PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A noteworthy case of rewilding Chinese yew from a garden population in eastern China
items: Genome-wide association study and population structure analysis of seed-bound amino acids and total protein in watermelon
items: Perception of footwear comfort and its relationship with the foot structure among youngest-old women and men
items: Migration effects on the intestinal microbiota of Tibetans
items: Differential response of distinct copepod life history types to spring environmental forcing in Rivers Inlet, British Columbia, Canada
items: Identification and validation of a novel zinc finger protein-related gene-based prognostic model for breast cancer
items: Differential transcriptome analysis and identification of genes related to resistance to blight in three varieties of Bambusa pervariabilis × Dendrocalamopsis grandis
items: Changes in the spike and nucleocapsid protein of porcine epidemic diarrhea virus strain in Vietnam—a molecular potential for the vaccine development?
items: Variation of soil microbial carbon use efficiency (CUE) and its Influence mechanism in the context of global environmental change: a review
items: Effect of yeast and essential oil-enriched diets on critical determinants of health and immune function in Africanized Apis mellifera

A noteworthy case of rewilding Chinese yew from a garden population in eastern China
type: item
type: AcademicArticle
description: Chinese yew (Taxus wallichiana var. mairei) is ranked as a rare and endangered plant of first-grade protection of China. It has been widely cultivated in 17 provinces of China over the past few decades. However, little is known about the dispersion, rewilding, and ecological influence of Chinese yew’s offspring during cultivation. Here, we report a noteworthy case of this species, via ex situ conservation, which has successfully spread into different secondary forests, thus forming a stable regenerating population in eastern China. The establishment of this yew population, which has > 900 individuals and 7 ha area, can be ascribed to two key ecological factors: (1) secondary forest near the parent yews that provided suitable microhabitats in which progeny yews could germinate and grow, and (2) seed-foraging and transportation by native birds. Thus, this case may offer a pathway for conserving endangered Chinese Taxus species, which can attract frugivorous birds to disperse their seeds. In addition, it is necessary to monitor the growth performance of progeny population in the field.
format: application/pdf
format: text/html
creator: Kaidi Li
creator: Guangfu Zhang
creator: Ying Zhang
creator: M. Patrick Griffith
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.12341
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Chinese yew (Taxus wallichiana var. mairei) is ranked as a rare and endangered plant of first-grade protection of China. It has been widely cultivated in 17 provinces of China over the past few decades. However, little is known about the dispersion, rewilding, and ecological influence of Chinese yew’s offspring during cultivation. Here, we report a noteworthy case of this species, via ex situ conservation, which has successfully spread into different secondary forests, thus forming a stable regenerating population in eastern China. The establishment of this yew population, which has > 900 individuals and 7 ha area, can be ascribed to two key ecological factors: (1) secondary forest near the parent yews that provided suitable microhabitats in which progeny yews could germinate and grow, and (2) seed-foraging and transportation by native birds. Thus, this case may offer a pathway for conserving endangered Chinese Taxus species, which can attract frugivorous birds to disperse their seeds. In addition, it is necessary to monitor the growth performance of progeny population in the field.
bibliographic citation: Li et al. (2021) A noteworthy case of rewilding Chinese yew from a garden population in eastern China. PeerJ 9:e12341 https://doi.org/10.7717/peerj.12341
date submitted: 2021-05-22
date accepted: 2021-09-28
issued: 2021-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Kaidi
author list: Agent
  family name: Zhang
  given name: Guangfu
author list: Agent
  family name: Zhang
  given name: Ying
author list: Agent
  family name: Griffith
  given name: M. Patrick
doi: 10.7717/peerj.12341
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-19
copyright: ©2021 Li et al.
attribution name: Li et al.

Genome-wide association study and population structure analysis of seed-bound amino acids and total protein in watermelon
type: item
type: AcademicArticle
description: Background Watermelon seeds are a powerhouse of value-added traits such as proteins, free amino acids, vitamins, and essential minerals, offering a paleo-friendly dietary option. Despite the availability of substantial genetic variation, there is no sufficient information on the natural variation in seed-bound amino acids or proteins across the watermelon germplasm. This study aimed to analyze the natural variation in watermelon seed amino acids and total protein and explore underpinning genetic loci by genome-wide association study (GWAS). Methods The study evaluated the distribution of seed-bound free amino acids and total protein in 211 watermelon accessions of Citrullus spp, including 154 of Citrullus lanatus, 54 of Citrullus mucosospermus (egusi) and three of Citrullus amarus. We used the GWAS approach to associate seed phenotypes with 11,456 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS). Results Our results demonstrate a significant natural variation in different free amino acids and total protein content across accessions and geographic regions. The accessions with high protein content and proportion of essential amino acids warrant its use for value-added benefits in the food and feed industries via biofortification. The GWAS analysis identified 188 SNPs coinciding with 167 candidate genes associated with watermelon seed-bound amino acids and total protein. Clustering of SNPs associated with individual amino acids found by principal component analysis was independent of the speciation or cultivar groups and was not selected during the domestication of sweet watermelon. The identified candidate genes were involved in metabolic pathways associated with amino acid metabolism, such as Argininosuccinate synthase, explaining 7% of the variation in arginine content, which validate their functional relevance and potential for marker-assisted analysis selection. This study provides a platform for exploring potential gene loci invo…
format: application/pdf
format: text/html
creator: Vijay Joshi
creator: Padma Nimmakayala
creator: Qiushuo Song
creator: Venkata Abburi
creator: Purushothaman Natarajan
creator: Amnon Levi
creator: Kevin Crosby
creator: Umesh K. Reddy
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
subject: Nutrition
description: doi:10.7717/peerj.12343
publisher: PeerJ Inc.
