Phylogeny and biogeography of the African Bathyergidae: a review of patterns and processes
Background We review genealogical relationships, biogeographic patterns and broad historical drivers of speciation within the Bathyergidae, a group of endemic African rodents, as well as identify key taxa which need further research. Methods We sourced comparable cytochrome b sequence data (comparable data available for all members for the Family) and geographic information for all six genera of the African subterranean rodent. This information was combined into the most comprehensive and geographically representative evolutionary study for the Bathyergidae to date. Results Species richness within the Bathyergidae appears to be underestimated, with undescribed taxa in five of the six genera. Biogeographic patterns suggest large historical distributions, which were repeatedly fragmented by major landscape changes (especially rifting, uplift and drainage evolution) since the Miocene. Aside from vicariant events, other factors (ecological specialization, population-level responses and climatic change) may have been instrumental in driving divergences in the Bathyergidae. As such, adaptive differences may exist among both populations and species across their discrete ranges, driving independent evolutionary trajectories among taxa. In addition, highly fragmented distributions of divergent (and often relict) lineages indicates the possibility of narrow endemics restricted to diminishing suitable habitats. From this, it is clear that a systematic revision of the Bathyergidae is necessary; such a revision should include comprehensive sampling of all putative taxa, the addition of genomic information to assess adaptive differences, as well as ecological information.
Visser et al. (2019) Phylogeny and biogeography of the African Bathyergidae: a review of patterns and processes. PeerJ 7:e7730 https://doi.org/10.7717/peerj.7730
Plant and insect herbivore community variation across the Paleocene–Eocene boundary in the Hanna Basin, southeastern Wyoming
Ecosystem function and stability are highly affected by internal and external stressors. Utilizing paleobotanical data gives insight into the evolutionary processes an ecosystem undergoes across long periods of time, allowing for a more complete understanding of how plant and insect herbivore communities are affected by ecosystem imbalance. To study how plant and insect herbivore communities change during times of disturbance, we quantified community turnover across the Paleocene­–Eocene boundary in the Hanna Basin, southeastern Wyoming. This particular location is unlike other nearby Laramide basins because it has an abundance of late Paleocene and Eocene coal and carbonaceous shales and paucity of well-developed paleosols, suggesting perpetually high water availability. We sampled approximately 800 semi-intact dicot leaves from five stratigraphic levels, one of which occurs late in the Paleocene–Eocene thermal maximum (PETM). Field collections were supplemented with specimens at the Denver Museum of Nature & Science. Fossil leaves were classified into morphospecies and herbivore damage was documented for each leaf. We tested for changes in plant and insect herbivore damage diversity using rarefaction and community composition using non-metric multidimensional scaling ordinations. We also documented changes in depositional environment at each stratigraphic level to better contextualize the environment of the basin. Plant diversity was highest during the mid-late Paleocene and decreased into the Eocene, whereas damage diversity was highest at the sites with low plant diversity. Plant communities significantly changed during the late PETM and do not return to pre-PETM composition. Insect herbivore communities also changed during the PETM, but, unlike plant communities, rebound to their pre-PETM structure. These results suggest that insect herbivore communities responded more strongly to plant community composition than to the diversity of species present.
Azevedo Schmidt et al. (2019) Plant and insect herbivore community variation across the Paleocene–Eocene boundary in the Hanna Basin, southeastern Wyoming. PeerJ 7:e7798 https://doi.org/10.7717/peerj.7798
Differences in tail feather growth rate in storm-petrels breeding in the Northern and Southern hemisphere: a ptilochronological approach
Moulting and breeding are costly stages in the avian annual cycle and may impose trade-offs in energy allocation between both stages or in their timing. Here, we compared feather growth rates (FGR) of rectrices in adults between two pairs of small pelagic Procellariiformes species differing in moult-breeding strategies: the European storm-petrel Hydrobates pelagicus and Leach’s storm-petrel Oceanodroma leucorhoa breeding in the Northern Hemisphere (Faroe Islands), showing moult-breeding overlap in tail feathers; and the Wilson’s storm-petrel Oceanites oceanicus and black-bellied storm-petrel Fregetta tropica, breeding in the Southern Hemisphere (South Shetlands), temporally separating moult and breeding. We used ptilochronology (i.e., feather growth bar width) to reconstruct FGR reflecting relative energy availability during moult. Based on previous research, we expected positive correlations between feather length (FL) and FGR. Additionally, we expected to find differences in FGR relative to FL between the moult-breeding strategies, where a relatively higher FGR to FL indicates a higher energy availability for moult. To investigate if energy availability during moult in the studied species is similar to species from other avian orders, we used FGR and FL found in literature (n = 164) and this study. We fitted a phylogenetic generalized least squares (PGLS) model to FGR with FL, group (i.e., Procellariiformes vs. non-Procellariiformes) and the interaction FL * group as predictors. As it has been suggested that Procellariiformes may form two growth bars per 24 h, we fitted the same model but with doubled FGR for Procellariiformes (PGLSadj). The group term was significant in the PGLS model, but was not in the PGLSadj model, confirming this suggestion. Individually predicted FGR by the PGLSadj model based on FL, showed that the Southern species have a significantly higher FGR relative to FL compared to the Northern species. Additionally, we found no correlation between FL and FGR in the Northern species, and a positive correlation between FL and FGR in the Southern species, suggesting differences in the trade-off between feather growth and size between species from both hemispheres. The observed differences between the Northern and Southern species may be caused by different moult-breeding strategies. The Southern species may have had more energy available for moult as they are free from breeding duties during moult, while the Northern species may have had less free energy due to a trade-off in energy allocation between breeding and moulting. Our study shows how different moult-breeding strategies may affect relative nutritional condition or energy allocation during moult of migratory pelagic seabirds.
