A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
The emergence of diseases such as white spot disease has become a threat to Penaeus monodon cultivation. Although there have been a few studies utilizing RNA-Seq, the cellular processes of host-virus interaction in this species remain mostly anonymous. In the present study, P. monodon was challenged with WSSV by intramuscular injection and survived for 12 days. The effect of the host gene expression by WSSV infection in the haemocytes, hepatopancreas and muscle of P. monodon was studied using Illumina HiSeq 2000. The RNA-Seq of cDNA libraries was developed from surviving WSSV-challenged shrimp as well as from normal healthy shrimp as control. A comparison of the transcriptome data of the two groups showed 2,644 host genes to be significantly up-regulated and 2,194 genes significantly down-regulated as a result of the infection with WSSV. Among the differentially expressed genes, our study discovered HMGB, TNFSF and c-Jun in P. monodon as new potential candidate genes for further investigation for the development of potential disease resistance markers. Our study also provided significant data on the differential expression of genes in the survived WSSV infected P. monodon that will help to improve understanding of host-virus interactions in this species.
Mohd Ghani et al. (2019) A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon. PeerJ 7:e8107 https://doi.org/10.7717/peerj.8107
Comparative RNA-sequencing profiled the differential gene expression of liver in response to acetyl-CoA carboxylase inhibitor GS-0976 in a mouse model of NASH
Background Non-alcoholic steatohepatitis (NASH) is a progressive liver disease characterized by hepatic steatosis, lobular inflammation and fibrosis. Acetyl-CoA carboxylase (ACC) isoform 1 and 2 involved in de novo lipogenesis (DNL) and fatty acid oxidation have been identified as a therapeutic target in NASH. GS-0976, the inhibitor of ACC1 and ACC2, has achieved favorable therapeutic effects in clinical trials with NASH. The purpose of this study was to explore the transcriptional alterations regulated by GS-0976 in NASH. Methods C57BL/6 mice were fed on a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) or normal diet for 12 weeks. Mice were treated with or without GS-0976 (3 mg/kg per day) in the last 8 weeks. Oil Red O, Haematoxylin-eosin (H & E), and Sirius Red were used to evaluate hepatic steatosis, inflammation and fibrosis. The comparative RNA-sequencing was conducted to analyse the hepatic gene expression profiles in mice. Reverse transcription–polymerase chain reaction analysis was performed to validate the differential expression of representative genes. Results GS-0976 attenuated the steatosis, inflammation, and fibrosis of NASH in CDAHFD mouse model. High-throughput sequencing and differential gene expression analysis showed that there were 516 up-regulated genes and 525 down-regulated genes after GS-0976 treatment. Genes involved in the metabolic process, extracellular matrix formation, immune response, and angiogenesis were significantly enriched. The “Metabolic pathways” and “ECM-receptor interaction” pathways were the most significantly enriched KEGG pathways in the up-regulated and down-regulated differentially expressed genes (DEGs), respectively. Conclusions Transcriptome analysis showed that GS-0976 could regulate the expression of genes related to metabolism, inflammation and fibrosis in NASH. The global transcriptomic changes in gene expression promote the further understanding for the inhibition mechanisms of GS-0976 in NASH.
Lu et al. (2019) Comparative RNA-sequencing profiled the differential gene expression of liver in response to acetyl-CoA carboxylase inhibitor GS-0976 in a mouse model of NASH. PeerJ 7:e8115 https://doi.org/10.7717/peerj.8115
Genetic links between endometriosis and cancers in women
Endometriosis is a chronic disease occurring during the reproductive stage of women. Although there is only limited association between endometriosis and gynecological cancers with regard to clinical features, the molecular basis of the relationship between these diseases is unexplored. We conducted a systematic study by integrating literature-based evidence, gene expression and large-scale cancer genomics data in order to reveal any genetic relationships between endometriosis and cancers in women. We curated 984 endometriosis-related genes from 3270 PubMed articles and then conducted a meta-analysis of the two public gene expression profiles related to endometriosis which identified Differential Expression of Genes (DEGs). Following an overlapping analysis, we identified 39 key endometriosis-related genes common in both literature and DEG analysis. Finally, the functional analysis confirmed that all the 39 genes were associated with the vital processes of tumour formation and cancer progression and that two genes (PGR and ESR1) were common to four cancers of women. From network analysis, we identified a novel linker gene, C3AR1, which had not been implicated previously in endometriosis. The shared genetic mechanisms of endometriosis and cancers in women identified in this study provided possible new avenues of multiple disease management and treatments through early diagnosis.
Bhyan et al. (2019) Genetic links between endometriosis and cancers in women. PeerJ 7:e8135 https://doi.org/10.7717/peerj.8135
Evaluation of human-papillomavirus screening for cervical cancer in China’s rural population
Background and Objective Human papillomavirus (HPV) testing has become a preferred cervical cancer screening. However, most HPV infections are harmless and additional tests are required to screen HPV positive women. The objective of this study is to determine the optimal triage strategies for HPV positive women in China’s rural population. Methods A population-based screening was performed at seven rural counties of Jiangxi province, between October 2014 to January 2016. A total of 18,000 women aged 35–64 years were enrolled in this study. The primary screening was performed using CareHPV, HC-2, Cobas ®4,800 or HybriMax. Positive women were further screened with five triage tests: (1) Liquid-based cytology test (LBC); (2) conventional Pap cytology test (Pap smear); (3) HPV16, 18 detection; (4) viral load; and (5) visual inspection with acetic acid and Lugol’s iodine (VIA/VILI). Women who were tested positive were referred for colposcopy. The five triage tests were compared with respect to sensitivity, specificity, referral rate, cost and diagnostic time. Results Complete data were available for 17,782 women. The HPV prevalence was 13.6%. Referral rates for colposcopy were 4.5%, 2.8%, 2.8%, 6.6%, and 3.7% with LBC, Pap smear, HPV16/18, viral load, and VIA/VILI, respectively. The sensitivity of the above triage tests was 65.8%, 51.9%, 86.8%, 73.3%, and 41.7%, respectively. The specificity was 69.8%, 81.0%, 85.8%, 52.2% and 65.3%, respectively. The average time to diagnosis was significantly lower with HPV16/18, viral load and VIA/VILI than LBC and Pap smear. In addition, screening cost that leads to identify one HSIL+ woman was the lowest with viral load. Conclusion Our data indicate that HPV16/18 and viral load are the optimal triage strategies for HPV screening in China’s rural population.
Li et al. (2019) Evaluation of human-papillomavirus screening for cervical cancer in China’s rural population. PeerJ 7:e8152 https://doi.org/10.7717/peerj.8152
Systematic evaluation of the gut microbiome of swamp eel (Monopterus albus) by 16S rRNA gene sequencing
Background The swamp eel (Monopterus albus) is a commercially important farmed species in China. The dysbiosis and homeostasis of gut microbiota has been suggested to be associated with the swamp eel’s disease pathogenesis and food digestion. Although the contributions of gut microbiome in fish growth and health has been increasingly recognized, little is known about the microbial community in the intestine of the swamp eel (Monopterus albus). Methods The intestinal microbiomes of the five distinct gut sections (midgut content and mucosa, hindgut content and mucosa, and stools) of swamp eel were compared using Illumina MiSeq sequencing of the bacterial 16S rRNA gene sequence and statistical analysis. Results The results showed that the number of observed OTUs in the intestine decreased proximally to distally. Principal coordinate analysis revealed significant separations among samples from different gut sections. There were 54 core OTUs shared by all gut sections and 36 of these core OTUs varied significantly in their abundances. Additionally, we discovered 66 section-specific enriched KEGG pathways. These section-specific enriched microbial taxa (e.g., Bacillus, Lactobacillus) and potential function capacities (e.g., amino acid metabolism, carbohydrate metabolism) might play vital roles in nutrient metabolism, immune modulation and host-microbe interactions of the swamp eel. Conclusions Our results showed that microbial diversity, composition and function capacity varied substantially across different gut sections. The gut section-specific enriched core microbial taxa and function capacities may perform important roles in swamp eel’s nutrient metabolism, immune modulation, and host-microbe interactions. This study should provide insights into the gut microbiome of the swamp eel.
Chen et al. (2019) Systematic evaluation of the gut microbiome of swamp eel (Monopterus albus) by 16S rRNA gene sequencing. PeerJ 7:e8176 https://doi.org/10.7717/peerj.8176
Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
Viruses drive microbial diversity, function and evolution and influence important biogeochemical cycles in aquatic ecosystems. Despite their relevance, we currently lack an understanding of their potential impacts on stream biofilm structure and function. This is surprising given the critical role of biofilms for stream ecosystem processes. Currently, the study of viruses in stream biofilms is hindered by the lack of an optimized protocol for their extraction, concentration and purification. Here, we evaluate a range of methods to separate viral particles from stream biofilms, and to concentrate and purify them prior to DNA extraction and metagenome sequencing. Based on epifluorescence microscopy counts of viral-like particles (VLP) and DNA yields, we optimize a protocol including treatment with tetrasodium pyrophosphate and ultra-sonication to disintegrate biofilms, tangential-flow filtration to extract and concentrate VLP, followed by ultracentrifugation in a sucrose density gradient to isolate VLP from the biofilm slurry. Viromes derived from biofilms sampled from three different streams were dominated by Siphoviridae, Myoviridae and Podoviridae and provide first insights into the viral diversity of stream biofilms. Our protocol optimization provides an important step towards a better understanding of the ecological role of viruses in stream biofilms.
Bekliz et al. (2019) Benchmarking protocols for the metagenomic analysis of stream biofilm viromes. PeerJ 7:e8187 https://doi.org/10.7717/peerj.8187
Genome size, chromosome number determination, and analysis of the repetitive elements in Cissus quadrangularis
Cissus quadrangularis (Vitaceae) is a perennial climber endemic to Africa and is characterized by succulent angular stems. The plant grows in arid and semi-arid regions of Africa especially in the African savanna. The stem of C. quadrangularis has a wide range of applications in both human and animal medicine, but there is limited cytogenetic information available for this species. In this study, the chromosome number, genome size, and genome composition for C. quadrangularis were determined. Flow cytometry results indicated that the genome size of C. quadrangularis is approximately 2C = 1.410 pg. Fluorescence microscopy combined with DAPI stain showed the chromosome numbers to be 2n = 48. It is likely that C. quadrangularis has a tetraploid genome after considering the basic chromosome numbers in Cissus genus (n = 10, 11, or 12). A combination of low-throughput genome sequencing and bioinformatics analysis allowed identification and quantification of repetitive elements that make up about 52% of the C. quadrangularis genome, which was dominated by LTR-retrotransposons. Two LTR superfamilies were identified as Copia and Gypsy, with 24% and 15% of the annotated clusters, respectively. The comparison of repeat elements for C. quadrangularis, Vitis vinifera, and four other selected members in the Cissus genus revealed a high diversity in the repetitive element components, which could suggest recent amplification events in the Cissus genus. Our data provides a platform for further studies on the phylogeny and karyotype evolution in this genus and in the family Vitaceae.
Gichuki et al. (2019) Genome size, chromosome number determination, and analysis of the repetitive elements in Cissus quadrangularis. PeerJ 7:e8201 https://doi.org/10.7717/peerj.8201
Reduced GRAMD1C expression correlates to poor prognosis and immune infiltrates in kidney renal clear cell carcinoma
There has been an increase in the mortality rate and morbidity of kidney cancer (KC) with kidney renal clear cell carcinoma (KIRC) being the most common subtype of KC. GRAMD1C (GRAM Domain Containing 1C) has not been reported to relate to prognosis and immunotherapy in any cancers. Using bioinformatics methods, we judged the prognostic value of GRAMD1C expression in KIRC and investigated the underlying mechanisms of GRAMD1C affecting the overall survival of KIRC based on data downloaded from The Cancer Genome Atlas (TCGA). The outcome revealed that reduced GRAMD1C expression could be a promising predicting factor of poor prognosis in kidney renal clear cell carcinoma. Meanwhile, GRAMDIC expression was significantly correlated to several tumor-infiltrating immune cells (TIICs), particularly the regulatory T cells (Tregs). Furthermore, GRAMD1C was most significantly associated with the mTOR signaling pathway, RNA degradation, WNT signaling pathway, toll pathway and AKT pathway in KIRC. Thus, GRAMD1C has the potential to become a novel predictor to evaluate prognosis and immune infiltration for KIRC patients.
Hao et al. (2019) Reduced GRAMD1C expression correlates to poor prognosis and immune infiltrates in kidney renal clear cell carcinoma. PeerJ 7:e8205 https://doi.org/10.7717/peerj.8205
Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium ‘Summit’
Background Sweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear. Methods In this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium ‘Summit’ from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively. Results The complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium ‘Summit’ was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and ‘Summit’ cherry. A total of 73 simple sequence repeats (SSRs) were identified in ‘Summit’ cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus species.
Zhao et al. (2019) Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium ‘Summit’. PeerJ 7:e8210 https://doi.org/10.7717/peerj.8210
Modelling the effect of curves on distance running performance
Background Although straight ahead running appears to be faster, distance running races are predominately contested on tracks or roads that involve curves. How much faster could world records be run on straight courses? Methods Here,we propose a model to explain the slower times observed for races involving curves compared to straight running. For a given running velocity, on a curve, the average axial leg force ( ${\overline{F}}_{a}$ F ¯ a ) of a runner is increased due to the need to exert centripetal force. The increased ${\overline{F}}_{a}$ F ¯ a presumably requires a greater rate of metabolic energy expenditure than straight running at the same velocity. We assumed that distance runners maintain a constant metabolic rate and thus slow down on curves accordingly. We combined published equations to estimate the change in the rate of gross metabolic energy expenditure as a function of ${\overline{F}}_{a}$ F ¯ a , where ${\overline{F}}_{a}$ F ¯ a depends on curve radius and velocity, with an equation for the gross rate of oxygen uptake as a function of velocity. We compared performances between straight courses and courses with different curve radii and geometries. Results The differences between our model predictions and the actual indoor world records, are between 0.45% in 3,000 m and 1.78% in the 1,500 m for males, and 0.59% in the 5,000 m and 1.76% in the 3,000 m for females. We estimate that a 2:01:39 marathon on a 400 m track, corresponds to 2:01:32 on a straight path and to 2:02:00 on a 200 m track. Conclusion Our model predicts that compared to straight racecourses, the increased time due to curves, is notable for smaller curve radii and for faster velocities. But, for larger radii and slower speeds, the time increase is negligible and the general perception of the magnitude of the effects of curves on road racing performance is not supported by our calculations.
Taboga et al. (2019) Modelling the effect of curves on distance running performance. PeerJ 7:e8222 https://doi.org/10.7717/peerj.8222
New titanosauriform (Dinosauria: Sauropoda) specimens from the Upper Cretaceous Daijiaping Formation of southern China
Titanosauriform sauropod dinosaurs were once considered rare in the Upper Cretaceous of Asia, but a number of titanosauriforms from this stratigraphic interval have been discovered in China in recent years. In fact, all adequately known Cretaceous Asian sauropods are titanosauriforms, but only a few have been well studied, lending significance to any new anatomical information that can be extracted from Asia’s Cretaceous sauropod record. Here we give a detailed description of some titanosauriform bones recovered recently from the Upper Cretaceous Daijiaping Formation of Tianyuan County, Zhuzhou City, Hunan Province, southern China. The occurrence of this material in Hunan increases the known geographic range of titanosauriforms in eastern Asia. Although all of the specimens discussed in this paper can be assigned to Titanosauriformes at least tentatively, some bones display a limited number of features that are more typical of basal sauropods and/or derived diplodocoids, suggesting complex patterns of character evolution within Neosauropoda.
Han et al. (2019) New titanosauriform (Dinosauria: Sauropoda) specimens from the Upper Cretaceous Daijiaping Formation of southern China. PeerJ 7:e8237 https://doi.org/10.7717/peerj.8237
Toward insights on determining factors for high activity in antimicrobial peptides via machine learning
The continued and general rise of antibiotic resistance in pathogenic microbes is a well-recognized global threat. Host defense peptides (HDPs), a component of the innate immune system have demonstrated promising potential to become a next generation antibiotic effective against a plethora of pathogens. While the effectiveness of antimicrobial HDPs has been extensively demonstrated in experimental studies, theoretical insights on the mechanism by which these peptides function is comparably limited. In particular, experimental studies of AMP mechanisms are limited in the number of different peptides investigated and the type of peptide parameters considered. This study makes use of the random forest algorithm for classifying the antimicrobial activity as well for identifying molecular descriptors underpinning the antimicrobial activity of investigated peptides. Subsequent manual interpretation of the identified important descriptors revealed that polarity-solubility are necessary for the membrane lytic antimicrobial activity of HDPs.
Li et al. (2019) Toward insights on determining factors for high activity in antimicrobial peptides via machine learning. PeerJ 7:e8265 https://doi.org/10.7717/peerj.8265
A new species of Atrimitra Dall, 1918 (Gastropoda: Mitridae) from seamounts of the recently created Nazca-Desventuradas Marine Park, Chile
We describe Atrimitra isolata sp. n. (Gastropoda: Mitridae), collected on the summit of seamounts (~200 m water depth) in the vicinity of Desventuradas Islands, Chile insular territory. Additionally, we provide some insight into the habitat of this new species based on underwater imagery taken with a remotely operated vehicle. A. isolata sp. n. is characterized by its small size (up to 26 mm), elongate-ovate shape, solid shell and smooth appearance. It has a base brown color, with some specimens being tan or yellow. It is morphologically related to counterparts from shallow depths on the west coast of North, Central and South America (i.e., Atrimitra idae, Atrimitra orientalis and Atrimitra semigranosa), but has no affinities with species of the family reported from around Easter Island, on the far western side of the Salas y Gómez ridge (e.g., Strigatella flavocingulata, Imbricariopsis punctata and Neocancilla takiisaoi), or with other Indo-Pacific species. The present contribution adds to the knowledge of the poorly studied fauna of the seamounts in the southern portion of the Nazca ridge and easternmost section of the Sala y Gómez ridge, an area characterized by the high degree of endemism of its benthic fauna, and now protected within the large and newly created Nazca-Desventuradas Marine Park.
Sellanes et al. (2019) A new species of Atrimitra Dall, 1918 (Gastropoda: Mitridae) from seamounts of the recently created Nazca-Desventuradas Marine Park, Chile. PeerJ 7:e8279 https://doi.org/10.7717/peerj.8279
Production and characteristics of fish protein hydrolysate from parrotfish (Chlorurus sordidus) head
Background Fish byproducts are commonly recognized as low-value resources. In order to increase the value, fish byproducts need to be converted into new products with high functionality such as fish protein hydrolysate (FPH). In this study, FPH manufactured from parrotfish (Chlorurus sordidus) heads using different pH, time and sample ratio was investigated. Methods Hydrolysis reactions were conducted under different pHs (5, 7, and 9) and over different durations (12 and 24 h). Control treatment (without pH adjustment (pH 6.4)) and 0 h hydrolsisis duration were applied. Hydrolysates were characterized with respect to proximate composition, amino acid profile, and molecular weight distribution. The antioxidant activity of the hydrolysate was also observed. Results The pH and duration of hydrolysis significantly affected (p < 0.05) the characteristics of FPH. The highest yield of hydrolysate (49.04 ± 0.90%), with a degree of hydrolysis of 30.65 ± 1.82%, was obtained at pH 9 after 24 h incubation. In addition, the FPH had high antioxidant activity (58.20 ± 0.55%), with a high level of essential amino acids. Results suggested that FPH produced using endogenous enzymes represents a promising additive for food and industrial applications.
Prihanto et al. (2019) Production and characteristics of fish protein hydrolysate from parrotfish (Chlorurus sordidus) head. PeerJ 7:e8297 https://doi.org/10.7717/peerj.8297
Expression and prognostic analyses of ITGA11, ITGB4 and ITGB8 in human non-small cell lung cancer
Background Integrins play a crucial role in the regulation process of cell proliferation, migration, differentiation, tumor invasion and metastasis. ITGA11, ITGB4 and ITGB8 are three encoding genes of integrins family. Accumulative evidences have proved that abnormal expression of ITGA11, ITGB4 and ITGB8 are a common phenomenon in different malignances. However, their expression patterns and prognostic roles for patients with non-small cell lung cancer (NSCLC) have not been completely illustrated. Methods We investigated the expression patterns and prognostic values of ITGA11, ITGB4 and ITGB8 in patients with NSCLC through using a series of databases and various datasets, including ONCOMINE, GEPIA, HPA, TCGA and GEO datasets. Results We found that the expression levels of ITGA11 and ITGB4 were significantly upregulated in both LUAD and LUSC, while ITGB8 was obviously upregulated in LUSC. Additionally, higher expression level of ITGB4 revealed a worse OS in LUAD. Conclusion Our findings suggested that ITGA11 and ITGB4 might have the potential ability to act as diagnostic biomarkers for both LUAD and LUSC, while ITGB8 might serve as diagnostic biomarker for LUSC. Furthermore, ITGB4 could serve as a potential prognostic biomarker for LUAD.
Wu et al. (2019) Expression and prognostic analyses of ITGA11, ITGB4 and ITGB8 in human non-small cell lung cancer. PeerJ 7:e8299 https://doi.org/10.7717/peerj.8299
Heterologous expression, purification and biochemical characterization of a glutamate racemase (MurI) from Streptococcus mutans UA159
Background Glutamate racemase (MurI) is a cofactor-independent enzyme that is essential to the bacterial peptidoglycan biosynthesis pathway and has therefore been considered an attractive target for the development of antimicrobial drugs. While in our previous study the essentiality of the murI gene was shown in Streptococcus mutans, the primary aetiologic agent of human dental caries, studies on S. mutans MurI have not yet provided definitive results. This study aimed to produce and characterize the biochemical properties of the MurI from the S. mutans UA159 genome. Methods Structure characterization prediction and multiple sequence alignment were performed by bioinformatic analysis. Recombinant His6-tagged S. mutans MurI was overexpressed in the expression vector pColdII and further purified using a Ni2+ affinity chromatography method. Protein solubility, purity and aggregation state were analyzed by SDS–PAGE, Western blotting, native PAGE and SEC-HPLC. Kinetic parameters were assessed by a circular dichroism (CD) assay. Kinetic constants were calculated based on the curve fit for the Michaelis–Menten equation. The effects of temperature and pH on enzymatic activity were determined by a series of coupled enzyme reaction mixtures. Results The glutamate racemase gene from S. mutans UA159 was amplified by PCR, cloned and expressed in Escherichia coli BL21 (DE3). The 264-amino-acid protein, as a mixture of dimeric and monomeric enzymes, was purified to electrophoretic homogeneity. In the CD assay, S. mutans MurI displayed unique kinetic parameters (Km, d-Glu→l-Glu = 0.3631 ± 0.3205 mM, Vmax, d-Glu→l-Glu = 0.1963 ± 0.0361 mM min−1, kcat, d-Glu→l-Glu = 0.0306 ± 0.0065 s−1, kcat/Km, d-Glu→l-Glu = 0.0844 ± 0.0128 s−1 mM−1, with d-glutamate as substrate; Km, l-Glu→d-Glu = 0.8077 ± 0.5081 mM, Vmax, l-Glu→d-Glu = 0.2421 ± 0.0418 mM min−1, kcat, l-Glu→d-Glu = 0.0378 ± 0.0056 s−1, kcat/Km, l-Glu→d-Glu = 0.0468 ± 0.0176 s−1 mM−1, with l-glutamate as substrate). S. mutans MurI possessed an assay temperature optimum of 37.5 °C and its optimum pH was 8.0. Conclusion The findings of this study provide insight into the structure and biochemical traits of the glutamate racemase in S. mutans and supply a conceivable guideline for employing glutamate racemase in anti-caries drug design.
Wang et al. (2019) Heterologous expression, purification and biochemical characterization of a glutamate racemase (MurI) from Streptococcus mutans UA159. PeerJ 7:e8300 https://doi.org/10.7717/peerj.8300
Effect of induced hyperopia on fall risk and Fourier transformation of postural sway
Background and Purpose Fall accidents are a social challenge in Korea and elsewhere. Most previous studies have focused on the effects of reduced visual acuity due to myopia on falls and body balance. The objective of this study was to investigate whether uncorrected hyperopia was a major risk factor for falls and to establish whether the risk of falls was absolutely correlated with visual acuity. Methods Fifty-one young subjects with a mean age of 22.75 ± 2.13 years were enrolled in this study. To induce hyperopic and myopic refractive errors, spherical lenses of ±1.0–6.0 D (1.0 D stepwise) were used. Under each induced condition, fall risk index and sway power were assessed via Fourier transformation of postural sway using a TETRAX system. Results The fall risk index for eyes-closed was significantly greater than that of eyes-open with full correction (t = −5.876, p < 0.05). The fall risk index increased significantly from hyperopia induced with −4.0 D lenses (with visual acuity of 0.69 ± 0.32) compared to eyes-open with full correction (F = 3.213, p < 0.05). However, there was no significant change in the induced myopia conditions, despite a drastic decline in decimal visual acuity. Sway power increased significantly in the low-to-medium frequency band derived from the peripheral vestibular system when hyperopia was induced. A significant difference was detected in hyperopia induced with −6.0 D lenses compared to eyes-open with full correction (F = 4.981, p = 0.017). Conclusion An uncorrected hyperopia rather than myopia may increase the risk of falls, although eyes may show normal visual acuity due to the inherent accommodation mechanism. Our findings suggest that the corrected state of refractive errors is more important than the level of visual acuity as the criteria for appropriate visual input, which contributes to stable posture. Therefore, clinicians should consider the refractive condition, especially the characteristics of hyperopia, when analyzing body balance, and appropriate correction of uncorrected hyperopia to prevent falls.
Moon et al. (2019) Effect of induced hyperopia on fall risk and Fourier transformation of postural sway. PeerJ 7:e8329 https://doi.org/10.7717/peerj.8329
Crowdsourcing visual perception experiments: a case of contrast threshold
Crowdsourcing has commonly been used for psychological research but not for studies on sensory perception. A reason is that in online experiments, one cannot ensure that the rigorous settings required for the experimental environment are replicated. The present study examined the suitability of online experiments on basic visual perception, particularly the contrast threshold. We conducted similar visual experiments in the laboratory and online, employing three experimental conditions. The first was a laboratory experiment, where a small sample of participants (n = 24; laboratory condition) completed a task with 10 iterations. The other two conditions were online experiments: participants were either presented with a task without repetition of trials (n = 285; online non-repetition condition) or one with 10 iterations (n = 166; online repetition condition). The results showed significant equivalence in the contrast thresholds between the laboratory and online repetition conditions, although a substantial amount of data needed to be excluded from the analyses in the latter condition. The contrast threshold was significantly higher in the online non-repetition condition compared with the laboratory and online repetition conditions. To make crowdsourcing more suitable for investigating the contrast threshold, ways to reduce data wastage need to be formulated.
