PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Arboreal twig-nesting ants form dominance hierarchies over nesting resources
items: Sarc-F and muscle function in community dwelling adults with aged care service needs: baseline and post-training relationship
items: Effect of vibration vs non-vibration foam rolling techniques on flexibility, dynamic balance and perceived joint stability after fatigue
items: A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean
items: Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae
items: Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology
items: Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma
items: Oxidative stress and antioxidants in the trabecular meshwork
items: Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia
items: Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)

Arboreal twig-nesting ants form dominance hierarchies over nesting resources
type: item
type: AcademicArticle
description: Interspecific dominance hierarchies have been widely reported across animal systems. High-ranking species are expected to monopolize more resources than low-ranking species via resource monopolization. In some ant species, dominance hierarchies have been used to explain species coexistence and community structure. However, it remains unclear whether or in what contexts dominance hierarchies occur in tropical ant communities. This study seeks to examine whether arboreal twig-nesting ants competing for nesting resources in a Mexican coffee agricultural ecosystem are arranged in a linear dominance hierarchy. We described the dominance relationships among 10 species of ants and measured the uncertainty and steepness of the inferred dominance hierarchy. We also assessed the orderliness of the hierarchy by considering species interactions at the network level. Based on the randomized Elo-rating method, we found that the twig-nesting ant species Myrmelachista mexicana ranked highest in the ranking, while Pseudomyrmex ejectus was ranked as the lowest in the hierarchy. Our results show that the hierarchy was intermediate in its steepness, suggesting that the probability of higher ranked species winning contests against lower ranked species was fairly high. Motif analysis and significant excess of triads further revealed that the species networks were largely transitive. This study highlights that some tropical arboreal ant communities organize into dominance hierarchies.
format: application/pdf
format: text/html
creator: Senay Yitbarek
creator: Stacy M. Philpott
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Population Biology
description: doi:10.7717/peerj.8124
publisher: PeerJ Inc.
rights: © 2019 Yitbarek and Philpott
abstract: Interspecific dominance hierarchies have been widely reported across animal systems. High-ranking species are expected to monopolize more resources than low-ranking species via resource monopolization. In some ant species, dominance hierarchies have been used to explain species coexistence and community structure. However, it remains unclear whether or in what contexts dominance hierarchies occur in tropical ant communities. This study seeks to examine whether arboreal twig-nesting ants competing for nesting resources in a Mexican coffee agricultural ecosystem are arranged in a linear dominance hierarchy. We described the dominance relationships among 10 species of ants and measured the uncertainty and steepness of the inferred dominance hierarchy. We also assessed the orderliness of the hierarchy by considering species interactions at the network level. Based on the randomized Elo-rating method, we found that the twig-nesting ant species Myrmelachista mexicana ranked highest in the ranking, while Pseudomyrmex ejectus was ranked as the lowest in the hierarchy. Our results show that the hierarchy was intermediate in its steepness, suggesting that the probability of higher ranked species winning contests against lower ranked species was fairly high. Motif analysis and significant excess of triads further revealed that the species networks were largely transitive. This study highlights that some tropical arboreal ant communities organize into dominance hierarchies.
bibliographic citation: Yitbarek et al. (2019) Arboreal twig-nesting ants form dominance hierarchies over nesting resources. PeerJ 7:e8124 https://doi.org/10.7717/peerj.8124
date submitted: 2019-08-08
date accepted: 2019-10-30
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yitbarek
  given name: Senay
author list: Agent
  family name: Philpott
  given name: Stacy M.
