PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of aerobic exercise on event-related potentials related to cognitive performance: a systematic review
items: Food taboos during pregnancy: meta-analysis on cross cultural differences suggests specific, diet-related pressures on childbirth among agriculturalists
items: An impact assessment of insecticides application on the non-targeted mosquito Aedes albopictus (Skuse) in Punjab rice fields, Pakistan
items: Niche diversification of Mediterranean and southwestern Asian tortoises
items: TBX3 regulates the transcription of VEGFA to promote osteoblasts proliferation and microvascular regeneration
items: Wide space sowing achieved high productivity and effective nitrogen use of irrigated wheat in South Shanxi, China
items: Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México
items: Identification and subcellular localization analysis of membrane protein Ycf 1 in the microsporidian Nosema bombycis
items: Ecological restoration stimulates environmental outcomes but exacerbates water shortage in the Loess Plateau
items: Evaluating pharmacists’ knowledge, attitude, and practices toward amiodarone cross-reactivity with iodine: a cross-sectional pilot study

Effects of aerobic exercise on event-related potentials related to cognitive performance: a systematic review
type: item
type: AcademicArticle
description: Introduction Aerobic exercise interventions may affect different cognitive domains such as attention, working memory, inhibition, etc. However, the neural mechanisms underlying this relationship, remains uncertain. Objective To perform a systematic review on exercise intervention studies that use event-related potentials (ERPs) as outcome for cognitive performance. Methods We identified studies through searches in four databases reporting the effects of either an acute bout or chronic exercise on any ERP associated with cognitive performance. Study population included participants >17 years of age with or without a diagnosis. Results A total of 5,797 records were initially identified through database searching of which 52 were eligible for inclusion. Most studies were of acute aerobic exercise with moderate intensity. Results were heterogenious across studies, but there was a trend that ERP amplitude increased and (to a lesser extent) latencies decreased post-exercise. The P3 ERP was the most often reported ERP. Conclusion Heterogeneity across studies regarding methodology limited the possibility to draw definitive conclusions but the most consistent findings were that acute aerobic exercise was associated with higher amplitudes, and to a lesser extent shorter latencies, of ERPs.
format: application/pdf
format: text/html
creator: Julia Gusatovic
creator: Mathias Holsey Gramkow
creator: Steen Gregers Hasselbalch
creator: Kristian Steen Frederiksen
subject: Biophysics
subject: Neuroscience
subject: Kinesiology
description: doi:10.7717/peerj.13604
publisher: PeerJ Inc.
rights: © 2022 Gusatovic et al.
abstract: Introduction Aerobic exercise interventions may affect different cognitive domains such as attention, working memory, inhibition, etc. However, the neural mechanisms underlying this relationship, remains uncertain. Objective To perform a systematic review on exercise intervention studies that use event-related potentials (ERPs) as outcome for cognitive performance. Methods We identified studies through searches in four databases reporting the effects of either an acute bout or chronic exercise on any ERP associated with cognitive performance. Study population included participants >17 years of age with or without a diagnosis. Results A total of 5,797 records were initially identified through database searching of which 52 were eligible for inclusion. Most studies were of acute aerobic exercise with moderate intensity. Results were heterogenious across studies, but there was a trend that ERP amplitude increased and (to a lesser extent) latencies decreased post-exercise. The P3 ERP was the most often reported ERP. Conclusion Heterogeneity across studies regarding methodology limited the possibility to draw definitive conclusions but the most consistent findings were that acute aerobic exercise was associated with higher amplitudes, and to a lesser extent shorter latencies, of ERPs.
bibliographic citation: Gusatovic et al. (2022) Effects of aerobic exercise on event-related potentials related to cognitive performance: a systematic review. PeerJ 10:e13604 https://doi.org/10.7717/peerj.13604
date submitted: 2022-03-04
date accepted: 2022-05-26
issued: 2022-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gusatovic
  given name: Julia
author list: Agent
  family name: Gramkow
  given name: Mathias Holsey
author list: Agent
  family name: Hasselbalch
  given name: Steen Gregers
author list: Agent
  family name: Frederiksen
  given name: Kristian Steen
doi: 10.7717/peerj.13604
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-11
copyright: ©2022 Gusatovic et al.
attribution name: Gusatovic et al.

