Ontogenetic variation in the diet of the anuran community from a semi-arid environment in the southeastern Chihuahuan Desert
Although ontogeny influences dietary composition and trophic niche breadth in many anurans, its effects on diet have been little analyzed in sympatric species. In this study, we analyzed interspecific and ontogenetic variation in dietary composition and trophic niche width in an anuran community from a semi-arid environment. We found a more profound effect of species identity than body size on dietary composition, with the diet of four species dominated by formicids, that of two others by coleopterans and formicids, and that of the remaining species not dominated by specific prey types. We found ontogenetic changes in dietary composition in three of four species analyzed, in which consumption of some small insects decreased as predator size increased, regardless of species. Additionally, we did not find ontogenetic change in prey number consumed in any of the four species, but prey size increased with increasing predator size in all of them. Most species exhibited a narrow trophic niche, which was even narrower in adults in three of the four species analyzed. Costello’s modified plots revealed a high variation among individuals in termite consumption in Anaxyrus punctatus, and in more prey types in Spea multiplicata. Our results suggest that this community is not size-structured, and that ontogenetic diet shifts are mainly caused by passive sampling toward prey of different sizes. Finally, comparisons with previous data revealed an interpopulation pattern, in which trophic niche width contracts as aridity increases, possibly because of an increase in interspecific competition for trophic resources.
© 2019 Luría-Manzano and Ramírez-Bautista
Luría-Manzano et al. (2019) Ontogenetic variation in the diet of the anuran community from a semi-arid environment in the southeastern Chihuahuan Desert. PeerJ 7:e7908 https://doi.org/10.7717/peerj.7908
Effects of particle size of ground alfalfa hay on caecal bacteria and archaea populations of rabbits
This work was aimed to investigate the effects of the different particle size of ground alfalfa hay on caecal microbial and archeal communities of rabbits. One hundred-twenty New Zealand rabbits (950.3 ± 8.82 g) were allocated into four treatments, with five replicates in each treatment and six rabbits in each replicate. The particle sizes of the alfalfa meal in the four treatment diets were 2,500, 1,000, 100 and 10 µm respectively, while the other ingredients were ground through a 2.5 mm sieve. High-throughput sequencing technology was applied to examine the differences in bacteria and methanogenic archaea diversity in the caecum of the four treatment groups of rabbits. A total of 745,946 bacterial sequences (a mean of 31,081 ± 13,901 sequences per sample) and 539,227 archaeal sequences (a mean of 22,468 ± 2,443 sequences per sample) were recovered from twenty-four caecal samples, and were clustered into 9,953 and 2,246 OTUs respectively. A total of 26 bacterial phyla with 465 genera and three archaeal phyla with 10 genera were identified after taxonomic summarization. Bioinformatic analyses illustrated that Firmicutes (58.69% ∼ 68.50%) and Bacteroidetes (23.96% ∼ 36.05%) were the two most predominant bacterial phyla and Euryarchaeota (over 99.9%) was the most predominant archaeal phyla in the caecum of all rabbits. At genus level, as the particle size of alfalfa decreased from 2,500 to 10 µm, the relative abundances of Ruminococcaceae UCG-014 (P < 0.001) and Lactobacillus (P = 0.043) were increased and Ruminococcaceae UCG-005 (P = 0.012) was increased first and then decreased when the alfalfa particle size decreased, while Lachnospiraceae NK4A136 group (P = 0.016), Ruminococcaceae NK4A214 (P = 0.044), Christensenellaceae R-7 group (P = 0.019), Lachnospiraceae other (Family) (P = 0.011) and Ruminococcaceae UCG-013 (P = 0.021) were decreased. The relative abundance of Methanobrevibacter was increased from 62.48% to 90.40% (P < 0.001), whereas the relative abundance of Methanosphaera was reduced from 35.47% to 8.62% (P < 0.001). In conclusion, as the particle size of alfalfa meal decreased, both the bacterial and archaeal population in the caecum of rabbit experienced alterations, however archaea response earlier than bacteria to the decrease of alfalfa meal particle size.