doi: 10.7717/peerj.8124
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: ©2019 Yitbarek and Philpott
attribution name: Yitbarek and Philpott

Sarc-F and muscle function in community dwelling adults with aged care service needs: baseline and post-training relationship
type: item
type: AcademicArticle
description: Background This study sought to better understand the psychometric properties of the SARC-F, by examining the baseline and training-related relationships between the five SARC-F items and objective measures of muscle function. Each of the five items of the SARC-F are scored from 0 to 2, with total score of four or more indicative of likely sarcopenia. Methods This manuscript describes a sub-study of a larger step-wedge, randomised controlled 24-week progressive resistance and balance training (PRBT) program trial for Australian community dwelling older adults accessing government supported aged care. Muscle function was assessed using handgrip strength, isometric knee extension, 5-time repeated chair stand and walking speed over 4 m. Associations within and between SARC-F categories and muscle function were assessed using multiple correspondence analysis (MCA) and multinomial regression, respectively. Results Significant associations were identified at baseline between SARC-F total score and measures of lower-body muscle function (r = − 0.62 to 0.57; p ≤ 0.002) in 245 older adults. MCA analysis indicated the first three dimensions of the SARC-F data explained 48.5% of the cumulative variance. The initial dimension represented overall sarcopenia diagnosis, Dimension 2 the ability to displace the body vertically, and Dimension 3 walking ability and falls status. The majority of the 168 older adults who completed the PRBT program reported no change in their SARC-F diagnosis or individual item scores (56.5–79.2%). However, significant associations were obtained between training-related changes in SARC-F total and item scores and changes in walking speed and chair stand test performance (r = − 0.30 to 0.33; p < 0.001 and relative risk ratio = 0.40–2.24; p < 0.05, respectively). MCA analysis of the change score data indicated that the first two dimensions explained 32.2% of the cumulative variance, with these dimensions representing whether a change occurred and the direc…
format: application/pdf
format: text/html
creator: Justin W.L. Keogh
creator: Tim Henwood
creator: Paul A. Gardiner
creator: Anthony G. Tuckett
creator: Sharon Hetherington
creator: Kevin Rouse
creator: Paul Swinton
subject: Geriatrics
subject: Kinesiology
description: doi:10.7717/peerj.8140
publisher: PeerJ Inc.
rights: © 2019 Keogh et al.
abstract: Background This study sought to better understand the psychometric properties of the SARC-F, by examining the baseline and training-related relationships between the five SARC-F items and objective measures of muscle function. Each of the five items of the SARC-F are scored from 0 to 2, with total score of four or more indicative of likely sarcopenia. Methods This manuscript describes a sub-study of a larger step-wedge, randomised controlled 24-week progressive resistance and balance training (PRBT) program trial for Australian community dwelling older adults accessing government supported aged care. Muscle function was assessed using handgrip strength, isometric knee extension, 5-time repeated chair stand and walking speed over 4 m. Associations within and between SARC-F categories and muscle function were assessed using multiple correspondence analysis (MCA) and multinomial regression, respectively. Results Significant associations were identified at baseline between SARC-F total score and measures of lower-body muscle function (r = − 0.62 to 0.57; p ≤ 0.002) in 245 older adults. MCA analysis indicated the first three dimensions of the SARC-F data explained 48.5% of the cumulative variance. The initial dimension represented overall sarcopenia diagnosis, Dimension 2 the ability to displace the body vertically, and Dimension 3 walking ability and falls status. The majority of the 168 older adults who completed the PRBT program reported no change in their SARC-F diagnosis or individual item scores (56.5–79.2%). However, significant associations were obtained between training-related changes in SARC-F total and item scores and changes in walking speed and chair stand test performance (r = − 0.30 to 0.33; p < 0.001 and relative risk ratio = 0.40–2.24; p < 0.05, respectively). MCA analysis of the change score data indicated that the first two dimensions explained 32.2% of the cumulative variance, with these dimensions representing whether a change occurred and the direc…
bibliographic citation: Keogh et al. (2019) Sarc-F and muscle function in community dwelling adults with aged care service needs: baseline and post-training relationship. PeerJ 7:e8140 https://doi.org/10.7717/peerj.8140
date submitted: 2019-06-17
date accepted: 2019-11-01
issued: 2019-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Keogh
  given name: Justin W.L.
author list: Agent
  family name: Henwood
  given name: Tim
author list: Agent
  family name: Gardiner
  given name: Paul A.
author list: Agent
  family name: Tuckett
  given name: Anthony G.
author list: Agent
  family name: Hetherington
  given name: Sharon
author list: Agent
  family name: Rouse
  given name: Kevin
author list: Agent
  family name: Swinton
  given name: Paul
doi: 10.7717/peerj.8140
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-27
copyright: ©2019 Keogh et al.
attribution name: Keogh et al.

