PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Advances in the diagnosis of non-occlusive mesenteric ischemia and challenges in intra-abdominal sepsis patients: a narrative review
items: Association between Vitamin D receptor (VDR) gene polymorphisms and hypertensive disorders of pregnancy: a systematic review and meta-analysis
items: Pyrus calleryana extracts reduce germination of native grassland species, suggesting the potential for allelopathic effects during ecological invasion
items: Annual changes in biomass amount and feeding potential of shrubby rangelands in maquis formation
items: CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability
items: Characterization of the populations of upside-down jellyfish in Jardines de la Reina National Park, Cuba
items: Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera
items: East Timor as an important source of cashew (Anacardium occidentale L.) genetic diversity
items: Personality traits, rank attainment, and siring success throughout the lives of male chimpanzees of Gombe National Park
items: In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease

Advances in the diagnosis of non-occlusive mesenteric ischemia and challenges in intra-abdominal sepsis patients: a narrative review
type: item
type: AcademicArticle
description: Non-occlusive mesenteric ischemia (NOMI) is a type of acute mesenteric ischemia (AMI) with a high mortality rate mainly because of a delayed or misdiagnosis. Intra-abdominal sepsis is one of the risk factors for developing NOMI, and its presence makes early diagnosis much more difficult. An increase in routine abdominal surgeries carries a corresponding risk of abdominal infection, which is a complication that should not be overlooked. It is critical that physicians are aware of the possibility for intestinal necrosis in abdominal sepsis patients due to the poor survival rate of NOMI. This review aims to summarize advances in the diagnosis of NOMI, and focuses on the diagnostic challenges of mesenteric ischemia in patients with intra-abdominal sepsis.
format: application/pdf
format: text/html
creator: Zhou Chen
creator: Xiaosun Liu
creator: Chunhui Shou
creator: Weili Yang
creator: Jiren Yu
subject: Emergency and Critical Care
subject: Infectious Diseases
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.15307
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Non-occlusive mesenteric ischemia (NOMI) is a type of acute mesenteric ischemia (AMI) with a high mortality rate mainly because of a delayed or misdiagnosis. Intra-abdominal sepsis is one of the risk factors for developing NOMI, and its presence makes early diagnosis much more difficult. An increase in routine abdominal surgeries carries a corresponding risk of abdominal infection, which is a complication that should not be overlooked. It is critical that physicians are aware of the possibility for intestinal necrosis in abdominal sepsis patients due to the poor survival rate of NOMI. This review aims to summarize advances in the diagnosis of NOMI, and focuses on the diagnostic challenges of mesenteric ischemia in patients with intra-abdominal sepsis.
bibliographic citation: Chen et al. (2023) Advances in the diagnosis of non-occlusive mesenteric ischemia and challenges in intra-abdominal sepsis patients: a narrative review. PeerJ 11:e15307 https://doi.org/10.7717/peerj.15307
date submitted: 2022-12-27
date accepted: 2023-04-06
issued: 2023-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Zhou
author list: Agent
  family name: Liu
  given name: Xiaosun
author list: Agent
  family name: Shou
  given name: Chunhui
author list: Agent
  family name: Yang
  given name: Weili
author list: Agent
  family name: Yu
  given name: Jiren
doi: 10.7717/peerj.15307
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-26
copyright: © 2023 Chen et al.
attribution name: Chen et al.

Association between Vitamin D receptor (VDR) gene polymorphisms and hypertensive disorders of pregnancy: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Hypertensive disorders of pregnancy (HDP) are currently one of the major causes of pregnancy-related maternal and fetal morbidity and mortality worldwide. Recent studies provide evidence that maternal Vitamin D receptor (VDR) gene polymorphisms probably play a key role by affecting the biological function of vitamin D in some adverse pregnancy outcomes, while the relationship between the VDR gene polymorphisms and the risk of HDP remains controversial in current studies. This systematic review and meta-analysis aimed to comprehensively evaluate the association of the VDR gene polymorphisms with HDP susceptibility. Methods This meta-analysis follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement and a protocol has been registered in the PROSPERO (ID: CRD42022344383) before commencing this review. PubMed, Web of Science, Embase, and the Cochrane Library databases were searched until January 21, 2023. Case-control and cohort studies that reported the association of the VDR gene polymorphisms with HDP were included. The quality of the included studies was assessed using the Newcastle-Ottawa Scale (NOS) for non-randomized studies. The odds ratios (ORs) with corresponding 95% confidence intervals (CIs) of the five models (allele model, dominant model, recessive model, homozygous model, heterozygous model) were pooled respectively, and subgroup analysis was performed based on ethnicity. Results A total of ten studies were included. The VDR gene ApaI polymorphism was associated with HDP susceptibility in the dominant model (OR: 1.38; 95% CI [1.07–1.79]; P = 0.014) and the heterozygote model (OR: 1.48; 95% CI [1.12–1.95]; P = 0.006). In subgroup analysis, the heterozygote model (OR: 2.06; 95% CI [1.21–3.52]; P = 0.008) of the ApaI polymorphism was associated with HDP in Asians, but not in Caucasians. Conclusion The VDR gene ApaI polymorphism may be associated with HDP susceptibility. Insufficient evidence to support the e…
format: application/pdf
format: text/html
creator: Yicong Guo
creator: Yu Zhang
creator: Xiangling Tang
creator: Xionghao Liu
creator: Huilan Xu
subject: Cardiology
subject: Gynecology and Obstetrics
subject: Public Health
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.15181
publisher: PeerJ Inc.
