PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma
items: Stable isotope compositions of precipitation over Central Asia
items: Phenotypic, molecular and pathogenic characterization of Colletotrichum scovillei infecting Capsicum species in Rio de Janeiro, Brazil
items: Mediterraneibacter catenae SW178 sp. nov., an intestinal bacterium of feral chicken
items: Mitogenomics of five Olidiana leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications
items: Dysregulation of miR-381-3p and miR-23b-3p in skeletal muscle could be a possible estimator of early post-mortem interval in rats
items: Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries)
items: Methyl jasmonate enhances ursolic, oleanolic and rosmarinic acid production and sucrose induced biomass accumulation, in hairy roots of Lepechinia caulescens
items: Pre- and post-partum variation in wool cortisol and wool micron in Australian Merino ewe sheep (Ovis aries)
items: Beneficial effects of an intergenerational exercise intervention on health-related physical and psychosocial outcomes in Swiss preschool children and residential seniors: a clinical trial

Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Hepatocellular carcinoma (HCC) is considered to be a malignant tumor with a high incidence and a high mortality. Accurate prognostic models are urgently needed. The present study was aimed at screening the critical genes for prognosis of HCC. Methods The GSE25097, GSE14520, GSE36376 and GSE76427 datasets were obtained from Gene Expression Omnibus (GEO). We used GEO2R to screen differentially expressed genes (DEGs). A protein-protein interaction network of the DEGs was constructed by Cytoscape in order to find hub genes by module analysis. The Metascape was performed to discover biological functions and pathway enrichment of DEGs. MCODE components were calculated to construct a module complex of DEGs. Then, gene set enrichment analysis (GSEA) was used for gene enrichment analysis. ONCOMINE was employed to assess the mRNA expression levels of key genes in HCC, and the survival analysis was conducted using the array from The Cancer Genome Atlas (TCGA) of HCC. Then, the LASSO Cox regression model was performed to establish and identify the prognostic gene signature. We validated the prognostic value of the gene signature in the TCGA cohort. Results We screened out 10 hub genes which were all up-regulated in HCC tissue. They mainly enrich in mitotic cell cycle process. The GSEA results showed that these data sets had good enrichment score and significance in the cell cycle pathway. Each candidate gene may be an indicator of prognostic factors in the development of HCC. However, hub genes expression was weekly associated with overall survival in HCC patients. LASSO Cox regression analysis validated a five-gene signature (including CDC20, CCNB2, NCAPG, ASPM and NUSAP1). These results suggest that five-gene signature model may provide clues for clinical prognostic biomarker of HCC.
format: application/pdf
format: text/html
creator: Lei Yang
creator: Weilong Yin
creator: Xuechen Liu
creator: Fangcun Li
creator: Li Ma
creator: Dong Wang
creator: Hongxing Li
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.11273
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Background Hepatocellular carcinoma (HCC) is considered to be a malignant tumor with a high incidence and a high mortality. Accurate prognostic models are urgently needed. The present study was aimed at screening the critical genes for prognosis of HCC. Methods The GSE25097, GSE14520, GSE36376 and GSE76427 datasets were obtained from Gene Expression Omnibus (GEO). We used GEO2R to screen differentially expressed genes (DEGs). A protein-protein interaction network of the DEGs was constructed by Cytoscape in order to find hub genes by module analysis. The Metascape was performed to discover biological functions and pathway enrichment of DEGs. MCODE components were calculated to construct a module complex of DEGs. Then, gene set enrichment analysis (GSEA) was used for gene enrichment analysis. ONCOMINE was employed to assess the mRNA expression levels of key genes in HCC, and the survival analysis was conducted using the array from The Cancer Genome Atlas (TCGA) of HCC. Then, the LASSO Cox regression model was performed to establish and identify the prognostic gene signature. We validated the prognostic value of the gene signature in the TCGA cohort. Results We screened out 10 hub genes which were all up-regulated in HCC tissue. They mainly enrich in mitotic cell cycle process. The GSEA results showed that these data sets had good enrichment score and significance in the cell cycle pathway. Each candidate gene may be an indicator of prognostic factors in the development of HCC. However, hub genes expression was weekly associated with overall survival in HCC patients. LASSO Cox regression analysis validated a five-gene signature (including CDC20, CCNB2, NCAPG, ASPM and NUSAP1). These results suggest that five-gene signature model may provide clues for clinical prognostic biomarker of HCC.
bibliographic citation: Yang et al. (2021) Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma. PeerJ 9:e11273 https://doi.org/10.7717/peerj.11273
date submitted: 2020-11-10
date accepted: 2021-03-23
issued: 2021-04-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Lei
author list: Agent
  family name: Yin
  given name: Weilong
author list: Agent
  family name: Liu
  given name: Xuechen
author list: Agent
  family name: Li
  given name: Fangcun
author list: Agent
  family name: Ma
  given name: Li
author list: Agent
  family name: Wang
  given name: Dong
author list: Agent
  family name: Li
  given name: Hongxing
doi: 10.7717/peerj.11273
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-28
copyright: ©2021 Yang et al.
attribution name: Yang et al.