Sasaki et al. (2019) Crowdsourcing visual perception experiments: a case of contrast threshold. PeerJ 7:e8339 https://doi.org/10.7717/peerj.8339
Hole in One: an element reduction approach to modeling bone porosity in finite element analysis
Finite element analysis has been an increasingly widely applied biomechanical modeling method in many different science and engineering fields over the last decade. In the biological sciences, there are many examples of FEA in areas such as paleontology and functional morphology. Despite this common use, the modeling of trabecular bone remains a key issue because their highly complex and porous geometries are difficult to replicate in the solid mesh format required for many simulations. A common practice is to assign uniform model material properties to whole or portions of models that represent trabecular bone. In this study we aimed to demonstrate that a physical, element reduction approach constitutes a valid protocol for addressing this problem in addition to the wholesale mathematical approach. We tested a customized script for element reduction modeling on five exemplar trabecular geometry models of carnivoran temporomandibular joints, and compared stress and strain energy results of both physical and mathematical trabecular modeling to models incorporating actual trabecular geometry. Simulation results indicate that that the physical, element reduction approach generally outperformed the mathematical approach: physical changes in the internal structure of experimental cylindrical models had a major influence on the recorded stress values throughout the model, and more closely approximates values obtained in models containing actual trabecular geometry than solid models with modified trabecular material properties. In models with both physical and mathematical adjustments for bone porosity, the physical changes exhibit more weight than material properties changes in approximating values of control models. Therefore, we conclude that maintaining or mimicking the internal porosity of a trabecular structure is a more effective method of approximating trabecular bone behavior in finite element models than modifying material properties.
Santaella et al. (2019) Hole in One: an element reduction approach to modeling bone porosity in finite element analysis. PeerJ 7:e8112 https://doi.org/10.7717/peerj.8112
Functioning of autobiographical memory specificity and self-defining memories in people with cancer diagnosis
Objectives Cognitive and emotional disturbances have been associated with the diagnosis and treatment of cancer. Autobiographical memory is one of the specific cognitive processes affected during this disease. The current study had two main aims: (1) to compare the functioning of autobiographical memory specificity and its related variables (executive functioning, depression and perceived stress) in a group of persons with cancer and a control group; and (2) to analyze whether the experience of cancer evolved into a self-defining memory in the sample of participants diagnosed with this disease. Method The study sample comprised 62 participants, 31 in the group with a cancer diagnosis and 31 in the control group. Autobiographical memory specificity, executive functions, depression, stress and self-defining memory were evaluated in the current study. Results Depressive symptomatology and reduced executive functioning, but not perceived stress levels, are related and are predictors of autobiographical memory specificity. In addition, the identified characteristics of the self-defining memories were associated with the cancer experience as a threat to physical integrity and an awareness of the meaning of life. Conclusion This emerging research line is especially important in view of its possible impacts on patients’ well-being, due to the importance of psychological processes in cancer disease.
Nieto et al. (2019) Functioning of autobiographical memory specificity and self-defining memories in people with cancer diagnosis. PeerJ 7:e8126 https://doi.org/10.7717/peerj.8126
Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea
Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: Acropora aspera, Acropora formosa, Cyphastrea sp., and Isopora sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where Proteobacteria and Firmicutes were pre-dominated followed by Bacteroidetes together with Actinobacteria, Fusobacteria, and Lentisphaerae as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. Fusibacter was found as the major bacterial genus across all corals. The lower number of Fusibacter was found in A. aspera infected with white band disease and Isopora sp. with white plaque disease, but marked increases of Vibrio and Acrobacter, respectively, were observed. This was in contrast to A. formosa infected by a black band and Cyphastrea sp. infected by yellow blotch diseases which showed an increasing abundance of Fusibacter but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals.
Mhuantong et al. (2019) Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea. PeerJ 7:e8137 https://doi.org/10.7717/peerj.8137
Simulating more realistic predation threat using attack playbacks
Use of virtual proxies of live animals are rapidly gaining ground in studies of animal behaviour. Such proxies help to reduce the number of live experimental animals needed to stimulate the behaviour of experimental individuals and to increase standardisation. However, using too simplistic proxies may fail to induce a desired effect and/or lead to quick habituation. For instance, in a predation context, prey often employ multimodal cues to detect predators or use specific aspects of predator behaviour to assess threat. In a live interaction, predator and prey often show behaviours directed towards each other, which are absent in virtual proxies. Here we compared the effectiveness of chemical and visual predator cues in the cooperatively breeding cichlid Neolamprologus pulcher, a species in which predation pressure has been the evolutionary driver of its sociality. We created playbacks of predators simulating an attack and tested their effectiveness in comparison to a playback showing regular activity and to a live predator. We further compared the effectiveness of predator odour and conspecific skin extracts on behaviours directed towards a predator playback. Regular playbacks of calmly swimming predators were less effective than live predators in stimulating a focal individual’s aggression and attention. However, playbacks mimicking an attacking predator induced responses much like a live predator. Chemical cues did not affect predator directed behaviour.
Watve et al. (2019) Simulating more realistic predation threat using attack playbacks. PeerJ 7:e8149 https://doi.org/10.7717/peerj.8149
Heatstroke-induced hepatocyte exosomes promote liver injury by activating the NOD-like receptor signaling pathway in mice
Background Liver injury is a common and important clinical issue of severe heat stress (HS), which has toxic effects and promotes subsequent multiple organ failure. The pathogenesis of HS-induced liver injury has not been fully elucidated. Passively injured hepatocytes also drive liver injury. Exosomes, extracellular vesicles secreted by hepatocytes as “danger signals,” mediate the intercellular transportation of diverse functional protein cargoes and modulate the biological processes of target cells. However, whether hepatocyte exosomes are involved in HS-induced liver injury has not been reported. The purpose of the current study was to clarify the release of hepatocyte exosomes under HS conditions and to explore their role in mediating HS-induced liver injury. Methods HS was induced in hepatocytes or mice by hyperthermic treatment at 43.0 °C for 1 h. Exosomes from control and HS-exposed hepatocytes were isolated by standard differential ultracentrifugation. The hepatocyte exosomes were characterized, and the differentially expressed proteins of the control and HS exosomes were identified by isobaric tags for relative and absolute quantitation (iTRAQ) mass spectrometry and subjected to Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Recipient hepatocytes were treated with control or HS exosomes, whereas in vivo, the exosomes were infused into mice. The internalization of HS hepatocyte exosomes by hepatocytes or the liver was tracked. The effect of HS exosomes on the activation of the NOD-like receptor signaling pathway and liver injury was demonstrated in vitro and in vivo. Results HS induced an increase in the release of exosomes from hepatocytes, which were internalized by recipient liver cells in vitro and taken up by the liver in vivo. HS significantly changed the proteomic profiles of hepatocyte exosomes based on the iTRAQ analysis. The KEGG pathway analysis revealed the enrichment of proteins associated with injury and inflammatory signaling pathways, especially the NOD-like receptor signaling pathway, the activity of which was upregulated. Subsequently, the capacity of HS hepatocyte exosomes to activate the NOD-like receptor signaling pathway was verified and found to aggrevate liver damage and inflammation in vitro and in vivo. Conclusions This study is the first preliminary study to demonstrate the induction of acute liver injury by hepatic exosomes in the setting of severe HS and reveals potentially related pathways. These results provide a basis for future research and the identification of new targets for clinical intervention.
Li et al. (2019) Heatstroke-induced hepatocyte exosomes promote liver injury by activating the NOD-like receptor signaling pathway in mice. PeerJ 7:e8216 https://doi.org/10.7717/peerj.8216
Bacterial microbiota composition of Ixodes ricinus ticks: the role of environmental variation, tick characteristics and microbial interactions
Ecological factors, host characteristics and/or interactions among microbes may all shape the occurrence of microbes and the structure of microbial communities within organisms. In the past, disentangling these factors and determining their relative importance in shaping within-host microbiota communities has been hampered by analytical limitations to account for (dis)similar environmental preferences (‘environmental filtering’). Here we used a joint species distribution modelling (JSDM) approach to characterize the bacterial microbiota of one of the most important disease vectors in Europe, the sheep tick Ixodes ricinus, along ecological gradients in the Swiss Alps. Although our study captured extensive environmental variation along elevational clines, the explanatory power of such large-scale ecological factors was comparably weak, suggesting that tick-specific traits and behaviours, microhabitat and -climate experienced by ticks, and interactions among microbes play an important role in shaping tick microbial communities. Indeed, when accounting for shared environmental preferences, evidence for significant patterns of positive or negative co-occurrence among microbes was found, which is indicative of competition or facilitation processes. Signals of facilitation were observed primarily among human pathogens, leading to co-infection within ticks, whereas signals of competition were observed between the tick endosymbiont Spiroplasma and human pathogens. These findings highlight the important role of small-scale ecological variation and microbe-microbe interactions in shaping tick microbial communities and the dynamics of tick-borne disease.
Aivelo et al. (2019) Bacterial microbiota composition of Ixodes ricinus ticks: the role of environmental variation, tick characteristics and microbial interactions. PeerJ 7:e8217 https://doi.org/10.7717/peerj.8217
The effect of pupil size and peripheral brightness on detection and discrimination performance
It is easier to read dark text on a bright background (positive polarity) than to read bright text on a dark background (negative polarity). This positive-polarity advantage is often linked to pupil size: A bright background induces small pupils, which in turn increases visual acuity. Here we report that pupil size, when manipulated through peripheral brightness, has qualitatively different effects on discrimination of fine stimuli in central vision and detection of faint stimuli in peripheral vision. Small pupils are associated with improved discrimination performance, consistent with the positive-polarity advantage, but only for very small stimuli that are at the threshold of visual acuity. In contrast, large pupils are associated with improved detection performance. These results are likely due to two pupil-size related factors: Small pupils increase visual acuity, which improves discrimination of fine stimuli; and large pupils increase light influx, which improves detection of faint stimuli. Light scatter is likely also a contributing factor: When a display is bright, light scatter creates a diffuse veil of retinal illumination that reduces perceived image contrast, thus impairing detection performance. We further found that pupil size was larger during the detection task than during the discrimination task, even though both tasks were equally difficult and similar in visual input; this suggests that the pupil may automatically assume an optimal size for the current task. Our results may explain why pupils dilate in response to arousal: This may reflect an increased emphasis on detection of unpredictable danger, which is crucially important in many situations that are characterized by high levels of arousal. Finally, we discuss the implications of our results for the ergonomics of display design.
Mathôt et al. (2019) The effect of pupil size and peripheral brightness on detection and discrimination performance. PeerJ 7:e8220 https://doi.org/10.7717/peerj.8220
Effect of music listening on hypertonia in neurologically impaired patients—systematic review
Background As music listening is able to induce self-perceived and physiological signs of relaxation, it might be an interesting tool to induce muscle relaxation in patients with hypertonia. To this date effective non-pharmacological rehabilitation strategies to treat hypertonia in neurologically impaired patients are lacking. Therefore the aim is to investigate the effectiveness of music listening on muscle activity and relaxation. Methodology The search strategy was performed by the PRISMA guidelines and registered in the PROSPERO database (no. 42019128511). Seven databases were systematically searched until March 2019. Six of the 1,684 studies met the eligibility criteria and were included in this review. Risk of bias was assessed by the PEDro scale. In total 171 patients with a variety of neurological conditions were included assessing hypertonia with both clinicall and biomechanical measures. Results The analysis showed that there was a large treatment effect of music listening on muscle performance (SMD 0.96, 95% CI [0.29–1.63], I2 = 10%, Z = 2.82, p = 0.005). Music can be used as either background music during rehabilitation (dual-task) or during rest (single-task) and musical preferences seem to play a major role in the observed treatment effect. Conclusions Although music listening is able to induce muscle relaxation, several gaps in the available literature were acknowledged. Future research is in need of an accurate and objective assessment of hypertonia.
Van Criekinge et al. (2019) Effect of music listening on hypertonia in neurologically impaired patients—systematic review. PeerJ 7:e8228 https://doi.org/10.7717/peerj.8228
The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis
Background The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences. Methods Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups. Results The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.
Chen et al. (2019) The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis. PeerJ 7:e8274 https://doi.org/10.7717/peerj.8274
Biomarker potential of repetitive-element transcriptome in lung cancer
Since repetitive elements (REs) account for nearly 53% of the human genome, profiling its transcription after an oncogenic change might help in the search for new biomarkers. Lung cancer was selected as target since it is the most frequent cause of cancer death. A bioinformatic workflow based on well-established bioinformatic tools (such as RepEnrich, RepBase, SAMTools, edgeR and DESeq2) has been developed to identify differentially expressed RNAs from REs. It was trained and tested with public RNA-seq data from matched sequencing of tumour and healthy lung tissues from the same patient to reveal differential expression within the RE transcriptome. Healthy lung tissues express a specific set of REs whose expression, after an oncogenic process, is strictly and specifically changed. Discrete sets of differentially expressed REs were found for lung adenocarcinoma, for small-cell lung cancer, and for both cancers. Differential expression affects more HERV-than LINE-derived REs and seems biased towards down-regulation in cancer cells. REs behaving consistently in all patients were tested in a different patient cohort to validate the proposed biomarkers. Down-regulation of AluYg6 and LTR18B was confirmed as potential lung cancer biomarkers, while up-regulation of HERVK11D-Int is specific for lung adenocarcinoma and up-regulation of UCON88 is specific for small cell lung cancer. Hence, the study of RE transcriptome might be considered another research target in cancer, making REs a promising source of lung cancer biomarkers.
Arroyo et al. (2019) Biomarker potential of repetitive-element transcriptome in lung cancer. PeerJ 7:e8277 https://doi.org/10.7717/peerj.8277
Genetic characteristics of non-familial epilepsy
Background Knowledge of the genetic etiology of epilepsy can provide essential prognostic information and influence decisions regarding treatment and management, leading us into the era of precision medicine. However, the genetic basis underlying epileptogenesis or epilepsy pharmacoresistance is not well-understood, particularly in non-familial epilepsies with heterogeneous phenotypes that last until or start in adulthood. Methods We sought to determine the contribution of known epilepsy-associated genes (EAGs) to the causation of non-familial epilepsies with heterogeneous phenotypes and to the genetic basis underlying epilepsy pharmacoresistance. We performed a multi-center study for whole exome sequencing-based screening of 178 selected EAGs in 243 non-familial adult patients with primarily focal epilepsy (122 drug-resistant and 121 drug-responsive epilepsies). The pathogenicity of each variant was assessed through a customized stringent filtering process and classified according to the American College of Medical Genetics and Genomics guidelines. Results Possible causal genetic variants of epilepsy were uncovered in 13.2% of non-familial patients with primarily focal epilepsy. The diagnostic yield according to the seizure onset age was 25% (2/8) in the neonatal and infantile period, 11.1% (14/126) in childhood and 14.7% (16/109) in adulthood. The higher diagnostic yields were from ion channel-related genes and mTOR pathway-related genes, which does not significantly differ from the results of previous studies on familial or early-onset epilepsies. These potentially pathogenic variants, which were identified in genes that have been mainly associated with early-onset epilepsies with severe phenotypes, were also linked to epilepsies that start in or last until adulthood in this study. This finding suggested the presence of one or more disease-modifying factors that regulate the onset time or severity of epileptogenesis. The target hypothesis of epilepsy pharmacoresistance was not verified in our study. Instead, neurodevelopment-associated epilepsy genes, such as TSC2 or RELN, or structural brain lesions were more strongly associated with epilepsy pharmacoresistance. Conclusions We revealed a fraction of possible causal genetic variants of non-familial epilepsies in which genetic testing is usually overlooked. In this study, we highlight the importance of earlier identification of the genetic etiology of non-familial epilepsies, which leads us to the best treatment options in terms of precision medicine and to future neurobiological research for novel drug development. This should be considered a justification for physicians determining the hidden genetics of non-familial epilepsies that last until or start in adulthood.
Kang et al. (2019) Genetic characteristics of non-familial epilepsy. PeerJ 7:e8278 https://doi.org/10.7717/peerj.8278
Identification of target genes in neuroinflammation and neurodegeneration after traumatic brain injury in rats
Background Traumatic brain injury (TBI) is a common neurological emergency observed in hospitals. A considerable number of patients suffer from long-term disabilities after TBI. This study aimed to identify altered gene expression signatures and mechanisms related to TBI-induced chronic neuroinflammation and neurodegeneration. Methods An integrated analysis was performed using published RNA-sequencing studies to determine TBI-induced differentially expressed genes (DEGs). Based on the DEG data, functional annotation, signal-net, and transcription factor analyses were conducted to understand the mechanism of chronic neuroinflammation and neurodegeneration induced after TBI. Results Two datasets were obtained using the Gene Expression Omnibus database, of which, 6,513 DEGs were identified (6,464 upregulated and 49 downregulated). Positive regulation of biological process, positive regulation of cellular process, nucleus, and heterocyclic compound binding were Gene Ontology terms significantly enriched in post-TBI rat models. Leukocyte transendothelial migration, chemokine signaling pathway, neurotrophin signaling pathway, and longevity-regulating pathway were significantly enriched after TBI. With regard to the signal-net analysis, FOXO3, DGKZ and ILK were considered the most critical genes derived using high–betweenness centrality calculation. A total of 44 TFs, including FOXO1, SRY and KLF4, were predicted to play an important role in the upregulation of gene expression. Using integrated bioinformatics analysis, TBI was found to be associated with a significant inflammatory response and neurodegeneration. FOXO3, apolipoprotein (APOE), microtubule-associated protein tau (MAPT), and TREM2 were probably associated with the TBI pathological process. The mitochondrial electron transport chain may be associated with neurodegeneration in patients with TBI, serving as a potential therapeutic target.
Zhao et al. (2019) Identification of target genes in neuroinflammation and neurodegeneration after traumatic brain injury in rats. PeerJ 7:e8324 https://doi.org/10.7717/peerj.8324
Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis
Background G. boninense is a hemibiotrophic fungus that infects oil palms (Elaeis guineensis Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released during saprophytic and necrotrophic stage of infection of the oil palm host. However, there is a lack of information available on the essentiality of CWDEs in wood-decaying process and pathogenesis of this oil palm pathogen especially at molecular and genome levels. Methods In this study, comparative genome analysis was carried out using the G. boninense NJ3 genome to identify and characterize carbohydrate-active enzyme (CAZymes) including CWDE in the fungal genome. Augustus pipeline was employed for gene identification in G. boninense NJ3 and the produced protein sequences were analyzed via dbCAN pipeline and PhiBase 4.5 database annotation for CAZymes and plant-host interaction (PHI) gene analysis, respectively. Comparison of CAZymes from G. boninense NJ3 was made against G. lucidum, a well-studied model Ganoderma sp. and five selected pathogenic fungi for CAZymes characterization. Functional annotation of PHI genes was carried out using Web Gene Ontology Annotation Plot (WEGO) and was used for selecting candidate PHI genes related to cell wall degradation of G. boninense NJ3. Results G. boninense was enriched with CAZymes and CWDEs in a similar fashion to G. lucidum that corroborate with the lignocellulolytic abilities of both closely-related fungal strains. The role of polysaccharide and cell wall degrading enzymes in the hemibiotrophic mode of infection of G. boninense was investigated by analyzing the fungal CAZymes with necrotrophic Armillaria solidipes, A. mellea, biotrophic Ustilago maydis, Melampsora larici-populina and hemibiotrophic Moniliophthora perniciosa. Profiles of the selected pathogenic fungi demonstrated that necrotizing pathogens including G. boninense NJ3 exhibited an extensive set of CAZymes as compared to the more CAZymes-limited biotrophic pathogens. Following PHI analysis, several candidate genes including polygalacturonase, endo β-1,3-xylanase, β-glucanase and laccase were identified as potential CWDEs that contribute to the plant host interaction and pathogenesis. Discussion This study employed bioinformatics tools for providing a greater understanding of the biological mechanisms underlying the production of CAZymes in G. boninense NJ3. Identification and profiling of the fungal polysaccharide- and lignocellulosic-degrading enzymes would further facilitate in elucidating the infection mechanisms through the production of CWDEs by G. boninense. Identification of CAZymes and CWDE-related PHI genes in G. boninense would serve as the basis for functional studies of genes associated with the fungal virulence and pathogenicity using systems biology and genetic engineering approaches.
Ramzi et al. (2019) Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis. PeerJ 7:e8065 https://doi.org/10.7717/peerj.8065
Charge and hydrophobicity are key features in sequence-trained machine learning models for predicting the biophysical properties of clinical-stage antibodies
Improved understanding of properties that mediate protein solubility and resistance to aggregation are important for developing biopharmaceuticals, and more generally in biotechnology and synthetic biology. Recent acquisition of large datasets for antibody biophysical properties enables the search for predictive models. In this report, machine learning methods are used to derive models for 12 biophysical properties. A physicochemical perspective is maintained in analysing the models, leading to the observation that models cluster largely according to charge (cross-interaction measurements) and hydrophobicity (self-interaction methods). These two properties also overlap in some cases, for example in a new interpretation of variation in hydrophobic interaction chromatography. Since the models are developed from differences of antibody variable loops, the next stage is to extend models to more diverse protein sets. Availability The web application for the sequence-based algorithms are available on the protein-sol webserver, at https://protein-sol.manchester.ac.uk/abpred, with models and virtualisation software available at https://protein-sol.manchester.ac.uk/software.
Hebditch et al. (2019) Charge and hydrophobicity are key features in sequence-trained machine learning models for predicting the biophysical properties of clinical-stage antibodies. PeerJ 7:e8199 https://doi.org/10.7717/peerj.8199
Epidemiology of multiple sclerosis and vitamin D levels in Lanzarote, Canary Islands, Spain
Background Low levels of 25-hydroxyvitamin D (25(OH)D) have been described as one of the possible environmental factors involved in multiple sclerosis (MS) etiopathogenesis. Objectives To study epidemiology of MS and 25(OH)D serum levels of patients in Lanzarote (29°02′06″N), a region with high ultraviolet radiation values during the whole year which is located far apart from Iberian Peninsula (36°–43°N), but without genetic/ethnic differences with it. Methods Incidence in Lanzarote was assessed according to McDonald 2005 criteria between January 2008 and December 2015 and prevalence date was 12/31/15. For 25(OH)D serum levels analyses, samples from 60 MS patients and 60 healthy donors (HD) were collected monthly in a one-year prospective study. Results The prevalence of MS in Lanzarote was 50.0/100,000 and the incidence per year was 2.5/100,000. Median 25(OH)D levels values were 29.1 ng/ml for MS patients (maximum = 36.1 ng/ml, minimum = 22.5 ng/ml) and 27.1 ng/ml for HD (maximum = 34.8 ng/ml, minimum = 22.8 ng/ml). There were no significant differences between 25(OH)D serum levels between MS patients and HD. Conclusions Lanzarote possesses lower prevalence and incidence values than peninsular Spain. Moreover, 25(OH)D serum levels do not differ between MS patients and HD.
Pérez-Pérez et al. (2019) Epidemiology of multiple sclerosis and vitamin D levels in Lanzarote, Canary Islands, Spain. PeerJ 7:e8235 https://doi.org/10.7717/peerj.8235
First evidence of underwater vocalisations in hunting penguins
Seabirds are highly vocal on land where acoustic communication plays a crucial role in reproduction. Yet, seabirds spend most of their life at sea. They have developed a number of morphological, physiological and behavioural adaptations to forage in the marine environment. The use of acoustic signals at sea could potentially enhance seabirds’ foraging success, but remains largely unexplored. Penguins emit vocalisations from the sea surface when commuting, a behaviour possibly associated with group formation at sea. Still, they are unique in their exceptional diving abilities and feed entirely underwater. Other air-breathing marine predators that feed under water, like cetaceans, pinnipeds and marine turtles, are known to emit sound underwater, but such behaviour has not yet been described in seabirds. We aimed to assess the potential prevalence and diversity of vocalisations emitted underwater by penguins. We chose three study species from three different genera, and equipped foraging adults with video cameras with built-in microphones. We recorded a total of 203 underwater vocalisation from all three species during 4 h 43 min of underwater footage. Vocalisations were very short in duration (0.06 s on average), with a frequency of maximum amplitude averaging 998 Hz, 1097 Hz and 680 Hz for King, Gentoo and Macaroni penguins, respectively. All vocalisations were emitted during feeding dives and more than 50% of them were directly associated with hunting behaviour, preceeded by an acceleration (by 2.2 s on average) and/or followed by a prey capture attempt (after 0.12 s on average). The function of these vocalisations remain speculative. Although it seems to be related to hunting behaviour, these novel observations warrant further investigation.
Thiebault et al. (2019) First evidence of underwater vocalisations in hunting penguins. PeerJ 7:e8240 https://doi.org/10.7717/peerj.8240
Sipha maydis sensitivity to defences of Lolium multiflorum and its endophytic fungus Epichloë occultans
Background Plants possess a sophisticated immune system to defend from herbivores. These defence responses are regulated by plant hormones including salicylic acid (SA) and jasmonic acid (JA). Sometimes, plant defences can be complemented by the presence of symbiotic microorganisms. A remarkable example of this are grasses establishing symbiotic associations with Epichloë fungal endophytes. We studied the level of resistance provided by the grass’ defence hormones, and that provided by Epichloë fungal endophytes, against an introduced herbivore aphid. These fungi protect their hosts against herbivores by producing bioactive alkaloids. We hypothesized that either the presence of fungal endophytes or the induction of the plant salicylic acid (SA) defence pathway would enhance the level of resistance of the grass to the aphid. Methods Lolium multiflorum plants, with and without the fungal endophyte Epichloë occultans, were subjected to an exogenous application of SA followed by a challenge with the aphid, Sipha maydis. Results Our results indicate that neither the presence of E. occultans nor the induction of the plant’s SA pathway regulate S. maydis populations. However, endophyte-symbiotic plants may have been more tolerant to the aphid feeding because these plants produced more aboveground biomass. We suggest that this insect insensitivity could be explained by a combination between the ineffectiveness of the specific alkaloids produced by E. occultans in controlling S. maydis aphids and the capacity of this herbivore to deal with hormone-dependent defences of L. multiflorum.