rights: © 2021 Joshi et al.
abstract: Background Watermelon seeds are a powerhouse of value-added traits such as proteins, free amino acids, vitamins, and essential minerals, offering a paleo-friendly dietary option. Despite the availability of substantial genetic variation, there is no sufficient information on the natural variation in seed-bound amino acids or proteins across the watermelon germplasm. This study aimed to analyze the natural variation in watermelon seed amino acids and total protein and explore underpinning genetic loci by genome-wide association study (GWAS). Methods The study evaluated the distribution of seed-bound free amino acids and total protein in 211 watermelon accessions of Citrullus spp, including 154 of Citrullus lanatus, 54 of Citrullus mucosospermus (egusi) and three of Citrullus amarus. We used the GWAS approach to associate seed phenotypes with 11,456 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS). Results Our results demonstrate a significant natural variation in different free amino acids and total protein content across accessions and geographic regions. The accessions with high protein content and proportion of essential amino acids warrant its use for value-added benefits in the food and feed industries via biofortification. The GWAS analysis identified 188 SNPs coinciding with 167 candidate genes associated with watermelon seed-bound amino acids and total protein. Clustering of SNPs associated with individual amino acids found by principal component analysis was independent of the speciation or cultivar groups and was not selected during the domestication of sweet watermelon. The identified candidate genes were involved in metabolic pathways associated with amino acid metabolism, such as Argininosuccinate synthase, explaining 7% of the variation in arginine content, which validate their functional relevance and potential for marker-assisted analysis selection. This study provides a platform for exploring potential gene loci invo…
bibliographic citation: Joshi et al. (2021) Genome-wide association study and population structure analysis of seed-bound amino acids and total protein in watermelon. PeerJ 9:e12343 https://doi.org/10.7717/peerj.12343
date submitted: 2021-04-30
date accepted: 2021-09-28
issued: 2021-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Joshi
  given name: Vijay
author list: Agent
  family name: Nimmakayala
  given name: Padma
author list: Agent
  family name: Song
  given name: Qiushuo
author list: Agent
  family name: Abburi
  given name: Venkata
author list: Agent
  family name: Natarajan
  given name: Purushothaman
author list: Agent
  family name: Levi
  given name: Amnon
author list: Agent
  family name: Crosby
  given name: Kevin
author list: Agent
  family name: Reddy
  given name: Umesh K.
doi: 10.7717/peerj.12343
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-19
copyright: © 2021 Joshi et al.
attribution name: Joshi et al.

Perception of footwear comfort and its relationship with the foot structure among youngest-old women and men
type: item
type: AcademicArticle
description: Background Adequate footwear comfort and functionality are important regardless of age, but they become particularly important in the youngest-old women and men, mainly due to the fact that this age range is the initial period of old age with changes in shoe preferences. The aim of this study was to assess the perception of footwear comfort and its relationship with the feet structure in youngest-old women and men. Methods The cross-sectional study covered community dwellers living on their own aged 65–74 years (50 women; 50 men). The feet characteristics were measured using the CQ-ST podoscope (Electronic System, Ltd, EU), and the perception of footwear comfort was assessed with a visual analogue scale. The assessment took into account gender-specific footwear of a certain brand (Befado Dr orto). Results Statistically significant intergender differences were observed in the perception of footwear comfort with respect to the shoe heel width (p = 0.022), the arch height (p = 0.013), the overall comfort (p = 0.049) and the material properties of the footwear (p = 0.017). In women, there were statistically significant positive relationships among the heel angle (γ) and the perception of footwear comfort in terms of heel cushioning (p = 0.021), forefoot cushioning (p = 0.015), arch height (p = 0.029). In men, there was a statistically significant negative relationship of the left foot Clarke’s angle with the heel height (p = 0.043), and a positive relationship between the right foot width and the arch height (p = 0.044). Conclusions Youngest-old women, compared to men of the same age range, have a higher perception of shoe comfort in terms of the shoe heel width, the arch height, the overall comfort of the footwear and the material properties of the footwear. The appropriate profile and construction of the shoe allows for an increase in the contact surface of the foot with the shoe, hence the improvement in the perception of footwear comfort in people with lowered arch …
format: application/pdf
format: text/html
creator: Ewa Puszczalowska-Lizis
creator: Karolina Koziol
creator: Jaroslaw Omorczyk
subject: Anesthesiology and Pain Management
subject: Geriatrics
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.12385
publisher: PeerJ Inc.
