PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Necked strawberries are especially susceptible to cracking
items: Zinc solubilizing bacteria and their potential as bioinoculant for growth promotion of green soybean (Glycine max L. Merr.)
items: Precipitation extremes observed over and around the Taklimakan Desert, China
items: CPJSdraw: analysis and visualization of junction sites of chloroplast genomes
items: Regenerative plantlets with improved agronomic characteristics caused by anther culture of tetraploid potato (Solanum tuberosum L.)
items: Factors shaping the gut microbiome of five species of lizards from different habitats
items: A systematic review of informal supporters of intimate partner violence survivors: the intimate partner violence model of informal supporter readiness
items: Two new syntopic species of glassfrogs (Amphibia, Centrolenidae, Centrolene) from the southwestern Andes of Ecuador
items: Epithelial to mesenchymal transition in mammary gland tissue fibrosis and insights into drug therapeutics
items: Prognostic significance of SH2D5 expression in lung adenocarcinoma and its relation to immune cell infiltration

Necked strawberries are especially susceptible to cracking
type: item
type: AcademicArticle
description: Fruit cracking is a commercially important disorder that reduces both quantity and quality of strawberries (Fragaria × ananassa Duch.). The objective was to identify the physiological mechanism of cracking and the factors affecting cracking. Cracking is more common in necked than in normal-shaped fruit. Most macroscopic cracks (‘macrocracks’) occur in the seedless neck. Large fruit is more cracking susceptible than medium size or small fruit. Macrocrack orientation is predominantly latitudinal in the proximal region of the neck and longitudinal in the mid and distal regions of the neck. The neck region of necked fruit has a thicker cuticle than the body of necked or normal-shaped fruit. The vascular bundles in the neck (seedless) are orientated longitudinally, while those in the body (with seeds) are both longitudinal and radial. Epidermal cells in the neck region are elongated longitudinally, with those in the proximal region of the neck being more elongated than those in the mid or distal regions of the neck. Cuticular microcracking was more severe in necked fruit than in normal-shaped fruit. The orientations of the microcracks matched those of the macrocracks, i.e., latitudinal in the proximal neck and longitudinal in the mid and distal neck regions. Following artificial incisions (blade), gaping was significantly more pronounced in necked than in normal-shaped fruit. Incubation of fruit in deionized water induced macrocracks in about 75% of fruit. Necked fruit cracked more than normal-shaped fruit. Most macrocracks were oriented latitudinally in the proximal neck and longitudinally in the distal neck regions. The results indicate cracking results from excessive growth strains which are further increased by surface water uptake.
format: application/pdf
format: text/html
creator: Grecia Hurtado
creator: Moritz Knoche
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.15402
publisher: PeerJ Inc.
rights: © 2023 Hurtado and Knoche
abstract: Fruit cracking is a commercially important disorder that reduces both quantity and quality of strawberries (Fragaria × ananassa Duch.). The objective was to identify the physiological mechanism of cracking and the factors affecting cracking. Cracking is more common in necked than in normal-shaped fruit. Most macroscopic cracks (‘macrocracks’) occur in the seedless neck. Large fruit is more cracking susceptible than medium size or small fruit. Macrocrack orientation is predominantly latitudinal in the proximal region of the neck and longitudinal in the mid and distal regions of the neck. The neck region of necked fruit has a thicker cuticle than the body of necked or normal-shaped fruit. The vascular bundles in the neck (seedless) are orientated longitudinally, while those in the body (with seeds) are both longitudinal and radial. Epidermal cells in the neck region are elongated longitudinally, with those in the proximal region of the neck being more elongated than those in the mid or distal regions of the neck. Cuticular microcracking was more severe in necked fruit than in normal-shaped fruit. The orientations of the microcracks matched those of the macrocracks, i.e., latitudinal in the proximal neck and longitudinal in the mid and distal neck regions. Following artificial incisions (blade), gaping was significantly more pronounced in necked than in normal-shaped fruit. Incubation of fruit in deionized water induced macrocracks in about 75% of fruit. Necked fruit cracked more than normal-shaped fruit. Most macrocracks were oriented latitudinally in the proximal neck and longitudinally in the distal neck regions. The results indicate cracking results from excessive growth strains which are further increased by surface water uptake.
bibliographic citation: Hurtado et al. (2023) Necked strawberries are especially susceptible to cracking. PeerJ 11:e15402 https://doi.org/10.7717/peerj.15402
date submitted: 2023-01-30
date accepted: 2023-04-20
issued: 2023-05-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hurtado
  given name: Grecia
author list: Agent
  family name: Knoche
  given name: Moritz
doi: 10.7717/peerj.15402
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-11
copyright: © 2023 Hurtado and Knoche
attribution name: Hurtado and Knoche

Zinc solubilizing bacteria and their potential as bioinoculant for growth promotion of green soybean (Glycine max L. Merr.)