rights: © 2023 Guo et al.
abstract: Background Hypertensive disorders of pregnancy (HDP) are currently one of the major causes of pregnancy-related maternal and fetal morbidity and mortality worldwide. Recent studies provide evidence that maternal Vitamin D receptor (VDR) gene polymorphisms probably play a key role by affecting the biological function of vitamin D in some adverse pregnancy outcomes, while the relationship between the VDR gene polymorphisms and the risk of HDP remains controversial in current studies. This systematic review and meta-analysis aimed to comprehensively evaluate the association of the VDR gene polymorphisms with HDP susceptibility. Methods This meta-analysis follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement and a protocol has been registered in the PROSPERO (ID: CRD42022344383) before commencing this review. PubMed, Web of Science, Embase, and the Cochrane Library databases were searched until January 21, 2023. Case-control and cohort studies that reported the association of the VDR gene polymorphisms with HDP were included. The quality of the included studies was assessed using the Newcastle-Ottawa Scale (NOS) for non-randomized studies. The odds ratios (ORs) with corresponding 95% confidence intervals (CIs) of the five models (allele model, dominant model, recessive model, homozygous model, heterozygous model) were pooled respectively, and subgroup analysis was performed based on ethnicity. Results A total of ten studies were included. The VDR gene ApaI polymorphism was associated with HDP susceptibility in the dominant model (OR: 1.38; 95% CI [1.07–1.79]; P = 0.014) and the heterozygote model (OR: 1.48; 95% CI [1.12–1.95]; P = 0.006). In subgroup analysis, the heterozygote model (OR: 2.06; 95% CI [1.21–3.52]; P = 0.008) of the ApaI polymorphism was associated with HDP in Asians, but not in Caucasians. Conclusion The VDR gene ApaI polymorphism may be associated with HDP susceptibility. Insufficient evidence to support the e…
bibliographic citation: Guo et al. (2023) Association between Vitamin D receptor (VDR) gene polymorphisms and hypertensive disorders of pregnancy: a systematic review and meta-analysis. PeerJ 11:e15181 https://doi.org/10.7717/peerj.15181
date submitted: 2022-12-27
date accepted: 2023-03-14
issued: 2023-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Yicong
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Tang
  given name: Xiangling
author list: Agent
  family name: Liu
  given name: Xionghao
author list: Agent
  family name: Xu
  given name: Huilan
doi: 10.7717/peerj.15181
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-25
copyright: ©2023 Guo et al.
attribution name: Guo et al.

Pyrus calleryana extracts reduce germination of native grassland species, suggesting the potential for allelopathic effects during ecological invasion
type: item
type: AcademicArticle
description: Invasive plant species’ success may be a result of allelopathy, or the release of secondary metabolites that are harmful for surrounding plant species. Allelopathy can be mediated through the abiotic environment by chemical sorption or transformation, so the substrate on which interactions occur can lead to differential outcomes in allelopathic potential. One aggressive invader, Pyrus calleryana, has become dominant in many ecosystems throughout Eastern US, and has reduced the abundance of native species where it invades. Thus, our goal was to identify if P. calleryana had allelopathic potential by testing the impact of leaf and flower leachate on gemination of six common grassland species (three grasses and three forbs) in either sterilized sand or field collected soils. Germination of five out of six tested species was reduced by P. calleryana leaf litter, with weaker impacts from flower leachate. This suggests that allelopathy is one mechanism driving the success of P. calleryana and that allelopathic effects may change with plant phenology. For instance, P. calleryana has late leaf senescence in the fall and copious blooming in the spring that may elongate the timeframe that allelopathic inhibition can occur. Further, germination was higher in sand than in soil, suggesting that the context of the abiotic environment can mediate this relationship. In our study, two grass species that could be overabundant in restored grasslands had higher germination rates in soil than sand and one was not altered by P. calleryana suggesting that this relationship could further promote the overabundance of grass species. Taken together, P. calleryana likely inhibits the germination of native species where it invades, but there is context dependency of this relationship with both soil chemistry and seasonality.