rights: © 2021 Puszczalowska-Lizis et al.
abstract: Background Adequate footwear comfort and functionality are important regardless of age, but they become particularly important in the youngest-old women and men, mainly due to the fact that this age range is the initial period of old age with changes in shoe preferences. The aim of this study was to assess the perception of footwear comfort and its relationship with the feet structure in youngest-old women and men. Methods The cross-sectional study covered community dwellers living on their own aged 65–74 years (50 women; 50 men). The feet characteristics were measured using the CQ-ST podoscope (Electronic System, Ltd, EU), and the perception of footwear comfort was assessed with a visual analogue scale. The assessment took into account gender-specific footwear of a certain brand (Befado Dr orto). Results Statistically significant intergender differences were observed in the perception of footwear comfort with respect to the shoe heel width (p = 0.022), the arch height (p = 0.013), the overall comfort (p = 0.049) and the material properties of the footwear (p = 0.017). In women, there were statistically significant positive relationships among the heel angle (γ) and the perception of footwear comfort in terms of heel cushioning (p = 0.021), forefoot cushioning (p = 0.015), arch height (p = 0.029). In men, there was a statistically significant negative relationship of the left foot Clarke’s angle with the heel height (p = 0.043), and a positive relationship between the right foot width and the arch height (p = 0.044). Conclusions Youngest-old women, compared to men of the same age range, have a higher perception of shoe comfort in terms of the shoe heel width, the arch height, the overall comfort of the footwear and the material properties of the footwear. The appropriate profile and construction of the shoe allows for an increase in the contact surface of the foot with the shoe, hence the improvement in the perception of footwear comfort in people with lowered arch …
bibliographic citation: Puszczalowska-Lizis et al. (2021) Perception of footwear comfort and its relationship with the foot structure among youngest-old women and men. PeerJ 9:e12385 https://doi.org/10.7717/peerj.12385
date submitted: 2021-07-05
date accepted: 2021-10-04
issued: 2021-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Puszczalowska-Lizis
  given name: Ewa
author list: Agent
  family name: Koziol
  given name: Karolina
author list: Agent
  family name: Omorczyk
  given name: Jaroslaw
doi: 10.7717/peerj.12385
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-19
copyright: ©2021 Puszczalowska-Lizis et al.
attribution name: Puszczalowska-Lizis et al.

Migration effects on the intestinal microbiota of Tibetans
type: item
type: AcademicArticle
description: Background Diet, environment, and genomic context have a significant impact on humans’ intestinal microbiota. Moreover, migration may be accompanied by changes in human eating habits and living environment, which could, in turn, affect the intestinal microbiota. Located in southwestern China, Tibet has an average altitude of 4,000 meters and is known as the world’s roof. Xianyang is situated in the plains of central China, with an average altitude of about 400 meters. Methods To understand the association between intestinal microbiota and population migration, we collected the fecal samples from 30 Tibetan women on the first day (as TI1st), six months (as TI2nd), and ten months (as TI3rd) following migration from Tibet to Xianyang. Fecal samples were collected from 29 individuals (belonging to the Han women) as a control. The dietary information of the Tibetan women and the Han women was gathered. We performed a 16S rRNA gene survey of the collected fecal samples using Illumina MiSeq sequencing. Results Following the migration, the alpha and beta diversity of Tibetan women’s intestinal microbiota appeared unaffected. Linear discriminant analysis effect size (LEfSe) analysis showed that Klebsiella, Blautia, and Veillonella are potential biomarkers at TI1st, while Proteobacteria and Enterobacteriaceae were common in TI3rd. Finally, functional prediction by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) found no significant up-regulation or down-regulation gene pathway in the intestinal microbiota of Tibetan women after migration. The present study reveals that the higher stability in Tibetan women’s intestinal microbiota was less affected by the environment and diet, indicating that Tibetan women’s intestinal microbiota is relatively stable. The main limitations of the study were the small sample size and all volunteers were women.
format: application/pdf
format: text/html
creator: Tian Liang
creator: Fang Liu
creator: Lifeng Ma
creator: Zhiying Zhang
creator: Lijun Liu
creator: Tingting Huang
creator: Jing Li
creator: Wenxue Dong
creator: Han Zhang
creator: Yansong Li
creator: Yaqiong Jiang
creator: Weimin Ye
creator: Su Bai
creator: Longli Kang
subject: Anthropology
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.12036
publisher: PeerJ Inc.