Yuan et al. (2019) Effects of particle size of ground alfalfa hay on caecal bacteria and archaea populations of rabbits. PeerJ 7:e7910 https://doi.org/10.7717/peerj.7910
Combining simulation modeling and stable isotope analyses to reconstruct the last known movements of one of Nature’s giants
The spatial ecology of rare, migratory oceanic animals is difficult to study directly. Where incremental tissues are available, their chemical composition can provide valuable indirect observations of movement and diet. Interpreting the chemical record in incremental tissues can be highly uncertain, however, as multiple mechanisms interact to produce the observed data. Simulation modeling is one approach for considering alternative hypotheses in ecology and can be used to consider the relative likelihood of obtaining an observed record under different combinations of ecological and environmental processes. Here we show how a simulation modeling approach can help to infer movement behaviour based on stable carbon isotope profiles measured in incremental baleen tissues of a blue whale (Balaenoptera musculus). The life history of this particular specimen, which stranded in 1891 in the UK, was selected as a case study due to its cultural significance as part of a permanent display at the Natural History Museum, London. We specifically tested whether measured variations in stable isotope compositions across the analysed baleen plate were more consistent with residency or latitudinal migrations. The measured isotopic record was most closely reproduced with a period of residency in sub-tropical waters for at least a full year followed by three repeated annual migrations between sub-tropical and high latitude regions. The latitudinal migration cycle was interrupted in the year prior to stranding, potentially implying pregnancy and weaning, but isotopic data alone cannot test this hypothesis. Simulation methods can help reveal movement information coded in the biochemical compositions of incremental tissues such as those archived in historic collections, and provides context and inferences that are useful for retrospective studies of animal movement, especially where other sources of individual movement data are sparse or challenging to validate.
Trueman et al. (2019) Combining simulation modeling and stable isotope analyses to reconstruct the last known movements of one of Nature’s giants. PeerJ 7:e7912 https://doi.org/10.7717/peerj.7912
The phylogeny of desmostylians revisited: proposal of new clades based on robust phylogenetic hypotheses
Background Desmostylia is a clade of extinct aquatic mammals with no living members. Today, this clade is considered belonging to either Afrotheria or Perissodactyla. In the currently-accepted taxonomic scheme, Desmostylia includes two families, 10 to 12 genera, and 13–14 species. There have been relatively few phylogenetic analyses published on desmostylian interrelationship compared to other vertebrate taxa, and two main, alternative phylogenetic hypotheses have been proposed in previous studies. One major problem with those previous studies is that the numbers of characters and OTUs were small. Methods In this study, we analyzed the phylogenetic interrelationship of Desmostylia based on a new data matrix that includes larger numbers of characters and taxa than in any previous studies. The new data matrix was compiled mainly based on data matrices of previous studies and included three outgroups and 13 desmostylian ingroup taxa. Analyses were carried out using five kinds of parsimonious methods. Results Strict consensus trees of the most parsimonious topologies obtained in all analyses supported the monophyly of Desmostylidae and paraphyly of traditional Paleoparadoxiidae. Based on these results, we propose phylogenetic definitions of the clades Desmostylidae and Paleoparadoxiidae based on common ancestry.
Matsui et al. (2019) The phylogeny of desmostylians revisited: proposal of new clades based on robust phylogenetic hypotheses. PeerJ 7:e7430 https://doi.org/10.7717/peerj.7430
Rosiglitazone accelerates wound healing by improving endothelial precursor cell function and angiogenesis in db/db mice
Background & Aims Endothelial precursor cell (EPC) dysfunction is one of the risk factors for diabetes mellitus (DM) which results in delayed wound healing. Rosiglitazone (RSG) is a frequently prescribed oral glucose-lowering drug. Previous studies have shown the positive effects of RSG on ameliorating EPC dysfunction in diabetic patients. Interestingly, knowledge about RSG with regard to the wound healing process caused by DM is scarce. Therefore, in this study, we investigated the possible actions of RSG on wound healing and the related mechanisms involved in db/db diabetic mice. Methods Db/db mice with spontaneous glucose metabolic disorder were used as a type 2 DM model. RSG (20 mg/kg/d, i.g.,) was administered for 4 weeks before wound creation and bone marrow derived EPC (BM-EPC) isolation. Wound closure was assessed by wound area and CD31 staining. Tubule formation and migration assays were used to judge the function of the BM-EPCs. The level of vascular endothelial growth factor (VEGF), stromal cell derived factor-1α (SDF-1α) and insulin signaling was determined by ELISA. Cell viability of the BM-EPCs was measured by CCK-8 assay. Results RSG significantly accelerated wound healing and improved angiogenesis in db/db mice. Bioactivities of tube formation and migration were decreased in db/db mice but were elevated by RSG. Level of both VEGF and SDF-1α was increased by RSG in the BM-EPCs of db/db mice. Insulin signaling was elevated by RSG reflected in the phosphorylated-to-total AKT in the BM-EPCs. In vitro, RSG improved impaired cell viability and tube formation of BM-EPCs induced by high glucose, but this was prevented by the VEGF inhibitor avastin. Conclusion Our data demonstrates that RSG has benefits for wound healing and angiogenesis in diabetic mice, and was partially associated with improvement of EPC function through activation of VEGF and stimulation of SDF-1α in db/db mice.
