PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Biomaterials research of China from 2013 to 2017 based on bibliometrics and visualization analysis
items: Elevated limb-bud and heart development (LBH) expression indicates poor prognosis and promotes gastric cancer cell proliferation and invasion via upregulating Integrin/FAK/Akt pathway
items: Examining the assumptions of heterogeneity-based management for promoting plant diversity in a disturbance-prone ecosystem
items: Physiological and biochemical responses of sugar beet (Beta vulgaris L) to ultraviolet-B radiation
items: Gene drives as a new quality in GMO releases—a comparative technology characterization
items: Applying and refining DNA analysis to determine the identity of plant material extracted from the digestive tracts of katydids
items: Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize
items: Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.)
items: Prefrontal cortical activation measured by fNIRS during walking: effects of age, disease and secondary task
items: Leptin-a mediates transcription of genes that participate in central endocrine and phosphatidylinositol signaling pathways in 72-hour embryonic zebrafish (Danio rerio)

Biomaterials research of China from 2013 to 2017 based on bibliometrics and visualization analysis
type: item
type: AcademicArticle
description: Objectives This study aims to evaluate the changes of development trends and research hotspots of biomaterials research from 2013 to 2017, which can identify the general information of papers and explore the changes of research content, thus providing perspectives for the development of biomaterials in China and other countries. Methods Data of the paper were retrieved from the Web of Science Core Collection, and then analyzed by the bibliometric and CiteSpace visualization analysis. Results It was found that a total of 3,839 related papers had been published from the year 2013 to 2017. The analysis of the articles showed that the annual quantity and quality of the articles in the biomaterials research have been increasing since 2013, and the Wang L / Chinese Academy of Sciences were the most productive author/institution. Meanwhile, the keywords “in vitro”, “scaffold”, “nanoparticle” , “mechanical property”, and “biocompatibility” have the relatively higher frequency, and the keywords “apatite”, “deposition”, and “surface modification” have the strongest burst citation. Conclusions After statistics and analysis, we found that biomaterials is a promising research field. The study may be helpful in understanding research trends in this field.
format: application/pdf
format: text/html
creator: Dandan Hou
creator: Xuewei Bi
creator: Zhinan Mao
creator: Yubo Fan
creator: Xiangming Hu
creator: Xiaoming Li
subject: Bioengineering
subject: Bioinformatics
description: doi:10.7717/peerj.6859
publisher: PeerJ Inc.
rights: © 2019 Hou et al.
abstract: Objectives This study aims to evaluate the changes of development trends and research hotspots of biomaterials research from 2013 to 2017, which can identify the general information of papers and explore the changes of research content, thus providing perspectives for the development of biomaterials in China and other countries. Methods Data of the paper were retrieved from the Web of Science Core Collection, and then analyzed by the bibliometric and CiteSpace visualization analysis. Results It was found that a total of 3,839 related papers had been published from the year 2013 to 2017. The analysis of the articles showed that the annual quantity and quality of the articles in the biomaterials research have been increasing since 2013, and the Wang L / Chinese Academy of Sciences were the most productive author/institution. Meanwhile, the keywords “in vitro”, “scaffold”, “nanoparticle” , “mechanical property”, and “biocompatibility” have the relatively higher frequency, and the keywords “apatite”, “deposition”, and “surface modification” have the strongest burst citation. Conclusions After statistics and analysis, we found that biomaterials is a promising research field. The study may be helpful in understanding research trends in this field.
bibliographic citation: Hou et al. (2019) Biomaterials research of China from 2013 to 2017 based on bibliometrics and visualization analysis. PeerJ 7:e6859 https://doi.org/10.7717/peerj.6859
date submitted: 2019-01-03
date accepted: 2019-03-21
issued: 2019-05-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: Dandan
author list: Agent
  family name: Bi
  given name: Xuewei
author list: Agent
  family name: Mao
  given name: Zhinan
author list: Agent
  family name: Fan
  given name: Yubo
author list: Agent
  family name: Hu
  given name: Xiangming
author list: Agent
  family name: Li
  given name: Xiaoming
doi: 10.7717/peerj.6859
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-06
copyright: ©2019 Hou et al.
attribution name: Hou et al.