Stable isotope compositions of precipitation over Central Asia
type: item
type: AcademicArticle
description: Central Asia is one of the driest regions in the world with a unique water cycle and a complex moisture transport process. However, there is little information on the precipitation δ18O content in Central Asia. We compiled a precipitation δ18O database from 47 meteorological stations across Central Asia to reveal its spatial-temporal characteristics. We determined the relationship between precipitation δ18O and environmental variables and investigated the relationship between δ18O and large-scale atmospheric circulation. The Central Asia meteoric water line was established as δ2H = 7.30 δ18O + 3.12 (R2 = 0.95, n = 727, p < 0.01), and precipitation δ18O ranged from +2‰ to −25.4‰ with a mean of −8.7‰. The precipitation δ18O over Central Asia was related to environmental variables. The δ18O had a significant positive correlation with temperature, and the δ18O-temperature gradient ranged from 0.28‰/°C to 0.68‰/°C. However, the dependence of δ18O on precipitation was unclear; a significant precipitation effect was only observed at the Zhangye and Teheran stations, showing δ18O-precipitation gradients of 0.20‰/mm and −0.08‰/mm, respectively. Latitude and altitude were always significantly correlated with annual δ18O, when considering geographical controls on δ18O, with δ18O/LAT and δ18O/ALT gradients of −0.42‰/° and −0.001‰/m, respectively. But both latitude and longitude were significantly correlated with δ18O in winter. The relationship between δ18O and large-scale atmospheric circulation suggested that the moisture in Central Asia is mainly transported by westerly circulation and is indirectly affected by the Indian monsoon. Meanwhile, the East Asian monsoon may affect the precipitation δ18O content in westerly and monsoon transition regions. These results improve our understanding of the precipitation δ18O and moisture transport in Central Asia, as well as the paleoclimatology and hydrology processes in Central Asia.
format: application/pdf
format: text/html
creator: Junqiang Yao
creator: Xinchun Liu
creator: Wenfeng Hu
subject: Atmospheric Chemistry
subject: Ecohydrology
description: doi:10.7717/peerj.11312
publisher: PeerJ Inc.
rights: © 2021 Yao et al.
abstract: Central Asia is one of the driest regions in the world with a unique water cycle and a complex moisture transport process. However, there is little information on the precipitation δ18O content in Central Asia. We compiled a precipitation δ18O database from 47 meteorological stations across Central Asia to reveal its spatial-temporal characteristics. We determined the relationship between precipitation δ18O and environmental variables and investigated the relationship between δ18O and large-scale atmospheric circulation. The Central Asia meteoric water line was established as δ2H = 7.30 δ18O + 3.12 (R2 = 0.95, n = 727, p < 0.01), and precipitation δ18O ranged from +2‰ to −25.4‰ with a mean of −8.7‰. The precipitation δ18O over Central Asia was related to environmental variables. The δ18O had a significant positive correlation with temperature, and the δ18O-temperature gradient ranged from 0.28‰/°C to 0.68‰/°C. However, the dependence of δ18O on precipitation was unclear; a significant precipitation effect was only observed at the Zhangye and Teheran stations, showing δ18O-precipitation gradients of 0.20‰/mm and −0.08‰/mm, respectively. Latitude and altitude were always significantly correlated with annual δ18O, when considering geographical controls on δ18O, with δ18O/LAT and δ18O/ALT gradients of −0.42‰/° and −0.001‰/m, respectively. But both latitude and longitude were significantly correlated with δ18O in winter. The relationship between δ18O and large-scale atmospheric circulation suggested that the moisture in Central Asia is mainly transported by westerly circulation and is indirectly affected by the Indian monsoon. Meanwhile, the East Asian monsoon may affect the precipitation δ18O content in westerly and monsoon transition regions. These results improve our understanding of the precipitation δ18O and moisture transport in Central Asia, as well as the paleoclimatology and hydrology processes in Central Asia.
bibliographic citation: Yao et al. (2021) Stable isotope compositions of precipitation over Central Asia. PeerJ 9:e11312 https://doi.org/10.7717/peerj.11312
date submitted: 2020-11-11
date accepted: 2021-03-30
issued: 2021-04-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Junqiang
author list: Agent
  family name: Liu
  given name: Xinchun
author list: Agent
  family name: Hu
  given name: Wenfeng
doi: 10.7717/peerj.11312
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-28
copyright: © 2021 Yao et al.
attribution name: Yao et al.

Phenotypic, molecular and pathogenic characterization of Colletotrichum scovillei infecting Capsicum species in Rio de Janeiro, Brazil
type: item
type: AcademicArticle
description: Anthracnose is a disease caused by Colletotrichum spp., one of the world’s most damaging sweet and chili pepper pathogens, especially in tropical and subtropical regions. In the state of Rio de Janeiro, anthracnose is one of the main obstacles for pepper crops. However, to date no research has focused on the identification and characterization of the pathogen, which is fundamental to understand the scope of the disease in the state. Thus, the correct identification of the fungal species and pathogenicity studies can provide important support for disease management and control, apart from identifying possible resistance sources for exploitation in peppers breeding programs. In this study, 11 Colletotrichum isolates were collected from peppers with typical symptoms in the Rio de Janeiro state. These isolates were characterized based on morpho-cultural characteristics and sequencing data from five regions (ITS, ACT, CAL, β-TUB and GAPDH), and the genetic variability was estimated by AFLP markers. Simultaneously, microscopy images of the colonization by the fungal species on unripe Capsicum annuum fruits were taken. Pathogenicity was tested and resistance sources were sought by means of infection of ripe and unripe fruits of 50 Capsicum baccatum accessions. The resulting data showed that all isolates belong to Colletotrichum scovillei specie. About the pathogenicity of Capsicum baccatum, differentiated, stage-specific responses, with higher resistance of ripe fruits were recorded. In addition, four possible sources of Colletotrichum scovillei resistance were detected among the tested accessions. The combination of these data can contribute to future studies on the interaction of Colletotrichum scovillei-Capsicum spp., a research line that is still unexploited in the main areas of this anthracnose fungus.
