title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=859 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Early effects of crop tree management on undergrowth plant diversity and soil physicochemical properties in a Pinus massoniana plantation link: https://peerj.com/articles/11852 last-modified: 2021-07-29 description: BackgroundSoil and understory vegetation are vital components of forest ecosystems. Identifying the interaction of plantation management to vegetation and soil is crucial for developing sustainable plantation ecosystem management strategies. As one of the main measures of close-to-nature management of forest plantation, few studies have paid attention to the effect of crop tree management on the soil properties and understory vegetation.MethodsA 36-year-old Pinus massoniana plantation in Huaying city, Sichuan Province was taken as the research object to analyse the changes in undergrowth plant diversity and soil physicochemical properties under three different crop tree densities (100, 150, and 200 N/ha).ResultsOur results showed that the contents of available phosphorus, organic matter and hydrolysable nitrogen in the topsoil increased significantly after crop tree management, while content of available potassium decreased. The composition of shrub and herb layer was richer, and the dominant species were obviously replaced after crop tree management. The Shannon–Wiener index and Richness index of shrub layer, and the diversity of herb layer increased significantly after crop tree management. Herb layer diversity indexes and Richness index of shrub layer were closely related to soil organic matter, available phosphorus, hydrolysable nitrogen, available potassium, soil moisture and bulk density. As the main limiting factors for plant growth, nitrogen, phosphorus and potassium were closely related to plant diversity and to the distribution of the dominant species. At the initial stage of crop tree management, each treatment significantly improved the soil physicochemical properties and plant diversity of Pinus massoniana plantation, and the comprehensive evaluation was 200 N/ha >100 N/ha >150 N/ha >CK. Compared with other treatments, 200 N/ha had the best effect on improving the undergrowth environment of the Pinus massoniana plantation in the initial stage of crop tree management. creator: Qian Lyu creator: Yi Shen creator: Xianwei Li creator: Gang Chen creator: Dehui Li creator: Chuan Fan uri: https://doi.org/10.7717/peerj.11852 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lyu et al. title: Sequence analysis and mRNA expression of prolactin receptor gene isoforms in different tissues of sheep during lactation and the post-weaning period link: https://peerj.com/articles/11868 last-modified: 2021-07-29 description: Few studies on mRNA expression of the prolactin receptor (PRLR) isoforms in different tissues of sheep were reported. The objective of this study was to analyze the gene sequence and mRNA expression of PRLR isoforms in the uterus, mammary gland, ovary, spleen and lymph tissue of ewes during the lactation and post-weaning periods. Ten lactating crossbred ewes (Dorper×Hu sheep) with twin lambs were used in this study. Five ewes were chosen randomly and slaughtered at mid-lactation (35 days after lambing). The remaining five ewes were slaughtered on the 5th day after weaning. Samples of uterus, mammary gland, ovary, spleen and lymph tissue were collected from each ewe to determine the mRNA expression of long PRLR (L-PRLR) and short PRLR (S-PRLR) by RT-qPCR. The physical and chemical properties, the similarity of the nucleotides L-PRLR and S-PRLR genes and the secondary and tertiary structure of the L-PRLR and S-PRLR proteins of sheep were analyzed. The results indicated that the predicted protein molecular weights of L-PRLR and S-PRLR are 65235.36 KD and 33847.48 KD, respectively, with isoelectric points of 5.12 and 8.34, respectively. The secondary protein structures of L-PRLR and S-PRLR are different. For L-PRLR these include alpha helix, extended strand and random coils and β-turns for which the content was 16.01%, 21%, 59.55% and 3.44%, respectively, whereas the secondary protein structures of S-PRLR contain only alpha helices, extended strand and random coils, comprising 18.24%, 30.07% and 48.99%, respectively. The L-PRLR and S-PRLR genes of the sheep (Ovis aries) had nucleotide sequences showing much similarity among ruminants. In these sheep, mRNA expression of L-PRLR and S-PRLR was highest in the uterus and differed between the uterus, ovary, mammary gland, spleen and lymph tissue. The mRNA expression of L-PRLR in lymph tissue was higher during lactation than