Elevated limb-bud and heart development (LBH) expression indicates poor prognosis and promotes gastric cancer cell proliferation and invasion via upregulating Integrin/FAK/Akt pathway
type: item
type: AcademicArticle
description: The limb-bud and heart development (LBH) gene is a highly conserved, tissue-specific transcription cofactor in vertebrates that regulates multiple key genes in embryonic development. The role of LBH in various cancer types is still controversial, and its specific role and molecular mechanism in the oncogenesis of gastric cancer (GC) remains largely unexplored. In the present study, the prognostic significance and clinicopathological characteristics of LBH in GC was determined. The LBH mRNA expression was first investigated in four independent public datasets (TCGA-STAD, GSE15459, GSE29272, and GSE62254) and then validated with our samples at the protein level. LBH was overexpressed at both the mRNA and protein levels in cancer compared with normal tissues. High LBH expression was correlated with advanced T, N, and M stages. Kaplan–Meier analysis and log-rank test indicated that higher LBH expression was statistically correlated with shorter overall survival (OS) in the public datasets and our study samples. Univariate and multivariate Cox regression analysis showed that LBH was an independent prognostic biomarker for survival in TCGA-STAD, GSE15459, GSE62254 cohorts, and our GC patients. In vitro experiments showed that knockdown of LBH can significantly inhibit the proliferation and invasion of HGC-27 cells, while overexpression of LBH can significantly enhance the proliferation and invasion of BGC-823 cells. Gene Set Enrichment Analysis (GSEA), Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomics (KEGG) indicated that high LBH expression is associated with the PI3K-Akt pathway, focal adhesion, and extracellular matrix (ECM)-receptor interaction. Western blot analysis showed that knockdown of LBH significantly inhibited the expression of integrin α5, integrin β1, p-FAK, and p-Akt. Therefore, results from the present study indicate that LBH is a potential independent prognostic biomarker and promotes proliferation and invasion of GC cells by activating th…
format: application/pdf
format: text/html
creator: Ruoxi Yu
creator: Zhi Li
creator: Chuang Zhang
creator: Huicong Song
creator: Mingming Deng
creator: Liping Sun
creator: Ling Xu
creator: Xiaofang Che
creator: Xuejun Hu
creator: Xiujuan Qu
creator: Yunpeng Liu
creator: Ye Zhang
subject: Bioinformatics
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.6885
publisher: PeerJ Inc.
rights: © 2019 Yu et al.
abstract: The limb-bud and heart development (LBH) gene is a highly conserved, tissue-specific transcription cofactor in vertebrates that regulates multiple key genes in embryonic development. The role of LBH in various cancer types is still controversial, and its specific role and molecular mechanism in the oncogenesis of gastric cancer (GC) remains largely unexplored. In the present study, the prognostic significance and clinicopathological characteristics of LBH in GC was determined. The LBH mRNA expression was first investigated in four independent public datasets (TCGA-STAD, GSE15459, GSE29272, and GSE62254) and then validated with our samples at the protein level. LBH was overexpressed at both the mRNA and protein levels in cancer compared with normal tissues. High LBH expression was correlated with advanced T, N, and M stages. Kaplan–Meier analysis and log-rank test indicated that higher LBH expression was statistically correlated with shorter overall survival (OS) in the public datasets and our study samples. Univariate and multivariate Cox regression analysis showed that LBH was an independent prognostic biomarker for survival in TCGA-STAD, GSE15459, GSE62254 cohorts, and our GC patients. In vitro experiments showed that knockdown of LBH can significantly inhibit the proliferation and invasion of HGC-27 cells, while overexpression of LBH can significantly enhance the proliferation and invasion of BGC-823 cells. Gene Set Enrichment Analysis (GSEA), Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomics (KEGG) indicated that high LBH expression is associated with the PI3K-Akt pathway, focal adhesion, and extracellular matrix (ECM)-receptor interaction. Western blot analysis showed that knockdown of LBH significantly inhibited the expression of integrin α5, integrin β1, p-FAK, and p-Akt. Therefore, results from the present study indicate that LBH is a potential independent prognostic biomarker and promotes proliferation and invasion of GC cells by activating th…
bibliographic citation: Yu et al. (2019) Elevated limb-bud and heart development (LBH) expression indicates poor prognosis and promotes gastric cancer cell proliferation and invasion via upregulating Integrin/FAK/Akt pathway. PeerJ 7:e6885 https://doi.org/10.7717/peerj.6885
date submitted: 2018-11-22
date accepted: 2019-03-31
issued: 2019-05-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Ruoxi
author list: Agent
  family name: Li
  given name: Zhi
author list: Agent
  family name: Zhang
  given name: Chuang
author list: Agent
  family name: Song
  given name: Huicong
author list: Agent
  family name: Deng
  given name: Mingming
author list: Agent
  family name: Sun
  given name: Liping
author list: Agent
  family name: Xu
  given name: Ling
author list: Agent
  family name: Che
  given name: Xiaofang
author list: Agent
  family name: Hu
  given name: Xuejun
author list: Agent
  family name: Qu
  given name: Xiujuan
author list: Agent
  family name: Liu
  given name: Yunpeng
author list: Agent
  family name: Zhang
  given name: Ye
doi: 10.7717/peerj.6885
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-06
copyright: ©2019 Yu et al.
attribution name: Yu et al.

