PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: https://peerj.com/articles/11283
items: Effects of different resistance training frequencies on body composition and muscular performance adaptations in men
items: Photoperiod induced the pituitary differential regulation of lncRNAs and mRNAs related to reproduction in sheep
items: Identification of a novel autophagy signature for predicting survival in patients with lung adenocarcinoma
items: A novel Tick Carousel Assay for testing efficacy of repellents on Amblyomma americanum L.
items: Understanding experiments and research practices for reproducibility: an exploratory study
items: Transfection types, methods and strategies: a technical review
items: Genome-wide identification and expression analysis of the EXO70 gene family in grape (Vitis vinifera L)
items: Chemosensitivity and role of swimming legs of mud crab, Scylla paramamosain, in feeding activity as determined by electrocardiographic and behavioural observations
items: First remains of the enormous alligatoroid Deinosuchus from the Upper Cretaceous Menefee Formation, New Mexico

https://peerj.com/articles/11283
type: item
type: AcademicArticle
title: Stable isotope and fatty acid analyses reveal significant differences in trophic niches of smooth hammerhead Sphyrna zygaena (Carcharhiniformes) among three nursery areas in northern Humboldt Current System
description: Fishery pressure on nursery areas of smooth hammerhead in northern Peruvian coast have become a serious threat to sustainability of this resource. Even though, some management actions focused on conservation of the smooth hammerhead populations were proposed in recent years, their scientific foundations are often limited, and biomass of smooth hammerhead in Peruvian waters continues to decrease. To inform management and conservation, this study aims to evaluate the trophic niche of smooth hammerhead juveniles from three nursery areas in the northern Peruvian coast using stable isotope and fatty acid analyses. First, we compared the environmental characteristics of each nursery area (i.e., sea surface temperature and chlorophyll-a concentration) and concluded that nursery areas differed significantly and consistently in sea surface temperature. Subsequently, we evaluated isotopic composition of carbon and nitrogen and fatty acid profiles of muscle and liver tissues collected from juvenile smooth hammerhead from each nursery area. We found that juvenile smooth hammerhead captured in San José were enriched in heavier 13C and 15N isotopes compared to those captured in Máncora and Salaverry. Furthermore, the broadest isotopic niches were observed in juveniles from Máncora, whereas isotopic niches of juveniles from Salaverry and San José were narrower. This difference is primarily driven by the Humboldt Current System and associated upwelling of cold and nutrient rich water that drives increased primary production in San José and, to a less extent, in Salaverry. Compared to smooth hammerhead juveniles from Máncora, those from San José and Salaverry were characterised by higher essential fatty acid concentrations related to pelagic and migratory prey. We conclude that smooth hammerhead juveniles from three nursery areas in the northern Peruvian coast differ significantly in their trophic niches. Thus, management and conservation efforts should consider each nursery area as…
format: application/pdf
format: text/html
creator: Eduardo Segura-Cobeña
creator: Joanna Alfaro-Shigueto
creator: Jeffrey Mangel
creator: Angel Urzua
creator: Konrad Górski
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.11283
publisher: PeerJ Inc.
rights: © 2021 Segura-Cobeña et al.
abstract: Fishery pressure on nursery areas of smooth hammerhead in northern Peruvian coast have become a serious threat to sustainability of this resource. Even though, some management actions focused on conservation of the smooth hammerhead populations were proposed in recent years, their scientific foundations are often limited, and biomass of smooth hammerhead in Peruvian waters continues to decrease. To inform management and conservation, this study aims to evaluate the trophic niche of smooth hammerhead juveniles from three nursery areas in the northern Peruvian coast using stable isotope and fatty acid analyses. First, we compared the environmental characteristics of each nursery area (i.e., sea surface temperature and chlorophyll-a concentration) and concluded that nursery areas differed significantly and consistently in sea surface temperature. Subsequently, we evaluated isotopic composition of carbon and nitrogen and fatty acid profiles of muscle and liver tissues collected from juvenile smooth hammerhead from each nursery area. We found that juvenile smooth hammerhead captured in San José were enriched in heavier 13C and 15N isotopes compared to those captured in Máncora and Salaverry. Furthermore, the broadest isotopic niches were observed in juveniles from Máncora, whereas isotopic niches of juveniles from Salaverry and San José were narrower. This difference is primarily driven by the Humboldt Current System and associated upwelling of cold and nutrient rich water that drives increased primary production in San José and, to a less extent, in Salaverry. Compared to smooth hammerhead juveniles from Máncora, those from San José and Salaverry were characterised by higher essential fatty acid concentrations related to pelagic and migratory prey. We conclude that smooth hammerhead juveniles from three nursery areas in the northern Peruvian coast differ significantly in their trophic niches. Thus, management and conservation efforts should consider each nursery area as…
bibliographic citation: Segura-Cobeña et al. (2021) Stable isotope and fatty acid analyses reveal significant differences in trophic niches of smooth hammerhead Sphyrna zygaena (Carcharhiniformes) among three nursery areas in northern Humboldt Current System. PeerJ 9:e11283 https://doi.org/10.7717/peerj.11283
date submitted: 2020-12-07
date accepted: 2021-03-24
issued: 2021-04-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Segura-Cobeña
  given name: Eduardo
author list: Agent
  family name: Alfaro-Shigueto
  given name: Joanna
author list: Agent
  family name: Mangel
  given name: Jeffrey
author list: Agent
  family name: Urzua
  given name: Angel
author list: Agent
  family name: Górski
  given name: Konrad
doi: 10.7717/peerj.11283
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-22
copyright: ©2021 Segura-Cobeña et al.