format: application/pdf
format: text/html
creator: Michaela J. Woods
creator: Jonathan T. Bauer
creator: Dena Schaeffer
creator: Ryan W. McEwan
subject: Ecology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.15189
publisher: PeerJ Inc.
rights: © 2023 Woods et al.
abstract: Invasive plant species’ success may be a result of allelopathy, or the release of secondary metabolites that are harmful for surrounding plant species. Allelopathy can be mediated through the abiotic environment by chemical sorption or transformation, so the substrate on which interactions occur can lead to differential outcomes in allelopathic potential. One aggressive invader, Pyrus calleryana, has become dominant in many ecosystems throughout Eastern US, and has reduced the abundance of native species where it invades. Thus, our goal was to identify if P. calleryana had allelopathic potential by testing the impact of leaf and flower leachate on gemination of six common grassland species (three grasses and three forbs) in either sterilized sand or field collected soils. Germination of five out of six tested species was reduced by P. calleryana leaf litter, with weaker impacts from flower leachate. This suggests that allelopathy is one mechanism driving the success of P. calleryana and that allelopathic effects may change with plant phenology. For instance, P. calleryana has late leaf senescence in the fall and copious blooming in the spring that may elongate the timeframe that allelopathic inhibition can occur. Further, germination was higher in sand than in soil, suggesting that the context of the abiotic environment can mediate this relationship. In our study, two grass species that could be overabundant in restored grasslands had higher germination rates in soil than sand and one was not altered by P. calleryana suggesting that this relationship could further promote the overabundance of grass species. Taken together, P. calleryana likely inhibits the germination of native species where it invades, but there is context dependency of this relationship with both soil chemistry and seasonality.
bibliographic citation: Woods et al. (2023) Pyrus calleryana extracts reduce germination of native grassland species, suggesting the potential for allelopathic effects during ecological invasion. PeerJ 11:e15189 https://doi.org/10.7717/peerj.15189
date submitted: 2022-12-09
date accepted: 2023-03-15
issued: 2023-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Woods
  given name: Michaela J.
author list: Agent
  family name: Bauer
  given name: Jonathan T.
author list: Agent
  family name: Schaeffer
  given name: Dena
author list: Agent
  family name: McEwan
  given name: Ryan W.
doi: 10.7717/peerj.15189
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-25
copyright: ©2023 Woods et al.
attribution name: Woods et al.

Annual changes in biomass amount and feeding potential of shrubby rangelands in maquis formation
type: item
type: AcademicArticle
description: Background This study evaluated the extent to which the endemic herbaceous and woody species of shrubby rangelands met the roughage needs of grazing animals throughout the year. Methods The biomass, botanical composition, and quality of hay were investigated in the shrubby rangelands in Paşaköy of the Ayvacık districts in Çanakkale over the course of a year. Plant samples were taken from the herbaceous species monthly and from the grazing parts of the shrubs in May and November. Results The total amount of biomass (hay + shrub) in the rangeland was found to be 30.448 kg/ha. Shrubs made up 18.78% of the rangeland, while the annual species comprised 54.96%, and perennial herbs covered 26.26% of the total biomass. Crude protein (CP) ratios of herbaceous species decreased continuously from March (13.58%) to September (6.73%), and then increased. A similar change was also seen in pure ash (PA) ratios. The CP ratios in the shrub species were high in spring and decreased in autumn and there was an irregular variation in PA rates. Oak had the highest PA ratio during the spring, while thuja had the highest ratio in autumn, and Juniperus oxycedrus during the winter months. In herbaceous species, cell wall components (NDF, ADF, and ADL) reached their highest levels in summer and decreased in spring and winter. However, in shrubs, these components varied according to the species and were generally lowest in spring and then increased in autumn and winter. Here, it was determined that year-round grazing is a suitable grazing system in the shrubby rangelands of the Mediterranean zone, and animals are able to find fresh forage in the rangelands due to the presence of shrubs. However, since the contribution of shrubs to the total forage production is low, additional roughage should be provided, except in the spring when the production and quality of hay increase. These practices may contribute to better livestock management.
format: application/pdf
format: text/html
creator: Fırat Alatürk
creator: Hülya Hanoğlu Oral
creator: Ahmet Gökkuş
creator: Baboo Ali
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.15204
publisher: PeerJ Inc.
rights: © 2023 Alatürk et al.