Food taboos during pregnancy: meta-analysis on cross cultural differences suggests specific, diet-related pressures on childbirth among agriculturalists
type: item
type: AcademicArticle
description: Pregnancy is the most delicate stage of human life history as well as a common target of food taboos across cultures. Despite puzzling evidence that many pregnant women across the world reduce their intake of nutritious foods to accomplish cultural norms, no study has provided statistical analysis of cross-cultural variation in food taboos during pregnancy. Moreover, antenatal practices among forager and agriculturalists have never been compared, despite subsistence mode being known to affect staple foods and lifestyle directly. This gap hinders to us from understanding the overall threats attributed to pregnancy, and their perceived nutritional causes around the world. The present study constitutes the first cross-cultural meta-analysis on food taboos during pregnancy. We examined thirty-two articles on dietary antenatal restrictions among agricultural and non-agricultural societies, in order to: (i) identify cross-culturally targeted animal, plant and miscellaneous foods; (ii) define major clusters of taboo focus; (iii) test the hypothesis that food types and clusters of focus distribute differently between agricultural and non-agricultural taboos; and (iv) test the hypothesis that food types distribute differently across the clusters of taboo focus. All data were analysed in SPSS and RStudio using chi-squared tests and Fisher’s exact tests. We detected a gradient in taboo focus that ranged from no direct physiological interest to the fear of varied physiological complications to a very specific concern over increased birth weight and difficult delivery. Non-agricultural taboos were more likely to target non-domesticated animal foods and to be justified by concerns not directly linked to the physiological sphere, whereas agricultural taboos tended to targed more cultivated and processed products and showed a stronger association with concerns over increased birth weight. Despite some methodological discrepancies in the existing literature on food taboos during pre…
format: application/pdf
format: text/html
creator: Ornella Maggiulli
creator: Fabrizio Rufo
creator: Sarah E. Johns
creator: Jonathan C.K. Wells
subject: Anthropology
subject: Evolutionary Studies
subject: Global Health
subject: Gynecology and Obstetrics
subject: Nutrition
description: doi:10.7717/peerj.13633
publisher: PeerJ Inc.
rights: © 2022 Maggiulli et al.
abstract: Pregnancy is the most delicate stage of human life history as well as a common target of food taboos across cultures. Despite puzzling evidence that many pregnant women across the world reduce their intake of nutritious foods to accomplish cultural norms, no study has provided statistical analysis of cross-cultural variation in food taboos during pregnancy. Moreover, antenatal practices among forager and agriculturalists have never been compared, despite subsistence mode being known to affect staple foods and lifestyle directly. This gap hinders to us from understanding the overall threats attributed to pregnancy, and their perceived nutritional causes around the world. The present study constitutes the first cross-cultural meta-analysis on food taboos during pregnancy. We examined thirty-two articles on dietary antenatal restrictions among agricultural and non-agricultural societies, in order to: (i) identify cross-culturally targeted animal, plant and miscellaneous foods; (ii) define major clusters of taboo focus; (iii) test the hypothesis that food types and clusters of focus distribute differently between agricultural and non-agricultural taboos; and (iv) test the hypothesis that food types distribute differently across the clusters of taboo focus. All data were analysed in SPSS and RStudio using chi-squared tests and Fisher’s exact tests. We detected a gradient in taboo focus that ranged from no direct physiological interest to the fear of varied physiological complications to a very specific concern over increased birth weight and difficult delivery. Non-agricultural taboos were more likely to target non-domesticated animal foods and to be justified by concerns not directly linked to the physiological sphere, whereas agricultural taboos tended to targed more cultivated and processed products and showed a stronger association with concerns over increased birth weight. Despite some methodological discrepancies in the existing literature on food taboos during pre…
bibliographic citation: Maggiulli et al. (2022) Food taboos during pregnancy: meta-analysis on cross cultural differences suggests specific, diet-related pressures on childbirth among agriculturalists. PeerJ 10:e13633 https://doi.org/10.7717/peerj.13633
date submitted: 2021-12-23
date accepted: 2022-06-03
issued: 2022-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maggiulli
  given name: Ornella
author list: Agent
  family name: Rufo
  given name: Fabrizio
author list: Agent
  family name: Johns
  given name: Sarah E.
author list: Agent
  family name: Wells
  given name: Jonathan C.K.
doi: 10.7717/peerj.13633
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-11
copyright: ©2022 Maggiulli et al.
attribution name: Maggiulli et al.

