Brain structural and functional changes in patients with major depressive disorder: a literature review
Depression is a mental disorder characterized by low mood and anhedonia that involves abnormalities in multiple brain regions and networks. Epidemiological studies demonstrated that depression has become one of the most important diseases affecting human health and longevity. The pathogenesis of the disease has not been fully elucidated. The clinical effect of treatment is not satisfactory in many cases. Neuroimaging studies have provided rich and valuable evidence that psychological symptoms and behavioral deficits in patients with depression are closely related to structural and functional abnormalities in specific areas of the brain. There were morphological differences in several brain regions, including the frontal lobe, temporal lobe, and limbic system, in people with depression compared to healthy people. In addition, people with depression also had abnormal functional connectivity to the default mode network, the central executive network, and the salience network. These findings provide an opportunity to re-understand the biological mechanisms of depression. In the future, magnetic resonance imaging (MRI) may serve as an important auxiliary tool for psychiatrists in the process of early and accurate diagnosis of depression and finding the appropriate treatment target for each patient to optimize clinical response.
Dai et al. (2019) Brain structural and functional changes in patients with major depressive disorder: a literature review. PeerJ 7:e8170 https://doi.org/10.7717/peerj.8170
Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.)
Background Plant cell metabolism inevitably forms reactive oxygen species (ROS), which can damage cells or lead to their death. The antioxidant system (AOS) evolved to eliminate a high concentration of ROS. For plants, this system consists of the seven classes of antioxidant enzymes and antioxidant compounds. Each enzymatic class contains a various number of genes which may vary from species to species. In such a multi-copy genetic system, the integration of evolutionary characteristics and expression data makes it possible to effectively predict promising breeding targets for the design of highly-yielding cultivars. In the plant cells, ROS production can increase as a result of abiotic stresses. Accordingly, AOS responds to stress by altering the expression of the genes of its components. Expression profiles of AOS enzymes, including their changes under stress, remains incomplete. A comprehensive study of the system behavior in response to stress for different species gives the key to identify the general mechanisms of AOS regulation. In this article, we studied stress-induced changes in the expression of AOS genes in photosynthetic tissues for rice and bread wheat. Methods A meta-analysis of genome-wide transcriptome data on stress-induced changes in expression profiles of antioxidant genes using microarray and next generation sequencing (NGS) experiments from the GEO NCBI database for rice and bread wheat was carried out. Experimental study of expression changes in short (6 h) and prolonged (24 h) cold stress responses for selected AOS genes of bread wheat cultivars Saratovskaya29 and Yanetzkis Probat was conducted using qPCR. Results The large-scale meta-transcriptome and complementary experimental analysis revealed a summary of fold changes in the AOS gene expression in response to cold and water deficiency for rice and bread wheat.
Ermakov et al. (2019) Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.). PeerJ 7:e7791 https://doi.org/10.7717/peerj.7791
Taxonomic assessment of species of the genus Octopus from the northeastern Pacific via morphological, molecular and morphometric analyses
Species of the genus Octopus from the northeastern Pacific are ecologically and economically important; however, their taxonomy is confusing and has not been comprehensively assessed. In this study, we performed a taxonomic evaluation of these species considering the morphological characteristics of the original descriptions, a molecular analysis of partial COI-gene sequences, and a traditional morphometry analysis of nine body measurements. Several interesting findings were obtained with our results: for instance, we updated the diagnoses of some species by including characters such as the number of lamellae per demibranch and the presence of chromatophores in the visceral sac; we deposited partial COI-gene sequences of species that had not been incorporated into the GenBank repository; and according to the morphometric analysis, we confirmed that the lengths of arms I–IV are relevant to discriminate the species under study. The taxa evaluated were morphologically, molecularly and morphometrically well-delimited; however, features such as funnel organ shape and arm length proportions in regard to dorsal mantle length are either not included in the diagnosis of the genus Octopus or overlap with other genera. Hence, this information, combined with the results obtained from the molecular analysis, supports the generic re-assignation of two of the species evaluated.
Díaz-Santana-Iturrios et al. (2019) Taxonomic assessment of species of the genus Octopus from the northeastern Pacific via morphological, molecular and morphometric analyses. PeerJ 7:e8118 https://doi.org/10.7717/peerj.8118
Relationship between the Dark Triad and depressive symptoms
The Dark Triad (DT) is composed of three closely related personality traits: psychopathy, Machiavellianism and narcissism. These traits have been linked to emotional deficits. The aim of the present study was to analyze the relationship between the DT traits, including sub-dimensions, and depressive symptoms in order to identify those factors most strongly associated with the development of depression in individuals scoring high on DT. For these purposes, a total of 791 adults (M = 35.76 years; 24.91% males) completed a questionnaire battery including DT traits and depression measures. A positive significant correlation was found between psychopathy and Machiavellianism traits (total score and all sub-dimensions) and depressive symptoms. For narcissism, the direction of the correlation was dependent on the sub-dimension assessed. A model explaining 26.2% of the depressive symptoms scores was composed of the callous affect and criminal tendencies sub-dimensions of psychopathy, cynical view of human nature, which is a sub-dimension of Machiavellianism, and entitlement and self-sufficiency, which are sub-dimensions of narcissism. In addition, some of the relationships found between DT sub-dimensions and depressive symptoms appeared to depend on gender. Our results could have implications for detection and intervention programs aimed at decreasing the negative emotional consequences suffered by individuals with high DT scores. Limitations and future lines of research are discussed.
Gómez-Leal et al. (2019) Relationship between the Dark Triad and depressive symptoms. PeerJ 7:e8120 https://doi.org/10.7717/peerj.8120
Identification of prognostic gene signature associated with microenvironment of lung adenocarcinoma
Background Lung cancer has the highest morbidity and mortality worldwide, and lung adenocarcinoma (LADC) is the most common pathological subtype. Accumulating evidence suggests the tumor microenvironment (TME) is correlated with the tumor progress and the patient’s outcome. As the major components of TME, the tumor-infiltrated immune cells and stromal cells have attracted more and more attention. In this study, differentially expressed immune and stromal signature genes were used to construct a TME-related prognostic model for predicting the outcomes of LADC patients. Methods The expression profiles of LADC samples with clinical information were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) related to the TME of LADC were identified using TCGA dataset by Wilcoxon rank sum test. The prognostic effects of TME-related DEGs were analyzed using univariate Cox regression. Then, the least absolute shrinkage and selection operator (LASSO) regression was performed to reduce the overfit and the number of genes for further analysis. Next, the prognostic model was constructed by step multivariate Cox regression and risk score of each sample was calculated. Then, survival and Receiver Operating Characteristic (ROC) analyses were conducted to validate the model using TCGA and GEO datasets, respectively. The Kyoto Encyclopedia of Genes and Genomes analysis of gene signature was performed using Gene Set Enrichment Analysis (GSEA). Finally, the overall immune status, tumor purity and the expression profiles of HLA genes of high- and low-risk samples was further analyzed to reveal the potential mechanisms of prognostic effects of the model. Results A total of 93 TME-related DEGs were identified, of which 23 DEGs were up-regulated and 70 DEGs were down-regulated. The univariate cox analysis indicated that 23 DEGs has the prognostic effects, the hazard ratio ranged from 0.65 to 1.25 (p < 0.05). Then, seven genes were screened out from the 23 DEGs by LASSO regression method and were further analyzed by step multivariate Cox regression. Finally, a three-gene (ADAM12, Bruton Tyrosine Kinase (BTK), ERG) signature was constructed, and ADAM12, BTK can be used as independent prognostic factors. The three-gene signature well stratified the LADC patients in both training (TCGA) and testing (GEO) datasets as high-risk and low-risk groups, the 3-year area under curve (AUC) of ROC curves of three GEO sets were 0.718 (GSE3141), 0.646 (GSE30219) and 0.643 (GSE50081). The GSEA analysis indicated that highly expressed ADAM12, BTK, ERG mainly correlated with the activation of pathways involving in focal adhesion, immune regulation. The immune analysis indicated that the low-risk group has more immune activities and higher expression of HLA genes than that of the high-risk group. In sum, we identified and constructed a three TME-related DEGs signature, which could be used to predict the prognosis of LADC patients.
Yue et al. (2019) Identification of prognostic gene signature associated with microenvironment of lung adenocarcinoma. PeerJ 7:e8128 https://doi.org/10.7717/peerj.8128
Characteristics of the vaginal microbiome in cross-border female sex workers in China: a case-control study
Background Female sex workers (FSWs) are key groups in the transmission of sexual transmitted infections (STI), and vaginal microbiome variations play an important role in transmission. We aimed to explore the characteristics of vaginal microbiome among FSWs. Materials and Methods A total of 24 cross-border FSWs were randomly selected from a cross-sectional survey for female sex workers in southwest China. Thirty-seven female non-sex workers (FNSWs) were randomly selected from the gynecology clinic and health examination center. Vaginal swabs were collected, bacterial DNA extracted and 16S rRNA genes were sequenced. Differences in the vaginal microbiome between both groups were compared using bioinformatics analysis. Results One DNA sample was excluded due to unqualified concentration, therefore 60 samples were sequenced. FSWs had significantly different vaginal microbiota β diversity, but undifferentiated α diversity when compared with non-sex workers. The average relative abundance of Sneathia, Shigella, Neisseria, Chlamydia, Prevotella, Enterococcus and Ureaplasma among FSWs was higher than FNSWs, and relative abundance of Atopobium in FSWs was lower than FNSWs. The Lactobacillus genus was the major genus in both groups. At the species level, Lactobacllus crispatus, Lactobacllus gasseri and Lactobacllus jensenii, in female sex workers, were lower when compared to FNSWs. Conclusion There were distinct differences in vaginal bacteria variety between FSWs and FNSWs. Some disease-related genus were also more abundant in FSWs. Based on these observations, further research is required to identify microbiome communities related to high STI risks and other diseases in these cohorts.
Hong et al. (2019) Characteristics of the vaginal microbiome in cross-border female sex workers in China: a case-control study. PeerJ 7:e8131 https://doi.org/10.7717/peerj.8131
Combined effects of body mass index and unhealthy behaviors on disability in older Japanese adults: the Okayama study
Background Body mass index (BMI) is a significant predictor of functional disability in older adults. However, when evaluated, the association between BMI and incident functional disability, considering behaviors only as covariates or not, may not be appropriate. The primary purpose of the study was to investigate the combined effects of BMI and unhealthy behaviors on the risk of incident functional disability. Methods This was a retrospective cohort study that took place in Okayama City, Japan. Data on BMI and unhealthy behaviors were obtained using the health check-up questionnaire. The certification of Long-Term Care Insurance was used to measure functional disability. Cox proportional hazard models were used; adjusted hazard ratios (HRs) with 95% confidence interval (CI) were calculated for incidence of functional disability across categories of BMI and number of unhealthy behaviors. Results The relationship between BMI and incident functional disability was U-shaped (HR = 1.18, 95% CI [1.11–1.25], among the underweight range; and 1.26 [1.19–1.34] among the obesity range), and its risk was significantly higher within the normal-to-overweight range of BMI values with co-occurring unhealthy behaviors (with normal weight range and one, 1.17 [1.01–1.21]; two, 1.29 [1.18–1.41]; and three or four unhealthy behaviors 1.38 [1.24–1.54]; as well as among overweight range and one, 1.16 [1.05–1.27]; two, 1.26 [1.15–1.38]; and three or four unhealthy behaviors, 1.47 [1.31–1.64]). In each BMI category, the risk of incident functional disability increased with increasing number of unhealthy behaviors (p < 0.05 for linear tread), with the highest risk (1.87 [1.58–2.20]) occurring in combination with at least three unhealthy behaviors with BMI ≥ 27.5, for both sexes (2.20 [1.64–2.92] in men and 1.66 [1.35–2.04] in women). Conclusion It is necessary to consider the combined effects of BMI and behaviors on incident functional disability. Furthermore, interventions targeting multiple behaviors should be considered as such interventions may offer greater benefits than simple interventions.
Liu et al. (2019) Combined effects of body mass index and unhealthy behaviors on disability in older Japanese adults: the Okayama study. PeerJ 7:e8146 https://doi.org/10.7717/peerj.8146
1H-NMR spectroscopy identifies potential biomarkers in serum metabolomic signatures for early stage esophageal squamous cell carcinoma
Background Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent types of upper gastrointestinal malignancies. Here, we used 1H nuclear magnetic resonance spectroscopy (1H-NMR) to identify potential serum biomarkers in patients with early stage ESCC. Methods Sixty-five serum samples from early stage ESCC patients (n = 25) and healthy controls (n = 40) were analysed using 1H-NMR spectroscopy. We distinguished between different metabolites through principal component analysis, partial least squares-discriminant analysis, and orthogonal partial least squares-discriminant analysis (OPLS-DA) using SIMCA-P+ version 14.0 software. Receiver operating characteristic (ROC) analysis was conducted to verify potential biomarkers. Results Using OPLS-DA, 31 altered serum metabolites were successfully identified between the groups. Based on the area under the ROC curve (AUROC), and the biomarker panel with AUROC of 0.969, six serum metabolites (α-glucose, choline, glutamine, glutamate, valine, and dihydrothymine) were selected as potential biomarkers for early stage ESCC. Dihydrothymine particularly was selected as a new feasible biomarker associated with tumor occurrence. Conclusions 1H-NMR spectroscopy may be a useful tumour detection approach in identifying useful metabolic ESCC biomarkers for early diagnosis and in the exploration of the molecular pathogenesis of ESCC.
Liu et al. (2019) 1H-NMR spectroscopy identifies potential biomarkers in serum metabolomic signatures for early stage esophageal squamous cell carcinoma. PeerJ 7:e8151 https://doi.org/10.7717/peerj.8151
Life history response of Echinops gmelinii Turcz. to variation in the rainfall pattern in a temperate desert
Background Current and future changes in rainfall amount and frequency may particularly impact annual plants in desert ecosystems. The winter annual Echinops gmelinii Turcz. is widely distributed in the desert habitats of northern China and is a dominant pioneer annual plant following sand stabilization in the Tengger Desert. This species plays a vital role in dune stabilization during spring and early summer, when wind erosion is the most severe and frequent. However, seedling emergence and regeneration in sandy soil are mainly determined by rainfall patterns. Therefore, understanding the life history response of this species to rainfall variation is necessary for understanding the change of population dynamics under the future climate change. Methods A field simulation rainfall pot experiment using rainout shelter was conducted that included five amounts and five frequencies of rainfall based on historical and predicted values to monitor the life history responses of E. gmelinii in a near-natural habitat. Results We found that rainfall amount and frequency significantly affected seedling survival, growth and reproduction. The plant height, biomass, capitula number, seed number, seed mass and reproductive effort, but not the root/shoot ratio, significantly increased with increasing rainfall. Further, these traits exhibited the greatest response to low-frequency and larger rainfall events, especially the optimal rainfall frequency of 10-day intervals. Offspring seed germination showed increasing trends with decreasing rainfall, suggesting that the maternal effects may have occurred. Conclusions Our study shows that the plasticity in growth and reproduction of E. gmelinii in response to rainfall variations may help it to gain dominance in the harsh and unpredictable desert environment. Furthermore, population development of this winter annual species should be promoted under the likely future scenarios of large rainfall events and increasing cool-season precipitation in temperate desert.
Wang et al. (2019) Life history response of Echinops gmelinii Turcz. to variation in the rainfall pattern in a temperate desert. PeerJ 7:e8159 https://doi.org/10.7717/peerj.8159
Screening and identification of key candidate genes and pathways in myelodysplastic syndrome by bioinformatic analysis
Myelodysplastic syndrome (MDS) is a heterogeneous hematologic malignancy derived from hematopoietic stem cells and the molecular mechanism of MDS remains unclear. This study aimed to elucidate potential markers of diagnosis and prognosis of MDS. The gene expression profiles GSE19429 and GSE58831 were obtained and downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in MDS were screened using GEO2R and overlapped DEGs were obtained with Venn Diagrams. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway functional enrichment analyses, protein–protein interaction network establishment and survival analyses were performed. Functional enrichment analysis indicated that these DEGs were significantly enriched in the interferon signaling pathway, immune response, hematopoietic cell lineage and the FOXO signaling pathway. Four hub genes and four significant modules including 25 module genes were obtained via Cytoscape MCODE. Survival analysis showed that the overall survival of MDS patients having BLNK, IRF4, IFITM1, IFIT1, ISG20, IFI44L alterations were worse than that without alterations. In conclusion, the identification of these genes and pathways helps understand the underlying molecular mechanisms of MDS and provides candidate targets for the diagnosis and prognosis of MDS.
Le (2019) Screening and identification of key candidate genes and pathways in myelodysplastic syndrome by bioinformatic analysis. PeerJ 7:e8162 https://doi.org/10.7717/peerj.8162
Polyphenol-rich Trapa quadrispinosa pericarp extract ameliorates high-fat diet induced non-alcoholic fatty liver disease by regulating lipid metabolism and insulin resistance in mice
In China, Trapa quadrispinosa (also called water caltrop) has long been used as a function food and folk medicine to treat diabetes mellitus for years. In the present study, the extract of T. quadrispinosa pericarp (TQPE) which mainly contains hydrolysable tannins was prepared to investigate the potential therapeutic action in non-alcoholic fatty liver disease (NAFLD) mice induced by high fat-diet (HFD). After the administration of TQPE (15, 30 mg/kg/day) for 8 weeks, the increased weight of body and liver were significantly suppressed. TQPE also ameliorated liver lipid deposition and reduced lipids parameters of blood in mice. Moreover, TQPE attenuated oxidative stress and showed a hepatoprotective effect in mice. TQPE was also found to decrease the value of homeostatic model assessment for insulin resistance. In addition, TQPE administration increased the phosphorylation of AMP-activated protein kinase (AMPK) and Acetyl-CoA carboxylase (ACC) and inhibited sterol regulatory element-binding protein (SREBP) in the liver tissue. Meanwhile, TQPE elevated insulin receptor substrate-1 (IRs-1) and protein kinase B (Akt) phosphorylation. These results reflected that, as a nature product, TQPE is a potential agent for suppressing the process of NAFLD via regulation of the AMPK/SREBP/ACC and IRs-1/Akt pathways.
Jian et al. (2019) Polyphenol-rich Trapa quadrispinosa pericarp extract ameliorates high-fat diet induced non-alcoholic fatty liver disease by regulating lipid metabolism and insulin resistance in mice. PeerJ 7:e8165 https://doi.org/10.7717/peerj.8165
Characterization and expression profiling of the ICE-CBF-COR genes in wheat
Cold stress is one of the major abiotic stresses that limit crop production. The ICE-CBF-COR pathway is associated with cold stress response in a wide variety of crop species. However, the ICE-CBF-COR genes has not been well characterized in wheat (Triticum aestivum). This study identified, characterized and examined the expression profiles of the ICE, CBF and COR genes for cold defense in wheat. Five ICE (inducer of CBF expression) genes, 37 CBF (C-repeat binding factor) genes and 11 COR (cold-responsive or cold-regulated) genes were discovered in the wheat genome database. Phylogenetic trees based on all 53 genes revealed that CBF genes were more diverse than ICE and COR genes. Twenty-two of the 53 genes appeared to include 11 duplicated pairs. Twenty rice (Oryza sativa) genes and 21 sorghum (Sorghum bicolor) and maize (Zea mays) genes showed collinearity with the wheat ICE, CBF and COR genes. Transcriptome data and qRT-PCR analyses revealed tissue-specific expression patterns of the ICE, CBF and COR genes, and identified similarities in the expression pattern of genes from the same family when subjected to drought, heat, drought plus heat, and cold stress. These results provide information for better understanding the biological roles of ICE, CBF, COR genes in wheat.
Guo et al. (2019) Characterization and expression profiling of the ICE-CBF-COR genes in wheat. PeerJ 7:e8190 https://doi.org/10.7717/peerj.8190
Does bone preparation impact its shape: consequences for comparative analyses of bone shape
Vertebrate osteological collections provide comparative material for morphological analysis. Before being stored in the collection and studied by researchers, specimens are treated by preparators or curators and are cleaned. The preparation protocol employed ideally should not damage the material. Here, we explore the potential deformation of bones due to preparation using geometric morphometric methods. We focus both on intraspecific and interspecific variability. Our data on the scapular girdle of birds show that, at an intraspecific level, the effect of preparation on bone shape cannot be neglected. Paired and unpaired bones did not respond to the preparation process in the same way, possibly due to differences in function and their anatomical characteristics. Moreover, deformations due to preparation can be estimated by looking at the texture of the bone. At the interspecific level, we found no significant differences as the deformations induced by preparation are relatively small compared to differences among species. This study highlights the importance of carefully selecting preparation methods in order to avoid physical damage that could impact the shape of bones, especially for studies at the intraspecific level.
Pagès et al. (2019) Does bone preparation impact its shape: consequences for comparative analyses of bone shape. PeerJ 7:e7932 https://doi.org/10.7717/peerj.7932
Invasions of gladiolus rust in North America are caused by a widely-distributed clone of Uromycestransversalis
Uromyces transversalis, the causal agent of Gladiolus rust, is an invasive plant pathogen in the United States and is regulated as a quarantine pathogen in Europe. The aim of this research was to: (i) determine the origin of introductions of U. transversalis to the United States, (ii) track the movement of genotypes, and (iii) understand the worldwide genetic diversity of the species. To develop molecular markers for genotyping, whole genome sequencing was performed on three isolates collected in the United States. Genomes were assembled de novo and searched for microsatellite regions. Primers were developed and tested on ten isolates from the United States resulting in the identification of 24 polymorphic markers. Among 92 isolates collected from Costa Rica, Mexico, New Zealand, Australia, and the United States there were polymorphisms within isolates with no genotypic diversity detected among isolates; however, missing data among the New Zealand and Australia isolates due to either poor amplification of degraded DNA or null alleles as a result of genetic differences made it difficult to generate conclusions about these populations. The microsatellite loci and flanking regions showed high diversity and two divergent genomes within dikaryotic individuals, yet no diversity among individuals, suggesting that the invasive U. transversalis populations from North America are strictly clonal.
DeLong et al. (2019) Invasions of gladiolus rust in North America are caused by a widely-distributed clone of Uromycestransversalis. PeerJ 7:e7986 https://doi.org/10.7717/peerj.7986
Long noncoding RNA MEG3 suppresses podocyte injury in diabetic nephropathy by inactivating Wnt/β-catenin signaling
Background Diabetic nephropathy (DN) is one of the principal complications of diabetes and podocyte injury plays an important role in the DN pathogenesis. Wnt/β-catenin signaling overactivation confers podocyte injury and promotes multiple types of renal disease. However, the underlying mechanism of Wnt/β-catenin signaling activation in DN progression has not been fully elucidated. Long noncoding RNA (lncRNA) is a large class of endogenous RNA molecules lacking functional code capacity and which participates in the pathogenesis of human disease, including DN. Method A diabetes model was constructed by intraperitoneal injection of Streptozotocin in rats. The MPC5 cells were used to create the in vitro model. Western blot and Quantitative reverse-transcriptase-PCR were used to examine the expression of protein and mRNA. The migrated capacity was analyzed by Transwell migration assay. The cell viability was detected by CCK8. Results In the present study, we revealed the association of lncRNA Maternally Expressed Gene 3 (MEG3) with aberrant activation of Wnt/β-catenin signaling and the role of MEG3/Wnt axis in podocyte injury. We found that high glucose (HG) treatment suppressed MEG3 expression in cultured podocytes, activated Wnt/β-catenin signaling and caused podocyte injury as indicated by the downregulation of podocyte-specific markers (podocin and synaptopodin) and the upregulation of snail1 and α-smooth muscle actin. Overexpression of MEG3 attenuated HG-induced podocyte injury by reducing Wnt/β-catenin activity, repressing cell migration, reactive oxygen species production and increasing the viability of podocytes. Furthermore, we provided evidences that restoration of Wnt/β-catenin signaling by specific agonist impeded the protective effect of MEG3 on podocyte injury. Current results demonstrated that MEG3/Wnt axis plays an important role in fostering podocyte injury and may serve as a potential therapeutic target for the treatment of DN. Conclusion lncRNA MEG3 ameliorates podocyte injury in DN via inactivating Wnt/β-catenin signaling.
Che et al. (2019) Long noncoding RNA MEG3 suppresses podocyte injury in diabetic nephropathy by inactivating Wnt/β-catenin signaling. PeerJ 7:e8016 https://doi.org/10.7717/peerj.8016
Multiple ecosystem services from field margin vegetation for ecological sustainability in agriculture: scientific evidence and knowledge gaps
Background Field margin and non-crop vegetation in agricultural systems are potential ecosystem services providers because they offer semi-natural habitats for both below and above ground animal groups such as soil organisms, small mammals, birds and arthropods that are service supplying units. They are considered as a target area for enhancing farm biodiversity. Methodology To explore the multiple potential benefits of these semi-natural habitats and to identify research trends and knowledge gaps globally, a review was carried out following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. A total of 235 publications from the year 2000 to 2016 in the Scopus and Web of Science databases were reviewed. Results The literature showed an increasing trend in the number of published articles over time with European studies leading in the proportion of studies conducted, followed by North America, Asia, South America, Africa and Australia. Several functional groups of organisms were studied from field margin and non-crop vegetation around agricultural lands including natural enemies (37%), insect pests (22%), birds (17%), pollinators (16%), soil macro fauna (4%) and small mammals (4%). Ecosystem services derived from the field margin included natural pest regulation, pollination, nutrient cycling and reduced offsite erosion. Some field margin plants were reported to host detrimental crop pests, a major ecosystem dis-service, potentially leading to increased pest infestation in the field. Conclusion The majority of studies revealed the importance of field margin and non-crop vegetation around arable fields in enhancing ecosystem biodiversity. Promotion of field margin plants that selectively enhance the population of beneficial organisms would support sustainable food security rather than simply boosting plant diversity. Our analyses also highlight that agro-ecological studies remain largely overlooked in some regions.
Mkenda et al. (2019) Multiple ecosystem services from field margin vegetation for ecological sustainability in agriculture: scientific evidence and knowledge gaps. PeerJ 7:e8091 https://doi.org/10.7717/peerj.8091
Concentrated ambient PM2.5 exposure affects mice sperm quality and testosterone biosynthesis
Background Studies suggested that PM2.5 exposure could lead to adverse reproductive effects on male animals. However, the underlying mechanism is still not clear. Besides, animals in the majority of previous studies were exposed to PM2.5 through intratracheal instillation which should be improved. In addition, limited amount of research has been conducted in China where the PM2.5 concentration is higher and the PM2.5 components are different. The aim of this work is to explore the effects of concentrated ambient PM2.5 (CAP) on mice sperm quality and testosterone biosynthesis. Methods A total of 12 male C57BL/6 mice were exposed to filtered air (FA) or CAP for 125 days using the Shanghai Meteorological and Environmental Animal Exposure System. The mice sperm concentration, sperm motility, DNA fragmentation index, high DNA stainability and plasma testosterone were analyzed. Testicular histology and sperm morphology were observed through optical microscope. Testosterone biosynthesis related gene expressions were analyzed using real-time PCR, including cytochrome P450 CHOL side-chain cleavage enzyme (P450scc), steroidogenic acute regulatory protein (StAR), 3β-hydroxysteroid dehydrogenase (3β HSD), 17β-hydroxysteroid dehydrogenase, cytochrome P450 aromatase (P450arom), estrogen receptor (ER), androgen receptor (AR) and follicle stimulating hormone receptor (FSHR). Results Exposure to CAP resulted in disturbance of various stages of spermatogenesis and significant higher percentage of abnormal sperm (FA vs. CAP: 24.37% vs. 44.83%) in mice testis. CAP exposure significantly decreased sperm concentration (43.00 × 106 vs. 25.33 × 106) and motility (PR: 63.58% vs. 55.15%; PR + NP: 84.00% vs. 77.08%) in epididymis. Plasma testosterone concentration were significantly declined (0.28 ng/ml vs. 0.69 ng/ml) under CAP exposure. Notably, the levels of testosterone biosynthesis related genes, StAR, P450scc, P450arom, ER and FSHR were significantly decreased with CAP exposure. Conclusion Concentrated ambient PM2.5 exposure altered mice sperm concentration, motility and morphology, which might be mediated primarily by the decline in testosterone concentration and testosterone biosynthesis process.
Yang et al. (2019) Concentrated ambient PM2.5 exposure affects mice sperm quality and testosterone biosynthesis. PeerJ 7:e8109 https://doi.org/10.7717/peerj.8109
Analysis of miRNA expression profiles in the liver of ClockΔ19 mutant mice
The circadian clock controls the physiological functions of many tissues including the liver via an autoregulatory transcriptional−translational feedback loop, of which CLOCK is a core positive component. In addition, many studies have indicated that microRNAs (miRNAs) regulate liver function. However, how CLOCK-regulated miRNAs are linked to liver function remains largely unknown. In this study, miRNAs expression profiles were performed in the liver of ClockΔ19 mutant mice. Compared to wild type mice, totals of 61 and 57 putative CLOCK-regulated miRNAs were differentially expressed (fold change absolute value ≥2) at zeitgeber time 2 and zeitgeber time 14, respectively. According to the pathway analyses, the target genes of differentially expressed miRNAs were mainly involved in pathways in cancer, the PI3K-Akt signaling pathway and the MAPK signaling pathway. Protein−protein interaction analyses revealed that the hub genes were primarily associated with pathway in cancer and circadian rhythms. Expression validation showed that while the expression levels of miR-195 and miR-340 were up-regulated, the rhythms of these two miRNAs were always maintained. The expression level of nr1d2 mRNA was down-regulated. We identified a number of prospective CLOCK-regulated miRNAs that play roles in the various physiological processes of the liver, providing a reference to better understanding the potential regulatory mechanisms in the liver.
Wang et al. (2019) Analysis of miRNA expression profiles in the liver of ClockΔ19 mutant mice. PeerJ 7:e8119 https://doi.org/10.7717/peerj.8119
The discriminative power of the ReproQ: a client experience questionnaire in maternity care
Background The aim of the ReproQuestionnaire (ReproQ) is to measure the client’s experience with maternity care, following WHO’s responsiveness model. To support quality improvement, ReproQ should be able to discriminate best from worst organisational units. Methods We sent questionnaires to 27,487 third-trimester pregnant women (response 31%) and to 37,230 women 6 weeks after childbirth (response 39%). For analysis we first summarized the ReproQ domain scores into three summary scores: total score (all eight domains), personal score (four personal domains), and setting score (four setting domains). Second, we estimated the proportion of variance across perinatal units attributable to the ‘actual’ difference across perinatal units using intraclass correlation coefficients (ICCs). Third, we assessed the ability of ReproQ to discriminate between perinatal units based on both a statistical approach using multilevel regression analyses, and a relevance approach based on the minimally important difference (MID). Finally, we compared the domain scores of the best and underperforming units. Results ICCs ranged between 0.004 and 0.025 for the summary scores, and between 0.002 and 0.125 for the individual domains. ReproQ was able to identify the best and worst performing units with both the statistical and relevance approach. The statistical approach was able to identify four underperforming units during childbirth (total score), while the relevance approach identified 10 underperforming units. Conclusions ReproQ, a valid and efficient measure of client experiences in maternity care, has the ability to discriminate well across perinatal units, and is suitable for benchmarking under routine conditions.
Scheerhagen et al. (2019) The discriminative power of the ReproQ: a client experience questionnaire in maternity care. PeerJ 7:e7575 https://doi.org/10.7717/peerj.7575
Comparative proteomic analysis of pepper (Capsicum annuum L.) seedlings under selenium stress
Selenium (Se) is an essential trace element for human and animal health. Se fertilizer has been used to increase the Se content in crops to meet the Se requirements in humans and animals. To address the challenge of Se poisoning in plants, the mechanisms underlying Se-induced stress in plants must be understood. Here, to elucidate the effects of Se stress on the protein levels in pepper, we used an integrated approach involving tandem mass tag labeling, high performance liquid chromatography fractionation, and mass spectrometry-based analysis. A total of 4,693 proteins were identified, 3,938 of which yielded quantitative information. Among them, the expression of 172 proteins was up-regulated, and the expression of 28 proteins was down-regulated in the Se/mock treatment comparison. According to the above data, we performed a systematic bioinformatics analysis of all identified proteins and differentially expressed proteins (DEPs). The DEPs were most strongly associated with the terms “metabolic process,” “posttranslational modification, protein turnover, chaperones,” and “protein processing in endoplasmic reticulum” according to Gene Ontology, eukaryotic orthologous groups classification, and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, respectively. Furthermore, several heat shock proteins were identified as DEPs. These results provide insights that may facilitate further studies on the pepper proteome expressed downstream of the Se stress response. Our data revealed that the responses of pepper to Se stress involve various pathways.
Environmental Contamination and Remediation
Zhang et al. (2019) Comparative proteomic analysis of pepper (Capsicum annuum L.) seedlings under selenium stress. PeerJ 7:e8020 https://doi.org/10.7717/peerj.8020
Intra-individual heteroplasmy in the Gentiana tongolensis plastid genome (Gentianaceae)
Chloroplasts are typically inherited from the female parent and are haploid in most angiosperms, but rare intra-individual heteroplasmy in plastid genomes has been reported in plants. Here, we report an example of plastome heteroplasmy and its characteristics in Gentiana tongolensis (Gentianaceae). The plastid genome of G. tongolensis is 145,757 bp in size and is missing parts of petD gene when compared with other Gentiana species. A total of 112 single nucleotide polymorphisms (SNPs) and 31 indels with frequencies of more than 2% were detected in the plastid genome, and most were located in protein coding regions. Most sites with SNP frequencies of more than 10% were located in six genes in the LSC region. After verification via cloning and Sanger sequencing at three loci, heteroplasmy was identified in different individuals. The cause of heteroplasmy at the nucleotide level in plastome of G. tongolensis is unclear from the present data, although biparental plastid inheritance and transfer of plastid DNA seem to be most likely. This study implies that botanists should reconsider the heredity and evolution of chloroplasts and be cautious with using chloroplasts as genetic markers, especially in Gentiana.