Bastías et al. (2019) Sipha maydis sensitivity to defences of Lolium multiflorum and its endophytic fungus Epichloë occultans. PeerJ 7:e8257 https://doi.org/10.7717/peerj.8257
qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data
Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern medicine. We propose a new classification method based on a model where the data is marginally negative binomial but dependent, thereby incorporating the dependence known to be present between measurements from different genes. The method, called qtQDA, works by first performing a quantile transformation (qt) then applying Gaussian quadratic discriminant analysis (QDA) using regularized covariance matrix estimates. We show that qtQDA has excellent performance when applied to real data sets and has advantages over some existing approaches. An R package implementing the method is also available on https://github.com/goknurginer/qtQDA.
Koçhan et al. (2019) qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data. PeerJ 7:e8260 https://doi.org/10.7717/peerj.8260
Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics
Recent advances in statistical machine learning techniques have led to the creation of probabilistic programming frameworks. These frameworks enable probabilistic models to be rapidly prototyped and fit to data using scalable approximation methods such as variational inference. In this work, we explore the use of the Stan language for probabilistic programming in application to phylogenetic models. We show that many commonly used phylogenetic models including the general time reversible substitution model, rate heterogeneity among sites, and a range of coalescent models can be implemented using a probabilistic programming language. The posterior probability distributions obtained via the black box variational inference engine in Stan were compared to those obtained with reference implementations of Markov chain Monte Carlo (MCMC) for phylogenetic inference. We find that black box variational inference in Stan is less accurate than MCMC methods for phylogenetic models, but requires far less compute time. Finally, we evaluate a custom implementation of mean-field variational inference on the Jukes–Cantor substitution model and show that a specialized implementation of variational inference can be two orders of magnitude faster and more accurate than a general purpose probabilistic implementation.
Fourment et al. (2019) Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics. PeerJ 7:e8272 https://doi.org/10.7717/peerj.8272
A systematic review of the application of machine learning in the detection and classification of transposable elements
Background Transposable elements (TEs) constitute the most common repeated sequences in eukaryotic genomes. Recent studies demonstrated their deep impact on species diversity, adaptation to the environment and diseases. Although there are many conventional bioinformatics algorithms for detecting and classifying TEs, none have achieved reliable results on different types of TEs. Machine learning (ML) techniques can automatically extract hidden patterns and novel information from labeled or non-labeled data and have been applied to solving several scientific problems. Methodology We followed the Systematic Literature Review (SLR) process, applying the six stages of the review protocol from it, but added a previous stage, which aims to detect the need for a review. Then search equations were formulated and executed in several literature databases. Relevant publications were scanned and used to extract evidence to answer research questions. Results Several ML approaches have already been tested on other bioinformatics problems with promising results, yet there are few algorithms and architectures available in literature focused specifically on TEs, despite representing the majority of the nuclear DNA of many organisms. Only 35 articles were found and categorized as relevant in TE or related fields. Conclusions ML is a powerful tool that can be used to address many problems. Although ML techniques have been used widely in other biological tasks, their utilization in TE analyses is still limited. Following the SLR, it was possible to notice that the use of ML for TE analyses (detection and classification) is an open problem, and this new field of research is growing in interest.
Orozco-Arias et al. (2019) A systematic review of the application of machine learning in the detection and classification of transposable elements. PeerJ 7:e8311 https://doi.org/10.7717/peerj.8311
Comparison of diversity and composition of macrofungal species between intensive mushroom harvesting and non-harvesting areas in Oaxaca, Mexico
Wild edible mushrooms have been collected and consumed by human groups for centuries, and today they represent a relevant source of food and income for many rural families worldwide. Preserving these non-timber forest products is of great interest, and there is concern about the damage caused by intensive mushroom harvesting on macromycete communities. The aim of this study was to evaluate variation in diversity and composition of macromycete species between areas regularly used for mushroom harvesting and non-harvested areas in the Mixteca region of Oaxaca, Mexico, as well as to assess the influence of microclimatic and environmental factors on this variation. We selected two harvested and two non-harvested sites within the study area. In each one, we established 10 permanent plots of 10 m × 10 m where we sampled all the observed fruit bodies weekly from June to October 2017. We recorded a total of 856 individuals corresponding to 138 species, and 23 of these were identified as edible. Overall macromycete diversity, edible species diversity and composition were similar in Sites 1 (non-harvested) and 3 (harvested), and in Sites 2 (non-harvested) and 4 (harvested). Variation of diversity and species composition along the studied area was mainly related to microclimatic variables, while most environmental variables and variables related to vegetation structure similarly affected macromycete species in the four sites. Our results indicate that intensive harvesting of wild edible mushrooms is not affecting the diversity and distribution of macromycete species in our study area. Knowledge on the sustainability of mushroom harvesting practices can help improve current regulations regarding the management of these valuable non-timber forest products.
Ruiz-Almenara et al. (2019) Comparison of diversity and composition of macrofungal species between intensive mushroom harvesting and non-harvesting areas in Oaxaca, Mexico. PeerJ 7:e8325 https://doi.org/10.7717/peerj.8325
Ontogenetic and inter-elemental osteohistological variability in the leopard tortoise Stigmochelys pardalis
Testudines are a group of reptiles characterized by the presence of a shell covered by keratinous shields. Stigmochelys pardalis is the most widely distributed terrestrial testudine in southern Africa. Although relatively common with some life history traits being well known, the growth of this species has yet to be studied in any detail. The bone microanatomy of this clade differs from that found in other amniotes, where terrestrial species tend to display characteristics normally seen in aquatic species and vice versa. A detailed histological analysis of the limb bones of S. pardalis reveals extensive variation through ontogeny. Cortical bone becomes increasingly thicker through ontogeny and is finally resorbed in the late sub-adult stage, resulting in a thin cortex and a large infilled medullary cavity. The predominant bone tissues are parallel-fibred and lamellar-zonal for the forelimbs and hind limbs respectively. The oldest individual displayed an External Fundamental System indicating that the growth rate had decreased substantially by this stage. Variability is prevalent between the forelimb and hind limb as well as between early and late sub-adults Forelimb elements exhibit characteristics such as faster growing parallel-fibered bone tissue, slightly higher vascularization and a predominance of annuli over Lines of Arrested Growth (LAG) compared to the hind limb which exhibits poorly vascularized, slower growing lamellar-zonal bone interrupted by LAGs. These differences indicate that the forelimb grew more rapidly than the hind limb, possibly due to the method of locomotion seen in terrestrial species. The extensive bone resorption that occurs from the early sub-adult stage destroys much of the primary cortex and results in a significantly different ratio of inner and outer bone diameter (p = 3.59 × 10­−5; df = 28.04) as well as compactness (p = 2.91 × 10­−5; df = 31.27) between early and late sub-adults. The extensive bone resorption seen also destroys the ecological signal and infers an aquatic lifestyle for this species despite it being clearly terrestrial. This supports the results of other studies that have found that using bone microanatomy to determine lifestyle in testudines does not produce accurate results.
Botha et al. (2019) Ontogenetic and inter-elemental osteohistological variability in the leopard tortoise Stigmochelys pardalis. PeerJ 7:e8030 https://doi.org/10.7717/peerj.8030
Exploring snake occurrence records: Spatial biases and marginal gains from accessible social media
A species’ distribution provides fundamental information on: climatic niche, biogeography, and conservation status. Species distribution models often use occurrence records from biodiversity databases, subject to spatial and taxonomic biases. Deficiencies in occurrence data can lead to incomplete species distribution estimates. We can incorporate other data sources to supplement occurrence datasets. The general public is creating (via GPS-enabled cameras to photograph wildlife) incidental occurrence records that may present an opportunity to improve species distribution models. We investigated (1) occurrence data of a cryptic group of animals: non-marine snakes, in a biodiversity database (Global Biodiversity Information Facility (GBIF)) and determined (2) whether incidental occurrence records extracted from geo-tagged social media images (Flickr) could improve distribution models for 18 tropical snake species. We provide R code to search for and extract data from images using Flickr’s API. We show the biodiversity database’s 302,386 records disproportionately originate from North America, Europe and Oceania (250,063, 82.7%), with substantial gaps in tropical areas that host the highest snake diversity. North America, Europe and Oceania averaged several hundred records per species; whereas Asia, Africa and South America averaged less than 35 per species. Occurrence density showed similar patterns; Asia, Africa and South America have roughly ten-fold fewer records per 100 km2than other regions. Social media provided 44,687 potential records. However, including them in distribution models only marginally impacted niche estimations; niche overlap indices were consistently over 0.9. Similarly, we show negligible differences in Maxent model performance between models trained using GBIF-only and Flickr-supplemented datasets. Model performance appeared dependent on species, rather than number of occurrences or training dataset. We suggest that for tropical snakes, accessible social media currently fails to deliver appreciable benefits for estimating species distributions; but due to the variation between species and the rapid growth in social media data, may still be worth considering in future contexts.
Marshall et al. (2019) Exploring snake occurrence records: Spatial biases and marginal gains from accessible social media. PeerJ 7:e8059 https://doi.org/10.7717/peerj.8059
Expression of extraocular opsin genes and light-dependent basal activity of blind cavefish
Background Animals living in well-lit environments utilize optical stimuli for detecting visual information, regulating the homeostatic pacemaker, and controlling patterns of body pigmentation. In contrast, many subterranean animal species without optical stimuli have evolved regressed binocular eyes and body pigmentation. Interestingly, some fossorial and cave-dwelling animals with regressed eyes still respond to light. These light-dependent responses may be simply evolutionary residuals or they may be adaptive, where negative phototaxis provides avoidance of predator-rich surface environments. However, the relationship between these non-ocular light responses and the underlying light-sensing Opsin proteins has not been fully elucidated. Methods To highlight the potential functions of opsins in a blind subterranean animal, we used the Mexican cave tetra to investigate opsin gene expression in the eyes and several brain regions of both surface and cave-dwelling adults. We performed database surveys, expression analyses by quantitative reverse transcription PCR (RT-qPCR), and light-dependent locomotor activity analysis using pinealectomized fish, one of the high-opsin expressing organs of cavefish. Results Based on conservative criteria, we identified 33 opsin genes in the cavefish genome. Surveys of available RNAseq data found 26 of these expressed in the surface fish eye as compared to 24 expressed in cavefish extraocular tissues, 20 of which were expressed in the brain. RT-qPCR of 26 opsins in surface and cavefish eye and brain tissues showed the highest opsin-expressing tissue in cavefish was the pineal organ, which expressed exo-rhodopsin at 72.7% of the expression levels in surface fish pineal. However, a pinealectomy resulted in no change to the light-dependent locomotor activity in juvenile cavefish and surface fish. Therefore, we conclude that, after 20,000 or more years of evolution in darkness, cavefish light-dependent basal activity is regulated by a non-pineal extraocular organ.
Simon et al. (2019) Expression of extraocular opsin genes and light-dependent basal activity of blind cavefish. PeerJ 7:e8148 https://doi.org/10.7717/peerj.8148
Social information affects Canada goose alert and escape responses to vehicle approach: implications for animal–vehicle collisions
Background Animal–vehicle collisions represent substantial sources of mortality for a variety of taxa and can pose hazards to property and human health. But there is comparatively little information available on escape responses by free-ranging animals to vehicle approach versus predators/humans. Methods We examined responses (alert distance and flight-initiation distance) of focal Canada geese (Branta canadensis maxima) to vehicle approach (15.6 m·s−1) in a semi-natural setting and given full opportunity to escape. We manipulated the direction of the vehicle approach (direct versus tangential) and availability of social information about the vehicle approach (companion group visually exposed or not to the vehicle). Results We found that both categorical factors interacted to affect alert and escape behaviors. Focal geese used mostly personal information to become alert to the vehicle under high risk scenarios (direct approach), but they combined personal and social information to become alert in low risk scenarios (tangential approach). Additionally, when social information was not available from the companion group, focal birds escaped at greater distances under direct compared to tangential approaches. However, when the companion group could see the vehicle approaching, focal birds escaped at similar distances irrespective of vehicle direction. Finally, geese showed a greater tendency to take flight when the vehicle approached directly, as opposed to a side step or walking away from the vehicle. Conclusions We suggest that the perception of risk to vehicle approach (likely versus unlikely collision) is weighted by the availability of social information in the group; a phenomenon not described before in the context of animal–vehicle interactions. Notably, when social information is available, the effects of heightened risk associated with a direct approach might be reduced, leading to the animal delaying the escape, which could ultimately increase the chances of a collision. Also, information on a priori escape distances required for surviving a vehicle approach (based on species behavior and vehicle approach speeds) can inform planning, such as location of designated cover or safe areas. Future studies should assess how information from vehicle approach flows within a flock, including aspects of vehicle speed and size, metrics that affect escape decision-making.
Blackwell et al. (2019) Social information affects Canada goose alert and escape responses to vehicle approach: implications for animal–vehicle collisions. PeerJ 7:e8164 https://doi.org/10.7717/peerj.8164
The interplay between movement, morphology and dispersal in Tetrahymena ciliates
Understanding how and why individual movement translates into dispersal between populations is a long-term goal in ecology. Movement is broadly defined as ‘any change in the spatial location of an individual’, whereas dispersal is more narrowly defined as a movement that may lead to gene flow. Because the former may create the condition for the latter, behavioural decisions that lead to dispersal may be detectable in underlying movement behaviour. In addition, dispersing individuals also have specific sets of morphological and behavioural traits that help them coping with the costs of movement and dispersal, and traits that mitigate costs should be under selection and evolve if they have a genetic basis. Here, we experimentally study the relationships between movement behaviour, morphology and dispersal across 44 genotypes of the actively dispersing unicellular, aquatic model organism Tetrahymena thermophila. We used two-patch populations to quantify individual movement trajectories, as well as activity, morphology and dispersal rate. First, we studied variation in movement behaviour among and within genotypes (i.e. between dispersers and residents) and tested whether this variation can be explained by morphology. Then, we addressed how much the dispersal rate is driven by differences in the underlying movement behaviour. Genotypes revealed clear differences in terms of movement speed and linearity. We also detected marked movement differences between resident and dispersing individuals, mediated by the genotype. Movement variation was partly explained by morphological properties such as cell size and shape, with larger cells consistently showing higher movement speed and higher linearity. Genetic differences in activity and movement were positively related to the observed dispersal and jointly explained 47% of the variation in dispersal rate. Our study shows that a detailed understanding of the interplay between morphology, movement and dispersal may have potential to improve dispersal predictions over broader spatio-temporal scales.
Pennekamp et al. (2019) The interplay between movement, morphology and dispersal in Tetrahymena ciliates. PeerJ 7:e8197 https://doi.org/10.7717/peerj.8197
Feeding intensity of insect herbivores is associated more closely with key metabolite profiles than phylogenetic relatedness of their potential hosts
Determinants of the host ranges of insect herbivores are important from an evolutionary perspective and also have implications for applications such as biological control. Although insect herbivore host ranges typically are phylogenetically constrained, herbivore preference and performance ultimately are determined by plant traits, including plant secondary metabolites. Where such traits are phylogenetically labile, insect hervivore host ranges are expected to be phylogenetically disjunct, reflecting phenotypic similarities rather than genetic relatedness among potential hosts. We tested this hypothesis in the laboratory with a Brassicaceae-specialized weevil, Ceutorhynchus cardariae Korotyaev (Coleoptera: Curculionidae), on 13 test plant species differing in their suitability as hosts for the weevil. We compared the associations between feeding by C. cardariae and either phenotypic similarity (secondary chemistry—glucosinolate profile) or genetic similarity (sequence of the chloroplast gene ndhF) using two methods—simple correlations or strengths of association between feeding by each species, and dendrograms based on either glucosinolates or ndhF sequence (i.e., a phylogram). For comparison, we performed a similar test with the oligophagous Plutella xylostella (L.) (Lepidoptera: Plutellidae) using the same plant species. We found using either method that phenotypic similarity was more strongly associated with feeding intensity by C. cardariae than genetic similarity. In contrast, neither genetic nor phenotypic similarity was significantly associated with feeding intensity on the test species by P. xylostella. The result indicates that phenotypic traits can be more reliable indicators of the feeding preference of a specialist than phylogenetic relatedness of its potential hosts. This has implications for the evolution and maintenance of host ranges and host specialization in phytophagous insects. It also has implications for identifying plant species at risk of nontarget attack by potential weed biological control agents and hence the approach to prerelease testing.
Rapo et al. (2019) Feeding intensity of insect herbivores is associated more closely with key metabolite profiles than phylogenetic relatedness of their potential hosts. PeerJ 7:e8203 https://doi.org/10.7717/peerj.8203
Genetic and serologic surveillance of canine (CIV) and equine (EIV) influenza virus in Nuevo León State, México
Background Despite the uncontrolled distribution of the Influenza A virus through wild birds, the detection of canine influenza virus and equine influenza virus in Mexico was absent until now. Recently, outbreaks of equine and canine influenza have been reported around the world; the virus spreads quickly among animals and there is potential for zoonotic transmission. Methods Amplification of the Influenza A virus matrix gene from necropsies, nasal and conjunctival swabs from trash service horses and pets/stray dogs was performed through RT-PCR. The seroprevalence was carried out through Sandwich enzyme-linked immunosorbent assay system using the M1 recombinant protein and polyclonal antibodies anti-M1. Results The matrix gene was amplified from 13 (19.11%) nasal swabs, two (2.94%) conjunctival swabs and five (7.35%) lung necropsies, giving a total of 20 (29.41%) positive samples in a pet dog population. A total of six (75%) positive samples of equine nasal swab were amplified. Sequence analysis showed 96–99% identity with sequences of Influenza A virus matrix gene present in H1N1, H1N2 and H3N2 subtypes. The phylogenetic analysis of the sequences revealed higher identity with matrix gene sequences detected from zoonotic isolates of subtype H1N1/2009. The detection of anti-M1 antibodies in stray dogs showed a prevalence of 123 (100%) of the sampled population, whereas in horses, 114 (92.68%) positivity was obtained. Conclusion The results unveil the prevalence of Influenza A virus in the population of horses and dogs in the state of Nuevo Leon, which could indicate a possible outbreak of equine and Canine Influenza in Mexico. We suggest that the prevalence of Influenza virus in companion animals be monitored to investigate its epizootic and zoonotic potential, in addition to encouraging the regulation of vaccination in these animal species in order to improve their quality of life.
Plata-Hipólito et al. (2019) Genetic and serologic surveillance of canine (CIV) and equine (EIV) influenza virus in Nuevo León State, México. PeerJ 7:e8239 https://doi.org/10.7717/peerj.8239
Resolution-agnostic tissue segmentation in whole-slide histopathology images with convolutional neural networks
Modern pathology diagnostics is being driven toward large scale digitization of microscopic tissue sections. A prerequisite for its safe implementation is the guarantee that all tissue present on a glass slide can also be found back in the digital image. Whole-slide scanners perform a tissue segmentation in a low resolution overview image to prevent inefficient high-resolution scanning of empty background areas. However, currently applied algorithms can fail in detecting all tissue regions. In this study, we developed convolutional neural networks to distinguish tissue from background. We collected 100 whole-slide images of 10 tissue samples—staining categories from five medical centers for development and testing. Additionally, eight more images of eight unfamiliar categories were collected for testing only. We compared our fully-convolutional neural networks to three traditional methods on a range of resolution levels using Dice score and sensitivity. We also tested whether a single neural network can perform equivalently to multiple networks, each specialized in a single resolution. Overall, our solutions outperformed the traditional methods on all the tested resolutions. The resolution-agnostic network achieved average Dice scores between 0.97 and 0.98 across the tested resolution levels, only 0.0069 less than the resolution-specific networks. Finally, its excellent generalization performance was demonstrated by achieving averages of 0.98 Dice score and 0.97 sensitivity on the eight unfamiliar images. A future study should test this network prospectively.
Bándi et al. (2019) Resolution-agnostic tissue segmentation in whole-slide histopathology images with convolutional neural networks. PeerJ 7:e8242 https://doi.org/10.7717/peerj.8242
Why do we transition from walking to running? Energy cost and lower leg muscle activity before and after gait transition under body weight support
Background Minimization of the energetic cost of transport (CoT) has been suggested for the walk-run transition in human locomotion. More recent literature argues that lower leg muscle activities are the potential triggers of the walk-run transition. We examined both metabolic and muscular aspects for explaining walk-run transition under body weight support (BWS; supported 30% of body weight) and normal walking (NW), because the BWS can reduce both leg muscle activity and metabolic rate. Methods Thirteen healthy young males participated in this study. The energetically optimal transition speed (EOTS) was determined as the intersection between linear CoT and speed relationship in running and quadratic CoT-speed relationship in walking under BWS and NW conditions. Preferred transition speed (PTS) was determined during constant acceleration protocol (velocity ramp protocol at 0.00463 m·s−2 = 1 km·h−1 per min) starting from 1.11 m·s−1. Muscle activities and mean power frequency (MPF) were measured using electromyography of the primary ankle dorsiflexor (tibialis anterior; TA) and synergetic plantar flexors (calf muscles including soleus) before and after the walk-run transition. Results The EOTS was significantly faster than the PTS under both conditions, and both were faster under BWS than in NW. In both conditions, MPF decreased after the walk-run transition in the dorsiflexor and the combined plantar flexor activities, especially the soleus. Discussion The walk-run transition is not triggered solely by the minimization of whole-body energy expenditure. Walk-run transition is associated with reduced TA and soleus activities with evidence of greater slow twitch fiber recruitment, perhaps to avoid early onset of localized muscle fatigue.
Abe et al. (2019) Why do we transition from walking to running? Energy cost and lower leg muscle activity before and after gait transition under body weight support. PeerJ 7:e8290 https://doi.org/10.7717/peerj.8290
Prognostic factors and survival outcomes according to tumor subtype in patients with breast cancer lung metastases
Background Reports on the incidence and prognoses of lung metastases when diagnosing breast cancer patients with different subtypes are limited. Our study investigated the effect of molecular sub-typing stratification on the prognoses of lung metastatic breast caner patients. Methods Patients with breast cancer and lung metastases were identified from Surveillance, Epidemiology and End Results population-based data between 2010 and 2015. Univariate and multivariate Cox regression analyses were performed to identify risk factors and prognoses, overall survival (OS) and breast cancer-specific survival for patients with breast cancer lung metastases. Results We identified 6,516 patients with lung metastatic breast cancer, representing 1.7% of the entire cohort and 30.4% of the subset with metastatic disease. This included 2,940 hormone receptor (HR)+/HER2− patients, 852 HR+/HER2+ patients, 547 HR−/HER2+ patients and 983 triple-negative patients. The median OS for all lung metastatic patients was 13 months. Multivariate analysis revealed that those lung metastatic breast cancer patients of older age (>80), black race, with poorly differentiated tumors, carcinoma histology, triple-negative subtype, more metastatic sites and no surgery, and no chemotherapy showed significantly poor survival, both overall and breast cancer-specific. Conclusions Our findings show that molecular sub-type and more metastatic sites might have significant influence on the incidence and prognosis of breast cancer lung metastases. We also identified several prognostic factors that could guide therapy selection in the treatment of lung metastatic patients.
Chen et al. (2019) Prognostic factors and survival outcomes according to tumor subtype in patients with breast cancer lung metastases. PeerJ 7:e8298 https://doi.org/10.7717/peerj.8298
Prey-tracking behavior and prey preferences in a tree-climbing firefly
Prey-tracking behavior is common in snail-killing predators, but in the family Lampyridae, this behavior has been validated in only a single species even though this Coleopteran family includes many specialist snail predators. The endemic firefly Pyrocoelia atripennis is a major snail-killing predator in the Yaeyama Islands of Japan, and the larvae often climb on the trees and grasses at night. This tree-climbing behavior is relevant to larval food choices and anti-predatory defenses of land snails. This study examined whether lampyrid larvae can track snail mucus trails and examined larval prey preferences using alternative choice experiments. In addition, predation trials were conducted to evaluate which snail species are potential prey. P. atripennis larvae significantly selected mucous trails over distilled water or control (no-trail) treatments. In addition, a semi-arboreal species was preferred over a ground-dwelling species. In predation trials, the larvae preyed on five out of 10 endemic snail species, all of which were semi-arboreal or arboreal species. Ground-dwelling Cyclophoridae and Aegista species have effective anti-predatory defenses consisting of an operculum or “foamy-lid” that fills the shell aperture. Whether the prey has a lid affects the predation success of lampyrid larvae, and larval tree-climbing behavior may be an adaptation used to search for semi-arboreal and arboreal land snails that lack defensive lids. Furthermore, snail mucus left on the plant stem may help the lampyrid larvae to locate their prey.
Sato (2019) Prey-tracking behavior and prey preferences in a tree-climbing firefly. PeerJ 7:e8080 https://doi.org/10.7717/peerj.8080
Managing migraine with over-the-counter provision of triptans: the perspectives and readiness of Western Australian community pharmacists
Background Down-scheduling one or more triptans to Schedule 3 (Pharmacist Only Medicine) from Schedule 4 (Prescription Only Medicine) has been debated in Australia for a decade. This study aimed to evaluate the perspectives and readiness of Western Australian (WA) community pharmacists to manage migraine including over-the-counter (OTC) provision of triptans. Methods Data were collected using a self-administered paper-based questionnaire, posted to a random sample of 178 metropolitan and 97 regional pharmacies in WA. Respondent pharmacists were surveyed regarding: knowledge of optimal migraine treatment as per current guidelines, resources required to appropriately recommend triptans and attitudes and perspective toward down-scheduling. Data were analysed using descriptive statistics and multivariate regression analysis. Pharmacist/pharmacy characteristics influencing readiness were evaluated by assigning respondents a score based on responses to Likert scale questions. These questions were assigned to five domains based on an implementation model and these scores were used in a general linear model to identify demographic characteristics associated with readiness across each domain. Results A total of 114 of the 275 pharmacies returned useable questionnaires (response rate: 41.5%). The two most commonly recommended first line OTC agents were a combined paracetamol/non-steroidal anti-inflammatory drugs and aspirin (44/104; 42.3% and 22/104; 21.2%, respectively) which provided context to the respondents’ knowledge of optimal migraine treatment. Responses to questions in relation to triptans and the warning signs requiring referral were in line with current guidelines, demonstrating respondents’ knowledge in these areas. Nevertheless, most respondents demonstrated uncertainty in relation to the pathogenesis of migraine. If triptans were available OTC, 66/107 (61.7%) would recommend them first-line. The majority (107/113; 94.7%) agreed that down-scheduling would improve timely access to effective migraine medication and 105/113 (92.9%) agreed that if triptans were down-scheduled, pharmacists may be better able to assist people in the treatment of migraine. Most respondents agreed that additional training and resources, including a guideline for OTC supply of triptans and the management of first-time and repeat migraine would be necessary if triptans were down-scheduled. No single demographic characteristic influenced readiness across all five domains. Discussion Pharmacists were knowledgeable regarding triptans and recognised symptoms requiring referral; migraine knowledge could be improved. Pharmacists supported down-scheduling of one or more triptans in Australia, however they highlighted a need for further training and resources to support migraine diagnosis and provision of OTC triptans. Professional pharmacy bodies should consider these findings when recommending drugs suitable for down-scheduling for pharmacist recommendation.