An impact assessment of insecticides application on the non-targeted mosquito Aedes albopictus (Skuse) in Punjab rice fields, Pakistan
type: item
type: AcademicArticle
description: Insecticidal control of insect pests of rice crop may influence the environment and nontarget species in rice fields. Aedes albopictus, one of the most common nontarget species present in rice fields, received lethal and sublethal exposures to insecticides used in rice cultivated fields. The present work explores the effects of insecticides in six non-targeted Ae. albopictus strains collected from rice fields with a history of insecticidal usage in comparison with a laboratory susceptible reference strain (REF) and a strain (LHR) collected from a rice field with no, or minimal, history of insecticidal usage. Two types of effects, the resistance development and performance of biological traits, were studied by selecting seven commonly used insecticides in rice fields in Punjab, Pakistan. The results revealed that the strains collected from the rice fields with histories of insecticidal usage exhibited significant levels of resistance to flonicamid, chlorantraniliprole, gamma-cyhalothrin, fipronil, monomehypo, triazophos, and carbofuran, when compared with REF and LHR strains. In addition, Ae. albopictus strains revealed a significantly weaker performance of biological traits (rate of pupae formation, survival of male and female adults (except females of OKR and MTN strains), and ovipositing females) than those of the REF and LHR strains. However, the fecundity of all field strains was only significantly different with that of the REF strain. In conclusion, the results highlight the problem of the negative effects of insecticidal usage in rice fields on nontarget species present in the same environment, and emphasize the need to adopt pest management activities that are safe for the environment.
format: application/pdf
format: text/html
creator: Hafiz Azhar Ali Khan
subject: Agricultural Science
subject: Ecology
subject: Entomology
subject: Zoology
subject: Ecotoxicology
description: doi:10.7717/peerj.13697
publisher: PeerJ Inc.
rights: © 2022 Khan
abstract: Insecticidal control of insect pests of rice crop may influence the environment and nontarget species in rice fields. Aedes albopictus, one of the most common nontarget species present in rice fields, received lethal and sublethal exposures to insecticides used in rice cultivated fields. The present work explores the effects of insecticides in six non-targeted Ae. albopictus strains collected from rice fields with a history of insecticidal usage in comparison with a laboratory susceptible reference strain (REF) and a strain (LHR) collected from a rice field with no, or minimal, history of insecticidal usage. Two types of effects, the resistance development and performance of biological traits, were studied by selecting seven commonly used insecticides in rice fields in Punjab, Pakistan. The results revealed that the strains collected from the rice fields with histories of insecticidal usage exhibited significant levels of resistance to flonicamid, chlorantraniliprole, gamma-cyhalothrin, fipronil, monomehypo, triazophos, and carbofuran, when compared with REF and LHR strains. In addition, Ae. albopictus strains revealed a significantly weaker performance of biological traits (rate of pupae formation, survival of male and female adults (except females of OKR and MTN strains), and ovipositing females) than those of the REF and LHR strains. However, the fecundity of all field strains was only significantly different with that of the REF strain. In conclusion, the results highlight the problem of the negative effects of insecticidal usage in rice fields on nontarget species present in the same environment, and emphasize the need to adopt pest management activities that are safe for the environment.
bibliographic citation: Khan (2022) An impact assessment of insecticides application on the non-targeted mosquito Aedes albopictus (Skuse) in Punjab rice fields, Pakistan. PeerJ 10:e13697 https://doi.org/10.7717/peerj.13697
date submitted: 2022-04-14
date accepted: 2022-06-17
issued: 2022-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khan
  given name: Hafiz Azhar Ali
doi: 10.7717/peerj.13697
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-11
copyright: © 2022 Khan
attribution name: Khan

Niche diversification of Mediterranean and southwestern Asian tortoises
type: item
type: AcademicArticle
description: Background Tortoises of the genus Testudo are widely distributed throughout the Mediterranean region and southwestern Asia. However, the evolutionary mechanisms of diversification in this genus are still poorly understood. Methods In this study, we assessed the evolutionary patterns in the climate niches of five species and 11 subspecies of the genus Testudo using ecological niche models and evaluated the niche overlap based on species phylogenetic distances. Results The ecological models indicated that most species differ in their climate niches, but show overlap, with gradual transitions at range boundaries. As expected, the ecological divergence among subspecies was lower than that among species. Evaluation of the phylogenetic signal indicated that climate niches have been weakly conserved, but sister species also show high evolutionary divergence.
format: application/pdf
format: text/html
creator: Daniel Escoriza
creator: Jihene Ben Hassine
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.13702
publisher: PeerJ Inc.
rights: © 2022 Escoriza and Ben Hassine
abstract: Background Tortoises of the genus Testudo are widely distributed throughout the Mediterranean region and southwestern Asia. However, the evolutionary mechanisms of diversification in this genus are still poorly understood. Methods In this study, we assessed the evolutionary patterns in the climate niches of five species and 11 subspecies of the genus Testudo using ecological niche models and evaluated the niche overlap based on species phylogenetic distances. Results The ecological models indicated that most species differ in their climate niches, but show overlap, with gradual transitions at range boundaries. As expected, the ecological divergence among subspecies was lower than that among species. Evaluation of the phylogenetic signal indicated that climate niches have been weakly conserved, but sister species also show high evolutionary divergence.