type: item
type: AcademicArticle
description: Zinc-solubilizing rhizobacteria can convert insoluble zinc to an accessible form and increase Zn bioavailability in soil, which help mitigate Zn deficiency in crops. In this work, 121 bacterial isolates were isolated from the rhizosphere soils of peanuts, sweet potatoes, and cassava, and their capability to solubilize Zn was evaluated using Bunt and Rovira’s agar containing 0.1% ZnO and ZnCO3. Among these isolates, six showed high Zn solubilization efficiencies ranging from 1.32 to 2.84 and 1.93 to 2.27 on the medium supplemented with 0.1% ZnO and ZnCO3, respectively. In a quantitative analysis of soluble Zn in liquid medium supplemented with 0.1% ZnO, the isolate KAH109 showed the maximum soluble zinc concentration of 62.89 mg L−1. Among the six isolates, the isolate KAH109 also produced the most indole-3-acetic acid (IAA) at 33.44 mg L−1, whereas the isolate KEX505 also produced IAA at 17.24 mg L−1 along with showing zinc and potassium solubilization activity. These strains were identified as Priestia megaterium KAH109 and Priestia aryabhattai KEX505 based on 16S rDNA sequence analysis. In a greenhouse experiment conducted in Nakhon Pathom, Thailand the ability of P. megaterium KAH109 and P. aryabhattai KEX505 to stimulate the growth and production of green soybeans was examined. The results revealed that inoculation with P. megaterium KAH109 and P. aryabhattai KEX505 considerably increased plant dry weight by 26.96% and 8.79%, respectively, and the number of grains per plant by 48.97% and 35.29% when compared to those of the uninoculated control. According to these results, both strains can be considered as a potential zinc solubilizing bioinoculant to promote the growth and production yield of green soybeans.
format: application/pdf
format: text/html
creator: Moltira Srithaworn
creator: Jieb Jaroenthanyakorn
creator: Janpen Tangjitjaroenkun
creator: Chanwit Suriyachadkun
creator: Orawan Chunhachart
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15128
publisher: PeerJ Inc.
rights: © 2023 Srithaworn et al.
abstract: Zinc-solubilizing rhizobacteria can convert insoluble zinc to an accessible form and increase Zn bioavailability in soil, which help mitigate Zn deficiency in crops. In this work, 121 bacterial isolates were isolated from the rhizosphere soils of peanuts, sweet potatoes, and cassava, and their capability to solubilize Zn was evaluated using Bunt and Rovira’s agar containing 0.1% ZnO and ZnCO3. Among these isolates, six showed high Zn solubilization efficiencies ranging from 1.32 to 2.84 and 1.93 to 2.27 on the medium supplemented with 0.1% ZnO and ZnCO3, respectively. In a quantitative analysis of soluble Zn in liquid medium supplemented with 0.1% ZnO, the isolate KAH109 showed the maximum soluble zinc concentration of 62.89 mg L−1. Among the six isolates, the isolate KAH109 also produced the most indole-3-acetic acid (IAA) at 33.44 mg L−1, whereas the isolate KEX505 also produced IAA at 17.24 mg L−1 along with showing zinc and potassium solubilization activity. These strains were identified as Priestia megaterium KAH109 and Priestia aryabhattai KEX505 based on 16S rDNA sequence analysis. In a greenhouse experiment conducted in Nakhon Pathom, Thailand the ability of P. megaterium KAH109 and P. aryabhattai KEX505 to stimulate the growth and production of green soybeans was examined. The results revealed that inoculation with P. megaterium KAH109 and P. aryabhattai KEX505 considerably increased plant dry weight by 26.96% and 8.79%, respectively, and the number of grains per plant by 48.97% and 35.29% when compared to those of the uninoculated control. According to these results, both strains can be considered as a potential zinc solubilizing bioinoculant to promote the growth and production yield of green soybeans.
bibliographic citation: Srithaworn et al. (2023) Zinc solubilizing bacteria and their potential as bioinoculant for growth promotion of green soybean (Glycine max L. Merr.). PeerJ 11:e15128 https://doi.org/10.7717/peerj.15128
date submitted: 2022-09-15
date accepted: 2023-03-04
issued: 2023-05-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Srithaworn
  given name: Moltira
author list: Agent
  family name: Jaroenthanyakorn
  given name: Jieb
author list: Agent
  family name: Tangjitjaroenkun
  given name: Janpen
author list: Agent
  family name: Suriyachadkun
  given name: Chanwit
author list: Agent
  family name: Chunhachart
  given name: Orawan
doi: 10.7717/peerj.15128
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-10
copyright: ©2023 Srithaworn et al.
attribution name: Srithaworn et al.

Precipitation extremes observed over and around the Taklimakan Desert, China
type: item
type: AcademicArticle
description: The Taklimakan Desert (TD) is the largest desert in China located in the Tarim Basin (TB) in China’s arid region. This study is a review of the change in precipitation and its extremes since 1961 and the high-impact extreme precipitation events in 2012–2021, particularly in 2021, with a focus on the TD along with the surrounding oases and mountainous regions.The TB has experienced significantly warmer and wetter trends since 1961, and extreme rainfall has increased significantly in the TD and its surrounding areas during the 2000s. In the TB, the year 2021 was identified as the 4th warmest for 1961–2021, and was remembered for unprecedented extreme events. Three high-impact extreme events that occurred in 2021 are highlighted, including extreme heavy rainfall over Hetian in mid-June. The earliest extreme rainfall event occurred over North Bazhou in early spring, and the strongest heavy snowfall over Baicheng in April. In addition, we also discussed the underlying physical mechanisms of extreme events over the TB and proposed novel perspectives and unresolved questions on the sciences of heavy rainfall in arid regions. Our results provide a reference for the physical mechanism, attribution, and high-resolution modeling of extreme events.
