Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods
Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently.
Santamaria et al. (2017) Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods. PeerJ 5:e3894 https://doi.org/10.7717/peerj.3894
Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
Background As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines. Methods We identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches). These are ideal benchmark datasets, as the trees, WGS data, and epidemiological data for each are all in agreement. We have placed these sequence data, sample metadata, and “known” phylogenetic trees in publicly-accessible databases and developed a standard descriptive spreadsheet format describing each dataset. To facilitate easy downloading of these benchmarks, we developed an automated script that uses the standard descriptive spreadsheet format. Results Our “outbreak” benchmark datasets represent the four major foodborne bacterial pathogens (Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni) and one simulated dataset where the “known tree” can be accurately called the “true tree”. The downloading script and associated table files are available on GitHub: https://github.com/WGS-standards-and-analysis/datasets. Discussion These five benchmark datasets will help standardize comparison of current and future phylogenomic pipelines, and facilitate important cross-institutional collaborations. Our work is part of a global effort to provide collaborative infrastructure for sequence data and analytic tools—we welcome additional benchmark datasets in our recommended format, and, if relevant, we will add these on our GitHub site. Together, these datasets, dataset format, and the underlying GitHub infrastructure present a recommended path for worldwide standardization of phylogenomic pipelines.
Timme et al. (2017) Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance. PeerJ 5:e3893 https://doi.org/10.7717/peerj.3893
Hearing assessment during deep brain stimulation of the central nucleus of the inferior colliculus and dentate cerebellar nucleus in rat
Background Recently it has been shown in animal studies that deep brain stimulation (DBS) of auditory structures was able to reduce tinnitus-like behavior. However, the question arises whether hearing might be impaired when interfering in auditory-related network loops with DBS. Methods The auditory brainstem response (ABR) was measured in rats during high frequency stimulation (HFS) and low frequency stimulation (LFS) in the central nucleus of the inferior colliculus (CIC, n = 5) or dentate cerebellar nucleus (DCBN, n = 5). Besides hearing thresholds using ABR, relative measures of latency and amplitude can be extracted from the ABR. In this study ABR thresholds, interpeak latencies (I–III, III–V, I–V) and V/I amplitude ratio were measured during off-stimulation state and during LFS and HFS. Results In both the CIC and the CNBN groups, no significant differences were observed for all outcome measures. Discussion DBS in both the CIC and the CNBN did not have adverse effects on hearing measurements. These findings suggest that DBS does not hamper physiological processing in the auditory circuitry.
Smit et al. (2017) Hearing assessment during deep brain stimulation of the central nucleus of the inferior colliculus and dentate cerebellar nucleus in rat. PeerJ 5:e3892 https://doi.org/10.7717/peerj.3892
Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos
Tibetan chickens have unique adaptations to the extreme high-altitude environment that they inhabit. Epigenetic DNA methylation affects many biological processes, including hypoxic adaptation; however, the regulatory genes for DNA methylation in hypoxic adaptation remain unknown. In this study, methylated DNA immunoprecipitation with high-throughput sequencing (MeDIP-seq) was used to provide an atlas of the DNA methylomes of the heart tissue of hypoxic highland Tibetan and lowland Chahua chicken embryos. A total of 31.2 gigabases of sequence data were generated from six MeDIP-seq libraries. We identified 1,049 differentially methylated regions (DMRs) and 695 related differentially methylated genes (DMGs) between the two chicken breeds. The DMGs are involved in vascular smooth muscle contraction, VEGF signaling pathway, calcium signaling pathway, and other hypoxia-related pathways. Five candidate genes that had low methylation (EDNRA, EDNRB2, BMPR1B, BMPRII, and ITGA2) might play key regulatory roles in the adaptation to hypoxia in Tibetan chicken embryos. Our study provides significant explanations for the functions of genes and their epigenetic regulation for hypoxic adaptation in Tibetan chickens.
