A set of novel SNP loci for differentiating continental populations and three Chinese populations
In recent years, forensic geneticists have begun to develop some ancestry informative marker (AIM) panels for ancestry analysis of regional populations. In this study, we chose 48 single nucleotide polymorphisms (SNPs) from SPSmart database to infer ancestry origins of continental populations and Chinese subpopulations. Based on the genetic data of four continental populations (African, American, East Asian and European) from the CEPH-HGDP database, the power of these SNPs for differentiating continental populations was assessed. Population genetic structure revealed that distinct ancestry components among these continental populations could be discerned by these SNPs. Another novel population set from 1000 Genomes Phase 3 was treated as testing populations to further validate the efficiency of the selected SNPs. Twenty-two populations from CEPH-HGDP database were classified into three known populations (African, East Asian, and European) based on their biogeographical regions. Principal component analysis and Bayes analysis of testing populations and three known populations indicated these testing populations could be correctly assigned to their corresponding biogeographical origins. For three Chinese populations (Han, Mongolian, and Uygur), multinomial logistic regression analyses indicated that these 48 SNPs could be used to estimate ancestry origins of these populations. Therefore, these SNPs possessed the promising potency in ancestry analysis among continental populations and some Chinese populations, and they could be used in population genetics and forensic research.
Jin et al. (2019) A set of novel SNP loci for differentiating continental populations and three Chinese populations. PeerJ 7:e6508 https://doi.org/10.7717/peerj.6508
Understanding the experience of psychopathology after intimate partner violence: the role of personality
Objective(s) To fully understand the dynamics of Intimate Partner Violence (IPV) it is necessary to understand the role of personality. The current understanding of which personality characteristics are associated with IPV victimization is, however, far from comprehensive. Given this gap in the literature, our objective was to examine the associations between the dimensions of the psychobiological model of personality and psychopathological symptoms in women who had experienced IPV. Methods Using a case-control design, a group of women who had experienced IPV and who were living in shelters (n = 50) were compared to a group of control women who had not experienced IPV (n = 50). All women completed the Temperament and Character Inventory–Revised and the Brief Symptom Inventory. Results Victims of IPV showed significantly higher levels of Harm Avoidance and Self-Transcendence, and lower levels of Reward Dependence and Self-Directedness, than the non-IPV control group. Victims of IPV also reported elevated levels of psychopathological symptoms. Personality dimensions showed a broadly consistent pattern of associations across different psychopathological symptoms. A regression analysis indicated that Novelty Seeking was negatively associated with psychopathological symptoms in victims of IPV, but not significantly associated in non-victims. Conclusions The study highlights the important role of Harm Avoidance and Self-Directedness for understanding psychopathological symptoms. Novelty Seeking appears to play an important role in the expression of individuals’ experiences of IPV. These results have important implications for research and practice, particularly the development and implementation of interventions.
Moreira et al. (2019) Understanding the experience of psychopathology after intimate partner violence: the role of personality. PeerJ 7:e6647 https://doi.org/10.7717/peerj.6647
Using road patrol data to identify factors associated with carnivore roadkill counts
As the global road network expands, roads pose an emerging threat to wildlife populations. One way in which roads can affect wildlife is wildlife-vehicle collisions, which can be a significant cause of mortality through roadkill. In order to successfully mitigate these problems, it is vital to understand the factors that can explain the distribution of roadkill. Collecting the data required to enable this can be expensive and time consuming, but there is significant potential in partnering with organisations that conduct existing road patrols to obtain the necessary data. We assessed the feasibility of using roadkill data collected daily between 2014 and 2017 by road patrol staff from a private road agency on a 410 km length of the N3 road in South Africa. We modelled the relationship between a set of environmental and anthropogenic variables on the number of roadkill carcasses, using serval (Leptailurus serval) as a model species. We recorded 5.24 serval roadkill carcasses/100 km/year. The number of carcasses was related to season, the amount of wetland, and NDVI, but was not related to any of the anthropogenic variables we included. This suggests that roadkill patterns may differ greatly depending on the ecology of species of interest, but targeting mitigation measures where roads pass through wetlands may help to reduce serval roadkill. Partnering with road agencies for data collection offers powerful opportunities to identify factors related to roadkill distribution and reduce the threats posed by roads to wildlife.
Williams et al. (2019) Using road patrol data to identify factors associated with carnivore roadkill counts. PeerJ 7:e6650 https://doi.org/10.7717/peerj.6650
IOCBIO Sparks detection and analysis software
Analysis of calcium sparks in cardiomyocytes can provide valuable information about functional changes of calcium handling in health and disease. As a part of the calcium sparks analysis, sparks detection and characterization is necessary. Here, we describe a new open-source platform for automatic calcium sparks detection from line scan confocal images. The developed software is tailored for detecting only calcium sparks, allowing us to design a graphical user interface specifically for this task. The software enables detecting sparks automatically as well as adding, removing, or adjusting regions of interest marking each spark. The results of the analysis are stored in an SQL database, allowing simple integration with statistical tools. We have analyzed the performance of the algorithm using a large set of synthetic images with varying spark sizes and noise levels and also compared the analysis results with results obtained by software established in the field. The use of our software is illustrated by an analysis of the effect of isoprenaline (ISO) on spark frequency, amplitude, and spatial and temporal characteristics. For that, cardiomyocytes from C57BL/6 mice were used. We demonstrated an increase in spark frequency, tendency of having larger spark amplitudes, sparks with a longer duration, and occurrence of multiple sparks from the same site in the presence of ISO. We also show that the duration and the width of sparks with the same amplitude were similar in the absence and presence of ISO. The software was released as an open source repository and is available for free use and collaborative development.
Laasmaa et al. (2019) IOCBIO Sparks detection and analysis software. PeerJ 7:e6652 https://doi.org/10.7717/peerj.6652
Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China
Background The gut microbiota plays an important role in host immunity and metabolic homeostasis. Although analyses of gut microbiotas have been used to assess host health and foster disease prevention and treatment, no comparative comprehensive study, assessing gut microbiotas among several species of farmed snake, is yet available. In this study, we characterized and compared the gut microbiotas of four species of farmed snakes (Naja atra, Ptyas mucosa, Elaphe carinata, and Deinagkistrodon acutus) using high-throughput sequencing of the 16S rDNA gene in southern China and tested whether there was a relationship between gut microbiotal composition and host species. Results A total of 629 operational taxonomic units across 22 samples were detected. The five most abundant phyla were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria, while the five most abundant genera were Bacteroides, Cetobacterium, Clostridium, Plesiomonas, and Paeniclostridium. This was the first report of the dominance of Fusobacteria and Cetobacterium in the snake gut. Our phylogenetic analysis recovered a relatively close relationship between Fusobacteria and Bacteroidetes. Alpha diversity analysis indicated that species richness and diversity were highest in the gut microbiota of D. acutus and lowest in that of E. carinata. Significant differences in alpha diversity were detected among the four farmed snake species. The gut microbiotas of conspecifics were more similar to each other than to those of heterospecifics. Conclusion This study provides the first comparative study of gut microbiotas among several species of farmed snakes, and provides valuable data for the management of farmed snakes. In farmed snakes, host species affected the species composition and diversity of the gut microbiota.
Zhang et al. (2019) Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China. PeerJ 7:e6658 https://doi.org/10.7717/peerj.6658
Music-performance regulates microRNAs in professional musicians
Musical training and performance require precise integration of multisensory and motor centres of the human brain and can be regarded as an epigenetic modifier of brain functions. Numerous studies have identified structural and functional differences between the brains of musicians and non-musicians and superior cognitive functions in musicians. Recently, music-listening and performance has also been shown to affect the regulation of several genes, many of which were identified in songbird singing. MicroRNAs affect gene regulation and studying their expression may give new insights into the epigenetic effect of music. Here, we studied the effect of 2 hours of classical music-performance on the peripheral blood microRNA expressions in professional musicians with respect to a control activity without music for the same duration. As detecting transcriptomic changes in the functional human brain remains a challenge for geneticists, we used peripheral blood to study music-performance induced microRNA changes and interpreted the results in terms of potential effects on brain function, based on the current knowledge about the microRNA function in blood and brain. We identified significant (FDR <0.05) up-regulation of five microRNAs; hsa-miR-3909, hsa-miR-30d-5p, hsa-miR-92a-3p, hsa-miR-222-3p and hsa-miR-30a-5p; and down-regulation of two microRNAs; hsa-miR-6803-3p and hsa-miR-1249-3p. hsa-miR-222-3p and hsa-miR-92a-3p putatively target FOXP2, which was found down-regulated by microRNA regulation in songbird singing. miR-30d and miR-222 corroborate microRNA response observed in zebra finch song-listening/learning. miR-222 is induced by ERK cascade, which is important for memory formation, motor neuron functions and neuronal plasticity. miR-222 is also activated by FOSL1, an immediate early gene from the FOS family of transcriptional regulators which are activated by auditory-motor stimuli. miR-222 and miR-92 promote neurite outgrowth by negatively regulating the neuronal growth inhibitor, PTEN, and by activating CREB expression and phosphorylation. The up-regulation of microRNAs previously found to be regulators of auditory and nervous system functions (miR-30d, miR-92a and miR-222) is indicative of the sensory perception processes associated with music-performance. Akt signalling pathway which has roles in cell survival, cell differentiation, activation of CREB signalling and dopamine transmission was one of the functions regulated by the up-regulated microRNAs; in accordance with functions identified from songbird learning. The up-regulated microRNAs were also found to be regulators of apoptosis, suggesting repression of apoptotic mechanisms in connection with music-performance. Furthermore, comparative analyses of the target genes of differentially expressed microRNAs with that of the song-responsive microRNAs in songbirds suggest convergent regulatory mechanisms underlying auditory perception.
Nair et al. (2019) Music-performance regulates microRNAs in professional musicians. PeerJ 7:e6660 https://doi.org/10.7717/peerj.6660
Green potential of Pleurotus spp. in biotechnology
Background The genus Pleurotus is most exploitable xylotrophic fungi, with valuable biotechnological, medical, and nutritional properties. The relevant features of the representatives of this genus to provide attractive low-cost industrial tools have been reported in numerous studies to resolve the pressure of ecological issues. Additionally, a number of Pleurotus species are highly adaptive, do not require any special conditions for growth, and possess specific resistance to contaminating diseases and pests. The unique properties of Pleurotus species widely used in many environmental technologies, such as organic solid waste recycling, chemical pollutant degradation, and bioethanol production. Methodology The literature study encompasses peer-reviewed journals identified by systematic searches of electronic databases such as Google Scholar, NCBI, Springer, ResearchGate, ScienceDirect, and ISI Web of Knowledge. The search scheme was divided into several steps, as described below. Results In this review, we describe studies examining the biotechnological feasibility of Pleurotus spp. to elucidate the importance of this genus for use in green technology. Here, we review areas of application of the genus Pleurotus as a prospective biotechnological tool. Conclusion The incomplete description of some fungal biochemical pathways emphasises the future research goals for this fungal culture.
Environmental Contamination and Remediation
Sekan et al. (2019) Green potential of Pleurotus spp. in biotechnology. PeerJ 7:e6664 https://doi.org/10.7717/peerj.6664
Transcriptional factor regulation network and competitive endogenous RNA (ceRNA) network determining response of esophageal squamous cell carcinomas to neoadjuvant chemoradiotherapy
Background Neoadjuvant chemoradiotherapy (nCRT) followed by surgery benefits survival for patients with esophageal squamous cell carcinomas (ESCC) compared with surgery alone, but the clinical outcomes of nCRT are heterogeneous. This study aimed to elucidate transcriptional factor (TF) regulation network and competitive endogenous RNA (ceRNA) network determining response of ESCC to nCRT. Materials and Methods RNA microarray data of GSE59974 and GSE45670 were analyzed to investigate the significant changes of lincRNAs, miRNAs, mRNAs in responders and non-responders of nCRT in ESCC. Functional and enrichment analyses were conducted by clusterProfiler. The target lincRNAs and mRNAs of miRNAs were predicted by miRWalk. The ceRNA and TF regulatory networks were constructed using Cytoscape. Results Differentially expressed genes between responders and non-responders mainly enriched in biological process including Wnt signaling pathway and regulation of cell development and morphogenesis involved in differentiation. Besides, these genes showed enrichment in molecular function of glycosaminoglycan binding, metalloendopeptidase inhibitor and growth factor activity. KEGG analysis enriched these genes in pathways of neurotrophin signaling pathway, cell adhesion molecules and Wnt signaling pathway. We also constructed ceRNA network and TF network regulating response of ESCC to nCRT. Core regulatory miRNAs were miR-520a, miR-548am, miR-3184, miR-548d, miR-4725, miR-148a, miR-4659a and key regulatory TFs included MBNL1, SLC26A3, BMP4, ZIC1 and ANKRD7. Conclusion We identified significantly altered lincRNAs, miRNAs and mRNAs involved in the nCRT response of ESCC. In addition, the ceRNA regulatory network of lincRNA-miRNA-mRNA and TF regulatory network were constructed, which would elucidate novel molecular mechanisms determining nCRT response of ESCC, thus providing promising clues for clinical therapy.
Shao et al. (2019) Transcriptional factor regulation network and competitive endogenous RNA (ceRNA) network determining response of esophageal squamous cell carcinomas to neoadjuvant chemoradiotherapy. PeerJ 7:e6668 https://doi.org/10.7717/peerj.6668
Using opportunistic sightings to infer differential spatio-temporal use of western Mediterranean waters by the fin whale
The fin whale (Balaenoptera physalus) is a cosmopolitan species with a resident population in the Mediterranean Sea. Due to its habitat, open seas often far from ports and airfields, and its long-distance migratory behaviour, studying and monitoring its distribution is costly. Currently, many opportunistic sightings (OS) reports are available, which provide a source of potentially useful, low-cost information about the spatio-temporal distribution of this species. Since 1993, the Spanish Institute of Oceanography has compiled a dataset comprising 874 records of OS of nine species of cetaceans in the western Mediterranean Sea and adjacent waters. The aim of this study was to use this dataset to investigate the differential use of these waters by the fin whale when compared with other cetaceans. We compared the presence of fin whales with the presence of any other cetacean species in the dataset. Binary logistic regression was then used to model these occurrences according to several spatio-temporal variables expected to reflect their habitat use. Several significant models reveal that fin whales are more prone than other cetaceans to use the waters over the slope of the Gulf of Lion in summer. This finding confirms that the Gulf of Lion is an area of importance for this species and suggests that the slope of the continental shelf could be particularly important. Our study shows how OS can be a source of useful information when appropriately analyzed.
Torreblanca et al. (2019) Using opportunistic sightings to infer differential spatio-temporal use of western Mediterranean waters by the fin whale. PeerJ 7:e6673 https://doi.org/10.7717/peerj.6673
Up-regulation of Grb2-associated binder 1 promotes hepatocyte growth factor-induced endothelial progenitor cell proliferation and migration
Objectives Grb2-associated binder 1 (Gab1), a scaffolding adaptor protein, plays an important role in transmitting key signals that control cell growth, migration, and function from multiple tyrosine kinase receptors. This study was designed to investigate the influence of upregulation of Gab1 in endothelial progenitor cells (EPCs) stimulated with hepatocyte growth factor (HGF), and the underlying molecular mechanisms. Materials and Methods Endothelial progenitor cells isolated from human umbilical cord blood were identified and divided into four groups. EPCs in the Control group were cultured normally; those in the Control+HGF group were treated with HGF stimulation; those in the AD-Gab1 group were transfected with adenovirus containing the Gab1 gene but not treated with HGF stimulation; and, those in the AD-Gab1+HGF group were treated with both HGF stimulation and transfection with adenovirus containing the Gab1 gene. Subsequently, Gab1 expression and proliferation and migration ability were compared for EPCs grown under different conditions. Furthermore, we measured phosphorylation levels of three key proteins Gab1, SHP2, and ERK1/2. Results The AD-Gab1+HGF group had the highest expression of Gab1 and higher proliferation and migration than the other three groups. Conclusions Upregulation of Gab1 promoted HGF-induced EPC proliferation and migration. Mechanistically, HGF stimulated Gab1 tyrosine phosphorylation in EPCs, thus leading to activation of extracellular regulated MAP kinase 1/2, which is involved in proliferation and migration signaling.
Fan et al. (2019) Up-regulation of Grb2-associated binder 1 promotes hepatocyte growth factor-induced endothelial progenitor cell proliferation and migration. PeerJ 7:e6675 https://doi.org/10.7717/peerj.6675
Factors that influence response classifications in chemotherapy treated patient-derived xenografts (PDX)
In this study, we investigated the impact of initial tumor volume, rate of tumor growth, cohort size, study duration, and data analysis method on chemotherapy treatment response classifications in patient-derived xenografts (PDXs). The analyses were conducted on cisplatin treatment response data for 70 PDX models representing ten cancer types with up to 28-day study duration and cohort sizes of 3–10 tumor-bearing mice. The results demonstrated that a 21-day dosing study using a cohort size of eight was necessary to reliably detect responsive models (i.e., tumor volume ratio of treated animals to control between 0.1 and 0.42)—independent of analysis method. A cohort of three tumor-bearing animals led to a reliable classification of models that were both highly responsive and highly nonresponsive to cisplatin (i.e., tumor volume ratio of treated animals to control animals less than 0.10). In our set of PDXs, we found that tumor growth rate in the control group impacted treatment response classification more than initial tumor volume. We repeated the study design factors using docetaxel treated PDXs with consistent results. Our results highlight the importance of defining endpoints for PDX dosing studies when deciding the size of cohorts to use in dosing studies and illustrate that response classifications for a study do not differ significantly across the commonly used analysis methods that are based on tumor volume changes in treatment versus control groups.
Malcolm et al. (2019) Factors that influence response classifications in chemotherapy treated patient-derived xenografts (PDX). PeerJ 7:e6586 https://doi.org/10.7717/peerj.6586
Evaluation of a toxoid fusion protein vaccine produced in plants to protect poultry against necrotic enteritis
Background Necrotic enteritis (NE) is caused by type A strains of the bacterium Clostridium perfringens. Total global economic losses to the poultry industry due to NE is estimated to be over two billion dollars annually. Traditionally, NE has been effectively controlled by inclusion of antibiotics in the diet of poultry. However, recent concerns regarding the impact of this practice on increasing antibiotic resistance in human pathogens have led us to consider alternative approaches, such as vaccination, for controlling this disease. NE strains of C. perfringens produce two major toxins, a-toxin and NetB. Immune responses against either toxin can provide partial protection against NE. Methods We have developed a fusion protein combining a non-toxic carboxyl-terminal domain of a-toxin (PlcC) and an attenuated, mutant form of NetB (NetB-W262A) for use as a vaccine antigen to immunize poultry against NE. We utilized a DNA sequence that was codon-optimized for Nicotiana benthamiana to enable high levels of expression. The 6-His tagged PlcC-NetB fusion protein was synthesized in N. benthamiana using a geminiviral replicon transient expression system, purified by metal affinity chromatography, and used to immunize broiler birds. Results Immunized birds produced a strong serum IgY response against both the plant produced PlcC-NetB protein and against bacterially produced His-PlcC and His-NetB. Immunized birds were significantly protected against a subsequent in-feed challenge with virulent C. perfringens when treated with the fusion protein. These results indicate that a plant-produced PlcC-NetB toxoid is a promising vaccine candidate for controlling NE in poultry.
Hunter et al. (2019) Evaluation of a toxoid fusion protein vaccine produced in plants to protect poultry against necrotic enteritis. PeerJ 7:e6600 https://doi.org/10.7717/peerj.6600
Underwater sound production varies within not between species in sympatric newts
Sound production is a widespread phenomenon among animals. Effective sound use for mate or species recognition requires some acoustic differentiation at an individual or species level. Several species of caudate amphibians produce underwater sounds, but information about intra- and interspecific variation in their acoustic production is missing. We examined individual, sex, and species variation in underwater sound production in adults of two sympatric newt taxa, Ichthyosaura alpestris and Lissotriton vulgaris. Individual newts produced simple low- (peak frequency = 7–8 kHz) and mid-high frequency (14–17 kHz) clicks, which greatly overlap between sexes and species. Individual differences explained about 40–50% of total variation in sound parameters. These results provide foundations for further studies on the mechanisms and eco-evolutionary consequences of underwater acoustics in newts.
Hubáček et al. (2019) Underwater sound production varies within not between species in sympatric newts. PeerJ 7:e6649 https://doi.org/10.7717/peerj.6649
Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing
The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.
Han et al. (2019) Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing. PeerJ 7:e6684 https://doi.org/10.7717/peerj.6684
Mammut pacificus sp. nov., a newly recognized species of mastodon from the Pleistocene of western North America
A new species of mastodon from the Pleistocene of western North America, Mammut pacificus sp. nov. is herein recognized, with specimens identified throughout California and from two localities in southern Idaho. This new taxon differs from the contemporaneous M. americanum in having narrower teeth, most prominently in M3/m3, as well as six sacral vertebrae, femur with a proportionally greater mid-shaft diameter, and no mandibular tusks at any growth stage. All known Pleistocene Mammut remains from California are consistent with our diagnosis of M. pacificus, which indicates that M. americanum was not present in California.
Dooley et al. (2019) Mammut pacificus sp. nov., a newly recognized species of mastodon from the Pleistocene of western North America. PeerJ 7:e6614 https://doi.org/10.7717/peerj.6614
Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains
Background The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated. Methods In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses. Results Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1. Discussion In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence in this area. Moreover, the unexpected discovery of a 24,700-year-old sample carrying a haplotype that, from the fragment here obtained, falls within the canine clade A, could represent the oldest evidence in Europe of such dog-rich clade. All these findings suggest complex population dynamics that deserve to be further investigated based on mitochondrial or whole genome sequencing.
Ciucani et al. (2019) Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains. PeerJ 7:e6424 https://doi.org/10.7717/peerj.6424
Clinicopathological characteristics, treatment and survival of pulmonary large cell neuroendocrine carcinoma: a SEER population-based study
Background This study was designed to investigate the clinicopathological characteristics, treatment and survival of patients with pulmonary large cell neuroendocrine carcinoma (LCNEC). Methods The Surveillance, Epidemiology and End Results database was utilized to identify patients diagnosed with pulmonary LCNEC between 2004 and 2013. Kaplan–Meier analysis was conducted to determine the overall survival (OS) and cancer-specific survival (CSS) rate. Univariate survival analysis along with log-rank test, and Cox proportional hazards model were employed to detect independent prognostic factors. Results Pulmonary LCNEC accounted for 0.58% (2972/510607) of the total number of lung and bronchus carcinoma. And a total of 1,530 eligible cases were identified, with the median follow-up time of 11 months. To be specific, the 3-, 5-year OS and CSS rates were 22.8%, 16.8% and 26.5%, 20.8% respectively. Generally, pulmonary LCNEC was commonly detected in the elderly (72.2%), males (55.9%), the upper lobe (62.0%) and advanced AJCC stage (65.5%). Multivariate analysis revealed that elderly [(≥60 and <80 years) HR:1.203, 95% CI [1.053–1.375], P = 0.007; (≥80 years) HR:1.530, 95% CI [1.238–1.891], P < 0.001] and advanced AJCC stage [(stage III) HR:2.606, 95% CI [2.083–3.260], P < 0.001; (stage IV) HR:4.881, 95% CI [3.923–6.072], P < 0.001] were independent unfavorable prognostic factors, and that female (HR:0.845, 95% CI [0.754–0.947], P = 0.004)), surgery [(Segmentectomy/wedge resection) HR:0.526, 95% CI [0.413–0.669], P < 0.001; (Lobectomy/Bilobectomy) HR:0.357, 95% CI [0.290–0.440], P < 0.001;(Pneumonectomy) HR:0.491, 95% CI [0.355–0.679], P < 0.001] , chemotherapy (HR:0.442, 95% CI [0.389–0.503], P < 0.001) and radiation (HR:0.837, 95% CI [0.738–0.949], P = 0.005) were independent favorable prognostic factors. Conclusion To sum up, age at diagnosis, sex, AJCC 8th edition stage, surgery, chemotherapy and radiation were significantly associated with OS of patients with pulmonary LCNEC.
Cao et al. (2019) Clinicopathological characteristics, treatment and survival of pulmonary large cell neuroendocrine carcinoma: a SEER population-based study. PeerJ 7:e6539 https://doi.org/10.7717/peerj.6539
Associated bacteria of Botryococcus braunii (Chlorophyta)
Botryococcus braunii (Chlorophyta) is a green microalga known for producing hydrocarbons and exopolysaccharides (EPS). Improving the biomass productivity of B. braunii and hence, the productivity of the hydrocarbons and of the EPS, will make B. braunii more attractive for industries. Microalgae usually cohabit with bacteria which leads to the formation of species-specific communities with environmental and biological advantages. Bacteria have been found and identified with a few B. braunii strains, but little is known about the bacterial community across the different strains. A better knowledge of the bacterial community of B. braunii will help to optimize the biomass productivity, hydrocarbons, and EPS accumulation. To better understand the bacterial community diversity of B. braunii, we screened 12 strains from culture collections. Using 16S rRNA gene analysis by MiSeq we described the bacterial diversity across 12 B. braunii strains and identified possible shared communities. We found three bacterial families common to all strains: Rhizobiaceae, Bradyrhizobiaceae, and Comamonadaceae. Additionally, the results also suggest that each strain has its own specific bacteria that may be the result of long-term isolated culture.
Gouveia et al. (2019) Associated bacteria of Botryococcus braunii (Chlorophyta). PeerJ 7:e6610 https://doi.org/10.7717/peerj.6610
Evaluating the effects of a temporary fostering program on shelter dog welfare
One of the greatest stressors for dogs living in animal shelters is social isolation. Many studies have demonstrated that human interaction reduces cortisol in shelter dogs, with the possibility that longer periods of interaction may yield greater effects. These types of interventions are contingent upon removing the dog from the kennel and any such reductions in cortisol are often lost when the dog returns to the kennel. More recently, animal shelters are utilizing short-term fostering programs to provide relief from the perceived stresses of kennel life; however the effects of these programs are not well understood. This study assessed the impacts of one- and two-night fostering programs on the urinary cortisol levels, resting pulse rates, longest bout of uninterrupted rest, and proportion of time spent resting of dogs awaiting adoption. Five animal shelters, open and limited-admission facilities, from across the United States participated in the study. During the study, dogs’ urine was collected in the morning before, during, and after fostering stays for cortisol: creatinine analysis. Non-invasive health monitors were worn by the dogs, which collected heart rates and activity levels, in the shelter and in foster homes. In total, 207 dogs participated in the study, and 1,076 cortisol values were used in our analysis. Across all shelters, we found that dogs’ cortisol: creatinine ratios dropped significantly during their fostering stay, but returned to baseline levels after return to the shelter. However, the observed reduction in cortisol varied in magnitude across shelters. We found that dogs of greater weight, age, and average resting pulse rate had higher cortisol levels; and dogs with longer bouts of uninterrupted rest had lower cortisol levels. Dogs had their longest bouts of rest during sleepovers, followed by in the shelter after their sleepovers. Lastly, significant differences were found when comparing in-shelter cortisol values at our five shelters, differences that were in some cases greater than the impact of the fostering intervention itself. Considering the diversity of facilities that participated in this study, it is possible that as yet unstudied, shelter-specific, environmental factors could be contributing to the overall welfare of shelter dogs. Thus while a reprieve from the shelter is impactful for dogs awaiting adoption, mitigating the stressors present in kenneling conditions should also be addressed to improve the lives of shelter dogs.
Gunter et al. (2019) Evaluating the effects of a temporary fostering program on shelter dog welfare. PeerJ 7:e6620 https://doi.org/10.7717/peerj.6620
Pixel: a content management platform for quantitative omics data
Background In biology, high-throughput experimental technologies, also referred as “omics” technologies, are increasingly used in research laboratories. Several thousands of gene expression measurements can be obtained in a single experiment. Researchers are routinely facing the challenge to annotate, store, explore and mine all the biological information they have at their disposal. We present here the Pixel web application (Pixel Web App), an original content management platform to help people involved in a multi-omics biological project. Methods The Pixel Web App is built with open source technologies and hosted on the collaborative development platform GitHub (https://github.com/Candihub/pixel). It is written in Python using the Django framework and stores all the data in a PostgreSQL database. It is developed in the open and licensed under the BSD 3-clause license. The Pixel Web App is also heavily tested with both unit and functional tests, a strong code coverage and continuous integration provided by CircleCI. To ease the development and the deployment of the Pixel Web App, Docker and Docker Compose are used to bundle the application as well as its dependencies. Results The Pixel Web App offers researchers an intuitive way to annotate, store, explore and mine their multi-omics results. It can be installed on a personal computer or on a server to fit the needs of many users. In addition, anyone can enhance the application to better suit their needs, either by contributing directly on GitHub (encouraged) or by extending Pixel on their own. The Pixel Web App does not provide any computational programs to analyze the data. Still, it helps to rapidly explore and mine existing results and holds a strategic position in the management of research data.
