PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey
items: New sources of Sym2A allele in the pea (Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX
items: Transcriptional characterization and response to defense elicitors of mevalonate pathway genes in cotton (Gossypium arboreum L.)
items: Roles of phytohormone changes in the grain yield of rice plants exposed to heat: a review
items: Low expression or hypermethylation of PLK2 might predict favorable prognosis for patients with glioblastoma multiforme
items: Hematological convergence between Mesozoic marine reptiles (Sauropterygia) and extant aquatic amniotes elucidates diving adaptations in plesiosaurs
items: Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum)
items: Environmental sampling to assess the bioburden of Mycobacterium avium subspecies paratuberculosis in drylot pens on California dairies
items: The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster
items: Decrease in walking speed increases hip moment impulse in the frontal plane during the stance phase

Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey
type: item
type: AcademicArticle
description: Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children’s health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.
format: application/pdf
format: text/html
creator: Roberto Cabrera-Contreras
creator: Rosa I. Santamaría
creator: Patricia Bustos
creator: Irma Martínez-Flores
creator: Enrique Meléndez-Herrada
creator: Rubén Morelos-Ramírez
creator: Martín Barbosa-Amezcua
creator: Vanessa González-Covarrubias
creator: Eugenia Silva-Herzog
creator: Xavier Soberón
creator: Víctor González
subject: Genomics
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.8068
publisher: PeerJ Inc.
rights: © 2019 Cabrera-Contreras et al.
abstract: Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children’s health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.
bibliographic citation: Cabrera-Contreras et al. (2019) Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey. PeerJ 7:e8068 https://doi.org/10.7717/peerj.8068
date submitted: 2019-04-29
date accepted: 2019-10-20
issued: 2019-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cabrera-Contreras
  given name: Roberto
author list: Agent
  family name: Santamaría
  given name: Rosa I.
author list: Agent
  family name: Bustos
  given name: Patricia
author list: Agent
  family name: Martínez-Flores
  given name: Irma
author list: Agent
  family name: Meléndez-Herrada
  given name: Enrique
author list: Agent
  family name: Morelos-Ramírez
  given name: Rubén
author list: Agent
  family name: Barbosa-Amezcua
  given name: Martín
author list: Agent
  family name: González-Covarrubias
  given name: Vanessa
author list: Agent
  family name: Silva-Herzog
  given name: Eugenia
author list: Agent
  family name: Soberón
  given name: Xavier
author list: Agent
  family name: González
  given name: Víctor
doi: 10.7717/peerj.8068
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-20
copyright: ©2019 Cabrera-Contreras et al.
attribution name: Cabrera-Contreras et al.

New sources of Sym2A allele in the pea (Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX
type: item
type: AcademicArticle
description: At the onset of legume-rhizobial symbiosis, the mutual recognition of partners occurs based on a complicated interaction between signal molecules and receptors. Bacterial signal molecules named Nod factors (“nodulation factors”) are perceived by the plant LysM-containing receptor-like kinases (LysM-RLKs) that recognize details of its structure (i.e., unique substitutions), thus providing the conditions particular to symbiosis. In the garden pea (Pisum sativum L.), the allelic state of Sym2 gene has long been reported to regulate the symbiotic specificity: for infection to be successful, plants with the Sym2A allele (for “Sym2 Afghan”, as these genotypes originate mostly from Afghanistan) require an additional acetylation of the Nod factor which is irrelevant for genotypes with the Sym2E allele (for “Sym2 European”). Despite being described about 90 years ago, Sym2 has not yet been cloned, though phenotypic analysis suggests it probably encodes a receptor for the Nod factor. Recently, we described a novel pea gene LykX (PsLykX) from the LysM-RLK gene family that demonstrates a perfect correlation between its allelic state and the symbiotic specificity of the Sym2A-type. Here we report on a series of Middle-Eastern pea genotypes exhibiting the phenotype of narrow symbiotic specificity discovered in the VIR plant genetic resources gene bank (Saint-Petersburg, Russia). These genotypes are new sources of Sym2A, as has been confirmed by an allelism test with Sym2A pea cv. Afghanistan. Within these genotypes, LykX is present either in the allelic state characteristic for cv. Afghanistan, or in another, minor allelic state found in two genotypes from Tajikistan and Turkmenistan. Plants carrying the second allele demonstrate the same block of rhizobial infection as cv. Afghanistan when inoculated with an incompatible strain. Intriguingly, this “Tajik” allele of LykX differs from the “European” one by a single nucleotide polymorphism leading to an R75P change in the receptor …
format: application/pdf
format: text/html
creator: Anton S. Sulima
creator: Vladimir A. Zhukov
creator: Olga A. Kulaeva
creator: Ekaterina N. Vasileva
creator: Alexey Y. Borisov
creator: Igor A. Tikhonovich
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.8070
publisher: PeerJ Inc.
rights: © 2019 Sulima et al.