Zhang et al. (2017) Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos. PeerJ 5:e3891 https://doi.org/10.7717/peerj.3891
voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data
RNA-Seq is a recent and efficient technique that uses the capabilities of next-generation sequencing technology for characterizing and quantifying transcriptomes. One important task using gene-expression data is to identify a small subset of genes that can be used to build diagnostic classifiers particularly for cancer diseases. Microarray based classifiers are not directly applicable to RNA-Seq data due to its discrete nature. Overdispersion is another problem that requires careful modeling of mean and variance relationship of the RNA-Seq data. In this study, we present voomDDA classifiers: variance modeling at the observational level (voom) extensions of the nearest shrunken centroids (NSC) and the diagonal discriminant classifiers. VoomNSC is one of these classifiers and brings voom and NSC approaches together for the purpose of gene-expression based classification. For this purpose, we propose weighted statistics and put these weighted statistics into the NSC algorithm. The VoomNSC is a sparse classifier that models the mean-variance relationship using the voom method and incorporates voom’s precision weights into the NSC classifier via weighted statistics. A comprehensive simulation study was designed and four real datasets are used for performance assessment. The overall results indicate that voomNSC performs as the sparsest classifier. It also provides the most accurate results together with power-transformed Poisson linear discriminant analysis, rlog transformed support vector machines and random forests algorithms. In addition to prediction purposes, the voomNSC classifier can be used to identify the potential diagnostic biomarkers for a condition of interest. Through this work, statistical learning methods proposed for microarrays can be reused for RNA-Seq data. An interactive web application is freely available at http://www.biosoft.hacettepe.edu.tr/voomDDA/.
Zararsiz et al. (2017) voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data. PeerJ 5:e3890 https://doi.org/10.7717/peerj.3890
The isolation and identification of pathogenic fungi from Tessaratoma papillosa Drury (Hemiptera: Tessaratomidae)
Background Litchi stink-bug, Tessaratoma papillosa Drury (Hemiptera: Tessaratomidae), is one of the most widespread and destructive pest species on Litchi chinensis Sonn and Dimocarpus longan Lour in Southern China. Inappropriate use of chemical pesticides has resulted in serious environmental problems and food pollution. Generating an improved Integrated Pest Management (IPM) strategy for litchi stink-bug in orchard farming requires development of an effective biological control agent. Entomopathogenic fungi are regarded as a vital ecological factor in the suppression of pest populations under field conditions. With few effective fungi and pathogenic strains available to control litchi stink-bug, exploration of natural resources for promising entomopathogenic fungi is warranted. Methods & Results In this study, two pathogenic fungi were isolated from cadavers of adult T. papillosa. They were identified as Paecilomyces lilacinus and Beauveria bassiana by morphological identification and rDNA-ITS homogeneous analysis. Infection of T. papillosa with B. bassiana and P. lilacinus occurred initially from the antennae, metameres, and inter-segmental membranes. Biological tests showed that the two entomopathogenic fungi induced high mortality in 2nd and 5th instar nymphs of T. papillosa. B. bassiana was highly virulent on 2nd instar nymphs of T. papillosa, with values for cadaver rate, LC50 and LT50 of 88.89%, 1.92 × 107 conidia/mL and 4.34 days respectively. Discussion This study provides two valuable entomopathogenic fungi from T. papillosa. This finding suggests that the highly virulent P. lilacinus and B. bassiana play an important role in the biocontrol of T. papillosa in China. These pathogenic fungi had no pollution or residue risk, and could provide an alternative option for IPM of litchi stink-bug.
Meng et al. (2017) The isolation and identification of pathogenic fungi from Tessaratoma papillosa Drury (Hemiptera: Tessaratomidae). PeerJ 5:e3888 https://doi.org/10.7717/peerj.3888
Anti-apoptotic properties of carbon monoxide in porcine oocyte during in vitro aging
If fertilization of matured oocyte does not occur, unfertilized oocyte undergoes aging, resulting in a time-dependent reduction of the oocyte’s quality. The aging of porcine oocytes can lead to apoptosis. Carbon monoxide (CO), a signal molecule produced by the heme oxygenase (HO), possesses cytoprotective and anti-apoptotic effects that have been described in somatic cells. However, the effects of CO in oocytes have yet to be investigated. By immunocytochemistry method we detected that both isoforms of heme oxygenase (HO-1 and HO-2) are present in the porcine oocytes. Based on the morphological signs of oocyte aging, it was found that the inhibition of both HO isoforms by Zn-protoporphyrin IX (Zn-PP IX) leads to an increase in the number of apoptotic oocytes and decrease in the number of intact oocytes during aging. Contrarily, the presence of CO donors (CORM-2 or CORM-A1) significantly decrease the number of apoptotic oocytes while increasing the number of intact oocytes. We also determined that CO donors significantly decrease the caspase-3 (CAS-3) activity. Our results suggest that HO/CO contributes to the sustaining viability through regulation of apoptosis during in vitro aging of porcine oocytes.