format: application/pdf
format: text/html
creator: Moyan Li
creator: Junqiang Yao
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.15256
publisher: PeerJ Inc.
rights: © 2023 Li and Yao
abstract: The Taklimakan Desert (TD) is the largest desert in China located in the Tarim Basin (TB) in China’s arid region. This study is a review of the change in precipitation and its extremes since 1961 and the high-impact extreme precipitation events in 2012–2021, particularly in 2021, with a focus on the TD along with the surrounding oases and mountainous regions.The TB has experienced significantly warmer and wetter trends since 1961, and extreme rainfall has increased significantly in the TD and its surrounding areas during the 2000s. In the TB, the year 2021 was identified as the 4th warmest for 1961–2021, and was remembered for unprecedented extreme events. Three high-impact extreme events that occurred in 2021 are highlighted, including extreme heavy rainfall over Hetian in mid-June. The earliest extreme rainfall event occurred over North Bazhou in early spring, and the strongest heavy snowfall over Baicheng in April. In addition, we also discussed the underlying physical mechanisms of extreme events over the TB and proposed novel perspectives and unresolved questions on the sciences of heavy rainfall in arid regions. Our results provide a reference for the physical mechanism, attribution, and high-resolution modeling of extreme events.
bibliographic citation: Li et al. (2023) Precipitation extremes observed over and around the Taklimakan Desert, China. PeerJ 11:e15256 https://doi.org/10.7717/peerj.15256
date submitted: 2022-11-17
date accepted: 2023-03-28
issued: 2023-05-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Li
  given name: Moyan
author list: Agent
  family name: Yao
  given name: Junqiang
doi: 10.7717/peerj.15256
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-10
copyright: ©2023 Li and Yao
attribution name: Li and Yao

CPJSdraw: analysis and visualization of junction sites of chloroplast genomes
type: item
type: AcademicArticle
description: Background Chloroplast genomes are usually circular molecules, and most of them are tetrad structures with two inverted repeat (IR) regions, a large single-copy region, and a small single-copy region. IR contraction and expansion are among the genetic diversities during the evolution of plant chloroplast genomes. The only previously released tool for the visualization of junction sites of the regions does not consider the diversity of the starting point of genomes, which leads to incorrect results or even no results for the examination of IR contraction and expansion. Results In this work, a new tool named CPJSdraw was developed for visualizing the junction sites of chloroplast genomes. CPJSdraw can format the starting point of the irregular linearized genome, correct the junction sites of IR and single-copy regions, display the tetrad structure, visualize the junction sites of any number (≥1) of chloroplast genomes, show the transcription direction of genes adjacent to junction sites, and indicate the IR expansion or contraction of chloroplast genomes. Conclusions CPJSdraw is a software that is universal and reliable in analysis and visualization of IR expansion or contraction of chloroplast genomes. CPJSdraw has more accurate analysis and more complete functions when compared with previously released tool. CPJSdraw as a perl package and tested data are available at http://dx.doi.org/10.5281/zenodo.7669480 for English users. In addition, an online version with a Chinese interface is available at http://cloud.genepioneer.com:9929/#/tool/alltool/detail/335.
format: application/pdf
format: text/html
creator: Huie Li
creator: Qiqiang Guo
creator: Lei Xu
creator: Haidong Gao
creator: Lei Liu
creator: Xiangyang Zhou
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.15326
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background Chloroplast genomes are usually circular molecules, and most of them are tetrad structures with two inverted repeat (IR) regions, a large single-copy region, and a small single-copy region. IR contraction and expansion are among the genetic diversities during the evolution of plant chloroplast genomes. The only previously released tool for the visualization of junction sites of the regions does not consider the diversity of the starting point of genomes, which leads to incorrect results or even no results for the examination of IR contraction and expansion. Results In this work, a new tool named CPJSdraw was developed for visualizing the junction sites of chloroplast genomes. CPJSdraw can format the starting point of the irregular linearized genome, correct the junction sites of IR and single-copy regions, display the tetrad structure, visualize the junction sites of any number (≥1) of chloroplast genomes, show the transcription direction of genes adjacent to junction sites, and indicate the IR expansion or contraction of chloroplast genomes. Conclusions CPJSdraw is a software that is universal and reliable in analysis and visualization of IR expansion or contraction of chloroplast genomes. CPJSdraw has more accurate analysis and more complete functions when compared with previously released tool. CPJSdraw as a perl package and tested data are available at http://dx.doi.org/10.5281/zenodo.7669480 for English users. In addition, an online version with a Chinese interface is available at http://cloud.genepioneer.com:9929/#/tool/alltool/detail/335.
bibliographic citation: Li et al. (2023) CPJSdraw: analysis and visualization of junction sites of chloroplast genomes. PeerJ 11:e15326 https://doi.org/10.7717/peerj.15326
date submitted: 2023-01-12
date accepted: 2023-04-10
issued: 2023-05-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Huie
author list: Agent
  family name: Guo
  given name: Qiqiang
author list: Agent
  family name: Xu
  given name: Lei
author list: Agent
  family name: Gao
  given name: Haidong
author list: Agent
  family name: Liu
  given name: Lei
author list: Agent
  family name: Zhou
  given name: Xiangyang
doi: 10.7717/peerj.15326
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-10
copyright: ©2023 Li et al.
attribution name: Li et al.

