PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The prognostic and clinicopathological significance of desmoglein 2 in human cancers: a systematic review and meta-analysis
items: Bird protection treatments reduce bird-window collision risk at low-rise buildings within a Pacific coastal protected area
items: Evaluation of change in trabecular bone structure surrounding dental implants by fractal dimension analysis and comparison with radiomorphometric indicators: a retrospective study
items: Transcription factor 7-like 2 single nucleotide polymorphisms rs290487 and rs290481 are associated with dyslipidemia in the Balinese population
items: The biogeography of bent-toed geckos, Cyrtodactylus (Squamata: Gekkonidae)
items: Comparative transcriptome analysis of cold-tolerant and -sensitive asparagus bean under chilling stress and recovery
items: N-mixture models provide informative crocodile (Crocodylus moreletii) abundance estimates in dynamic environments
items: Individuals with fibromyalgia have a different gait pattern and a reduced walk functional capacity: a systematic review with meta-analysis
items: Exploring interactions between Beauveria and Metarhizium strains through co-inoculation and responses of perennial ryegrass in a one-year trial
items: Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility

The prognostic and clinicopathological significance of desmoglein 2 in human cancers: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective The survival and clinicopathological significance of desmoglein 2 (DSG2) in various cancers is controversial. Thus, we performed this systematic review and meta-analysis to explore the preliminary prognostic value of DSG2. Methods Eligible studies were identified from databases including PubMed, the Cochrane Library, Embase, Web of Science and Scopus. Hand searches were also conducted in relevant bibliographies. We then extracted and pooled hazard ratio (HR) of overall survival (OS) and odds ratio (OR) of clinicopathological features. Results A total of 11 eligible studies containing 1,488 patients were included. Our results demonstrated that in non-small cell lung cancer (NSCLC), high DSG2 expression is associated with poor OS. However, in digestive system cancer and female reproductive system cancer, there were no statistically significant associations between OS and DSG2. Conclusions Based on the findings of this study, high DSG2 expression is associated with worse prognosis in patients with NSCLC, and thus DSG2 expression could be a biomarker for prognosis in NSCLC.
format: application/pdf
format: text/html
creator: Jiantao Wang
creator: Siyuan Hao
creator: Junjie Gu
creator: Sean G. Rudd
creator: Yan Wang
subject: Evidence Based Medicine
subject: Oncology
subject: Translational Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.13141
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Objective The survival and clinicopathological significance of desmoglein 2 (DSG2) in various cancers is controversial. Thus, we performed this systematic review and meta-analysis to explore the preliminary prognostic value of DSG2. Methods Eligible studies were identified from databases including PubMed, the Cochrane Library, Embase, Web of Science and Scopus. Hand searches were also conducted in relevant bibliographies. We then extracted and pooled hazard ratio (HR) of overall survival (OS) and odds ratio (OR) of clinicopathological features. Results A total of 11 eligible studies containing 1,488 patients were included. Our results demonstrated that in non-small cell lung cancer (NSCLC), high DSG2 expression is associated with poor OS. However, in digestive system cancer and female reproductive system cancer, there were no statistically significant associations between OS and DSG2. Conclusions Based on the findings of this study, high DSG2 expression is associated with worse prognosis in patients with NSCLC, and thus DSG2 expression could be a biomarker for prognosis in NSCLC.
bibliographic citation: Wang et al. (2022) The prognostic and clinicopathological significance of desmoglein 2 in human cancers: a systematic review and meta-analysis. PeerJ 10:e13141 https://doi.org/10.7717/peerj.13141
date submitted: 2021-12-09
date accepted: 2022-02-28
issued: 2022-03-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jiantao
author list: Agent
  family name: Hao
  given name: Siyuan
author list: Agent
  family name: Gu
  given name: Junjie
author list: Agent
  family name: Rudd
  given name: Sean G.
author list: Agent
  family name: Wang
  given name: Yan
doi: 10.7717/peerj.13141
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-22
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Bird protection treatments reduce bird-window collision risk at low-rise buildings within a Pacific coastal protected area
type: item
type: AcademicArticle
description: Background In North America, up to one billion birds are estimated to die annually due to collisions with glass. The transparent and reflective properties of glass present the illusion of a clear flight passage or continuous habitat. Approaches to reducing collision risk involve installing visual cues on glass that enable birds to perceive glass as a solid hazard at a sufficient distance to avoid it. Methods We monitored for bird-window collisions between 2013 and 2018 to measure response to bird protection window treatments at two low-rise buildings at the Alaksen National Wildlife Area in Delta, British Columbia, Canada. After 2 years of collision monitoring in an untreated state, we retrofitted one building with Feather Friendly® circular adhesive markers applied in a grid pattern across all windows, enabling a field-based assessment of the relative reduction in collisions in the 2 years of monitoring following treatment. An adjacent building that had been constructed with a bird protective UV-treated glass called ORNILUX® Mikado, was monitored throughout the two study periods. Carcass persistence trials were conducted to evaluate the likelihood that carcasses were missed due to carcass removal between scheduled searches. Results and Conclusions After accounting for differences in area of glass between the two buildings, year, and observer effects, our best-fit model for explaining collision risk included the building’s treatment group, when compared to models that included building and season only. We found that the Feather Friendly® markers reduced collision risk at the retrofitted building by 95%. Collision incidence was also lower at the two monitored façades of the building with ORNILUX® glass compared to the building with untreated glass. Although more research is needed on the effectiveness of bird-protection products across a range of conditions, our results highlight the benefit of these products for reducing avian mortality due to collisions with glass.
