PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Organic acids and 2,4-Di-tert-butylphenol: major compounds of Weissella confusa WM36 cell-free supernatant against growth, survival and virulence of Salmonella Typhi
items: Ecology of an ocelot population at the northern edge of the species’ distribution in northern Sonora, Mexico
items: Integrated bioinformatics analysis of potential pathway biomarkers using abnormal proteins in clubfoot
items: Comparative analysis of cutaneous bacterial communities of farmed Rana dybowskii after gentamycin bath
items: Gini coefficients for measuring the distribution of sexually transmitted infections among individuals with different levels of sexual activity
items: Comparative analysis of the demographic parameters of seven spotted ladybird beetle (Coleoptera: Coccinellidae) reared on various host aphid species
items: Evolution of sexual size dimorphism in the wing musculature of Drosophila
items: Identification of key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis
items: Isolation, sequencing, and expression analysis of 30 AP2/ERF transcription factors in apple
items: Autophagy-related genes prognosis signature as potential predictive markers for immunotherapy in hepatocellular carcinoma

Organic acids and 2,4-Di-tert-butylphenol: major compounds of Weissella confusa WM36 cell-free supernatant against growth, survival and virulence of Salmonella Typhi
type: item
type: AcademicArticle
description: Background Salmonella Typhi (S. Typhi), the causative agent of typhoid fever, causes serious systemic disease in humans. Antibiotic treatment is required for the S. Typhi infection, while the inappropriate use of antibiotics causes increased drug-resistant S. Typhi. Hence, alternative therapies through non-antibiotic approaches are urgently needed. The use of beneficial lactic acid bacterium and/or its metabolites to control typhoid fever represent a promising approach, as it may exert protective actions through various mechanisms. Method In this study, the cell-free culture supernatant (CFCS) of Weissella confusa WM36 was evaluated via the antibacterial activity, and its metabolites were identified. In addition, the effects of CFCS on Salmonella virulence behaviors were also investigated. Result Based on strong inhibition the growth of S. Typhi DMST 22842, organic acids (lactic acid and acetic acid) and 2,4-Di-tert-butylphenol (2,4 DTBP), were the main antibacterial metabolites presented in CFCS of strain WM36. Minimum inhibitory concentration (MIC) at 40% WM36–CFCS dramatically reduced the S. Typhi population to more than 99.99% at 4 h and completely inhibited biofilm formation, while sub-MIC at 20% (v/v) and MIC could reduce 100% of motility. Additionally, sub-MIC at only 10% (v/v) WM36–CFCS did down-regulate the expression of virulence genes which are responsible for the type-III secretion system, effector proteins, and quorum sensing system in this pathogen. Conclusion W. confusa WM36 and its metabolites are shown to be a promising candidates, and an effective approach against typhoid Salmonella burden.
format: application/pdf
format: text/html
creator: Wattana Pelyuntha
creator: Chaiyavat Chaiyasut
creator: Duangporn Kantachote
creator: Sasithorn Sirilun
subject: Biotechnology
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.8410
publisher: PeerJ Inc.
rights: © 2020 Pelyuntha et al.
abstract: Background Salmonella Typhi (S. Typhi), the causative agent of typhoid fever, causes serious systemic disease in humans. Antibiotic treatment is required for the S. Typhi infection, while the inappropriate use of antibiotics causes increased drug-resistant S. Typhi. Hence, alternative therapies through non-antibiotic approaches are urgently needed. The use of beneficial lactic acid bacterium and/or its metabolites to control typhoid fever represent a promising approach, as it may exert protective actions through various mechanisms. Method In this study, the cell-free culture supernatant (CFCS) of Weissella confusa WM36 was evaluated via the antibacterial activity, and its metabolites were identified. In addition, the effects of CFCS on Salmonella virulence behaviors were also investigated. Result Based on strong inhibition the growth of S. Typhi DMST 22842, organic acids (lactic acid and acetic acid) and 2,4-Di-tert-butylphenol (2,4 DTBP), were the main antibacterial metabolites presented in CFCS of strain WM36. Minimum inhibitory concentration (MIC) at 40% WM36–CFCS dramatically reduced the S. Typhi population to more than 99.99% at 4 h and completely inhibited biofilm formation, while sub-MIC at 20% (v/v) and MIC could reduce 100% of motility. Additionally, sub-MIC at only 10% (v/v) WM36–CFCS did down-regulate the expression of virulence genes which are responsible for the type-III secretion system, effector proteins, and quorum sensing system in this pathogen. Conclusion W. confusa WM36 and its metabolites are shown to be a promising candidates, and an effective approach against typhoid Salmonella burden.
bibliographic citation: Pelyuntha et al. (2020) Organic acids and 2,4-Di-tert-butylphenol: major compounds of Weissella confusa WM36 cell-free supernatant against growth, survival and virulence of Salmonella Typhi. PeerJ 8:e8410 https://doi.org/10.7717/peerj.8410
date submitted: 2019-10-09
date accepted: 2019-12-16
issued: 2020-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pelyuntha
  given name: Wattana
author list: Agent
  family name: Chaiyasut
  given name: Chaiyavat
author list: Agent
  family name: Kantachote
  given name: Duangporn
author list: Agent
  family name: Sirilun
  given name: Sasithorn
doi: 10.7717/peerj.8410
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-20
copyright: © 2020 Pelyuntha et al.
attribution name: Pelyuntha et al.