Examining the assumptions of heterogeneity-based management for promoting plant diversity in a disturbance-prone ecosystem
type: item
type: AcademicArticle
description: Background Patch-burn management approaches attempt to increase overall landscape biodiversity by creating a mosaic of habitats using a patchy application of fire and grazing. We tested two assumptions of the patch-burn approach, namely that: (1) fire and grazing drive spatial patch differentiation in community structure and (2) species composition of patches change through time in response to disturbance. Methods We analyzed species cover data on 100 m2 square quadrats from 128 sites located on a 1 × 1 km UTM grid in the grassland habitats of the Tallgrass Prairie Preserve. A total of 20 of these sites were annually sampled for 12 years. We examined how strongly changes in species richness and species composition correlated with changes in management variables relative to independent spatial and temporal drivers using multiple regression and direct ordination, respectively. Results Site effects, probably due to edaphic differences, explained the majority of variation in richness and composition. Interannual variation in fire and grazing management was relatively unimportant relative to inherent site and year drivers with respect to both richness and composition; however, the effects of fire and grazing variables were statistically significant and interpretable, and bison management was positively correlated with plant richness. Conclusions There was some support for the two assumptions of patch-burn management we examined; however, in situ spatial and temporal environmental heterogeneity played a much larger role than management in shaping both plant richness and composition. Our results suggest that fine-tuning the application of fire and grazing may not be critical for maintaining landscape scale plant diversity in disturbance-prone ecosystems.
format: application/pdf
format: text/html
creator: Daniel J. McGlinn
creator: Michael W. Palmer
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.6738
publisher: PeerJ Inc.
rights: © 2019 McGlinn and Palmer
abstract: Background Patch-burn management approaches attempt to increase overall landscape biodiversity by creating a mosaic of habitats using a patchy application of fire and grazing. We tested two assumptions of the patch-burn approach, namely that: (1) fire and grazing drive spatial patch differentiation in community structure and (2) species composition of patches change through time in response to disturbance. Methods We analyzed species cover data on 100 m2 square quadrats from 128 sites located on a 1 × 1 km UTM grid in the grassland habitats of the Tallgrass Prairie Preserve. A total of 20 of these sites were annually sampled for 12 years. We examined how strongly changes in species richness and species composition correlated with changes in management variables relative to independent spatial and temporal drivers using multiple regression and direct ordination, respectively. Results Site effects, probably due to edaphic differences, explained the majority of variation in richness and composition. Interannual variation in fire and grazing management was relatively unimportant relative to inherent site and year drivers with respect to both richness and composition; however, the effects of fire and grazing variables were statistically significant and interpretable, and bison management was positively correlated with plant richness. Conclusions There was some support for the two assumptions of patch-burn management we examined; however, in situ spatial and temporal environmental heterogeneity played a much larger role than management in shaping both plant richness and composition. Our results suggest that fine-tuning the application of fire and grazing may not be critical for maintaining landscape scale plant diversity in disturbance-prone ecosystems.
bibliographic citation: McGlinn et al. (2019) Examining the assumptions of heterogeneity-based management for promoting plant diversity in a disturbance-prone ecosystem. PeerJ 7:e6738 https://doi.org/10.7717/peerj.6738
date submitted: 2017-05-23
date accepted: 2019-03-06
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McGlinn
  given name: Daniel J.
author list: Agent
  family name: Palmer
  given name: Michael W.
doi: 10.7717/peerj.6738
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 McGlinn and Palmer
attribution name: McGlinn and Palmer

Physiological and biochemical responses of sugar beet (Beta vulgaris L) to ultraviolet-B radiation
type: item
type: AcademicArticle
description: Ultraviolet radiation can cause many serious problems for all living organisms. With a growing population, the UV sensitivity of crop plants presents a particular problem. To evaluate the suitability of growing in areas under UV irradiance, the influence of different doses of UV-B (3.042, 6.084 and 9.126 kJm−2d−1) on the sugar beet (Beta vulgaris L) plants was studied. UV-B induced a significant decrease in growth displayed as reduced height and fresh and dry weight. This reduction is not dose dependent and was associated with diminishing photosynthetic O2 evolution, relative chlorophyll content, photosynthetic pigments and chlorophyll fluorescence. On the other hand, antioxidant enzyme activities, total protein content, compatible solutes, total free amino acids and total betalain content were increased under 9.126 kJm−2d−1 UV-B treatments, representing mechanisms by which the plants coped with the stress. The oxidative stress upon UV-B treatment was evident by increased malondialdehyde (MDA) content, however, hydrogen peroxide (H2O2) was not affected in UV-B exposed plants. Thus, the studied sugar beet variety BR1seems to be suitable particularly for areas with high doses of UV-B irradiation.
