PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Developmental exposure to the DE-71 mixture of polybrominated diphenyl ether (PBDE) flame retardants induce a complex pattern of endocrine disrupting effects in rats
items: Predicting continuous ground reaction forces from accelerometers during uphill and downhill running: a recurrent neural network solution
items: Efficacy of bakuchiol-garlic combination against virulent genes of Candida albicans
items: Role of miR-100-5p and CDC25A in breast carcinoma cells
items: Characteristics of Central American brocket deer resting sites in a tropical mountain cloud forest in eastern Mexico
items: https://peerj.com/articles/12632
items: Assessment of health-related quality of life in hypertensive hemodialysis patients
items: Land-use history impacts spatial patterns and composition of woody plant species across a 35-hectare temperate forest plot
items: Identification of the occurrence and potential mechanisms of heterotopic ossification associated with 17-beta-estradiol targeting MKX by bioinformatics analysis and cellular experiments
items: First report of fatty acids in Mimosadiplotricha bee pollen with in vitro lipase inhibitory activity

Developmental exposure to the DE-71 mixture of polybrominated diphenyl ether (PBDE) flame retardants induce a complex pattern of endocrine disrupting effects in rats
type: item
type: AcademicArticle
description: Polybrominated diphenyl ethers (PBDEs) are legacy compounds with continued widespread human exposure. Despite this, developmental toxicity studies of DE-71, a mixture of PBDEs, are scarce and its potential for endocrine disrupting effects in vivo is not well covered. To address this knowledge gap, we carried out a developmental exposure study with DE-71. Pregnant Wistar rat dams were exposed to 0, 40 or 60 mg/kg bodyweight/day from gestation day 7 to postnatal day 16, and both sexes were examined. Developmental exposure affected a range of reproductive toxicity endpoints. Effects were seen for both male and female anogenital distances (AGD), with exposed offspring of either sex displaying around 10% shorter AGD compared to controls. Both absolute and relative prostate weights were markedly reduced in exposed male offspring, with about 40% relative to controls. DE-71 reduced mammary gland outgrowth, especially in male offspring. These developmental in vivo effects suggest a complex effect pattern involving anti-androgenic, anti-estrogenic and maybe estrogenic mechanisms depending on tissues and developmental stages. Irrespective of the specific underlying mechanisms, these in vivo results corroborate that DE-71 causes endocrine disrupting effects and raises concern for the effects of PBDE-exposure on human reproductive health, including any potential long-term consequences of disrupted mammary gland development.
format: application/pdf
format: text/html
creator: Louise Ramhøj
creator: Karen Mandrup
creator: Ulla Hass
creator: Terje Svingen
creator: Marta Axelstad
subject: Developmental Biology
subject: Toxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.12738
publisher: PeerJ Inc.
rights: © 2022 Ramhøj et al.
abstract: Polybrominated diphenyl ethers (PBDEs) are legacy compounds with continued widespread human exposure. Despite this, developmental toxicity studies of DE-71, a mixture of PBDEs, are scarce and its potential for endocrine disrupting effects in vivo is not well covered. To address this knowledge gap, we carried out a developmental exposure study with DE-71. Pregnant Wistar rat dams were exposed to 0, 40 or 60 mg/kg bodyweight/day from gestation day 7 to postnatal day 16, and both sexes were examined. Developmental exposure affected a range of reproductive toxicity endpoints. Effects were seen for both male and female anogenital distances (AGD), with exposed offspring of either sex displaying around 10% shorter AGD compared to controls. Both absolute and relative prostate weights were markedly reduced in exposed male offspring, with about 40% relative to controls. DE-71 reduced mammary gland outgrowth, especially in male offspring. These developmental in vivo effects suggest a complex effect pattern involving anti-androgenic, anti-estrogenic and maybe estrogenic mechanisms depending on tissues and developmental stages. Irrespective of the specific underlying mechanisms, these in vivo results corroborate that DE-71 causes endocrine disrupting effects and raises concern for the effects of PBDE-exposure on human reproductive health, including any potential long-term consequences of disrupted mammary gland development.
bibliographic citation: Ramhøj et al. (2022) Developmental exposure to the DE-71 mixture of polybrominated diphenyl ether (PBDE) flame retardants induce a complex pattern of endocrine disrupting effects in rats. PeerJ 10:e12738 https://doi.org/10.7717/peerj.12738
date submitted: 2021-09-28
date accepted: 2021-12-13
issued: 2022-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramhøj
  given name: Louise
author list: Agent
  family name: Mandrup
  given name: Karen
author list: Agent
  family name: Hass
  given name: Ulla
author list: Agent
  family name: Svingen
  given name: Terje
author list: Agent
  family name: Axelstad
  given name: Marta
doi: 10.7717/peerj.12738
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-04
copyright: ©2022 Ramhøj et al.
attribution name: Ramhøj et al.