rights: © 2021 Liang et al.
abstract: Background Diet, environment, and genomic context have a significant impact on humans’ intestinal microbiota. Moreover, migration may be accompanied by changes in human eating habits and living environment, which could, in turn, affect the intestinal microbiota. Located in southwestern China, Tibet has an average altitude of 4,000 meters and is known as the world’s roof. Xianyang is situated in the plains of central China, with an average altitude of about 400 meters. Methods To understand the association between intestinal microbiota and population migration, we collected the fecal samples from 30 Tibetan women on the first day (as TI1st), six months (as TI2nd), and ten months (as TI3rd) following migration from Tibet to Xianyang. Fecal samples were collected from 29 individuals (belonging to the Han women) as a control. The dietary information of the Tibetan women and the Han women was gathered. We performed a 16S rRNA gene survey of the collected fecal samples using Illumina MiSeq sequencing. Results Following the migration, the alpha and beta diversity of Tibetan women’s intestinal microbiota appeared unaffected. Linear discriminant analysis effect size (LEfSe) analysis showed that Klebsiella, Blautia, and Veillonella are potential biomarkers at TI1st, while Proteobacteria and Enterobacteriaceae were common in TI3rd. Finally, functional prediction by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) found no significant up-regulation or down-regulation gene pathway in the intestinal microbiota of Tibetan women after migration. The present study reveals that the higher stability in Tibetan women’s intestinal microbiota was less affected by the environment and diet, indicating that Tibetan women’s intestinal microbiota is relatively stable. The main limitations of the study were the small sample size and all volunteers were women.
bibliographic citation: Liang et al. (2021) Migration effects on the intestinal microbiota of Tibetans. PeerJ 9:e12036 https://doi.org/10.7717/peerj.12036
date submitted: 2021-01-11
date accepted: 2021-08-02
issued: 2021-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Tian
author list: Agent
  family name: Liu
  given name: Fang
author list: Agent
  family name: Ma
  given name: Lifeng
author list: Agent
  family name: Zhang
  given name: Zhiying
author list: Agent
  family name: Liu
  given name: Lijun
author list: Agent
  family name: Huang
  given name: Tingting
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Dong
  given name: Wenxue
author list: Agent
  family name: Zhang
  given name: Han
author list: Agent
  family name: Li
  given name: Yansong
author list: Agent
  family name: Jiang
  given name: Yaqiong
author list: Agent
  family name: Ye
  given name: Weimin
author list: Agent
  family name: Bai
  given name: Su
author list: Agent
  family name: Kang
  given name: Longli
doi: 10.7717/peerj.12036
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-18
copyright: ©2021 Liang et al.
attribution name: Liang et al.

Differential response of distinct copepod life history types to spring environmental forcing in Rivers Inlet, British Columbia, Canada
type: item
type: AcademicArticle
description: The temporal dynamics of five copepod species common to coastal waters of the Pacific Northwest were examined in relation to variability in spring temperature and phytoplankton dynamics in 2008, 2009, and 2010 in Rivers Inlet, British Columbia, Canada. The five species were differentiated by life history strategies. Acartia longiremis, Metridia pacifica, and Paraeuchaeta elongata remained active over most of the year. By contrast, the reproductive effort of Eucalanus bungii and Calanus marshallae was concentrated over the spring period and they spent most of the year in diapause as C5 copepodites. A delay in the timing of the spring bloom was associated with a shift in the phenology of all species. However, following the delay in spring bloom timing, recruitment to the G1 cohort was reduced only for E. bungii and C. marshallae. Recruitment successes of E. bungii and C. marshallae was also drastically reduced in 2010, an El Niño year, when spring temperatures were highest. Reasons for the observed differential response to spring environmental forcing, and its effect on upper trophic levels, are discussed.
format: application/pdf
format: text/html
creator: Desiree Tommasi
creator: Brian P.V. Hunt
creator: Evgeny A. Pakhomov
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12238
publisher: PeerJ Inc.
rights: © 2021 Tommasi et al.
abstract: The temporal dynamics of five copepod species common to coastal waters of the Pacific Northwest were examined in relation to variability in spring temperature and phytoplankton dynamics in 2008, 2009, and 2010 in Rivers Inlet, British Columbia, Canada. The five species were differentiated by life history strategies. Acartia longiremis, Metridia pacifica, and Paraeuchaeta elongata remained active over most of the year. By contrast, the reproductive effort of Eucalanus bungii and Calanus marshallae was concentrated over the spring period and they spent most of the year in diapause as C5 copepodites. A delay in the timing of the spring bloom was associated with a shift in the phenology of all species. However, following the delay in spring bloom timing, recruitment to the G1 cohort was reduced only for E. bungii and C. marshallae. Recruitment successes of E. bungii and C. marshallae was also drastically reduced in 2010, an El Niño year, when spring temperatures were highest. Reasons for the observed differential response to spring environmental forcing, and its effect on upper trophic levels, are discussed.