Denecker et al. (2019) Pixel: a content management platform for quantitative omics data. PeerJ 7:e6623 https://doi.org/10.7717/peerj.6623
Biodegradation of thiocyanate by a native groundwater microbial consortium
Gold ore processing typically generates large amounts of thiocyanate (SCN−)-contaminated effluent. When this effluent is stored in unlined tailings dams, contamination of the underlying aquifer can occur. The potential for bioremediation of SCN−-contaminated groundwater, either in situ or ex situ, remains largely unexplored. This study aimed to enrich and characterise SCN−-degrading microorganisms from mining-contaminated groundwater under a range of culturing conditions. Mildly acidic and suboxic groundwater, containing ∼135 mg L−1 SCN−, was collected from an aquifer below an unlined tailings dam. An SCN−-degrading consortium was enriched from contaminated groundwater using combinatory amendments of air, glucose and phosphate. Biodegradation occurred in all oxic cultures, except with the sole addition of glucose, but was inhibited by NH4+ and did not occur under anoxic conditions. The SCN−-degrading consortium was characterised using 16S and 18S rRNA gene sequencing, identifying a variety of heterotrophic taxa in addition to sulphur-oxidising bacteria. Interestingly, few recognised SCN−-degrading taxa were identified in significant abundance. These results provide both proof-of-concept and the required conditions for biostimulation of SCN− degradation in groundwater by native aquifer microorganisms.
Spurr et al. (2019) Biodegradation of thiocyanate by a native groundwater microbial consortium. PeerJ 7:e6498 https://doi.org/10.7717/peerj.6498
Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)
Background Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.
Shen et al. (2019) Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia). PeerJ 7:e6542 https://doi.org/10.7717/peerj.6542
Proteomics alterations in chicken jejunum caused by 24 h fasting
The small intestine is the longest part of the chicken (Gallus gallus) gastrointestinal system that is specialized for nutrient absorption. It is known that decrease in intestinal villi area or height in early age can cause a reduction in essential nutrient intake, which may lead to delayed growth and consequently poorer performance of broiler chickens. The small intestinal absorptive surface is known to be affected by various factors, among others things the nutritional state. In our experiment, we aimed to investigate the possible protein expression alterations that lie behind the villus area and height decrease caused by feed deprivation. A total of 24 chickens were divided into three groups, namely ad libitum fed, fasted for 24 h, fasted for 24 h then refed for 2 h. The morphometric parameters were also measured in the duodenum, jejunum and ileum tissue sections using image analysis. Differential proteome analyses from jejunum samples were performed using two-dimensional difference gel electrophoresis followed by tryptic digestion and protein identification by matrix-assisted laser desorption/ionization mass spectrometry. Overall 541 protein spots were detected after 2D. Among them, eleven showed 1.5-fold or higher significant difference in expression and were successfully identified. In response to 24 h fasting, the expression of nine proteins was higher and that of two proteins was lower compared to the ad libitum fed group. The functions of the differentially expressed proteins indicate that the 24 h fasting mainly affects the expression of structural proteins, and proteins involved in lipid transport, general stress response, and intestinal defense.
Simon et al. (2019) Proteomics alterations in chicken jejunum caused by 24 h fasting. PeerJ 7:e6588 https://doi.org/10.7717/peerj.6588
Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri)
The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD genes.
Su et al. (2019) Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri). PeerJ 7:e6628 https://doi.org/10.7717/peerj.6628
Isolation of cancer stem cells by selection for miR-302 expressing cells
Background Cancer stem cells are believed to be a major reason for long-term therapy failure because they are multi-drug resistant and able to rest mitotically inactive in the hypoxic center of tumors. Due to their variable number and their often low proliferation rate, cancer stem cells are difficult to purify in decent quantities and to grow in cell culture systems, where they are easily outcompeted by faster growing more ‘differentiated’, i.e., less stem cell-like tumor cells. Methods Here we present a proof of principle study based on the idea to select cancer stem cells by means of the expression of a stem cell-specific gene. A selectable egfp-neo coding sequence was inserted in the last exon of the non-coding murine miR-302 host gene. As a stem cell specific regulatory element, 2.1 kb of the genomic region immediately upstream of the miR-302 host gene transcription start site was used. Stable transgenic CJ7 embryonic stem cells were used to induce teratomas. Results After three weeks, tumors were removed for analysis and primary cultures were established. Stem cell-like cells were selected from these culture based on G418 selection. When the selection was removed, stem cell morphology and miR-302 expression were rapidly lost, indicating that it was not the original ES cells that had been isolated. Conclusions We show the possibility to use drug resistance expressed from a regulatory sequence of a stem cell-specific marker, to isolate and propagate cancer stem cells that otherwise might be hidden in the majority of tumor cells.
Rahimi et al. (2019) Isolation of cancer stem cells by selection for miR-302 expressing cells. PeerJ 7:e6635 https://doi.org/10.7717/peerj.6635
Robust and automatic definition of microbiome states
Analysis of microbiome dynamics would allow elucidation of patterns within microbial community evolution under a variety of biologically or economically important circumstances; however, this is currently hampered in part by the lack of rigorous, formal, yet generally-applicable approaches to discerning distinct configurations of complex microbial populations. Clustering approaches to define microbiome “community state-types” at a population-scale are widely used, though not yet standardized. Similarly, distinct variations within a state-type are well documented, but there is no rigorous approach to discriminating these more subtle variations in community structure. Finally, intra-individual variations with even fewer differences will likely be found in, for example, longitudinal data, and will correlate with important features such as sickness versus health. We propose an automated, generic, objective, domain-independent, and internally-validating procedure to define statistically distinct microbiome states within datasets containing any degree of phylotypic diversity. Robustness of state identification is objectively established by a combination of diverse techniques for stable cluster verification. To demonstrate the efficacy of our approach in detecting discreet states even in datasets containing highly similar bacterial communities, and to demonstrate the broad applicability of our method, we reuse eight distinct longitudinal microbiome datasets from a variety of ecological niches and species. We also demonstrate our algorithm’s flexibility by providing it distinct taxa subsets as clustering input, demonstrating that it operates on filtered or unfiltered data, and at a range of different taxonomic levels. The final output is a set of robustly defined states which can then be used as general biomarkers for a wide variety of downstream purposes such as association with disease, monitoring response to intervention, or identifying optimally performant populations.
García-Jiménez et al. (2019) Robust and automatic definition of microbiome states. PeerJ 7:e6657 https://doi.org/10.7717/peerj.6657
Comparative analysis of the complete mitochondrial genomes of five Achilidae species (Hemiptera: Fulgoroidea) and other Fulgoroidea reveals conserved mitochondrial genome organization
In the present study, the complete mitochondrial genomes (mitogenomes) of five Achilidae (Hemiptera: Fulgoroidea), Betatropis formosana, two new species (Magadhaideus luodiana sp. nov and Peltatavertexalis horizontalis sp. nov), Plectoderini sp. and Paracatonidia sp., were sequenced for the first time through next-generation sequencing. The five mitogenomes ranged from 15,214 to 16,216 bp in length, with the typical gene content and arrangement usually observed in Hexapods. The motif “ATGATAA” between atp8 and atp6 was found in all the analyzed species. An overlap “AAGCTTA” between trnW and trnC was observed in the mitogenomes of most Fulgoroidea. The structural and compositional analyses of 26 Fulgoroidea mitogenomes, including the gene rearrangement of five tRNAs (trnW, trnC and trnY; trnT and trnP), the A + T content and AT-skew of the whole mitogenomes, and the nuclear acid and amino acid compositions of the protein-coding genes (PCGs), revealed family-level differences between Delphacidae and other families (Achilidae, Flatidae, Fulgoridae, Issidae and Ricaniidae). Phylogenetic analyses of 13 protein-coding genes from 26 Fulgoroidea species by maximum likelihood and Bayesian Inference were consistent and well supported the basal position of Delphacidae, a close affinity among the families Flatidae, Issidae and Ricaniidae, and a close relationship between Achilidae and Fulgoridae.
Xu et al. (2019) Comparative analysis of the complete mitochondrial genomes of five Achilidae species (Hemiptera: Fulgoroidea) and other Fulgoroidea reveals conserved mitochondrial genome organization. PeerJ 7:e6659 https://doi.org/10.7717/peerj.6659
Pharmacokinetic comparison of quercetin, isoquercitrin, and quercetin-3-O-β-D-glucuronide in rats by HPLC-MS
Background Quercetin (Qr), isoquercitrin (IQ), and quercetin-3-O-β-D-glucuronide (QG) are powerful phytochemicals that have been shown to exhibit disease prevention and health promotion properties. However, there may exist transformations between Qr, IQ, and QG in vivo. And the pharmacokinetic profiles of Qr, IQ, and QG have not been systematically compared. The pharmacokinetics study would be helpful to better understand the pharmacological actions of them. Methods Herein, we developed a reliable HPLC-MS method to compare the pharmacokinetics of Qr, IQ, and QG after separate (50 mg/kg) oral administration of them in rats, using puerarin as internal standard. The detection was performed using negative selected ion monitoring. This method was validated in terms of selectivity, linearity, precision, accuracy, extraction recovery, matrix effect, and stability; and shows reliabilities in monitoring the pharmacokinetic behaviors of these three compounds. Results Our results showed that after separate oral administration of Qr, IQ, and QG, all of the compounds could be detected in plasma. In addition, QG could be detected in the Qr group; Qr and QG could be measured in the IQ group; and Qr could be found in rat plasma after 1.5 h of QG administration. Moreover, the AUC0−t of Qr in the; Qr group (2,590.5 ± 987.9 mg/L*min), IQ group (2,212.7 ± 914.1 mg/L*min), and QG group (3,505.7 ± 1,565.0 mg/L*min) was larger than the AUC0−t of QG in the; Qr group (1,550.0 ± 454.2 mg/L*min), IQ group (669.3 ± 188.3 mg/L*min), and QG group (962.7 ± 602.3 mg/L*min). The AUC0−t of IQ was the lowest among all groups. Discussion Quercetin, IQ, and QG can all be absorbed into plasma. A mutual transformation exists between Qr and QG, and IQ can be metabolized into Qr and QG in SD rats. These results would provide a meaningful basis for understanding the pharmacological actions of these three compounds.
Yin et al. (2019) Pharmacokinetic comparison of quercetin, isoquercitrin, and quercetin-3-O-β-D-glucuronide in rats by HPLC-MS. PeerJ 7:e6665 https://doi.org/10.7717/peerj.6665
The relationship between serum uric acid within the normal range and β-cell function in Chinese patients with type 2 diabetes: differences by body mass index and gender
Background Elevated serum uric acid (SUA) has a positive correlation with insulin secretion and insulin resistance indexes. However, whether weight- and gender-specific differences regarding the relationship between SUA within the normal range and β-cell function and insulin resistance exist is unknown in type 2 diabetes mellitus (T2DM) patients. Methods A total of 380 patients with type 2 diabetes were divided into two groups as overweight/obesity (n = 268) and normal weight (n = 112). Each group were again divided into low (LSUA) and high normal SUA (HSUA). The HbA1c, C-peptide, SUA, creatinine, and lipids profiles were measured. HOMA2IR and HOMA%2B were estimated using fasting glucose and C-peptide by homeostasis model assessment (HOMA). Pearson’s correlations and multiple linear regression analyses were conducted to assess the associations between SUA levels and islet function indexes. Results In overweight/obesity subgroup, the levels of body mass index, fasting C-peptide (FCP), P2hCP, fasting CPI (FCPI), postprandial CPI (PPCPI), ΔC-peptide, HOMA2%B, and HOMA2IR were higher in HSUA group than in LSUA group. In contrast, the HbA1c, FBS, and P2hBS were lower in HSUA than in LSUA. In normal weight subgroup, there were no differences between the HSUA than LSUA group in terms of clinical characteristics. Pearson’s correlations indicated that there were no significant correlations between SUA and insulin secretory capacity in normal weight group, but in overweight/obesity group, SUA had positive significant correlations with P2hCP, FCPI, PPCPI, ΔC-peptide, and HOMA2%B. In the female group, there were no significant correlations between SUA and insulin secretory capacity. However, in the male group, SUA had positive significant correlations with insulin secretory capacity include P2hCP, FCPI, PPCPI, ΔC-peptide, and HOMA2%B. Multiple linear regression showed that SUA was significantly associated with HOMA2%B, but not with HOMA2IR in overweight/obesity and male group. Conclusions Our study shows that SUA levels within normal range were associated with β-cell function in T2DM patients with overweight/obesity or male. This finding supports that the association between SUA within normal range and insulin secretion ability differs by weight and sex.
Zhong et al. (2019) The relationship between serum uric acid within the normal range and β-cell function in Chinese patients with type 2 diabetes: differences by body mass index and gender. PeerJ 7:e6666 https://doi.org/10.7717/peerj.6666
Loancorhynchus catrillancai gen. et sp. nov., a new swordfish (Xiphioidei, Blochiidae) from the Middle Eocene of central Chile
This contribution describes the skull remains of a swordfish (Perciformes, Xiphioidei), recovered from Middle Eocene beds of central Chile. Comparison with known fossil and extant xiphioids reveals derived traits only present in the Neogene swordfish Xiphias gladius (Xiphiidae, Xiphiinae), these being a elongated rostrum composed of premaxillaries and possible prenasals, a dorsoventrally high and slender hyomandibular-metapterygoid complex, and a rounded, convex operculum. Also, strong ridges and sulci are present in the dorsal part of the rostrum, a feature only present in the billfish genera Aglyptorhynchus and Xiphiorhynchus, and in the swordfish genus Blochius. In addition, the specimen also has villiform teeth in the rostrum and lower jaw, a feature previously documented only in the Paleocene genus Hemingwaya. Such a unique combination of characters in the specimen allows classifying it as a new genus and species, Loancorhynchus catrillancai. Phylogenetic analyses obtained Xiphiorhynchus outside the Xiphiidae, suggesting instead narrow relationships to the Paleocene-Eocene genera Hemingwaya + Palaeorhynchus + Homorhynchus. Loancorhynchus is obtained as an intermediate form between Xiphias and Blochius. The specimen represents the first Paleogene swordfish described in the southeastern Pacific.
Otero (2019) Loancorhynchus catrillancai gen. et sp. nov., a new swordfish (Xiphioidei, Blochiidae) from the Middle Eocene of central Chile. PeerJ 7:e6671 https://doi.org/10.7717/peerj.6671
Translating the hemodynamic response: why focused interdisciplinary integration should matter for the future of functional neuroimaging
The amount of information acquired with functional neuroimaging techniques, particularly fNIRS and fMRI, is rapidly growing and has enormous potential for studying human brain functioning. Therefore, many scientists focus on solving computational neuroimaging and Big Data issues to advance the discipline. However, the main obstacle—the accurate translation of the hemodynamic response (HR) by the investigation of a physiological phenomenon called neurovascular coupling—is still not fully overcome and, more importantly, often overlooked in this context. This article provides a brief and critical overview of significant findings from cellular biology and in vivo brain physiology with a focus on advancing existing HR modelling paradigms. A brief historical timeline of these disciplines of neuroscience is presented for readers to grasp the concept better, and some possible solutions for further scientific discussion are provided.
Cinciute (2019) Translating the hemodynamic response: why focused interdisciplinary integration should matter for the future of functional neuroimaging. PeerJ 7:e6621 https://doi.org/10.7717/peerj.6621
Dual effects of biochar and hyperaccumulator Solanum nigrum L. on the remediation of Cd-contaminated soil
Biochar was widely developed for the soil amendment and remediation of heavy metal contaminated soil. The Cd hyperaccumulator, Solanum nigrum L., has been paid much more attention with the wide application of phytoremediation. The effects of biochar on the growth and accumulation capacity of Solanum nigrum L. in Cd contaminated soil have not been explored so far. The objectives of this study were to explore the dual effects of biochar addition on available Cd in the soil and hyperaccumulation of Cd in Solanum nigrum L. under different Cd contaminated levels. The correlations of soil physicochemical and biochemical properties and Cd absorption of Solanum nigrum L. were analyzed after a 60-day pot experiment under three biochar doses (0%, 1% and 5%) and four Cd concentrations (0, 25, 50 and 100 mg kg−1). The availability of Cd obtained by DTPA extraction significantly decreased after biochar application (P = 0.003, P = 0.0001, P = 0.0001 under 1% biochar addition for 25, 50, and 100 mg kg−1 Cd concentrations, P = 0.0001, P = 0.0001, P = 0.0001 under 5% biochar addition for 25, 50, and 100 mg kg−1 Cd concentrations, n ≥ 3). The 1% biochar dose significantly increased leaf dry weight (P = 0.039, P = 0.002 for the Cd concentrations of 50 and 100 mg kg−1, n ≥ 3) compared with the control in higher Cd concentrations (50 and 100 100 mg kg−1). In the presence of biochar, the bioconcentration factor (BCF) increased under the Cd concentrations of 50 and 100 mg kg−1. The translocation factors (TF) decreased with the biochar doses under the Cd concentration of 100 mg kg−1. The dose of 5% biochar significantly increased the urease activity by 41.18% compared to the 1% biochar addition in the Cd contaminated soil of 50 mg kg−1 concentration. The activities of acid phosphatase were inhibited by 1% biochar dose in all the Cd contaminated soils. The dry weight of the root of Solanum nigrum L. was significantly negatively correlated with acid phosphatase activity and BCF, respectively, indicating acid phosphatase in the rhizosphere soil of Solanum nigrum L. were repressed by Cd toxicity despite of biochar amendment. Biochar had no negative effect on Cd accumulation ability of Solanum nigrum L. Two-way ANOVA analysis showed that both biochar and Cd significantly affected the height of Solanum nigrum L. and the dry weight of leaf and stem. This study implied that biochar addition does not limit the absorption of hyperaccumulator Solanum nigrum L. in the remediation of Cd-contaminated soil. This study implied that the simultaneous application of biochar and hyperccumulator Solanum nigrum L. is promising during the remediation of Cd-contaminated soil.
Li et al. (2019) Dual effects of biochar and hyperaccumulator Solanum nigrum L. on the remediation of Cd-contaminated soil. PeerJ 7:e6631 https://doi.org/10.7717/peerj.6631
Capacity for heat absorption by the wings of the butterfly Tirumala limniace (Cramer)
Butterflies can directly absorb heat from the sun via their wings to facilitate autonomous flight. However, how is the heat absorbed by the butterfly from sunlight stored and transmitted in the wing? The answer to this scientific question remains unclear. The butterfly Tirumala limniace (Cramer) is a typical heat absorption insect, and its wing surface color is only composed of light and dark colors. Thus, in this study, we measured a number of wing traits relevant for heat absorption including the thoracic temperature at different light intensities and wing opening angles, the thoracic temperature of butterflies with only one right fore wing or one right hind wing; In addition, the spectral reflectance of the wing surfaces, the thoracic temperature of butterflies with the scales removed or present in light or dark areas, and the real-time changes in heat absorption by the wing surfaces with temperature were also measured. We found that high intensity light (600–60,000 lx) allowed the butterflies to absorb more heat and 60−90° was the optimal angle for heat absorption. The heat absorption capacity was stronger in the fore wings than the hind wings. Dark areas on the wing surfaces were heat absorption areas. The dark areas in the lower region of the fore wing surface and the inside region of the hind wing surface were heat storage areas. Heat was transferred from the heat storage areas to the wing base through the veins near the heat storage areas of the fore and hind wings.
Liao et al. (2019) Capacity for heat absorption by the wings of the butterfly Tirumala limniace (Cramer). PeerJ 7:e6648 https://doi.org/10.7717/peerj.6648
Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)
Schneider’s dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.
Bittencourt et al. (2019) Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae). PeerJ 7:e6580 https://doi.org/10.7717/peerj.6580
Objectives The Internet in general, and YouTube in particular, is now one of the most popular sources of health-related information. Pain neuroscience education has become a primary tool for managing persistent pain, based in part on the discovery that information about pain can change pain. Our objective was to examine the availability, characteristics, and content of YouTube videos that address the neuroscience of pain. Methods We conducted a systematic review of videos on YouTube using the search terms “pain education”, “what is pain”, and “pain brain” in January 2018. Videos were included if they were in English, were under 10 minutes long, and included information on the neuroscience of pain. Videos were coded for (i) descriptive characteristics (e.g., number of views, duration on YouTube), (ii) source and style, (iii) whether or not they addressed seven pre-determined target concepts of pain neuroscience education (e.g., ‘Pain is not an accurate marker of tissue state’), and (iv) how engaging they were. Results We found 106 unique videos that met the inclusion criteria. The videos ranged from having four views to over five million views (Mdn = 1,163 views), with the three most highly viewed videos accounting for 75% of the total views. Animated videos were much more highly viewed than non-animated videos. Only a small number of videos had been posted by a clearly-identifiable reputable source such as an academic or medical institution (10%), although a number of videos were posted by healthcare professionals and professional medical societies. For a small number of videos (7%), the source was unclear. We found 17 videos that addressed at least one target concept of pain neuroscience science education, only nine of which were considered to be at least somewhat engaging. The target concept ‘Pain is a brain output’ was considered to be well addressed by the most videos (N = 11), followed by ‘Pain is a protector’ (N = 10). We found only one video that adequately addressed all seven target concepts of pain neuroscience education. Discussion YouTube contains a variety of videos that practitioners, patients, and families may view to access pain neuroscience education information. A small portion of these videos addressed one or more target concepts of pain neuroscience education in an engaging manner. It is yet to be determined to what extent patients are able to learn information from these videos, to what extent the videos promote behavior change, and thus to what extent the videos may be useful for clinical practice.
Heathcote et al. (2019) Pain neuroscience education on YouTube. PeerJ 7:e6603 https://doi.org/10.7717/peerj.6603
The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula
Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and grains. However understanding of this process in the temperate legumes of the Fabaceae family, which are important both agriculturally and ecologically, is incomplete. Previous work in the reference legume Medicago truncatula has shown that the FT-like gene MtFTa1 is a potent floral activator. While MtFTa1 is upregulated by long-day photoperiods (LD) and vernalisation, the molecular basis of this is unknown as functional homologues of key regulatory genes present in other species, notably CONSTANS in A. thaliana, have not been identified. In LD MtFTa1 maintains a near constant diurnal pattern of expression unlike its homologue FT in A. thaliana, which has a notable peak in expression at dusk. This suggests a different manner of regulation. Furthermore, M. truncatula possesses other FT-like genes such as two LD induced MtFTb genes which may also act in the regulation of flowering time. MtFTb genes have a diurnal pattern of expression with peaks at both four and sixteen hours after dawn. This study utilises RNA-Seq to analyse the transcriptome of M. truncatula leaves to identify genes which may regulate or be co-expressed with these FT-like genes following a shift from short-day photoperiods to inductive long-days. Specifically this study focuses on the first four hours of the day in the young leaves, which coincides with the first diurnal peak of the FTb genes. Following differential expression analysis at each timepoint, genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering and identifies a number of potential candidate photoperiod flowering time genes for future studies to consider.
Thomson et al. (2019) The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula. PeerJ 7:e6626 https://doi.org/10.7717/peerj.6626
Identification of key genes, pathways and potential therapeutic agents for liver fibrosis using an integrated bioinformatics analysis
Background Liver fibrosis is often a consequence of chronic liver injury, and has the potential to progress to cirrhosis and liver cancer. Despite being an important human disease, there are currently no approved anti-fibrotic drugs. In this study, we aim to identify the key genes and pathways governing the pathophysiological processes of liver fibrosis, and to screen therapeutic anti-fibrotic agents. Methods Expression profiles were downloaded from the Gene Expression Omnibus (GEO), and differentially expressed genes (DEGs) were identified by R packages (Affy and limma). Gene functional enrichments of each dataset were performed on the DAVID database. Protein–protein interaction (PPI) network was constructed by STRING database and visualized in Cytoscape software. The hub genes were explored by the CytoHubba plugin app and validated in another GEO dataset and in a liver fibrosis cell model by quantitative real-time PCR assay. The Connectivity Map L1000 platform was used to identify potential anti-fibrotic agents. Results We integrated three fibrosis datasets of different disease etiologies, incorporating a total of 70 severe (F3–F4) and 116 mild (F0–F1) fibrotic tissue samples. Gene functional enrichment analyses revealed that cell cycle was a pathway uniquely enriched in a dataset from those patients infected by hepatitis B virus (HBV), while the immune-inflammatory response was enriched in both the HBV and hepatitis C virus (HCV) datasets, but not in the nonalcoholic fatty liver disease (NAFLD) dataset. There was overlap between these three datasets; 185 total shared DEGs that were enriched for pathways associated with extracellular matrix constitution, platelet-derived growth-factor binding, protein digestion and absorption, focal adhesion, and PI3K-Akt signaling. In the PPI network, 25 hub genes were extracted and deemed to be essential genes for fibrogenesis, and the expression trends were consistent with GSE14323 (an additional dataset) and liver fibrosis cell model, confirming the relevance of our findings. Among the 10 best matching anti-fibrotic agents, Zosuquidar and its corresponding gene target ABCB1 might be a novel anti-fibrotic agent or therapeutic target, but further work will be needed to verify its utility. Conclusions Through this bioinformatics analysis, we identified that cell cycle is a pathway uniquely enriched in HBV related dataset and immune-inflammatory response is clearly enriched in the virus-related datasets. Zosuquidar and ABCB1 might be a novel anti-fibrotic agent or target.
Zhan et al. (2019) Identification of key genes, pathways and potential therapeutic agents for liver fibrosis using an integrated bioinformatics analysis. PeerJ 7:e6645 https://doi.org/10.7717/peerj.6645
Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades
Lake Sinai Viruses (Sinaivirus) are commonly detected in honey bees (Apis mellifera) but no disease phenotypes or fitness consequences have yet been demonstrated. This viral group is genetically diverse, lacks obvious geographic structure, and multiple lineages can co-infect individual bees. While phylogenetic analyses have been performed, the molecular evolution of LSV has not been studied extensively. Here, I use LSV isolates from GenBank as well as contigs assembled from honey bee Sequence Read Archive (SRA) accessions to better understand the evolutionary history of these viruses. For each ORF, substitution rate variation, codon usage, and tests of positive selection were evaluated. Outlier regions of high or low diversity were sought with sliding window analysis and the role of recombination in creating LSV diversity was explored. Phylogenetic analysis consistently identified two large clusters of sequences that correspond to the current LSV1 and LSV2 nomenclature, however lineages sister to LSV1 were the most frequently detected in honey bee SRA accessions. Different expression levels among ORFs suggested the occurrence of subgenomic transcripts. ORF1 and RNA-dependent RNA polymerase had higher evolutionary rates than the capsid and ORF4. A hypervariable region of the ORF1 protein-coding sequence was identified that had reduced selective constraint, but a site-based model of positive selection was not significantly more likely than a neutral model for any ORF. The only significant recombination signals detected between LSV1 and LSV2 initiated within this hypervariable region, but assumptions of the test (single-frame coding and independence of substitution rate by site) were violated. LSV codon usage differed strikingly from that of honey bees and other common honey-bee viruses, suggesting LSV is not strongly co-evolved with that host. LSV codon usage was significantly correlated with that of Varroa destructor, however, despite the relatively weak codon bias exhibited by the latter. While codon usage between the LSV1 and LSV2 clusters was similar for three ORFs, ORF4 codon usage was uncorrelated between these clades, implying rapid divergence of codon use for this ORF only. Phylogenetic placement and relative abundance of LSV isolates reconstructed from SRA accessions suggest that detection biases may be over-representing LSV1 and LSV2 in public databases relative to their sister lineages.
