title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=579
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Bacterial composition along the digestive tract of the Horned Screamer (Anhima cornuta), a tropical herbivorous bird
link: https://peerj.com/articles/14805
last-modified: 2023-02-13
description: BackgroundThe Horned Screamer (Anhima cornuta) is an herbivorous bird that inhabits wetlands of the South American tropical region. We hypothesize that due to its herbivorous niche, its digestive tract compartments may have bacteria specialized in fermenting complex plant carbohydrates. To test this hypothesis, we compared the bacterial communities along the gastrointestinal tract (GIT) of a Horned Screamer captured in Venezuela.MethodsSamples were taken from tissues and content of the proventriculus and the small intestine (considered for this study as upper GIT), and the large intestine and cecum (lower GIT). The bacterial community was characterized by sequencing the V4 region of the 16S rRNA gene. Bioinformatic analysis was performed using QIIME, QIITA and Microbiome Analyst. The association between microbial taxonomy and function was analyzed using their Greengenes OTU IDs and a custom KEGG BRITE hierarchical tree and visualized with BURRITO.ResultsThe Screamer’s gastrointestinal microbiota was composed by seven phyla being Firmicutes and Bacteroidetes the most predominant. The dominant taxa in the upper GIT were Helicobacter, Vibrio, Enterobacter, Acinetobacter and Staphylococcus. The dominant taxa in the lower GIT were Oribacterium, Blautia, Roseburia, Ruminococcus, Desulfovibrio, Intestinimonas, Marvinbryantia and Parabacteroides. Complete degradation of cellulose to the end-products acetate, propanoate, butanoate and acetoacetate was found in the upper and lower GIT without significant differences.ConclusionOur study confirmed changes in bacterial community composition throughout the GIT of the Horned Screamer primarily associated with the production of metabolic end-products of carbohydrate digestion essential for the fermentation of the herbivorous diet.
creator: María Alexandra García-Amado
creator: Carla A. Rudolf
creator: Maria del Mar Fuentes-Fuentes
creator: Nataliya Chorna
creator: Leoncia Margarita Martínez
creator: Filipa Godoy-Vitorino
uri: https://doi.org/10.7717/peerj.14805
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 García-Amado et al.

title: Breviscapine alleviates podocyte injury by inhibiting NF-κB/NLRP3-mediated pyroptosis in diabetic nephropathy
link: https://peerj.com/articles/14826
last-modified: 2023-02-13
description: Podocyte injury is a critical factor in the pathogenesis of diabeticnephropathy (DN). Emerging evidence has demonstrated that breviscapine (Bre) exerts a renoprotective effect on diabetic rats. However, the effects of Bre on regulating podocyte injury under high glucose (HG) conditions remain unclear. In this study, an experimental mouse model of DN was induced by intraperitoneal injections of streptozotocin (STZ) in vivo. The effects of Bre on podocyte injury were assessed using cell counting kit-8 (CCK-8) assay, TdT-mediated dUTPnick-endlabelling (TUNEL) staining, quantitative real-time PCR (qRT‒PCR) and western blot analysis. We found that renal function was significantly decreased in diabetic mice, and this effect was blocked by Bre treatment. Bre effectively increased podocyte viability and inhibited HG-induced cell apoptosis. Furthermore, Bre ameliorated HG-induced podocyte injury, as evidenced by decreased α-smooth muscle actin (α-SMA) expression and increased podocin and synaptopodin expression. Mechanistically, Bre inhibited HG-induced nuclear factorkappaB (NF-κB) signalling activation and subsequently decreased NLR family pyrin domain containing 3 (NLRP3) inflammasome activation, resulting in a decrease in pyroptosis. Pharmacological inhibition of NLRP3 decreased HG-induced podocyte injury, whereas the NLRP3 agonist abrogated the effects of Bre on inhibiting podocyte injury. In summary, these results demonstrate that Bre alleviates HG-induced podocyte injury and improves renal function in diabetic mice, at least in part by inhibiting NF-κB/NLRP3-mediated pyroptosis.
creator: Linlin Sun
creator: Miao Ding
creator: Fuhua Chen
creator: Dingyu Zhu
creator: Xinmiao Xie
uri: https://doi.org/10.7717/peerj.14826
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Sun et al.