bibliographic citation: Escoriza et al. (2022) Niche diversification of Mediterranean and southwestern Asian tortoises. PeerJ 10:e13702 https://doi.org/10.7717/peerj.13702
date submitted: 2022-03-08
date accepted: 2022-06-17
issued: 2022-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Escoriza
  given name: Daniel
author list: Agent
  family name: Ben Hassine
  given name: Jihene
doi: 10.7717/peerj.13702
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-11
copyright: ©2022 Escoriza and Ben Hassine
attribution name: Escoriza and Ben Hassine

TBX3 regulates the transcription of VEGFA to promote osteoblasts proliferation and microvascular regeneration
type: item
type: AcademicArticle
description: Objective Osteochondral decellularization can promote local vascular regeneration, but the exact mechanism is unknown. The aim of this study is to study osteogenic microvascular regeneration in single cells. Methods The scRNA-seq dataset of human periosteal-derived cells (hPDCs) were analyzed by pySCENIC. To examine the role of TBX3 in osteogenesis and vascularization, cell transfection, qRT-PCR, western blot, and CCK-8 cell proliferation assays were performed. Results TCF7L2, TBX3, FLI1, NFKB2, and EZH2 were found to be transcription factors (TFs) most closely associated with corresponding cells. The regulatory network of these TFs was then visualized. Our study knocked down the expression of TBX3 in human osteoblast cell lines. In the TBX3 knockdown group, we observed decreased expression of VEGFA, VEGFB, and VEGFC. Moreover, Western blot analysis showed that downregulating TBX3 resulted in a reduction of VEGFA expression. And TBX3 stimulated osteoblast proliferation in CCK-8 assays. Conclusion TBX3 regulates VEGFA expression and promotes osteoblast proliferation in skeletal microvasculature formation. The findings provide a theoretical basis for investigating the role of TBX3 in promoting local vascular regeneration.
format: application/pdf
format: text/html
creator: Lichuang Wu
creator: Chenxian Su
creator: Chuanhua Yang
creator: Jinxing Liu
creator: Yiheng Ye
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Orthopedics
description: doi:10.7717/peerj.13722
publisher: PeerJ Inc.
rights: © 2022 Wu et al.
abstract: Objective Osteochondral decellularization can promote local vascular regeneration, but the exact mechanism is unknown. The aim of this study is to study osteogenic microvascular regeneration in single cells. Methods The scRNA-seq dataset of human periosteal-derived cells (hPDCs) were analyzed by pySCENIC. To examine the role of TBX3 in osteogenesis and vascularization, cell transfection, qRT-PCR, western blot, and CCK-8 cell proliferation assays were performed. Results TCF7L2, TBX3, FLI1, NFKB2, and EZH2 were found to be transcription factors (TFs) most closely associated with corresponding cells. The regulatory network of these TFs was then visualized. Our study knocked down the expression of TBX3 in human osteoblast cell lines. In the TBX3 knockdown group, we observed decreased expression of VEGFA, VEGFB, and VEGFC. Moreover, Western blot analysis showed that downregulating TBX3 resulted in a reduction of VEGFA expression. And TBX3 stimulated osteoblast proliferation in CCK-8 assays. Conclusion TBX3 regulates VEGFA expression and promotes osteoblast proliferation in skeletal microvasculature formation. The findings provide a theoretical basis for investigating the role of TBX3 in promoting local vascular regeneration.
bibliographic citation: Wu et al. (2022) TBX3 regulates the transcription of VEGFA to promote osteoblasts proliferation and microvascular regeneration. PeerJ 10:e13722 https://doi.org/10.7717/peerj.13722
date submitted: 2022-05-05
date accepted: 2022-06-22
issued: 2022-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Lichuang
author list: Agent
  family name: Su
  given name: Chenxian
author list: Agent
  family name: Yang
  given name: Chuanhua
author list: Agent
  family name: Liu
  given name: Jinxing
author list: Agent
  family name: Ye
  given name: Yiheng
doi: 10.7717/peerj.13722
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-11
copyright: ©2022 Wu et al.
attribution name: Wu et al.