format: application/pdf
format: text/html
creator: Parisa Rahimzadeh Karvansara
creator: Seyed Mehdi Razavi
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.6790
publisher: PeerJ Inc.
rights: © 2019 Rahimzadeh Karvansara and Razavi
abstract: Ultraviolet radiation can cause many serious problems for all living organisms. With a growing population, the UV sensitivity of crop plants presents a particular problem. To evaluate the suitability of growing in areas under UV irradiance, the influence of different doses of UV-B (3.042, 6.084 and 9.126 kJm−2d−1) on the sugar beet (Beta vulgaris L) plants was studied. UV-B induced a significant decrease in growth displayed as reduced height and fresh and dry weight. This reduction is not dose dependent and was associated with diminishing photosynthetic O2 evolution, relative chlorophyll content, photosynthetic pigments and chlorophyll fluorescence. On the other hand, antioxidant enzyme activities, total protein content, compatible solutes, total free amino acids and total betalain content were increased under 9.126 kJm−2d−1 UV-B treatments, representing mechanisms by which the plants coped with the stress. The oxidative stress upon UV-B treatment was evident by increased malondialdehyde (MDA) content, however, hydrogen peroxide (H2O2) was not affected in UV-B exposed plants. Thus, the studied sugar beet variety BR1seems to be suitable particularly for areas with high doses of UV-B irradiation.
bibliographic citation: Rahimzadeh Karvansara et al. (2019) Physiological and biochemical responses of sugar beet (Beta vulgaris L) to ultraviolet-B radiation. PeerJ 7:e6790 https://doi.org/10.7717/peerj.6790
date submitted: 2018-12-02
date accepted: 2019-03-12
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rahimzadeh Karvansara
  given name: Parisa
author list: Agent
  family name: Razavi
  given name: Seyed Mehdi
doi: 10.7717/peerj.6790
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: ©2019 Rahimzadeh Karvansara and Razavi
attribution name: Rahimzadeh Karvansara and Razavi

Gene drives as a new quality in GMO releases—a comparative technology characterization
type: item
type: AcademicArticle
description: Compared to previous releases of genetically modified organisms (GMOs) which were primarily plants, gene drives represent a paradigm shift in the handling of GMOs: Current regulation of the release of GMOs assumes that for specific periods of time a certain amount of GMOs will be released in a particular region. However, now a type of genetic technology arises whose innermost principle lies in exceeding these limits—the transformation or even eradication of wild populations. The invasive character of gene drives demands a thorough analysis of their functionalities, reliability and potential impact. But such investigations are hindered by the fact that an experimental field test would hardly be reversible. Therefore, an appropriate prospective assessment is of utmost importance for an estimation of the risk potential associated with the application of gene drives. This work is meant to support the inevitable characterization of gene drives by a comparative approach of prospective technology assessment with a focus on potential sources of risk. Therein, the hazard and exposure potential as well as uncertainties with regard to the performance of synthetic gene drives are addressed. Moreover, a quantitative analysis of their invasiveness should enable a differentiated evaluation of their power to transform wild populations.
format: application/pdf
format: text/html
creator: Johannes L. Frieß
creator: Arnim von Gleich
creator: Bernd Giese
subject: Biotechnology
subject: Ecology
subject: Genetics
subject: Coupled Natural and Human Systems
subject: Population Biology
description: doi:10.7717/peerj.6793
publisher: PeerJ Inc.
rights: © 2019 Frieß et al.
abstract: Compared to previous releases of genetically modified organisms (GMOs) which were primarily plants, gene drives represent a paradigm shift in the handling of GMOs: Current regulation of the release of GMOs assumes that for specific periods of time a certain amount of GMOs will be released in a particular region. However, now a type of genetic technology arises whose innermost principle lies in exceeding these limits—the transformation or even eradication of wild populations. The invasive character of gene drives demands a thorough analysis of their functionalities, reliability and potential impact. But such investigations are hindered by the fact that an experimental field test would hardly be reversible. Therefore, an appropriate prospective assessment is of utmost importance for an estimation of the risk potential associated with the application of gene drives. This work is meant to support the inevitable characterization of gene drives by a comparative approach of prospective technology assessment with a focus on potential sources of risk. Therein, the hazard and exposure potential as well as uncertainties with regard to the performance of synthetic gene drives are addressed. Moreover, a quantitative analysis of their invasiveness should enable a differentiated evaluation of their power to transform wild populations.
bibliographic citation: Frieß et al. (2019) Gene drives as a new quality in GMO releases—a comparative technology characterization. PeerJ 7:e6793 https://doi.org/10.7717/peerj.6793
date submitted: 2018-11-28
date accepted: 2019-03-15
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frieß
  given name: Johannes L.
author list: Agent
  family name: von Gleich
  given name: Arnim
author list: Agent
  family name: Giese
  given name: Bernd
doi: 10.7717/peerj.6793
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: ©2019 Frieß et al.
attribution name: Frieß et al.