format: application/pdf
format: text/html
creator: Krista L. De Groot
creator: Amy G. Wilson
creator: René McKibbin
creator: Sarah A. Hudson
creator: Kimberly M. Dohms
creator: Andrea R. Norris
creator: Andrew C. Huang
creator: Ivy B. J. Whitehorne
creator: Kevin T. Fort
creator: Christian Roy
creator: Julie Bourque
creator: Scott Wilson
subject: Biodiversity
subject: Conservation Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.13142
publisher: PeerJ Inc.
rights: © 2022 De Groot et al.
abstract: Background In North America, up to one billion birds are estimated to die annually due to collisions with glass. The transparent and reflective properties of glass present the illusion of a clear flight passage or continuous habitat. Approaches to reducing collision risk involve installing visual cues on glass that enable birds to perceive glass as a solid hazard at a sufficient distance to avoid it. Methods We monitored for bird-window collisions between 2013 and 2018 to measure response to bird protection window treatments at two low-rise buildings at the Alaksen National Wildlife Area in Delta, British Columbia, Canada. After 2 years of collision monitoring in an untreated state, we retrofitted one building with Feather Friendly® circular adhesive markers applied in a grid pattern across all windows, enabling a field-based assessment of the relative reduction in collisions in the 2 years of monitoring following treatment. An adjacent building that had been constructed with a bird protective UV-treated glass called ORNILUX® Mikado, was monitored throughout the two study periods. Carcass persistence trials were conducted to evaluate the likelihood that carcasses were missed due to carcass removal between scheduled searches. Results and Conclusions After accounting for differences in area of glass between the two buildings, year, and observer effects, our best-fit model for explaining collision risk included the building’s treatment group, when compared to models that included building and season only. We found that the Feather Friendly® markers reduced collision risk at the retrofitted building by 95%. Collision incidence was also lower at the two monitored façades of the building with ORNILUX® glass compared to the building with untreated glass. Although more research is needed on the effectiveness of bird-protection products across a range of conditions, our results highlight the benefit of these products for reducing avian mortality due to collisions with glass.
bibliographic citation: De Groot et al. (2022) Bird protection treatments reduce bird-window collision risk at low-rise buildings within a Pacific coastal protected area. PeerJ 10:e13142 https://doi.org/10.7717/peerj.13142
date submitted: 2021-12-07
date accepted: 2022-02-28
issued: 2022-03-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Groot
  given name: Krista L.
author list: Agent
  family name: Wilson
  given name: Amy G.
author list: Agent
  family name: McKibbin
  given name: René
author list: Agent
  family name: Hudson
  given name: Sarah A.
author list: Agent
  family name: Dohms
  given name: Kimberly M.
author list: Agent
  family name: Norris
  given name: Andrea R.
author list: Agent
  family name: Huang
  given name: Andrew C.
author list: Agent
  family name: Whitehorne
  given name: Ivy B. J.
author list: Agent
  family name: Fort
  given name: Kevin T.
author list: Agent
  family name: Roy
  given name: Christian
author list: Agent
  family name: Bourque
  given name: Julie
author list: Agent
  family name: Wilson
  given name: Scott
doi: 10.7717/peerj.13142
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-22
copyright: © 2022 De Groot et al.
attribution name: De Groot et al.

Evaluation of change in trabecular bone structure surrounding dental implants by fractal dimension analysis and comparison with radiomorphometric indicators: a retrospective study
type: item
type: AcademicArticle
description: Background The trabecular bone surrounding dental implant show some structural changes during healing period. The purpose of this study is to observe the change in trabecular bone with fractal dimensional analysis from baseline to 3rd month of implant placement. It was also aimed to determine the correlation of fractal dimension (FD) change with morphometric indices, mandibular cortical index (MCI) and mandibular cortical width (MCW). Methods Digital panoramic radiographs taken from 14 patients were evaluated in this study. A total of 30 implants which were placed on mandibular premolar or molar region were included. MCI and MCW assessments were made on baseline radiograph and FD were analyzed on baseline and 3rd month radiograph. FD change by time was recorded separately for every ROI. A paired sample t-test was used to evaluate the change between FD-baseline and FD-3rdmonth values. One-way ANOVA was used to determine the relationship between FD change and MCI. FD change and MCW measurements correlation was calculated by Pearson correlation analysis Results FD value increased in 75 of 90 implant-adjacent regions evaluated in the 3rd month and it was observed that the FD values were statistically significantly increased in the mesial, distal and apical regions at the 3rd month measurements. There was no statistically significant relationship between mean FD change and MCI, and there was no correlation between mean FD change and MCW value. Discussion There are many studies evaluating the resorptive changes in bone. However, there are few studies investigating whether there is a correlation between pre- and post-operative trabecular pattern with MCI and MCW. The results of this study indicate that the implants have an improving effect on bone trabeculation in the region where they are placed.
format: application/pdf
format: text/html
creator: Ilkim Karadag
creator: Hasan Guney Yilmaz
subject: Dentistry
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.13145
publisher: PeerJ Inc.