abstract: At the onset of legume-rhizobial symbiosis, the mutual recognition of partners occurs based on a complicated interaction between signal molecules and receptors. Bacterial signal molecules named Nod factors (“nodulation factors”) are perceived by the plant LysM-containing receptor-like kinases (LysM-RLKs) that recognize details of its structure (i.e., unique substitutions), thus providing the conditions particular to symbiosis. In the garden pea (Pisum sativum L.), the allelic state of Sym2 gene has long been reported to regulate the symbiotic specificity: for infection to be successful, plants with the Sym2A allele (for “Sym2 Afghan”, as these genotypes originate mostly from Afghanistan) require an additional acetylation of the Nod factor which is irrelevant for genotypes with the Sym2E allele (for “Sym2 European”). Despite being described about 90 years ago, Sym2 has not yet been cloned, though phenotypic analysis suggests it probably encodes a receptor for the Nod factor. Recently, we described a novel pea gene LykX (PsLykX) from the LysM-RLK gene family that demonstrates a perfect correlation between its allelic state and the symbiotic specificity of the Sym2A-type. Here we report on a series of Middle-Eastern pea genotypes exhibiting the phenotype of narrow symbiotic specificity discovered in the VIR plant genetic resources gene bank (Saint-Petersburg, Russia). These genotypes are new sources of Sym2A, as has been confirmed by an allelism test with Sym2A pea cv. Afghanistan. Within these genotypes, LykX is present either in the allelic state characteristic for cv. Afghanistan, or in another, minor allelic state found in two genotypes from Tajikistan and Turkmenistan. Plants carrying the second allele demonstrate the same block of rhizobial infection as cv. Afghanistan when inoculated with an incompatible strain. Intriguingly, this “Tajik” allele of LykX differs from the “European” one by a single nucleotide polymorphism leading to an R75P change in the receptor …
bibliographic citation: Sulima et al. (2019) New sources of Sym2A allele in the pea (Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX. PeerJ 7:e8070 https://doi.org/10.7717/peerj.8070
date submitted: 2019-07-31
date accepted: 2019-10-20
issued: 2019-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sulima
  given name: Anton S.
author list: Agent
  family name: Zhukov
  given name: Vladimir A.
author list: Agent
  family name: Kulaeva
  given name: Olga A.
author list: Agent
  family name: Vasileva
  given name: Ekaterina N.
author list: Agent
  family name: Borisov
  given name: Alexey Y.
author list: Agent
  family name: Tikhonovich
  given name: Igor A.
doi: 10.7717/peerj.8070
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-20
copyright: ©2019 Sulima et al.
attribution name: Sulima et al.

Transcriptional characterization and response to defense elicitors of mevalonate pathway genes in cotton (Gossypium arboreum L.)
type: item
type: AcademicArticle
description: The mevalonate (MVA) pathway is responsible for the biosynthesis of cytosolic terpenes including gossypol and its derivatives, which play an important role in the cotton plant’s defense against pathogens and herbivores. In this study, we identified and cloned 17 potentially functional genes encoding enzymes that catalyze the six steps of the MVA pathway in Gossypium arboreum. Expression pattern analysis by qRT-PCR demonstrated that these genes had tissue-specific expression profiles and were most prevalently expressed in roots. Moreover, these genes were up-regulated in response to several elicitors, including methyl jasmonate and salicylic acid, as well as Verticillium dahliae infection and Helicoverpa armigera infestation. This indicates that the MVA pathway genes are involved in the signaling pathway regulated by exogenous hormones and the resistance of cotton plants to pathogens and herbivores. Our results improve the understanding of cytosolic terpene biosynthesis in Gossypium species and lay the foundation for further research on gossypol biosynthesis.
format: application/pdf
format: text/html
creator: Zhiqiang Zhang
creator: Wei Liu
creator: Zongbin Ma
creator: Wei Zhu
creator: Lin Jia
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.8123
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: The mevalonate (MVA) pathway is responsible for the biosynthesis of cytosolic terpenes including gossypol and its derivatives, which play an important role in the cotton plant’s defense against pathogens and herbivores. In this study, we identified and cloned 17 potentially functional genes encoding enzymes that catalyze the six steps of the MVA pathway in Gossypium arboreum. Expression pattern analysis by qRT-PCR demonstrated that these genes had tissue-specific expression profiles and were most prevalently expressed in roots. Moreover, these genes were up-regulated in response to several elicitors, including methyl jasmonate and salicylic acid, as well as Verticillium dahliae infection and Helicoverpa armigera infestation. This indicates that the MVA pathway genes are involved in the signaling pathway regulated by exogenous hormones and the resistance of cotton plants to pathogens and herbivores. Our results improve the understanding of cytosolic terpene biosynthesis in Gossypium species and lay the foundation for further research on gossypol biosynthesis.