title: Variable level of genetic dominance controls important agronomic traits in rice populations under water deficit condition
link: https://peerj.com/articles/14833
last-modified: 2023-02-13
description: Plant hybridization is an important breeding technique essential for producing a genotype (hybrid) with favorable traits (e.g., stress tolerance, pest resistance, high yield potential etc.) to increase agronomic, economic and commercial values. Studying of genetic dominance among the population helps to determine gene action, heritability and candidate gene selection for plant breeding program. Therefore, this investigation was aimed to evaluate gene action, heritability, genetic advance and heterosis of rice root, agronomic, and yield component traits under water deficit conditions. In this study, crossing was performed among the four different water-deficit tolerant rice genotypes to produce better hybrid (F1), segregating (F2) and back-cross (BC1 and BC2) populations. The Giza 178, WAB56-204, and Sakha104 × WAB56-104 populations showed the better physiological and agronomical performances, which provided better adaptability of the populations to water deficit condition. Additionally, the estimation of heterosis and heterobeltiosis of some quantitative traits in rice populations were also studied. The inheritance of all studied traits was influenced by additive gene actions. Dominance gene actions played a major role in controlling the genetic variance among studied traits in both crossed populations under well-watered and drought conditions. The additive × additive type of gene interactions was essential for the inheritance of root length, root/shoot ratio, 1,000-grain weight, and sterility % of two crossed populations under both conditions. On the contrary, the additive × dominance type of gene interactions was effective in the inheritance of all studied traits, except duration in Giza178 × Sakha106, and plant height in Sakha104 × WAB56-104 under water deficit condition. In both crosses, the dominance × dominance type of gene interactions was effective in the inheritance of root volume, root/shoot ratio, number of panicles/plant and 1,000-grain weight under both conditions. Moreover, dominance × dominance type of gene interaction played a major role in the inheritance of root length, number of roots/plant, plant height, panicle length, number of filled grain/panicle and grain yield/plant in Giza178 × Sakha106 under both conditions. The studied traits in both crossed populations indicated better genetic advance as they showed advanced qualitative and quantitative characters in rice populations under water deficit condition. Overall, our findings open a new avenue of future phenotypic and genotypic association studies in rice. These insights might be useful to the plant breeders and farmers for developing water deficit tolerant rice cultivars.
creator: Hamada M. Hassan
creator: Adel A. Hadifa
creator: Sara A. El-leithy
creator: Maria Batool
creator: Ahmed Sherif
creator: Ibrahim Al-Ashkar
creator: Akihiro Ueda
creator: Md Atikur Rahman
creator: Mohammad Anwar Hossain
creator: Ayman Elsabagh
uri: https://doi.org/10.7717/peerj.14833
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Hassan et al.

title: Leaf color change and photosystem function evaluation under heat treatment revealed the stress resistance variation between Loropetalum chinense and L. chinense var. rubrum
link: https://peerj.com/articles/14834
last-modified: 2023-02-13
description: This research mainly focused on the leaf color change and photosystem function differentiation between Loropetalum chinense and its variety L. chinense var. rubrum under heat stress, which were tightly concerned about their ornamental traits and growth. L. chinense ‘Xiangnong Xiangyun’ (X) and L. chinense var. rubrum ‘Xiangnong Fendai’ (F) and L. chinense var. rubrum ‘Hei Zhenzhu’ (H) were chosen to be experimented on to investigate whether leaf color morphology and pigment composition could influence the adaptability of plants to high temperature in order to select foliage plants which posses stable leaf color and better adaptability for hot regions. The plants were cultured in hot environment (40 °C/33 °C, day/night) and normal environment (25 °C/18 °C, day/night). Phenotype and anatomic observation of three cultivars were made and leaf color indices and pigment contents were measured. During the experiment, H and F gradually turned green, total anthocyanins contents significantly decreased in them, however, chlorophyll b contents increased in all three cultivars. In addition, the initial fluorescence (Fo) decreased in X, while increased in H and F. For the maximum fluorescence (Fm) and maximum photochemical efficiency of PSII (Fv/Fm), they only increased in H and decreased in both F and X. The non-photochemical chlorophyll fluorescence quenching (NPQ) also increased in H and decreased in F. For X, it increased at first then gradually decreased. The coefficient of photochemical quenching all increased at first then gradually decreased. Correlation analysis between showed that there was relatively strong connection between anthocyanins, flavonoids and chlorophyll fluorescence parameters, especially NPQ, proved anthocyanins and flavonoids might not only involved in enriching leaf color, but also interfered with the protection of photosystem. Generally speaking, we found higher anthocyanin and flavonoids content level not only dramatically enriched the leaf color of L. chinense var. rubrum cultivars, but also offered more potential antioxidant to keep their normal growth when encountered heat stress.
creator: Wenqi Cai
creator: Damao Zhang
creator: Xia Zhang
creator: Qianru Chen
creator: Yang Liu
creator: Ling Lin
creator: Lili Xiang
creator: Yujie Yang
creator: Lu Xu
creator: Xiaoying Yu
creator: Yanlin Li
uri: https://doi.org/10.7717/peerj.14834
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Cai et al.

