Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau
The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.
Wang et al. (2017) Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau. PeerJ 5:e3770 https://doi.org/10.7717/peerj.3770
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine
Background The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. Methods The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC. Results We present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. Discussion This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.
Gerritsen et al. (2017) Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. PeerJ 5:e3698 https://doi.org/10.7717/peerj.3698
Development and evaluation of rapid novel isothermal amplification assays for important veterinary pathogens: Chlamydia psittaci and Chlamydia pecorum
Background Chlamydia psittaci and Chlamydia pecorum are important veterinary pathogens, with the former also being responsible for zoonoses, and the latter adversely affecting koala populations in Australia and livestock globally. The rapid detection of these organisms is still challenging, particularly at the point-of-care (POC). In the present study, we developed and evaluated rapid, sensitive and robust C. psittaci-specific and C. pecorum-specific Loop Mediated Isothermal Amplification (LAMP) assays for detection of these pathogens. Methods and Materials The LAMP assays, performed in a Genie III real-time fluorometer, targeted a 263 bp region of the C. psittaci-specific Cps_0607 gene or a 209 bp region of a C. pecorum-specific conserved gene CpecG_0573, and were evaluated using a range of samples previously screened using species-specific quantitative PCRs (qPCRs). Species-specificity for C. psittaci and C. pecorum LAMP targets was tested against DNA samples from related chlamydial species and a range of other bacteria. In order to evaluate pathogen detection in clinical samples, C. psittaci LAMP was evaluated using a total of 26 DNA extracts from clinical samples from equine and avian hosts, while for C. pecorum LAMP, we tested a total of 63 DNA extracts from clinical samples from koala, sheep and cattle hosts. A subset of 36 C. pecorum samples was also tested in a thermal cycler (instead of a real-time fluorometer) using newly developed LAMP and results were determined as an end point detection. We also evaluated rapid swab processing (without DNA extraction) to assess the robustness of these assays. Results Both LAMP assays were demonstrated to species-specific, highly reproducible and to be able to detect as little as 10 genome copy number/reaction, with a mean amplification time of 14 and 24 min for C. psittaci and C. pecorum, respectively. When testing clinical samples, the overall congruence between the newly developed LAMP assays and qPCR was 92.3% for C. psittaci (91.7% sensitivity and 92.9% specificity); and 84.1% for C. pecorum (90.6% sensitivity and 77.4% specificity). For a subset of 36 C. pecorum samples tested in a thermal cycler using newly developed LAMP, we observed 34/36 (94.4%) samples result being congruent between LAMP performed in fluorometer and in thermal cycler. Rapid swab processing method evaluated in this study also allows for chlamydial DNA detection using LAMP. Discussion In this study, we describe the development of novel, rapid and robust C. psittaci-specific and C. pecorum-specific LAMP assays that are able to detect these bacteria in clinical samples in either the laboratory or POC settings. With further development and a focus on the preparation of these assays at the POC, it is anticipated that both tests may fill an important niche in the repertoire of ancillary diagnostic tools available to clinicians.
Jelocnik et al. (2017) Development and evaluation of rapid novel isothermal amplification assays for important veterinary pathogens: Chlamydia psittaci and Chlamydia pecorum. PeerJ 5:e3799 https://doi.org/10.7717/peerj.3799
Variance component testing for identifying differentially expressed genes in RNA-seq data
RNA sequencing (RNA-Seq) enables the measurement and comparison of gene expression with isoform-level quantification. Differences in the effect of each isoform may make traditional methods, which aggregate isoforms, ineffective. Here, we introduce a variance component-based test that can jointly test multiple isoforms of one gene to identify differentially expressed (DE) genes, especially those with isoforms that have differential effects. We model isoform-level expression data from RNA-Seq using a negative binomial distribution and consider the baseline abundance of isoforms and their effects as two random terms. Our approach tests the global null hypothesis of no difference in any of the isoforms. The null distribution of the derived score statistic is investigated using empirical and theoretical methods. The results of simulations suggest that the performance of the proposed set test is superior to that of traditional algorithms and almost reaches optimal power when the variance of covariates is large. This method is also applied to analyze real data. Our algorithm, as a supplement to traditional algorithms, is superior at selecting DE genes with sparse or opposite effects for isoforms.