attribution name: Segura-Cobeña et al.

Effects of different resistance training frequencies on body composition and muscular performance adaptations in men
type: item
type: AcademicArticle
description: Background The aim of this study was to compare the effects of 8 weeks resistance training (RT) with two sessions versus four sessions per week under volume load-equated conditions on body composition, maximal strength, and explosive actions performance in recreationally trained men. Methods Thirty-five healthy young men participated in the study and were randomly divided into a two sessions per-week RT (RT2, n = 12), four sessions per-week RT (RT4, n = 13) or a control group (CG, n = 10). All subjects were evaluated for thigh, chest and arm circumference, countermovement jump (CMJ), medicine ball throw (MBT), 1-repetition maximum (1RM) leg press, bench press, arm curl, muscular endurance (i.e., 60% of 1RM to failure) for leg press, and bench press at pre, mid (week 4) and post an 8-week training intervention. Results A two-way analysis of variance with repeated measures (3 [group] × 3 [time]) revealed that both training groups increased chest and thigh circumferences, strength and explosive actions performance tests in comparison to CG following 8 weeks of training (p = 0.01 to 0.04). Group × time interactions were also noted in 1RM bench press (effects size [ES] = 1.07 vs. 0.89) and arm curl (ES = 1.15 vs. 0.89), with greater gains for RT4 than RT2 (p = 0.03). Conclusion RT improved muscle strength, explosive actions performance and markers of muscle size in recreationally trained men; however, four sessions of resistance training per week produced greater gains in muscular strength for the upper body measures (i.e., 1RM bench press and arm curl) when compared to two sessions per week under volume-equated conditions.
format: application/pdf
format: text/html
creator: Hamid Arazi
creator: Abbas Asadi
creator: Paulo Gentil
creator: Rodrigo Ramírez-Campillo
creator: Pooria Jahangiri
creator: Adel Ghorbani
creator: Anthony C. Hackney
creator: Hassane Zouhal
subject: Anthropology
subject: Anatomy and Physiology
subject: Clinical Trials
subject: Kinesiology
description: doi:10.7717/peerj.10537
publisher: PeerJ Inc.
rights: © 2021 Arazi et al.
abstract: Background The aim of this study was to compare the effects of 8 weeks resistance training (RT) with two sessions versus four sessions per week under volume load-equated conditions on body composition, maximal strength, and explosive actions performance in recreationally trained men. Methods Thirty-five healthy young men participated in the study and were randomly divided into a two sessions per-week RT (RT2, n = 12), four sessions per-week RT (RT4, n = 13) or a control group (CG, n = 10). All subjects were evaluated for thigh, chest and arm circumference, countermovement jump (CMJ), medicine ball throw (MBT), 1-repetition maximum (1RM) leg press, bench press, arm curl, muscular endurance (i.e., 60% of 1RM to failure) for leg press, and bench press at pre, mid (week 4) and post an 8-week training intervention. Results A two-way analysis of variance with repeated measures (3 [group] × 3 [time]) revealed that both training groups increased chest and thigh circumferences, strength and explosive actions performance tests in comparison to CG following 8 weeks of training (p = 0.01 to 0.04). Group × time interactions were also noted in 1RM bench press (effects size [ES] = 1.07 vs. 0.89) and arm curl (ES = 1.15 vs. 0.89), with greater gains for RT4 than RT2 (p = 0.03). Conclusion RT improved muscle strength, explosive actions performance and markers of muscle size in recreationally trained men; however, four sessions of resistance training per week produced greater gains in muscular strength for the upper body measures (i.e., 1RM bench press and arm curl) when compared to two sessions per week under volume-equated conditions.