Ecology of an ocelot population at the northern edge of the species’ distribution in northern Sonora, Mexico
type: item
type: AcademicArticle
description: We used data from eight years of camera trapping at Rancho El Aribabi, a cattle ranch and conservation property in northern Sonora, Mexico, to examine the ecology of the northern-most known breeding population of ocelots (Leopardus pardalis). Ocelots were found mostly in two discrete and disjunct areas: a riverine riparian canyon at just less than 1,000 masl elevation and along arroyos in an oak-mesquite savanna in the Sierra Azul at 1,266–1,406 masl. An ocelot was also detected at a site between those two areas, in an area of a Sonoran desertscrub-foothills thornscrub ecotone at 1,300 masl. At least 18 ocelots, both males and females, were detected during the 2007–2011 and 2014–2018 sampling periods. A female with a kitten was documented in 2011. No individual ocelots were photographed in both areas, which are separated by a minimum of 11.29 km, and no individuals were photographed in both time periods. In a binary logistic regression, key environmental variables predicting ocelot presence were, in order of importance, distance to a paved road, distance to human habitation, proximity to water, and an anthropogenic influences index that was dominated by cattle. Another analysis corroborated the finding regarding ocelot presence and cattle. Contrary to previous studies, ocelot presence was not tied to vegetation cover close to the ground. We present information about the types of habitats and sites ocelots used, short-term movements, daily and seasonal activity patterns, and behavior, including occurrence of different individuals at or near the same site over short periods of time. We discuss ocelot home range, density, and movements, but small sample sizes and study design problems limit the value of estimates derived from our work. Rancho El Aribabi is a private, conservation ranch for which the owners have made voluntary conservation commitments that provide habitat and protection for ocelots and other animals and plants. This northern-most known breeding populati…
format: application/pdf
format: text/html
creator: James C. Rorabaugh
creator: Jan Schipper
creator: Sergio Avila-Villegas
creator: Jessica A. Lamberton-Moreno
creator: Timothy Flood
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Natural Resource Management
subject: Population Biology
description: doi:10.7717/peerj.8414
publisher: PeerJ Inc.
rights: © 2020 Rorabaugh et al.
abstract: We used data from eight years of camera trapping at Rancho El Aribabi, a cattle ranch and conservation property in northern Sonora, Mexico, to examine the ecology of the northern-most known breeding population of ocelots (Leopardus pardalis). Ocelots were found mostly in two discrete and disjunct areas: a riverine riparian canyon at just less than 1,000 masl elevation and along arroyos in an oak-mesquite savanna in the Sierra Azul at 1,266–1,406 masl. An ocelot was also detected at a site between those two areas, in an area of a Sonoran desertscrub-foothills thornscrub ecotone at 1,300 masl. At least 18 ocelots, both males and females, were detected during the 2007–2011 and 2014–2018 sampling periods. A female with a kitten was documented in 2011. No individual ocelots were photographed in both areas, which are separated by a minimum of 11.29 km, and no individuals were photographed in both time periods. In a binary logistic regression, key environmental variables predicting ocelot presence were, in order of importance, distance to a paved road, distance to human habitation, proximity to water, and an anthropogenic influences index that was dominated by cattle. Another analysis corroborated the finding regarding ocelot presence and cattle. Contrary to previous studies, ocelot presence was not tied to vegetation cover close to the ground. We present information about the types of habitats and sites ocelots used, short-term movements, daily and seasonal activity patterns, and behavior, including occurrence of different individuals at or near the same site over short periods of time. We discuss ocelot home range, density, and movements, but small sample sizes and study design problems limit the value of estimates derived from our work. Rancho El Aribabi is a private, conservation ranch for which the owners have made voluntary conservation commitments that provide habitat and protection for ocelots and other animals and plants. This northern-most known breeding populati…
bibliographic citation: Rorabaugh et al. (2020) Ecology of an ocelot population at the northern edge of the species’ distribution in northern Sonora, Mexico. PeerJ 8:e8414 https://doi.org/10.7717/peerj.8414
date submitted: 2019-07-08
date accepted: 2019-12-16
issued: 2020-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rorabaugh
  given name: James C.
author list: Agent
  family name: Schipper
  given name: Jan
author list: Agent
  family name: Avila-Villegas
  given name: Sergio
author list: Agent
  family name: Lamberton-Moreno
  given name: Jessica A.
author list: Agent
  family name: Flood
  given name: Timothy
doi: 10.7717/peerj.8414
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-20
copyright: ©2020 Rorabaugh et al.
attribution name: Rorabaugh et al.