Predicting continuous ground reaction forces from accelerometers during uphill and downhill running: a recurrent neural network solution
type: item
type: AcademicArticle
description: Background Ground reaction forces (GRFs) are important for understanding human movement, but their measurement is generally limited to a laboratory environment. Previous studies have used neural networks to predict GRF waveforms during running from wearable device data, but these predictions are limited to the stance phase of level-ground running. A method of predicting the normal (perpendicular to running surface) GRF waveform using wearable devices across a range of running speeds and slopes could allow researchers and clinicians to predict kinetic and kinematic variables outside the laboratory environment. Purpose We sought to develop a recurrent neural network capable of predicting continuous normal (perpendicular to surface) GRFs across a range of running speeds and slopes from accelerometer data. Methods Nineteen subjects ran on a force-measuring treadmill at five slopes (0°, ±5°, ±10°) and three speeds (2.5, 3.33, 4.17 m/s) per slope with sacral- and shoe-mounted accelerometers. We then trained a recurrent neural network to predict normal GRF waveforms frame-by-frame. The predicted versus measured GRF waveforms had an average ± SD RMSE of 0.16 ± 0.04 BW and relative RMSE of 6.4 ± 1.5% across all conditions and subjects. Results The recurrent neural network predicted continuous normal GRF waveforms across a range of running speeds and slopes with greater accuracy than neural networks implemented in previous studies. This approach may facilitate predictions of biomechanical variables outside the laboratory in near real-time and improves the accuracy of quantifying and monitoring external forces experienced by the body when running.
format: application/pdf
format: text/html
creator: Ryan S. Alcantara
creator: W. Brent Edwards
creator: Guillaume Y. Millet
creator: Alena M. Grabowski
subject: Data Mining and Machine Learning
subject: Biomechanics
description: doi:10.7717/peerj.12752
publisher: PeerJ Inc.
rights: © 2022 Alcantara et al.
abstract: Background Ground reaction forces (GRFs) are important for understanding human movement, but their measurement is generally limited to a laboratory environment. Previous studies have used neural networks to predict GRF waveforms during running from wearable device data, but these predictions are limited to the stance phase of level-ground running. A method of predicting the normal (perpendicular to running surface) GRF waveform using wearable devices across a range of running speeds and slopes could allow researchers and clinicians to predict kinetic and kinematic variables outside the laboratory environment. Purpose We sought to develop a recurrent neural network capable of predicting continuous normal (perpendicular to surface) GRFs across a range of running speeds and slopes from accelerometer data. Methods Nineteen subjects ran on a force-measuring treadmill at five slopes (0°, ±5°, ±10°) and three speeds (2.5, 3.33, 4.17 m/s) per slope with sacral- and shoe-mounted accelerometers. We then trained a recurrent neural network to predict normal GRF waveforms frame-by-frame. The predicted versus measured GRF waveforms had an average ± SD RMSE of 0.16 ± 0.04 BW and relative RMSE of 6.4 ± 1.5% across all conditions and subjects. Results The recurrent neural network predicted continuous normal GRF waveforms across a range of running speeds and slopes with greater accuracy than neural networks implemented in previous studies. This approach may facilitate predictions of biomechanical variables outside the laboratory in near real-time and improves the accuracy of quantifying and monitoring external forces experienced by the body when running.
bibliographic citation: Alcantara et al. (2022) Predicting continuous ground reaction forces from accelerometers during uphill and downhill running: a recurrent neural network solution. PeerJ 10:e12752 https://doi.org/10.7717/peerj.12752
date submitted: 2021-08-30
date accepted: 2021-12-15
issued: 2022-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alcantara
  given name: Ryan S.
author list: Agent
  family name: Edwards
  given name: W. Brent
author list: Agent
  family name: Millet
  given name: Guillaume Y.
author list: Agent
  family name: Grabowski
  given name: Alena M.
doi: 10.7717/peerj.12752
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-04
copyright: ©2022 Alcantara et al.
attribution name: Alcantara et al.

Efficacy of bakuchiol-garlic combination against virulent genes of Candida albicans
type: item
type: AcademicArticle
description: Background Polymicrobial biofilms are notorious for causing intraoral tissue destruction. Streptococcus sanguinis and Streptococcus mitis, commensals of oral cavities, have been found co-existing with C. albicans in resistant oral infections. There is an urgent need to find alternative treatment options. This study aims to assess the efficacy of garlic (G) and bakuchiol (Bk) combination against candida virulent genes and their subsequently secreted proteins. Methods In vitro single species biofilms of C. albicans, and mixed species biofilms formed in combination with streptococci were exposed to bakuchiol and garlic extract (Bk+G). Gene expression of agglutinin-like sequence (ALS1), (ALS3), adhesin-like wall proteins (HWP1) and aspartyl proteinases (SAP5) were determined using qPCR and their subsequent proteins were assessed through Western blotting. Results Virulent genes were significantly downregulated in single species biofilms when they were treated with Bk+G combination. However, Bk+G did not have significant effect on ALS1 and HWP1 gene in polymicrobial biofilms. ALS3 and SAP5 were significantly downregulated in Bk+G treated polymicrobial biofilm. Similar results were portrayed in Western blotting. Conclusion Bk+G combination exhibited antimicrobial effects against single and mixed species biofilms. The findings might provide insights for treating resistant candida infections. This combination could potentially serve as an herbal alternative to traditional antifungals following further research.
format: application/pdf
format: text/html
creator: Ayesha Fahim
creator: Wan Harun Himratul-Aznita
creator: Puteri Shafinaz Abdul-Rahman
creator: Mohammad K. Alam
subject: Biochemistry
subject: Microbiology
subject: Molecular Biology
subject: Dentistry
description: doi:10.7717/peerj.12251
publisher: PeerJ Inc.
rights: © 2022 Fahim et al.