Regenerative plantlets with improved agronomic characteristics caused by anther culture of tetraploid potato (Solanum tuberosum L.)
type: item
type: AcademicArticle
description: Objective As the primary means of plant-induced haploid, anther culture is of great significance in quickly obtaining pure lines and significantly shortening the potato breeding cycle. Nevertheless, the methods of anther culture of tetraploid potato were still not well established. Methods In this study, 16 potato cultivars (lines) were used for anther culture in vitro. The corresponding relation between the different development stages of microspores and the external morphology of buds was investigated. A highly-efficient anther culture system of tetraploid potatoes was established. Results It was shown in the results that the combined use of 0.5 mg/L 1-Naphthylacetic acid (NAA), 1.0 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D), and 1.0 mg/L Kinetin (KT) was the ideal choice of hormone pairing for anther callus. Ten of the 16 potato cultivars examined could be induced callus with their respective anthers, and the induction rate ranged from 4.44% to 22.67% using this hormone combination. According to the outcome from the orthogonal design experiments of four kinds of appendages, we found that the medium with sucrose (40 g/L), AgNO3 (30 mg/L), activated carbon (3 g/L), potato extract (200 g/L) had a promotive induction effect on the anther callus. In contrast, adding 1 mg/L Zeatin (ZT) effectively facilitated callus differentiation. Conclusion Finally, 201 anther culture plantlets were differentiated from 10 potato cultivars. Among these, Qingshu 168 and Ningshu 15 had higher efficiency than anther culture. After identification by flow cytometry and fluorescence in situ hybridization, 10 haploid plantlets (5%), 177 tetraploids (88%), and 14 octoploids (7%) were obtained. Some premium anther-cultured plantlets were further selected by morphological and agronomic comparison. Our findings provide important guidance for potato ploidy breeding.
format: application/pdf
format: text/html
creator: Li Zhang
creator: Feng-jie Nie
creator: Lei Gong
creator: Xiao-yan Gan
creator: Guo-hui Zhang
creator: Xuan Liu
creator: Wen-jing Yang
creator: Lei Shi
creator: Yu-chao Chen
creator: Rui-xia Xie
creator: Zhi-qian Guo
creator: Yuxia Song
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.14984
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Objective As the primary means of plant-induced haploid, anther culture is of great significance in quickly obtaining pure lines and significantly shortening the potato breeding cycle. Nevertheless, the methods of anther culture of tetraploid potato were still not well established. Methods In this study, 16 potato cultivars (lines) were used for anther culture in vitro. The corresponding relation between the different development stages of microspores and the external morphology of buds was investigated. A highly-efficient anther culture system of tetraploid potatoes was established. Results It was shown in the results that the combined use of 0.5 mg/L 1-Naphthylacetic acid (NAA), 1.0 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D), and 1.0 mg/L Kinetin (KT) was the ideal choice of hormone pairing for anther callus. Ten of the 16 potato cultivars examined could be induced callus with their respective anthers, and the induction rate ranged from 4.44% to 22.67% using this hormone combination. According to the outcome from the orthogonal design experiments of four kinds of appendages, we found that the medium with sucrose (40 g/L), AgNO3 (30 mg/L), activated carbon (3 g/L), potato extract (200 g/L) had a promotive induction effect on the anther callus. In contrast, adding 1 mg/L Zeatin (ZT) effectively facilitated callus differentiation. Conclusion Finally, 201 anther culture plantlets were differentiated from 10 potato cultivars. Among these, Qingshu 168 and Ningshu 15 had higher efficiency than anther culture. After identification by flow cytometry and fluorescence in situ hybridization, 10 haploid plantlets (5%), 177 tetraploids (88%), and 14 octoploids (7%) were obtained. Some premium anther-cultured plantlets were further selected by morphological and agronomic comparison. Our findings provide important guidance for potato ploidy breeding.
bibliographic citation: Zhang et al. (2023) Regenerative plantlets with improved agronomic characteristics caused by anther culture of tetraploid potato (Solanum tuberosum L.). PeerJ 11:e14984 https://doi.org/10.7717/peerj.14984
date submitted: 2022-08-31
date accepted: 2023-02-10
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Li
author list: Agent
  family name: Nie
  given name: Feng-jie
author list: Agent
  family name: Gong
  given name: Lei
author list: Agent
  family name: Gan
  given name: Xiao-yan
author list: Agent
  family name: Zhang
  given name: Guo-hui
author list: Agent
  family name: Liu
  given name: Xuan
author list: Agent
  family name: Yang
  given name: Wen-jing
author list: Agent
  family name: Shi
  given name: Lei
author list: Agent
  family name: Chen
  given name: Yu-chao
author list: Agent
  family name: Xie
  given name: Rui-xia
author list: Agent
  family name: Guo
  given name: Zhi-qian
author list: Agent
  family name: Song
  given name: Yuxia
doi: 10.7717/peerj.14984
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Zhang et al.
attribution name: Zhang et al.