Yang et al. (2017) Variance component testing for identifying differentially expressed genes in RNA-seq data. PeerJ 5:e3797 https://doi.org/10.7717/peerj.3797
Age, growth, mortality and reproductive seasonality of jolthead porgy, Calamus bajonado, from Florida waters
Ages of jolthead porgy (Calamus bajonado Schneider 1801) (n = 635) from Florida commercial and recreational fisheries from 2008–2016 were determined using sectioned sagittal otoliths. We determined, using edge-type analysis, that opaque zones were annular, forming March–June (peaking in April). Jolthead porgy ranged from 1–13 years, and the largest fish measured 680 mm TL (total length, mm). Body size relationships for jolthead porgy were TL = 1.09FL + 20.44 (n = 622, r2 = 0.99), FL = 0.90 TL –14.26 (n = 622, r2 = 0.99), and W = 1.1 × 10−5 TL3.06 (n = 577), where W is total weight (grams, g) and FL is fork length (mm). The von Bertalanffy growth equation for jolthead porgy was Lt = 737(1 − e−0.14(t+2.02)) (n = 635). Point estimate of natural mortality was M = 0.32, while age-specific estimates of M ranged from 0.58–0.17 y−1 for ages 1–13. Catch curve analysis estimated the instantaneous rate of total mortality Z = 0.70, while instantaneous rate of fishing mortality F was 0.38. Macroscopic staging of female gonads indicated the presence of hydrated oocytes from December–March, and GSI data indicates that peak spawning in females occurs during March. This study presents the first published findings of life history parameters for jolthead porgy from the Atlantic waters off the southeastern United States.
Burton et al. (2017) Age, growth, mortality and reproductive seasonality of jolthead porgy, Calamus bajonado, from Florida waters. PeerJ 5:e3774 https://doi.org/10.7717/peerj.3774
Current practice in the management of new-onset atrial fibrillation in critically ill patients: a UK-wide survey
Background New-onset atrial fibrillation (AF) is the most common arrhythmia in critically ill patients. Although evidence base and expert consensus opinion for management have been summarised in several international guidelines, no specific considerations for critically ill patients have been included. We aimed to establish current practice of management of critically ill patients with new-onset AF. Methods We designed a short user-friendly online questionnaire. All members of the Intensive Care Society were invited via email containing a link to the questionnaire, which comprised 21 questions. The online survey was conducted between November 2016 and December 2016. Results The response rate was 397/3152 (12.6%). The majority of respondents (81.1%) worked in mixed Intensive Care Units and were consultants (71.8%). Most respondents (39.5%) would start intervention on patients with fast new-onset AF and stable blood pressure at a heart rate between 120 and 139 beats/min. However, 34.8% of participants would treat all patients who developed new-onset fast AF. Amiodarone and beta-blockers (80.9% and 11.6% of answers) were the most commonly used anti-arrhythmics. A total of 63.8% of respondents do not regularly anti-coagulate critically ill patients with new-onset fast AF, while 30.8% anti-coagulate within 72 hours. A total of 68.0% of survey respondents do not routinely use stroke risk scores in critically ill patients with new-onset AF. A total of 85.4% of participants would consider taking part in a clinical trial investigating treatment of new-onset fast AF in the critically ill. Discussion Our results suggest a considerable disparity between contemporary practice of management of new-onset AF in critical illness and treatment recommendations for the general patient population suffering from AF, particularly with regard to anti-arrhythmics and anti-coagulation used. Amongst intensivists, there is a substantial interest in research for management of new-onset AF in critically ill patients.