Wide space sowing achieved high productivity and effective nitrogen use of irrigated wheat in South Shanxi, China
type: item
type: AcademicArticle
description: Wheat (Triticum aestivum L.) is a staple crop worldwide, and its yield has improved since the green revolution, which was attributed to chemical nitrogen (N) fertilizer application. However, regular N application decreases N use efficiency (NUE, the ratio of grain dry matter yield to N supply from soil and fertilizer). Various practices have been implemented to maintain high crop yield and improve NUE. Nowadays, the enhanced sowing method, i.e., wide space sowing (WS), has improved the productivity of wheat crops. However, how the sowing method and N application rate affect N use and yield productivity has not been fully elucidated. Field experiments with treatments using two sowing methods (WS, and drill sowing, DS) and four N application rates (0, 180, 240, and 300 kg ha−1, represented as N0, N180, N240, and N300, respectively) were conducted from 2017 to 2019. The results showed that grain yield under WS was 13.57–16.38% higher than that under DS. The yield advantage under WS was attributed to an increased ear number. Both the higher stem and productive stem percentage accounted for the increased ear number under WS. Higher total N quantity and larger leaf area index at anthesis under WS contributed to higher dry matter production, resulting in higher grain yield. Higher dry matter production was due to pre-anthesis dry weight and post-anthesis dry weight. The wheat crop under WS had a 12.44–15.00% higher NUE than that under DS. The increased NUE under WS was attributed to higher N uptake efficiency (the ratio of total N quantity at maturity to N supply from soil and fertilizer), which was the result of greater total N quantity. The higher total N quantity under WS was due to both higher pre-anthesis N uptake and post-anthesis N uptake. Remarkably, compared to DS with 240 kg N ha−1, WS with 180 kg N ha−1 had almost equal grain yield, dry matter, and total N quantity. Therefore, wheat crops under WS could achieve both high NUE and grain yield simultaneously with o…
format: application/pdf
format: text/html
creator: Qiang Wang
creator: Hafeez Noor
creator: Min Sun
creator: Aixia Ren
creator: Yu Feng
creator: Peng Qiao
creator: Jingjing Zhang
creator: Zhiqiang Gao
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.13727
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Wheat (Triticum aestivum L.) is a staple crop worldwide, and its yield has improved since the green revolution, which was attributed to chemical nitrogen (N) fertilizer application. However, regular N application decreases N use efficiency (NUE, the ratio of grain dry matter yield to N supply from soil and fertilizer). Various practices have been implemented to maintain high crop yield and improve NUE. Nowadays, the enhanced sowing method, i.e., wide space sowing (WS), has improved the productivity of wheat crops. However, how the sowing method and N application rate affect N use and yield productivity has not been fully elucidated. Field experiments with treatments using two sowing methods (WS, and drill sowing, DS) and four N application rates (0, 180, 240, and 300 kg ha−1, represented as N0, N180, N240, and N300, respectively) were conducted from 2017 to 2019. The results showed that grain yield under WS was 13.57–16.38% higher than that under DS. The yield advantage under WS was attributed to an increased ear number. Both the higher stem and productive stem percentage accounted for the increased ear number under WS. Higher total N quantity and larger leaf area index at anthesis under WS contributed to higher dry matter production, resulting in higher grain yield. Higher dry matter production was due to pre-anthesis dry weight and post-anthesis dry weight. The wheat crop under WS had a 12.44–15.00% higher NUE than that under DS. The increased NUE under WS was attributed to higher N uptake efficiency (the ratio of total N quantity at maturity to N supply from soil and fertilizer), which was the result of greater total N quantity. The higher total N quantity under WS was due to both higher pre-anthesis N uptake and post-anthesis N uptake. Remarkably, compared to DS with 240 kg N ha−1, WS with 180 kg N ha−1 had almost equal grain yield, dry matter, and total N quantity. Therefore, wheat crops under WS could achieve both high NUE and grain yield simultaneously with o…
bibliographic citation: Wang et al. (2022) Wide space sowing achieved high productivity and effective nitrogen use of irrigated wheat in South Shanxi, China. PeerJ 10:e13727 https://doi.org/10.7717/peerj.13727
date submitted: 2022-01-20
date accepted: 2022-06-22
issued: 2022-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Qiang
author list: Agent
  family name: Noor
  given name: Hafeez
author list: Agent
  family name: Sun
  given name: Min
author list: Agent
  family name: Ren
  given name: Aixia
author list: Agent
  family name: Feng
  given name: Yu
author list: Agent
  family name: Qiao
  given name: Peng
author list: Agent
  family name: Zhang
  given name: Jingjing
author list: Agent
  family name: Gao
  given name: Zhiqiang
doi: 10.7717/peerj.13727
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-11
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México
type: item
type: AcademicArticle
description: Background The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities. Methods We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses. Results As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6–V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may…
format: application/pdf
format: text/html
creator: David Ramirez-Delgado
creator: Francesco Cicala
creator: Ricardo A. Gonzalez-Sanchez
creator: Rosalia Avalos-Tellez
creator: Elena Solana-Arellano
creator: Alexei Licea-Navarro
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.13235
publisher: PeerJ Inc.
rights: © 2022 Ramirez-Delgado et al.