Effect of vibration vs non-vibration foam rolling techniques on flexibility, dynamic balance and perceived joint stability after fatigue
type: item
type: AcademicArticle
description: Background Foam roller and vibration techniques are currently used to assist in recovery after fatigue. The main purpose of this study was to determine the effects of the use of a foam roller with and without vibration on dynamic balance, ankle dorsiflexion, hamstring and lumbar spine flexibility and perceived knee and ankle stability after an induced fatigue protocol. Methods A total of 24 healthy recreationally active participants (17 males and seven females) were recruited to a randomized cross over trial consisting of; no treatment (NT), foam roller treatment (FR) and vibration foam roller treatment (VFR). The assessments included; the Sit & Reach test, Y balance test and post-treatment perceived knee and ankle stability. Measurements were taken after a standardized warm up (baseline) and repeated following an exercise-induced muscle fatigue protocol consisting of repeated lunges until volitional fatigue. The three treatment conditions were assessed on three separate days in a randomized order. A 3 × 3 repeated measures ANOVA was used to investigate differences between the three treatments over the three time points and a one factor repeated measures ANOVA was used to determine any differences between treatments using the Global Rate of Change scale when considering perceived stability. Results FR and VFR conditions both showed a greater ankle dorsiflexion range of motion (ROM) (p < 0.001), greater posteromedial and posterolateral reach distances (p < 0.001) and a better knee and ankle perceived stability (p < 0.001) when compared to the NT condition. A trend toward significance was observed in the hamstring and lumbar spine flexibility (p = 0.074) in both treatment conditions when compared to the NT condition. However, no differences were seen between the FR and VFR conditions. Conclusions Both FR conditions seem to assist in exercise-induced muscle fatigue recovery with improvements in ROM, balance and perceived stability.
format: application/pdf
format: text/html
creator: Ana María de Benito
creator: Raúl Valldecabres
creator: Diego Ceca
creator: Jim Richards
creator: Joaquín Barrachina Igual
creator: Ana Pablos
subject: Kinesiology
description: doi:10.7717/peerj.8000
publisher: PeerJ Inc.
rights: © 2019 de Benito et al.
abstract: Background Foam roller and vibration techniques are currently used to assist in recovery after fatigue. The main purpose of this study was to determine the effects of the use of a foam roller with and without vibration on dynamic balance, ankle dorsiflexion, hamstring and lumbar spine flexibility and perceived knee and ankle stability after an induced fatigue protocol. Methods A total of 24 healthy recreationally active participants (17 males and seven females) were recruited to a randomized cross over trial consisting of; no treatment (NT), foam roller treatment (FR) and vibration foam roller treatment (VFR). The assessments included; the Sit & Reach test, Y balance test and post-treatment perceived knee and ankle stability. Measurements were taken after a standardized warm up (baseline) and repeated following an exercise-induced muscle fatigue protocol consisting of repeated lunges until volitional fatigue. The three treatment conditions were assessed on three separate days in a randomized order. A 3 × 3 repeated measures ANOVA was used to investigate differences between the three treatments over the three time points and a one factor repeated measures ANOVA was used to determine any differences between treatments using the Global Rate of Change scale when considering perceived stability. Results FR and VFR conditions both showed a greater ankle dorsiflexion range of motion (ROM) (p < 0.001), greater posteromedial and posterolateral reach distances (p < 0.001) and a better knee and ankle perceived stability (p < 0.001) when compared to the NT condition. A trend toward significance was observed in the hamstring and lumbar spine flexibility (p = 0.074) in both treatment conditions when compared to the NT condition. However, no differences were seen between the FR and VFR conditions. Conclusions Both FR conditions seem to assist in exercise-induced muscle fatigue recovery with improvements in ROM, balance and perceived stability.
bibliographic citation: de Benito et al. (2019) Effect of vibration vs non-vibration foam rolling techniques on flexibility, dynamic balance and perceived joint stability after fatigue. PeerJ 7:e8000 https://doi.org/10.7717/peerj.8000
date submitted: 2019-07-18
date accepted: 2019-10-07
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Benito
  given name: Ana María
author list: Agent
  family name: Valldecabres
  given name: Raúl
author list: Agent
  family name: Ceca
  given name: Diego
author list: Agent
  family name: Richards
  given name: Jim
author list: Agent
  family name: Barrachina Igual
  given name: Joaquín
author list: Agent
  family name: Pablos
  given name: Ana
doi: 10.7717/peerj.8000
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: © 2019 de Benito et al.
attribution name: de Benito et al.

A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean
type: item
type: AcademicArticle
description: Caribbean reef corals have experienced unprecedented declines from climate change, anthropogenic stressors and infectious diseases in recent decades. Since 2014, a highly lethal, new disease, called stony coral tissue loss disease, has impacted many reef-coral species in Florida. During the summer of 2018, we noticed an anomalously high disease prevalence affecting different coral species in the northern portion of the Mexican Caribbean. We assessed the severity of this outbreak in 2018/2019 using the AGRRA coral protocol to survey 82 reef sites across the Mexican Caribbean. Then, using a subset of 14 sites, we detailed information from before the outbreak (2016/2017) to explore the consequences of the disease on the condition and composition of coral communities. Our findings show that the disease outbreak has already spread across the entire region by affecting similar species (with similar disease patterns) to those previously described for Florida. However, we observed a great variability in prevalence and tissue mortality that was not attributable to any geographical gradient. Using long-term data, we determined that there is no evidence of such high coral disease prevalence anywhere in the region before 2018, which suggests that the entire Mexican Caribbean was afflicted by the disease within a few months. The analysis of sites that contained pre-outbreak information showed that this event considerably increased coral mortality and severely changed the structure of coral communities in the region. Given the high prevalence and lethality of this disease, and the high number of susceptible species, we encourage reef researchers, managers and stakeholders across the Western Atlantic to accord it the highest priority for the near future.