Integrated bioinformatics analysis of potential pathway biomarkers using abnormal proteins in clubfoot
type: item
type: AcademicArticle
description: Background As one of the most common major congenital distal skeletal abnormalities, congenital talipes equinovarus (clubfoot) affects approximately one in one thousandth newborns. Although several etiologies of clubfoot have been proposed and several genes have been identified as susceptible genes, previous studies did not further explore signaling pathways and potential upstream and downstream regulatory networks. Therefore, the aim of the present investigation is to explore abnormal pathways and their interactions in clubfoot using integrated bioinformatics analyses. Methods KEGG, gene ontology (GO), Reactome (REAC), WikiPathways (WP) or human phenotype ontology (HP) enrichment analysis were performed using WebGestalt, g:Profiler and NetworkAnalyst. Results A large number of signaling pathways were enriched e.g. signal transduction, disease, metabolism, gene expression (transcription), immune system, developmental biology, cell cycle, and ECM. Protein-protein interactions (PPIs) and gene regulatory networks (GRNs) analysis results indicated that extensive and complex interactions occur in these proteins, enrichment pathways, and TF-miRNA coregulatory networks. Transcription factors such as SOX9, CTNNB1, GLI3, FHL2, TGFBI and HOXD13, regulated these candidate proteins. Conclusion The results of the present study supported previously proposed hypotheses, such as ECM, genetic, muscle, neurological, skeletal, and vascular abnormalities. More importantly, the enrichment results also indicated cellular or immune responses to external stimuli, and abnormal molecular transport or metabolism may be new potential etiological mechanisms of clubfoot.
format: application/pdf
format: text/html
creator: Guiquan Cai
creator: Xuan Yang
creator: Ting Chen
creator: Fangchun Jin
creator: Jing Ding
creator: Zhenkai Wu
subject: Bioinformatics
subject: Orthopedics
subject: Pathology
subject: Pediatrics
subject: Computational Science
description: doi:10.7717/peerj.8422
publisher: PeerJ Inc.
rights: © 2020 Cai et al.
abstract: Background As one of the most common major congenital distal skeletal abnormalities, congenital talipes equinovarus (clubfoot) affects approximately one in one thousandth newborns. Although several etiologies of clubfoot have been proposed and several genes have been identified as susceptible genes, previous studies did not further explore signaling pathways and potential upstream and downstream regulatory networks. Therefore, the aim of the present investigation is to explore abnormal pathways and their interactions in clubfoot using integrated bioinformatics analyses. Methods KEGG, gene ontology (GO), Reactome (REAC), WikiPathways (WP) or human phenotype ontology (HP) enrichment analysis were performed using WebGestalt, g:Profiler and NetworkAnalyst. Results A large number of signaling pathways were enriched e.g. signal transduction, disease, metabolism, gene expression (transcription), immune system, developmental biology, cell cycle, and ECM. Protein-protein interactions (PPIs) and gene regulatory networks (GRNs) analysis results indicated that extensive and complex interactions occur in these proteins, enrichment pathways, and TF-miRNA coregulatory networks. Transcription factors such as SOX9, CTNNB1, GLI3, FHL2, TGFBI and HOXD13, regulated these candidate proteins. Conclusion The results of the present study supported previously proposed hypotheses, such as ECM, genetic, muscle, neurological, skeletal, and vascular abnormalities. More importantly, the enrichment results also indicated cellular or immune responses to external stimuli, and abnormal molecular transport or metabolism may be new potential etiological mechanisms of clubfoot.
bibliographic citation: Cai et al. (2020) Integrated bioinformatics analysis of potential pathway biomarkers using abnormal proteins in clubfoot. PeerJ 8:e8422 https://doi.org/10.7717/peerj.8422
date submitted: 2019-08-19
date accepted: 2019-12-17
issued: 2020-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Guiquan
author list: Agent
  family name: Yang
  given name: Xuan
author list: Agent
  family name: Chen
  given name: Ting
author list: Agent
  family name: Jin
  given name: Fangchun
author list: Agent
  family name: Ding
  given name: Jing
author list: Agent
  family name: Wu
  given name: Zhenkai
doi: 10.7717/peerj.8422
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-20
copyright: ©2020 Cai et al.
attribution name: Cai et al.

Comparative analysis of cutaneous bacterial communities of farmed Rana dybowskii after gentamycin bath
type: item
type: AcademicArticle
description: Introduction Pathogenic bacteria limit the success of Rana dybowskii breeding. Gentamicin is used to treat R. dybowskii disease. To understand the effects of gentamicin on the composition and structure of the cutaneous bacterial community of R. dybowskii, three groups (control, gentamicin and recovery) were established in this study. Materials & Methods The V3–V4 hypervariable region of the 16S rRNA gene was analyzed in samples by high-throughput sequencing. Alpha diversity and beta diversity were evaluated to compare the cutaneous bacterial community diversity. Results A total of 1,159,668 valid sequences and 3,132 operational taxonomic units (OTUs) were obtained from these three experimental groups. The number of OTUs obtained in the control group, gentamicin group and recovery group were 2,194, 2,288, and 2,047, respectively, and the number of shared OTUs was 1,313. The alpha diversity of the cutaneous bacterial community was not significantly affected by gentamicin, while beta diversity was significantly affected. Discussion & Conclusions The effect of a gentamicin bath on relative species abundance was greater than the effect on the species composition. The changes in Proteobacteria, Acinetobacter, and Chryseobacterium were significant, and reductions were observed after the recovery period. Six potentially pathogenic genera were detected, including Aeromonas, Citrobacter, Chryseobacterium, Pseudomonas, Staphylococcus, and Streptococcus. Among them, Aeromonas and Chryseobacterium were significantly inhibited by the gentamicin bath. The results of this study provide a theoretical basis for the application of gentamicin in R. dybowskii breeding.