abstract: Background This study evaluated the extent to which the endemic herbaceous and woody species of shrubby rangelands met the roughage needs of grazing animals throughout the year. Methods The biomass, botanical composition, and quality of hay were investigated in the shrubby rangelands in Paşaköy of the Ayvacık districts in Çanakkale over the course of a year. Plant samples were taken from the herbaceous species monthly and from the grazing parts of the shrubs in May and November. Results The total amount of biomass (hay + shrub) in the rangeland was found to be 30.448 kg/ha. Shrubs made up 18.78% of the rangeland, while the annual species comprised 54.96%, and perennial herbs covered 26.26% of the total biomass. Crude protein (CP) ratios of herbaceous species decreased continuously from March (13.58%) to September (6.73%), and then increased. A similar change was also seen in pure ash (PA) ratios. The CP ratios in the shrub species were high in spring and decreased in autumn and there was an irregular variation in PA rates. Oak had the highest PA ratio during the spring, while thuja had the highest ratio in autumn, and Juniperus oxycedrus during the winter months. In herbaceous species, cell wall components (NDF, ADF, and ADL) reached their highest levels in summer and decreased in spring and winter. However, in shrubs, these components varied according to the species and were generally lowest in spring and then increased in autumn and winter. Here, it was determined that year-round grazing is a suitable grazing system in the shrubby rangelands of the Mediterranean zone, and animals are able to find fresh forage in the rangelands due to the presence of shrubs. However, since the contribution of shrubs to the total forage production is low, additional roughage should be provided, except in the spring when the production and quality of hay increase. These practices may contribute to better livestock management.
bibliographic citation: Alatürk et al. (2023) Annual changes in biomass amount and feeding potential of shrubby rangelands in maquis formation. PeerJ 11:e15204 https://doi.org/10.7717/peerj.15204
date submitted: 2022-09-08
date accepted: 2023-03-17
issued: 2023-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alatürk
  given name: Fırat
author list: Agent
  family name: Hanoğlu Oral
  given name: Hülya
author list: Agent
  family name: Gökkuş
  given name: Ahmet
author list: Agent
  family name: Ali
  given name: Baboo
doi: 10.7717/peerj.15204
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-25
copyright: ©2023 Alatürk et al.
attribution name: Alatürk et al.

CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability
type: item
type: AcademicArticle
description: Genomic instability is an important hallmark of cancer and more recently has been identified in others like neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by measuring structural and numerical chromosomal alterations. There have been multiple chromosomal instability scores developed across many studies in the literature; however, these scores have not been compared because of the lack of a single tool available to calculate and facilitate these various metrics. Here, we provide an R package CINmetrics, that calculates six different chromosomal instability scores and allows direct comparison between them. We also demonstrate how these scores differ by applying CINmetrics to breast cancer data from The Cancer Genome Atlas (TCGA). The package is available on CRAN at https://cran.rproject.org/package=CINmetrics and on GitHub at https://github.com/lasseignelab/CINmetrics.
format: application/pdf
format: text/html
creator: Vishal H. Oza
creator: Jennifer L. Fisher
creator: Roshan Darji
creator: Brittany N. Lasseigne
subject: Computational Biology
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.15244
publisher: PeerJ Inc.
rights: © 2023 Oza et al.
abstract: Genomic instability is an important hallmark of cancer and more recently has been identified in others like neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by measuring structural and numerical chromosomal alterations. There have been multiple chromosomal instability scores developed across many studies in the literature; however, these scores have not been compared because of the lack of a single tool available to calculate and facilitate these various metrics. Here, we provide an R package CINmetrics, that calculates six different chromosomal instability scores and allows direct comparison between them. We also demonstrate how these scores differ by applying CINmetrics to breast cancer data from The Cancer Genome Atlas (TCGA). The package is available on CRAN at https://cran.rproject.org/package=CINmetrics and on GitHub at https://github.com/lasseignelab/CINmetrics.
bibliographic citation: Oza et al. (2023) CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability. PeerJ 11:e15244 https://doi.org/10.7717/peerj.15244
date submitted: 2022-11-11
date accepted: 2023-03-28
issued: 2023-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oza
  given name: Vishal H.
author list: Agent
  family name: Fisher
  given name: Jennifer L.
author list: Agent
  family name: Darji
  given name: Roshan
author list: Agent
  family name: Lasseigne
  given name: Brittany N.
doi: 10.7717/peerj.15244
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-25
copyright: ©2023 Oza et al.
attribution name: Oza et al.