format: application/pdf
format: text/html
creator: Lorenzo Alvarez-Filip
creator: Nuria Estrada-Saldívar
creator: Esmeralda Pérez-Cervantes
creator: Ana Molina-Hernández
creator: Francisco J. González-Barrios
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.8069
publisher: PeerJ Inc.
rights: © 2019 Alvarez-Filip et al.
abstract: Caribbean reef corals have experienced unprecedented declines from climate change, anthropogenic stressors and infectious diseases in recent decades. Since 2014, a highly lethal, new disease, called stony coral tissue loss disease, has impacted many reef-coral species in Florida. During the summer of 2018, we noticed an anomalously high disease prevalence affecting different coral species in the northern portion of the Mexican Caribbean. We assessed the severity of this outbreak in 2018/2019 using the AGRRA coral protocol to survey 82 reef sites across the Mexican Caribbean. Then, using a subset of 14 sites, we detailed information from before the outbreak (2016/2017) to explore the consequences of the disease on the condition and composition of coral communities. Our findings show that the disease outbreak has already spread across the entire region by affecting similar species (with similar disease patterns) to those previously described for Florida. However, we observed a great variability in prevalence and tissue mortality that was not attributable to any geographical gradient. Using long-term data, we determined that there is no evidence of such high coral disease prevalence anywhere in the region before 2018, which suggests that the entire Mexican Caribbean was afflicted by the disease within a few months. The analysis of sites that contained pre-outbreak information showed that this event considerably increased coral mortality and severely changed the structure of coral communities in the region. Given the high prevalence and lethality of this disease, and the high number of susceptible species, we encourage reef researchers, managers and stakeholders across the Western Atlantic to accord it the highest priority for the near future.
bibliographic citation: Alvarez-Filip et al. (2019) A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean. PeerJ 7:e8069 https://doi.org/10.7717/peerj.8069
date submitted: 2019-08-12
date accepted: 2019-10-20
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alvarez-Filip
  given name: Lorenzo
author list: Agent
  family name: Estrada-Saldívar
  given name: Nuria
author list: Agent
  family name: Pérez-Cervantes
  given name: Esmeralda
author list: Agent
  family name: Molina-Hernández
  given name: Ana
author list: Agent
  family name: González-Barrios
  given name: Francisco J.
doi: 10.7717/peerj.8069
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: © 2019 Alvarez-Filip et al.
attribution name: Alvarez-Filip et al.

Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae
type: item
type: AcademicArticle
description: Background Coelidiinae, a relatively large subfamily within the family Cicadellidae, includes 129 genera and ∼1,300 species distributed worldwide. However, the mitogenomes of only two species (Olidiana sp. and Taharana fasciana) in the subfamily Coelidiinae have been assembled. Here, we report the first complete mitogenome assembly of the genus Olidiana. Methods Specimens were collected from Wenxian County (Gansu Province, China) and identified on the basis of their morphology. Mitogenomes were sequenced by next-generation sequencing, following which an NGS template was generated, and this was confirmed using polymerase chain reaction and Sanger sequencing. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. Results The mitogenome of O. ritcheriina was 15,166 bp long, with an A + T content of 78.0%. Compared with the mitogenome of other Cicadellidae sp., the gene order, gene content, gene size, base composition, and codon usage of protein-coding genes (PCGs) in O. ritcheriina were highly conserved. The standard start codon of all PCGs was ATN and stop codon was TAA or TAG; COII, COIII, and ND4L ended with a single T. All tRNA genes showed the typical cloverleaf secondary structure, except for trnSer, which did not have the dihydrouridine arm. Furthermore, the secondary structures of rRNAs (rrnL and rrnS) in O. ritcheriina were predicted. Overall, five domains and 42 helices were predicted for rrnL (domain III is absent in arthropods), and three structural domains and 27 helices were predicted for rrnS. Maximum likelihood and Bayesian analyses indicated that O. ritcheriina and other Coelidiinae members were clustered into a clade, indicating the relationships among their subfamilies; the main topology was as follows: (Deltocephalinae + ((Coelidiinae + Iassinae) + ((Typhlocybinae + Cicadellinae) + (Idiocerinae + (Treehopper + Megophthalminae))))). The phylogenetic relationships indicated that the molecular taxonomy of O. ritcheriina is co…
format: application/pdf
format: text/html
creator: Xian-Yi Wang
creator: Jia-Jia Wang
creator: Zhi-Hua Fan
creator: Ren-Huai Dai