format: application/pdf
format: text/html
creator: Jia Bie
creator: Qing Tong
creator: Xiaoning Liu
creator: Xianhao Zhang
creator: Hongbin Wang
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.8430
publisher: PeerJ Inc.
rights: © 2020 Bie et al.
abstract: Introduction Pathogenic bacteria limit the success of Rana dybowskii breeding. Gentamicin is used to treat R. dybowskii disease. To understand the effects of gentamicin on the composition and structure of the cutaneous bacterial community of R. dybowskii, three groups (control, gentamicin and recovery) were established in this study. Materials & Methods The V3–V4 hypervariable region of the 16S rRNA gene was analyzed in samples by high-throughput sequencing. Alpha diversity and beta diversity were evaluated to compare the cutaneous bacterial community diversity. Results A total of 1,159,668 valid sequences and 3,132 operational taxonomic units (OTUs) were obtained from these three experimental groups. The number of OTUs obtained in the control group, gentamicin group and recovery group were 2,194, 2,288, and 2,047, respectively, and the number of shared OTUs was 1,313. The alpha diversity of the cutaneous bacterial community was not significantly affected by gentamicin, while beta diversity was significantly affected. Discussion & Conclusions The effect of a gentamicin bath on relative species abundance was greater than the effect on the species composition. The changes in Proteobacteria, Acinetobacter, and Chryseobacterium were significant, and reductions were observed after the recovery period. Six potentially pathogenic genera were detected, including Aeromonas, Citrobacter, Chryseobacterium, Pseudomonas, Staphylococcus, and Streptococcus. Among them, Aeromonas and Chryseobacterium were significantly inhibited by the gentamicin bath. The results of this study provide a theoretical basis for the application of gentamicin in R. dybowskii breeding.
bibliographic citation: Bie et al. (2020) Comparative analysis of cutaneous bacterial communities of farmed Rana dybowskii after gentamycin bath. PeerJ 8:e8430 https://doi.org/10.7717/peerj.8430
date submitted: 2019-08-07
date accepted: 2019-12-18
issued: 2020-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bie
  given name: Jia
author list: Agent
  family name: Tong
  given name: Qing
author list: Agent
  family name: Liu
  given name: Xiaoning
author list: Agent
  family name: Zhang
  given name: Xianhao
author list: Agent
  family name: Wang
  given name: Hongbin
doi: 10.7717/peerj.8430
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-20
copyright: ©2020 Bie et al.
attribution name: Bie et al.

Gini coefficients for measuring the distribution of sexually transmitted infections among individuals with different levels of sexual activity
type: item
type: AcademicArticle
description: Objectives Gini coefficients have been used to describe the distribution of Chlamydia trachomatis (CT) infections among individuals with different levels of sexual activity. The objectives of this study were to investigate Gini coefficients for different sexually transmitted infections (STIs), and to determine how STI control interventions might affect the Gini coefficient over time. Methods We used population-based data for sexually experienced women from two British National Surveys of Sexual Attitudes and Lifestyles (Natsal-2: 1999–2001; Natsal-3: 2010–2012) to calculate Gini coefficients for CT, Mycoplasma genitalium (MG), and human papillomavirus (HPV) types 6, 11, 16 and 18. We applied bootstrap methods to assess uncertainty and to compare Gini coefficients for different STIs. We then used a mathematical model of STI transmission to study how control interventions affect Gini coefficients. Results Gini coefficients for CT and MG were 0.33 (95% CI [0.18–0.49]) and 0.16 (95% CI [0.02–0.36]), respectively. The relatively small coefficient for MG suggests a longer infectious duration compared with CT. The coefficients for HPV types 6, 11, 16 and 18 ranged from 0.15 to 0.38. During the decade between Natsal-2 and Natsal-3, the Gini coefficient for CT did not change. The transmission model shows that higher STI treatment rates are expected to reduce prevalence and increase the Gini coefficient of STIs. In contrast, increased condom use reduces STI prevalence but does not affect the Gini coefficient. Conclusions Gini coefficients for STIs can help us to understand the distribution of STIs in the population, according to level of sexual activity, and could be used to inform STI prevention and treatment strategies.
format: application/pdf
format: text/html
creator: Sandro Gsteiger
creator: Nicola Low
creator: Pam Sonnenberg
creator: Catherine H. Mercer
creator: Christian L. Althaus
subject: Mathematical Biology
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.8434
publisher: PeerJ Inc.
rights: © 2020 Gsteiger et al.
abstract: Objectives Gini coefficients have been used to describe the distribution of Chlamydia trachomatis (CT) infections among individuals with different levels of sexual activity. The objectives of this study were to investigate Gini coefficients for different sexually transmitted infections (STIs), and to determine how STI control interventions might affect the Gini coefficient over time. Methods We used population-based data for sexually experienced women from two British National Surveys of Sexual Attitudes and Lifestyles (Natsal-2: 1999–2001; Natsal-3: 2010–2012) to calculate Gini coefficients for CT, Mycoplasma genitalium (MG), and human papillomavirus (HPV) types 6, 11, 16 and 18. We applied bootstrap methods to assess uncertainty and to compare Gini coefficients for different STIs. We then used a mathematical model of STI transmission to study how control interventions affect Gini coefficients. Results Gini coefficients for CT and MG were 0.33 (95% CI [0.18–0.49]) and 0.16 (95% CI [0.02–0.36]), respectively. The relatively small coefficient for MG suggests a longer infectious duration compared with CT. The coefficients for HPV types 6, 11, 16 and 18 ranged from 0.15 to 0.38. During the decade between Natsal-2 and Natsal-3, the Gini coefficient for CT did not change. The transmission model shows that higher STI treatment rates are expected to reduce prevalence and increase the Gini coefficient of STIs. In contrast, increased condom use reduces STI prevalence but does not affect the Gini coefficient. Conclusions Gini coefficients for STIs can help us to understand the distribution of STIs in the population, according to level of sexual activity, and could be used to inform STI prevention and treatment strategies.
