DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework
Background A prime objective in metagenomics is to classify DNA sequence fragments into taxonomic units. It usually requires several stages: read’s quality control, de novo assembly, contig annotation, gene prediction, etc. These stages need very efficient programs because of the number of reads from the projects. Furthermore, the complexity of metagenomes requires efficient and automatic tools that orchestrate the different stages. Method DATMA is a pipeline for fast metagenomic analysis that orchestrates the following: sequencing quality control, 16S rRNA-identification, reads binning, de novo assembly and evaluation, gene prediction, and taxonomic annotation. Its distributed computing model can use multiple computing resources to reduce the analysis time. Results We used a controlled experiment to show DATMA functionality. Two pre-annotated metagenomes to compare its accuracy and speed against other metagenomic frameworks. Then, with DATMA we recovered a draft genome of a novel Anaerolineaceae from a biosolid metagenome. Conclusions DATMA is a bioinformatics tool that automatically analyzes complex metagenomes. It is faster than similar tools and, in some cases, it can extract genomes that the other tools do not. DATMA is freely available at https://github.com/andvides/DATMA.
Benavides et al. (2020) DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework. PeerJ 8:e9762 https://doi.org/10.7717/peerj.9762
Generalized Linear Models outperform commonly used canonical analysis in estimating spatial structure of presence/absence data
Background Ecological communities tend to be spatially structured due to environmental gradients and/or spatially contagious processes such as growth, dispersion and species interactions. Data transformation followed by usage of algorithms such as Redundancy Analysis (RDA) is a fairly common approach in studies searching for spatial structure in ecological communities, despite recent suggestions advocating the use of Generalized Linear Models (GLMs). Here, we compared the performance of GLMs and RDA in describing spatial structure in ecological community composition data. We simulated realistic presence/absence data typical of many β-diversity studies. For model selection we used standard methods commonly used in most studies involving RDA and GLMs. Methods We simulated communities with known spatial structure, based on three real spatial community presence/absence datasets (one terrestrial, one marine and one freshwater). We used spatial eigenvectors as explanatory variables. We varied the number of non-zero coefficients of the spatial variables, and the spatial scales with which these coefficients were associated and then compared the performance of GLMs and RDA frameworks to correctly retrieve the spatial patterns contained in the simulated communities. We used two different methods for model selection, Forward Selection (FW) for RDA and the Akaike Information Criterion (AIC) for GLMs. The performance of each method was assessed by scoring overall accuracy as the proportion of variables whose inclusion/exclusion status was correct, and by distinguishing which kind of error was observed for each method. We also assessed whether errors in variable selection could affect the interpretation of spatial structure. Results Overall GLM with AIC-based model selection (GLM/AIC) performed better than RDA/FW in selecting spatial explanatory variables, although under some simulations the methods performed similarly. In general, RDA/FW performed unpredictably, often retaining too many explanatory variables and selecting variables associated with incorrect spatial scales. The spatial scale of the pattern had a negligible effect on GLM/AIC performance but consistently affected RDA’s error rates under almost all scenarios. Conclusion We encourage the use of GLM/AIC for studies searching for spatial drivers of species presence/absence patterns, since this framework outperformed RDA/FW in situations most likely to be found in natural communities. It is likely that such recommendations might extend to other types of explanatory variables.