in the post-weaning period (P < 0.01), whereas mRNA expression of S-PRLR in the uterus and the mammary gland was lower during lactation than during the post-weaning period (P < 0.01). In the uterus, mRNA expression of L-PRLR was higher than that of S-PRLR during lactation (P < 0.01) but there were no significant differences (P < 0.05) for the other five tissues. This study that the L-PRLR and S-PRLR proteins in ewes are mainly composed of extended fragments and random coils. The data also indicate that mRNA expression of L-PRLR and S-PRLR genes varies among different tissues in sheep and is higher in the uterus than in the ovary, spleen, mammary gland and lymph tissue throughout lactation and the post-weaning period. creator: Ruochen Yang creator: Chunhui Duan creator: Yunxia Guo creator: Yujing Ma creator: Nazi Niu creator: Yingjie Zhang creator: Yueqin Liu uri: https://doi.org/10.7717/peerj.11868 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Network analysis of miRNA targeting m6A-related genes in patients with esophageal cancer link: https://peerj.com/articles/11893 last-modified: 2021-07-29 description: BackgroundWe investigated the miRNA-m6A related gene network and identified a miRNA-based prognostic signature in patients with esophageal cancer using integrated genomic analysis.MethodsWe obtained expression data for m6A-related genes and miRNAs from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Survival analysis was conducted to identify potential prognostic biomarkers. LASSO Cox regression was performed to construct the overall survival (OS) associated prediction signature. We used the Kaplan–Meier (K–M) curve and receiver operating characteristic (ROC) curves to explore the signature’s efficiency and accuracy. Interactions between the m6A-related genes and miRNAs were identified in starBase3.0 and used to construct the miRNA-m6A related gene network.ResultsWe found that HNRNPC, YTHDF, ZC3H13, YTHDC2, and METTL14 were dysregulated in esophageal cancer tissues. Multivariate Cox regression analysis revealed that HNRNPC may be an independent risk factor for OS. Five hundred twenty-two potential upstream miRNAs were obtained from starBase3.0. Four miRNAs (miR-186, miR-320c, miR-320d, and miR-320b) were used to construct a prognostic signature, which could serve as a prognostic predictor independent from routine clinicopathological features. Finally, we constructed a key miRNA-m6A related gene network and used one m6A-related gene and four miRNAs associated with the prognosis. The results of our bioinformatics analysis were successfully validated in the human esophageal carcinoma cell lines KYSE30 and TE-1.ConclusionOur study identified a 4-miRNA prognostic signature and established a key miRNA-m6A related gene network. These tools may reliably assist with esophageal cancer patient prognosis. creator: Lili Li creator: Rongrong Xie creator: Qichun Wei uri: https://doi.org/10.7717/peerj.11893 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Population and distribution of wild Asian elephants (Elephas maximus) in Phu Khieo Wildlife Sanctuary, Thailand link: https://peerj.com/articles/11896 last-modified: 2021-07-29 description: BackgroundThe populations of wild Asian elephants (Elephas maximus) have increased recently after a period of worldwide decline in protected areas. It is important to understand the dynamics and distribution of the remaining populations to ensure their conservation and prevent human-elephant conflicts.MethodsWe monitored the population distribution of elephants between 2016 and 2019 in the Phu Khieo Wildlife Sanctuary, Thailand. We set one hundred forty-nine camera trap locations; cameras recorded 38,834 photos over 6,896 trap nights. Elephants were captured in 4,319 photographs. The maximum entropy modeling software MaxEntwas used to identify elephants’ habitat preferences within 49 of the 149 total camera trap locations according to five environmental factors.ResultsOne hundred fourteen elephants were identified. We identified 30 adult males, 43 adult females, 14 sub-adult males, nine sub-adult females, 11 juveniles, and seven calves. The age structure ratio based on adult femaleswas 0.7:1:0.3:0.2:0.3:0.2, and the ratio of reproductive ability between adult females, juveniles, and calves was 1:0.2:0.1. A suitable elephant habitat was determined to be 1,288.9 km2 using Area Under the Curve (AUC). An AUC = 0.061 indicated good performance. Our model classified habitat preferences associated with elevation, forests, salt licks, human activity, and slope.ConclusionsAccording to our probability map this sanctuary can provide a suitable habitat for elephants. Our results