Cornman (2019) Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades. PeerJ 7:e6305 https://doi.org/10.7717/peerj.6305
Oceanographic moorings as year-round laboratories for investigating growth performance and settlement dynamics in the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902)
Background Oceanographic moorings (OMs) are standard marine platforms composed of wires, buoys, weights and instruments, and are used as in situ observatories to record water column properties. However, OMs are also comprised of hard substrates on which a variety of invertebrates can settle when they encounter these structures along their dispersal routes. In this contribution, we studied the fouling communities found on two OMs deployed in the Ross Sea (Antarctica). Furthermore, a cage containing the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902) was incorporated in the OM. The growth of the caged A. colbecki were evaluated after 1 year and their shells used as biological proxy for seawater temperature and salinity. Methods A variety of settlers were collected from two different OMs deployed in the Ross Sea (Antarctica) and species identified using a combination of morphological and genetic (mainly through DNA barcoding) characteristics. Caged scallops were individually marked with permanent tags and their growth studied in terms of size-increment data (SID). Cages were specifically designed to prevent damage to individuals due to water drag during OM deployment and retrieval. Growth parameters from the caged individuals were applied to the A. colbecki juveniles that had settled on the mooring, to trace the likely settlement period. Results The growth performance of caged A. colbecki was similar to that from previous growth studies of this species. The remarkable survival rate of caged specimens (96.6%) supports the feasibility of caging experiments, even for a species with a fragile shell such as the Antarctic scallop. Some of the new recruits found on the mooring were A. colbecki, the same species we put into special cages fixed to it. The settlement of the A. colbecki juveniles started during the Austral spring with a peak in summer months and, remarkably, coincided with seasonal changes in water temperature and flow direction, which were recorded by the mooring’s instruments. Genetic data from other settlers provided new information about their larval ecology and connectivity. Discussion Oceanographic moorings are expensive and complex experimental platforms that, at present, are strictly used for the acquisition of physical and biogeochemical data. Their use for in situ ecological experiments on model organisms suitable for caging and to study fouling species has yet to be fully explored. We present the outcomes of a study, which represents a baseline for the characterization of Antarctic fouling biodiversity. We hope that in the near future an internationally coordinated systematic study of settlers could be initiated around the Antarctic continent. This could utilize “new generation OMs” equipped with standardized settlement structures and agreed sampling protocols for the study of fouling communities.
Schiaparelli et al. (2019) Oceanographic moorings as year-round laboratories for investigating growth performance and settlement dynamics in the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902). PeerJ 7:e6373 https://doi.org/10.7717/peerj.6373
Human gut resistome can be country-specific
The emergence and spread of antibiotic resistance have become emerging threats to human health. The human gut is a large reservoir for antibiotic resistance genes. The gut resistome may be influenced by many factors, but the consumption of antibiotics at both individual and country level should be one of the most significant factors. Previous studies have suggested that the gut resistome of different populations may vary, but lack quantitative characterization supported with relatively large datasets. In this study, we filled the gap by analyzing a large gut resistome dataset of 1,267 human gut samples of America, China, Denmark, and Spain. We built a stacking machine-learning model to determine whether the gut resistome can act as the sole feature to identify the nationality of an individual reliably. It turned out that the machine learning method could successfully identify American, Chinese, Danish, and Spanish populations with F1 score of 0.964, 0.987, 0.971, and 0.986, respectively. Our finding does highlight the significant differences in the composition of the gut resistome among different nationalities. Our study should be valuable for policy-makers to look into the influences of country-specific factors of the human gut resistome.
Xia et al. (2019) Human gut resistome can be country-specific. PeerJ 7:e6389 https://doi.org/10.7717/peerj.6389
Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress
The red-eared slider (Trachemys scripta elegans), identified as one of the 100 most invasive species in the world, is a freshwater turtle originally from the eastern United States and northeastern Mexico. Field investigations have shown that T. s. elegans can survive and lay eggs in saline habitats. In order to understand the molecular mechanisms of salinity adaptation, high-throughput RNA-Seq was utilized to identify the changes in gene expression profiles in the liver of T. s. elegans in response to elevated salinity. We exposed individuals to 0, 5, or 15 psu (practical salinity units) for 30 days. A total of 157.21 million reads were obtained and assembled into 205138 unigenes with an average length of 620 bp and N50 of 964 bp. Of these, 1019 DEGs (differentially expressed genes) were found in the comparison of 0 vs. 5 psu, 1194 DEGs in 0 vs. 15 psu and 1180 DEGs in 5 vs. 15 psu, which are mainly related to macromolecule metabolic process, ion transport, oxidoreductase activity and generation of precursor metabolites and energy by GO (Gene Ontology) enrichment analyses. T. s. elegans can adapt itself into salinity by balancing the entry of sodium and chloride ions via the up-regulation expression genes of ion transport (potassium voltage-gated channel subfamily H member 5, KCNH5; erine/threonine-protein kinase 32, STK32; salt-inducible kinase 1, SIK1; adiponectin, ACDC), and by accumulating plasma urea and free amino acid via the up-regulation expression genes of amino acid metabolism (ornithine decarboxylase antizyme 3, OAZ3; glutamine synthetase, GLUL; asparaginase-like protein 1b, ASRGL; L-amino-acid oxidase-like, LAAO; sodium-dependent neutral amino acid transporter B, SLC6A15s; amino acid permease, SLC7A9) in response to osmotic regulation. An investment of energy to maintain their homeostatic balance is required to salinity adaptation, therefore, the genes related to energy production and conversion (F-ATPase protein 6, ATP6; cytochrome c oxidase subunit I, COX1; cytochrome c oxidase subunit III, COX3; cytochrome b, CYTb; cytochrome P450 17A1, CYP17A1) were up-regulated with the increase of gene expression associated with lipid metabolism (apolipoprotein E precursor, APoE; coenzyme Q-binding protein, CoQ10; high-density lipoprotein particle, SAA) and carbohydrate metabolism (HK, MIP). These findings improve our understanding of the underlying molecular mechanisms involved in salinity adaptation and provide general guidance to illuminate the invasion potential of T. s. elegans into saline environments.
Hong et al. (2019) Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress. PeerJ 7:e6538 https://doi.org/10.7717/peerj.6538
Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California
Background In this study cull dairy cows from six California dairy herds were sampled seasonally over the course of a year. The objectives were to determine the prevalence of antimicrobial resistant (AMR) Salmonella spp. shed in cull cow feces, and the factors associated with fecal shedding of AMR and multidrug resistant (MDR) Salmonella. Methods Six dairy farms located in the San Joaquin Valley of California were identified and enrolled as a convenience sample. On each dairy, and once during each of the four seasons, 10 cull cows were randomly selected for fecal sampling on the day of their removal from the herd. In addition, study personnel completed a survey based on responses of the herd manager to questions related to the previous 4 month’s herd management and the specific cattle sampled. Fecal samples were submitted to the California Animal Health and Food Safety laboratory for Salmonella isolation. Antimicrobial resistance was evaluated using broth microdilution method and a gram-negative assay plate following Clinical Laboratory Standards Institute (CLSI) guidelines and breakpoint references. All statistical models were survey adjusted for number of animals on sampling day. Results A total of 62 Salmonella were isolated from 60 of the 239 fecal samples collected. For 12% (95% confidence interval (CI) [3–20]) of fecal samples a multidrug resistant Salmonella was isolated. The survey-weighted results for the two most common drug classes for which isolates were resistant were tetracycline (39%; 95% CI [27–51]) and ampicillin (18%; 95% CI [9–27]). An important finding was the identification of cephalosporin as the third most common drug class for which isolates were resistant, with ceftriaxone (10%; 95% CI [2–17]) being the most common drug associated with resistance in that class. At the cow-level, reason for culling, prior treatment with antimicrobial drugs as the reason for culling was associated with higher odds of isolating an AMR Salmonella isolate. At the herd-level, percent of animals monthly culled on the farm as well as number of milking cows in the herd were associated with isolation of antimicrobial resistant Salmonella in cull cows. Discussion Salmonella isolated from fecal samples from cull cows were resistant to important antimicrobials, such as ceftriaxone. The most common drug classes for which isolates were resistant were tetracyclines and beta-lactams, with ampicillin, ceftriaxone and ceftiofur being the three most common drugs within the latter. Cow and herd level factors were associated with isolating antimicrobial resistant Salmonella that should be further investigated for their potential role in promoting occurrence of AMR Salmonella. Our results also highlight the importance of monitoring dairy cattle sent to slaughter for shedding of Salmonella resistant to medically important antimicrobial drugs.
Pereira et al. (2019) Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California. PeerJ 7:e6546 https://doi.org/10.7717/peerj.6546
Sea stars of the genus Henricia Gray, 1840 (Echinodermata, Asteroidea) from Vostok Bay, Sea of Japan
We report seven species of the genus Henricia Gray, 1840 that were found in Vostok Bay, and two species from adjacent area, known from museum collection or seen in underwater footage. while existing literature reported no confirmed species from this area. Most of these species: H. djakonovi, H. alexeyi, H. densispina, H. hayashii, H. granulifera, H. pacifica, H. asiatica, and H. oculata robusta were reported from the Sea of Japan previously. H. nipponica, known from Japan, is reported from Russian seas for the first time. All studied taxa are re-described here using a range of morphological characters and partial 16S rRNA nucleotide sequences, life colorations of several species are reported for the first time, and an identification key is provided. Lectotype designations are fixed for studied series of species described by AM Djakonov.
Chichvarkhin et al. (2019) Sea stars of the genus Henricia Gray, 1840 (Echinodermata, Asteroidea) from Vostok Bay, Sea of Japan. PeerJ 7:e6585 https://doi.org/10.7717/peerj.6585
Spatial near future modeling of land use and land cover changes in the temperate forests of Mexico
The loss of temperate forests of Mexico has continued in recent decades despite wide recognition of their importance to maintaining biodiversity. This study analyzes land use/land cover change scenarios, using satellite images from the Landsat sensor. Images corresponded to the years 1990, 2005 and 2017. The scenarios were applied for the temperate forests with the aim of getting a better understanding of the patterns in land use/land cover changes. The Support Vector Machine (SVM) multispectral classification technique served to determine the land use/land cover types, which were validated through the Kappa Index. For the simulation of land use/land cover dynamics, a model developed in Dinamica-EGO was used, which uses stochastic models of Markov Chains, Cellular Automata and Weight of Evidences. For the study, a stationary, an optimistic and a pessimistic scenario were proposed. The projections based on the three scenarios were simulated for the year 2050. Five types of land use/land cover were identified and evaluated. They were primary forest, secondary forest, human settlements, areas without vegetation and water bodies. Results from the land use/land cover change analysis show a substantial gain for the secondary forest. The surface area of the primary forest was reduced from 55.8% in 1990 to 37.7% in 2017. Moreover, the three projected scenarios estimate further losses of the surface are for the primary forest, especially under the stationary and pessimistic scenarios. This highlights the importance and probably urgent implementation of conservation and protection measures to preserve these ecosystems and their services. Based on the accuracy obtained and on the models generated, results from these methodologies can serve as a decision tool to contribute to the sustainable management of the natural resources of a region.
Spatial and Geographic Information Science
Prieto-Amparán et al. (2019) Spatial near future modeling of land use and land cover changes in the temperate forests of Mexico. PeerJ 7:e6617 https://doi.org/10.7717/peerj.6617
Improvement of hydrogen production from Chlorella sp. biomass by acid-thermal pretreatment
Background Owing to the high growth rate, high protein and carbohydrate contents, and an ability to grow autotrophically, microalgal biomass is regarded as a promising feedstock for fermentative hydrogen production. However, the rigid cell wall of microalgae impedes efficient hydrolysis of the biomass, resulting in low availability of assimilable nutrients and, consequently, low hydrogen production. Therefore, pretreatment of the biomass is necessary in order to achieve higher hydrogen yield (HY). In the present study, acid-thermal pretreatment of Chlorella sp. biomass was investigated. Conditions for the pretreatment, as well as those for hydrogen production from the pretreated biomass, were optimized. Acid pretreatment was also conducted for comparison. Results Under optimum conditions (0.75% (v/v) H2SO4, 160 °C, 30 min, and 40 g-biomass/L), acid-thermal pretreatment yielded 151.8 mg-reducing-sugar/g-biomass. This was around 15 times that obtained from the acid pretreatment under optimum conditions (4% (v/v) H2SO4, 150 min, and 40 g-biomass/L). Fermentation of the acid-thermal pretreated biomass gave 1,079 mL-H2/L, with a HY of 54.0 mL-H2/g-volatile-solids (VS), while only 394 mL/L and 26.3 mL-H2/g-VS were obtained from the acid-pretreated biomass. Conclusions Acid-thermal pretreatment was effective in solubilizing the biomass of Chlorella sp. Heat exerted synergistic effect with acid to release nutrients from the biomass. Satisfactory HY obtained with the acid-thermal pretreated biomass demonstrates that this pretreatment method was effective, and that it should be implemented to achieve high HY.
Giang et al. (2019) Improvement of hydrogen production from Chlorella sp. biomass by acid-thermal pretreatment. PeerJ 7:e6637 https://doi.org/10.7717/peerj.6637
The chemical composition of a new “mica sandwich” foraminiferal species from the East Coast of Korea: Capsammina crassa sp. nov.
We describe a new agglutinated monothalamous foraminiferal species, Capsammina crassa sp. nov., based on integrated observations of the test morphology and the chemical characteristics of materials composing the test. The new species was found at a depth of <60 m on the East coast of Korea. The test morphology is typical of the genus Capsammina, comprising two or more mica plates with a ring of finely agglutinated mineral grains sandwiched between them and surrounding the cell body. There is no distinct test aperture. Elemental analyses of the agglutinated grains revealed 15 different types of mineral grains of which quartz is the most abundant. The surface areas of grains exposed on fractured surfaces ranged from 1.6 to 7,700 μm2 and the large plate-like grains forming the upper and lower surfaces measured about 420–2,350 μm in maximum width. The new species is morphologically similar to C. patelliformis, however, the differences in size, distribution area and depth support that these two species are distinct. This discovery is the first record of the genus Capsammina from the North Pacific. Therefore, it extends the biodiversity and geographical distribution of the genus Capsammina, which has been reported only from the bathyal NE Atlantic. Our finding also suggests the possibility of additional discovery of monothalamous foraminifera from around Korea.
Lee et al. (2019) The chemical composition of a new “mica sandwich” foraminiferal species from the East Coast of Korea: Capsammina crassa sp. nov.. PeerJ 7:e6642 https://doi.org/10.7717/peerj.6642
Dose-dependent and strain-dependent anti-obesity effects of Lactobacillus sakei in a diet induced obese murine model
Background Overweight and abdominal obesity, in addition to medical conditions such as high blood pressure, high blood sugar and triglyceride levels, are typical risk factors associated with metabolic syndrome. Yet, considering the complexity of factors and underlying mechanisms leading to these inflammatory conditions, a deeper understanding of this area is still lacking. Some probiotics have a reputation of a relatively-long history of safe use, and an increasing number of studies are confirming benefits including anti-obesity effects when administered in adequate amounts. Recent reports demonstrate that probiotic functions may widely differ with reference to either intra-species or inter-species related data. Such differences do not necessarily reflect or explain strain-specific functions of a probiotic, and thus require further assessment at the intra-species level. Various anti-obesity clinical trials with probiotics have shown discrepant results and require additional consolidated studies in order to clarify the correct dose of application for reliable and constant efficacy over a long period. Methods Three different strains of Lactobacillus sakei were administered in a high-fat diet induced obese murine model using three different doses, 1 × 1010, 1 × 109 and 1 × 108 CFUs, respectively, per day. Changes in body and organ weight were monitored, and serum chemistry analysis was performed for monitoring obesity associated biomarkers. Results Only one strain of L. sakei (CJLS03) induced a dose-dependent anti-obesity effect, while no correlation with either dose or body or adipose tissue weight loss could be detected for the other two L. sakei strains (L338 and L446). The body weight reduction primarily correlated with adipose tissue and obesity-associated serum biomarkers such as triglycerides and aspartate transaminase. Discussion This study shows intraspecies diversity of L. sakei and suggests that anti-obesity effects of probiotics may vary in a strain- and dose-specific manner.
Ji et al. (2019) Dose-dependent and strain-dependent anti-obesity effects of Lactobacillus sakei in a diet induced obese murine model. PeerJ 7:e6651 https://doi.org/10.7717/peerj.6651
Maintenance of dominant populations in heavily grazed grassland: Inference from a Stipa breviflora seed germination experiment
An understanding of population adaptation and maintenance mechanisms under interference from large herbivores is lacking and is a major focus of ecological research. In the Eurasian steppe, which has been subjected to continuous interference from domesticated ungulates throughout history and shows increased grazing, it is particularly urgent to analyze the ecological adaptation strategies of widely distributed Stipa plants. In this study, Stipa breviflora in a group of desert steppes in the Mongolian Plateau was selected to study the potential mechanism underlying the maintenance of dominant populations under the continuous interference of heavy grazing from the new perspective of seed germination rate. Laboratory experimental results showed that the values of the phenotypic traits of S. breviflora seeds were lower under a heavy grazing treatment than under a non-grazing treatment, but the seed germination rate did not decrease. The awns of non-grazed seeds significantly affected the seed germination rate, while those of heavily grazed seeds did not. Field observations showed that grazing does not significantly affect the population density of S. breviflora at different growth stages except in extremely wet and dry years. Our study suggests that under heavy grazing, S. breviflora uses an “opportunistic” ecological strategy to ensure population maintenance by increasing the seed germination rate and reducing dispersal via changes in associated seed phenotypic traits.
Liu et al. (2019) Maintenance of dominant populations in heavily grazed grassland: Inference from a Stipa breviflora seed germination experiment. PeerJ 7:e6654 https://doi.org/10.7717/peerj.6654
Minimum inhibitory concentration of nano-silver bactericides for beneficial microbes and its effect on Ralstonia solanacearum and seed germination of Japanese Cucumber (Cucumis sativus)
Background Plant growth-promoting rhizobacteria (PGPR) are highly promising biofertilizers that contribute to eco-friendly sustainable agriculture. There have been many reports on the anti-microbial properties of nanoparticles (NPs). Toxic effects of NPs under laboratory conditions have also reported; however, there is a lack of information about their uptake and mobility in organisms under environmental conditions. There is an urgent need to determine the highest concentration of NPs which is not detrimental for growth and proliferation of PGPR. Methods Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were used to measure the size and shape of NPs. Minimum inhibitory concentrations (MIC) of nano-silver on selected beneficial microbes and Ralstonia solanacearum were measured using the microdilution broth method. The percentage of seed germination was measured under in vitro conditions. Results NPs were spherical with a size of 16 ± 6 nm. Nano-silver at 12–40 mg l−1 inhibited the growth of bacteria. Seed application at 40 mg l−1 protected seeds from R. solanacearum and improved the rate of seed germination.
Sotoodehnia et al. (2019) Minimum inhibitory concentration of nano-silver bactericides for beneficial microbes and its effect on Ralstonia solanacearum and seed germination of Japanese Cucumber (Cucumis sativus). PeerJ 7:e6418 https://doi.org/10.7717/peerj.6418
Identification of an eight-gene signature for survival prediction for patients with hepatocellular carcinoma based on integrated bioinformatics analysis
Background Hepatocellular carcinoma (HCC) remains one of the leading causes of cancer-related death worldwide. Despite recent advances in imaging techniques and therapeutic intervention for HCC, the low overall 5-year survival rate of HCC patients remains unsatisfactory. This study aims to find a gene signature to predict clinical outcomes in HCC. Methods Bioinformatics analysis including Cox’s regression analysis, Kaplan-Meier (KM) and receiver operating characteristic curve (ROC) analysis and the random survival forest algorithm were performed to mine the expression profiles of 553 hepatocellular carcinoma (HCC) patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) public database. Results We selected a signature comprising eight protein-coding genes (DCAF13, FAM163A, GPR18, LRP10, PVRIG, S100A9, SGCB, and TNNI3K) in the training dataset (AUC = 0.77 at five years, n = 332). The signature stratified patients into high- and low-risk groups with significantly different survival in the training dataset (median 2.20 vs. 8.93 years, log-rank test P < 0.001) and in the test dataset (median 2.68 vs. 4.24 years, log-rank test P = 0.004, n = 221, GSE14520). Further multivariate Cox regression analysis showed that the signature was an independent prognostic factor for patients with HCC. Compared with TNM stage and another reported three-gene model, the signature displayed improved survival prediction power in entire dataset (AUC signature = 0.66 vs. AUC TNM = 0.64 vs. AUC gene model = 0.60, n = 553). Stratification analysis shows that it can be used as an auxiliary marker for many traditional staging models. Conclusions We constructed an eight-gene signature that can be a novel prognostic marker to predict the survival of HCC patients.
Qiao et al. (2019) Identification of an eight-gene signature for survival prediction for patients with hepatocellular carcinoma based on integrated bioinformatics analysis. PeerJ 7:e6548 https://doi.org/10.7717/peerj.6548
Effects of handling and short-term captivity: a multi-behaviour approach using red sea urchins, Mesocentrotus franciscanus
Understanding the effects of captivity-induced stress on wild-caught animals after their release back into the wild is critical for the long-term success of relocation and reintroduction programs. To date, most of the research on captivity stress has focused on vertebrates, with far less attention paid to invertebrates. Here, we examine the effect of short-term captivity (i.e., up to four days) on self-righting, aggregation, and predator-escape behaviours in wild-caught red sea urchins, Mesocentrotus franciscanus, after their release back into the wild. Aggregation behaviour, which has been linked to feeding in sea urchins, was not affected by handling or captivity. In contrast, the sea urchins that had been handled and released immediately, as well as those that were handled and held captive, took longer to right themselves and were poorer at fleeing from predators than wild, unhandled sea urchins. These results indicate that handling rather than captivity impaired these behaviours in the short term. The duration of captivity did not influence the sea urchin behaviours examined. Longer-term monitoring is needed to establish what the fitness consequences of these short-term behavioural changes might be. Our study nevertheless highlights the importance of considering a suite of responses when examining the effects of capture and captivity. Our findings, which are based on a locally abundant species, can inform translocation efforts aimed at bolstering populations of ecologically similar but depleted invertebrate species to retain or restore important ecosystem functions.
Bose et al. (2019) Effects of handling and short-term captivity: a multi-behaviour approach using red sea urchins, Mesocentrotus franciscanus. PeerJ 7:e6556 https://doi.org/10.7717/peerj.6556
High virulence gene diversity in Streptococcus pyogenes isolated in Central Italy
Globally, Streptococcus pyogenes poses a continuous burden on human health, causing both self-limiting and life-threatening diseases. Therefore, studying the profile of virulence genes and their combinations is essential to monitor the epidemiology and pathogenic potential of this important species. Thus, the aim of this study was to analyze related genetic features of clinical strains collected in Italy in 2012 in order to obtain a valid picture of their virulence profile that could be compared to similar studies made in other countries approximately in the same period. We conducted emm typing and fibronectin-collagen-T antigen (FCT) region typing in 122 Streptococcus pyogenes strains. Furthermore, several additional virulence genes were screened by polymerase chain reaction. We found correlations between emm types and FCT region profiles. emm1 strains were mainly associated with FCT2 and FCT6, while emm89 and emm12 strains were associated with FCT4. FCT5 was mainly represented in emm4, emm6, and emm75 strains. Significantly, we defined subtypes for each FCT type based on the differences in single and double loci compared to the reference scheme used for the classification of the FCT region. In addition, new FCT-region variants with differences in multiple loci were also recorded. Cluster analysis based on virulence gene profiling showed a non-random distribution within each emm type. This study added new data to existing studies conducted worldwide and revealed new variability scores in circulating Streptococcus pyogenes strains and new assortments in well-established virulence gene signatures.
Bencardino et al. (2019) High virulence gene diversity in Streptococcus pyogenes isolated in Central Italy. PeerJ 7:e6613 https://doi.org/10.7717/peerj.6613
Evolution of host plant use and diversification in a species complex of parasitic weevils (Coleoptera: Curculionidae)
Weevils (Coleoptera: Curculionoidea) represent one of the most diverse groups of organisms on Earth; interactions with their host plants have been recognized to play a central role in their remarkable diversity, yet the exact mechanisms and factors still remain poorly understood. Using phylogenetic comparative analyses, here we investigate the evolution of host use and its possible role in diversification processes of Rhinusa and Gymnetron, two closely related groups of weevils that feed and develop inside plant tissues of hosts within the families Scrophulariaceae and Plantaginaceae. We found strong evidence for phylogenetic conservatism of host use at the plant family level, most likely due to substantial differences in the chemical composition of hosts, reducing the probability of shifts between host families. In contrast, the use of different plant organs represents a more labile ecological trait and ecological niche expansion that allows a finer partitioning of resources. Rhinusa and Gymnetron weevils initially specialized on plants within Scrophulariaceae and then shifted to the closely related Plantaginaceae; likewise, a gall inducing behavior evolved from non-galler weevils, possibly in response to resource competition, as galls facilitate larval development by providing enhanced nutrition and a favorable microhabitat. Results from trait-dependent diversification analyses suggest that both use of hosts within Plantaginaceae and parasitism on fruits and seed capsules are associated with enhanced diversification of Rhinusa and Gymnetron via low extinction rates. Our study provides quantitative evidence and insights on the ecological factors that can promote diversification in phytophagous insects that feed and develop inside plant tissues.
Hernández-Vera et al. (2019) Evolution of host plant use and diversification in a species complex of parasitic weevils (Coleoptera: Curculionidae). PeerJ 7:e6625 https://doi.org/10.7717/peerj.6625
Transcriptome sequencing of olfactory-related genes in olfactory transduction of large yellow croaker (Larimichthy crocea) in response to bile salts
Fish produce and release bile salts as chemical signalling substances that act as sensitive olfactory stimuli. To investigate how bile salts affect olfactory signal transduction in large yellow croaker (Larimichthy crocea), deep sequencing of olfactory epithelium was conducted to analyse olfactory-related genes in olfactory transduction. Sodium cholates (SAS) have typical bile salt chemical structures, hence we used four different concentrations of SAS to stimulate L. crocea, and the fish displayed a significant behavioural preference for 0.30% SAS. We then sequenced olfactory epithelium tissues, and identified 9938 unigenes that were significantly differentially expressed between SAS-stimulated and control groups, including 9055 up-regulated and 883 down-regulated unigenes. Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses found eight categories linked to the olfactory transduction pathway that was highly enriched with some differentially expressed genes (DEGs), including the olfactory receptor (OR), Adenylate cyclase type 3 (ADCY3) and Calmodulin (CALM). Genes in these categories were analysed by RT-qPCR, which revealed aspects of the pathway transformation between odor detection, and recovery and adaptation. The results provide new insight into the effects of bile salt stimulation in olfactory molecular mechanisms in fishes, and expands our knowledge of olfactory transduction, and signal generation and decline.
Hu et al. (2019) Transcriptome sequencing of olfactory-related genes in olfactory transduction of large yellow croaker (Larimichthy crocea) in response to bile salts. PeerJ 7:e6627 https://doi.org/10.7717/peerj.6627
Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites
Background Captive populations permit research and conservation of endangered species in which these efforts are hardly implemented in wild populations. Thus, analysing genetic diversity and structure of captive populations offers unique opportunities. One example is the critically endangered Blue-crowned Laughingthrush, Garrulax courtoisi, which has only two known wild populations in Wuyuan, Jiangxi and Simao, Yunnan, China. We carried out the first conservation genetic study, in order to provide useful implications that allow for successful ex situ conservation and management of the Blue-crowned Laughingthrush. Methods Using the novel microsatellite markers developed by whole-genome sequencing, we genotyped two captive populations, from the Ocean Park Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the Wuyuan wild population since the year 2010–2011, respectively. The genetic diversity of captive Blue-crowned Laughingthrush populations was estimated based on genetic polymorphisms revealed by a new microsatellite data set and mitochondrial sequences. Then, we characterised the population structure using STRUCTURE, principal coordinates analysis, population assignment test using the microsatellite data, and haplotype analysis of mitochondrial data. Additionally, we quantified genetic relatedness based on the microsatellite data with ML-Relate. Results Our results showed equally low levels of genetic diversity of the two captive Blue-crowned Laughingthrush populations. The population structure analysis, population assignment test using the microsatellite data, and haplotype analysis of the mitochondrial data showed weak population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified. Discussion This study offers a genetic tool and consequently reveals a low level of genetic diversity within populations of a critically endangered bird species. Furthermore, our results indicate that we cannot exclude the probability that the origin of the Hong Kong captive population was the wild population from Wuyuan. These results provide valuable knowledge that can help improve conservation management and planning for both captive and wild Blue-crowned Laughingthrush populations.