Spatial and Geographic Information Science
Carlos-Júnior et al. (2020) Generalized Linear Models outperform commonly used canonical analysis in estimating spatial structure of presence/absence data. PeerJ 8:e9777 https://doi.org/10.7717/peerj.9777
Comparing the gastrointestinal barrier function between growth-retarded and normal yaks on the Qinghai-Tibetan Plateau
Background Yak (Bos grunniens) is an ancient bovine species on the Qinghai-Tibetan Plateau. Due to extremely harsh condition in the plateau, the growth retardation of yaks commonly exist, which can reduce the incomes of herdsman. The gastrointestinal barrier function plays a vital role in the absorption of nutrients and healthy growth. Functional deficiencies of the gastrointestinal barrier may be one of the contributors for yaks with growth retardation. Methods To this end, we compared the growth performance and gastrointestinal barrier function of growth-retarded (GRY) and normal yaks (GNY) based on average daily gain (ADG), serum parameters, tissue slice, real-time PCR, and western blotting, with eight yaks in each group. Results GRY exhibited lower (P < 0.05) average daily gain as compared to GNY. The diamine oxidase, D-lactic acid, and lipopolysaccharide concentrations in the serum of GRY were significantly higher (P < 0.05) than those of GNY. Compared to GNY, the papillae height in the rumen of GRY exhibited lower (P = 0.004). In jejunum, with the exception of higher villus height, width, and surface area in GNY, numerical difference (P = 0.61) was detected between two groups for crypt depth. Both in rumen and jejunum, the mRNA expression of interleukin-1beta in GRY was markedly higher (P < 0.05) than that in GNY, but an opposite trend was found in interleukin-10 expression. Moreover, GRY showed a higher (P < 0.05) tumor necrosis factor-alpha mRNA expression in the rumen. The claudin-1 (CLDN1), occludin (OCLN), and zonula occludens-1 (ZO1) expressions of GRY in rumen and jejunum were significantly down-regulated (P < 0.05) as compared to GNY. The correlation analysis identified that in rumen and jejunum, there was a positive correlation between interleukin-10 and CLDN1, OCLN, and ZO1 mRNA expressions, but the tumor necrosis factor-alpha was negatively correlated with CLDN1, OCLN, and ZO1. In the rumen, the ADG was positively correlated with papillae surface area, and a same relationship between ADG and CLDN1, OCLN, and ZO1 expressions was found. Conclusion The results indicated that the ruminal and jejunal barrier functions of GRY are disrupted as compared to GNY. In addition, our study provides a potential solution for promoting the growth of GRY by enhancing the gastrointestinal barrier function.
Ma et al. (2020) Comparing the gastrointestinal barrier function between growth-retarded and normal yaks on the Qinghai-Tibetan Plateau. PeerJ 8:e9851 https://doi.org/10.7717/peerj.9851
Collaborative networks enable the rapid establishment of serological assays for SARS-CoV-2 during nationwide lockdown in New Zealand
Background Serological assays that detect antibodies to SARS-CoV-2 are critical for determining past infection and investigating immune responses in the COVID-19 pandemic. We established ELISA-based immunoassays using locally produced antigens when New Zealand went into a nationwide lockdown and the supply chain of diagnostic reagents was a widely held domestic concern. The relationship between serum antibody binding measured by ELISA and neutralising capacity was investigated using a surrogate viral neutralisation test (sVNT). Methods A pre-pandemic sera panel (n = 113), including respiratory infections with symptom overlap with COVID-19, was used to establish assay specificity. Sera from PCR‑confirmed SARS-CoV-2 patients (n = 21), and PCR-negative patients with respiratory symptoms suggestive of COVID-19 (n = 82) that presented to the two largest hospitals in Auckland during the lockdown period were included. A two-step IgG ELISA based on the receptor binding domain (RBD) and spike protein was adapted to determine seropositivity, and neutralising antibodies that block the RBD/hACE‑2 interaction were quantified by sVNT. Results The calculated cut-off (>0.2) in the two-step ELISA maximised specificity by classifying all pre-pandemic samples as negative. Sera from all PCR-confirmed COVID-19 patients were classified as seropositive by ELISA ≥7 days after symptom onset. There was 100% concordance between the two-step ELISA and the sVNT with all 7+ day sera from PCR‑confirmed COVID-19 patients also classified as positive with respect to neutralising antibodies. Of the symptomatic PCR-negative cohort, one individual with notable travel history was classified as positive by two-step ELISA and sVNT, demonstrating the value of serology in detecting prior infection. Conclusions These serological assays were established and assessed at a time when human activity was severely restricted in New Zealand. This was achieved by generous sharing of reagents and technical expertise by the international scientific community, and highly collaborative efforts of scientists and clinicians across the country. The assays have immediate utility in supporting clinical diagnostics, understanding transmission in high-risk cohorts and underpinning longer‑term ‘exit’ strategies based on effective vaccines and therapeutics.