bibliographic citation: Tommasi et al. (2021) Differential response of distinct copepod life history types to spring environmental forcing in Rivers Inlet, British Columbia, Canada. PeerJ 9:e12238 https://doi.org/10.7717/peerj.12238
date submitted: 2021-02-25
date accepted: 2021-09-10
issued: 2021-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tommasi
  given name: Desiree
author list: Agent
  family name: Hunt
  given name: Brian P.V.
author list: Agent
  family name: Pakhomov
  given name: Evgeny A.
doi: 10.7717/peerj.12238
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-18
copyright: © 2021 Tommasi et al.
attribution name: Tommasi et al.

Identification and validation of a novel zinc finger protein-related gene-based prognostic model for breast cancer
type: item
type: AcademicArticle
description: Background Breast invasive carcinoma (BRCA) is a commonly occurring malignant tumor. Zinc finger proteins (ZNFs) constitute the largest transcription factor family in the human genome and play a mechanistic role in many cancers’ development. The prognostic value of ZNFs has yet to be approached systematically for BRCA. Methods We analyzed the data of a training set from The Cancer Genome Atlas (TCGA) database and two validation cohort from GSE20685 and METABRIC datasets, composed of 3,231 BRCA patients. After screening the differentially expressed ZNFs, univariate Cox regression, LASSO, and multiple Cox regression analysis were performed to construct a risk-based predictive model. ESTIMATE algorithm, single-sample gene set enrichment analysis (ssGSEA), and gene set enrichment analyses (GSEA) were utilized to assess the potential relations among the tumor immune microenvironment and ZNFs in BRCA. Results In this study, we profiled ZNF expression in TCGA based BRCA cohort and developed a novel prognostic model based on 14 genes with ZNF relations. This model was composed of high and low-score groups for BRCA classification. Based upon Kaplan-Meier survival curves, risk-status-based prognosis illustrated significant differences. We integrated the 14 ZNF-gene signature with patient clinicopathological data for nomogram construction with accurate 1-, 3-, and 5-overall survival predictive capabilities. We then accessed the Genomics of Drug Sensitivity in Cancer database for therapeutic drug response prediction of signature-defined BRCA patient groupings for our selected TCGA population. The signature also predicts sensitivity to chemotherapeutic and molecular-targeted agents in high- and low-risk patients afflicted with BRCA. Functional analysis suggested JAK STAT, VEGF, MAPK, NOTCH TOLL-like receptor, NOD-like receptor signaling pathways, apoptosis, and cancer-based pathways could be key for ZNF-related BRCA development. Interestingly, based on the results of ESTIMATE, s…
format: application/pdf
format: text/html
creator: Min Ye
creator: Liang Li
creator: Donghua Liu
creator: Qiuming Wang
creator: Yunuo Zhang
creator: Jinfeng Zhang
subject: Bioinformatics
subject: Oncology
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.12276
publisher: PeerJ Inc.
rights: © 2021 Ye et al.
abstract: Background Breast invasive carcinoma (BRCA) is a commonly occurring malignant tumor. Zinc finger proteins (ZNFs) constitute the largest transcription factor family in the human genome and play a mechanistic role in many cancers’ development. The prognostic value of ZNFs has yet to be approached systematically for BRCA. Methods We analyzed the data of a training set from The Cancer Genome Atlas (TCGA) database and two validation cohort from GSE20685 and METABRIC datasets, composed of 3,231 BRCA patients. After screening the differentially expressed ZNFs, univariate Cox regression, LASSO, and multiple Cox regression analysis were performed to construct a risk-based predictive model. ESTIMATE algorithm, single-sample gene set enrichment analysis (ssGSEA), and gene set enrichment analyses (GSEA) were utilized to assess the potential relations among the tumor immune microenvironment and ZNFs in BRCA. Results In this study, we profiled ZNF expression in TCGA based BRCA cohort and developed a novel prognostic model based on 14 genes with ZNF relations. This model was composed of high and low-score groups for BRCA classification. Based upon Kaplan-Meier survival curves, risk-status-based prognosis illustrated significant differences. We integrated the 14 ZNF-gene signature with patient clinicopathological data for nomogram construction with accurate 1-, 3-, and 5-overall survival predictive capabilities. We then accessed the Genomics of Drug Sensitivity in Cancer database for therapeutic drug response prediction of signature-defined BRCA patient groupings for our selected TCGA population. The signature also predicts sensitivity to chemotherapeutic and molecular-targeted agents in high- and low-risk patients afflicted with BRCA. Functional analysis suggested JAK STAT, VEGF, MAPK, NOTCH TOLL-like receptor, NOD-like receptor signaling pathways, apoptosis, and cancer-based pathways could be key for ZNF-related BRCA development. Interestingly, based on the results of ESTIMATE, s…
bibliographic citation: Ye et al. (2021) Identification and validation of a novel zinc finger protein-related gene-based prognostic model for breast cancer. PeerJ 9:e12276 https://doi.org/10.7717/peerj.12276
date submitted: 2021-06-15
date accepted: 2021-09-19
issued: 2021-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Min
author list: Agent
  family name: Li
  given name: Liang
author list: Agent
  family name: Liu
  given name: Donghua
author list: Agent
  family name: Wang
  given name: Qiuming
author list: Agent
  family name: Zhang
  given name: Yunuo
author list: Agent
  family name: Zhang
  given name: Jinfeng
doi: 10.7717/peerj.12276
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-18
copyright: © 2021 Ye et al.
