PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations
items: 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
items: Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench)
items: Effect of humic acid derived from leonardite on the redistribution of uranium fractions in soil
items: Effect of salt stress and nitrogen supply on seed germination and early seedling growth of three coastal halophytes
items: Spatiotemporal relationships of coyotes and free-ranging domestic cats as indicators of conflict in Culver City, California
items: Regional water footprint assessment for a semi-arid basin in India
items: The cloacal microbiome of a cavity-nesting raptor, the lesser kestrel (Falco naumanni)
items: Vegetation height and structure drive foraging habitat selection of the lesser kestrel (Falco naumanni) in intensive agricultural landscapes
items: Incidence rate, risk factors, and management of Bell’s palsy in the Qurayyat region of Saudi Arabia

Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Hossam Nada
creator: Ahmed Elkamhawy
creator: Kyeong Lee
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Computational Science
subject: COVID-19
description: doi:10.7717/peerj.14120
publisher: PeerJ Inc.
rights: © 2022 Nada et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-06-10
date accepted: 2022-09-05
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nada
  given name: Hossam
author list: Agent
  family name: Elkamhawy
  given name: Ahmed
author list: Agent
  family name: Lee
  given name: Kyeong
doi: 10.7717/peerj.14120
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: © 2022 Nada et al.
attribution name: Nada et al.

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
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Rongrong Zhang
creator: Peiru Wang
creator: Wenxiang Wang
creator: Aixia Ren
creator: Hafeez Noor
creator: Rong Zhong
creator: Zhiqiang Gao
creator: Min Sun
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.14153
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-05-30
date accepted: 2022-09-07
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Rongrong
author list: Agent
  family name: Wang
  given name: Peiru
author list: Agent
  family name: Wang
  given name: Wenxiang
author list: Agent
  family name: Ren
  given name: Aixia
author list: Agent
  family name: Noor
  given name: Hafeez
author list: Agent
  family name: Zhong
  given name: Rong
author list: Agent
  family name: Gao
  given name: Zhiqiang
author list: Agent
  family name: Sun
  given name: Min
doi: 10.7717/peerj.14153
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench)
type: item
type: AcademicArticle
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 …
format: application/pdf
format: text/html
creator: Aixia Zhang
creator: Jingjing Xu
creator: Xin Xu
creator: Junping Wu
creator: Ping Li
creator: Baohua Wang
creator: Hui Fang
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14156
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: 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 …
bibliographic citation: 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
date submitted: 2022-03-15
date accepted: 2022-09-08
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Aixia
author list: Agent
  family name: Xu
  given name: Jingjing
author list: Agent
  family name: Xu
  given name: Xin
author list: Agent
  family name: Wu
  given name: Junping
author list: Agent
  family name: Li
  given name: Ping
author list: Agent
  family name: Wang
  given name: Baohua
author list: Agent
  family name: Fang
  given name: Hui
doi: 10.7717/peerj.14156
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

Effect of humic acid derived from leonardite on the redistribution of uranium fractions in soil
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Fande Meng
creator: Qiuxiang Huang
creator: Yongbing Cai
creator: Guodong Yuan
creator: Liang Xiao
creator: Fengxiang X. Han
subject: Soil Science
subject: Ecotoxicology
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.14162
publisher: PeerJ Inc.
rights: © 2022 Meng et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-07-28
date accepted: 2022-09-09
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Fande
author list: Agent
  family name: Huang
  given name: Qiuxiang
author list: Agent
  family name: Cai
  given name: Yongbing
author list: Agent
  family name: Yuan
  given name: Guodong
author list: Agent
  family name: Xiao
  given name: Liang
author list: Agent
  family name: Han
  given name: Fengxiang X.
doi: 10.7717/peerj.14162
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: ©2022 Meng et al.
attribution name: Meng et al.

Effect of salt stress and nitrogen supply on seed germination and early seedling growth of three coastal halophytes
type: item
type: AcademicArticle
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 und…
format: application/pdf
format: text/html
creator: Yanfeng Chen
creator: Yan Liu
creator: Lan Zhang
creator: Lingwei Zhang
creator: Nan Wu
creator: Huiliang Liu
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.14164
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: 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 und…
bibliographic citation: 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
date submitted: 2022-04-29
date accepted: 2022-09-12
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yanfeng
author list: Agent
  family name: Liu
  given name: Yan
author list: Agent
  family name: Zhang
  given name: Lan
author list: Agent
  family name: Zhang
  given name: Lingwei
author list: Agent
  family name: Wu
  given name: Nan
author list: Agent
  family name: Liu
  given name: Huiliang
doi: 10.7717/peerj.14164
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: © 2022 Chen et al.
attribution name: Chen et al.

Spatiotemporal relationships of coyotes and free-ranging domestic cats as indicators of conflict in Culver City, California
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Rebecca N. Davenport
creator: Melinda Weaver
creator: Katherine C. B. Weiss
creator: Eric G. Strauss
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.14169
publisher: PeerJ Inc.
rights: © 2022 Davenport et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-01-11
date accepted: 2022-09-12
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Davenport
  given name: Rebecca N.
author list: Agent
  family name: Weaver
  given name: Melinda
author list: Agent
  family name: Weiss
  given name: Katherine C. B.
author list: Agent
  family name: Strauss
  given name: Eric G.
doi: 10.7717/peerj.14169
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: © 2022 Davenport et al.
attribution name: Davenport et al.

