PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of different training modalities on phosphate homeostasis and local vitamin D metabolism in rat bone
items: GPs’ motivation for teaching medical students in a rural area—development of the Motivation for Medical Education Questionnaire (MoME-Q)
items: Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in northwest China
items: Association of TIMP4 gene variants with steroid-induced osteonecrosis of the femoral head in the population of northern China
items: Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data
items: Prioritizing bona fide bacterial small RNAs with machine learning classifiers
items: Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum (Burramys parvus) in the Kosciuszko National Park, New South Wales, Australia
items: A turiasaurian sauropod dinosaur from the Early Cretaceous Wealden Supergroup of the United Kingdom
items: Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma
items: Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube

Effects of different training modalities on phosphate homeostasis and local vitamin D metabolism in rat bone
type: item
type: AcademicArticle
description: Objectives Mechanical loading may be an important factor in the regulation of bone derived hormones involved in phosphate homeostasis. This study investigated the effects of peak power and endurance training on expression levels of fibroblast growth factor 23 (FGF23) and 1α-hydroxylase (CYP27b1) in bone. Methods Thirty-eight rats were assigned to six weeks of training in four groups: peak power (PT), endurance (ET), PT followed by ET (PET) or no training (control). In cortical bone, FGF23 was quantified using immunohistochemistry. mRNA expression levels of proteins involved in phosphate and vitamin D homeostasis were quantified in cortical bone and kidney. C-terminal FGF23, 25-hydroxyvitamin D3, parathyroid hormone (PTH), calcium and phosphate concentrations were measured in plasma or serum. Results Neither FGF23 mRNA and protein expression levels in cortical bone nor FGF23 plasma concentrations differed between the groups. In cortical bone, mRNA expression levels of sclerostin (SOST), dental matrix protein 1 (DMP1), phosphate-regulating gene with homologies to endopeptidases on the X chromosome (PHEX) and matrix extracellular phosphoglycoprotein (MEPE) were lower after PT compared to ET and PET. Expression levels of CYP27b1 and vitamin D receptor (VDR) in tibial bone were decreased after PT compared to ET. In kidney, no differences between groups were observed for mRNA expression levels of CYP27b1, 24-hydroxylase (CYP24), VDR, NaPi-IIa cotransporter (NPT2a) and NaPi-IIc cotransporter (NPT2c). Serum PTH concentrations were higher after PT compared to controls. Conclusion After six weeks, none of the training modalities induced changes in FGF23 expression levels. However, PT might have caused changes in local phosphate regulation within bone compared to ET and PET. CYP27b1 and VDR expression in bone was reduced after PT compared to ET, suggesting high intensity peak power training in this rat model is associated with decreased vitamin D signalling in bone.
format: application/pdf
format: text/html
creator: Joost Buskermolen
creator: Karen van der Meijden
creator: Regula Furrer
creator: Dirk-Jan Mons
creator: Huib W. van Essen
creator: Annemieke C. Heijboer
creator: Paul Lips
creator: Richard T. Jaspers
creator: Nathalie Bravenboer
subject: Anatomy and Physiology
subject: Diabetes and Endocrinology
subject: Internal Medicine
subject: Kinesiology
description: doi:10.7717/peerj.6184
publisher: PeerJ Inc.
rights: © 2019 Buskermolen et al.
abstract: Objectives Mechanical loading may be an important factor in the regulation of bone derived hormones involved in phosphate homeostasis. This study investigated the effects of peak power and endurance training on expression levels of fibroblast growth factor 23 (FGF23) and 1α-hydroxylase (CYP27b1) in bone. Methods Thirty-eight rats were assigned to six weeks of training in four groups: peak power (PT), endurance (ET), PT followed by ET (PET) or no training (control). In cortical bone, FGF23 was quantified using immunohistochemistry. mRNA expression levels of proteins involved in phosphate and vitamin D homeostasis were quantified in cortical bone and kidney. C-terminal FGF23, 25-hydroxyvitamin D3, parathyroid hormone (PTH), calcium and phosphate concentrations were measured in plasma or serum. Results Neither FGF23 mRNA and protein expression levels in cortical bone nor FGF23 plasma concentrations differed between the groups. In cortical bone, mRNA expression levels of sclerostin (SOST), dental matrix protein 1 (DMP1), phosphate-regulating gene with homologies to endopeptidases on the X chromosome (PHEX) and matrix extracellular phosphoglycoprotein (MEPE) were lower after PT compared to ET and PET. Expression levels of CYP27b1 and vitamin D receptor (VDR) in tibial bone were decreased after PT compared to ET. In kidney, no differences between groups were observed for mRNA expression levels of CYP27b1, 24-hydroxylase (CYP24), VDR, NaPi-IIa cotransporter (NPT2a) and NaPi-IIc cotransporter (NPT2c). Serum PTH concentrations were higher after PT compared to controls. Conclusion After six weeks, none of the training modalities induced changes in FGF23 expression levels. However, PT might have caused changes in local phosphate regulation within bone compared to ET and PET. CYP27b1 and VDR expression in bone was reduced after PT compared to ET, suggesting high intensity peak power training in this rat model is associated with decreased vitamin D signalling in bone.