attribution name: Ye et al.

Differential transcriptome analysis and identification of genes related to resistance to blight in three varieties of Bambusa pervariabilis × Dendrocalamopsis grandis
type: item
type: AcademicArticle
description: Background Bambusa pervariabilis × Dendrocalamopsis grandis is a fast-growing bamboo that is widely introduced in southern China and has great economic and ecological benefits. In recent years, a blight of B. pervariabilis × D. grandis caused by Arthrinium phaeospermum has led to much branch damage and even death of entire bamboo forests. Methods To screen for resistance genes in B. pervariabilis × D. grandis, transcriptome sequencing technology was used to compare the gene expression profiles of different varieties of B. pervariabilis × D. grandis with variable resistance and the same varieties under different treatments. The Clusters of Orthologous Groups of Proteins (COG) database; the Gene Ontology (GO) database; and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were used to annotate and analyse the differentially expressed genes. Results A total of 26,157 and 11,648 differentially expressed genes were obtained in the different varieties after inoculation with A. phaeospermum and the same varieties after inoculation A. phaeospermum or sterile water, respectively. There were 23 co-upregulated DGEs and 143 co-downregulated DEGs in #3 and #8, #6 and #8, #6 and #3. There were 50 co-upregulated DGEs and 24 co-downregulated DEGs in the same varieties after inoculation A. phaeospermum or sterile water. The results showed that many genes involved in cell wall composition synthesis, redox reactions and signal transduction were significantly different after pathogen infection. Twenty-one candidate genes for blight resistance, such as pme53, cad5, pod, gdsl-ll and Myb4l, were found. The qRT-PCR results were consistent with the sequencing results, verifying their authenticity. These results provide a foundation for the further exploration of resistance genes and their functions.
format: application/pdf
format: text/html
creator: Fengying Luo
creator: Xinmei Fang
creator: Han Liu
creator: Tianhui Zhu
creator: Shan Han
creator: Qi Peng
creator: Shujiang Li
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12301
publisher: PeerJ Inc.
rights: © 2021 Luo et al.
abstract: Background Bambusa pervariabilis × Dendrocalamopsis grandis is a fast-growing bamboo that is widely introduced in southern China and has great economic and ecological benefits. In recent years, a blight of B. pervariabilis × D. grandis caused by Arthrinium phaeospermum has led to much branch damage and even death of entire bamboo forests. Methods To screen for resistance genes in B. pervariabilis × D. grandis, transcriptome sequencing technology was used to compare the gene expression profiles of different varieties of B. pervariabilis × D. grandis with variable resistance and the same varieties under different treatments. The Clusters of Orthologous Groups of Proteins (COG) database; the Gene Ontology (GO) database; and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were used to annotate and analyse the differentially expressed genes. Results A total of 26,157 and 11,648 differentially expressed genes were obtained in the different varieties after inoculation with A. phaeospermum and the same varieties after inoculation A. phaeospermum or sterile water, respectively. There were 23 co-upregulated DGEs and 143 co-downregulated DEGs in #3 and #8, #6 and #8, #6 and #3. There were 50 co-upregulated DGEs and 24 co-downregulated DEGs in the same varieties after inoculation A. phaeospermum or sterile water. The results showed that many genes involved in cell wall composition synthesis, redox reactions and signal transduction were significantly different after pathogen infection. Twenty-one candidate genes for blight resistance, such as pme53, cad5, pod, gdsl-ll and Myb4l, were found. The qRT-PCR results were consistent with the sequencing results, verifying their authenticity. These results provide a foundation for the further exploration of resistance genes and their functions.
bibliographic citation: Luo et al. (2021) Differential transcriptome analysis and identification of genes related to resistance to blight in three varieties of Bambusa pervariabilis × Dendrocalamopsis grandis. PeerJ 9:e12301 https://doi.org/10.7717/peerj.12301
date submitted: 2021-07-01
date accepted: 2021-09-22
issued: 2021-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Fengying
author list: Agent
  family name: Fang
  given name: Xinmei
author list: Agent
  family name: Liu
  given name: Han
author list: Agent
  family name: Zhu
  given name: Tianhui
author list: Agent
  family name: Han
  given name: Shan
author list: Agent
  family name: Peng
  given name: Qi
author list: Agent
  family name: Li
  given name: Shujiang
doi: 10.7717/peerj.12301
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-18
copyright: ©2021 Luo et al.
attribution name: Luo et al.