Applying and refining DNA analysis to determine the identity of plant material extracted from the digestive tracts of katydids
type: item
type: AcademicArticle
description: Background Feeding habits are central to animal ecology, but it is often difficult to characterize the diet of organisms that are arboreal, nocturnal, rare, or highly mobile. Genetic analysis of gut contents is a promising approach for expanding our understanding of animal feeding habits. Here, we adapt a laboratory protocol for extracting and sequencing plant material from gut contents and apply it to Neotropical forest katydids (Orthoptera: Tettigoniidae) on Barro Colorado Island (BCI) in Panama. Methods Our approach uses three chloroplast primer sets that were previously developed to identify vegetation on BCI. We describe the utility and success rate of each primer set. We then test whether there is a significant difference in the amplification and sequencing success of gut contents based on the size or sex of the katydid, the time of day that it was caught, and the color of the extracted gut contents. Results We find that there is a significant difference in sequencing success as a function of gut color. When extracts were yellow, green, or colorless the likelihood of successfully amplifying DNA ranged from ~30–60%. When gut extracts were red, orange, or brown, amplification success was exceptionally low (0–8%). Amplification success was also higher for smaller katydids and tended to be more successful in katydids that were captured earlier in the night. Strength of the amplified product was indicative of the likelihood of sequencing success, with strong bands having a high likelihood of success. By anticipating which samples are most likely to succeed, we provide information useful for estimating the number of katydids that need to be collected and minimizing the costs of purifying, amplifying, and sequencing samples that are unlikely to succeed. This approach makes it possible to understand the herbivory patterns of these trophically important katydids and can be applied more broadly to understand the diet of other tropical herbivores.
format: application/pdf
format: text/html
creator: Laurel B. Symes
creator: Nicole L. Wershoven
creator: Lars-Olaf Hoeger
creator: Jessica S. Ralston
creator: Sharon J. Martinson
creator: Hannah M. ter Hofstede
creator: Christine M. Palmer
subject: Ecology
subject: Entomology
subject: Molecular Biology
description: doi:10.7717/peerj.6808
publisher: PeerJ Inc.
rights: © 2019 Symes et al.
abstract: Background Feeding habits are central to animal ecology, but it is often difficult to characterize the diet of organisms that are arboreal, nocturnal, rare, or highly mobile. Genetic analysis of gut contents is a promising approach for expanding our understanding of animal feeding habits. Here, we adapt a laboratory protocol for extracting and sequencing plant material from gut contents and apply it to Neotropical forest katydids (Orthoptera: Tettigoniidae) on Barro Colorado Island (BCI) in Panama. Methods Our approach uses three chloroplast primer sets that were previously developed to identify vegetation on BCI. We describe the utility and success rate of each primer set. We then test whether there is a significant difference in the amplification and sequencing success of gut contents based on the size or sex of the katydid, the time of day that it was caught, and the color of the extracted gut contents. Results We find that there is a significant difference in sequencing success as a function of gut color. When extracts were yellow, green, or colorless the likelihood of successfully amplifying DNA ranged from ~30–60%. When gut extracts were red, orange, or brown, amplification success was exceptionally low (0–8%). Amplification success was also higher for smaller katydids and tended to be more successful in katydids that were captured earlier in the night. Strength of the amplified product was indicative of the likelihood of sequencing success, with strong bands having a high likelihood of success. By anticipating which samples are most likely to succeed, we provide information useful for estimating the number of katydids that need to be collected and minimizing the costs of purifying, amplifying, and sequencing samples that are unlikely to succeed. This approach makes it possible to understand the herbivory patterns of these trophically important katydids and can be applied more broadly to understand the diet of other tropical herbivores.
bibliographic citation: Symes et al. (2019) Applying and refining DNA analysis to determine the identity of plant material extracted from the digestive tracts of katydids. PeerJ 7:e6808 https://doi.org/10.7717/peerj.6808
date submitted: 2019-01-07
date accepted: 2019-03-18
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Symes
  given name: Laurel B.
author list: Agent
  family name: Wershoven
  given name: Nicole L.
author list: Agent
  family name: Hoeger
  given name: Lars-Olaf
author list: Agent
  family name: Ralston
  given name: Jessica S.
author list: Agent
  family name: Martinson
  given name: Sharon J.
author list: Agent
  family name: ter Hofstede
  given name: Hannah M.
author list: Agent
  family name: Palmer
  given name: Christine M.
doi: 10.7717/peerj.6808
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Symes et al.
attribution name: Symes et al.

Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize
type: item
type: AcademicArticle
description: Background The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana, prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation. Methods We used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F2 population derived from a cross between lowland and highland maize individuals. Results Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize. Discussion Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized.
format: application/pdf
format: text/html
creator: Eric Gonzalez-Segovia
creator: Sergio Pérez-Limon
creator: G. Carolina Cíntora-Martínez
creator: Alejandro Guerrero-Zavala
creator: Garrett M. Janzen
creator: Matthew B. Hufford
creator: Jeffrey Ross-Ibarra
creator: Ruairidh J. H. Sawers
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.6815
publisher: PeerJ Inc.
rights: © 2019 Gonzalez-Segovia et al.
abstract: Background The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana, prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation. Methods We used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F2 population derived from a cross between lowland and highland maize individuals. Results Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize. Discussion Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized.
bibliographic citation: Gonzalez-Segovia et al. (2019) Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize. PeerJ 7:e6815 https://doi.org/10.7717/peerj.6815
date submitted: 2019-01-15
date accepted: 2019-03-19
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gonzalez-Segovia
  given name: Eric
author list: Agent
  family name: Pérez-Limon
  given name: Sergio
author list: Agent
  family name: Cíntora-Martínez
  given name: G. Carolina
author list: Agent
  family name: Guerrero-Zavala
  given name: Alejandro
author list: Agent
  family name: Janzen
  given name: Garrett M.
author list: Agent
  family name: Hufford
  given name: Matthew B.
author list: Agent
  family name: Ross-Ibarra
  given name: Jeffrey
author list: Agent
  family name: Sawers
  given name: Ruairidh J. H.
doi: 10.7717/peerj.6815
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Gonzalez-Segovia et al.
attribution name: Gonzalez-Segovia et al.

Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.)
type: item
type: AcademicArticle
description: In plants, heat shock proteins (Hsps) play important roles in response to diverse stresses. Hsp20 is the major family of Hsps, but their role remains poorly understood in barley (Hordeum vulgare L.). To reveal the mechanisms of barley Hsp20s (HvHsp20s) response to stress conditions, we performed a comprehensive genome-wide analysis of the HvHsp20 gene family using bioinformatics-based methods. In total, 38 putative HvHsp20s were identified in barley and grouped into four subfamilies (C, CP, PX, and MT) based on predicted subcellular localization and their phylogenetic relationships. A sequence analysis indicated that most HvHsp20 genes have no intron or one with a relatively short length. In addition, the same group of HvHsp20 proteins in the phylogenetic tree shared similar gene structure and motifs, indicating that they were highly conserved and might have similar function. Based on RNA-seq data analysis, we showed that the transcript levels of HvHsp20 genes could be induced largely by abiotic and biotic stresses such as heat, salt, and powdery mildew. Three HvHsp20 genes, HORVU7Hr1G036540, HORVU7Hr1G036470, and HORVU3Hr1G007500, were up-regulated under biotic and abiotic stresses, suggesting their potential roles in mediating the response of barley plants to environment stresses. These results provide valuable information for further understanding the complex mechanisms of HvHsp20 gene family in barley.
format: application/pdf
format: text/html
creator: Jie Li
creator: Xinhao Liu
subject: Agricultural Science
subject: Bioinformatics
description: doi:10.7717/peerj.6832
publisher: PeerJ Inc.
rights: © 2019 Li and Liu
abstract: In plants, heat shock proteins (Hsps) play important roles in response to diverse stresses. Hsp20 is the major family of Hsps, but their role remains poorly understood in barley (Hordeum vulgare L.). To reveal the mechanisms of barley Hsp20s (HvHsp20s) response to stress conditions, we performed a comprehensive genome-wide analysis of the HvHsp20 gene family using bioinformatics-based methods. In total, 38 putative HvHsp20s were identified in barley and grouped into four subfamilies (C, CP, PX, and MT) based on predicted subcellular localization and their phylogenetic relationships. A sequence analysis indicated that most HvHsp20 genes have no intron or one with a relatively short length. In addition, the same group of HvHsp20 proteins in the phylogenetic tree shared similar gene structure and motifs, indicating that they were highly conserved and might have similar function. Based on RNA-seq data analysis, we showed that the transcript levels of HvHsp20 genes could be induced largely by abiotic and biotic stresses such as heat, salt, and powdery mildew. Three HvHsp20 genes, HORVU7Hr1G036540, HORVU7Hr1G036470, and HORVU3Hr1G007500, were up-regulated under biotic and abiotic stresses, suggesting their potential roles in mediating the response of barley plants to environment stresses. These results provide valuable information for further understanding the complex mechanisms of HvHsp20 gene family in barley.