bibliographic citation: Zhang et al. (2019) Transcriptional characterization and response to defense elicitors of mevalonate pathway genes in cotton (Gossypium arboreum L.). PeerJ 7:e8123 https://doi.org/10.7717/peerj.8123
date submitted: 2019-07-29
date accepted: 2019-10-30
issued: 2019-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Zhiqiang
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Ma
  given name: Zongbin
author list: Agent
  family name: Zhu
  given name: Wei
author list: Agent
  family name: Jia
  given name: Lin
doi: 10.7717/peerj.8123
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-20
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Roles of phytohormone changes in the grain yield of rice plants exposed to heat: a review
type: item
type: AcademicArticle
description: During its reproductive phase, rice is susceptible to heat stress. Heat events will occur at all stages during the reproductive phase of rice as a result of global warming. Moreover, rice yield traits respond differently to heat stress during panicle initiation, flowering and grain filling. The reduction in the number of spikelets per panicle of heat-stressed plants is due to the attenuated differentiation of secondary branches and their attached florets as well as the promotion of their degradation during the panicle-initiation stage but is not affected by heat stress thereafter. Spikelet sterility as a result of heat stress is attributed not only to physiological abnormalities in the reproductive organs during the flowering stage but also to structural and morphological abnormalities in reproductive organs during the panicle-initiation stage. The reduced grain weight of heat-stressed plants is due to a reduction in nonstructural carbohydrates, undeveloped vascular bundles, and a reduction in glume size during the panicle-initiation stage, while a shortened grain-filling duration, reduced grain-filling rate, and decreased grain width contribute to reduced grain weight during the grain-filling stage. Thus, screening and breeding rice varieties that have comprehensive tolerance to heat stress at all time points during their reproductive stage may be possible to withstand unpredictable heat events in the future. The responses of yield traits to heat stress are regulated by phytohormone levels, which are determined by phytohormone homeostasis. Currently, the biosynthesis and transport of phytohormones are the key processes that determine phytohormone levels in and grain yield of rice under heat stress. Studies on phytohormone homeostatic responses are needed to further reveal the key processes that determine phytohormone levels under heat conditions.
format: application/pdf
format: text/html
creator: Chao Wu
creator: She Tang
creator: Ganghua Li
creator: Shaohua Wang
creator: Shah Fahad
creator: Yanfeng Ding
subject: Agricultural Science
subject: Plant Science
subject: Environmental Impacts
description: doi:10.7717/peerj.7792
publisher: PeerJ Inc.
rights: © 2019 Wu et al.
abstract: During its reproductive phase, rice is susceptible to heat stress. Heat events will occur at all stages during the reproductive phase of rice as a result of global warming. Moreover, rice yield traits respond differently to heat stress during panicle initiation, flowering and grain filling. The reduction in the number of spikelets per panicle of heat-stressed plants is due to the attenuated differentiation of secondary branches and their attached florets as well as the promotion of their degradation during the panicle-initiation stage but is not affected by heat stress thereafter. Spikelet sterility as a result of heat stress is attributed not only to physiological abnormalities in the reproductive organs during the flowering stage but also to structural and morphological abnormalities in reproductive organs during the panicle-initiation stage. The reduced grain weight of heat-stressed plants is due to a reduction in nonstructural carbohydrates, undeveloped vascular bundles, and a reduction in glume size during the panicle-initiation stage, while a shortened grain-filling duration, reduced grain-filling rate, and decreased grain width contribute to reduced grain weight during the grain-filling stage. Thus, screening and breeding rice varieties that have comprehensive tolerance to heat stress at all time points during their reproductive stage may be possible to withstand unpredictable heat events in the future. The responses of yield traits to heat stress are regulated by phytohormone levels, which are determined by phytohormone homeostasis. Currently, the biosynthesis and transport of phytohormones are the key processes that determine phytohormone levels in and grain yield of rice under heat stress. Studies on phytohormone homeostatic responses are needed to further reveal the key processes that determine phytohormone levels under heat conditions.
bibliographic citation: Wu et al. (2019) Roles of phytohormone changes in the grain yield of rice plants exposed to heat: a review. PeerJ 7:e7792 https://doi.org/10.7717/peerj.7792
date submitted: 2018-07-24
date accepted: 2019-08-29
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Chao
author list: Agent
  family name: Tang
  given name: She
author list: Agent
  family name: Li
  given name: Ganghua
author list: Agent
  family name: Wang
  given name: Shaohua
author list: Agent
  family name: Fahad
  given name: Shah
author list: Agent
  family name: Ding
  given name: Yanfeng
doi: 10.7717/peerj.7792
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: © 2019 Wu et al.
attribution name: Wu et al.