abstract: Background Polymicrobial biofilms are notorious for causing intraoral tissue destruction. Streptococcus sanguinis and Streptococcus mitis, commensals of oral cavities, have been found co-existing with C. albicans in resistant oral infections. There is an urgent need to find alternative treatment options. This study aims to assess the efficacy of garlic (G) and bakuchiol (Bk) combination against candida virulent genes and their subsequently secreted proteins. Methods In vitro single species biofilms of C. albicans, and mixed species biofilms formed in combination with streptococci were exposed to bakuchiol and garlic extract (Bk+G). Gene expression of agglutinin-like sequence (ALS1), (ALS3), adhesin-like wall proteins (HWP1) and aspartyl proteinases (SAP5) were determined using qPCR and their subsequent proteins were assessed through Western blotting. Results Virulent genes were significantly downregulated in single species biofilms when they were treated with Bk+G combination. However, Bk+G did not have significant effect on ALS1 and HWP1 gene in polymicrobial biofilms. ALS3 and SAP5 were significantly downregulated in Bk+G treated polymicrobial biofilm. Similar results were portrayed in Western blotting. Conclusion Bk+G combination exhibited antimicrobial effects against single and mixed species biofilms. The findings might provide insights for treating resistant candida infections. This combination could potentially serve as an herbal alternative to traditional antifungals following further research.
bibliographic citation: Fahim et al. (2022) Efficacy of bakuchiol-garlic combination against virulent genes of Candida albicans. PeerJ 10:e12251 https://doi.org/10.7717/peerj.12251
date submitted: 2021-07-29
date accepted: 2021-09-13
issued: 2022-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fahim
  given name: Ayesha
author list: Agent
  family name: Himratul-Aznita
  given name: Wan Harun
author list: Agent
  family name: Abdul-Rahman
  given name: Puteri Shafinaz
author list: Agent
  family name: Alam
  given name: Mohammad K.
doi: 10.7717/peerj.12251
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-03
copyright: © 2022 Fahim et al.
attribution name: Fahim et al.

Role of miR-100-5p and CDC25A in breast carcinoma cells
type: item
type: AcademicArticle
description: Objective To inquiry about mechanism of miR-100-5p/CDC25A axis in breast carcinoma (BC), thus offering a new direction for BC targeted treatment. Methods qRT-PCR was employed to explore miR-100-5p and CDC25A mRNA levels. Western blot was employed for detecting protein expression of CDC25A. Targeting relationship of miR-100-5p and CDC25A was verified by dual-luciferase assay. In vitro experiments were used for assessment of cell functions. Results In BC tissue and cells, miR-100-5p was significantly lowly expressed (P < 0.05) while CDC25A was highly expressed. Besides, miR-100-5p downregulated CDC25A level. miR-100-5p had a marked influence on the prognosis of patients. The forced miR-100-5p expression hindered BC cell proliferation, migration and invasion, and facilitated cell apoptosis. Upregulated miR-100-5p weakened promotion of CDC25A on BC cell growth. Conclusion Together, these findings unveiled that CDC25A may be a key target of miR-100-5p that mediated progression of BC cells. Hence, miR-100-5p overexpression or CDC25A suppression may contribute to BC diagnosis.
format: application/pdf
format: text/html
creator: Xiaoping Li
creator: Yanli Ren
creator: Donghong Liu
creator: Xi Yu
creator: Keda Chen
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.12263
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Objective To inquiry about mechanism of miR-100-5p/CDC25A axis in breast carcinoma (BC), thus offering a new direction for BC targeted treatment. Methods qRT-PCR was employed to explore miR-100-5p and CDC25A mRNA levels. Western blot was employed for detecting protein expression of CDC25A. Targeting relationship of miR-100-5p and CDC25A was verified by dual-luciferase assay. In vitro experiments were used for assessment of cell functions. Results In BC tissue and cells, miR-100-5p was significantly lowly expressed (P < 0.05) while CDC25A was highly expressed. Besides, miR-100-5p downregulated CDC25A level. miR-100-5p had a marked influence on the prognosis of patients. The forced miR-100-5p expression hindered BC cell proliferation, migration and invasion, and facilitated cell apoptosis. Upregulated miR-100-5p weakened promotion of CDC25A on BC cell growth. Conclusion Together, these findings unveiled that CDC25A may be a key target of miR-100-5p that mediated progression of BC cells. Hence, miR-100-5p overexpression or CDC25A suppression may contribute to BC diagnosis.
bibliographic citation: Li et al. (2022) Role of miR-100-5p and CDC25A in breast carcinoma cells. PeerJ 10:e12263 https://doi.org/10.7717/peerj.12263
date submitted: 2021-02-24
date accepted: 2021-09-16
issued: 2022-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xiaoping
author list: Agent
  family name: Ren
  given name: Yanli
author list: Agent
  family name: Liu
  given name: Donghong
author list: Agent
  family name: Yu
  given name: Xi
author list: Agent
  family name: Chen
  given name: Keda
doi: 10.7717/peerj.12263
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-03
copyright: ©2022 Li et al.
attribution name: Li et al.