bibliographic citation: Gsteiger et al. (2020) Gini coefficients for measuring the distribution of sexually transmitted infections among individuals with different levels of sexual activity. PeerJ 8:e8434 https://doi.org/10.7717/peerj.8434
date submitted: 2019-08-12
date accepted: 2019-12-19
issued: 2020-01-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gsteiger
  given name: Sandro
author list: Agent
  family name: Low
  given name: Nicola
author list: Agent
  family name: Sonnenberg
  given name: Pam
author list: Agent
  family name: Mercer
  given name: Catherine H.
author list: Agent
  family name: Althaus
  given name: Christian L.
doi: 10.7717/peerj.8434
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-20
copyright: © 2020 Gsteiger et al.
attribution name: Gsteiger et al.

Comparative analysis of the demographic parameters of seven spotted ladybird beetle (Coleoptera: Coccinellidae) reared on various host aphid species
type: item
type: AcademicArticle
description: Background The demographic parameters of the predacious seven spotted ladybird beetle Coccinella septempunctata Linnaeus (Coleoptera: Coccinellidae) reared on the following four host aphid species were compared: Rhopalosiphum padi Linnaeus (Hemiptera: Aphididae), Rhopalosiphum maidis Fitch (Hemiptera: Aphididae), Sitobion avenae Fabricius (Hemiptera: Aphididae), and Schizaphis graminum Rondani (Hemiptera: Aphididae). Methods The developmental period, fecundity, adult preoviposition period, total preoviposition period and population parameters were evaluated based on the two-sex age-stage life table. The duration of the developmental stages and the population parameters were calculated with the TWOSEX-MSChart program, whereas population size was projected based on the two-sex age-stage life table data with the TIMING-MSChart program. Results The intrinsic rate of increase (r) was the highest in the R. padi predators (0.1946 per day), followed by the S. graminum (0.1435 per day), S. avenae (0.1400 per day), and R. maidis (0.1180 per day) predators. The differences in the net reproductive rate (R0) and the finite rate of increase (λ) when C. septempunctata was reared on the four aphid species were consistent with the r values. This trend was reversed for the mean generation time (T), which ranged from 29.02 days for the lady beetles reared on R. padi to 39.75 days for the lady beetles reared on R. maidis. Interestingly, R. padi was the most suitable host, while the congeneric R. maidis was the least suitable. The results of this study may be useful for future investigations regarding the ecological effects of predatory species and the mass-production of C. septempunctata in the laboratory for an augmentative release of an aphid predator.
format: application/pdf
format: text/html
creator: Muhammad Farooq
creator: Xun Zhu
creator: Muhammad Shakeel
creator: Ayesha Iftikhar
creator: Muhammad Rafiq Shahid
creator: Nadia Saeed
creator: Muhammad Shahid Arain
subject: Agricultural Science
subject: Animal Behavior
subject: Entomology
description: doi:10.7717/peerj.8313
publisher: PeerJ Inc.
rights: © 2020 Farooq et al.
abstract: Background The demographic parameters of the predacious seven spotted ladybird beetle Coccinella septempunctata Linnaeus (Coleoptera: Coccinellidae) reared on the following four host aphid species were compared: Rhopalosiphum padi Linnaeus (Hemiptera: Aphididae), Rhopalosiphum maidis Fitch (Hemiptera: Aphididae), Sitobion avenae Fabricius (Hemiptera: Aphididae), and Schizaphis graminum Rondani (Hemiptera: Aphididae). Methods The developmental period, fecundity, adult preoviposition period, total preoviposition period and population parameters were evaluated based on the two-sex age-stage life table. The duration of the developmental stages and the population parameters were calculated with the TWOSEX-MSChart program, whereas population size was projected based on the two-sex age-stage life table data with the TIMING-MSChart program. Results The intrinsic rate of increase (r) was the highest in the R. padi predators (0.1946 per day), followed by the S. graminum (0.1435 per day), S. avenae (0.1400 per day), and R. maidis (0.1180 per day) predators. The differences in the net reproductive rate (R0) and the finite rate of increase (λ) when C. septempunctata was reared on the four aphid species were consistent with the r values. This trend was reversed for the mean generation time (T), which ranged from 29.02 days for the lady beetles reared on R. padi to 39.75 days for the lady beetles reared on R. maidis. Interestingly, R. padi was the most suitable host, while the congeneric R. maidis was the least suitable. The results of this study may be useful for future investigations regarding the ecological effects of predatory species and the mass-production of C. septempunctata in the laboratory for an augmentative release of an aphid predator.