abstract: Background The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities. Methods We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses. Results As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6–V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may…
bibliographic citation: Ramirez-Delgado et al. (2022) Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México. PeerJ 10:e13235 https://doi.org/10.7717/peerj.13235
date submitted: 2021-11-17
date accepted: 2022-03-17
issued: 2022-07-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramirez-Delgado
  given name: David
author list: Agent
  family name: Cicala
  given name: Francesco
author list: Agent
  family name: Gonzalez-Sanchez
  given name: Ricardo A.
author list: Agent
  family name: Avalos-Tellez
  given name: Rosalia
author list: Agent
  family name: Solana-Arellano
  given name: Elena
author list: Agent
  family name: Licea-Navarro
  given name: Alexei
doi: 10.7717/peerj.13235
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-08
copyright: © 2022 Ramirez-Delgado et al.
attribution name: Ramirez-Delgado et al.

Identification and subcellular localization analysis of membrane protein Ycf 1 in the microsporidian Nosema bombycis
type: item
type: AcademicArticle
description: Microsporidia are obligate intracellular parasites that can infect a wide range of vertebrates and invertebrates including humans and insects, such as silkworm and bees. The microsporidium Nosema bombycis can cause pebrine in Bombyx mori, which is the most destructive disease in the sericulture industry. Although membrane proteins are involved in a wide range of cellular functions and part of many important metabolic pathways, there are rare reports about the membrane proteins of microsporidia up to now. We screened a putative membrane protein Ycf 1 from the midgut transcriptome of the N. bombycis-infected silkworm. Gene cloning and bioinformatics analysis showed that the Ycf 1 gene contains a complete open reading frame (ORF) of 969 bp in length encoding a 322 amino acid polypeptide that has one signal peptide and one transmembrane domain. Indirect immunofluorescence results showed that Ycf 1 protein is distributed on the plasma membrane. Expression pattern analysis showed that the Ycf 1 gene expressed in all developmental stages of N. bombycis. Knockdown of the Ycf 1 gene by RNAi effectively inhibited the proliferation of N. bombycis. These results indicated that Ycf 1 is a membrane protein and plays an important role in the life cycle of N. bombycis.
format: application/pdf
format: text/html
creator: Yong Chen
creator: Erjun Wei
creator: Ying Chen
creator: Ping He
creator: Runpeng Wang
creator: Qiang Wang
creator: Xudong Tang
creator: Yiling Zhang
creator: Feng Zhu
creator: Zhongyuan Shen
subject: Agricultural Science
subject: Entomology
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.13530
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: Microsporidia are obligate intracellular parasites that can infect a wide range of vertebrates and invertebrates including humans and insects, such as silkworm and bees. The microsporidium Nosema bombycis can cause pebrine in Bombyx mori, which is the most destructive disease in the sericulture industry. Although membrane proteins are involved in a wide range of cellular functions and part of many important metabolic pathways, there are rare reports about the membrane proteins of microsporidia up to now. We screened a putative membrane protein Ycf 1 from the midgut transcriptome of the N. bombycis-infected silkworm. Gene cloning and bioinformatics analysis showed that the Ycf 1 gene contains a complete open reading frame (ORF) of 969 bp in length encoding a 322 amino acid polypeptide that has one signal peptide and one transmembrane domain. Indirect immunofluorescence results showed that Ycf 1 protein is distributed on the plasma membrane. Expression pattern analysis showed that the Ycf 1 gene expressed in all developmental stages of N. bombycis. Knockdown of the Ycf 1 gene by RNAi effectively inhibited the proliferation of N. bombycis. These results indicated that Ycf 1 is a membrane protein and plays an important role in the life cycle of N. bombycis.
bibliographic citation: Chen et al. (2022) Identification and subcellular localization analysis of membrane protein Ycf 1 in the microsporidian Nosema bombycis. PeerJ 10:e13530 https://doi.org/10.7717/peerj.13530
date submitted: 2022-01-24
date accepted: 2022-05-11
issued: 2022-07-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yong
author list: Agent
  family name: Wei
  given name: Erjun
author list: Agent
  family name: Chen
  given name: Ying
author list: Agent
  family name: He
  given name: Ping
author list: Agent
  family name: Wang
  given name: Runpeng
author list: Agent
  family name: Wang
  given name: Qiang
author list: Agent
  family name: Tang
  given name: Xudong
author list: Agent
  family name: Zhang
  given name: Yiling
author list: Agent
  family name: Zhu
  given name: Feng
author list: Agent
  family name: Shen
  given name: Zhongyuan
doi: 10.7717/peerj.13530
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-08
copyright: ©2022 Chen et al.
attribution name: Chen et al.