bibliographic citation: Arazi et al. (2021) Effects of different resistance training frequencies on body composition and muscular performance adaptations in men. PeerJ 9:e10537 https://doi.org/10.7717/peerj.10537
date submitted: 2020-06-16
date accepted: 2020-11-19
issued: 2021-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arazi
  given name: Hamid
author list: Agent
  family name: Asadi
  given name: Abbas
author list: Agent
  family name: Gentil
  given name: Paulo
author list: Agent
  family name: Ramírez-Campillo
  given name: Rodrigo
author list: Agent
  family name: Jahangiri
  given name: Pooria
author list: Agent
  family name: Ghorbani
  given name: Adel
author list: Agent
  family name: Hackney
  given name: Anthony C.
author list: Agent
  family name: Zouhal
  given name: Hassane
doi: 10.7717/peerj.10537
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-21
copyright: © 2021 Arazi et al.
attribution name: Arazi et al.

Photoperiod induced the pituitary differential regulation of lncRNAs and mRNAs related to reproduction in sheep
type: item
type: AcademicArticle
description: The pituitary is a vital endocrine organ that regulates animal seasonal reproduction by controlling the synthesis and secretion of the hormone. The change of photoperiod is the key factor affecting the function of the pituitary in animals, but the mechanism is unclear. Here, we studied the transcriptomic variation in pars distalis (PD) of the pituitary between short photoperiod (SP) and long photoperiod (LP) using RNA sequencing based on the OVX+E2 sheep. 346 differentially expressed (DE) lncRNAs and 186 DE-mRNA were found in the PD. Moreover, function annotation analysis indicated that the reproductive hormones and photoperiod response-related pathways including aldosterone synthesis and secretion, insulin secretion, thyroid hormone synthesis, and circadian entrainment were enriched. The interaction analysis of mRNA-lncRNA suggested that MSTRG.240648, MSTRG.85500, MSTRG.32448, and MSTRG.304959 targeted CREB3L1 and DUSP6, which may be involved in the photoperiodic regulation of the PD. These findings provide resources for further study on the seasonal reproductive in ewes.
format: application/pdf
format: text/html
creator: Xiaoyun He
creator: Lin Tao
creator: Yingjie Zhong
creator: Ran Di
creator: Qing Xia
creator: Xiangyu Wang
creator: Xiaofei Guo
creator: Shangquan Gan
creator: Xiaosheng Zhang
creator: Jinlong Zhang
creator: Qiuyue Liu
creator: Mingxing Chu
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.10953
publisher: PeerJ Inc.
rights: © 2021 He et al.
abstract: The pituitary is a vital endocrine organ that regulates animal seasonal reproduction by controlling the synthesis and secretion of the hormone. The change of photoperiod is the key factor affecting the function of the pituitary in animals, but the mechanism is unclear. Here, we studied the transcriptomic variation in pars distalis (PD) of the pituitary between short photoperiod (SP) and long photoperiod (LP) using RNA sequencing based on the OVX+E2 sheep. 346 differentially expressed (DE) lncRNAs and 186 DE-mRNA were found in the PD. Moreover, function annotation analysis indicated that the reproductive hormones and photoperiod response-related pathways including aldosterone synthesis and secretion, insulin secretion, thyroid hormone synthesis, and circadian entrainment were enriched. The interaction analysis of mRNA-lncRNA suggested that MSTRG.240648, MSTRG.85500, MSTRG.32448, and MSTRG.304959 targeted CREB3L1 and DUSP6, which may be involved in the photoperiodic regulation of the PD. These findings provide resources for further study on the seasonal reproductive in ewes.
bibliographic citation: He et al. (2021) Photoperiod induced the pituitary differential regulation of lncRNAs and mRNAs related to reproduction in sheep. PeerJ 9:e10953 https://doi.org/10.7717/peerj.10953
date submitted: 2020-05-06
date accepted: 2021-01-27
issued: 2021-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Xiaoyun
author list: Agent
  family name: Tao
  given name: Lin
author list: Agent
  family name: Zhong
  given name: Yingjie
author list: Agent
  family name: Di
  given name: Ran
author list: Agent
  family name: Xia
  given name: Qing
author list: Agent
  family name: Wang
  given name: Xiangyu
author list: Agent
  family name: Guo
  given name: Xiaofei
author list: Agent
  family name: Gan
  given name: Shangquan
author list: Agent
  family name: Zhang
  given name: Xiaosheng
author list: Agent
  family name: Zhang
  given name: Jinlong
author list: Agent
  family name: Liu
  given name: Qiuyue
author list: Agent
  family name: Chu
  given name: Mingxing
doi: 10.7717/peerj.10953
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-21
copyright: ©2021 He et al.
attribution name: He et al.