Chen et al. (2019) Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites. PeerJ 7:e6643 https://doi.org/10.7717/peerj.6643
Fine-scale substrate heterogeneity does not affect arthropod communities on green roofs
Green roofs, which are roofs with growing substrate and vegetation, can provide habitat for arthropods in cities. Maintaining a diversity of arthropods in an urban environment can enhance the functions they fill, such as pest control and soil development. Theory suggests that the creation of a heterogeneous environment on green roofs would enhance arthropod diversity. Several studies have examined how arthropod diversity can be enhanced on green roofs, and particularly whether substrate properties affect the arthropod community, but a gap remains in identifying the effect of substrate heterogeneity within a green roof on the arthropod community. In this paper, it is hypothesized that creating heterogeneity in the substrate would directly affect the diversity and abundance of some arthropod taxa, and indirectly increase arthropod diversity through increased plant diversity. These hypotheses were tested using green roof plots in four treatments of substrate heterogeneity: (1) homogeneous dispersion; (2) mineral heterogeneity—with increased tuff concentration in subplots; (3) organic heterogeneity—with decreased compost concentrations in subplots; (4) both mineral and organic heterogeneity. Each of the four treatments was replicated twice on each of three roofs (six replicates per treatment) in a Mediterranean region. There was no effect of substrate heterogeneity on arthropod diversity, abundance, or community composition, but there were differences in arthropod communities among roofs. This suggests that the location of a green roof, which can differ in local climatic conditions, can have a strong effect on the composition of the arthropod community. Thus, arthropod diversity may be promoted by building green roofs in a variety of locations throughout a city, even if the roof construction is similar on all roofs.
Schindler et al. (2019) Fine-scale substrate heterogeneity does not affect arthropod communities on green roofs. PeerJ 7:e6445 https://doi.org/10.7717/peerj.6445
Large carnivore habitat suitability modelling for Romania and associated predictions for protected areas
Habitat characteristics associated with species occurrences represent important baseline information for wildlife management and conservation, but have rarely been assessed for countries recently joining the EU. We used footprint tracking data and landscape characteristics in Romania to investigate the occurrence of brown bear (Ursus arctos), gray wolf (Canis lupus) and Eurasian lynx (Lynx lynx) and to compare model predictions between Natura 2000 and national-level protected areas (gap analysis). Wolves were more likely to occur where rugged terrain was present. Increasing proportion of forest was positively associated with occurrence of all large carnivores, but forest type (broadleaf, mixed, or conifer) generally varied with carnivore species. Areas where cultivated lands were extensive had little suitable habitat for lynx, whereas bear occurrence probability decreased with increasing proportion of built areas. Pastures were positively associated with wolf and lynx occurrence. Brown bears occurred primarily where national roads with high traffic volumes were at low density, while bears and lynx occurred at medium-high densities of communal roads that had lower traffic volumes. Based on predictions of carnivore distributions, natural areas protected in national parks were most suitable for carnivores, nature parks were less suitable, whereas EU-legislated Natura 2000 sites had the lowest probability of carnivore presence. Our spatially explicit carnivore habitat suitability predictions can be used by managers to amend borders of existing sites, delineate new protected areas, and establish corridors for ecological connectivity. To assist recovery and recolonization, management could also focus on habitat predicted to be suitable but where carnivores were not tracked.
Cristescu et al. (2019) Large carnivore habitat suitability modelling for Romania and associated predictions for protected areas. PeerJ 7:e6549 https://doi.org/10.7717/peerj.6549
Identification of gene-phenotype connectivity associated with flavanone naringenin by functional network analysis
Naringenin, extracted from grapefruits and citrus fruits, is a bioactive flavonoid with antioxidative, anti-inflammatory, antifibrogenic, and anticancer properties. In the past two decades, the growth of publications of naringenin in PubMed suggests that naringenin is quickly gaining interest. However, systematically regarding its biological functions connected to its direct and indirect target proteins remains difficult but necessary. Herein, we employed a set of bioinformatic platforms to integrate and dissect available published data of naringenin. Analysis based on DrugBank and the Search Tool for the Retrieval of Interacting Genes/Proteins revealed seven direct protein targets and 102 indirect protein targets. The protein–protein interaction (PPI) network of total 109 naringenin-mediated proteins was next visualized using Cytoscape. What’s more, all naringenin-mediated proteins were subject to Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis by the Database for Annotation, Visualization and Integrated Discovery, which resulted in three ESR1-related signaling pathways and prostate cancer pathway. Refined analysis of PPI network and KEGG pathway identified four genes (ESR1, PIK3CA, AKT1, and MAPK1). Further genomic analysis of four genes using cBioPortal indicated that naringenin might exert biological effects via ESR1 signaling axis. In general, this work scrutinized naringenin-relevant knowledge and provided an insight into the regulation and mediation of naringenin on prostate cancer.
Fu et al. (2019) Identification of gene-phenotype connectivity associated with flavanone naringenin by functional network analysis. PeerJ 7:e6611 https://doi.org/10.7717/peerj.6611
Increased risk of thyroid disease in patients with Sjogren's syndrome: a systematic review and meta-analysis
Background Sjogren’s syndrome (SS) is a chronic autoimmune epithelitis characterized by disruption of epithelial cells, ensuing lymphoplasmocytic infiltration of exocrine glands, and subsequent dryness of the mouth and eyes. Individuals with SS are more likely to have the thyroid disease. However, this association remains controversial. This meta-analysis aimed to evaluate the risk of thyroid disease in patients with SS. Methods We performed this systematic review by searching both English and Chinese literature databases. Random- or fixed-effects models were used to summarize the association between thyroid disease and SS. The results were subjected to meta-analysis with odds ratios (ORs) and corresponding 95% confidence intervals (CIs). Results The eight articles in this meta-analysis included 988 SS cases and 2,884 controls. Overall, the risk of thyroid disease in patients with SS was significantly increased compared with controls (OR, 3.29; 95% CI [2.08–5.21]). The risk of autoimmune thyroid disease (AITD) and non-AITD were also higher in patients with SS than in controls (OR, 3.48; 95% CI [1.59–7.63]; and OR, 2.90; 95% CI [1.51–5.57], respectively). Conclusions To the best of our knowledge, this systematic review is the first to demonstrate that the risk of thyroid disease was increased in SS compared to controls, suggesting that SS patients should be screened for thyroid disease.
Sun et al. (2019) Increased risk of thyroid disease in patients with Sjogren's syndrome: a systematic review and meta-analysis. PeerJ 7:e6737 https://doi.org/10.7717/peerj.6737
Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets
Background Current environmental pollution factors, particularly the distribution and diffusion of heavy metals in soil and water, are a high risk to local environments and humans. Despite striking advances in methods to detect contaminants by a variety of chemical and physical solutions, these methods have inherent limitations such as small dimensions and very low coverage. Therefore, identifying novel contaminant biomarkers are urgently needed. Methods To better track heavy metal contaminations in soil and water, integrated bioinformatics analysis to identify biomarkers of relevant heavy metal, such as As, Cd, Pb and Cu, is a suitable method for long-term and large-scale surveys of such heavy metal pollutants. Subsequently, the accuracy and stability of the results screened were experimentally validated by quantitative PCR experiment. Results We obtained 168 differentially expressed genes (DEGs) which contained 59 up-regulated genes and 109 down-regulated genes through comparative bioinformatics analyses. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of these DEGs were performed, respectively. GO analyses found that these DEGs were mainly related to responses to chemicals, responses to stimulus, responses to stress, responses to abiotic stimulus, and so on. KEGG pathway analyses of DEGs were mainly involved in the protein degradation process and other biologic process, such as the phenylpropanoid biosynthesis pathways and nitrogen metabolism. Moreover, we also speculated that nine candidate core biomarker genes (namely, NILR1, PGPS1, WRKY33, BCS1, AR781, CYP81D8, NR1, EAP1 and MYB15) might be tightly correlated with the response or transport of heavy metals. Finally, experimental results displayed that these genes had the same expression trend response to different stresses as mentioned above (Cd, Pb and Cu) and no mentioned above (Zn and Cr). Conclusion In general, the identified biomarker genes could help us understand the potential molecular mechanisms or signaling pathways responsive to heavy metal stress in plants, and could be applied as marker genes to track heavy metal pollution in soil and water through detecting their expression in plants growing in those environments.
Niu et al. (2019) Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets. PeerJ 7:e6495 https://doi.org/10.7717/peerj.6495
Long-term high physical activity modulates event-related potential indices of inhibitory control in postmenopausal women
Background Inhibition processing is sensitive to aging, and an age-related decline in inhibition processing has been associated with an accelerated rate of progression to Alzheimer disease. Elderly women are two to three times more likely than age-matched men to have Alzheimer disease. Therefore, this study examined whether long-term high physical activity affects inhibitory processing, specifically among postmenopausal women. Methods In total, 251 candidates were screened using the Montreal Cognitive Assessment and the Raven’s Standard Progressive Matrices to assess their cognitive abilities and the International Physical Activity Questionnaire (Chinese version) to assess their physical activity levels. The participants were then grouped into either a long-term high physical activity group (defined as more than 3 days of high intensity activity per week and gross metabolic equivalent minutes (MET-minutes) higher than 1,500 MET-minutes/week or a gross MET higher than 3,000 MET-minutes/week obtained through walking or other moderate or high intensity activity) or a control group and matched for demographic and health characteristics as well as cognitive scores. Event-related potentials (ERPs) were recorded as participants performed a Go/No-go task to assess inhibition processing. Results The long-term high physical activity group (n = 30) had faster Go reaction times than the control group (n = 30), whereas no significant difference between the two groups was found in their performance accuracy on the No-go task. For the ERP results, the latency of N2 component was significantly shorter in the long-term high physical activity group than that in the control group. Discussion The results of this study suggested that long-term high physical activity may increase the efficiency of the inhibitory control system by increasing the activity of response monitoring processes.
Xu et al. (2019) Long-term high physical activity modulates event-related potential indices of inhibitory control in postmenopausal women. PeerJ 7:e6523 https://doi.org/10.7717/peerj.6523
Estimating probabilistic context-free grammars for proteins using contact map constraints
Interactions between amino acids that are close in the spatial structure, but not necessarily in the sequence, play important structural and functional roles in proteins. These non-local interactions ought to be taken into account when modeling collections of proteins. Yet the most popular representations of sets of related protein sequences remain the profile Hidden Markov Models. By modeling independently the distributions of the conserved columns from an underlying multiple sequence alignment of the proteins, these models are unable to capture dependencies between the protein residues. Non-local interactions can be represented by using more expressive grammatical models. However, learning such grammars is difficult. In this work, we propose to use information on protein contacts to facilitate the training of probabilistic context-free grammars representing families of protein sequences. We develop the theory behind the introduction of contact constraints in maximum-likelihood and contrastive estimation schemes and implement it in a machine learning framework for protein grammars. The proposed framework is tested on samples of protein motifs in comparison with learning without contact constraints. The evaluation shows high fidelity of grammatical descriptors to protein structures and improved precision in recognizing sequences. Finally, we present an example of using our method in a practical setting and demonstrate its potential beyond the current state of the art by creating a grammatical model of a meta-family of protein motifs. We conclude that the current piece of research is a significant step towards more flexible and accurate modeling of collections of protein sequences. The software package is made available to the community.
Dyrka et al. (2019) Estimating probabilistic context-free grammars for proteins using contact map constraints. PeerJ 7:e6559 https://doi.org/10.7717/peerj.6559
Impact of El Niño-Southern Oscillation 2015-2016 on the soluble proteomic profile and cytolytic activity of Millepora alcicornis (“fire coral”) from the Mexican Caribbean
Reef-forming cnidarians are extremely susceptible to the “bleaching” phenomenon caused by global warming. The effect of elevated seawater temperature has been extensively studied on Anthozoans; however, to date the impact of thermal stress on the expression of genes and proteins in Hydrozoan species has not been investigated. The present study aimed to determine the differential proteomic profile of Millepora alcicornis, which inhabits the Mexican Caribbean, in response to the El Niño-Southern Oscillation 2015–2016. Additionally, the cytolytic activity of the soluble proteomes obtained from normal and bleached M. alcicornis was assessed. Bleached specimens showed decreased symbiont’s density and chlorophyll a and c2 levels. After bleaching, we observed a differential expression of 17 key proteins, tentatively identified as related to exocytosis, calcium homeostasis, cytoskeletal organization, and potential toxins, including a metalloprotease, a phospholipase A2 (PLA2), and an actitoxin. Although, some of the differentially expressed proteins included potential toxins, the hemolytic, PLA2, and proteolytic activities elicited by the soluble proteomes from bleached and normal specimens were not significantly different. The present study provides heretofore-unknown evidence that thermal stress produces a differential expression of proteins involved in essential cellular processes of Hydrozoan species. Even though our results showed an over-expression of some potential toxin-related proteins, the cytolytic effect (as assessed by hemolytic, PLA2, and caseinolytic activities) was not increased in bleached M. alcicornis, which suggests that the cytolysis is mainly produced by toxins whose expression was not affected by temperature stress. These findings allow hypothesizing that this hydrocoral is able to prey heterotrophically when suffering from moderate bleaching, giving it a better chance to withstand the effects of high temperature.
Olguín-López et al. (2019) Impact of El Niño-Southern Oscillation 2015-2016 on the soluble proteomic profile and cytolytic activity of Millepora alcicornis (“fire coral”) from the Mexican Caribbean. PeerJ 7:e6593 https://doi.org/10.7717/peerj.6593
Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys
Background Endogenous retroviruses (ERV) are remnants of former exogenous retroviruses that had previously invaded the germ line of the host that can be vertically transmitted across generations. While the majority of ERVs lack infectious capacity due to the accumulation of deleterious mutations, some ERVs remain active and produce potentially infectious viral particles. ERV sequences have been reported in all mammals; however, the distribution and diversity of ERVs in several primate taxa remains unclear. The aim of this study was to identify and classify the ERV sequences in the genomes of the golden snub-nosed monkey (Rhinopithecus roxellana) and the black and white snub-nosed monkey (Rhinopithecus bieti), two endangered primate species that exploit high altitude (2,500–4,500 m) temperate forests in southern and central China. Methods We used a TBLASTN program to search the ERV sequences of golden snub-nosed monkey genome and the black and white snub-nosed monkey genome. We retrieved all complete accession sequences from the homology search and then used the program, RetroTector, to check and identify the ERV sequences. Results We identified 284 and 263 endogenous retrovirus sequences in R. roxellana and R. bieti respectively. The proportion of full-length sequences of all ERV was 30% in R. roxellana and 21% in R. bieti and they were described as class I and class II or gamma-retrovirus and beta-retrovirus genera. The truncation pattern distribution in the two species was virtually identical. By analyzing and comparing ERV orthologues among 6 primate species, we identified the co-evolution of ERVs with their host. We also examined ERV-like sequences and found 48 such genes in R. roxellana and 63 in R. bieti. Some of those genes are associated with diseases, suggesting that ERVs might have involved the abnormal expression of certain genes that have contributed to deleterious consequences for the host. Conclusions Our results indicate that ERV sequences are widely distributed in snub-nosed monkeys, and their phylogenetic history can mirror that of their hosts over long evolutionary time scales. In addition, ERV sequences appear to have an important influence on the evolution of host pathology.
Wang et al. (2019) Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys. PeerJ 7:e6602 https://doi.org/10.7717/peerj.6602
Phytobiomes are compositionally nested from the ground up
Plant-associated microbes are critical players in host health, fitness and productivity. Despite microbes’ importance in plants, seeds are mostly sterile, and most plant microbes are recruited from an environmental pool. Surprisingly little is known about the processes that govern how environmental microbes assemble on plants in nature. In this study we examine how bacteria are distributed across plant parts, and how these distributions interact with spatial gradients. We sequenced amplicons of bacteria from the surfaces of six plant parts and adjacent soil of Scaevola taccada, a common beach shrub, along a 60 km transect spanning O’ahu island’s windward coast, as well as within a single intensively-sampled site. Bacteria are more strongly partitioned by plant part as compared with location. Within S. taccada plants, microbial communities are highly nested: soil and rhizosphere communities contain much of the diversity found elsewhere, whereas reproductive parts fall at the bottom of the nestedness hierarchy. Nestedness patterns suggest either that microbes follow a source/sink gradient from the ground up, or else that assembly processes correlate with other traits, such as tissue persistence, that are vertically stratified. Our work shines light on the origins and determinants of plant-associated microbes across plant and landscape scales.
Amend et al. (2019) Phytobiomes are compositionally nested from the ground up. PeerJ 7:e6609 https://doi.org/10.7717/peerj.6609
A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya
Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I–III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV and PVBV indicate that these viruses have likely been underreported due to the unavailability of diagnostic tools.
Wainaina et al. (2019) A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya. PeerJ 7:e6465 https://doi.org/10.7717/peerj.6465
Vocal recognition of a nest-predator in black grouse
Corvids count among the important predators of bird nests. They are vocal animals and one can expect that birds threatened by their predation, such as black grouse, are sensitive to and recognize their calls. Within the framework of field studies, we noticed that adult black grouse were alerted by raven calls during periods outside the breeding season. Since black grouse are large, extremely precocial birds, this reaction can hardly be explained by sensitization specifically to the threat of nest predation by ravens. This surprising observation prompted us to study the phenomenon more systematically. According to our knowledge, the response of birds to corvid vocalization has been studied in altricial birds only. We tested whether the black grouse distinguishes and responds specifically to playback calls of the common raven. Black grouse recognized raven calls and were alerted, displaying typical neck stretching, followed by head scanning, and eventual escape. Surprisingly, males tended to react faster and exhibited a longer duration of vigilance behavior compared to females. Although raven calls are recognized by adult black grouse out of the nesting period, they are not directly endangered by the raven. We speculate that the responsiveness of adult grouse to raven calls might be explained as a learned response in juveniles from nesting hens that is then preserved in adults, or by a known association between the raven and the red fox. In that case, calls of the raven would be rather interpreted as a warning signal of probable proximity of the red fox.
Policht et al. (2019) Vocal recognition of a nest-predator in black grouse. PeerJ 7:e6533 https://doi.org/10.7717/peerj.6533
Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia)
Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes ‘Ursidae’ and ‘Ursinae-Tremarctinae’. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical events involving varying food and environmental preferences. The high phylogenetic signal in the node Tremarctinae probably indicates that the basicranium configuration of these bears was obtained early in their evolutionary history. Finally, our results of the basicranium and skull length ratios indicate that in Tremarctinae, the basicranium size was not determined by phylogeny but instead by other factors, such as adaptive responses to climatic changes and competition with other carnivores.
Arnaudo et al. (2019) Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia). PeerJ 7:e6597 https://doi.org/10.7717/peerj.6597
Predicting electrocardiogram interpretation performance in Advanced Cardiovascular Life Support simulation: comparing knowledge tests and simulation performance among Mexican medical students
Background Simulation plays a key role in assessing performance in Advanced Cardiovascular Life Support (ACLS). Traditional knowledge tests are also important for assessing the cognitive elements of ACLS performance. However, the association between the two has not been established. In this study, we focus on one important element in ACLS—interpretation of electrocardiograms (ECG)—and the potential of knowledge tests to serve as predictors of improvement in ACLS performance. Methods We looked at the correlation between Mexican medical students’ improvement in ECG interpretation performance in ACLS megacode simulations (from the start of the semester to the end of the semester), and their scores on ECG interpretation knowledge tests. Results We found significant improvement in ECG interpretation in ACLS megacode simulation (from pre-semester to post-semester), but this was not predicted by the ECG interpretation knowledge test scores. The correlation was .079 (p = 0.66). Conclusions These results suggest that even cognitive tasks such as ECG interpretation can be expressed and assessed differently in simulation versus traditional knowledge testing.
Smith et al. (2019) Predicting electrocardiogram interpretation performance in Advanced Cardiovascular Life Support simulation: comparing knowledge tests and simulation performance among Mexican medical students. PeerJ 7:e6632 https://doi.org/10.7717/peerj.6632
Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood
Caffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuable timber tree species in China . We performed a comprehensive analysis of COMT genes in the C. bungei genome by describing the gene structure and phylogenetic relationships of each family member using bioinformatics-based methods. A total of 23 putative COMT genes were identified using the conserved domain sequences and amino acid sequences of COMTs from Arabidopsis thaliana and Populus trichocarpa as probes. Phylogenetic analysis showed that 23 CbuCOMTs can be divided into three groups based on their structural characteristics; five conserved domains were found in the COMT family. Promoter analysis indicated that the CbuCOMT promoters included various cis-acting elements related to growth and development. Real-time quantitative polymerase chain reaction (PCR) analysis showed differential expression among CbuCOMTs. CbuCOMT2, 7, 8, 9, 10, 12, 13, 14, 21, and 23 were mainly expressed in xylem. Only CbuCOMT23 was significantly downregulated in tension wood and upregulated in opposite wood compared to normal wood. Our study provides new information about the CbuCOMT gene family and will facilitate functional characterisation in further research.
Lu et al. (2019) Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood. PeerJ 7:e6520 https://doi.org/10.7717/peerj.6520
Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA
Background Adrenocortical carcinoma (ACC) is a rare and aggressive malignant cancer in the adrenal cortex with poor prognosis. Though previous research has attempted to elucidate the progression of ACC, its molecular mechanism remains poorly understood. Methods Gene transcripts per million (TPM) data were downloaded from the UCSC Xena database, which included ACC (The Cancer Genome Atlas, n = 77) and normal samples (Genotype Tissue Expression, n = 128). We used weighted gene co-expression network analysis to identify gene connections. Overall survival (OS) was determined using the univariate Cox model. A protein–protein interaction (PPI) network was constructed by the search tool for the retrieval of interacting genes. Results To determine the critical genes involved in ACC progression, we obtained 2,953 significantly differentially expressed genes and nine modules. Among them, the blue module demonstrated significant correlation with the “Stage” of ACC. Enrichment analysis revealed that genes in the blue module were mainly enriched in cell division, cell cycle, and DNA replication. Combined with the PPI and co-expression networks, we identified four hub genes (i.e., TOP2A, TTK, CHEK1, and CENPA) that were highly expressed in ACC and negatively correlated with OS. Thus, these identified genes may play important roles in the progression of ACC and serve as potential biomarkers for future diagnosis.
Xia et al. (2019) Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA. PeerJ 7:e6555 https://doi.org/10.7717/peerj.6555
Acute toxicity and responses of antioxidant systems to dibutyl phthalate in neonate and adult Daphnia magna
Dibutyl phthalate (DBP) poses a severe threat to aquatic ecosystems, introducing hazards to both aquatic species and human health. The ecotoxic effects of DBP on aquatic organisms have not been fully investigated. This study investigates acute toxicity, oxidative damage, and antioxidant enzyme parameters in neonate and adult Daphnia magna exposed to DBP. The obtained results show comparable DBP toxic responses in neonates and adults. The median lethal concentrations (LC50) of DBP in neonates exposed for 24 and 48 h were 3.48 and 2.83 mg/L, respectively. The LC50 of adults for the same DBP exposure durations were 4.92 and 4.31 mg/L, respectively. Increased hydrogen peroxide and malondialdehyde were found in neonates and adults at both 24 and 48 h, while the total antioxidant capacity decreased. Superoxide dismutase activity increased significantly in neonates and adults exposed to 0.5 mg/L DBP, and subsequently diminished at higher DBP concentrations and prolonged exposure. Catalase and glutathione S-transferases activities both decreased markedly in neonates and adults. The changes observed were found to be time and concentration dependent. Overall, these data indicated that the acute toxic effects of DBP exposure on neonates were more pronounced than in adults, and oxidative injury may be the main mechanism of DBP toxicity. These results provide a functional link for lipid peroxidation, antioxidant capacity, and antioxidant enzyme levels in the Daphnia magna response to DBP exposure.
Shen et al. (2019) Acute toxicity and responses of antioxidant systems to dibutyl phthalate in neonate and adult Daphnia magna. PeerJ 7:e6584 https://doi.org/10.7717/peerj.6584
Staphylococcus spp. associated with subclinical bovine mastitis in central and northeast provinces of Thailand
Background Staphylococcus spp. are major cause of bovine mastitis (BM) worldwide leading to economic damage to dairy farms and public health threat. Recently, a newly emerged Staphylococcus argenteus has been found as a human and animal pathogen. Molecular characteristics, virulence and antibiotic resistant phenotypes of bacteria causing BM in Thailand are rare. This study aimed to investigated Staphylococcus spp. associated with subclinical bovine mastitis (SCM) in Thailand. Methods Milk samples were collected from 224 cows of 52 dairy herds in four central and northeast provinces. Total somatic cell counts (SCC) and California mastitis test (CMT) were used to identify SCM cows. Milk samples were cultured for Staphylococcus spp. Coagulase-positive isolates were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Organisms suspected as S. argenteus were verified by detecting nonribosomal peptide synthetase gene. All isolates were checked for antibiograms and the presence of various virulence genes. Results From the 224 milk samples of 224 cows, 132 (59%) were positive for SCM by SCC and CMT and 229 staphylococcal isolates were recovered. They were 32 coagulase-positive (24 S. aureus and eight S. argenteus) and 197 coagulase-negative. PFGE of the S. aureus and S. argenteus revealed 11 clusters and a non-typeable pattern. MLST of representatives of the 11 PFGE clusters, three PFGE non-typeable S. aureus isolates from different locations and S. argenteus showed 12 sequence types. The eight S. argenteus isolates belonged to ST1223 (three isolates), ST2250 (two isolates), and ST2793 (two isolates). The antimicrobial tests identified 11 (46%) methicillin-resistant S. aureus and 25 (13%) methicillin-resistant coagulase-negative isolates, while seven S. argenteus were methicillin-susceptible and one isolate was methicillin-resistant. All of the 229 isolates were multiply resistant to other antibiotics. The most prevalent virulence genes of the 24 S. aureus isolates were clfA, coa and spa (X and IgG-binding region) (100%), hla (96%), pvl (96%) and sec (79%). Six S. argenteus isolates carried one enterotoxin gene each and other virulence genes including coa, clfA, hla/hlb, spa, tsst and pvl, indicating their pathogenic potential. Conclusion and perspective This is the first report on the S. argenteus from cow milk samples with SCM. Data on the molecular characteristics, virulence genes and antibiograms of the Staphylococcus spp. obtained from the present study showed a wide spread and increasing trend of methicillin-resistance and multiple resistance to other antibiotics. This suggests that the “One Health” practice should be nurtured, not only at the dairy farm level, but also at the national or even the international levels through cooperation of different sectors (dairy farmers, veterinarians, medical and public health personnel and scientists) in order to effectively combat and control the spread of these pathogens.
Pumipuntu et al. (2019) Staphylococcus spp. associated with subclinical bovine mastitis in central and northeast provinces of Thailand. PeerJ 7:e6587 https://doi.org/10.7717/peerj.6587
Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken
The gut microbiota is crucial for metabolic homeostasis, immunity, growth and overall health, and it is recognized that early-life microbiota acquisition is a pivotal event for later-life health. Recent studies show that gut microbiota diversity and functional activity are synchronized with the host circadian rhythms in healthy individuals, and circadian disruption elicits dysbiosis in mammalian models. However, no studies have determined the associations between circadian disruption in early life, microbiota colonization, and the consequences for microbiota structure in birds. Chickens, as a major source of protein around the world, are one of the most important agricultural species, and their gut and metabolic health are significant concerns. The poultry industry routinely employs extended photoperiods (>18 h light) as a management tool, and their impacts on the chicken circadian, its role in gut microbiota acquisition in early life (first 3 weeks of life), and consequences for later life microbiota structure remain unknown. In this study, the objectives were to (a) characterize circadian activity under two different light regimes in layer chicken (12/12 h′ Light/Dark (LD) and 23/1 h LD), (b) characterize gut microbiota acquisition and composition in the first 4 weeks of life, (c) determine if gut microbiota oscillate in synchrony with the host circadian rhythm, and (d) to determine if fecal microbiota is representative of cecal microbiota in early life. Expression of clock genes (clock, bmal1, and per2) was assayed, and fecal and cecal microbiotas were characterized using 16S rRNA gene amplicon analyses from birds raised under two photoperiod treatments. Chickens raised under 12/12 LD photoperiods exhibited rhythmic clock gene activity, which was absent in birds raised under the extended (23/1 LD) photoperiod. There was differential microbiota acquisition under different photoperiod regimes in newly hatched chicks. Gut microbiota members showed a similar oscillating pattern as the host, but this association was not as strong as found in mammals. Finally, the fecal microbiota was found to be not representative of cecal microbiota membership and structure in young birds. This is one of the first studies to demonstrate the use of photoperiods to modulate microbiota acquisition in newly hatched chicks, and show their potential as a tool to promote the colonization of beneficial microorganisms.