Low expression or hypermethylation of PLK2 might predict favorable prognosis for patients with glioblastoma multiforme
type: item
type: AcademicArticle
description: Background As the most aggressive brain tumor, patients with glioblastoma multiforme (GBM) have a poor prognosis. Our purpose was to explore prognostic value of Polo-like kinase 2 (PLK2) in GBM, a member of the PLKs family. Methods The expression profile of PLK2 in GBM was obtained from The Cancer Genome Atlas database. The PLK2 expression in GBM was tested. Kaplan–Meier curves were generated to assess the association between PLK2 expression and overall survival (OS) in patients with GBM. Furthermore, to assess its prognostic significance in patients with primary GBM, we constructed univariate and multivariate Cox regression models. The association between PLK2 expression and its methylation was then performed. Differentially expressed genes correlated with PLK2 were identified by Pearson test and functional enrichment analysis was performed. Results Overall survival results showed that low PLK2 expression had a favorable prognosis of patients with GBM (P-value = 0.0022). Furthermore, PLK2 (HR = 0.449, 95% CI [0.243–0.830], P-value = 0.011) was positively associated with OS by multivariate Cox regression analysis. In cluster 5, DNA methylated PLK2 had the lowest expression, which implied that PLK2 expression might be affected by its DNA methylation status in GBM. PLK2 in CpG island methylation phenotype (G-CIMP) had lower expression than non G-CIMP group (P = 0.0077). Regression analysis showed that PLK2 expression was negatively correlated with its DNA methylation (P = 0.0062, Pearson r = −0.3855). Among all differentially expressed genes of GBM, CYGB (r = 0.5551; P < 0.0001), ISLR2 (r = 0.5126; P < 0.0001), RPP25 (r = 0.5333; P < 0.0001) and SOX2 (r = −0.4838; P < 0.0001) were strongly correlated with PLK2. Functional enrichment analysis results showed that these genes were enriched several biological processes or pathways that were associated with GBM. Conclusion Polo-like kinase 2 expression is regulated by DNA methylation in GBM, and its low expression or hyper…
format: application/pdf
format: text/html
creator: Xiangping Xia
creator: Fang Cao
creator: Xiaolu Yuan
creator: Qiang Zhang
creator: Wei Chen
creator: Yunhu Yu
creator: Hua Xiao
creator: Chong Han
creator: Shengtao Yao
subject: Bioinformatics
subject: Neurology
subject: Surgery and Surgical Specialties
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.7974
publisher: PeerJ Inc.
rights: © 2019 Xia et al.
abstract: Background As the most aggressive brain tumor, patients with glioblastoma multiforme (GBM) have a poor prognosis. Our purpose was to explore prognostic value of Polo-like kinase 2 (PLK2) in GBM, a member of the PLKs family. Methods The expression profile of PLK2 in GBM was obtained from The Cancer Genome Atlas database. The PLK2 expression in GBM was tested. Kaplan–Meier curves were generated to assess the association between PLK2 expression and overall survival (OS) in patients with GBM. Furthermore, to assess its prognostic significance in patients with primary GBM, we constructed univariate and multivariate Cox regression models. The association between PLK2 expression and its methylation was then performed. Differentially expressed genes correlated with PLK2 were identified by Pearson test and functional enrichment analysis was performed. Results Overall survival results showed that low PLK2 expression had a favorable prognosis of patients with GBM (P-value = 0.0022). Furthermore, PLK2 (HR = 0.449, 95% CI [0.243–0.830], P-value = 0.011) was positively associated with OS by multivariate Cox regression analysis. In cluster 5, DNA methylated PLK2 had the lowest expression, which implied that PLK2 expression might be affected by its DNA methylation status in GBM. PLK2 in CpG island methylation phenotype (G-CIMP) had lower expression than non G-CIMP group (P = 0.0077). Regression analysis showed that PLK2 expression was negatively correlated with its DNA methylation (P = 0.0062, Pearson r = −0.3855). Among all differentially expressed genes of GBM, CYGB (r = 0.5551; P < 0.0001), ISLR2 (r = 0.5126; P < 0.0001), RPP25 (r = 0.5333; P < 0.0001) and SOX2 (r = −0.4838; P < 0.0001) were strongly correlated with PLK2. Functional enrichment analysis results showed that these genes were enriched several biological processes or pathways that were associated with GBM. Conclusion Polo-like kinase 2 expression is regulated by DNA methylation in GBM, and its low expression or hyper…
bibliographic citation: Xia et al. (2019) Low expression or hypermethylation of PLK2 might predict favorable prognosis for patients with glioblastoma multiforme. PeerJ 7:e7974 https://doi.org/10.7717/peerj.7974
date submitted: 2019-01-25
date accepted: 2019-10-02
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xia
  given name: Xiangping
author list: Agent
  family name: Cao
  given name: Fang
author list: Agent
  family name: Yuan
  given name: Xiaolu
author list: Agent
  family name: Zhang
  given name: Qiang
author list: Agent
  family name: Chen
  given name: Wei
author list: Agent
  family name: Yu
  given name: Yunhu
author list: Agent
  family name: Xiao
  given name: Hua
author list: Agent
  family name: Han
  given name: Chong
author list: Agent
  family name: Yao
  given name: Shengtao
doi: 10.7717/peerj.7974
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: © 2019 Xia et al.
attribution name: Xia et al.