Sun et al. (2019) Intra-individual heteroplasmy in the Gentiana tongolensis plastid genome (Gentianaceae). PeerJ 7:e8025 https://doi.org/10.7717/peerj.8025
Field evaluation of Mosq-ovitrap, Ovitrap and a CO2-light trap for Aedes albopictus sampling in Shanghai, China
Background The Mosq-ovitrap (MOT) is currently used for routine surveillance of container-breeding Aedes in China. However, the effectiveness of monitoring Aedes albopictus using the MOT and other mosquito monitoring methods, such as the Ovitrap (OT) and the CO2-light trap (CLT), have not been extensively compared. Moreover, little is known about the spatial-temporal correlations of eggs with adult Ae. albopictus abundance among these three types of traps. Methods Comparative field evaluation of MOT, OT and CLT for Ae. albopictus monitoring was conducted simultaneously at two city parks and three residential neighborhoods in downtown Shanghai for 8 months from April 21 to December 21, 2017. Results Significantly more Ae. albopictus eggs were collected from both MOTs and OTs when traps remained in the field for 10 d or 7 d compared with 3 d (MOT: 50.16, 34.15 vs. 12.38 per trap, P < 0.001; OT: 3.98, 2.92 vs. 0.63 per trap, P < 0.001). Egg collections of MOTs were significantly greater than OTs for all three exposure durations (Percent positive: X2 = 72.251, 52.420 and 51.429, P value all < 0.001; egg collections: t = 8.068, 8.517 and 10.021, P value all <0.001). Significant temporal correlations were observed between yields of MOT and CLT in all sampling locations and 3 different MOT exposure durations (correlation coefficient r ranged from 0.439 to 0.850, P values all < 0.05). However, great variation was found in the spatial distributions of Ae. albopictus density between MOT and CLT. MOT considerably underestimated Ae. albopictus abundances in areas with high Ae. albopictus density (>25.56 per day ⋅ trap by CLT). Conclusion The MOT was more efficient than the OT in percent positive scores and egg collections of Ae. albopictus. The minimum length of time that MOTs are deployed in the field should not be less than 7 d, as Ae. albopictus collections during this period were much greater than for 3 d of monitoring. MOT considerably underestimated Ae. albopictus abundance in areas with high Aedes albopictus density compared to CLT. In areas with moderate Aedes albopictus densities, MOT results were significantly correlated with CLT catches.
Gao et al. (2019) Field evaluation of Mosq-ovitrap, Ovitrap and a CO2-light trap for Aedes albopictus sampling in Shanghai, China. PeerJ 7:e8031 https://doi.org/10.7717/peerj.8031
Effects of elevated pCO2 and nutrient enrichment on the growth, photosynthesis, and biochemical compositions of the brown alga Saccharina japonica (Laminariaceae, Phaeophyta)
Ocean acidification and eutrophication are two major environmental issues affecting kelp mariculture. In this study, the growth, photosynthesis, and biochemical compositions of adult sporophytes of Saccharina japonica were evaluated at different levels of pCO2 (400 and 800 µatm) and nutrients (nutrient-enriched and non-enriched seawater). The relative growth rate (RGR), net photosynthetic rate, and all tested biochemical contents (including chlorophyll (Chl) a, Chl c, soluble carbohydrates, and soluble proteins) were significantly lower at 800 µatm than at 400 µatm pCO2. The RGR and the contents of Chl a and soluble proteins were significantly higher under nutrient-enriched conditions than under non-enriched conditions. Moreover, the negative effects of the elevated pCO2 level on the RGR, net photosynthetic rate, Chl c and the soluble carbohydrates and proteins contents were synergized by the elevated nutrient availability. These results implied that increased pCO2could suppress the growth and biochemical composition of adult sporophytes of S. japonica. The interactive effects of ocean acidification and eutrophication constitute a great threat to the cultivation of S. japonica due to growth inhibition and a reduction in quality.
Chu et al. (2019) Effects of elevated pCO2 and nutrient enrichment on the growth, photosynthesis, and biochemical compositions of the brown alga Saccharina japonica (Laminariaceae, Phaeophyta). PeerJ 7:e8040 https://doi.org/10.7717/peerj.8040
Seasonal variation in apparent conductivity and soil salinity at two Narragansett Bay, RI salt marshes
Measurement of the apparent conductivity of salt marsh sediments using electromagnetic induction (EMI) is a rapid alternative to traditional methods of salinity determination that can be used to map soil salinity across a marsh surface. Soil salinity measures can provide information about marsh processes, since salinity is important in determining the structure and function of tidally influenced marsh communities. While EMI has been shown to accurately reflect salinity to a specified depth, more information is needed on the potential for spatial and temporal variability in apparent conductivity measures that may impact the interpretation of salinity data. In this study we mapped soil salinity at two salt marshes in the Narragansett Bay, RI estuary monthly over the course of several years to examine spatial and temporal trends in marsh salinity. Mean monthly calculated salinity was 25.8 ± 5.5 ppt at Narrow River marsh (NAR), located near the mouth of the Bay, and 17.7 ± 5.3 ppt at Passeonkquis marsh (PAS) located in the upper Bay. Salinity varied seasonally with both marshes, showing the lowest values (16.3 and 8.3 ppt, respectively) in April and highest values (35.4 and 26.2 ppt, respectively) in August. Contour plots of calculated salinities showed that while the mean whole-marsh calculated salinity at both sites changed over time, within-marsh patterns of higher versus lower salinity were maintained at NAR but changed over time at PAS. Calculated salinity was significantly negatively correlated with elevation at NAR during a sub-set of 12 sample events, but not at PAS. Best-supported linear regression models for both sites included one-month and 6-month cumulative rainfall, and tide state as potential factors driving observed changes in calculated salinity. Mapping apparent conductivity of salt marsh sediments may be useful both identifying within-marsh micro-habitats, and documenting marsh-wide changes in salinity over time.
McKinney et al. (2019) Seasonal variation in apparent conductivity and soil salinity at two Narragansett Bay, RI salt marshes. PeerJ 7:e8074 https://doi.org/10.7717/peerj.8074
Diatoms as indicators of the effects of river impoundment at multiple spatial scales
River impoundment constitutes one of the most important anthropogenic impacts on the World’s rivers. An increasing number of studies have tried to quantify the effects of river impoundment on riverine ecosystems over the past two decades, often focusing on the effects of individual large reservoirs. This study is one of the first to use a large-scale, multi-year diatom dataset from a routine biomonitoring network to analyse sample sites downstream of a large number of water supply reservoirs (n = 77) and to compare them with paired unregulated control sites. We analysed benthic diatom assemblage structure and a set of derived indices, including ecological guilds, in tandem with multiple spatio-temporal variables to disclose patterns of ecological responses to reservoirs beyond the site-specific scale. Diatom assemblage structure at sites downstream of water supply reservoirs was significantly different to control sites, with the effect being most evident at the regional scale. We found that regional influences were important drivers of differences in assemblage structure at the national scale, although this effect was weaker at downstream sites, indicating the homogenising effect of river impoundment on diatom assemblages. Sites downstream of reservoirs typically exhibited a higher taxonomic richness, with the strongest increases found within the motile guild. In addition, Trophic Diatom Index (TDI) values were typically higher at downstream sites. Water quality gradients appeared to be an important driver of diatom assemblages, but the influence of other abiotic factors could not be ruled out and should be investigated further. Our results demonstrate the value of diatom assemblage data from national-scale biomonitoring networks to detect the effects of water supply reservoirs on instream communities at large spatial scales. This information may assist water resource managers with the future implementation of mitigation measures such as setting environmental flow targets.
Krajenbrink et al. (2019) Diatoms as indicators of the effects of river impoundment at multiple spatial scales. PeerJ 7:e8092 https://doi.org/10.7717/peerj.8092
Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants
Background Genomics diagnostic tests are done for a wide spectrum of complex genetics conditions such as autism and cancer. The growth of technology has not only aided in successfully decoding the genetic variants that causes or trigger these disorders. However, interpretation of these variants is not a trivial task even at a level of distinguish pathogenic vs benign variants. Methods We used the clinically significant variants from ClinVar database to evaluate the performance of 14 most popular in-silico predictors using supervised learning methods. We implemented a feature selection and random forest classification algorithm to identify the best combination of predictors to evaluate the pathogenicity of a variant. Finally, we have also utilized this combination of predictors to reclassify the variants of unknown significance in MeCP2 gene that are associated with the Rett syndrome. Results The results from analysis shows an optimized selection of prediction algorithm and developed a combinatory predictor method. Our combinatory approach of using both best performing independent and ensemble predictors reduces any algorithm biases in variant characterization. The reclassification of variants (such as VUS) in MECP2 gene associated with RETT syndrome suggest that the combinatory in-silico predictor approach had a higher success rate in categorizing their pathogenicity.
Ganakammal et al. (2019) Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants. PeerJ 7:e8106 https://doi.org/10.7717/peerj.8106
Arboreal twig-nesting ants form dominance hierarchies over nesting resources
Interspecific dominance hierarchies have been widely reported across animal systems. High-ranking species are expected to monopolize more resources than low-ranking species via resource monopolization. In some ant species, dominance hierarchies have been used to explain species coexistence and community structure. However, it remains unclear whether or in what contexts dominance hierarchies occur in tropical ant communities. This study seeks to examine whether arboreal twig-nesting ants competing for nesting resources in a Mexican coffee agricultural ecosystem are arranged in a linear dominance hierarchy. We described the dominance relationships among 10 species of ants and measured the uncertainty and steepness of the inferred dominance hierarchy. We also assessed the orderliness of the hierarchy by considering species interactions at the network level. Based on the randomized Elo-rating method, we found that the twig-nesting ant species Myrmelachista mexicana ranked highest in the ranking, while Pseudomyrmex ejectus was ranked as the lowest in the hierarchy. Our results show that the hierarchy was intermediate in its steepness, suggesting that the probability of higher ranked species winning contests against lower ranked species was fairly high. Motif analysis and significant excess of triads further revealed that the species networks were largely transitive. This study highlights that some tropical arboreal ant communities organize into dominance hierarchies.
Yitbarek et al. (2019) Arboreal twig-nesting ants form dominance hierarchies over nesting resources. PeerJ 7:e8124 https://doi.org/10.7717/peerj.8124
Sarc-F and muscle function in community dwelling adults with aged care service needs: baseline and post-training relationship
Background This study sought to better understand the psychometric properties of the SARC-F, by examining the baseline and training-related relationships between the five SARC-F items and objective measures of muscle function. Each of the five items of the SARC-F are scored from 0 to 2, with total score of four or more indicative of likely sarcopenia. Methods This manuscript describes a sub-study of a larger step-wedge, randomised controlled 24-week progressive resistance and balance training (PRBT) program trial for Australian community dwelling older adults accessing government supported aged care. Muscle function was assessed using handgrip strength, isometric knee extension, 5-time repeated chair stand and walking speed over 4 m. Associations within and between SARC-F categories and muscle function were assessed using multiple correspondence analysis (MCA) and multinomial regression, respectively. Results Significant associations were identified at baseline between SARC-F total score and measures of lower-body muscle function (r = − 0.62 to 0.57; p ≤ 0.002) in 245 older adults. MCA analysis indicated the first three dimensions of the SARC-F data explained 48.5% of the cumulative variance. The initial dimension represented overall sarcopenia diagnosis, Dimension 2 the ability to displace the body vertically, and Dimension 3 walking ability and falls status. The majority of the 168 older adults who completed the PRBT program reported no change in their SARC-F diagnosis or individual item scores (56.5–79.2%). However, significant associations were obtained between training-related changes in SARC-F total and item scores and changes in walking speed and chair stand test performance (r = − 0.30 to 0.33; p < 0.001 and relative risk ratio = 0.40–2.24; p < 0.05, respectively). MCA analysis of the change score data indicated that the first two dimensions explained 32.2% of the cumulative variance, with these dimensions representing whether a change occurred and the direction of change, respectively. Discussion The results advance our comprehension of the psychometric properties on the SARC-F, particularly its potential use in assessing changes in muscle function. Older adults’ perception of their baseline and training-related changes in their function, as self-reported by the SARC-F, closely matched objectively measured muscle function tests. This is important as there may be a lack of concordance between self-reported and clinician-measured assessments of older adults’ muscle function. However, the SARC-F has a relative lack of sensitivity to detecting training-related changes, even over a period of 24 weeks. Conclusions Results of this study may provide clinicians and researchers a greater understanding of how they may use the SARC-F and its potential limitations. Future studies may wish to further examine the SARC-F’s sensitivity of change, perhaps by adding a few additional items or an additional category of performance to each item.
Keogh et al. (2019) Sarc-F and muscle function in community dwelling adults with aged care service needs: baseline and post-training relationship. PeerJ 7:e8140 https://doi.org/10.7717/peerj.8140
Effect of vibration vs non-vibration foam rolling techniques on flexibility, dynamic balance and perceived joint stability after fatigue
Background Foam roller and vibration techniques are currently used to assist in recovery after fatigue. The main purpose of this study was to determine the effects of the use of a foam roller with and without vibration on dynamic balance, ankle dorsiflexion, hamstring and lumbar spine flexibility and perceived knee and ankle stability after an induced fatigue protocol. Methods A total of 24 healthy recreationally active participants (17 males and seven females) were recruited to a randomized cross over trial consisting of; no treatment (NT), foam roller treatment (FR) and vibration foam roller treatment (VFR). The assessments included; the Sit & Reach test, Y balance test and post-treatment perceived knee and ankle stability. Measurements were taken after a standardized warm up (baseline) and repeated following an exercise-induced muscle fatigue protocol consisting of repeated lunges until volitional fatigue. The three treatment conditions were assessed on three separate days in a randomized order. A 3 × 3 repeated measures ANOVA was used to investigate differences between the three treatments over the three time points and a one factor repeated measures ANOVA was used to determine any differences between treatments using the Global Rate of Change scale when considering perceived stability. Results FR and VFR conditions both showed a greater ankle dorsiflexion range of motion (ROM) (p < 0.001), greater posteromedial and posterolateral reach distances (p < 0.001) and a better knee and ankle perceived stability (p < 0.001) when compared to the NT condition. A trend toward significance was observed in the hamstring and lumbar spine flexibility (p = 0.074) in both treatment conditions when compared to the NT condition. However, no differences were seen between the FR and VFR conditions. Conclusions Both FR conditions seem to assist in exercise-induced muscle fatigue recovery with improvements in ROM, balance and perceived stability.
de Benito et al. (2019) Effect of vibration vs non-vibration foam rolling techniques on flexibility, dynamic balance and perceived joint stability after fatigue. PeerJ 7:e8000 https://doi.org/10.7717/peerj.8000
A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean
Caribbean reef corals have experienced unprecedented declines from climate change, anthropogenic stressors and infectious diseases in recent decades. Since 2014, a highly lethal, new disease, called stony coral tissue loss disease, has impacted many reef-coral species in Florida. During the summer of 2018, we noticed an anomalously high disease prevalence affecting different coral species in the northern portion of the Mexican Caribbean. We assessed the severity of this outbreak in 2018/2019 using the AGRRA coral protocol to survey 82 reef sites across the Mexican Caribbean. Then, using a subset of 14 sites, we detailed information from before the outbreak (2016/2017) to explore the consequences of the disease on the condition and composition of coral communities. Our findings show that the disease outbreak has already spread across the entire region by affecting similar species (with similar disease patterns) to those previously described for Florida. However, we observed a great variability in prevalence and tissue mortality that was not attributable to any geographical gradient. Using long-term data, we determined that there is no evidence of such high coral disease prevalence anywhere in the region before 2018, which suggests that the entire Mexican Caribbean was afflicted by the disease within a few months. The analysis of sites that contained pre-outbreak information showed that this event considerably increased coral mortality and severely changed the structure of coral communities in the region. Given the high prevalence and lethality of this disease, and the high number of susceptible species, we encourage reef researchers, managers and stakeholders across the Western Atlantic to accord it the highest priority for the near future.
Alvarez-Filip et al. (2019) A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean. PeerJ 7:e8069 https://doi.org/10.7717/peerj.8069
Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae
Background Coelidiinae, a relatively large subfamily within the family Cicadellidae, includes 129 genera and ∼1,300 species distributed worldwide. However, the mitogenomes of only two species (Olidiana sp. and Taharana fasciana) in the subfamily Coelidiinae have been assembled. Here, we report the first complete mitogenome assembly of the genus Olidiana. Methods Specimens were collected from Wenxian County (Gansu Province, China) and identified on the basis of their morphology. Mitogenomes were sequenced by next-generation sequencing, following which an NGS template was generated, and this was confirmed using polymerase chain reaction and Sanger sequencing. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. Results The mitogenome of O. ritcheriina was 15,166 bp long, with an A + T content of 78.0%. Compared with the mitogenome of other Cicadellidae sp., the gene order, gene content, gene size, base composition, and codon usage of protein-coding genes (PCGs) in O. ritcheriina were highly conserved. The standard start codon of all PCGs was ATN and stop codon was TAA or TAG; COII, COIII, and ND4L ended with a single T. All tRNA genes showed the typical cloverleaf secondary structure, except for trnSer, which did not have the dihydrouridine arm. Furthermore, the secondary structures of rRNAs (rrnL and rrnS) in O. ritcheriina were predicted. Overall, five domains and 42 helices were predicted for rrnL (domain III is absent in arthropods), and three structural domains and 27 helices were predicted for rrnS. Maximum likelihood and Bayesian analyses indicated that O. ritcheriina and other Coelidiinae members were clustered into a clade, indicating the relationships among their subfamilies; the main topology was as follows: (Deltocephalinae + ((Coelidiinae + Iassinae) + ((Typhlocybinae + Cicadellinae) + (Idiocerinae + (Treehopper + Megophthalminae))))). The phylogenetic relationships indicated that the molecular taxonomy of O. ritcheriina is consistent with the current morphological classification.
Wang et al. (2019) Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae. PeerJ 7:e8072 https://doi.org/10.7717/peerj.8072
Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology
Background There are abundant sheep breed resources in the Xinjiang region of China attributing to its diverse ecological system, which include several high-litter size sheep populations. Previous studies have confirmed that the major high prolificacy gene cannot be used to detect high litter size. Our research team found a resource group in Pishan County, southern Xinjiang. It showed high fertility with an average litter size of two to four in one birth, excellent breast development, and a high survival rate of lambs. In the present study, we used this resource as an ideal sample for studying the genetic mechanisms of high prolificacy in sheep. Methods Indigenous sheep populations from Xinjiang, with different litter sizes, were selected for the research, and specific-locus amplified fragment sequencing (SLAF-seq) technology was used to comprehensively screen single nucleotide polymorphisms (SNPs) from the whole genome that may cause differences in litter size. Novel genes associated with litter size of sheep were detected using genome-wide association studies (GWAS), providing new clues revealing the regulation mechanism of sheep fecundity. Candidate genes related to ovulation and litter size were selected for verification using Kompetitive Allele Specific polymerase chain reaction (KASP) cluster analysis. Results We identified 685,300 SNPs using the SLAF-seq technique for subsequent genome-wide analysis. Subsequently, 155 SNPs were detected at the genome-wide level. Fourteen genes related to sheep reproduction were notated: COIL, SLK, FSHR, Plxna3, Ddx24, CXCL12, Pla2g7, ATP5F1A, KERA, GUCY1A1, LOC101107541, LOC101107119, LOC101107809, and BRAF. Based on literature reports, 30 loci of seven genes and candidate genes (CXCL12, FSHR, SLK, GUCY1A1, COIL, LOC101107541, and LOC101107119) related to ovulation and litter size were selected for verification using KASP cluster analysis. Among them, nine loci of three genes were successfully genotyped. Three loci of FSHR (GenBank ID: 443299, g. 75320741G>A site), GUCY1A1 (GenBank ID: 101110000, g. 43266624C>T site), and COIL (GenBank ID: 101123134, g. 7321466C>G site) were found to be significantly or extremely significantly associated with litter size. These three loci are expected to be used as molecular markers to determine differences in litter size in sheep.
Ma et al. (2019) Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology. PeerJ 7:e8079 https://doi.org/10.7717/peerj.8079
Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma
Clear cell renal cell carcinoma (ccRCC) is one of the most common and lethal types of cancer within the urinary system. Great efforts have been made to elucidate the pathogeny. However, the molecular mechanism of ccRCC is still not well understood. The aim of this study is to identify key genes in the carcinogenesis and progression of ccRCC. The mRNA microarray dataset GSE53757 was downloaded from the Gene Expression Omnibus database. The GSE53757 dataset contains tumor and matched paracancerous specimens from 72 ccRCC patients with clinical stage I to IV. The linear model of microarray data (limma) package in R language was used to identify differentially expressed genes (DEGs). The protein–protein interaction (PPI) network of the DEGs was constructed using the search tool for the retrieval of interacting genes (STRING). Subsequently, we visualized molecular interaction networks by Cytoscape software and analyzed modules with MCODE. A total of 1,284, 1,416, 1,610 and 1,185 up-regulated genes, and 932, 1,236, 1,006 and 929 down-regulated genes were identified from clinical stage I to IV ccRCC patients, respectively. The overlapping DEGs among the four clinical stages contain 870 up-regulated and 645 down-regulated genes. The enrichment analysis of DEGs in the top module was carried out with DAVID. The results showed the DEGs of the top module were mainly enriched in microtubule-based movement, mitotic cytokinesis and mitotic chromosome condensation. Eleven up-regulated genes and one down-regulated gene were identified as hub genes. Survival analysis showed the high expression of CENPE, KIF20A, KIF4A, MELK, NCAPG, NDC80, NUF2, TOP2A, TPX2 and UBE2C, and low expression of ACADM gene could be involved in the carcinogenesis, invasion or recurrence of ccRCC. Literature retrieval results showed the hub gene NDC80, CENPE and ACADM might be novel targets for the diagnosis, clinical treatment and prognosis of ccRCC. In conclusion, the findings of present study may help us understand the molecular mechanisms underlying the carcinogenesis and progression of ccRCC, and provide potential diagnostic, therapeutic and prognostic biomarkers.
Zhang et al. (2019) Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma. PeerJ 7:e8096 https://doi.org/10.7717/peerj.8096
Oxidative stress and antioxidants in the trabecular meshwork
Glaucoma is an age-dependent disease closely related to oxidative stress and is regarded as the second leading cause of irreversible blindness worldwide. In recent years, many studies have shown that morphological and functional abnormalities of the trabecular meshwork (TM) are closely related to glaucoma, especially with respect to oxidative stress. In this review, the mechanisms of oxidative stress in the TM and treatment strategies for this condition, including strategies involving antioxidants, noncoding RNAs and exogenous compounds, are discussed. Although many questions remain to be answered, the reviewed findings provide insights for further research on oxidative stress alleviation in glaucoma and suggest new targets for glaucoma prevention.
Wang et al. (2019) Oxidative stress and antioxidants in the trabecular meshwork. PeerJ 7:e8121 https://doi.org/10.7717/peerj.8121
Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia
The best facultative anaerobes among vertebrates are members of the genera Trachemys (pond slider turtles) and Chrysemys (painted turtles), and are able to survive without oxygen for up to 12 to 18 weeks at ∼3 °C. In this study, we utilized RNAseq to profile the transcriptomic changes that take place in response to 20 hrs of anoxia at 5 °C in the liver of the red eared slide turtle (Trachemys scripta elegans). Sequencing reads were obtained from at least 18,169 different genes and represented a minimum 49x coverage of the C. picta bellii exome. A total of 3,105 genes showed statistically significant changes in gene expression between the two animal groups, of which 971 also exhibited a fold change equal to or greater than 50% of control normoxic values. This study also highlights a number of anoxia-responsive molecular pathways that are may be important to navigating anoxia survival. These pathways were enriched in mRNA found to significantly increase in response to anoxia and included molecular processes such as DNA damage repair and metabolic reprogramming. For example, our results indicate that the anoxic turtle may utilize succinate metabolism to yield a molecule of GTP in addition to the two molecules that results from lactate production, and agrees with other established models of anoxia tolerance. Collectively, our analysis provides a snapshot of the molecular landscape of the anoxic turtle and may provide hints into the how this animal is capable of surviving this extreme environmental stress.
Biggar et al. (2019) Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia. PeerJ 7:e8144 https://doi.org/10.7717/peerj.8144
Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)
The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.
Hu et al. (2019) Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.). PeerJ 7:e7929 https://doi.org/10.7717/peerj.7929
Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications
The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.
Mitra et al. (2019) Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications. PeerJ 7:e8033 https://doi.org/10.7717/peerj.8033
Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research
Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research.
Cobb et al. (2019) Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research. PeerJ 7:e8086 https://doi.org/10.7717/peerj.8086
Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference
Background The exoskeleton of an insect could be an important factor in the success of its evolutionary process. This reaches its maximum expression in beetles, which constitute the most diversified animal taxon. The involvement in the management of environmental radiation could be one of the most important functions of the exoskeleton due to the passive contributions to the thermoregulation of body temperature. We study whether the elytra of two sympatric and closely related beetle species respond differentially to the radiation of distinct wavelengths in agreement with their ecological preferences. Methods Onthophagus coenobita (Herbst) and O. medius (Kugelaan) occupy different habitats and environmental conditions (shaded vs. unshaded from solar radiation). The potential adaptive variations to thermoregulation under these different ecological conditions were studied using the responses of their exoskeletons to radiation of different wavelengths (ultraviolet, visible and near-infrared). For these two species, the amounts of the three wavelengths that were reflected, transmitted or absorbed by the exoskeleton were measured using of a spectrophotometer. In addition, the darkness and thickness of the elytra were examined to determine whether these two features influence the management of radiation by the exoskeleton. Results Both species differ in the management of visible and near-infrared radiation. In agreement with habitat preferences, the species inhabiting shaded conditions would allow infrared and visible radiation to penetrate the elytra more easily to heat internal body parts, while the elytra of the heliophilous species would have increased absorbance of these same types of radiation. An increase in body size (and therefore in elytron thickness) and the quantity of dark spots may serve as barriers against exogenous heat gain. However, the maintenance of between-species differences independent of the effects of these two morphological features led us to suspect that an unconsidered elytron characteristic may also be affecting these differences. Discussion The results of the involvement of the exoskeleton thickness and spots in the thermoregulation of insects opens new research lines to obtain a better understanding of the function of the exoskeleton as a passive thermoregulation mechanism in Coleoptera.
Cuesta et al. (2019) Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference. PeerJ 7:e8104 https://doi.org/10.7717/peerj.8104
Familiarity with visual stimuli boosts recency bias in macaques
To probe how non-human primates (NHPs) decode temporal dynamic stimuli, we used a two-alternative forced choice task (2AFC), where the cue was dynamic: a movie snippet drawn from an animation that transforms one image into another. When the cue was drawn from either the beginning or end of the animation, thus heavily weighted towards one (the target) of both images (the choice pair), then primates performed at high levels of accuracy. For a subset of trials, however, the cue was ambiguous, drawn from the middle of the animation, containing information that could be associated to either image. Those trials, rewarded randomly and independent of choice, offered an opportunity to study the strategy the animals used trying to decode the cue. Despite being ambiguous, the primates exhibited a clear strategy, suggesting they were not aware that reward was given non-differentially. More specifically, they relied more on information provided at the end than at the beginning of those cues, consistent with the recency effect reported by numerous serial position studies. Interestingly and counterintuitively, this effect became stronger for sessions where the primates were already familiar with the stimuli. In other words, despite having rehearsed with the same stimuli in a previous session, the animals relied even more on a decision strategy that did not yield any benefits during a previous session. In the discussion section we speculate on what might cause this behavioral shift towards stronger bias, as well as why this behavior shows similarities with a repetition bias in humans known as the illusory truth effect.
Brunet et al. (2019) Familiarity with visual stimuli boosts recency bias in macaques. PeerJ 7:e8105 https://doi.org/10.7717/peerj.8105
Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry
Background The production of photocatalytic nanoparticles such as TiO2 has received increasing interest for biomedical and wastewater treatment applications. However, the conventional synthesis of such materials faces several environmental concerns. Methods In this work, green synthesis is addressed to prepare TiO2 nanoparticles at large scale using Lemongrass (Cymbopogon citratus) and titanium isopropoxide (TTIP). This process was designed and modeled using computer-aided process engineering (CAPE) in order to obtain the extended mass/energy balances, as well as operating parameters. Process simulation was carried out using the commercial software Aspen Plus®. In addition, energy performance of large-scale nanoparticle production was analyzed to identify alternatives for process improvement from an exergetic point of view. Results The production capacity of the plant was estimated as 1,496 t/y of TiO2 nanoparticles by the conversion of 32,675 t/y lemongrass and 5,724 t/y TTIP. Hence, the overall production yield is 0.26 kg TiO2/kg TTIP. Exergy analysis reported an overall exergy efficiency of 0.27% and an exergy loss of 159,824.80 MJ/h. These results suggest that such a process requires the implementation of process improvement strategies to reach a more sustainable design from energy and thermodynamic viewpoints.
Meramo-Hurtado et al. (2019) Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry. PeerJ 7:e8113 https://doi.org/10.7717/peerj.8113
Application of open field, tonic immobility, and attention bias tests to hens with different ranging patterns
Assessment of negative affective states is a key component of animal welfare research. In laying hens, excessive fearfulness results in reduced production and increased sensitivity to stress. Fearfulness can be defined as a response to a known threat, but anxiety is a response to an unknown threat and may have similar negative consequences. The open field test and tonic immobility test are commonly applied to measure fearfulness in laying hens. An attention bias test that measured individual hen’s responses to playback of a conspecific alarm call in the presence of food was recently pharmacologically validated using an anxiogenic drug but was confounded by the hen’s typical motionless response in a novel environment. The current study used 56-week old free-range layers to further assess the validity of an attention bias test to differentiate ranging treatment groups in comparison with the open field and tonic immobility tests. The selected hens varied in their range use patterns as tracked by radio-frequency identification technology. ‘Indoor’ hens did not access the range and ‘outdoor’ hens ranged daily; previous research has confirmed higher fearfulness in hens that remain indoors. The tonic immobility test did not differentiate ranging groups (P = 0.34), but indoor birds were slower to first step (P = 0.03) and stepped less (P = 0.02) in the open field test. The attention bias test occurred in an isolated wooden box using a conspecific alarm call playback (a threat) and mixed grain (a positive stimulus). The behavioural response of latency to resume eating following playback of the alarm call was measured to differentiate the anxiety states of the indoor and outdoor ranging birds. Before the attention bias test could occur, birds had to be habituated to the test box across three separate 5-minute sessions to increase the willingness to feed within the novel test environment. All birds ate faster across time (P < 0.001) but the indoor birds were slower to eat than the outdoor birds (P < 0.001). In this study, the latency to resume eating following an alarm call was determined to be a poor measure for highly anxious birds as they failed to eat at all. Forty-six percent of indoor hens were excluded for not eating across the 5-minute test. Of the birds that did eat, only 7% of indoor hens ate following playback of the alarm call, compared with 36% of outdoor hens. This repetition of an attention bias test for laying hens highlights the challenges in assessing hens with extreme fearful/anxious responses and that information may be missed when non-performing hens are excluded from behavioural tests. We suggest that latency to eat in a novel arena without any alarm call playback is an informative measure of anxious state that can be applied to all hens but consideration must be made of potential differences in food motivation.
Campbell et al. (2019) Application of open field, tonic immobility, and attention bias tests to hens with different ranging patterns. PeerJ 7:e8122 https://doi.org/10.7717/peerj.8122
Introducing a new tool to navigate, understand and use International Codes of Nomenclature
Background In order to designate the various concepts of taxa in biology, evolution and paleontology, scientists have developed various rules on how to create unique names for taxa. Different Codes of Nomenclature have been developed for animals, plants, fungi, bacteria etc., with standard sets of Rules that govern the formation, publication and application of the nomina of extant and extinct species. These Codes are the result of decades of discussions, workshops, publications and revisions. The structure and complexity of these Codes have been criticized many times by zoologists. This project aims, using the International Code of Zoological Nomenclature as a case study, to show that the structure of these Codes is better reflected and understood as networks. Methods The majority of the text of the Code has been divided into hundreds of Nodes of different types, connected to each other with different types of Edges to form a network. The various mathematical descriptors of the entire system, as well as for the elements of the network, have been conceptually framed to help describing and understanding the Code as a network. Results The network of the Code comprises 1,379 Nodes, which are connected with 11,276 Edges. The structure of the Code can be accurately described as a network, a mathematical structure that is better suited than any kind of linear text publication to reflect its structure. Discussion Thinking of the Code as a network allows a better, in-depth understanding of the Code itself, as the user can navigate in a more efficient way, as well as to depict and analyze all the implied connections between the various parts of the Code that are not visible immediately. The network of the Code is an open access tool that could also help teaching, using and disseminating the Code. More importantly, this network is a powerful tool that allows identifying a priori the parts of the Code that could be potentially affected by upcoming amendment and revisions. This kind of analysis is not limited to nomenclature, as it could be applied to other fields that use complex textbooks with long editing history, such as Law, Medicine and Linguistics.
Vlachos (2019) Introducing a new tool to navigate, understand and use International Codes of Nomenclature. PeerJ 7:e8127 https://doi.org/10.7717/peerj.8127
Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction
Mycobacterium avium subsp. paratuberculosis (MAP) is a pathogen causing paratuberculosis in cattle and small ruminants. During the long asymptomatic subclinical stage, high numbers of MAP are excreted and can be transmitted to food for human consumption, where they survive many of the standard techniques of food decontamination. Whether MAP is a human pathogen is currently under debate. The aim of this study was a better understanding of the host-pathogen response by analyzing the interaction of peripheral blood lymphocytes (PBL) from cattle with MAP in their exoproteomes/secretomes to gain more information about the pathogenic mechanisms of MAP. Because in other mycobacterial infections, the immune phenotype correlates with susceptibility, we additionally tested the interaction of MAP with recently detected cattle with a different immune capacity referred as immune deviant (ID) cows. In PBL, different biological pathways were enhanced in response to MAP dependent on the immune phenotype of the host. PBL of control cows activated members of cell activation and chemotaxis of leukocytes pathway as well as IL-12 mediated signaling. In contrast, in ID cows CNOT1 was detected as highly abundant protein, pointing to a different immune response, which could be favorable for MAP. Additionally, MAP exoproteomes differed in either GroEL1 or DnaK abundance, depending on the interacting host immune response. These finding point to an interdependent, tightly regulated response of the bovine immune system to MAP and vise versa.
Kleinwort et al. (2019) Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction. PeerJ 7:e8130 https://doi.org/10.7717/peerj.8130
Mapping theme trends and recognizing hot spots in postmenopausal osteoporosis research: a bibliometric analysis
Background This study aimed to draw a series of scientific maps to quantitatively and qualitatively evaluate hot spots and trends in postmenopausal osteoporosis research using bibliometric analysis. Methods Scientific papers published on postmenopausal osteoporosis were extracted from the Web of Science Core Collection and PubMed database. Extracted information was analyzed quantitatively with bibliometric analysis by CiteSpace, the Online Analysis Platform of Literature Metrology and Bibliographic Item Co-Occurrence Matrix Builder (BICOMB). To explore the hot spots in this field, co-word biclustering analysis was conducted by gCLUTO based on the major MeSH terms/MeSH subheading terms-source literatures matrix. Results We identified that a total of 5,247 publications related to postmenopausal osteoporosis were published between 2013 and 2017. The overall trend decreased from 1,071 literatures in 2013 to 1,048 literatures in 2017. Osteoporosis International is the leading journal in the field of postmenopausal osteoporosis research, both in terms of impact factor score (3.819) and H-index value (157). The United States has retained a top position and has exerted a pivotal influence in this field. The University of California, San Francisco was identified as a leading institution for research collaboration, and Professors Reginster and Kanis have made great achievements in this area. Eight research hot spots were identified. Conclusions Our study found that in the past few years, the etiology and drug treatment of postmenopausal osteoporosis have been research hot spots. They provide a basis for the study of the pathogenesis of osteoporosis and guidelines for the drug treatment of osteoporosis.