Booth et al. (2019) Managing migraine with over-the-counter provision of triptans: the perspectives and readiness of Western Australian community pharmacists. PeerJ 7:e8134 https://doi.org/10.7717/peerj.8134
A novel approach to immunoapheresis of C3a/C3 and proteomic identification of associates
Background Complement factor C3 represents the central component of the complement cascade and its activation split product C3a plays an important role in inflammation and disease. Many human disorders are linked to dysregulation of the complement system and alteration in interaction molecules. Therefore, various therapeutic approaches to act on the complement system have been initiated. Methods and Results Aiming to develop a tool to eliminate C3a/C3 from the circulation, in a first step a high affine murine monoclonal antibody (mAb) (3F7E2-mAb) was generated against complement factor C3 and selected for binding to the C3a region to serve as immunoaffinity reagent. Functional testing of the 3F7E2-mAb revealed an inhibition of Zymosan-induced cleavage of C3a from C3. Subsequently, a C3a/C3 specific 3F7E2-immunoaffinity column was developed and apheresis of C3a/C3 and associates was performed. Finally, a proteomic analysis was carried out for identification of apheresis products. C3a/C3 was liberated from the 3F7E2-column together with 278 proteins. C3a/C3 interaction specificity was validated by using a haptoglobin immunoaffinity column as control and biostatistic analysis revealed 39 true C3a/C3 interactants. Conclusion A novel and functionally active mAb was developed against complement factor C3a/C3 and used in a specific immunoaffinity column that allows apheresis of C3a/C3 and associates and their identification by proteomic analysis. This methodological approach of developing specific antibodies that can be used as immunoaffinity reagents to design immunoaffinity columns for elimination and further identification of associated proteins could open new avenues for the development of tailored immunotherapy in various complement-mediated or autoimmune diseases.
Winnicki et al. (2019) A novel approach to immunoapheresis of C3a/C3 and proteomic identification of associates. PeerJ 7:e8218 https://doi.org/10.7717/peerj.8218
The fast–slow continuum of longevity among yellow-bellied toad populations (Bombina variegata): intrinsic and extrinsic drivers of variation
Yellow-bellied toad populations (Bombina variegata) show a wide fast–slow continuum of the life-history trait longevity ranging from 5 to 23 years. We investigated populations in Germany (n = 8) and Austria (n = 1) to determine their position within the continuum of longevity and the potential drivers of adult survival at the local and the continental scale. Intrinsic and extrinsic factors considered were local weather, nutritional state, allocation of ingested energy to somatic growth, pathogen prevalence, and geographical clines (latitude, altitude, and longitude). Capture-mark-recapture (CMR) monitoring and direct age assessment by skeletochronology allowed for reliable estimates of longevity and adult survival. Raw and corrected recapture rates as well as a probabilistic estimate of the lifespan of the eldest 1% adults of a cohort (CMR data) were used as surrogates for adult survival and thus longevity in a population. Additionally, survival rates were calculated from static life tables based on the age structure (skeletochronological data) of eight populations. Populations in Germany were short-lived with a maximum lifespan of annual cohorts varying from 5 to 8 years, whereas the population in Austria was long-lived with a cohort longevity of 13 to 23 years. We provide evidence that annual survival rates and longevity differ among years and between short- and long-lived populations, but there was no decrease of survival in older toads (i.e. absence of senescence). Variation of weather among years accounted for 90.7% of variance in annual survival rates of short-lived populations, whereas the sources of variation in the long-lived population remained unidentified. At the continental scale, longevity variation among B. variegata populations studied so far did not correspond to geographical clines or climate variation. Therefore, we propose that a population’s position within the fast–slow continuum integrates the response to local environmental stochasticity (extrinsic source of variation) and the efficiency of chemical antipredator protection determining the magnitude of longevity (intrinsic source of variation).
Hantzschmann et al. (2019) The fast–slow continuum of longevity among yellow-bellied toad populations (Bombina variegata): intrinsic and extrinsic drivers of variation. PeerJ 7:e8233 https://doi.org/10.7717/peerj.8233
Significance of TP53 mutation in bladder cancer disease progression and drug selection
Background The tumor protein p53 (TP53) mutant is one of the most frequent mutant genes in bladder cancer. In this study, we assessed the importance of the TP53 mutation in bladder cancer progression and drug selection, and identified potential pathways and core genes associated with the underlying mechanisms. Methods Gene expression data used in this study were downloaded from The Cancer Genome Atlas and cBioportal databases. Drug sensitivity data were obtained from the Genomics of Drug Sensitivity in Cancer. We did functional enrichment analysis by gene set enrichment analysis (GSEA) and the Database for Annotation, Visualization and Integrated Discovery (DAVID). Results We found the TP53 mutation in 50% of bladder cancer patients. Patients with the TP53 mutation were associated with a lower TP53 mRNA expression level, more advanced tumor stage and higher histologic grade. Three drugs, mitomycin-C, doxorubicin and gemcitabine, were especially more sensitive to bladder cancer with the TP53 mutation. As for the mechanisms, we identified 863 differentially expressed genes (DEGs). Functional enrichment analysis suggested that DEGs were primarily enriched in multiple metabolic progressions, chemical carcinogenesis and cancer related pathways. The protein–protein interaction network identified the top 10 hub genes. Our results have suggested the significance of TP53 mutation in disease progression and drug selection in bladder cancer, and identified multiple genes and pathways related in such program, offering novel basis for bladder cancer individualized treatment.
Wu et al. (2019) Significance of TP53 mutation in bladder cancer disease progression and drug selection. PeerJ 7:e8261 https://doi.org/10.7717/peerj.8261
Algorithms for efficiently collapsing reads with Unique Molecular Identifiers
Background Unique Molecular Identifiers (UMI) are used in many experiments to find and remove PCR duplicates. There are many tools for solving the problem of deduplicating reads based on their finding reads with the same alignment coordinates and UMIs. However, many tools either cannot handle substitution errors, or require expensive pairwise UMI comparisons that do not efficiently scale to larger datasets. Results We reformulate the problem of deduplicating UMIs in a manner that enables optimizations to be made, and more efficient data structures to be used. We implement our data structures and optimizations in a tool called UMICollapse, which is able to deduplicate over one million unique UMIs of length 9 at a single alignment position in around 26 s, using only a single thread and much less than 10 GB of memory. Conclusions We present a new formulation of the UMI deduplication problem, and show that it can be solved faster, with more sophisticated data structures.
Liu (2019) Algorithms for efficiently collapsing reads with Unique Molecular Identifiers. PeerJ 7:e8275 https://doi.org/10.7717/peerj.8275
Limited initial impacts of biomass harvesting on composition of wood-inhabiting fungi within residual stumps
Growing pressures linked to global warming are prompting governments to put policies in place to find alternatives to fossil fuels. In this study, we compared the impact of tree-length harvesting to more intensive full-tree harvesting on the composition of fungi residing in residual stumps 5 years after harvest. In the tree-length treatment, a larger amount of residual material was left around the residual stumps in contrast to the full-tree treatment where a large amount of woody debris was removed. We collected sawdust from five randomly selected residual stumps in five blocks in each of the tree-length and full-tree treatments, yielding a total of 50 samples (25 in each treatment). We characterized the fungal operational taxonomic units (OTUs) present in each stump using high-throughput DNA sequencing of the fungal ITS region. We observed no differences in Shannon diversity between tree-length and full-tree harvesting. Likewise, we observed few differences in the composition of fungal OTUs among tree-length and full-tree samples using non-metric multidimensional scaling. Using the differential abundance analysis implemented with DESeq2, we did, however, detect several associations between specific fungal taxa and the intensity of residual biomass harvest. For example, Peniophorella pallida (Bres.) KH Larss. and Tephromela sp. were found mainly in the full-tree treatment, while Phlebia livida (Pers.) Bres. and Cladophialophora chaetospira (Grove) Crous & Arzanlou were found mainly in the tree-length treatment. While none of the 20 most abundant species in our study were identified as pathogens we did identify one conifer pathogen species Serpula himantioides (Fr.) P. Karst found mainly in the full-tree treatment.
Boué et al. (2019) Limited initial impacts of biomass harvesting on composition of wood-inhabiting fungi within residual stumps. PeerJ 7:e8027 https://doi.org/10.7717/peerj.8027
Invasive alien plants in Polish national parks—threats to species diversity
Due to the relevance of protected areas to the conservation of native biota, the magnitude of invasions and threats posed by alien plants are currently important issues for the preservation of these areas. The paper summarises data on invasive alien plant species presence in the most valuable protected areas in Poland, i.e. national parks (NPs). We investigated the distribution of invasive alien plant species and management attempts concerning those species. We analysed data obtained from 23 national parks originating from published and unpublished sources. Invasive plants were present in all protected areas analysed, from two to 42 species in a particular national park, and 68 in total. The most widely distributed species were: Impatiens parviflora (present in 19 NPs), I. glandulifera (17), Solidago gigantea (17), Reynoutria japonica (17), and Robinia pseudoacacia (16). The conducted analyses showed that the number of invasive species decreased with the higher altitude (asl) of the national park. The most often managed species were Impatiens glandulifera (being removed in seven NPs), I. parviflora (six), Padus serotina (four) and Quercus rubra (four). In the majority of NPs, control activities are limited to small areas and singular species, thus having an incidental character. Only in five objects (Białowieża NP, Biebrza NP, Kampinos NP, Tuchola NP, Wigry NP), management has been focused on several species. We conclude that a lack of comprehensive management of invasive plant species in the majority of national parks currently limits the effectiveness of IAS (invasive alien species) eradication. Exchange of expertise among protected areas, documenting best practice examples, synthesising lessons learnt in IAS management, as well as the development of minimum standards for invasive plants surveillance and management are pivotal.
Bomanowska et al. (2019) Invasive alien plants in Polish national parks—threats to species diversity. PeerJ 7:e8034 https://doi.org/10.7717/peerj.8034
Embryo aggregation regulates in vitro stress conditions to promote developmental competence in pigs
Embryo aggregation is a useful method to produce blastocysts with high developmental competence to generate more offspring in various mammals, but the underlying mechanism(s) regarding the beneficial effects are largely unknown. In this study, we investigated the effects of embryo aggregation using 4-cell stage embryos in in vitro developmental competence and the relationship of stress conditions in porcine early embryogenesis. We conducted aggregation using the well of the well system and confirmed that aggregation using two or three embryos was useful for obtaining blastocysts. Aggregated embryos significantly improved developmental competence, including blastocyst formation rate, blastomere number, ICM/TE ratio, and cellular survival rate, compared to non-aggregated embryos. Investigation into the relationship between embryo aggregation and stress conditions revealed that mitochondrial function increased, and oxidative and endoplasmic reticulum (ER)-stress decreased compared to 1X (non-aggregated embryos) blastocysts. In addition, 3X (three-embryo aggregated) blastocysts increased the expression of pluripotency, anti-apoptosis, and implantation related genes, and decreased expression of pro-apoptosis related genes. Therefore, these findings indicate that embryo aggregation regulates in vitro stress conditions to increase developmental competence and contributes to the in vitro production of high-quality embryos and the large-scale production of transgenic and chimeric pigs.
Jeong et al. (2019) Embryo aggregation regulates in vitro stress conditions to promote developmental competence in pigs. PeerJ 7:e8143 https://doi.org/10.7717/peerj.8143
Resident microbes of lactation rooms and daycares
Dedicated lactation rooms are a modern development as mothers return to work while still providing breastmilk to their absent infants. This study describes the built environment microbiome of lactation rooms and daycares, and explores the influence of temperature and humidity on the microbiome of lactation rooms. Sterile swabs were used to collect samples from five different sites in lactation rooms at University of California, Davis and from five different sites in daycares located in Davis, California. DNA from the swabs was extracted and the V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Temperature and relative humidity data were collected on a subset of the lactation rooms. Sampled lactation rooms could be either dedicated lactation rooms or could also serve other functions (e.g., combined lactation room and restroom lounge). The majority of sequence reads were identified as belonging to family Moraxellaceae, with 73% of all reads included in analysis identified as an unknown species of Acinetobacter. Alpha diversity was analyzed using the Shannon index, while beta diversity was analyzed using unweighted and weighted UniFrac distance. The Jaccard distance was used to measure amount of change at sampling locations between time points for analysis of the impact of temperature and humidity on the microbiome. There were significant differences in the beta diversity of the microbiome of lactation rooms by room type. There were also significant differences in the beta diversity of the microbiome by sample collection location. There were no significant differences in either alpha or beta diversity associated with room temperature or humidity. Additional studies are needed to understand if the differences in lactation room type may result in differences in the breastmilk microbiome of milk collected in those rooms, and to what extent any such differences may influence the infant microbiome.
Taft et al. (2019) Resident microbes of lactation rooms and daycares. PeerJ 7:e8168 https://doi.org/10.7717/peerj.8168
consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Extensive evaluation of RNA-seq methods have demonstrated that no single algorithm consistently outperforms all others. Removal of unwanted variation (RUV) has also been proposed as a method for stabilizing differential expression (DE) results. Despite this, it remains a challenge to run multiple RNA-seq algorithms to identify significant differences common to multiple algorithms, whilst also integrating and assessing the impact of RUV into all algorithms. consensusDE was developed to automate the process of identifying significant DE by combining the results from multiple algorithms with minimal user input and with the option to automatically integrate RUV. consensusDE only requires a table describing the sample groups, a directory containing BAM files or preprocessed count tables and an optional transcript database for annotation. It supports merging of technical replicates, paired analyses and outputs a compendium of plots to guide the user in subsequent analyses. Herein, we assess the ability of RUV to improve DE stability when combined with multiple algorithms and between algorithms, through application to real and simulated data. We find that, although RUV increased fold change stability between algorithms, it demonstrated improved FDR in a setting of low replication for the intersect, the effect was algorithm specific and diminished with increased replication, reinforcing increased replication for recovery of true DE genes. We finish by offering some rules and considerations for the application of RUV in a consensus-based setting. consensusDE is freely available, implemented in R and available as a Bioconductor package, under the GPL-3 license, along with a comprehensive vignette describing functionality: http://bioconductor.org/packages/consensusDE/.
Waardenberg et al. (2019) consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction. PeerJ 7:e8206 https://doi.org/10.7717/peerj.8206
Vegetation dynamic analysis based on multisource remote sensing data in the east margin of the Qinghai-Tibet Plateau, China
This study focuses on the vegetation dynamic caused by global environmental change in the eastern margin of the Qinghai-Tibet Plateau (EMQTP). The Qinghai–Tibet Plateau (QTP) is one of the most sensitive areas responding to global environmental change, particularly global climate change, and has been recognized as a hotspot for coupled studies on changes in global terrestrial ecosystems and global climates. An important component of terrestrial ecosystems, vegetation dynamic has become a key issue in global environmental change, and numerous case studies have been conducted on vegetation dynamic trends using multi-source data and multi-scale methods across different study periods. The EMQTP is regarded as a transitional area located between the QTP and the Sichuan basin, and has special geographical and climatic conditions. Although this area is ecologically fragile and sensitive to climate change, few studies about vegetation dynamics have been carried out in this area. Thus, in this study, we used long-term series datasets of GIMMS 3g NDVI and VGT/PROBA-V NDVI to analyze the vegetation dynamics and phenological changes from 1982 to 2018. Validation was performed based on Landsat NDVI and Vegetation Index & Phenology (VIP) data. The results reveal that the year 1998 was a vital turning point in the start of growing season (SGS) in vegetation ecosystems. Before this turning point, the SGS had an average slope of 9.2 days/decade, and after, the average slope was 3.9 days/decade. The length of growing season (LGS) was slightly prolonged between 1982 to 2015. Additionally, the largest national alpine wetland grassland experienced significant vegetation degradation; in autumn, the degraded area accounted for 63.4%. Vegetation degradation had also appeared in the arid valleys of the Yalong River and the Jinsha River. Through validation analysis, we found that the main causes of vegetation degradation are the natural degradation of wetland grassland and human activities, specifically agricultural development and residential area expansion.
Spatial and Geographic Information Science
Wang et al. (2019) Vegetation dynamic analysis based on multisource remote sensing data in the east margin of the Qinghai-Tibet Plateau, China. PeerJ 7:e8223 https://doi.org/10.7717/peerj.8223
Development and characterization of a multiplex panel of microsatellite markers for the Reunion free-tailed bat Mormopterus francoismoutoui
The ecology and conservation status of many island-restricted bats remain largely unexplored. The free-tailed bat Mormopterus francoismoutoui is a small insectivorous tropical bat, endemic to Reunion Island (Indian Ocean). Despite being widely distributed on the island, the fine-scale genetic structure and evolutionary ecology of M. francoismoutoui remain under-investigated, and therefore its ecology is poorly known. Here, we used Illumina paired-end sequencing to develop microsatellite markers for M. francoismoutoui, based on the genotyping of 31 individuals from distinct locations all over the island. We selected and described 12 polymorphic microsatellite loci with high levels of heterozygosity, which provide novel molecular markers for future genetic population-level studies of M. francoismoutoui.
Dietrich et al. (2019) Development and characterization of a multiplex panel of microsatellite markers for the Reunion free-tailed bat Mormopterus francoismoutoui. PeerJ 7:e8036 https://doi.org/10.7717/peerj.8036
Body height and waist circumference of young Swiss men as assessed by 3D laser-based photonic scans and by manual anthropometric measurements
Overweight and obesity are considered among the major health concerns worldwide. The body mass index is a frequently used measure for overweight and obesity and is associated with common non-communicable diseases such as diabetes type II, cardiovascular diseases and certain cancers. However, the body mass index does not account for the distribution of body fat and relative fat to muscle mass. 3D laser-based photonic full body scans provide detailed information on various body circumferences, surfaces, and volumes as well as body height and weight (using an integrated scale). In the literature, body scans showed good feasibility, reliability, and validity, while also demonstrating a good correlation with health parameters linked to the metabolic syndrome. However, systematic differences between body scan derived measurements and manual measurements remain an issue. This study aimed to assess these systematic differences for body height, waist circumference, and body mass index using cross-sectional data from a homogenous sample of 52 young Swiss male volunteers. In addition to 3D laser-based photonic full body scans and correlative manual measurements, body fat distribution was assessed through bioelectrical impedance analysis. Overall, an excellent correlation was found between measurements of waist circumference and body mass index, and good correlation between body mass index and total fat mass, as well as between waist circumference and visceral fat mass as assessed by bioelectrical impedance analysis. Volunteers were shorter in height measured by body scan when compared to manual measurements. This systematic difference became smaller when volunteers stood in the scanner in a completely upright position with their feet together. Waist circumference was slightly smaller for manual measurements than for body scan derived values. This systematic difference was larger in overweight volunteers compared to leaner volunteers.
Beckmann et al. (2019) Body height and waist circumference of young Swiss men as assessed by 3D laser-based photonic scans and by manual anthropometric measurements. PeerJ 7:e8095 https://doi.org/10.7717/peerj.8095
Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences
Background Species in the genus Morus (Moraceae) are deciduous woody plants of great economic importance. The classification and phylogenetic relationships of Morus, especially the abundant mulberry resources in China, is still undetermined. Internal transcribed spacer (ITS) regions are among the most widely used molecular markers in phylogenetic analyses of angiosperms. However, according to the previous phylogenetic analyses of ITS sequences, most of the mulberry accessions collected in China were grouped into the largest clade lacking for phylogenetic resolution. Compared with functional ITS sequences, ITS pseudogenes show higher sequence diversity, so they can provide useful phylogenetic information. Methods We sequenced the ITS regions and the chloroplast DNA regions TrnL-TrnF and TrnT-TrnL from 33 mulberry accessions, and performed phylogenetic analyses to explore the evolution of mulberry. Results We found ITS pseudogenes in 11 mulberry accessions. In the phylogenetic tree constructed from ITS sequences, clade B was separated into short-type sequence clades (clades 1 and 2), and a long-type sequence clade (clade 3). Pseudogene sequences were separately clustered into two pseudogroups, designated as pseudogroup 1 and pseudogroup 2. The phylogenetic tree generated from cpDNA sequences also separated clade B into two clades. Conclusions Two species were separated in clade B. The existence of three connection patterns and incongruent distribution patterns between the phylogenetic trees generated from cpDNA and ITS sequences suggested that the ITS pseudogene sequences connect with genetic information from the female progenitor. Hybridization has played important roles in the evolution of mulberry, resulting in low resolution of the phylogenetic analysis based on ITS sequences. An evolutionary pattern illustrating the evolution history of mulberry is proposed. These findings have significance for the conservation of local mulberry resources. Polyploidy, hybridization, and concerted evolution have all played the roles in the evolution of ITS sequences in mulberry. This study will expand our understanding of mulberry evolution.
Xuan et al. (2019) Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences. PeerJ 7:e8158 https://doi.org/10.7717/peerj.8158
MemCat: a new category-based image set quantified on memorability
Images differ in their memorability in consistent ways across observers. What makes an image memorable is not fully understood to date. Most of the current insight is in terms of high-level semantic aspects, related to the content. However, research still shows consistent differences within semantic categories, suggesting a role for factors at other levels of processing in the visual hierarchy. To aid investigations into this role as well as contributions to the understanding of image memorability more generally, we present MemCat. MemCat is a category-based image set, consisting of 10K images representing five broader, memorability-relevant categories (animal, food, landscape, sports, and vehicle) and further divided into subcategories (e.g., bear). They were sampled from existing source image sets that offer bounding box annotations or more detailed segmentation masks. We collected memorability scores for all 10 K images, each score based on the responses of on average 99 participants in a repeat-detection memory task. Replicating previous research, the collected memorability scores show high levels of consistency across observers. Currently, MemCat is the second largest memorability image set and the largest offering a category-based structure. MemCat can be used to study the factors underlying the variability in image memorability, including the variability within semantic categories. In addition, it offers a new benchmark dataset for the automatic prediction of memorability scores (e.g., with convolutional neural networks). Finally, MemCat allows the study of neural and behavioral correlates of memorability while controlling for semantic category.
Goetschalckx et al. (2019) MemCat: a new category-based image set quantified on memorability. PeerJ 7:e8169 https://doi.org/10.7717/peerj.8169
The effect of voluntary head movements on postural kinetics in the standing cat
Background Although the postural instability accompanying bilateral vestibular loss in human and quadrupeds during lateral head movements are well-known, it is still unclear whether or not lateral head turns would indeed activate the postural control system to maintain balance. This study aimed to examine the kinetic parameters in freely standing intact cats during head movements in order to further answer the above question. Methods Six intact cats were trained to stand, unrestrained on a force plate and perform voluntary head movements to the left and right positions in response to visual cues. Each trial was divided into two phases, quiet standing with the cat’s head maintaining a straight forward and lateral head position after voluntary head movements. Kinetic parameters including peak pressure and contact area under each limb as well as center of pressure (COP) displacements of the whole body were measured. Results Compared to the neutral head position, peak pressure and contact area of the left head position were significantly smaller for the left forelimb while greatly larger for the right forelimb. An exact opposite case of peak pressure and contact area in the forelimbs was found between the right and neutral head positions. In addition, the COP displacements altered oppositely to the head movements, and presented a significantly right shift in the left position and a significantly left shift in the right position. Conclusion These results demonstrate that the lateral displacement of the head in standing intact cats does activate the postural adjustment to maintain balance, which is consistent with the concept that vestibular input can contribute to postural balance during voluntary head turns.
Song et al. (2019) The effect of voluntary head movements on postural kinetics in the standing cat. PeerJ 7:e8186 https://doi.org/10.7717/peerj.8186
Identification of key genes in non-small cell lung cancer by bioinformatics analysis
Background Non-small cell lung cancer (NSCLC) is one of the most common malignant tumors in the world, and it has become the leading cause of death of malignant tumors. However, its mechanisms are not fully clear. The aim of this study is to investigate the key genes and explore their potential mechanisms involving in NSCLC. Methods We downloaded gene expression profiles GSE33532, GSE30219 and GSE19804 from the Gene Expression Omnibus (GEO) database and analyzed them by using GEO2R. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for the functional and pathway enrichment analysis. We constructed the protein-protein interaction (PPI) network by STRING and visualized it by Cytoscape. Further, we performed module analysis and centrality analysis to find the potential key genes. Finally, we carried on survival analysis of key genes by GEPIA. Results In total, we obtained 685 DEGs. Moreover, GO analysis showed that they were mainly enriched in cell adhesion, proteinaceous extracellular region, heparin binding. KEGG pathway analysis revealed that transcriptional misregulation in cancer, ECM-receptor interaction, cell cycle and p53 signaling pathway were involved in. Furthermore, PPI network was constructed including 249 nodes and 1,027 edges. Additionally, a significant module was found, which included eight candidate genes with high centrality features. Further, among the eight candidate genes, the survival of NSCLC patients with the seven high expression genes were significantly worse, including CDK1, CCNB1, CCNA2, BIRC5, CCNB2, KIAA0101 and MELK. In summary, these identified genes should play an important role in NSCLC, which can provide new insight for NSCLC research.
Zhang et al. (2019) Identification of key genes in non-small cell lung cancer by bioinformatics analysis. PeerJ 7:e8215 https://doi.org/10.7717/peerj.8215
Fossil fern rhizomes as a model system for exploring epiphyte community structure across geologic time: evidence from Patagonia
Background In extant ecosystems, complex networks of ecological interactions between organisms can be readily studied. In contrast, understanding of such interactions in ecosystems of the geologic past is incomplete. Specifically, in past terrestrial ecosystems we know comparatively little about plant biotic interactions besides saprotrophy, herbivory, mycorrhizal associations, and oviposition. Due to taphonomic biases, epiphyte communities are particularly rare in the plant-fossil record, despite their prominence in modern ecosystems. Accordingly, little is known about how terrestrial epiphyte communities have changed across geologic time. Here, we describe a tiny in situ fossil epiphyte community that sheds light on plant-animal and plant-plant interactions more than 50 million years ago. Methods A single silicified Todea (Osmundaceae) rhizome from a new locality of the early Eocene (ca. 52 Ma) Tufolitas Laguna del Hunco (Patagonia, Argentina) was studied in serial thin sections using light microscopy. The community of organisms colonizing the tissues of the rhizome was characterized by identifying the organisms and mapping and quantifying their distribution. A 200 × 200 µm grid was superimposed onto the rhizome cross section, and the colonizers present at each node of the grid were tallied. Results Preserved in situ, this community offers a rare window onto aspects of ancient ecosystems usually lost to time and taphonomic processes. The community is surprisingly diverse and includes the first fossilized leafy liverworts in South America, also marking the only fossil record of leafy bryophyte epiphytes outside of amber deposits; as well as several types of fungal hyphae and spores; microsclerotia with possible affinities in several ascomycete families; and evidence for oribatid mites. Discussion The community associated with the Patagonian rhizome enriches our understanding of terrestrial epiphyte communities in the distant past and adds to a growing body of literature on osmundaceous rhizomes as important hosts for component communities in ancient ecosystems, just as they are today. Because osmundaceous rhizomes represent an ecological niche that has remained virtually unchanged over time and space and are abundant in the fossil record, they provide a paleoecological model system that could be used to explore epiphyte community structure through time.