title: Genome-wide identification and analysis of the evolution and expression pattern of the HVA22 gene family in three wild species of tomatoes
link: https://peerj.com/articles/14844
last-modified: 2023-02-13
description: Wild tomato germplasm is a valuable resource for improving biotic and abiotic stresses in tomato breeding. The HVA22 is widely present in eukaryotes and involved in growth and development as well as stress response, such as cold, salt, drought, and biotic stress. In the present study, we identified 45 HVA22 genes in three wild species of tomatoes. The phylogenetic relationships, gene localization to chromosomes, gene structure, gene collinearity, protein interactions, and cis-acting element prediction of all 45 HVA22 genes (14 in Solanum pennellii, 15 in S. pimpinellifolium, and 16 in S. lycopersicoides) were analyzed. The phylogenetic analysis showed that the all HVA22 proteins from the family Solanaceae were divided into three branches. The identified 45 HVA22 genes were grouped into four subfamilies, which displayed similar number of exons and expanded in a fragmentary replication manner. The distribution of HVA22 genes on the chromosomes of the three wild tomato species was also highly similar. RNA-seq and qRT-PCR revealed that HVA22 genes were expressed in different tissues and induced by drought, salt, and phytohormone treatments. These results might be useful for explaining the evolution, expression patterns, and functional divergence of HVA22 genes in Lycopersicon.
creator: LaiPeng Zhao
creator: Baike Wang
creator: Tao Yang
creator: Huizhuan Yan
creator: Qinghui Yu
creator: Juan Wang
uri: https://doi.org/10.7717/peerj.14844
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Zhao et al.

title: Mismatch between IUCN range maps and species interactions data illustrated using the Serengeti food web
link: https://peerj.com/articles/14620
last-modified: 2023-02-10
description: BackgroundRange maps are a useful tool to describe the spatial distribution of species. However, they need to be used with caution, as they essentially represent a rough approximation of a species’ suitable habitats. When stacked together, the resulting communities in each grid cell may not always be realistic, especially when species interactions are taken into account. Here we show the extent of the mismatch between range maps, provided by the International Union for Conservation of Nature (IUCN), and species interactions data. More precisely, we show that local networks built from those stacked range maps often yield unrealistic communities, where species of higher trophic levels are completely disconnected from primary producers.MethodologyWe used the well-described Serengeti food web of mammals and plants as our case study, and identify areas of data mismatch within predators’ range maps by taking into account food web structure. We then used occurrence data from the Global Biodiversity Information Facility (GBIF) to investigate where data is most lacking.ResultsWe found that most predator ranges comprised large areas without any overlapping distribution of their prey. However, many of these areas contained GBIF occurrences of the predator.ConclusionsOur results suggest that the mismatch between both data sources could be due either to the lack of information about ecological interactions or the geographical occurrence of prey. We finally discuss general guidelines to help identify defective data among distributions and interactions data, and we recommend this method as a valuable way to assess whether the occurrence data that are being used, even if incomplete, are ecologically accurate.
creator: Gracielle T. Higino
creator: Francis Banville
creator: Gabriel Dansereau
creator: Norma Rocio Forero Muñoz
creator: Fredric Windsor
creator: Timothée Poisot
uri: https://doi.org/10.7717/peerj.14620
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Higino et al.