format: application/pdf
format: text/html
creator: Renata Mussoi Giacomin
creator: Claudete de Fátima Ruas
creator: Viviane Yumi Baba
creator: Sara Mataroli De Godoy
creator: Claudia Pombo Sudré
creator: Cintia dos Santos Bento
creator: Maura Da Cunha
creator: Ingrid Gaspar Da Costa Geronimo
creator: Rosana Rodrigues
creator: Leandro SA Gonçalves
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.10782
publisher: PeerJ Inc.
rights: © 2021 Giacomin et al.
abstract: Anthracnose is a disease caused by Colletotrichum spp., one of the world’s most damaging sweet and chili pepper pathogens, especially in tropical and subtropical regions. In the state of Rio de Janeiro, anthracnose is one of the main obstacles for pepper crops. However, to date no research has focused on the identification and characterization of the pathogen, which is fundamental to understand the scope of the disease in the state. Thus, the correct identification of the fungal species and pathogenicity studies can provide important support for disease management and control, apart from identifying possible resistance sources for exploitation in peppers breeding programs. In this study, 11 Colletotrichum isolates were collected from peppers with typical symptoms in the Rio de Janeiro state. These isolates were characterized based on morpho-cultural characteristics and sequencing data from five regions (ITS, ACT, CAL, β-TUB and GAPDH), and the genetic variability was estimated by AFLP markers. Simultaneously, microscopy images of the colonization by the fungal species on unripe Capsicum annuum fruits were taken. Pathogenicity was tested and resistance sources were sought by means of infection of ripe and unripe fruits of 50 Capsicum baccatum accessions. The resulting data showed that all isolates belong to Colletotrichum scovillei specie. About the pathogenicity of Capsicum baccatum, differentiated, stage-specific responses, with higher resistance of ripe fruits were recorded. In addition, four possible sources of Colletotrichum scovillei resistance were detected among the tested accessions. The combination of these data can contribute to future studies on the interaction of Colletotrichum scovillei-Capsicum spp., a research line that is still unexploited in the main areas of this anthracnose fungus.
bibliographic citation: Giacomin et al. (2021) Phenotypic, molecular and pathogenic characterization of Colletotrichum scovillei infecting Capsicum species in Rio de Janeiro, Brazil. PeerJ 9:e10782 https://doi.org/10.7717/peerj.10782
date submitted: 2020-08-03
date accepted: 2020-12-23
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giacomin
  given name: Renata Mussoi
author list: Agent
  family name: Ruas
  given name: Claudete de Fátima
author list: Agent
  family name: Baba
  given name: Viviane Yumi
author list: Agent
  family name: De Godoy
  given name: Sara Mataroli
author list: Agent
  family name: Sudré
  given name: Claudia Pombo
author list: Agent
  family name: Bento
  given name: Cintia dos Santos
author list: Agent
  family name: Da Cunha
  given name: Maura
author list: Agent
  family name: Da Costa Geronimo
  given name: Ingrid Gaspar
author list: Agent
  family name: Rodrigues
  given name: Rosana
author list: Agent
  family name: Gonçalves
  given name: Leandro SA
doi: 10.7717/peerj.10782
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: © 2021 Giacomin et al.
attribution name: Giacomin et al.

Mediterraneibacter catenae SW178 sp. nov., an intestinal bacterium of feral chicken
type: item
type: AcademicArticle
description: A Gram-positive, coccobacillus, white raised and circular with an entire edge colony, and obligately anaerobic bacterium, strain SW178 was isolated from the cecum content of feral chickens in Brookings, South Dakota, USA. The most closely related strain based on 16S rRNA gene sequence analysis of strain SW178 was Mediterraneibacter torques ATCC 27756T (Ruminococcus torques ATCC 27756T) with 96.94% similarity. The genome of strain SW178 is 3.18 Mbp with G+C content of 46.9 mol%. The optimal temperature and pH for growth in modified brain heart infusion (BHI-M) medium were 45 °C and pH 7.5, respectively. The sole carbon sources of the strain were dextrin, L-fucose, D-galacturonic, α-D-glucose, L-rhamnose and D-sorbitol. The primary cellular fatty acids were C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal (DMA). Based on the genotypic and phenotypic comparison, we proposed that strain SW178 belong to the genus Mediterraneibacter in the family Lachnospiraceae as a novel species, in which the name Mediterraneibacter catenae is proposed. The type strain is SW178 (= DSM 109242T = CCOS 1886T).
format: application/pdf
format: text/html
creator: Supapit Wongkuna
creator: Sudeep Ghimire
creator: Surang Chankhamhaengdecha
creator: Tavan Janvilisri
creator: Joy Scaria
subject: Ecology
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.11050
publisher: PeerJ Inc.
rights: © 2021 Wongkuna et al.
abstract: A Gram-positive, coccobacillus, white raised and circular with an entire edge colony, and obligately anaerobic bacterium, strain SW178 was isolated from the cecum content of feral chickens in Brookings, South Dakota, USA. The most closely related strain based on 16S rRNA gene sequence analysis of strain SW178 was Mediterraneibacter torques ATCC 27756T (Ruminococcus torques ATCC 27756T) with 96.94% similarity. The genome of strain SW178 is 3.18 Mbp with G+C content of 46.9 mol%. The optimal temperature and pH for growth in modified brain heart infusion (BHI-M) medium were 45 °C and pH 7.5, respectively. The sole carbon sources of the strain were dextrin, L-fucose, D-galacturonic, α-D-glucose, L-rhamnose and D-sorbitol. The primary cellular fatty acids were C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal (DMA). Based on the genotypic and phenotypic comparison, we proposed that strain SW178 belong to the genus Mediterraneibacter in the family Lachnospiraceae as a novel species, in which the name Mediterraneibacter catenae is proposed. The type strain is SW178 (= DSM 109242T = CCOS 1886T).