rights: © 2022 Karadag and Yilmaz
abstract: Background The trabecular bone surrounding dental implant show some structural changes during healing period. The purpose of this study is to observe the change in trabecular bone with fractal dimensional analysis from baseline to 3rd month of implant placement. It was also aimed to determine the correlation of fractal dimension (FD) change with morphometric indices, mandibular cortical index (MCI) and mandibular cortical width (MCW). Methods Digital panoramic radiographs taken from 14 patients were evaluated in this study. A total of 30 implants which were placed on mandibular premolar or molar region were included. MCI and MCW assessments were made on baseline radiograph and FD were analyzed on baseline and 3rd month radiograph. FD change by time was recorded separately for every ROI. A paired sample t-test was used to evaluate the change between FD-baseline and FD-3rdmonth values. One-way ANOVA was used to determine the relationship between FD change and MCI. FD change and MCW measurements correlation was calculated by Pearson correlation analysis Results FD value increased in 75 of 90 implant-adjacent regions evaluated in the 3rd month and it was observed that the FD values were statistically significantly increased in the mesial, distal and apical regions at the 3rd month measurements. There was no statistically significant relationship between mean FD change and MCI, and there was no correlation between mean FD change and MCW value. Discussion There are many studies evaluating the resorptive changes in bone. However, there are few studies investigating whether there is a correlation between pre- and post-operative trabecular pattern with MCI and MCW. The results of this study indicate that the implants have an improving effect on bone trabeculation in the region where they are placed.
bibliographic citation: Karadag et al. (2022) Evaluation of change in trabecular bone structure surrounding dental implants by fractal dimension analysis and comparison with radiomorphometric indicators: a retrospective study. PeerJ 10:e13145 https://doi.org/10.7717/peerj.13145
date submitted: 2021-10-21
date accepted: 2022-03-01
issued: 2022-03-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karadag
  given name: Ilkim
author list: Agent
  family name: Yilmaz
  given name: Hasan Guney
doi: 10.7717/peerj.13145
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-22
copyright: © 2022 Karadag and Yilmaz
attribution name: Karadag and Yilmaz

Transcription factor 7-like 2 single nucleotide polymorphisms rs290487 and rs290481 are associated with dyslipidemia in the Balinese population
type: item
type: AcademicArticle
description: Background Dyslipidemia is one of the major risks for the development of cardiovascular diseases which has been the leading cause of death in developing countries. Previously, common polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene have been associated with altered lipid profiles. In this study, we investigated the associations of TCF7L2 SNPs, rs290487 and rs290481, with dyslipidemia and altered lipid profile in the Balinese. Methods A total of 565 subjects from four locations in the Bali Province, Indonesia, were recruited. Serum lipid concentrations (triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC)) were measured using standard protocol. SNP genotyping was done using the amplification refractory system mutation polymerase chain reaction (ARMS-PCR) method. Results We found the shifted major/minor allele frequencies of both SNPs (0.56 for rs290487 T allele, 0.53 for rs290481 T allele) in the Balinese, as compared to dbSNP. The rs290487 and rs290481 C alleles were significantly associated with dyslipidemia, particularly high TC and high LDL-C. These associations were independent of age, sex, population, obesity, diabetes mellitus, and high TyG index as a proxy for insulin resistance. The haplotype CC also showed similar association with these traits. Our findings indicate that TCF7L2 polymorphisms are associated with dyslipidemia and altered lipid profile in the Balinese.
format: application/pdf
format: text/html
creator: Prisca C. Limardi
creator: Sukma Oktavianthi
creator: Lidwina Priliani
creator: Retno Lestari
creator: Made Ratna Saraswati
creator: Ketut Suastika
creator: Safarina G. Malik
subject: Molecular Biology
subject: Diabetes and Endocrinology
subject: Hematology
subject: Medical Genetics
description: doi:10.7717/peerj.13149
publisher: PeerJ Inc.
rights: © 2022 Limardi et al.
abstract: Background Dyslipidemia is one of the major risks for the development of cardiovascular diseases which has been the leading cause of death in developing countries. Previously, common polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene have been associated with altered lipid profiles. In this study, we investigated the associations of TCF7L2 SNPs, rs290487 and rs290481, with dyslipidemia and altered lipid profile in the Balinese. Methods A total of 565 subjects from four locations in the Bali Province, Indonesia, were recruited. Serum lipid concentrations (triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC)) were measured using standard protocol. SNP genotyping was done using the amplification refractory system mutation polymerase chain reaction (ARMS-PCR) method. Results We found the shifted major/minor allele frequencies of both SNPs (0.56 for rs290487 T allele, 0.53 for rs290481 T allele) in the Balinese, as compared to dbSNP. The rs290487 and rs290481 C alleles were significantly associated with dyslipidemia, particularly high TC and high LDL-C. These associations were independent of age, sex, population, obesity, diabetes mellitus, and high TyG index as a proxy for insulin resistance. The haplotype CC also showed similar association with these traits. Our findings indicate that TCF7L2 polymorphisms are associated with dyslipidemia and altered lipid profile in the Balinese.
bibliographic citation: Limardi et al. (2022) Transcription factor 7-like 2 single nucleotide polymorphisms rs290487 and rs290481 are associated with dyslipidemia in the Balinese population. PeerJ 10:e13149 https://doi.org/10.7717/peerj.13149
date submitted: 2021-11-29
date accepted: 2022-03-01
issued: 2022-03-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Limardi
  given name: Prisca C.
author list: Agent
  family name: Oktavianthi
  given name: Sukma
author list: Agent
  family name: Priliani
  given name: Lidwina
author list: Agent
  family name: Lestari
  given name: Retno
author list: Agent
  family name: Saraswati
  given name: Made Ratna
author list: Agent
  family name: Suastika
  given name: Ketut
author list: Agent
  family name: Malik
  given name: Safarina G.
doi: 10.7717/peerj.13149
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-22
copyright: © 2022 Limardi et al.
attribution name: Limardi et al.