indicate that effective management practices can protect wild Asian elephants in the region and reduce conflict between humans and elephants. creator: Nyi Nyi Phyo Htet creator: Rattanawat Chaiyarat creator: Nikorn Thongthip creator: Panat Anuracpreeda creator: Namphung Youngpoy creator: Phonlugsamee Chompoopong uri: https://doi.org/10.7717/peerj.11896 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Htet et al. title: Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil link: https://peerj.com/articles/11903 last-modified: 2021-07-29 description: Rhodoliths are free-living and morphologically diverse marine calcareous algae commonly distributed over the continental shelf seafloor. They increase the seabed structural complexity and are of potential value as feeding and reproductive grounds for a myriad of marine fauna. The higher structural seabed complexity within rhodolith beds may also increase benthic diversity by creating microhabitats, but this relationship has been rarely explored within rhodolith beds worldwide. Here we compared benthic macrofaunal (>500 µm) structure on rhodolith beds (nodule epifauna) and within unconsolidated sediments (sediment infauna) under high and low-density beds to test whether rhodolith bed density and nodule morphology influenced macrofaunal assemblages. We observed that macrofaunal density on nodules (2538 ± 288.7 ind·m−2) was 15-fold higher when compared to sediments under those beds (166 ± 38.8 ind·m−2). Rhodolith bed density was positively related to macrofaunal density, composition, and functional diversity on the rhodoliths. Low-density beds (61 ± 27.1 nodules·m−2) with discoid-shape nodules were dominated by peracarid crustaceans whereas high-density beds (204 ± 18.7 nodules·m−2) with spheroidal nodules were dominated by Annelid polychaetes. The sediment macrofauna was also positively influenced by the density of rhodolith nodules, which increased sediment carbonate and organic quality (protein and lipids) under high-density beds. Macrofaunal functional diversity was generally higher on rhodoliths, with low similarity (low nestedness) and high taxa turnover between macrofaunal assemblages of rhodoliths and sediments. These findings indicate that rhodolith beds provide an unique habitat for benthic macrofaunal communities, with exclusive functional and taxonomic richness that are likely not typical in the unconsolidated sediment below these beds in SE Brazil. This study highlights the importance of protecting rhodolith beds from multiple sources of anthropogenic disturbance and exploration on continental shelves. creator: Patricia Sarcinelli Stelzer creator: Ana Carolina A. Mazzuco creator: Luiz Eduardo Gomes creator: João Martins creator: Sergio Netto creator: Angelo F. Bernardino uri: https://doi.org/10.7717/peerj.11903 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Stelzer et al. title: Why a landscape view is important: nearby urban and agricultural land affects bird abundances in protected areas link: https://peerj.com/articles/10719 last-modified: 2021-07-28 description: Protected areas are one of the primary conservation tools used worldwide. However, they are often embedded in a landscape that is intensely used by people, such as for agriculture or urban development. The proximity of these land-use types to protected areas can potentially affect the ecological effectiveness (or conservation effectiveness) of protected areas. In this article, we examine to what degree adjacent agricultural and urban land uses affect the ecological effectiveness of protected areas over the greater Gauteng region of South Africa. We selected 198 common, resident bird species, and analysed detection/non-detection data for these species collected over regular grid cells (approximately 61 km2 in area). For each species, we estimated abundance per grid cell with the Royle-Nichols model in relation to the proportion of protected area as a covariate. Our study focused on how this relationship between proportion of protected area and abundance (which we term the ‘protection–abundance relationship’) changed as a function of other land-use types in the grid cell. Specifically, we examined the interaction effects between protected area and both urban and agricultural land-use type per grid cell on bird abundance. We assigned each species to one of seven guilds, namely: frugivores, gleaners, granivores, ground-feeders, hawkers, predators and vegivores, and examined how the protection–abundance relationship varied across guilds in relation to agriculture and urban area. As urban area within a grid cell increased, the protection–abundance relationship became more positive for 