bibliographic citation: Buskermolen et al. (2019) Effects of different training modalities on phosphate homeostasis and local vitamin D metabolism in rat bone. PeerJ 7:e6184 https://doi.org/10.7717/peerj.6184
date submitted: 2018-05-23
date accepted: 2018-11-29
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buskermolen
  given name: Joost
author list: Agent
  family name: van der Meijden
  given name: Karen
author list: Agent
  family name: Furrer
  given name: Regula
author list: Agent
  family name: Mons
  given name: Dirk-Jan
author list: Agent
  family name: van Essen
  given name: Huib W.
author list: Agent
  family name: Heijboer
  given name: Annemieke C.
author list: Agent
  family name: Lips
  given name: Paul
author list: Agent
  family name: Jaspers
  given name: Richard T.
author list: Agent
  family name: Bravenboer
  given name: Nathalie
doi: 10.7717/peerj.6184
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Buskermolen et al.
attribution name: Buskermolen et al.

GPs’ motivation for teaching medical students in a rural area—development of the Motivation for Medical Education Questionnaire (MoME-Q)
type: item
type: AcademicArticle
description: Background The establishment of a medical education program in the rural area of Siegen is planned to be the first step against a shortage of physicians in this region. General practitioners (GPs) will be extensively involved in this program as Family Medicine (Allgemeinmedizin) will become a core subject in the curriculum nationwide. Based on this situation we aim to figure out GPs motivation to participate in medical education. For this purpose, we had to construct and test a new questionnaire. Methods A survey was conducted among general practitioners (GPs) in the region of Siegen-Wittgenstein regarding their motivation to participate in medical education. For this purpose, the Motivation for Medical Education Questionnaire (MoME-Q), a 24-item questionnaire, was developed. Structural characteristics of GPs, the Maslach Burnout Inventory (MBI) and the Work Satisfaction Questionnaire (WSQ) were used for validation purposes. Results A representative number of GPs took part in the study (53.8%). Although the majority had no connection to a university (86%), 83% can imagine participating in the education of medical students. The items of the MoME-Q load on two factors (commitment and personal benefit). The confirmatory factor analysis shows a good model fit. Subscales of the MoME-Q were able to differentiate between physicians with and without authorization to train GP residents, between practices with and without a specialized practice nurse, and between physicians with and without previous experience in medical education. The MoME-Q subscale “commitment” correlated significantly with all three subscales of the MBI. Correlations were in the medium range around |.30|. Conclusion The MoME-Q seems to be an appropriate tool to assess motivation to participate in medical education of GPs. In our sample, a large number of GPs was motivated to participate in the education of medical students. Future studies with larger number of GPs should be carried out to validate and con…
format: application/pdf
format: text/html
creator: Charles Christian Adarkwah
creator: Annette Schwaffertz
creator: Joachim Labenz
creator: Annette Becker
creator: Oliver Hirsch
subject: Public Health
subject: Science and Medical Education
description: doi:10.7717/peerj.6235
publisher: PeerJ Inc.
rights: © 2019 Adarkwah et al.
abstract: Background The establishment of a medical education program in the rural area of Siegen is planned to be the first step against a shortage of physicians in this region. General practitioners (GPs) will be extensively involved in this program as Family Medicine (Allgemeinmedizin) will become a core subject in the curriculum nationwide. Based on this situation we aim to figure out GPs motivation to participate in medical education. For this purpose, we had to construct and test a new questionnaire. Methods A survey was conducted among general practitioners (GPs) in the region of Siegen-Wittgenstein regarding their motivation to participate in medical education. For this purpose, the Motivation for Medical Education Questionnaire (MoME-Q), a 24-item questionnaire, was developed. Structural characteristics of GPs, the Maslach Burnout Inventory (MBI) and the Work Satisfaction Questionnaire (WSQ) were used for validation purposes. Results A representative number of GPs took part in the study (53.8%). Although the majority had no connection to a university (86%), 83% can imagine participating in the education of medical students. The items of the MoME-Q load on two factors (commitment and personal benefit). The confirmatory factor analysis shows a good model fit. Subscales of the MoME-Q were able to differentiate between physicians with and without authorization to train GP residents, between practices with and without a specialized practice nurse, and between physicians with and without previous experience in medical education. The MoME-Q subscale “commitment” correlated significantly with all three subscales of the MBI. Correlations were in the medium range around |.30|. Conclusion The MoME-Q seems to be an appropriate tool to assess motivation to participate in medical education of GPs. In our sample, a large number of GPs was motivated to participate in the education of medical students. Future studies with larger number of GPs should be carried out to validate and con…
bibliographic citation: Adarkwah et al. (2019) GPs’ motivation for teaching medical students in a rural area—development of the Motivation for Medical Education Questionnaire (MoME-Q). PeerJ 7:e6235 https://doi.org/10.7717/peerj.6235
date submitted: 2018-09-27
date accepted: 2018-12-07
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adarkwah
  given name: Charles Christian
author list: Agent
  family name: Schwaffertz
  given name: Annette
author list: Agent
  family name: Labenz
  given name: Joachim
author list: Agent
  family name: Becker
  given name: Annette
author list: Agent
  family name: Hirsch
  given name: Oliver
doi: 10.7717/peerj.6235
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Adarkwah et al.
attribution name: Adarkwah et al.

Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in northwest China
type: item
type: AcademicArticle
description: Climatic fluctuations during the Quaternary significantly affect many species in their intraspecific divergence and population structure across northwest China. In order to investigate the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Sequences of two chloroplast DNA (cpDNA) intergenic spacers (trnH-psbA and rpoB-trnC) and a nuclear ribosomal region (nrDNA, ITS) were generated from 27 populations of Panzerina lanata and resulted in the identification of seven chloroplast haplotypes and thirty-two nuclear haplotypes. We applied AMOVA, neutrality test and mismatch distribution analysis to estimate genetic differentiation and demographic characteristics. The divergence times of the seven cpDNA haplotypes were estimated using BEAST. Our results revealed high levels of genetic diversity (cpDNA: Hcp = 0.6691, HT = 0.673; nrDNA: Hnr = 0.5668, HT = 0.577). High level of genetic differentiation (GST = 0.950) among populations was observed in the cpDNA sequences, while the genetic differentiation values (GST = 0.348) were low in nuclear sequences. AMOVA results revealed major genetic variation among the three groups: northern, central, and eastern group. However, the genetic differentiation in ITS data was not found. The species distribution modeling and demographic analysis indicated that P. lanata had not experienced recent range expansion. The occurrence of divergence between seven cpDNA haplotypes, probably during Pleistocene, coincides with aridification and expansion of the desert across northwest China that resulted in species diversification and habitat fragmentation. In addition, we discovered that the deserts and the Helan Mountains acted as effective geographic barriers that promoting the intraspecific diversity of P. lanata.
format: application/pdf
format: text/html
creator: Yanfen Zhao
creator: Hongxiang Zhang
creator: Borong Pan
creator: Mingli Zhang
subject: Biodiversity
subject: Biogeography
subject: Plant Science
description: doi:10.7717/peerj.6264
publisher: PeerJ Inc.
rights: © 2019 Zhao et al.
abstract: Climatic fluctuations during the Quaternary significantly affect many species in their intraspecific divergence and population structure across northwest China. In order to investigate the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Sequences of two chloroplast DNA (cpDNA) intergenic spacers (trnH-psbA and rpoB-trnC) and a nuclear ribosomal region (nrDNA, ITS) were generated from 27 populations of Panzerina lanata and resulted in the identification of seven chloroplast haplotypes and thirty-two nuclear haplotypes. We applied AMOVA, neutrality test and mismatch distribution analysis to estimate genetic differentiation and demographic characteristics. The divergence times of the seven cpDNA haplotypes were estimated using BEAST. Our results revealed high levels of genetic diversity (cpDNA: Hcp = 0.6691, HT = 0.673; nrDNA: Hnr = 0.5668, HT = 0.577). High level of genetic differentiation (GST = 0.950) among populations was observed in the cpDNA sequences, while the genetic differentiation values (GST = 0.348) were low in nuclear sequences. AMOVA results revealed major genetic variation among the three groups: northern, central, and eastern group. However, the genetic differentiation in ITS data was not found. The species distribution modeling and demographic analysis indicated that P. lanata had not experienced recent range expansion. The occurrence of divergence between seven cpDNA haplotypes, probably during Pleistocene, coincides with aridification and expansion of the desert across northwest China that resulted in species diversification and habitat fragmentation. In addition, we discovered that the deserts and the Helan Mountains acted as effective geographic barriers that promoting the intraspecific diversity of P. lanata.
bibliographic citation: Zhao et al. (2019) Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in northwest China. PeerJ 7:e6264 https://doi.org/10.7717/peerj.6264
date submitted: 2018-04-04
date accepted: 2018-12-11
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yanfen
author list: Agent
  family name: Zhang
  given name: Hongxiang
author list: Agent
  family name: Pan
  given name: Borong
author list: Agent
  family name: Zhang
  given name: Mingli
doi: 10.7717/peerj.6264
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Zhao et al.
attribution name: Zhao et al.