Chean et al. (2017) Current practice in the management of new-onset atrial fibrillation in critically ill patients: a UK-wide survey. PeerJ 5:e3716 https://doi.org/10.7717/peerj.3716
Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences
Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.
Campbell et al. (2017) Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences. PeerJ 5:e3548 https://doi.org/10.7717/peerj.3548
A comparison of the morphological and biochemical characteristics of Chlorella sorokiniana and Chlorella zofingiensis cultured under photoautotrophic and mixotrophic conditions
The responses of two species of microalgae, Chlorella sorokiniana and Chlorella zofingiensis, were compared regarding their morphological and biochemical properties under photoautotrophic and mixotrophic conditions. These microalgae were cultured under both conditions, and their crude ethanolic extracts were examined for their pigment and total phenolic contents. In addition, the microalgae’s antioxidant activities were determined using a DPPH radical scavenging assay and a ferric reducing antioxidant power (FRAP) assay. Both strains showed increases in cell size due to the accumulation of lipid bodies and other cell contents, especially carotenoids, under the mixotrophic condition. Notably, reductions in phenolic and chlorophyll contents were observed to be associated with lower antioxidant activity. C. zofingiensis compared with C. sorokiniana, demonstrated higher antioxidant activity and carotenoid content. This study showed that different species of microalgae responded differently to varying conditions by producing different types of metabolites, as evidenced by the production of higher levels of phenolic compounds under the photoautotrophic condition and the production of the same levels of carotenoids under both photoautotrophic and mixotrophic conditions.
Azaman et al. (2017) A comparison of the morphological and biochemical characteristics of Chlorella sorokiniana and Chlorella zofingiensis cultured under photoautotrophic and mixotrophic conditions. PeerJ 5:e3473 https://doi.org/10.7717/peerj.3473
MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes
Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide valuable insights into microbial ecology by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool—MetaCRAST) that constrains searches based on user-specified direct repeats (DRs). These DRs could be expected from assembly or taxonomic profiles of metagenomes. We compared the performance of MetaCRAST to those of two existing metagenomic CRISPR detection tools—Crass and MinCED—using both real and simulated acid mine drainage (AMD) and enhanced biological phosphorus removal (EBPR) metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to the de novo CRISPR detection methods Crass and MinCED. Evaluation on simulated metagenomes show it performs better than de novo tools for Illumina metagenomes and comparably for 454 metagenomes. It also has comparable performance dependence on read length and community composition, run time, and accuracy to these tools. MetaCRAST is implemented in Perl, parallelizable through the Many Core Engine (MCE), and takes metagenomic sequence reads and direct repeat queries (FASTA or FASTQ) as input. It is freely available for download at https://github.com/molleraj/MetaCRAST.
Moller et al. (2017) MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes. PeerJ 5:e3788 https://doi.org/10.7717/peerj.3788
Lectins: an effective tool for screening of potential cancer biomarkers
In recent years, the use of lectins for screening of potential biomarkers has gained increased importance in cancer research, given the development in glycobiology that highlights altered structural changes of glycans in cancer associated processes. Lectins, having the properties of recognizing specific carbohydrate moieties of glycoconjugates, have become an effective tool for detection of new cancer biomarkers in complex bodily fluids and tissues. The specificity of lectins provides an added advantage of selecting peptides that are differently glycosylated and aberrantly expressed in cancer patients, many of which are not possibly detected using conventional methods because of their low abundance in bodily fluids. When coupled with mass spectrometry, research utilizing lectins, which are mainly from plants and fungi, has led to identification of numerous potential cancer biomarkers that may be used in the future. This article reviews lectin-based methods that are commonly adopted in cancer biomarker discovery research.
Hashim et al. (2017) Lectins: an effective tool for screening of potential cancer biomarkers. PeerJ 5:e3784 https://doi.org/10.7717/peerj.3784