Ausems et al. (2019) Differences in tail feather growth rate in storm-petrels breeding in the Northern and Southern hemisphere: a ptilochronological approach. PeerJ 7:e7807 https://doi.org/10.7717/peerj.7807
Urban-rural disparity in the utilization of national community-based hypertension monitoring service—results from the China Health and Retirement Longitudinal Study, 2015
Background Since 2009, community-based hypertension monitoring service (CBHMS) has been provided free of charge by the Chinese government as part of the national Essential Public Health Services (EPHS) policy. This study aimed to examine the disparity in the utilization of CBHMS between urban and rural community-dwelling middle-aged and older adults with hypertension. Methods Subjects were 3,479 community-residing hypertensive patients, identified from the China Health and Retirement Longitudinal Study (CHARLS), 2015, a nationally representative survey of Chinese residents aged 45 years and older. The utilization of CBHMS was defined as having one’s blood pressure (BP) examined at least once a season by community or village doctors. Rates of CBHMS use of urban and rural residents with hypertension were compared by using chi-square test. Multiple logistic regression analyses were conducted to examine factors associated with the utilization of CBHMS of hypertensive patients. Results CBHMS was significantly more likely to be used by rural than urban middle-aged and older residents with hypertension (38.6% vs. 25.1%, P < 0.001). Results from multiple logistic regression analyses showed that urban patients who were living in central (OR = 0.37) and western (OR = 0.48) regions (vs. eastern region), had an educational attainment of middle school (OR = 0.33) and college and above (OR = 0.48) (vs. illiterate), and were not taking antihypertensive agents (OR = 0.26) were less likely to use CBHMS, while rural patients who had no medical insurance (OR = 0.56), and were not taking antihypertensive agents (OR = 0.31) were less likely to use CBHMS. Conclusions The national CBHMS is more likely to be used by rural middle-aged and older adults with hypertension in China. The urban-rural difference in the utilization of CBHMS may be resulted from the different demographics of urban and rural middle-aged and older residents and uneven distributions of health services resources between urban and rural areas. Urban-rural disparities in characteristics of CBHMS use should be taken into consideration when promoting the utilization of CBHMS in China.
Song et al. (2019) Urban-rural disparity in the utilization of national community-based hypertension monitoring service—results from the China Health and Retirement Longitudinal Study, 2015. PeerJ 7:e7842 https://doi.org/10.7717/peerj.7842
Refractory ascites—the contemporary view on pathogenesis and therapy
Refractory ascites (RA) refers to ascites that cannot be mobilized or that has an early recurrence that cannot be prevented by medical therapy. Every year, 5–10% of patients with liver cirrhosis and with an accumulation of fluid in the peritoneal cavity develop RA while undergoing standard treatment (low sodium diet and diuretic dose up to 400 mg/day of spironolactone and 160 mg/day of furosemide). Liver cirrhosis accounts for marked alterations in the splanchnic and systemic hemodynamics, causing hypovolemia and arterial hypotension. The consequent activation of renin-angiotensin and sympathetic systems and increased renal sodium re-absorption occurs during the course of the disease. Cirrhotic patients with RA have poor prognoses and are at risk of developing serious complications. Different treatment options are available, but only liver transplantation may improve the survival of such patients.