The biogeography of bent-toed geckos, Cyrtodactylus (Squamata: Gekkonidae)
type: item
type: AcademicArticle
description: The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins, land bridges, and mountain ranges—followed by in situ diversification within specific geographic areas. Ancestral ranges were reconstructed on a mitochondrial phylogeny with 346 described and undescribed species from which it was inferred that Cyrtodactylus evolved in a proto-Himalaya region during the early Eocene. From there, it dispersed to what is currently Indoburma and Indochina during the mid-Eocene—the latter becoming the first major center of origin for the remainder of the genus that seeded dispersals to the Indian subcontinent, Papua, and Sundaland. Sundaland became a second major center of radiation during the Oligocene and gave rise to a large number of species that radiated further within Sundaland and dispersed to Wallacea, the Philippines, and back to Indochina. One Papuan lineage dispersed west to recolonize and radiate in Sundaland. Currently, Indochina and Sundaland still harbor the vast majority of species of Cyrtodactylus.
format: application/pdf
format: text/html
creator: L. Lee Grismer
creator: Nikolay A. Poyarkov
creator: Evan S.H. Quah
creator: Jesse L. Grismer
creator: Perry L. Wood Jr
subject: Biodiversity
subject: Biogeography
subject: Bioinformatics
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.13153
publisher: PeerJ Inc.
rights: © 2022 Grismer et al.
abstract: The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins, land bridges, and mountain ranges—followed by in situ diversification within specific geographic areas. Ancestral ranges were reconstructed on a mitochondrial phylogeny with 346 described and undescribed species from which it was inferred that Cyrtodactylus evolved in a proto-Himalaya region during the early Eocene. From there, it dispersed to what is currently Indoburma and Indochina during the mid-Eocene—the latter becoming the first major center of origin for the remainder of the genus that seeded dispersals to the Indian subcontinent, Papua, and Sundaland. Sundaland became a second major center of radiation during the Oligocene and gave rise to a large number of species that radiated further within Sundaland and dispersed to Wallacea, the Philippines, and back to Indochina. One Papuan lineage dispersed west to recolonize and radiate in Sundaland. Currently, Indochina and Sundaland still harbor the vast majority of species of Cyrtodactylus.
bibliographic citation: Grismer et al. (2022) The biogeography of bent-toed geckos, Cyrtodactylus (Squamata: Gekkonidae). PeerJ 10:e13153 https://doi.org/10.7717/peerj.13153
date submitted: 2021-11-30
date accepted: 2022-03-01
issued: 2022-03-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grismer
  given name: L. Lee
author list: Agent
  family name: Poyarkov
  given name: Nikolay A.
author list: Agent
  family name: Quah
  given name: Evan S.H.
author list: Agent
  family name: Grismer
  given name: Jesse L.
author list: Agent
  family name: Wood Jr
  given name: Perry L.
doi: 10.7717/peerj.13153
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-22
copyright: ©2022 Grismer et al.
attribution name: Grismer et al.

Comparative transcriptome analysis of cold-tolerant and -sensitive asparagus bean under chilling stress and recovery
type: item
type: AcademicArticle
description: Background Low temperature is a type of abiotic stress that threatens the growth and yield of asparagus bean. However, the key genes and regulatory pathways involved in low temperature response in this legume are still poorly understood. Methodology. The present study analyzed the transcriptome of seedlings from two asparagus bean cultivars—Dubai bean and Ningjiang 3—using Illumina RNA sequencing (RNA-seq). Correlations between samples were determined by calculating Pearson correlation coefficients (PCC) and principal component analysis (PCA). Differentially expressed genes (DEGs) between two samples were identified using the DESeq package. Transcription factors (TF) prediction, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were also performed. Results Phenotypes and physiological indices indicated that Ningjiang 3 seedlings tolerated cold better than Dubai bean seedlings, in contrast to adult stage. The transcriptome dynamics of the two cultivars were closely compared using Illumina RNA-seq following 0, 3, 12, and 24 h of cold stress at 5 °C and recovery for 3 h at 25 °C room temperature. Global gene expression patterns displayed relatively high correlation between the two cultivars (>0.88), decreasing to 0.79 and 0.81, respectively, at 12 and 24 h of recovery, consistent with the results of principal component analysis. The major transcription factor families identified from differentially expressed genes between the two cultivars included bHLH, NAC, C2H2, MYB, WRKY, and AP2/ERF. The representative GO enrichment terms were protein phosphorylation, photosynthesis, oxidation-reduction process, and cellular glucan metabolic process. Moreover, KEGG analysis of DEGs within each cultivar revealed 36 transcription factors enriched in Dubai bean and Ningjiang 3 seedlings under cold stress. Conclusions These results reveal new information that will improve our understanding of the molecular mechanisms underlying the cold …
format: application/pdf
format: text/html
creator: Mingjun Miao
creator: Huaqiang Tan
creator: Le Liang
creator: Haitao Huang
creator: Wei Chang
creator: Jianwei Zhang
creator: Ju Li
creator: Yi Tang
creator: Zhi Li
creator: Yunsong Lai
creator: Liang Yang
creator: Huanxiu Li
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13167
publisher: PeerJ Inc.
