title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=638 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Dynamics of the gut microbiota in rats after hypobaric hypoxia exposure link: https://peerj.com/articles/14090 last-modified: 2022-10-07 description: BackgroundGut microbiota plays an important role in host health and is influenced by multiple factors. Hypobaric hypoxia usually existing at high altitude conditions can adversely affect normal physiological functions. However, the dynamic changes of gut microbiota influenced by hypobaric hypoxia have not been elucidated.MethodsIn this study, we collected fecal samples from seven rats at 14 time points from entering the hypobaric chamber (eight time points) to leaving the chamber (six time points) and five rats served as normoxic controls. Metagenome sequencing was performed on all samples and the dynamics of taxa and functions were analyzed.ResultsWe found that the α-diversity was changed in the first 5 days after entering or leaving the hypobaric chamber. The β-diversity analysis revealed that gut microbiota structure was significantly separated among 14 time points. After entering the chamber, the relative abundance of Bacteroides decreased and the most abundant genus turned into Prevotella. The abundance of Firmicutes and Bacteroidetes showed an opposite trend and both have a significant change within 5 days after entering or leaving the hypobaric hypoxia chamber. Some obligate anaerobic bacteria belonging to Desulfovibrio and Alistipes were significantly enriched after entering the chamber for 5 weeks, whereas Probiotics like Bifidobacterium and Lactococcus, and short-chain fatty acids producers like Butyrivibrio and Pseudobutyrivibrio were significantly enriched after leaving the chamber for 3 weeks. Microbial functions like ‘Two-component regulatory system’, ‘beta-carotene biosynthesis’ and ‘Fatty acid biosynthesis’ were significantly enriched after entering the chamber for 5 weeks. Hypobaric hypoxia conditions could deeply affect the diversity and structure of gut microbiota. The alterations of abundance of dominant taxa (Firmicutes and Bacteroidetes), increased anaerobes and decreased probiotics induced by hypobaric hypoxia conditions might affect the host health. creator: Yang Han creator: Jiayu Xu creator: Yan Yan creator: Xiaojing Zhao uri: https://doi.org/10.7717/peerj.14090 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Han et al. title: Comparative assessment of enamel remineralisation on the surface microhardness of demineralized enamel - an in vitro study link: https://peerj.com/articles/14098 last-modified: 2022-10-07 description: ObjectiveThe main objective of the study was to compare two different remineralising materials containing casein phosphopeptide-amorphous calcium phosphate, bioactive glass on enamel surface microhardness.Materials and MethodsThirty premolars were used for specimen preparation. Group 1 (the control group) consisted of intact enamel samples, group 2: CPP-ACPF (Tooth Mousse Plus), group 3: bioenamel remineralising gel (Prevest DenPro). All specimens were subjected to demineralisation except the control group, followed by which remineralising agents were applied. A universal hardness tester was used to assess the surface microhardness of all samples. Results were analysed using one-way ANOVA test and comparison was analysed using Scheffe’s post hoc least significant difference (LSD) test.ResultsBoth remineralising agents used in groups 2 and 3 have shown significant outcome in terms of improving the surface microhardness in comparison with the control group. Group 2 increased the enamel hardness by 8.34 where P = 0.023 whereas group 3 increased the hardness by 5.87, where P = 0.01.ConclusionGroup 2 has a superior hardness value than group 3; however, no statistically significant results were obtained between both the groups. creator: Bhavika Bhavsar creator: Mary Vijo creator: Pranjely Sharma creator: Tulika Patnaik creator: Mohammad Khursheed Alam creator: Santosh Patil uri: https://doi.org/10.7717/peerj.14098 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bhavsar et al. title: Interactions between two functionally distinct aquatic invertebrate herbivores complicate ecosystem- and population-level resilience link: https://peerj.com/articles/14103 last-modified: 2022-10-07 description: Resilience, the capacity for a system to bounce-back after a perturbation, is critical for conservation and restoration efforts. Different functional traits have differential effects on system-level resilience. We test this experimentally in a lab system consisting of algae consumed by zooplankton, snails, or both, using an eutrophication event as a perturbation. We examined seston settlement load, chlorophyll-a and ammonium concentration as gauges of resilience. We find that Daphnia magna increased our measures of resilience. But this effect is not consistent across ecosystem measures; in fact, D. magna increased the difference between disturbed and undisturbed treatments in seston settlement loads. We have some evidence of shifting reproductive strategy in response to perturbation in D. magna and in the presence of Physa