Zhou et al. (2019) Mapping theme trends and recognizing hot spots in postmenopausal osteoporosis research: a bibliometric analysis. PeerJ 7:e8145 https://doi.org/10.7717/peerj.8145
Molecular characterization of G-protein-coupled receptor (GPCR) and protein kinase A (PKA) cDNA in Perinereis aibuhitensis and expression during benzo(a)pyrene exposure
Background G-protein-coupled receptors (GPCRs) are one of the most important molecules that transfer signals across the plasma membrane, and play central roles in physiological systems. The molecular architecture of GPCRs allows them to bind to diverse chemicals, including environmental contaminants. Methods To investigate the effects of benzo(a)pyrene (B(a)P) on GPCR signaling, GPCR and the protein kinase A (PKA) catalytic subunit of Perinereis aibuhitensis were cloned. The expression patterns of these two genes during B(a)P exposure were determined with real-time fluorescence quantitative PCR. The PKA content in P. aibuhitensis under B(a)P exposure was examined. Results The full-length cDNAs of PaGPCR and the PaPKA catalytic subunit were 1,514 and 2,662 nucleotides, respectively, encoding 338 and 350 amino acids, respectively. Multiple sequence alignments indicated that the deduced amino acid sequence of PaGPCR shared a low level of similarity with the orphan GPCRs of polychaetes and echinoderms, whereas PaPKA shared a high level of identify with the PKA catalytic subunits of other invertebrates. B(a)P exposure time-dependently elevated the expression of PaGPCR and PaPKA. The expression of both PaGPCR and PaPKA was also dose-dependent, except at a dose of 10 μg/L B(a)P. The PKA content in concentration group was elevated on day 4, with time prolonging the PKA content was down-regulated to control level. Discussion These results suggested that GPCR signaling in P. aibuhitensis was involved in the polychaete’s response to environmental contaminants.
Huang et al. (2019) Molecular characterization of G-protein-coupled receptor (GPCR) and protein kinase A (PKA) cDNA in Perinereis aibuhitensis and expression during benzo(a)pyrene exposure. PeerJ 7:e8044 https://doi.org/10.7717/peerj.8044
Oral toxicity of arjunolic acid on hematological, biochemical and histopathological investigations in female Sprague Dawley rats
Background Arjunolic acid (AA) is a potent phytochemical with wider pharmacological activities. Despite potential medicinal properties on various in vitro and in vivo studies, there is still a dearth of scientific data related to its safety profile and toxicological parameters. The current study aimed to investigate acute toxicity of AA in normal female Sprague Dawley rats. Methods In this study, AA was administered orally at an individual dose of 300 and 2000 mg/kg body weight to group 1 and 2 respectively, while group 3 served as normal control. All the animals were observed for 2 weeks to determine any behavioral and physical changes. On day 15, blood was collected for hematological and biochemical investigation, later animals from all the three groups were euthanized to harvest and store essential organs for histopathological analysis. Four different staining techniques; hematoxylin and eosin, Masson trichrome, Periodic acid Schiff and Oil O Red were used to investigate any alterations in different tissues through microscopical observation. Results The results of the study showed no morbidity and mortality at two different dosage of AA treatment. Daily food & water intake, body weight, relative organ weight, hematological and biochemical parameters were detected to be normal with no severe alteration seen through microscopical investigation in the structure of harvested tissues. Our findings support the safety profile of AA, which was well tolerated at higher dose. Thus, an in-detail study on the subacute disease model is warranted.
Aamir et al. (2019) Oral toxicity of arjunolic acid on hematological, biochemical and histopathological investigations in female Sprague Dawley rats. PeerJ 7:e8045 https://doi.org/10.7717/peerj.8045
Lymph node detection in MR Lymphography: false positive reduction using multi-view convolutional neural networks
Purpose To investigate whether multi-view convolutional neural networks can improve a fully automated lymph node detection system for pelvic MR Lymphography (MRL) images of patients with prostate cancer. Methods A fully automated computer-aided detection (CAD) system had been previously developed to detect lymph nodes in MRL studies. The CAD system was extended with three types of 2D multi-view convolutional neural networks (CNN) aiming to reduce false positives (FP). A 2D multi-view CNN is an efficient approximation of a 3D CNN, and three types were evaluated: a 1-view, 3-view, and 9-view 2D CNN. The three deep learning CNN architectures were trained and configured on retrospective data of 240 prostate cancer patients that received MRL images as the standard of care between January 2008 and April 2010. The MRL used ferumoxtran-10 as a contrast agent and comprised at least two imaging sequences: a 3D T1-weighted and a 3D T2*-weighted sequence. A total of 5089 lymph nodes were annotated by two expert readers, reading in consensus. A first experiment compared the performance with and without CNNs and a second experiment compared the individual contribution of the 1-view, 3-view, or 9-view architecture to the performance. The performances were visually compared using free-receiver operating characteristic (FROC) analysis and statistically compared using partial area under the FROC curve analysis. Training and analysis were performed using bootstrapped FROC and 5-fold cross-validation. Results Adding multi-view CNNs significantly (p < 0.01) reduced false positive detections. The 3-view and 9-view CNN outperformed (p < 0.01) the 1-view CNN, reducing FP from 20.6 to 7.8/image at 80% sensitivity. Conclusion Multi-view convolutional neural networks significantly reduce false positives in a lymph node detection system for MRL images, and three orthogonal views are sufficient. At the achieved level of performance, CAD for MRL may help speed up finding lymph nodes and assessing them for potential metastatic involvement.
Debats et al. (2019) Lymph node detection in MR Lymphography: false positive reduction using multi-view convolutional neural networks. PeerJ 7:e8052 https://doi.org/10.7717/peerj.8052
Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ
Background In the predator–sea urchin–macrophyte trophic cascade, the ecological effect of sea urchins as grazers depends both on their density and the changes in foraging activity, which are influenced by various disturbing factors. However, the complete duration of the alarm reactions of echinoids has not been studied until now. Here, we tested a hypothesis that two cohabiting sea urchins, Mesocentrotus nudus and Strongylocentrotus intermedius, which differ morphologically, might display different behavioral responses to high hydrodynamic activity and predation. Methods We used continuous time-lapse video recording to clarify behavioral patterns of M. nudus and S. intermedius in presence of a large quantity of food (the kelp Saccharina japonica) but under different weather conditions and different types of predation threat: (1) calm weather conditions, (2) stormy weather conditions, (3) predation risk associated with the presence of several sea star species and (4) predation risk associated with an alarm stimulus (crushed conspecifics or heterospecifics). Three separate video recording experiments (134 days in total) were conducted under field conditions. Video recording analysis was performed to determine the number of specimens of each sea urchin species in the cameras’ field of view, size of sea urchins’ groups, movement patterns and the duration of the alarm responses of both sea urchin species. Results We showed that in the presence of kelp, M. nudus and S. intermedius exhibited both similar and different behavioral responses to hydrodynamics and predation threat. Under calm weather, movement patterns of both echinoids were similar but M. nudus exhibited the higher locomotion speed and distance traveled. Furthermore, S. intermedius but not M. nudus tended to group near the food substrate. The stormy weather caused a sharp decrease in movement activity followed by escape response in both echinoids. Six starfish species failed to predate on healthy sea urchins of either species and only a few attacks on ailing S. intermedius specimens were successful. The alarm response of S. intermedius lasted approximately 90 h and 20 h for starfish attacks on ailing conspecifics and for simulated attacks (crushed conspecifics or heterospecifics), respectively and involved several phases: (1) flight response, (2) grouping close to the food, (3) leaving the food and (4) return to the food. Phase three was the more pronounced in a case of starfish attack. M. nudus only responded to crushed conspecifics and exhibited no grouping behavior but displayed fast escape (during 4 h) and prolonged (up to 19 days) avoidance of the food source. This outcome is the longest alarm response reported for sea urchins. Discussion The most interesting finding is that two cohabiting sea urchin species, M. nudus and S. intermedius, display different alarm responses to predation threat. Both alarm responses are interpreted as defensive adaptations against visual predators.
Zhadan et al. (2019) Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ. PeerJ 7:e8087 https://doi.org/10.7717/peerj.8087
Munidopsis species (Crustacea: Decapoda: Munidopsidae) from carcass falls in Weijia Guyot, West Pacific, with recognition of a new species based on integrative taxonomy
Several squat lobster specimens of the genus Munidopsis were collected from an artificially placed carcass fall (cow bones) on Weijia Guyot in the western Pacific Ocean. Based on morphological comparisons and molecular analysis, three specimens were confirmed as juveniles of M. albatrossae Pequegnat & Pequegnat, 1973, which represents the first record of this species in the western Pacific. The other specimens collected are newly described as Munidopsis spinifrons sp. nov., which is distinguished from the closely related species in having a spinose rostrum and basal lateral eyespine on the eyestalk. The M. albatrossae from Weijia Guyot exhibited very low genetic distances when compared with a conspecific sample from Monterey Bay, USA, and the closely related species M. aries (A. Milne Edwards, 1880) from the northeastern Atlantic. A phylogenetic tree based on the mtCOI gene shows M. spinifrons sp. nov. as sister to M. vrijenhoeki Jones & Macpherson, 2007 and M. nitida (A. Milne Edwards, 1880), although M. vrijenhoeki presents a complex relationship with other species in the clade. The systematic status of the new species and the closely related species are discussed.
Dong et al. (2019) Munidopsis species (Crustacea: Decapoda: Munidopsidae) from carcass falls in Weijia Guyot, West Pacific, with recognition of a new species based on integrative taxonomy. PeerJ 7:e8089 https://doi.org/10.7717/peerj.8089
Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene
Delta bovine papillomaviruses (δBPVs) causes fibropapillomas or bladder cancer in cattle. E5 is the major oncogene of δBPVs; however, the influence that E5 oncogene has on host microRNA (miRNA) and mRNA expression profiles remains little elucidated. In the present study, small RNA sequencing and RNA sequencing were used to explore alterations in miRNAs and mRNAs in E5 over-expressing Madin-Darby bovine kidney (MDBK) cells compared with controls. In total, 77 miRNAs (including 30 bovine-derived miRNAs) and 223 genes were differentially expressed (DE) following E5 overexpression. The dysregulated genes were mainly involved in metabolic and biosynthetic processes. We constructed a potential miRNA-gene regulatory network from the differentially expressed genes (DEGs) and DE miRNAs. Finally, 22 DEGs and nine DE miRNAs were selected for RT-qPCR validation. Of these, downregulation of six miRNAs, bta-miR-34c, bta-miR-122, bta-miR-195, bta-miR-449b, bta-miR-2425-5p, and bta-miR-2428-3p were confirmed; In addition, upregulation of 16 genes, ACSS2, DDIT4, INHBE, INSIG1, PNRC1, PSAT1, PSPH, PYCR1, SC4MOL, SLC34A2, SCD, SPARC, IDI1, PCK2, HMGCS1, and SMIM14 and downregulation of two genes, BATF3 and WFDC2 were confirmed. Specially, bta-miR-34c and bta-miR-449b potentially regulated PYCR1 and DDIT4, which were involved in cancer progression and angiogenesis. Our study presented for the first time the comprehensive miRNA and mRNA alterations in MDBK cells expressing the BPV E5 oncogene, providing new insights into the tumorigenesis induced by BPV E5.
Pang et al. (2019) Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene. PeerJ 7:e8098 https://doi.org/10.7717/peerj.8098
Comparative morphology and trophic ecology in a population of the polymorphic lizard Sceloporus minor (Squamata: Phrynosomatidae) from central Mexico
Polymorphism among individuals of the same population has generally been linked to alternative reproductive tactics, where different morphs can exhibit differences in their morphological, ecological, and behavioral attributes. These differences may result in a divergence in diet between morphs due to differential exploitation of habitat, morphological differences that influence prey selection, or differential energy expenditure that results in different nutritional needs. The present study analyzes the morphology (morphometry and body mass) and diet of red and yellow male morphs in a population (El Enzuelado) of the lizard Sceloporus minor from central Mexico. No differences between morphs were found for any of the morphometric variables analyzed (snout-vent length, tail length, jaw length, jaw width, head length, head width, head height, tibia length, femur length, forearm length and ventral patch length). In both morphs, allometric growth was observed in all body features analyzed, as well as in morphometric features of the head across seasons. Analysis of stomach contents showed that the diet of red males was composed of 12 categories of prey, while that of yellow males was composed of 10 categories; those categories of diet not shared between morphs (e.g., Isoptera, Psocoptera) were consumed by their respective morph in very low proportions. Categories of diet with the highest values of food importance for both groups were Coleoptera, Orthoptera, and leaves; a similar pattern was seen across seasons. This, in turn, is reflected in low niche breadth values for each morph and a very high niche overlap. There were no significant differences between morphs overall, or between morphs per season, in the weight and volume of stomach contents or in the number of prey items found in stomachs; however, differences in these variables across all males (independent of morph) were recorded between seasons. Likewise, no significant correlations were found between body size (snout-vent length) and the volume of stomach contents for either morph or between lizard mandibular dimensions and the volume of stomach contents for red morph males. For the yellow morph, prey volume unexpectedly decreased significantly with jaw size rather than increasing as expected. Overall, this study adds new information about the morphology and feeding of males in this species, and suggests that in this population, color morphs lack the morphological and ecological differences found in some other species of polymorphic lizard.
García-Rosales et al. (2019) Comparative morphology and trophic ecology in a population of the polymorphic lizard Sceloporus minor (Squamata: Phrynosomatidae) from central Mexico. PeerJ 7:e8099 https://doi.org/10.7717/peerj.8099
The first North American Propterodon (Hyaenodonta: Hyaenodontidae), a new species from the late Uintan of Utah
The carnivorous mammalian fauna from the Uintan (late middle Eocene) of North America remains relatively poorly documented. This is unfortunate, as this is a critical interval in the transition from “creodont” to carnivoran dominated carnivore guilds. This study reports a new species from the Uinta Formation of the Uinta Basin, Utah, the first North American species of the otherwise Asian hyaenodont genus Propterodon. The new species, Propterodon witteri, represented by a dentary with M2-3 from the late Uintan Leota Quarry, is larger than the well-known P. morrisi and P. tongi and has a larger M3 talonid, but is otherwise very similar. A phylogenetic analysis of hyaenodont interrelationships recovers P. witteri as a hyaenodontine but is generally poorly resolved. A relationship between Hyaenodontinae and Oxyaenoides, recovered by many recent analyses, is not supported. Among the Asian species of Propterodon, P. pishigouensis is reidentified as a machaeroidine oxyaenid and recombined as Apataelurus pishigouensis new combination. Isphanatherium ferganensis may also represent an Asian machaeroidine. Identification of a North American species of Propterodon and an Asian Apataelurus increases the similarity of North American Uintan and Asian Irdinmanhan faunas and suggests that there was substantial exchange of carnivorous fauna during the late middle Eocene.
Zack (2019) The first North American Propterodon (Hyaenodonta: Hyaenodontidae), a new species from the late Uintan of Utah. PeerJ 7:e8136 https://doi.org/10.7717/peerj.8136
Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community
Di-2-ethylhexyl phthalate (DEHP) is a plasticizer used in consumer products and building materials, including polyvinyl chloride flooring material. DEHP adsorbs from material and leaches into soil, water, or dust and presents an exposure risk to building occupants by inhalation, ingestion, or absorption. A number of bacterial isolates are demonstrated to degrade DEHP in culture, but bacteria may be susceptible to it as well, thus this study examined the relation of DEHP to bacterial communities in dust. Polyvinyl chloride flooring was seeded with homogenized house dust and incubated for up to 14 days, and bacterial communities in dust were identified at days 1, 7, and 14 using the V3–V4 regions of the bacterial 16S rRNA gene. DEHP concentration in dust increased over time, as expected, and bacterial richness and Shannon diversity were negatively correlated with DEHP concentration. Some sequence variants of Bacillus, Corynebacterium jeddahense, Streptococcus, and Peptoniphilus were relatively more abundant at low concentrations of DEHP, while some Sphingomonas, Chryseobacterium, and a member of the Enterobacteriaceae family were relatively more abundant at higher concentrations. The built environment is known to host lower microbial diversity and biomass than natural environments, and DEHP or other chemicals indoors may contribute to this paucity.
Velazquez et al. (2019) Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community. PeerJ 7:e8147 https://doi.org/10.7717/peerj.8147
TLR4 polymorphisms may increase susceptibility to periodontitis in Pg-positive individuals
Objective To investigate the correlation between the single nucleotide polymorphisms (SNPs) in the toll-like receptor 4 (TLR4) gene and the susceptibility to chronic periodontitis. Design 241 Chinese subjects from the cohort of Beijing Shijingshan Community were recruited. Buccal swab samples, the whole unstimulated saliva and periodontal clinical parameters were collected. Human DNA extracted from buccal swab samples were used for genotyping eight SNPs of the TLR4 gene (rs11536889, rs1927906, rs1927911, rs2149356, rs4986790, rs4986791, rs2737190, rs787384) by the Sequenom MassARRAY system. Porphyromonas gingivalis (P. gingivalis) was detected from the deposition of the whole unstimulated saliva through polymerase chain reaction (PCR) method based on 16S rRNA. The correlation between SNPs of TLR4 and chronic periodontitis susceptibility in the whole subjects and the patients detected with P. gingivalis was investigated. Results The variants of rs4986790 and rs4986791 were not found in 241 Chinese subjects. Moreover, there was no significant difference in the distribution of theother6 SNPs of TLR4 between groups of none/mild -periodontitis and moderate/severe-periodontitis subjects. When combined with P. gingivalis infection, rs1927911 (TT/CC+CT), rs2149356 (TT/GG+GT) and rs2737190 (GG/AA+AG) were independent risk factors of chronic periodontitis. Conclusion Three SNPs of TLR4, i.e., rs1927911 (TT/CC+CT), rs2149356 (TT/GG+GT) and rs2737190 (GG/AA+AG), were associated with moderate/severe chronic periodontitis in Chinese population infected with P. gingivalis. P. gingivalis, which interacted with TLR4 gene plays an important role in the pathogenesis of periodontitis.
Li et al. (2019) TLR4 polymorphisms may increase susceptibility to periodontitis in Pg-positive individuals. PeerJ 7:e7828 https://doi.org/10.7717/peerj.7828
Charcot-Marie-Tooth type 4B2 demyelinating neuropathy in miniature Schnauzer dogs caused by a novel splicing SBF2 (MTMR13) genetic variant: a new spontaneous clinical model
Background Charcot-Marie-Tooth (CMT) disease is the most common neuromuscular disorder in humans affecting 40 out of 100,000 individuals. In 2008, we described the clinical, electrophysiological and pathological findings of a demyelinating motor and sensory neuropathy in Miniature Schnauzer dogs, with a suspected autosomal recessive mode of inheritance based on pedigree analysis. The discovery of additional cases has followed this work and led to a genome-wide association mapping approach to search for the underlying genetic cause of the disease. Methods For genome wide association screening, genomic DNA samples from affected and unaffected dogs were genotyped using the Illumina CanineHD SNP genotyping array. SBF2 and its variant were sequenced using primers and PCRs. RNA was extracted from muscle of an unaffected and an affected dog and RT-PCR performed. Immunohistochemistry for myelin basic protein was performed on peripheral nerve section specimens. Results The genome-wide association study gave an indicative signal on canine chromosome 21. Although the signal was not of genome-wide significance due to the small number of cases, the SBF2 (also known as MTMR13) gene within the region of shared case homozygosity was a strong positional candidate, as 22 genetic variants in the gene have been associated with demyelinating forms of Charcot-Marie-Tooth disease in humans. Sequencing of SBF2 in cases revealed a splice donor site genetic variant, resulting in cryptic splicing and predicted early termination of the protein based on RNA sequencing results. Conclusions This study reports the first genetic variant in Miniature Schnauzer dogs responsible for the occurrence of a demyelinating peripheral neuropathy with abnormally folded myelin. This discovery establishes a genotype/phenotype correlation in affected Miniature Schnauzers that can be used for the diagnosis of these dogs. It further supports the dog as a natural model of a human disease; in this instance, Charcot-Marie-Tooth disease. It opens avenues to search the biological mechanisms responsible for the disease and to test new therapies in a non-rodent large animal model. In particular, recent gene editing methods that led to the restoration of dystrophin expression in a canine model of muscular dystrophy could be applied to other canine models such as this before translation to humans.
Granger et al. (2019) Charcot-Marie-Tooth type 4B2 demyelinating neuropathy in miniature Schnauzer dogs caused by a novel splicing SBF2 (MTMR13) genetic variant: a new spontaneous clinical model. PeerJ 7:e7983 https://doi.org/10.7717/peerj.7983
Stability of the vaginal, oral, and gut microbiota across pregnancy among African American women: the effect of socioeconomic status and antibiotic exposure
Objective A growing body of research has investigated the human microbiota and pregnancy outcomes, especially preterm birth. Most studies of the prenatal microbiota have focused on the vagina, with fewer investigating other body sites during pregnancy. Although pregnancy involves profound hormonal, immunological and metabolic changes, few studies have investigated either shifts in microbiota composition across pregnancy at different body sites or variation in composition at any site that may be explained by maternal characteristics. The purpose of this study was to investigate: (1) the stability of the vaginal, oral, and gut microbiota from early (8–14 weeks) through later (24–30 weeks) pregnancy among African American women according to measures of socioeconomic status, accounting for prenatal antibiotic use; (2) whether measures of socioeconomic status are associated with changes in microbiota composition over pregnancy; and (3) whether exposure to prenatal antibiotics mediate any observed associations between measures of socioeconomic status and stability of the vaginal, oral, and gut microbiota across pregnancy. Methods We used paired vaginal, oral, or gut samples available for 16S rRNA gene sequencing from two time points in pregnancy (8–14 and 24–30 weeks) to compare within-woman changes in measures of alpha diversity (Shannon and Chao1) and beta-diversity (Bray–Curtis dissimilarity) among pregnant African American women (n = 110). Multivariable linear regression was used to examine the effect of level of education and prenatal health insurance as explanatory variables for changes in diversity, considering antibiotic exposure as a mediator, adjusting for age, obstetrical history, and weeks between sampling. Results For the oral and gut microbiota, there were no significant associations between measures of socioeconomic status or prenatal antibiotic use and change in Shannon or Chao1 diversity. For the vaginal microbiota, low level of education (high school or less) was associated with an increase in Shannon and Chao1 diversity over pregnancy, with minimal attenuation when controlling for prenatal antibiotic use. Conversely, for within-woman Bray–Curtis dissimilarity for early compared to later pregnancy, low level of education and prenatal antibiotics were associated with greater dissimilarity for the oral and gut sites, with minimal attenuation when controlling for prenatal antibiotics, and no difference in dissimilarity for the vaginal site. Conclusions Measures of maternal socioeconomic status are variably associated with changes in diversity across pregnancy for the vaginal, oral, and gut microbiota, with minimal attenuation by prenatal antibiotic exposure. Studies that evaluate stability of the microbiota across pregnancy in association with health outcomes themselves associated with socioeconomic status (such as preterm birth) should incorporate measures of socioeconomic status to avoid finding spurious relationships.
Dunlop et al. (2019) Stability of the vaginal, oral, and gut microbiota across pregnancy among African American women: the effect of socioeconomic status and antibiotic exposure. PeerJ 7:e8004 https://doi.org/10.7717/peerj.8004
Sequencing and analyses on chloroplast genomes of Tetrataenium candicans and two allies give new insights on structural variants, DNA barcoding and phylogeny in Apiaceae subfamily Apioideae
Background Tetrataenium candicans is a traditional Chinese folk herbal medicine used in the treatment of asthma and rheumatic arthritis. Alongside several Tordyliinae species with fleshy roots, it is also regarded as a substitute for a Chinese material medicine called ‘Danggui’. However, a lack of sufficient sampling and genomic information has impeded species identification and the protection of wild resources. Methods The complete chloroplast genomes of T. candicans from two populations, Tetrataenium yunnanense and Semenovia transilliensis, were assembled from two pipelines using data generated from next generation sequencing (NGS). Pseudogenes, inverted repeats (IRs) and hyper-variable regions were located by Geneious 11.1.5. Repeat motifs were searched using MISA and REPuter. DNA polymorphism and segment screening were processed by DNAsp5, and PCR product was sequenced with Sanger’s sequencing method. Phylogeny was inferred by MEGA 7.0 and PhyML 3.0. Results The complete chloroplast genomes of T. candicans from two populations, T. yunnanense and S. transilliensis, were 142,261 bp, 141,985 bp, 142,714 bp and 142,145 bp in length, respectively, indicating conservative genome structures and gene categories. We observed duplications of trnH and psbA caused by exceptional contractions and expansions of the IR regions when comparing the four chloroplast genomes with previously published data. Analyses on DNA polymorphism located 29 candidate cp DNA barcodes for the authentication of ‘Danggui’ counterfeits. Meanwhile, 34 hyper-variable markers were also located by the five Tordyliinae chloroplast genomes, and 11 of them were screened for population genetics of T. candicans based on plastome information from two individuals. The screening results indicated that populations of T.candicans may have expanded. Phylogeny inference on Apiaceae species by CDS sequences showed most lineages were well clustered, but the five Tordyliinae species failed to recover as a monophyletic group, and the phylogenetic relationship between tribe Coriandreae, tribe Selineae, subtribe Tordyliinae and Sinodielsia clade remains unclear. Discussion The four chloroplast genomes offer valuable information for further research on species identification, cp genome structure, population demography and phylogeny in Apiaceae subfamily Apioideae.
Kang et al. (2019) Sequencing and analyses on chloroplast genomes of Tetrataenium candicans and two allies give new insights on structural variants, DNA barcoding and phylogeny in Apiaceae subfamily Apioideae. PeerJ 7:e8063 https://doi.org/10.7717/peerj.8063
Experimental evidence of chemical attraction in the mutualistic zebra mussel-killer shrimp system
Invasion facilitation, whereby one species has a positive effect on the establishment of another species, could help explain the rapid colonisation shown by some freshwater invasive species, but the underlying mechanisms remain unclear. We employed two-choice test arenas to test whether the presence of zebra mussel (Dreissena polymorpha) could facilitate the establishment of the killer shrimp (Dikerogammarus villosus). Killer shrimp preferred to settle on mats of zebra mussel, but this was unrelated to mat size, and was not different from attraction shown to artificial grass, suggesting that zebra mussel primarily provides substrate and refuge to the killer shrimp. Killer shrimp were strongly attracted to water scented by zebra mussel, but not to water scented by fish. Chemical attraction to the zebra mussel’s scent did not differ between sympatric and allopatric populations of killer shrimp, suggesting that chemical attraction is not an acquired or learned trait. Our study shows, for the first time, chemical attraction between two highly invasive freshwater species, thereby providing a plausible mechanism for invasion facilitation. This has implications for managing the spread of killer shrimp, and perhaps other freshwater invasive species, because chemical attraction could significantly increase establishment success in mutualistic systems. Failure to consider invasion facilitation may underestimate the risk of establishment, and likely also the impact of some aquatic invaders.
Rolla et al. (2019) Experimental evidence of chemical attraction in the mutualistic zebra mussel-killer shrimp system. PeerJ 7:e8075 https://doi.org/10.7717/peerj.8075
Transcriptome profiling analysis reveals key genes of different coat color in sheep skin
Background To investigate the molecular mechanisms determining the coat color of native breed sheep in Xinjiang. Methods Bashibai sheep, Yemule white sheep and Tulufan black sheep were selected. Illumina HiSeq X Ten sequencing technology was used to detect the genes responsible for the white, light brown, black and cyan gray coat colors in sheep. Sequence analysis and functional gene annotation analysis were performed to analyze the results. The signal pathways and differentially expressed genes related to sheep hair color production regulation were screened and finally verified by real-time polymerase chain reaction. Results Functional annotation by Kyoto Encyclopedia of Genes and Genomes analysis revealed significant differences in enrichment of immunity-related pathways as well as melanogenesis synthetic and tyrosine metabolism pathways. Our results showed that the DCT, TYR, TYRP1, PMEL, SLC45A2 and MLANA six genes may be associated with the regulation of coat color development and provide a theoretical basis for selecting natural coat colors of sheep.
Yao et al. (2019) Transcriptome profiling analysis reveals key genes of different coat color in sheep skin. PeerJ 7:e8077 https://doi.org/10.7717/peerj.8077
Rehabilitation time has greater influences on soil mechanical composition and erodibility than does rehabilitation land type in the hilly-gully region of the Loess Plateau, China
Background The major landscape in the hilly-gully region of the Loess Plateau is greatly affected by vegetation rehabilitation on abandoned cropland. Although many studies have shown that the rehabilitation have greatly improved soil conditions and protected them from erosion, these effectiveness were not always in consensus possibly due to the land type of vegetation or to the rehabilitation time. To close this gap, we conducted a long term experiment as follows. Methods In this study, we analysed four land types of vegetation rehabilitation (shrub land, woodland, naturally revegetated grassland, and orchard land) with different rehabilitation times and investigated the mechanical composition and erodibility of the soil. Areas of slope croplandand natural forest were selected as controls. Results The results showed that soil depth, rehabilitation time and rehabilitation land type had strong impacts on soil mechanical composition, micro-aggregation and erodibility. Following rehabilitation, naturally revegetated grassland and shrub land had lower fractal dimensions of particle size distribution (fractal dimensions of PSD), fractal dimensions of micro-aggregation, and erodibility (K factor) than did cropland. Compared to the positive effects of rehabilitation mainly happened in the topsoil layer at other rehabilitation land type, that of woodland happened in the deeper soil layer. Besides, the indispensable rehabilitation time for the significant improvement of soil condition was shorter at naturally revegetated grassland than that at shrub land and woodland. Discussion Although rehabilitation time was more influential than was rehabilitation land type or soil depth, the differences among the rehabilitation land types showed that naturally revegetated grassland with native plants is the most time-saving rehabilitation vegetation for the Loess Plateau in the conversion from slope cropland. The success of rehabilitation in this forestry practice was mainly contributed by the suited species of rehabilitation land type to the local climate and soil. Based on the differences of rehabilitation effectiveness resulting from land type, we should be cautious to choose land types for the rehabilitation of soil conditions in the Loess Plateau.
Qiao et al. (2019) Rehabilitation time has greater influences on soil mechanical composition and erodibility than does rehabilitation land type in the hilly-gully region of the Loess Plateau, China. PeerJ 7:e8090 https://doi.org/10.7717/peerj.8090
From command-line bioinformatics to bioGUI
Bioinformatics is a highly interdisciplinary field providing (bioinformatics) applications for scientists from many disciplines. Installing and starting applications on the command-line (CL) is inconvenient and/or inefficient for many scientists. Nonetheless, most methods are implemented with a command-line interface only. Providing a graphical user interface (GUI) for bioinformatics applications is one step toward routinely making CL-only applications available to more scientists and, thus, toward a more effective interdisciplinary work. With our bioGUI framework we address two main problems of using CL bioinformatics applications: First, many tools work on UNIX-systems only, while many scientists use Microsoft Windows. Second, scientists refrain from using CL tools which, however, could well support them in their research. With bioGUI install modules and templates, installing and using CL tools is made possible for most scientists—even on Windows, due to bioGUI’s support for Windows Subsystem for Linux. In addition, bioGUI templates can easily be created, making the bioGUI framework highly rewarding for developers. From the bioGUI repository it is possible to download, install and use bioinformatics tools with just a few clicks.
Joppich et al. (2019) From command-line bioinformatics to bioGUI. PeerJ 7:e8111 https://doi.org/10.7717/peerj.8111
First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds
Background Intragenomic variability in 16S rDNA is a limiting factor for taxonomic and diversity characterization of Bacteria, and studies on its occurrence in natural/environmental populations are scarce. In this work, direct DNA amplicon sequencing coupled with frequent-cutter restriction analysis allowed detection of intragenomic 16S rDNA variation in culturable endophytic bacteria from cacao seeds in a fast and attractive manner. Methods Total genomic DNA from 65 bacterial strains was extracted and the 16S rDNA hyper variable V5–V9 regions were amplified for enzyme digestion and direct Sanger-type sequencing. The resulting electropherograms were visually inspected and compared to the corresponding AluI-restriction profiles, as well as to complete genome sequences in databases. Restriction analysis were employed to substitute the need of amplicon cloning and re-sequencing. A specifically improved polyacrylamide-gradient electrophoresis allowed to resolve 5-bp differences in restriction fragment sizes. Chi-square analysis on 2 × 2 contingency table tested for the independence between the ‘number of AluI bands’ and ‘type of eletropherogram’. Results Two types of electropherograms were obtained: unique template, with single peaks per base (clean chromatograms), and heterogeneous template, with various levels of multiple peaks per base (mixed chromatograms). Statistics revealed significant interaction between number of restriction fragments and type of electropherogram for the same amplicons: clean or mixed ones associated to ≤5 or ≥6 bands, respectively. The mixed-template pattern combined with the AluI-restriction profiles indicated a high proportion of 49% of the culturable endophytes from a tropical environment showing evidence of intragenomic 16S rDNA heterogeneity. Conclusion The approach presented here was useful for a rapid, first-tier detection of intragenomic variation in culturable isolates, which can be applied in studies of other natural populations; a preliminary view of intragenomic heterogeneity levels can complement culture-dependent and -independent methods. Consequences of these findings in taxonomic and diversity studies in complex bacterial communities are discussed.
da Silva et al. (2019) First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds. PeerJ 7:e7452 https://doi.org/10.7717/peerj.7452
Importance of considering interoceptive abilities in alexithymia assessment
Background Recent studies have shown that people with high alexithymia scores have decreased interoceptive abilities, which can be associated with psychological and physical disorders. Early assessments of the alexithymia trait included the evaluation of these abilities through the dimension measuring the difficulty in identifying and distinguishing between feelings and bodily sensations (the 26-item Toronto Alexithymia Scale; TAS-26). The revised version of the TAS, the TAS-20, contains a three-factor solution that does not involve a dimension assessing interoceptive abilities. However, the three items allowing the evaluation of these abilities are still present in the TAS-20. In this context, we hypothesized that the 3 items which assess interoceptive abilities in the TAS-20 should constitute an independent factor. In addition to exploring the internal structure of the TAS-20, we examined its external validity by assessing the relationships between the new factors and self-reported measures of personality trait and psychological and physical health. Method Two online studies (N = 253 and N = 287) were performed. The participants completed the TAS-20 and a set of psychological questionnaires (e.g., anxiety, depression) and health questions (e.g., “Do you suffer from a somatic disorder?”). The structure of the TAS-20 was examined using exploratory factor analysis (EFA), followed by an investigation of the relationships between the resulting new factors and other psychological and health data using regressions. In both studies, EFA revealed a new structure of the questionnaire consisting of four dimensions: (1) difficulty in the awareness of feelings, (2) externally oriented thinking, (3) difficulty in interoceptive abilities, and (4) poor affective sharing. The first factor was positively associated with all self-reported psychological and personality trait measures while the third factor was associated more with somatic disorders and medication intake. Results Our results suggest the presence of a new latent factor in the assessment of alexithymia that reflects interoceptive abilities specifically related to health and personality trait outcomes. In accordance with the results and the literature, it seems important to include an assessment of interoceptive abilities when considering the evaluation of alexithymia. The next step would be to develop a valid measure of these abilities.