Hieke et al. (2019) Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken. PeerJ 7:e6592 https://doi.org/10.7717/peerj.6592
Recognizing two new Hippolyte species (Decapoda, Caridea, Hippolytidae) from the South China Sea based on integrative taxonomy
Hippolyte shrimps exhibit abundant biological diversity and display great ecological significance in seaweed bed ecosystems. Dozens of Hippolyte specimens were collected from Hainan Island and the Xisha Islands in the South China Sea. Detailed examination indicates that some of these specimens represent new Hippolyte species. Based on morphological, genetic, and ecological data, Hippolyte chacei sp. nov. and H. nanhaiensis sp. nov. are described. H. chacei sp. nov. was collected from the Sargassum sp. biotope in Hainan Island and is distinguished from congeners by its unique mandible and the dactylus of the third to fifth pereiopods; this species has a basal position in the Indo-West Pacific species clade in the phylogenetic tree which is reconstructed based on 16S rRNA gene. H. nanhaiensis sp. nov. was collected from the biotopes of Galaxaura sp. or Halimeda sp. in the Xisha Islands, and it differs from congeners in a series of characters associated with rostrum, scaphocerite, antennular peduncle, and spines on the dactylus of the third to fifth pereiopods. Additionally, it is sister to H. australiensis in the phylogenetic tree. A key to identifying mature female Hippolyte species of the Indo-West Pacific and neighboring seas is provided.
Gan et al. (2019) Recognizing two new Hippolyte species (Decapoda, Caridea, Hippolytidae) from the South China Sea based on integrative taxonomy. PeerJ 7:e6605 https://doi.org/10.7717/peerj.6605
HOXC6 promotes migration, invasion and proliferation of esophageal squamous cell carcinoma cells via modulating expression of genes involved in malignant phenotypes
Background HOXC6 is a member of the HOX gene family. The elevated expression of this gene occurs in prostate and breast cancers. However, the role of HOXC6 in esophageal squamous cell carcinoma (ESCC) remains largely uninvestigated. Methods The expression of HOXC6 was examined by immunohistochemistry, quantitative real-time PCR and immunoblotting assays. The lentivirus-mediated expression of HOXC6 was verified at mRNA and protein levels. Wound healing and Matrigel assays were performed to assess the effect of HOXC6 on the migration and invasion of cancer cells. The growth curving, CCK8, and colony formation assays were utilized to access the proliferation capacities. RNA-seq was performed to evaluate the downstream targets of HOXC6. Bioinformatic tool was used to analyze the gene expression. Results HOXC6 was highly expressed in ESCC tissues. HOXC6 overexpression promoted the migration, invasion, and proliferation of both Eca109 and TE10 cells. There were 2,155 up-regulated and 759 down-regulated genes in Eca109-HOXC6 cells and 95 up-regulated and 47 down-regulated genes in TE10-HOXC6 cells compared with the results of control. Interestingly, there were only 20 common genes, including 17 up-regulated and three down-regulated genes with similar changes upon HOXC6 transfection in both cell lines. HOXC6 activated several crucial genes implicated in the malignant phenotype of cancer cells. Discussion HOXC6 is highly expressed in ESCC and promotes malignant phenotype of ESCC cells. HOXC6 can be used as a new therapeutic target of ESCC.
Tang et al. (2019) HOXC6 promotes migration, invasion and proliferation of esophageal squamous cell carcinoma cells via modulating expression of genes involved in malignant phenotypes. PeerJ 7:e6607 https://doi.org/10.7717/peerj.6607
Fatty liver is a risk factor for liver metastasis in Chinese patients with non-small cell lung cancer
Background The hepatic microenvironment, which may include chronic inflammation and fibrosis, is considered to contribute to the development of liver metastases. Hepatic steatosis (HS) might cause liver inflammation and fibrosis. However, to date, no studies have investigated the impact of HS on liver metastasis in patients with non-small cell lung cancer (NSCLC). Methods A retrospective cohort study was performed on patients who received NSCLC treatment at two hospitals affiliated with the Southern Medical University from January 2005 to December 2015. The patients were grouped according to the presence of HS. The clinicopathological features of patients between the two groups were compared. The effect of HS on liver metastasis and overall metastasis was evaluated, adjusting for other confounders using Cox regression analyses. Results In total, 1,873 patients with NSCLC with no distant metastases were included in this study, and 408 (21.8%) patients were diagnosed with HS (at the time of diagnosis or before diagnosis). Liver metastases occurred in 166 (8.9%) patients. Liver metastasis-free survival was significantly worse in the study (HS) group (hazard ratio (HR) 1.42; (95% CI [1.03–1.96]); P = 0.031). Multivariate regression analysis demonstrated that HS was an independent risk factor for liver metastasis (HR 1.43; 95% CI [1.02–2.01]; P = 0.039). However, HS was not associated with overall metastasis of NSCLC (HR 0.99; 95% CI [0.84–1.17]; P = 0.895). Conclusion Hepatic steatosis was an independent predictor of liver metastasis from in patients with NSCLC.
Wu et al. (2019) Fatty liver is a risk factor for liver metastasis in Chinese patients with non-small cell lung cancer. PeerJ 7:e6612 https://doi.org/10.7717/peerj.6612
Effects of habitat fragmentation and human disturbance on the population dynamics of the Yunnan snub-nosed monkey from 1994 to 2016
In this study, we integrate data from field investigations, spatial analysis, genetic analysis, and Generalized Linear Models (GLMs) to evaluate the effects of habitat fragmentation on the population dynamics, genetic diversity, and range shifts in the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti). The results indicate that from 1994 to 2016, R. bieti population size increased from less than 2,000 to approximately 3,000 individuals. A primary factor promoting population recovery was the establishment of protected nature reserves. We also found that subpopulation growth rates were uneven, with the groups in some areas, and the formation of new groups. Both the fragmentation index, defined as the ratio of the number of forest patches to the total area of forest patches (e.g., increased fragmentation), and increasing human population size had a negative effect on population growth in R. bieti. We recommend that government conservation plans prioritize the protection of particular R. bieti populations, such as the Baimei and Jisichang populations, which have uncommon haplotypes. In addition, effective conservation strategies need to include an expansion of migration corridors to enable individuals from larger populations such as Guyoulong (Guilong) to serve as a source population to increase the genetic diversity of smaller R. bieti subpopulations. We argue that policies designed to protect endangered primates should not focus solely on total population size but also need to determine the amount of genetic diversity present across different subpopulations and use this information as a measure of the effectiveness of current conservation policies and the basis for new conservation policies.
Zhao et al. (2019) Effects of habitat fragmentation and human disturbance on the population dynamics of the Yunnan snub-nosed monkey from 1994 to 2016. PeerJ 7:e6633 https://doi.org/10.7717/peerj.6633
The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates
Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. Accordingly, characterizing the effect of prior selection on phylogenies is an active area of research. The choice of priors may systematically bias phylogenetic reconstruction and, subsequently, affect conclusions drawn from the resulting phylogeny. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation and extinction rates) from these trees. When substitution rate heterogeneity is large, diversification rate estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.
Sarver et al. (2019) The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates. PeerJ 7:e6334 https://doi.org/10.7717/peerj.6334
Adaptation of metal and antibiotic resistant traits in novel β-Proteobacterium Achromobacter xylosoxidans BHW-15
Chromosomal co-existence of metal and antibiotic resistance genes in bacteria offers a new perspective to the bacterial resistance proliferation in contaminated environment. In this study, an arsenotrophic bacterium Achromobacter xylosoxidans BHW-15, isolated from Arsenic (As) contaminated tubewell water in the Bogra district of Bangladesh, was analyzed using high throughput Ion Torrent Personal Genome Machine (PGM) complete genome sequencing scheme to reveal its adaptive potentiality. The assembled draft genome of A. xylosoxidans BHW-15 was 6.3 Mbp containing 5,782 functional genes, 1,845 pseudo genes, and three incomplete phage signature regions. Comparative genome study suggested the bacterium to be a novel strain of A. xylosoxidans showing significant dissimilarity with other relevant strains in metal resistance gene islands. A total of 35 metal resistance genes along with arsenite-oxidizing aioSXBA, arsenate reducing arsRCDAB, and mercury resistance merRTPADE operonic gene cluster and 20 broad range antibiotic resistance genes including β-lactams, aminoglycosides, and multiple multidrug resistance (MDR) efflux gene complex with a tripartite system OM-IM-MFP were found co-existed within the genome. Genomic synteny analysis with reported arsenotrophic bacteria revealed the characteristic genetic organization of ars and mer operonic genes, rarely described in β-Proteobacteria. A transposon Tn21 and mobile element protein genes were also detected to the end of mer (mercury) operonic genes, possibly a carrier for the gene transposition. In vitro antibiotic susceptibility assay showed a broad range of resistance against antibiotics belonging to β-lactams, aminoglycosides, cephalosporins (1st, 2nd, and 3rd generations), monobactams and even macrolides, some of the resistome determinants were predicted during in silico analysis. KEGG functional orthology analysis revealed the potential of the bacterium to utilize multiple carbon sources including one carbon pool by folate, innate defense mechanism against multiple stress conditions, motility, a proper developed cell signaling and processing unit and secondary metabolism-combination of all exhibiting a robust feature of the cell in multiple stressed conditions. The complete genome of the strain BHW-15 stands as a genetic basis for the evolutionary adaptation of metal and the antibiotic coexistence phenomenon in an aquatic environment.
Istiaq et al. (2019) Adaptation of metal and antibiotic resistant traits in novel β-Proteobacterium Achromobacter xylosoxidans BHW-15. PeerJ 7:e6537 https://doi.org/10.7717/peerj.6537
Identification of Austwickia chelonae as cause of cutaneous granuloma in endangered crocodile lizards using metataxonomics
The crocodile lizard (Shinisaurus crocodilurus Ahl, 1930) is an endangered reptile species, and in recent years many have died from diseases, especially the rescued and breeding individuals. However, pathogens underlying these diseases are unclear. In this study, we report our effort in rapidly identifying and isolating the pathogen that causes high mortality in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. The typical symptom is cutaneous granuloma in the infected crocodile lizards. Metagenomic next-generation sequencing (mNGS) is a comprehensive approach for sequence-based identification of pathogenic microbes. In this study, 16S rDNA based mNGS was used for rapid identification of pathogens, and microscopy and microbe isolation were used to confirm the results. Austwickia chelonae was identified to be the dominant pathogen in the granuloma using 16S rDNA based mNGS. Chinese skinks were used as an animal model to verify the pathogenicity of A. chelonae to fulfill Koch’s postulates. As expected, subcutaneous inoculation of A. chelonae induced granulomas in the healthy Chinese skinks and the A. chelonae was re-isolated from the induced granulomas. Therefore, A. chelonae was the primary pathogen that caused this high mortality disease, cutaneous granuloma, in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. Antibiotics analysis demonstrated that A. chelonae was sensitive to cephalothin, minocycline and ampicillin, but not to kanamycin, gentamicin, streptomycin and clarithromycin, suggesting a possible treatment for the infected crocodile lizards. However, surgical resection of the nodules as early as possible was recommended. This study is the first report of pathogenic analysis in crocodile lizards and provides a reference for disease control and conservations of the endangered crocodile lizards and other reptiles. In addition, this study indicated that mNGS of lesions could be used to detect the pathogens in animals with benefits in speed and convenient.
Jiang et al. (2019) Identification of Austwickia chelonae as cause of cutaneous granuloma in endangered crocodile lizards using metataxonomics. PeerJ 7:e6574 https://doi.org/10.7717/peerj.6574
Geochemical characteristics of dissolved heavy metals in Zhujiang River, Southwest China: spatial-temporal distribution, source, export flux estimation, and a water quality assessment
To investigate the sources and spatial-temporal distribution of dissolved heavy metals in river water, and to evaluate the water quality, a total of 162 water samples were collected from 81 key sampling points in high and low flow seasons separately in the Zhujiang River, Southwest China. Ten dissolved heavy metals (V, Cr, Mn, Co, Ni, Cu, Mo, Cd, Ba, and Pb) in the Zhujiang River water exhibit little variation at temporal scale, but vary with a significant spatial heterogeneity. Furthermore, different metals present different variation trends along the main channel of the Zhujiang River. Our results suggest that Ba (14.72 μg L−1 in low flow season and 12.50 μg L−1 in high flow season) and Cr (6.85 μg L−1 in low flow season and 7.52 μg L−1 in high flow season) are consistently the most abundant metals in the two sampling periods. According to the water quality index (WQI values ranged from 1.3 to 43.9) and health risk assessment, metals investigated in Zhujiang River are below the hazard level (all hazard index (HI) < 1). Application of statistical approaches, including correlation matrix and principal component analysis (PCA), identify three principal components that account for 61.74% of the total variance, the results conclude that the anthropogenic heavy metals (V, Cr, Ni, and Cu) are greatly impacted by the dilution effect, and the heavy metals in Zhujiang River are mainly presented a natural sources signature from the perspective of entire basin. Moreover, our results reveal that the estimated export budget of several heavy metals including V (735.6 t year−1), Cr (1,561.1 t year−1), Ni (498.2 t year−1), and Mo (118.9 t year−1) to the ocean are higher than the world average.
Zeng et al. (2019) Geochemical characteristics of dissolved heavy metals in Zhujiang River, Southwest China: spatial-temporal distribution, source, export flux estimation, and a water quality assessment. PeerJ 7:e6578 https://doi.org/10.7717/peerj.6578
Just a small bunch of flowers: the botanical knowledge of students and the positive effects of courses in plant identification at German universities
Background In the light of the ongoing loss of species the knowledge about and the ability to identify species becomes increasingly important for effective monitoring and conservation measures. Learning about identifying biodiversity is a central task for future biologists and biology teachers and universities play an important role in educating future experts and multipliers. It builds one basis for conservation literacy. Methods We analyzed undergraduate students’ prior knowledge on plant species, identification and their knowledge gain from introductory plant identification courses at eight German universities. Using the Visual Classification Method—a combination of a presentation and standardized questionnaires—we evaluated the learning success of more than 500 students regarding (a) ‘declarative species knowledge’ of plant species names and (b) ‘taxonomic concept knowledge’, which is seen as knowledge on a higher level of complexity. From comparison of paired pre- and post-tests we calculated the individual knowledge gain. Using Linear Mixed Effects Models (LMMs) we analyzed effects of knowledge levels, learner-specific resources and learning environment on the knowledge gain. Results We found that university course instructors have to start teaching at an almost zero level with respect to undergraduates’ prior knowledge: on average 2.6 of 32 common plant species were known. Overall, the introductory courses resulted in a significant but weak knowledge gain. We detected a higher knowledge gain in ‘taxonomic concept knowledge’ than in ‘declarative species knowledge’. We showed that the learning success was influenced by learner-specific resources, such as prior knowledge or aspects of motivation towards the subject matter, and by learning environment such as teaching methodology. Discussion We discuss didactical demands and aspects of teaching methodologies that could facilitate learning the complex task of plant identification in university courses. Plant identification should be taught and supervised by experienced, highly motivated course instructors with profound expertise and outstanding didactical skills. In order to qualify future generations of biologists, biology teachers, or conservationists universities should aim at and encourage high-quality teaching.
Buck et al. (2019) Just a small bunch of flowers: the botanical knowledge of students and the positive effects of courses in plant identification at German universities. PeerJ 7:e6581 https://doi.org/10.7717/peerj.6581
Coral-algal interactions at Weizhou Island in the northern South China Sea: variations by taxa and the exacerbating impact of sediments trapped in turf algae
Competitive interactions between corals and benthic algae are increasingly frequent on degrading coral reefs, but the processes and mechanisms surrounding the interactions, as well as the exacerbating effects of sediments trapped in turf algae, are poorly described. We surveyed the frequency, proportion, and outcomes of interactions between benthic algae (turf algae and macroalgae) and 631 corals (genera: Porites, Favites, Favia, Platygyra, and Pavona) on a degenerating reef in the northern South China Sea, with a specific focus on the negative effects of algal contact on corals. Our data indicated that turf algae were the main algal competitors for each surveyed coral genus and the proportion of algal contact along the coral edges varied significantly among the coral genera and the algal types. The proportions of algal wins between corals and turf algae or macroalgae differed significantly among coral genera. Compared to macroalgae, turf algae consistently yielded more algal wins and fewer coral wins on all coral genera. Amongst the coral genera, Porites was the most easily damaged by algal competition. The proportions of turf algal wins on the coral genera increased 1.1–1.9 times in the presence of sediments. Furthermore, the proportions of algal wins on massive and encrusting corals significantly increased with the combination of sediments and turf algae as the algal type. However, the variation in proportions of algal wins between massive and encrusting corals disappeared as sediments became trapped in turf algae. Sediments bound within turf algae further induced damage to corals and reduced the competitive advantage of the different coral growth forms in their competitive interactions with adjacent turf algae.
Liao et al. (2019) Coral-algal interactions at Weizhou Island in the northern South China Sea: variations by taxa and the exacerbating impact of sediments trapped in turf algae. PeerJ 7:e6590 https://doi.org/10.7717/peerj.6590
Assessing alignment-based taxonomic classification of ancient microbial DNA
The field of palaeomicrobiology—the study of ancient microorganisms—is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.
Eisenhofer et al. (2019) Assessing alignment-based taxonomic classification of ancient microbial DNA. PeerJ 7:e6594 https://doi.org/10.7717/peerj.6594
Microgeographic variation in body condition of three Mexican garter snakes in central Mexico
Background Geographic variation in body size and condition can reveal differential local adaptation to resource availability or climatic factors. Body size and condition are related to fitness in garter snakes (Thamnophis), thus good body condition may increase survival, fecundity in females, and mating success in males. Phylogenetically related species in sympatry are predicted to exhibit similar body condition when they experience similar environmental conditions. We focused on interspecific and geographical variation in body size and condition in three sympatric Mexican garter snakes from the highlands of Central Mexico. Methods We assessed SVL, mass, and body condition (obtained from Major axis linear regression of ln-transformed body mass on ln-transformed SVL) in adults and juveniles of both sexes of Thamnophis eques, T. melanogaster, and T. scalaris sampled at different locations and ranges from 3–11 years over a 20-year period. Results We provide a heterogeneous pattern of sexual and ontogenic reproductive status variations of body size and condition among local populations. Each garter snake species shows locations with good and poor body condition; juvenile snakes show similar body condition between populations, adults show varying body condition between populations, and adults also show sex differences in body condition. We discuss variations in body condition as possibly related to the snakes’ life cycle differences.
Valencia-Flores et al. (2019) Microgeographic variation in body condition of three Mexican garter snakes in central Mexico. PeerJ 7:e6601 https://doi.org/10.7717/peerj.6601
Seroprevalence and risk factors of Toxoplasma gondii infection in children with leukemia in Shandong Province, Eastern China: a case—control prospective study
Limited information is available concerning the epidemiology of Toxoplasma gondii infection in children with leukemia in Eastern China. Therefore, a case-control study was conducted to estimate the seroprevalence of toxoplasmosis in this patient group and to identify risk factors and possible routes of infection. Serum samples were collected from 339 children with leukemia and 339 age matched health control subjects in Qingdao from September 2014 to March 2018. Enzyme linked immunoassays were used to screen anti- T. gondii IgG and anti- T. gondii IgM antibodies. Forty-eight (14.2%) children with leukemia and 31 (9.1%) control subjects were positive for anti-T. gondii IgG antibodies (P < 0.05), while 13 (3.8%) patients and 14 (4.1%) controls were positive for anti-T. gondii IgM antibodies (P = 0.84). Multivariate analysis showed exposure to soil and a history of blood transfusion were risk factors for T. gondii infection. Compared with IgG, patients with a history of blood transfusion were more likely to present anti- T. gondii IgM (P = 0.003). Moreover, patients with chronic lymphocytic leukemia and acute lymphocytic leukemia had higher T. gondii seroprevalence in comparison to control subjects (P = 0.002 and P = 0.016, respectively). The results indicated that the seroprevalence of T. gondii infection in children with leukemia is higher than that of healthy children in Eastern China. This information may be used to guide future research and clinical management, and further studies are necessary to elucidate the role of T. gondii in children with leukemia.
Zhou et al. (2019) Seroprevalence and risk factors of Toxoplasma gondii infection in children with leukemia in Shandong Province, Eastern China: a case—control prospective study. PeerJ 7:e6604 https://doi.org/10.7717/peerj.6604
A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India
The Western Ghats (WG) is an escarpment on the west coast of Peninsular India, housing one of the richest assemblages of frogs in the world, with three endemic families. Here, we report the discovery of a new ancient lineage from a high-elevation massif in the Wayanad Plateau of the southern WG. Phylogenetic analysis reveals that the lineage belongs to Natatanura and clusters with Nyctibatrachidae, a family endemic to the WG/Sri Lanka biodiversity hotspot. Based on geographic distribution, unique morphological traits, deep genetic divergence, and phylogenetic position that distinguishes the lineage from the two nyctibatrachid subfamilies Nyctibatrachinae Blommers-Schlösser, 1993 and Lankanectinae Dubois & Ohler, 2001, we erect a new subfamily Astrobatrachinae subfam. nov. (endemic to the WG, Peninsular India), and describe a new genus Astrobatrachus gen. nov. and species, Astrobatrachus kurichiyana sp. nov. The discovery of this species adds to the list of deeply divergent and monotypic or depauperate lineages with narrow geographic ranges in the southern massifs of the WG. The southern regions of the WG have long been considered geographic and climatic refugia, and this new relict lineage underscores their evolutionary significance. The small range of this species exclusively outside protected areas highlights the significance of reserve forest tracts in the WG in housing evolutionary novelty. This reinforces the need for intensive sampling to uncover new lineages and advance our understanding of the historical biogeography of this ancient landmass.
Vijayakumar et al. (2019) A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India. PeerJ 7:e6457 https://doi.org/10.7717/peerj.6457
Habitat differentiation and conservation gap of Magnolia biondii, M. denudata, and M. sprengeri in China
The flower buds of Magnolia biondii, M. denudata, and M. sprengeri are the materials of Xinyi, a traditional Chinese medicine. The harvest of flower buds and habitat fragmentation caused by human disturbance heavily threatens the natural regeneration and survival of these three Magnolia species. With the aim to support the conservation and improve the effectiveness of conservation, we performed an assessment on habitat suitability, influences of environmental variables on habitat suitability, and the conservation gap of these three Magnolia species, based on the Maxent modeling method. The results indicated that: (1) altitude, annual mean temperature, extreme temperature, temperature fluctuation, annual precipitation, and extreme precipitation are the most influential environmental variables for the distribution of M. sprengeri, M. biondii, and M. denudata; (2) obvious habitat differentiations were observed among M. biondii, M. denudata, and M. sprengeri. M. sprengeri tends to be located in further northern areas with higher altitudes, lower temperatures, and lower precipitation compared to M. biondii and M. denudata; and (3) a large proportion of suitable habitats have been left without protection. Woodland and forest shared the largest area out of the suitable habitats. However, grassland, agricultural land, residential land, and mining and industry areas also occupied large areas of suitable habitats.
Song et al. (2019) Habitat differentiation and conservation gap of Magnolia biondii, M. denudata, and M. sprengeri in China. PeerJ 6:e6126 https://doi.org/10.7717/peerj.6126
Determination of two fluoroquinolones and their combinations with hyaluronan effect in in vitro canine cartilage explants
Background Previous studies reported the effect of enrofloxacin (Enro) and marbofloxacin (Mar) on cell death and alteration of the key genes involved in catabolic and anabolic processes and demonstrated the beneficial effects of hyaluronan (HA) combined with fluoroquinolones (FQs) on primary canine chondrocytes. This study further determines the effects of these treatments on canine cartilage explants in both normal and interleukin-1 beta (IL-1β)-stimulated conditions. Methods We examined sulfate glycosaminoglycan (s-GAG) release, uronic acid (UA) content, and safranin-O staining, as well as the expression patterns of inflammatory, extracellular matrix (ECM) component and enzymes. Results Enro treatment alone effectively stimulated proteoglycan anabolism by increasing UA content and glycosaminoglycans (GAGs) in normal and pre-IL-1β-stimulated explant, whereas Mar showed opposite results. The combination of HA and FQs increased s-GAG release and UA content in normal explants in addition to effective down-regulated expression of MMP3. HA reduced the adverse effects of Mar by enhancing UA and GAG contents in both normal and pre-IL-1β-explants. Moreover, HA effectively induced HAS1and ACANup-regulation and reduced MMP9, TNF, PTGS2,and NFKB1 expression for a long term. Discussion Our results suggest the direct effects of Enro and Mar may selectively stimulate the conditioned explants to express MMP-codinggenes and promote gene expression involved in matrix production, pro-inflammatory cytokines, and cell degradation in different directions. HA successfully reduced the adverse effects of FQs by enhancing s-GAG and UA contents and down-regulated expression of MMPs.
Siengdee et al. (2019) Determination of two fluoroquinolones and their combinations with hyaluronan effect in in vitro canine cartilage explants. PeerJ 7:e6553 https://doi.org/10.7717/peerj.6553
The effects of Solidago canadensis water extracts on maize seedling growth in association with the biomass allocation pattern
Background Solidago canadensis L. is an aggressive exotic plant species in China that has potential allelopathic effects on competing plant species. Effects of hormesis are frequently observed in studies of allelopathy; however, the mechanisms of such effects need to be elucidated. Allelopathic compounds may affect the growth of recipient plants via alteration of biomass allocation patterns or photosynthetic capacity. The aim of this study was to determine how water extracts from S. canadensis affected the shoot and root growth of recipient plants and whether the underlying mechanism was related to the biomass allocation pattern or photosynthetic gas exchange capacity. Methods The water extracts from S. canadensis shoots at 12 different concentrations in the range of 0–0.25 g/ml were applied thrice in 9 days to maize seedlings cultivated in silica sand. The growth (shoot height, leaf length and area and root length) and biomass accumulation and allocation (specific leaf area (SLA), leaf area ratio (LAR) and leaf mass ratio (LMR)) were compared among maize seedlings exposed to different treatment concentrations. Gas exchange (photosynthetic light response curve) was measured and compared among maize seedlings exposed to three concentrations of water extract (0, 0.0125 and 0.2 g/ml) before and after the first application, and seedling growth was measured after the third and final application. Results The growth of seedlings (shoot height, leaf length and area and root length) was promoted at concentrations below 0.125 g/ml and inhibited at concentrations above this level (P < 0.05). The pattern of change in biomass accumulation and allocation was similar to that of shoot growth, but biomass accumulation and allocation was not significantly affected by the water extract treatments (P > 0.05). The water extract treatments did not significantly affect the photosynthetic capacity (P > 0.05), but the dark respiration rate was higher in the low-dose treatment than that in the high-dose treatment. Shoot height was positively correlated with the biomass allocation indicators SLA and LAR (P < 0.05) but not with LMR (P > 0.05). Conclusions The results suggested that the effects of the water extracts from S. canadensis were highly dependent on the concentration, with the growth of maize seedlings promoted at low concentrations of water extracts. The effects of the water extracts on the growth of maize seedlings were mainly due to the effects on the LAR, the allocation to leaf area growth, whereas the effects of the water extracts on leaf gas exchange capacity cannot explain variation of seedling growth. Thus, the stimulation of plant growth was very likely due to increased biomass allocation towards the shoot.