Association of TIMP4 gene variants with steroid-induced osteonecrosis of the femoral head in the population of northern China
type: item
type: AcademicArticle
description: Background In clinical treatment, the use of steroid hormones is an important etiological factor of non-traumatic osteonecrosis of the femoral head (ONFH) risk. As an endogenous inhibitor of matrix metalloproteinases (MMPs) in the extracellular matrix, the expression of tissue inhibitors of metalloprotease-4 (TIMP4) plays an essential role in cartilage and bone tissue damage and remodeling, vasculitis formation, intravascular thrombosis, and lipid metabolism. Methods This study aimed to detect the association between TIMP4 polymorphism and steroid-induced ONFH. We genotyped seven single-nucleotide polymorphisms (SNPs) in TIMP4 genes and analyzed the association with steroid-induced ONFH from 286 steroid-induced ONFH patients and 309 normal individuals. Results We performed allelic model analysis and found that the minor alleles of five SNPs (rs99365, rs308952, rs3817004, rs2279750, and rs3755724) were associated with decreased steroid-induced ONFH (p = 0.02, p = 0.03, p = 0.04, p = 0.01, p = 0.04, respectively). rs2279750 showed a significant association with decreased risk of steroid-induced ONFH in the Dominant and Log-additive models (p = 0.042, p = 0.028, respectively), and rs9935, rs30892, and rs3817004 were associated with decreased risk in the Log-additive model (p = 0.038, p = 0.044, p = 0.042, respectively). In further stratification analysis, TIMP4 gene variants showed a significant association with steroid-induced ONFH in gender under the genotypes. Haplotype analysis also revealed that “TCAGAC” and “CCGGAA” sequences have protective effect on steroid-induced ONFH. Conclusion Our results indicate that five TIMP4 SNPs (rs99365, rs308952, rs3817004 rs2279750, and rs3755724) are significantly associated with decreased risk of steroid-induced ONFH in the population of northern China.
format: application/pdf
format: text/html
creator: Jiaqi Wang
creator: Feimeng An
creator: Yuju Cao
creator: Hongyan Gao
creator: Mingqi Sun
creator: Chao Ma
creator: Hao Wu
creator: Baoxin Zhang
creator: Wanlin Liu
creator: Jianzhong Wang
subject: Genomics
subject: Orthopedics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.6270
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background In clinical treatment, the use of steroid hormones is an important etiological factor of non-traumatic osteonecrosis of the femoral head (ONFH) risk. As an endogenous inhibitor of matrix metalloproteinases (MMPs) in the extracellular matrix, the expression of tissue inhibitors of metalloprotease-4 (TIMP4) plays an essential role in cartilage and bone tissue damage and remodeling, vasculitis formation, intravascular thrombosis, and lipid metabolism. Methods This study aimed to detect the association between TIMP4 polymorphism and steroid-induced ONFH. We genotyped seven single-nucleotide polymorphisms (SNPs) in TIMP4 genes and analyzed the association with steroid-induced ONFH from 286 steroid-induced ONFH patients and 309 normal individuals. Results We performed allelic model analysis and found that the minor alleles of five SNPs (rs99365, rs308952, rs3817004, rs2279750, and rs3755724) were associated with decreased steroid-induced ONFH (p = 0.02, p = 0.03, p = 0.04, p = 0.01, p = 0.04, respectively). rs2279750 showed a significant association with decreased risk of steroid-induced ONFH in the Dominant and Log-additive models (p = 0.042, p = 0.028, respectively), and rs9935, rs30892, and rs3817004 were associated with decreased risk in the Log-additive model (p = 0.038, p = 0.044, p = 0.042, respectively). In further stratification analysis, TIMP4 gene variants showed a significant association with steroid-induced ONFH in gender under the genotypes. Haplotype analysis also revealed that “TCAGAC” and “CCGGAA” sequences have protective effect on steroid-induced ONFH. Conclusion Our results indicate that five TIMP4 SNPs (rs99365, rs308952, rs3817004 rs2279750, and rs3755724) are significantly associated with decreased risk of steroid-induced ONFH in the population of northern China.
bibliographic citation: Wang et al. (2019) Association of TIMP4 gene variants with steroid-induced osteonecrosis of the femoral head in the population of northern China. PeerJ 7:e6270 https://doi.org/10.7717/peerj.6270
date submitted: 2018-09-26
date accepted: 2018-12-09
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jiaqi
author list: Agent
  family name: An
  given name: Feimeng
author list: Agent
  family name: Cao
  given name: Yuju
author list: Agent
  family name: Gao
  given name: Hongyan
author list: Agent
  family name: Sun
  given name: Mingqi
author list: Agent
  family name: Ma
  given name: Chao
author list: Agent
  family name: Wu
  given name: Hao
author list: Agent
  family name: Zhang
  given name: Baoxin
author list: Agent
  family name: Liu
  given name: Wanlin
author list: Agent
  family name: Wang
  given name: Jianzhong
doi: 10.7717/peerj.6270
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data
type: item
type: AcademicArticle
description: The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogeno…
format: application/pdf
format: text/html
creator: Gabriel A. Vieira
creator: Francisco Prosdocimi
subject: Biodiversity
subject: Bioinformatics
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.6271
publisher: PeerJ Inc.
rights: © 2019 Vieira et al.
abstract: The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogeno…
bibliographic citation: Vieira et al. (2019) Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data. PeerJ 7:e6271 https://doi.org/10.7717/peerj.6271
date submitted: 2018-11-07
date accepted: 2018-12-10
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vieira
  given name: Gabriel A.
author list: Agent
  family name: Prosdocimi
  given name: Francisco
doi: 10.7717/peerj.6271
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Vieira and Prosdocimi
attribution name: Vieira et al.