Fournier et al. (2019) Importance of considering interoceptive abilities in alexithymia assessment. PeerJ 7:e7615 https://doi.org/10.7717/peerj.7615
Magnetically directed antioxidant and antimicrobial agent: synthesis and surface functionalization of magnetite with quercetin
Oxidative stress can be reduced substantially using nanoantioxidant materials by tuning its surface morphological features up to a greater extent. The physiochemical, biological and optical properties of the nanoantioxidants can be altered by controlling their size and shape. In view of that, an appropriate synthesis technique should be adopted with optimization of the process variables. Properties of magnetite nanoparticles (IONP) can be tailored to upgrade the performance of biomedicine. Present research deals with the functionalization IONP using a hydrophobic agent of quercetin (Q). The application of quercetin will control its size using both the functionalization method including in-situ and post-synthesis technique. In in-situ techniques, the functionalized magnetite nanoparticles (IONP@Q) have average particles size 6 nm which are smaller than the magnetite (IONP) without functionalization. After post functionalization technique, the average particle size of magnetite IONP@Q2 determined was 11 nm. The nanoparticles also showed high saturation magnetization of about 51–59 emu/g. Before starting the experimental lab work, Prediction Activity Spectra of Substances (PASS) software was used to have a preliminary idea about the biological activities of Q. The antioxidant activity was carried out using 2, 2-diphenyl-1-picrylhydrazyl (DPPH) assay. The antibacterial studies were carried out using well diffusion method. The results obtained were well supported by the simulated results. Furthermore, the values of the half maximal inhibitory concentration (IC50) of the DPPH antioxidant assay were decreased using the functionalized one and it exhibited a 2–3 fold decreasing tendency than the unfunctionalized IONP. This exhibited that the functionalization process can easily enhance the free radical scavenging properties of IONPs up to three times. MIC values confirms that functionalized IONP have excellent antibacterial properties against the strains used (Staphylococcus aureus, Bacillus subtilis and Escherichia coli) and fungal strains (Aspergillus niger, Candida albicans, Trichoderma sp. and Saccharomyces cerevisiae). The findings of this research showed that the synthesized nanocomposite has combinatorial properties (magnetic, antioxidant and antimicrobial) which can be considered as a promising candidate for biomedical applications. It can be successfully used for the development of biomedicines which can be subsequently applied as antioxidant, anti-inflammatory, antimicrobial and anticancer agents.
Shah et al. (2019) Magnetically directed antioxidant and antimicrobial agent: synthesis and surface functionalization of magnetite with quercetin. PeerJ 7:e7651 https://doi.org/10.7717/peerj.7651
Validating anthropogenic threat maps as a tool for assessing river ecological integrity in Andean–Amazon basins
Anthropogenic threat maps are commonly used as a surrogate for the ecological integrity of rivers in freshwater conservation, but a clearer understanding of their relationships is required to develop proper management plans at large scales. Here, we developed and validated empirical models that link the ecological integrity of rivers to threat maps in a large, heterogeneous and biodiverse Andean–Amazon watershed. Through fieldwork, we recorded data on aquatic invertebrate community composition, habitat quality, and physical-chemical parameters to calculate the ecological integrity of 140 streams/rivers across the basin. Simultaneously, we generated maps that describe the location, extent, and magnitude of impact of nine anthropogenic threats to freshwater systems in the basin. Through seven-fold cross-validation procedure, we found that regression models based on anthropogenic threats alone have limited power for predicting the ecological integrity of rivers. However, the prediction accuracy improved when environmental predictors (slope and elevation) were included, and more so when the predictions were carried out at a coarser scale, such as microbasins. Moreover, anthropogenic threats that amplify the incidence of other pressures (roads, human settlements and oil activities) are the most relevant predictors of ecological integrity. We concluded that threat maps can offer an overall picture of the ecological integrity pattern of the basin, becoming a useful tool for broad-scale conservation planning for freshwater ecosystems. While it is always advisable to have finer scale in situ measurements of ecological integrity, our study shows that threat maps provide fast and cost-effective results, which so often are needed for pressing management and conservation actions.
Spatial and Geographic Information Science
Lessmann et al. (2019) Validating anthropogenic threat maps as a tool for assessing river ecological integrity in Andean–Amazon basins. PeerJ 7:e8060 https://doi.org/10.7717/peerj.8060
Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey
Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children’s health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.
Cabrera-Contreras et al. (2019) Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey. PeerJ 7:e8068 https://doi.org/10.7717/peerj.8068
New sources of Sym2A allele in the pea (Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX
At the onset of legume-rhizobial symbiosis, the mutual recognition of partners occurs based on a complicated interaction between signal molecules and receptors. Bacterial signal molecules named Nod factors (“nodulation factors”) are perceived by the plant LysM-containing receptor-like kinases (LysM-RLKs) that recognize details of its structure (i.e., unique substitutions), thus providing the conditions particular to symbiosis. In the garden pea (Pisum sativum L.), the allelic state of Sym2 gene has long been reported to regulate the symbiotic specificity: for infection to be successful, plants with the Sym2A allele (for “Sym2 Afghan”, as these genotypes originate mostly from Afghanistan) require an additional acetylation of the Nod factor which is irrelevant for genotypes with the Sym2E allele (for “Sym2 European”). Despite being described about 90 years ago, Sym2 has not yet been cloned, though phenotypic analysis suggests it probably encodes a receptor for the Nod factor. Recently, we described a novel pea gene LykX (PsLykX) from the LysM-RLK gene family that demonstrates a perfect correlation between its allelic state and the symbiotic specificity of the Sym2A-type. Here we report on a series of Middle-Eastern pea genotypes exhibiting the phenotype of narrow symbiotic specificity discovered in the VIR plant genetic resources gene bank (Saint-Petersburg, Russia). These genotypes are new sources of Sym2A, as has been confirmed by an allelism test with Sym2A pea cv. Afghanistan. Within these genotypes, LykX is present either in the allelic state characteristic for cv. Afghanistan, or in another, minor allelic state found in two genotypes from Tajikistan and Turkmenistan. Plants carrying the second allele demonstrate the same block of rhizobial infection as cv. Afghanistan when inoculated with an incompatible strain. Intriguingly, this “Tajik” allele of LykX differs from the “European” one by a single nucleotide polymorphism leading to an R75P change in the receptor part of the putative protein. Thus, our new data are in agreement with the hypothesis concerning the identity of LykX and the elusive Sym2 gene.
Sulima et al. (2019) New sources of Sym2A allele in the pea (Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX. PeerJ 7:e8070 https://doi.org/10.7717/peerj.8070
Transcriptional characterization and response to defense elicitors of mevalonate pathway genes in cotton (Gossypium arboreum L.)
The mevalonate (MVA) pathway is responsible for the biosynthesis of cytosolic terpenes including gossypol and its derivatives, which play an important role in the cotton plant’s defense against pathogens and herbivores. In this study, we identified and cloned 17 potentially functional genes encoding enzymes that catalyze the six steps of the MVA pathway in Gossypium arboreum. Expression pattern analysis by qRT-PCR demonstrated that these genes had tissue-specific expression profiles and were most prevalently expressed in roots. Moreover, these genes were up-regulated in response to several elicitors, including methyl jasmonate and salicylic acid, as well as Verticillium dahliae infection and Helicoverpa armigera infestation. This indicates that the MVA pathway genes are involved in the signaling pathway regulated by exogenous hormones and the resistance of cotton plants to pathogens and herbivores. Our results improve the understanding of cytosolic terpene biosynthesis in Gossypium species and lay the foundation for further research on gossypol biosynthesis.
Zhang et al. (2019) Transcriptional characterization and response to defense elicitors of mevalonate pathway genes in cotton (Gossypium arboreum L.). PeerJ 7:e8123 https://doi.org/10.7717/peerj.8123
Roles of phytohormone changes in the grain yield of rice plants exposed to heat: a review
During its reproductive phase, rice is susceptible to heat stress. Heat events will occur at all stages during the reproductive phase of rice as a result of global warming. Moreover, rice yield traits respond differently to heat stress during panicle initiation, flowering and grain filling. The reduction in the number of spikelets per panicle of heat-stressed plants is due to the attenuated differentiation of secondary branches and their attached florets as well as the promotion of their degradation during the panicle-initiation stage but is not affected by heat stress thereafter. Spikelet sterility as a result of heat stress is attributed not only to physiological abnormalities in the reproductive organs during the flowering stage but also to structural and morphological abnormalities in reproductive organs during the panicle-initiation stage. The reduced grain weight of heat-stressed plants is due to a reduction in nonstructural carbohydrates, undeveloped vascular bundles, and a reduction in glume size during the panicle-initiation stage, while a shortened grain-filling duration, reduced grain-filling rate, and decreased grain width contribute to reduced grain weight during the grain-filling stage. Thus, screening and breeding rice varieties that have comprehensive tolerance to heat stress at all time points during their reproductive stage may be possible to withstand unpredictable heat events in the future. The responses of yield traits to heat stress are regulated by phytohormone levels, which are determined by phytohormone homeostasis. Currently, the biosynthesis and transport of phytohormones are the key processes that determine phytohormone levels in and grain yield of rice under heat stress. Studies on phytohormone homeostatic responses are needed to further reveal the key processes that determine phytohormone levels under heat conditions.
Wu et al. (2019) Roles of phytohormone changes in the grain yield of rice plants exposed to heat: a review. PeerJ 7:e7792 https://doi.org/10.7717/peerj.7792
Low expression or hypermethylation of PLK2 might predict favorable prognosis for patients with glioblastoma multiforme
Background As the most aggressive brain tumor, patients with glioblastoma multiforme (GBM) have a poor prognosis. Our purpose was to explore prognostic value of Polo-like kinase 2 (PLK2) in GBM, a member of the PLKs family. Methods The expression profile of PLK2 in GBM was obtained from The Cancer Genome Atlas database. The PLK2 expression in GBM was tested. Kaplan–Meier curves were generated to assess the association between PLK2 expression and overall survival (OS) in patients with GBM. Furthermore, to assess its prognostic significance in patients with primary GBM, we constructed univariate and multivariate Cox regression models. The association between PLK2 expression and its methylation was then performed. Differentially expressed genes correlated with PLK2 were identified by Pearson test and functional enrichment analysis was performed. Results Overall survival results showed that low PLK2 expression had a favorable prognosis of patients with GBM (P-value = 0.0022). Furthermore, PLK2 (HR = 0.449, 95% CI [0.243–0.830], P-value = 0.011) was positively associated with OS by multivariate Cox regression analysis. In cluster 5, DNA methylated PLK2 had the lowest expression, which implied that PLK2 expression might be affected by its DNA methylation status in GBM. PLK2 in CpG island methylation phenotype (G-CIMP) had lower expression than non G-CIMP group (P = 0.0077). Regression analysis showed that PLK2 expression was negatively correlated with its DNA methylation (P = 0.0062, Pearson r = −0.3855). Among all differentially expressed genes of GBM, CYGB (r = 0.5551; P < 0.0001), ISLR2 (r = 0.5126; P < 0.0001), RPP25 (r = 0.5333; P < 0.0001) and SOX2 (r = −0.4838; P < 0.0001) were strongly correlated with PLK2. Functional enrichment analysis results showed that these genes were enriched several biological processes or pathways that were associated with GBM. Conclusion Polo-like kinase 2 expression is regulated by DNA methylation in GBM, and its low expression or hypermethylation could be considered to predict a favorable prognosis for patients with GBM.
Xia et al. (2019) Low expression or hypermethylation of PLK2 might predict favorable prognosis for patients with glioblastoma multiforme. PeerJ 7:e7974 https://doi.org/10.7717/peerj.7974
Hematological convergence between Mesozoic marine reptiles (Sauropterygia) and extant aquatic amniotes elucidates diving adaptations in plesiosaurs
Plesiosaurs are a prominent group of Mesozoic marine reptiles, belonging to the more inclusive clades Pistosauroidea and Sauropterygia. In the Middle Triassic, the early pistosauroid ancestors of plesiosaurs left their ancestral coastal habitats and increasingly adapted to a life in the open ocean. This ecological shift was accompanied by profound changes in locomotion, sensory ecology and metabolism. However, investigations of physiological adaptations on the cellular level related to the pelagic lifestyle are lacking so far. Using vascular canal diameter, derived from osteohistological thin-sections, we show that inferred red blood cell size significantly increases in pistosauroids compared to more basal sauropterygians. This change appears to have occurred in conjunction with the dispersal to open marine environments, with cell size remaining consistently large in plesiosaurs. Enlarged red blood cells likely represent an adaptation of plesiosaurs repeated deep dives in the pelagic habitat and mirror conditions found in extant marine mammals and birds. Our results emphasize physiological aspects of adaptive convergence among fossil and extant marine amniotes and add to our current understanding of plesiosaur evolution.
Fleischle et al. (2019) Hematological convergence between Mesozoic marine reptiles (Sauropterygia) and extant aquatic amniotes elucidates diving adaptations in plesiosaurs. PeerJ 7:e8022 https://doi.org/10.7717/peerj.8022
Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum)
Superoxide dismutases (SODs) are a family of key antioxidant enzymes that play a crucial role in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, a genome-wide analysis of the SOD gene family in wheat were performed. Twenty-six SOD genes were identified from the whole genome of wheat, including 17 Cu/Zn-SODs, six Fe-SODs, and three Mn-SODs. The chromosomal location mapping analysis indicated that these three types of SOD genes were only distributed on 2, 4, and 7 chromosomes, respectively. Phylogenetic analyses of wheat SODs and several other species revealed that these SOD proteins can be assigned to two major categories. SOD1 mainly comprises of Cu/Zn-SODs, and SOD2 mainly comprises of Fe-SODs and Mn-SODs. Gene structure and motif analyses indicated that most of the SOD genes showed a relatively conserved exon/intron arrangement and motif composition. Analyses of transcriptional data indicated that most of the wheat SOD genes were expressed in almost all of the examined tissues and had important functions in abiotic stress resistance. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to reveal the regulating roles of wheat SOD gene family in response to NaCl, mannitol, and polyethylene glycol stresses. qRT-PCR showed that eight randomly selected genes with relatively high expression levels responded to all three stresses based on released transcriptome data. However, their degree of response and response patterns were different. Interestingly, among these genes, TaSOD1.7, TaSOD1.9, TaSOD2.1, and TaSOD2.3 feature research value owing to their remarkable expression-fold change in leaves or roots under different stresses. Overall, our results provide a basis of further functional research on the SOD gene family in wheat and facilitate their potential use for applications in the genetic improvement on wheat in drought and salt stress environments.
Jiang et al. (2019) Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum). PeerJ 7:e8062 https://doi.org/10.7717/peerj.8062
Environmental sampling to assess the bioburden of Mycobacterium avium subspecies paratuberculosis in drylot pens on California dairies
Mycobacterium avium subspecies paratuberculosis (MAP) is a bacterium that can cause substantial economic losses in infected dairy herds due to reduced milk production and increased cow-replacement costs. In order to control MAP in dairies with drylot pens, a standardized environmental sampling protocol to quantify MAP in fecal slurry was developed based on an existing protocol for freestall pens. Specifically, following a 24 h hold of the flush, a grab sample of approximately 10 ml of fecal slurry was collected every 1 m along the flush lane of the drylot pens, avoiding individual cow fecal pats. To determine the reliability and repatability of the new environmental sampling protocol for estimation of MAP bioburden at the pen level, two collectors simultaneously collected fecal slurry samples every day for 3 days from six drylot cow pens on two Central California dairies. During the study period no cow movement between pens was allowed with the exception of sick cows. The study herds had MAP seroprevalence of 5.8% and 3.2%, respectively, based on whole pen serum ELISA results. Variance components models for quantitative real-time PCR (qPCR) results showed samples collected from different pens on different dairies accounted for greater variablitiy in MAP concentration (65%), while samples collected by different collectors had the least variability (0.1%). In contrast, variability in MAP concentration in environmental samples collected on different days had 25% variability. The intraclass correlation coefficient showed high reliability (93%) of environmental sampling simultaneously by different collectors. In contrast, the reliability of environmental sampling at different days was 65%, which was similar to the reliability for sampling by different collectors on different days. Investigators can expect high reliability when employing the new environmental sampling protocol along with qPCR testing of environmental samples from drylot pens.
Chamchoy et al. (2019) Environmental sampling to assess the bioburden of Mycobacterium avium subspecies paratuberculosis in drylot pens on California dairies. PeerJ 7:e8081 https://doi.org/10.7717/peerj.8081
The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster
Microorganisms play a central role in the biology of vinegar flies such as Drosophila suzukii and Drosophila melanogaster: serving as a food source to both adults and larvae, and influencing a range of traits including nutrition, behavior, and development. The niches utilized by the fly species partially overlap, as do the microbiota that sustain them, and interactions among these players may drive the development of crop diseases. To learn more about how the microbiota of one species may affect the other, we isolated and identified microbes from field-caught D. suzukii, and then characterized their effects on D. melanogaster larval development time in the laboratory. We found that the D. suzukii microbiota consistently included both yeasts and bacteria. It was dominated by yeasts of the genus Hanseniaspora, and bacteria from the families Acetobacteraceae and Enterobacteriaceae. Raising D. melanogaster under gnotobiotic conditions with each microbial isolate individually, we found that some bacteria promoted larval development relative to axenic conditions, but most did not have a significant effect. In contrast, nearly all the yeasts tested significantly accelerated larval development. The one exception was Starmerella bacillaris, which had the opposite effect: significantly slowing larval developmental rate. We investigated the basis for this effect by examining whether S. bacillaris cells could sustain larval growth, and measuring the survival of S. bacillaris and other yeasts in the larval gut. Our results suggest S. bacillaris is not digested by D. melanogaster and therefore cannot serve as a source of nutrition. These findings have interesting implications for possible interactions between the two Drosophilia species and their microbiota in nature. Overall, we found that microbes isolated from D. suzukii promote D. melanogaster larval development, which is consistent with the model that infestation of fruit by D. suzukii can open up habitat for D. melanogaster. We propose that the microbiome is an important dimension of the ecological interactions between Drosophila species.
Solomon et al. (2019) The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster. PeerJ 7:e8097 https://doi.org/10.7717/peerj.8097
Decrease in walking speed increases hip moment impulse in the frontal plane during the stance phase
Background Increased daily cumulative hip moment in the frontal plane (i.e., the product of hip moment impulse in the frontal plane during the stance phase and mean steps per day) is a risk factor for progression of hip osteoarthritis. Although hip osteoarthritis generally causes a decrease in the walking speed, its effect on hip moment impulse in the frontal plane is unclear. The purpose of this study was to examine the relationship between decrease in walking speed and hip moment impulse in the frontal plane. Methods We used a public dataset of treadmill walking in 17 older adults (mean (SD) age: 63.2 (8.0) years). The subjects walked on the treadmill for 30 s under five conditions: (1) 40% of comfortable non-dimensional speed (CNDS), (2) 55% CNDS, (3) 70% CNDS, (4) 85% CNDS, and (5) 100% CNDS. The hip moment impulse in the frontal plane non-normalized (or normalized) to step length (Nm s/kg [or Nm s/(kg m)]) for each condition was calculated. Furthermore, the relationship between walking speed and hip moment impulse in the frontal plane non-normalized (or normalized) to step length was examined using regression analysis based on a previous study. Results A decrease in non-dimensional speed (i.e., walking speed) significantly increased the non-normalized (or normalized) hip moment impulse in the frontal plane during the stance phase. The relationship between walking speed and non-normalized (or normalized) hip moment impulse in the frontal plane was fitted by a second-order polynomial. Discussion This study revealed that a decrease in walking speed increased the non-normalized (or normalized) hip moment impulse in the frontal plane in healthy older adults. This finding is useful for understanding the relationship between walking speed and hip moment impulse in the frontal plane and suggests that a decrease in walking speed may actually increase the daily cumulative hip moment in the frontal plane of patients with hip osteoarthritis.
Inai et al. (2019) Decrease in walking speed increases hip moment impulse in the frontal plane during the stance phase. PeerJ 7:e8110 https://doi.org/10.7717/peerj.8110
First palaeoneurological study of a sauropod dinosaur from France and its phylogenetic significance
Despite continuous improvements, our knowledge of the palaeoneurology of sauropod dinosaurs is still deficient. This holds true even for Titanosauria, which is a particularly speciose clade of sauropods with representatives known from numerous Cretaceous sites in many countries on all continents. The data currently available regarding the palaeoneurology of titanosaurs is strongly biased towards Gondwanan forms (Argentina above all, but also India, Malawi and Australia). In contrast, the palaeoneurology of Laurasian titanosaurs is known only from a few taxa from Spain and Uzbekistan, despite the discovery in other countries of Laurasia of a number of neurocranial remains that would lend themselves well to investigations of this kind. To fill in this gap in our knowledge, we subjected a titanosaurian braincase from the uppermost Upper Cretaceous of southern France to X-ray computed tomographic scanning, allowing the generation of 3D renderings of the endocranial cavity enclosing the brain, cranial nerves and blood vessels, as well as the labyrinth of the inner ear. These reconstructions are used to clarify the phylogenetic position of the specimen from the Fox-Amphoux-Métisson site. A combination of characters, including the presence of two hypoglossal rami on the endocast, the average degree of development of the dorsal-head/caudal-middle-cerebral vein system and the relatively short and subequal lengths of the ipsilateral semicircular canals of the labyrinth, are particularly revealing in this respect. They suggest that, compared with the few other Laurasian titanosaurs for which in-depth palaeoneurological data are available, the French taxon is more derived than the distinctly more ancient, possibly non-lithostrotian titanosaur from the Uzbek site of Dzharakuduk but more basal than derived saltasaurids, such as the coeval or slightly more recent forms from the Spanish locality of Lo Hueco.
Knoll et al. (2019) First palaeoneurological study of a sauropod dinosaur from France and its phylogenetic significance. PeerJ 7:e7991 https://doi.org/10.7717/peerj.7991
Bibliographic revision of Mesacanthion Filipjev, 1927 (Nematoda: Thoracostomopsidae) with description of a new species from Jeju Island, South Korea
A new species of the genus Mesacanthion Filipjev, 1927 was discovered during a survey of natural beaches of Jeju Island in South Korea. The new species Mesacanthion jejuensis sp. nov. shares general morphology of the genus such as the outer labial and cephalic setae being situated at the middle of cephalic capsule, well-developed mandibles with two columns united by a curved bar, and three equally sized and shaped teeth shorter than the mandibles. The new species belongs to a group of Mesacanthion species in which spicules are shorter than two anal body diameters. The new species is most closely related to M. pannosum, first discovered in Puget Sound, Washington, in terms of having enlarged cervical setae flap at the end of cephalic capsule, spicules which are shorter than 2 anal body diameter, both supplementary organ and gubernaculum. It can be distinguished from M. pannosum by its stronger inner labial setae, longer outer labial setae, and difference in the index value of b and c’. Along with the description of Mesacanthion jejuensis sp. nov., the genus Mesacanthion Filipjev, 1927 is bibliographically reviewed and revised. Including the new species, a total of 48 species are described within the genus; 39 which are valid; eight which are considered to be species inquirenda due to misplacement of genus and poor description; one which is considered nomen nudum. An updated diagnosis of the genus is provided along with a compiled tabular key comparing different diagnostic morphological characters of all valid species, as well as a pictorial key consisting of 21 species with spicules shorter than two anal body diameters.
Jeong et al. (2019) Bibliographic revision of Mesacanthion Filipjev, 1927 (Nematoda: Thoracostomopsidae) with description of a new species from Jeju Island, South Korea. PeerJ 7:e8023 https://doi.org/10.7717/peerj.8023
Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies
Host-associated gut microbiota can have significant impacts on host ecology and evolution and are often host-specific. Multiple factors can contribute to such host-specificity: (1) host dietary specialization passively determining microbial colonization, (2) hosts selecting for specific diet-acquired microbiota, or (3) a combination of both. The latter possibilities indicate a functional association and should produce stable microbiota. We tested these alternatives by analyzing the gut bacterial communities of six species of wild adult dragonfly populations collected across several geographic locations. The bacterial community composition was predominantly explained by sampling location, and only secondarily by host identity. To distinguish the role of host dietary specialization and host-imposed selection, we identified prey in the guts of three dragonfly species. Surprisingly, the dragonflies–considered to be generalist predators–consumed distinct prey; and the prey diversity was strongly correlated with the gut bacterial profile. Such host dietary specialization and spatial variation in bacterial communities suggested passive rather than selective underlying processes. Indeed, the abundance and distribution of 72% of bacterial taxa were consistent with neutral community assembly; and fluorescent in situ hybridization revealed that bacteria only rarely colonized the gut lining. Our results contradict the expectation that host-imposed selection shapes the gut microbiota of most insects, and highlight the importance of joint analyses of diet and gut microbiota of natural host populations.
Deb et al. (2019) Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies. PeerJ 7:e8058 https://doi.org/10.7717/peerj.8058
A recombinase polymerase amplification-lateral flow dipstick assay for rapid detection of the quarantine citrus pathogen in China, Phytophthora hibernalis
Phytophthora hibernalis, the causal agent of brown rot of citrus fruit, is an important worldwide pathogen and a quarantine pest in China. Current diagnosis of the disease relies on disease symptoms, pathogen isolation and identification by DNA sequencing. However, symptoms caused by P. hibernalis can be confused with those by other Phytophthora and fungal species. Moreover, pathogen isolation, PCR amplification and sequencing are time-consuming. In this study, a rapid assay including 20-min recombinase polymerase amplification targeting the Ypt1 gene and 5-min visualization using lateral flow dipsticks was developed for detecting P. hibernalis. This assay was able to detect 0.2 ng of P. hibernalis genomic DNA in a 50-µL reaction system. It was specific to P. hibernalis without detection of other tested species including P. citrophthora, P. nicotianae, P. palmivora and P. syringae, four other important citrus pathogens. Using this assay, P. hibernalis was also detected from artificially inoculated orange fruits. Results in this study indicated that this assay has the potential application to detect P. hibernalis at diagnostic laboratories and plant quarantine departments of customs, especially under time- and resource-limited conditions.
Dai et al. (2019) A recombinase polymerase amplification-lateral flow dipstick assay for rapid detection of the quarantine citrus pathogen in China, Phytophthora hibernalis. PeerJ 7:e8083 https://doi.org/10.7717/peerj.8083
Acquisition of fungi from the environment modifies ambrosia beetle mycobiome during invasion
Microbial symbionts can play critical roles when their host attempts to colonize a new habitat. The lack of symbiont adaptation can in fact hinder the invasion process of their host. This scenario could change if the exotic species are able to acquire microorganisms from the invaded environment. Understanding the ecological factors that influence the take-up of new microorganisms is thus essential to clarify the mechanisms behind biological invasions. In this study, we tested whether different forest habitats influence the structure of the fungal communities associated with ambrosia beetles. We collected individuals of the most widespread exotic (Xylosandrus germanus) and native (Xyleborinus saxesenii) ambrosia beetle species in Europe in several old-growth and restored forests. We characterized the fungal communities associated with both species via metabarcoding. We showed that forest habitat shaped the community of fungi associated with both species, but the effect was stronger for the exotic X. germanus. Our results support the hypothesis that the direct contact with the mycobiome of the invaded environment might lead an exotic species to acquire native fungi. This process is likely favored by the occurrence of a bottleneck effect at the mycobiome level and/or the disruption of the mechanisms sustaining co-evolved insect-fungi symbiosis. Our study contributes to the understanding of the factors affecting insect-microbes interactions, helping to clarify the mechanisms behind biological invasions.
Rassati et al. (2019) Acquisition of fungi from the environment modifies ambrosia beetle mycobiome during invasion. PeerJ 7:e8103 https://doi.org/10.7717/peerj.8103
Angiogenic signaling in the lungs of a metabolically suppressed hibernating mammal (Ictidomys tridecemlineatus)
To conserve energy in times of limited resource availability, particularly during cold winters, hibernators suppress even the most basic of physiologic processes. Breathing rates decrease from 40 breaths/minute to less than 1 breath/min as they decrease body temperature from 37 °C to ambient. Nevertheless, after months of hibernation, these incredible mammals emerge from torpor unscathed. This study was conducted to better understand the protective and possibly anti-inflammatory adaptations that hibernator lungs may use to prevent damage associated with entering and emerging from natural torpor. We postulated that the differential protein expression of soluble protein receptors (decoy receptors that sequester soluble ligands to inhibit signal transduction) would help identify inhibited inflammatory signaling pathways in metabolically suppressed lungs. Instead, the only two soluble receptors that responded to torpor were sVEGFR1 and sVEGFR2, two receptors whose full-length forms are bound by VEGF-A to regulate endothelial cell function and angiogenesis. Decreased sVEGFR1/2 correlated with increased total VEGFR2 protein levels. Maintained or increased levels of key γ-secretase subunits suggested that decreased sVEGFR1/2 protein levels were not due to decreased levels of intramembrane cleavage complex subunits. VEGF-A protein levels did not change, suggesting that hibernators may regulate VEGFR1/2 signaling at the level of the receptor instead of increasing relative ligand abundance. A panel of angiogenic factors used to identify biomarkers of angiogenesis showed a decrease in FGF-1 and an increase in BMP-9. Torpid lungs may use VEGF and BMP-9 signaling to balance angiogenesis and vascular stability, possibly through the activation of SMAD signaling for adaptive tissue remodeling.
Logan et al. (2019) Angiogenic signaling in the lungs of a metabolically suppressed hibernating mammal (Ictidomys tridecemlineatus). PeerJ 7:e8116 https://doi.org/10.7717/peerj.8116
Single-molecule real-time sequencing identifies massive full-length cDNAs and alternative-splicing events that facilitate comparative and functional genomics study in the hexaploid crop sweet potato
Background Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important crops in many developing countries and provides a candidate source of bioenergy. However, neither a complete reference genome nor large-scale full-length cDNA sequences for this outcrossing hexaploid crop are available, which in turn impedes progress in research studies in I. batatas functional genomics and molecular breeding. Methods In this study, we sequenced full-length transcriptomes in I. batatas and its diploid ancestor I. trifida by single-molecule real-time sequencing and Illumina second-generation sequencing technologies. With the generated datasets, we conducted comprehensive intraspecific and interspecific sequence analyses and experimental characterization. Results A total of 53,861/51,184 high-quality long-read transcripts were obtained, which covered about 10,439/10,452 loci in the I. batatas/I. trifida genome. These datasets enabled us to predict open reading frames successfully in 96.83%/96.82% of transcripts and identify 34,963/33,637 full-length cDNA sequences, 1,401/1,457 transcription factors, 25,315/27,090 simple sequence repeats, 1,656/1,389 long non-coding RNAs, and 5,251/8,901 alternative splicing events. Approximately, 32.34%/38.54% of transcripts and 46.22%/51.18% multi-exon transcripts underwent alternative splicing in I. batatas/I. trifida. Moreover, we validated one alternative splicing event in each of 10 genes and identified tuberous-root-specific expressed isoforms from a starch-branching enzyme, an alpha-glucan phosphorylase, a neutral invertase, and several ABC transporters. Overall, the collection and analysis of large-scale long-read transcripts generated in this study will serve as a valuable resource for the I. batatas research community, which may accelerate the progress in its structural, functional, and comparative genomics studies.
Ding et al. (2019) Single-molecule real-time sequencing identifies massive full-length cDNAs and alternative-splicing events that facilitate comparative and functional genomics study in the hexaploid crop sweet potato. PeerJ 7:e7933 https://doi.org/10.7717/peerj.7933
Identification of novel BRCA1 large genomic rearrangements by a computational algorithm of amplicon-based Next-Generation Sequencing data
Background Genetic testing for BRCA1/2 germline mutations in hereditary breast/ovarian cancer patients requires screening for single nucleotide variants, small insertions/deletions and large genomic rearrangements (LGRs). These studies have long been run by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). The recent introduction of next-generation sequencing (NGS) platforms dramatically improved the speed and the efficiency of DNA testing for nucleotide variants, while the possibility to correctly detect LGRs by this mean is still debated. The purpose of this study was to establish whether and to which extent the development of an analytical algorithm could help us translating NGS sequencing via an Ion Torrent PGM platform into a tool suitable to identify LGRs in hereditary breast-ovarian cancer patients. Methods We first used NGS data of a group of three patients (training set), previously screened in our laboratory by conventional methods, to develop an algorithm for the calculation of the dosage quotient (DQ) to be compared with the Ion Reporter (IR) analysis. Then, we tested the optimized pipeline with a consecutive cohort of 85 uncharacterized probands (validation set) also subjected to MLPA analysis. Characterization of the breakpoints of three novel BRCA1 LGRs was obtained via long-range PCR and direct sequencing of the DNA products. Results In our cohort, the newly defined DQ-based algorithm detected 3/3 BRCA1 LGRs, demonstrating 100% sensitivity and 100% negative predictive value (NPV) (95% CI [87.6–99.9]) compared to 2/3 cases detected by IR (66.7% sensitivity and 98.2% NPV (95% CI [85.6–99.9])). Interestingly, DQ and IR shared 12 positive results, but exons deletion calls matched only in five cases, two of which confirmed by MLPA. The breakpoints of the 3 novel BRCA1 deletions, involving exons 16–17, 21–22 and 20, have been characterized. Conclusions Our study defined a DQ-based algorithm to identify BRCA1 LGRs using NGS data. Whether confirmed on larger data sets, this tool could guide the selection of samples to be subjected to MLPA analysis, leading to significant savings in time and money.