Hematological convergence between Mesozoic marine reptiles (Sauropterygia) and extant aquatic amniotes elucidates diving adaptations in plesiosaurs
type: item
type: AcademicArticle
description: Plesiosaurs are a prominent group of Mesozoic marine reptiles, belonging to the more inclusive clades Pistosauroidea and Sauropterygia. In the Middle Triassic, the early pistosauroid ancestors of plesiosaurs left their ancestral coastal habitats and increasingly adapted to a life in the open ocean. This ecological shift was accompanied by profound changes in locomotion, sensory ecology and metabolism. However, investigations of physiological adaptations on the cellular level related to the pelagic lifestyle are lacking so far. Using vascular canal diameter, derived from osteohistological thin-sections, we show that inferred red blood cell size significantly increases in pistosauroids compared to more basal sauropterygians. This change appears to have occurred in conjunction with the dispersal to open marine environments, with cell size remaining consistently large in plesiosaurs. Enlarged red blood cells likely represent an adaptation of plesiosaurs repeated deep dives in the pelagic habitat and mirror conditions found in extant marine mammals and birds. Our results emphasize physiological aspects of adaptive convergence among fossil and extant marine amniotes and add to our current understanding of plesiosaur evolution.
format: application/pdf
format: text/html
creator: Corinna V. Fleischle
creator: P. Martin Sander
creator: Tanja Wintrich
creator: Kai R. Caspar
subject: Evolutionary Studies
subject: Paleontology
subject: Histology
description: doi:10.7717/peerj.8022
publisher: PeerJ Inc.
rights: © 2019 Fleischle et al.
abstract: Plesiosaurs are a prominent group of Mesozoic marine reptiles, belonging to the more inclusive clades Pistosauroidea and Sauropterygia. In the Middle Triassic, the early pistosauroid ancestors of plesiosaurs left their ancestral coastal habitats and increasingly adapted to a life in the open ocean. This ecological shift was accompanied by profound changes in locomotion, sensory ecology and metabolism. However, investigations of physiological adaptations on the cellular level related to the pelagic lifestyle are lacking so far. Using vascular canal diameter, derived from osteohistological thin-sections, we show that inferred red blood cell size significantly increases in pistosauroids compared to more basal sauropterygians. This change appears to have occurred in conjunction with the dispersal to open marine environments, with cell size remaining consistently large in plesiosaurs. Enlarged red blood cells likely represent an adaptation of plesiosaurs repeated deep dives in the pelagic habitat and mirror conditions found in extant marine mammals and birds. Our results emphasize physiological aspects of adaptive convergence among fossil and extant marine amniotes and add to our current understanding of plesiosaur evolution.
bibliographic citation: Fleischle et al. (2019) Hematological convergence between Mesozoic marine reptiles (Sauropterygia) and extant aquatic amniotes elucidates diving adaptations in plesiosaurs. PeerJ 7:e8022 https://doi.org/10.7717/peerj.8022
date submitted: 2019-07-23
date accepted: 2019-10-10
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fleischle
  given name: Corinna V.
author list: Agent
  family name: Sander
  given name: P. Martin
author list: Agent
  family name: Wintrich
  given name: Tanja
author list: Agent
  family name: Caspar
  given name: Kai R.
doi: 10.7717/peerj.8022
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: © 2019 Fleischle et al.
attribution name: Fleischle et al.

Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum)
type: item
type: AcademicArticle
description: Superoxide dismutases (SODs) are a family of key antioxidant enzymes that play a crucial role in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, a genome-wide analysis of the SOD gene family in wheat were performed. Twenty-six SOD genes were identified from the whole genome of wheat, including 17 Cu/Zn-SODs, six Fe-SODs, and three Mn-SODs. The chromosomal location mapping analysis indicated that these three types of SOD genes were only distributed on 2, 4, and 7 chromosomes, respectively. Phylogenetic analyses of wheat SODs and several other species revealed that these SOD proteins can be assigned to two major categories. SOD1 mainly comprises of Cu/Zn-SODs, and SOD2 mainly comprises of Fe-SODs and Mn-SODs. Gene structure and motif analyses indicated that most of the SOD genes showed a relatively conserved exon/intron arrangement and motif composition. Analyses of transcriptional data indicated that most of the wheat SOD genes were expressed in almost all of the examined tissues and had important functions in abiotic stress resistance. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to reveal the regulating roles of wheat SOD gene family in response to NaCl, mannitol, and polyethylene glycol stresses. qRT-PCR showed that eight randomly selected genes with relatively high expression levels responded to all three stresses based on released transcriptome data. However, their degree of response and response patterns were different. Interestingly, among these genes, TaSOD1.7, TaSOD1.9, TaSOD2.1, and TaSOD2.3 feature research value owing to their remarkable expression-fold change in leaves or roots under different stresses. Overall, our results provide a basis of further functional research on the SOD gene family in wheat and facilitate their potential use for applications in the genetic improvement on wheat in drought and salt stress environments.
format: application/pdf
format: text/html
creator: Wenqiang Jiang
creator: Lei Yang
creator: Yiqin He
creator: Haotian Zhang
creator: Wei Li
creator: Huaigu Chen
creator: Dongfang Ma
creator: Junliang Yin
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.8062
publisher: PeerJ Inc.
rights: © 2019 Jiang et al.