rights: © 2022 Miao et al.
abstract: Background Low temperature is a type of abiotic stress that threatens the growth and yield of asparagus bean. However, the key genes and regulatory pathways involved in low temperature response in this legume are still poorly understood. Methodology. The present study analyzed the transcriptome of seedlings from two asparagus bean cultivars—Dubai bean and Ningjiang 3—using Illumina RNA sequencing (RNA-seq). Correlations between samples were determined by calculating Pearson correlation coefficients (PCC) and principal component analysis (PCA). Differentially expressed genes (DEGs) between two samples were identified using the DESeq package. Transcription factors (TF) prediction, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were also performed. Results Phenotypes and physiological indices indicated that Ningjiang 3 seedlings tolerated cold better than Dubai bean seedlings, in contrast to adult stage. The transcriptome dynamics of the two cultivars were closely compared using Illumina RNA-seq following 0, 3, 12, and 24 h of cold stress at 5 °C and recovery for 3 h at 25 °C room temperature. Global gene expression patterns displayed relatively high correlation between the two cultivars (>0.88), decreasing to 0.79 and 0.81, respectively, at 12 and 24 h of recovery, consistent with the results of principal component analysis. The major transcription factor families identified from differentially expressed genes between the two cultivars included bHLH, NAC, C2H2, MYB, WRKY, and AP2/ERF. The representative GO enrichment terms were protein phosphorylation, photosynthesis, oxidation-reduction process, and cellular glucan metabolic process. Moreover, KEGG analysis of DEGs within each cultivar revealed 36 transcription factors enriched in Dubai bean and Ningjiang 3 seedlings under cold stress. Conclusions These results reveal new information that will improve our understanding of the molecular mechanisms underlying the cold …
bibliographic citation: Miao et al. (2022) Comparative transcriptome analysis of cold-tolerant and -sensitive asparagus bean under chilling stress and recovery. PeerJ 10:e13167 https://doi.org/10.7717/peerj.13167
date submitted: 2021-10-20
date accepted: 2022-03-04
issued: 2022-03-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miao
  given name: Mingjun
author list: Agent
  family name: Tan
  given name: Huaqiang
author list: Agent
  family name: Liang
  given name: Le
author list: Agent
  family name: Huang
  given name: Haitao
author list: Agent
  family name: Chang
  given name: Wei
author list: Agent
  family name: Zhang
  given name: Jianwei
author list: Agent
  family name: Li
  given name: Ju
author list: Agent
  family name: Tang
  given name: Yi
author list: Agent
  family name: Li
  given name: Zhi
author list: Agent
  family name: Lai
  given name: Yunsong
author list: Agent
  family name: Yang
  given name: Liang
author list: Agent
  family name: Li
  given name: Huanxiu
doi: 10.7717/peerj.13167
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-22
copyright: ©2022 Miao et al.
attribution name: Miao et al.

N-mixture models provide informative crocodile (Crocodylus moreletii) abundance estimates in dynamic environments
type: item
type: AcademicArticle
description: Estimates of animal abundance provide essential information for population ecological studies. However, the recording of individuals in the field can be challenging, and accurate estimates require analytical techniques which account for imperfect detection. Here, we quantify local abundances and overall population size of Morelet’s crocodiles (Crocodylus moreletii) in the region of Calakmul (Campeche, Mexico), comparing traditional approaches for crocodylians (Minimum Population Size—MPS; King’s Visible Fraction Method—VFM) with binomial N-mixture models based on Poisson, zero-inflated Poisson (ZIP) and negative binomial (NB) distributions. A total of 191 nocturnal spotlight surveys were conducted across 40 representative locations (hydrologically highly dynamic aquatic sites locally known as aguadas) over a period of 3 years (2017–2019). Local abundance estimates revealed a median of 1 both through MPS (min–max: 0–89; first and third quartiles, Q1–Q3: 0–7) and VFM (0–112; Q1–Q3: 0–9) non-hatchling C. moreletii for each aguada, respectively. The ZIP based N-mixture approach shown overall superior confidence over Poisson and NB, and revealed a median of 6 ± 3 individuals (min = 0; max = 120 ± 18; Q1 = 0; Q3 = 18 ± 4) jointly with higher detectabilities in drying aguadas with low and intermediate vegetation cover. Extrapolating these inferences across all waterbodies in the study area yielded an estimated ~10,000 (7,000–11,000) C. moreletii present, highlighting Calakmul as an important region for this species. Because covariates enable insights into population responses to local environmental conditions, N-mixture models applied to spotlight count data result in particularly insightful estimates of crocodylian detection and abundance.