McGregor et al. (2020) Collaborative networks enable the rapid establishment of serological assays for SARS-CoV-2 during nationwide lockdown in New Zealand. PeerJ 8:e9863 https://doi.org/10.7717/peerj.9863
Structural and functional microbial diversity of sandy soil under cropland and grassland
Background Land use change significantly alters soil organic carbon content and the microbial community. Therefore, in the present study, the effect of changing cropland to grassland on structural and functional soil microbial diversity was evaluated. The specific aims were (i) to identify the most prominent members of the fungal communities and their relevant ecological guild groups; (ii) to assess changes in the diversity of ammonia-oxidizing archaea; (iii) to determine the relationships between microbial diversity and selected physical and chemical properties. Methods We investigated microbial diversity and activity indicators, bulk density and the water-holding capacity of sandy soil under both cropland and 25-year-old grassland (formerly cropland) in Trzebieszów, in the Podlasie Region, Poland. Microbial diversity was assessed by: the relative abundance of ammonia-oxidizing archaea, fungal community composition and functional diversity. Microbial activity was assessed by soil enzyme (dehydrogenase, β-glucosidase) and respiration tests. Results It was shown that compared to cropland, grassland has a higher soil organic carbon content, microbial biomass, basal respiration, rate of enzyme activity, richness and diversity of the microbial community, water holding capacity and the structure of the fungal and ammonia-oxidizing archaea communities was also altered. The implications of these results for soil quality and soil health are also discussed. The results suggest that grassland can have a significant phytosanitary capacity with regard to ecosystem services, due to the prominent presence of beneficial and antagonistic microbes. Moreover, the results also suggest that grassland use may improve the status of soil organic carbon and nitrogen dynamics, thereby increasing the relative abundance of fungi and ammonia-oxidizing archaea.
Frąc et al. (2020) Structural and functional microbial diversity of sandy soil under cropland and grassland. PeerJ 8:e9501 https://doi.org/10.7717/peerj.9501
Postcranial elements of small mammals as indicators of locomotion and habitat
Many studies have shown a correlation between postcranial anatomy and locomotor behavior in mammals, but the postcrania of small mammals (<5 kg) is often considered to be uninformative of their mode of locomotion due to their more generalized overall anatomy. Such small body size was true of all mammals during the Mesozoic. Anatomical correlates of locomotor behavior are easier to determine in larger mammals, but useful information can be obtained from the smaller ones. Limb bone proportions (e.g., brachial index) can be useful locomotor indicators; but complete skeletons, or even complete long bones, are rare for Mesozoic mammals, although isolated articular surfaces are often preserved. Here we examine the correlation of the morphology of long bone joint anatomy (specifically articular surfaces) and locomotor behavior in extant small mammals and demonstrate that such anatomy may be useful for determining the locomotor mode of Mesozoic mammals, at least for the therian mammals.