bibliographic citation: Farooq et al. (2020) Comparative analysis of the demographic parameters of seven spotted ladybird beetle (Coleoptera: Coccinellidae) reared on various host aphid species. PeerJ 8:e8313 https://doi.org/10.7717/peerj.8313
date submitted: 2019-08-08
date accepted: 2019-11-28
issued: 2020-01-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Farooq
  given name: Muhammad
author list: Agent
  family name: Zhu
  given name: Xun
author list: Agent
  family name: Shakeel
  given name: Muhammad
author list: Agent
  family name: Iftikhar
  given name: Ayesha
author list: Agent
  family name: Shahid
  given name: Muhammad Rafiq
author list: Agent
  family name: Saeed
  given name: Nadia
author list: Agent
  family name: Arain
  given name: Muhammad Shahid
doi: 10.7717/peerj.8313
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-17
copyright: ©2020 Farooq et al.
attribution name: Farooq et al.

Evolution of sexual size dimorphism in the wing musculature of Drosophila
type: item
type: AcademicArticle
description: Male courtship songs in Drosophila are exceedingly diverse across species. While much of this variation is understood to have evolved from changes in the central nervous system, evolutionary transitions in the wing muscles that control the song may have also contributed to song diversity. Here, focusing on a group of four wing muscles that are known to influence courtship song in Drosophila melanogaster, we investigate the evolutionary history of wing muscle anatomy of males and females from 19 Drosophila species. We find that three of the wing muscles have evolved sexual dimorphisms in size multiple independent times, whereas one has remained monomorphic in the phylogeny. These data suggest that evolutionary changes in wing muscle anatomy may have contributed to species variation in sexually dimorphic wing-based behaviors, such as courtship song. Moreover, wing muscles appear to differ in their propensity to evolve size dimorphisms, which may reflect variation in the functional constraints acting upon different wing muscles.
format: application/pdf
format: text/html
creator: Claire B. Tracy
creator: Janet Nguyen
creator: Rayna Abraham
creator: Troy R. Shirangi
subject: Animal Behavior
subject: Entomology
subject: Evolutionary Studies
subject: Neuroscience
description: doi:10.7717/peerj.8360
publisher: PeerJ Inc.
rights: © 2020 Tracy et al.
abstract: Male courtship songs in Drosophila are exceedingly diverse across species. While much of this variation is understood to have evolved from changes in the central nervous system, evolutionary transitions in the wing muscles that control the song may have also contributed to song diversity. Here, focusing on a group of four wing muscles that are known to influence courtship song in Drosophila melanogaster, we investigate the evolutionary history of wing muscle anatomy of males and females from 19 Drosophila species. We find that three of the wing muscles have evolved sexual dimorphisms in size multiple independent times, whereas one has remained monomorphic in the phylogeny. These data suggest that evolutionary changes in wing muscle anatomy may have contributed to species variation in sexually dimorphic wing-based behaviors, such as courtship song. Moreover, wing muscles appear to differ in their propensity to evolve size dimorphisms, which may reflect variation in the functional constraints acting upon different wing muscles.
bibliographic citation: Tracy et al. (2020) Evolution of sexual size dimorphism in the wing musculature of Drosophila. PeerJ 8:e8360 https://doi.org/10.7717/peerj.8360
date submitted: 2019-07-12
date accepted: 2019-12-05
issued: 2020-01-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tracy
  given name: Claire B.
author list: Agent
  family name: Nguyen
  given name: Janet
author list: Agent
  family name: Abraham
  given name: Rayna
author list: Agent
  family name: Shirangi
  given name: Troy R.
doi: 10.7717/peerj.8360
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-17
copyright: ©2020 Tracy et al.
attribution name: Tracy et al.

Identification of key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis
type: item
type: AcademicArticle
description: Background Osteoarthritis (OA) is the most common chronic degenerative joint disease and is mainly characterized by cartilage degeneration, subcartilage bone hyperplasia, osteophyte formation and joint space stenosis. Recent studies showed that synovitis might also be an important pathological change of OA. However, the molecular mechanisms of synovitis in OA are still not well understood. Objective This study was designed to identify key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis. Materials and Methods The gene expression profiles of GSE12021, GSE55235 and GSE55457 were downloaded from the GEO database. The differentially expressed genes (DEGs) were identified by the LIMMA package in Bioconductor, and functional enrichment analyses were performed. A protein-protein interaction network (PPI) was constructed, and module analysis was performed using STRING and Cytoscape. The CIBERSORT algorithm was used to analyze the immune infiltration of synovial tissue between OA and normal controls. Results A total of 106 differentially expressed genes, including 68 downregulated genes and 38 upregulated genes, were detected. The PPI network was assessed, and the most significant module containing 14 hub genes was identified. Gene Ontology analysis revealed that the hub genes were significantly enriched in immune cell chemotaxis and cytokine activity. KEGG pathway analysis showed that the hub genes were significantly enriched in the rheumatoid arthritis signaling pathway, IL-17 signaling pathway and cytokine-cytokine receptor interaction signaling pathway. The immune infiltration profiles varied significantly between osteoarthritis and normal controls. Compared with normal tissue, OA synovial tissue contained a higher proportion of memory B cells, naive CD4+ T cells, regulatory T cells, resting dendritic cells and resting mast cells, while naive CD4+ T cells, activated NK cells, activated mast cells and eosinophils contr…
format: application/pdf
format: text/html
creator: Weisong Cai
creator: Haohuan Li
creator: Yubiao Zhang
creator: Guangtao Han
subject: Bioinformatics
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Orthopedics
description: doi:10.7717/peerj.8390
publisher: PeerJ Inc.