Characterization of the populations of upside-down jellyfish in Jardines de la Reina National Park, Cuba
type: item
type: AcademicArticle
description: Upside-down jellyfish are a group of benthic scyphozoans belonging to the genus Cassiopea, whose members are in symbiosis with dinoflagellates and inhabit tropical and subtropical waters. Although there are some studies of the genus in the Caribbean, these are limited. In Cuba, the group’s studies are restricted to reports on taxonomic lists and, as far as we know, no one has performed any analyzes of the densities of these jellyfish in seagrass or mangrove ecosystems in Cuba. In this work, the populations of Cassiopea spp. in Jardines de la Reina National Park (JRNP) were characterized, for the first time for this Marine Protected Area and Cuba. One hundred 1m2 square frames were placed at 14 JRNP sites. For each site, the species, density, size of the individuals and abiotic factors were determined. Density and diameter comparisons were made between sites, zones and regions within the JRNP. The percentage of the benthic cover was determined and a correlation was made between density and diameter. A total of 10,803 individuals were recorded, of which 7,618 belong to Cassiopea xamachana and 3,185 belong to Cassiopea frondosa. Both species share a niche and no evident segregation was detected according to abiotic variables. Significant differences were detected in comparisons of density and size across sites and zones. Density and size in the JRNP were negatively correlated, and higher aggregations of the species were observed at lower sizes. Density mean values ranged from 2.18 to 14.52 ind. /m2 with maximum values of 79 ind. /m2. Cayo Alcatraz was the site found to have the highest density while Cachiboca was the site with the lowest density. The average bell diameter size of the individuals ranged from 9.34 to 15.31 cm for the sampled sites, with minimum and maximum values of 2.5 cm and 32.6 cm. The smallest size was recorded at Cayo Alcatraz while the largest size was reported for Boca de las Anclitas. The environmental factors evaluated showed no significant rel…
format: application/pdf
format: text/html
creator: Ramón Damián Morejón-Arrojo
creator: Leandro Rodriguez-Viera
subject: Marine Biology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.15254
publisher: PeerJ Inc.
rights: © 2023 Morejón-Arrojo et al.
abstract: Upside-down jellyfish are a group of benthic scyphozoans belonging to the genus Cassiopea, whose members are in symbiosis with dinoflagellates and inhabit tropical and subtropical waters. Although there are some studies of the genus in the Caribbean, these are limited. In Cuba, the group’s studies are restricted to reports on taxonomic lists and, as far as we know, no one has performed any analyzes of the densities of these jellyfish in seagrass or mangrove ecosystems in Cuba. In this work, the populations of Cassiopea spp. in Jardines de la Reina National Park (JRNP) were characterized, for the first time for this Marine Protected Area and Cuba. One hundred 1m2 square frames were placed at 14 JRNP sites. For each site, the species, density, size of the individuals and abiotic factors were determined. Density and diameter comparisons were made between sites, zones and regions within the JRNP. The percentage of the benthic cover was determined and a correlation was made between density and diameter. A total of 10,803 individuals were recorded, of which 7,618 belong to Cassiopea xamachana and 3,185 belong to Cassiopea frondosa. Both species share a niche and no evident segregation was detected according to abiotic variables. Significant differences were detected in comparisons of density and size across sites and zones. Density and size in the JRNP were negatively correlated, and higher aggregations of the species were observed at lower sizes. Density mean values ranged from 2.18 to 14.52 ind. /m2 with maximum values of 79 ind. /m2. Cayo Alcatraz was the site found to have the highest density while Cachiboca was the site with the lowest density. The average bell diameter size of the individuals ranged from 9.34 to 15.31 cm for the sampled sites, with minimum and maximum values of 2.5 cm and 32.6 cm. The smallest size was recorded at Cayo Alcatraz while the largest size was reported for Boca de las Anclitas. The environmental factors evaluated showed no significant rel…
bibliographic citation: Morejón-Arrojo et al. (2023) Characterization of the populations of upside-down jellyfish in Jardines de la Reina National Park, Cuba. PeerJ 11:e15254 https://doi.org/10.7717/peerj.15254
date submitted: 2023-01-11
date accepted: 2023-03-28
issued: 2023-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morejón-Arrojo
  given name: Ramón Damián
author list: Agent
  family name: Rodriguez-Viera
  given name: Leandro
doi: 10.7717/peerj.15254
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-25
copyright: ©2023 Morejón-Arrojo et al.
attribution name: Morejón-Arrojo et al.

Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera
type: item
type: AcademicArticle
description: Ribosomal intragenomic variability in prokaryotes and eukaryotes is a genomic feature commonly studied for its inflationary impact on molecular diversity assessments. However, the evolutionary mechanisms and distribution of this phenomenon within a microbial group are rarely explored. Here, we investigate the intragenomic variability in 33 species of planktonic foraminifera, calcifying marine protists, by inspecting 2,403 partial SSU sequences obtained from single-cell clone libraries. Our analyses show that polymorphisms are common among planktonic foraminifera species, but the number of polymorphic sites significantly differs among clades. With our molecular simulations, we could assess that most of these mutations are located in paired regions that do not affect the secondary structure of the SSU fragment. Finally, by mapping the number of polymorphic sites on the phylogeny of the clades, we were able to discuss the evolution and potential sources of intragenomic variability in planktonic foraminifera, linking this trait to the distinctive nuclear and genomic dynamics of this microbial group.