Janis et al. (2020) Postcranial elements of small mammals as indicators of locomotion and habitat. PeerJ 8:e9634 https://doi.org/10.7717/peerj.9634
Extreme dispersal or human-transport? The enigmatic case of an extralimital freshwater occurrence of a Southern elephant seal from Indiana
Elephant seals (Mirounga spp.) are the largest living pinnipeds, and the spatial scales of their ecology, with dives over 1 km in depth and foraging trips over 10,000 km long, are unrivalled by their near relatives. Here we report the discovery of an incomplete Holocene age Southern elephant seal (M. leonina) rostrum from Indiana, USA. The surviving material are two casts of the original specimen, which was collected in a construction excavation close to the Wabash River near Lafayette, Indiana. The original specimen was mostly destroyed for radiometric dating analyses in the 1970s, which resulted in an age of 1,260 ± 90 years before the present. The existence of sediments in the original specimen suggests some type of post depositional fluvial transportation. The prevalent evidence suggests that this male Southern elephant seal crossed the equator and the Gulf of Mexico, and then entered the Mississippi River system, stranding far upriver in Indiana or adjacent areas, similar to other reported examples of lost marine mammals in freshwater systems. Based on potential cut marks, we cannot exclude human-mediated transportation or scavenging by Indigenous peoples as a contributing factor of this occurrence. The material reported here represents by far the northernmost occurrence of a Southern elephant seal in the Northern Hemisphere ever recorded. The unusual occurrence of a top marine predator >1,000 km from the closest marine effluent as a potential extreme case of dispersal emphasizes how marine invasions of freshwater systems have happened frequently through historical (and likely geological) time.
Valenzuela-Toro et al. (2020) Extreme dispersal or human-transport? The enigmatic case of an extralimital freshwater occurrence of a Southern elephant seal from Indiana. PeerJ 8:e9665 https://doi.org/10.7717/peerj.9665
Peritumoral immune infiltrates in primary tumours are not associated with the presence of axillary lymph node metastasis in breast cancer: a retrospective cohort study
Background The axillary lymph nodes (ALNs) in breast cancer patients are the body regions to where tumoral cells most often first disseminate. The tumour immune response is important for breast cancer patient outcome, and some studies have evaluated its involvement in ALN metastasis development. Most studies have focused on the intratumoral immune response, but very few have evaluated the peritumoral immune response. The aim of the present article is to evaluate the immune infiltrates of the peritumoral area and their association with the presence of ALN metastases. Methods The concentration of 11 immune markers in the peritumoral areas was studied in 149 patients diagnosed with invasive breast carcinoma of no special type (half of whom had ALN metastasis at diagnosis) using tissue microarrays, immunohistochemistry and digital image analysis procedures. The differences in the concentration of the immune response of peritumoral areas between patients diagnosed with and without metastasis in their ALNs were evaluated. A multivariate logistic regression model was developed to identify the clinical-pathological variables and the peritumoral immune markers independently associated with having or not having ALN metastases at diagnosis. Results No statistically significant differences were found in the concentrations of the 11 immune markers between patients diagnosed with or without ALN metastases. Patients with metastases in their ALNs had a higher histological grade, more lymphovascular and perineural invasion and larger-diameter tumours. The multivariate analysis, after validation by bootstrap simulation, revealed that only tumour diameter (OR = 1.04; 95% CI [1.00–1.07]; p = 0.026), lymphovascular invasion (OR = 25.42; 95% CI [9.57–67.55]; p < 0.001) and histological grades 2 (OR = 3.84; 95% CI [1.11–13.28]; p = 0.033) and 3 (OR = 5.18; 95% CI [1.40–19.17]; p = 0.014) were associated with the presence of ALN metastases at diagnosis. This study is one of the first to study the association of the peritumoral immune response with ALN metastasis. We did not find any association of peritumoral immune infiltrates with the presence of ALN metastasis. Nevertheless, this does not rule out the possibility that other peritumoral immune populations are associated with ALN metastasis. This matter needs to be examined in greater depth, broadening the types of peritumoral immune cells studied, and including new peritumoral areas, such as the germinal centres of the peritumoral tertiary lymphoid structures found in extensively infiltrated neoplastic lesions.