bibliographic citation: Wongkuna et al. (2021) Mediterraneibacter catenae SW178 sp. nov., an intestinal bacterium of feral chicken. PeerJ 9:e11050 https://doi.org/10.7717/peerj.11050
date submitted: 2020-10-16
date accepted: 2021-02-10
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wongkuna
  given name: Supapit
author list: Agent
  family name: Ghimire
  given name: Sudeep
author list: Agent
  family name: Chankhamhaengdecha
  given name: Surang
author list: Agent
  family name: Janvilisri
  given name: Tavan
author list: Agent
  family name: Scaria
  given name: Joy
doi: 10.7717/peerj.11050
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: © 2021 Wongkuna et al.
attribution name: Wongkuna et al.

Mitogenomics of five Olidiana leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications
type: item
type: AcademicArticle
description: Similar morphological characteristics and limited molecular data of Olidiana resulted in their unknown phylogenetic statuses and equivocal relationships. To further understand the genus Olidiana, we sequenced and annotated five Olidiana complete mitochondrial genomes (mitogenomes). Our results show that Olidiana mitogenomes range from 15,205 bp to 15,993 bp in length and include 37 typical genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and a control region. Their nucleotide composition, codon usage, features of control region, and tRNA secondary structures are similar to other members of Cicadellidae. We constructed the phylogenetic tree of Cicadellidae using the maximum likelihood (ML) and Bayesian inference (BI) methods based on all valid mitogenome sequences. The most topological structure of the obtained phylogenetic tree is consistent. Our results support the monophyletic relationships among 10 subfamilies within Cicadellidae and confirm Iassinae and Coelidiinae to be sister groups with high approval ratings. Interestingly, Olidiana was inferred as a paraphyletic group with strong support via both ML and BI analyses. These complete mitogenomes of five Olidiana species could be useful in further studies for species diagnosis, evolution, and phylogeny research within Cicadellidae.
format: application/pdf
format: text/html
creator: Xianyi Wang
creator: Jiajia Wang
creator: Ren-Huai Dai
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.11086
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Similar morphological characteristics and limited molecular data of Olidiana resulted in their unknown phylogenetic statuses and equivocal relationships. To further understand the genus Olidiana, we sequenced and annotated five Olidiana complete mitochondrial genomes (mitogenomes). Our results show that Olidiana mitogenomes range from 15,205 bp to 15,993 bp in length and include 37 typical genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and a control region. Their nucleotide composition, codon usage, features of control region, and tRNA secondary structures are similar to other members of Cicadellidae. We constructed the phylogenetic tree of Cicadellidae using the maximum likelihood (ML) and Bayesian inference (BI) methods based on all valid mitogenome sequences. The most topological structure of the obtained phylogenetic tree is consistent. Our results support the monophyletic relationships among 10 subfamilies within Cicadellidae and confirm Iassinae and Coelidiinae to be sister groups with high approval ratings. Interestingly, Olidiana was inferred as a paraphyletic group with strong support via both ML and BI analyses. These complete mitogenomes of five Olidiana species could be useful in further studies for species diagnosis, evolution, and phylogeny research within Cicadellidae.
bibliographic citation: Wang et al. (2021) Mitogenomics of five Olidiana leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications. PeerJ 9:e11086 https://doi.org/10.7717/peerj.11086
date submitted: 2020-10-23
date accepted: 2021-02-18
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xianyi
author list: Agent
  family name: Wang
  given name: Jiajia
author list: Agent
  family name: Dai
  given name: Ren-Huai
doi: 10.7717/peerj.11086
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Dysregulation of miR-381-3p and miR-23b-3p in skeletal muscle could be a possible estimator of early post-mortem interval in rats
type: item
type: AcademicArticle
description: Background The post-mortem interval (PMI) is the time elapsed since the dead of an individual until the body is found, which is relevant for forensic purposes. The miRNAs regulate the expression of some genes; and due to their small size, they can better support degradation, which makes them suitable for forensic analysis. In the present work, we evaluated the gene expression of miR-381-3p, miR-23b-3p, and miR-144-3p in skeletal muscle in a murine model at the early PMI. Methods We designed a rat model to evaluate the early PMI under controlled conditions. This model consisted in 25 rats divided into five groups of rats, that correspond to the 0, 3, 6, 12 and 24 hours of PMI. The 0 h-PMI was considered as the control group. Muscle samples were taken from each rat to analyze the expression of miR-381-3p, miR-23b-3p, and miR-144-3p by quantitative RT-PCR. The gene expression of each miRNA was expressed as Fold Change (FC) and compared among groups. To find the targets of these miRNAs and the pathways where they participate, we performed an in-silico analysis. From the gene targets of miR-381-3p identified in the silico analysis, the EPC1 gene was selected for gene expression analysis by quantitative RT-PCR in these samples. Also, to evaluate if miR-381-3p could predict the early PMI, a mixed effects model was calculated using its gene expression. Results An upregulation of miR-381-3p was found at 24 h-PMI compared with the control group of 0 h-PMI and (FC = 1.02 vs. FC = 1.96; p = 0.0079). This was the opposite for miR-23b-3p, which had a down-regulation at 24 h-PMI compared to 0 h-PMI (FC = 1.22 vs. FC = 0.13; p = 0.0079). Moreover, the gene expression of miR-381-3p increased throughout the first 24 h of PMI, contrary to miR-23b-3p. The targets of these two miRNAs, participate in biological pathways related to hypoxia, apoptosis, and RNA metabolism. The gene expression of EPC1 was found downregulated at 3 and 12 h of PMI, whereas it remained unchanged at 6 h and 24 h…
format: application/pdf
format: text/html
creator: Vanessa Martínez-Rivera
creator: Christian A. Cárdenas-Monroy
creator: Oliver Millan-Catalan
creator: Jessica González-Corona
creator: N. Sofia Huerta-Pacheco
creator: Antonio Martínez-Gutiérrez
creator: Alexa Villavicencio-Queijeiro
creator: Carlos Pedraza-Lara
creator: Alfredo Hidalgo-Miranda
creator: María Elena Bravo-Gómez
creator: Carlos Pérez-Plasencia
creator: Mariano Guardado-Estrada
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.11102
publisher: PeerJ Inc.