58% of all species. At the level of guilds, the protection–abundance relationship became more positive for two guilds (granivores and ground-feeders), more negative for frugivores, and remained unchanged for the other four guilds (gleaners, hawkers, predators and vegivores). As agricultural area within a grid cell increased, the protection–abundance relationship became more positive for 49% of all species. At the guild level, the protection–abundance relationship became more positive for six guilds (frugivores, gleaners, ground-feeders, hawkers, predators and vegivores) and remained unchanged for the granivores. Our results show land-use type near protected areas modified the effect protected areas had on bird abundances, and hence the ecological effectiveness of protected areas. Our results suggest that protected areas should be viewed as constituents within the landscape, rather than islands of protection. creator: Gregory Duncan Duckworth creator: Res Altwegg uri: https://doi.org/10.7717/peerj.10719 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Duckworth and Altwegg title: Bioactive marine metabolites derived from the Persian Gulf compared to the Red Sea: similar environments and wide gap in drug discovery link: https://peerj.com/articles/11778 last-modified: 2021-07-28 description: Marine life has provided mankind with unique and extraordinary chemical structures and scaffolds with potent biological activities. Many organisms and secondary metabolites derived from fungi and symbionts are found to be more environmentally friendly to study than the marine corals per se. Marine symbionts such as Aspergillus sp., a fungus, which can be isolated and grown in the lab would be a potential and continuous source of bioactive natural compounds without affecting the marine environment. The Red Sea is known for its biodiversity and is well-studied in terms of its marine-derived bioactive metabolites. The harsh environmental conditions lead to the development of unique metabolic pathways. This, in turn, results in enhanced synthesis and release of toxic and bioactive chemicals. Interestingly, the Persian Gulf and the Gulf of Oman carry a variety of environmental stresses, some of which are similar to the Red Sea. When compared to the Red Sea, the Persian Gulf has been shown to be rich in marine fungi as well, and is, therefore, expected to contain elaborate and interesting bioactive compounds. Such compounds may or may not be similar to the ones isolated from the Red Sea environment. Astoundingly, there are a very limited number of studies on the bioactive portfolio of marine-derived metabolites from the Persian Gulf and the Gulf of Oman. In this perspective, we are looking at the Red Sea as a comparator marine environment and bioactive materials repertoire to provide a futuristic perspective on the potential of the understudied and possibly overlooked bioactive metabolites derived from the marine life of the Persian Gulf and the Gulf of Oman despite its proven biodiversity and harsher environmental stress. creator: Reham K. Abuhijjleh creator: Samiullah Shabbir creator: Ahmed M. Al-Abd creator: Nada H. Jiaan creator: Shahad Alshamil creator: Eman M. El-labbad creator: Sherief I. Khalifa uri: https://doi.org/10.7717/peerj.11778 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Abuhijjleh et al. title: Large chromosomal deletions and impaired homologous recombination repairing in HEK293T cells exposed to polychlorinated biphenyl 153 link: https://peerj.com/articles/11816 last-modified: 2021-07-28 description: BackgroundPolychlorinated biphenyls (PCBs) are persistent pollutants with carcinogenesis and mutagenesis effects which have been closely associated with PCBs-induced DNA damage. However, the detailed DNA damage events and corresponding pathway alterations under PCBs poisoning is still not well understood.MethodsWhole-genome sequencing (WGS) and RNA sequencing (RNA-seq) were used to explore genome wide variations and related pathway changes in HEK293T cells that challenged by 15 µM PCB153 for 96 h in vitro. Double strand breaks (DSBs) were measured by 53BP1 foci detection, altered pathways were confirmed by quantitative real-time PCR (qPCR).ResultsThe results indicated that abundant copy number variations (CNVs), including four duplications and 30 deletions, occurred in PCB153-exposed HEK293T cells. Multiple large fragment deletions (>1 Mb) involving up to 245 Mb regions on many chromosomes. Missense mutations were found in six tumor susceptibility genes, two of which are key members participating in homologous recombination (HR) repair response, BRCA1 and BRCA2. RNA-seq data showed that PCB153 poisoning