Bippus et al. (2019) Fossil fern rhizomes as a model system for exploring epiphyte community structure across geologic time: evidence from Patagonia. PeerJ 7:e8244 https://doi.org/10.7717/peerj.8244
Unprofessional peer reviews disproportionately harm underrepresented groups in STEM
Background Peer reviewed research is paramount to the advancement of science. Ideally, the peer review process is an unbiased, fair assessment of the scientific merit and credibility of a study; however, well-documented biases arise in all methods of peer review. Systemic biases have been shown to directly impact the outcomes of peer review, yet little is known about the downstream impacts of unprofessional reviewer comments that are shared with authors. Methods In an anonymous survey of international participants in science, technology, engineering, and mathematics (STEM) fields, we investigated the pervasiveness and author perceptions of long-term implications of receiving of unprofessional comments. Specifically, we assessed authors’ perceptions of scientific aptitude, productivity, and career trajectory after receiving an unprofessional peer review. Results We show that survey respondents across four intersecting categories of gender and race/ethnicity received unprofessional peer review comments equally. However, traditionally underrepresented groups in STEM fields were most likely to perceive negative impacts on scientific aptitude, productivity, and career advancement after receiving an unprofessional peer review. Discussion Studies show that a negative perception of aptitude leads to lowered self-confidence, short-term disruptions in success and productivity and delays in career advancement. Therefore, our results indicate that unprofessional reviews likely have and will continue to perpetuate the gap in STEM fields for traditionally underrepresented groups in the sciences.
Silbiger et al. (2019) Unprofessional peer reviews disproportionately harm underrepresented groups in STEM. PeerJ 7:e8247 https://doi.org/10.7717/peerj.8247
Quantitative estimation of wastewater quality parameters by hyperspectral band screening using GC, VIP and SPA
Water pollution has been hindering the world’s sustainable development. The accurate inversion of water quality parameters in sewage with visible-near infrared spectroscopy can improve the effectiveness and rational utilization and management of water resources. However, the accuracy of spectral models of water quality parameters is usually prone to noise information and high dimensionality of spectral data. This study aimed to enhance the model accuracy through optimizing the spectral models based on the sensitive spectral intervals of different water quality parameters. To this end, six kinds of sewage water taken from a biological sewage treatment plant went through laboratory physical and chemical tests. In total, 87 samples of sewage water were obtained by adding different amount of pure water to them. The raw reflectance (Rraw) of the samples were collected with analytical spectral devices. The Rraw-SNV were obtained from the Rraw processed with the standard normal variable. Then, the sensitive spectral intervals of each of the six water quality parameters, namely, chemical oxygen demand (COD), biological oxygen demand (BOD), NH3-N, the total dissolved substances (TDS), total hardness (TH) and total alkalinity (TA), were selected using three different methods: gray correlation (GC), variable importance in projection (VIP) and set pair analysis (SPA). Finally, the performance of both extreme learning machine (ELM) and partial least squares regression (PLSR) was investigated based on the sensitive spectral intervals. The results demonstrated that the model accuracy based on the sensitive spectral ranges screened through different methods appeared different. The GC method had better performance in reducing the redundancy and the VIP method was better in information preservation. The SPA method could make the optimal trade-offs between information preservation and redundancy reduction and it could retain maximal spectral band intervals with good response to the inversion parameters. The accuracy of the models based on varied sensitive spectral ranges selected by the three analysis methods was different: the GC was the highest, the SPA came next and the VIP was the lowest. On the whole, PLSR and ELM both achieved satisfying model accuracy, but the prediction accuracy of the latter was higher than the former. Great differences existed among the optimal inversion accuracy of different water quality parameters: COD, BOD and TN were very high; TA relatively high; and TDS and TH relatively low. These findings can provide a new way to optimize the spectral model of wastewater biochemical parameters and thus improve its prediction precision.
Environmental Contamination and Remediation
Xing et al. (2019) Quantitative estimation of wastewater quality parameters by hyperspectral band screening using GC, VIP and SPA. PeerJ 7:e8255 https://doi.org/10.7717/peerj.8255
Organ health and development in larval kingfish are unaffected by ocean acidification and warming
Anthropogenic CO2 emissions are causing global ocean warming and ocean acidification. The early life stages of some marine fish are vulnerable to elevated ocean temperatures and CO2 concentrations, with lowered survival and growth rates most frequently documented. Underlying these effects, damage to different organs has been found as a response to elevated CO2 in larvae of several species of marine fish, yet the combined effects of acidification and warming on organ health are unknown. Yellowtail kingfish, Seriola lalandi, a circumglobal subtropical pelagic fish of high commercial and recreational value, were reared from fertilization under control (21 °C) and elevated (25 °C) temperature conditions fully crossed with control (500 µatm) and elevated (1,000 µatm) pCO2 conditions. Larvae were sampled at 11 days and 21 days post hatch for histological analysis of the eye, gills, gut, liver, pancreas, kidney and liver. Previous work found elevated temperature, but not elevated CO2, significantly reduced larval kingfish survival while increasing growth and developmental rate. The current histological analysis aimed to determine whether there were additional sublethal effects on organ condition and development and whether underlying organ damage could be responsible for the documented effects of temperature on survivorship. While damage to different organs was found in a number of larvae, these effects were not related to temperature and/or CO2 treatment. We conclude that kingfish larvae are generally vulnerable during organogenesis of the digestive system in their early development, but that this will not be exacerbated by near-future ocean warming and acidification.
Frommel et al. (2019) Organ health and development in larval kingfish are unaffected by ocean acidification and warming. PeerJ 7:e8266 https://doi.org/10.7717/peerj.8266
Effect of temperature on pollen germination for several Rosaceae species: influence of freezing conservation time on germination patterns
Between February 2018 and April 2018, flowers were collected from eight Rosaceae species. Flowers were kept in a freezer at −20 °C for three freezing times (Treatment 1, two months; Treatment 2, four months; Treatment 3, six months). After extracting pollen, in vitro germination was induced in a culture medium and incubated at six different temperatures for 72 h. The percentage of pollen germination, average pollen tube length and maximum pollen tube length were measured. Pollen germination was maximum for all species between 15 °C and 30 °C. Cydonia oblonga, Malus sylvestris, Prunus avium, Prunus domestica, Prunus dulcis, Prunus persica and Pyrus communis obtained 30–52% pollen germination between 15 °C and 20 °C. Prunus cerasifera had 40% pollen germination at 30 °C. All species studied reached the maximum pollen tube length between 10 °C and 25 °C. Germination did not change significantly for any of the species with freezing time, but we found significant differences in the three parameters measured between treatments. The highest germination percentages were obtained in Treatment 2 (four months frozen at −20 °C), while the maximum pollen tube length was reached in Treatment 1 (two months frozen at −20 °C). According to our results, freezing time affected the germination-temperature patterns. This could indicate that studies on the effect of temperature on pollen germination should always be carried out with fresh pollen to obtain more conclusive data.
Beltrán et al. (2019) Effect of temperature on pollen germination for several Rosaceae species: influence of freezing conservation time on germination patterns. PeerJ 7:e8195 https://doi.org/10.7717/peerj.8195
Differential responses of the acidobacterial community in the topsoil and subsoil to fire disturbance in Pinus tabulaeformis stands
Acidobacteria is found to be dominant and abundant in forest soil, and performs specific ecological functions (such as cellulose decomposition and photosynthetic capacity, etc.). However, relative limited is known about its changing patterns after a fire interruption. In this study, the response of soil Acidobacteria to a wildfire disturbance was investigated using the Illumina MiSeq sequencing system. The research area was classified by different severities of fire damage (high, moderate, and low severity, and an unburnt area), and samples were collected from various soil layers (0–10 cm as topsoil; 10–20 cm as subsoil). We obtained a total of 986,036 sequence reads; 31.77% of them belonged to Acidobacteria. Overall, 18 different Acidobacteria subgroups were detected, with subgroups 4, 6, 1, 3, and 2 the most abundant, accounting for 31.55%, 30.84%, 17.42%, 6.02%, and 5.81% of acidobacterial sequences across all samples, respectively. Although no significant differences in acidobacterial diversity were found in the same soil layer across different fire severities, we observed significantly lower numbers of reads, but higher Shannon and Simpson indices, in the topsoil of the high-severity fire area than in the subsoil. Non-metric multidimensional scaling (NMDS) analysis and permutational multivariate analysis of variance (PERMANOVA) also revealed significant differences in the acidobacterial community structure between the two soil layers. Soil pH, total nitrogen, NH4+-N, the Shannon index of understory vegetation and canopy density were the major drivers for acidobacterial community structure in the topsoil, while soil pH and organic matter were significant factors in the subsoil. A variance partitioning analysis (VPA) showed that edaphic factors explained the highest variation both in the topsoil (15.6%) and subsoil (56.3%). However, there are large gaps in the understanding of this field of research that still need to be explored in future studies.
Li et al. (2019) Differential responses of the acidobacterial community in the topsoil and subsoil to fire disturbance in Pinus tabulaeformis stands. PeerJ 7:e8047 https://doi.org/10.7717/peerj.8047
Response of colonial Peruvian guano birds to flying UAVs: effects and feasibility for implementing new population monitoring methods
Background Drones are reliable tools for estimating colonial seabird numbers. Although most research has focused on methods of improving the accuracy of bird counts, few studies have evaluated the impacts of these methods on bird behavior. In this study, we examined the effects of the DJI Phantom 3 drone approach (altitude, horizontal and vertical descent speeds) on changes in the intensity of behavioral response of guano birds: guanay cormorants (Phalacrocorax bougainvilli), Peruvian boobies (Sula variegata) and Peruvian pelicans (Pelecanus thagus). The breeding and non-breeding condition was also evaluated. Methods Eleven locations along the Peruvian coast were visited in 2016–2017. Drone flight tests considered an altitude range from 5 to 80 m from the colony level, a horizontal speed range from 0.5 to 15 m/s, and a vertical descent speed range from 0.5 to 3 m/s. The intensity of the behavioral response of birds was scored and categorized as: 0-no reacting, 1-head pointing to the drone (HP), 2-wing flapping (WF), 3-walking/running (WR) and 4-taking-off/flying (TK). Drone noise at specific altitudes was recorded with a sound meter close to the colony to discriminate visual from auditory effects of the drone. Results In 74% of all test flights (N = 507), guano birds did not react to the presence of the drone, whereas in the remaining flights, birds showed a sign of discomfort: HP (47.7%, N = 130), WF (18.5%), WR (16.9%) and TK (16.9%). For the drone approach tests, only flight altitude had a significant effect in the intensity of the behavioral response of guano birds (intensity behavioral response <2). No birds reacted at drone altitudes above 50 m from the colony. Birds, for all species either in breeding or non-breeding condition, reacted more often at altitudes of 5 and 10 m. Chick-rearing cormorants and pelicans were less sensitive than their non-breeding counterparts in the range of 5–30 m of drone altitude, but boobies reacted similarly irrespective of their condition. At 5 m above the colony, cormorants were more sensitive to the drone presence than the other two species. Horizontal and vertical flights at different speeds had negligible effects (intensity behavioral response <1). At 2 m above the ground, the noise of the cormorant colony was in average 71.34 ± 4.05 dB (N = 420). No significant differences were observed in the drone noise at different flight altitudes because the background noise of the colony was as loud as the drone. Conclusions It is feasible to use the drone DJI Phantom 3 for surveys on the guano islands of Peru. We recommend performing drone flights at altitudes greater than 50 m from guano bird colonies and to select take-off spots far from gulls. Likewise, this study provides a first step to develop guidelines and protocols of drone use for other potential activities on the Peruvian guano islands and headlands such as surveys of other seabirds and pinnipeds, filming and surveillance.
Irigoin-Lovera et al. (2019) Response of colonial Peruvian guano birds to flying UAVs: effects and feasibility for implementing new population monitoring methods. PeerJ 7:e8129 https://doi.org/10.7717/peerj.8129
The association between mental rotation capacity and motor impairment in children with obesity—an exploratory study
Background Motor impairments are relatively common in children with obesity and evidence suggests that these difficulties go beyond those expected based on the extra weight. This study aimed to investigate the mental rotation capacity in children with obesity, i.e., the ability to mentally view and rotate spatial information, which is a function of both visual-spatial and action representation processes. In particular, we examined whether children with obesity solved mental hand rotation tasks using an egocentric perspective (i.e., motor imagery) and if performance was related to their motor competence. Methods Fifty children (age range: 7–11 y) of which 19 with obesity and motor impairments (OB-) as assessed by the Movement Assessment Battery for Children (2nd version), 13 with obesity without motor impairments (OB+) and 18 control children with a healthy weight (HW) and normal motor competence, were submitted to a classic hand rotation task. Sitting at a desk the children were instructed to indicate the laterality of a picture of a hand displayed on a monitor as quickly and as accurately as possible. Results The results indicate no differences in response time between groups (2,648 ms, 2,558 ms, 2,664 ms for OB-, OB+ and HW respectively). The OB- group, however, had significantly lower accuracy rates and inverse efficiency scores than the HW group (Accuracy: 72% vs. 89%; Inverse efficiency: 4,428 vs. 3,238). No difference was observed in accuracy and inverse efficiency between the OB+ and HW group (Accuracy: 86%; Inverse efficiency: 3,432). In all groups, slower and more error-prone responses were observed when the angle of rotation was larger and when the hand on display was incongruent with the posture of the participants, which indicates that judgments were made from an egocentric perspective and involved motor imagery. Conclusion All children, including those with obesity, appear to engage in motor imagery. This notion needs to be investigated further in children with obesity and motor impairments, given their generally lower accuracy and decreased efficiency, which may indicate a reduced mental rotation capacity.
Deconinck et al. (2019) The association between mental rotation capacity and motor impairment in children with obesity—an exploratory study. PeerJ 7:e8150 https://doi.org/10.7717/peerj.8150
Prosaposin in seminal plasma on the day of oocyte retrieval is associated with normal fertilization and embryo development in in vitro fertilization cycles
The prospective study including 166 participants aims to evaluate the association between seminal prosaposin and the outcomes of in vitro fertilization (IVF) cycles in humans. The generalized linear model (GLM) was used to analyze the associations between seminal prosaposin concentrations and normal fertilization rates and good embryos proportion. The generalized estimating equation (GEE) was used to evaluate the association between embryo parameters and the prosaposin concentrations. Each model was adjusted for age of the couples, female basal FSH, AFC and BMI, starting dose and oocyte yield of IVF cycles and smoker. GLM models suggested that prosaposin was significantly associated with fertilization rate (P = 0.005) and good embryo proportion (P = 0.038) while none of the semen parameters (sperm concentration, motility, progressive motility, normal morphology rate, postwash sperm concentration and motility) was significantly associated with the parameters in the cohort. Using GEE, it was also shown that prosaposin was positively associated with the occurrence of early cleavage and negatively associated with uneven cleavage pattern on day 3. In both the overall population and the normozoospermia patients, the prosaposin was significantly associated with pregnancy with adjustment with covariates. In conclusion, our data suggested that seminal prosaposin concentration could provide more information regarding normal fertilization and embryo development in IVF than traditional semen parameters.
Xu et al. (2019) Prosaposin in seminal plasma on the day of oocyte retrieval is associated with normal fertilization and embryo development in in vitro fertilization cycles. PeerJ 7:e8177 https://doi.org/10.7717/peerj.8177
Soil and plant phytoliths from the Acacia-Commiphora mosaics at Oldupai Gorge (Tanzania)
This article studies soil and plant phytoliths from the Eastern Serengeti Plains, specifically the Acacia-Commiphora mosaics from Oldupai Gorge, Tanzania, as present-day analogue for the environment that was contemporaneous with the emergence of the genus Homo. We investigate whether phytolith assemblages from recent soil surfaces reflect plant community structure and composition with fidelity. The materials included 35 topsoil samples and 29 plant species (20 genera, 15 families). Phytoliths were extracted from both soil and botanical samples. Quantification aimed at discovering relationships amongst the soil and plant phytoliths relative distributions through Chi–square independence tests, establishing the statistical significance of the relationship between categorical variables within the two populations. Soil assemblages form a spectrum, or cohort of co-ocurring phytolith classes, that will allow identifying environments similar to those in the Acacia-Commiphora ecozone in the fossil record.
Mercader et al. (2019) Soil and plant phytoliths from the Acacia-Commiphora mosaics at Oldupai Gorge (Tanzania). PeerJ 7:e8211 https://doi.org/10.7717/peerj.8211
Identification of miRNA precursors in the phloem of Cucurbita maxima
Plant development and responses to environmental cues largely depend on mobile signals including microRNAs (miRNAs) required for post-transcriptional silencing of specific genes. Short-range cell-to-cell transport of miRNA in developing tissues and organs is involved in transferring positional information essential for determining cell fate. Among other RNA species, miRNAs are found in the phloem sap. Long-distance transport of miRNA via the phloem takes a part in regulation of physiological responses to changing environmental conditions. As shown for regulation of inorganic phosphorus and sulfate homeostasis, mature miRNAs rather than miRNAs precursors are transported in the phloem as signaling molecules. Here, a bioinformatics analysis of transcriptomic data for Cucurbita maxima phloem exudate RNAs was carried out to elucidate whether miRNA precursors could also be present in the phloem. We demonstrated that the phloem transcriptome contained a subset of C. maxima pri-miRNAs that differed from a subset of pri-miRNA sequences abundant in a leaf transcriptome. Differential accumulation of pri-miRNA was confirmed by PCR analysis of C. maxima phloem exudate and leaf RNA samples. Therefore, the presented data indicate that a number of C. maxima pri-miRNAs are selectively recruited to the phloem translocation pathway. This conclusion was validated by inter-species grafting experiments, in which C. maxima pri-miR319a was found to be transported across the graft union via the phloem, confirming the presence of pri-miR319a in sieve elements and showing that phloem miRNA precursors could play a role in long-distance signaling in plants.
Tolstyko et al. (2019) Identification of miRNA precursors in the phloem of Cucurbita maxima. PeerJ 7:e8269 https://doi.org/10.7717/peerj.8269
The landscape and prognostic value of tumor-infiltrating immune cells in gastric cancer
Background Gastric cancer (GC) is the fourth most frequently diagnosed malignancy and the second leading cause of cancer-associated mortality worldwide. The tumor microenvironment, especially tumor-infiltrating immune cells (TIICs), exhibits crucial roles both in promoting and inhibiting cancer growth. The aim of the present study was to evaluate the landscape of TIICs and develop a prognostic nomogram in GC. Materials and Methods A gene expression profile obtained from a dataset from The Cancer Genome Atlas (TCGA) was used to quantify the proportion of 22 TIICs in GC by the CIBERSORT algorithm. LASSO regression analysis and multivariate Cox regression were applied to select the best survival-related TIICs and develop an immunoscore formula. Based on the immunoscore and clinical information, a prognostic nomogram was built, and the predictive accuracy of it was evaluated by the area under the curve (AUC) of the receiver operating characteristic curve (ROC) and the calibration plot. Furthermore, the nomogram was validated by data from the International Cancer Genome Consortium (ICGC) dataset. Results In the GC samples, macrophages (25.3%), resting memory CD4 T cells (16.2%) and CD8 T cells (9.7%) were the most abundant among 22 TIICs. Seven TIICs were filtered out and used to develop an immunoscore formula. The AUC of the prognostic nomogram in the TCGA set was 0.772, similar to that in the ICGC set (0.730) and whole set (0.748), and significantly superior to that of TNM staging alone (0.591). The calibration plot demonstrated an outstanding consistency between the prediction and actual observation. Survival analysis revealed that patients with GC in the high-immunoscore group exhibited a poor clinical outcome. The result of multivariate analysis revealed that the immunoscore was an independent prognostic factor. Discussion The immunoscore could be used to reinforce the clinical outcome prediction ability of the TNM staging system and provide a convenient tool for risk assessment and treatment selection for patients with GC.
Li et al. (2019) The landscape and prognostic value of tumor-infiltrating immune cells in gastric cancer. PeerJ 7:e7993 https://doi.org/10.7717/peerj.7993
Cellular components in tumor microenvironment of neuroblastoma and the prognostic value
Background Tumor microenvironment (TME) contributes to tumor development, progression, and treatment response. In this study, we detailed the cell composition of the TME in neuroblastoma (NB) and constructed a cell risk score model to predict the prognosis of NB. Methods xCell score was calculated through transcriptomic data from the datasets GSE49711 and GSE45480 based on the xCell algorithm. The random forest method was employed to select important features and the coefficient was obtained via multivariate cox regression analysis to construct a prognostic model, and the performance was validated in another two independent datasets, GSE16476 and TARGET-NBL. Results We found that both immune and non-immune cells varies significantly in different prognostic groups, and were correlated with survival time. The proposed prognostic cell risk score (pCRS) model we constructed can be an independent prognostic indicator for overall survival (OS) and event-free survival (EFS) (training: OS, HR 1.579, EFS, HR 1.563; validation: OS, HR 1.665, 3.848, EFS, HR 2.203, all p-values < 0.01) and only independent prognostic factor in International Neuroblastoma Risk Group high risk patients (HR 1.339, 3.631; p-value 1.76e–2, 3.71e–5), rather than MYCN amplification. Besides, pCRS model showed good performance in grouping, in discriminating MYCN status, the area under the curve (AUC) was 0.889, 0.933, and 0.861 in GSE49711, GSE45480, and GSE16476, respectively. In separating high risk groups, the AUC was 0.904 in GSE49711. Conclusion This study details the cellular components in the TME of NB through gene expression data, the proposed pCRS model might provide a basis for treatment selection of high risk patients or targeting cellular components of TME in NB.
Zhong et al. (2019) Cellular components in tumor microenvironment of neuroblastoma and the prognostic value. PeerJ 7:e8017 https://doi.org/10.7717/peerj.8017
motoRneuron: an open-source R toolbox for time-domain motor unit analyses
Motor unit synchronization is the tendency of motor neurons and their associated muscle fibers to discharge near-simultaneously. It has been theorized as a control mechanism for force generation by common excitatory inputs to these motor neurons. Magnitude of synchronization is calculated from peaks in cross-correlation histograms between motor unit discharge trains. However, there are many different methods for detecting these peaks and even more indices for calculating synchronization from them. Methodology is diverse, typically laboratory-specific and requires expensive software, like Matlab or LabView. This lack of standardization makes it difficult to draw definitive conclusions about motor unit synchronization. A free, open-source toolbox, “motoRneuron”, for the R programming language, has been developed which contains functions for calculating time domain synchronization using different methods found in the literature. The objective of this paper is to detail the toolbox’s functionality and present a case study showing how the same synchronization index can differ when different methods are used to compute it. A pair of motor unit action potential trains were collected from the forearm during a isometric finger flexion task using fine wire electromyography. The motoRneuron package was used to analyze the discharge time of the motor units for time-domain synchronization. The primary function “mu_synch” automatically performed the cross-correlation analysis using three different peak detection methods, the cumulative sum method, the z-score method, and a subjective visual method. As function parameters defined by the user, only first order recurrence intervals were calculated and a 1 ms bin width was used to create the cross correlation histogram. Output from the function were six common synchronization indices, the common input strength (CIS), k′, k′ − 1, E, S, and Synch Index. In general, there was a high degree of synchronization between the two motor units. However, there was a varying degree of synchronization between methods. For example, the widely used CIS index, which represents a rate of synchronized discharges, shows a 45% difference between the visual and z-score methods. This singular example demonstrates how a lack of consensus in motor unit synchronization methodologies may lead to substantially differing results between studies. The motoRneuron toolbox provides researchers with a standard interface and software to examine time-domain motor unit synchronization.
Tweedell et al. (2019) motoRneuron: an open-source R toolbox for time-domain motor unit analyses. PeerJ 7:e7907 https://doi.org/10.7717/peerj.7907
Species recovery and recolonization of past habitats: lessons for science and conservation from sea otters in estuaries
Recovering species are often limited to much smaller areas than they historically occupied. Conservation planning for the recovering species is often based on this limited range, which may simply be an artifact of where the surviving population persisted. Southern sea otters (Enhydra lutris nereis) were hunted nearly to extinction but recovered from a small remnant population on a remote stretch of the California outer coast, where most of their recovery has occurred. However, studies of recently-recolonized estuaries have revealed that estuaries can provide southern sea otters with high quality habitats featuring shallow waters, high production and ample food, limited predators, and protected haul-out opportunities. Moreover, sea otters can have strong effects on estuarine ecosystems, fostering seagrass resilience through their consumption of invertebrate prey. Using a combination of literature reviews, population modeling, and prey surveys we explored the former estuarine habitats outside the current southern sea otter range to determine if these estuarine habitats can support healthy sea otter populations. We found the majority of studies and conservation efforts have focused on populations in exposed, rocky coastal habitats. Yet historical evidence indicates that sea otters were also formerly ubiquitous in estuaries. Our habitat-specific population growth model for California’s largest estuary—San Francisco Bay—determined that it alone can support about 6,600 sea otters, more than double the 2018 California population. Prey surveys in estuaries currently with (Elkhorn Slough and Morro Bay) and without (San Francisco Bay and Drakes Estero) sea otters indicated that the availability of prey, especially crabs, is sufficient to support healthy sea otter populations. Combining historical evidence with our results, we show that conservation practitioners could consider former estuarine habitats as targets for sea otter and ecosystem restoration. This study reveals the importance of understanding how recovering species interact with all the ecosystems they historically occupied, both for improved conservation of the recovering species and for successful restoration of ecosystem functions and processes.