© 2019 Kasztelan-Szczerbinska and Cichoz-Lach
Kasztelan-Szczerbinska et al. (2019) Refractory ascites—the contemporary view on pathogenesis and therapy. PeerJ 7:e7855 https://doi.org/10.7717/peerj.7855
Effects of soil pH and texture on soil carbon and nitrogen in soil profiles under different land uses in Mun River Basin, Northeast Thailand
Soil carbon and nitrogen are essential factors for agricultural production and climate changes. A total of 106 soil samples from three agricultural lands (including two rice fields and one sugarcane field) and four non-agricultural lands (including two forest lands, one wasteland and one built-up land) in the Mun River Basin were collected to determine soil carbon, nitrogen, soil pH, soil particle sizes and explore the influence of pH and soil texture on soil C and N. The results show that total organic carbon (TOC) and nitrogen (TON) contents in topsoil (TOC: 2.78 ~ 18.83 g kg−1; TON: 0.48 ~ 2.05 g kg−1) are much higher than those in deep soil (TOC: 0.35 ~ 6.08 g kg−1; TON: <0.99 g kg−1). In topsoil, their contents of forest lands and croplands (TOC: average 15.37 g kg−1; TON: average 1.29 g kg−1) are higher than those of other land uses (TOC: average 5.28 g kg−1; TON: average 0.38 g kg−1). The pH values range from 4.2 to 6.1 in topsoil, and with increase in soil depth, they tend to increase and then decrease. Soil carbon, nitrogen and the C/N (TC/TN ratio) are negatively correlated with soil pH, demonstrating that relatively low pH benefits the accumulation of organic matter. Most soil samples are considered as sandy loam and silt loam from the percentages of clay, silt and sand. For soil profiles below 50 cm, the TOC and TON average contents of soil samples which contain more clay and silt are higher than those of other soil samples.
Zhou et al. (2019) Effects of soil pH and texture on soil carbon and nitrogen in soil profiles under different land uses in Mun River Basin, Northeast Thailand. PeerJ 7:e7880 https://doi.org/10.7717/peerj.7880
Downregulated miR-383-5p contributes to the proliferation and migration of gastric cancer cells and is associated with poor prognosis
Aim The study aims to identify differentially expressed microRNAs (DEMs) in gastric cancer (GC) and explore the expression, prognosis and downstream regulation role of miR-383-5p in GC. Methods The GC miRNA-Seq and clinical information were downloaded from Firebrowse which stores integrated data sourced from The Cancer Genome Atlas database. The DEMs were identified with limma package in R software at the cut-off criteria of P < 0.05 and |log2 fold change| > 1.0 (|log2FC| > 1.0). The expression of miR-383-5p in GC cell lines and 54 paired GC tissues was measured by quantitative real-time polymerase chain reaction (qRT-PCR). The overall survival curve of miR-383-5p and the association between its expression and clinicopathological features were explored. Wound healing and cell counting kit-8 assays were performed to investigate the capacity of miR-383-5p in cell proliferation and migration. The downstream target genes were predicted by bioinformatics tools (miRDB, TargetScan and starBase). The consensus target genes were selected for gene functional enrichment analysis by FunRich v3.0 software. The luciferase reporter assay was performed to verify the potential targeting sites of miR-383-5p on lactate dehydrogenase A (LDHA). Results A total of 21 down-regulated miRNAs (including miR-383-5p) and 202 up-regulated miRNAs were identified by analyzing GC miRNA-Seq data. Survival analysis found that patients with low miR-383-5p expression had a shorter survival time (median survival time 21.1 months) than those with high expression (46.9 months). The results of qRT-PCR indicated that miR-383-5p was downregulated in GC cell lines and tissues, which was consistent with miRNA-Seq data. The expression of miR-383-5p was significantly associated with tumor size and differentiation grade. Besides, overexpression of miR-383-5p suppressed GC cells proliferation and migration. A total of 49 common target genes of miR-383-5p were obtained by bioinformatics tools and gene functional enrichment analysis showed that these predicted genes participated in PI3K, mTOR, c-MYC, TGF-beta receptor, VEGF/VEGFR and E-cadherin signaling pathways. The data showed that expression of miR-383-5p was negatively correlated with target LDHA (r = −0.203). Luciferase reporter assay suggested that LDHA was a target of miR-383-5p. Conclusion The present study concluded that miR-383-5p was downregulated and may act as a tumor suppressor in GC. Furthermore, its target genes were involved in important signaling pathways. It could be a prognostic biomarker and play a vital role in exploring the molecular mechanism of GC.