Factors shaping the gut microbiome of five species of lizards from different habitats
type: item
type: AcademicArticle
description: Background Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as systematics, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota. Methods In this study, we investigate the influence of systematics, sex, host size, and locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal: Podarcis bocagei and Podarcis lusitanicus, living in syntopy in a rural area in northern Portugal (Moledo); the invasive Podarcis siculus and the native Podarcis virescens, living in sympatry in an urbanized environment (Lisbon); and the invasive Teira dugesii also living in an urban area (Lisbon). We also infer the potential microbial transmission occurring between species living in sympatry and syntopy. To achieve these goals, we use a metabarcoding approach to characterize the bacterial communities from the cloaca of lizards, sequencing the V4 region of the 16S rRNA. Results Habitat/locality was an important factor explaining differences in gut bacterial composition and structure, with species from urbanized environments having higher bacterial diversity. Host systematics (i.e., species) influenced gut bacterial community structure only in lizards from the urbanized environment. We also detected a significant positive correlation between lizard size and gut bacterial alpha-diversity in the invasive species P. siculus, which could be due to its higher exploratory behavior. Moreover, estimates of bacterial transmission indicate that P. siculus may have acquired a high proportion of local microbiota after its introduction. These findings confirm that a diverse array of host and environmental factors can influence lizards’ gut microbiota.
format: application/pdf
format: text/html
creator: Diana S. Vasconcelos
creator: D. James Harris
creator: Isabel Damas-Moreira
creator: Ana Pereira
creator: Raquel Xavier
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.15146
publisher: PeerJ Inc.
rights: © 2023 Vasconcelos et al.
abstract: Background Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as systematics, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota. Methods In this study, we investigate the influence of systematics, sex, host size, and locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal: Podarcis bocagei and Podarcis lusitanicus, living in syntopy in a rural area in northern Portugal (Moledo); the invasive Podarcis siculus and the native Podarcis virescens, living in sympatry in an urbanized environment (Lisbon); and the invasive Teira dugesii also living in an urban area (Lisbon). We also infer the potential microbial transmission occurring between species living in sympatry and syntopy. To achieve these goals, we use a metabarcoding approach to characterize the bacterial communities from the cloaca of lizards, sequencing the V4 region of the 16S rRNA. Results Habitat/locality was an important factor explaining differences in gut bacterial composition and structure, with species from urbanized environments having higher bacterial diversity. Host systematics (i.e., species) influenced gut bacterial community structure only in lizards from the urbanized environment. We also detected a significant positive correlation between lizard size and gut bacterial alpha-diversity in the invasive species P. siculus, which could be due to its higher exploratory behavior. Moreover, estimates of bacterial transmission indicate that P. siculus may have acquired a high proportion of local microbiota after its introduction. These findings confirm that a diverse array of host and environmental factors can influence lizards’ gut microbiota.
bibliographic citation: Vasconcelos et al. (2023) Factors shaping the gut microbiome of five species of lizards from different habitats. PeerJ 11:e15146 https://doi.org/10.7717/peerj.15146
date submitted: 2022-11-07
date accepted: 2023-03-09
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vasconcelos
  given name: Diana S.
author list: Agent
  family name: Harris
  given name: D. James
author list: Agent
  family name: Damas-Moreira
  given name: Isabel
author list: Agent
  family name: Pereira
  given name: Ana
author list: Agent
  family name: Xavier
  given name: Raquel
doi: 10.7717/peerj.15146
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Vasconcelos et al.
attribution name: Vasconcelos et al.

A systematic review of informal supporters of intimate partner violence survivors: the intimate partner violence model of informal supporter readiness
type: item
type: AcademicArticle
description: Background Intimate partner violence (IPV) is a serious public health issue that consists of physical, sexual, and psychological violence perpetrated by a current or former partner. Informal supporters (e.g., family and friends) of survivors are more often witness to IPV or are the first people a survivor will disclose abuse to and are more able to provide consistent ongoing support than professional services. Therefore, greater understanding of informal supporters is warranted to aid in reducing the risks experienced by survivors. This systematic review aimed to: (1) identify factors associated with either an increase or decrease in helping behaviour toward a survivor, (2), identify the most effective self-care strategies employed by informal supporters, and (3) consider the current theoretical approaches used to understand informal supporters help-giving behavioural intention. Methods A systematic literature search was conducted following the PRISMA guidelines. The search included English language articles published between 2005 and 2021 in the databases Psych Articles, Scopus, Proquest Social Services Abstracts, and Ebscohost. Studies were included if the primary research aims explored the motivators and inhibitors of helping intention or self-care strategies of adult social network members of adult IPV survivors. Two reviewers independently screened all identified articles for inclusion suitability. Results One hundred and twenty articles were subjected to full text screening resulting in 31 articles being identified as meeting inclusion criteria. Synthesis of the findings identified the following three key areas associated with help-giving behavioural intentions: normative factors, individual factors, and situational factors. There were no articles identified that considered self-care of informal supporters. Of the 31 articles, 22 had a theoretical underpinning. None of the utilised theories explained all three of the identified factors of help-giving behaviour…
format: application/pdf
format: text/html
creator: Ryan L. Davies
creator: Kylie Rice
creator: Adam J. Rock
subject: Psychiatry and Psychology
subject: Women’s Health
subject: Mental Health
subject: Healthcare Services
description: doi:10.7717/peerj.15160
publisher: PeerJ Inc.
