SCelVis: exploratory single cell data analysis on the desktop and in the cloud
Background Single cell omics technologies present unique opportunities for biomedical and life sciences from lab to clinic, but the high dimensional nature of such data poses challenges for computational analysis and interpretation. Furthermore, FAIR data management as well as data privacy and security become crucial when working with clinical data, especially in cross-institutional and translational settings. Existing solutions are either bound to the desktop of one researcher or come with dependencies on vendor-specific technology for cloud storage or user authentication. Results To facilitate analysis and interpretation of single-cell data by users without bioinformatics expertise, we present SCelVis, a flexible, interactive and user-friendly app for web-based visualization of pre-processed single-cell data. Users can survey multiple interactive visualizations of their single cell expression data and cell annotation, define cell groups by filtering or manual selection and perform differential gene expression, and download raw or processed data for further offline analysis. SCelVis can be run both on the desktop and cloud systems, accepts input from local and various remote sources using standard and open protocols, and allows for hosting data in the cloud and locally. We test and validate our visualization using publicly available scRNA-seq data. Methods SCelVis is implemented in Python using Dash by Plotly. It is available as a standalone application as a Python package, via Conda/Bioconda and as a Docker image. All components are available as open source under the permissive MIT license and are based on open standards and interfaces, enabling further development and integration with third party pipelines and analysis components. The GitHub repository is https://github.com/bihealth/scelvis.
Obermayer et al. (2020) SCelVis: exploratory single cell data analysis on the desktop and in the cloud. PeerJ 8:e8607 https://doi.org/10.7717/peerj.8607
‘Remote’ behavioural ecology: do megaherbivores consume vegetation in proportion to its presence in the landscape?
Examination of the feeding habits of mammalian species such as the African elephant (Loxodonta africana) that range over large seasonally dynamic areas is exceptionally challenging using field-based methods alone. Although much is known of their feeding preferences from field studies, conclusions, especially in relation to differing habits in wet and dry seasons, are often contradictory. Here, two remote approaches, stable carbon isotope analysis and remote sensing, were combined to investigate dietary changes in relation to tree and grass abundances to better understand elephant dietary choice in the Kruger National Park, South Africa. A composited pair of Landsat Enhanced Thematic Mapper satellite images characterising flushed and senescent vegetation states, typical of wet and dry seasons respectively, were used to generate land-cover maps focusing on the forest to grassland gradient. Stable carbon isotope analysis of elephant faecal samples identified the proportion of C3 (typically browse)/C4 (typically grass) in elephant diets in the 1–2 days prior to faecal deposition. The proportion of surrounding C4 land-cover was extracted using concentric buffers centred on faecal sample locations, and related to the faecal %C4 content. Results indicate that elephants consume C4 vegetation in proportion to its availability in the surrounding area during the dry season, but during the rainy season there was less of a relationship between C4 intake and availability, as elephants targeted grasses in these periods. This study illustrates the utility of coupling isotope and cost-free remote sensing data to conduct complementary landscape analysis at highly-detailed, biologically meaningful resolutions, offering an improved ability to monitor animal behavioural patterns at broad geographical scales. This is increasingly important due to potential impacts of climate change and woody encroachment on broad-scale landscape habitat composition, allowing the tracking of shifts in species utilisation of these changing landscapes in a way impractical using field based methods alone.
Spatial and Geographic Information Science
Marston et al. (2020) ‘Remote’ behavioural ecology: do megaherbivores consume vegetation in proportion to its presence in the landscape?. PeerJ 8:e8622 https://doi.org/10.7717/peerj.8622
The expression of small RNAs in exosomes of follicular fluid altered in human polycystic ovarian syndrome
Polycystic ovary syndrome (PCOS) can cause reproductive disorders that may affect oocyte quality from punctured follicles in human follicular fluid (HFF). The non-coding RNA family includes micro RNA (miRNA), piwi-interacting RNA (piRNA) and transfer RNA (tRNA); these non-coding RNA transcripts play diverse functions and are implicated in a variety of diseases and health conditions, including infertility. In this study, to explore the role of HFF exosomes in PCOS, we extracted and sequenced RNA from HFF exosomes of PCOS patients and compared the analysis results with those of non-PCOS control group. The HFF exosomes were successfully isolated and characterized in a variety of ways. The sequencing results of the HFF exosomal RNA showed that about 6.6% of valid reads in the PCOS group and 8.6% in the non-PCOS group were successfully mapped to the human RNA database. Using a hierarchical clustering method, we found there were ten small RNA sequences whose expression was significantly different between the PCOS and non-PCOS groups. We chose six of them to predict target genes of interest for further GO analysis, and pathway analysis showed that the target genes are mainly involved in biosynthesis of amino acids, glycine, serine and glycosaminoglycan, as well as threonine metabolism. Therefore, the small RNA sequences contained in HFF EXs may play a key role in the mechanism that drives PCOS pathogenesis, and thereby can act as molecular biomarkers for PCOS diagnosis in the future.