rights: © 2021 Martínez-Rivera et al.
abstract: Background The post-mortem interval (PMI) is the time elapsed since the dead of an individual until the body is found, which is relevant for forensic purposes. The miRNAs regulate the expression of some genes; and due to their small size, they can better support degradation, which makes them suitable for forensic analysis. In the present work, we evaluated the gene expression of miR-381-3p, miR-23b-3p, and miR-144-3p in skeletal muscle in a murine model at the early PMI. Methods We designed a rat model to evaluate the early PMI under controlled conditions. This model consisted in 25 rats divided into five groups of rats, that correspond to the 0, 3, 6, 12 and 24 hours of PMI. The 0 h-PMI was considered as the control group. Muscle samples were taken from each rat to analyze the expression of miR-381-3p, miR-23b-3p, and miR-144-3p by quantitative RT-PCR. The gene expression of each miRNA was expressed as Fold Change (FC) and compared among groups. To find the targets of these miRNAs and the pathways where they participate, we performed an in-silico analysis. From the gene targets of miR-381-3p identified in the silico analysis, the EPC1 gene was selected for gene expression analysis by quantitative RT-PCR in these samples. Also, to evaluate if miR-381-3p could predict the early PMI, a mixed effects model was calculated using its gene expression. Results An upregulation of miR-381-3p was found at 24 h-PMI compared with the control group of 0 h-PMI and (FC = 1.02 vs. FC = 1.96; p = 0.0079). This was the opposite for miR-23b-3p, which had a down-regulation at 24 h-PMI compared to 0 h-PMI (FC = 1.22 vs. FC = 0.13; p = 0.0079). Moreover, the gene expression of miR-381-3p increased throughout the first 24 h of PMI, contrary to miR-23b-3p. The targets of these two miRNAs, participate in biological pathways related to hypoxia, apoptosis, and RNA metabolism. The gene expression of EPC1 was found downregulated at 3 and 12 h of PMI, whereas it remained unchanged at 6 h and 24 h…
bibliographic citation: Martínez-Rivera et al. (2021) Dysregulation of miR-381-3p and miR-23b-3p in skeletal muscle could be a possible estimator of early post-mortem interval in rats. PeerJ 9:e11102 https://doi.org/10.7717/peerj.11102
date submitted: 2020-08-14
date accepted: 2021-02-22
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez-Rivera
  given name: Vanessa
author list: Agent
  family name: Cárdenas-Monroy
  given name: Christian A.
author list: Agent
  family name: Millan-Catalan
  given name: Oliver
author list: Agent
  family name: González-Corona
  given name: Jessica
author list: Agent
  family name: Huerta-Pacheco
  given name: N. Sofia
author list: Agent
  family name: Martínez-Gutiérrez
  given name: Antonio
author list: Agent
  family name: Villavicencio-Queijeiro
  given name: Alexa
author list: Agent
  family name: Pedraza-Lara
  given name: Carlos
author list: Agent
  family name: Hidalgo-Miranda
  given name: Alfredo
author list: Agent
  family name: Bravo-Gómez
  given name: María Elena
author list: Agent
  family name: Pérez-Plasencia
  given name: Carlos
author list: Agent
  family name: Guardado-Estrada
  given name: Mariano
doi: 10.7717/peerj.11102
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Martínez-Rivera et al.
attribution name: Martínez-Rivera et al.

Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries)
type: item
type: AcademicArticle
description: Background Minxian black fur (MBF) sheep are found in the northwestern parts of China. These sheep have developed several special traits. Skin color is a phenotype subject to strong natural selection and diverse skin colors are likely a consequence of differences in gene regulation. Methods Skin structure, color differences, and gene expression (determined by RNA sequencing) were evaluated the Minxian black fur and Small-tail Han sheep (n = 3 each group), which are both native Chinese sheep breeds. Results Small-tail Han sheep have a thicker skin and dermis than the Minxian black fur sheep (P < 0.01); however, the quantity of melanin granules is greater (P < 0.01) in Minxian black fur sheep with a more extensive distribution in skin tissue and hair follicles. One hundred thirty-three differentially expressed genes were significantly associated with 37 ontological terms and two critical KEGG pathways for pigmentation (“tyrosine metabolism” and “melanogenesis” pathways). Important genes from those pathways with known involvement in pigmentation included OCA2 melanosomal transmembrane protein (OCA2), dopachrome tautomerase (DCT), tyrosinase (TYR) and tyrosinase related protein (TYRP1), melanocortin 1 receptor (MC1R), and premelanosome protein (PMEL). The results from our histological and transcriptome analyses will form a foundation for additional investigation into the genetic basis and regulation of pigmentation in these sheep breeds.