Prioritizing bona fide bacterial small RNAs with machine learning classifiers
type: item
type: AcademicArticle
description: Bacterial small (sRNAs) are involved in the control of several cellular processes. Hundreds of putative sRNAs have been identified in many bacterial species through RNA sequencing. The existence of putative sRNAs is usually validated by Northern blot analysis. However, the large amount of novel putative sRNAs reported in the literature makes it impractical to validate each of them in the wet lab. In this work, we applied five machine learning approaches to construct twenty models to discriminate bona fide sRNAs from random genomic sequences in five bacterial species. Sequences were represented using seven features including free energy of their predicted secondary structure, their distances to the closest predicted promoter site and Rho-independent terminator, and their distance to the closest open reading frames (ORFs). To automatically calculate these features, we developed an sRNA Characterization Pipeline (sRNACharP). All seven features used in the classification task contributed positively to the performance of the predictive models. The best performing model obtained a median precision of 100% at 10% recall and of 64% at 40% recall across all five bacterial species, and it outperformed previous published approaches on two benchmark datasets in terms of precision and recall. Our results indicate that even though there is limited sRNA sequence conservation across different bacterial species, there are intrinsic features in the genomic context of sRNAs that are conserved across taxa. We show that these features are utilized by machine learning approaches to learn a species-independent model to prioritize bona fide bacterial sRNAs.
format: application/pdf
format: text/html
creator: Erik J.J. Eppenhof
creator: Lourdes Peña-Castillo
subject: Bioinformatics
subject: Microbiology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6304
publisher: PeerJ Inc.
rights: © 2019 Eppenhof and Peña-Castillo
abstract: Bacterial small (sRNAs) are involved in the control of several cellular processes. Hundreds of putative sRNAs have been identified in many bacterial species through RNA sequencing. The existence of putative sRNAs is usually validated by Northern blot analysis. However, the large amount of novel putative sRNAs reported in the literature makes it impractical to validate each of them in the wet lab. In this work, we applied five machine learning approaches to construct twenty models to discriminate bona fide sRNAs from random genomic sequences in five bacterial species. Sequences were represented using seven features including free energy of their predicted secondary structure, their distances to the closest predicted promoter site and Rho-independent terminator, and their distance to the closest open reading frames (ORFs). To automatically calculate these features, we developed an sRNA Characterization Pipeline (sRNACharP). All seven features used in the classification task contributed positively to the performance of the predictive models. The best performing model obtained a median precision of 100% at 10% recall and of 64% at 40% recall across all five bacterial species, and it outperformed previous published approaches on two benchmark datasets in terms of precision and recall. Our results indicate that even though there is limited sRNA sequence conservation across different bacterial species, there are intrinsic features in the genomic context of sRNAs that are conserved across taxa. We show that these features are utilized by machine learning approaches to learn a species-independent model to prioritize bona fide bacterial sRNAs.
bibliographic citation: Eppenhof et al. (2019) Prioritizing bona fide bacterial small RNAs with machine learning classifiers. PeerJ 7:e6304 https://doi.org/10.7717/peerj.6304
date submitted: 2018-05-31
date accepted: 2018-12-16
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eppenhof
  given name: Erik J.J.
author list: Agent
  family name: Peña-Castillo
  given name: Lourdes
doi: 10.7717/peerj.6304
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Eppenhof and Peña-Castillo
attribution name: Eppenhof and Peña-Castillo

Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum (Burramys parvus) in the Kosciuszko National Park, New South Wales, Australia
type: item
type: AcademicArticle
description: Background The Mountain Pygmy-possum (Burramys parvus) is a critically endangered marsupial, endemic to alpine regions of southern Australia. We investigated the diet of a recently discovered population of the possum in northern Kosciuszko National Park, NSW, Australia. This new population occurs at elevations well below the once-presumed lower elevation limit of 1,600 m. Goals and Methods Faecal material was analysed to determine if dietary composition differed between individuals in the newly discovered northern population and those in the higher elevation southern population, and to examine how diet was influenced by rainfall in the southern population and seasonal changes in resource availability in the northern population. Results and Discussion The diet of B. parvus in the northern population comprised of arthropods, fruits and seeds. Results indicate the diet of both populations shares most of the same invertebrate orders and plant species. However, in the absence of preferred food types available to the southern population, individuals of the northern population opportunistically consumed different species that were similar to those preferred by individuals in higher altitude populations. Differing rainfall amounts had a significant effect on diet, with years of below average rainfall having a greater percentage composition and diversity of invertebrates. Seasonal variation was also recorded, with the northern population increasing the diversity of invertebrates in their diet during the Autumn months when Bogong Moths (Agrotis infusa) were absent from those sites, raising questions about the possum’s dependence on the species Conclusions Measurable effects of rainfall amount and seasonal variation on the dietary composition suggest that predicted climatic variability will have a significant impact on its diet, potentially impacting its future survival. Findings suggest that it is likely that B. parvus is not restricted by dietary requirements to its current …
format: application/pdf
format: text/html
creator: Tahneal Hawke
creator: Hayley Bates
creator: Suzanne Hand
creator: Michael Archer
creator: Linda Broome
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6307
publisher: PeerJ Inc.