bibliographic citation: Li et al. (2019) Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.). PeerJ 7:e6832 https://doi.org/10.7717/peerj.6832
date submitted: 2018-12-31
date accepted: 2019-03-22
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Liu
  given name: Xinhao
doi: 10.7717/peerj.6832
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Li and Liu
attribution name: Li and Liu

Prefrontal cortical activation measured by fNIRS during walking: effects of age, disease and secondary task
type: item
type: AcademicArticle
description: Background Cognitive processes are required during walking to appropriately respond to environmental and task demands. There are now many studies that have used functional Near-Infrared Spectroscopy (fNIRS) to record brain activation to investigate neural bases of cognitive contributions in gait. The aim of this systematic review was to summarize the published research regarding Prefrontal cortical (PFC) activation patterns during simple and complex walking tasks in young adults, older adults and clinical groups with balance disorders using fNIRS. Our secondary aim was to evaluate each included study based on methodological reporting criteria important for good data quality. Methods We conducted searches in June 2018 using four databases: Embase, PubMed, Scopus and PsycINFO. The strategy search used was: (((((near infrared spectroscopy) OR functional near infrared spectroscopy) OR nirs) OR fnirs) AND (((gait) OR walking) OR locomotion) AND (((((young) OR adult) OR older) OR elderly) NOT children)) AND (((Brain) OR cortex) OR cortical) for our search. The papers included met the specific review criteria: (i) used fNIRS to measure PFC activation patterns; (ii) included walking tasks (simple and complex) and; (iii) assessed young people, older people and/or clinical groups with balance disorders. Results Thirty five (describing 75 brain activation comparisons) of the 308 studies retrieved through our search met the inclusion criteria. Based on 6 methodological reporting considerations, 20 were of high quality, 10 were of medium quality and 5 were of low quality. Eleven/20 comparisons in young people, 23/37 comparisons in older people and 15/18 comparisons in clinical groups reported increased PFC activation with increased walking task complexity. The majority of comparisons that used verbal fluency, counting backwards or secondary motor tasks reported increases in PFC activation (83%, 64% and 58% of these studies, respectively). In contrast, no studies found secondary …
format: application/pdf
format: text/html
creator: Paulo H.S. Pelicioni
creator: Mylou Tijsma
creator: Stephen R. Lord
creator: Jasmine Menant
subject: Bioengineering
subject: Neuroscience
subject: Cognitive Disorders
subject: Geriatrics
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.6833
publisher: PeerJ Inc.
rights: © 2019 Pelicioni et al.
abstract: Background Cognitive processes are required during walking to appropriately respond to environmental and task demands. There are now many studies that have used functional Near-Infrared Spectroscopy (fNIRS) to record brain activation to investigate neural bases of cognitive contributions in gait. The aim of this systematic review was to summarize the published research regarding Prefrontal cortical (PFC) activation patterns during simple and complex walking tasks in young adults, older adults and clinical groups with balance disorders using fNIRS. Our secondary aim was to evaluate each included study based on methodological reporting criteria important for good data quality. Methods We conducted searches in June 2018 using four databases: Embase, PubMed, Scopus and PsycINFO. The strategy search used was: (((((near infrared spectroscopy) OR functional near infrared spectroscopy) OR nirs) OR fnirs) AND (((gait) OR walking) OR locomotion) AND (((((young) OR adult) OR older) OR elderly) NOT children)) AND (((Brain) OR cortex) OR cortical) for our search. The papers included met the specific review criteria: (i) used fNIRS to measure PFC activation patterns; (ii) included walking tasks (simple and complex) and; (iii) assessed young people, older people and/or clinical groups with balance disorders. Results Thirty five (describing 75 brain activation comparisons) of the 308 studies retrieved through our search met the inclusion criteria. Based on 6 methodological reporting considerations, 20 were of high quality, 10 were of medium quality and 5 were of low quality. Eleven/20 comparisons in young people, 23/37 comparisons in older people and 15/18 comparisons in clinical groups reported increased PFC activation with increased walking task complexity. The majority of comparisons that used verbal fluency, counting backwards or secondary motor tasks reported increases in PFC activation (83%, 64% and 58% of these studies, respectively). In contrast, no studies found secondary …
bibliographic citation: Pelicioni et al. (2019) Prefrontal cortical activation measured by fNIRS during walking: effects of age, disease and secondary task. PeerJ 7:e6833 https://doi.org/10.7717/peerj.6833
date submitted: 2018-12-03
date accepted: 2019-03-22
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pelicioni
  given name: Paulo H.S.
author list: Agent
  family name: Tijsma
  given name: Mylou
author list: Agent
  family name: Lord
  given name: Stephen R.
author list: Agent
  family name: Menant
  given name: Jasmine
doi: 10.7717/peerj.6833
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: ©2019 Pelicioni et al.
attribution name: Pelicioni et al.