format: application/pdf
format: text/html
creator: Xiaolei Shi
creator: Jianping Wu
creator: Xia Lang
creator: Cailian Wang
creator: Yan Bai
creator: David Greg Riley
creator: Lishan Liu
creator: Xiaoming Ma
subject: Biodiversity
subject: Genetics
subject: Molecular Biology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.11122
publisher: PeerJ Inc.
rights: © 2021 Shi et al.
abstract: Background Minxian black fur (MBF) sheep are found in the northwestern parts of China. These sheep have developed several special traits. Skin color is a phenotype subject to strong natural selection and diverse skin colors are likely a consequence of differences in gene regulation. Methods Skin structure, color differences, and gene expression (determined by RNA sequencing) were evaluated the Minxian black fur and Small-tail Han sheep (n = 3 each group), which are both native Chinese sheep breeds. Results Small-tail Han sheep have a thicker skin and dermis than the Minxian black fur sheep (P < 0.01); however, the quantity of melanin granules is greater (P < 0.01) in Minxian black fur sheep with a more extensive distribution in skin tissue and hair follicles. One hundred thirty-three differentially expressed genes were significantly associated with 37 ontological terms and two critical KEGG pathways for pigmentation (“tyrosine metabolism” and “melanogenesis” pathways). Important genes from those pathways with known involvement in pigmentation included OCA2 melanosomal transmembrane protein (OCA2), dopachrome tautomerase (DCT), tyrosinase (TYR) and tyrosinase related protein (TYRP1), melanocortin 1 receptor (MC1R), and premelanosome protein (PMEL). The results from our histological and transcriptome analyses will form a foundation for additional investigation into the genetic basis and regulation of pigmentation in these sheep breeds.
bibliographic citation: Shi et al. (2021) Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries). PeerJ 9:e11122 https://doi.org/10.7717/peerj.11122
date submitted: 2020-08-25
date accepted: 2021-02-25
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Xiaolei
author list: Agent
  family name: Wu
  given name: Jianping
author list: Agent
  family name: Lang
  given name: Xia
author list: Agent
  family name: Wang
  given name: Cailian
author list: Agent
  family name: Bai
  given name: Yan
author list: Agent
  family name: Riley
  given name: David Greg
author list: Agent
  family name: Liu
  given name: Lishan
author list: Agent
  family name: Ma
  given name: Xiaoming
doi: 10.7717/peerj.11122
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Shi et al.
attribution name: Shi et al.

Methyl jasmonate enhances ursolic, oleanolic and rosmarinic acid production and sucrose induced biomass accumulation, in hairy roots of Lepechinia caulescens
type: item
type: AcademicArticle
description: Background Ursolic (UA), oleanolic (OA) and rosmarinic (RA) acids are bioactive metabolites found in Lepechinia caulescens that have generated interest for their health benefits, which include antimicrobial, antioxidant, antimutagenic, gastroprotective, antidiabetic, antihypertensive and anti-inflammatory properties, among others. To date, very few attempts have been made to evaluate the potential for simultaneous production of these bioactive compounds, using a biotechnological approach. Hairy root cultures offer a biotechnology approach that can be used to study the factors affecting the biosynthesis and the production of UA, OA and RA. In the current study, we established hairy root cultures of L. caulescens and evaluated the effect of sucrose on biomass accumulation, and the effect of different concentrations and times of exposure of methyl jasmonate (MeJA), on the accumulation of UA, OA and RA. Methods Leaves from plants of L. caulescens were inoculated with Agrobacterium rhizogenes strain ATCC 15834. PCR of rolB gene confirmed the transgenic nature of hairy roots. Hairy roots were subcultured in semisolid MSB5 medium, supplemented with 15, 30, 45 or 60 g/L sucrose and after 4 weeks, dry weight was determined. The accumulation of UA, OA and RA of wild plants and hairy roots were determined by HPLC. Finally, the hairy roots were treated with 0, 100, 200 and 300 µM of MeJA and the content of bioactive compounds was analyzed, after 24, 48 and 72 h. Results High frequency transformation (75%) was achieved, using leaf explants from axenic seedlings, infected with A. rhizogenes. The hairy roots showed an enhanced linear biomass accumulation, in response to the increase in sucrose concentration. The hairy root cultures in MSB5 medium, supplemented with 45 g/L sucrose, were capable to synthesizing UA (0.29 ± 0.00 mg/g DW), OA (0.57 ± 0.00 mg/g DW) and RA (41.66 ± 0.31 mg/g DW), about two, seven and three times more, respectively, than in roots from wild plants. Elicita…
format: application/pdf
format: text/html
creator: Victor M. Vergara-Martínez
creator: Samuel E. Estrada-Soto
creator: Susana Valencia-Díaz
creator: Karlina Garcia-Sosa
creator: Luis Manuel Peña-Rodríguez
creator: José de Jesús Arellano-García
creator: Irene Perea-Arango
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11279
publisher: PeerJ Inc.
rights: © 2021 Vergara-Martínez et al.
