Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony
The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including DQA, DRA, DQB, and DRB, and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. DRA had the lowest dN/dS ratio (0.560) compared with the other three loci, indicating that DRA was conserved and could be conserved after undergoing selective processes. Nine DQA, five DQB, nine DRA, and seven DRB codons were under significant positive selection at the antigen binding sites (ABS), suggesting that the selected residues in ABS may play a significant role in the innate immune system of the GZP. Two GZP alleles were shared with Przewalski’s horse, and six older GZP haplotypes had a better relationship with other horse species by one or two mutational steps, indicating that the GZP may be a natural ancient variety of equid. The specific diversity of ABS and the numbers of unique haplotypes in the evolutionary process affords this species a better genetic fitness and ability to adapt to the native environment.
Liu et al. (2020) Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony. PeerJ 8:e9889 https://doi.org/10.7717/peerj.9889
Native trees of Mexico: diversity, distribution, uses and conservation
Background Mexico is one of the most floristically rich countries in the world. Despite significant contributions made on the understanding of its unique flora, the knowledge on its diversity, geographic distribution and human uses, is still largely fragmented. Unfortunately, deforestation is heavily impacting this country and native tree species are under threat. The loss of trees has a direct impact on vital ecosystem services, affecting the natural capital of Mexico and people’s livelihoods. Given the importance of trees in Mexico for many aspects of human well-being, it is critical to have a more complete understanding of their diversity, distribution, traditional uses and conservation status. We aimed to produce the most comprehensive database and catalogue on native trees of Mexico by filling those gaps, to support their in situ and ex situ conservation, promote their sustainable use, and inform reforestation and livelihoods programmes. Methods A database with all the tree species reported for Mexico was prepared by compiling information from herbaria and reviewing the available floras. Species names were reconciled and various specialised sources were used to extract additional species information, i.e. endemic status, threat status, availability in seed collections, reports on plant uses and conservation actions currently in place. With this information, a comprehensive catalogue of native trees from Mexico was redacted. Available georeferenced records were used to map each species distribution and perform spatial analyses to identify gaps of information and priority areas for their conservation and exploration. Results Mexico has at least 2,885 native tree species, belonging to 612 genera and 128 families. Fabaceae is the most represented family and Quercus the most represented genus. Approximately 44% of tree species are endemic to the country. The southern part of the country showed the highest values of species richness. Six hundred and seventy-four species have at least one documented human use. In terms of conservation assessment, ca. 33% of species have been assessed by either the IUCN Red List (919) or the National protection catalogue “NORMA Oficial Mexicana NOM-059” (29) or both (45). Additionally, 98 species have been included in the CITES listing for protection. In terms of existing conservation efforts, 19% of species have ex situ protection in seed banks, while protected areas overlap with all the identified peaks of species richness, except for those in the states of Veracruz and Chiapas. This work constitutes a key milestone for the knowledge, management, and conservation of the Mexican native trees. The two areas with high density of tree species identified in Veracruz and Chiapas represent two priority areas for tree conservation in Mexico, where integrated in situ and ex situ conservation efforts should be focused.
Tellez et al. (2020) Native trees of Mexico: diversity, distribution, uses and conservation. PeerJ 8:e9898 https://doi.org/10.7717/peerj.9898
Life-history traits and intra-cohort divergence of clearhead icefish (Protosalanx chinensis), indicating cannibalism increased fitness
Cannibalism is considered one of the causes of intra-cohort size divergence in fish and is usually believed to result in increased fitness in terms of survival and reproduction, but direct evidence of this is lacking. Population demographics of the clearhead icefish (Protosalanx chinensis) from Lake Xingkai (Khanka) were investigated for one year. Size-frequencies exhibited a bimodal distribution from July through January, where the population diverged into an upper and a lower modal group based on size. Stomach content analysis confirmed the occurrence of cannibalism, where fish belonging to the larger, upper modal group preyed upon those of the smaller, lower modal group. We found P. chinensis does not spawn until all of the oocytes have reached maturity and then a single spawning event occurs although the oocytes may develope asynchronously in the ovary. Upper modal group females matured slightly earlier than those of the lower modal group, and reproductive investment was considerably greater in the upper modal group than the lower modal group. The lower modal males made up the majority of the population after the spawning period, which meant they may have few opportunities to participate in reproduction. Therefore, piscivory and cannibalism of P. chinensis appears to have increased fitness of the fish belonging to the upper modal group and greatly reduced the fitness of those belonging to the lower modal group.