format: application/pdf
format: text/html
creator: Mattia Greco
creator: Raphaël Morard
creator: Kate Darling
creator: Michal Kucera
subject: Evolutionary Studies
subject: Genetics
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.15255
publisher: PeerJ Inc.
rights: © 2023 Greco et al.
abstract: Ribosomal intragenomic variability in prokaryotes and eukaryotes is a genomic feature commonly studied for its inflationary impact on molecular diversity assessments. However, the evolutionary mechanisms and distribution of this phenomenon within a microbial group are rarely explored. Here, we investigate the intragenomic variability in 33 species of planktonic foraminifera, calcifying marine protists, by inspecting 2,403 partial SSU sequences obtained from single-cell clone libraries. Our analyses show that polymorphisms are common among planktonic foraminifera species, but the number of polymorphic sites significantly differs among clades. With our molecular simulations, we could assess that most of these mutations are located in paired regions that do not affect the secondary structure of the SSU fragment. Finally, by mapping the number of polymorphic sites on the phylogeny of the clades, we were able to discuss the evolution and potential sources of intragenomic variability in planktonic foraminifera, linking this trait to the distinctive nuclear and genomic dynamics of this microbial group.
bibliographic citation: Greco et al. (2023) Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera. PeerJ 11:e15255 https://doi.org/10.7717/peerj.15255
date submitted: 2022-10-24
date accepted: 2023-03-28
issued: 2023-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Greco
  given name: Mattia
author list: Agent
  family name: Morard
  given name: Raphaël
author list: Agent
  family name: Darling
  given name: Kate
author list: Agent
  family name: Kucera
  given name: Michal
doi: 10.7717/peerj.15255
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-25
copyright: © 2023 Greco et al.
attribution name: Greco et al.

East Timor as an important source of cashew (Anacardium occidentale L.) genetic diversity
type: item
type: AcademicArticle
description: Background Cashew (Anacardium occidentale L.) is a crop currently grown in several tropical countries because of the economic importance of cashew nuts. Despite its enormous economic worth, limited research has been conducted on the molecular diversity of cashew genetic resources. In this study, a wide comprehensive assessment of the genetic diversity of cashew trees in East Timor was performed using microsatellites (SSRs) to evaluate intraspecific diversity and population structuring. Methods A total of 207 individual cashew trees, including trees from East Timor (11), and outgroup populations from Indonesia (one) and Mozambique (two), were analyzed with 16 cashew-specific SSRs. A comprehensive sampling of cashew trees within East Timor was performed, covering the distribution of cashew orchards in the country. Genetic diversity indices were calculated, and population structuring was determined using three different approaches: genetic distances (UPGMA and NJ), AMOVA, and individual-based clustering methods through Bayesian (STRUCTURE) and multivariate (DAPC) analyses. Results The population structuring analysis revealed that the genetic diversity of cashew populations in East Timor was higher in this study than previously reported for cashew trees. A higher allelic richness was found within cashew populations in East Timor compared with the outgroup populations (Mozambique and Indonesia), reinforced by the presence of private alleles. Moreover, our study showed that cashew populations in East Timor are grouped into two dissimilar genetic groups, which may suggest multiple cashew introductions over time. These new cashew genetic resources could be explored for future crop improvement. Conclusions Crop diversity underpins the productivity, resilience, and adaptive capacity of agriculture. Therefore, this study provides useful information regarding genetic diversity and population structure that can be harnessed to improve cashew production in East Timor. This data i…
format: application/pdf
format: text/html
creator: Lara Guterres
creator: João Barnabé
creator: André Barros
creator: Alberto Bento Charrua
creator: Maria Cristina Duarte
creator: Maria M. Romeiras
creator: Filipa Monteiro
subject: Agricultural Science
subject: Genetics
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.14894
publisher: PeerJ Inc.
rights: © 2023 Guterres et al.