title: Comparative chloroplast genomics of three species of Bulbophyllum section Cirrhopetalum (Orchidaceae), with an emphasis on the description of a new species from Eastern Himalaya
link: https://peerj.com/articles/14721
last-modified: 2023-02-10
description: BackgroundChloroplast (cp) genomes are useful and informative molecular markers used for species determination and phylogenetic analysis. Bulbophyllum is one of the most taxonomically complex taxa in Orchidaceae. However, the genome characteristics of Bulbophyllum are poorly understood.MethodsBased on comparative morphological and genomic analysis, a new species Bulbophyllum pilopetalum from eastern Himalaya belonging to section Cirrhopetalum is described and illustrated. This study used chloroplast genomic sequences and ribosomal DNA (nrDNA) analysis to distinguish the new Bulbophyllum species and determine its phylogenetic position. An additional phylogenetic analysis was conducted using 74 coding sequences from 15 complete chloroplast genomes from the genus Bulbophyllum, as well as nrDNA sequences and two chloroplast DNA sequences from 33 Bulbophyllun species.ResultsThe new species is morphologically similar to B. pingnanense, B. albociliatum, and B. brevipedunculatum in vegetative and floral morphology, but it can be distinguished by its ovate-triangle dorsal sepal without a marginal ciliate. The chloroplast genome of the new Bulbophyllum species is 151,148 bp in length, and includes a pair of inverted repeats (IRs) of 25,833 bp, a large single-copy region (LSC) of 86,138 bp, and a small single-copy region (SSC) of 13,300 bp. The chloroplast genome includes 108 unique genes encoding 75 proteins, 30 tRNAs, and four rRNAs. Compared with the cp genomes of its two most closely-related species, B. pingnanense and B. albociliatum, this chloroplast genome exhibited great interspecific divergence and contained several Indels that were specific to the new species. The plastid tree showed that B. pilopetalum is most closely-related to B. pingnanense. The phylogenetic tree based on combined nrDNA and chloroplast DNA sequences indicated that section Cirrhopetalum was monophyletic and B. pilopetalum was a member of this section.DiscussionThe taxonomic status of the new species is strongly supported by cp genome data. Our study highlights the importance of using the complete cp genome to identify species, elucidate the taxonomy, and reconstruct the phylogeny of plant groups with complicated taxonomic problems.
creator: Mengkai Li
creator: Lu Tang
creator: Jianping Deng
creator: Hanqing Tang
creator: Shicheng Shao
creator: Zhen Xing
creator: Yan Luo
uri: https://doi.org/10.7717/peerj.14721
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Li et al.

title: Low-stress livestock handling protects cattle in a five-predator habitat
link: https://peerj.com/articles/14788
last-modified: 2023-02-10
description: Given the ecological importance of top predators, societies are turning to non-lethal methods for coexistence. Coexistence is challenging when livestock graze within wild predator habitats. We report a randomized, controlled experiment to evaluate low-stress livestock handling (L-SLH), a form of range riding, to deter grizzly (brown) bears, gray wolves, cougars, black bears, and coyotes in Southwestern Alberta. The treatment condition was supervision by two newly hired and trained range riders and an experienced L-SLH-practicing range rider. This treatment was compared against a baseline pseudo-control condition of the experienced range rider working alone. Cattle experienced zero injuries or deaths in either condition. We infer that inexperienced range riders trained and supervised by an experienced rider did not raise or lower the risk to cattle. Also, predators did not shift to the cattle herds protected by fewer range riders. We found a correlation suggesting grizzly bears avoided herds visited more frequently by range riders practicing L-SLH. More research is required to compare different forms of range riding. However, pending experimental evaluation of other designs, we recommend use of L-SLH. We discuss the cobenefits of this husbandry method.
creator: Naomi X. Louchouarn
creator: Adrian Treves
uri: https://doi.org/10.7717/peerj.14788
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Louchouarn and Treves