Nicolussi et al. (2019) Identification of novel BRCA1 large genomic rearrangements by a computational algorithm of amplicon-based Next-Generation Sequencing data. PeerJ 7:e7972 https://doi.org/10.7717/peerj.7972
Differences in the importance of microcephaly, dysmorphism, and epilepsy in the detection of pathogenic CNVs in ID and ASD patients
Background Autism spectrum disorders (ASD) and intellectual disabilities (ID) are heterogeneous and complex developmental diseases with significant genetic backgrounds and overlaps of genetic susceptibility loci. Copy number variants (CNVs) are known to be frequent causes of these impairments. However, the clinical heterogeneity of both disorders causes the diagnostic efficacy of CNV analysis to be modest. This could be resolved by stratifying patients according to their clinical features. Aim First, we sought to assess the significance of particular clinical features for the detection of pathogenic CNVs in separate groups of ID and ASD patients and determine whether and how these groups differ from each other in the significance of these variables. Second, we aimed to create a statistical model showing how particular clinical features affect the probability of pathogenic CNV findings. Method We tested a cohort of 204 patients with ID (N = 90) and ASD (N = 114) for the presence of pathogenic CNVs. We stratified both groups according to their clinical features. Fisher’s exact test was used to determine the significance of these variables for pathogenic CNV findings. Logistic regression was used to create a statistical model of pathogenic CNV findings. Results The frequency of pathogenic CNV was significantly higher in the ID group than in the ASD group: 18 (19.78%) versus 8 (7%) (p < 0.004). Microcephaly showed a significant association with pathogenic findings in ID patients (p < 0.01) according to Fisher’s exact test, whereas epilepsy showed a significant association with pathogenic findings in ASD patients (p < 0.01). The probability of pathogenic CNV findings when epilepsy occurred in ASD patients was more than two times higher than if epilepsy co-occurred with ID (29.6%/14.0%). Facial dysmorphism was a significant variable for detecting pathogenic CNVs in both groups (ID p = 0.05, ASD p = 0.01). However, dysmorphism increased the probability of pathogenic CNV detection in the ID group nearly twofold compared to the ASD group (44.4%/23.7%). The presence of macrocephaly in the ASD group showed a 25% probability of pathogenic CNV findings by logistic regression, but this was insignificant according to Fisher’s exact test. The probability of detecting pathogenic CNVs decreases up to 1% in the absence of dysmorphism, macrocephaly, and epilepsy in the ASD group. Conclusion Dysmorphism, microcephaly, and epilepsy increase the probability of pathogenic CNV findings in ID and ASD patients. The significance of each feature as a predictor for pathogenic CNV detection differs depending on whether the patient has only ASD or ID. The probability of pathogenic CNV findings without dysmorphism, macrocephaly, or epilepsy in ASD patients is low. Therefore the efficacy of CNV analysis is limited in these patients.
Capkova et al. (2019) Differences in the importance of microcephaly, dysmorphism, and epilepsy in the detection of pathogenic CNVs in ID and ASD patients. PeerJ 7:e7979 https://doi.org/10.7717/peerj.7979
Two new species and the molecular phylogeography of the freshwater crab genus Bottapotamon (Crustacea: Decapoda: Brachyura: Potamidae)
Bottapotamon chenzhouense sp. n. and B. luxiense sp. n. are described from Hunan Province and Jiangxi Province, respectively. These species both have diagnostic features of the genus Bottapotamon and discernible characteristics as new species. B. chenzhouense sp. n. can be distinguished from co-geners by features such as the G1, which has a fold covering the surface of the entire subterminal article with a distal region. B. luxiense sp. n. has an elliptical carapace, and a sturdy and blunt terminal article of G1. The molecular phylogeny and biogeography of the genus Bottapotamon (Decapoda: Brachyura: Potamidae) were studied, using mitochondrial cytochrome oxidase I (mtDNA COI), 16S rRNA and nuclear histone H3 gene fragments. The results support the assignment of the two new species to the genus Bottapotamon. In addition, the divergence time of the genus Bottapotamon was estimated to be 3.49–1.08 Ma, which coincided with various vicariant and dispersal events that occurred in the geological area where the genus Bottapotamon is commonly distributed. Mountains appear to have played an important role in the distribution of this genus. The Wuyi Mountains gradually formed offshore and inland of southeastern China by the compression of the Pacific plate and the Indian plate in the Neogene-Quaternary, and the Luoxiao Mountains formed continuously in the continued forming in the north-south direction because of neotectonic movement, have resulted in the geographical distribution pattern of the genus Bottapotamon, which was also established gradually.
Gao et al. (2019) Two new species and the molecular phylogeography of the freshwater crab genus Bottapotamon (Crustacea: Decapoda: Brachyura: Potamidae). PeerJ 7:e7980 https://doi.org/10.7717/peerj.7980
High-throughput sequence analysis reveals variation in the relative abundance of components of the bacterial and fungal microbiota in the rhizosphere of Ginkgo biloba
Background The narrow region of soil, in contact with and directly influenced by plant roots, is called the rhizosphere. Microbes living in the rhizosphere are considered to be important factors for the normal growth and development of plants. In this research, the structural and functional diversities of microbiota between the Ginkgo biloba root rhizosphere and the corresponding bulk soil were investigated. Methods Three independent replicate sites were selected, and triplicate soil samples were collected from the rhizosphere and the bulk soil at each sampling site. The communities of bacteria and fungi were investigated using high-throughput sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) of the rRNA gene, respectively. Results A number of bacterial genera showed significantly different abundance in the rhizosphere compared to the bulk soil, including Bradyrhizobium, Rhizobium, Sphingomonas, Streptomyces and Nitrospira. Functional enrichment analysis of bacterial microbiota revealed consistently increased abundance of ATP-binding cassette (ABC) transporters and decreased abundance of two-component systems in the rhizosphere community, compared to the bulk soil community. In contrast, the situation was more complex and inconsistent for fungi, indicating the independency of the rhizosphere fungal community on the local microenvironment.
Ruan et al. (2019) High-throughput sequence analysis reveals variation in the relative abundance of components of the bacterial and fungal microbiota in the rhizosphere of Ginkgo biloba. PeerJ 7:e8051 https://doi.org/10.7717/peerj.8051
Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral
Corals are in decline worldwide due to local anthropogenic stressors, such as nutrient loading, and global stressors, such as ocean warming. Anthropogenic nutrient loading, which is often rich in nitrate, inhibits coral growth and worsens corals’ response to warming while natural sources of nitrogen, such as ammonium from fish excretion, promotes coral growth. Although the effects of nutrient loading and ocean warming have been well-studied, it remains unclear how these factors may interact with biotic processes, such as corallivory, to alter coral health and the coral microbiome. This study examined how nitrate vs. ammonium enrichment altered the effects of increased seawater temperature and simulated parrotfish corallivory on the health of Pocillopora meandrina and its microbial community. We tested the effects of nitrogen source on the response to corallivory under contrasting temperatures (control: 26 °C, warming: 29 °C) in a factorial mesocosm experiment in Moorea, French Polynesia. Corals were able to maintain growth rates despite simultaneous stressors. Seawater warming suppressed wound healing rates by nearly 66%. However, both ammonium and nitrate enrichment counteracted the effect of higher temperatures on would healing rates. Elevated seawater temperature and ammonium enrichment independently increased Symbiodiniaceae densities relative to controls, yet there was no effect of nitrate enrichment on algal symbiont densities. Microbiome variability increased with the addition of nitrate or ammonium. Moreover, microbial indicator analysis showed that Desulfovibrionaceae Operational taxonomic units (OTUs) are indicators of exclusively temperature stress while Rhodobacteraceae and Saprospiraceae OTUs were indicators of high temperature, wounding, and nitrogen enrichment. Overall, our results suggest that nitrogen source may not alter the response of the coral host to simultaneous stressors, but that the associated microbial community may be distinct depending on the source of enrichment.
Rice et al. (2019) Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral. PeerJ 7:e8056 https://doi.org/10.7717/peerj.8056
Characterization of preferential flow in soils near Zarqa river (Jordan) using in situ tension infiltrometer measurements
Background The Zarqa River (ZR) is located in the northern part of Jordan and supplies King Talal Dam (KTD). The streamflow that discharges into KTD is composed of treated wastewater from the Khirbat Es-Samra water treatment plant (KTP) and runoff generated during the winter season. Thus, during the summer, the streamflow of the ZR is dominated by effluent from the KTP. Due to the severe scarcity of water in Jordan, a portion of the streamflow is utilized for irrigated agriculture in the ZR valley, located between the KTP and KTD. The groundwater in the vicinity of the ZR is vulnerable to contamination—a risk that may be exacerbated by the potential occurrence of preferential flow (PF). Therefore, the PF in the soils near the ZR should be carefully considered. Methods The macropore flux fraction (Qmacro) and macroscopic capillary length (λc) were determined from in situ measurements using a tension infiltrometer equipped with an infiltration disc with a diameter of 20 cm. The macropore was defined as the pore size that drains at a tension of less than —-3— cm. The λc less than 80 mm was considered to be an indication of PF. The measurements were taken at 69 sites along the ZR between the KTP and KTD. At each measurement site, the soil organic matter content (OM) and soil texture were determined using a composite soil sample obtained by excavating the soil beneath the infiltration disc to a depth of 10 cm. Results The data was split into two groups: the matrix flow group (MF), which includes data associated with λc > 80 mm, and the PF group, which includes data associated with λc < 80 mm. The Qmacro values of 0.67 and 0.57, respectively, for PF and MF were significantly different at p < 0.01 (t-test). The flow rates at h=0 were generally well associated with λc, as attested to by a significant difference between the averages of PF (57.8 mm/hr) and MF (21.0 mm/hr) at p < 0.01 (t-test). The OM was positively associated with PF. This was statistically confirmed by a t-test at p < 0.01. The average sand and clay contents of PF and MF were not statistically different. Analysis of the ratio of Soil Organic Carbon (SOC) to clay showed that the average SOC/clay of the PF (14%) was larger than that of the MF (13.3%). After the exclusion of soils with clay content less than 8%, the differences between the SOC/clay averages of PF (9.8%) and MF (7.5%) were significant at p < 0.05, as shown by a WM-test. Conclusion The OM was positively associated with PF. Soil texture—and clay content in particular—influenced the λcvalues. However, the association of clay content with PF was not statistically significant. Consideration of the SOC/clay ratio showed that the tendency toward PF increases as the complexation of the clay content increases. This was most obvious in soils with a clay content of greater than 8% and SOC/clay of approximately 10%. The OM either influences or is inter-correlated with the processes responsible for the formation of macropores.
Rahbeh (2019) Characterization of preferential flow in soils near Zarqa river (Jordan) using in situ tension infiltrometer measurements. PeerJ 7:e8057 https://doi.org/10.7717/peerj.8057
Association between the degree of fibrosis in fibrotic focus and the unfavorable clinicopathological prognostic features of breast cancer
Objective To explore the association between the degree of fibrosis in fibrotic focus (FF) and the unfavorable clinicopathological prognostic features of breast cancer. Methods A total of 169 cases of breast invasive ductal carcinoma (IDC) were included in the study. Hematoxylin and eosin (H&E) staining was performed in the primary lesion of breast IDC and the degree of fibrosis in tumor-stromal FF was assessed. The association between the degree of fibrosis in FF and the well-known clinicopathologic features of breast cancer was investigated and the influence of the degree of fibrosis in FF on the survival was analyzed. Results Tumor size >2 cm (P = 0.023), vascular invasion (P = 0.011), lymphatic vessel invasion (P < 0.001) and HER-2+ (P = 0.032) were positively correlated with the degree of fibrosis in FF in breast IDC. The result of multivariate analysis showed that lymphatic vessel invasion was the only independent correlation factor of high fibrosis in FF in breast IDC (OR = 3.82, 95% CI[1.13 ∼ 12.82], P = 0.031). The Nottingham prognostic index (NPI) of high fibrosis in FF was significantly higher than that of mild and moderate fibrosis in FF in the no vascular infiltration subgroup, the no nerve infiltration subgroup, and the Luminal A subgroup (P = 0.014, 0.039, and 0.018; respectively). Conclusions The high fibrosis in FF is closely associated with the strong invasiveness and the high malignancy of breast IDC. The degree of fibrosis in FF might be considered as a very practical and meaningful pathological feature of breast cancer.
Li et al. (2019) Association between the degree of fibrosis in fibrotic focus and the unfavorable clinicopathological prognostic features of breast cancer. PeerJ 7:e8067 https://doi.org/10.7717/peerj.8067
Up-regulation of cryptochrome 1 gene expression in cotton bollworm (Helicoverpa armigera) during migration over the Bohai Sea
Cryptochromes (CRYs) are flavoproteins and play a pivotal role in circadian clocks which mediate behavior of organisms such as feeding, mating and migrating navigation. Herein, we identified novel transcripts in Helicoverpa armigera of six isoforms of cry1 and seven isoforms of cry2 by Sanger sequencing. Phylogenetic analysis showed that the transcripts of cry1 and cry2 align closely with other insect crys, indicating within-species divergence of Hacry. A dn/ds analysis revealed that the encoding sequence of the cry1 was under purifying selection by a strong negative selection pressure whereas the cry2 was less constraint and showed a less strong purification selection than cry1. In general, Hacrys were more abundantly transcribed in wild migrating populations than that in laboratory maintained populations, and expression of the cry2 was lower than cry1 in all samples tested. Moreover, when compared with the migrating parental population, offspring reared in laboratory conditions showed a significant reduction on transcription of the cry1 but not cry2. These results strongly suggest that cry1 was more related to the migration behavior of H. armigera than cry2.
Yang et al. (2019) Up-regulation of cryptochrome 1 gene expression in cotton bollworm (Helicoverpa armigera) during migration over the Bohai Sea. PeerJ 7:e8071 https://doi.org/10.7717/peerj.8071
Land use is the main driver of soil organic carbon spatial distribution in a high mountain ecosystem
Background Terrestrial ecosystems play a significant role in carbon (C) storage. Human activities, such as urbanization, infrastructure, and land use change, can reduce significantly the C stored in the soil. The aim of this research was to measure the spatial variability of soil organic C (SOC) in the national park La Malinche (NPLM) in the central highlands of Mexico as an example of highland ecosystems and to determine the impact of land use change on the SOC stocks through deterministic and geostatistical geographic information system (GIS) based methods. Methods The soil was collected from different landscapes, that is, pine, fir, oak and mixed forests, natural grassland, moor and arable land, and organic C content determined. Different GIS-based deterministic (inverse distance weighting, local polynomial interpolation and radial basis function) and geostatistical interpolation techniques (ordinary kriging, cokriging and empirical Bayes kriging) were used to map the SOC stocks and other environmental variables of the top soil layer. Results All interpolation GIS-based methods described the spatial distribution of SOC of the NPLM satisfactorily. The total SOC stock of the NPLM was 2.45 Tg C with 85.3% in the forest (1.26 Tg C in the A horizon and 0.83 Tg C in the O horizon), 11.4% in the arable soil (0.23 Tg in the A horizon and only 0.05 Tg C in the O horizon) and 3.3% in the high moor (0.07 Tg C in the A horizon and <0.01 Tg C in the O horizon). The estimated total SOC stock in a preserved part of the forest in NPLM was 4.98 Tg C in 1938 and has nearly halved since then. Continuing this trend of converting all the remaining forest to arable land will decrease the total SOC stock to 0.52 Tg C. Discussion Different factors explain the large variations in SOC stocks found in this study but the change in land use (conversion of forests into agricultural lands) was the major reason for the reduction of the SOC stocks in the high mountain ecosystem of the NPLM. Large amounts of C, however, could be stored potentially in this ecosystem if the area was used more sustainable. The information derived from this study could be used to recommend strategies to reverse the SOC loss in NPLM and other high-altitude temperate forests and sequester larger quantities of C. This research can serve as a reference for the analysis of SOC distribution in similar mountain ecosystems in central part of Mexico and in other parts of the world.
Fusaro et al. (2019) Land use is the main driver of soil organic carbon spatial distribution in a high mountain ecosystem. PeerJ 7:e7897 https://doi.org/10.7717/peerj.7897
Genome-wide identification, characterization, interaction network and expression profile of GAPDH gene family in sweet orange (Citrus sinensis)
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key glycolytic enzyme that plays important roles in multiple cellular processes including phytohormone signaling, plant development, and transcriptional regulation. Although GAPDH genes have been well characterized in various plant species such as Arabidopsis, tobacco, wheat, rice, and watermelon, comprehensive analysis has yet to be completed at the whole genome level in sweet orange (Citrus sinensis). In this study, six GAPDH genes distributed across four chromosomes were identified within the sweet orange genome. Their gene structures, conserved subunits, and subcellular localization were also characterized. Cis-element analysis of CsGAPDHs’ promoter regions and the results of dark treatments indicate that CsGAPDH may be involved in photosynthesis. CsGAPDH genes expressed either in a tissue-specific manner or constitutively were ultimately identified along with their expression response to phosphorus deficiency treatments. In addition, a dual-luciferase transient assay was performed to reveal the transcriptional activation of CsGAPDH proteins. Gene Ontology (GO) analysis for proteins interacting with CsGAPDHs helped to uncover the roles these CsGAPDHs play in other plant processes such as citrus seed germination. This study provides a systematic analysis of the CsGAPDH gene family in the sweet orange genome, which can serve as a strong foundation for further research into the biochemical properties and physiological functions of CsGAPDHs.
Miao et al. (2019) Genome-wide identification, characterization, interaction network and expression profile of GAPDH gene family in sweet orange (Citrus sinensis). PeerJ 7:e7934 https://doi.org/10.7717/peerj.7934
Pilates versus resistance training on trunk strength and balance adaptations in older women: a randomized controlled trial
Background The neuromuscular decline impact in the functional independence of older women is determining the necessity of implementing new strategies focused on core strength training and postural stability maintenance to promote healthy aging. Objectives To define whether Pilates or resistance training is better at improving (a) core isometric and isokinetic muscular strength, and (b) static and dynamic balance, in older women. Methods This was a cluster randomized controlled trial. Physically independent older women (60–80 years) from day centers were randomly allocated to Pilates, Muscular and Control Groups (PG, MG and CG) using a block randomization method. Only the research staff performing the assessment and statistical analysis were blinded. Exercise groups trained twice a week (1 h per session) for 18 weeks in a moderate-to-vigorous intensity. Core strength (primary outcome): trunk and hip isometric and hip isokinetic muscular strength (Biodex System III Pro Isokinetic Dynamometer), alongside one leg static balance (portable force platform Kistler 9286AA) and dynamic balance (timed up and go (TUG)) were assessed. Results A total of 60 participants were randomized (PG, n = 20; MG, n = 20; CG, n = 20) and 49 completed the trial (PG, n = 16; MG, n = 19; CG, n = 14). Regarding hip isometric extension strength, PG was statistically better than CG (P = 0.004). There were no differences between groups regarding isokinetic strength or balance. Intra-group comparisons showed significant improvements (P < 0.05) in the dynamic balance and trunk and hip isometric extension strength for PG and MG, whereas every hip isokinetic measurement was improved in MG. Exercise programs did not produce any adverse event. Conclusions The Pilates training program was more effective for improving isometric hip and trunk extension strength, while the Muscular training program generated greater benefits on trunk and hip isokinetic strength. Moreover, both training programs showed moderate effects for the TUG. Clinical Trial Registration The trial was registered at ClinicalTrials.gov (identifier: NCT02506491).
Carrasco-Poyatos et al. (2019) Pilates versus resistance training on trunk strength and balance adaptations in older women: a randomized controlled trial. PeerJ 7:e7948 https://doi.org/10.7717/peerj.7948
Long non-coding RNA, LINC01614 as a potential biomarker for prognostic prediction in breast cancer
Background Dysregulated long non-coding RNAs (lncRNAs) may serve as potential biomarkers of cancers including breast cancer (BRCA). This study aimed to identify lncRNAs with strong prognostic value for BRCA. Methods LncRNA expression profiles of 929 tissue samples were downloaded from TANRIC database. We performed differential expression analysis between paired BRCA and adjacent normal tissues. Survival analysis was used to identify lncRNAs with prognostic value. Univariate and multivariate Cox regression analyses were performed to confirm the independent prognostic value of potential lncRNAs. Dysregulated signaling pathways associated with lncRNA expression were evaluated using gene set enrichment analysis. Results We found that a total of 398 lncRNAs were significantly differentially expressed between BRCA and adjacent normal tissues (adjusted P value <= 0.0001 and |logFC| >= 1). Additionally, 381 potential lncRNAs were correlated Overall Survival (OS) (P value < 0.05). A total of 48 lncRNAs remained when differentially expressed lncRNAs overlapped with lncRNAs that had prognostic value. Among the 48 lncRNAs, one lncRNA (LINC01614) had stronger prognostic value and was highly expressed in BRCA tissues. LINC01614 expression was validated as an independent prognostic factor using univariate and multivariate analyses. Higher LINC01614 expression was observed in several molecular subgroups including estrogen receptors+, progesterone receptors+ and human epidermal growth factor receptor 2 (HER2)+ subgroup, respectively. Also, BRCA carrying one of four gene mutations had higher expression of LINC01614 including AOAH, CIT, HER2 and ODZ1. Higher expression of LINC01614 was positively correlated with several gene sets including TGF-β1 response, CDH1 signals and cell adhesion pathways. Conclusions A novel lncRNA LINC01614 was identified as a potential biomarker for prognosis prediction of BRCA. This study emphasized the importance of LINC01614 and further research should be focused on it.
Wang et al. (2019) Long non-coding RNA, LINC01614 as a potential biomarker for prognostic prediction in breast cancer. PeerJ 7:e7976 https://doi.org/10.7717/peerj.7976
Genetic and phylogenetic analysis of Chinese sacbrood virus isolates from Apis mellifera
Background Sacbrood virus (SBV) is one of the most pathogenic honeybee viruses that exhibits host specificity and regional variations. The SBV strains that infect the Chinese honeybee Apis cerana are called Chinese SBVs (CSBVs). Methods In this study, a CSBV strain named AmCSBV-SDLY-2016 (GenBank accession No. MG733283) infecting A. mellifera was identified by electron microscopy, its protein composition was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis and agar gel immunodiffusion assay, and its nucleotide sequence was identified using a series of reverse-transcription polymerase chain reaction fragments of AmCSBV-SDLY-2016 generated using SBV/CSBV-specific primers. To investigate phylogenetic relationships of the CSBV isolates, a phylogenetic tree of the complete open reading frames (ORF) of the CSBV sequences was constructed using MEGA 6.0; then, the similarity and recombination events among the isolated CSBV strains were analyzed using SimPlot and RDP4 software, respectively. Results Sequencing results revealed the complete 8,794-nucleotide long complete genomic RNA of the strain, with a single large ORF (189–8,717) encoding 2,843 amino acids. Comparison of the deduced amino acid sequence with the SBV/CSBV reference sequences deposited in the GenBank database identified helicase, protease, and RNA-dependent RNA polymerase domains; the structural genes were located at the 5′ end, whereas the non-structural genes were found at the 3′ end. Multiple sequence alignment showed that AmCSBV-SDLY-2016 had a 17-amino acid (aa) and a single aa deletion at positions 711–729 and 2,128, respectively, as compared with CSBV-GD-2002, and a 16-aa deletion (positions 711–713 and 715–728) as compared with AmSBV-UK-2000. However, AmCSBV-SDLY-2016 was similar to the CSBV-JLCBS-2014 strain, which infects A. cerana. AmCSBV-SDLY-2016 ORF shared 92.4–97.1% identity with the genomes of other CSBV strains (94.5–97.7% identity for deduced amino acids). AmCSBV-SDLY-2016 was least similar (89.5–90.4% identity) to other SBVs but showed maximum similarity with the previously reported CSBV-FZ-2014 strain. The phylogenetic tree constructed from AmCSBV-SDLY-2016 and 43 previously reported SBV/CSBV sequences indicated that SBV/CSBV strains clustered according to the host species and country of origin; AmCSBV-SDLY-2016 clustered with other previously reported Chinese and Asian strains (AC genotype SBV, as these strains originated from A. cerana) but was separate from the SBV genomes originating from Europe (AM genotype SBV, originating from A. mellifera). A SimPlot graph of SBV genomes confirmed the high variability, especially between the AC genotype SBV and AM genotype SBV. This genomic diversity may reflect the adaptation of SBV to specific hosts, ability of CSBV to cross the species barrier, and the spatial distances that separate CSBVs from other SBVs.
Li et al. (2019) Genetic and phylogenetic analysis of Chinese sacbrood virus isolates from Apis mellifera. PeerJ 7:e8003 https://doi.org/10.7717/peerj.8003
Brittle stars looking like starfish: the first fossil record of the Astrophiuridae and a remarkable case of convergent evolution
The genus Astrophiura, which ranks among the most extraordinary of modern brittle stars, is the type genus of the recently resurrected family Astrophiuridae within the order Ophiurida. On account of its absurdly enlarged and strongly modified lateral arm plates, Astrophiura bears a closer resemblance to a pentagonal starfish than to a typical ophiuroid. Although molecular evidence suggests an ancient origin of the Astrophiuridae, dating back at least to the Early Jurassic, not a single fossil astrophiurid has been reported so far. Here, we describe dissociated lateral arm plates from the Campanian of Cringleford near Norwich, UK, and the Maastrichtian of Rügen, Germany (both Upper Cretaceous) with unambiguous astrophiurid affinities and assign these to a new species, Astrophiura markbeneckei. This represents the first fossil record of the family. In addition, the Rügen material included lateral arm plates that superficially resemble those of A. markbeneckei sp. nov. but differ in having spine articulations that are typical of the ophionereidoid family Amphilimnidae. We assign these plates to a new genus and species, Astrosombra rammsteinensis, an extinct amphilimnid with morphological modifications similar to those of Astrophiura, and thus representing a remarkable case of parallel evolution amongst brittle stars looking like starfish.
Thuy et al. (2019) Brittle stars looking like starfish: the first fossil record of the Astrophiuridae and a remarkable case of convergent evolution. PeerJ 7:e8008 https://doi.org/10.7717/peerj.8008
First microsatellite markers for the pine catkin sawfly Xyela concava (Hymenoptera, Xyelidae) and their application in phylogeography and population genetics
Microsatellites are widely used as powerful markers in population genetics because of their ability to access recent genetic variation and to resolve subtle population genetic structures. However, their development, especially for non-model organisms with no available genome-wide sequence data has been difficult and time-consuming. Here, a commercial high-throughput sequencing approach (HTS) was used for the very first identification of microsatellite motifs in the genome of Xyela concava and the design of primer pairs flanking those motifs. Sixteen of those primer pairs were selected and implemented successfully to answer questions on the phylogeography and population genetics of X. concava. The markers were characterized in three geographically distinct populations of X. concava and tested for cross-species amplification in two additional Xyela and one Pleroneura species (Xyelidae). All markers showed substantial polymorphism as well as revealing subtle genetic structures among the three genotyped populations. We also analyzed a fragment of the nuclear gene region of sodium/potassium-transporting ATPase subunit alpha (NaK) and a partial mitochondrial gene region coding for cytochrome oxidase subunit I (COI) to demonstrate different genetic resolutions and sex-biased patterns of these markers, and their potential for combined use in future studies on the phylogeography and population genetics of X. concava. Although a limited number of populations was analyzed, we nevertheless obtained new insights on the latter two topics. The microsatellites revealed a generally high gene flow between the populations, but also suggested a deep historical segregation into two genetic lineages. This deep genetic segregation was confirmed by NaK. While the high gene flow was unexpected, because of assumed restricted dispersal ability of X. concava and the discontinuous distribution of the host trees between the populations, the segregation of two lineages is comprehensible and could be explained by different refuge areas of the hosts during glacial times. The COI results showed a discordant strong genetic structure between all populations, which might be explained by the smaller effective population size of the mitochondrial genome. However, given the frequent evidence of a similar nature in recent studies on sawflies, we also consider and discuss mitochondrial introgression on population level as an alternative explanation.
Kulanek et al. (2019) First microsatellite markers for the pine catkin sawfly Xyela concava (Hymenoptera, Xyelidae) and their application in phylogeography and population genetics. PeerJ 7:e8010 https://doi.org/10.7717/peerj.8010
Effects of miniaturization in the anatomy of the minute springtail Mesaphorura sylvatica (Hexapoda: Collembola: Tullbergiidae)
Smaller animals display pecular characteristics related to their small body size, and miniaturization has recently been intensely studied in insects, but not in other arthropods. Collembola, or springtails, are abundant soil microarthropods and form one of the four basal groups of hexapods. Many of them are notably smaller than 1 mm long, which makes them a good model for studying miniaturization effects in arthropods. In this study we analyze for the first time the anatomy of the minute springtail Mesaphorura sylvatica (body length 400 µm). It is described using light and scanning electron microscopy and 3D computer reconstruction. Possible effects of miniaturization are revealed based on a comparative analysis of data from this study and from studies on the anatomy of larger collembolans. Despite the extremely small size of M. sylvatica, some organ systems, e.g., muscular and digestive, remain complex. On the other hand, the nervous system displays considerable changes. The brain has two pairs of apertures with three pairs of muscles running through them, and all ganglia are shifted posteriad by one segment. The relative volumes of the skeleton, brain, and musculature are smaller than those of most microinsects, while the relative volumes of other systems are greater than or the same as in most microinsects. Comparison of the effects of miniaturization in collembolans with those of insects has shown that most of the miniaturization-related features of M. sylvatica have also been found in microinsects (shift of the brain into the prothorax, absent heart, absence of midgut musculature, etc.), but also has revealed unique features (brain with two apertures and three pairs of muscles going through them), which have not been described before.
Panina et al. (2019) Effects of miniaturization in the anatomy of the minute springtail Mesaphorura sylvatica (Hexapoda: Collembola: Tullbergiidae). PeerJ 7:e8037 https://doi.org/10.7717/peerj.8037
Phylogenetic revision of the psammophilic Trogloderus LeConte (Coleoptera: Tenebrionidae), with biogeographic implications for the Intermountain Region
The genus Trogloderus LeConte, 1879, which is restricted to dunes and sandy habitats in the western United States, is revised using morphological and molecular information. Six new species are described from desert regions: Trogloderus arcanus New Species (Lahontan Trough); Trogloderus kandai New Species (Owens Valley); Trogloderus major New Species (Mohave Desert); Trogloderus skillmani New Species (eastern Great Basin and Mohave Desert); Trogloderus verpus New Species (eastern Colorado Plateau); and Trogloderus warneri New Species (western Colorado Plateau). A molecular phylogeny is presented for the genus and used to infer its historical biogeography. The most recent common ancestor of Trogloderus is dated to 5.2 mya and is inferred to have inhabited the Colorado Plateau. Current species most likely arose during the mid-Pleistocene where the geographic features of the Lahontan Trough, Bouse Embayment and Kaibab Plateau were significant factors driving speciation.
Johnston (2019) Phylogenetic revision of the psammophilic Trogloderus LeConte (Coleoptera: Tenebrionidae), with biogeographic implications for the Intermountain Region. PeerJ 7:e8039 https://doi.org/10.7717/peerj.8039
Oxidative stress as a potential target in acute kidney injury
Background Acute kidney injury (AKI) is a major problem for health systems being directly related to short and long-term morbidity and mortality. In the last years, the incidence of AKI has been increasing. AKI and chronic kidney disease (CKD) are closely interconnected, with a growing rate of CKD linked to repeated and severe episodes of AKI. AKI and CKD can occur also secondary to imbalanced oxidative stress (OS) reactions, inflammation, and apoptosis. The kidney is particularly sensitive to OS. OS is known as a crucial pathogenetic factor in cellular damage, with a direct role in initiation, development, and progression of AKI. The aim of this review is to focus on the pathogenetic role of OS in AKI in order to gain a better understanding. We exposed the potential relationships between OS and the perturbation of renal function and we also presented the redox-dependent factors that can contribute to early kidney injury. In the last decades, promising advances have been made in understanding the pathophysiology of AKI and its consequences, but more studies are needed in order to develop new therapies that can address OS and oxidative damage in early stages of AKI. Methods We searched PubMed for relevant articles published up to May 2019. In this review we incorporated data from different types of studies, including observational and experimental, both in vivo and in vitro, studies that provided information about OS in the pathophysiology of AKI. Results The results show that OS plays a major key role in the initiation and development of AKI, providing the chance to find new targets that can be therapeutically addressed. Discussion Acute kidney injury represents a major health issue that is still not fully understood. Research in this area still provides new useful data that can help obtain a better management of the patient. OS represents a major focus point in many studies, and a better understanding of its implications in AKI might offer the chance to fight new therapeutic strategies.
Tomsa et al. (2019) Oxidative stress as a potential target in acute kidney injury. PeerJ 7:e8046 https://doi.org/10.7717/peerj.8046
Limits to load-lifting performance in a passerine bird: the effects of intraspecific variation in morphological and kinematic parameters
Although more massive flight muscles along with larger wings, higher wingbeat frequencies and greater stroke amplitudes enhance force and power production in flapping flight, the extent to which these parameters may be correlated with other morphological features relevant to flight physiology and biomechanics remains unclear. Intraspecifically, we hypothesized that greater vertical load-lifting capacity would correlate with higher wingbeat frequencies and relatively more massive flight muscles, along with relatively bigger hearts, lungs, and stomachs to enhance metabolic capacity and energy supply, but also with smaller body size given the overall negative allometric dependence of maximum flight performance in volant taxa. To explore intraspecific correlates of flight performance, we assembled a large dataset that included 13 morphological and kinematic variables for a non-migratory passerine, the Eurasian tree sparrow (Passer montanus). We found that heavier flight muscles and larger wings, heavier stomachs and shorter bills were the most important correlates of maximum load-lifting capacity. Surprisingly, wingbeat frequency, wing stroke amplitude and masses of the heart, lungs and digestive organs (except for the stomach) were non-significant predictor variables relative to lifting capacity. The best-fit structural equation model (SEM) indicated that load-lifting capacity was positively correlated with flight muscle mass, wing area and stomach mass, but was negatively correlated with bill length. Characterization of individual variability in flight performance in a free-ranging passerine indicates the subtlety of interaction effects among morphological features, some of which differ from those that have been identified interspecifically for maximum flight performance in birds.
Wang et al. (2019) Limits to load-lifting performance in a passerine bird: the effects of intraspecific variation in morphological and kinematic parameters. PeerJ 7:e8048 https://doi.org/10.7717/peerj.8048
Prediction of clusters of miRNA binding sites in mRNA candidate genes of breast cancer subtypes
The development of breast cancer (BC) subtypes is controlled by distinct sets of candidate genes, and the expression of these genes is regulated by the binding of their mRNAs with miRNAs. Predicting miRNA associations and target genes is thus essential when studying breast cancer. The MirTarget program identifies the initiation of miRNA binding to mRNA, the localization of miRNA binding sites in mRNA regions, and the free energy from the binding of all miRNA nucleotides with mRNA. Candidate gene mRNAs have clusters (miRNA binding sites with overlapping nucleotide sequences). mRNAs of EPOR, MAZ and NISCH candidate genes of the HER2 subtype have clusters, and there are four clusters in mRNAs of MAZ, BRCA2 and CDK6 genes. Candidate genes of the triple-negative subtype are targets for multiple miRNAs. There are 11 sites in CBL mRNA, five sites in MMP2 mRNA, and RAB5A mRNA contains two clusters in each of the three sites. In SFN mRNA, there are two clusters in three sites, and one cluster in 21 sites. Candidate genes of luminal A and B subtypes are targets for miRNAs: there are 21 sites in FOXA1 mRNA and 15 sites in HMGA2 mRNA. There are clusters of five sites in mRNAs of ITGB1 and SOX4 genes. Clusters of eight sites and 10 sites are identified in mRNAs of SMAD3 and TGFB1 genes, respectively. Organizing miRNA binding sites into clusters reduces the proportion of nucleotide binding sites in mRNAs. This overlapping of miRNA binding sites creates a competition among miRNAs for a binding site. From 6,272 miRNAs studied, only 29 miRNAs from miRBase and 88 novel miRNAs had binding sites in clusters of target gene mRNA in breast cancer. We propose using associations of miRNAs and their target genes as markers in breast cancer subtype diagnosis.