Characteristics of Central American brocket deer resting sites in a tropical mountain cloud forest in eastern Mexico
type: item
type: AcademicArticle
description: The Central American brocket deer is a vulnerable species. Geographically isolated populations have been affected by poaching and habitat fragmentation, leading to local extinctions. It is therefore important to understand this species’ habitat characteristics, particularly of resting sites, which play a crucial role in survival and fitness. We describe the characteristics and distribution patterns of Central American brocket deer resting sites at the microhabitat and landscape scales in San Bartolo Tutotepec, Hidalgo, México. We conducted eight bimonthly field surveys between November 2017 and March 2019, consisting of 32 transects of 500 m length to search for fecal pellets, footprints, scrapes, and browsed plants. At each resting site we identified, we measured canopy closure, horizontal thermal cover, protection from predators for fawns and adults, escape routes, slope from the ground, presence of scrapes, cumulative importance value of the edible plant species, and distance from the resting site to the nearest water resource to characterize the site at the microhabitat scale. At the landscape scale, we identified the type of biotope, elevation, aspect, and slope. We compared all of these parameters from resting sites with a paired randomly selected site to serve as a control. We performed a multiple logistic regression to identify the parameters associated with the resting sites and a point pattern analysis to describe their distribution. We characterized 43 resting sites and their corresponding control plots. At the microhabitat scale, resting sites were associated with higher vertical thermal cover, more concealment cover, more escape routes, more edible plant species, higher slope from the ground, and closer distance to water resources. At the landscape scale, resting sites were associated with beech forest, oak forest, secondary forest, and ravine biotopes and negatively associated with pine forest, houses, and roads. Resting sites had an aggregated spatial…
format: application/pdf
format: text/html
creator: Brenda Muñoz Vazquez
creator: Sonia Gallina Tessaro
creator: Livia León-Paniagua
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.12587
publisher: PeerJ Inc.
rights: © 2022 Muñoz Vazquez et al.
abstract: The Central American brocket deer is a vulnerable species. Geographically isolated populations have been affected by poaching and habitat fragmentation, leading to local extinctions. It is therefore important to understand this species’ habitat characteristics, particularly of resting sites, which play a crucial role in survival and fitness. We describe the characteristics and distribution patterns of Central American brocket deer resting sites at the microhabitat and landscape scales in San Bartolo Tutotepec, Hidalgo, México. We conducted eight bimonthly field surveys between November 2017 and March 2019, consisting of 32 transects of 500 m length to search for fecal pellets, footprints, scrapes, and browsed plants. At each resting site we identified, we measured canopy closure, horizontal thermal cover, protection from predators for fawns and adults, escape routes, slope from the ground, presence of scrapes, cumulative importance value of the edible plant species, and distance from the resting site to the nearest water resource to characterize the site at the microhabitat scale. At the landscape scale, we identified the type of biotope, elevation, aspect, and slope. We compared all of these parameters from resting sites with a paired randomly selected site to serve as a control. We performed a multiple logistic regression to identify the parameters associated with the resting sites and a point pattern analysis to describe their distribution. We characterized 43 resting sites and their corresponding control plots. At the microhabitat scale, resting sites were associated with higher vertical thermal cover, more concealment cover, more escape routes, more edible plant species, higher slope from the ground, and closer distance to water resources. At the landscape scale, resting sites were associated with beech forest, oak forest, secondary forest, and ravine biotopes and negatively associated with pine forest, houses, and roads. Resting sites had an aggregated spatial…
bibliographic citation: Muñoz Vazquez et al. (2022) Characteristics of Central American brocket deer resting sites in a tropical mountain cloud forest in eastern Mexico. PeerJ 10:e12587 https://doi.org/10.7717/peerj.12587
date submitted: 2021-05-18
date accepted: 2021-11-11
issued: 2022-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Muñoz Vazquez
  given name: Brenda
author list: Agent
  family name: Gallina Tessaro
  given name: Sonia
author list: Agent
  family name: León-Paniagua
  given name: Livia
doi: 10.7717/peerj.12587
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-03
copyright: ©2022 Muñoz Vazquez et al.
attribution name: Muñoz Vazquez et al.

https://peerj.com/articles/12632
type: item
type: AcademicArticle
title: Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles
description: Black-rot disease caused by the phytopathogen Xanthomonas campestris pv. campestris (Xcc) continues to have considerable impacts on the productivity of cruciferous crops in Trinidad and Tobago and the wider Caribbean region. While the widespread occurrence of resistance of Xcc against bactericidal agrochemicals can contribute to the high disease burdens, the role of virulence and pathogenicity features of local strains on disease prevalence and severity has not been investigated yet. In the present study, a comparative genomic analysis was performed on 6 pathogenic Xcc and 4 co-isolated non-pathogenic Xanthomonas melonis (Xmel) strains from diseased crucifer plants grown in fields with heavy chemical use in Trinidad. Native isolates were grouped into two known and four newly assigned ribosomal sequence types (rST). Mobile genetic elements were identified which belonged to the IS3, IS5 family, Tn3 transposon, resolvases, and tra T4SS gene clusters. Additionally, exogenous plasmid derived sequences with origins from other bacterial species were characterised. Although several instances of genomic rearrangements were observed, native Xcc and Xmel isolates shared a significant level of structural homology with reference genomes, Xcc ATCC 33913 and Xmel CFBP4644, respectively. Complete T1SS hlyDB, T2SS, T4SS vir and T5SS xadA, yapH and estA gene clusters were identified in both species. Only Xmel strains contained a complete T6SS but no T3SS. Both species contained a complex repertoire of extracellular cell wall degrading enzymes. Native Xcc strains contained 37 T3SS and effector genes but a variable and unique profile of 8 avr, 4 xop and 1 hpa genes. Interestingly, Xmel strains contained several T3SS effectors with low similarity to references including avrXccA1 (~89%), hrpG (~73%), hrpX (~90%) and xopAZ (~87%). Furthermore, only Xmel genomes contained a CRISPR-Cas I-F array, but no lipopolysaccharide wxc gene cluster. Xmel strains were confirmed to be non-pathogenic by…
format: application/pdf
format: text/html
creator: Stephen D. B. Jr. Ramnarine
creator: Jayaraj Jayaraman
creator: Adesh Ramsubhag
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.12632
publisher: PeerJ Inc.