title: Abnormal expression of SLIT3 induces intravillous vascularization dysplasia in ectopic pregnancy
link: https://peerj.com/articles/14850
last-modified: 2023-02-10
description: ObjectiveTo investigate whether the morphology, capillary number, and transcriptome expression profiles of ectopic pregnancy (EP) villi differ from those of normal pregnancy (NP) villi.MethodsHematoxylin-eosin (HE) and immunohistochemistry (IHC) staining for CD31 were conducted to compare differences in morphology and capillary number between EP and NP villi. Differentially expressed (DE) miRNAs and mRNAs were determined from transcriptome sequencing of both types of villi and used to construct a miRNA–mRNA network, from which hub genes were identified. Candidate DE-miRNAs and DE-mRNAs were validated by quantitative reverse transcription (qRT)-PCR. Correlations were identified between the number of capillaries and serum beta human chorionic gonadotropin (β-HCG) levels and between the expression levels of hub genes associated with angiogenesis and β-HCG levels.ResultsThe mean and total cross-sectional areas of placental villi were significantly increased in EP compared with NP villi. Capillary density was greatly reduced in EP villi and was positively correlated with β-HCG levels. A total of 49 DE-miRNAs and 625 DE-mRNAs were identified from the sequencing data. An integrated analysis established a miRNA–mRNA network containing 32 DE-miRNAs and 103 DE-mRNAs. Based on the validation of hub mRNAs and miRNAs in the network, a regulatory pathway involving miR-491-5p–SLIT3 was discovered, which may have a role in the development of villous capillaries.ConclusionVillus morphology, capillary number, and miRNA/mRNA expression profiles in villous tissues were aberrant in EP placentas. Specifically, SLIT3, which is regulated by miR-491-5p, may contribute to the regulation of villous angiogenesis and was established as a putative predictor of chorionic villus development, providing a basis for future research.
creator: Qian Zhu
creator: Xiaoya Zhao
creator: Duo Zhang
creator: Wei Xia
creator: Jian Zhang
uri: https://doi.org/10.7717/peerj.14850
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Zhu et al.

title: Rapid growth in Late Cretaceous sea turtles reveals life history strategies similar to extant leatherbacks
link: https://peerj.com/articles/14864
last-modified: 2023-02-10
description: Modern sea turtle long bone osteohistology has been surprisingly well-studied, as it is used to understand sea turtle growth and the timing of life history events, thus informing conservation decisions. Previous histologic studies reveal two distinct bone growth patterns in extant sea turtle taxa, with Dermochelys (leatherbacks) growing faster than the cheloniids (all other living sea turtles). Dermochelys also has a unique life history compared to other sea turtles (large size, elevated metabolism, broad biogeographic distribution, etc.) that is likely linked to bone growth strategies. Despite the abundance of data on modern sea turtle bone growth, extinct sea turtle osteohistology is virtually unstudied. Here, long bone microstructure of the large, Cretaceous sea turtle Protostega gigas is examined to better understand its life history. Humeral and femoral analysis reveals bone microstructure patterns similar to Dermochelys with variable but sustained rapid growth through early ontogeny. Similarities between Progostegea and Dermochelys osteohistology suggest similar life history strategies like elevated metabolic rates with rapid growth to large body size and sexual maturity. Comparison to the more basal protostegid Desmatochelys indicates elevated growth rates are not present throughout the entire Protostegidae, but evolved in larger and more derived taxa, possibly in response to Late Cretaceous ecological changes. Given the uncertainties in the phylogenetic placement of the Protostegidae, these results either support convergent evolution towards rapid growth and elevated metabolism in both derived protostegids and dermochelyids, or a close evolutionary relationship between the two taxa. Better understanding the evolution and diversity of sea turtle life history strategies during the Late Cretaceous greenhouse climate can also impact current sea turtle conservation decisions.
creator: Laura E. Wilson
uri: https://doi.org/10.7717/peerj.14864
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Wilson