sp. These shifts correspond with altered population levels in D. magna, suggesting feedback loops between the herbivore species. While these results suggest only an ambiguous connection between functional traits to ecosystem resilience, they point to the difficulties in establishing such a link: indirect effects of one species on reproduction of another and different scales of response among components of the system, are just two examples that may compromise the power of simple predictions. creator: Jo A. Werba creator: Alexander C. Phong creator: Lakhdeep Brar creator: Acacia Frempong-Manso creator: Ofure Vanessa Oware creator: Jurek Kolasa uri: https://doi.org/10.7717/peerj.14103 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Werba et al. title: Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations link: https://peerj.com/articles/14120 last-modified: 2022-10-07 description: The rapid spread of the coronavirus since its first appearance in 2019 has taken the world by surprise, challenging the global economy, and putting pressure on healthcare systems across the world. The introduction of preventive vaccines only managed to slow the rising death rates worldwide, illuminating the pressing need for developing effective antiviral therapeutics. The traditional route of drug discovery has been known to require years which the world does not currently have. In silico approaches in drug design have shown promising results over the last decade, helping to decrease the required time for drug development. One of the vital non-structural proteins that are essential to viral replication and transcription is the SARS-CoV-2 main protease (Mpro). Herein, using a test set of recently identified COVID-19 inhibitors, a pharmacophore was developed to screen 20 million drug-like compounds obtained from a freely accessible Zinc database. The generated hits were ranked using a structure based virtual screening technique (SBVS), and the top hits were subjected to in-depth molecular docking studies and MM-GBSA calculations over SARS-COV-2 Mpro. Finally, the most promising hit, compound (1), and the potent standard (III) were subjected to 100 ns molecular dynamics (MD) simulations and in silico ADME study. The result of the MD analysis as well as the in silico pharmacokinetic study reveal compound 1 to be a promising SARS-Cov-2 MPro inhibitor suitable for further development. creator: Hossam Nada creator: Ahmed Elkamhawy creator: Kyeong Lee uri: https://doi.org/10.7717/peerj.14120 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Nada et al. title: Deep ploughing in the summer fallow season and optimizing nitrogen rate can increase yield, water, and nitrogen efficiencies of rain-fed winter wheat in the Loess Plateau region of China link: https://peerj.com/articles/14153 last-modified: 2022-10-07 description: BackgroundAbout 60% of the annual precipitation in the Loess Plateau occurs during the summer fallow season, and does not align with the wheat growing season. In addition, the nitrogen use efficiency is low in this area because nutrient availability is affected by drought. As a result, rainwater storage during the summer fallow season is very important to increasing nitrogen use efficiency, and to the stable production of dryland wheat in the Loess Plateau.MethodsA 3-year field experiment in the eastern part of the Loess Plateau was conducted with two tillage methods (no tillage (NT) and deep ploughing (DP)) and five N rates (0, 120, 150, 180, and 210 kg N ha−1) to study the effect of tillage on soil water utilization, plant nitrogen utilization, and wheat yield.ResultCompared to NT, DP showed a larger increase in soil water storage (SWSf) and precipitation storage efficiency (PSEf) during the two dry summer fallow seasons than in the normal summer fallow season. DP substantially increased the pre-anthesis soil water consumption (SWCpre) and N translocation. The average yield under DP was 12.46% and 14.92–18.29% higher than under NT in the normal and dry seasons, respectively. A 1 mm increase in SWCpre could increase grain yield by 25.28 kg ha−1, water use efficiency (WUE) by 0.069 kg ha−1 mm−1, and nitrogen utilization efficiency (NUtE) by 0.029 kg kg−1. DP could reduce the N rate by 11.49–53.34% in the normal seasons and 40.97–65.07% in the dry seasons compared to the same highest point of yield, WUE, and NUtE under NT.ConclusionDeep ploughing in the summer fallow season, paired with optimized N application, could help increase wheat yield and nitrogen efficiency in dryland. creator: Rongrong Zhang creator: Peiru Wang creator: Wenxiang Wang creator: Aixia Ren creator: Hafeez Noor creator: Rong Zhong creator: Zhiqiang Gao creator: Min Sun uri: https://doi.org/10.7717/peerj.14153 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench) link: https://peerj.com/articles/14156 last-modified: 2022-10-07 description: The aboveground parts of plants are covered with cuticle, a hydrophobic layer composed of cutin polyester and cuticular wax that can protect plants from various environmental stresses. β-Ketoacyl-CoA synthase (KCS) is the key rate-limiting enzyme in plant wax synthesis. Although the properties of KCS family genes