abstract: Superoxide dismutases (SODs) are a family of key antioxidant enzymes that play a crucial role in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, a genome-wide analysis of the SOD gene family in wheat were performed. Twenty-six SOD genes were identified from the whole genome of wheat, including 17 Cu/Zn-SODs, six Fe-SODs, and three Mn-SODs. The chromosomal location mapping analysis indicated that these three types of SOD genes were only distributed on 2, 4, and 7 chromosomes, respectively. Phylogenetic analyses of wheat SODs and several other species revealed that these SOD proteins can be assigned to two major categories. SOD1 mainly comprises of Cu/Zn-SODs, and SOD2 mainly comprises of Fe-SODs and Mn-SODs. Gene structure and motif analyses indicated that most of the SOD genes showed a relatively conserved exon/intron arrangement and motif composition. Analyses of transcriptional data indicated that most of the wheat SOD genes were expressed in almost all of the examined tissues and had important functions in abiotic stress resistance. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to reveal the regulating roles of wheat SOD gene family in response to NaCl, mannitol, and polyethylene glycol stresses. qRT-PCR showed that eight randomly selected genes with relatively high expression levels responded to all three stresses based on released transcriptome data. However, their degree of response and response patterns were different. Interestingly, among these genes, TaSOD1.7, TaSOD1.9, TaSOD2.1, and TaSOD2.3 feature research value owing to their remarkable expression-fold change in leaves or roots under different stresses. Overall, our results provide a basis of further functional research on the SOD gene family in wheat and facilitate their potential use for applications in the genetic improvement on wheat in drought and salt stress environments.
bibliographic citation: Jiang et al. (2019) Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum). PeerJ 7:e8062 https://doi.org/10.7717/peerj.8062
date submitted: 2018-11-29
date accepted: 2019-10-20
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Wenqiang
author list: Agent
  family name: Yang
  given name: Lei
author list: Agent
  family name: He
  given name: Yiqin
author list: Agent
  family name: Zhang
  given name: Haotian
author list: Agent
  family name: Li
  given name: Wei
author list: Agent
  family name: Chen
  given name: Huaigu
author list: Agent
  family name: Ma
  given name: Dongfang
author list: Agent
  family name: Yin
  given name: Junliang
doi: 10.7717/peerj.8062
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: ©2019 Jiang et al.
attribution name: Jiang et al.

Environmental sampling to assess the bioburden of Mycobacterium avium subspecies paratuberculosis in drylot pens on California dairies
type: item
type: AcademicArticle
description: Mycobacterium avium subspecies paratuberculosis (MAP) is a bacterium that can cause substantial economic losses in infected dairy herds due to reduced milk production and increased cow-replacement costs. In order to control MAP in dairies with drylot pens, a standardized environmental sampling protocol to quantify MAP in fecal slurry was developed based on an existing protocol for freestall pens. Specifically, following a 24 h hold of the flush, a grab sample of approximately 10 ml of fecal slurry was collected every 1 m along the flush lane of the drylot pens, avoiding individual cow fecal pats. To determine the reliability and repatability of the new environmental sampling protocol for estimation of MAP bioburden at the pen level, two collectors simultaneously collected fecal slurry samples every day for 3 days from six drylot cow pens on two Central California dairies. During the study period no cow movement between pens was allowed with the exception of sick cows. The study herds had MAP seroprevalence of 5.8% and 3.2%, respectively, based on whole pen serum ELISA results. Variance components models for quantitative real-time PCR (qPCR) results showed samples collected from different pens on different dairies accounted for greater variablitiy in MAP concentration (65%), while samples collected by different collectors had the least variability (0.1%). In contrast, variability in MAP concentration in environmental samples collected on different days had 25% variability. The intraclass correlation coefficient showed high reliability (93%) of environmental sampling simultaneously by different collectors. In contrast, the reliability of environmental sampling at different days was 65%, which was similar to the reliability for sampling by different collectors on different days. Investigators can expect high reliability when employing the new environmental sampling protocol along with qPCR testing of environmental samples from drylot pens.
format: application/pdf
format: text/html
creator: Tapakorn Chamchoy
creator: Deneice R. Williams
creator: John M. Adaska
creator: Randall J. Anderson
creator: Sharif S. Aly
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.8081
publisher: PeerJ Inc.
rights: © 2019 Chamchoy et al.
abstract: Mycobacterium avium subspecies paratuberculosis (MAP) is a bacterium that can cause substantial economic losses in infected dairy herds due to reduced milk production and increased cow-replacement costs. In order to control MAP in dairies with drylot pens, a standardized environmental sampling protocol to quantify MAP in fecal slurry was developed based on an existing protocol for freestall pens. Specifically, following a 24 h hold of the flush, a grab sample of approximately 10 ml of fecal slurry was collected every 1 m along the flush lane of the drylot pens, avoiding individual cow fecal pats. To determine the reliability and repatability of the new environmental sampling protocol for estimation of MAP bioburden at the pen level, two collectors simultaneously collected fecal slurry samples every day for 3 days from six drylot cow pens on two Central California dairies. During the study period no cow movement between pens was allowed with the exception of sick cows. The study herds had MAP seroprevalence of 5.8% and 3.2%, respectively, based on whole pen serum ELISA results. Variance components models for quantitative real-time PCR (qPCR) results showed samples collected from different pens on different dairies accounted for greater variablitiy in MAP concentration (65%), while samples collected by different collectors had the least variability (0.1%). In contrast, variability in MAP concentration in environmental samples collected on different days had 25% variability. The intraclass correlation coefficient showed high reliability (93%) of environmental sampling simultaneously by different collectors. In contrast, the reliability of environmental sampling at different days was 65%, which was similar to the reliability for sampling by different collectors on different days. Investigators can expect high reliability when employing the new environmental sampling protocol along with qPCR testing of environmental samples from drylot pens.