subject: Biodiversity
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Taxonomy
description: doi:10.7717/peerj.8072
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Coelidiinae, a relatively large subfamily within the family Cicadellidae, includes 129 genera and ∼1,300 species distributed worldwide. However, the mitogenomes of only two species (Olidiana sp. and Taharana fasciana) in the subfamily Coelidiinae have been assembled. Here, we report the first complete mitogenome assembly of the genus Olidiana. Methods Specimens were collected from Wenxian County (Gansu Province, China) and identified on the basis of their morphology. Mitogenomes were sequenced by next-generation sequencing, following which an NGS template was generated, and this was confirmed using polymerase chain reaction and Sanger sequencing. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. Results The mitogenome of O. ritcheriina was 15,166 bp long, with an A + T content of 78.0%. Compared with the mitogenome of other Cicadellidae sp., the gene order, gene content, gene size, base composition, and codon usage of protein-coding genes (PCGs) in O. ritcheriina were highly conserved. The standard start codon of all PCGs was ATN and stop codon was TAA or TAG; COII, COIII, and ND4L ended with a single T. All tRNA genes showed the typical cloverleaf secondary structure, except for trnSer, which did not have the dihydrouridine arm. Furthermore, the secondary structures of rRNAs (rrnL and rrnS) in O. ritcheriina were predicted. Overall, five domains and 42 helices were predicted for rrnL (domain III is absent in arthropods), and three structural domains and 27 helices were predicted for rrnS. Maximum likelihood and Bayesian analyses indicated that O. ritcheriina and other Coelidiinae members were clustered into a clade, indicating the relationships among their subfamilies; the main topology was as follows: (Deltocephalinae + ((Coelidiinae + Iassinae) + ((Typhlocybinae + Cicadellinae) + (Idiocerinae + (Treehopper + Megophthalminae))))). The phylogenetic relationships indicated that the molecular taxonomy of O. ritcheriina is co…
bibliographic citation: Wang et al. (2019) Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae. PeerJ 7:e8072 https://doi.org/10.7717/peerj.8072
date submitted: 2019-04-27
date accepted: 2019-10-21
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xian-Yi
author list: Agent
  family name: Wang
  given name: Jia-Jia
author list: Agent
  family name: Fan
  given name: Zhi-Hua
author list: Agent
  family name: Dai
  given name: Ren-Huai
doi: 10.7717/peerj.8072
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology
type: item
type: AcademicArticle
description: Background There are abundant sheep breed resources in the Xinjiang region of China attributing to its diverse ecological system, which include several high-litter size sheep populations. Previous studies have confirmed that the major high prolificacy gene cannot be used to detect high litter size. Our research team found a resource group in Pishan County, southern Xinjiang. It showed high fertility with an average litter size of two to four in one birth, excellent breast development, and a high survival rate of lambs. In the present study, we used this resource as an ideal sample for studying the genetic mechanisms of high prolificacy in sheep. Methods Indigenous sheep populations from Xinjiang, with different litter sizes, were selected for the research, and specific-locus amplified fragment sequencing (SLAF-seq) technology was used to comprehensively screen single nucleotide polymorphisms (SNPs) from the whole genome that may cause differences in litter size. Novel genes associated with litter size of sheep were detected using genome-wide association studies (GWAS), providing new clues revealing the regulation mechanism of sheep fecundity. Candidate genes related to ovulation and litter size were selected for verification using Kompetitive Allele Specific polymerase chain reaction (KASP) cluster analysis. Results We identified 685,300 SNPs using the SLAF-seq technique for subsequent genome-wide analysis. Subsequently, 155 SNPs were detected at the genome-wide level. Fourteen genes related to sheep reproduction were notated: COIL, SLK, FSHR, Plxna3, Ddx24, CXCL12, Pla2g7, ATP5F1A, KERA, GUCY1A1, LOC101107541, LOC101107119, LOC101107809, and BRAF. Based on literature reports, 30 loci of seven genes and candidate genes (CXCL12, FSHR, SLK, GUCY1A1, COIL, LOC101107541, and LOC101107119) related to ovulation and litter size were selected for verification using KASP cluster analysis. Among them, nine loci of three genes were successfully genotyped. Three loci of FSHR (G…
format: application/pdf
format: text/html
creator: Haiyu Ma
creator: Chao Fang
creator: Lingling Liu
creator: Qiong Wang
creator: Jueken Aniwashi
creator: Yiming Sulaiman
creator: Kezierkailedi Abudilaheman
creator: Wujun Liu
subject: Developmental Biology
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.8079
publisher: PeerJ Inc.