Zhou et al. (2019) Rosiglitazone accelerates wound healing by improving endothelial precursor cell function and angiogenesis in db/db mice. PeerJ 7:e7815 https://doi.org/10.7717/peerj.7815
Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue
The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals, and its conservation has significant ecosystem and cultural service value. Cytosine DNA methylation (5mC) is a stable epigenetic modification to the genome and has multiple functions such as gene regulation. However, DNA methylome of giant panda and its function have not been reported as of yet. Bisulfite sequencing was performed on a 4-day-old male giant panda’s brain, liver and pancreatic tissues. We found that the whole genome methylation level was about 0.05% based on reads normalization and mitochondrial DNA was not methylated. Three tissues showed similar methylation tendency in the protein-coding genes of their genomes, but the brain genome had a higher count of methylated genes. We obtained 467 and 1,013 different methylation regions (DMR) genes in brain vs. pancreas and liver, while only 260 DMR genes were obtained in liver vs pancreas. Some lncRNA were also DMR genes, indicating that methylation may affect biological processes by regulating other epigenetic factors. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that low methylated promoter, high methylated promoter and DMR genes were enriched at some important and tissue-specific items and pathways, like neurogenesis, metabolism and immunity. DNA methylation may drive or maintain tissue specificity and organic functions and it could be a crucial regulating factor for the development of newborn cubs. Our study offers the first insight into giant panda’s DNA methylome, laying a foundation for further exploration of the giant panda’s epigenetics.
Ren et al. (2019) Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue. PeerJ 7:e7847 https://doi.org/10.7717/peerj.7847
Relationships between key functional traits of the waterlily Nuphar lutea and wetland nutrient content
Little attention has been paid to how aquatic habitat characteristics affect the traits of plant species. Nuphar lutea (L.) Sm. is a keystone species distributed across temperate regions of Europe, northwest Africa and western Asia. Its apparently low phenotypic variability compared to other aquatic plants led us to test whether the species exhibited significant phenotypic variability and whether trait values correlated to environmental parameters. The hypotheses were that (1) the environmental variation within our set of wetlands (both water and sediment characteristics) led to significant variation among four sets of traits related respectively to growth, reproduction, defence and storage and (2) that nutrient limitation (nitrogen and especially phosphorus) should affect plant traits towards a higher investment in storage and defence and a lower investment in growth and reproduction, thereby negatively affecting the success of N. lutea. To test these hypotheses, 11 populations of N. lutea were sampled in wetlands differing in physicochemical characteristics and spread along three rivers. A total of 15 traits, grouped into four sets (growth, reproduction, storage and defence), were measured during the growing season. Most N. lutea traits were related to the environmental characteristics of wetlands. The growth and reproduction traits were mostly positively related to habitat resource conditions, whereas the defence traits were positively correlated with both ammonium concentration and temperature, outlining possible anoxic stress (habitat adversity). Nitrogen or phosphorus limitation led to the variation of only a few traits: the rhizome starch content was higher in phosphorus-limited wetlands, while the rhizome length and volume, and the number of flowers were higher in nitrogen-limited wetlands.
Henriot et al. (2019) Relationships between key functional traits of the waterlily Nuphar lutea and wetland nutrient content. PeerJ 7:e7861 https://doi.org/10.7717/peerj.7861
Differences between medically treated and untreated non-fatal self-harm reported by hotline callers in China
Background Many self-harmers do not present in hospitals due to the self-harm. It is still unclear on the differences between medically treated and untreated self-harm in China. This study described the differences of the two groups of self-harmers using the largest psychological aid hotline data. Methods The present observational study recruited 3,403 hotline callers who reported episodes of self-harm before the call. In routine assessment, information about the most recent episode of self-harm was collected, including the method of self-harm, the wish to die, goals of the self-harm, and any medical treatment (irrespective of psychological services) in the hospital. The callers were divided into two groups: those who received hospital-based medical treatment due to the most recent self-harm (treated self-harm callers) and those who did not (untreated self-harm callers). Results In the most recent episode of self-harm, 65% (n = 2,217) of callers were untreated and 55% (1,226/2,217) of the untreated self-harm callers reported a wish to die. A total of 67% of the callers reported that their main goal of self-harm was to relieve suffering. The most common self-harm methods were using instruments (knife or rope) and overdosing on medicines. Compared with treated self-harm callers, the untreated self-harm callers were less likely to have a wish to die (OR = 0.57), engage in self-harm outside the home (OR = 0.71 and 0.78), and attribute their self-harm to romantic relationship problems (OR = 0.76); however, they were more likely to use instruments, to jump, or to choose other methods (OR = 3.73, 3.83, and 7.71, respectively). Conclusions Among hotline callers, many episodes of self-harm did not receive medical treatment, despite over half reporting a wish to die. Characteristics of self-harm behaviors were different between treated and untreated self-harm callers. Our findings suggest that more strategies should improve access to hospital-based medical treatment and coverage for post-intervention for self-harmers who are not presented in hospitals.