Identification of a novel autophagy signature for predicting survival in patients with lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Lung adenocarcinoma (LUAD) is the most commonhistological lung cancer subtype, with an overall five-year survivalrate of only 17%. In this study, we aimed to identify autophagy-related genes (ARGs) and develop an LUAD prognostic signature. Methods In this study, we obtained ARGs from three databases and downloaded gene expression profiles from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. We used TCGA-LUAD (n = 490) for a training and testing dataset, and GSE50081 (n = 127) as the external validation dataset.The least absolute shrinkage and selection operator (LASSO) Cox and multivariate Cox regression models were used to generate an autophagy-related signature. We performed gene set enrichment analysis (GSEA) and immune cell analysis between the high- and low-risk groups. A nomogram was built to guide the individual treatment for LUAD patients. Results We identified a total of 83 differentially expressed ARGs (DEARGs) from the TCGA-LUAD dataset, including 33 upregulated DEARGs and 50 downregulated DEARGs, both with thresholds of adjusted P < 0.05 and |Fold change| > 1.5. Using LASSO and multivariate Cox regression analyses, we identified 10 ARGs that we used to build a prognostic signature with areas under the curve (AUCs) of 0.705, 0.715, and 0.778 at 1, 3, and 5 years, respectively. Using the risk score formula, the LUAD patients were divided into low- or high-risk groups. Our GSEA results suggested that the low-risk group were enriched in metabolism and immune-related pathways, while the high-risk group was involved in tumorigenesis and tumor progression pathways. Immune cell analysis revealed that, when compared to the high-risk group, the low-risk group had a lower cell fraction of M0- and M1- macrophages, and higher CD4 and PD-L1 expression levels. Conclusion Our identified robust signature may provide novel insight into underlying autophagy mechanisms as well as therapeutic strategies for LUAD treatment.
format: application/pdf
format: text/html
creator: Jin Duan
creator: Youming Lei
creator: Guoli Lv
creator: Yinqiang Liu
creator: Wei Zhao
creator: Qingmei Yang
creator: Xiaona Su
creator: Zhijian Song
creator: Leilei Lu
creator: Yunfei Shi
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.11074
publisher: PeerJ Inc.
rights: © 2021 Duan et al.
abstract: Background Lung adenocarcinoma (LUAD) is the most commonhistological lung cancer subtype, with an overall five-year survivalrate of only 17%. In this study, we aimed to identify autophagy-related genes (ARGs) and develop an LUAD prognostic signature. Methods In this study, we obtained ARGs from three databases and downloaded gene expression profiles from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. We used TCGA-LUAD (n = 490) for a training and testing dataset, and GSE50081 (n = 127) as the external validation dataset.The least absolute shrinkage and selection operator (LASSO) Cox and multivariate Cox regression models were used to generate an autophagy-related signature. We performed gene set enrichment analysis (GSEA) and immune cell analysis between the high- and low-risk groups. A nomogram was built to guide the individual treatment for LUAD patients. Results We identified a total of 83 differentially expressed ARGs (DEARGs) from the TCGA-LUAD dataset, including 33 upregulated DEARGs and 50 downregulated DEARGs, both with thresholds of adjusted P < 0.05 and |Fold change| > 1.5. Using LASSO and multivariate Cox regression analyses, we identified 10 ARGs that we used to build a prognostic signature with areas under the curve (AUCs) of 0.705, 0.715, and 0.778 at 1, 3, and 5 years, respectively. Using the risk score formula, the LUAD patients were divided into low- or high-risk groups. Our GSEA results suggested that the low-risk group were enriched in metabolism and immune-related pathways, while the high-risk group was involved in tumorigenesis and tumor progression pathways. Immune cell analysis revealed that, when compared to the high-risk group, the low-risk group had a lower cell fraction of M0- and M1- macrophages, and higher CD4 and PD-L1 expression levels. Conclusion Our identified robust signature may provide novel insight into underlying autophagy mechanisms as well as therapeutic strategies for LUAD treatment.
bibliographic citation: Duan et al. (2021) Identification of a novel autophagy signature for predicting survival in patients with lung adenocarcinoma. PeerJ 9:e11074 https://doi.org/10.7717/peerj.11074
date submitted: 2020-05-01
date accepted: 2021-02-17
issued: 2021-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duan
  given name: Jin
author list: Agent
  family name: Lei
  given name: Youming
author list: Agent
  family name: Lv
  given name: Guoli
author list: Agent
  family name: Liu
  given name: Yinqiang
author list: Agent
  family name: Zhao
  given name: Wei
author list: Agent
  family name: Yang
  given name: Qingmei
author list: Agent
  family name: Su
  given name: Xiaona
author list: Agent
  family name: Song
  given name: Zhijian
author list: Agent
  family name: Lu
  given name: Leilei
author list: Agent
  family name: Shi
  given name: Yunfei
doi: 10.7717/peerj.11074
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-21
copyright: ©2021 Duan et al.
attribution name: Duan et al.