Ye et al. (2019) The effects of Solidago canadensis water extracts on maize seedling growth in association with the biomass allocation pattern. PeerJ 7:e6564 https://doi.org/10.7717/peerj.6564
Anywhere but here: local conditions motivate dispersal in Daphnia
Dispersal is fundamental to population dynamics. However, it is increasingly apparent that, despite most models treating dispersal as a constant, many organisms make dispersal decisions based upon information gathered from the environment. Ideally, organisms would make fully informed decisions, with knowledge of both intra-patch conditions (conditions in their current location) and extra-patch conditions (conditions in alternative locations). Acquiring information is energetically costly, however, and extra-patch information will typically be costlier to obtain than intra-patch information. As a consequence, theory suggests that organisms will often make partially informed dispersal decisions, utilising intra-patch information only. We test this proposition in an experimental two-patch system using populations of the aquatic crustacean, Daphnia carinata. We manipulated conditions (food availability) in the population’s home patch, and in its alternative patch. We found that D. carinata made use of intra-patch information (resource availability in the home patch induced a 10-fold increase in dispersal probability) but either ignored or were incapable of using of extra-patch information (resource availability in the alternative patch did not affect dispersal probability). We also observed a small apparent increase in dispersal in replicates with higher population densities, but this effect was smaller than the effect of resource constraint, and not found to be significant. Our work highlights the considerable influence that information can have on dispersal probability, but also that dispersal decisions will often be made in only a partially informed manner. The magnitude of the response we observed also adds to the growing chorus that condition-dependence may be a significant driver of variation in dispersal.
Erm et al. (2019) Anywhere but here: local conditions motivate dispersal in Daphnia. PeerJ 7:e6599 https://doi.org/10.7717/peerj.6599
Quality-of-life among Syrian refugees residing outside camps in Jordan relative to Jordanians and other countries
Background Since the beginning of the Syrian humanitarian crisis, Syrians sought refuge in many safer countries. Many aspects of Syrian refugees’ lives have been affected, hence affecting the overall quality of their lives. However, only one study has investigated their quality of life (QOL). The aim of this study was to assess the QOL of Syrian refugees residing outside camps in Jordan and compare it to the QOL of Jordanians and to other refugees and populations around the globe. Methods Data were obtained from Syrian refugees residing outside camps in Jordan, and from two Jordanian groups; low socioeconomic status (LSES) Jordanians and average socioeconomic status (ASES) Jordanians in 2017. A total of 661 Syrians, 208 LSES Jordanians and 714 ASES Jordanians, aged between 18 and 75 years were included. The World Health Organization Quality of Life instrument (WHOQOL-BREF) questionnaire was used as the QOL assessment tool. Analysis of Variance “ANOVA” and post hoc Tukey-Honest tests were used to find the differences between the means of QOL questions in the three groups (Syrians, ASES, and LSES). Stepwise multivariate linear regression was performed for each domain to determine the most associated risk factors. Results No significant difference was found between Syrian refugees and LSES Jordanians in the physical health domain. Syrian refugees scored significantly lower than LSES Jordanians in the psychological health and social relationship domain. Syrian refugees scored significantly higher than LSES Jordanians in the environmental domain. ASES Jordanians scored significantly higher than the other two groups in all domains, with all its scores above the average. Discussion Despite the support Jordan provides to the Syrian refugees, they still seem to suffer from poor psychological health, social relationships and environmental domains, with scores below 50 on (0–100) scale. Nonetheless, no significant difference was found between Syrian refugees and LSES Jordanians in the physical health domain, furthermore they scored significantly higher than LSES Jordanians in the environmental domain despite both scoring below 50 on (0–100) scale in this domain. Physical, psychological, and social domains were mainly affected by having a job, having higher income, and being married and free from diseases.
Abdo et al. (2019) Quality-of-life among Syrian refugees residing outside camps in Jordan relative to Jordanians and other countries. PeerJ 7:e6454 https://doi.org/10.7717/peerj.6454
The effect of sewage sludge and BAF inoculant on plant condition and yield as well as biochemical and microbial activity of soil in willow (Salix viminalis L.) culture as an energy crop
Excessive amounts of sewage sludge produced in sewage treatment plants along with the ban on its storage and dumping require rapid solutions to the problem of sewage sludge management. An example of a rational and environmentally viable method may be provided by its application in agriculture and environmental management. The optimal solution is to use sludge as a fertiliser for industrial plants, including energy crops, that is, those not used in food production. For environmental reasons it is essential to control soil quality and condition following sludge application. Analyses of the residual effect of sewage sludge and bacteria, actinobacteria, fungi microbial inoculant (BAF) on selected physiological parameters of plants and microbial activity of soil were conducted in the years 2013–2015 on experimental fields of the Poznan University of Life Sciences. The results indicate that the application of sewage sludge increased yields and improved selected photosynthesis activity and biometric traits of willow. Among the tested combinations the best results were obtained following the application of sewage sludge combined with the BAF medium microbial inoculant. Similar dependencies were observed when evaluating soil microbial activity.
Panasiewicz et al. (2019) The effect of sewage sludge and BAF inoculant on plant condition and yield as well as biochemical and microbial activity of soil in willow (Salix viminalis L.) culture as an energy crop. PeerJ 7:e6434 https://doi.org/10.7717/peerj.6434
Draft Aphaenogaster genomes expand our view of ant genome size variation across climate gradients
Given the abundance, broad distribution, and diversity of roles that ants play in many ecosystems, they are an ideal group to serve as ecosystem indicators of climatic change. At present, only a few whole-genome sequences of ants are available (19 of >16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genus Aphaenogaster, a genus with important seed dispersers. In total, we sampled seven colonies of six species: Aphaenogaster ashmeadi, Aphaenogaster floridana, Aphaenogaster fulva, Aphaenogaster miamiana, Aphaenogaster picea, and Aphaenogaster rudis. The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The Aphaenogaster genomes displayed high levels of completeness with 96.1% to 97.6% of Hymenoptera BUSCOs completely represented, relative to currently sequenced ant genomes which ranged from 88.2% to 98.5%. Additionally, the mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8–396.0 Mb) and flow cytometry estimates (210.7–690.4 Mb). In an analysis of currently sequenced ant genomes and the new Aphaenogaster sequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature, and annual precipitation had the strongest correlations with genome size, with ants from locations with colder minimum temperatures and higher levels of precipitation having larger genomes. These results suggest that climate extremes could be a selective force acting on ant genomes and point to the need for more extensive sequencing of ant genomes.
Lau et al. (2019) Draft Aphaenogaster genomes expand our view of ant genome size variation across climate gradients. PeerJ 7:e6447 https://doi.org/10.7717/peerj.6447
A systematic comparison of eight new plastome sequences from Ipomoea L
Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.
Sun et al. (2019) A systematic comparison of eight new plastome sequences from Ipomoea L. PeerJ 7:e6563 https://doi.org/10.7717/peerj.6563
The distributive and structural characteristics of bronchus-associated lymphoid tissue (BALT) in Bactrian camels (Camelus bactrianus)
Background Bronchus-associated lymphoid tissue (BALT), distributed in the bronchial mucosa, plays a critical role in maintaining the mucosal immune homeostasis of the lower respiratory tract. The bronchial tree is a functional structure for gas exchange with the outside environment and maintains basic lung morphology. Methods To explore the structural and distributive characteristics of BALT in Bactrian camels, twelve healthy adult Bactrian camels were divided into two groups (six in each group). The lungs, bronchial tree and BALT were observed and analysed systematically through anatomical and histological methods. Results The results showed that Bactrian camel lungs were constituted by the left cranial lobe, left caudal lobe, right cranial lobe, right caudal lobe and accessory lobe, but lacked the middle lobe. The cranial lobe was narrow and small, the caudal lobe was extremely developed (almost four times the cranial lobe in size), and the accessory lobe was smaller than the cranial lobe; the bronchial tree, an unequal dichotomy with a tracheobronchial branch, was composed of dorsal, ventral, lateral and medial bronchiole systems. Isolated lymphoid follicles (the chief type) and aggregates of lymphoid follicles revealed two types of BALT, and germinal centres, follicle-associated epithelium and high endothelial venules could be observed in some well-developed BALT. Additionally, BALT was scattered along the bronchial tree in the entire lung, and the density increased from the trachea to the lower graded branches (densest in the bronchioles) and then decreased, with the occasional location around respiratory bronchioles or among the pulmonary mesenchyme. In the conducting portion, BALT was primarily located in the mucosa lamina propria but was also found in the submucosa, under the muscular layer, and around the submucosal glands and cartilage. Conclusion The results demonstrated that the lung morphology of Bactrian camels was similar to that of horses, but the bronchial branches were more closely related to those of ruminants. These characteristics were in accordance with the morphological and structural variation regularity of lungs with species evolution. BALT was mainly scattered in the conducting portion, and bronchioles, as the final “checkpoint” in the surveillance, capture and recognition of antigens before pulmonary exchange, were the pivotal locational position of BALT. However, BALT at different depths of the bronchial wall of the conducting portion might be at different developmental stages. Our study provided evidence for further insight into the mucosal immunomodulatory mechanism of BALT in the respiratory system of Bactrian camels.
He et al. (2019) The distributive and structural characteristics of bronchus-associated lymphoid tissue (BALT) in Bactrian camels (Camelus bactrianus). PeerJ 7:e6571 https://doi.org/10.7717/peerj.6571
Anatomical location of AICA loop in CPA as a prognostic factor for ISSNHL
The cerebellopontine angle (CPA) is a triangular-shaped space that lies at the junction of the pons and cerebellum. It contains cranial nerves and the anterior inferior cerebellar artery (AICA). The anatomical shape and location of the AICA is variable within the CPA and internal auditory canal (IAC). A possible etiology of idiopathic sudden sensorineural hearing loss (ISSNHL) is ischemia of the labyrinthine artery, which is a branch of the AICA. As such, the position of the AICA within the CPA and IAC may be related to the clinical development of ISSNHL. We adopted two methods to classify the anatomic position of the AICA, then analyzed whether these classifications affected the clinical features and prognosis of ISSNHL. We retrospectively reviewed patient data from January 2015 to March 2018. Two established classification methods designed by Cahvada and Gorrie et al. were used. Pure tone threshold at four different frequencies (0.5, 1, 4, and 8 kHz), at two different time points (at initial presentation and three months after treatment), were analyzed. We compared the affected and unaffected ears, and investigated whether there were any differences in hearing recovery and symptoms between the two classification types. There was no difference in AICA types between ears with and without ISSNHL. Patients who had combined symptoms such as tinnitus and vertigo did not show a different AICA distribution compared with patients who did not. There were differences in quantitative hearing improvement between AICA types, although without statistic significance (p = 0.09–0.13). At two frequencies, 1 and 4 kHz, there were differences in Chavda types between hearing improvement and no improvement (p < 0.05). Anatomical variances of the AICA loop position did not affect the incidence of ISSNHL or co-morbid symptoms including tinnitus and vertigo. In contrast, comparisons of hearing improvement based on Chavda type classification showed a statistical difference, with a higher proportion of Chavda type 1 showing improvements in hearing (AICA outside IAC).
Kim et al. (2019) Anatomical location of AICA loop in CPA as a prognostic factor for ISSNHL. PeerJ 7:e6582 https://doi.org/10.7717/peerj.6582
Numerical ability and improvement through interindividual cooperation varied between two cyprinid fish species, qingbo and crucian carp
We used qingbo (Spinibarbus sinensis) and Chinese crucian carp (Carassius auratus) to test whether numerical discrimination could be improved by the coexistence and possible cooperation of conspecies or heterospecies. We conducted a spontaneous shoal choice test of singletons, conspecific dyads and heterospecific dyads under different numerical comparisons (8 vs. 12, 9 vs. 12 and 10 vs. 12). Singletons of qingbo could discriminate only 8 vs. 12, whereas the dyads of qingbo showed better numerical acuity, as they could discriminate 10 vs. 12. Crucian carp may have poor numerical ability, as both singleton and dyads showed no significant preference for larger stimulus shoals, even at the ‘easier’ numerical discrimination, that is, 8 vs. 12. Furthermore, heterospecific dyads of crucian carp and qingbo did not show significant preference for larger shoals at any numerical comparison in the present study. It is suggested that both the numerical ability and the possibility for improvement by interindividual interaction and hence cooperation might vary among fish species, and the interaction between heterospecies in the present study showed negative effect on numerical ability possibly due to the different behavioural and cognitive traits which make the information transfer and consensus difficult to reach.
Xiong et al. (2019) Numerical ability and improvement through interindividual cooperation varied between two cyprinid fish species, qingbo and crucian carp. PeerJ 7:e6619 https://doi.org/10.7717/peerj.6619
Chronic fluoxetine treatment of juvenile zebrafish (Danio rerio) does not elicit changes in basal cortisol levels and anxiety-like behavior in adulthood
Exposure to selective serotonin reuptake inhibitors (SSRIs) during development may elicit long-term neuroadaptive changes that could alter the basal regulation of stress-associated physiological and behavioral processes later in life. Currently, the effects of juvenile fluoxetine exposure in rodent models appear to be dependent on the developmental window targeted as well as the duration of drug exposure. The zebrafish (Danio rerio) model is rapidly becoming a useful tool in pharmacological research and can be used to help elucidate some of the long-term effects of fluoxetine exposure prior to sexual maturation on neuroendocrine and behavioral stress markers. In the current study, juvenile zebrafish were chronically exposed to fluoxetine hydrochloride (0 or 100 μg/L) for 14 days (31–44 days post-fertilization (dpf)), then were left untreated until young adulthood. Starting at 90 dpf, basal neuroendocrine stress and behavioral responses of zebrafish were assessed. Cortisol was extracted from the young adult zebrafish body (trunk) and quantified via enzyme-linked immunosorbent assay (ELISA). Anxiety-like behaviors were assessed in response to introduction to the novel tank test. It was expected that juvenile exposure to fluoxetine would (1) reduce basal cortisol levels and (2) elicit anxiolytic effects in the novel tank test in adulthood. However, fluoxetine exposure during the juvenile period was not associated with alterations in basal levels of cortisol nor were there any significant changes in anxiety-like behavior in the young adult zebrafish. Thus, in zebrafish, it does not appear that SSRI exposure during the juvenile period has a long-term adverse or maladaptive impact on the basal expression of cortisol and anxiety-like behavior in adulthood. Further studies are needed to determine if SSRI exposure during this developmental window influences neuroendocrine and behavioral responses to acute stress.
Petrunich-Rutherford (2019) Chronic fluoxetine treatment of juvenile zebrafish (Danio rerio) does not elicit changes in basal cortisol levels and anxiety-like behavior in adulthood. PeerJ 7:e6407 https://doi.org/10.7717/peerj.6407
In vitro observation: the GFP-E. coli adhering to porcine erythrocytes can be removed by porcine alveolar macrophages
Although the activation of pathogen phagocytosis via complement system has been studied, erythrocyte-phagocyte interactions in pigs are not clearly understood. Therefore, we sought to investigate the ability of porcine erythrocytes to clear immune complexes (ICs) by using laser confocal microscopy and flow cytometry to observe the immune adhesion of porcine erythrocytes to fluorescent bacilli and the immune presentation process of transferring fluorescent bacilli to macrophages. Isolated porcine alveolar macrophages (PAMs) had uniform morphology and size, and a survival rate of 97.2%. The phagocytosis rate was 98.8%. After WT E. coli was labeled with Fluorescein Isothiocyanate (FITC), the bacteria showed a bright green fluorescence, and the labeling rate was 92.3%. When laser confocal microscopy was utilized to observe the co-incubation system of porcine erythrocytes, PAM, and fluorescent E. coli, the fluorescence intensity of bacilli decreased with increasing observation time and even disappeared. Flow Cytometry examination showed that the average fluorescence intensity of PAMs co-incubated with porcine erythrocytes adhered to WT-E. coli-FITC, was significantly higher than that of normal PAMs. Furthermore, when porcine erythrocytes adhered to WT E. coli were incubated with PAMs, the surface mean fluorescence intensity of porcine erythrocytes was significantly higher than that of the blank control group. This shows that PAMs can competitively bind to the oposinized E. coli adhered to the surface of porcine erythrocytes, and these oposinized pathogens can enter macrophages by the process of phagocytosis, which promoting the internalization of ICs or pathogens. During this process, the physical morphology of porcine erythrocytes was not damaged, but the levels of its main functional protein CR1-like were reduced.
Yin et al. (2019) In vitro observation: the GFP-E. coli adhering to porcine erythrocytes can be removed by porcine alveolar macrophages. PeerJ 7:e6439 https://doi.org/10.7717/peerj.6439
A multi-year experiment shows that lower precipitation predictability encourages plants’ early life stages and enhances population viability
Climate change is a key factor that may cause the extinction of species. The associated reduced weather predictability may alter the survival of plants, especially during their early life stages, when individuals are most fragile. While it is expected that extreme weather events will be highly detrimental for species, the effects of more subtle environmental changes have been little considered. In a four-year experiment on two herbaceous plants, Papaver rhoeas and Onobrychis viciifolia, we manipulated the predictability of precipitation by changing the temporal correlation of precipitation events while maintaining average precipitation constant, leading to more and less predictable treatments. We assessed the effect of predictability on plant viability in terms of seedling emergence, survival, seed production, and population growth rate. We found greater seedling emergence, survival, and population growth for plants experiencing lower intra-seasonal predictability, but more so during early compared to late life stages. Since predictability levels were maintained across four generations, we have also tested whether descendants exhibited transgenerational responses to previous predictability conditions. In P. rhoeas, descendants had increased the seedling emergence compared to ancestors under both treatments, but more so under lower precipitation predictability. However, higher predictability in the late treatment induced higher survival in descendants, showing that these conditions may benefit long-term survival. This experiment highlights the ability of some plants to rapidly exploit environmental resources and increase their survival under less predictable conditions, especially during early life stages. Therefore, this study provides relevant evidence of the survival capacity of some species under current and future short-term environmental alterations.
March-Salas et al. (2019) A multi-year experiment shows that lower precipitation predictability encourages plants’ early life stages and enhances population viability. PeerJ 7:e6443 https://doi.org/10.7717/peerj.6443
Modulating pain thresholds through classical conditioning
Background Classical conditioning has frequently been shown to be capable of evoking fear of pain and avoidance behavior in the context of chronic pain. However, whether pain itself can be conditioned has rarely been investigated and remains a matter of debate. Therefore, the present study investigated whether pain threshold ratings can be modified by the presence of conditioned non-nociceptive sensory stimuli in healthy participant. Methods In 51 healthy volunteers, pain threshold to electrocutaneous stimuli was determined prior to participation in a simultaneous conditioning paradigm. Participants underwent an acquisition phase in which one non-painful vibrotactile stimulus (CS+) was repeatedly paired with a painful electrocutaneous stimulus, whereas a second vibrotactile stimulus of the same quality and intensity (CS−) was paired with a non-painful electrocutaneous stimulus. Stimulation was provided on the lower back with close proximity between the conditioned stimulus and the unconditioned stimulus. In the test phase, electrocutaneous stimuli at the individually-set threshold intensity were simultaneously delivered together with either a CS+ or CS−. Pain intensity ratings were obtained after each trial; expectancy ratings were obtained after each block. The primary outcome was the percentage of test stimuli that were rated as painful. Results Test stimuli were more likely to be rated as painful when they were paired with the CS+ than when they were paired with the CS−. This effect was not influenced by contingency awareness, nor by expectancies or mood states. Discussion The findings support the notion that the judgement of an event being painful or non-painful can be influenced by classical conditioning and corroborate the possible role of associative learning in the development and maintenance of chronic pain.
Traxler et al. (2019) Modulating pain thresholds through classical conditioning. PeerJ 7:e6486 https://doi.org/10.7717/peerj.6486
Aboveground carbon of community-managed Chirpine (Pinus roxburghii Sarg.) forests of Nepal based on stand types and geographic aspects
On a global scale, about 15.5% of forests are administered through community-based forestry programs that offer the opportunity for enhanced carbon sequestration while maintaining the supply of more traditional goods and services such as cooking fuels, animal fodder and bedding. A challenge in community forest (CF) management is to realize their carbon value without compromising their role in the provision of these traditional goods and services. In this study of CF dominated by Pinus roxburghii in the Phalebas region of Nepal, the impacts of stand composition and geographic aspect on aboveground forest carbon is investigated as a means to optimize CF management for both traditional values and for emerging carbon market values. The aboveground carbon of mixed and monospecific stands of Pinus roxburghii was estimated using a combination of destructive sampling and species-specific allometric equations. On average, monospecific stands contained 106.2 Mg C ha−1 in aboveground tree biomass, significantly more than mixed stands at 73.1 Mg C ha−1 (p = 0.022). Similarly, stands growing on northern aspects (northeast 124.8 Mg C ha−1, northwest 100.9 Mg C ha−1) stored significantly more carbon (p = 0.002) than southern aspects (southeast 75.3 Mg C ha−1, southwest 57.6 Mg C ha−1), reflecting the more favorable growing conditions of northern aspects. These results suggest monospecific stands planted on northern aspects may be best suited for management to achieve carbon benefits, whilst mixed-species stands on southern aspects may be better suited for biodiversity conservation and supporting livelihoods. To maintain and increase carbon value, community forestry may need to implement nutrient return practices to limit the impact of sustained nutrient removals on stand productivity.
Pariyar et al. (2019) Aboveground carbon of community-managed Chirpine (Pinus roxburghii Sarg.) forests of Nepal based on stand types and geographic aspects. PeerJ 7:e6494 https://doi.org/10.7717/peerj.6494
cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer
Background Transcription factors and microRNAs play a critical role in regulating the gene expression in normal physiology and pathological conditions. Many bioinformatics tools were built to predict and identify transcription factor and microRNA targets and their role in the development of diseases including cancers. The availability of public access high-throughput data allows researchers to make data-driven predictions. Implementation Here, we developed an R package called cRegulome to access, manage and visualize data from open source databases. The package provides a programmatic access to the regulome (transcription factor and microRNA) expression correlations with target genes of different cancer types. It obtains a local instance of Cistrome Cancer and miRCancerdb databases and provides classes and methods to query, interact with and visualize the correlation data. Availability cRegulome is available on the comprehensive R archive network (CRAN) and the source code is hosted on GitHub as part of the ROpenSci on-boarding collection, https://github.com/ropensci/cRegulome.
Ahmed et al. (2019) cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer. PeerJ 7:e6509 https://doi.org/10.7717/peerj.6509
Comparison of laboratory indices of non-alcoholic fatty liver disease for the detection of incipient kidney dysfunction
Non-alcoholic fatty liver disease (NAFLD) is closely linked to insulin resistance and related adverse health outcomes. We investigated the non-invasive index of NAFLD that has the best performance in estimating the renal manifestations of metabolic disturbances. This nation-wide, cross-sectional study included 11,836 subjects, using various non-invasive assessments comprising routinely measured clinical and laboratory variables. The subjects were native Koreans aged 20 years or older and had no diabetes, history of liver or kidney disease. All participants were divided into quintiles according to their fibrosis-4 (FIB-4) results. Participants in the highest quintile were more hypertensive and obese with greater glycemic exposure, poor lipid profiles, and impaired kidney function, than those in the other quintiles. Multiple logistic regression, adjusted for age, sex, smoking, systolic blood pressure, white blood cell, platelet, fasting plasma glucose, and triglyceride, demonstrated that FIB-4, the hepatic steatosis index, the aspartate aminotransferase/alanine aminotransferase (AST/ALT) ratio, Gholam’s model for non-alcoholic steatohepatitis, and the BARD score were independently associated with kidney dysfunction. ROC curve analysis revealed that FIB-4 (AUC = 0.6227, 95% CI [0.5929–0.6526], p = 0.0258) was the most precise in predicting kidney dysfunction. Our findings suggest that FIB-4 may be a favorable screening tool for the renal manifestation of hepatic metabolic disturbances.
Choi et al. (2019) Comparison of laboratory indices of non-alcoholic fatty liver disease for the detection of incipient kidney dysfunction. PeerJ 7:e6524 https://doi.org/10.7717/peerj.6524
Transcriptome sequencing and comparative analysis of adult ovary and testis identify potential gonadal maintenance-related genes in Mauremys reevesii with temperature-dependent sex determination
Mauremys reevesii is a classical organism with temperature-dependent sex determination (TSD). Gonad development in early life has recently received considerable attention but gonadal maintenance after sex differentiation in turtles with TSD remains a mystery. In this study, we sequenced the transcriptomes for the adult testis and ovary using RNA-seq, and 36,221 transcripts were identified. In total, 1,594 differentially expressed genes (DEGs) were identified where 756 DEGs were upregulated in the testis and 838 DEGs were upregulated in the ovary. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that the TGF-beta signaling pathway and Hedgehog signaling pathway have important roles in testis maintenance and spermatogenesis, whereas the Hippo signaling pathway and Wnt signaling pathway are likely to participate in ovary maintenance. We determined the existence of antagonistic networks containing significant specific-expressed genes and pathways related to gonadal maintenance and gametogenesis in the adult gonads of M. reevesii. The candidate gene Fibronectin type 3 and ankyrin repeat domains 1 (FANK1) might be involved with the regulation of testis spermatogenesis.
Xiong et al. (2019) Transcriptome sequencing and comparative analysis of adult ovary and testis identify potential gonadal maintenance-related genes in Mauremys reevesii with temperature-dependent sex determination. PeerJ 7:e6557 https://doi.org/10.7717/peerj.6557
Patterns of hepatitis B virus S gene escape mutants and reverse transcriptase mutations among genotype D isolates in Jordan
Background Hepatitis B virus (HBV) is an important infectious cause of morbidity and mortality in Jordan. HBV genotype D is the most prevalent in the country. Virus escape mutants in the HBV S region is an important public health problem halting preventive efforts. The aim of the current study was to investigate patterns of HBV escape and resistance mutations and to assess domestic transmission of the virus. Methods Patients infected with HBV were recruited at Jordan University Hospital (n = 56) and were diagnosed during (1984–2012). A total of 37 partial HBV S sequences were generated using Sanger’s method. Mutation analysis was done using the HIV grade HBV drug resistance interpretation online tool and Geno2pheno (HBV) online tools. Domestic transmission of HBV was assessed using maximum likelihood phylogenetic inference with similar GenBank sequences. Results Genotyping revealed an exclusive presence of sub-genotype D1. Typical HBV escape mutants were identified in seven patients. These mutations included: L109R, Q129R, M133L, S143L and D144E with overall prevalence of 18.9% (95% CI [9.5–34.2]). Reverse transcriptase (RT) sequence analysis showed mutations in three patients with overall prevalence of 8.1% (95% CI [2.8–21.3]). RT mutations included: V173L, S202I, L180M, M204V and T184A. Transmission cluster analysis revealed a relatively high proportion of infections taking place as a result of domestic spread (29.7%). Conclusions Based on our findings, RT mutation analysis appears to be of high value before the initiation of therapy in patients with chronic HBV infection in Jordan. Phylogenetic analyses revealed a considerable proportion of local spread in the country which should be considered in the preventive infection control efforts.
Ababneh et al. (2019) Patterns of hepatitis B virus S gene escape mutants and reverse transcriptase mutations among genotype D isolates in Jordan. PeerJ 7:e6583 https://doi.org/10.7717/peerj.6583
Osteogenic capacity and cytotherapeutic potential of periodontal ligament cells for periodontal regeneration in vitro and in vivo
Background The periodontal ligament cells (PDLCs) contain heterogeneous cell populations and possess stem-cell-like properties. PDLCs have attracted considerable attention as an option for periodontal regeneration. However, the osteogenic differentiation of PDLCs remains obscure owing to variable osteo-inductive methods and whether PDLCs could be directly used for periodontal regeneration without stem cell enrichment is uncertain. The aim of the present study was to clarify the osteogenic differentiation capacity of PDLCs and test PDLCs as an alternative to stem cells for periodontal regeneration. Methods We tested the performance of human PDLCs in osteo-inductive culture and transplantation in vivo while taking human bone marrow derived mesenchymal stem cells (hMSCs) as positive control. Proliferation of PDLCs and hMSCs in osteo-inductive condition were examined by MTT assay and colony formation assay. The osteogenic differentiations of PDLCs and hMSCs were assessed by Alkaline phosphatase (ALP) activity measurement, von Kossa staining, Alizarin red S staining and quantitative RT-PCR of osteogenic marker gene including RUNX2, ALP, OCN, Col I, BSP, OPN. We transplanted osteo-inductive PDLCs and hMSCs with hydroxyapatite/tricalcium phosphate (HA/TCP) scaffolds to immunodeficient mice to explore their biological behaviors in vivo by histological staining and immunohistochemical evaluation. Results After 14 days of osteo-induction, PDLCs exhibited significantly higher proliferation rate but lower colony-forming ability comparing with hMSCs. PDLCs demonstrated lower ALP activity and generated fewer mineralized nodules than hMSCs. PDLCs showed overall up-regulated expression of RUNX2, ALP, OCN, Col I, BSP, OPN after osteo-induction. Col I level of PDLCs in osteo-inductive group was significantly higher while RUNX2, ALP, OCN were lower than that of hMSCs. Massive fiber bundles were produced linking or circling the scaffold while the bone-like structures were limited in the PDLCs-loaded HA/TCP samples. The fiber bundles displayed strong positive Col I, but weak OCN and OPN staining. The in vivo results were consistent with the in vitro data, which confirmed strong collagen forming ability and considerable osteogenic potential of PDLCs. Conclusion It is encouraging to find that PDLCs exhibit higher proliferation, stronger collagen fiber formation capacity, but lower osteogenic differentiation ability in comparison with hMSCs. This characteristic is essential for the successful periodontal reconstruction which is based on the synchronization of fiber formation and bone deposition. Moreover, PDLCs have advantages such as good accessibility, abundant source, vigorous proliferation and evident osteogenic differentiation capacity when triggered properly. They can independently form PDL-like structure in vivo without specific stem cell enrichment procedure. The application of PDLCs may offer a novel cytotherapeutic option for future clinical periodontal reconstruction.