have been investigated in many plant species, the understanding of this gene family in sorghum is still limited. Here, a total of 25 SbKCS genes were identified in the sorghum genome, which were named from SbKCS1 to SbKCS25. Evolutionary analysis among different species divided the KCS family into five subfamilies and the SbKCSs were more closely related to maize, implying a closer evolutionary relationship between sorghum and maize. All SbKCS genes were located on chromosomes 1, 2, 3, 4, 5, 6, 9 and 10, respectively, while Chr 1 and Chr 10 contained more KCS genes than other chromosomes. The prediction results of subcellular localization showed that SbKCSs were mainly expressed in the plasma membrane and mitochondria. Gene structure analysis revealed that there was 0–1 intron in the sorghum KCS family and SbKCSs within the same subgroup were similar. Multiple cis-acting elements related to abiotic stress, light and hormone response were enriched in the promoters of SbKCS genes, which indicated the functional diversity among these genes. The three-dimensional structure analysis showed that a compact spherical space structure was formed by various secondary bonds to maintain the stability of SbKCS proteins, which was necessary for their biological activity. qRT-PCR results revealed that nine randomly selected SbKCS genes expressed differently under drought and salt treatments, among which SbKCS8 showed the greatest fold of expression difference at 12 h after drought and salt stresses, which suggested that the SbKCS genes played a potential role in abiotic stress responses. Taken together, these results provided an insight into investigating the functions of KCS family in sorghum and in response to abiotic stress. creator: Aixia Zhang creator: Jingjing Xu creator: Xin Xu creator: Junping Wu creator: Ping Li creator: Baohua Wang creator: Hui Fang uri: https://doi.org/10.7717/peerj.14156 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Effect of humic acid derived from leonardite on the redistribution of uranium fractions in soil link: https://peerj.com/articles/14162 last-modified: 2022-10-07 description: Humic acids (HAs) are complex organic substances with abundant functional groups (e.g., carboxyl, phenolic-OH, etc.). They are commonly distributed in the soil environment and exert a double-edged sword effect in controlling the migration and transformation of uranium. However, the effects of HAs on dynamic processes associated with uranium transformation are still unclear. In this study, we used HAs derived from leonardite (L-HA) and commercial HA (C-HA) as exogenous organic matter and C-HA as the reference. UO2, UO3, and UO2(NO3)2 were used as the sources of U to explore the fractionations of uranium in the soil. We also studied the behavior of the HA. The incubation experiments were designed to investigate the effects of HA on the soil pH, uranium fraction transformation, dynamic behavior of exchangeable, weak acid, and labile uranium. The observations were made for one month. The results showed that soil pH decreased for L-HA but increased for C-HA. Under these conditions, uranium tended to transform into an inactive fraction. The dynamic behavior of exchangeable, weak acid, and labile uranium varied with the sources of HA and uranium. This study highlighted that HA could affect soil pH and the dynamic redistribution of U fractions. The results suggest that the sources of HA and U should be considered when using HA as the remediation material for uranium-contaminated soils. creator: Fande Meng creator: Qiuxiang Huang creator: Yongbing Cai creator: Guodong Yuan creator: Liang Xiao creator: Fengxiang X. Han uri: https://doi.org/10.7717/peerj.14162 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Meng et al. title: Effect of salt stress and nitrogen supply on seed germination and early seedling growth of three coastal halophytes link: https://peerj.com/articles/14164 last-modified: 2022-10-07 description: Due to high salinity and low nutrient concentrations, the coastal zone is considered as one of the most vulnerable of the earth’s habitats. Thus, the effect of salt and nitrogen on growth and development of coastal halophytes has been extensively investigated in recent years, but insufficient attention has been paid to the crucial stages of plant establishment, such as seed germination and seedling growth. Thus, we carried out a field experiment to evaluate the effects of salt stress (6, 10 and 20 g/kg NaCl) and nitrogen supply (0, 6 and 12 gm−2year−1) on seed germination and seedling growth of three coastal halophytes (including two dominant herb species Glehnia littoralis and Calystegia soldanella, one constructive shrub species Vitex rotundifolia) from September 2020 to June 2021. The results of our experiment showed that seeds of G. littoralis exhibited an explosive germination strategy in the early spring of 2021 with 70% of the seeds germinating. Conversely, the seeds of V. rotundifolia exhibited slow germination in the late spring of 2021 with only 60% of the seeds germinating. C. soldanella seed germination exhibited two obvious peak periods, but only 6% of the seeds germinated, which means that most