rights: © 2019 Hawke et al.
abstract: Background The Mountain Pygmy-possum (Burramys parvus) is a critically endangered marsupial, endemic to alpine regions of southern Australia. We investigated the diet of a recently discovered population of the possum in northern Kosciuszko National Park, NSW, Australia. This new population occurs at elevations well below the once-presumed lower elevation limit of 1,600 m. Goals and Methods Faecal material was analysed to determine if dietary composition differed between individuals in the newly discovered northern population and those in the higher elevation southern population, and to examine how diet was influenced by rainfall in the southern population and seasonal changes in resource availability in the northern population. Results and Discussion The diet of B. parvus in the northern population comprised of arthropods, fruits and seeds. Results indicate the diet of both populations shares most of the same invertebrate orders and plant species. However, in the absence of preferred food types available to the southern population, individuals of the northern population opportunistically consumed different species that were similar to those preferred by individuals in higher altitude populations. Differing rainfall amounts had a significant effect on diet, with years of below average rainfall having a greater percentage composition and diversity of invertebrates. Seasonal variation was also recorded, with the northern population increasing the diversity of invertebrates in their diet during the Autumn months when Bogong Moths (Agrotis infusa) were absent from those sites, raising questions about the possum’s dependence on the species Conclusions Measurable effects of rainfall amount and seasonal variation on the dietary composition suggest that predicted climatic variability will have a significant impact on its diet, potentially impacting its future survival. Findings suggest that it is likely that B. parvus is not restricted by dietary requirements to its current …
bibliographic citation: Hawke et al. (2019) Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum (Burramys parvus) in the Kosciuszko National Park, New South Wales, Australia. PeerJ 7:e6307 https://doi.org/10.7717/peerj.6307
date submitted: 2018-07-17
date accepted: 2018-12-18
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hawke
  given name: Tahneal
author list: Agent
  family name: Bates
  given name: Hayley
author list: Agent
  family name: Hand
  given name: Suzanne
author list: Agent
  family name: Archer
  given name: Michael
author list: Agent
  family name: Broome
  given name: Linda
doi: 10.7717/peerj.6307
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Hawke et al.
attribution name: Hawke et al.

A turiasaurian sauropod dinosaur from the Early Cretaceous Wealden Supergroup of the United Kingdom
type: item
type: AcademicArticle
description: The Jurassic/Cretaceous (J/K) boundary, 145 million years ago, has long been recognised as an extinction event or faunal turnover for sauropod dinosaurs, with many ‘basal’ lineages disappearing. However, recently, a number of ‘extinct’ groups have been recognised in the Early Cretaceous, including diplodocids in Gondwana, and non-titanosauriform macronarians in Laurasia. Turiasauria, a clade of non-neosauropod eusauropods, was originally thought to have been restricted to the Late Jurassic of western Europe. However, its distribution has recently been extended to the Late Jurassic of Tanzania (Tendaguria tanzaniensis), as well as to the Early Cretaceous of the USA (Mierasaurus bobyoungi and Moabosaurus utahensis), demonstrating the survival of another ‘basal’ clade across the J/K boundary. Teeth from the Middle Jurassic–Early Cretaceous of western Europe and North Africa have also tentatively been attributed to turiasaurs, whilst recent phylogenetic analyses recovered Late Jurassic taxa from Argentina and China as further members of Turiasauria. Here, an anterior dorsal centrum and neural arch (both NHMUK 1871) from the Early Cretaceous Wealden Supergroup of the UK are described for the first time. NHMUK 1871 shares several synapomorphies with Turiasauria, especially the turiasaurs Moabosaurus and Tendaguria, including: (1) a strongly dorsoventrally compressed centrum; (2) the retention of prominent epipophyses; and (3) an extremely low, non-bifid neural spine. NHMUK 1871 therefore represents the first postcranial evidence for Turiasauria from European deposits of Early Cretaceous age. Although turiasaurs show clear heterodont dentition, only broad, characteristically ‘heart’-shaped teeth can currently be attributed to Turiasauria with confidence. As such, several putative turiasaur occurrences based on isolated teeth from Europe, as well as the Middle Jurassic and Early Cretaceous of Africa, cannot be confidently referred to Turiasauria. Unequivocal evidence for tu…
format: application/pdf
format: text/html
creator: Philip D. Mannion
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.6348
publisher: PeerJ Inc.