Tong et al. (2019) Differences between medically treated and untreated non-fatal self-harm reported by hotline callers in China. PeerJ 7:e7868 https://doi.org/10.7717/peerj.7868
A novel form of wasp mimicry in a new species of praying mantis from the Amazon rainforest, Vespamantoida wherleyi gen. nov. sp. nov. (Mantodea, Mantoididae)
A wasp mimicking praying mantis (Mantodea) of the early evolving Mantoididae family was discovered in 2013 at a research station near the Amazon River in Northern Peru. This adult specimen exhibited a striking bright red/orange and black coloration pattern that was undocumented in all known praying mantis species. We tested the status of this new specimen using external morphology, male genital dissections, and geographic distribution. Our findings demonstrate the specimen to represent a new species, Vespamantoida wherleyi gen. nov. sp. nov., that is closely allied with a recently described species, Mantoida toulgoeti Roy, 2010, both of which are included within the newly erected genus. To support our actions, we present high resolution images of museum preserved and living specimens, morphological illustrations, a generic-level distribution map, and recorded video of the behavior of the holotype taken in the field at the time of collection. The bright red/orange coloration contrasted with black markings, the general appearance of a hymenopteran that includes a narrowed wasp waist, and the locomotory patterns and antennal movements mark this newly discovered species as unique among all hymenopteran mimicking Mantoididae as well as all other praying mantises.
Svenson et al. (2019) A novel form of wasp mimicry in a new species of praying mantis from the Amazon rainforest, Vespamantoida wherleyi gen. nov. sp. nov. (Mantodea, Mantoididae). PeerJ 7:e7886 https://doi.org/10.7717/peerj.7886
Identification of key genes and multiple molecular pathways of metastatic process in prostate cancer
Background Cancer metastasis is well known as the most adverse outcome and the major cause of mortality in cancer patients, including prostate cancer (PCa). There are no credible predictors, to this day, that can reflect the metastatic ability of localized PCa. In the present study, we firstly identified the differentially expressed genes (DEGs) and molecular pathways involved in the metastaic process of PCa by comparing gene expressions of metastaic PCa with localized PCa directly, with the purpose of identifying potential markers or therapeutic targets. Methods The gene expression profiles (GSE6919 and GSE32269) were downloaded from the Gene Expression Omnibus database, which contained 141 tissue samples, including 87 primary localized PCa samples and 54 metastaic PCa samples. After data processing, DEGs were identified by R language using the Student’s t-test adjusted via the Beniamini–Hochberg method. Subsequently, the gene ontology functional and pathway enrichment analyses of DEGs were performed and the protein–protein interaction network was constructed. Hub genes were identified using the plug-in cytoHubba in Cytoscape software by MCC and degree. Furthermore, validation and prognostic significance analysis of the hub genes were performed by UALCAN and gene expression profiling interactive analysis (GEPIA). Results A total of 90 DEGs were identified between localized and metastaic PCa, which consisted of 47 upregulated and 43 downregulated genes. The enriched functions and pathways of the DEGs include catabolic process, cell cycle, response to steroid hormone, extracellular matrix (ECM)-receptor interaction and vascular smooth muscle contraction. A total of 10 genes were identified as hub genes and biological process analysis of hub genes showed that cell cycle phase, cell division, and mitotic cell cycle process were mainly enriched. The expression of hub genes were confirmed in metastaic PCa when compared with localized PCa tissues by The Cancer Genome Atlas database. Moreover, the disease-free survival analysis of hub genes revealed that these genes may play an important role in invasion, progression or recurrence. Therefore, these hub genes might be the key genes contributed to tumor progression or metastasis in PCa and provide candidate therapeutic targets for PCa. Conclusions The present study identified some DEGs between localized and metastaic PCa tissue samples. These key genes might be potential therapeutic targets and biomarkers for the metastaic process of PCa.
Guo et al. (2019) Identification of key genes and multiple molecular pathways of metastatic process in prostate cancer. PeerJ 7:e7899 https://doi.org/10.7717/peerj.7899