Ecological restoration stimulates environmental outcomes but exacerbates water shortage in the Loess Plateau
type: item
type: AcademicArticle
description: Restoration is the natural and intervention-assisted set of processes designed to promote and facilitate the recovery of an ecosystem that has been degraded, damaged, or destroyed. However, it can also have an adverse effect on the environment. Thus, assessing an ecological restoration project’s impact is crucial to determining its success and optimum management strategies. We performed a meta-analysis concerning the environmental outcomes during the years 2000–2015 resulting from the “Grain for Green” Project (GFGP) implementation in the Loess Plateau (LP). Data were gathered from 40 peer-reviewed English-language articles chosen from a pool of 332 articles. The results showed that, on average, GFGP increased forest coverage by 35.7% (95% CI [24.15–47.52%]), and grassland by 1.05% (95% CI [0.8–1.28%]). At the same time, GFGP has a positive impact on soil carbon (C) sequestration, net ecosystem production (NEP), and net primary production (NPP), from the years 2000 to 2015 by an average of 36% (95% CI [28.96–43.18%]), 22.7% (95% CI [9.10–36.79%]), and 13.5% (95% CI [9.44–17.354%]), respectively. Soil erosion, sediment load, runoff coefficient, and water yield were reduced by 13.3% (95% CI [0.27–25.76%]), 21.5% (95% CI [1.50–39.99%]), 22.4% (95% CI [5.28–40.45%]) and 43.3% (95% CI [27.03–82.86%]), respectively, from the years 2000 to 2015. Our results indicate that water supply decreased with the increase of vegetation coverage. Therefore, to balance the needs for green space, GFGP policies and strategies should recover, enhance, and sustain more resilient ecosystems.
format: application/pdf
format: text/html
creator: Mbezele Junior Yannick Ngaba
creator: Yves Uwiragiye
creator: Hongzhi Miao
creator: Zhiqin Li
creator: Paulo Pereira
creator: Jianbin Zhou
subject: Ecology
subject: Natural Resource Management
subject: Ecohydrology
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.13658
publisher: PeerJ Inc.
rights: © 2022 Ngaba et al.
abstract: Restoration is the natural and intervention-assisted set of processes designed to promote and facilitate the recovery of an ecosystem that has been degraded, damaged, or destroyed. However, it can also have an adverse effect on the environment. Thus, assessing an ecological restoration project’s impact is crucial to determining its success and optimum management strategies. We performed a meta-analysis concerning the environmental outcomes during the years 2000–2015 resulting from the “Grain for Green” Project (GFGP) implementation in the Loess Plateau (LP). Data were gathered from 40 peer-reviewed English-language articles chosen from a pool of 332 articles. The results showed that, on average, GFGP increased forest coverage by 35.7% (95% CI [24.15–47.52%]), and grassland by 1.05% (95% CI [0.8–1.28%]). At the same time, GFGP has a positive impact on soil carbon (C) sequestration, net ecosystem production (NEP), and net primary production (NPP), from the years 2000 to 2015 by an average of 36% (95% CI [28.96–43.18%]), 22.7% (95% CI [9.10–36.79%]), and 13.5% (95% CI [9.44–17.354%]), respectively. Soil erosion, sediment load, runoff coefficient, and water yield were reduced by 13.3% (95% CI [0.27–25.76%]), 21.5% (95% CI [1.50–39.99%]), 22.4% (95% CI [5.28–40.45%]) and 43.3% (95% CI [27.03–82.86%]), respectively, from the years 2000 to 2015. Our results indicate that water supply decreased with the increase of vegetation coverage. Therefore, to balance the needs for green space, GFGP policies and strategies should recover, enhance, and sustain more resilient ecosystems.
bibliographic citation: Ngaba et al. (2022) Ecological restoration stimulates environmental outcomes but exacerbates water shortage in the Loess Plateau. PeerJ 10:e13658 https://doi.org/10.7717/peerj.13658
date submitted: 2022-03-09
date accepted: 2022-06-09
issued: 2022-07-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ngaba
  given name: Mbezele Junior Yannick
author list: Agent
  family name: Uwiragiye
  given name: Yves
author list: Agent
  family name: Miao
  given name: Hongzhi
author list: Agent
  family name: Li
  given name: Zhiqin
author list: Agent
  family name: Pereira
  given name: Paulo
author list: Agent
  family name: Zhou
  given name: Jianbin
doi: 10.7717/peerj.13658
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-08
copyright: © 2022 Ngaba et al.
attribution name: Ngaba et al.