Changes in the spike and nucleocapsid protein of porcine epidemic diarrhea virus strain in Vietnam—a molecular potential for the vaccine development?
type: item
type: AcademicArticle
description: Background Porcine epidemic diarrhea virus (PEDV) is a dangerous virus causing large piglet losses. PEDV spread rapidly between pig farms and caused the death of up to 90% of infected piglets. Current vaccines are only partially effective in providing immunity to suckling due to the rapid dissemination and ongoing evolution of PEDV. Methods In this study, the complete genome of a PEDV strain in Vietnam 2018 (IBT/VN/2018 strain) has been sequenced. The nucleotide sequence of each fragment was assembled to build a continuous complete sequence using the DNASTAR program. The complete nucleotide sequences and amino acid sequences of S, N, and ORF3 genes were aligned and analyzed to detect the mutations. Results The full-length genome was determined with 28,031 nucleotides in length which consisted of the 5′UTR, ORF1ab, S protein, ORF3, E protein, M protein, N protein, and 3′UTR region. The phylogenetic analysis showed that the IBT/VN/2018 strain was highly virulent belonged to the G2b subgroup along with the Northern American and Asian S-INDEL strains. Multiple sequence alignment of deduced amino acids revealed numerous mutations in the S, N, and ORF3 regions including one substitution 766P > L766 in the epitope SS6; two in the S0subdomain (135DN136 > 135SI136 and N144> D144); two in subdomain SHR1 at aa 1009L > M1009 and 1089S > L1089; one at aa 1279P > S1279 in subdomain SHR2 of the S protein; two at aa 364N > I364 and 378N > S378 in the N protein; four at aa 25L > S25, 70I > V70, 107C > F107, and 168D > N168 in the ORF3 protein. We identified two insertions (at aa 59NQGV62 and aa 145N) and one deletion (at aa 168DI169) in S protein. Remarkable, eight amino acid substitutions (294I > M294, 318A > S318, 335V > I335, 361A > T361, 497R > T497, 501SH502 > 501IY502, 506I > T506, 682V > I682, and 777P > L777) were found in SA subdomain. Besides, N- and O-glycosylation analysis of S, N, and ORF3 protein reveals three known sites (25G+, 123N+, and 62V+) and three novel sites (…
format: application/pdf
format: text/html
creator: Thach Xuan Tran
creator: Nguyen T.K. Lien
creator: Ha T. Thu
creator: Nguyen Dinh Duy
creator: Bui T.T. Duong
creator: Dong Van Quyen
subject: Molecular Biology
subject: Veterinary Medicine
subject: Virology
description: doi:10.7717/peerj.12329
publisher: PeerJ Inc.
rights: © 2021 Tran et al.
abstract: Background Porcine epidemic diarrhea virus (PEDV) is a dangerous virus causing large piglet losses. PEDV spread rapidly between pig farms and caused the death of up to 90% of infected piglets. Current vaccines are only partially effective in providing immunity to suckling due to the rapid dissemination and ongoing evolution of PEDV. Methods In this study, the complete genome of a PEDV strain in Vietnam 2018 (IBT/VN/2018 strain) has been sequenced. The nucleotide sequence of each fragment was assembled to build a continuous complete sequence using the DNASTAR program. The complete nucleotide sequences and amino acid sequences of S, N, and ORF3 genes were aligned and analyzed to detect the mutations. Results The full-length genome was determined with 28,031 nucleotides in length which consisted of the 5′UTR, ORF1ab, S protein, ORF3, E protein, M protein, N protein, and 3′UTR region. The phylogenetic analysis showed that the IBT/VN/2018 strain was highly virulent belonged to the G2b subgroup along with the Northern American and Asian S-INDEL strains. Multiple sequence alignment of deduced amino acids revealed numerous mutations in the S, N, and ORF3 regions including one substitution 766P > L766 in the epitope SS6; two in the S0subdomain (135DN136 > 135SI136 and N144> D144); two in subdomain SHR1 at aa 1009L > M1009 and 1089S > L1089; one at aa 1279P > S1279 in subdomain SHR2 of the S protein; two at aa 364N > I364 and 378N > S378 in the N protein; four at aa 25L > S25, 70I > V70, 107C > F107, and 168D > N168 in the ORF3 protein. We identified two insertions (at aa 59NQGV62 and aa 145N) and one deletion (at aa 168DI169) in S protein. Remarkable, eight amino acid substitutions (294I > M294, 318A > S318, 335V > I335, 361A > T361, 497R > T497, 501SH502 > 501IY502, 506I > T506, 682V > I682, and 777P > L777) were found in SA subdomain. Besides, N- and O-glycosylation analysis of S, N, and ORF3 protein reveals three known sites (25G+, 123N+, and 62V+) and three novel sites (…
bibliographic citation: Tran et al. (2021) Changes in the spike and nucleocapsid protein of porcine epidemic diarrhea virus strain in Vietnam—a molecular potential for the vaccine development?. PeerJ 9:e12329 https://doi.org/10.7717/peerj.12329
date submitted: 2021-05-20
date accepted: 2021-09-27
issued: 2021-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tran
  given name: Thach Xuan
author list: Agent
  family name: Lien
  given name: Nguyen T.K.