apparently suppressedHR repairing genes. Besides, 15 µM PCB153 exposure significantly increased 53BP1 foci formation and effectively reduced BRCA1, RAD51B and RAD51C expression, indicating an elevated DSBs and impaired HR repairing.ConclusionThis study firstly reported multiple large chromosomal deletions and impaired HR repairing in PCB153-exposed HEK293T cells, which provided a new insight into the understanding of early response and the mechanism underlying PCB153 genotoxicity. The chromosomal instabilities might be related to the impaired HR repairing that induced by PCB153; however, further investigations, especially on actual toxic effects of human body, are needed to confirm such speculation. creator: Jiaci Li creator: Yaqing Jing creator: Yi Liu creator: Yawei Ru creator: Mingyan Ju creator: Yuxia Zhao creator: Guang Li uri: https://doi.org/10.7717/peerj.11816 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides link: https://peerj.com/articles/11839 last-modified: 2021-07-28 description: BackgroundLignocellulose is a renewable and enormous biomass resource, which can be degraded efficiently by a range of cocktails of carbohydrate-active enzymes secreted by termite gut symbiotic bacteria. There is an urgent need to find enzymes with novel characteristics for improving the conversion processes in the production of lignocellulosic-based products. Although various studies dedicated to the genus Cellulosimicrobium as gut symbiont, genetic potential related to plant biomass-acting enzymes and exopolysaccharides production has been fully untapped to date.MethodsThe cellulolytic bacterial strain MP1 was isolated from termite guts and identified to the species level by phenotypic, phylogenetic, and genomic analysis. To further explore genes related to cellulose and hemicellulose degradation, the draft genome of strain MP1 was obtained by using whole-genome sequencing, assembly, and annotation through the Illumina platform. Lignocellulose degrading enzymes and levan production in the liquid medium were also examined to shed light on bacterial activities.ResultsAmong 65 isolates obtained, the strain MP1 was the most efficient cellulase producer with cellulase activity of 0.65 ± 0.02 IU/ml. The whole genome analysis depicted that strain MP1 consists of a circular chromosome that contained 4,580,223 bp with an average GC content of 73.9%. The genome comprises 23 contigs including 67 rRNA genes, three tRNA genes, a single tmRNA gene, and 4,046 protein-coding sequences. In support of the phenotypic identification, the 16S rRNA gene sequence, average nucleotide identity, and whole-genome-based taxonomic analysis demonstrated that the strain MP1 belongs to the species Cellulosimicrobium cellulans. A total of 30 genes related to the degradation of cellulases and hemicellulases were identified in the C. cellulans MP1 genome. Of note, the presence of sacC1-levB-sacC2-ls operon responsible for levan and levan-type fructooligosaccharides biosynthesis was detected in strain MP1 genome, but not with closely related C. cellulans strains, proving this strain to be a potential candidate for further studies. Endoglucanases, exoglucanases, and xylanase were achieved by using cheaply available agro-residues such as rice bran and sugar cane bagasse. The maximum levan production by C. cellulans MP1 was 14.8 ± 1.2 g/l after 20 h of cultivation in media containing 200 g/l sucrose. To the best of our knowledge, the present study is the first genome-based analysis of a Cellulosimicrobium species which focuses on lignocellulosic enzymes and levan biosynthesis, illustrating that the C. cellulans MP1 has a great potential to be an efficient platform for basic research and industrial exploitation. creator: Nguyen Thi-Hanh Vu creator: Tung Ngoc Quach creator: Xuan Thi-Thanh Dao creator: Ha Thanh Le creator: Chi Phuong Le creator: Lam Tung Nguyen creator: Lam Tung Le creator: Cuong Cao Ngo creator: Ha Hoang creator: Ha Hoang Chu creator: Quyet-Tien Phi uri: https://doi.org/10.7717/peerj.11839 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Vu et al. title: Comparative development and ocular histology between epigean and subterranean salamanders (Eurycea) from central Texas link: https://peerj.com/articles/11840 last-modified: 2021-07-28 description: The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes—the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of adult E. rathbuni. creator: Ruben U. Tovar creator: Valentin Cantu creator: Brian Fremaux creator: Pedro Gonzalez Jr creator: Amanda Spikes creator: Dana M. García uri: https://doi.org/10.7717/peerj.11840 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tovar et al.