abstract: Background Cashew (Anacardium occidentale L.) is a crop currently grown in several tropical countries because of the economic importance of cashew nuts. Despite its enormous economic worth, limited research has been conducted on the molecular diversity of cashew genetic resources. In this study, a wide comprehensive assessment of the genetic diversity of cashew trees in East Timor was performed using microsatellites (SSRs) to evaluate intraspecific diversity and population structuring. Methods A total of 207 individual cashew trees, including trees from East Timor (11), and outgroup populations from Indonesia (one) and Mozambique (two), were analyzed with 16 cashew-specific SSRs. A comprehensive sampling of cashew trees within East Timor was performed, covering the distribution of cashew orchards in the country. Genetic diversity indices were calculated, and population structuring was determined using three different approaches: genetic distances (UPGMA and NJ), AMOVA, and individual-based clustering methods through Bayesian (STRUCTURE) and multivariate (DAPC) analyses. Results The population structuring analysis revealed that the genetic diversity of cashew populations in East Timor was higher in this study than previously reported for cashew trees. A higher allelic richness was found within cashew populations in East Timor compared with the outgroup populations (Mozambique and Indonesia), reinforced by the presence of private alleles. Moreover, our study showed that cashew populations in East Timor are grouped into two dissimilar genetic groups, which may suggest multiple cashew introductions over time. These new cashew genetic resources could be explored for future crop improvement. Conclusions Crop diversity underpins the productivity, resilience, and adaptive capacity of agriculture. Therefore, this study provides useful information regarding genetic diversity and population structure that can be harnessed to improve cashew production in East Timor. This data i…
bibliographic citation: Guterres et al. (2023) East Timor as an important source of cashew (Anacardium occidentale L.) genetic diversity. PeerJ 11:e14894 https://doi.org/10.7717/peerj.14894
date submitted: 2022-04-28
date accepted: 2023-01-24
issued: 2023-04-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guterres
  given name: Lara
author list: Agent
  family name: Barnabé
  given name: João
author list: Agent
  family name: Barros
  given name: André
author list: Agent
  family name: Charrua
  given name: Alberto Bento
author list: Agent
  family name: Duarte
  given name: Maria Cristina
author list: Agent
  family name: Romeiras
  given name: Maria M.
author list: Agent
  family name: Monteiro
  given name: Filipa
doi: 10.7717/peerj.14894
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-24
copyright: ©2023 Guterres et al.
attribution name: Guterres et al.

Personality traits, rank attainment, and siring success throughout the lives of male chimpanzees of Gombe National Park
type: item
type: AcademicArticle
description: Personality traits in many taxa correlate with fitness. Several models have been developed to try to explain how variation in these traits is maintained. One model proposes that variation persists because it is linked to trade-offs between current and future adaptive benefits. Tests of this model’s predictions, however, are scant in long-lived species. To test this model, we studied male chimpanzees living in Gombe National Park, Tanzania. We operationalized six personality traits using ratings on 19 items. We used 37 years of behavioral and genetic data to assemble (1) daily rank scores generated from submissive vocalizations and (2) records of male siring success. We tested whether the association between two personality traits, Dominance and Conscientiousness, and either rank or reproductive success, varied over the life course. Higher Dominance and lower Conscientiousness were associated with higher rank, but the size and direction of these relationships did not vary over the life course. In addition, independent of rank at the time of siring, higher Dominance and lower Conscientiousness were related to higher siring success. Again, the size and direction of these relationships did not vary over the life course. The trade-off model, therefore, may not hold in long-lived and/or slowly reproducing species. These findings also demonstrate that ratings are a valid way to measure animal personality; they are related to rank and reproductive success. These traits could therefore be used to test alternative models, including one that posits that personality variation is maintained by environmental heterogeneity, in studies of multiple chimpanzee communities.
format: application/pdf
format: text/html
creator: Alexander Weiss
creator: Joseph T. Feldblum
creator: Drew M. Altschul
creator: David Anthony Collins
creator: Shadrack Kamenya
creator: Deus Mjungu
creator: Steffen Foerster
creator: Ian C. Gilby
creator: Michael L. Wilson
creator: Anne E. Pusey
subject: Animal Behavior
subject: Anthropology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.15083
publisher: PeerJ Inc.
rights: © 2023 Weiss et al.
abstract: Personality traits in many taxa correlate with fitness. Several models have been developed to try to explain how variation in these traits is maintained. One model proposes that variation persists because it is linked to trade-offs between current and future adaptive benefits. Tests of this model’s predictions, however, are scant in long-lived species. To test this model, we studied male chimpanzees living in Gombe National Park, Tanzania. We operationalized six personality traits using ratings on 19 items. We used 37 years of behavioral and genetic data to assemble (1) daily rank scores generated from submissive vocalizations and (2) records of male siring success. We tested whether the association between two personality traits, Dominance and Conscientiousness, and either rank or reproductive success, varied over the life course. Higher Dominance and lower Conscientiousness were associated with higher rank, but the size and direction of these relationships did not vary over the life course. In addition, independent of rank at the time of siring, higher Dominance and lower Conscientiousness were related to higher siring success. Again, the size and direction of these relationships did not vary over the life course. The trade-off model, therefore, may not hold in long-lived and/or slowly reproducing species. These findings also demonstrate that ratings are a valid way to measure animal personality; they are related to rank and reproductive success. These traits could therefore be used to test alternative models, including one that posits that personality variation is maintained by environmental heterogeneity, in studies of multiple chimpanzee communities.