rights: © 2022 Ramnarine et al.
abstract: Black-rot disease caused by the phytopathogen Xanthomonas campestris pv. campestris (Xcc) continues to have considerable impacts on the productivity of cruciferous crops in Trinidad and Tobago and the wider Caribbean region. While the widespread occurrence of resistance of Xcc against bactericidal agrochemicals can contribute to the high disease burdens, the role of virulence and pathogenicity features of local strains on disease prevalence and severity has not been investigated yet. In the present study, a comparative genomic analysis was performed on 6 pathogenic Xcc and 4 co-isolated non-pathogenic Xanthomonas melonis (Xmel) strains from diseased crucifer plants grown in fields with heavy chemical use in Trinidad. Native isolates were grouped into two known and four newly assigned ribosomal sequence types (rST). Mobile genetic elements were identified which belonged to the IS3, IS5 family, Tn3 transposon, resolvases, and tra T4SS gene clusters. Additionally, exogenous plasmid derived sequences with origins from other bacterial species were characterised. Although several instances of genomic rearrangements were observed, native Xcc and Xmel isolates shared a significant level of structural homology with reference genomes, Xcc ATCC 33913 and Xmel CFBP4644, respectively. Complete T1SS hlyDB, T2SS, T4SS vir and T5SS xadA, yapH and estA gene clusters were identified in both species. Only Xmel strains contained a complete T6SS but no T3SS. Both species contained a complex repertoire of extracellular cell wall degrading enzymes. Native Xcc strains contained 37 T3SS and effector genes but a variable and unique profile of 8 avr, 4 xop and 1 hpa genes. Interestingly, Xmel strains contained several T3SS effectors with low similarity to references including avrXccA1 (~89%), hrpG (~73%), hrpX (~90%) and xopAZ (~87%). Furthermore, only Xmel genomes contained a CRISPR-Cas I-F array, but no lipopolysaccharide wxc gene cluster. Xmel strains were confirmed to be non-pathogenic by…
bibliographic citation: Ramnarine et al. (2022) Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles. PeerJ 10:e12632 https://doi.org/10.7717/peerj.12632
date submitted: 2021-07-27
date accepted: 2021-11-22
issued: 2022-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramnarine
  given name: Stephen D. B. Jr.
author list: Agent
  family name: Jayaraman
  given name: Jayaraj
author list: Agent
  family name: Ramsubhag
  given name: Adesh
doi: 10.7717/peerj.12632
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-03
copyright: © 2022 Ramnarine et al.
attribution name: Ramnarine et al.

Assessment of health-related quality of life in hypertensive hemodialysis patients
type: item
type: AcademicArticle
description: Background and Objectives Globally, the prevalence of hypertension (HTN) with the coexistence of chronic kidney disease (CKD) is increasing, resulting in poor quality of life. The main objective of the study was to measure the health-related quality of life (HRQoL) of hypertensive hemodialysis patients. Methods A multicenter follow-up study was carried out in six public and two private dialysis centers in Pakistan. A total of 517 hypertensive hemodialysis patients responded by completing the questionnaire at baseline and two subsequent phases. The quality of life of these patients was assessed using the EQ-5D-5L questionnaire (a standardized instrument for measuring generic health status). Statistical analysis was done using a multivariate linear regression model, Friedman test and Kruskal Wallis test. Results The majority of patients (58.2%) had normal body mass index and about 60.5% of the patients were taking less salt due to HTN. Friedman test gave the statistically significant results (p ≤ 0.001) in systolic blood pressure (BP), diastolic BP and EQ-5D visual analogue scale (VAS) score between three phases (initial visit, first follow-up and second follow-up). A significant improvement was observed in self-care and usual activities from initial visit to first follow-up (p < 0.05). The most problematic dimension among the hypertensive patients with CKD was pain/discomfort (86.5%). Conclusions HTN with coexisting CKD in hemodialysis patients severely affected HRQoL. Pain/discomfort was the most problematic dimension among the participants.
format: application/pdf
format: text/html
creator: Ayesha Aslam
creator: Shahid Shah
creator: Ghulam Abbas
creator: Anees ur Rehman
creator: Tauqeer Hussain Malhi
creator: Nasser Hadal Alotaibi
creator: Abdulaziz Ibrahim Alzarea
creator: Muhammad Fawad Rasool
creator: Haris Khurram
creator: Sibgha Noureen
creator: Muhammad Talha Saeed Bokhari
subject: Cardiology
subject: Psychiatry and Psychology
subject: Public Health
subject: Urology
description: doi:10.7717/peerj.12690
publisher: PeerJ Inc.
rights: © 2022 Aslam et al.
abstract: Background and Objectives Globally, the prevalence of hypertension (HTN) with the coexistence of chronic kidney disease (CKD) is increasing, resulting in poor quality of life. The main objective of the study was to measure the health-related quality of life (HRQoL) of hypertensive hemodialysis patients. Methods A multicenter follow-up study was carried out in six public and two private dialysis centers in Pakistan. A total of 517 hypertensive hemodialysis patients responded by completing the questionnaire at baseline and two subsequent phases. The quality of life of these patients was assessed using the EQ-5D-5L questionnaire (a standardized instrument for measuring generic health status). Statistical analysis was done using a multivariate linear regression model, Friedman test and Kruskal Wallis test. Results The majority of patients (58.2%) had normal body mass index and about 60.5% of the patients were taking less salt due to HTN. Friedman test gave the statistically significant results (p ≤ 0.001) in systolic blood pressure (BP), diastolic BP and EQ-5D visual analogue scale (VAS) score between three phases (initial visit, first follow-up and second follow-up). A significant improvement was observed in self-care and usual activities from initial visit to first follow-up (p < 0.05). The most problematic dimension among the hypertensive patients with CKD was pain/discomfort (86.5%). Conclusions HTN with coexisting CKD in hemodialysis patients severely affected HRQoL. Pain/discomfort was the most problematic dimension among the participants.