A novel Tick Carousel Assay for testing efficacy of repellents on Amblyomma americanum L.
type: item
type: AcademicArticle
description: Ticks are important vectors of human and veterinary diseases. A primary way ticks gain access to human hosts is by engaging to clothing. Repellents or acaricides sprayed onto fabric are used to deter ticks’ access to human hosts. However, there are a limited amount of standardized laboratory assays that can determine the potency and efficacy of repellents. We present a novel fabric-engagement assay referred to as the ‘Tick Carousel Assay’. This assay utilizes fabric brushing past ticks located on an artificial grass patch and measures tick engagements to fabric over time. After screening a variety of tick species, we used the lone star tick (Amblyomma americanum) to test the efficacy of four commonly used active ingredients in repellents: DEET, Picaridin, IR3535, and Oil of Lemon Eucalyptus. Repellency was tested immediately, after three hours, and six hours post application to fabric. Our data show that each repellent we tested significantly reduced the number of tick engagements to fabric for at least 6 hours. We did not find significant differences in repellent efficacy between the four active ingredients tested directly and three hours after application. After six hours, Oil of Lemon Eucalyptus repelled ticks more than the other active ingredients. We show that our Tick Carousel Assay provides an affordable, repeatable, and standardized way to compare and test repellent efficacy on treated fabrics. Our results confirm that commonly used repellents applied to fabric are an effective way to reduce tick engagement.
format: application/pdf
format: text/html
creator: Hailey A. Luker
creator: Stacy Rodriguez
creator: Yashoda Kandel
creator: Julia Vulcan
creator: Immo A. Hansen
subject: Animal Behavior
subject: Entomology
subject: Toxicology
subject: Zoology
description: doi:10.7717/peerj.11138
publisher: PeerJ Inc.
rights: © 2021 Luker et al.
abstract: Ticks are important vectors of human and veterinary diseases. A primary way ticks gain access to human hosts is by engaging to clothing. Repellents or acaricides sprayed onto fabric are used to deter ticks’ access to human hosts. However, there are a limited amount of standardized laboratory assays that can determine the potency and efficacy of repellents. We present a novel fabric-engagement assay referred to as the ‘Tick Carousel Assay’. This assay utilizes fabric brushing past ticks located on an artificial grass patch and measures tick engagements to fabric over time. After screening a variety of tick species, we used the lone star tick (Amblyomma americanum) to test the efficacy of four commonly used active ingredients in repellents: DEET, Picaridin, IR3535, and Oil of Lemon Eucalyptus. Repellency was tested immediately, after three hours, and six hours post application to fabric. Our data show that each repellent we tested significantly reduced the number of tick engagements to fabric for at least 6 hours. We did not find significant differences in repellent efficacy between the four active ingredients tested directly and three hours after application. After six hours, Oil of Lemon Eucalyptus repelled ticks more than the other active ingredients. We show that our Tick Carousel Assay provides an affordable, repeatable, and standardized way to compare and test repellent efficacy on treated fabrics. Our results confirm that commonly used repellents applied to fabric are an effective way to reduce tick engagement.
bibliographic citation: Luker et al. (2021) A novel Tick Carousel Assay for testing efficacy of repellents on Amblyomma americanum L.. PeerJ 9:e11138 https://doi.org/10.7717/peerj.11138
date submitted: 2020-12-07
date accepted: 2021-03-01
issued: 2021-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luker
  given name: Hailey A.
author list: Agent
  family name: Rodriguez
  given name: Stacy
author list: Agent
  family name: Kandel
  given name: Yashoda
author list: Agent
  family name: Vulcan
  given name: Julia
author list: Agent
  family name: Hansen
  given name: Immo A.
doi: 10.7717/peerj.11138
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-21
copyright: ©2021 Luker et al.
attribution name: Luker et al.

Understanding experiments and research practices for reproducibility: an exploratory study
type: item
type: AcademicArticle
description: Scientific experiments and research practices vary across disciplines. The research practices followed by scientists in each domain play an essential role in the understandability and reproducibility of results. The “Reproducibility Crisis”, where researchers find difficulty in reproducing published results, is currently faced by several disciplines. To understand the underlying problem in the context of the reproducibility crisis, it is important to first know the different research practices followed in their domain and the factors that hinder reproducibility. We performed an exploratory study by conducting a survey addressed to researchers representing a range of disciplines to understand scientific experiments and research practices for reproducibility. The survey findings identify a reproducibility crisis and a strong need for sharing data, code, methods, steps, and negative and positive results. Insufficient metadata, lack of publicly available data, and incomplete information in study methods are considered to be the main reasons for poor reproducibility. The survey results also address a wide number of research questions on the reproducibility of scientific results. Based on the results of our explorative study and supported by the existing published literature, we offer general recommendations that could help the scientific community to understand, reproduce, and reuse experimental data and results in the research data lifecycle.