Němeček et al. (2017) Anti-apoptotic properties of carbon monoxide in porcine oocyte during in vitro aging. PeerJ 5:e3876 https://doi.org/10.7717/peerj.3876
Effects of astragalus polysaccharide on the adhesion-related immune response of endothelial cells stimulated with CSFV in vitro
Background Astragalus polysaccharide (APS) has immunomodulatory activities on porcine peripheral blood mononuclear cells. The immunomodulatory effects of APS on porcine endothelial cells (ECs) expose to classical swine fever virus (CSFV) remain unknown. Methods The virus was titrated using an indirect immune biotin enzyme standard method to confirm that porcine ECs were susceptible to CSFV infection and to determine the TCID50 of CSFV (C-strain). Porcine ECs were cultured with CSFV in the presence of APS. Relative quantitative PCR was used to assess the mRNA expression of factors that influence EC adhesion and immunity. Results The expression of adhesion factors mRNA increased following stimulation with CSFV; this effect was inhibited by pre-exposing the cells to APS. In addition, the expression of growth factors and some immune factors increased after infection with CSFV; this increase in tissue factor (TF), transforming growth factor (TGF-β), and interleukin-8 (IL-8) could be inhibited by the addition of APS. The immune response mediated by Toll-like receptor 4 (TLR4) in ECs may be unregulated by CSFV as it was also inhibited by pre-treatment with APS. Discussion The addition of APS to the culture can obviously regulate the expression of molecules related to the adhesion, growth, and immune response of ECs, as well as the production of cytokines. Therefore, it may have the potential to be an effective component in vaccines against CSFV.
Zhuge et al. (2017) Effects of astragalus polysaccharide on the adhesion-related immune response of endothelial cells stimulated with CSFV in vitro. PeerJ 5:e3862 https://doi.org/10.7717/peerj.3862
Enhanced conflict monitoring via a short-duration, video-assisted deep breathing in healthy young adults: an event-related potential approach through the Go/NoGo paradigm
Objectives Practitioners of mindfulness are reported to have greater cognitive control especially in conflict monitoring, response inhibition and sustained attention. However, due to the various existing methods in each mindfulness practices and also, the high commitment factor, a barrier still exists for an individual to pick up the practices. Therefore, the effect of short duration deep breathing on the cognitive control is investigated here. Methods Short duration guided deep breathing videos consisting of 5, 7 and 9 min respectively were created and used on subjects training. The effect on cognitive control was assessed using a Go/NoGo task along with event-related potential (ERP) measurements at Fz, Cz, and Pz. Results From the study, the significant outcome showed at the follow-up session in which participants engaged for 5 min deep breathing group showed a profound NoGo N2 amplitude increment as compared to the control group, indicating an enhanced conflict monitoring ability. An inverse relationship between the NoGo N2 amplitude and the breathing duration is observed as well at the follow-up session. Conclusion These results indicated the possibility of performing short duration deep breathing guided by a video to achieve an enhanced conflict monitoring as an alternative to other mindfulness practices and 5 min is found to be the optimum practice duration. Significant This study is the first to establish a relationship between deep breathing and conflict monitoring through ERP. The study population of young adults taken from the same environment reduces the variance in ERP results due to age and environment. Limitation A larger sample size would provide a greater statistical power. A longer duration of deep breathing should be investigated to further clarify the relationship between the practice duration and the NoGo N2 amplitude. The result can be split by gender and analyzed separately due to the different brain structure of males and females.
Cheng et al. (2017) Enhanced conflict monitoring via a short-duration, video-assisted deep breathing in healthy young adults: an event-related potential approach through the Go/NoGo paradigm. PeerJ 5:e3857 https://doi.org/10.7717/peerj.3857
Effects of invasion history on physiological responses to immune system activation in invasive Australian cane toads
The cane toad (Rhinella marina) has undergone rapid evolution during its invasion of tropical Australia. Toads from invasion front populations (in Western Australia) have been reported to exhibit a stronger baseline phagocytic immune response than do conspecifics from range core populations (in Queensland). To explore this difference, we injected wild-caught toads from both areas with the experimental antigen lipopolysaccharide (LPS, to mimic bacterial infection) and measured whole-blood phagocytosis. Because the hypothalamic-pituitary-adrenal axis is stimulated by infection (and may influence immune responses), we measured glucocorticoid response through urinary corticosterone levels. Relative to injection of a control (phosphate-buffered saline), LPS injection increased both phagocytosis and the proportion of neutrophils in the blood. However, responses were similar in toads from both populations. This null result may reflect the ubiquity of bacterial risks across the toad’s invaded range; utilization of this immune pathway may not have altered during the process of invasion. LPS injection also induced a reduction in urinary corticosterone levels, perhaps as a result of chronic stress.
Selechnik et al. (2017) Effects of invasion history on physiological responses to immune system activation in invasive Australian cane toads. PeerJ 5:e3856 https://doi.org/10.7717/peerj.3856