Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations
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.
Nada et al. (2022) Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations. PeerJ 10:e14120 https://doi.org/10.7717/peerj.14120
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
Background About 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. Methods A 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. Result Compared 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. Conclusion Deep ploughing in the summer fallow season, paired with optimized N application, could help increase wheat yield and nitrogen efficiency in dryland.
Zhang et al. (2022) 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. PeerJ 10:e14153 https://doi.org/10.7717/peerj.14153
Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench)
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.
Zhang et al. (2022) Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench). PeerJ 10:e14156 https://doi.org/10.7717/peerj.14156
Effect of humic acid derived from leonardite on the redistribution of uranium fractions in soil
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.
Environmental Contamination and Remediation
Meng et al. (2022) Effect of humic acid derived from leonardite on the redistribution of uranium fractions in soil. PeerJ 10:e14162 https://doi.org/10.7717/peerj.14162
Effect of salt stress and nitrogen supply on seed germination and early seedling growth of three coastal halophytes
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.
Chen et al. (2022) Effect of salt stress and nitrogen supply on seed germination and early seedling growth of three coastal halophytes. PeerJ 10:e14164 https://doi.org/10.7717/peerj.14164
Spatiotemporal relationships of coyotes and free-ranging domestic cats as indicators of conflict in Culver City, California
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.
Davenport et al. (2022) Spatiotemporal relationships of coyotes and free-ranging domestic cats as indicators of conflict in Culver City, California. PeerJ 10:e14169 https://doi.org/10.7717/peerj.14169
Regional water footprint assessment for a semi-arid basin in India
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.
Spatial and Geographic Information Science
Mehla (2022) Regional water footprint assessment for a semi-arid basin in India. PeerJ 10:e14207 https://doi.org/10.7717/peerj.14207
The cloacal microbiome of a cavity-nesting raptor, the lesser kestrel (Falco naumanni)
Background Microbial communities are found on any part of animal bodies exposed to the environment, and are particularly prominent in the gut, where they play such a major role in the host metabolism and physiology to be considered a “second genome”. These communities, collectively known as “microbiome”, are well studied in humans and model species, while studies on wild animals have lagged behind. This is unfortunate, as different studies suggested the central role of the gut microbiome in shaping the evolutionary trajectories of species and their population dynamics. Among bird species, only few descriptions of raptor gut microbiomes are available, and mainly carried out on captive individuals. Objectives In this study, we aimed at improving the knowledge of raptor microbiomes by providing the first description of the gut microbiome of the lesser kestrel (Falco naumanni), a cavity-nesting raptor. Results The gut microbiome of the lesser kestrel was dominated by Actinobacteria (83.9%), Proteobacteria (8.6%) and Firmicutes (4.3%). We detected no differences in microbiome composition between males and females. Furthermore, the general composition of the microbiome appears similar to that of phylogenetically distant cavity-nesting species. Conclusions Our results broaden the knowledge of raptor gut microbial communities and let us hypothesize that the distinct nest environment in terms of microclimate and presence of organic material from previous breeding attempts, to which cavity-nesting species that reuse the nest are exposed, might be an important driver shaping microbiomes.
Costanzo et al. (2022) The cloacal microbiome of a cavity-nesting raptor, the lesser kestrel (Falco naumanni). PeerJ 10:e13927 https://doi.org/10.7717/peerj.13927
Vegetation height and structure drive foraging habitat selection of the lesser kestrel (Falco naumanni) in intensive agricultural landscapes
Habitat selection in animals is a fundamental ecological process with key conservation implications. Assessing habitat selection in endangered species and populations occupying the extreme edges of their distribution range, or living in highly anthropized landscapes, may be of particular interest as it may provide hints to mechanisms promoting potential range expansions. We assessed second- and third-order foraging habitat selection in the northernmost European breeding population of the lesser kestrel (Falco naumanni), a migratory falcon of European conservation interest, by integrating results obtained from 411 direct observations with those gathered from nine GPS-tracked individuals. The study population breeds in the intensively cultivated Po Plain (northern Italy). Direct observations and GPS data coincide in showing that foraging lesser kestrels shifted their habitat preferences through the breeding cycle. They positively selected alfalfa and other non-irrigated crops during the early breeding season, while winter cereals were selected during the nestling-rearing phase. Maize was selected during the early breeding season, after sowing, but significantly avoided later. Overall, vegetation height emerged as the main predictor of foraging habitat selection, with birds preferring short vegetation, which is likely to maximise prey accessibility. Such a flexibility in foraging habitat selection according to spatio-temporal variation in the agricultural landscape determined by local crop management practices may have allowed the species to successfully thrive in one of the most intensively cultivated areas of Europe. In the southeastern Po Plain, the broad extent of hay and non-irrigated crops is possibly functioning as a surrogate habitat for the pseudo-steppe environment where most of the European breeding population is settled, fostering the northward expansion of the species in Europe. In intensive agricultural landscapes, the maintenance of alfalfa and winter cereals crops and an overall high crop heterogeneity (deriving from crop rotation) is fundamental to accommodate the ecological requirements of the species in different phases of its breeding cycle.