format: application/pdf
format: text/html
creator: Sheeba Samuel
creator: Birgitta König-Ries
subject: Science Policy
subject: Human-Computer Interaction
subject: Computational Science
subject: Data Science
description: doi:10.7717/peerj.11140
publisher: PeerJ Inc.
rights: © 2021 Samuel et al.
abstract: Scientific experiments and research practices vary across disciplines. The research practices followed by scientists in each domain play an essential role in the understandability and reproducibility of results. The “Reproducibility Crisis”, where researchers find difficulty in reproducing published results, is currently faced by several disciplines. To understand the underlying problem in the context of the reproducibility crisis, it is important to first know the different research practices followed in their domain and the factors that hinder reproducibility. We performed an exploratory study by conducting a survey addressed to researchers representing a range of disciplines to understand scientific experiments and research practices for reproducibility. The survey findings identify a reproducibility crisis and a strong need for sharing data, code, methods, steps, and negative and positive results. Insufficient metadata, lack of publicly available data, and incomplete information in study methods are considered to be the main reasons for poor reproducibility. The survey results also address a wide number of research questions on the reproducibility of scientific results. Based on the results of our explorative study and supported by the existing published literature, we offer general recommendations that could help the scientific community to understand, reproduce, and reuse experimental data and results in the research data lifecycle.
bibliographic citation: Samuel et al. (2021) Understanding experiments and research practices for reproducibility: an exploratory study. PeerJ 9:e11140 https://doi.org/10.7717/peerj.11140
date submitted: 2020-09-09
date accepted: 2021-03-01
issued: 2021-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Samuel
  given name: Sheeba
author list: Agent
  family name: König-Ries
  given name: Birgitta
doi: 10.7717/peerj.11140
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-21
copyright: ©2021 Samuel et al.
attribution name: Samuel et al.

Transfection types, methods and strategies: a technical review
type: item
type: AcademicArticle
description: Transfection is a modern and powerful method used to insert foreign nucleic acids into eukaryotic cells. The ability to modify host cells’ genetic content enables the broad application of this process in studying normal cellular processes, disease molecular mechanism and gene therapeutic effect. In this review, we summarized and compared the findings from various reported literature on the characteristics, strengths, and limitations of various transfection methods, type of transfected nucleic acids, transfection controls and approaches to assess transfection efficiency. With the vast choices of approaches available, we hope that this review will help researchers, especially those new to the field, in their decision making over the transfection protocol or strategy appropriate for their experimental aims.
format: application/pdf
format: text/html
creator: Zhi Xiong Chong
creator: Swee Keong Yeap
creator: Wan Yong Ho
subject: Biotechnology
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.11165
publisher: PeerJ Inc.
rights: © 2021 Chong et al.
abstract: Transfection is a modern and powerful method used to insert foreign nucleic acids into eukaryotic cells. The ability to modify host cells’ genetic content enables the broad application of this process in studying normal cellular processes, disease molecular mechanism and gene therapeutic effect. In this review, we summarized and compared the findings from various reported literature on the characteristics, strengths, and limitations of various transfection methods, type of transfected nucleic acids, transfection controls and approaches to assess transfection efficiency. With the vast choices of approaches available, we hope that this review will help researchers, especially those new to the field, in their decision making over the transfection protocol or strategy appropriate for their experimental aims.
bibliographic citation: Chong et al. (2021) Transfection types, methods and strategies: a technical review. PeerJ 9:e11165 https://doi.org/10.7717/peerj.11165
date submitted: 2020-07-22
date accepted: 2021-03-05
issued: 2021-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chong
  given name: Zhi Xiong
author list: Agent
  family name: Yeap
  given name: Swee Keong
author list: Agent
  family name: Ho
  given name: Wan Yong
doi: 10.7717/peerj.11165
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-21
copyright: © 2021 Chong et al.
attribution name: Chong et al.