López et al. (2020) Peritumoral immune infiltrates in primary tumours are not associated with the presence of axillary lymph node metastasis in breast cancer: a retrospective cohort study. PeerJ 8:e9779 https://doi.org/10.7717/peerj.9779
Applied phylogeography of Cyclopia intermedia (Fabaceae) highlights the need for ‘duty of care’ when cultivating honeybush
Background The current cultivation and plant breeding of Honeybush tea (produced from members of CyclopiaVent.) do not consider the genetic diversity nor structuring of wild populations. Thus, wild populations may be at risk of genetic contamination if cultivated plants are grown in the same landscape. Here, we investigate the spatial distribution of genetic diversity within Cyclopia intermedia E. Mey.—this species is widespread and endemic in the Cape Floristic Region (CFR) and used in the production of Honeybush tea. Methods We applied High Resolution Melt analysis (HRM), with confirmation Sanger sequencing, to screen two non-coding chloroplast DNA regions (two fragments from the atpI-aptH intergenic spacer and one from the ndhA intron) in wild C. intermedia populations. A total of 156 individuals from 17 populations were analyzed for phylogeographic structuring. Statistical tests included analyses of molecular variance and isolation-by-distance, while relationships among haplotypes were ascertained using a statistical parsimony network. Results Populations were found to exhibit high levels of genetic structuring, with 62.8% of genetic variation partitioned within mountain ranges. An additional 9% of genetic variation was located amongst populations within mountains, suggesting limited seed exchange among neighboring populations. Despite this phylogeographic structuring, no isolation-by-distance was detected (p > 0.05) as nucleotide variation among haplotypes did not increase linearly with geographic distance; this is not surprising given that the configuration of mountain ranges dictates available habitats and, we assume, seed dispersal kernels. Conclusions Our findings support concerns that the unmonitored redistribution of Cyclopia genetic material may pose a threat to the genetic diversity of wild populations, and ultimately the genetic resources within the species. We argue that ‘duty of care’ principles be used when cultivating Honeybush and that seed should not be translocated outside of the mountain range of origin. Secondarily, given the genetic uniqueness of wild populations, cultivated populations should occur at distance from wild populations that is sufficient to prevent unintended gene flow; however, further research is needed to assess gene flow within mountain ranges.
Galuszynski et al. (2020) Applied phylogeography of Cyclopia intermedia (Fabaceae) highlights the need for ‘duty of care’ when cultivating honeybush. PeerJ 8:e9818 https://doi.org/10.7717/peerj.9818
Simulating highly disturbed vegetation distribution: the case of China’s Jing-Jin-Ji region
Background Simulating vegetation distribution is an effective method for identifying vegetation distribution patterns and trends. The primary goal of this study was to determine the best simulation method for a vegetation in an area that is heavily affected by human disturbance. Methods We used climate, topographic, and spectral data as the input variables for four machine learning models (random forest (RF), decision tree (DT), support vector machine (SVM), and maximum likelihood classification (MLC)) on three vegetation classification units (vegetation group (I), vegetation type (II), and formation and subformation (III)) in Jing-Jin-Ji, one of China’s most developed regions. We used a total of 2,789 vegetation points for model training and 974 vegetation points for model assessment. Results Our results showed that the RF method was the best of the four models, as it could effectively simulate vegetation distribution in all three classification units. The DT method could only simulate vegetation distribution in units I and II, while the other two models could not simulate vegetation distribution in any of the units. Kappa coefficients indicated that the DT and RF methods had more accurate predictions for units I and II than for unit III. The three vegetation classification units were most affected by six variables: three climate variables (annual mean temperature, mean diurnal range, and annual precipitation), one geospatial variable (slope), and two spectral variables (Mid-infrared ratio of winter vegetation index and brightness index of summer vegetation index). Variables Combination 7, including annual mean temperature, annual precipitation, mean diurnal range and precipitation of driest month, produced the highest simulation accuracy. Conclusions We determined that the RF model was the most effective for simulating vegetation distribution in all classification units present in the Jing-Jin-Ji region. The RF model produced high accuracy vegetation distributions in classification units I and II, but relatively low accuracy in classification unit III. Four climate variables were sufficient for vegetation distribution simulation in such region.
Yi et al. (2020) Simulating highly disturbed vegetation distribution: the case of China’s Jing-Jin-Ji region. PeerJ 8:e9839 https://doi.org/10.7717/peerj.9839