bibliographic citation: Aslam et al. (2022) Assessment of health-related quality of life in hypertensive hemodialysis patients. PeerJ 10:e12690 https://doi.org/10.7717/peerj.12690
date submitted: 2021-07-02
date accepted: 2021-12-04
issued: 2022-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aslam
  given name: Ayesha
author list: Agent
  family name: Shah
  given name: Shahid
author list: Agent
  family name: Abbas
  given name: Ghulam
author list: Agent
  family name: Rehman
  given name: Anees ur
author list: Agent
  family name: Malhi
  given name: Tauqeer Hussain
author list: Agent
  family name: Alotaibi
  given name: Nasser Hadal
author list: Agent
  family name: Alzarea
  given name: Abdulaziz Ibrahim
author list: Agent
  family name: Rasool
  given name: Muhammad Fawad
author list: Agent
  family name: Khurram
  given name: Haris
author list: Agent
  family name: Noureen
  given name: Sibgha
author list: Agent
  family name: Saeed Bokhari
  given name: Muhammad Talha
doi: 10.7717/peerj.12690
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-03
copyright: ©2022 Aslam et al.
attribution name: Aslam et al.

Land-use history impacts spatial patterns and composition of woody plant species across a 35-hectare temperate forest plot
type: item
type: AcademicArticle
description: Land-use history is the template upon which contemporary plant and tree populations establish and interact with one another and exerts a legacy on the structure and dynamics of species assemblages and ecosystems. We use the first census (2010–2014) of a 35-ha forest-dynamics plot at the Harvard Forest in central Massachusetts to describe the composition and structure of the woody plants in this plot, assess their spatial associations within and among the dominant species using univariate and bivariate spatial point-pattern analysis, and examine the interactions between land-use history and ecological processes. The plot includes 108,632 live stems ≥ 1 cm in diameter (2,215 individuals/ha) and 7,595 standing dead stems ≥ 5 cm in diameter. Live tree basal area averaged 42.25 m2/ha, of which 84% was represented by Tsuga canadensis (14.0 m2/ ha), Quercus rubra (northern red oak; 9.6 m2/ ha), Acer rubrum (7.2 m2/ ha) and Pinus strobus (eastern white pine; 4.4 m2/ ha). These same four species also comprised 78% of the live aboveground biomass, which averaged 245.2 Mg/ ha. Across all species and size classes, the forest contains a preponderance (> 80,000) of small stems (<10-cm diameter) that exhibit a reverse-J size distribution. Significant spatial clustering of abundant overstory species was observed at all spatial scales examined. Spatial distributions of A. rubrum and Q. rubra showed negative intraspecific correlations in diameters up to at least a 150-m spatial lag, likely indicative of crowding effects in dense forest patches following intensive past land use. Bivariate marked point-pattern analysis, showed that T. canadensis and Q. rubra diameters were negatively associated with one another, indicating resource competition for light. Distribution and abundance of the common overstory species are predicted best by soil type, tree neighborhood effects, and two aspects of land-use history: when fields were abandoned in the late 19th century and the succeeding forest t…
format: application/pdf
format: text/html
creator: David A. Orwig
creator: Jason A. Aylward
creator: Hannah L. Buckley
creator: Bradley S. Case
creator: Aaron M. Ellison
subject: Ecology
subject: Plant Science
subject: Natural Resource Management
subject: Forestry
description: doi:10.7717/peerj.12693
publisher: PeerJ Inc.
rights: © 2022 Orwig et al.
abstract: Land-use history is the template upon which contemporary plant and tree populations establish and interact with one another and exerts a legacy on the structure and dynamics of species assemblages and ecosystems. We use the first census (2010–2014) of a 35-ha forest-dynamics plot at the Harvard Forest in central Massachusetts to describe the composition and structure of the woody plants in this plot, assess their spatial associations within and among the dominant species using univariate and bivariate spatial point-pattern analysis, and examine the interactions between land-use history and ecological processes. The plot includes 108,632 live stems ≥ 1 cm in diameter (2,215 individuals/ha) and 7,595 standing dead stems ≥ 5 cm in diameter. Live tree basal area averaged 42.25 m2/ha, of which 84% was represented by Tsuga canadensis (14.0 m2/ ha), Quercus rubra (northern red oak; 9.6 m2/ ha), Acer rubrum (7.2 m2/ ha) and Pinus strobus (eastern white pine; 4.4 m2/ ha). These same four species also comprised 78% of the live aboveground biomass, which averaged 245.2 Mg/ ha. Across all species and size classes, the forest contains a preponderance (> 80,000) of small stems (<10-cm diameter) that exhibit a reverse-J size distribution. Significant spatial clustering of abundant overstory species was observed at all spatial scales examined. Spatial distributions of A. rubrum and Q. rubra showed negative intraspecific correlations in diameters up to at least a 150-m spatial lag, likely indicative of crowding effects in dense forest patches following intensive past land use. Bivariate marked point-pattern analysis, showed that T. canadensis and Q. rubra diameters were negatively associated with one another, indicating resource competition for light. Distribution and abundance of the common overstory species are predicted best by soil type, tree neighborhood effects, and two aspects of land-use history: when fields were abandoned in the late 19th century and the succeeding forest t…
bibliographic citation: Orwig et al. (2022) Land-use history impacts spatial patterns and composition of woody plant species across a 35-hectare temperate forest plot. PeerJ 10:e12693 https://doi.org/10.7717/peerj.12693
date submitted: 2021-09-08
date accepted: 2021-12-06
issued: 2022-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Orwig
  given name: David A.