bibliographic citation: Chamchoy et al. (2019) Environmental sampling to assess the bioburden of Mycobacterium avium subspecies paratuberculosis in drylot pens on California dairies. PeerJ 7:e8081 https://doi.org/10.7717/peerj.8081
date submitted: 2019-06-10
date accepted: 2019-10-21
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chamchoy
  given name: Tapakorn
author list: Agent
  family name: Williams
  given name: Deneice R.
author list: Agent
  family name: Adaska
  given name: John M.
author list: Agent
  family name: Anderson
  given name: Randall J.
author list: Agent
  family name: Aly
  given name: Sharif S.
doi: 10.7717/peerj.8081
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: © 2019 Chamchoy et al.
attribution name: Chamchoy et al.

The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster
type: item
type: AcademicArticle
description: Microorganisms play a central role in the biology of vinegar flies such as Drosophila suzukii and Drosophila melanogaster: serving as a food source to both adults and larvae, and influencing a range of traits including nutrition, behavior, and development. The niches utilized by the fly species partially overlap, as do the microbiota that sustain them, and interactions among these players may drive the development of crop diseases. To learn more about how the microbiota of one species may affect the other, we isolated and identified microbes from field-caught D. suzukii, and then characterized their effects on D. melanogaster larval development time in the laboratory. We found that the D. suzukii microbiota consistently included both yeasts and bacteria. It was dominated by yeasts of the genus Hanseniaspora, and bacteria from the families Acetobacteraceae and Enterobacteriaceae. Raising D. melanogaster under gnotobiotic conditions with each microbial isolate individually, we found that some bacteria promoted larval development relative to axenic conditions, but most did not have a significant effect. In contrast, nearly all the yeasts tested significantly accelerated larval development. The one exception was Starmerella bacillaris, which had the opposite effect: significantly slowing larval developmental rate. We investigated the basis for this effect by examining whether S. bacillaris cells could sustain larval growth, and measuring the survival of S. bacillaris and other yeasts in the larval gut. Our results suggest S. bacillaris is not digested by D. melanogaster and therefore cannot serve as a source of nutrition. These findings have interesting implications for possible interactions between the two Drosophilia species and their microbiota in nature. Overall, we found that microbes isolated from D. suzukii promote D. melanogaster larval development, which is consistent with the model that infestation of fruit by D. suzukii can open up habitat for D. melanogaster…
format: application/pdf
format: text/html
creator: Gabrielle M. Solomon
creator: Hiruni Dodangoda
creator: Tylea McCarthy-Walker
creator: Rita Ntim-Gyakari
creator: Peter D. Newell
subject: Entomology
subject: Microbiology
description: doi:10.7717/peerj.8097
publisher: PeerJ Inc.
rights: © 2019 Solomon et al.
abstract: Microorganisms play a central role in the biology of vinegar flies such as Drosophila suzukii and Drosophila melanogaster: serving as a food source to both adults and larvae, and influencing a range of traits including nutrition, behavior, and development. The niches utilized by the fly species partially overlap, as do the microbiota that sustain them, and interactions among these players may drive the development of crop diseases. To learn more about how the microbiota of one species may affect the other, we isolated and identified microbes from field-caught D. suzukii, and then characterized their effects on D. melanogaster larval development time in the laboratory. We found that the D. suzukii microbiota consistently included both yeasts and bacteria. It was dominated by yeasts of the genus Hanseniaspora, and bacteria from the families Acetobacteraceae and Enterobacteriaceae. Raising D. melanogaster under gnotobiotic conditions with each microbial isolate individually, we found that some bacteria promoted larval development relative to axenic conditions, but most did not have a significant effect. In contrast, nearly all the yeasts tested significantly accelerated larval development. The one exception was Starmerella bacillaris, which had the opposite effect: significantly slowing larval developmental rate. We investigated the basis for this effect by examining whether S. bacillaris cells could sustain larval growth, and measuring the survival of S. bacillaris and other yeasts in the larval gut. Our results suggest S. bacillaris is not digested by D. melanogaster and therefore cannot serve as a source of nutrition. These findings have interesting implications for possible interactions between the two Drosophilia species and their microbiota in nature. Overall, we found that microbes isolated from D. suzukii promote D. melanogaster larval development, which is consistent with the model that infestation of fruit by D. suzukii can open up habitat for D. melanogaster…
bibliographic citation: Solomon et al. (2019) The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster. PeerJ 7:e8097 https://doi.org/10.7717/peerj.8097
date submitted: 2019-08-13
date accepted: 2019-10-24
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Solomon
  given name: Gabrielle M.
author list: Agent
  family name: Dodangoda
  given name: Hiruni
author list: Agent
  family name: McCarthy-Walker
  given name: Tylea
author list: Agent
  family name: Ntim-Gyakari
  given name: Rita
author list: Agent
  family name: Newell
  given name: Peter D.
doi: 10.7717/peerj.8097
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: ©2019 Solomon et al.
attribution name: Solomon et al.