rights: © 2023 Davies et al.
abstract: Background Intimate partner violence (IPV) is a serious public health issue that consists of physical, sexual, and psychological violence perpetrated by a current or former partner. Informal supporters (e.g., family and friends) of survivors are more often witness to IPV or are the first people a survivor will disclose abuse to and are more able to provide consistent ongoing support than professional services. Therefore, greater understanding of informal supporters is warranted to aid in reducing the risks experienced by survivors. This systematic review aimed to: (1) identify factors associated with either an increase or decrease in helping behaviour toward a survivor, (2), identify the most effective self-care strategies employed by informal supporters, and (3) consider the current theoretical approaches used to understand informal supporters help-giving behavioural intention. Methods A systematic literature search was conducted following the PRISMA guidelines. The search included English language articles published between 2005 and 2021 in the databases Psych Articles, Scopus, Proquest Social Services Abstracts, and Ebscohost. Studies were included if the primary research aims explored the motivators and inhibitors of helping intention or self-care strategies of adult social network members of adult IPV survivors. Two reviewers independently screened all identified articles for inclusion suitability. Results One hundred and twenty articles were subjected to full text screening resulting in 31 articles being identified as meeting inclusion criteria. Synthesis of the findings identified the following three key areas associated with help-giving behavioural intentions: normative factors, individual factors, and situational factors. There were no articles identified that considered self-care of informal supporters. Of the 31 articles, 22 had a theoretical underpinning. None of the utilised theories explained all three of the identified factors of help-giving behaviour…
bibliographic citation: Davies et al. (2023) A systematic review of informal supporters of intimate partner violence survivors: the intimate partner violence model of informal supporter readiness. PeerJ 11:e15160 https://doi.org/10.7717/peerj.15160
date submitted: 2022-11-22
date accepted: 2023-03-13
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Davies
  given name: Ryan L.
author list: Agent
  family name: Rice
  given name: Kylie
author list: Agent
  family name: Rock
  given name: Adam J.
doi: 10.7717/peerj.15160
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Davies et al.
attribution name: Davies et al.

Two new syntopic species of glassfrogs (Amphibia, Centrolenidae, Centrolene) from the southwestern Andes of Ecuador
type: item
type: AcademicArticle
description: We describe two new species of glassfrogs of the genus Centrolene living in syntopy at La Enramada, province of Azuay, southwestern Ecuador. They were found in a small creek in montane evergreen forests at 2,900 m elevation. The first new species is distinguished from all other members of the genus Centrolene by having the following combination of characters: dentigerous process of vomer absent; sloping snout in lateral view; thick, white labial stripe and a faint white line between the lip and anterior ¼ of body; humeral spine in adult males; parietal peritoneum covered by iridophores, visceral peritonea translucent (except pericardium); ulnar and tarsal ornamentation; dorsal skin shagreen with dispersed warts; uniform green dorsum with light yellowish green warts; and green bones. The new species is remarkable by being sister to a species from the opposite Andean versant, C. condor. The second new species is distinguished from all other Centrolene by having the following combination of characters: dentigerous process of vomer absent; round snout in lateral view; thin, yellowish labial stripe with a row of white tubercles between the lip and arm insertion, and a yellowish line between arm insertion and groin; uniform green dorsum; humeral spine in adult males; parietal peritoneum covered by iridophores, visceral peritonea translucent (except pericardium); dorsal skin shagreen with dispersed spicules; ulnar and tarsal ornamentation; and green bones. The second new species is sister to C. sabini and an undescribed species of Centrolene from southeastern Ecuador. Based on nuclear and mitochondrial DNA sequences, we present a new phylogeny for Centrolene and comment on the phylogenetic relationships inside the genus.
format: application/pdf
format: text/html
creator: Diego F. Cisneros-Heredia
creator: Mario H. Yánez-Muñoz
creator: Juan C. Sánchez-Nivicela
creator: Santiago R. Ron
subject: Biodiversity
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15195
publisher: PeerJ Inc.
rights: © 2023 Cisneros-Heredia et al.
abstract: We describe two new species of glassfrogs of the genus Centrolene living in syntopy at La Enramada, province of Azuay, southwestern Ecuador. They were found in a small creek in montane evergreen forests at 2,900 m elevation. The first new species is distinguished from all other members of the genus Centrolene by having the following combination of characters: dentigerous process of vomer absent; sloping snout in lateral view; thick, white labial stripe and a faint white line between the lip and anterior ¼ of body; humeral spine in adult males; parietal peritoneum covered by iridophores, visceral peritonea translucent (except pericardium); ulnar and tarsal ornamentation; dorsal skin shagreen with dispersed warts; uniform green dorsum with light yellowish green warts; and green bones. The new species is remarkable by being sister to a species from the opposite Andean versant, C. condor. The second new species is distinguished from all other Centrolene by having the following combination of characters: dentigerous process of vomer absent; round snout in lateral view; thin, yellowish labial stripe with a row of white tubercles between the lip and arm insertion, and a yellowish line between arm insertion and groin; uniform green dorsum; humeral spine in adult males; parietal peritoneum covered by iridophores, visceral peritonea translucent (except pericardium); dorsal skin shagreen with dispersed spicules; ulnar and tarsal ornamentation; and green bones. The second new species is sister to C. sabini and an undescribed species of Centrolene from southeastern Ecuador. Based on nuclear and mitochondrial DNA sequences, we present a new phylogeny for Centrolene and comment on the phylogenetic relationships inside the genus.