author list: Agent
  family name: Aylward
  given name: Jason A.
author list: Agent
  family name: Buckley
  given name: Hannah L.
author list: Agent
  family name: Case
  given name: Bradley S.
author list: Agent
  family name: Ellison
  given name: Aaron M.
doi: 10.7717/peerj.12693
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-03
copyright: ©2022 Orwig et al.
attribution name: Orwig et al.

Identification of the occurrence and potential mechanisms of heterotopic ossification associated with 17-beta-estradiol targeting MKX by bioinformatics analysis and cellular experiments
type: item
type: AcademicArticle
description: Background Tendon heterotopic ossification (HO) is a common condition occurring secondary to tendon injury or surgical trauma that significantly affects the patient’s quality of life. The treatment of tendon HO remains challenging due to a lack of clarity regarding the pathological mechanism. Mohawk (MKX) is a key factor in preventing tendon HO; however, its upstream regulatory mechanism remains to be understood. This study aimed to identify potential compounds that target and regulate MKX and explore their functional mechanisms. Methods Bioinformatics analysis of MKX-related compounds and proteins was performed based on data from the STITCH and OncoBinder databases. Subsequently, the SymMap database was used to study MKX-related traditional Chinese medicine drugs and symptoms. Next, the OncoBinder genomic and proteomic discovery model was applied to identify potential regulators of MKX. The analytical tool Expert Protein Analysis System for proteomics was used to predict the three-dimensional structure of MKX, and the AutoDockTools software was used to identify pockets of activity at potential sites for molecular docking. Furthermore, we evaluated the effect of different doses of 17-beta-estradiol on bone marrow-derived mesenchymal stem cells (BM-MSCs). Results By predicting the three-dimensional structure of MKX and simulating molecular docking, Pro-Tyr and 17-beta-Estradiol were found to target and bind to MKX. Analysis of the STITCH and OncoBinder databases showed that MKX had a significant regulatory correlation with suppressor interacting 3 A/histone deacetylase 1 (SIN3A/HDAC1). The GO and KEGG pathway enrichment analysis revealed that the functions of MKX and its associated proteins were mainly enriched in osteogenic-related pathways. Assessment of the proliferation of BM-MSCs revealed that 17-beta-estradiol possibly upregulated the mRNA expression of the HDAC1-SIN3A/BMP pathway-related RUNX2, thereby promoting the proliferation of BM-MSCs. Conclusions The co…
format: application/pdf
format: text/html
creator: Yunpeng Zhang
creator: Jingwei Zhang
creator: Chenyu Sun
creator: Fan Wu
subject: Drugs and Devices
subject: Orthopedics
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.12696
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Tendon heterotopic ossification (HO) is a common condition occurring secondary to tendon injury or surgical trauma that significantly affects the patient’s quality of life. The treatment of tendon HO remains challenging due to a lack of clarity regarding the pathological mechanism. Mohawk (MKX) is a key factor in preventing tendon HO; however, its upstream regulatory mechanism remains to be understood. This study aimed to identify potential compounds that target and regulate MKX and explore their functional mechanisms. Methods Bioinformatics analysis of MKX-related compounds and proteins was performed based on data from the STITCH and OncoBinder databases. Subsequently, the SymMap database was used to study MKX-related traditional Chinese medicine drugs and symptoms. Next, the OncoBinder genomic and proteomic discovery model was applied to identify potential regulators of MKX. The analytical tool Expert Protein Analysis System for proteomics was used to predict the three-dimensional structure of MKX, and the AutoDockTools software was used to identify pockets of activity at potential sites for molecular docking. Furthermore, we evaluated the effect of different doses of 17-beta-estradiol on bone marrow-derived mesenchymal stem cells (BM-MSCs). Results By predicting the three-dimensional structure of MKX and simulating molecular docking, Pro-Tyr and 17-beta-Estradiol were found to target and bind to MKX. Analysis of the STITCH and OncoBinder databases showed that MKX had a significant regulatory correlation with suppressor interacting 3 A/histone deacetylase 1 (SIN3A/HDAC1). The GO and KEGG pathway enrichment analysis revealed that the functions of MKX and its associated proteins were mainly enriched in osteogenic-related pathways. Assessment of the proliferation of BM-MSCs revealed that 17-beta-estradiol possibly upregulated the mRNA expression of the HDAC1-SIN3A/BMP pathway-related RUNX2, thereby promoting the proliferation of BM-MSCs. Conclusions The co…
bibliographic citation: Zhang et al. (2022) Identification of the occurrence and potential mechanisms of heterotopic ossification associated with 17-beta-estradiol targeting MKX by bioinformatics analysis and cellular experiments. PeerJ 10:e12696 https://doi.org/10.7717/peerj.12696
date submitted: 2021-08-31
date accepted: 2021-12-06
issued: 2022-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yunpeng
author list: Agent
  family name: Zhang
  given name: Jingwei
author list: Agent
  family name: Sun
  given name: Chenyu
author list: Agent
  family name: Wu