format: application/pdf
format: text/html
creator: José António Lemos Barão-Nóbrega
creator: Mauricio González-Jaurégui
creator: Robert Jehle
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.12906
publisher: PeerJ Inc.
rights: © 2022 Lemos Barão-Nóbrega et al.
abstract: Estimates of animal abundance provide essential information for population ecological studies. However, the recording of individuals in the field can be challenging, and accurate estimates require analytical techniques which account for imperfect detection. Here, we quantify local abundances and overall population size of Morelet’s crocodiles (Crocodylus moreletii) in the region of Calakmul (Campeche, Mexico), comparing traditional approaches for crocodylians (Minimum Population Size—MPS; King’s Visible Fraction Method—VFM) with binomial N-mixture models based on Poisson, zero-inflated Poisson (ZIP) and negative binomial (NB) distributions. A total of 191 nocturnal spotlight surveys were conducted across 40 representative locations (hydrologically highly dynamic aquatic sites locally known as aguadas) over a period of 3 years (2017–2019). Local abundance estimates revealed a median of 1 both through MPS (min–max: 0–89; first and third quartiles, Q1–Q3: 0–7) and VFM (0–112; Q1–Q3: 0–9) non-hatchling C. moreletii for each aguada, respectively. The ZIP based N-mixture approach shown overall superior confidence over Poisson and NB, and revealed a median of 6 ± 3 individuals (min = 0; max = 120 ± 18; Q1 = 0; Q3 = 18 ± 4) jointly with higher detectabilities in drying aguadas with low and intermediate vegetation cover. Extrapolating these inferences across all waterbodies in the study area yielded an estimated ~10,000 (7,000–11,000) C. moreletii present, highlighting Calakmul as an important region for this species. Because covariates enable insights into population responses to local environmental conditions, N-mixture models applied to spotlight count data result in particularly insightful estimates of crocodylian detection and abundance.
bibliographic citation: Lemos Barão-Nóbrega et al. (2022) N-mixture models provide informative crocodile (Crocodylus moreletii) abundance estimates in dynamic environments. PeerJ 10:e12906 https://doi.org/10.7717/peerj.12906
date submitted: 2020-09-17
date accepted: 2022-01-17
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lemos Barão-Nóbrega
  given name: José António
author list: Agent
  family name: González-Jaurégui
  given name: Mauricio
author list: Agent
  family name: Jehle
  given name: Robert
doi: 10.7717/peerj.12906
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 Lemos Barão-Nóbrega et al.
attribution name: Lemos Barão-Nóbrega et al.

Individuals with fibromyalgia have a different gait pattern and a reduced walk functional capacity: a systematic review with meta-analysis
type: item
type: AcademicArticle
description: Background The aim of the present study was to perform a systematic review and meta-analysis comparing walking test performance and gait pattern between individuals with and without fibromyalgia (FM). Methodology This systematic review was registered in PROSPERO with the following reference: CRD42018116200.The search for the scientific articles in this systematic review was carried out using the MEDLINE, SCOPUS, PEDRO, CINHAL and WEB OF SCIENCE databases. A combination of three conceptual groups of terms was used: (1) fibromyalgia; (2) walk (performance) tests; and (3) gait analysis. The included articles were analyzed for both functional and pattern of walking data of patients with FM. In order to provide a better estimate of the difference between individuals with and without FM on gait, a meta-analysis was performed on the 6MWT (6-minute walk test). Results Thirty-six studies were analyzed, with a total population of 4.078 participants (3.369 FM and 709 individuals without FM). From a functional point of view, the 6MWT distance covered by the group of individuals without FM was significantly greater than that of the individuals with FM in all the analyzed studies. In addition, when comparing the results obtained in the gait pattern analysis, it was observed that individuals with FM walked slower, with a shorter stride length and lower cadence compare to individuals without FM. Conclusions It is possible to affirm that individuals with FM perform walking tests differently than individuals without FM. It was observed that individuals with FM walk performing a cycle of shorter length and lower frequency, producing a slower gait, which results in a shorter distance traveled, in the same period of time, with respect to healthy subjects.
format: application/pdf
format: text/html
creator: Elio Carrasco-Vega
creator: María Ruiz-Muñoz
creator: Antonio Cuesta-Vargas
creator: Rita Pilar Romero-Galisteo
creator: Manuel González-Sánchez
subject: Anesthesiology and Pain Management
subject: Kinesiology
subject: Rheumatology
subject: Women’s Health
description: doi:10.7717/peerj.12908
publisher: PeerJ Inc.
rights: © 2022 Carrasco-Vega et al.
abstract: Background The aim of the present study was to perform a systematic review and meta-analysis comparing walking test performance and gait pattern between individuals with and without fibromyalgia (FM). Methodology This systematic review was registered in PROSPERO with the following reference: CRD42018116200.The search for the scientific articles in this systematic review was carried out using the MEDLINE, SCOPUS, PEDRO, CINHAL and WEB OF SCIENCE databases. A combination of three conceptual groups of terms was used: (1) fibromyalgia; (2) walk (performance) tests; and (3) gait analysis. The included articles were analyzed for both functional and pattern of walking data of patients with FM. In order to provide a better estimate of the difference between individuals with and without FM on gait, a meta-analysis was performed on the 6MWT (6-minute walk test). Results Thirty-six studies were analyzed, with a total population of 4.078 participants (3.369 FM and 709 individuals without FM). From a functional point of view, the 6MWT distance covered by the group of individuals without FM was significantly greater than that of the individuals with FM in all the analyzed studies. In addition, when comparing the results obtained in the gait pattern analysis, it was observed that individuals with FM walked slower, with a shorter stride length and lower cadence compare to individuals without FM. Conclusions It is possible to affirm that individuals with FM perform walking tests differently than individuals without FM. It was observed that individuals with FM walk performing a cycle of shorter length and lower frequency, producing a slower gait, which results in a shorter distance traveled, in the same period of time, with respect to healthy subjects.