Genome-wide identification and expression analysis of the EXO70 gene family in grape (Vitis vinifera L)
type: item
type: AcademicArticle
description: EXO70 is the pivotal protein subunit of exocyst, which has a very crucial role in enhancing the shielding effect of the cell wall, resisting abiotic and hormonal stresses. This experiment aims to identify family members of the EXO70 gene family in grape and predict the characteristics of this gene family, so as to lay the foundation of further exploring the mechanism of resisting abiotic and hormone stresses of VvEXO70s. Therefore, the Vitis vinifera ‘Red Globe’ tube plantlet were used as materials. Bioinformatics was used to inquire VvEXO70 genes family members, gene structure, system evolution, cis-acting elements, subcellular and chromosomal localization, collinearity, selective pressure, codon bias and tissue expression. All of VvEXO70s had the conserved pfam03081 domain which maybe necessary for interacting with other proteins. Microarray analysis suggested that most genes expressed to varying degrees in tendrils, leaves, seeds, buds, roots and stems. Quantitative Real-Time PCR (qRT-PCR) showed that the expression levels of all genes with 5 mM salicylic acid (SA), 0.1 mM methy jasmonate (MeJA), 20% PEG6000 and 4 °C for 24 h were higher than for 12 h. With 20% PEG6000 treatment about 24 h, the relative expression of VvEXO70-02 was significantly up-regulated and 361 times higher than CK. All genes’ relative expression was higher at 12 h than that at 24 h after treatment with 7 mM hydrogen peroxide (H2O2) and 0.1 mM ethylene (ETH). In conclusion, the expression levels of 14 VvEXO70 genes are distinguishing under these treatments, which play an important role in the regulation of anti-stress signals in grape. All of these test results provide a reference for the future research on the potential function analysis and plant breeding of VvEXO70 genes.
format: application/pdf
format: text/html
creator: Han Wang
creator: Zong-Huan Ma
creator: Juan Mao
creator: Bai-Hong Chen
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11176
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: EXO70 is the pivotal protein subunit of exocyst, which has a very crucial role in enhancing the shielding effect of the cell wall, resisting abiotic and hormonal stresses. This experiment aims to identify family members of the EXO70 gene family in grape and predict the characteristics of this gene family, so as to lay the foundation of further exploring the mechanism of resisting abiotic and hormone stresses of VvEXO70s. Therefore, the Vitis vinifera ‘Red Globe’ tube plantlet were used as materials. Bioinformatics was used to inquire VvEXO70 genes family members, gene structure, system evolution, cis-acting elements, subcellular and chromosomal localization, collinearity, selective pressure, codon bias and tissue expression. All of VvEXO70s had the conserved pfam03081 domain which maybe necessary for interacting with other proteins. Microarray analysis suggested that most genes expressed to varying degrees in tendrils, leaves, seeds, buds, roots and stems. Quantitative Real-Time PCR (qRT-PCR) showed that the expression levels of all genes with 5 mM salicylic acid (SA), 0.1 mM methy jasmonate (MeJA), 20% PEG6000 and 4 °C for 24 h were higher than for 12 h. With 20% PEG6000 treatment about 24 h, the relative expression of VvEXO70-02 was significantly up-regulated and 361 times higher than CK. All genes’ relative expression was higher at 12 h than that at 24 h after treatment with 7 mM hydrogen peroxide (H2O2) and 0.1 mM ethylene (ETH). In conclusion, the expression levels of 14 VvEXO70 genes are distinguishing under these treatments, which play an important role in the regulation of anti-stress signals in grape. All of these test results provide a reference for the future research on the potential function analysis and plant breeding of VvEXO70 genes.
bibliographic citation: Wang et al. (2021) Genome-wide identification and expression analysis of the EXO70 gene family in grape (Vitis vinifera L). PeerJ 9:e11176 https://doi.org/10.7717/peerj.11176
date submitted: 2020-09-11
date accepted: 2021-03-08
issued: 2021-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Han
author list: Agent
  family name: Ma
  given name: Zong-Huan
author list: Agent
  family name: Mao
  given name: Juan
author list: Agent
  family name: Chen
  given name: Bai-Hong
doi: 10.7717/peerj.11176
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-21
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Chemosensitivity and role of swimming legs of mud crab, Scylla paramamosain, in feeding activity as determined by electrocardiographic and behavioural observations
type: item
type: AcademicArticle
description: Swimming crabs have a characteristic fifth pair of legs that are flattened into paddles for swimming purposes. The dactyl of these legs bears a thick seta along its edge. The chemoreceptive and feeding properties of the seta are supported with scientific evidence; however, there is no available data on the sensitivity of the setae in portunid crabs. The underlying mechanisms of the chemo- and mechano-sensitivity of appendages and their involvement in feeding activities of the mud crab (Scylla paramamosain) were investigated using electrocardiography and behavioural assay, which focused on the responses of the mud crab to chemical and touch stimulus. Electrocardiography revealed the sensory properties of the appendages. The dactyls of swimming legs and the antennules were chemosensitive, but not mechanosensitive and vice versa for the antennae. However, the mouthparts, claws, and walking legs were chemo- and mechanosensitive. Only the chemosensitive appendages, including the swimming legs, were directly involved in feeding. The flattened dactyls of the swimming legs were more efficient than the pointed dactyls of the walking legs in detecting the food organism crawling on the substrate. The structural features enhanced the capacity of the crab in coming into contact with scattered food items. This study revealed that the swimming legs are important appendages for feeding in the mud crab.