rights: © 2020 Cai et al.
abstract: Background Osteoarthritis (OA) is the most common chronic degenerative joint disease and is mainly characterized by cartilage degeneration, subcartilage bone hyperplasia, osteophyte formation and joint space stenosis. Recent studies showed that synovitis might also be an important pathological change of OA. However, the molecular mechanisms of synovitis in OA are still not well understood. Objective This study was designed to identify key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis. Materials and Methods The gene expression profiles of GSE12021, GSE55235 and GSE55457 were downloaded from the GEO database. The differentially expressed genes (DEGs) were identified by the LIMMA package in Bioconductor, and functional enrichment analyses were performed. A protein-protein interaction network (PPI) was constructed, and module analysis was performed using STRING and Cytoscape. The CIBERSORT algorithm was used to analyze the immune infiltration of synovial tissue between OA and normal controls. Results A total of 106 differentially expressed genes, including 68 downregulated genes and 38 upregulated genes, were detected. The PPI network was assessed, and the most significant module containing 14 hub genes was identified. Gene Ontology analysis revealed that the hub genes were significantly enriched in immune cell chemotaxis and cytokine activity. KEGG pathway analysis showed that the hub genes were significantly enriched in the rheumatoid arthritis signaling pathway, IL-17 signaling pathway and cytokine-cytokine receptor interaction signaling pathway. The immune infiltration profiles varied significantly between osteoarthritis and normal controls. Compared with normal tissue, OA synovial tissue contained a higher proportion of memory B cells, naive CD4+ T cells, regulatory T cells, resting dendritic cells and resting mast cells, while naive CD4+ T cells, activated NK cells, activated mast cells and eosinophils contr…
bibliographic citation: Cai et al. (2020) Identification of key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis. PeerJ 8:e8390 https://doi.org/10.7717/peerj.8390
date submitted: 2019-08-22
date accepted: 2019-12-13
issued: 2020-01-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Weisong
author list: Agent
  family name: Li
  given name: Haohuan
author list: Agent
  family name: Zhang
  given name: Yubiao
author list: Agent
  family name: Han
  given name: Guangtao
doi: 10.7717/peerj.8390
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-17
copyright: ©2020 Cai et al.
attribution name: Cai et al.

Isolation, sequencing, and expression analysis of 30 AP2/ERF transcription factors in apple
type: item
type: AcademicArticle
description: Background AP2/ERF transcription factors are involved in the regulation of plant growth, development, and stress responses. Our research objective was to characterize novel apple (Malus × domestica Borkh.) genes encoding AP2/ERF transcription factors involved in regulation of plant growth, development, and stress response. The transcriptional level of apple AP2/ERF genes in different tissues and under various biotic and abiotic stress was determined to provide valuable insights into the function of AP2/ERF transcription factors in apple. Methods Thirty full-length cDNA sequences of apple AP2/ERF genes were isolated from ‘Zihong Fuji’ apple (Malus × domestica cv. Zihong Fuji) via homologous comparison and RT-PCR confirmation, and the obtained cDNA sequences and the deduced amino acid sequences were analyzed with bioinformatics methods. Expression levels of apple AP2/ERF genes were detected in 16 different tissues using a known array. Expression patterns of apple AP2/ERF genes were detected in response to Alternaria alternata apple pathotype (AAAP) infection using RNA-seq with existing data, and the expression of apple AP2/ERF genes was analyzed under NaCl and mannitol treatments using qRT-PCR. Results The sequencing results produced 30 cDNAs (designated as MdERF3-8, MdERF11, MdERF16-19, MdERF22-28, MdERF31-35, MdERF39, MdAP2D60, MdAP2D62-65, and MdRAV2). Phylogenetic analysis revealed that MdERF11/16, MdERF33/35, MdERF34/39, and MdERF18/23 belonged to groups A-2, A-4, A-5, and A-6 of the DREB subfamily, respectively; MdERF31, MdERF19, MdERF4/25/28/32, MdERF24, MdERF5/6/27, and MdERF3/7/8/17/22/26 belonged to groups B-1, B-2, B-3, B-4, B-5, and B-6 of the ERF subfamily, respectively; MdAP2D60 and MdAP2D62/63/64/65 belonged to the AP2 subfamily; and MdRAV2 belonged to the RAV subfamily. Array results indicated that 30 apple AP2/ERF genes were expressed in all examined tissues to different degrees. RNA-seq results using previously reported data showed that many members …
format: application/pdf
format: text/html
creator: Huifeng Li
creator: Qinglong Dong
creator: Qiang Zhao
creator: Song Shi
creator: Kun Ran
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.8391