Hughes et al. (2019) Species recovery and recolonization of past habitats: lessons for science and conservation from sea otters in estuaries. PeerJ 7:e8100 https://doi.org/10.7717/peerj.8100
Exploring profile and potential influencers of vaginal microbiome among asymptomatic pregnant Chinese women
Background This study was designed to explore the profile and potential influencers of the vaginal microbiome (VMB) among asymptomatic pregnant Chinese women and its possible association with pregnancy outcomes. Methods A prospective study was conducted among pregnant Chinese women receiving regular prenatal care at a hospital in Shanghai, China from March 2017 to March 2018. Vaginal swabs were obtained from 113 asymptomatic pregnant women in mid-pregnancy and sequenced by the V3–V4 region of 16S rRNA on an Ion S5™ XL platform. Demographic characteristics and major pregnancy outcomes were collected through questionnaires and electronic medical records. Results The predominant vaginal community state types (CSTs) were CST I (45.1%) and CST III (31.9%). Participants were divided into a lactobacilli-dominant group (LD, CST I/II/III/I–III/V, n = 100, 88.5%) and a less lactobacilli-dominant group (LLD, CST IV-A/B, n = 13, 11.5%). Women in the LLD group showed an increased alpha diversity [median (interquartile range, IQR): 2.41 (1.67, 2.49) vs. 0.30 (0.17, 0.59), P < 0.001], which was related to a lower pre-pregnancy body mass index (BMI) (P = 0.012), and a greater instance of passive smoking (P = 0.033). The relative abundance of Lactobacillus was correlated positively with the pre-pregnancy BMI (r = 0.177, P = 0.041), but negatively with passive smoking (r = − 0.204, P = 0.030). Conclusion The vaginal flora of asymptomatic pregnant Chinese women was mostly dominated by Lactobacillus crispatus and L. iners. A lower BMI and greater instance of passive smoking may contribute to a less lactobacilli-dominant VMB. However, a larger sample size is needed.
He et al. (2019) Exploring profile and potential influencers of vaginal microbiome among asymptomatic pregnant Chinese women. PeerJ 7:e8172 https://doi.org/10.7717/peerj.8172
The accumulation of Mn and Cu in the morphological parts of Solidago canadensis under different soil conditions
Solidago canadensis L. is a drought-tolerant, invasive plant, characterized by a large biomass of underground and aboveground parts. The aim of this study was to assess the accumulation of manganese (Mn) and copper (Cu) in the roots and rhizomes and the stems, leaves, and inflorescence parts in S. canadensis from two locations that differed in soil pH, organic carbon, and Mn and Cu concentrations. The concentration of the metals in the samples was determined by the AAS method; the pH was determined by the potentiometric method; and the content of organic carbon was determined using Tiurin’s method. The concentration of Mn and Cu in the roots of S. candensis correlated with the concentrations of the metals in the soil without regard to the soil condition or its organic carbon content. With a low soil pH and organic carbon content, Mn accumulation per 1 ramet in the aboveground parts of S. canadensis consisted over 50% of the total Mn content in the plant. In neutral or alkaline soils, the amount of Mn per 1 ramet accumulated in underground parts was over 60%. Regardless of the soil conditions, about 35% of Mn accumulated in rhizomes. Approximately 60% of copper accumulated in the underground parts of S. candensis (45% in rhizomes) without regard to the soil reaction or organic carbon content. The ability of the plant to accumulate large amounts of metals disposes Solidago canadensis as a candidate for the phytoremediation of soils contaminated with heavy metals.
Bielecka et al. (2019) The accumulation of Mn and Cu in the morphological parts of Solidago canadensis under different soil conditions. PeerJ 7:e8175 https://doi.org/10.7717/peerj.8175
Retrospective clinical study of renin-angiotensin system blockers in lung cancer patients with hypertension
Purpose Renin-angiotensin system blockers (RASBs), which include angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin-2 receptor 1 blockers (ARBs), have been reported to be associated with lung cancer metastasis, radiotherapy and chemotherapy. Until now, very limited clinical data for RASBs’ diagnostic and prognostic effects has existed for lung cancer chemotherapy in Chinese patients. Methods There were a total of 678 lung cancer patients with hypertension, of which 461 (68%) were in the non-RASBs group and 217 (32%) were in the RASBs group. Patients’ gender, age, smoking status, histologic differentiation, tumor size, pathological grade, lymph node metastasis, pathological stage and progression-free survival (PFS) were retrospectively analyzed between these two groups. The clinical effects of ACEIs and ARBs in lung cancer patients were compared via t tests, and χ2 test, and potential prognostic factors for progression-free survival (PFS) were evaluated by Kaplan–Meier analysis. Results Significant differences were observed in lymph node metastasis between the RASBs and non-RASBs groups. The RASBs group (62.8% vs 71.7%, p = 0.037) and ARBs group (60.0% vs 71.7%, p = 0.030) had lower lymph node metastasis, and patients with RASBs had a lower pathological stage than those in non-RASBs groups (67.1% vs 77.4%, p = 0.044 ). The PFS of the RASBs (10.7 vs. 6.7 months, p = 0.040) and ACEIs (12.9 vs 6.7 months, p = 0.021) groups were longer than that of the non-RASBs group, while no statistical difference was shown between the ACEIs and ARBs groups. Moreover, the significant results of PFS were further confirmed in pathological stage III–IV patients. In the non-RASB group, 55% of patients took calcium channel blockers (CCBs), and the ACEIs group have a significantly longer PFS compared to the non-CCBs group (6.4 vs 12.9 months, p = 0.036). Conclusion In this study, we showed that the use of RASBs is a positive factor for pathological stage and prognosis of lung cancer patients. Therefore, it is necessary to actively evaluate medical history, especially the use of anti-hypertension medication, in patients with lung cancer and reflect medical history in the treatment and management plans of these patients.
Wei et al. (2019) Retrospective clinical study of renin-angiotensin system blockers in lung cancer patients with hypertension. PeerJ 7:e8188 https://doi.org/10.7717/peerj.8188
A comparison of random-field-theory and false-discovery-rate inference results in the analysis of registered one-dimensional biomechanical datasets
Background The inflation of falsely rejected hypotheses associated with multiple hypothesis testing is seen as a threat to the knowledge base in the scientific literature. One of the most recently developed statistical constructs to deal with this problem is the false discovery rate (FDR), which aims to control the proportion of the falsely rejected null hypotheses among those that are rejected. FDR has been applied to a variety of problems, especially for the analysis of 3-D brain images in the field of Neuroimaging, where the predominant form of statistical inference involves the more conventional control of false positives, through Gaussian random field theory (RFT). In this study we considered FDR and RFT as alternative methods for handling multiple testing in the analysis of 1-D continuum data. The field of biomechanics has recently adopted RFT, but to our knowledge FDR has not previously been used to analyze 1-D biomechanical data, nor has there been a consideration of how FDR vs. RFT can affect biomechanical interpretations. Methods We reanalyzed a variety of publicly available experimental datasets to understand the characteristics which contribute to the convergence and divergence of RFT and FDR results. We also ran a variety of numerical simulations involving smooth, random Gaussian 1-D data, with and without true signal, to provide complementary explanations for the experimental results. Results Our results suggest that RFT and FDR thresholds (the critical test statistic value used to judge statistical significance) were qualitatively identical for many experimental datasets, but were highly dissimilar for others, involving non-trivial changes in data interpretation. Simulation results clarified that RFT and FDR thresholds converge as the true signal weakens and diverge when the signal is broad in terms of the proportion of the continuum size it occupies. Results also showed that, while sample size affected the relation between RFT and FDR results for small sample sizes (<15), this relation was stable for larger sample sizes, wherein only the nature of the true signal was important. Discussion RFT and FDR thresholds are both computationally efficient because both are parametric, but only FDR has the ability to adapt to the signal features of particular datasets, wherein the threshold lowers with signal strength for a gain in sensitivity. Additional advantages and limitations of these two techniques as discussed further. This article is accompanied by freely available software for implementing FDR analyses involving 1-D data and scripts to replicate our results.
Naouma et al. (2019) A comparison of random-field-theory and false-discovery-rate inference results in the analysis of registered one-dimensional biomechanical datasets. PeerJ 7:e8189 https://doi.org/10.7717/peerj.8189
Differentiation between maxillary and malar midface position within the facial profile
Aims To define midfacial position differentiating maxillary and zygomatic regions and to evaluate the corresponding cephalometric characteristics discerning midfacial flatness and fullness. Material and Methods A total of 183 pretreatment lateral cephalometric radiographs of non-growing orthodontic patients (age 25.98 ± 8.43 years) screened at our university orthodontic clinic. The lateral cephalographs of the orthodontic patients were stratified in four groups: flat, normal toward flat, normal toward full, full,according to distances from nasion and sella to points J and G (NJ, SJ, NG and SG). J is the midpoint of the distance connecting orbitale to point A, and G the center of the triangle connecting orbit, key ridge and pterygomaxillary fissure. Statistics included the Kendall tau-b test for best associations among measurements. Results All measurements were statistically significantly different between flat and full groups. The highest associations were between NJ and SJ (τb = 0.71; p < 0.001) and NG and SG (τb = 0.70; p < 0.001). Flat midfaces were characterized by canting of the cranial base and palatal plane, hyperdivergent pattern and maxillary retrognathism. The opposite was true for fuller midfaces. Conclusion Midface skeletal location was assessed differentially in the naso-maxillary and malo-zygomatic structures differentially. Craniofacial characteristics were identified according to this stratification, indicating the potential for application in facial diagnosis and need for testing on 3D cone-beam computed tomography images.
Chalala et al. (2019) Differentiation between maxillary and malar midface position within the facial profile. PeerJ 7:e8200 https://doi.org/10.7717/peerj.8200
Concentration-dependent polymorphism of insulin amyloid fibrils
Protein aggregation into highly structured fibrils has long been associated with several neurodegenerative disorders, such as Alzheimer’s or Parkinson’s disease. Polymorphism of amyloid fibrils increases the complexity of disease mechanisms and may be one of the reasons for the slow progress in drug research. Here we report protein concentration as another factor leading to polymorphism of insulin amyloid fibrils. Moreover, our data suggests that insulin amyloid conformation can self-replicate only via elongation, while seed-induced nucleation will lead to environment-defined conformation of fibrils. As similar observations were already described for a couple of other amyloid proteins, we suggest it to be a generic mechanism for self-replication of different amyloid fibril conformations.
Sakalauskas et al. (2019) Concentration-dependent polymorphism of insulin amyloid fibrils. PeerJ 7:e8208 https://doi.org/10.7717/peerj.8208
Icaritin, an inhibitor of beta-site amyloid cleaving enzyme-1, inhibits secretion of amyloid precursor protein in APP-PS1-HEK293 cells by impeding the amyloidogenic pathway
Background Icaritin (ICT) is a prenylflavonoid derivative from Epimedium brevicornum Maxim. ICT has been shown to have neuroprotective effects. We investigate how ICT affects secretion of amyloid precursor protein (APP). Methods We exposed APP-PS1-HEK293 cells to ICT to investigate its effect on beta-site amyloid cleaving enzyme (BACE)1. Cell viability was evaluated by MTT and lactate dehydrogenase (LDH) assays. The half-maximal inhibitory concentration (IC50) of ICT for BACE1 was measured using fluorescence resonance energy transfer. Effects of ICT on the mRNA expression of APP were assessed by quantitative polymerase chain reaction, and protein expression was measured by western blotting and immunofluorescence. Results Icaritin inhibited BACE1 activity and IC50 was 5.70 ± 1.09 μM. Compared with the control group, at ICT concentrations of 5 μM and 10 μM, the viability increased and LDH leakage decreased in APP-PS1-293 cells. Also, mRNA expression of A disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) increased, while that of BACE1 and presenilin-1 (PS1) decreased, upon ICT treatment. Western blotting and immunofluorescence confirmed that protein expression of ADAM10, BACE1 and PS1 showed the same trend. Expression of the APP fragments sAPPβ and C-terminal fragment β decreased, while that of sAPPα increased, upon ICT treatment. Expression of amyloid β peptides in APP-PS1-HEK293 cells was lower in ICT-treated groups compared with that in the control group. Conclusions Icaritin, as a BACE1 inhibitor, inhibits APP secretion in APP-PS1-HEK293 cells by impeding the amyloidogenic pathway.
Feng et al. (2019) Icaritin, an inhibitor of beta-site amyloid cleaving enzyme-1, inhibits secretion of amyloid precursor protein in APP-PS1-HEK293 cells by impeding the amyloidogenic pathway. PeerJ 7:e8219 https://doi.org/10.7717/peerj.8219
Effects of maximum residue limit of triflumezopyrim exposure on fitness of the red imported fire ant Solenopsis invicta
The impact of exposure to free feeding concentrations of triflumezopyrim to the red imported fire ant, Solenopsis invicta, in maximum residue tolerances for 56 days was investigated to understand whether triflumezopyrim, a novel neonicotinoid, poses unacceptable risks to the environment. Our results demonstrated that neither 0.5 μg/ml nor 0.2 μg/ml triflumezopyrim have a significant impact on the growth of the S. invicta colony and their food consumption (sugar water and locusts) during the length of treatment. While both 0.5 μg/ml and 0.2 μg/ml triflumezopyrim improved the grasping ability of S. invicta, and 0.5 μg/ml not 0.2 μg/ml triflumezopyrim increased their rate of locomotion. In addition, although 0.5 μg/ml and 0.2 μg/ml triflumezopyrim increased their individual aggressiveness index, the probability of the survival of S. invicta was not impacted by triflumezopyrim treatments in aggressive group encounters. This study suggests that triflumezopyrim did not have a negative impact on the fitness of S. invicta at 0.5 μg/ml and 0.2 μg/ml exposures.
Li et al. (2019) Effects of maximum residue limit of triflumezopyrim exposure on fitness of the red imported fire ant Solenopsis invicta. PeerJ 7:e8241 https://doi.org/10.7717/peerj.8241
Synthesis of silver nanoparticles using a Mentha spicata extract and evaluation of its anticancer and cytotoxic activity
In this study, silver nanoparticles (NP) were synthesized by two methods: using an aqueous extract of Mentha spicata leaves and using citrate ions as stabilizing agent, and the cytotoxicity and anticancer activity of both NP were evaluated in vitro. The particles synthesized with the aqueous extract were spherical with a size ranging from 15 to 45 nm. These NP decreased cell viability in all of the cells studied; however, the IC50 could only be estimated in the Chang liver cells (IC50 = 21.37 µg/mL). These particles also decreased the generation of reactive oxygen species in Chang and SiHa cells. Additionally, the dispersions decreased the activity of caspase-3. There was no significant difference between the biological activities of the NP obtained with the aqueous extract and the NP synthesized using citrate ions. This study showed that an aqueous extract of M. spicata is an excellent alternative for the synthesis of silver NP. These NP showed cytotoxicity and anticancer activity in vitro. Although more experiments are required, the cell death occurs probably through a mechanism different from apoptosis.
Torres-Martínez et al. (2019) Synthesis of silver nanoparticles using a Mentha spicata extract and evaluation of its anticancer and cytotoxic activity. PeerJ 7:e8142 https://doi.org/10.7717/peerj.8142
Expression and prognostic analyses of early growth response proteins (EGRs) in human breast carcinoma based on database analysis
Background Early growth response proteins (EGRs), as a transcriptional regulatory family, are involved in the process of cell growth, differentiation, apoptosis, and even carcinogenesis. However, the role of EGRs in tumors, their expression levels, and their prognostic value remain unclear. Methods Using the Oncomine database, Kaplan–Meier Plotter, bcGenExMiner v4.2, cBioPortal, and other tools, the association between the survival data of breast carcinoma (BC) patients and transcriptional levels of four EGRs was investigated. Results According to the Oncomine database, in comparison to normal tissues, the expression level of EGR2/3 mRNA in BC tissues was decreased, but there was no difference in the expression level of EGR4 mRNA. On the basis of the Scarff-Bloom-Richardson (SBR) grading system, the downregulated expression level of EGR1/2/3 and upregulated expression level of EGR4 were correlated with an increased histological differentiation level, with significant differences (p < 0.05). Kaplan–Meier curves suggest that a reduction in EGR2/3 mRNA expression is related to recurrence-free survival (RFS) in BC patients. In addition, the mRNA expression level of EGR1/2/3 was related to metastatic relapse-free survival (MRFS) in BC patients with metastatic recurrence (p < 0.05). Conclusion EGR1/2/3 can be utilized as an important factor for evaluating prognosis and may be relevant to diagnosis. EGR4 may play a role in the occurrence and development of BC. The specific function and mechanism of EGRs in BC deserve further study.
Fei et al. (2019) Expression and prognostic analyses of early growth response proteins (EGRs) in human breast carcinoma based on database analysis. PeerJ 7:e8183 https://doi.org/10.7717/peerj.8183
Effects of salinity on photosynthetic traits, ion homeostasis and nitrogen metabolism in wild and cultivated soybean
Background Carbon and nitrogen metabolism need to be highly regulated to achieve cell acclimation to changing environmental conditions. The understanding of physio-biochemical responses of crops to salinity stress could help to stabilize their performance and yield. In this study we have analyzed the roles of photosynthesis, ion physiology and nitrate assimilation toward saline/alkaline stress acclimation in wild and cultivated soybean seedlings. Methods Growth and photosynthetic parameters, ion concentrations and the activity of enzymes involved in nitrogen assimilation were determined in seedlings of one wild and one cultivated soybean accession subjected to saline or alkaline stresses. Results Both saline and alkaline stresses had a negative impact on the growth and metabolism of both wild and cultivated soybean.The growth, photosynthesis, and gas exchange parameters showed a significant decrease in response to increasing salt concentration. Additionally, a significant increase in root Na+ and Cl– concentration was observed. However, photosynthetic performance and ion regulation were higher in wild than in cultivated soybean under saline and alkaline stresses. Nitrate reductase (NR) and the glutamine synthetase/glutamate synthase (GS/GOGAT) cycle showed a significant decrease in leaves of both genotypes. The reduction in the GS/GOGAT cycle was accompanied by high aminating glutamate dehydrogenase (NADH-glutamate dehydrogenase) activity, indicating the assimilation of high levels of NH4+. A significant increase in the activities of aminating and deaminating enzymes, including glutamate dehydrogenase (GDH), alanine aminotransferase (AlaAT) and aspartate aminotransferase (AspAT), was observed, probably due to the high glutamate demand and maintenance of the Krebs cycle to correct the C: N status. Conclusions Cultivated soybean was much more stress sensitive than was the wild soybean. The decrease in growth, photosynthesis, ion regulation and nitrogen assimilation enzymes was greater in cultivated soybean than in wild soybean. The impact of alkaline stress was more pronounced than that of saline stress. Wild soybean regulated the physiological mechanisms of photosynthesis and nitrate assimilation more effectively than did cultivated soybean. The present findings provide a theoretical basis with which to screen and utilize wild and cultivated soybean germplasm for breeding new stress-tolerant soybean.
Ullah et al. (2019) Effects of salinity on photosynthetic traits, ion homeostasis and nitrogen metabolism in wild and cultivated soybean. PeerJ 7:e8191 https://doi.org/10.7717/peerj.8191
Pelvic floor pressure distribution profile in urinary incontinence: a classification study with feature selection
Background Pelvic floor pressure distribution profiles, obtained by a novel instrumented non-deformable probe, were used as the input to a feature extraction, selection, and classification approach to test their potential for an automatic diagnostic system for objective female urinary incontinence assessment. We tested the performance of different feature selection approaches and different classifiers, as well as sought to establish the group of features that provides the greatest discrimination capability between continent and incontinent women. Methods The available data for evaluation consisted of intravaginal spatiotemporal pressure profiles acquired from 24 continent and 24 incontinent women while performing four pelvic floor maneuvers: the maximum contraction maneuver, Valsalva maneuver, endurance maneuver, and wave maneuver. Feature extraction was guided by previous studies on the characterization of pressure profiles in the vaginal canal, where the extracted features were tested concerning their repeatability. Feature selection was achieved through a combination of a ranking method and a complete non-exhaustive subset search algorithm: branch and bound and recursive feature elimination. Three classifiers were tested: k-nearest neighbors (k-NN), support vector machine, and logistic regression. Results Of the classifiers employed, there was not one that outperformed the others; however, k-NN presented statistical inferiority in one of the maneuvers. The best result was obtained through the application of recursive feature elimination on the features extracted from all the maneuvers, resulting in 77.1% test accuracy, 74.1% precision, and 83.3 recall, using SVM. Moreover, the best feature subset, obtained by observing the selection frequency of every single feature during the application of branch and bound, was directly employed on the classification, thus reaching 95.8% accuracy. Although not at the level required by an automatic system, the results show the potential use of pelvic floor pressure distribution profiles data and provide insights into the pelvic floor functioning aspects that contribute to urinary incontinence.
Carafini et al. (2019) Pelvic floor pressure distribution profile in urinary incontinence: a classification study with feature selection. PeerJ 7:e8207 https://doi.org/10.7717/peerj.8207
Systematic analysis and prediction model construction of alternative splicing events in hepatocellular carcinoma: a study on the basis of large-scale spliceseq data from The Cancer Genome Atlas
Growing evidence showed that alternative splicing (AS) event is significantly related to tumor occurrence and progress. This study was performed to make a systematic analysis of AS events and constructed a robust prediction model of hepatocellular carcinoma (HCC). The clinical information and the genes expression profile data of 335 HCC patients were collected from The Cancer Genome Atlas (TCGA). Information of seven types AS events were collected from the TCGA SpliceSeq database. Overall survival (OS) related AS events and splicing factors (SFs) were identified using univariate Cox regression analysis. The corresponding genes of OS-related AS events were sent for gene network analysis and functional enrichment analysis. Optimal OS-related AS events were selected by LASSO regression to construct prediction model using multivariate Cox regression analysis. Prognostic value of the prediction models were assessed by receiver operating characteristic (ROC) curve and KaplanMeir survival analysis. The relationship between the Percent Spliced In (PSI) value of OS-related AS events and SFs expression were analyzed using Spearman correlation analysis. And the regulation network was generated by Cytoscape. A total of 34,163 AS events were identified, which consist of 3,482 OS-related AS events. UBB, UBE2D3, SF3A1 were the hub genes in the gene network of the top 800 OS-related AS events. The area under the curve (AUC) of the final prediction model based on seven types OS-related AS events was 0.878, 0.843, 0.821 in 1, 3, 5 years, respectively. Upon multivariate analysis, risk score (All) served as the risk factor to independently predict OS for HCC patients. SFs HNRNPH3 and HNRNPL were overexpressed in tumor samples and were signifcantly associated with the OS of HCC patients. The regulation network showed prominent correlation between the expression of SFs and OS-related AS events in HCC patients. The final prediction model performs well in predicting the prognosis of HCC patients. And the findings in this study improve our understanding of the association between AS events and HCC.
Yang et al. (2019) Systematic analysis and prediction model construction of alternative splicing events in hepatocellular carcinoma: a study on the basis of large-scale spliceseq data from The Cancer Genome Atlas. PeerJ 7:e8245 https://doi.org/10.7717/peerj.8245
Assessing the effect of fish size on species distribution model performance in southern Chilean rivers
Despite its theoretical relationship, the effect of body size on the performance of species distribution models (SDM) has only been assessed in a few studies, and to date, the evidence shows unclear results. In this context, Chilean fishes provide an ideal case to evaluate this relationship due to their short size (fishes between 5 cm and 40 cm) and conservation status, providing evidence for species at the lower end of the worldwide fish size distribution and representing a relevant management tool for species conservation. We assessed the effect of body size on the performance of SDM in nine Chilean river fishes, considering the number of records, performance metrics, and predictor importance. The study was developed in the Bueno and Valdivia basins of southern Chile. We used a neural network modeling algorithm, training models with a cross-validation scheme. The effect of fish size on selected metrics was assessed using linear models and beta regressions. While no relationship between fish size and the number of presences was found, our results indicate that the model specificity increases with fish size. Additionally, the predictive importance of Riparian Vegetation and Within-Channel Structures variables decreases for larger species. Our results suggest that the relationship between the grain of the dataset and the home range of the species could bias SDM, leading in our case, to overprediction of absences. We also suggest that evolutionary adaptation to low slopes among Chilean fishes increases the relevance of riparian vegetation in the SDMs of smaller species. This study provides evidence on how species size may bias SDM, which could potentially be corrected by adjusting the model grain.
Zamorano et al. (2019) Assessing the effect of fish size on species distribution model performance in southern Chilean rivers. PeerJ 7:e7771 https://doi.org/10.7717/peerj.7771
Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)
In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.
Wang et al. (2019) Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max). PeerJ 7:e7950 https://doi.org/10.7717/peerj.7950
Improving the prediction accuracy of river inflow using two data pre-processing techniques coupled with data-driven model
River inflow prediction plays an important role in water resources management and power-generating systems. But the noises and multi-scale nature of river inflow data adds an extra layer of complexity towards accurate predictive model. To overcome this issue, we proposed a hybrid model, Variational Mode Decomposition (VMD), based on a singular spectrum analysis (SSA) denoising technique. First, SSA his applied to denoise the river inflow data. Second, VMD, a signal processing technique, is employed to decompose the denoised river inflow data into multiple intrinsic mode functions (IMFs), each with a relative frequency scale. Third, Empirical Bayes Threshold (EBT) is applied on non-linear IMF to smooth out. Fourth, predicted models of denoised and decomposed IMFs are established by learning the feature values of the Support Vector Machine (SVM). Finally, the ensemble predicted results are formulated by adding the predicted IMFs. The proposed model is demonstrated using daily river inflow data from four river stations of the Indus River Basin (IRB) system, which is the largest water system in Pakistan. To fully illustrate the superiority of our proposed approach, the SSA-VMD-EBT-SVM hybrid model was compared with SSA-VMD-SVM, VMD-SVM, Empirical Mode Decomposition (EMD) based i.e., EMD-SVM, SSA-EMD-SVM, Ensemble EMD (EEMD) based i.e., EEMD-SVM and SSA-EEMD-SVM. We found that our proposed hybrid SSA-EBT-VMD-SVM model outperformed than others based on following performance measures: the Nash-Sutcliffe Efficiency (NSE), Mean Absolute Percentage Error (MAPE) and Root Mean Square Error (RMSE). Therefore, SSA-VMD-EBT-SVM model can be used for water resources management and power-generating systems using non-linear time series data.