  given name: Fan
doi: 10.7717/peerj.12696
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-03
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

First report of fatty acids in Mimosadiplotricha bee pollen with in vitro lipase inhibitory activity
type: item
type: AcademicArticle
description: Bee pollen (BP) is full of nutrients and phytochemicals, and so it is widely used as a health food and alternative medicine. Its composition and bioactivity mainly depend on the floral pollens. In this work, BP collected by Apis mellifera with different monoculture flowering crops (BP1-6) were used. The types of floral pollen in each BP were initially identified by morphology, and subsequently confirmed using molecular phylogenetic analysis. Data from both approaches were consistent and revealed each BP to be monofloral and derived from the flowers of Camellia sinensis L., Helianthus annuus L., Mimosa diplotricha, Nelumbo nucifera, Xyris complanata, and Ageratum conyzoides for BP1 to BP6, respectively. The crude extracts of all six BPs were prepared by sequential partition with methanol, dichloromethane (DCM), and hexane. The crude extracts were then tested for the in vitro (i) α-amylase inhibitory, (ii) acetylcholinesterase inhibitory (AChEI), and (iii) porcine pancreatic lipase inhibitory (PPLI) activities in terms of the percentage enzyme inhibition and half maximum inhibitory concentration (IC50). The DCM partitioned extract of X. complanata BP (DCMXBP) had the highest active α-amylase inhibitory activity with an IC50 value of 1,792.48 ± 50.56 µg/mL. The DCM partitioned extracts of C. sinensis L. BP (DCMCBP) and M. diplotricha BP (DCMMBP) had the highest PPLI activities with an IC50 value of 458.5 ± 13.4 and 500.8 ± 24.8 µg/mL, respectively), while no crude extract showed any marked AChEI activity. Here, the in vitro PPLI activity was focused on. Unlike C. sinensis L. BP, there has been no previous report of M. diplotricha BP having PPLI activity. Hence, DCMMBP was further fractionated by silica gel 60 column chromatography, pooling fractions with the same thin layer chromatography profile. The pooled fraction of DCMMBP2-1 was found to be the most active (IC50 of 52.6 ± 3.5 µg/mL), while nuclear magnetic resonance analysis revealed the presence of unsaturated fr…
format: application/pdf
format: text/html
creator: Phanthiwa Khongkarat
creator: Prapun Traiyasut
creator: Preecha Phuwapraisirisan
creator: Chanpen Chanchao
subject: Agricultural Science
subject: Biochemistry
subject: Entomology
subject: Food Science and Technology
subject: Molecular Biology
description: doi:10.7717/peerj.12722
publisher: PeerJ Inc.
rights: © 2022 Khongkarat et al.
abstract: Bee pollen (BP) is full of nutrients and phytochemicals, and so it is widely used as a health food and alternative medicine. Its composition and bioactivity mainly depend on the floral pollens. In this work, BP collected by Apis mellifera with different monoculture flowering crops (BP1-6) were used. The types of floral pollen in each BP were initially identified by morphology, and subsequently confirmed using molecular phylogenetic analysis. Data from both approaches were consistent and revealed each BP to be monofloral and derived from the flowers of Camellia sinensis L., Helianthus annuus L., Mimosa diplotricha, Nelumbo nucifera, Xyris complanata, and Ageratum conyzoides for BP1 to BP6, respectively. The crude extracts of all six BPs were prepared by sequential partition with methanol, dichloromethane (DCM), and hexane. The crude extracts were then tested for the in vitro (i) α-amylase inhibitory, (ii) acetylcholinesterase inhibitory (AChEI), and (iii) porcine pancreatic lipase inhibitory (PPLI) activities in terms of the percentage enzyme inhibition and half maximum inhibitory concentration (IC50). The DCM partitioned extract of X. complanata BP (DCMXBP) had the highest active α-amylase inhibitory activity with an IC50 value of 1,792.48 ± 50.56 µg/mL. The DCM partitioned extracts of C. sinensis L. BP (DCMCBP) and M. diplotricha BP (DCMMBP) had the highest PPLI activities with an IC50 value of 458.5 ± 13.4 and 500.8 ± 24.8 µg/mL, respectively), while no crude extract showed any marked AChEI activity. Here, the in vitro PPLI activity was focused on. Unlike C. sinensis L. BP, there has been no previous report of M. diplotricha BP having PPLI activity. Hence, DCMMBP was further fractionated by silica gel 60 column chromatography, pooling fractions with the same thin layer chromatography profile. The pooled fraction of DCMMBP2-1 was found to be the most active (IC50 of 52.6 ± 3.5 µg/mL), while nuclear magnetic resonance analysis revealed the presence of unsaturated fr…
bibliographic citation: Khongkarat et al. (2022) First report of fatty acids in Mimosadiplotricha bee pollen with in vitro lipase inhibitory activity. PeerJ 10:e12722 https://doi.org/10.7717/peerj.12722
date submitted: 2021-09-20
date accepted: 2021-12-09
issued: 2022-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khongkarat
  given name: Phanthiwa
author list: Agent
  family name: Traiyasut
  given name: Prapun
author list: Agent
  family name: Phuwapraisirisan
  given name: Preecha
author list: Agent
  family name: Chanchao
  given name: Chanpen
doi: 10.7717/peerj.12722
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-03
copyright: ©2022 Khongkarat et al.
attribution name: Khongkarat et al.

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