bibliographic citation: Carrasco-Vega et al. (2022) Individuals with fibromyalgia have a different gait pattern and a reduced walk functional capacity: a systematic review with meta-analysis. PeerJ 10:e12908 https://doi.org/10.7717/peerj.12908
date submitted: 2021-04-30
date accepted: 2022-01-18
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carrasco-Vega
  given name: Elio
author list: Agent
  family name: Ruiz-Muñoz
  given name: María
author list: Agent
  family name: Cuesta-Vargas
  given name: Antonio
author list: Agent
  family name: Romero-Galisteo
  given name: Rita Pilar
author list: Agent
  family name: González-Sánchez
  given name: Manuel
doi: 10.7717/peerj.12908
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: ©2022 Carrasco-Vega et al.
attribution name: Carrasco-Vega et al.

Exploring interactions between Beauveria and Metarhizium strains through co-inoculation and responses of perennial ryegrass in a one-year trial
type: item
type: AcademicArticle
description: Perennial ryegrass (Lolium perenne L.) possesses a high level of nutritional quality and is widely used as a forage species to establish permanent pastures in southern Chile. However, the productivity of most such pastures is limited by various environmental agents, such as insect pests and drought. In this context, our work stresses the need for elucidating the ability of fungal endophytes to establish interactions with plants, and to understand how these processes contribute to plant performance and fitness. Therefore, we evaluated the colonization and impact of two native strains of the endophytic insect-pathogenic fungus (EIPF) group isolated from permanent ryegrass pastures in southern Chile. Roots and seeds of ryegrass and scarabaeid larvae were collected from nine different ryegrass pastures in the Los Ríos region of southern Chile to specifically isolate EIPFs belonging to the genera Beauveria and Metarhizium. Fungal isolations were made on 2% water agar with antibiotics, and strains were identified by analyzing the entire internal transcribed spacer (ITS) 1-5.8S-ITS2 ribosomal DNA region. Four strains of Beauveria and 33 strains of Metarhizium were isolated only in scarabaeid larvae from ryegrass pastures across four sites. Experimental mini-pastures that were either not inoculated (control) or co-inoculated with conidia of the strains Beauveria vermiconia NRRL B-67993 (P55_1) and Metarhizium aff. lepidiotae NRRL B-67994 (M25_2) under two soil humidity levels were used. Ryegrass plants were randomly collected from the mini-pastures to characterize EIPF colonization in the roots by real-time PCR and fluorescence microscopy. Aboveground biomass was measured to analyze the putative impact of colonization on the mini-pastures’ aboveground phenotypic traits with R software using a linear mixed-effects model and the ANOVA statistical test. Seasonal variation in the relative abundance of EIPFs was observed, which was similar between both strains from autumn to spr…
format: application/pdf
format: text/html
creator: Milena Vera
creator: Sarah Zuern
creator: Carlos Henríquez-Valencia
creator: Carlos Loncoman
creator: Javier Canales
creator: Frank Waller
creator: Esteban Basoalto
creator: Sigisfredo Garnica
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.12924
publisher: PeerJ Inc.
rights: © 2022 Vera et al.
abstract: Perennial ryegrass (Lolium perenne L.) possesses a high level of nutritional quality and is widely used as a forage species to establish permanent pastures in southern Chile. However, the productivity of most such pastures is limited by various environmental agents, such as insect pests and drought. In this context, our work stresses the need for elucidating the ability of fungal endophytes to establish interactions with plants, and to understand how these processes contribute to plant performance and fitness. Therefore, we evaluated the colonization and impact of two native strains of the endophytic insect-pathogenic fungus (EIPF) group isolated from permanent ryegrass pastures in southern Chile. Roots and seeds of ryegrass and scarabaeid larvae were collected from nine different ryegrass pastures in the Los Ríos region of southern Chile to specifically isolate EIPFs belonging to the genera Beauveria and Metarhizium. Fungal isolations were made on 2% water agar with antibiotics, and strains were identified by analyzing the entire internal transcribed spacer (ITS) 1-5.8S-ITS2 ribosomal DNA region. Four strains of Beauveria and 33 strains of Metarhizium were isolated only in scarabaeid larvae from ryegrass pastures across four sites. Experimental mini-pastures that were either not inoculated (control) or co-inoculated with conidia of the strains Beauveria vermiconia NRRL B-67993 (P55_1) and Metarhizium aff. lepidiotae NRRL B-67994 (M25_2) under two soil humidity levels were used. Ryegrass plants were randomly collected from the mini-pastures to characterize EIPF colonization in the roots by real-time PCR and fluorescence microscopy. Aboveground biomass was measured to analyze the putative impact of colonization on the mini-pastures’ aboveground phenotypic traits with R software using a linear mixed-effects model and the ANOVA statistical test. Seasonal variation in the relative abundance of EIPFs was observed, which was similar between both strains from autumn to spr…
bibliographic citation: Vera et al. (2022) Exploring interactions between Beauveria and Metarhizium strains through co-inoculation and responses of perennial ryegrass in a one-year trial. PeerJ 10:e12924 https://doi.org/10.7717/peerj.12924
date submitted: 2021-07-15
date accepted: 2022-01-20
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vera
  given name: Milena
author list: Agent
  family name: Zuern
  given name: Sarah
author list: Agent
  family name: Henríquez-Valencia
  given name: Carlos
author list: Agent
  family name: Loncoman
  given name: Carlos
author list: Agent
  family name: Canales
  given name: Javier
author list: Agent
  family name: Waller
  given name: Frank
author list: Agent
  family name: Basoalto
  given name: Esteban
author list: Agent
  family name: Garnica
  given name: Sigisfredo
doi: 10.7717/peerj.12924
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 Vera et al.