abstract: Background Ursolic (UA), oleanolic (OA) and rosmarinic (RA) acids are bioactive metabolites found in Lepechinia caulescens that have generated interest for their health benefits, which include antimicrobial, antioxidant, antimutagenic, gastroprotective, antidiabetic, antihypertensive and anti-inflammatory properties, among others. To date, very few attempts have been made to evaluate the potential for simultaneous production of these bioactive compounds, using a biotechnological approach. Hairy root cultures offer a biotechnology approach that can be used to study the factors affecting the biosynthesis and the production of UA, OA and RA. In the current study, we established hairy root cultures of L. caulescens and evaluated the effect of sucrose on biomass accumulation, and the effect of different concentrations and times of exposure of methyl jasmonate (MeJA), on the accumulation of UA, OA and RA. Methods Leaves from plants of L. caulescens were inoculated with Agrobacterium rhizogenes strain ATCC 15834. PCR of rolB gene confirmed the transgenic nature of hairy roots. Hairy roots were subcultured in semisolid MSB5 medium, supplemented with 15, 30, 45 or 60 g/L sucrose and after 4 weeks, dry weight was determined. The accumulation of UA, OA and RA of wild plants and hairy roots were determined by HPLC. Finally, the hairy roots were treated with 0, 100, 200 and 300 µM of MeJA and the content of bioactive compounds was analyzed, after 24, 48 and 72 h. Results High frequency transformation (75%) was achieved, using leaf explants from axenic seedlings, infected with A. rhizogenes. The hairy roots showed an enhanced linear biomass accumulation, in response to the increase in sucrose concentration. The hairy root cultures in MSB5 medium, supplemented with 45 g/L sucrose, were capable to synthesizing UA (0.29 ± 0.00 mg/g DW), OA (0.57 ± 0.00 mg/g DW) and RA (41.66 ± 0.31 mg/g DW), about two, seven and three times more, respectively, than in roots from wild plants. Elicita…
bibliographic citation: Vergara-Martínez et al. (2021) Methyl jasmonate enhances ursolic, oleanolic and rosmarinic acid production and sucrose induced biomass accumulation, in hairy roots of Lepechinia caulescens. PeerJ 9:e11279 https://doi.org/10.7717/peerj.11279
date submitted: 2020-11-20
date accepted: 2021-03-24
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vergara-Martínez
  given name: Victor M.
author list: Agent
  family name: Estrada-Soto
  given name: Samuel E.
author list: Agent
  family name: Valencia-Díaz
  given name: Susana
author list: Agent
  family name: Garcia-Sosa
  given name: Karlina
author list: Agent
  family name: Peña-Rodríguez
  given name: Luis Manuel
author list: Agent
  family name: Arellano-García
  given name: José de Jesús
author list: Agent
  family name: Perea-Arango
  given name: Irene
doi: 10.7717/peerj.11279
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Vergara-Martínez et al.
attribution name: Vergara-Martínez et al.

Pre- and post-partum variation in wool cortisol and wool micron in Australian Merino ewe sheep (Ovis aries)
type: item
type: AcademicArticle
description: An individual merino sheep’s output of wool production is influenced by synergistic interactions of sheep genetics, climate, farm management, and nutrition available to the whole flock. The price paid to the producer for this wool commodity is determined via numerous tested parameters and /or subjective appraisal of the raw greasy wool. This research investigated the level of variation in wool cortisol (a physiological stress biomarker) and wool micron (MIC) in Merino ewes (Ovis aries), pre-partum and post-lambing (lactation/lambs at foot), using maiden ewe (n = 38) managed in an outdoor paddock in a commercial farm. The key findings of this study are; (1) wool quality indicators showed a significant variation between pre- and post- parturition including significant reduction in MIC and (2) there was a negative correlation between wool cortisol levels and wool micron pre-parturition (rs = − 0.179, p < 0.05). This relationship between wool cortisol and wool micron was positive (rs = + 0.29, p < 0.05) during post-parturition suggesting that ewes with lambs at foot ended up with finer wool (reduction in fibre diameter) but they also maintained high levels of wool cortisol. Furthermore, the comfort factor, curvature, standard deviation and spin fineness of the wool were also significantly reduced post-parturition. The results of this study show that metabolic resources partitioning in ewe associated with pregnancy and lambing can result in a reduction in wool quality indices. The activity of the HPA-axis is attenuated during late gestation and parturition as a maternal adaptation; however, the results of our study show that wool cortisol remained similar between pre- and post- lambing. This result indicates that environmental stressors that may have been operating on farm (e.g., cold winter period) could influence on maternal physiological stress response however the exact level of influence of environment conditions on ewe stress levels and productivity traits (e.g., l…
format: application/pdf
format: text/html
creator: Gregory Sawyer
creator: Dylan Russell Fox
creator: Edward Narayan
subject: Agricultural Science
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.11288
publisher: PeerJ Inc.
rights: © 2021 Sawyer et al.
abstract: An individual merino sheep’s output of wool production is influenced by synergistic interactions of sheep genetics, climate, farm management, and nutrition available to the whole flock. The price paid to the producer for this wool commodity is determined via numerous tested parameters and /or subjective appraisal of the raw greasy wool. This research investigated the level of variation in wool cortisol (a physiological stress biomarker) and wool micron (MIC) in Merino ewes (Ovis aries), pre-partum and post-lambing (lactation/lambs at foot), using maiden ewe (n = 38) managed in an outdoor paddock in a commercial farm. The key findings of this study are; (1) wool quality indicators showed a significant variation between pre- and post- parturition including significant reduction in MIC and (2) there was a negative correlation between wool cortisol levels and wool micron pre-parturition (rs = − 0.179, p < 0.05). This relationship between wool cortisol and wool micron was positive (rs = + 0.29, p < 0.05) during post-parturition suggesting that ewes with lambs at foot ended up with finer wool (reduction in fibre diameter) but they also maintained high levels of wool cortisol. Furthermore, the comfort factor, curvature, standard deviation and spin fineness of the wool were also significantly reduced post-parturition. The results of this study show that metabolic resources partitioning in ewe associated with pregnancy and lambing can result in a reduction in wool quality indices. The activity of the HPA-axis is attenuated during late gestation and parturition as a maternal adaptation; however, the results of our study show that wool cortisol remained similar between pre- and post- lambing. This result indicates that environmental stressors that may have been operating on farm (e.g., cold winter period) could influence on maternal physiological stress response however the exact level of influence of environment conditions on ewe stress levels and productivity traits (e.g., l…
bibliographic citation: Sawyer et al. (2021) Pre- and post-partum variation in wool cortisol and wool micron in Australian Merino ewe sheep (Ovis aries). PeerJ 9:e11288 https://doi.org/10.7717/peerj.11288
date submitted: 2020-12-24
date accepted: 2021-03-26
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sawyer
  given name: Gregory
author list: Agent
  family name: Fox
  given name: Dylan Russell
author list: Agent
  family name: Narayan
  given name: Edward
doi: 10.7717/peerj.11288
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Sawyer et al.