rights: © 2019 Mannion
abstract: The Jurassic/Cretaceous (J/K) boundary, 145 million years ago, has long been recognised as an extinction event or faunal turnover for sauropod dinosaurs, with many ‘basal’ lineages disappearing. However, recently, a number of ‘extinct’ groups have been recognised in the Early Cretaceous, including diplodocids in Gondwana, and non-titanosauriform macronarians in Laurasia. Turiasauria, a clade of non-neosauropod eusauropods, was originally thought to have been restricted to the Late Jurassic of western Europe. However, its distribution has recently been extended to the Late Jurassic of Tanzania (Tendaguria tanzaniensis), as well as to the Early Cretaceous of the USA (Mierasaurus bobyoungi and Moabosaurus utahensis), demonstrating the survival of another ‘basal’ clade across the J/K boundary. Teeth from the Middle Jurassic–Early Cretaceous of western Europe and North Africa have also tentatively been attributed to turiasaurs, whilst recent phylogenetic analyses recovered Late Jurassic taxa from Argentina and China as further members of Turiasauria. Here, an anterior dorsal centrum and neural arch (both NHMUK 1871) from the Early Cretaceous Wealden Supergroup of the UK are described for the first time. NHMUK 1871 shares several synapomorphies with Turiasauria, especially the turiasaurs Moabosaurus and Tendaguria, including: (1) a strongly dorsoventrally compressed centrum; (2) the retention of prominent epipophyses; and (3) an extremely low, non-bifid neural spine. NHMUK 1871 therefore represents the first postcranial evidence for Turiasauria from European deposits of Early Cretaceous age. Although turiasaurs show clear heterodont dentition, only broad, characteristically ‘heart’-shaped teeth can currently be attributed to Turiasauria with confidence. As such, several putative turiasaur occurrences based on isolated teeth from Europe, as well as the Middle Jurassic and Early Cretaceous of Africa, cannot be confidently referred to Turiasauria. Unequivocal evidence for tu…
bibliographic citation: Mannion (2019) A turiasaurian sauropod dinosaur from the Early Cretaceous Wealden Supergroup of the United Kingdom. PeerJ 7:e6348 https://doi.org/10.7717/peerj.6348
date submitted: 2018-10-08
date accepted: 2018-12-27
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mannion
  given name: Philip D.
doi: 10.7717/peerj.6348
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: © 2019 Mannion
attribution name: Mannion

Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma
type: item
type: AcademicArticle
description: ZBTB38 belongs to the zinc finger protein family and contains the typical BTB domains. As a transcription factor, ZBTB38 is involved in cell regulation, proliferation and apoptosis, whereas, functional deficiency of ZBTB38 induces the human neuroblastoma (NB) cell death potentially. To have some insight into the role of ZBTB38 in NB development, high throughput RNA sequencing was performed using the human NB cell line SH-SY5Y with the deletion of ZBTB38. In the present study, 2,438 differentially expressed genes (DEGs) in ZBTB38−/− SH-SY5Y cells were obtained, 83.5% of which was down-regulated. Functional annotation of the DEGs in the Kyoto Encyclopedia of Genes and Genomes database revealed that most of the identified genes were enriched in the neurotrophin TRK receptor signaling pathway, including PI3K/Akt and MAPK signaling pathway. we also observed that ZBTB38 affects expression of CDK4/6, Cyclin E, MDM2, ATM, ATR, PTEN, Gadd45, and PIGs in the p53 signaling pathway. In addition, ZBTB38 knockdown significantly suppresses the expression of autophagy-related key genes including PIK3C2A and RB1CC1. The present meeting provides evidence to molecular mechanism of ZBTB38 modulating NB development and targeted anti-tumor therapies.
format: application/pdf
format: text/html
creator: Jie Chen
creator: Chaofeng Xing
creator: Li Yan
creator: Yabing Wang
creator: Haosen Wang
creator: Zongmeng Zhang
creator: Daolun Yu
creator: Jie Li
creator: Honglin Li
creator: Jun Li
creator: Yafei Cai
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Nephrology
subject: Oncology
description: doi:10.7717/peerj.6352
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: ZBTB38 belongs to the zinc finger protein family and contains the typical BTB domains. As a transcription factor, ZBTB38 is involved in cell regulation, proliferation and apoptosis, whereas, functional deficiency of ZBTB38 induces the human neuroblastoma (NB) cell death potentially. To have some insight into the role of ZBTB38 in NB development, high throughput RNA sequencing was performed using the human NB cell line SH-SY5Y with the deletion of ZBTB38. In the present study, 2,438 differentially expressed genes (DEGs) in ZBTB38−/− SH-SY5Y cells were obtained, 83.5% of which was down-regulated. Functional annotation of the DEGs in the Kyoto Encyclopedia of Genes and Genomes database revealed that most of the identified genes were enriched in the neurotrophin TRK receptor signaling pathway, including PI3K/Akt and MAPK signaling pathway. we also observed that ZBTB38 affects expression of CDK4/6, Cyclin E, MDM2, ATM, ATR, PTEN, Gadd45, and PIGs in the p53 signaling pathway. In addition, ZBTB38 knockdown significantly suppresses the expression of autophagy-related key genes including PIK3C2A and RB1CC1. The present meeting provides evidence to molecular mechanism of ZBTB38 modulating NB development and targeted anti-tumor therapies.
bibliographic citation: Chen et al. (2019) Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma. PeerJ 7:e6352 https://doi.org/10.7717/peerj.6352
date submitted: 2018-09-25
date accepted: 2018-12-27
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Xing
  given name: Chaofeng
author list: Agent
  family name: Yan
  given name: Li
author list: Agent
  family name: Wang
  given name: Yabing
author list: Agent
  family name: Wang
  given name: Haosen
author list: Agent
  family name: Zhang
  given name: Zongmeng
author list: Agent
  family name: Yu
  given name: Daolun
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Li
  given name: Honglin
author list: Agent
  family name: Li
  given name: Jun
author list: Agent
  family name: Cai
  given name: Yafei
doi: 10.7717/peerj.6352
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: © 2019 Chen et al.
attribution name: Chen et al.

Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube
type: item
type: AcademicArticle
description: The MYB transcription factor (TF) superfamily, one of the largest gene superfamilies, regulates a variety of physiological processes in plants. Although many MYB superfamily genes have been identified in plants, the MYB TFs in Chinese jujube (Ziziphus jujuba Mill.) have not been fully identified and characterized. Additionally, the functions of these genes remain unclear. In total, we identified 171 MYB superfamily genes in jujube and divided them into five subfamilies containing 99 genes of the R2R3-MYB subfamily, 58 genes of the MYB-related subfamily, four genes of the R1R2R3-MYB subfamily, one gene of the 4R-MYB subfamily, and nine genes of the atypical MYB subfamily. The 99 R2R3-MYB genes of jujube were divided into 35 groups, C1–C35, and the 58 MYB-related genes were divided into the following groups: the R-R-type, CCA1-like, I-box-binding-like, TBP-like, CPC-like, and Chinese jujube-specific groups. ZjMYB genes in jujube were well supported by additional highly conserved motifs and exon/intron structures. Most R1 repeats of MYB-related proteins comprised the R2 repeat and had highly conserved EED and EEE residue groups in jujube. Three tandem duplicated gene pairs were found on 12 chromosomes in jujube. According to an expression analysis of 126 ZjMYB genes, MYB-related genes played important roles in jujube development and fruit-related biological processes. The total flavonoid content of jujube fruit decreased as ripening progressed. A total of 93 expressed genes were identified in the RNA-sequencing data from jujube fruit, and 56 ZjMYB members presented significant correlations with total flavonoid contents by correlation analysis. Five pairs of paralogous MYB genes within jujube were composed of nine jujube MYB genes. A total of 14 ZjMYB genes had the same homology to the MYB genes of Arabidopsis and peach, indicating that these 14 MYB genes and their orthologs probably existed before the ancestral divergence of the MYB superfamily. We used a synteny analy…
format: application/pdf
format: text/html
creator: Ji Qing
creator: Wang Dawei
creator: Zhou Jun
creator: Xu Yulan
creator: Shen Bingqi
creator: Zhou Fan
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6353
publisher: PeerJ Inc.
rights: © 2019 Qing et al.
abstract: The MYB transcription factor (TF) superfamily, one of the largest gene superfamilies, regulates a variety of physiological processes in plants. Although many MYB superfamily genes have been identified in plants, the MYB TFs in Chinese jujube (Ziziphus jujuba Mill.) have not been fully identified and characterized. Additionally, the functions of these genes remain unclear. In total, we identified 171 MYB superfamily genes in jujube and divided them into five subfamilies containing 99 genes of the R2R3-MYB subfamily, 58 genes of the MYB-related subfamily, four genes of the R1R2R3-MYB subfamily, one gene of the 4R-MYB subfamily, and nine genes of the atypical MYB subfamily. The 99 R2R3-MYB genes of jujube were divided into 35 groups, C1–C35, and the 58 MYB-related genes were divided into the following groups: the R-R-type, CCA1-like, I-box-binding-like, TBP-like, CPC-like, and Chinese jujube-specific groups. ZjMYB genes in jujube were well supported by additional highly conserved motifs and exon/intron structures. Most R1 repeats of MYB-related proteins comprised the R2 repeat and had highly conserved EED and EEE residue groups in jujube. Three tandem duplicated gene pairs were found on 12 chromosomes in jujube. According to an expression analysis of 126 ZjMYB genes, MYB-related genes played important roles in jujube development and fruit-related biological processes. The total flavonoid content of jujube fruit decreased as ripening progressed. A total of 93 expressed genes were identified in the RNA-sequencing data from jujube fruit, and 56 ZjMYB members presented significant correlations with total flavonoid contents by correlation analysis. Five pairs of paralogous MYB genes within jujube were composed of nine jujube MYB genes. A total of 14 ZjMYB genes had the same homology to the MYB genes of Arabidopsis and peach, indicating that these 14 MYB genes and their orthologs probably existed before the ancestral divergence of the MYB superfamily. We used a synteny analy…
bibliographic citation: Qing et al. (2019) Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube. PeerJ 7:e6353 https://doi.org/10.7717/peerj.6353
date submitted: 2018-10-16
date accepted: 2018-12-27
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qing
  given name: Ji
author list: Agent
  family name: Dawei
  given name: Wang
author list: Agent
  family name: Jun
  given name: Zhou
author list: Agent
  family name: Yulan
  given name: Xu
author list: Agent
  family name: Bingqi
  given name: Shen
author list: Agent
  family name: Fan
  given name: Zhou
doi: 10.7717/peerj.6353
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: © 2019 Qing et al.
attribution name: Qing et al.

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