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Background AP2/ERF transcription factors are involved in the regulation of plant growth, development, and stress responses. Our research objective was to characterize novel apple (Malus × domestica Borkh.) genes encoding AP2/ERF transcription factors involved in regulation of plant growth, development, and stress response. The transcriptional level of apple AP2/ERF genes in different tissues and under various biotic and abiotic stress was determined to provide valuable insights into the function of AP2/ERF transcription factors in apple. Methods Thirty full-length cDNA sequences of apple AP2/ERF genes were isolated from ‘Zihong Fuji’ apple (Malus × domestica cv. Zihong Fuji) via homologous comparison and RT-PCR confirmation, and the obtained cDNA sequences and the deduced amino acid sequences were analyzed with bioinformatics methods. Expression levels of apple AP2/ERF genes were detected in 16 different tissues using a known array. Expression patterns of apple AP2/ERF genes were detected in response to Alternaria alternata apple pathotype (AAAP) infection using RNA-seq with existing data, and the expression of apple AP2/ERF genes was analyzed under NaCl and mannitol treatments using qRT-PCR. Results The sequencing results produced 30 cDNAs (designated as MdERF3-8, MdERF11, MdERF16-19, MdERF22-28, MdERF31-35, MdERF39, MdAP2D60, MdAP2D62-65, and MdRAV2). Phylogenetic analysis revealed that MdERF11/16, MdERF33/35, MdERF34/39, and MdERF18/23 belonged to groups A-2, A-4, A-5, and A-6 of the DREB subfamily, respectively; MdERF31, MdERF19, MdERF4/25/28/32, MdERF24, MdERF5/6/27, and MdERF3/7/8/17/22/26 belonged to groups B-1, B-2, B-3, B-4, B-5, and B-6 of the ERF subfamily, respectively; MdAP2D60 and MdAP2D62/63/64/65 belonged to the AP2 subfamily; and MdRAV2 belonged to the RAV subfamily. Array results indicated that 30 apple AP2/ERF genes were expressed in all examined tissues to different degrees. RNA-seq results using previously reported data showed that many members …
bibliographic citation: Li et al. (2020) Isolation, sequencing, and expression analysis of 30 AP2/ERF transcription factors in apple. PeerJ 8:e8391 https://doi.org/10.7717/peerj.8391
date submitted: 2019-07-08
date accepted: 2019-12-13
issued: 2020-01-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Huifeng
author list: Agent
  family name: Dong
  given name: Qinglong
author list: Agent
  family name: Zhao
  given name: Qiang
author list: Agent
  family name: Shi
  given name: Song
author list: Agent
  family name: Ran
  given name: Kun
doi: 10.7717/peerj.8391
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-17
copyright: ©2020 Li et al.
attribution name: Li et al.

Autophagy-related genes prognosis signature as potential predictive markers for immunotherapy in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Autophagy-related genes (ATGs) depress tumorigenesis. However, in tumor tissue, it promotes tumor progression. Here, we demonstrated that 63 ATGs were differentially expressed in normal tissues and tumor tissues of hepatocellular carcinoma (HCC), and seven prognostic-related genes were chosen to establish prognostic risk signatures. It is not just an independent prognostic factor for HCC, but also closely related to the degree of malignancy of HCC. Further, the hallmarks of PI3K–AKT–mTOR signaling was significantly enriched in the high-risk group. Moreover, AKT–pS473 and mTOR–pS2448 expression was down-regulated and correlated with patient prognosis in high-risk group. Finally, we demonstrate that the prognosis signature of ATGs is closely related to immune cell infiltration and PD-L1 expression. In conclusion, ATGs are a crucial factor in the malignant progression of HCC and will be a new prognostic marker for diagnosis and treatment. ATGs prognostic signatures are potentially useful for predicting PD-L1 therapeutic effects.
format: application/pdf
format: text/html
creator: Deli Mao
creator: Zhe Zhang
creator: Xin Zhao
creator: Xiaoqiang Dong
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.8383
publisher: PeerJ Inc.
rights: © 2020 Mao et al.
abstract: Autophagy-related genes (ATGs) depress tumorigenesis. However, in tumor tissue, it promotes tumor progression. Here, we demonstrated that 63 ATGs were differentially expressed in normal tissues and tumor tissues of hepatocellular carcinoma (HCC), and seven prognostic-related genes were chosen to establish prognostic risk signatures. It is not just an independent prognostic factor for HCC, but also closely related to the degree of malignancy of HCC. Further, the hallmarks of PI3K–AKT–mTOR signaling was significantly enriched in the high-risk group. Moreover, AKT–pS473 and mTOR–pS2448 expression was down-regulated and correlated with patient prognosis in high-risk group. Finally, we demonstrate that the prognosis signature of ATGs is closely related to immune cell infiltration and PD-L1 expression. In conclusion, ATGs are a crucial factor in the malignant progression of HCC and will be a new prognostic marker for diagnosis and treatment. ATGs prognostic signatures are potentially useful for predicting PD-L1 therapeutic effects.
bibliographic citation: Mao et al. (2020) Autophagy-related genes prognosis signature as potential predictive markers for immunotherapy in hepatocellular carcinoma. PeerJ 8:e8383 https://doi.org/10.7717/peerj.8383
date submitted: 2019-10-10
date accepted: 2019-12-10
issued: 2020-01-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mao
  given name: Deli
author list: Agent
  family name: Zhang
  given name: Zhe
author list: Agent
  family name: Zhao
  given name: Xin
author list: Agent
  family name: Dong
  given name: Xiaoqiang
doi: 10.7717/peerj.8383
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-17
copyright: © 2020 Mao et al.
attribution name: Mao et al.

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