Nazir et al. (2019) Improving the prediction accuracy of river inflow using two data pre-processing techniques coupled with data-driven model. PeerJ 7:e8043 https://doi.org/10.7717/peerj.8043
Dynamic changes in prescription opioids from 2006 to 2017 in Texas
Background The US is experiencing an epidemic of opioid overdoses which may be at least partially due to an over-reliance on opioid analgesics in the treatment of chronic non-cancer pain and subsequent escalation to heroin or illicit fentanyl. As Texas was reported to be among the lowest in the US for opioid use and misuse, further examination of this state is warranted. Materials and Methods This study was conducted to quantify prescription opioid use in Texas. Data was obtained from the publicly available US Drug Enforcement Administration’s Automation of Reports and Consolidated Orders System (ARCOS) which monitors controlled substances transactions from manufacture to commercial distribution. Data for 2006–2017 from Texas for ten prescription opioids including eight primarily used to relieve pain (codeine, fentanyl, hydrocodone, hydromorphone, meperidine, morphine, oxycodone, oxymorphone) and two (buprenorphine and methadone) for the treatment of an Opioid Use Disorder (OUD) were examined. Results The change in morphine mg equivalent (MME) of all opioids (+23.3%) was only slightly greater than the state’s population gains (21.1%). Opioids used to treat an OUD showed pronounced gains (+90.8%) which were four-fold faster than population growth. Analysis of individual agents revealed pronounced elevations in codeine (+387.5%), hydromorphone (+106.7%), and oxycodone (+43.6%) and a reduction in meperidine (−80.3%) in 2017 relative to 2006. Methadone in 2017 accounted for a greater portion (39.5%) of the total MME than hydrocodone, oxycodone, morphine, hydromorphone, oxymorphone, and meperidine, combined. There were differences between urban and rural areas in the changes in hydrocodone and buprenorphine. Conclusions Collectively, these findings indicate that continued vigilance is needed in Texas to appropriately treat pain and an OUD while minimizing the potential for prescription opioid diversion and misuse. Texas may lead the US in a return to pre-opioid epidemic prescription levels.
Ighodaro et al. (2019) Dynamic changes in prescription opioids from 2006 to 2017 in Texas. PeerJ 7:e8108 https://doi.org/10.7717/peerj.8108
A multiple comparative study of putative endosymbionts in three coexisting apple snail species
We here compare morphological and molecular characters of some putative endosymbiotic elements of the digestive gland of three ampullariid species (Pomacea canaliculata, Pomacea scalaris and Asolene platae) which coexist in Lake Regatas (Palermo, Buenos Aires). The putative endosymbionts were reported in these species and were identified as C and K corpuscles. The three species show tubuloacinar glands, each adenomere was constituted mainly by two distinct cell types (columnar and pyramidal). C and K corpuscles together occupied from one-fourth to one-fifth of the tissue area in the three host species, where C corpuscles were round and greenish-brown, were delimited by a distinct wall, stained positively with Alcian Blue and were associated with columnar cells. K corpuscles were oval, dark-brown multilamellar bodies and were associated with pyramidal cells. Under TEM, C corpuscles occurred within vacuoles of columnar cells and contained many electron-dense clumps and irregular membrane stacks and vesicles spread in an electron-lucent matrix. Sometimes a membrane appeared detached from the inner surface of the wall, suggesting the existence of a plasma membrane. In turn, K corpuscles were contained within vacuoles of pyramidal cells and were made of concentric lamellae, which were in turn made of an electron-dense fibrogranular material. No membranes were seen in them. Interspecifically, C corpuscles vary significantly in width and inner contents. K corpuscles were also variable in length and width. However, both C and K corpuscles in the three studied species hybridised with generalised cyanobacterial/chloroplast probes for 16S rRNA. Also, both corpuscle types (isolated from gland homogenates) were sensitive to lysozyme digestion, which indicates that bacterial peptidoglycans are an integral part of their covers. The reported data confirm and extend previous studies on P. canaliculata in which the endosymbiotic nature of C and K corpuscles were first proposed. We further propose that the endosymbiotic corpuscles are related to the Cyanobacteria/chloroplasts clade. Based on the known distribution of these corpuscles in the major clades of Ampullariidae, we hypothesise they may be universally distributed in this family, and that may constitute an interesting model for studying the co-evolution of endosymbionts and their gastropod hosts.
Dellagnola et al. (2019) A multiple comparative study of putative endosymbionts in three coexisting apple snail species. PeerJ 7:e8125 https://doi.org/10.7717/peerj.8125
Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality
Environmental DNA (eDNA) is a powerful tool for monitoring the distribution of aquatic macro-organisms. However, environmental factors, including the water temperature and water quality, can affect the inhibition and/or degradation of eDNA, which complicates accurate estimations of eDNA concentrations and the detection of the presence/absence of species in natural habitats. Further very few eDNA studies have been conducted for reptiles, especially with respect to estimating their biomass and/or abundances. Here we examined the relationship between the visually-observed number of red-eared sliders (Trachemys scripta elegans) and eDNA concentrations across 100 ponds. Additionally, we evaluated the effect of water quality on red-eared slider eDNA concentration in these ponds. We found that there was a significant positive correlation between the observed number of red-eared sliders and the eDNA concentration in the ponds. On comparing various water quality indicators, including dissolved nitrogen, dissolved phosphorous, organic matter, and chlorophyll a (Chl. a), we found that only Chl. a had a negative correlation with the red-eared slider eDNA concentration, while we did not find any inhibition in the quantitative PCR. We conclude that concentrations of eDNA can potentially be used for estimating the abundance of the red-eared slider. Additionally, Chl. a might indirectly influence the degradation of eDNA through the microorganisms bonded to the phytoplankton in the ponds, as microbial activity is thought to decrease eDNA persistence.
Kakuda et al. (2019) Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality. PeerJ 7:e8155 https://doi.org/10.7717/peerj.8155
According, against, and above dietary norms: a key to understanding the relationship between personality style and taste preferences
Background Understanding individual food preferences is critical for creating tailored strategies that promote healthy individual eating behaviors. Individual sensory liking appears to be an essential determinant of dietary intake. Taste preferences influence satisfaction and satiety, and may consequently influence weight status and psychological adjustment. The purpose of this study was to identify the association between taste preferences (sweet, salty, sweet & fatty, salty & fatty) and personality features. Methods The Millon Clinical Multiaxial Inventory-III (MCMI-III) was used for the assessment of personality traits and PrefQuest (PQ) was used for measuring recalled food preferences. A total of 137 participants were included in the study. The relationship between compulsive and antisocial features and taste preferences was assessed by hierarchical multiple linear regression, while controlling for age, gender, BMI, marital status, and educational level. Results The antisocial personality traits were a negative explanatory variable for sweet & fatty taste preference, R2 = .15, t(132) = − 2.40, p = .018, 95% [−.57, −.06] and salty & fatty taste preference, R2 = .16, t(133) = − 2.38, p = .019, 95% [−.07, −.01], while controlling for anthropological factors. In addition, men showed a higher preference than women for sweet & fatty food, such as chocolate or desserts, rsp = .19, p = .021, and for the salty & fatty food, rsp = .30, p < .001. BMI was not found to moderate the relationship between personality and taste preference. No significant association was found between compulsive personality traits and food preference, as assessed by sensory liking. Conclusions The findings can bring a much better understanding of the relationship between the compulsive or antisocial personality and taste preferences. In addition, it may help build psychotherapeutic and nutritional strategies that promote healthy eating behaviors, tailored to a particular personality style.
Petre et al. (2019) According, against, and above dietary norms: a key to understanding the relationship between personality style and taste preferences. PeerJ 7:e8198 https://doi.org/10.7717/peerj.8198
In vitro histomorphometric comparison of dental pulp tissue in different teeth
Background Dental pulp (DP) represents an accessible and valuable source promising of stem cells for clinical application. However, there are some disadvantages associated with the isolation of dental pulp stem cells (DPSCs), which include the size and weight of the pulp tissue needed to yield sufficient cells for culturing in vitro. Therefore, the objective of this study was to compare in vitro histomorphometry of DP from permanent (premolars, third molar), supernumerary and deciduous teeth of patients between 5 and 25 years old with regards to weight, length, width and the cell density in the four regions of the DP in order to obtain quantitative parameters in a tissue that represents a valuable source of stem cells. Methods DPs were obtained from 10 central incisors deciduous, 20 permanent teeth (10 premolars, 10 third molars) and 10 supernumeraries (six mesiodents and four inferior premolar shapes). The pulps were carefully removed, and the entire tissue was weighed. The pulp length and the width were measured with a digital Vernier caliper. The cellular density analysis was performed according to the four regions of the DP (coronal, cervical, medial and apical) in histological slides using photography and the ImageJ® program for quantification. Results The Pearson correlation test revealed that DP weight among different types of teeth is correlated with age in male patients. A significant positive correlation was noted between length and width of the DP with age in both genders. The mean DP weight for supernumerary and third molar teeth was greater than deciduous and premolar teeth. Finally, the histological analysis showed that the coronal and apical portions of DP in supernumerary and premolar teeth have the highest cell density. Conclusions The DP of supernumerary teeth has quantitatively the best morphometric parameters and cell density comparable with the quality of DP obtained from deciduous teeth.
Guerrero-Jiménez et al. (2019) In vitro histomorphometric comparison of dental pulp tissue in different teeth. PeerJ 7:e8212 https://doi.org/10.7717/peerj.8212
VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs
In the past decades a number of software programs have been developed to infer phylogenetic relationships between populations. However, most of these programs typically use alignments of sequences from genes to build phylogeny. Recently, many standalone or web applications have been developed to handle large-scale whole genome data, but they are either computationally intensive, dependent on third party software or required significant time and resource of a web server. In the post-genomic era, researchers are able to obtain bioinformatically processed high-quality publication-ready whole genome data for many individuals in a population from next generation sequencing companies due to the reduction in the cost of sequencing and analysis. Such genotype data is typically presented in the Variant Call Format (VCF) and there is no simple software available that directly uses this data format to construct the phylogeny of populations in a short time. To address this limitation, we have developed a user-friendly software, VCF2PopTree that uses genome-wide SNPs to construct and display phylogenetic trees in seconds to minutes. For example, it reads a VCF file containing 4 million SNPs and draws a tree in less than 30 seconds. VCF2PopTree accepts genotype data from a local machine, constructs a tree using UPGMA and Neighbour-Joining algorithms and displays it on a web-browser. It also produces pairwise-diversity matrix in MEGA and PHYLIP file formats as well as trees in the Newick format which could be directly used by other popular phylogenetic software programs. The software including the source code, a test VCF file and a documentation are available at: https://github.com/sansubs/vcf2pop.
Subramanian et al. (2019) VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs. PeerJ 7:e8213 https://doi.org/10.7717/peerj.8213
Critical multi-stranded approach for determining the ecological values of diatoms in unique aquatic ecosystems of anthropogenic origin
Background The ecological state of surface waters is typically assessed by a multi-aspect approach based on a determination of its chemical and physical parameters, by hydromorphology and the use of indicator organisms such as benthic diatoms. By assigning ecological indicator values, it is possible to create diatom indices which serve as the basic tool in assessing the ecological status of surface waters. These ecological indicator values are set according to classification systems, such as the Van Dam, Mertens & Sinkeldam (1994) system, which classifies species of diatoms according to seven different ecological factors. However, recent studies on the autecology of diatoms have shown the need to verify and establish new ecological indicator values. To this end, aquatic ecosystems are good environments to observe the range of tolerance of benthic diatoms to environmental conditions due to their unique physical and chemical parameters. The aim of the present study was to propose the establishment of new, or altered, ecological indicator values, according to the Van Dam, Mertens & Sinkeldam (1994) classification, of species of diatoms characteristic of three post-mining aquatic ecosystems. Methods In total, 36 species were identified that were characteristic of three waterbodies: a salt aquatic complex (water outflow, a drainage ditch and a pond), mined iron ore reservoirs and a mined lignite reservoir. Their ecological indicator values were specified using OMNIDIA software, and the environmental conditions prevailing in the studied ecosystems were determined. Of the 36 characteristic species, 16 lacking at least one assigned ecological indicator value were analyzed further. The analysis identified three groups of selected characteristic species which showed a correlation, or lack of such, to the tested physical and chemical parameters. Results Based on this multistage study of the autecology of characteristic diatoms, comprising an analysis of environmental conditions, literature analysis and reference ecological indicator values of other species, it is proposed that 32 ecological indicator values be established or adjusted for 16 species, and that Planothidium frequentissimum be excluded from water quality assessments.
Olszyński et al. (2019) Critical multi-stranded approach for determining the ecological values of diatoms in unique aquatic ecosystems of anthropogenic origin. PeerJ 7:e8117 https://doi.org/10.7717/peerj.8117
Design and preliminary application of affinity peptide based on the structure of the porcine circovirus type II Capsid (PCV2 Cap)
Background Affinity peptides, as a core part of affinity chromatography, play an important role in the purification of target molecules. Methods Here we describe the use of molecular docking technology for virtual screening of affinity peptides that specifically recognize the PCV2 Cap protein for the first time. Thirteen candidate peptides with high scores were obtained and then further characterized. Experimentally, the affinity and sensitivity of the peptides studied were identified by ELISA and LSPR, respectively. In order to investigate the purification effect of a selected peptide (L11) for the recombinant PCV2 Cap protein, it was coupled to NHS agarose magnetic beads as an affinity adsorbent (NaMB-L11); and the ligand density of the affinity adsorbent and pH value in the purification of the recombinant PCV2 Cap protein were optimized. Results Our data showed that the peptide L11- DYWWQSWE has the smallest KD = 103 nM with higher specificity for PCV2 Cap protein recognition. The NaMB-L11 affinity adsorbent yielded a purified Cap sample with 98% purity at 90% recovery in a single step. Conclusion Based on the structure, we obtained a high affinity peptide L11 binding to the PCV2 Cap protein by molecular docking technology. It not only provides a theoretical basis for the design of PCV2 Cap affinity peptide, but a new method for the purification of the PCV2 Cap protein.
Hao et al. (2019) Design and preliminary application of affinity peptide based on the structure of the porcine circovirus type II Capsid (PCV2 Cap). PeerJ 7:e8132 https://doi.org/10.7717/peerj.8132
Bleaching and post-bleaching mortality of Acropora corals on a heat-susceptible reef in 2016
In 2016, global temperatures were the highest on record, and mass coral bleaching occurred world-wide. However, around Sesoko Island, Okinawa, southwestern Japan, the heat stress assessed by degree heating week (DHW) based on local temperature measurements was moderate in 2016; in 1998, DHW was three times higher than in 2016 (10.6 vs. 3.3 in September in respective years). On a reef flat of Sesoko Island where the effect of severe coral bleaching on coral assemblage was monitored in 1998, significant coral bleaching occurred in 2016. Bleaching of the heat stress sensitive Acropora corals began in July 2016 on the reef flat as seawater temperature rose. We observed the bleaching and post-bleaching mortality status of individual colonies of Acropora spp. in 2016 in fixed plots on the reef flat. In total, 123 Acropora colonies were followed for six months after seawater temperature became normal by multiple surveys. At the beginning of September 2016, 99.2% of colonies, were either completely (92.7%) or partially (6.5%) bleached. Of those, the dominant species or species groups were A. gemmifera (Ag), A. digitifera (Ad), and tabular Acropora (tA). For all Acropora colonies, the overall whole and partial mortality was 41.5% and 11.4%, respectively. Whole mortality rate differed significantly among species; 72.5%, 17.9%, and 27.8% in Ag, Ad, and tA, respectively. Mortality rates at the end of the surveys were similar in smaller (≤10 cm in diameter) and larger Ag, but the former suffered mortality earlier than the latter. Higher survival of smaller colonies was observed only in tA (100%), which may be associated with large morphological differences between smaller and larger colonies. Some of the dominant Acropora colonies had survived without partial mortality including 15.0% survival of the most vulnerable Ag at the end of the surveys. These results suggest that moderate heat stress may have a potential for selecting heat-tolerant genotypes. A longer period of mortality lasting for six months, was observed in Ag in addition to immediate whole mortality after bleaching, due to the continuous loss of living tissue by partial mortality. This highlights the need for multiple surveys at least during several months to accurately assess the impact of thermal stress event to corals. In contrast to DHW based on local measurements, DHW obtained from satellite data were similar between 1998 and 2016. Although satellite-based measurement of sea surface temperature is very useful to reveal variations in heat stress at a large spatial scale, temperature should be measured on site when variations at smaller spatial scales are of interest.
Sakai et al. (2019) Bleaching and post-bleaching mortality of Acropora corals on a heat-susceptible reef in 2016. PeerJ 7:e8138 https://doi.org/10.7717/peerj.8138
TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
Introduction Recent studies highlight the crucial regulatory roles of transposable elements (TEs) on proximal gene expression in distinct biological contexts such as disease and development. However, computational tools extracting potential TE –proximal gene expression associations from RNA-sequencing data are still missing. Implementation Herein, we developed a novel R package, using a linear regression model, for studying the potential influence of TE species on proximal gene expression from a given RNA-sequencing data set. Our R package, namely TEffectR, makes use of publicly available RepeatMasker TE and Ensembl gene annotations as well as several functions of other R-packages. It calculates total read counts of TEs from sorted and indexed genome aligned BAM files provided by the user, and determines statistically significant relations between TE expression and the transcription of nearby genes under diverse biological conditions. Availability TEffectR is freely available at https://github.com/karakulahg/TEffectR along with a handy tutorial as exemplified by the analysis of RNA-sequencing data including normal and tumour tissue specimens obtained from breast cancer patients.
Karakülah et al. (2019) TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model. PeerJ 7:e8192 https://doi.org/10.7717/peerj.8192
A high latitude Devonian lungfish, from the Famennian of South Africa
New fossil lungfish remains comprising two parasphenoids, tooth plates and scales from the Famennian Witpoort Formation of South Africa are described. From the parasphenoid material, which bears similarity to Oervigia and Sagenodus but is nevertheless unique, a new genus, Isityumzi mlomomde gen. et sp. nov. is erected. Tooth plates and scales from the same locality may be conspecific but are not yet assigned until further material becomes available. The tooth plates closely resemble those of some taxa in the Carboniferous genus Ctenodus. The new taxon is significant as only the second Devonian lungfish described from the African continent, and for hailing from the high-latitude (polar) Waterloo Farm environment situated close to 70° south during the Famennian.
Gess et al. (2019) A high latitude Devonian lungfish, from the Famennian of South Africa. PeerJ 7:e8073 https://doi.org/10.7717/peerj.8073
Rediscovery of Osteocephalus vilarsi (Anura: Hylidae): an overlooked but widespread Amazonian spiny-backed treefrog
Osteocephalus vilarsi (Melin, 1941) is an Amazonian treefrog species known for over 75 years from its holotype only. Due to a lack of published data on its morphological diagnostic characters and their variations, as well as the absence of molecular, acoustic and ecological data supporting its identity, a highly dynamic taxonomic history has led this species to be confused and even synonymised with other Osteocephalus species from distinct species groups. The molecular phylogenetic relationships of O. vilarsi were investigated based on recently collected specimens from eight Northwestern Brazilian localities in the state of Amazonas, leading to its removal from the Osteocephalus taurinus species group and placement in the Osteocephalus planiceps species group. Furthermore, detailed data on morphology and colour variation are provided, as well as advertisement call and tadpole descriptions. Finally, the currently known geographic range of O. vilarsi is considerably extended, first data on the natural history of the species are provided, and the possible ecological preference of O. vilarsi for Amazonian white-sand forests is discussed.
Ferrão et al. (2019) Rediscovery of Osteocephalus vilarsi (Anura: Hylidae): an overlooked but widespread Amazonian spiny-backed treefrog. PeerJ 7:e8160 https://doi.org/10.7717/peerj.8160
Management of recurrent ureteral stricture: a retrospectively comparative study with robot-assisted laparoscopic surgery versus open approach
Background Management of recurrent ureteral stricture is challenging. Consensus on the best surgical choice has not been demonstrated. In this study, we aim to report our experience in treating recurrent ureteral stricture and demonstrate whether robot-assisted procedure for redo ureteral surgery is as effective as open procedure while remaining less invasive. Methods We retrospectively assessed 41 patients (22 robot-assisted surgeries and 19 open surgeries) who underwent consecutive robot-assisted and open procedures for redo ureteral surgery from January 2014 to 2018 in our institution. Perioperative outcomes, including demographics, operative time, estimated blood loss, complications, pain scores, success rate and cost, were compared between two groups. Results There was no significant intergroup difference in terms of age, body mass index, gender composition and American Society of Anesthesiologists scores. A total of 31 patients underwent redo pyeloplasty and ten underwent redo uretero-ureterostomy. Compared with open group, robot-assisted group showed shorter operative time (124.55 min vs. 185.11 min, p < 0.0001), less estimated blood loss (100.00 mL vs. 182.60 mL, p = 0.008) and higher cost (61161.77¥ vs. 39470.79¥, p < 0.0001). Complication rate and pain scores were similar between two groups. Median follow-up periods were 30 and 48 months for robot-assisted and open group respectively. Success rate in the robot-assisted (85.71%) and the open group (82.35%) was not significantly different. Conclusions Robot-assisted surgery for recurrent stricture after previous ureteral reconstruction is as effective as open procedure and is associated with shorter operative time and less estimated blood loss.
Wang et al. (2019) Management of recurrent ureteral stricture: a retrospectively comparative study with robot-assisted laparoscopic surgery versus open approach. PeerJ 7:e8166 https://doi.org/10.7717/peerj.8166
The response of fine root morphological and physiological traits to added nitrogen in Schrenk’s spruce (Picea schrenkiana) of the Tianshan mountains, China
Fine roots are essential for water and nutrient uptake in plants, but little is known about the variation in fine root traits and the underlying mechanisms that drive it. Understanding the responses of fine root function traits to changing environmental conditions and the role of fine root traits as drivers of forest ecosystem processes are critical for informing physiological and ecological theory as well as ecosystem management. We measured morphological and physiological traits of fine roots from six soil layers and three diameter classes in Schrenk’s spruce (Picea shrenkiana) forests of the Tianshan mountains, China. We found significant effects of nitrogen addition on these morphological and physiological traits, which varied by soil layer and root diameter. Specifically, specific root length (SRL) was higher in medium N addition group (N2) than in control group (N0). Specific root area (SRA) was higher in the control group (N0) than fertilized groups (N1, N2 and N3). Root tissue density (RTD) was higher in low N addition group (N1) than in the other group. Root dry matter content had no significant difference among four treatment groups. SRL, SRA, and RTD of fine roots in different diameter classes were all significantly different between high N addition (N3) and the control (N0) groups. The physiological characteristics of fine roots showed that soluble sugar (SS), fine root vitality (FRV), and tissue water content (TWC) in different soil layers were higher in the control group than in the fertilized groups. While soluble protein (SP), malondialdehyde (MDA) and free proline (FP) were lower in the control group (N0) than in the fertilized groups. In addition, SS, FRV, SP, TWC, FP, and MDA in all N addition treatments groups were significantly different from the control group. Fine root morphological traits were closely related to physiological traits, and added nitrogen inputs change these correlations. Our study confirms that nitrogen addition has specific effects on the morphological and physiological traits of fine roots of Schrenk’s spruce, and the effects of N addition vary according to the amount added.
Gong et al. (2019) The response of fine root morphological and physiological traits to added nitrogen in Schrenk’s spruce (Picea schrenkiana) of the Tianshan mountains, China. PeerJ 7:e8194 https://doi.org/10.7717/peerj.8194
Migraine aura, a predictor of near-death experiences in a crowdsourced study
Background Near-death experiences (NDE) occur with imminent death and in situations of stress and danger but are poorly understood. Evidence suggests that NDE are associated with rapid eye movement (REM) sleep intrusion, a feature of narcolepsy. Previous studies further found REM abnormalities and an increased frequency of dream-enacting behavior in migraine patients, as well as an association between migraine with aura and narcolepsy. We therefore investigated if NDE are more common in people with migraine aura. Methods We recruited 1,037 laypeople from 35 countries and five continents, without any filters except for English language and age ≥18 years, via a crowdsourcing platform. Reports were validated using the Greyson NDE Scale. Results Eighty-one of 1,037 participants had NDE (7.8%; CI [6.3–9.7%]). There were no significant associations between NDE and age (p > 0.6, t-test independent samples) or gender (p > 0.9, Chi-square test). The only significant association was between NDE and migraine aura: 48 (6.1%) of 783 subjects without migraine aura and 33 (13.0%) of 254 subjects with migraine aura had NDE (p < 0.001, odds ratio (OR) = 2.29). In multiple logistic regression analysis, migraine aura remained significant after adjustment for age (p < 0.001, OR = 2.31), gender (p < 0.001, OR = 2.33), or both (p < 0.001, OR = 2.33). Conclusions In our sample, migraine aura was a predictor of NDE. This indirectly supports the association between NDE and REM intrusion and might have implications for the understanding of NDE, because a variant of spreading depolarization (SD), terminal SD, occurs in humans at the end of life, while a short-lasting variant of SD is considered the pathophysiological correlate of migraine aura.
Kondziella et al. (2019) Migraine aura, a predictor of near-death experiences in a crowdsourced study. PeerJ 7:e8202 https://doi.org/10.7717/peerj.8202
Amino acids and acylcarnitine production by Chlorella vulgaris and Chlorella sorokiniana microalgae from wastewater culture
Background Microalgae are a widely distributed group of prokaryotic and eukaryotic photosynthetic microorganisms that use a number of substances present in wastewater to produce a variety of biotechnological and nutritional biomolecules. Methods Production ofamino acids and acylcarnitine by Chlorella vulgaris and Chlorella sorokiniana was determined after 13 d of culture in wastewater, under various culture conditions. Wastewater was collected from “La Encantada” stream, located in Saltillo, Coahuila, Mexico. Microalgae was cultured at 23°C and natural day light, including the use of the following conditions: (1) extra light (12:12 light:dark cycles, 1,380 lumens), (2) agitation (130 rpm), and (3) both conditions, until exponential phase. Supernatant products were then analyzed by liquid chromatograph coupled to mass spectrometry. In addition, metabolomic profiles related to growing conditions were evaluated. Results Amino acids and acylcarnitine production by C. sorokiniana and C. vulgaris resulted in higher Ala and Leu concentrations by C. vulgaris compared with control, where control produced Gly and Pro in higher amounts compared with C. sorokiniana. Tyr, Phe, Val, and Cit were detected in lower amounts under light and shaking culture conditions. High concentrations of C0 acylcarnitines were produced by both microalgae compared with control, where C. sorokiniana production was independent of culture conditions, whereas C. vulgaris one was stimulated by shaking. C4 production was higher by C. sorokiniana compared with control. Furthermore, C4, C6DC, C14:1, C14:2, and C18:1OH production by microalga was low in all culture conditions. Conclusion Microalgae produced essential amino acids and nutritionally important carnitines from wastewater. In addition, C. sorokiniana biomass has higher potential as animal nutrient supplement, as compared with that of C. vulgaris.