Cioccarelli et al. (2022) Vegetation height and structure drive foraging habitat selection of the lesser kestrel (Falco naumanni) in intensive agricultural landscapes. PeerJ 10:e13979 https://doi.org/10.7717/peerj.13979
Incidence rate, risk factors, and management of Bell’s palsy in the Qurayyat region of Saudi Arabia
Background Bell’s palsy is an idiopathic facial nerve dysfunction causing temporary paralysis of muscles of facial expression. This study aimed to determine the incidence rate, common risk factors, and preferred treatment by the Saudi patients with Bell’s palsy. Method This cross-sectional study was carried out in the Qurayyat region of Saudi Arabia. The retrospective medical records were searched from 2015–2020 of patients diagnosed with Bell’s palsy at Qurayyat General Hospital and King Fahad hospital. A 28-item questionnaire was developed by a team of experts and pre-tested among patients with Bell’s palsy before being sent to the eligible participants. The data were analyzed using summary statistics, Chi-square test, Fisher exact test and Likelihood ratio test. Results We identified 279 cases of Bell’s palsy from the medical records of the hospitals from the years 2015 to 2020, accounting for 46.5 cases per year and an incidence rate of 25.7 per 100,000 per year. Out of 279 patients with Bell’s palsy, only 171 returned the questionnaire accounting for a response rate of 61.2%. Out of 171 patients with Bell’s palsy, females (n = 147, 86.0%) accounted for the majority of cases. The most affected age group among participants with Bell’s palsy was 21–30 years (n = 76, 44.4%). There were 153 (89.5%) cases who reported Bell’s palsy for the first time. The majority of the participants experienced right-sided facial paralysis (n = 96, 56.1%). Likelihood ratio test revealed significant relationship between exposure to cold air and common cold with age groups (χ2(6, N = 171) = 14.92, p = 0.021), χ2(6, N = 171) = 16.35, pp = 0.012 respectively. The post hoc analyses revealed that participants in the age group of 20–31-years were mostly affected due to exposure to cold air and common cold than the other age groups. The main therapeutic approach preferred was physiotherapy (n = 149, 87.1%), followed by corticosteroids and antivirals medications (n = 61, 35.7%), acupressure (n = 35, 20.5%), traditional Saudi herb medicine (n = 32, 18.7%), cauterization by hot iron rod (n = 23, 13.5%), supplementary therapy (n = 2, 1.2%), facial cosmetic surgery (n = 1, 0.6%) and no treatment (n = 1, 0.6%). The most preferred combined therapy was physiotherapy (87.6%) with corticosteroid and antiviral drugs (35.9%), and acupressure (17.6%). Conclusion The rate of Bell’s palsy was approximately 25.7 per 100,000 per year in the Qurayyat region of Saudi Arabia. Exposure to cold air and common cold were the significant risk factors associated with Bell’s palsy. Females were predominantly affected by Bell’s palsy in the Qurayyat region of Saudi Arabia. Bell’s palsy most commonly occurred in the age group 21–30 years. The most favored treatment was physiotherapy following Bell’s palsy.
Alanazi et al. (2022) Incidence rate, risk factors, and management of Bell’s palsy in the Qurayyat region of Saudi Arabia. PeerJ 10:e14076 https://doi.org/10.7717/peerj.14076