Tang et al. (2020) Life-history traits and intra-cohort divergence of clearhead icefish (Protosalanx chinensis), indicating cannibalism increased fitness. PeerJ 8:e9900 https://doi.org/10.7717/peerj.9900
Different responses of plant N and P resorption to overgrazing in three dominant species in a typical steppe of Inner Mongolia, China
Nutrient resorption from senesced leaves is an important mechanism for nutrient conservation in plants. However, little is known about the effect of grazing on plant nutrient resorption from senesced leaves, especially in semiarid ecosystems. Here, we evaluated the effects of grazing on N and P resorption in the three most dominant grass species in a typical steppe in northern China. We identified the key pathways of grazing-induced effects on N and P resorption efficiency. Grazing increased N and P concentrations in the green leaves of Leymus chinensis and Stipa grandis but not in Cleistogenes squarossa. Both L. chinensis and S. grandis exhibited an increasing trend of leaf N resorption, whereas C. squarrosa recorded a decline in both leaf N and P resorption efficiency under grazing. Structural equation models showed that grazing is the primary driver of the changes in N resorption efficiency of the three dominant grass species. For L. chinensis, the P concentration in green and senesced leaves increased the P resorption efficiency, whereas the senesced leaf P concentration played an important role in the P resorption efficiency of C. squarrosa. Grazing directly drove the change in P resorption efficiency of S. grandis. Our results suggest that large variations in nutrient resorption patterns among plant species depend on leaf nutritional status and nutrient-use strategies under overgrazing, and indicate that overgrazing may have indirect effects on plant-mediated nutrient cycling via inducing shifts in the dominance of the three plant species.
Wang et al. (2020) Different responses of plant N and P resorption to overgrazing in three dominant species in a typical steppe of Inner Mongolia, China. PeerJ 8:e9915 https://doi.org/10.7717/peerj.9915
Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies
Dietary habits in extinct species cannot be directly observed; thus, in the absence of extraordinary evidence, they must be reconstructed with a combination of morphological proxies. Such proxies often include information on dental organization and function such as tooth formation time and tooth replacement rate. In extinct organisms, tooth formation times and tooth replacement rate are calculated, in part via extrapolation of the space between incremental lines in dental tissues representing daily growth (von Ebner Line Increment Width; VEIW). However, to date, little work has been conducted testing assumptions about the primary data underpinning these calculations, specifically, the potential impact of differential sampling and data extrapolation protocols. To address this, we tested a variety of intradental, intramandibular, and ontogentic sampling effects on calculations of mean VEIW, tooth formation times, and replacement rates using histological sections and CT reconstructions of a growth series of three specimens of the extant archosaurian Alligator mississippiensis. We find transect position within the tooth and transect orientation with respect to von Ebner lines to have the greatest impact on calculations of mean VEIW—a maximum number of VEIW measurements should be made as near to the central axis (CA) as possible. Measuring in regions away from the central axis can reduce mean VEIW by up to 36%, causing inflated calculations of tooth formation time. We find little demonstrable impact to calculations of mean VEIW from the practice of subsampling along a transect, or from using mean VEIW derived from one portion of the dentition to extrapolate for other regions of the dentition. Subsampling along transects contributes only minor variations in mean VEIW (<12%) that are dwarfed by the standard deviation (SD). Moreover, variation in VEIW with distance from the pulp cavity likely reflects idiosyncratic patterns related to life history, which are difficult to control for; however, we recommend increasing the number of VEIW measured to minimize this effect. Our data reveal only a weak correlation between mean VEIW and body length, suggesting minimal ontogenetic impacts. Finally, we provide a relative SD of mean VEIW for Alligator of 29.94%, which can be used by researchers to create data-driven error bars for tooth formation times and replacement rates in fossil taxa with small sample sizes. We caution that small differences in mean VEIW calculations resulting from non-standardized sampling protocols, especially in a comparative context, will produce inflated error in tooth formation time estimations that intensify with crown height. The same holds true for applications of our relative SD to calculations of tooth formation time in extinct taxa, which produce highly variable maximum and minimum estimates in large-toothed taxa (e.g., 718–1,331 days in Tyrannosaurus).