Ballesteros-Torres et al. (2019) Amino acids and acylcarnitine production by Chlorella vulgaris and Chlorella sorokiniana microalgae from wastewater culture. PeerJ 7:e7977 https://doi.org/10.7717/peerj.7977
The effect of diet on the structure of gut bacterial community of sympatric pair of whitefishes (Coregonus lavaretus): one story more
In the Coregonus lavaretus complex may be found lacustrine sympatric pairs, which serves as an intriguing model for studying different aspects of fish evolutionary biology. One such sympatric whitefish pair inhabits Teletskoye Lake (West Siberia, Russia) and includes a “large” form (Coregonus lavaretus pidschian (Gmelin, 1789)) and a “small” form (C. l. pravdinellus (Dulkeit, 1949)). C. l. pravdinellus has a narrow trophic specialization and feeds on zooplankton, whereas the diet of C. l. pidschian is based on benthic prey. In the present study we aimed to address the question of how the gut microbial community reflects the divergence in diet of a sympatric pair of whitefish. Studied samples included the mucosa and content were collected for cardiac and pyloric stomach, anterior, middle, and posterior intestine, but only mucosa was collected for the pyloric caeca. In addition, water, sediment, macrophyte (environmental microbiota) and invertebrate (microbiota of prey) samples were collected in the same location. The V3–V4 region of the 16S rRNA genes was chosen for microbiome analysis and the software PICRUSt used to estimate the difference functional roles of the microbiota. The number of OTUs and Chao1 index in mucosa and content of cardiac and pyloric stomach were significantly different between whitefish. Significant differences were observed between whitefish for content from different parts of the intestine in terms of OTU number and Chao1 indices, whereas for mucosa from the same parts of intestine these differences were absent. No significant differences were found for diversity estimates of mucosa and content of different parts of the gut (there were a few exceptions) between whitefish. The form of whitefish and the segment of the digestive system were factors with a significant determinative effect on the structure of the microbiota from gut mucosa and content. The most dominant phyla in mucosa and content of cardiac and pyloric stomach was Proteobacteria (57.0–84.0%) for both whitefish. Throughout the intestine of C. l. pidschian the dominant phyla in mucosa were Proteobacteria (38.8%) and Firmicutes (15.6%), whereas for C. l. pravdinellus–Tenericutes (49.6%) and Proteobacteria (28.1%). For both forms, the phylum Spirochaetes was found in a significant amount (20.0–25.0%) in the mucosa of the posterior intestine. While for the content obtained from anterior, middle and posterior intestines, the dominant bacterial phyla were the same as those described for mucosa from the same parts of the intestine for both whitefish. The bacterial community of the prey and environment was significantly different from bacterial communities found for all parts of the gut mucosa for both whitefish, with the exception of the mucosa of the cardiac stomach. According to PICRUSt the highest level of differences between whitefish at the L3 level were found for the intestinal mucosa (75.3%), whereas the lowest one was registered for stomach content (38.8%).
Solovyev et al. (2019) The effect of diet on the structure of gut bacterial community of sympatric pair of whitefishes (Coregonus lavaretus): one story more. PeerJ 7:e8005 https://doi.org/10.7717/peerj.8005
Phospholipase A2 from krait Bungarus fasciatus venom induces human cancer cell death in vitro
Background Snake venoms are the complex mixtures of different compounds manifesting a wide array of biological activities. The venoms of kraits (genus Bungarus, family Elapidae) induce mainly neurological symptoms; however, these venoms show a cytotoxicity against cancer cells as well. This study was conducted to identify in Bungarus fasciatus venom an active compound(s) exerting cytotoxic effects toward MCF7 human breast cancer cells and A549 human lung cancer cells. Methods The crude venom of B. fasciatus was separated by gel-filtration on Superdex HR 75 column and reversed phase HPLC on C18 column. The fractions obtained were screened for cytotoxic effect against MCF7, A549, and HK2 cell lines using colorimetric assay with the tetrazolium dye MTT- 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide. The primary structure of active protein was established by ultra high resolution LC-MS/MS. The molecular mechanism of the isolated protein action on MCF7 cells was elucidated by flow cytometry. Results MTT cell viability assays of cancer cells incubated with fractions isolated from B. fasciatus venom revealed a protein with molecular mass of about 13 kDa possessing significant cytotoxicity. This protein manifested the dose and time dependent cytotoxicity for MCF7 and A549 cell lines while showed no toxic effect on human normal kidney HK2 cells. In MCF7, flow cytometry analysis revealed a decrease in the proportion of Ki-67 positive cells. As Ki-67 protein is a cellular marker for proliferation, its decline indicates the reduction in the proliferation of MCF7 cells treated with the protein. Flow cytometry analysis of MCF7 cells stained with propidium iodide and Annexin V conjugated with allophycocyanin showed that a probable mechanism of cell death is apoptosis. Mass spectrometric studies showed that the cytotoxic protein was phospholipase A2. The amino acid sequence of this enzyme earlier was deduced from cloned cDNA, and in this work it was isolated from the venom as a protein for the first time. It is also the first krait phospholipase A2 manifesting the cytotoxicity for cancer cells.
Tran et al. (2019) Phospholipase A2 from krait Bungarus fasciatus venom induces human cancer cell death in vitro. PeerJ 7:e8055 https://doi.org/10.7717/peerj.8055
Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic sponge Isodictya sp.
Although the cellular and molecular responses to exposure to relatively high temperatures (acute thermal stress or heat shock) have been studied previously, only sparse empirical evidence of how it affects cold-water species is available. As climate change becomes more pronounced in areas such as the Western Antarctic Peninsula, both long-term and occasional acute temperature rises will impact species found there, and it has become crucial to understand the capacity of these species to respond to such thermal stress. Here, we use the Antarctic sponge Isodictya sp. to investigate how sessile organisms (particularly Porifera) can adjust to acute short-term heat stress, by exposing this species to 3 and 5 °C for 4 h, corresponding to predicted temperatures under high-end 2080 IPCC-SRES scenarios. Assembling a de novo reference transcriptome (90,188 contigs, >93.7% metazoan BUSCO genes) we have begun to discern the molecular response employed by Isodictya to adjust to heat exposure. Our initial analyses suggest that TGF-β, ubiquitin and hedgehog cascades are involved, alongside other genes. However, the degree and type of response changed little from 3 to 5 °C in the time frame examined, suggesting that even moderate rises in temperature could cause stress at the limits of this organism’s capacity. Given the importance of sponges to Antarctic ecosystems, our findings are vital for discerning the consequences of short-term increases in Antarctic ocean temperature on these and other species.
González-Aravena et al. (2019) Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic sponge Isodictya sp.. PeerJ 7:e8088 https://doi.org/10.7717/peerj.8088
Effectiveness of water-saving technologies during early stages of restoration of endemic Opuntia cacti in the Galápagos Islands, Ecuador
Restoration of keystone species is a primary strategy used to combat biodiversity loss and recover ecological services. This is particularly true for oceanic islands, which despite their small land mass, host a large fraction of the planet’s imperiled species. The endemic Opuntia spp. cacti are one example and a major focus for restoration in the Galápagos archipelago, Ecuador. These cacti are keystone species that support much of the unique vertebrate animal community in arid zones, yet human activities have substantially reduced Opuntia populations. Extreme aridity poses an obstacle for quickly restoring Opuntia populations though water-saving technologies may provide a solution. The aim of this study was to evaluate current restoration efforts and the utility of two water-saving technologies as tools for the early stages of restoring Opuntia populations in the Galápagos archipelago. We planted 1,425 seedlings between 2013 and 2018, of which 66% had survived by the end of 2018. Compared with no-technology controls, seedlings planted with Groasis Waterboxx® water-saving technology (polypropylene trays with water reservoir and protective refuge for germinants) had a greater rate of survival in their first two-years of growth on one island (Plaza Sur) and greater growth rate on four islands whereas the “Cocoon” water-saving technology (similar technology but made of biodegradable fiber) did not affect growth and actually reduced seedling survival. Survival and growth rate were also influenced by vegetation zone, elevation, and precipitation in ways largely contingent on island. Overall, our findings suggest that water-saving technologies are not always universally applicable but can substantially increase the survival and growth rate of seedlings in certain conditions, providing in some circumstances a useful tool for improving restoration outcomes for rare plants of arid ecosystems.
Tapia et al. (2019) Effectiveness of water-saving technologies during early stages of restoration of endemic Opuntia cacti in the Galápagos Islands, Ecuador. PeerJ 7:e8156 https://doi.org/10.7717/peerj.8156
Different distant metastasis patterns based on tumor size could be found in extensive-stage small cell lung cancer patients: a large, population-based SEER study
Background Small-cell lung cancer (SCLC) is a malignant cancer with the ability to metastasize quickly. The relationship between tumor size and the distant metastasis patterns of Extensive-Stage Small Cell Lung Cancer (ES-SCLC) has not been reported. Objectives The aim of this study was to determine the different distant metastasis patterns as they related to tumor size in ES-SCLC. Patients and Methods We used Surveillance, Epidemiology, and End Results (SEER) population-based data collected from 2010 through 2013 to identify 11058 ES-SCLC patients with definite evidence of distant metastases. Multivariate logistic regression analysis was used to demonstrate the association between tumor size and distant metastasis patterns including bone, liver, brain, and lung metastases. Age, race, sex, and N stage were also selected in the logistic regression model. Results Subtle differences in metastasis patterns were found among patients based on different tumor sizes. Patients with tumors 3–7 cm have a higher risk of bone metastasis compared with those that have tumors ≤3 cm (OR 1.165, 95% CI [1.055–1.287], P = 0.003) and patients with tumors ≥7 cm have a higher risk of lung metastasis (OR 1.183, 95% CI [1.039–1.347], P = 0.011). In addition, patients with tumors ≥7 cm had a lower risk of brain metastasis and liver metastasis than patients with tumors ≤3 cm (OR 0.799, 95% CI [0.709–0.901], P < 0.001; OR 0.747, 95% CI [0.672–0.830], P < 0.001). Interestingly, there was no correlation between a larger tumor and a higher risk of metastasis. However, the tumor metastasis pattern did have some correlation with age, gender, race and N-status. Conclusion The pattern of distant metastasis of ES-SCLC is related to the tumor size and the tumor size is indicative of the metastatic site. Larger tumor sizes did not correlate with a higher risk of distant metastasis, but the size is related to the pattern of distant metastasis. The study of different distant metastasis patterns based on tumor size and other clinical features (e.g., age, race, sex, and N stage) in ES-SCLC is clinically valuable.
Li et al. (2019) Different distant metastasis patterns based on tumor size could be found in extensive-stage small cell lung cancer patients: a large, population-based SEER study. PeerJ 7:e8163 https://doi.org/10.7717/peerj.8163
Switching between standard coral reef benthic monitoring protocols is complicated: proof of concept
Monitoring the state of coral reefs is necessary to identify drivers of change and assess effectiveness of management actions. There are several widely-used survey methods, each of which is likely to exhibit different biases that should be quantified if the purpose is to combine datasets obtained via different survey methods. The latter is a particularly important consideration when switching methodologies in long-term monitoring programs and is highly relevant to the Caribbean today. This is because of the continuing need for regionally comparable coral reef monitoring datasets and the fact that the Global Coral Reef Monitoring Network (GCRMN)-Caribbean node is now recommending a photoquadrat (PQ) method over the chain intercept transect method widely adopted by the members of the first truly regional monitoring network, Caribbean Coastal Marine Productivity Program (CARICOMP), in the early-1990s. Barbados, a member of the CARICOMP network, has been using a variation of the chain intercept method in its long-term coral reef monitoring program for more than two decades. Now a member of GCRMN-Caribbean, Barbados is considering switching to the PQ method in conformity with other regional members. Since we expect differences between methods, this study seeks to quantify the nature of those differences to inform Barbados and others considering switching methods. In 2017, both methods were concurrently implemented at 21 permanent monitoring plots across three major reef types in Barbados. Differences in % cover estimates for the six major benthic components, that is, hard corals, sponges, gorgonians, macroalgae, turf algae and crustose coralline algae, were examined within and among reef types. Overall, we found a complex pattern of differences between methods that depended on the benthic component, its relative abundance, and the reef type. We conclude that most benthic components would require a different conversion procedure depending on the reef type, and we provide an example of these procedures for Barbados. The factors that likely contribute to the complex pattern of between-method differences are discussed. Overall, our findings highlight that switching methods will be complicated, but not impossible. Finally, our study fills an important gap by underscoring a promising analytical framework to guide the comparison of ecological survey methods on coral reefs.
Vallès et al. (2019) Switching between standard coral reef benthic monitoring protocols is complicated: proof of concept. PeerJ 7:e8167 https://doi.org/10.7717/peerj.8167
Sentence comprehension in patients with dementia of the Alzheimer’s type
Sentence comprehension is diminished in patients with dementia of the Alzheimer’s type (DAT). However, the underlying reason for such deficits is still not entirely clear. The Syntactic Deficit Hypothesis attributes sentence comprehension deficits in DAT patients to the impairment in syntactic ability, whereas the Processing Resource Deficit Hypothesis proposes that sentence comprehension deficits are the result of working memory deficiency. This study investigated the deficits in sentence comprehension in Chinese-speaking DAT patients with different degrees of severity using sentence-picture matching tasks. The study revealed a significant effect of syntactic complexity in patients and healthy controls, but the effect was stronger in patients than in healthy controls. When working memory demand was minimized, the effect of syntactic complexity was only significant in patients with moderate DAT, but not in healthy controls or those with mild DAT. The findings suggest that in patients with mild DAT, working memory decline was the major source of sentence comprehension difficulty and in patients with moderate DAT, working memory decline and syntactic impairment jointly contributed to the impairments in sentence comprehension. The source of sentence comprehension deficits varied with degree of dementia severity.
Liu et al. (2019) Sentence comprehension in patients with dementia of the Alzheimer’s type. PeerJ 7:e8181 https://doi.org/10.7717/peerj.8181
Overexpression of VEGF-C and MMP-9 predicts poor prognosis in Kazakh patients with esophageal squamous cell carcinoma
Vascular endothelial growth factor (VEGF) and Matrix metalloproteinases (MMPs) are believed to participate in infiltration of tumors. High mortality of esophageal squamous cell carcinoma (ESCC) related to its primary infiltration; however, it is not clear whether the expression of VEGF and MMPs is involved in this process. Screening of The Cancer Genome Atlas (TCGA) database showed that among the VEGF family and MMP9, VEGF-A, VEGF-C, and MMP-9 mRNA were overexpression in ESCC. This result was verified using the Oncomine database and in Kazakh patients with ESCC. Overexpression of VEGF-C and MMP-9 and positive association with advanced esophageal cancer and invading ESCC cells (Gene Expression Omnibus (GEO): GSE21293). Immunohistochemical staining revealed that VEGF-C and MMP-9 were overexpressed in Kazakh ESCCs. VEGF-C expression was related to invasive depth, tumor-node-metastasis (TNM) staging, lymphatic, and lymph node metastasis of ESCC. The linear association between them was further confirmed in TCGA database and the specimens from Kazakh patients with ESCC. Patients with both proteins expression had tumors with greater aggressiveness, suffered from poor prognosis compared with patients who did not express either protein or expressed protein alone. Both proteins expression predicted high invasiveness of ESCC, which is related to worse prognosis of Kazakh ESCCs.
Li et al. (2019) Overexpression of VEGF-C and MMP-9 predicts poor prognosis in Kazakh patients with esophageal squamous cell carcinoma. PeerJ 7:e8182 https://doi.org/10.7717/peerj.8182
Comparative genomic analysis of the PAL genes in five Rosaceae species and functional identification of Chinese white pear
Phenylalanine ammonia lyase (PAL) plays an important role in the biosynthesis of secondary metabolites regulating plant growth response. To date, the evolutionary history of the PAL family in Rosaceae plants remains unclear. In this study, we identified 16 PAL homologous genes in five Rosaceae plants (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Prunus persica, and Malus × domestica). We classified these PALs into three categories based on phylogenetic analysis, and all PALs were distributed on 13 chromosomes. We tracked gene duplication events and performed sliding window analysis. These results revealed the evolution of PALs in five Rosaceae plants. We predicted the promoter of the PbPALs by PLANT CARE online software, and found that the promoter region of both PbPAL1 and PbPAL3 have at least one AC element. The results of qRT-PCR analysis found that PbPAL1 and PbPAL2 were highly expressed in the stems and roots, while expression level of PbPAL3 was relatively low in different tissues. The expression of PbPAL1 and PbPAL2 increased firstly and then decreased at different developmental periods of pear fruit. Among them, the expression of PbPAL1 reached the highest level 55 days after flowering. Three PbPALs were induced by abiotic stress to varying degrees. We transfected PbPAL1 and PbPAL2 into Arabidopsis thaliana, which resulted in an increase in lignin content and thickening of the cell walls of intervascular fibres and xylem cells. In summary, this research laid a foundation for better understanding the molecular evolution of PALs in five Rosaceae plants. Furthermore, the present study revealed the role of PbPALs in lignin synthesis, and provided basic data for regulating lignin synthesis and stone cells development in pear plants.
Li et al. (2019) Comparative genomic analysis of the PAL genes in five Rosaceae species and functional identification of Chinese white pear. PeerJ 7:e8064 https://doi.org/10.7717/peerj.8064
Impact of habitat loss on the diversity and structure of ecological networks between oxyurid nematodes and spur-thighed tortoises (Testudo graeca L.)
Habitat loss and fragmentation are recognized as affecting the nature of biotic interactions, although we still know little about such changes for reptilian herbivores and their hindgut nematodes, in which endosymbiont interactions could range from mutualistic to commensal and parasitic. We investigated the potential cost and benefit of endosymbiont interactions between the spur-thighed tortoise (Testudo graeca L.) and adult oxyurid nematodes (Pharyngodonidae order Oxyurida) in scrublands of southern Spain. For this, we assessed the association between richness and abundance of oxyurid species with tortoises’ growth rates and body traits (weight and carapace length) across levels of habitat loss (low, intermediate and high). Furthermore, by using an intrapopulation ecological network approach, we evaluated the structure and diversity of tortoise–oxyurid interactions by focusing on oxyurid species infesting individual tortoises with different body traits and growth rates across habitats. Overall, tortoise body traits were not related to oxyurid infestation across habitats. Oxyurid richness and abundance however, showed contrasting relationships with growth rates across levels of habitat loss. At low habitat loss, oxyurid infestation was positively associated with growth rates (suggesting a mutualistic oxyurid–tortoise relationship), but the association became negative at high habitat loss (suggesting a parasitic relationship). Furthermore, no relationship was observed when habitat loss was intermediate (suggesting a commensal relationship). The network analysis showed that the oxyurid community was not randomly assembled but significantly nested, revealing a structured pattern for all levels of habitat loss. The diversity of interactions was lowest at low habitat loss. The intermediate level, however, showed the greatest specialization, which indicates that individuals were infested by fewer oxyurids in this landscape, whereas at high habitat loss individuals were the most generalized hosts. Related to the latter, connectance was greatest at high habitat loss, reflecting a more uniform spread of interactions among oxyurid species. At an individual level, heavier and larger tortoises tended to show a greater number of oxyurid species interactions. We conclude that there is an association between habitat loss and the tortoise–oxyurid interaction. Although we cannot infer causality in their association, we hypothesize that such oxyurids could have negative, neutral and positive consequences for tortoise growth rates. Ecological network analysis can help in the understanding of the nature of such changes in tortoise–oxyurid interactions by showing how generalized or specialized such interactions are under different environmental conditions and how vulnerable endosymbiont interactions might be to further habitat loss.
Benítez-Malvido et al. (2019) Impact of habitat loss on the diversity and structure of ecological networks between oxyurid nematodes and spur-thighed tortoises (Testudo graeca L.). PeerJ 7:e8076 https://doi.org/10.7717/peerj.8076
Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma
Background Hepatocellular carcinoma (HCC) is the most common primary liver cancer in the world, with a high degree of malignancy and recurrence. The influence of the ceRNA network in tumor on the biological function of liver cancer is very important, It has been reported that many lncRNA play a key role in liver cancer development. In our study, integrated data analysis revealed potential eight novel lncRNA biomarkers in hepatocellular carcinoma. Methods Transcriptome data and clinical data were downloaded from the The Cancer Genome Atlas (TCGA) data portal. Weighted gene co-expression network analysis was performed to identify the expression pattern of genes in liver cancer. Then, the ceRNA network was constructed using transcriptome data. Results The integrated analysis of miRNA and RNAseq in the database show eight novel lncRNAs that may be involved in important biological pathways, including TNM and disease development in liver cancer. We performed function enrichment analysis of mRNAs affected by these lncRNAs. Conclusions By identifying the ceRNA network and the lncRNAs that affect liver cancer, we showed that eight novel lncRNAs play an important role in the development and progress of liver cancer.
Zou et al. (2019) Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma. PeerJ 7:e8101 https://doi.org/10.7717/peerj.8101
The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity
Background Multiple factors can influence stool sample integrity upon sample collection. Preservation of faecal samples for microbiome studies is therefore an important step, particularly in tropical regions where resources are limited and high temperatures may significantly influence microbiota profiles. Freezing is the accepted standard to preserve faecal samples however, cold chain methods are often unfeasible in fieldwork scenarios particularly in low and middle-income countries and alternatives are required. This study therefore aimed to address the impact of different preservative methods, time-to-freezing at ambient tropical temperatures, and stool heterogeneity on stool microbiome diversity and composition under real-life physical environments found in resource-limited fieldwork conditions. Methods Inner and outer stool samples collected from one specimen obtained from three children were stored using different storage preservation methods (raw, ethanol and RNAlater) in a Ugandan field setting. Mixed stool was also stored using these techniques and frozen at different time-to-freezing intervals post-collection from 0–32 h. Metataxonomic profiling was used to profile samples, targeting the V1–V2 regions of 16S rRNA with samples run on a MiSeq platform. Reads were trimmed, combined and aligned to the Greengenes database. Microbial diversity and composition data were generated and analysed using Quantitative Insights Into Microbial Ecology and R software. Results Child donor was the greatest predictor of microbiome variation between the stool samples, with all samples remaining identifiable to their child of origin despite the stool being stored under a variety of conditions. However, significant differences were observed in composition and diversity between preservation techniques, but intra-preservation technique variation was minimal for all preservation methods, and across the time-to-freezing range (0–32 h) used. Stool heterogeneity yielded no apparent microbiome differences. Conclusions Stool collected in a fieldwork setting for comparative microbiome analyses should ideally be stored as consistently as possible using the same preservation method throughout.
Carruthers et al. (2019) The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity. PeerJ 7:e8133 https://doi.org/10.7717/peerj.8133
Propofol inhibits stromatoxin-1-sensitive voltage-dependent K+ channels in pancreatic β-cells and enhances insulin secretion
Background Proper glycemic control is an important goal of critical care medicine, including perioperative patient care that can influence patients’ prognosis. Insulin secretion from pancreatic β-cells is generally assumed to play a critical role in glycemic control in response to an elevated blood glucose concentration. Many animal and human studies have demonstrated that perioperative drugs, including volatile anesthetics, have an impact on glucose-stimulated insulin secretion (GSIS). However, the effects of the intravenous anesthetic propofol on glucose metabolism and insulin sensitivity are largely unknown at present. Methods The effect of propofol on insulin secretion under low glucose or high glucose was examined in mouse MIN6 cells, rat INS-1 cells, and mouse pancreatic β-cells/islets. Cellular oxygen or energy metabolism was measured by Extracellular Flux Analyzer. Expression of glucose transporter 2 (GLUT2), potassium channels, and insulin mRNA was assessed by qRT-PCR. Protein expression of voltage-dependent potassium channels (Kv2) was also assessed by immunoblot. Propofol’s effects on potassium channels including stromatoxin-1-sensitive Kv channels and cellular oxygen and energy metabolisms were also examined. Results We showed that propofol, at clinically relevant doses, facilitates insulin secretion under low glucose conditions and GSIS in MIN6, INS-1 cells, and pancreatic β-cells/islets. Propofol did not affect intracellular ATP or ADP concentrations and cellular oxygen or energy metabolism. The mRNA expression of GLUT2 and channels including the voltage-dependent calcium channels Cav1.2, Kir6.2, and SUR1 subunit of KATP, and Kv2 were not affected by glucose or propofol. Finally, we demonstrated that propofol specifically blocks Kv currents in β-cells, resulting in insulin secretion in the presence of glucose. Conclusions Our data support the hypothesis that glucose induces membrane depolarization at the distal site, leading to KATP channel closure, and that the closure of Kv channels by propofol depolarization in β-cells enhances Ca2+ entry, leading to insulin secretion. Because its activity is dependent on GSIS, propofol and its derivatives are potential compounds that enhance and initiate β-cell electrical activity.
Kusunoki et al. (2019) Propofol inhibits stromatoxin-1-sensitive voltage-dependent K+ channels in pancreatic β-cells and enhances insulin secretion. PeerJ 7:e8157 https://doi.org/10.7717/peerj.8157
Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo
Background Water buffalo (Bubalus bubalis) are divided into river buffalo and swamp buffalo subspecies and are essential livestock for agriculture and the local economy. Studies on buffalo reproduction have primarily focused on optimal fertility and embryonic mortality. There is currently limited knowledge on buffalo embryonic development, especially during the preimplantation period. Assembly of the river buffalo genome offers a reference for omics studies and facilitates transcriptomic analysis of preimplantation embryo development (PED). Methods We revealed transcriptomic profile of four stages (2-cell, 8-cell, Morula and Blastocyst) of PED via RNA-seq (Illumina HiSeq4000). Each stage comprised three biological replicates. The data were analyzed according to the basic RNA-seq analysis process. Ingenuity analysis of cell lineage control, especially transcription factor (TF) regulatory networks, was also performed. Results A total of 21,519 expressed genes and 67,298 transcripts were predicted from approximately 81.94 Gb of raw data. Analysis of transcriptome-wide expression, gene coexpression networks, and differentially expressed genes (DEGs) allowed for the characterization of gene-specific expression levels and relationships for each stage. The expression patterns of TFs, such as POU5F1, TEAD4, CDX4 and GATAs, were elucidated across diverse time series; most TF expression levels were increased during the blastocyst stage, during which time cell differentiation is initiated. All of these TFs were involved in the composition of the regulatory networks that precisely specify cell fate. These findings offer a deeper understanding of PED at the transcriptional level in the river buffalo.
Pang et al. (2019) Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo. PeerJ 7:e8185 https://doi.org/10.7717/peerj.8185