seeds may be stored in the soil by stratification or died. All three halophytes showed greater sensitivity to nitrogen than salt stress during the seed germination stage. Nitrogen supply significantly delayed seed germination and reduced the cumulative germination percentage, particularly for G. littoralis. Despite the large impact of nitrogen on seed germination, nitrogen had a larger impact on seedling growth suggesting that the seedling growth stage of halophytes is more vulnerable to changes in nitrogen supply. Moreover, nitrogen supply significantly reduced the individual biomass of G. littoralis, C. soldanella and V. rotundifolia, with greater decreases seen in the dominant species than in the constructive species. Conversely, nitrogen supply increased underground biomass allocation of G. littoralis and C. soldanella, suggesting that the constructive species were less sensitive to nitrogen and exhibited a stronger anti-interference ability than the dominant species. Therefore, increasing nitrogen supply may firstly affect the seed germination and seedling growth of the dominant species, but not the constructive species. creator: Yanfeng Chen creator: Yan Liu creator: Lan Zhang creator: Lingwei Zhang creator: Nan Wu creator: Huiliang Liu uri: https://doi.org/10.7717/peerj.14164 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Spatiotemporal relationships of coyotes and free-ranging domestic cats as indicators of conflict in Culver City, California link: https://peerj.com/articles/14169 last-modified: 2022-10-07 description: As habitat generalists, urban coyote (Canis latrans) populations often utilize an abundance of diverse food sources in cities. Within southern California, domestic cats (Felis catus) comprise a higher proportion of coyote diets than in other studied urban areas throughout the United States. However, it is unclear which ecological factors contribute to higher rates of cat depredation by coyotes in this region. While previous research suggests that coyote presence may have a negative effect on free-ranging domestic cat distributions, few studies have determined whether urban green spaces affect coyote or free-ranging domestic cat occurrence and activity within a predominantly urbanized landscape. We placed 20 remote wildlife cameras across a range of green spaces and residential sites in Culver City, California, an area of Los Angeles County experiencing pronounced coyote-domestic cat conflict. Using data collected across 6 months from 2019–2020, we assessed the influence of green space and prey species (i.e., cottontail rabbits (Sylvilagus spp.) and domestic cats) on coyote habitat use and activity. Coyotes exhibited a preference for sites with higher amounts of green space, while domestic cat habitat use was high throughout our study region. Although cottontail rabbit habitat use was also highly associated with urban green space, neither cottontails nor domestic cats appeared to temporally overlap significantly with coyotes. Unlike other cities where coyotes and domestic cats exhibit strong habitat partitioning across the landscape, domestic cats and coyotes spatially overlapped in green space fragments throughout Culver City. We suggest that this pattern of overlap may be responsible for the frequent cases of domestic cat depredation by coyotes in Culver City. creator: Rebecca N. Davenport creator: Melinda Weaver creator: Katherine C. B. Weiss creator: Eric G. Strauss uri: https://doi.org/10.7717/peerj.14169 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Davenport et al. title: Regional water footprint assessment for a semi-arid basin in India link: https://peerj.com/articles/14207 last-modified: 2022-10-07 description: Water footprint assessment enables us to pinpoint the impacts and limitations of the current systems. Identifying vulnerabilities across various regions and times helps us prepare for suitable actions for improving water productivity and promoting sustainable water use. This study aims to provide a comprehensive evaluation of the sector-wise water footprint in the Banas River Basin from 2008–2020. The water footprint of the Banas River Basin was estimated as 20.2 billion cubic meters (BCM)/year from all sectors. The water footprint has increased over the year with the increase in population, the number of industries, and crop production demand. The average annual water footprint of crop production varied from 11.4–23.1 BCM/year (mean 19.3 BCM/year) during the study period. Results indicate that the water footprint has nearly doubled in the past decade. Wheat, bajra, maize, and rapeseed & mustard make up 67.4% of crop production’s total average annual water footprint. Suitable measures should be implemented in the basin to improve water productivity and promote sustainable water use in agriculture, which accounts for nearly 95.5% of the total water footprint (WF) of the Banas basin. The outcomes of the study provide a reference point for further research and planning of appropriate actions to combat water scarcity challenges in the Banas basin. creator: Mukesh Kumar Mehla uri: https://doi.org/10.7717/peerj.14207 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mehla