format: application/pdf
format: text/html
creator: Gunzo Kawamura
creator: Chi Keong Loke
creator: Leong Seng Lim
creator: Annita Seok Kian Yong
creator: Saleem Mustafa
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.11248
publisher: PeerJ Inc.
rights: © 2021 Kawamura et al.
abstract: Swimming crabs have a characteristic fifth pair of legs that are flattened into paddles for swimming purposes. The dactyl of these legs bears a thick seta along its edge. The chemoreceptive and feeding properties of the seta are supported with scientific evidence; however, there is no available data on the sensitivity of the setae in portunid crabs. The underlying mechanisms of the chemo- and mechano-sensitivity of appendages and their involvement in feeding activities of the mud crab (Scylla paramamosain) were investigated using electrocardiography and behavioural assay, which focused on the responses of the mud crab to chemical and touch stimulus. Electrocardiography revealed the sensory properties of the appendages. The dactyls of swimming legs and the antennules were chemosensitive, but not mechanosensitive and vice versa for the antennae. However, the mouthparts, claws, and walking legs were chemo- and mechanosensitive. Only the chemosensitive appendages, including the swimming legs, were directly involved in feeding. The flattened dactyls of the swimming legs were more efficient than the pointed dactyls of the walking legs in detecting the food organism crawling on the substrate. The structural features enhanced the capacity of the crab in coming into contact with scattered food items. This study revealed that the swimming legs are important appendages for feeding in the mud crab.
bibliographic citation: Kawamura et al. (2021) Chemosensitivity and role of swimming legs of mud crab, Scylla paramamosain, in feeding activity as determined by electrocardiographic and behavioural observations. PeerJ 9:e11248 https://doi.org/10.7717/peerj.11248
date submitted: 2020-08-04
date accepted: 2021-03-18
issued: 2021-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kawamura
  given name: Gunzo
author list: Agent
  family name: Loke
  given name: Chi Keong
author list: Agent
  family name: Lim
  given name: Leong Seng
author list: Agent
  family name: Yong
  given name: Annita Seok Kian
author list: Agent
  family name: Mustafa
  given name: Saleem
doi: 10.7717/peerj.11248
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-21
copyright: ©2021 Kawamura et al.
attribution name: Kawamura et al.

First remains of the enormous alligatoroid Deinosuchus from the Upper Cretaceous Menefee Formation, New Mexico
type: item
type: AcademicArticle
description: The neosuchian Deinosuchus is known from numerous localities throughout the Campanian of North America, from New Jersey to Montana (USA) and as far south as Coahuila (Mexico). Here we describe six osteoderms, two vertebrae, and a partial tooth discovered in the Menefee Formation of New Mexico and assign them to Deinosuchus sp., representing one of the earliest occurrences of this genus on the Laramidian subcontinent, and among the earliest known occurrences of this large alligatoroid in all of North America. The osteoderms are morphologically distinct in their inflated construction, with deep and radially distributed pitting, which closely matches osteoderms of Deinosuchus.
format: application/pdf
format: text/html
creator: Benjamin F. Mohler
creator: Andrew T. McDonald
creator: Douglas G. Wolfe
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.11302
publisher: PeerJ Inc.
rights: © 2021 Mohler et al.
abstract: The neosuchian Deinosuchus is known from numerous localities throughout the Campanian of North America, from New Jersey to Montana (USA) and as far south as Coahuila (Mexico). Here we describe six osteoderms, two vertebrae, and a partial tooth discovered in the Menefee Formation of New Mexico and assign them to Deinosuchus sp., representing one of the earliest occurrences of this genus on the Laramidian subcontinent, and among the earliest known occurrences of this large alligatoroid in all of North America. The osteoderms are morphologically distinct in their inflated construction, with deep and radially distributed pitting, which closely matches osteoderms of Deinosuchus.
bibliographic citation: Mohler et al. (2021) First remains of the enormous alligatoroid Deinosuchus from the Upper Cretaceous Menefee Formation, New Mexico. PeerJ 9:e11302 https://doi.org/10.7717/peerj.11302
date submitted: 2021-01-07
date accepted: 2021-03-29
issued: 2021-04-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohler
  given name: Benjamin F.
author list: Agent
  family name: McDonald
  given name: Andrew T.
author list: Agent
  family name: Wolfe
  given name: Douglas G.
doi: 10.7717/peerj.11302
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-21
copyright: © 2021 Mohler et al.
attribution name: Mohler et al.

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