Evaluating pharmacists’ knowledge, attitude, and practices toward amiodarone cross-reactivity with iodine: a cross-sectional pilot study
type: item
type: AcademicArticle
description: Introduction Iodine is a vital mineral of the human body that acts by maintaining the health of the thyroid gland. Research has shown that iodine-rich food allergy (i.e., seafood allergy) is not caused by iodine itself; instead, it is caused by other proteins including tropomyosin and parvalbumin in shellfish and fish, respectively. Amiodarone is a commonly used antiarrhythmic agent containing a significant amount of iodine. Objective This study’s objective was to assess pharmacists’ knowledge, attitude, and practices toward the misconception of iodine allergy and the cross-reactivity with amiodarone. Methods In February 2020, a cross-sectional study was conducted by sending out an online survey to three pharmaceutical organizations (Saudi Pharmaceutical Society, Kuwait Pharmaceutical Association, and Oman Pharmaceutical Society). Additionally, an electronic questionnaire was administered to pharmacists attending the Dubai International Pharmaceuticals and Technologies Conference and Exhibition 2020 (DUPHAT). Chi-square or Fisher’s exact test, when appropriate, were used to compare categorical variables. The statistical analyses were carried out using SPSS software. Results Data were collected from 66 respondents. However, only 61 (92.4%) were included in the final analysis following the exclusion of incomplete responses. The mean age of participants was 35 ± 8.48 years. The majority of participants did not have the Board of Pharmacy Specialties Certification (54.1%). Moreover, (41%) of participants licensed as pharmacists with more than 10 years of initial pharmacy licensure. Forty-three (70.5%) of participants had the misconception that iodine allergy should be considered before amiodarone administration, 20/32 (62.5%) of whom considered iodine allergy alone thought that premedication with corticosteroids and/or antihistamines is necessary. Concerning iodine allergy and amiodarone use, there was no significant difference in knowledge between the pharmacists who ha…
format: application/pdf
format: text/html
creator: Nura Abdullah Alshehab
creator: Munirah Abdullah Alhumaid
creator: Mohammed Abdulrazaq Alabdulwahed
creator: Abdulaziz Saleh Almulhim
subject: Allergy and Clinical Immunology
subject: Internal Medicine
subject: Pharmacology
description: doi:10.7717/peerj.13665
publisher: PeerJ Inc.
rights: © 2022 Alshehab et al.
abstract: Introduction Iodine is a vital mineral of the human body that acts by maintaining the health of the thyroid gland. Research has shown that iodine-rich food allergy (i.e., seafood allergy) is not caused by iodine itself; instead, it is caused by other proteins including tropomyosin and parvalbumin in shellfish and fish, respectively. Amiodarone is a commonly used antiarrhythmic agent containing a significant amount of iodine. Objective This study’s objective was to assess pharmacists’ knowledge, attitude, and practices toward the misconception of iodine allergy and the cross-reactivity with amiodarone. Methods In February 2020, a cross-sectional study was conducted by sending out an online survey to three pharmaceutical organizations (Saudi Pharmaceutical Society, Kuwait Pharmaceutical Association, and Oman Pharmaceutical Society). Additionally, an electronic questionnaire was administered to pharmacists attending the Dubai International Pharmaceuticals and Technologies Conference and Exhibition 2020 (DUPHAT). Chi-square or Fisher’s exact test, when appropriate, were used to compare categorical variables. The statistical analyses were carried out using SPSS software. Results Data were collected from 66 respondents. However, only 61 (92.4%) were included in the final analysis following the exclusion of incomplete responses. The mean age of participants was 35 ± 8.48 years. The majority of participants did not have the Board of Pharmacy Specialties Certification (54.1%). Moreover, (41%) of participants licensed as pharmacists with more than 10 years of initial pharmacy licensure. Forty-three (70.5%) of participants had the misconception that iodine allergy should be considered before amiodarone administration, 20/32 (62.5%) of whom considered iodine allergy alone thought that premedication with corticosteroids and/or antihistamines is necessary. Concerning iodine allergy and amiodarone use, there was no significant difference in knowledge between the pharmacists who ha…
bibliographic citation: Alshehab et al. (2022) Evaluating pharmacists’ knowledge, attitude, and practices toward amiodarone cross-reactivity with iodine: a cross-sectional pilot study. PeerJ 10:e13665 https://doi.org/10.7717/peerj.13665
date submitted: 2022-02-22
date accepted: 2022-06-10
issued: 2022-07-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alshehab
  given name: Nura Abdullah
author list: Agent
  family name: Alhumaid
  given name: Munirah Abdullah
author list: Agent
  family name: Alabdulwahed
  given name: Mohammed Abdulrazaq
author list: Agent
  family name: Almulhim
  given name: Abdulaziz Saleh
doi: 10.7717/peerj.13665
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-08
copyright: © 2022 Alshehab et al.
attribution name: Alshehab et al.

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