Leptin-a mediates transcription of genes that participate in central endocrine and phosphatidylinositol signaling pathways in 72-hour embryonic zebrafish (Danio rerio)
type: item
type: AcademicArticle
description: We analyzed microarray expression data to highlight biological pathways that respond to embryonic zebrafish Leptin-a (lepa) signaling. Microarray expression measures for 26,046 genes were evaluated from lepa morpholino oligonucleotide “knockdown”, recombinant Leptin-a “rescue”, and uninjected control zebrafish at 72-hours post fertilization. In addition to KEGG pathway enrichment for phosphatidylinositol signaling and neuroactive ligand-receptor interactions, Gene Ontology (GO) data from lepa rescue zebrafish include JAK/STAT cascade, sensory perception, nervous system processes, and synaptic signaling. In the zebrafish lepa rescue treatment, we found changes in the expression of homologous genes that align with mammalian leptin signaling cascades including AMPK (prkaa2), ACC (acacb), Ca2+/calmodulin-dependent kinase (camkk2), PI3K (pik3r1), Ser/Thr protein kinase B (akt3), neuropeptides (agrp2, cart1), mitogen-activated protein kinase (MAPK), and insulin receptor substrate (LOC794738, LOC100537326). Notch signaling pathway and ribosome biogenesis genes respond to knockdown of Leptin-a. Differentially expressed transcription factors in lepa knockdown zebrafish regulate neurogenesis, neural differentiation, and cell fate commitment. This study presents a role for zebrafish Leptin-a in influencing expression of genes that mediate phosphatidylinositol and central endocrine signaling.
format: application/pdf
format: text/html
creator: Matthew Tuttle
creator: Mark R. Dalman
creator: Qin Liu
creator: Richard L. Londraville
subject: Evolutionary Studies
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.6848
publisher: PeerJ Inc.
rights: © 2019 Tuttle et al.
abstract: We analyzed microarray expression data to highlight biological pathways that respond to embryonic zebrafish Leptin-a (lepa) signaling. Microarray expression measures for 26,046 genes were evaluated from lepa morpholino oligonucleotide “knockdown”, recombinant Leptin-a “rescue”, and uninjected control zebrafish at 72-hours post fertilization. In addition to KEGG pathway enrichment for phosphatidylinositol signaling and neuroactive ligand-receptor interactions, Gene Ontology (GO) data from lepa rescue zebrafish include JAK/STAT cascade, sensory perception, nervous system processes, and synaptic signaling. In the zebrafish lepa rescue treatment, we found changes in the expression of homologous genes that align with mammalian leptin signaling cascades including AMPK (prkaa2), ACC (acacb), Ca2+/calmodulin-dependent kinase (camkk2), PI3K (pik3r1), Ser/Thr protein kinase B (akt3), neuropeptides (agrp2, cart1), mitogen-activated protein kinase (MAPK), and insulin receptor substrate (LOC794738, LOC100537326). Notch signaling pathway and ribosome biogenesis genes respond to knockdown of Leptin-a. Differentially expressed transcription factors in lepa knockdown zebrafish regulate neurogenesis, neural differentiation, and cell fate commitment. This study presents a role for zebrafish Leptin-a in influencing expression of genes that mediate phosphatidylinositol and central endocrine signaling.
bibliographic citation: Tuttle et al. (2019) Leptin-a mediates transcription of genes that participate in central endocrine and phosphatidylinositol signaling pathways in 72-hour embryonic zebrafish (Danio rerio). PeerJ 7:e6848 https://doi.org/10.7717/peerj.6848
date submitted: 2018-12-07
date accepted: 2019-03-26
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tuttle
  given name: Matthew
author list: Agent
  family name: Dalman
  given name: Mark R.
author list: Agent
  family name: Liu
  given name: Qin
author list: Agent
  family name: Londraville
  given name: Richard L.
doi: 10.7717/peerj.6848
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: ©2019 Tuttle et al.
attribution name: Tuttle et al.

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