Kosch et al. (2020) Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies. PeerJ 8:e9918 https://doi.org/10.7717/peerj.9918
Mesenchymal stem cell exosomes reverse acute lung injury through Nrf-2/ARE and NF-κB signaling pathways
Acute lung injury (ALI) is associated with histopathological diffuse alveolar damage. The potential role of mesenchymal stem cells (MSCs) in the treatment of various clinical disorders have been widely documented, such as those for ALI. Recent evidence has demonstrated that exosomes from endothelial progenitor cells can improve outcomes of the lipopolysaccharide (LPS)-induced ALI. However, there has been no research on the potential role of MSC-exosomes in the treatment of sepsis-induced ALI, which is worth further exploration. Thus, the objective of our study was to identify whether the MSC-exosomes could reverse ALI. The ALI model induced by LPS was established in this study. MTT assay was performed to test cell proliferation. Expression of inflammatory factors (TNF-α, IL-6, and IL-10) in the LPS-treated type II alveolar epithelial cells (AECs) (MLE-12) was detected by ELISA. After co-culture of MSC-exosomes with LPS-treated MLE-12 cells, we found that the cell proliferation of MLE-12 cells gradually increased. Furthermore, we selected five of the Nrf-2/ARE- and NF-κB signaling pathway-related genes to explore if MSC-exosomes could reverse LPS-induced ALI through Nrf-2/ARE and NF-κB signaling pathways. QRT-PCR and western blot experiment results showed that the expression of these five genes were significantly regulated after stimulation with high-concentration LPS and exosome intervention. Taken together, these findings highlighted the fact that MSC-exosomes could reverse ALI through the Nrf-2/ARE and NF-κB signaling pathways. The MSC-exosome may be the potential future therapeutic strategy for the treatment of ALI.
Li et al. (2020) Mesenchymal stem cell exosomes reverse acute lung injury through Nrf-2/ARE and NF-κB signaling pathways. PeerJ 8:e9928 https://doi.org/10.7717/peerj.9928
Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs
Using the crystal structure of SARS-CoV-2 papain-like protease (PLpro) as a template, we developed a pharmacophore model of functional centers of the PLpro inhibitor-binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. This search identified 147 compounds that can be potential inhibitors of SARS-CoV-2 PLpro. The conformations of these compounds underwent 3D fingerprint similarity clusterization, followed by docking of possible conformers to the binding pocket of PLpro. Docking of random compounds to the binding pocket of protease was also done for comparison. Free energies of the docking interaction for the selected compounds were lower than for random compounds. The drug list obtained includes inhibitors of HIV, hepatitis C, and cytomegalovirus (CMV), as well as a set of drugs that have demonstrated some activity in MERS, SARS-CoV, and SARS-CoV-2 therapy. We recommend testing of the selected compounds for treatment of COVID-19
Kouznetsova et al. (2020) Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs. PeerJ 8:e9965 https://doi.org/10.7717/peerj.9965
Radiolarian assemblages in the shelf area of the East China Sea and Yellow Sea and their ecological indication of the Kuroshio Current derivative branches
We analyzed the radiolarian assemblages of 59 surface sediment samples collected from the Yellow Sea and East China Sea of the northwestern Pacific. In the study region, the Kuroshio Current and its derivative branches exerted a crucial impact on radiolarian composition and distribution. Radiolarians in the Yellow Sea shelf showed a quite low abundance as no tests were found in 15 of 25 Yellow Sea samples. Radiolarians in the East China Sea shelf could be divided into three regional groups: the East China Sea north region group, the East China Sea middle region group, and the East China Sea south region group. The results of the redundancy analysis suggested that the Sea Surface Temperature and Sea Surface Salinity were primary environmental variables explaining species-environment relationship. The gradients of temperature, salinity, and species diversity reflect the powerful influence of the Kuroshio Current in the study area.