Li et al. (2019) Osteogenic capacity and cytotherapeutic potential of periodontal ligament cells for periodontal regeneration in vitro and in vivo. PeerJ 7:e6589 https://doi.org/10.7717/peerj.6589
Environmental inactivation and irrigation-mediated regrowth of Escherichia coli O157:H7 on romaine lettuce when inoculated in a fecal slurry matrix
Field trials were conducted in July–August and October 2012 to quantify the inactivation rate of Escherichia coli O157:H7 when mixed with fecal slurry and applied to romaine lettuce leaves. Lettuce was grown under commercial conditions in Salinas Valley, California. One-half milliliter of rabbit, chicken, or pig fecal slurry, containing an average of 4.05 × 107 CFU E. coli O157:H7 (C0), was inoculated onto the upper (adaxial) surface of a lower leaf on 288 heads of lettuce per trial immediately following a 2.5 h irrigation event. To estimate the bacterial inactivation rate as a function of time, fecal matrix, irrigation and seasonal climate effects, sets of lettuce heads (n = 28) were sampled each day over 10 days and the concentration of E. coli O157:H7 (Ct) determined. E. coli O157:H7 was detected on 100% of heads during the 10-day duration, with concentrations ranging from ≤340 MPN/head (∼5-log reduction) to >3.45 × 1012 MPN/head (∼5-log growth). Relative to C0, on day 10 (Ct = 12) we observed an overall 2.6-log and 3.2-log mean reduction of E. coli O157:H7 in July and October, respectively. However, we observed relative maximum concentrations due to bacterial growth on day 6 (maximum Ct = 8) apparently stimulated by foliar irrigation on day 5. From this maximum there was a mean 5.3-log and 5.1-log reduction by day 10 (Ct = 12) for the July and October trials, respectively. This study provides insight into the inactivation and growth kinetics of E. coli O157:H7 on romaine lettuce leaves under natural field conditions. This study provides evidence that harvesting within 24 h post irrigation has the potential to increase the concentration of E. coli O157:H7 contamination, if present on heads of romaine lettuce; foliar irrigation can temporarily stimulate substantial regrowth of E. coli O157:H7.
Chase et al. (2019) Environmental inactivation and irrigation-mediated regrowth of Escherichia coli O157:H7 on romaine lettuce when inoculated in a fecal slurry matrix. PeerJ 7:e6591 https://doi.org/10.7717/peerj.6591
Exotic urban trees conserve similar natural enemy communities to native congeners but have fewer pests
Urban trees serve a critical conservation function by supporting arthropod and vertebrate communities but are often subject to arthropod pest infestations. Native trees are thought to support richer arthropod communities than exotic trees but may also be more susceptible to herbivorous pests. Exotic trees may be less susceptible to herbivores but provide less conservation value as a consequence. We tested the hypotheses that native species in Acer and Quercus would have more herbivorous pests than exotic congeners and different communities of arthropod natural enemies. The density of scale insects, common urban tree pests, was greatest on a native Acer and a native Quercus than exotic congeners in both years of our research (2012 and 2016) and sometimes reached damaging levels. However, differences in predator and parasitoid abundance, diversity, and communities were not consistent between native and exotic species in either genus and were generally similar. For example, in 2012 neither predator nor parasitoid abundance differed among native and exotic Acer congeners but in 2016 a native species, A. saccharum, had the least of both groups. A native, Q. phellos, had significantly more predators and parasitoids in 2012 than its native and exotic congeners but no differences in 2016. Parasitoid communities were significantly different among Acer species and Quercus species due in each case to greater abundance of a single family on one native tree species. These native and exotic tree species could help conserve arthropod natural enemies and achieve pest management goals.
Frank et al. (2019) Exotic urban trees conserve similar natural enemy communities to native congeners but have fewer pests. PeerJ 7:e6531 https://doi.org/10.7717/peerj.6531
Experimental mechanical strain measurement of tissues
Strain, an important biomechanical factor, occurs at different scales from molecules and cells to tissues and organs in physiological conditions. Under mechanical strain, the strength of tissues and their micro- and nanocomponents, the structure, proliferation, differentiation and apoptosis of cells and even the cytokines expressed by cells probably shift. Thus, the measurement of mechanical strain (i.e., relative displacement or deformation) is critical to understand functional changes in tissues, and to elucidate basic relationships between mechanical loading and tissue response. In the last decades, a great number of methods have been developed and applied to measure the deformations and mechanical strains in tissues comprising bone, tendon, ligament, muscle and brain as well as blood vessels. In this article, we have reviewed the mechanical strain measurement from six aspects: electro-based, light-based, ultrasound-based, magnetic resonance-based and computed tomography-based techniques, and the texture correlation-based image processing method. The review may help solving the problems of experimental and mechanical strain measurement of tissues under different measurement environments.
Huang et al. (2019) Experimental mechanical strain measurement of tissues. PeerJ 7:e6545 https://doi.org/10.7717/peerj.6545
Identification of differentially expressed key genes between glioblastoma and low-grade glioma by bioinformatics analysis
Gliomas are a very diverse group of brain tumors that are most commonly primary tumor and difficult to cure in central nervous system. It’s necessary to distinguish low-grade tumors from high-grade tumors by understanding the molecular basis of different grades of glioma, which is an important step in defining new biomarkers and therapeutic strategies. We have chosen the gene expression profile GSE52009 from gene expression omnibus (GEO) database to detect important differential genes. GSE52009 contains 120 samples, including 60 WHO II samples and 24 WHO IV samples that were selected in our analysis. We used the GEO2R tool to pick out differently expressed genes (DEGs) between low-grade glioma and high-grade glioma, and then we used the database for annotation, visualization and integrated discovery to perform gene ontology analysis and Kyoto encyclopedia of gene and genome pathway analysis. Furthermore, we used the Cytoscape search tool for the retrieval of interacting genes with molecular complex detection plug-in applied to achieve the visualization of protein–protein interaction (PPI). We selected 15 hub genes with higher degrees of connectivity, including tissue inhibitors metalloproteinases-1 and serum amyloid A1; additionally, we used GSE53733 containing 70 glioblastoma samples to conduct Gene Set Enrichment Analysis. In conclusion, our bioinformatics analysis showed that DEGs and hub genes may be defined as new biomarkers for diagnosis and for guiding the therapeutic strategies of glioblastoma.
Xu et al. (2019) Identification of differentially expressed key genes between glioblastoma and low-grade glioma by bioinformatics analysis. PeerJ 7:e6560 https://doi.org/10.7717/peerj.6560
The explosion in volumes and types of data has led to substantial challenges in data management. These challenges are often faced by front-line researchers who are already dealing with rapidly changing technologies and have limited time to devote to data management. There are good high-level guidelines for managing and processing scientific data. However, there is a lack of simple, practical tools to implement these guidelines. This is particularly problematic in a highly distributed research environment where needs differ substantially from group to group and centralised solutions are difficult to implement and storage technologies change rapidly. To meet these challenges we have developed dtool, a command line tool for managing data. The tool packages data and metadata into a unified whole, which we call a dataset. The dataset provides consistency checking and the ability to access metadata for both the whole dataset and individual files. The tool can store these datasets on several different storage systems, including a traditional file system, object store (S3 and Azure) and iRODS. It includes an application programming interface that can be used to incorporate it into existing pipelines and workflows. The tool has provided substantial process, cost, and peace-of-mind benefits to our data management practices and we want to share these benefits. The tool is open source and available freely online at http://dtool.readthedocs.io.
Olsson et al. (2019) Lightweight data management with dtool. PeerJ 7:e6562 https://doi.org/10.7717/peerj.6562
Climate change and conservation in a warm North American desert: effect in shrubby plants
Background Deserts are biologically rich habitats with a vast array of animals and plants adapted to xeric conditions, and most deserts are among the planet’s last remaining areas of total wilderness. Among North American deserts, the Chihuahuan Desert has the highest levels of diversity and endemism. To understand the effect of future climate change on plants distributed in this arid land and propose effective conservation planning, we focused on five endemic shrubby species that characterize the Chihuahuan Desert and used an integrative approach. Methods Ecological niche-based modeling, spatial genetics and ecological resistance analyses were carried out to identify the effect of global warming on the studied five shrubby species. Key areas that need to be preserved were identified taking into account the existing protected areas within the Chihuahuan Desert. Results The extent of future distribution will vary among these species, and on average expansion will occur in the western part of the Chihuahuan Desert. For most species low environmental resistance to gene flow was predicted, while higher future resistance was predicted for one species that would lead to increased population isolation. The highest haplotype diversity was identified in three hotspots. Based on future suitability of habitat and in the haplotype diversity we suggest preserving two hotspots of genetic diversity in the Sierra Madre Oriental, located in areas without protection. The third hotspot was detected in the well preserved Tehuacán-Cuicatlán Man and Biosphere Reserve. Conclusion Global climate change will have an effect in arid adapted plants, favoring expansion in the western of the Chihuahuan Desert however negatively affecting others with high ecological resistance disrupting gene flow. Two hotspots of genetic diversity in the Sierra Madre Oriental should be protected.
Sosa et al. (2019) Climate change and conservation in a warm North American desert: effect in shrubby plants. PeerJ 7:e6572 https://doi.org/10.7717/peerj.6572
Three odorant-binding proteins are involved in the behavioral response of Sogatella furcifera to rice plant volatiles
Plant volatiles play an important role in regulating insect behavior. Odorant binding proteins (OBPs) are involved in the first step of the olfactory signal transduction pathway and plant volatiles recognition. Sogatella furcifera is one of the most destructive pests of rice crops. Understanding the functions of S. furcifera OBPs (SfurOBPs) in the host plant location and the behavioral responses of S. furcifera to rice plant volatiles could lead to improved, more environmentally-friendly, methods for controlling this pest. We found that SfurOBP1 displayed only weak binding with all the tested volatiles. SfurOBP2, SfurOBP3 and SfurOBP11 had different binding affinities to β-ionone. SfurOBP2 and SfurOBP11 had strong binding affinities to β-caryophyllene (Ki = 2.23 µM) and plant alcohol (Ki = 2.98 µM), respectively. The results of Y-olfactometer experiments indicate that S. furcifera was significantly repelled by octanal and n-octane but strongly attracted by (+)-limonene, acetophenone, 2-heptanone, n-hendecane, α-farnesene and β-ionone. Furthermore, the dsRNA-mediated gene silencing of SfurOBP2, SfurOBP3 and SfurOBP11 shifted the olfactory behavior of S. furcifera for β-ionone, α-farnesene and plant alcohol, respectively. These results suggest that the SfurOBPs are involved in the recognition of rice plant volatiles, and several potential repellants and lures for controlling this pest.
Hu et al. (2019) Three odorant-binding proteins are involved in the behavioral response of Sogatella furcifera to rice plant volatiles. PeerJ 7:e6576 https://doi.org/10.7717/peerj.6576
An assessment for health education and health promotion in chronic disease demonstration districts: a comparative study from Hunan Province, China
Background Cost-effective strategies of chronic disease control, integrated health education and health promotion play important roles in the programs of chronic disease demonstration districts in China. The performance of these districts can be directly assessed by their health education and promotion work. However, there have been only a few performance assessments done on these programs, most of which made without the inclusion of proper quality indicators. This study was designed to establish a framework of indicators for outcome evaluation of health education and promotion efforts in Chinese districts, and explore the factors involved in promoting these efforts. Methods A modified two-round Delphi survey was first used to construct quality indicators on a nine-point Likert scale. With those indicators, the rank sum ratio (RSR) method was then conducted through rank conversion and parametric statistics, to assess and classify the performance of ten districts or counties randomly chosen both from demonstration and non-demonstration districts in the Hunan province. Results The Delphi process produced seven themes and 25 sub-themes as quality indicators. The seven themes included organizational management, financial support, professional personnel, health education and promotion, residents’ health awareness and behaviors, residents’ satisfaction, and residents’ health literacy. The districts were classified into four levels by RSR as follows: One demonstration district at the first-ranked level, five other demonstration districts at the second-ranked level, all non-demonstration districts at the third-ranked level. None were at the fourth-qualified level. Discussion Chronic disease demonstration districts performed better on the work of health education and health promotion than the non-demonstration districts. The work should be focused on the following measures of chronic diseases: organizational management, financial support, media-related broadcasting, technical support, community-based promotion and supportive environment, and people’s enhanced awareness and health literacy.
Xu et al. (2019) An assessment for health education and health promotion in chronic disease demonstration districts: a comparative study from Hunan Province, China. PeerJ 7:e6579 https://doi.org/10.7717/peerj.6579
Ultra-performance liquid chromatography-mass spectrometry for precise fatty acid profiling of oilseed crops
Oilseed crops are one of the most important sources of vegetable oils for food and industry. Nutritional and technical properties of vegetable oil are primarily determined by its fatty acid (FA) composition. The content and composition of FAs in plants are commonly determined using gas chromatography-mass spectrometry (GS-MS) or gas chromatography-flame ionization detection (GC-FID) techniques. In the present work, we applied ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) technique to FA profiling of sunflower and rapeseed seeds and compared this method with the GC-FID technique. GC-FID detected 11 FAs in sunflower and 13 FAs in rapeseed, while UPLC-MS appeared to be more sensitive, detecting about 2.5 times higher numbers of FAs in both plants. In addition to even-chain FAs, UPLC-MS was able to detect odd-chain FAs. The longest FA detected using GC-FID was an FA with 24 carbon atoms, whereas UPLC-MS could reveal the presence of longer FAs with the tails of up to 28 carbon atoms. Based on our results, we may conclude that UPLC-MS has great potential to be used for the assessment of FA profiles of oil crops.
Chernova et al. (2019) Ultra-performance liquid chromatography-mass spectrometry for precise fatty acid profiling of oilseed crops. PeerJ 7:e6547 https://doi.org/10.7717/peerj.6547
Agrobacterium rhizogenes—mediated transformation of Pisum sativum L. roots as a tool for studying the mycorrhizal and root nodule symbioses
In this study, we demonstrated the successful transformation of two pea (Pisum sativum L.) cultivars using Agrobacterium rhizogenes, whereby transgenic roots in the resulting composite plants showed expression of the gene encoding the green fluorescent protein. Subsequent to infection with A. rhizogenes, approximately 70%–80% of pea seedlings developed transgenic hairy roots. We found out that the transgenic roots can be efficiently nodulated by Rhizobium leguminosarum bv. viciae and infected by the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis. The morphology of nodules in the transgenic roots was found to be identical to that of nodules observed in wild-type roots, and we also observed the effective induction of markers typical of the symbiotic association with AM fungi. The convenient protocol for highly efficient A. rhizogenes-mediated transformation developed in this study would be a rapid and effective tool for investigating those genes involved in the development of the two types of symbioses found in pea plants.
Leppyanen et al. (2019) Agrobacterium rhizogenes—mediated transformation of Pisum sativum L. roots as a tool for studying the mycorrhizal and root nodule symbioses. PeerJ 7:e6552 https://doi.org/10.7717/peerj.6552
Association of late-onset postpartum depression of mothers with expressive language development during infancy and early childhood: the HBC study
Background While it has been implied that an infant’s exposure to maternal postpartum depression (PPD) may be associated with delayed development of expressive language, it remains unclear whether such a delay persists into childhood and whether the onset of PPD onset—early (within 4 weeks after childbirth) vs. late (between 5 and 12 weeks postpartum)—is relevant in this context. Objective To examine whether children of mothers with early- or late-onset PPD have reduced expressive language scores during infancy and early childhood (up to 40 months of age). Methods This longitudinal, observational study was conducted as a part of the Hamamatsu Birth Cohort for Mothers and Children (HBC Study), a population-representative sample in Japan. A total of 969 neonates and their mothers were included in the analysis. Exposures Early- and late-onset PPD was measured using the Edinburgh Postnatal Depression Scale. Main Outcomes and Measures Expressive language development was measured using the Mullen Scales of Early Learning. Six points over time were monitored (10, 14, 18, 24, 32, and 40 months postpartum). The relationship between the exposure variable and any change in expressive language score was evaluated using multiple linear regression analysis and growth curve analysis, both adjusted for covariates. Results Results from the adjusted regression analysis showed that children of mothers with late-onset PPD had significantly lower expressive language scores at 18 months of age and beyond, with a score reduction of approximately 0.6 standard deviations from the reference value at 40 months of age (95% CI [−0.888 to −0.265], p < .001). This association was confirmed on growth curve analysis, which revealed a significant, monotonic decline of expressive language development between 10 and 40 months of age among children of mothers with late-onset PPD, but not among children of mothers with early-onset PPD. Conclusion Exposure to late-onset PPD may lead to a persistent decline in the rate of expressive language development in offspring during infancy and early childhood, highlighting the significance of monitoring for late-onset PPD to facilitate early detection and intervention.
Aoyagi et al. (2019) Association of late-onset postpartum depression of mothers with expressive language development during infancy and early childhood: the HBC study. PeerJ 7:e6566 https://doi.org/10.7717/peerj.6566
A glucagon-like peptide-1 analog, liraglutide, ameliorates endothelial dysfunction through miRNAs to inhibit apoptosis in rats
Background and Aims Many studies have revealed that glucagon-like peptide-1 has vasoprotective effects. In this study, we investigated whether liraglutide suppressed endothelial dysfunction and explored the mechanism involved. Methods Experimental diabetes was induced through combined high-fat diet administration and intraperitoneal streptozotocin injections. Rats were randomly divided into the following four groups: control, diabetes, diabetes + a low liraglutide dose (0.2 mg/kg/d), and diabetes + a high liraglutide dose (0.4 mg/kg/d). Endothelial function and metabolic parameters were measured after 8 weeks of treatment. miRNA arrays were analyzed to identify the differentially expressed miRNAs. Results We found that liraglutide significantly improved aortic endothelial function in diabetic rats. Liraglutide inhibited miR-93-5p, miR-181a-5p and miR-34a-5p expression, and activated miR-26a-5p expression. miRNA mimic transfection experiments indicated negative relationships between miR-93-5p, miR-181a-5p, miR-34a-5p, and miR-26a-5p and Sirt1, Creb, Bcl-2, and Pten expression, respectively. Moreover, liraglutide increased Sirt1, Creb, and Bcl-2 expression levels and reduced Pten expression level. Conclusion Our results demonstrate the role of key miRNAs in the liraglutide-mediated regulation of endothelial cell function in diabetic rats.
Zhang et al. (2019) A glucagon-like peptide-1 analog, liraglutide, ameliorates endothelial dysfunction through miRNAs to inhibit apoptosis in rats. PeerJ 7:e6567 https://doi.org/10.7717/peerj.6567
Public perception of the vegetative state/unresponsive wakefulness syndrome: a crowdsourced study
Background The vegetative state (VS)/unresponsive wakefulness syndrome (UWS) denotes brain-injured, awake patients who are seemingly without awareness. Still, up to 15% of these patients show signs of covert consciousness when examined by functional magnetic resonance imaging (fMRI) or EEG, which is known as cognitive motor dissociation (CMD). Experts often prefer the term unresponsive wakefulness syndrome to avoid the negative connotations associated with vegetative state and to highlight the possibility for CMD. However, the perception of VS/UWS by the public has never been studied systematically. Methods Using an online crowdsourcing platform, we recruited 1,297 lay people from 32 countries. We investigated if vegetative state and unresponsive wakefulness syndrome might have a different influence on attitudes towards VS/UWS and the concept of CMD. Results Participants randomized to be inquired about the vegetative state believed that CMD was less plausible (mean estimated frequency in unresponsive patients 38.07% ± SD 25.15) than participants randomized to unresponsive wakefulness syndrome (42.29% ± SD 26.63; Cohen’s d 0.164; p = 0.016). Attitudes towards treatment withdrawal were similar. Most participants preferred unresponsive wakefulness syndrome (60.05%), although a sizeable minority favored vegetative state (24.21%; difference 35.84%, 95% CI 29.36 to 41.87; p < 0.0001). Searches on PubMed and Google Trends revealed that unresponsive wakefulness syndrome is increasingly used by academics but not lay people. Discussion Simply replacing vegetative state with unresponsive wakefulness syndrome may not be fully appropriate given that one of four prefer the first term. We suggest that physicians take advantage of the controversy around the terminology to explain relatives the concept of CMD and its ethical implications.
Kondziella et al. (2019) Public perception of the vegetative state/unresponsive wakefulness syndrome: a crowdsourced study. PeerJ 7:e6575 https://doi.org/10.7717/peerj.6575
Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing
Porcine circovirus-associated disease (PCVAD), which is induced by porcine circovirus type 2 (PCV2), is responsible for severe economic losses. Recently, the role of noncoding RNAs, and in particular microRNAs, in PCV2 infection has received great attention. However, the role of long noncoding RNA (lncRNA) in PCV2 infection is unclear. Here, for the first time, we describe the expression profiles of lncRNAs in an intestinal porcine epithelial cell line (IPEC-J2) after PCV2 infection, and analyze the features of differently expressed lncRNAs and their potential target genes. After strict filtering of approximately 150 million reads, we identified 13,520 lncRNAs, including 199 lncRNAs that were differentially expressed in non-infected and PCV2-infected cells. Furthermore, trans analysis found lncRNA-regulated target genes enriched for specific Gene Ontology terms (P < 0.05), such as DNA binding, RNA binding, and transcription factor activity, which are closely associated with PCV2 infection. In addition, we analyzed the predicted target genes of differentially expressed lncRNAs, including SOD2, TNFAIP3, and ARG1, all of which are involved in infectious diseases. Our study identifies many candidate lncRNAs involved in PCV2 infection and provides new insight into the mechanisms underlying the pathogenesis of PCVAD.
Fang et al. (2019) Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing. PeerJ 7:e6577 https://doi.org/10.7717/peerj.6577
Electric resistance tomography and stress wave tomography for decay detection in trees—a comparison study
Background To ensure the safety of trees, two NDT (nondestructive testing) techniques, electric resistance tomography and stress wave tomography, were employed to quantitatively detect and characterize the internal decay of standing trees. Comparisons between those two techniques were done to make full use of the individual capability for decay detection. Methods Eighty trees (40 Manchurian ash and 40 Populus simonii) were detected, then wood increment cores were obtained from each cross disc trial. The Dt, which was defined as the value determined by the mass loss ratio of each wood core, was regarded as the true severity of decay. Using ordinary least-squares regression to analyze the relationship between Dt and De (De was defined as the severity of decay determined by electric resistance tomography) and between Dt and Ds (Ds was defined as the severity of decay determined by stress wave tomography). Results The results showed that both methods could estimate the severity of decay in trees. In terms of different stages of decay, when Dt < 30%, De had a strong positive correlation with Dt (R2 = 0.677, P < 0.01), while, when Dt ≥ 30%, Ds had a significant positive correlation relationship with Dt (R2 = 0.645, P < 0.01). Conclusion Electric resistance tomography was better than stress wave tomography for testing in the early stages of decay, while stress wave tomography can be used effectively in the late stage of decay. It is suggested that each technique can be used in the practice of internal decay testing of standing trees based on decay stages and operating conditions.
Yue et al. (2019) Electric resistance tomography and stress wave tomography for decay detection in trees—a comparison study. PeerJ 7:e6444 https://doi.org/10.7717/peerj.6444
Potential invasive plant expansion in global ecoregions under climate change
Climate change is increasing the risk of invasive plant expansion worldwide. However, few studies have specified the relationship between invasive plant expansion and ecoregions at the global scale under climate change. To address this gap, we provide risk maps highlighting the response of invasive plant species (IPS), with a focus on terrestrial and freshwater ecoregions to climate change, and further explore the climatic features of ecosystems with a high potential for invasive plant expansion under climate change. We use species distribution modelling to predict the suitable habitats of IPS with records at the global scale. Hotspots with a potential risk of IPS (such as aquatic plants, trees, and herbs) expanding in global ecoregions were distributed in Northern Europe, the UK, South America, North America, southwest China, and New Zealand. Temperature changes were related to the potential of IPS expansion in global ecoregions under climate change. Coastal and high latitude ecoregions, such as temperate forests, alpine vegetation, and coastal rivers, were severely infiltrated by IPS under climate change. Monitoring strategies should be defined for climate change for IPS, particularly for aquatic plants, trees, and herbs in the biomes of regions with coastal or high latitudes. The role of climate change on the potential for IPS expansion should be taken into consideration for biological conservation and risk evaluation of IPS at ecoregional scales.
Wang et al. (2019) Potential invasive plant expansion in global ecoregions under climate change. PeerJ 7:e6479 https://doi.org/10.7717/peerj.6479
Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework
The taxonomy and associated nomenclature of many taxa of rumen bacteria are poorly defined within databases of 16S rRNA genes. This lack of resolution results in inadequate definition of microbial community structures, with large parts of the community designated as incertae sedis, unclassified, or uncultured within families, orders, or even classes. We have begun resolving these poorly-defined groups of rumen bacteria, based on our desire to name these for use in microbial community profiling. We used the previously-reported global rumen census (GRC) dataset consisting of >4.5 million partial bacterial 16S rRNA gene sequences amplified from 684 rumen samples and representing a wide range of animal hosts and diets. Representative sequences from the 8,985 largest operational units (groups of sequence sharing >97% sequence similarity, and covering 97.8% of all sequences in the GRC dataset) were used to identify 241 pre-defined clusters (mainly at genus or family level) of abundant rumen bacteria in the ARB SILVA 119 framework. A total of 99 of these clusters (containing 63.8% of all GRC sequences) had no unique or had inadequate taxonomic identifiers, and each was given a unique nomenclature. We assessed this improved framework by comparing taxonomic assignments of bacterial 16S rRNA gene sequence data in the GRC dataset with those made using the original SILVA 119 framework, and three other frameworks. The two SILVA frameworks performed best at assigning sequences to genus-level taxa. The SILVA 119 framework allowed 55.4% of the sequence data to be assigned to 751 uniquely identifiable genus-level groups. The improved framework increased this to 87.1% of all sequences being assigned to one of 871 uniquely identifiable genus-level groups. The new designations were included in the SILVA 123 release (https://www.arb-silva.de/documentation/release-123/) and will be perpetuated in future releases.
Henderson et al. (2019) Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework. PeerJ 7:e6496 https://doi.org/10.7717/peerj.6496
The Malacca Strait separates distinct faunas of poorly-flying Cautires net-winged beetles
We investigated the spatial and temporal patterns of Cautires diversification on the Malay Peninsula and Sumatra to understand if the narrow and frequently dry Malacca Strait separates different faunas. Moreover, we analyzed the origin of Cautires in Malayan and Sumatran mountains. We sampled 18 localities and present the mtDNA-based phylogeny of 76 species represented by 388 individuals. The phylogenetic tree was dated using mtDNA evolution rates and the ancestral ranges were estimated using the maximum likelihood approach. The phylogeny identified multiple lineages on the Malay Peninsula since the Upper Eocene (35 million years ago, mya) and a delayed evolution of diversity in Sumatra since the Upper Oligocene (26 mya). A limited number of colonization events across the Malacca Strait was identified up to the Pliocene and more intensive faunal exchange since the Pleistocene. The early colonization events were commonly followed by in situ diversification. As a result, the Malacca Strait now separates two faunas with a high species-level turnover. The montane fauna diversified in a limited space and seldom took part in colonization events across the Strait. Besides isolation by open sea or a savannah corridor, mimetic patterns could decrease the colonization capacity of Cautires. The Malay fauna is phylogenetically more diverse and has a higher value if conservation priorities should be defined.