attribution name: Vera et al.

Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility
type: item
type: AcademicArticle
description: Background Impaired meiosis can result in absence of sperm in the seminal fluid. This condition, namely non-obstructive azoospermia (NOA), is one of the reasons of male infertility. Despite the low number of studies on meiosis 1-associated protein (M1AP) in the literature, M1AP is known to be crucial for spermatogenesis. Recently, seven variants (five missense, one frameshift, one splice-site) have been reported in the M1AP gene as associated with NOA, cryptozoospermia and oligozoospermia in two separate studies. However, all missense variants were evaluated as variant of uncertain significance by these studies. Therefore, we aimed to analyze their structural impacts on the M1AP protein that could lead to NOA. Methods We firstly performed an evolutionary conservation analysis for the variant positions. Afterwards, a comprehensive molecular modelling study was performed for the M1AP structure. By utilizing this model, protein dynamics were sampled for the wild-type and variants by performing molecular dynamics (MD) simulations. Results All variant positions are highly conserved, indicating that they are potentially important for function. In MD simulations, none of the variants led to a general misfolding or loss of stability in the protein structure, but they did cause severe modifications in the conformational dynamics of M1AP, particularly through changes in local interactions affecting flexibility, hinge and secondary structure. Conclusions Due to critical perturbations in protein dynamics, we propose that these variants may cause NOA by affecting important interactions regulating meiosis, particularly in wild-type M1AP deficiency since the variants are reported to be homozygous or bi-allelic in the infertile individuals. Our results provided reasonable insights about the M1AP structure and the effects of the variants to the structure and dynamics, which should be further investigated by experimental studies to validate.
format: application/pdf
format: text/html
creator: Umut Gerlevik
creator: Mahmut Cerkez Ergoren
creator: Osman Uğur Sezerman
creator: Sehime Gulsun Temel
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Andrology
subject: Medical Genetics
description: doi:10.7717/peerj.12947
publisher: PeerJ Inc.
rights: © 2022 Gerlevik et al.
abstract: Background Impaired meiosis can result in absence of sperm in the seminal fluid. This condition, namely non-obstructive azoospermia (NOA), is one of the reasons of male infertility. Despite the low number of studies on meiosis 1-associated protein (M1AP) in the literature, M1AP is known to be crucial for spermatogenesis. Recently, seven variants (five missense, one frameshift, one splice-site) have been reported in the M1AP gene as associated with NOA, cryptozoospermia and oligozoospermia in two separate studies. However, all missense variants were evaluated as variant of uncertain significance by these studies. Therefore, we aimed to analyze their structural impacts on the M1AP protein that could lead to NOA. Methods We firstly performed an evolutionary conservation analysis for the variant positions. Afterwards, a comprehensive molecular modelling study was performed for the M1AP structure. By utilizing this model, protein dynamics were sampled for the wild-type and variants by performing molecular dynamics (MD) simulations. Results All variant positions are highly conserved, indicating that they are potentially important for function. In MD simulations, none of the variants led to a general misfolding or loss of stability in the protein structure, but they did cause severe modifications in the conformational dynamics of M1AP, particularly through changes in local interactions affecting flexibility, hinge and secondary structure. Conclusions Due to critical perturbations in protein dynamics, we propose that these variants may cause NOA by affecting important interactions regulating meiosis, particularly in wild-type M1AP deficiency since the variants are reported to be homozygous or bi-allelic in the infertile individuals. Our results provided reasonable insights about the M1AP structure and the effects of the variants to the structure and dynamics, which should be further investigated by experimental studies to validate.
bibliographic citation: Gerlevik et al. (2022) Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility. PeerJ 10:e12947 https://doi.org/10.7717/peerj.12947
date submitted: 2021-03-12
date accepted: 2022-01-25
issued: 2022-03-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gerlevik
  given name: Umut
author list: Agent
  family name: Ergoren
  given name: Mahmut Cerkez
author list: Agent
  family name: Sezerman
  given name: Osman Uğur
author list: Agent
  family name: Temel
  given name: Sehime Gulsun
doi: 10.7717/peerj.12947
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-21
copyright: © 2022 Gerlevik et al.
attribution name: Gerlevik et al.

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