Decrease in walking speed increases hip moment impulse in the frontal plane during the stance phase
type: item
type: AcademicArticle
description: Background Increased daily cumulative hip moment in the frontal plane (i.e., the product of hip moment impulse in the frontal plane during the stance phase and mean steps per day) is a risk factor for progression of hip osteoarthritis. Although hip osteoarthritis generally causes a decrease in the walking speed, its effect on hip moment impulse in the frontal plane is unclear. The purpose of this study was to examine the relationship between decrease in walking speed and hip moment impulse in the frontal plane. Methods We used a public dataset of treadmill walking in 17 older adults (mean (SD) age: 63.2 (8.0) years). The subjects walked on the treadmill for 30 s under five conditions: (1) 40% of comfortable non-dimensional speed (CNDS), (2) 55% CNDS, (3) 70% CNDS, (4) 85% CNDS, and (5) 100% CNDS. The hip moment impulse in the frontal plane non-normalized (or normalized) to step length (Nm s/kg [or Nm s/(kg m)]) for each condition was calculated. Furthermore, the relationship between walking speed and hip moment impulse in the frontal plane non-normalized (or normalized) to step length was examined using regression analysis based on a previous study. Results A decrease in non-dimensional speed (i.e., walking speed) significantly increased the non-normalized (or normalized) hip moment impulse in the frontal plane during the stance phase. The relationship between walking speed and non-normalized (or normalized) hip moment impulse in the frontal plane was fitted by a second-order polynomial. Discussion This study revealed that a decrease in walking speed increased the non-normalized (or normalized) hip moment impulse in the frontal plane in healthy older adults. This finding is useful for understanding the relationship between walking speed and hip moment impulse in the frontal plane and suggests that a decrease in walking speed may actually increase the daily cumulative hip moment in the frontal plane of patients with hip osteoarthritis.
format: application/pdf
format: text/html
creator: Takuma Inai
creator: Tomoya Takabayashi
creator: Mutsuaki Edama
creator: Masayoshi Kubo
subject: Kinesiology
subject: Rheumatology
description: doi:10.7717/peerj.8110
publisher: PeerJ Inc.
rights: © 2019 Inai et al.
abstract: Background Increased daily cumulative hip moment in the frontal plane (i.e., the product of hip moment impulse in the frontal plane during the stance phase and mean steps per day) is a risk factor for progression of hip osteoarthritis. Although hip osteoarthritis generally causes a decrease in the walking speed, its effect on hip moment impulse in the frontal plane is unclear. The purpose of this study was to examine the relationship between decrease in walking speed and hip moment impulse in the frontal plane. Methods We used a public dataset of treadmill walking in 17 older adults (mean (SD) age: 63.2 (8.0) years). The subjects walked on the treadmill for 30 s under five conditions: (1) 40% of comfortable non-dimensional speed (CNDS), (2) 55% CNDS, (3) 70% CNDS, (4) 85% CNDS, and (5) 100% CNDS. The hip moment impulse in the frontal plane non-normalized (or normalized) to step length (Nm s/kg [or Nm s/(kg m)]) for each condition was calculated. Furthermore, the relationship between walking speed and hip moment impulse in the frontal plane non-normalized (or normalized) to step length was examined using regression analysis based on a previous study. Results A decrease in non-dimensional speed (i.e., walking speed) significantly increased the non-normalized (or normalized) hip moment impulse in the frontal plane during the stance phase. The relationship between walking speed and non-normalized (or normalized) hip moment impulse in the frontal plane was fitted by a second-order polynomial. Discussion This study revealed that a decrease in walking speed increased the non-normalized (or normalized) hip moment impulse in the frontal plane in healthy older adults. This finding is useful for understanding the relationship between walking speed and hip moment impulse in the frontal plane and suggests that a decrease in walking speed may actually increase the daily cumulative hip moment in the frontal plane of patients with hip osteoarthritis.
bibliographic citation: Inai et al. (2019) Decrease in walking speed increases hip moment impulse in the frontal plane during the stance phase. PeerJ 7:e8110 https://doi.org/10.7717/peerj.8110
date submitted: 2019-07-09
date accepted: 2019-10-28
issued: 2019-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Inai
  given name: Takuma
author list: Agent
  family name: Takabayashi
  given name: Tomoya
author list: Agent
  family name: Edama
  given name: Mutsuaki
author list: Agent
  family name: Kubo
  given name: Masayoshi
doi: 10.7717/peerj.8110
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-19
copyright: ©2019 Inai et al.
attribution name: Inai et al.

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