bibliographic citation: Weiss et al. (2023) Personality traits, rank attainment, and siring success throughout the lives of male chimpanzees of Gombe National Park. PeerJ 11:e15083 https://doi.org/10.7717/peerj.15083
date submitted: 2022-05-09
date accepted: 2023-02-25
issued: 2023-04-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weiss
  given name: Alexander
author list: Agent
  family name: Feldblum
  given name: Joseph T.
author list: Agent
  family name: Altschul
  given name: Drew M.
author list: Agent
  family name: Collins
  given name: David Anthony
author list: Agent
  family name: Kamenya
  given name: Shadrack
author list: Agent
  family name: Mjungu
  given name: Deus
author list: Agent
  family name: Foerster
  given name: Steffen
author list: Agent
  family name: Gilby
  given name: Ian C.
author list: Agent
  family name: Wilson
  given name: Michael L.
author list: Agent
  family name: Pusey
  given name: Anne E.
doi: 10.7717/peerj.15083
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-24
copyright: ©2023 Weiss et al.
attribution name: Weiss et al.

In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease
type: item
type: AcademicArticle
description: Yellow head virus (YHV) is one of the most important pathogens in prawn cultivation. The outbreak of YHV could potentially result in collapses in aquaculture industries. Although a flurry of development has been made in searching for preventive and therapeutic approaches against YHV, there is still no effective therapy available in the market. Previously, computational screening has suggested a few cancer drugs to be used as YHV protease (3CLpro) inhibitors. However, their toxic nature is still of concern. Here, we exploited various computational approaches, such as deep learning-based structural modeling, molecular docking, pharmacological prediction, and molecular dynamics simulation, to search for potential YHV 3CLpro inhibitors. A total of 272 chalcones and flavonoids were in silico screened using molecular docking. The bioavailability, toxicity, and specifically drug-likeness of hits were predicted. Among the hits, molecular dynamics simulation and trajectory analysis were performed to scrutinize the compounds with high binding affinity. Herein, the four selected compounds including chalcones cpd26, cpd31 and cpd50, and a flavonoid DN071_f could be novel potent compounds to prevent YHV and GAV propagation in shrimp. The molecular mechanism at the atomistic level is also enclosed that can be used to further antiviral development.
format: application/pdf
format: text/html
creator: Kanpong Boonthaworn
creator: Kowit Hengphasatporn
creator: Yasuteru Shigeta
creator: Warinthorn Chavasiri
creator: Thanyada Rungrotmongkol
creator: Puey Ounjai
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Computational Biology
subject: Virology
description: doi:10.7717/peerj.15086
publisher: PeerJ Inc.
rights: © 2023 Boonthaworn et al.
abstract: Yellow head virus (YHV) is one of the most important pathogens in prawn cultivation. The outbreak of YHV could potentially result in collapses in aquaculture industries. Although a flurry of development has been made in searching for preventive and therapeutic approaches against YHV, there is still no effective therapy available in the market. Previously, computational screening has suggested a few cancer drugs to be used as YHV protease (3CLpro) inhibitors. However, their toxic nature is still of concern. Here, we exploited various computational approaches, such as deep learning-based structural modeling, molecular docking, pharmacological prediction, and molecular dynamics simulation, to search for potential YHV 3CLpro inhibitors. A total of 272 chalcones and flavonoids were in silico screened using molecular docking. The bioavailability, toxicity, and specifically drug-likeness of hits were predicted. Among the hits, molecular dynamics simulation and trajectory analysis were performed to scrutinize the compounds with high binding affinity. Herein, the four selected compounds including chalcones cpd26, cpd31 and cpd50, and a flavonoid DN071_f could be novel potent compounds to prevent YHV and GAV propagation in shrimp. The molecular mechanism at the atomistic level is also enclosed that can be used to further antiviral development.
bibliographic citation: Boonthaworn et al. (2023) In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease. PeerJ 11:e15086 https://doi.org/10.7717/peerj.15086
date submitted: 2022-09-06
date accepted: 2023-02-26
issued: 2023-04-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boonthaworn
  given name: Kanpong
author list: Agent
  family name: Hengphasatporn
  given name: Kowit
author list: Agent
  family name: Shigeta
  given name: Yasuteru
author list: Agent
  family name: Chavasiri
  given name: Warinthorn
author list: Agent
  family name: Rungrotmongkol
  given name: Thanyada
author list: Agent
  family name: Ounjai
  given name: Puey
doi: 10.7717/peerj.15086
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-04-24
copyright: ©2023 Boonthaworn et al.
attribution name: Boonthaworn et al.

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