Aisina et al. (2019) Prediction of clusters of miRNA binding sites in mRNA candidate genes of breast cancer subtypes. PeerJ 7:e8049 https://doi.org/10.7717/peerj.8049
Ciglitazone—a human PPARγ agonist—disrupts dorsoventral patterning in zebrafish
Peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-activated transcription factor that regulates lipid/glucose homeostasis and adipocyte differentiation. While the role of PPARγ in adipogenesis and diabetes has been extensively studied, little is known about PPARγ function during early embryonic development. Within zebrafish, maternally-loaded pparγ transcripts are present within the first 6 h post-fertilization (hpf), and de novo transcription of zygotic pparγ commences at ~48 hpf. Since maternal pparγ transcripts are elevated during a critical window of cell fate specification, the objective of this study was to test the hypothesis that PPARγ regulates gastrulation and dorsoventral patterning during zebrafish embryogenesis. To accomplish this objective, we relied on (1) ciglitazone as a potent PPARγ agonist and (2) a splice-blocking, pparγ-specific morpholino to knockdown pparγ. We found that initiation of ciglitazone—a potent human PPARγ agonist—exposure by 4 hpf resulted in concentration-dependent effects on dorsoventral patterning in the absence of epiboly defects during gastrulation, leading to ventralized embryos by 24 hpf. Interestingly, ciglitazone-induced ventralization was reversed by co-exposure with dorsomorphin, a bone morphogenetic protein signaling inhibitor that induces strong dorsalization within zebrafish embryos. Moreover, mRNA-sequencing revealed that lipid- and cholesterol-related processes were affected by exposure to ciglitazone. However, pparγ knockdown did not block ciglitazone-induced ventralization, suggesting that PPARγ is not required for dorsoventral patterning nor involved in ciglitazone-induced toxicity within zebrafish embryos. Our findings point to a novel, PPARγ-independent mechanism of action and phenotype following ciglitazone exposure during early embryonic development.
Cheng et al. (2019) Ciglitazone—a human PPARγ agonist—disrupts dorsoventral patterning in zebrafish. PeerJ 7:e8054 https://doi.org/10.7717/peerj.8054
Identification of genes and functional coexpression modules closely related to ulcerative colitis by gene datasets analysis
Background Ulcerative colitis is a type of inflammatory bowel disease posing a great threat to the public health worldwide. Previously, gene expression studies of mucosal colonic biopsies have provided some insight into the pathophysiological mechanisms in ulcerative colitis; however, the exact pathogenesis is unclear. The purpose of this study is to identify the most related genes and pathways of UC by bioinformatics, so as to reveal the core of the pathogenesis. Methods Genome-wide gene expression datasets involving ulcerative colitis patients were collected from gene expression omnibus database. To identify most close genes, an integrated analysis of gene expression signature was performed by employing robust rank aggregation method. We used weighted gene co-expression network analysis to explore the functional modules involved in ulcerative colitis pathogenesis. Besides, biological process and pathways analysis of co-expression modules were figured out by gene ontology enrichment analysis using Metascape. Results A total of 328 ulcerative colitis patients and 138 healthy controls were from 14 datasets. The 150 most significant differentially expressed genes are likely to include causative genes of disease, and further studies are needed to demonstrate this. Seven main functional modules were identified, which pathway enrichment analysis indicated were associated with many biological processes. Pathways such as ‘extracellular matrix, immune inflammatory response, cell cycle, material metabolism’ are consistent with the core mechanism of ulcerative colitis. However, ‘defense response to virus’ and ‘herpes simplex infection’ suggest that viral infection is one of the aetiological agents. Besides, ‘Signaling by Receptor Tyrosine Kinases’ and ‘pathway in cancer’ provide new clues for the study of the risk and process of ulcerative colitis cancerization.
Zhu et al. (2019) Identification of genes and functional coexpression modules closely related to ulcerative colitis by gene datasets analysis. PeerJ 7:e8061 https://doi.org/10.7717/peerj.8061
Inconsistent response of soil bacterial and fungal communities in aggregates to litter decomposition during short-term incubation
Background Soil aggregate-size classes and microbial communities within the aggregates are important factors regulating the soil organic carbon (SOC) turnover. However, the response of soil bacterial and fungal communities in aggregates to litter decomposition in different aggregate-size classes is poorly understand. Methods Soil samples from un-grazed natural grassland were separated into four dry aggregate classes of different sizes (2–4 mm, 1–2 mm, 0.25–1 mm and <0.25 mm). Two types of plant litter (leaf and stem) of Leymus chinensis were added to each of the four aggregate class samples. The CO2 release rate, SOC storage and soil microbial communities were measured at the end of the 56-day incubation. Results The results showed that the 1–2 mm aggregate had the highest bacterial Shannon and CO2 release in CK and leaf addition treatments, and the SOC in the <0.25 mm aggregate was higher than that in the others across the treatments. The relative abundance of Ascomycota was higher in the 2–4 mm and <0.25 mm aggregates than in the 1–2 mm and 0.25–1 mm aggregates in the treatment without litter addition, and the relative abundance of Aphelidiomycota was lower in the 2–4 mm and <0.25 mm aggregates than in the 1–2 mm and 0.25–1 mm aggregates. Also, litter addition increased the relative abundance of Proteobacteria and Bacteroidetes, but decreased the relative abundance of Acidobacteria, Gemmatimonadetes, and Actinobacteria. The relative abundance of Ascomycota and Aphelidiomycota increased by more than 10% following leaf litter addition. The bacterial Shannon index had a significantly positive and direct effect on SOC concentration and CO2 release, while the fungal Shannon index was significantly correlated with SOC concentration. Our results indicate that the soil bacterial diversity contributes positively to both carbon emissions and carbon storage, whereas soil fungal diversity can promote carbon storage and decrease carbon emissions.
Li et al. (2019) Inconsistent response of soil bacterial and fungal communities in aggregates to litter decomposition during short-term incubation. PeerJ 7:e8078 https://doi.org/10.7717/peerj.8078
Adaptation, phylogeny, and covariance in milk macronutrient composition
Background Milk is a complicated chemical mixture often studied through macronutrient concentrations of fat, protein, and sugar. There is a long-standing natural history tradition describing interspecific diversity in these concentrations. However, recent work has shown little influence of ecological or life history variables on them, aside from maternal diet effects, along with a strong phylogenetic signal. Methods I used multivariate phylogenetic comparative methods to revisit the ecological and life history correlates of milk macronutrient composition and elaborate on the nature of the phylogenetic signal using the phylogenetic mixed model. I also identified clades with distinctive milks through nonparametric tests (KSI) and PhylogeneticEM evolutionary modeling. Results In addition to the previously reported diet effects, I found increasingly aquatic mammals have milk that this is lower in sugar and higher in fat. Phylogenteic heritabilities for each concentration were high and phylogenetic correlations were moderate to strong indicating coevolution among the concentrations. Primates and pinnipeds had the most outstanding milks according to KSI and PhylogeneticEM, with perissodactyls and marsupials as other noteworthy clades with distinct selection regimes. Discussion Mammalian milks are diverse but often characteristic of certain higher taxa. This complicates identifying the ecological and life history correlates of milk composition using common phylogenetic comparative methods because those traits are also conservative and clade-specific. Novel methods, careful assessment of data quality and hypotheses, and a “phylogenetic natural history” perspective provide alternatives to these traditional tools.
Blomquist (2019) Adaptation, phylogeny, and covariance in milk macronutrient composition. PeerJ 7:e8085 https://doi.org/10.7717/peerj.8085
Lake trophic state classifications provide information about the condition of lentic ecosystems and are indicative of both ecosystem services (e.g., clean water, recreational opportunities, and aesthetics) and disservices (e.g., cyanobacteria blooms). The current classification schemes have been criticized for developing indices that are single-variable based (vs. a complex aggregate of multi-variables), discrete (vs. a continuous), and/or deterministic (vs. an inherently random). We present an updated lake trophic classification model using a Bayesian multilevel ordered categorical regression. The model consists of a proportional odds logistic regression (POLR) that models ordered, categorical, lake trophic state using Secchi disk depth, elevation, nitrogen concentration (N), and phosphorus concentration (P). The overall accuracy, when compared to existing classifications of trophic state index (TSI), for the POLR model was 0.68 and the balanced accuracy ranged between 0.72 and 0.93. This work delivers an index that is multi-variable based, continuous, and classifies lakes in probabilistic terms. While our model addresses aforementioned limitations of the current approach to lake trophic classification, the addition of uncertainty quantification is important, because the trophic state response to predictors varies among lakes. Our model successfully addresses concerns with the current approach and performs well across trophic states in a large spatial extent.
Nojavan A. et al. (2019) Rethinking the lake trophic state index. PeerJ 7:e7936 https://doi.org/10.7717/peerj.7936
Accurate spatiotemporal predictions of daily stream temperature from statistical models accounting for interactions between climate and landscape
Spatial and temporal patterns in stream temperature are primary factors determining species composition, diversity and productivity in stream ecosystems. The availability of spatially and temporally continuous estimates of stream temperature would improve the ability of biologists to fully explore the effects of stream temperature on biota. Most statistical stream temperature modeling techniques are limited in their ability to account for the influence of variables changing across spatial and temporal gradients. We identified and described important interactions between climate and spatial variables that approximate mechanistic controls on spatiotemporal patterns in stream temperature. With identified relationships we formed models to generate reach-scale basin-wide spatially and temporally continuous predictions of daily mean stream temperature in four Columbia River tributaries watersheds of the Pacific Northwest, USA. Models were validated with a testing dataset composed of completely distinct sites and measurements from different years. While some patterns in residuals remained, testing dataset predictions of selected models demonstrated high accuracy and precision (averaged RMSE for each watershed ranged from 0.85–1.54 °C) and was only 17% higher on average than training dataset prediction error. Aggregating daily predictions to monthly predictions of mean stream temperature reduced prediction error by an average of 23%. The accuracy of predictions was largely consistent across diverse climate years, demonstrating the ability of the models to capture the influences of interannual climatic variability and extend predictions to timeframes with limited temperature logger data. Results suggest that the inclusion of a range of interactions between spatial and climatic variables can approximate dynamic mechanistic controls on stream temperatures.
Siegel et al. (2019) Accurate spatiotemporal predictions of daily stream temperature from statistical models accounting for interactions between climate and landscape. PeerJ 7:e7892 https://doi.org/10.7717/peerj.7892
Characterization of aminopeptidase encoding gene anp-1 and its association with development in Caenorhabditis elegans
Background Aminopeptidases play important roles in various biological processes in nematodes including growth, development and reproduction. Although the aminopeptidases have been shown to regulate reproduction in Caenorhabditis elegans (C. elegans), the role of aminopeptidases in development and aging has not been reported. This study focused on the function of aminopeptidase AlaNyl aminopeptidase 1 (ANP-1) on development in C. elegans. Methods In the present study, we reported the identification of ANP-1 in C. elegans along with sequence analysis and its functional expression and characterization. The phenotype changes were observed when anp-1 mutated. Then, differential expression genes (DEGs) between wild type strain (N2) and anp-1 deletion strain (RB804) were identified using transcriptome sequencing method. Finally, DEGs were verified by qRT-PCR assay. Results Our observations suggested that anp-1 mutation induced small body size in the L4/young adult stage of C. elegans, however, there was no difference between N2 and RB804 in adult stage. Moreover, deletion of anp-1 resulted in shortening lifespan and laying fewer eggs. DEGs (184 genes) were observed between N2 groups and RB804 groups by transcriptome sequencing. According to GO annotations and KEGG enrichment analysis, these DEGs play vital roles in development regulation in C. elegans. These data demonstrate ANP-1 participates in development and aging of C. elegans and will considerably contribute to the existing knowledge of aminopeptidase function in C. elegans.
Su et al. (2019) Characterization of aminopeptidase encoding gene anp-1 and its association with development in Caenorhabditis elegans. PeerJ 7:e7944 https://doi.org/10.7717/peerj.7944
Kinetic analysis of felines landing from different heights
Background Kinetic motion analysis has been used in canines and equines as a fundamental objective evaluation measurement. Cats are very capable jumpers, and this ability has biomimetic applications. It is essential to understand movement patterns and physical adaptations of this species, as cats are popular pets for humans. Further to this, motion analysis of a cat’s movement patterns may provide potentially valuable information in relation to limb disease and injury. Therefore, the aim of this study was to investigate kinetic differences in cats when landing from varying preselected controlled heights. Methods The peak vertical force (PVF) and paw contact area (CA) of both the forelimbs and hindlimbs were collected from seven healthy Chinese domesticated cats while landing from heights of 30 cm, 50 cm, 70 cm and 90 cm respectively. The falling motivation for the cats was facilitated with the use of a flip board. This device provided the basis for the cats to land passively. Results The results indicated that the PVF of all examined limbs (fore right, fore left, hind right, hind left) significantly increased as the height increased. When the PVF from the hindlimbs and forelimbs were compared, the forelimbs recorded significantly greater values for all heights examined (P < 0.001). The PVF of the hindlimbs was symmetrical at all heights, but forelimb symmetry only occurred at the lower heights. The hindlimbs demonstrated larger CA than the forelimbs measured from all heights on landing (P < 0.001). Moreover, the paw CA on the left and right limbs were symmetrical. Discussion The paw CA of cats may be an effective parameter to evaluate abnormalities or diseases in the limbs of cats. Additionally, these findings highlight how cats land from varying heights, which may also provide reference values for the bionic design of artificial limbs for felines and treatment for limb diseases in this species.
Wang et al. (2019) Kinetic analysis of felines landing from different heights. PeerJ 7:e8007 https://doi.org/10.7717/peerj.8007
Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers
Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread Elymus species. Elymus excelsus Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of E. excelsus germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of E. excelsus from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei’s genetic diversity (H) and Shannon’s diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of E. excelsus germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (Fst = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (He = 0.197) was greater than that of the GSC (He = 0.176) and XJC (He = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that E. excelsus accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable E. excelsus germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.
Xiong et al. (2019) Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers. PeerJ 7:e8038 https://doi.org/10.7717/peerj.8038
Effects of a blend of green tea and curcuma extract supplementation on lipopolysaccharide-induced inflammation in horses and ponies
Background In horses and ponies numerous medical conditions are known to be linked with inflammation in different tissues, especially in the liver. Besides affecting other metabolic pathways such as the expression of certain interleukins (IL), inflammation is associated with stress of the endoplasmic reticulum (ER). In particular, ER stress leads to adaptive stress response and can be measured by several markers of inflammatory and stress signalling pathways, like nuclear factor κB (NF-kB). Objectives To investigate lipopolysaccharide (LPS)-induced inflammatory reactions and their modulation in horses and ponies by feeding a polyphenol-rich supplement consisting of green tea and curcuma. Methods In a cross-over study, 11 animals were allocated to either a placebo or a supplement group and supplemented with 10 g of a blend of green tea and curcuma extract (GCE) or a placebo (calcium carbonate) once daily. After 21 days of supplementation, all animals underwent a LPS challenge to induce moderate systemic inflammation. Blood samples and liver biopsies were taken at standardized time points: 24 hours before and 12 hours after LPS challenge. Inflammatory blood parameters such as serum amyloid A (SAA), haptoglobin and retinol binding protein 4 (RBP4) were measured in serum. Hepatic mRNA levels of selected markers of inflammation such as haptoglobin, tumor necrosis factor α (TNF-α), IL-1β, IL-6, cluster of differentiation 68 (CD68), fibroblast growth factor 21 (FGF-21), NF-κB, activating transcription factor 4 (ATF4) were quantified by RT-qPCR. In addition, liver biopsies were examined histologically for inflammatory alterations. Results Blood markers of acute inflammatory response increased after LPS challenge. In the liver, the proinflammatory cytokine IL-1β showed significantly lower mRNA levels after LPS challenge in the supplemented group (P = 0.04) compared to the placebo group. Levels of the hepatic CD68 mRNA increased significantly in the placebo group (P = 0.04). There were no significant differences between supplemented and placebo groups concerning other markers of inflammation and markers of ER stress within the liver. The number of hepatic macrophages were not different after LPS challenge in both feeding groups. Conclusion LPS was able to induce inflammation but seemed less suitable to induce ER stress in the horses and ponies. The polyphenol-rich supplement showed some potential to reduce inflammatory responses. Nevertheless, the supplementation did not exert an overall anti-inflammatory effect in horses and ponies.
Starzonek et al. (2019) Effects of a blend of green tea and curcuma extract supplementation on lipopolysaccharide-induced inflammation in horses and ponies. PeerJ 7:e8053 https://doi.org/10.7717/peerj.8053
Genome-wide identification and characterization of heat shock protein family 70 provides insight into its divergent functions on immune response and development of Paralichthys olivaceus
Flatfish undergo extreme morphological development and settle to a benthic in the adult stage, and are likely to be more susceptible to environmental stress. Heat shock proteins 70 (hsp70) are involved in embryonic development and stress response in metazoan animals. However, the evolutionary history and functions of hsp70 in flatfish are poorly understood. Here, we identified 15 hsp70 genes in the genome of Japanese flounder (Paralichthys olivaceus), a flatfish endemic to northwestern Pacific Ocean. Gene structure and motifs of the Japanese flounder hsp70 were conserved, and there were few structure variants compared to other fish species. We constructed a maximum likelihood tree to understand the evolutionary relationship of the hsp70 genes among surveyed fish. Selection pressure analysis suggested that four genes, hspa4l, hspa9, hspa13, and hyou1, showed signs of positive selection. We then extracted transcriptome data on the Japanese flounder with Edwardsiella tarda to induce stress, and found that hspa9, hspa12b, hspa4l, hspa13, and hyou1 were highly expressed, likely to protect cells from stress. Interestingly, expression patterns of hsp70 genes were divergent in different developmental stages of the Japanese flounder. We found that at least one hsp70 gene was always highly expressed at various stages of embryonic development of the Japanese flounder, thereby indicating that hsp70 genes were constitutively expressed in the Japanese flounder. Our findings provide basic and useful resources to better understand hsp70 genes in flatfish.
Liu et al. (2019) Genome-wide identification and characterization of heat shock protein family 70 provides insight into its divergent functions on immune response and development of Paralichthys olivaceus. PeerJ 7:e7781 https://doi.org/10.7717/peerj.7781
Vitis flower types: from the wild to crop plants
Vitis vinifera can be divided into two subspecies, V. vinifera subsp. vinifera, one of the most important agricultural crops in the world, and its wild ancestor, V. vinifera subsp. sylvestris. Three flower types can be observed: hermaphrodite and female (on some varieties) in vinifera, and male or female flowers in sylvestris. It is assumed that the different flower types in the wild ancestor arose through specific floral patterns of organ abortion. A considerable amount of data about the diversity of sexual systems in grapevines has been collected over the past century. Several grapevine breeding studies led to the hypothesis that dioecy in vinifera is derived from a hermaphrodite ancestor and could be controlled by either, one or two linked genetic determinants following Mendelian inherence. More recently, experiments using molecular approaches suggested that these loci were located in a specific region of the chromosome 2 of vinifera. Based on the works published so far, its seems evident that a putative sex locus is present in chromosome 2. However, it is still not fully elucidated whether flower types are regulated by two linked loci or by one locus with three alleles. Nevertheless, several genes could contribute to sex determination in grapevine. This review presents the results from early studies, combined with the recent molecular approaches, which may contribute to the design of new experiments towards a better understanding of the sex inheritance in grapevine.
Coito et al. (2019) Vitis flower types: from the wild to crop plants. PeerJ 7:e7879 https://doi.org/10.7717/peerj.7879
The acute effect of match-play on hip range of motion and isometric strength in elite tennis players
Background Groin injuries are some of the most common injuries tennis players suffer. Several factors (e.g., post-match decrease in hip adductor (ADD) strength) have been proposed as possible mechanisms for increasing the incidence of this type of injury. However, the risk factors of developing groin injuries after a tennis match have not yet been delineated. Objective The aim of this study was to determine the effect of tennis match-play on isometric ADD and abductor (ABD) strength and passive hip range of motion (ROM). Methods Twenty-six male tennis players (20.30 ± 4.98 years) took part in this study. Participants completed an evaluation of strength and flexibility hip measurements before and after a simulated tennis match. Dominant and non-dominant passive hip ROM, ADD and ABD isometric strength, and the ADD/ABD strength ratio were measured before and immediately post-match. A global positioning system (GPS) and a session rating of perceived exertion (RPE) were used to assess the locomotive demands and internal match load. Results Isometric dominant ADD strength (17.8%, p ≤ 0.01) and ADD/ABD strength ratio (11.6%, p = 0.04) were lower post-match compared to the pre-match values. No between-limbs differences were observed for isometric ADD strength, ABD strength, and passive hip ROM tests. RPE showed an expected increase between pre- vs. post-match (pre- vs. post-warming-up, 3.42 ± 2.08 vs. 5.62 ± 2.29, p < 0.01). In addition, a significant relationship between ADD strength and the volume of tennis practice per week was found, stablishing that tennis players with lower volume of training per week suffered a reduction in ADD strength in their dominant limb after match-play (r = 0.420, p = 0.04). Conclusion The assessment of ADD strength and the ADD/ABD strength ratio in the dominant limb may be considered a post-match tool that can be used to identify players who require rest and additional recovery strategies before competing again.
Moreno-Pérez et al. (2019) The acute effect of match-play on hip range of motion and isometric strength in elite tennis players. PeerJ 7:e7940 https://doi.org/10.7717/peerj.7940
A combined morphological and molecular approach for hair identification to comply with the European ban on dog and cat fur trade
Animal furs are encountering more and more the detriment of public opinion, that is increasingly sensitive to animals, their welfare and protection. The feeling of outrage against animal suffering is particularly intense when cats and dogs are involved, since these are the most popular pets in Western countries. However, in some Asian countries breeding of dogs and cats for the fur industry is a common practice. These furs and their finished garments are often mislabelled in order to be imported and sold to unaware consumers in Western countries. The European Union has issued the Regulation 1523/2007, which bans the use and trade of dog and cat furs. The main purposes of the Regulation were to normalise the internal market and to address the concerns of European consumers about the risk of inadvertently buying products containing these species. The Regulation states that several analytical methods (microscopy, DNA testing and mass spectrometry) can be used to exclude dogs and cats as source species, but an official analytical protocol was not provided. In this paper, we report on the development of a reliable and affordable method for species identification in furs, based on a combined morphological and molecular approach. Our protocol provides an initial morphological analysis as a time and cost effective screening test. Only samples that are morphologically not excluded as canid/felid furs, based on few selected microscopic features, are then submitted to DNA testing. The application of this protocol on seized furs reached 92% identification of species. Our approach assists in identifying frauds and reinforcing the ban on dog and cat fur trade, allowing (1) rapid inexpensive recognition of fake furs, (2) exclusion of non-canid/non-felid furs through fast microscopic morphological screening, (3) overall cost reduction with lower number of samples to be submitted to DNA analysis, (4) analytical protocol to stand in court in case criminal sanctions are to be applied.
Mariacher et al. (2019) A combined morphological and molecular approach for hair identification to comply with the European ban on dog and cat fur trade. PeerJ 7:e7955 https://doi.org/10.7717/peerj.7955
Development of molecular markers for invasive alien plants in Korea: a case study of a noxious weed, Cenchrus longispinus (Hack.) Fernald, based on next generation sequencing data
Background Genomic data play an important role in plant research because of its implications in studying genomic evolution, phylogeny, and developing molecular markers. Although the information of invasive alien plants was collected, the genomic data of those species have not been intensively studied. Methods We employ the next generation sequencing and PCR methods to explore the genomic data as well as to develop and test the molecular markers. Results In this study, we characterize the chloroplast genomes (cpDNA) of Cenchrus longispinus and C. echinatus, of which the lengths are 137,144 and 137,131 bp, respectively. These two newly sequenced genomes include 78 protein-coding genes, 30 tRNA, and four rRNA. There are 56 simple single repeats and 17 forward repeats in the chloroplast genome of C. longispinus. Most of the repeats locate in non-coding regions. However, repeats can be found in infA, ndhD, ndhH, ndhK, psbC, rpl22, rpoC2, rps14, trnA-UGC, trnC-GCA, trnF-GAA, trnQ-UUG, trnS-UGA, trnS-GCU, and ycf15. The phylogenomic analysis revealed the monophyly of Cenchrus but not Panicum species in tribe Paniceae. The single nucleotide polymorphism sites in atpB, matK, and ndhD were successfully used for developing molecular markers to distinguish C. longispinus and related taxa. The simple PCR protocol for using the newly developed molecular markers was also provided.
Hyun et al. (2019) Development of molecular markers for invasive alien plants in Korea: a case study of a noxious weed, Cenchrus longispinus (Hack.) Fernald, based on next generation sequencing data. PeerJ 7:e7965 https://doi.org/10.7717/peerj.7965
Ghosts from the past: a review of fossil Hepialoidea (Lepidoptera)
We critically re-examine nine of the ten fossil specimens currently assigned to Hepialidae. Three fossils with impressions of wing veins and scales placed in the fossil genus Prohepialus Piton, 1940, and two mummified larvae that show apomorphic characters, have features that support placement in Hepialidae. The other four fossils that we evaluate, Prohepialus incertus Piton, 1940; Oiophassus nycterus Zhang, 1989; Protohepialus comstocki Pierce, 1945; and a fossil scale, lack definitive hepialid characters. One of these, Prohepialus incertus Piton, 1940, appears to represent a symphytan (Hymenoptera), and is excluded from Lepidoptera. The fossilized wings placed in Prohepialus by Jarzembowski display numerous features that indicate a proximate phylogenetic relationship to extant members of the hepialid genus Sthenopis Packard and related genera.
Simonsen et al. (2019) Ghosts from the past: a review of fossil Hepialoidea (Lepidoptera). PeerJ 7:e7982 https://doi.org/10.7717/peerj.7982
Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs
Crossbreeding is widely used aimed at improving crossbred performance for poultry and livestock. Alleles that are specific to different purebreds will yield a large number of heterozygous single-nucleotide polymorphisms (SNPs) in crossbred individuals, which are supposed to have the power to alter gene function or regulate gene expression. For pork production, a classic three-way crossbreeding system of Duroc × (Landrace × Yorkshire) (DLY) is generally used to produce terminal crossbred pigs with stable and prominent performance. Nonetheless, little is known about the breed-of-origin effects from purebreds on DLY pigs. In this study, we first estimated the distribution of heterozygous SNPs in three kinds of three-way crossbred pigs via whole genome sequencing data originated from three purebreds. The result suggested that DLY is a more effective strategy for three-way crossbreeding as it could yield more stably inherited heterozygous SNPs. We then sequenced a DLY pig family and identified 95, 79, 132 and 42 allele-specific expression (ASE) genes in adipose, heart, liver and skeletal muscle, respectively. Principal component analysis and unrestricted clustering analyses revealed the tissue-specific pattern of ASE genes, indicating the potential roles of ASE genes for development of DLY pigs. In summary, our findings provided a lot of candidate SNP markers and ASE genes for DLY three-way crossbreeding system, which may be valuable for pig breeding and production in the future.
Lin et al. (2019) Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs. PeerJ 7:e8009 https://doi.org/10.7717/peerj.8009
Another look at the eigenvalues of a population matrix model
Population matrix models are important tools in resource management, in part because they are used to calculate the finite rate of growth (“dominant eigenvalue”). But understanding how a population matrix model converts life history traits into the finite rate of growth can be tricky. We introduce interactive software (“IsoPOPd”) that uses the characteristic equation to display how vital rates (survival and fertility) contribute to the finite rate of growth. Higher-order interactions among vital rates complicate the linkage between a management intervention and a population’s growth rate. We illustrate the use of the software for investigating the consequences of three management interventions in a 3-stage model of white-tailed deer (Odocoileus virginianus). The software is applicable to any species with 2- or 3-stages, but the mathematical concepts underlying the software are applicable to a population matrix model of any size. The IsoPOPd software is available at: https://cwhl.vet.cornell.edu/tools/isopopd.
Hanley et al. (2019) Another look at the eigenvalues of a population matrix model. PeerJ 7:e8018 https://doi.org/10.7717/peerj.8018
Long-term dynamics of urban thermal comfort in China’s four major capital cities across different climate zones
China has experienced intensive urbanization over the past decades. However, it is still unclear about the influence of urbanization on urban thermal comfort and how the effect varies with climate condition. Based on long-term daily meteorological data from 1990 to 2015 in four Chinese cities undergoing rapid urbanization, our study tried to detect the long-term dynamics of summer urban thermal comfort across different climate zones and analyze their relationships with urbanization. Our results showed that urbanization can increase urban temperature and decrease relative humidity and wind velocity. Urban thermal comfort and discomfort days also changed greatly, especially in Harbin, Northeast China from 1990 to 2015. However, such changes for different cities across different climate zones are inconsistent. Results also showed that urbanization especially for social economic activities can have a significant influence on the physiological Equivalent Temperature (PET). Compared with southern cities, the PET in northern cities such as Harbin and Changchun in this study is more sensitive to urbanization. These results reveal that the changing patterns of urban thermal comfort in Chinese cities under rapid urbanization, and help government take some effective measures to improve urban thermal environment.
Fu et al. (2019) Long-term dynamics of urban thermal comfort in China’s four major capital cities across different climate zones. PeerJ 7:e8026 https://doi.org/10.7717/peerj.8026
Alien species as a potential threat for Natura 2000 habitats: a national survey
Invasion by alien species (AS) is one of the most serious threats to ecosystems. In Europe, the Natura 2000 habitats network was established to protect habitats vital for the conservation of biodiversity and function of ecosystems. Therefore, the appearance of AS in Natura 2000 habitats is a warning signal that the most valuable European habitats may be endangered. However, quantitative studies encompassing a wide spectrum of habitats are lacking, and there is no insight into the differences in the level of invasion among habitats. Our survey is based on the State Monitoring of Natura 2000 data and aimed at an assessment of the level of invasion in natural habitat types in Poland. The percentage of invaded locations, number and frequency of alien plant species was assessed in 79 Natura 2000 habitats, both terrestrial and water, investigated on 5,941 locations. The most invaded habitats (with the highest percentage of invaded plots) were dunes with Hippophaë rhamnoides (habitat code 2160), rivers with muddy banks (habitat code 3270), and alpine rivers and herbaceous and ligneous vegetation along their banks (habitat codes: 3220, 3230, 3240). Grassland, forest and most of the bog, mire and fen habitats and also some habitats on a rock were invaded by a relatively large number of AS, but their frequency was comparatively low. In contrast, a high frequency of AS was found in the majority of dune and costal habitats and calaminarian grasslands. Compared with the period 2000–2010, the number of AS in some riparian, grassland and forest habitats rose noticeably. The occurrence of AS showed a negative correlation with conservation status of the habitats. This study has demonstrated that standard monitoring of Natura 2000 habitats provides the basis for the detection of AS, including invasive ones, in all types of habitats, and can be used for development rapid and effective response programs.
Perzanowska et al. (2019) Alien species as a potential threat for Natura 2000 habitats: a national survey. PeerJ 7:e8032 https://doi.org/10.7717/peerj.8032
Transcriptome sequencing of Verticillium dahliae from a cotton farm reveals positive correlation between virulence and tolerance of sugar-induced hyperosmosis
Verticillium dahliae causes disease symptoms in its host plants; however, due to its rapid variability, V. dahliae is difficult to control. To analyze the reason for this pathogenic differentiation, 22 V. dahliae strains with different virulence were isolated from a cotton farm. The genetic diversity of cotton varieties make cotton cultivars have different Verticillium wilt resistance, so the Xinluzao 7 (susceptible to V. dahliae), Zhongmian 35 (tolerant), and Xinluzao 33 (resistant) were used to investigate the pathogenicity of the strains in a green house. Vegetative compatibility groups (VCGs) assays, Internal Transcribed Spacer (ITS) PCR, and pathogenicity analysis showed that SHZ-4, SHZ-5, and SHZ-9 had close kinship and significantly different pathogenicity. Transcriptome sequencing of the three strains identified 19 of 146 unigenes in SHZ-4_vs_ SHZ-5, SHZ-5_vs_ SHZ-9, and SHZ-4_vs_ SHZ-9. In these unigenes, three proteinase and four polysaccharide degrading hydrolases were found to be associated with the pathogenicity. However, due to a number of differentially expressed genes in the transport, these unigenes not only played a role in nutrition absorption but might also contribute to the resistance of sugar-induced hyperosmosis. Moreover, the tolerance ability was positively related to the pathogenicity of V. dahliae. This resistance to sugar-induced hyperosmosis might help V. dahliae to access the nutrition of the host. The pathogenicity of V. dahliae correlated with the resistance of sugar-induced-hyperosmosis, which provides clues for the cultivation of V. dahliae resistant varieties.
Li et al. (2019) Transcriptome sequencing of Verticillium dahliae from a cotton farm reveals positive correlation between virulence and tolerance of sugar-induced hyperosmosis. PeerJ 7:e8035 https://doi.org/10.7717/peerj.8035
Gnathovorax cabreirai: a new early dinosaur and the origin and initial radiation of predatory dinosaurs
Predatory dinosaurs were an important ecological component of terrestrial Mesozoic ecosystems. Though theropod dinosaurs carried this role during the Jurassic and Cretaceous Periods (and probably the post-Carnian portion of the Triassic), it is difficult to depict the Carnian scenario, due to the scarcity of fossils. Until now, knowledge on the earliest predatory dinosaurs mostly relies on herrerasaurids recorded in Carnian strata of South America. Phylogenetic investigations recovered the clade in different positions within Dinosauria, whereas fewer studies challenged its monophyly. Although herrerasaurid fossils are much better recorded in present-day Argentina than in Brazil, Argentinean strata so far yielded no fairly complete skeleton representing a single individual. Here, we describe Gnathovorax cabreirai, a new herrerasaurid based on an exquisite specimen found as part of a multitaxic association from southern Brazil. The type specimen comprises a complete and well-preserved articulated skeleton, preserved in close association (side by side) with rhynchosaur and cynodont remains. Given its superb state of preservation and completeness, the new specimen sheds light into poorly understood aspects of the herrerasaurid anatomy, including endocranial soft tissues. The specimen also reinforces the monophyletic status of the group, and provides clues on the ecomorphology of the early carnivorous dinosaurs. Indeed, an ecomorphological analysis employing dental traits indicates that herrerasaurids occupy a particular area in the morphospace of faunivorous dinosaurs, which partially overlaps the area occupied by post-Carnian theropods. This indicates that herrerasaurid dinosaurs preceded the ecological role that later would be occupied by large to medium-sized theropods.