bibliographic citation: Cisneros-Heredia et al. (2023) Two new syntopic species of glassfrogs (Amphibia, Centrolenidae, Centrolene) from the southwestern Andes of Ecuador. PeerJ 11:e15195 https://doi.org/10.7717/peerj.15195
date submitted: 2023-01-19
date accepted: 2023-03-15
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cisneros-Heredia
  given name: Diego F.
author list: Agent
  family name: Yánez-Muñoz
  given name: Mario H.
author list: Agent
  family name: Sánchez-Nivicela
  given name: Juan C.
author list: Agent
  family name: Ron
  given name: Santiago R.
doi: 10.7717/peerj.15195
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: © 2023 Cisneros-Heredia et al.
attribution name: Cisneros-Heredia et al.

Epithelial to mesenchymal transition in mammary gland tissue fibrosis and insights into drug therapeutics
type: item
type: AcademicArticle
description: Background The epithelial-mesenchymal transition (EMT) is a multi-step morphogenetic process in which epithelial cells lose their epithelial properties and gain mesenchymal characteristics. The process of EMT has been shown to mediate mammary gland fibrosis. Understanding how mesenchymal cells emerge from an epithelial default state will aid in unravelling the mechanisms that control fibrosis and, ultimately, in identifying therapeutic targets to alleviate fibrosis. Methods The effects of EGF and high glucose (HG) on EMT in mammary epithelial cells, MCF10A and GMECs, as well as their pathogenic role, were studied. In-silico analysis was used to find interacting partners and protein-chemical/drug molecule interactions. Results On treatment with EGF and/or HG, qPCR analysis showed a significant increase in the gene expression of EMT markers and downstream signalling genes. The expression of these genes was reduced on treatment with EGF+HG combination in both cell lines. The protein expression of COL1A1 increased as compared to the control in cells treated with EGF or HG alone, but when the cells were treated with EGF and HG together, the protein expression of COL1A1 decreased. ROS levels and cell death increased in cells treated with EGF and HG alone, whereas cells treated with EGF and HG together showed a decrease in ROS production and apoptosis. In-silico analysis of protein-protein interactions suggest the possible role of MAPK1, actin alpha 2 (ACTA2), COL1A1, and NFκB1 in regulating TGFβ1, ubiquitin C (UBC), specificity protein 1 (SP1) and E1A binding protein P300 (EP300). Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment suggests advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signalling pathway, relaxin signalling pathway and extra cellular matrix (ECM) receptor interactions underlying fibrosis mechanism. Conclusion This study demonstrates that EGF and HG induce EMT in mammary epithelial cells and may also have a …
format: application/pdf
format: text/html
creator: Mudasir Ahmad Syed
creator: Basharat Bhat
creator: Abiza Wali
creator: Afnan Saleem
creator: Lateef Ahmad Dar
creator: Mudasir Bashir Gugjoo
creator: Shakil Bhat
creator: Sahar Saleem Bhat
subject: Biochemistry
subject: Biotechnology
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.15207
publisher: PeerJ Inc.
rights: © 2023 Syed et al.
abstract: Background The epithelial-mesenchymal transition (EMT) is a multi-step morphogenetic process in which epithelial cells lose their epithelial properties and gain mesenchymal characteristics. The process of EMT has been shown to mediate mammary gland fibrosis. Understanding how mesenchymal cells emerge from an epithelial default state will aid in unravelling the mechanisms that control fibrosis and, ultimately, in identifying therapeutic targets to alleviate fibrosis. Methods The effects of EGF and high glucose (HG) on EMT in mammary epithelial cells, MCF10A and GMECs, as well as their pathogenic role, were studied. In-silico analysis was used to find interacting partners and protein-chemical/drug molecule interactions. Results On treatment with EGF and/or HG, qPCR analysis showed a significant increase in the gene expression of EMT markers and downstream signalling genes. The expression of these genes was reduced on treatment with EGF+HG combination in both cell lines. The protein expression of COL1A1 increased as compared to the control in cells treated with EGF or HG alone, but when the cells were treated with EGF and HG together, the protein expression of COL1A1 decreased. ROS levels and cell death increased in cells treated with EGF and HG alone, whereas cells treated with EGF and HG together showed a decrease in ROS production and apoptosis. In-silico analysis of protein-protein interactions suggest the possible role of MAPK1, actin alpha 2 (ACTA2), COL1A1, and NFκB1 in regulating TGFβ1, ubiquitin C (UBC), specificity protein 1 (SP1) and E1A binding protein P300 (EP300). Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment suggests advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signalling pathway, relaxin signalling pathway and extra cellular matrix (ECM) receptor interactions underlying fibrosis mechanism. Conclusion This study demonstrates that EGF and HG induce EMT in mammary epithelial cells and may also have a …
bibliographic citation: Syed et al. (2023) Epithelial to mesenchymal transition in mammary gland tissue fibrosis and insights into drug therapeutics. PeerJ 11:e15207 https://doi.org/10.7717/peerj.15207
date submitted: 2022-11-14
date accepted: 2023-03-19
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Syed
  given name: Mudasir Ahmad
author list: Agent
  family name: Bhat
  given name: Basharat
author list: Agent
  family name: Wali
  given name: Abiza
author list: Agent
  family name: Saleem
  given name: Afnan
author list: Agent
  family name: Ahmad Dar
  given name: Lateef
author list: Agent
  family name: Gugjoo
  given name: Mudasir Bashir
author list: Agent
  family name: Bhat
  given name: Shakil
author list: Agent
  family name: Saleem Bhat
  given name: Sahar
doi: 10.7717/peerj.15207
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Syed et al.