rights: © 2019 Ma et al.
abstract: Background There are abundant sheep breed resources in the Xinjiang region of China attributing to its diverse ecological system, which include several high-litter size sheep populations. Previous studies have confirmed that the major high prolificacy gene cannot be used to detect high litter size. Our research team found a resource group in Pishan County, southern Xinjiang. It showed high fertility with an average litter size of two to four in one birth, excellent breast development, and a high survival rate of lambs. In the present study, we used this resource as an ideal sample for studying the genetic mechanisms of high prolificacy in sheep. Methods Indigenous sheep populations from Xinjiang, with different litter sizes, were selected for the research, and specific-locus amplified fragment sequencing (SLAF-seq) technology was used to comprehensively screen single nucleotide polymorphisms (SNPs) from the whole genome that may cause differences in litter size. Novel genes associated with litter size of sheep were detected using genome-wide association studies (GWAS), providing new clues revealing the regulation mechanism of sheep fecundity. Candidate genes related to ovulation and litter size were selected for verification using Kompetitive Allele Specific polymerase chain reaction (KASP) cluster analysis. Results We identified 685,300 SNPs using the SLAF-seq technique for subsequent genome-wide analysis. Subsequently, 155 SNPs were detected at the genome-wide level. Fourteen genes related to sheep reproduction were notated: COIL, SLK, FSHR, Plxna3, Ddx24, CXCL12, Pla2g7, ATP5F1A, KERA, GUCY1A1, LOC101107541, LOC101107119, LOC101107809, and BRAF. Based on literature reports, 30 loci of seven genes and candidate genes (CXCL12, FSHR, SLK, GUCY1A1, COIL, LOC101107541, and LOC101107119) related to ovulation and litter size were selected for verification using KASP cluster analysis. Among them, nine loci of three genes were successfully genotyped. Three loci of FSHR (G…
bibliographic citation: Ma et al. (2019) Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology. PeerJ 7:e8079 https://doi.org/10.7717/peerj.8079
date submitted: 2019-05-21
date accepted: 2019-10-21
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Haiyu
author list: Agent
  family name: Fang
  given name: Chao
author list: Agent
  family name: Liu
  given name: Lingling
author list: Agent
  family name: Wang
  given name: Qiong
author list: Agent
  family name: Aniwashi
  given name: Jueken
author list: Agent
  family name: Sulaiman
  given name: Yiming
author list: Agent
  family name: Abudilaheman
  given name: Kezierkailedi
author list: Agent
  family name: Liu
  given name: Wujun
doi: 10.7717/peerj.8079
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: ©2019 Ma et al.
attribution name: Ma et al.

Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma
type: item
type: AcademicArticle
description: Clear cell renal cell carcinoma (ccRCC) is one of the most common and lethal types of cancer within the urinary system. Great efforts have been made to elucidate the pathogeny. However, the molecular mechanism of ccRCC is still not well understood. The aim of this study is to identify key genes in the carcinogenesis and progression of ccRCC. The mRNA microarray dataset GSE53757 was downloaded from the Gene Expression Omnibus database. The GSE53757 dataset contains tumor and matched paracancerous specimens from 72 ccRCC patients with clinical stage I to IV. The linear model of microarray data (limma) package in R language was used to identify differentially expressed genes (DEGs). The protein–protein interaction (PPI) network of the DEGs was constructed using the search tool for the retrieval of interacting genes (STRING). Subsequently, we visualized molecular interaction networks by Cytoscape software and analyzed modules with MCODE. A total of 1,284, 1,416, 1,610 and 1,185 up-regulated genes, and 932, 1,236, 1,006 and 929 down-regulated genes were identified from clinical stage I to IV ccRCC patients, respectively. The overlapping DEGs among the four clinical stages contain 870 up-regulated and 645 down-regulated genes. The enrichment analysis of DEGs in the top module was carried out with DAVID. The results showed the DEGs of the top module were mainly enriched in microtubule-based movement, mitotic cytokinesis and mitotic chromosome condensation. Eleven up-regulated genes and one down-regulated gene were identified as hub genes. Survival analysis showed the high expression of CENPE, KIF20A, KIF4A, MELK, NCAPG, NDC80, NUF2, TOP2A, TPX2 and UBE2C, and low expression of ACADM gene could be involved in the carcinogenesis, invasion or recurrence of ccRCC. Literature retrieval results showed the hub gene NDC80, CENPE and ACADM might be novel targets for the diagnosis, clinical treatment and prognosis of ccRCC. In conclusion, the findings of present study may help us un…