Jiruskova et al. (2019) The Malacca Strait separates distinct faunas of poorly-flying Cautires net-winged beetles. PeerJ 7:e6511 https://doi.org/10.7717/peerj.6511
Transcriptome analysis of osmotic-responsive genes in ABA-dependent and -independent pathways in wheat (Triticum aestivum L.) roots
Bread wheat is one of the most important crops in the world. However, osmotic stress significantly inhibits wheat growth and development, and reduces crop yield and quality. Plants respond to osmotic stress mainly through abscisic acid (ABA)-dependent and -independent pathways. In this study, root transcriptome profiles of wheat seedlings exposed to osmotic stress and exogenous ABA were analysed to identify osmotic-responsive genes belonging to the ABA-dependent or -independent pathways. We found that osmotic stress promoted proline biosynthesis in the ABA-dependent pathway, and trehalose biosynthesis is likely promoted among soluble sugars to maintain protein bioactivity under osmotic stress. In wheat roots subjected to osmotic stress, calcium ions, and glutathione exert their functions mainly through calcium-binding protein (CaM/CML) and glutathione-S-transferase, respectively, depending on both pathways. In addition, a complex relationship among phytohormones signal transduction was observed in response to osmotic stress. The findings of this study deepen our understanding of the molecular mechanisms of osmotic-stress resistance, and provide several candidate osmotic-responsive genes for further study.
Li et al. (2019) Transcriptome analysis of osmotic-responsive genes in ABA-dependent and -independent pathways in wheat (Triticum aestivum L.) roots. PeerJ 7:e6519 https://doi.org/10.7717/peerj.6519
Serial monogamy benefits both sexes in the biparental convict cichlid
Monogamy can be either long-term or serial, with new pairs formed with each breeding bout. Costs and benefits are associated with each strategy. Because biparental convict cichlids (Amatitlania nigrofasciata) typically switch mates, exhibiting serial monogamy, we tested for the costs associated with forcing individuals to remain with the same mate. Convict cichlids were observed over two successive breeding bouts, either with the same or a new, equally experienced, mate. Parental behavior did not differ between breeding bouts, nor did brood size. Surprisingly, fish that remained with their original partner for a second bout took significantly longer to produce a brood compared to fish that paired with new partners. New partners were also more likely to successfully produce a second brood than re-mated partners. This is in contrast to the majority of bird studies that show many benefits to staying with the same partner for multiple broods. In convict cichlids, there seems to be no benefit associated with remaining with the same partner and switching mates reduces duration between broods for both males and females, potentially increasing overall reproductive success.
Snekser et al. (2019) Serial monogamy benefits both sexes in the biparental convict cichlid. PeerJ 7:e6535 https://doi.org/10.7717/peerj.6535
Effect of the flavonoid baicalin on the proliferative capacity of bovine mammary cells and their ability to regulate oxidative stress
Background High-yielding dairy cows are prone to oxidative stress due to the high metabolic needs of homeostasis and milk production. Oxidative stress and inflammation are tightly linked; therefore, anti-inflammatory and/or natural antioxidant compounds may help improve mammary cell health. Baicalin, one of the major flavonoids in Scutellaria baicalensis, has natural antioxidant and anti-inflammatory properties in various cell types, but its effects on bovine mammary epithelial cells (BMECs) have not been investigated. Methods Explants from bovine mammary glands were collected by biopsy at the peak of lactation (approximately 60 days after the start of lactation) (n = three animals) to isolate BMECs corresponding to mature secretory cells. Cell viability, apoptosis, proliferative capacity and reactive oxygen species (ROS) production by BMECs were measured after increasing doses of baicalin were added to the culture media in the absence or presence of H2O2, which was used as an in vitro model of oxidative stress. Results Low doses of baicalin (1–10 µg/mL) had no or only slightly positive effects on the proliferation and viability of BMECs, whereas higher doses (100 or 200 µg/mL) markedly decreased BMEC proliferation. Baicalin decreased apoptosis rate at low concentrations (10 µg/mL) but increased apoptosis at higher doses. ROS production was decreased in BMECs treated with increasing doses of baicalin compared with untreated cells, and this decreased production was associated with increased intracellular concentrations of catalase and NRF-2. Irrespective of the dose, baicalin pretreatment attenuated H2O2-induced ROS production. Discussion These results indicate that baicalin exerts protective antioxidant effects on bovine mammary cells. This finding suggests that baicalin could be used to prevent oxidative metabolic disorders in dairy cows.
Perruchot et al. (2019) Effect of the flavonoid baicalin on the proliferative capacity of bovine mammary cells and their ability to regulate oxidative stress. PeerJ 7:e6565 https://doi.org/10.7717/peerj.6565
DNA metabarcoding allows non-invasive identification of arthropod prey provisioned to nestling Rufous hummingbirds (Selasphorus rufus)
Hummingbirds consume sugars from nectar, sap and honeydew, and obtain protein, fat and minerals from arthropods. To date, the identity of arthropod taxa in hummingbird diets has been investigated by observation of foraging or examination of alimentary tract contents. Direct examination of nestling provisioning adds the extra complication of disturbance to the young and mother. Here, we show that arthropod food items provisioned to Rufous hummingbird (Selasphorus rufus) nestlings can be identified by a safe and non-invasive protocol using next-generation sequencing (NGS) of DNA from nestling fecal pellets collected post-fledging. We found that females on southern Vancouver Island (British Columbia, Canada) provisioned nestlings with a wide range of arthropod taxa. The samples examined contained three Classes, eight Orders, 48 Families, and 87 Genera, with from one to 15 Families being identified in a single pellet. Soft-bodied Dipterans were found most frequently and had the highest relative abundance; hard-bodied prey items were absent from almost all samples. Substantial differences in taxa were found within season and between years, indicating the importance of multi-year sampling when defining a prey spectrum.
Moran et al. (2019) DNA metabarcoding allows non-invasive identification of arthropod prey provisioned to nestling Rufous hummingbirds (Selasphorus rufus). PeerJ 7:e6596 https://doi.org/10.7717/peerj.6596
Capturing complexity: field-testing the use of ‘structure from motion’ derived virtual models to replicate standard measures of reef physical structure
Reef structural complexity provides important refuge habitat for a range of marine organisms, and is a useful indicator of the health and resilience of reefs as a whole. Marine scientists have recently begun to use ‘Structure from Motion’ (SfM) photogrammetry in order to accurately and repeatably capture the 3D structure of physical objects underwater, including reefs. There has however been limited research on the comparability of this new method with existing analogue methods already used widely for measuring and monitoring 3D structure, such as ‘tape and chain rugosity index (RI)’ and graded visual assessments. Our findings show that analogue and SfM RI can be reliably converted over a standard 10-m reef section (SfM RI = 1.348 × chain RI—0.359, r2 = 0.82; and Chain RI = 0.606 × SfM RI + 0.465) for RI values up to 2.0; however, SfM RI values above this number become increasingly divergent from traditional tape and chain measurements. Additionally, we found SfM RI correlates well with visual assessment grades of coral reefs over a 10 × 10 m area (SfM RI = 0.1461 × visual grade + 1.117; r2 = 0.83). The SfM method is shown to be affordable and non-destructive whilst also allowing the data collected to be archival, less biased by the observer, and broader in its scope of applications than standard methods. This work allows researchers to easily transition from analogue to digital structural assessment techniques, facilitating continued long-term monitoring, whilst also improving the quality and additional research value of the data collected.
Bayley et al. (2019) Capturing complexity: field-testing the use of ‘structure from motion’ derived virtual models to replicate standard measures of reef physical structure. PeerJ 7:e6540 https://doi.org/10.7717/peerj.6540
A new method of gall mite management: application of artificial defoliation to control Aceria pallida
Artificial defoliant is widely applied to cotton to facilitate mechanical harvesting and successfully controls leaf diseases by blocking pathogen epidemical cycles; however, this technique is rarely used to control herbivores. Because many eriophyoid mites live and reproduce in galls, the control of these mites by pesticides is usually limited. However, the abscission of galled foliage is lethal to tiny mites with low mobility. Therefore, artificial defoliation should be effective in controlling gall mites. Here, the effects of defoliant on the control of the goji berry Lycium barbarum L. gall mite Aceria pallida Keifer were compared with those of pesticides under field conditions over 3 years. Our results showed that artificial defoliation enabled almost complete defoliation and timely refoliation. A. pallida galls fell off with the defoliation, and then regenerated foliage escaped from mite attack. After defoliant application, the densities of mite galls decreased by 84.1%, 80.3% and 80.3% compared with those found in the pesticide (undefoliated) treatment in 2012, 2013 and 2014, respectively. Artificial defoliation achieved much better control of gall mites than pesticides.
Li et al. (2019) A new method of gall mite management: application of artificial defoliation to control Aceria pallida. PeerJ 7:e6503 https://doi.org/10.7717/peerj.6503
Amorphous silica nanoparticles induce tumorigenesis via regulating ATP5H/SOD1-related oxidative stress, oxidative phosphorylation and EIF4G2/PABPC1-associated translational initiation
Background Recent studies indicate amorphous silica nanoparticles (SiNPs), one of the widely applied nanomaterials, have potential toxicity in humans and induces cell malignant transformation. However, its carcinogenic mechanisms remain poorly understood. This study’s purpose was to investigate the underlying toxic mechanisms of amorphous SiNPs on human lung epithelial cells model by using microarray data. Methods Microarray dataset GSE82062 was collected from Gene Expression Omnibus database, including three repeats of Beas-2B exposed to amorphous SiNPs for 40 passages and three repeats of passage-matched control Beas-2B cells. Differentially expressed genes (DEGs) were identified using linear models for microarray data method. Protein–protein interaction (PPI) network was constructed using data from the STRING database followed by module analysis. The miRwalk2 database was used to predict the underlying target genes of differentially miRNAs. Function enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Results A total of 323 genes were identified as DEGs, including 280 downregulated (containing 12 pre-miRNAs) and 43 upregulated genes (containing 29 pre-miRNAs). Function enrichment indicated these genes were involved in translational initiation (i.e., eukaryotic translation initiation factor 4 gamma 2 (EIF4G2), poly (A) binding protein cytoplasmic 1 (PABPC1)), response to reactive oxygen species (i.e., superoxide dismutase 1 (SOD1)) and oxidative phosphorylation (i.e., ATP5H). PABPC1 (degree = 15), ATP5H (degree = 11) and SOD1 (degree = 8)] were proved to be hub genes after PPI-module analyses. ATP5H/SOD1 and EIF4G2/PABPC1 were overlapped with the target genes of differentially expressed pre-miR-3648/572/661 and pre-miR-4521. Conclusions Amorphous SiNPs may induce tumorigenesis via influencing ATP5H/SOD1-related oxidative stress, oxidative phosphorylation and EIF4G2/PABPC1-associated translational initiation which may be regulated by miR-3648/572/661 and miR-4521, respectively.
Xie et al. (2019) Amorphous silica nanoparticles induce tumorigenesis via regulating ATP5H/SOD1-related oxidative stress, oxidative phosphorylation and EIF4G2/PABPC1-associated translational initiation. PeerJ 7:e6455 https://doi.org/10.7717/peerj.6455
Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes
Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota are not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human GM. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human GM we developed TAGMA (toxin antitoxin genes for metagenomes analyses) software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strains of Lactobacillus and Bifidobacterium in metagenomes.
Klimina et al. (2019) Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes. PeerJ 7:e6554 https://doi.org/10.7717/peerj.6554
PCR effects of melting temperature adjustment of individual primers in degenerate primer pools
Deep sequencing of small subunit ribosomal RNA (SSU rRNA) gene amplicons continues to be the most common approach for characterization of complex microbial communities. PCR amplifications of conserved regions of SSU rRNA genes often employ degenerate pools of primers to enable targeting of a broad spectrum of organisms. One little noticed feature of such degenerate primer sets is the potential for a wide range of melting temperatures between the primer variants. The melting temperature variation of primers in a degenerate pool could lead to variable amplification efficiencies and PCR bias. Thus, we sought to adjust the melting temperature of each primer variant individually. Individual primer modifications were used to reduce theoretical melting temperature variation between primers, as well as to introduce inter-cluster nucleotide diversity during Illumina sequencing of primer regions. We demonstrate here the suitability of such primers for microbial community analysis. However, no substantial differences in microbial community structure were revealed when using primers with adjusted melting temperatures, though the optimal annealing temperature decreased.
Naqib et al. (2019) PCR effects of melting temperature adjustment of individual primers in degenerate primer pools. PeerJ 7:e6570 https://doi.org/10.7717/peerj.6570
Feeding traces attributable to juvenile Tyrannosaurus rex offer insight into ontogenetic dietary trends
Theropod dinosaur feeding traces and tooth marks yield paleobiological and paleoecological implications for social interactions, feeding behaviors, and direct evidence of cannibalism and attempted predation. However, ascertaining the taxonomic origin of a tooth mark is largely dependent on both the known regional biostratigraphy and the ontogenetic stage of the taxon. Currently, most recorded theropod feeding traces and bite marks are attributed to adult theropods, whereas juvenile and subadult tooth marks have been rarely reported in the literature. Here we describe feeding traces attributable to a late-stage juvenile Tyrannosaurus rex on a caudal vertebra of a hadrosaurid dinosaur. The dimensions and spacing of the traces were compared to the dentition of Tyrannosaurus rex maxillae and dentaries of different ontogenetic stages. These comparisons reveal that the tooth marks present on the vertebra closely match the maxillary teeth of a late-stage juvenile Tyrannosaurus rex specimen histologically determined to be 11–12 years of age. These results demonstrate that late-stage juvenile and subadult tyrannosaurs were already utilizing the same large-bodied food sources as adults despite lacking the bone-crushing abilities of adults. Further identification of tyrannosaur feeding traces coupled with experimental studies of the biomechanics of tyrannosaur bite forces from younger ontogenetic stages may reveal dynamic dietary trends and ecological roles of Tyrannosaurus rex throughout ontogeny.
Peterson et al. (2019) Feeding traces attributable to juvenile Tyrannosaurus rex offer insight into ontogenetic dietary trends. PeerJ 7:e6573 https://doi.org/10.7717/peerj.6573
Arbuscular mycorrhizal fungi in soil, roots and rhizosphere of Medicago truncatula: diversity and heterogeneity under semi-arid conditions
Mycorrhizal symbioses are considered indicators of ecosystem biodiversity. However, their diversity and relevance in arid and semi-arid ecosystems are poorly understood. This study addressed this subject, the main objective being to evaluate arbuscular mycorrhizal fungi (AMF) diversity and heterogeneity in a semi-arid region. Samples of bulk and rhizosphere soil and fine roots of Medicago truncatula were collected at four different sites with the same aridity index (6.1), in Bou-Hedma National Park, Tunisia, a semi-arid ecosystem. AMF taxa were assessed by 454- pyrosequencing and identified by BLAST matching of operational taxonomic units (OTUs) against the MaarjAM database, targeting AMF SSU rRNA gene diversity. Roots were the hotspots of AMF diversity (107 OTUs out of a total of 138). Of the 138 OTUs, 113 found correspondence in the MaarjAM database, with 32 AMF virtual taxa (VTX),19 Site-exclusive (SE) and 13 common to at least two sites (Non-site exclusive, NSE); the remaining 25 OTUs grouped in 16 putative new AMF taxa (pNTX), each one consisting of OTUs sharing pairwise distances not higher than 3%. We found a high diversity and heterogeneity of AMF across the four sites, which showed, in a regression analysis, significant relation to six out of the eight environmental parameters evaluated: grazing activity and soil texture, electrical conductivity, organic matter, total phosphorus and total nitrogen. AMF colonization of plants also presented significant differences among the four sites, as well as spore density, microbial biomass and several enzymatic activities (dehydrogenase, β-glucosidase and phosphatase) evaluated in rhizosphere soils. The four sites clustered in two groups in a hierarchical clustering evaluation based on their AMF diversity (total numbers of OTU, VTX and pNTX) and the parameters referred above. The crucial role of abiotic factors, other than aridity index, on AMF community composition, was evidenced by the high heterogeneity found between AMF communities across sites under identical aridity conditions.
Mahmoudi et al. (2019) Arbuscular mycorrhizal fungi in soil, roots and rhizosphere of Medicago truncatula: diversity and heterogeneity under semi-arid conditions. PeerJ 7:e6401 https://doi.org/10.7717/peerj.6401
Functional genomics screen with pooled shRNA library and gene expression profiling with extracts of Azadirachta indica identify potential pathways for therapeutic targets in head and neck squamous cell carcinoma
Tumor suppression by the extracts of Azadirachta indica (neem) works via anti-proliferation, cell cycle arrest, and apoptosis, demonstrated previously using cancer cell lines and live animal models. However, very little is known about the molecular targets and pathways that neem extracts and their associated compounds act through. Here, we address this using a genome-wide functional pooled shRNA screen on head and neck squamous cell carcinoma cell lines treated with crude neem leaf extracts, known for their anti-tumorigenic activity. We analyzed differences in global clonal sizes of the shRNA-infected cells cultured under no treatment and treatment with neem leaf extract conditions, assayed using next-generation sequencing. We found 225 genes affected the cancer cell growth in the shRNA-infected cells treated with neem extract. Pathway enrichment analyses of whole-genome gene expression data from cells temporally treated with neem extract revealed important roles played by the TGF-β pathway and HSF-1-related gene network. Our results indicate that neem extract affects various important molecular signaling pathways in head and neck cancer cells, some of which may be therapeutic targets for this devastating tumor.
Krishnan et al. (2019) Functional genomics screen with pooled shRNA library and gene expression profiling with extracts of Azadirachta indica identify potential pathways for therapeutic targets in head and neck squamous cell carcinoma. PeerJ 7:e6464 https://doi.org/10.7717/peerj.6464
Mitochondrial complex activity in permeabilised cells of chronic fatigue syndrome patients using two cell types
Abnormalities in mitochondrial function have previously been shown in chronic fatigue syndrome (CFS) patients, implying that mitochondrial dysfunction may contribute to the pathogenesis of disease. This study builds on previous work showing that mitochondrial respiratory parameters are impaired in whole cells from CFS patients by investigating the activity of individual mitochondrial respiratory chain complexes. Two different cell types were used in these studies in order to assess individual complex activity locally in the skeletal muscle (myotubes) (n = 6) and systemically (peripheral blood mononuclear cells (PBMCs)) (control n = 6; CFS n = 13). Complex I, II and IV activity and respiratory activitysupported by fatty acid oxidation and glutaminolysis were measured usingextracellular flux analysis. Cells were permeabilised and combinations of substrates and inhibitors were added throughout the assays to allow states of mitochondrial respiration to be calculated and the activity of specific aspects of respiratory activity to be measured. Results showed there to be no significant differences in individual mitochondrial complex activity or respiratory activity supported by fatty acid oxidation or glutaminolysis between healthy control and CFS cohorts in either skeletal muscle (p ≥ 0.190) or PBMCs (p ≥ 0.065). This is the first study to use extracellular flux analysisto investigate individual mitochondrial complex activity in permeabilised cells in the context of CFS. The lack of difference in complex activity in CFS PBMCs suggests that the previously observed mitochondrial dysfunction in whole PBMCs is due to causes upstream of the mitochondrial respiratory chain.
Tomas et al. (2019) Mitochondrial complex activity in permeabilised cells of chronic fatigue syndrome patients using two cell types. PeerJ 7:e6500 https://doi.org/10.7717/peerj.6500
The role of juvenile hormone in regulating reproductive physiology and dominance in Dinoponera quadriceps ants
Unequal reproductive output among members of the same sex (reproductive skew) is a common phenomenon in a wide range of communally breeding animals. In such species, reproductive dominance is often acquired during antagonistic interactions between group members that establish a reproductive hierarchy in which only a few individuals reproduce. Rank-specific syndromes of behavioural and physiological traits characterize such hierarchies, but how antagonistic behavioural interactions translate into stable rank-specific syndromes remains poorly understood. The pleiotropic nature of hormones makes them prime candidates for generating such syndromes as they physiologically integrate environmental (social) information, and often affect reproduction and behaviour simultaneously. Juvenile hormone (JH) is one of several hormones that occupy such a central regulatory role in insects and has been suggested to regulate reproductive hierarchies in a wide range of social insects including ants. Here we use experimental manipulation to investigate the effect of JH levels on reproductive physiology and social dominance in high-ranked workers of the eusocial ant Dinoponera quadriceps, a species that has secondarily reverted to queenless, simple societies. We show that JH regulated reproductive physiology, with ants in which JH levels were experimentally elevated having more regressed ovaries. In contrast, we found no evidence of JH levels affecting dominance in social interactions. This could indicate that JH and ovary development are decoupled from dominance in this species, however only high-ranked workers were investigated. The results therefore confirm that the regulatory role of JH in reproductive physiology in this ant species is in keeping with its highly eusocial ancestors rather than its secondary reversion to simple societies, but more investigation is needed to disentangle the relationships between hormones, behaviour and hierarchies.
Norman et al. (2019) The role of juvenile hormone in regulating reproductive physiology and dominance in Dinoponera quadriceps ants. PeerJ 7:e6512 https://doi.org/10.7717/peerj.6512
Synthesis of light-inducible and light-independent anthocyanins regulated by specific genes in grape ‘Marselan’ (V. vinifera L.)
Anthocyanin is an important parameter for evaluating the quality of wine grapes. However, the effects of different light intensities on anthocyanin synthesis in grape berry skin and its regulation mechanisms are still unclear. In this experiment, clusters of wine grape cv. ‘Marselan’ were bagged using fruit bags with different light transmittance of 50%, 15%, 5%, and 0, designated as treatment A, B, C and D, respectively. Fruits that were not bagged were used as the control, designated as CK. The anthocyanin composition and concentration, as well as gene expression profiles in the berry skin were determined. The results showed that the degree of coloration of the berry skin reduced with the decrease of the light transmittance, and the veraison was postponed for 10 days in D when compared with the CK. Total anthocyanin concentration in the berry skin treated with D decreased by 51.50% compared with CK at the harvest stage. A total of 24 and 21 anthocyanins were detected in CK and D, respectively. Among them, Malvidin-3-O-coumaroylglucoside (trans), which showed a significant positive correlation with the total concentration of anthocyanins at the harvest stage (r = 0.775) and was not detected in D, was presumed to be light-induced anthocyanin. Other anthocyanins which were both synthesized in CK and D were considered to be light-independent anthocyanins. Among them, Malvidin-3-O-coumaroylglucoside (cis) and Malvidin-3-O-acetylglucoside were typical representatives. Remarkably, the synthesis of light-inducible anthocyanins and light-independent anthocyanins were regulated by different candidate structural genes involved in flavonoid biosynthesis pathway and members of MYB and bHLH transcription factors.
Ma et al. (2019) Synthesis of light-inducible and light-independent anthocyanins regulated by specific genes in grape ‘Marselan’ (V. vinifera L.). PeerJ 7:e6521 https://doi.org/10.7717/peerj.6521
Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon)
Background Coral reefs are major hotspots of diversity for marine fishes, yet there is still ongoing debate on the mechanisms that promote divergence in these rich ecosystems. Our understanding of how diversity originates in this environment could be enhanced by investigating the evolutionary dynamics of closely related fishes with overlapping ranges. Here, we focus on grunts of the genus Haemulon, a group of coral reef fishes with 15 species in the Western Atlantic, 11 of which are syntopic. Methods Wild fish samples from three sympatric species of the Caribbean: Haemulon flavolineatum, H. carbonarium and H. macrostomum, were collected while SCUBA diving. RNA was extracted from livers, and the transcriptomes were assembled and annotated to investigate positive selection (Pairwise dN/dS) and patterns of gene expression between the three species. Results Pairwise dN/dS analyses showed evidence of positive selection for genes associated with immune response, cranial morphology and formation of the anterior–posterior axis. Analyses of gene expression revealed that despite their sympatric distribution, H. macrostomum showed upregulation of oxidation-reduction machinery, while there was evidence for activation of immune response in H. carbonarium. Discussion Overall, our analyses suggest closely related grunts show important differences in genes associated with body shape and feeding morphology, a result in-line with previous morphological studies in the group. Further, despite their overlapping distribution they interact with their environment in distinct fashions. This is the largest compendium of genomic information for grunts thus far, representing a valuable resource for future studies in this unique group of coral reef fishes.
Bernal et al. (2019) Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon). PeerJ 7:e6541 https://doi.org/10.7717/peerj.6541
An interpretable machine learning model for diagnosis of Alzheimer's disease
We present an interpretable machine learning model for medical diagnosis called sparse high-order interaction model with rejection option (SHIMR). A decision tree explains to a patient the diagnosis with a long rule (i.e., conjunction of many intervals), while SHIMR employs a weighted sum of short rules. Using proteomics data of 151 subjects in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset, SHIMR is shown to be as accurate as other non-interpretable methods (Sensitivity, SN = 0.84 ± 0.1, Specificity, SP = 0.69 ± 0.15 and Area Under the Curve, AUC = 0.86 ± 0.09). For clinical usage, SHIMR has a function to abstain from making any diagnosis when it is not confident enough, so that a medical doctor can choose more accurate but invasive and/or more costly pathologies. The incorporation of a rejection option complements SHIMR in designing a multistage cost-effective diagnosis framework. Using a baseline concentration of cerebrospinal fluid (CSF) and plasma proteins from a common cohort of 141 subjects, SHIMR is shown to be effective in designing a patient-specific cost-effective Alzheimer’s disease (AD) pathology. Thus, interpretability, reliability and having the potential to design a patient-specific multistage cost-effective diagnosis framework can make SHIMR serve as an indispensable tool in the era of precision medicine that can cater to the demand of both doctors and patients, and reduce the overwhelming financial burden of medical diagnosis.
Das et al. (2019) An interpretable machine learning model for diagnosis of Alzheimer's disease. PeerJ 7:e6543 https://doi.org/10.7717/peerj.6543
Use of Next Generation Sequencing to study two cowpox virus outbreaks
Background Between 2008 and 2011 about 40 cases of human cowpox were reported from Germany and France. Infections had been acquired via close contact to infected, young pet rats. An identical and unique sequence of the hemagglutinin gene was found in various cowpox virus (CPXV) isolates pointing to a common source of infection. In a second CPXV outbreak in cats in a small animal clinic in Germany in 2015, four out of five hospitalized cats showed identical hemagglutinin sequences and thus, a hospital-acquired transmission had been assumed. Next-Generation Sequencing was performed in order to re-investigate the outbreaks, as epidemiological data could not confirm all cases. Methods Homogenates of lesion material from rats, cats and humans were cultivated in cell culture. The genomes of four virus isolates, nine CPXVs from our strain collections and from DNA of three paraffin-embedded lesion materials were determined by Next Generation Sequencing (NGS). For phylogenetic analyses a MAFFT-alignment was generated. A distance matrix based on concatenated SNPs was calculated and plotted as dendrogram using Unweighted Pair Group Method with Arithmetic mean (UPGMA) for visualization. Results Aligning of about 200.000 nucleotides of 8 virus isolates associated with the pet rat outbreak revealed complete identity of six genomes, the remainder two genomes differed in as little as 3 SNPs. When comparing this dataset with four already published CPXV genomes also associated with the pet rat outbreak, again a maximum difference of 3 SNPs was found. The outbreak which lasted from 2008 till 2011 was indeed caused by a single strain which has maintained an extremely high level of clonality over 4 years. Aligning genomic sequences from four cases of feline cowpox revealed 3 identical sequences and one sequence which differed in 65 nucleotides. Although identical hemagglutinin sequences had been obtained from four hospitalized cats, genomic sequencing proved that a hospital-acquired transmission had occurred in only three cats. Conclusion Analyzing the rather short sequence of the hemagglutinin gene is not sufficient to conduct molecular trace back analyses. Instead, whole genome sequencing is the method of choice which can even be applied to paraffin-embedded specimens.
Antwerpen et al. (2019) Use of Next Generation Sequencing to study two cowpox virus outbreaks. PeerJ 7:e6561 https://doi.org/10.7717/peerj.6561