Hu et al. (2020) The expression of small RNAs in exosomes of follicular fluid altered in human polycystic ovarian syndrome. PeerJ 8:e8640 https://doi.org/10.7717/peerj.8640
The systematics of the Cervidae: a total evidence approach
Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub) classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervids. Several analyses using different data partitions, taxon sampling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon sampling was compiled including 168 cranial and dental characters of 41 extant and 29 fossil cervids. The morphological and molecular data were analysed in a combined approach and other comprehensive phylogenetic reconstructions. The results showed that most Miocene cervids were more closely related to each other than to any other cervids. They were often positioned between the outgroup and all other cervids or as the sister taxon to Muntiacini. Two Miocene cervids were frequently placed within Muntiacini. Plio- and Pleistocene cervids could often be affiliated to Cervini, Odocoileini or Capreolini. The phylogenetic analyses provide new insights into the evolutionary history of cervids. Several fossil cervids could be successfully related to living representatives, confirming previously assumed affiliations based on comparative morphology and introducing new hypotheses. New systematic relationships were observed, some uncertainties persisted and resolving systematics within certain taxa remained challenging.
Heckeberg (2020) The systematics of the Cervidae: a total evidence approach. PeerJ 8:e8114 https://doi.org/10.7717/peerj.8114
Personality underground: evidence of behavioral types in the solitary subterranean rodent Ctenomys talarum
Background Animal personalities have been studied in a wide variety of taxa, but among rodents, available studies are relatively scarce and have focused mainly on social species. In this study, we evaluated the existence of personality in the solitary subterranean rodent Ctenomys talarum. Specifically, we aimed to test individual differences in behavior that are stable over time and context in males of C. talarum captured in the wild. Methods Our experimental design included two series of three behavioral tests each, carried out with a 35 day time interval. Each series included an Open Field test, a Social Encounter test, and an Open Field test with a predator stimulus. Results Of the total recorded behaviors, 55.55% showed temporal consistency. Principal component analysis of consistent behaviors grouped them into four dimensions that explain inter individual behavioral variability, in order of importance: activity, socioaversion, boldness and exploration. Therefore, our results suggest that the concept of animal personality is applicable to C. talarum and the dimensions found are in accordance with the ecological and behavioral characteristics of this species.
Fanjul et al. (2020) Personality underground: evidence of behavioral types in the solitary subterranean rodent Ctenomys talarum. PeerJ 8:e8490 https://doi.org/10.7717/peerj.8490
Greenhouse gas emissions from riparian zone cropland in a tributary bay of the Three Gorges Reservoir, China
Background A huge reservoir was formed by the Three Gorges Dam in China, which also formed a riparian zone along the bank of the reservoir. In the period of low water-level, the riparian zone in tributary bays of the Three Gorges Reservoir (TGR) was always unordered cultivated, owing to its gentle slope and high soil fertility. This land-use practice creates high potential of generating greenhouse gas (GHG) emissions with periodic water level fluctuation. Methods To evaluate potential GHG emissions from the soil-air interface, the static opaque chamber method was adopted to evaluate the effect of elevations (180 m, 175 m, 170 m and 165 m) and land use types (dry lands, paddy fields and grass fields) from April to September in 2015 and 2016. Results The results showed that carbon dioxide (CO2) was the main contributor of GHG emission in riparian zone most likely because of high organic carbon from residues. Furthermore, high soil water content in paddy fields resulted in significantly higher methane (CH4) flux than that in dry lands and grass fields. Compared to grass fields, anthropogenic activities in croplands were attributed with a decrease of soil total carbon and GHG emissions. However, inundation duration of different elevations was found to have no significant effect on CH4 and CO2 emissions in the riparian zone, and the mean nitrous oxide (N2O) flux from dry lands at an elevation of 165 m was significantly higher than that of other elevations likely because of tillage and manure application. The high N2O fluxes produced from tillage and fertilizer suggested that, in order to potentially mitigate GHG emissions from the riparian zone, more attention must be paid to the farming practices in dry lands at low elevations (below 165 m) in the riparian zone. Understanding factors that contribute to GHG emissions will help guide ecological restoration of riparian zones in the TGR.
Environmental Contamination and Remediation
Wang et al. (2020) Greenhouse gas emissions from riparian zone cropland in a tributary bay of the Three Gorges Reservoir, China. PeerJ 8:e8503 https://doi.org/10.7717/peerj.8503
Taxonomic revision of Dasydorylas Skevington, 2001 (Diptera, Pipunculidae) in the Middle East
Species of the distinctive and cosmopolitan genus Dasydorylas Skevington, 2001 in the Middle East are revised. Seven species are documented, and three new species, Dasydorylas dactylos sp. nov., D. forcipus sp. nov. and D. parazardouei sp. nov., are described, and one synonym, D. derafshani Motamedinia & Kehlmaier, 2017, syn. nov. is proposed, based on sequence information from the mitochondrial COI barcoding gene and morphological parameters. Diagnoses, illustrations and distributional data are provided for all studied species. Descriptions of new species as well as an identification key to all known species in the Middle East are also provided.