format: application/pdf
format: text/html
creator: Haiping Zhang
creator: Jian Zou
creator: Ying Yin
creator: Bo Zhang
creator: Yaling Hu
creator: Jingjing Wang
creator: Huijun Mu
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Nephrology
subject: Oncology
description: doi:10.7717/peerj.8096
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Clear cell renal cell carcinoma (ccRCC) is one of the most common and lethal types of cancer within the urinary system. Great efforts have been made to elucidate the pathogeny. However, the molecular mechanism of ccRCC is still not well understood. The aim of this study is to identify key genes in the carcinogenesis and progression of ccRCC. The mRNA microarray dataset GSE53757 was downloaded from the Gene Expression Omnibus database. The GSE53757 dataset contains tumor and matched paracancerous specimens from 72 ccRCC patients with clinical stage I to IV. The linear model of microarray data (limma) package in R language was used to identify differentially expressed genes (DEGs). The protein–protein interaction (PPI) network of the DEGs was constructed using the search tool for the retrieval of interacting genes (STRING). Subsequently, we visualized molecular interaction networks by Cytoscape software and analyzed modules with MCODE. A total of 1,284, 1,416, 1,610 and 1,185 up-regulated genes, and 932, 1,236, 1,006 and 929 down-regulated genes were identified from clinical stage I to IV ccRCC patients, respectively. The overlapping DEGs among the four clinical stages contain 870 up-regulated and 645 down-regulated genes. The enrichment analysis of DEGs in the top module was carried out with DAVID. The results showed the DEGs of the top module were mainly enriched in microtubule-based movement, mitotic cytokinesis and mitotic chromosome condensation. Eleven up-regulated genes and one down-regulated gene were identified as hub genes. Survival analysis showed the high expression of CENPE, KIF20A, KIF4A, MELK, NCAPG, NDC80, NUF2, TOP2A, TPX2 and UBE2C, and low expression of ACADM gene could be involved in the carcinogenesis, invasion or recurrence of ccRCC. Literature retrieval results showed the hub gene NDC80, CENPE and ACADM might be novel targets for the diagnosis, clinical treatment and prognosis of ccRCC. In conclusion, the findings of present study may help us un…
bibliographic citation: Zhang et al. (2019) Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma. PeerJ 7:e8096 https://doi.org/10.7717/peerj.8096
date submitted: 2019-08-23
date accepted: 2019-10-24
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Haiping
author list: Agent
  family name: Zou
  given name: Jian
author list: Agent
  family name: Yin
  given name: Ying
author list: Agent
  family name: Zhang
  given name: Bo
author list: Agent
  family name: Hu
  given name: Yaling
author list: Agent
  family name: Wang
  given name: Jingjing
author list: Agent
  family name: Mu
  given name: Huijun
doi: 10.7717/peerj.8096
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Oxidative stress and antioxidants in the trabecular meshwork
type: item
type: AcademicArticle
description: Glaucoma is an age-dependent disease closely related to oxidative stress and is regarded as the second leading cause of irreversible blindness worldwide. In recent years, many studies have shown that morphological and functional abnormalities of the trabecular meshwork (TM) are closely related to glaucoma, especially with respect to oxidative stress. In this review, the mechanisms of oxidative stress in the TM and treatment strategies for this condition, including strategies involving antioxidants, noncoding RNAs and exogenous compounds, are discussed. Although many questions remain to be answered, the reviewed findings provide insights for further research on oxidative stress alleviation in glaucoma and suggest new targets for glaucoma prevention.
format: application/pdf
format: text/html
creator: Mingxuan Wang
creator: Yajuan Zheng
subject: Geriatrics
subject: Ophthalmology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.8121
publisher: PeerJ Inc.
rights: © 2019 Wang and Zheng
abstract: Glaucoma is an age-dependent disease closely related to oxidative stress and is regarded as the second leading cause of irreversible blindness worldwide. In recent years, many studies have shown that morphological and functional abnormalities of the trabecular meshwork (TM) are closely related to glaucoma, especially with respect to oxidative stress. In this review, the mechanisms of oxidative stress in the TM and treatment strategies for this condition, including strategies involving antioxidants, noncoding RNAs and exogenous compounds, are discussed. Although many questions remain to be answered, the reviewed findings provide insights for further research on oxidative stress alleviation in glaucoma and suggest new targets for glaucoma prevention.