attribution name: Syed et al.

Prognostic significance of SH2D5 expression in lung adenocarcinoma and its relation to immune cell infiltration
type: item
type: AcademicArticle
description: Objective Through analyzing the SH2D5 expression profiles, clinical features, and immune infiltration in lung adenocarcinoma (LUAD), the study was intended to discuss the correlations of SH2D5 with prognosis and immune infiltration in LUAD. Methods We downloaded transcriptome and clinical data of LUAD patients from TCGA, GEO, and CCLE databases. Sangerbox, R language, GEPIA, UALCAN, and Kaplan-Meier Plotter were adopted to analyze the SH2D5 expression patterns, prognosis, and clinical features. Spearman correlation analysis was performed to determine the association between SH2D5 expression and immune cell infiltration and immune checkpoint genes. The miRNA-SH2D5 relations were predicted by miRDB and starbase. Lastly, quantitative PCR, IHC and Western blot were implemented for validation. Results A prominent up-regulation of SH2D5 was noted in the LUAD group relative to the normal group, which was validated by quantitative PCR, IHC and Western blot. SH2D5 expression was inversely related to overall survival (OS) of LUAD patients as well as B cell immune infiltration. Additionally, SH2D5 expression was negatively correlated with dendritic cells resting (p < 0.001), plasma cells (p < 0.001), mast cells resting (p = 0.031) and T cells CD4 memory resting (p = 0.036) in LUAD patients with abundant SH2D5 expression correlated with poor prognosis. Furthermore, enrichment analysis suggested that SH2D5 was associated with lung cancer and immunity. Lastly, we investigated the relationship between the expression of SH2D5 and the use of antitumor drugs. Conclusion High SH2D5 expression shares an association with unfavorable prognosis in LUAD, and SH2D5 may also provide new ideas for immunotherapy as a potential therapeutic target.
format: application/pdf
format: text/html
creator: Hao Zhou
creator: Shengjun Li
creator: Yuansheng Lin
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Medical Genetics
description: doi:10.7717/peerj.15238
publisher: PeerJ Inc.
rights: © 2023 Zhou et al.
abstract: Objective Through analyzing the SH2D5 expression profiles, clinical features, and immune infiltration in lung adenocarcinoma (LUAD), the study was intended to discuss the correlations of SH2D5 with prognosis and immune infiltration in LUAD. Methods We downloaded transcriptome and clinical data of LUAD patients from TCGA, GEO, and CCLE databases. Sangerbox, R language, GEPIA, UALCAN, and Kaplan-Meier Plotter were adopted to analyze the SH2D5 expression patterns, prognosis, and clinical features. Spearman correlation analysis was performed to determine the association between SH2D5 expression and immune cell infiltration and immune checkpoint genes. The miRNA-SH2D5 relations were predicted by miRDB and starbase. Lastly, quantitative PCR, IHC and Western blot were implemented for validation. Results A prominent up-regulation of SH2D5 was noted in the LUAD group relative to the normal group, which was validated by quantitative PCR, IHC and Western blot. SH2D5 expression was inversely related to overall survival (OS) of LUAD patients as well as B cell immune infiltration. Additionally, SH2D5 expression was negatively correlated with dendritic cells resting (p < 0.001), plasma cells (p < 0.001), mast cells resting (p = 0.031) and T cells CD4 memory resting (p = 0.036) in LUAD patients with abundant SH2D5 expression correlated with poor prognosis. Furthermore, enrichment analysis suggested that SH2D5 was associated with lung cancer and immunity. Lastly, we investigated the relationship between the expression of SH2D5 and the use of antitumor drugs. Conclusion High SH2D5 expression shares an association with unfavorable prognosis in LUAD, and SH2D5 may also provide new ideas for immunotherapy as a potential therapeutic target.
bibliographic citation: Zhou et al. (2023) Prognostic significance of SH2D5 expression in lung adenocarcinoma and its relation to immune cell infiltration. PeerJ 11:e15238 https://doi.org/10.7717/peerj.15238
date submitted: 2022-09-21
date accepted: 2023-03-28
issued: 2023-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Hao
author list: Agent
  family name: Li
  given name: Shengjun
author list: Agent
  family name: Lin
  given name: Yuansheng
doi: 10.7717/peerj.15238
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-09
copyright: ©2023 Zhou et al.
attribution name: Zhou et al.

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