Motamedinia et al. (2020) Taxonomic revision of Dasydorylas Skevington, 2001 (Diptera, Pipunculidae) in the Middle East. PeerJ 8:e8511 https://doi.org/10.7717/peerj.8511
SpeciesPrimer: a bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species
Background Quantitative real-time PCR (qPCR) is a well-established method for detecting and quantifying bacteria, and it is progressively replacing culture-based diagnostic methods in food microbiology. High-throughput qPCR using microfluidics brings further advantages by providing faster results, decreasing the costs per sample and reducing errors due to automatic distribution of samples and reagents. In order to develop a high-throughput qPCR approach for the rapid and cost-efficient quantification of microbial species in complex systems such as fermented foods (for instance, cheese), the preliminary setup of qPCR assays working efficiently under identical PCR conditions is required. Identification of target-specific nucleotide sequences and design of specific primers are the most challenging steps in this process. To date, most available tools for primer design require either laborious manual manipulation or high-performance computing systems. Results We developed the SpeciesPrimer pipeline for automated high-throughput screening of species-specific target regions and the design of dedicated primers. Using SpeciesPrimer, specific primers were designed for four bacterial species of importance in cheese quality control, namely Enterococcus faecium, Enterococcus faecalis, Pediococcus acidilactici and Pediococcus pentosaceus. Selected primers were first evaluated in silico and subsequently in vitro using DNA from pure cultures of a variety of strains found in dairy products. Specific qPCR assays were developed and validated, satisfying the criteria of inclusivity, exclusivity and amplification efficiencies. Conclusion In this work, we present the SpeciesPrimer pipeline, a tool to design species-specific primers for the detection and quantification of bacterial species. We use SpeciesPrimer to design qPCR assays for four bacterial species and describe a workflow to evaluate the designed primers. SpeciesPrimer facilitates efficient primer design for species-specific quantification, paving the way for a fast and accurate quantitative investigation of microbial communities.
Dreier et al. (2020) SpeciesPrimer: a bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species. PeerJ 8:e8544 https://doi.org/10.7717/peerj.8544
Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata
We examined genetic structure in the lobe coral Porites lobata among pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oahu and Maui, Hawaii. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVA FST = 0.04∼0.19, P < 0.001), but no significant isolation by distance between islands. Strikingly, corals from the two nearshore sites with higher levels of environmental stressors on different islands over 100 km apart with similar environmentally stressful conditions were genetically closer (FST = 0.0, P = 0.73) than those within a single location less than 2 km apart (FST = 0.04∼0.08, P < 0.01). In contrast, a third site with a less impacted nearshore site (i.e., less pronounced environmental gradient) showed no significant structure from the offshore comparison. Our results show much stronger support for environment than distance separating these populations. Our finding suggests that ecological boundaries from human impacts may play a role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow might be explained by selective pressure across contrasting habitats.
Tisthammer et al. (2020) Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata. PeerJ 8:e8550 https://doi.org/10.7717/peerj.8550
Broad similarities in shoulder muscle architecture and organization across two amniotes: implications for reconstructing non-mammalian synapsids
The evolution of upright limb posture in mammals may have enabled modifications of the forelimb for diverse locomotor ecologies. A rich fossil record of non-mammalian synapsids holds the key to unraveling the transition from “sprawling” to “erect” limb function in the precursors to mammals, but a detailed understanding of muscle functional anatomy is a necessary prerequisite to reconstructing postural evolution in fossils. Here we characterize the gross morphology and internal architecture of muscles crossing the shoulder joint in two morphologically-conservative extant amniotes that form a phylogenetic and morpho-functional bracket for non-mammalian synapsids: the Argentine black and white tegu Salvator merianae and the Virginia opossum Didelphis virginiana. By combining traditional physical dissection of cadavers with nondestructive three-dimensional digital dissection, we find striking similarities in muscle organization and architectural parameters. Despite the wide phylogenetic gap between our study species, distal muscle attachments are notably similar, while differences in proximal muscle attachments are driven by modifications to the skeletal anatomy of the pectoral girdle that are well-documented in transitional synapsid fossils. Further, correlates for force production, physiological cross-sectional area (PCSA), muscle gearing (pennation), and working range (fascicle length) are statistically indistinguishable for an unexpected number of muscles. Functional tradeoffs between force production and working range reveal muscle specializations that may facilitate increased girdle mobility, weight support, and active stabilization of the shoulder in the opossum—a possible signal of postural transformation. Together, these results create a foundation for reconstructing the musculoskeletal anatomy of the non-mammalian synapsid pectoral girdle with greater confidence, as we demonstrate by inferring shoulder muscle PCSAs in the fossil non-mammalian cynodont Massetognathus pascuali.
Fahn-Lai et al. (2020) Broad similarities in shoulder muscle architecture and organization across two amniotes: implications for reconstructing non-mammalian synapsids. PeerJ 8:e8556 https://doi.org/10.7717/peerj.8556