bibliographic citation: Wang et al. (2019) Oxidative stress and antioxidants in the trabecular meshwork. PeerJ 7:e8121 https://doi.org/10.7717/peerj.8121
date submitted: 2019-06-14
date accepted: 2019-10-30
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Mingxuan
author list: Agent
  family name: Zheng
  given name: Yajuan
doi: 10.7717/peerj.8121
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: ©2019 Wang and Zheng
attribution name: Wang and Zheng

Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia
type: item
type: AcademicArticle
description: The best facultative anaerobes among vertebrates are members of the genera Trachemys (pond slider turtles) and Chrysemys (painted turtles), and are able to survive without oxygen for up to 12 to 18 weeks at ∼3 °C. In this study, we utilized RNAseq to profile the transcriptomic changes that take place in response to 20 hrs of anoxia at 5 °C in the liver of the red eared slide turtle (Trachemys scripta elegans). Sequencing reads were obtained from at least 18,169 different genes and represented a minimum 49x coverage of the C. picta bellii exome. A total of 3,105 genes showed statistically significant changes in gene expression between the two animal groups, of which 971 also exhibited a fold change equal to or greater than 50% of control normoxic values. This study also highlights a number of anoxia-responsive molecular pathways that are may be important to navigating anoxia survival. These pathways were enriched in mRNA found to significantly increase in response to anoxia and included molecular processes such as DNA damage repair and metabolic reprogramming. For example, our results indicate that the anoxic turtle may utilize succinate metabolism to yield a molecule of GTP in addition to the two molecules that results from lactate production, and agrees with other established models of anoxia tolerance. Collectively, our analysis provides a snapshot of the molecular landscape of the anoxic turtle and may provide hints into the how this animal is capable of surviving this extreme environmental stress.
format: application/pdf
format: text/html
creator: Kyle K. Biggar
creator: Jing Zhang
creator: Kenneth B. Storey
subject: Biochemistry
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.8144
publisher: PeerJ Inc.
rights: © 2019 Biggar et al.
abstract: The best facultative anaerobes among vertebrates are members of the genera Trachemys (pond slider turtles) and Chrysemys (painted turtles), and are able to survive without oxygen for up to 12 to 18 weeks at ∼3 °C. In this study, we utilized RNAseq to profile the transcriptomic changes that take place in response to 20 hrs of anoxia at 5 °C in the liver of the red eared slide turtle (Trachemys scripta elegans). Sequencing reads were obtained from at least 18,169 different genes and represented a minimum 49x coverage of the C. picta bellii exome. A total of 3,105 genes showed statistically significant changes in gene expression between the two animal groups, of which 971 also exhibited a fold change equal to or greater than 50% of control normoxic values. This study also highlights a number of anoxia-responsive molecular pathways that are may be important to navigating anoxia survival. These pathways were enriched in mRNA found to significantly increase in response to anoxia and included molecular processes such as DNA damage repair and metabolic reprogramming. For example, our results indicate that the anoxic turtle may utilize succinate metabolism to yield a molecule of GTP in addition to the two molecules that results from lactate production, and agrees with other established models of anoxia tolerance. Collectively, our analysis provides a snapshot of the molecular landscape of the anoxic turtle and may provide hints into the how this animal is capable of surviving this extreme environmental stress.
bibliographic citation: Biggar et al. (2019) Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia. PeerJ 7:e8144 https://doi.org/10.7717/peerj.8144
date submitted: 2019-05-21
date accepted: 2019-11-01
issued: 2019-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Biggar
  given name: Kyle K.
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.8144
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-26
copyright: ©2019 Biggar et al.
attribution name: Biggar et al.

Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)
type: item
type: AcademicArticle
description: The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.
format: application/pdf
format: text/html
creator: Xin Hu
creator: Lili Zhu
creator: Yi Zhang
creator: Li Xu
creator: Na Li
creator: Xingguo Zhang
creator: Yu Pan
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.7929
publisher: PeerJ Inc.
rights: © 2019 Hu et al.
abstract: The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.
bibliographic citation: Hu et al. (2019) Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.). PeerJ 7:e7929 https://doi.org/10.7717/peerj.7929
date submitted: 2019-05-09
date accepted: 2019-09-20
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Xin
author list: Agent
  family name: Zhu
  given name: Lili
author list: Agent
  family name: Zhang
  given name: Yi
author list: Agent
  family name: Xu
  given name: Li
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Zhang
  given name: Xingguo
author list: Agent
  family name: Pan
  given name: Yu
doi: 10.7717/peerj.7929
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Hu et al.
attribution name: Hu et al.

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