Qu et al. (2020) Radiolarian assemblages in the shelf area of the East China Sea and Yellow Sea and their ecological indication of the Kuroshio Current derivative branches. PeerJ 8:e9976 https://doi.org/10.7717/peerj.9976
Development of a noninvasive photograph-based method for the evaluation of body condition in free-ranging brown bears
Body condition is an important determinant of health, and its evaluation has practical applications for the conservation and management of mammals. We developed a noninvasive method that uses photographs to assess the body condition of free-ranging brown bears (Ursus arctos) in the Shiretoko Peninsula, Hokkaido, Japan. First, we weighed and measured 476 bears captured during 1998–2017 and calculated their body condition index (BCI) based on residuals from the regression of body mass against body length. BCI showed seasonal changes and was lower in spring and summer than in autumn. The torso height:body length ratio was strongly correlated with BCI, which suggests that it can be used as an indicator of body condition. Second, we examined the precision of photograph-based measurements using an identifiable bear in the Rusha area, a special wildlife protection area on the peninsula. A total of 220 lateral photographs of this bear were taken September 24–26, 2017, and classified according to bear posture. The torso height:body/torso length ratio was calculated with four measurement methods and compared among bear postures in the photographs. The results showed torso height:horizontal torso length (TH:HTL) to be the indicator that could be applied to photographs of the most diverse postures, and its coefficient of variation for measurements was <5%. In addition, when analyzing photographs of this bear taken from June to October during 2016–2018, TH:HTL was significantly higher in autumn than in spring/summer, which indicates that this ratio reflects seasonal changes in body condition in wild bears. Third, we calculated BCI from actual measurements of seven females captured in the Rusha area and TH:HTL from photographs of the same individuals. We found a significant positive relationship between TH:HTL and BCI, which suggests that the body condition of brown bears can be estimated with high accuracy based on photographs. Our simple and accurate method is useful for monitoring bear body condition repeatedly over the years and contributes to further investigation of the relationships among body condition, food habits, and reproductive success.
Shirane et al. (2020) Development of a noninvasive photograph-based method for the evaluation of body condition in free-ranging brown bears. PeerJ 8:e9982 https://doi.org/10.7717/peerj.9982
Soil fungal networks are more sensitive to grazing exclusion than bacterial networks
Soil microbial communities play a crucial role in ecological restoration, but it is unknown how co-occurrence networks within these communities respond to grazing exclusion. This lack of information was addressed by investigating the effects of eight years of grazing exclusion on microbial networks in an area of Stipa glareosa P. Smirn desert steppe in northern China. Here, we show that fungal networks were more sensitive to grazing exclusion than bacterial networks. Eight years of grazing exclusion decreased the soil fungal community stability via changes in plant composition and reductions in soil total organic carbon, in this case triggering negative effects on the S. glareosa desert steppe. The results provide new insights into the response mechanisms of soil microbes to grazing exclusion and offer possible solutions for management issues in the restoration of degraded desert steppe.
Chen et al. (2020) Soil fungal networks are more sensitive to grazing exclusion than bacterial networks. PeerJ 8:e9986 https://doi.org/10.7717/peerj.9986