Regional water footprint assessment for a semi-arid basin in India
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Mukesh Kumar Mehla
subject: Agricultural Science
subject: Natural Resource Management
subject: Ecohydrology
subject: Food, Water and Energy Nexus
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.14207
publisher: PeerJ Inc.
rights: © 2022 Mehla
abstract: 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.
bibliographic citation: Mehla (2022) Regional water footprint assessment for a semi-arid basin in India. PeerJ 10:e14207 https://doi.org/10.7717/peerj.14207
date submitted: 2022-08-11
date accepted: 2022-09-19
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mehla
  given name: Mukesh Kumar
doi: 10.7717/peerj.14207
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: © 2022 Mehla
attribution name: Mehla

The cloacal microbiome of a cavity-nesting raptor, the lesser kestrel (Falco naumanni)
type: item
type: AcademicArticle
description: 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.
format: application/pdf
format: text/html
creator: Alessandra Costanzo
creator: Roberto Ambrosini
creator: Andrea Franzetti
creator: Andrea Romano
creator: Jacopo G. Cecere
creator: Michelangelo Morganti
creator: Diego Rubolini
creator: Isabella Gandolfi
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.13927
publisher: PeerJ Inc.
rights: © 2022 Costanzo et al.
abstract: 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.
bibliographic citation: 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
date submitted: 2022-03-18
date accepted: 2022-07-30
issued: 2022-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Costanzo
  given name: Alessandra
author list: Agent
  family name: Ambrosini
  given name: Roberto
author list: Agent
  family name: Franzetti
  given name: Andrea
author list: Agent
  family name: Romano
  given name: Andrea
author list: Agent
  family name: Cecere
  given name: Jacopo G.
author list: Agent
  family name: Morganti
  given name: Michelangelo
author list: Agent
  family name: Rubolini
  given name: Diego
author list: Agent
  family name: Gandolfi
  given name: Isabella
doi: 10.7717/peerj.13927
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-06
copyright: ©2022 Costanzo et al.
attribution name: Costanzo et al.

Vegetation height and structure drive foraging habitat selection of the lesser kestrel (Falco naumanni) in intensive agricultural landscapes
type: item
type: AcademicArticle
description: 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 ce…
format: application/pdf
format: text/html
creator: Sara Cioccarelli
creator: Anna Terras
creator: Giacomo Assandri
creator: Alessandro Berlusconi
creator: Nunzio Grattini
creator: Alessandro Mercogliano
creator: Aliona Pazhera
creator: Andrea Sbrilli
creator: Jacopo G. Cecere
creator: Diego Rubolini
creator: Michelangelo Morganti
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.13979
publisher: PeerJ Inc.
rights: © 2022 Cioccarelli et al.
abstract: 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 ce…
bibliographic citation: 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
date submitted: 2022-01-06
date accepted: 2022-08-10
issued: 2022-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cioccarelli
  given name: Sara
author list: Agent
  family name: Terras
  given name: Anna
author list: Agent
  family name: Assandri
  given name: Giacomo
author list: Agent
  family name: Berlusconi
  given name: Alessandro
author list: Agent
  family name: Grattini
  given name: Nunzio
author list: Agent
  family name: Mercogliano
  given name: Alessandro
author list: Agent
  family name: Pazhera
  given name: Aliona
author list: Agent
  family name: Sbrilli
  given name: Andrea
author list: Agent
  family name: Cecere
  given name: Jacopo G.
author list: Agent
  family name: Rubolini
  given name: Diego
author list: Agent
  family name: Morganti
  given name: Michelangelo
doi: 10.7717/peerj.13979
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-06
copyright: ©2022 Cioccarelli et al.
attribution name: Cioccarelli et al.

Incidence rate, risk factors, and management of Bell’s palsy in the Qurayyat region of Saudi Arabia
type: item
type: AcademicArticle
description: 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 (…
format: application/pdf
format: text/html
creator: Fahad Alanazi
creator: Faizan Z. Kashoo
creator: Anas Alduhishy
creator: Mishal Aldaihan
creator: Fuzail Ahmad
creator: Ahmad Alanazi
subject: Neurology
subject: Rehabilitation
description: doi:10.7717/peerj.14076
publisher: PeerJ Inc.
rights: © 2022 Alanazi et al.
abstract: 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 (…
bibliographic citation: 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
date submitted: 2022-02-24
date accepted: 2022-08-27
issued: 2022-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alanazi
  given name: Fahad
author list: Agent
  family name: Kashoo
  given name: Faizan Z.
author list: Agent
  family name: Alduhishy
  given name: Anas
author list: Agent
  family name: Aldaihan
  given name: Mishal
author list: Agent
  family name: Ahmad
  given name: Fuzail
author list: Agent
  family name: Alanazi
  given name: Ahmad
doi: 10.7717/peerj.14076
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-06
copyright: ©2022 Alanazi et al.
attribution name: Alanazi et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359