attribution name: Sawyer et al.

Beneficial effects of an intergenerational exercise intervention on health-related physical and psychosocial outcomes in Swiss preschool children and residential seniors: a clinical trial
type: item
type: AcademicArticle
description: Background Intergenerational exercise possesses the potential to becoming an innovative strategy for promoting physical activity in seniors and children. Although this approach has gained attraction within the last decade, controlled trials on physical and psychosocial effects have not been performed yet. Methods Sixty-eight healthy preschool children (age: 4.9 y (SD 0.7)) and 47 residential seniors (age: 81.7 y (7.1)) participated in this five-armed intervention study. All participants were assigned to either an intergenerational (IG), peer (PG) or a control group (CON). Children were tested on gross motor skills (TGMD-2), jump performance and handgrip strength. Social-emotional skills questionnaires (KOMPIK) were assessed by kindergarten teachers. Seniors performed the Short Physical Performance Battery (SPPB), including gait speed. Arterial stiffness parameters were also examined. Questionnaires assessing psychosocial wellbeing were filled in with staff. IG and PG received one comparable exercise session a week lasting 45 minutes for 25-weeks. CON received no intervention. Measurements were performed before and after the intervention. Results In children: IG improved all measured physical parameters. When adjusted for baseline values, large effects were observed in favor of IG compared to CON in TGMD-2 (Cohen’s d=0.78 [0.33;1.24]) and in handgrip strength (d = 1.07 [0.63;1.51]). No relevant differences were found in KOMPIK between groups (−0.38<d≤0.14). In seniors: IG showed moderate to very large improvements in all main physical performance (0.61<d≤2.53) and psychosocial parameters (0.89<d≤1.20) compared to CON. Conclusion IG children showed large benefits in motor skills compared to CON while IG seniors benefit especially in psychosocial wellbeing and functional mobility necessary for everyday life. Intergenerational exercise is comparable and in certain dimensions superior to peer group exercise and a promising strategy to integratively improve mental health …
format: application/pdf
format: text/html
creator: Alice Minghetti
creator: Lars Donath
creator: Lukas Zahner
creator: Henner Hanssen
creator: Oliver Faude
subject: Geriatrics
subject: Kinesiology
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11292
publisher: PeerJ Inc.
rights: © 2021 Minghetti et al.
abstract: Background Intergenerational exercise possesses the potential to becoming an innovative strategy for promoting physical activity in seniors and children. Although this approach has gained attraction within the last decade, controlled trials on physical and psychosocial effects have not been performed yet. Methods Sixty-eight healthy preschool children (age: 4.9 y (SD 0.7)) and 47 residential seniors (age: 81.7 y (7.1)) participated in this five-armed intervention study. All participants were assigned to either an intergenerational (IG), peer (PG) or a control group (CON). Children were tested on gross motor skills (TGMD-2), jump performance and handgrip strength. Social-emotional skills questionnaires (KOMPIK) were assessed by kindergarten teachers. Seniors performed the Short Physical Performance Battery (SPPB), including gait speed. Arterial stiffness parameters were also examined. Questionnaires assessing psychosocial wellbeing were filled in with staff. IG and PG received one comparable exercise session a week lasting 45 minutes for 25-weeks. CON received no intervention. Measurements were performed before and after the intervention. Results In children: IG improved all measured physical parameters. When adjusted for baseline values, large effects were observed in favor of IG compared to CON in TGMD-2 (Cohen’s d=0.78 [0.33;1.24]) and in handgrip strength (d = 1.07 [0.63;1.51]). No relevant differences were found in KOMPIK between groups (−0.38<d≤0.14). In seniors: IG showed moderate to very large improvements in all main physical performance (0.61<d≤2.53) and psychosocial parameters (0.89<d≤1.20) compared to CON. Conclusion IG children showed large benefits in motor skills compared to CON while IG seniors benefit especially in psychosocial wellbeing and functional mobility necessary for everyday life. Intergenerational exercise is comparable and in certain dimensions superior to peer group exercise and a promising strategy to integratively improve mental health …
bibliographic citation: Minghetti et al. (2021) Beneficial effects of an intergenerational exercise intervention on health-related physical and psychosocial outcomes in Swiss preschool children and residential seniors: a clinical trial. PeerJ 9:e11292 https://doi.org/10.7717/peerj.11292
date submitted: 2020-12-17
date accepted: 2021-03-26
issued: 2021-04-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Minghetti
  given name: Alice
author list: Agent
  family name: Donath
  given name: Lars
author list: Agent
  family name: Zahner
  given name: Lukas
author list: Agent
  family name: Hanssen
  given name: Henner
author list: Agent
  family name: Faude
  given name: Oliver
doi: 10.7717/peerj.11292
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-27
copyright: ©2021 Minghetti et al.
attribution name: Minghetti et al.

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