Wei et al. (2019) Downregulated miR-383-5p contributes to the proliferation and migration of gastric cancer cells and is associated with poor prognosis. PeerJ 7:e7882 https://doi.org/10.7717/peerj.7882
Tissue-specific evaluation of suitable reference genes for RT-qPCR in the pond snail, Lymnaea stagnalis
Reverse transcription quantitative PCR (RT-qPCR) is a robust technique for the quantification and comparison of gene expression. To obtain reliable results with this method, one or more reference genes must be employed to normalize expression measurements among treatments or tissue samples. Candidate reference genes must be validated to ensure that they are stable prior to use in qPCR experiments. The pond snail (Lymnaea stagnalis) is a common research organism, particularly in the areas of learning and memory, and is an emerging model for the study of biological asymmetry, biomineralization, and evolution and development. However, no systematic assessment of qPCR reference genes has been performed in this animal. Therefore, the aim of our research was to identify stable reference genes to normalize gene expression data from several commonly studied tissues in L. stagnalis as well as across the entire body. We evaluated a panel of seven reference genes across six different tissues in L. stagnalis with RT-qPCR. The genes included: elongation factor 1-alpha, glyceraldehyde-3-phosphate dehydrogenase, beta-actin, beta-tubulin, ubiquitin, prenylated rab acceptor protein 1, and a voltage gated potassium channel. These genes exhibited a wide range of expression levels among tissues. The tissue-specific stability of each of the genes was consistent when measured by the standard stability assessment algorithms: geNorm, NormFinder, BestKeeper, and RefFinder. Our data indicate that the most stable reference genes vary among the tissues that we examined (central nervous system, tentacles, lips, penis, foot, mantle). Our results were generally congruent with those obtained from similar studies in other molluscs. Given that a minimum of two reference genes are recommended for data normalization, we provide suggestions for strong pairs of reference genes for single- and multi-tissue analyses of RT-qPCR data in L. stagnalis.
Young et al. (2019) Tissue-specific evaluation of suitable reference genes for RT-qPCR in the pond snail, Lymnaea stagnalis. PeerJ 7:e7888 https://doi.org/10.7717/peerj.7888
ncRNA2MetS: a manually curated database for non-coding RNAs associated with metabolic syndrome
Metabolic syndrome is a cluster of the most dangerous heart attack risk factors (diabetes and raised fasting plasma glucose, abdominal obesity, high cholesterol and high blood pressure), and has become a major global threat to human health. A number of studies have demonstrated that hundreds of non-coding RNAs, including miRNAs and lncRNAs, are involved in metabolic syndrome-related diseases such as obesity, type 2 diabetes mellitus, hypertension, etc. However, these research results are distributed in a large number of literature, which is not conducive to analysis and use. There is an urgent need to integrate these relationship data between metabolic syndrome and non-coding RNA into a specialized database. To address this need, we developed a metabolic syndrome-associated non-coding RNA database (ncRNA2MetS) to curate the associations between metabolic syndrome and non-coding RNA. Currently, ncRNA2MetS contains 1,068 associations between five metabolic syndrome traits and 627 non-coding RNAs (543 miRNAs and 84 lncRNAs) in four species. Each record in ncRNA2MetS database represents a pair of disease-miRNA (lncRNA) association consisting of non-coding RNA category, miRNA (lncRNA) name, name of metabolic syndrome trait, expressive patterns of non-coding RNA, method for validation, specie involved, a brief introduction to the association, the article referenced, etc. We also developed a user-friendly website so that users can easily access and download all data. In short, ncRNA2MetS is a complete and high-quality data resource for exploring the role of non-coding RNA in the pathogenesis of metabolic syndrome and seeking new treatment options. The website is freely available at http://www.biomed-bigdata.com:50020/index.html
Yao et al. (2019) ncRNA2MetS: a manually curated database for non-coding RNAs associated with metabolic syndrome. PeerJ 7:e7909 https://doi.org/10.7717/peerj.7909
Borrowing from Peter to pay Paul: managing threatened predators of endangered and declining prey species
Conservation policy and practice can sometimes run counter to their mutual aims of ensuring species survival. In Kenya, where threatened predators such as lion deplete endangered prey such as Grevy’s zebra, conservation practitioners seek to ensure species success through exclusive strategies of protection, population increase and preservation. We found strong selection for the endangered Grevy’s zebra by both lion and hyena on two small fenced conservancies in Kenya. Despite abundant diversity of available prey, Grevy’s zebra were selected disproportionately more than their availability, while other highly available species such as buffalo were avoided. Lions were therefore not alone in presenting a credible threat to Grevy’s zebra survival. Conservation practitioners must consider interlinked characteristics of prey selection, resource availability and quality, the interplay between carnivore guild members and landscape scale population trends performance in wildlife management decisions.
Davidson et al. (2019) Borrowing from Peter to pay Paul: managing threatened predators of endangered and declining prey species. PeerJ 7:e7916 https://doi.org/10.7717/peerj.7916