Pacheco et al. (2019) Gnathovorax cabreirai: a new early dinosaur and the origin and initial radiation of predatory dinosaurs. PeerJ 7:e7963 https://doi.org/10.7717/peerj.7963
Light intensity regulates phototaxis, foraging and righting behaviors of the sea urchin Strongylocentrotus intermedius
Small sea urchins Strongylocentrotus intermedius (1–2 cm of test diameter) are exposed to different environments of light intensities after being reseeded to the sea bottom. With little information available about the behavioral responses of S. intermedius to different light intensities in the environment, we carried out an investigation on how S. intermedius is affected by three light intensity environments in terms of phototaxis, foraging and righting behaviors. They were no light (zero lx), low light intensity (24–209 lx) and high light intensity (252–2,280 lx). Light intensity had obvious different effects on phototaxis. In low light intensity, sea urchins moved more and spent significantly more time at the higher intensity (69–209 lx) (P = 0.046). S. intermedius in high light intensity, in contrast, spent significantly more time at lower intensity (252–690 lx) (P = 0.005). Unexpectedly, no significant difference of movement (average velocity and total distance covered) was found among the three light intensities (P > 0.05). Foraging behavior of S. intermedius was significantly different among the light intensities. In the no light environment, only three of ten S. intermedius found food within 7 min. In low light intensity, nine of 10 sea urchins showed successful foraging behavior to the food placed at 209 lx, which was significantly higher than the ratio of the number (two of 10) when food was placed at 24 lx (P = 0.005). In the high light intensity, in contrast, significantly less sea urchins (three of 10) found food placed at the higher light intensity (2,280 lx) compared with the lower light intensity (252 lx) (10/10, P = 0.003). Furthermore, S. intermedius showed significantly longer righting response time in the high light intensity compared with both no light (P = 0.001) and low light intensity (P = 0.031). No significant difference was found in righting behavior between no light and low light intensity (P = 0.892). The present study indicates that light intensity significantly affects phototaxis, foraging and righting behaviors of S. intermedius and that ~200 lx might be the appropriate light intensity for reseeding small S. intermedius.
Sun et al. (2019) Light intensity regulates phototaxis, foraging and righting behaviors of the sea urchin Strongylocentrotus intermedius . PeerJ 7:e8001 https://doi.org/10.7717/peerj.8001
Long-term patient observation after conservative treatment of carpal tunnel syndrome: a summary of two randomised controlled trials
Background Physiotherapy of carpal tunnel syndrome (CTS) involves manual therapy based on neurodynamic techniques. Until now, two randomized controlled trials have shown that immediately after therapy, CTS patients who received neurodynamic techniques had significant improvement in nerve conduction, pain, symptom severity (SSS), functional state (FSS), muscle strength (MS) and two-point discrimination (2PD). However, long-term effects seem to be more important, as they are the only ones that can significantly improve the patient’s health and influence economic and social costs. Thus, the objective of this study was to evaluate the long-term (six months) effects of neurodynamic techniques in the conservative treatment of CTS patients. Methods Carpal tunnel syndrome patients (107) from two previously published randomised clinical trials were observed for six months after the treatment based on neurodynamic techniques. Results The sensory conduction velocity, motor conduction velocity, and motor latency were not subject to statistically significant changes within six months after therapy (p > 0.05). In both groups, there was further pain reduction (p < 0.05). In Group B, the symptom severity improved significantly (p < 0.05), while the functional status in both groups remained unchanged (p > 0.05). In both groups, there was muscle strength improvement (p < 0.05). Two-point discrimination remained unchanged six months after the therapy. Conclusion The use of manual therapy based on neurodynamic techniques maintains the beneficial effects 6 months after therapy in CTS patients.
Wolny et al. (2019) Long-term patient observation after conservative treatment of carpal tunnel syndrome: a summary of two randomised controlled trials. PeerJ 7:e8012 https://doi.org/10.7717/peerj.8012
Risk-taking behavior, the second-to-fourth digit ratio and psychological features in a sample of cavers
Background The risk-taking behavior is largely modulated by the subject’s history, its lifestyles, by the characteristics of the situations with which it is compared, and also by the effects of prenatal androgens. Thus, the personality of the single person is a significant predictor of such way of acting. Methods The present study aimed to explore the relationship between Digit Ratio Measurement (2D:4D) and personality factors capable to be good predictors for choosing highly risky activities, such as caving. Furthermore, our purpose was to investigate whether 2D:4D ratio is related to cavers’ affective states and to assess the personological and emotional features of 34 healthy cavers, aged between 24 and 71 years (M = 39.70, SD = 9.81). Results Data analysis showed several significant correlations between 2D:4D and Deliberate Risk Taking (RTI) and Precautionary Behavior (RTI), confirming that 2D:4D is a reliable index able to predict risk-taking behaviors. Furthermore, data analysis showed that Conscientiousness and its sub-dimension Scrupulousness (BFQ-2) are recurrent among significant correlations; in particular, the latter reports negative correlations with many factors of POMS. Moreover, all participants seemed to have a good attitude to collaboration, in terms of goal-direct strategy, and an adequate management of negative affective states, useful to maintaining a good level of stress within the group. Finally, the BFQ-2 factor Openness to culture seemed to be a predominant feature in the cavers, and this feature could be considered as predictive in the choice of an activity, such as caving, which requires curiosity, perseverance and a great planning of cave exploration.
Rinella et al. (2019) Risk-taking behavior, the second-to-fourth digit ratio and psychological features in a sample of cavers. PeerJ 7:e8029 https://doi.org/10.7717/peerj.8029
A new leptoceratopsid dinosaur from Maastrichtian-aged deposits of the Sustut Basin, northern British Columbia, Canada
A partial dinosaur skeleton from the Sustut Basin of northern British Columbia, Canada, previously described as an indeterminate neornithischian, is here reinterpreted as a leptoceratopsid ceratopsian, Ferrisaurus sustutensis, gen. et. sp. nov. The skeleton includes parts of the pectoral girdles, left forelimb, left hindlimb, and right pes. It can be distinguished from other named leptoceratopsids based on the proportions of the ulna and pedal phalanges. This is the first unique dinosaur species reported from British Columbia, and can be placed within a reasonably resolved phylogenetic context, with Ferrisaurus recovered as more closely related to Leptoceratops than Montanoceratops. At 68.2–67.2 Ma in age, Ferrisaurus falls between, and slightly overlaps with, both Montanoceratops and Leptoceratops, and represents a western range extension for Laramidian leptoceratopsids.
Arbour et al. (2019) A new leptoceratopsid dinosaur from Maastrichtian-aged deposits of the Sustut Basin, northern British Columbia, Canada. PeerJ 7:e7926 https://doi.org/10.7717/peerj.7926
Classifying Oryza sativa accessions into Indica and Japonica using logistic regression model with phenotypic data
In Oryza sativa, indica and japonica are pivotal subpopulations, and other subpopulations such as aus and aromatic are considered to be derived from indica or japonica. In this regard, Oryza sativa accessions are frequently viewed from the indica/japonica perspective. This study introduces a computational method for indica/japonica classification by applying phenotypic variables to the logistic regression model (LRM). The population used in this study included 413 Oryza sativa accessions, of which 280 accessions were indica or japonica. Out of 24 phenotypic variables, a set of seven phenotypic variables was identified to collectively generate the fully accurate indica/japonica separation power of the LRM. The resulting parameters were used to define the customized LRM. Given the 280 indica/japonica accessions, the classification accuracy of the customized LRM along with the set of seven phenotypic variables was estimated by 100 iterations of ten-fold cross-validations. As a result, the classification accuracy of 100% was achieved. This suggests that the LRM can be an effective tool to analyze the indica/japonica classification with phenotypic variables in Oryza sativa.
Kim (2019) Classifying Oryza sativa accessions into Indica and Japonica using logistic regression model with phenotypic data. PeerJ 7:e7259 https://doi.org/10.7717/peerj.7259
Scythes, sickles and other blades: defining the diversity of pectoral fin morphotypes in Pachycormiformes
The traditional terminology of ‘scythe’ or ‘sickle’ shaped is observed to be flawed as an effective descriptor for pectoral fin shape in pachycormids. The diversity of pachycormid pectoral fin shapes is assessed across the 14 recognised genera that preserve complete pectoral fins, and improved terms are defined to more effectively describe their form, supported by anatomical observation and aspect ratio analysis of individual fins, and corroborated by landmark analysis. Three clear and distinct pectoral fin structural morphotypes emerge (falceform, gladiform, falcataform), reflecting a diversity of pachycormid lifestyles throughout the Mesozoic, from agile pursuit predator to slow-cruising suspension feeder.
Liston et al. (2019) Scythes, sickles and other blades: defining the diversity of pectoral fin morphotypes in Pachycormiformes. PeerJ 7:e7675 https://doi.org/10.7717/peerj.7675
Vector distribution and transmission risk of the Zika virus in South and Central America
Background Zika is of great medical relevance due to its rapid geographical spread in 2015 and 2016 in South America and its serious implications, for example, certain birth defects. Recent epidemics urgently require a better understanding of geographic patterns of the Zika virus transmission risk. This study aims to map the Zika virus transmission risk in South and Central America. We applied the maximum entropy approach, which is common for species distribution modelling, but is now also widely in use for estimating the geographical distribution of infectious diseases. Methods As predictor variables we used a set of variables considered to be potential drivers of both direct and indirect effects on the emergence of Zika. Specifically, we considered (a) the modelled habitat suitability for the two main vector species Aedes aegypti and Ae. albopictus as a proxy of vector species distributions; (b) temperature, as it has a great influence on virus transmission; (c) commonly called evidence consensus maps (ECM) of human Zika virus infections on a regional scale as a proxy for virus distribution; (d) ECM of human dengue virus infections and, (e) as possibly relevant socio-economic factors, population density and the gross domestic product. Results The highest values for the Zika transmission risk were modelled for the eastern coast of Brazil as well as in Central America, moderate values for the Amazon basin and low values for southern parts of South America. The following countries were modelled to be particularly affected: Brazil, Colombia, Cuba, Dominican Republic, El Salvador, Guatemala, Haiti, Honduras, Jamaica, Mexico, Puerto Rico and Venezuela. While modelled vector habitat suitability as predictor variable showed the highest contribution to the transmission risk model, temperature of the warmest quarter contributed only comparatively little. Areas with optimal temperature conditions for virus transmission overlapped only little with areas of suitable habitat conditions for the two main vector species. Instead, areas with the highest transmission risk were characterised as areas with temperatures below the optimum of the virus, but high habitat suitability modelled for the two main vector species. Conclusion Modelling approaches can help estimating the spatial and temporal dynamics of a disease. We focused on the key drivers relevant in the Zika transmission cycle (vector, pathogen, and hosts) and integrated each single component into the model. Despite the uncertainties generally associated with modelling, the approach applied in this study can be used as a tool and assist decision making and managing the spread of Zika.
Cunze et al. (2019) Vector distribution and transmission risk of the Zika virus in South and Central America. PeerJ 7:e7920 https://doi.org/10.7717/peerj.7920
Combining data from different sampling methods to study the development of an alien crab Chionoecetes opilio invasion in the remote and pristine Arctic Kara Sea
Data obtained using three different types of sampling gear is compared and combined to assess the size composition and density of a non-indigenous snow crab population Chionoecetes opilio in the previously free of alien species Kara Sea benthos. The Sigsbee trawl has small mesh and catches even recently settled crabs. The large bottom trawl is able to catch large crabs, but does not retain younger crabs, due to its large mesh. Video sampling allows the observation of larger crabs, although some smaller crabs can also be spotted. The combined use of such gear could provide full scope data of the existing size groups in a population. The density of the crabs was calculated from the video footage. The highest figures were in Blagopoluchiya Bay at 0.87 crabs/m2, where the settlement seems to be reaching its first peak of population growth after the introduction. High density in the Kara Gates Strait at 0.55 crabs/m2, could be due to the close proximity of the Barents Sea from where the crabs can enter by both larval dispersal and active adult migration. All size groups have been present in most sampled areas, which suggest successful settlement and growth of crabs over a number of years. Again, this was not the case in Blagopoluchiya Bay with high density of small crabs (<30 mm CW), which confirms its recent population growth. Male to female ratio was strikingly different between the bays of the Novaya Zemlya Archipelago and west of the Yamal Peninsula (0.8 and 3.8 respectively). Seventy five ovigerous females were caught in 2016, which confirms the presence of a reproducing population in the Kara Sea. The spatial structure of the snow crab population in the Kara Sea is still in the process of formation. The presented data indicates that this process may lead to a complex system, which is based on local recruitment and transport of larvae from the Barents Sea and across the western Kara shelf; formation of nursery grounds; active migration of adults and their concentration in the areas of the shelf with appropriate feeding conditions.
Zalota et al. (2019) Combining data from different sampling methods to study the development of an alien crab Chionoecetes opilio invasion in the remote and pristine Arctic Kara Sea. PeerJ 7:e7952 https://doi.org/10.7717/peerj.7952
Zooplankton communities in the Drake Passage through environmental boundaries: a snapshot of 2010, early spring
Background Spatial distribution of zooplankton communities influenced by various environmental factors is always important for understanding pelagic ecosystems. The area of the Drake Passage (Southern Ocean) is of particular interest owing to the high spatial and temporal variability of hydrological parameters affecting marine fauna. This study provides a survey of zooplankton composition and spatial distribution along a transect in the Drake Passage sampled during the 31th Cruise of RV “Akademik Sergey Vavilov” in November, 2010. The main aim was to trace the main regularities in spatial zooplankton structure and its relationships with the environmental parameters. Methodology A total of 43 vertical hauls from the surface to 1,000 m depth were made at 13 stations using the Juday plankton net. 60 taxa were recorded, abundance and biomass of each were assessed. Environmental parameters including temperature, salinity, depth, horizontal distance between stations and surface chlorophyll concentration were tested as environmental factors possibly explaining plankton distribution. Results Higher zooplankton abundance and biomass with lower diversity were observed near the Polar Front. Cluster analysis revealed five different groups of zooplankton samples, four of which were arranged mostly by depth. Along the transect within the 1,000 m depth range, the qualitative taxonomical composition differed significantly with depth and to some extent differed also among horizontal hydrological regimes, while the quantitative structure of the communities (abundance of taxa) was mainly determined by depth. Plankton assemblages within the upper 300-m layer depended on hydrological fronts. Abundance of dominant taxa as well as total zooplankton abundance showed a clear correlation with depth, salinity and surface chlorophyll concentration. Some taxa also showed correlations with temperature and latitude. Between the stations the similarity in zooplankton structure was clearly dependent on the distance among them which indicates an importance of latitudinal gradient. Surface chlorophyll concentration was not correlated with zooplankton biomass, which can be explained by the uncompleted seasonal migrations of zooplankton from deeper waters in early spring.
Vedenin et al. (2019) Zooplankton communities in the Drake Passage through environmental boundaries: a snapshot of 2010, early spring. PeerJ 7:e7994 https://doi.org/10.7717/peerj.7994
Idiosyncratic changes in spring arrival dates of Pacific Northwest migratory birds
Shifts in the timing of bird migration have been associated with climatic change and species traits. However, climatic change does not affect all species or geographic locations equally. Climate in the Pacific Northwest has shifted during the last century with mean temperatures increasing by 1 °C but little change in total annual precipitation. Few long-term data on migration phenology of birds are available in the Pacific Northwest. We analyzed trends in spring arrival dates from a site in the Oregon Coast Range where nearly daily inventories of birds were conducted in 24 of 29 years. Several species showed statistically significant shifts in timing of first spring arrivals. Six of 18 species occur significantly earlier now than during the initial phase of the study. One species arrives significantly later. Eleven show no significant shifts in timing. We associated trends in spring migration phenology with regional climatic variables, weather (precipitation and temperature), traits of species such as migration strategy, foraging behavior, diet, and habitat use, and regional trends in abundance as indexed by Breeding Bird Survey data. We found no set of variables consistently correlated with avian phenological changes. Post hoc analyses of additional climate variables revealed an association of migratory arrival dates across the 18 species with rainfall totals in northern California, presumably indicating that songbird arrival dates in Oregon are slowed by spring storm systems in California. When only the six species with the most strongly advancing arrival dates were analyzed, winter maximum temperatures in the preceding three winters appeared consistently in top models, suggesting a possible role for food availability early in spring to promote the survival and successful reproduction of the earliest-arriving birds. However, additional data on food availability and avian survival and reproductive success are required to test that hypothesis. Despite the appearance of some climate variables in top models, there remains a mismatch between strongly advancing arrival dates in some songbirds and a lack of clear directional change in those climate variables. We conclude that either some previously unrecognized variable or combination of variables has affected the timing of migration in some species but not others, or the appearance of statistically significant directional changes over time can occur without being driven by consistent environmental or species-specific factors.
Robinson et al. (2019) Idiosyncratic changes in spring arrival dates of Pacific Northwest migratory birds. PeerJ 7:e7999 https://doi.org/10.7717/peerj.7999
The urban-rural disparity in the prevalence and risk factors of hypertension among the elderly in China—a cross-sectional study
Introduction This study aimed to assess the prevalence of hypertension and to explore the disparities of its risk factors among urban and rural elderly. Method Data of hypertensive patients were collected from the China Health and Retirement Longitudinal Study (CHARLS) 2015. Stratified sample households were selected from 450 villages or communities of 150 counties from 28 provinces. Multivariable logistic regression was performed to analyze the factors correlated with hypertension. Results Prevalence of HBP was 47.6% (95% CI [45.2%–50.1%]) in total and it was close between urban and rural population (48.6% vs 47.2%). Factors associated with HBP were different between urban and rural areas. In urban areas, hypertension was significantly associated with literacy and diabetes in both genders, high BMI level and smoke quitters in males, and physical activity and dyslipidemia in females. In rural areas, hypertension was significantly associated with older age, higher BMI level in both males and females, and dyslipidemia in males. Conclusions The prevalence are about the same among urban and rural residents, but their risk factors vary from each other. Disparity in the risk factors between urban and rural population should be taken into consideration for further intervention.
Song et al. (2019) The urban-rural disparity in the prevalence and risk factors of hypertension among the elderly in China—a cross-sectional study. PeerJ 7:e8015 https://doi.org/10.7717/peerj.8015
Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis
MADS-box genes encode transcription factors that participate in various plant growth and development processes, particularly floral organogenesis. To date, MADS-box genes have been reported in many species, the completion of the sequence of the willow genome provides us with the opportunity to conduct a comprehensive analysis of the willow MADS-box gene family. Here, we identified 60 willow MADS-box genes using bioinformatics-based methods and classified them into 22 M-type (11 Mα, seven Mβ and four Mγ) and 38 MIKC-type (32 MIKCc and six MIKC*) genes based on a phylogenetic analysis. Fifty-six of the 60 SsMADS genes were randomly distributed on 19 putative willow chromosomes. By combining gene structure analysis with evolutionary analysis, we found that the MIKC-type genes were more conserved and played a more important role in willow growth. Further study showed that the MIKC* type was a transition between the M-type and MIKC-type. Additionally, the number of MADS-box genes in gymnosperms was notably lower than that in angiosperms. Finally, the expression profiles of these willow MADS-box genes were analysed in five different tissues (root, stem, leave, bud and bark) and validated by RT-qPCR experiments. This study is the first genome-wide analysis of the willow MADS-box gene family, and the results establish a basis for further functional studies of willow MADS-box genes and serve as a reference for related studies of other woody plants.
Qu et al. (2019) Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis. PeerJ 7:e8019 https://doi.org/10.7717/peerj.8019
Competing endogenous RNA (ceRNA) hypothetic model based on comprehensive analysis of long non-coding RNA expression in lung adenocarcinoma
Background Non-small cell lung cancer (NSCLC) is a major subtype of lung cancer with high malignancy and bad prognosis, consisted of lung adenocarcinomas (LUAD) and lung squamous cell carcinomas (LUSC) chiefly. Multiple studies have indicated that competing endogenous RNA (ceRNA) network centered long noncoding RNAs (lncRNAs) can regulate gene expression and the progression of various cancers. However, the research about lncRNAs-mediated ceRNA network in LUAD is still lacking. Methods In this study, we analyzed the RNA-seq database from The Cancer Genome Atlas (TCGA) and obtained dysregulated lncRNAs in NSCLC, then further identified survival associated lncRNAs through Kaplan–Meier analysis. Quantitative real time PCR (qRT-PCR) was performed to confirm their expression in LUAD tissues and cell lines. The ceRNA networks were constructed based on DIANA-TarBase and TargetScan databases and visualized with OmicShare tools. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to investigate the potential function of ceRNA networks. Results In total, 1,437 and 1,699 lncRNAs were found to be up-regulated in LUAD and LUSC respectively with 895 lncRNAs overlapping (|log2FC| > 3, adjusted P value <0.01). Among which, 222 lncRNAs and 46 lncRNAs were associated with the overall survival (OS) of LUAD and LUSC, and 18 out of 222 up-regulated lncRNAs were found to have inverse correlation with LUAD patients’ OS (|log2FC| > 3, adjusted P value < 0.02). We selected 3 lncRNAs (CASC8, LINC01842 and VPS9D1-AS1) out of these 18 lncRNAs and confirmed their overexpression in lung cancer tissues and cells. CeRNA networks were further constructed centered CASC8, LINC01842 and VPS9D1-AS1 with 3 miRNAs and 100 mRNAs included respectively. Conclusion Through comprehensively analyses of TCGA, our study identified specific lncRNAs as candidate diagnostic and prognostic biomarkers for LUAD. The novel ceRNA network we created provided more insights into the regulatory mechanisms underlying LUAD.
Wang et al. (2019) Competing endogenous RNA (ceRNA) hypothetic model based on comprehensive analysis of long non-coding RNA expression in lung adenocarcinoma. PeerJ 7:e8024 https://doi.org/10.7717/peerj.8024
Effect of different ergonomic supports on muscle activity of dentists during posterior composite restoration
Background The aim of this study was to evaluate the effect of different ergonomic supports on the muscle activity of two trunk muscles while a group of dentists performed a common dental procedure on a phantom head, divided into three tasks. Methods A one-way repeated measures study (ANOVA) was conducted on a group of 36 dentists. The middle trapezius and lumbar erector spinae muscles were measured with and without the use of different ergonomic supports (ergonomic stool, magnification lenses and both) using a portable surface electromyography (sEMG) device. Intraclass correlation coefficients (ICCs) and the absolute standard error of measurement (SEM) were used to establish the reliability of the baseline measures without ergonomic supports. Results The sEMG showed excellent ICCs (ranging from 0.92 to 0.99) and SEM. Bonferroni post hoc tests showed differences between the three ergonomic supports (p < 0.001) in both muscles studied. The lowest muscle activity measurement occurred with the isolated used of magnification lenses. The use of the ergonomic stool increased the muscle activity of the middle trapezius and lumbar erector spinae muscles to a greater extent than the magnification lenses. The combination of the ergonomic stool and the magnification lenses produced a different effect on each muscle.
López-Nicolás et al. (2019) Effect of different ergonomic supports on muscle activity of dentists during posterior composite restoration. PeerJ 7:e8028 https://doi.org/10.7717/peerj.8028
Genome-wide analysis of transcription factors related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots
Carmine radish produced in Chongqing is famous for containing a natural red pigment (red radish pigment). However, the anthocyanin biosynthesis transcriptome and the expression of anthocyanin biosynthesis-related genes in carmine radish have not been fully investigated. Uncovering the mechanism of anthocyanin biosynthesis in the ‘Hongxin 1’ carmine radish cultivar has become a dominant research topic in this field. In this study, a local carmine radish cultivar named ‘Hongxin 1’ containing a highly natural red pigment was used to analyze transcription factors (TFs) related to anthocyanin biosynthesis during the dynamic development of fleshy roots. Based on RNA sequencing data, a total of 1,747 TFs in 64 TF families were identified according to their DNA-binding domains. Of those, approximately 71 differentially expressed transcription factors (DETFs) were commonly detected in any one stage compared with roots in the seedling stage (SS_root). Moreover, 26 transcripts of DETFs targeted by 74 miRNAs belonging to 25 miRNA families were identified, including MYB, WRKY, bHLH, ERF, GRAS, NF-YA, C2H2-Dof, and HD-ZIP. Finally, eight DETF transcripts belonging to the C2C2-Dof, bHLH and ERF families and their eight corresponding miRNAs were selected for qRT-PCR to verify their functions related to anthocyanin biosynthesis during the development of carmine radish fleshy roots. Finally, we propose a putative miRNA-target regulatory model associated with anthocyanin biosynthesis in carmine radish. Our findings suggest that sucrose synthase might act as an important regulator to modulate anthocyanin biosynthesis in carmine radish by inducing several miRNAs (miR165a-5p, miR172b, miR827a, miR166g and miR1432-5p) targeting different ERFs than candidate miRNAs in the traditional WMBW complex in biological processes.
Gao et al. (2019) Genome-wide analysis of transcription factors related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots. PeerJ 7:e8041 https://doi.org/10.7717/peerj.8041
Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA
Mine tailing disasters have occurred worldwide and contemporary release of tailings of large proportions raise concerns of the chronic impacts that trace metals may have on the aquatic biodiversity. Environmental metabarcoding (eDNA) offers an as yet poorly explored opportunity for biological monitoring of impacted aquatic ecosystems from mine tailings and contaminated sediments. eDNA has been increasingly recognized to be an effective method to detect previously unrecognized small-sized Metazoan taxa, but their ecological responses to environmental pollution has not been assessed by metabarcoding. Here, we evaluated chronic effects of trace metal contamination from sediment eDNA of the Rio Doce estuary, 1.7 years after the Samarco mine tailing disaster, which released over 40 million m3 of iron tailings in the Rio Doce river basin. We identified 123 new sequence variants environmental taxonomic units (eOTUs) of benthic taxa and an assemblage composition dominated by Nematoda, Crustacea and Platyhelminthes; typical of other estuarine ecosystems. We detected environmental filtering on the meiofaunal assemblages and multivariate analysis revealed strong influence of Fe contamination, supporting chronic impacts from mine tailing deposition in the estuary. This was in contrast to environmental filtering of meiofaunal assemblages of non-polluted estuaries. Here, we suggest that the eDNA metabarcoding technique provides an opportunity to fill up biodiversity gaps in coastal marine ecology and may become a valid method for long term monitoring studies in mine tailing disasters and estuarine ecosystems with high trace metals content.
Bernardino et al. (2019) Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA. PeerJ 7:e8042 https://doi.org/10.7717/peerj.8042
Effects of afforestation on water resource variations in the Inner Mongolian Plateau
Afforestation is a key approach used to effectively prevent ecosystem degradation, which in itself is a key reason for the obstruction of sustainable societal development. In order to suppress sand and dust storms as a result of ecological environmental degradation in North China, the Government of China has sanctioned the planting of a large number of trees in Inner Mongolia. However, water resources in the Inner Mongolian Plateau are insufficient to sustain this effort because such a large number of trees consume a large amount of water, which also significantly increases evapotranspiration. This study uses spatiotemporal trend analyses and abrupt change analyses to determine the effects of afforestation on water resource variations in the Inner Mongolian Plateau. Results show that even though water resources in Inner Mongolia fluctuate, this resource has generally exhibited a declining trend from 1980 to 2015, corresponding to the NDVI trend. On spatial-temporal scales, water resources decreased significantly in the eastern section of the plateau, especially in the Horqin District and the Hulunbuir Plateau. By contrast, water resources increased as a whole in the western section of the plateau (Alxa Plateau). Driving analysis results show that water resource variation is mainly due to the contribution of change in precipitation (positive effect), which accounted for 39.35% of total changes in water resources, followed by the evapotranspiration (negative effect). In other words, afforestation with the primary aim of improving ecosystem has effectually upset the water resource balance of Inner Mongolia Plateau.
Xiao et al. (2019) Effects of afforestation on water resource variations in the Inner Mongolian Plateau. PeerJ 7:e7525 https://doi.org/10.7717/peerj.7525
Neck mobility in the Jurassic plesiosaur Cryptoclidus eurymerus: finite element analysis as a new approach to understanding the cervical skeleton in fossil vertebrates
The sauropterygian clade Plesiosauria arose in the Late Triassic and survived to the very end of the Cretaceous. Plesiosauria evolved the greatest species diversity of any marine reptile clade, attaining a global distribution. Plesiosauria consist of two clades, Rhomaleosauridae and Neoplesiosauria. Basal Neoplesiosauria have long necks with at least 30 cervicals, but show qualitative osteological evidence for a stiff neck. Here we quantify neck mobility in lateral, ventral, and dorsal directions based on finite element modeling of neck vertebrae from the Middle Jurassic plesiosaur Cryptoclidus eurymerus. We model the mobility in a single motion segment, consisting of two adjacent cervical vertebrae and the joints connecting them. Based on the model with a maximum intervertebral spacing of 3 mm, we find that in Cryptoclidus, the maximum angle of lateral deflection in the motion segment was 2°. The maximum angle of ventral deflection was 5° and of dorsal deflection was 5°. When these values are multiplied by the number of cervical vertebrae, it becomes apparent that neck mobility was limited in all directions. The maximum angle of total lateral deflection in the neck was 67°. The maximum angle of total ventral deflection was 148° and of total dorsal deflection was 157°. This raises the question of the function of such a long, multi-segment but immobile neck. We posit that the long neck served in hydrodynamic and visual camouflage, hiding the bulk of the body from the small but abundant prey, such as schooling fish and squid. Neck immobility may have been advantageous in withstanding strong hydrodynamic forces acting on the neck during predatory strikes.
Wintrich et al. (2019) Neck mobility in the Jurassic plesiosaur Cryptoclidus eurymerus: finite element analysis as a new approach to understanding the cervical skeleton in fossil vertebrates. PeerJ 7:e7658 https://doi.org/10.7717/peerj.7658
Short-term vasoactive agent treatment driven by physicians’ preference in acute esophageal variceal bleeding in a tertiary center
Background Vasoactive drugs are frequently used in combination with endoscopic variceal ligation (EVL) in treatment of acute esophageal variceal bleeding (EVB). The aim of study was to assess physicians’ preference of vasoactive agents in acute EVB, their reasons of preference and efficacy and safety of these short course regimens. Methods Cirrhotic patients with suspected EVB were screened (n = 352). Eligible patients were assigned based on the physician’s preference to either somatostatin (group S) or terlipressin (group T) followed by EVL. In group S, intravenous bolus (250 µg) of somatostatin followed by 250 µg/hour was continued for three days. In group T, 2 mg bolus injection of terlipressin was followed by 1 mg infusion every 6 h for three days. Results A total of 150 patients were enrolled; 41 in group S and 109 in group T. Reasons for physician preference was convenience in administration (77.1%) for group T and good safety profile (73.2%) for group S. Very early rebleeding within 49–120 h occurred in one patient in groups S and T (p = 0.469). Four patients in group S and 14 patients in group T have variceal rebleeding episodes within 6–42 d (p = 0.781). Overall treatment-related adverse effects were compatible in groups S and T (p = 0.878), but the total cost of terlipressin and somatostatin differed i.e., USD 621.32 and USD 496.43 respectively. Conclusions Terlipressin is the preferred vasoactive agent by physicians in our institution for acute EVB. Convenience in administration and safety profile are main considerations of physicians. Safety and hemostatic effects did not differ significantly between short-course somatostatin or terlipressin, although terlipressin is more expensive.
Chuah et al. (2019) Short-term vasoactive agent treatment driven by physicians’ preference in acute esophageal variceal bleeding in a tertiary center. PeerJ 7:e7913 https://doi.org/10.7717/peerj.7913
Spatial genetic structure in Pinus cembroides Zucc. at population and landscape levels in central and northern Mexico
Background Spatial genetic structure (SGS) analysis is a powerful approach to quantifying gene flow between trees, thus clarifying the functional connectivity of trees at population and landscape scales. The findings of SGS analysis may be useful for conservation and management of natural populations and plantations. Pinus cembroides is a widely distributed tree species, covering an area of about 2.5 million hectares in Mexico. The aim of this study was to examine five natural seed stands of P. cembroides in the Sierra Madre Occidental to determine the SGS at population (within the seed stand) and landscape (among seed stands) levels in order to establish guidelines for the conservation and management of the species. We hypothesized that P. cembroides, in which the seeds are dispersed by birds and mammals, creates weaker SGS than species with wind-dispersed seeds. Methods DNA fingerprinting was performed using the amplified fragment length polymorphism (AFLP) technique. In order to estimate the SGS at population and landscape levels, we measured the geographical (spatial) distance as the Euclidean distance. We also estimated the genetic distances between individuals using the pairwise kinship coefficient. Results The results showed non-significant autocorrelation in four out of five seed stands studied (i.e., a mainly random distribution in the space of the genetic variants of P. cembroides at population level). Discussion SGS was detected at the landscape scale, supporting the theory of isolation by distance as a consequence of restricted pollen and seed dispersal. However, the SGS may also have been generated by our sampling strategy. We recommended establishing a close network of seed stands of P. cembroides to prevent greater loss of local genetic variants and alteration of SGS. We recommend seed stands of P. cembroides of a minimum width of 225 m.
García-Zubia et al. (2019) Spatial genetic structure in Pinus cembroides Zucc. at population and landscape levels in central and northern Mexico. PeerJ 7:e8002 https://doi.org/10.7717/peerj.8002
Enforced symmetry: the necessity of symmetric waxing and waning
A fundamental question in ecology is how the success of a taxon changes through time and what drives this change. This question is commonly approached using trajectories averaged over a group of taxa. Using results from probability theory, we show analytically and using examples that averaged trajectories will be more symmetric as the number of averaged trajectories increases, even if none of the original trajectories they were derived from is symmetric. This effect is not only based on averaging, but also on the introduction of noise and the incorporation of a priori known origination and extinction times. This implies that averaged trajectories are not suitable for deriving information about the processes driving the success of taxa. In particular, symmetric waxing and waning, which is commonly observed and interpreted to be linked to a number of different paleobiological processes, does not allow drawing any conclusions about the nature of the underlying process.
Hohmann et al. (2019) Enforced symmetry: the necessity of symmetric waxing and waning. PeerJ 7:e8011 https://doi.org/10.7717/peerj.8011
A new alligatoroid from the Eocene of Vietnam highlights an extinct Asian clade independent from extant Alligator sinensis
During systematic paleontological surveys in the Na Duong Basin in North Vietnam between 2009 and 2012, well-preserved fossilized cranial and postcranial remains belonging to at least 29 individuals of a middle to late Eocene (late Bartonian to Priabonian age (39–35 Ma)) alligatoroid were collected. Comparative anatomical study of the material warrants the diagnosis of a new taxon, Orientalosuchus naduongensis gen. et sp. nov. The combined presence of an enlarged fifth maxillary tooth, prominent preorbital ridges, a large supraoccipital exposure on the skull table, a palatine-pterygoid suture anterior to the posterior end of the suborbital fenestra, and a pterygoid forming a neck surrounding the choana is unique to this species. Unlike previous phylogenies, our parsimony analysis recovers a monophyletic Late Cretaceous to Paleogene East to Southeastern Asian alligatoroid group, here named Orientalosuchina. The group includes Orientalosuchus naduongensis, Krabisuchus siamogallicus, Eoalligator chunyii, Jiangxisuchus nankangensis and Protoalligator huiningensis, all of them sharing a medial shifted quadrate foramen aerum. The recognition of this clade indicates at least two separate dispersal events from North America to Asia: one during the Late Cretaceous by Orientalosuchina and one by the ancestor of Alligator sinensis during the Paleogene or Neogene, the timing of which is poorly constrained.
Massonne et al. (2019) A new alligatoroid from the Eocene of Vietnam highlights an extinct Asian clade independent from extant Alligator sinensis. PeerJ 7:e7562 https://doi.org/10.7717/peerj.7562
L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus
Phenotypic differences between Campylobacter fetus fetus and C. fetus venerealis subspecies allow the differential diagnosis of bovine genital campylobacteriosis. The hydrogen sulfide production, for example, is a trait exclusive to C. fetus fetus and C. fetus venerealis biovar intermedius. This gas that can be biochemically tested can be produced from L-cysteine (L-Cys). Herein, we report a novel multiplex-PCR to differentiate C. fetus based on the evaluation of a deletion of an ATP-binding cassette-type L-Cys transporter that could be involved in hydrogen sulfide production, as previously described. A wet lab approach combined with an in silico whole genome data analysis showed complete agreement between this L-Cys transporter-PCR and the hydrogen sulfide production biochemical test. This multiplex-PCR may complement the tests currently employed for the differential diagnosis of C. fetus.
Farace et al. (2019) L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus. PeerJ 7:e7820 https://doi.org/10.7717/peerj.7820
Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin
Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as “blue crab” and “Product of the USA” may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as “Product of the USA” and “Product of Venezuela.” In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise Fst values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide diversity values. Lineages 1 and 2 were separated by a mean pairwise distance (p-distance) of 3.15%, whereas Lineage 3 had a mean p-distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p-distances were 0.45%, 0.19%, and 0.07% for Lineages 1, 2, and 3, respectively. Among all vouchered reference specimens collected from the continental United States, Mexico, Puerto Rico, and Venezuela, we identified 22 phylogenetically informative sites that drive observed lineage divergences. Haplotypes identified from barcode COI sequences from commercial C. sapidus products labeled as originating from the US all aligned with haplotypes from Lineage 1 reference specimens and haplotypes from commercial products labeled as originating from Venezuela all aligned with Lineage 2, suggesting that these lineages may be useful for indicating whether products originate from the continental US or are imported when package labeling is in question.
Windsor et al. (2019) Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin. PeerJ 7:e7827 https://doi.org/10.7717/peerj.7827
Prey selectivity and the effect of diet on growth and development of a dragonfly, Sympetrum sanguineum
Despite a long tradition of research, our understanding of mechanisms driving prey selectivity in predatory insects is limited. According to optimal foraging theory, predators should prefer prey which provides the highest amount of energy per unit time. However, prey selectivity may also depend on previous diet and specific nutritional demands of the predator. From the long-term perspective, diet composition affects predator fitness. An open question is whether short-term selectivity of predators provides a diet which is optimal in the long-term. To shed more light on these issues, we conducted laboratory experiments on prey selectivity and its long-term consequences in larvae of the dragonfly Sympetrum sanguineum. We conditioned the larvae to one of two prey types, the cladoceran Daphnia magna and larvae of a non-biting midge Chironomus sp., and then exposed them to various combinations of the two prey types. We found that dragonfly larvae conditioned to Chironomus larvae consumed the same amount of D. magna, but significantly less Chironomus larvae compared to dragonfly larvae conditioned to D. magna. However, there was no effect of previous diet on their success of capture and handling time, suggesting a limited role of learning in their ability to process prey. We then tested the long-term effects of diets with different proportions of both prey for survival and growth of the dragonfly larvae. Individuals fed Chironomus-only diet had higher mortality and slower growth than dragonflies fed D. magna, while larvae fed a mixed diet had the highest survival and growth rate. In conclusion, we show that dragonfly larvae fed by Chironomus larvae performed poorly and compensated by preferring D. magna when both prey types were available. The superiority of the mixed diet suggests that a diverse diet may be needed to satisfy nutritional demands in S. sanguineum larvae. We demonstrate that merging short-term predation experiments with relevant data on predator fitness may provide better understanding of predator-prey interactions and conclude that detailed information on the (mis)matches between prey composition and predator nutritional demands is needed for further progress.
Dudová et al. (2019) Prey selectivity and the effect of diet on growth and development of a dragonfly, Sympetrum sanguineum. PeerJ 7:e7881 https://doi.org/10.7717/peerj.7881
Reconstructing the archosaur radiation using a Middle Triassic archosauriform tooth assemblage from Tanzania
Following the Permo–Triassic mass extinction, Archosauriformes—the clade that includes crocodylians, birds, and their extinct relatives outside crown Archosauria—rapidly diversified into many distinct lineages, became distributed globally, and, by the Late Triassic, filled a wide array of resource zones. Current scenarios of archosauriform evolution are ambiguous with respect to whether their taxonomic diversification in the Early–Middle Triassic coincided with the initial evolution of dietary specializations that were present by the Late Triassic or if their ecological disparity arose sometime after lineage diversification. Late Triassic archosauriform dietary specialization is recorded by morphological divergence from the plesiomorphic archosauriform tooth condition (laterally-compressed crowns with serrated carinae and a generally triangular lateral profile). Unfortunately, the roots of this diversification are poorly documented, with few known Early­–Middle Triassic tooth assemblages, limiting characterizations of morphological diversity during this critical, early period in archosaur evolution. Recent fieldwork (2007–2017) in the Middle Triassic Manda Beds of the Ruhuhu Basin, Tanzania, recovered a tooth assemblage that provides a window into this poorly sampled interval. To investigate the taxonomic composition of that collection, we built a dataset of continuous quantitative and discrete morphological characters based on in situ teeth of known taxonomic status (e.g., Nundasuchus, Parringtonia: N = 65) and a sample of isolated teeth (N = 31). Using crown heights from known taxa to predict tooth base ratio (= base length/width), we created a quantitative morphospace for the tooth assemblage. The majority of isolated, unassigned teeth fall within a region of morphospace shared by several taxa from the Manda Beds (e.g., Nundasuchus, Parringtonia); two isolated teeth fall exclusively within a “Pallisteria” morphospace. A non-metric multidimensional scaling ordination (N = 67) of 11 binary characters reduced overlap between species. The majority of the isolated teeth from the Manda assemblage fall within the Nundasuchus morphospace. This indicates these teeth are plesiomorphic for archosauriforms as Nundasuchus exhibits the predicted plesiomorphic condition of archosauriform teeth. Our model shows that the conservative tooth morphologies of archosauriforms can be differentiated and assigned to species and/or genus, rendering the model useful for identifying isolated teeth. The large overlap in tooth shape among the species present and their overall similarity indicates that dietary specialization lagged behind species diversification in archosauriforms from the Manda Beds, a pattern predicted by Simpson’s “adaptive zones” model. Although applied to a single geographic region, our methods offer a promising means to reconstruct ecological radiations and are readily transferable across a broad range of vertebrate taxa throughout Earth history.
Hoffman et al. (2019) Reconstructing the archosaur radiation using a Middle Triassic archosauriform tooth assemblage from Tanzania. PeerJ 7:e7970 https://doi.org/10.7717/peerj.7970
Screening of reference genes for expression analysis in the study of soldier caste differentiation of Formosan subterranean termite Coptotermes formosanus Shiraki
The Formosan subterranean termite, Coptotermes formosanus Shiraki, is a serious pest worldwide. Juvenile hormone analog (and its analogs such as methoprene) can induce the transformation of the worker caste into soldier caste in C. formosanus. However, several factors, such as feeding substrate and colony origin, influence the proportion of solider formation. The molecular mechanism of worker to soldier transformation of C. formosanus is still not clear. RT-qPCR is a powerful tool for molecular studies. Accurate gene quantification by the relative quantification method requires a stable expressed gene as the reference gene. However, no reference genes were available for this species in the methoprene bioassay. To study the problem of gene response to methoprene by RT-qPCR we have to first screen reference genes in C. formosanus. Workers were fed with methoprene. Termites were collected during the methoprene bioassay and separated into head and thorax+abdomen. Expression profiles of 10 candidate reference genes in the two body part types were investigated using RT-qPCR. The results were analyzed by a set of established methods (geNorm, NormFinder, BestKeeper, and RefFinder) as well as comparative ΔCt method. Our results suggest that RPS18 is the most stably-expressed gene both in the head and thorax+abdomen for expression analysis in the methoprene bioassay of C. formosanus. The screening of suitable reference genes in C. formosanus establishes the foundation for the molecular study of soldier caste differentiation in this species.
Du et al. (2019) Screening of reference genes for expression analysis in the study of soldier caste differentiation of Formosan subterranean termite Coptotermes formosanus Shiraki. PeerJ 7:e7981 https://doi.org/10.7717/peerj.7981
In recent years, the field of sexual selection has exploded, with advances in theoretical and empirical research complementing each other in exciting ways. This perspective piece is the product of a “stock-taking” workshop on sexual selection and sexual conflict. Our aim is to identify and deliberate on outstanding questions and to stimulate discussion rather than provide a comprehensive overview of the entire field. These questions are organized into four thematic sections we deem essential to the field. First we focus on the evolution of mate choice and mating systems. Variation in mate quality can generate both competition and choice in the opposite sex, with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems, especially with regard to polyandry. Second, we focus on how sender and receiver mechanisms shape signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are challenging to measure. We view the neuroethology of sensory and cognitive receiver biases as the main key to signal form and the ‘aesthetic sense’ proposed by Darwin. Since a receiver bias is sufficient to both initiate and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate ‘null model’ of sexual selection. Thirdly, we focus on the genetic architecture of sexually selected traits. Despite advances in modern molecular techniques, the number and identity of genes underlying performance, display and secondary sexual traits remains largely unknown. In-depth investigations into the genetic basis of sexual dimorphism in the context of long-term field studies will reveal constraints and trajectories of sexually selected trait evolution. Finally, we focus on sexual selection and conflict as drivers of speciation. Population divergence and speciation are often influenced by an interplay between sexual and natural selection. The extent to which sexual selection promotes or counteracts population divergence may vary depending on the genetic architecture of traits as well as the covariance between mating competition and local adaptation. Additionally, post-copulatory processes, such as selection against heterospecific sperm, may influence the importance of sexual selection in speciation. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection, and we offer potential avenues of research to advance this progress.
Lindsay et al. (2019) Endless forms of sexual selection. PeerJ 7:e7988 https://doi.org/10.7717/peerj.7988
Injury incidence, characteristics and burden among female sub-elite futsal players: a prospective study with three-year follow-up
The main purpose of the current study was to analyze the injury incidence, characteristics and burden among sub-elite female futsal players. Individual exposure to match play and training, injury incidence and characteristics (player position, injury mechanism, type of injuries, severity of injuries, recurrent vs. new injuries, season variation of injury pattern) in a female futsal team were prospectively recorded for three consecutive seasons (2015–2018). Incidences were calculated per 1,000 h of exposure. A total of 30 injuries were reported during the three seasons within a total exposure of 4,446.1 h. The overall, match and training incidence of injuries were 6.7, 6.4 and 6.8 injuries/1,000 h of exposure, respectively. Most injuries had a non-contact mechanism (93%), with the lower extremity being the most frequently injured anatomical region (5.62 injuries/1,000 h of exposure). The most common type of injury was muscle/tendon (4.9 injuries/1,000 h of exposure) followed by joint (non-bone) and ligament (1.3 injuries/1,000 h of exposure). The injuries with the highest injury burden were those that occurred at the knee (31.9 days loss/1,000 h exposure), followed by quadriceps (15.3 day loss/1,000 h) and hamstring (14.4 day loss/1,000 h) strains. The first few weeks of competition after pre-season and soon after the Christmas break were the time points when most injuries occurred. These data indicate that sub-elite female futsal players are exposed to a substantial risk of sustaining an injury. To reduce overall injury burden, efforts should be directed toward the design, implementation and assessment of preventative measures that target the most common diagnoses, namely, muscle/tendon and ligament injuries.
Ruiz-Pérez et al. (2019) Injury incidence, characteristics and burden among female sub-elite futsal players: a prospective study with three-year follow-up. PeerJ 7:e7989 https://doi.org/10.7717/peerj.7989
Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt
As one of the largest plant-specific gene families, the NAC transcription factor gene family plays important roles in various plant physiological processes that are related to plant development, hormone signaling, and biotic and abiotic stresses. However, systematic investigation of the NAC gene family in sea-island cotton (Gossypium babardense L.) has not been reported, to date. The recent release of the complete genome sequence of sea-island cotton allowed us to perform systematic analyses of G. babardense NAC GbNAC) genes. In this study, we performed a genome-wide survey and identified 270 GbNAC genes in the sea-island cotton genome. Genome mapping analysis showed that GbNAC genes were unevenly distributed on 26 chromosomes. Through phylogenetic analyses of GbNACs along with their Arabidopsis counterparts, these proteins were divided into 10 groups (I–X), and each contained a different number of GbNACs with a similar gene structure and conserved motifs. One hundred and fifty-four duplicated gene pairs were identified, and almost all of them exhibited strong purifying selection during evolution. In addition, various cis-acting regulatory elements in GbNAC genes were found to be related to major hormones, defense and stress responses. Notably, transcriptome data analyses unveiled the expression profiles of 62 GbNAC genes under Verticillium wilt (VW) stress. Furthermore, the expression profiles of 15 GbNAC genes tested by quantitative real-time PCR (qPCR) demonstrated that they were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatments and that they could be involved in pathogen-related hormone regulation. Taken together, the genome-wide identification and expression profiling pave new avenues for systematic functional analysis of GbNAC candidates, which may be useful for improving cotton defense against VW.
Liu et al. (2019) Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt. PeerJ 7:e7995 https://doi.org/10.7717/peerj.7995
Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales
Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.
Näpflin et al. (2019) Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales. PeerJ 7:e8013 https://doi.org/10.7717/peerj.8013
A pilot study—genetic diversity and population structure of snow leopards of Gilgit-Baltistan, Pakistan, using molecular techniques
Background The Hindu Kush and Karakoram mountain ranges in Pakistan’s northern areas are a natural habitat of the snow leopard (Panthera uncia syn. Uncia uncia) but the ecological studies on this animal are scarce since it is human shy by nature and lives in difficult mountainous tracts. The pilot study is conducted to exploit the genetic diversity and population structure of the snow leopard in this selected natural habitat of the member of the wildcat family in Pakistan. Method About 50 putative scat samples of snow leopard from five localities of Gilgit-Baltistan (Pakistan) along with a control sample of zoo maintained male snow leopard were collected for comparison. Significant quality and quantity of genomic DNA was extracted from scat samples using combined Zhang–phenol–chloroform method and successful amplification of cytochrome c oxidase I gene (190 bp) using mini-barcode primers, seven simple sequence repeats (SSR) markers and Y-linked AMELY gene (200 bp) was done. Results Cytochrome c oxidase I gene sequencing suggested that 33/50 (66%) scat samples were of snow leopard. AMELY primer suggested that out of 33 amplified samples, 21 (63.63%) scats were from male and 12 (36.36%) from female leopards. Through successful amplification of DNA of 25 out of 33 (75.75%) scat samples using SSR markers, a total of 68 alleles on seven SSR loci were identified, showing low heterozygosity, while high gene flow between population. Discussion The low gene flow rate among the population results in low genetic diversity causing decreased diversification. This affects the adaptability to climatic changes, thus ultimately resulting in decreased population size of the species.
Aruge et al. (2019) A pilot study—genetic diversity and population structure of snow leopards of Gilgit-Baltistan, Pakistan, using molecular techniques. PeerJ 7:e7672 https://doi.org/10.7717/peerj.7672
Characterization of the acoustic community of vocal fishes in the Azores
Sounds produced by teleost fishes are an important component of marine soundscapes, making passive acoustic monitoring (PAM) an effective way to map the presence of vocal fishes with a minimal impact on ecosystems. Based on a literature review, we list the known soniferous fish species occurring in Azorean waters and compile their sounds. We also describe new fish sounds recorded in Azores seamounts. From the literature, we identified 20 vocal fish species present in Azores. We analysed long-term acoustic recordings carried out since 2008 in Condor and Princesa Alice seamounts and describe 20 new putative fish sound sequences. Although we propose candidates as the source of some vocalizations, this study puts into evidence the myriad of fish sounds lacking species identification. In addition to identifying new sound sequences, we provide the first marine fish sound library for Azores. Our acoustic library will allow to monitor soniferous fish species for conservation and management purposes.
Carriço et al. (2019) Characterization of the acoustic community of vocal fishes in the Azores. PeerJ 7:e7772 https://doi.org/10.7717/peerj.7772
MHC class I allele diversity in cynomolgus macaques of Vietnamese origin
Cynomolgus macaques (Macaca fascicularis, Mafa) have been used as important experimental animal models for carrying out biomedical researches. The results of biomedical experiments strongly depend on the immunogenetic background of animals, especially on the diversity of major histocompatibility complex (MHC) alleles. However, there is much less information available on the polymorphism of MHC class I genes in cynomolgus macaques, than is currently available for humans. In this study, we have identified 40 Mafa-A and 60 Mafa-B exons 2 and 3 sequences from 30 unrelated cynomolgus macaques of Vietnamese origin. Among these alleles, 28 are novel. As for the remaining 72 known alleles, 15 alleles are shared with other cynomolgus macaque populations and 32 are identical to alleles previously reported in other macaque species. A potential recombination event was observed between Mafa-A1*091:02 and Mafa-A1*057:01. In addition, the Mafa-A1 genes were found to be more diverse than human HLA-A and the functional residues for peptide binding sites (PBS) or TCR binding sites (TBS) in Mafa-A1 have greater variability than that for non-PBS or non-TBS regions. Overall, this study provides important information on the diversity of Mafa-A and Mafa-B alleles from Vietnamese origin, which may help researchers to choose the most appropriate animals for their studies.
Huang et al. (2019) MHC class I allele diversity in cynomolgus macaques of Vietnamese origin. PeerJ 7:e7941 https://doi.org/10.7717/peerj.7941
Allelic variant in SLC6A3 rs393795 affects cerebral regional homogeneity and gait dysfunction in patients with Parkinson’s disease
Aims We sought to explore the role of the SLC6A3 rs393795 allelic variant in cerebral spontaneous activity and clinical features in Parkinson’s disease (PD) via imaging genetic approach. Methods Our study recruited 50 PD and 45 healthy control (HC) participants to provide clinical, genetic, and resting state functional magnetic resonance imaging (rs-fMRI) data. All subjects were separated into 16 PD-AA, 34 PD-CA/CC, 14 HC-AA, and 31 HC-CA/CC four subgroups according to SLC6A3 rs393795 genotyping. Afterwards, main effects and interactions of groups (PD versus HC) and genotypes (AA versus CA/CC) on cerebral function reflected by regional homogeneity (ReHo) were explored using two-way analysis of covariance (ANCOVA) after controlling age and gender. Finally, Spearman’ s correlations were employed to investigate the relationships between significantly interactive brain regions and clinical manifestations in PD subgroups. Results Compared with HC subjects, PD patients exhibited increased ReHo signals in left middle temporal gyrus and decreased ReHo signals in left pallidum. Compared with CA/CC carriers, AA genotype individuals showed abnormal increased ReHo signals in right inferior frontal gyrus (IFG) and supplementary motor area (SMA). Moreover, significant interactions (affected by both disease factor and allelic variation) were detected in right inferior temporal gyrus (ITG). Furthermore, aberrant increased ReHo signals in right ITG were observed in PD-AA in comparison with PD-CA/CC. Notably, ReHo values in right ITG were negatively associated with Tinetti Mobility Test (TMT) gait subscale scores and positively related to Freezing of Gait Questionnaire (FOG-Q) scores in PD-AA subgroup. Conclusions Our findings suggested that SLC6A3 rs393795 allelic variation might have a trend to aggravate the severity of gait disorders in PD patients by altering right SMA and IFG function, and ultimately result in compensatory activation of right ITG. It could provide us with a new perspective for exploring deeply genetic mechanisms of gait disturbances in PD.
Wang et al. (2019) Allelic variant in SLC6A3 rs393795 affects cerebral regional homogeneity and gait dysfunction in patients with Parkinson’s disease. PeerJ 7:e7957 https://doi.org/10.7717/peerj.7957
Squirrel monkey responses to information from social demonstration and individual exploration using touchscreen and object choice tasks
We aimed to study whether a non-human primate species responded differently to information acquired socially compared with that acquired individually. To do so, we attempted to train squirrel monkeys to perform binary discriminations. These involved exposure to either social information (human or puppet demonstrator performs an initial ‘information trial’) or individual exploration (monkey performs information trial as well as subsequent test trials). In Experiment 1, we presented the task on a touchscreen tablet. Only one monkey appeared to learn the significance of the information trial, and across the group there was no improvement in performance over sessions. The proficient individual showed little evidence of successful transfer to three-way discrimination problems, suggesting limited representation of the task structure. In Experiment 2, we used a logically identical task, presented as a physical object choice (inverted cups concealing a food reward). No monkeys learned to use the information trial cues, and success again did not increase over sessions. We concluded that the monkeys’ poor performance in Experiment 1 was not attributable to the mode of presentation (touchscreen), but reflected real difficulties with mastering the task structure. For both experiments, we analysed the monkeys’ spontaneous responses to the different trial types (social-win, social-lose, individual-win, and individual-lose). We found that monkeys had a tendency to repeat selections made during the information trial, whether these were made by themselves or by a demonstrator. This tendency to repeat was observed even following lose trials (i.e. when incorrect). Apparent ‘success’ following win trials was probably largely an artefact of behavioural inertia (individual learning conditions) and stimulus enhancement (social learning conditions), rather than sensitivity to the reward cues associated with that stimulus. Although monkeys did respond somewhat differently (more repeats) following win trials, compared with lose trials, this was no more apparent in the object choice task than the touchscreen task, again suggesting that the less ecologically valid presentation medium did not actively disrupt potential for learning the discrimination rule. Both touchscreen and physical object choice tasks appear to be valid methods to study learning in squirrel monkeys, with neither method giving a clear performance advantage over the other. However, this population did not master the contingencies in these tasks.
Renner et al. (2019) Squirrel monkey responses to information from social demonstration and individual exploration using touchscreen and object choice tasks. PeerJ 7:e7960 https://doi.org/10.7717/peerj.7960
Correction of estimation bias of predictive equations of energy expenditure based on wrist/waist-mounted accelerometers
Background Using wearable inertial sensors to accurately estimate energy expenditure (EE) during an athletic training process is important. Due to the characteristics of inertial sensors, however, the positions in which they are worn can produce signals of different natures. To understand and solve this issue, this study used the heart rate reserve (HRR) as a compensation factor to modify the traditional empirical equation of the accelerometer EE sensor and examine the possibility of improving the estimation of energy expenditure for sensors worn in different positions. Methods Indirect calorimetry was used as the criterion measure (CM) to measure the EE of 90 healthy adults on a treadmill (five speeds: 4.8, 6.4, 8.0, 9.7, and 11.3 km/h). The measurement was simultaneously performed with the ActiGraph GT9X-Link (placed on the wrist and waist) with the Polar H10 Heart Rate Monitor. Results At the same exercise intensity, the EE measurements of the GT9X on the wrist and waist had significant differences from those of the CM (p < 0.05). By using multiple regression analysis—utilizing values from vector magnitudes (VM), body weight (BW) and HRR parameters—accuracy of EE estimation was greatly improved compared to traditional equation. Modified models explained a greater proportion of variance (R2) (wrist: 0.802; waist: 0.805) and demonstrated a good ICC (wrist: 0.863, waist: 0.889) compared to Freedson’s VM3 Combination equation (R2: wrist: 0.384, waist: 0.783; ICC: wrist: 0.073, waist: 0.868). Conclusions The EE estimation equation combining the VM of accelerometer measurements, BW and HRR greatly enhanced the accuracy of EE estimation based on data from accelerometers worn in different positions, particularly from those on the wrist.
Ho et al. (2019) Correction of estimation bias of predictive equations of energy expenditure based on wrist/waist-mounted accelerometers. PeerJ 7:e7973 https://doi.org/10.7717/peerj.7973
Geographic origin and timing of colonization of the Pacific Coast of North America by the rocky shore gastropod Littorina sitkana
The demographic history of a species can have a lasting impact on its contemporary population genetic structure. Northeastern Pacific (NEP) populations of the rocky shore gastropod Littorina sitkana have very little mitochondrial DNA (mtDNA) sequence diversity and show no significant population structure despite lacking dispersive planktonic larvae. A contrasting pattern of high mtDNA diversity in the northwestern Pacific (NWP) suggests that L. sitkana may have recently colonized the NEP from the NWP via stepping-stone colonization through the Aleutian-Commander Archipelago (ACA) following the end of the last glacial 20,000 years ago. Here, we use multi-locus sequence data to test that hypothesis using a combination of descriptive statistics and population divergence modeling aimed at resolving the timing and the geographic origin of NEP populations. Our results show that NEP populations share a common ancestor with a population of L. sitkana on the Kamchatka Peninsula ∼46,900 years ago and that NEP populations diverged from each other ∼21,400 years ago. A more recent population divergence between Kamchatka and NEP populations, than between Kamchatka and other populations in the NWP, suggests that the ACA was the most probable dispersal route. Taking into account the confidence intervals for the estimates, we conservatively estimate that L. sitkana arrived in the NEP between 107,400 and 4,100 years ago, a range of dates that is compatible with post-glacial colonization of the NEP. Unlike other congeners that are relatively abundant in the Pleistocene fossil record of the NEP, only one report of L. sitkana exists from the NEP fossil record. Although broadly consistent with the molecular data, the biogeographic significance of these fossils is difficult to evaluate, as the shells cannot be distinguished from the closely-related congener L. subrotundata.
Marko et al. (2019) Geographic origin and timing of colonization of the Pacific Coast of North America by the rocky shore gastropod Littorina sitkana. PeerJ 7:e7987 https://doi.org/10.7717/peerj.7987
The effect of social information from live demonstrators compared to video playback on blue tit foraging decisions
Video playback provides a promising method to study social interactions, and the number of video playback experiments has been growing in recent years. Using videos has advantages over live individuals as it increases the repeatability of demonstrations, and enables researchers to manipulate the features of the presented stimulus. How observers respond to video playback might, however, differ among species, and the efficacy of video playback should be validated by investigating if individuals’ responses to videos are comparable to their responses to live demonstrators. Here, we use a novel foraging task to compare blue tits’ (Cyanistes caeruleus) responses to social information from a live conspecific vs video playback. Birds first received social information about the location of food, and were then presented with a three-choice foraging task where they could search for food from locations marked with different symbols (cross, square, plain white). Two control groups saw only a foraging tray with similar symbols but no information about the location of food. We predicted that socially educated birds would prefer the same location where a demonstrator had foraged, but we found no evidence that birds copied a demonstrator’s choice, regardless of how social information was presented. Social information, however, had an influence on blue tits’ foraging choices, as socially educated birds seemed to form a stronger preference for a square symbol (against two other options, cross and plain white) than the control birds. Our results suggest that blue tits respond to video playback of a conspecific similarly as to a live bird, but how they use this social information in their foraging decisions, remains unclear.
Hämäläinen et al. (2019) The effect of social information from live demonstrators compared to video playback on blue tit foraging decisions. PeerJ 7:e7998 https://doi.org/10.7717/peerj.7998
The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species
The medicinal orchid genus Dendrobium belonging to the Orchidaceae family is a huge genus comprising about 800–1,500 species. To better illustrate the species status in the genus Dendrobium, a comparative analysis of 33 available chloroplast genomes retrieved from NCBI RefSeq database was compared with that of the first complete chloroplast genome of D. nobile from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150). Our results provide comparative chloroplast genomic information for taxonomical identification, alignment-free phylogenomic inference and other statistical features of Dendrobium plastomes, which can also provide valuable information on their mutational events and sequence divergence.
Konhar et al. (2019) The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species. PeerJ 7:e7756 https://doi.org/10.7717/peerj.7756
Off-line and on-line optical monitoring of microalgal growth
The growth of Chlamydomonas reinhardtii microalgae cultures was successfully monitored, using classic off-line optical techniques (optical density and fluorescence) and on-line analysis of digital images. In this study, we found that the chlorophyll fluorescence ratio F685/F740 has a linear correlation with the logarithmic concentration of microalgae. By using digital images, the biomass concentration correlated with the luminosity of the images through an exponential equation and the length of penetration of a super luminescent blue beam (λ = 440 nm) through an inversely proportional function. The outcomes of this study are useful to monitor both research and industrial microalgae cultures.
Lazcano-Hernández et al. (2019) Off-line and on-line optical monitoring of microalgal growth. PeerJ 7:e7956 https://doi.org/10.7717/peerj.7956
TransPrise: a novel machine learning approach for eukaryotic promoter prediction
As interest in genetic resequencing increases, so does the need for effective mathematical, computational, and statistical approaches. One of the difficult problems in genome annotation is determination of precise positions of transcription start sites. In this paper we present TransPrise—an efficient deep learning tool for prediction of positions of eukaryotic transcription start sites. Our pipeline consists of two parts: the binary classifier operates the first, and if a sequence is classified as TSS-containing the regression step follows, where the precise location of TSS is being identified. TransPrise offers significant improvement over existing promoter-prediction methods. To illustrate this, we compared predictions of TransPrise classification and regression models with the TSSPlant approach for the well annotated genome of Oryza sativa. Using a computer equipped with a graphics processing unit, the run time of TransPrise is 250 minutes on a genome of 374 Mb long. The Matthews correlation coefficient value for TransPrise is 0.79, more than two times larger than the 0.31 for TSSPlant classification models. This represents a high level of prediction accuracy. Additionally, the mean absolute error for the regression model is 29.19 nt, allowing for accurate prediction of TSS location. TransPrise was also tested in Homo sapiens, where mean absolute error of the regression model was 47.986 nt. We provide the full basis for the comparison and encourage users to freely access a set of our computational tools to facilitate and streamline their own analyses. The ready-to-use Docker image with all necessary packages, models, code as well as the source code of the TransPrise algorithm are available at (http://compubioverne.group/). The source code is ready to use and customizable to predict TSS in any eukaryotic organism.
Pachganov et al. (2019) TransPrise: a novel machine learning approach for eukaryotic promoter prediction. PeerJ 7:e7990 https://doi.org/10.7717/peerj.7990
A biomechanical analysis of the stand-up paddle board stroke: a comparative study
Background Stand-up paddle boarding (SUP) is a rapidly growing global aquatic sport, with increasing popularity among participants within recreation, competition and rehabilitation. To date, few scientific studies have focused on SUP. Further, there is no research examining the biomechanics of the SUP paddle stroke. The purpose of this study was to investigate whether variations in kinematics existed among experienced and inexperienced SUP participants using three-dimensional motion analysis. This data could be of significance to participants, researchers, coaches and health practitioners to improve performance and inform injury minimization strategies. Methods A cross-sectional observational design study was performed with seven experienced and 19 inexperienced paddlers whereby whole-body kinematic data were acquired using a six-camera Vicon motion capture system. Participants paddled on a SUP ergometer while three-dimensional range of motion (ROM) and peak joint angles were calculated for the shoulders, elbows, hips and trunk. Mann–Whitney U tests were conducted on the non-normally distributed data to evaluate differences between level of expertise. Results Significant differences in joint kinematics were found between experienced and inexperienced participants, with inexperienced participants using greater overall shoulder ROM (78.9° ± 24.9° vs 56.6° ± 17.3°, p = 0.010) and less hip ROM than the experienced participants (50.0° ± 18.5° vs 66.4° ± 11.8°, p = 0.035). Experienced participants demonstrated increased shoulder motion at the end of the paddle stoke compared to the inexperienced participants (74.9° ± 16.3° vs 35.2° ± 28.5°, p = 0.001 minimum shoulder flexion) and more extension at the elbow (6.0° ± 9.2° minimum elbow flexion vs 24.8° ± 13.5°, p = 0.000) than the inexperienced participants. Discussion The results of this study indicate several significant kinematic differences between the experienced and inexperienced SUP participants. These variations in technique were noted in the shoulder, elbow and hip and are evident in other aquatic paddling sports where injury rates are higher in these joints. These finding may be valuable for coaches, therapists and participants needing to maximize performance and minimize injury risk during participation in SUP.
Schram et al. (2019) A biomechanical analysis of the stand-up paddle board stroke: a comparative study. PeerJ 7:e8006 https://doi.org/10.7717/peerj.8006
Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma
Background Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Although multiple efforts have been made to understand the development of HCC, morbidity, and mortality rates remain high. In this study, we aimed to discover the mRNAs and long non-coding RNAs (lncRNAs) that contribute to the progression of HCC. We constructed a lncRNA-related competitive endogenous RNA (ceRNA) network to elucidate the molecular regulatory mechanism underlying HCC. Methods A microarray dataset (GSE54238) containing information about both mRNAs and lncRNAs was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and lncRNAs (DElncRNAs) in tumor tissues and non-cancerous tissues were identified using the limma package of the R software. The miRNAs that are targeted by DElncRNAs were predicted using miRcode, while the target mRNAs of miRNAs were retrieved from miRDB, miRTarBas, and TargetScan. Functional annotation and pathway enrichment of DEGs were performed using the EnrichNet website. We constructed a protein–protein interaction (PPI) network of DEGs using STRING, and identified the hub genes using Cytoscape. Survival analysis of the hub genes and DElncRNAs was performed using the gene expression profiling interactive analysis database. The expression of molecules with prognostic values was validated on the UALCAN database. The hepatic expression of hub genes was examined using the Human Protein Atlas. The hub genes and DElncRNAs with prognostic values as well as the predictive miRNAs were selected to construct the ceRNA networks. Results We found that 10 hub genes (KPNA2, MCM7, CKS2, KIF23, HMGB2, ZWINT, E2F1, MCM4, H2AFX, and EZH2) and four lncRNAs (FAM182B, SNHG6, SNHG1, and SNHG3) with prognostic values were overexpressed in the hepatic tumor samples. We also constructed a network containing 10 lncRNA–miRNA–mRNA pathways, which might be responsible for regulating the biological mechanisms underlying HCC. Conclusion We found that the 10 significantly overexpressed hub genes and four lncRNAs were negatively correlated with the prognosis of HCC. Further, we suggest that lncRNA SNHG1 and the SNHG3-related ceRNAs can be potential research targets for exploring the molecular mechanisms of HCC.
Liu et al. (2019) Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma. PeerJ 7:e8021 https://doi.org/10.7717/peerj.8021