author list: Agent
  family name: Thu
  given name: Ha T.
author list: Agent
  family name: Duy
  given name: Nguyen Dinh
author list: Agent
  family name: Duong
  given name: Bui T.T.
author list: Agent
  family name: Quyen
  given name: Dong Van
doi: 10.7717/peerj.12329
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-18
copyright: ©2021 Tran et al.
attribution name: Tran et al.

Variation of soil microbial carbon use efficiency (CUE) and its Influence mechanism in the context of global environmental change: a review
type: item
type: AcademicArticle
description: Soil microbial carbon utilization efficiency (CUE) is the efficiency with which microorganisms convert absorbed carbon (C) into their own biomass C, also referred to as microorganism growth efficiency. Soil microbial CUE is a critical physiological and ecological parameter in the ecosystem’s C cycle, influencing the processes of C retention, turnover, soil mineralization, and greenhouse gas emission. Understanding the variation of soil microbial CUE and its influence mechanism in the context of global environmental change is critical for a better understanding of the ecosystem’s C cycle process and its response to global changes. In this review, the definition of CUE and its measurement methods are reviewed, and the research progress of soil microbial CUE variation and influencing factors is primarily reviewed and analyzed. Soil microbial CUE is usually expressed as the ratio of microbial growth and absorption, which is divided into methods based on the microbial growth rate, microbial biomass, substrate absorption rate, and substrate concentration change, and varies from 0.2 to 0.8. Thermodynamics, ecological environmental factors, substrate nutrient quality and availability, stoichiometric balance, and microbial community composition all influence this variation. In the future, soil microbial CUE research should focus on quantitative analysis of trace metabolic components, analysis of the regulation mechanism of biological-environmental interactions, and optimization of the carbon cycle model of microorganisms’ dynamic physiological response process.
format: application/pdf
format: text/html
creator: Samuel Adingo
creator: Jie-Ru Yu
creator: Liu Xuelu
creator: Xiaodan Li
creator: Sun Jing
creator: Zhang Xiaong
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.12131
publisher: PeerJ Inc.
rights: © 2021 Adingo et al.
abstract: Soil microbial carbon utilization efficiency (CUE) is the efficiency with which microorganisms convert absorbed carbon (C) into their own biomass C, also referred to as microorganism growth efficiency. Soil microbial CUE is a critical physiological and ecological parameter in the ecosystem’s C cycle, influencing the processes of C retention, turnover, soil mineralization, and greenhouse gas emission. Understanding the variation of soil microbial CUE and its influence mechanism in the context of global environmental change is critical for a better understanding of the ecosystem’s C cycle process and its response to global changes. In this review, the definition of CUE and its measurement methods are reviewed, and the research progress of soil microbial CUE variation and influencing factors is primarily reviewed and analyzed. Soil microbial CUE is usually expressed as the ratio of microbial growth and absorption, which is divided into methods based on the microbial growth rate, microbial biomass, substrate absorption rate, and substrate concentration change, and varies from 0.2 to 0.8. Thermodynamics, ecological environmental factors, substrate nutrient quality and availability, stoichiometric balance, and microbial community composition all influence this variation. In the future, soil microbial CUE research should focus on quantitative analysis of trace metabolic components, analysis of the regulation mechanism of biological-environmental interactions, and optimization of the carbon cycle model of microorganisms’ dynamic physiological response process.
bibliographic citation: Adingo et al. (2021) Variation of soil microbial carbon use efficiency (CUE) and its Influence mechanism in the context of global environmental change: a review. PeerJ 9:e12131 https://doi.org/10.7717/peerj.12131
date submitted: 2021-05-13
date accepted: 2021-08-17
issued: 2021-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adingo
  given name: Samuel
author list: Agent
  family name: Yu
  given name: Jie-Ru
author list: Agent
  family name: Xuelu
  given name: Liu
author list: Agent
  family name: Li
  given name: Xiaodan
author list: Agent
  family name: Jing
  given name: Sun
author list: Agent
  family name: Xiaong
  given name: Zhang
doi: 10.7717/peerj.12131
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-15
copyright: ©2021 Adingo et al.
attribution name: Adingo et al.

Effect of yeast and essential oil-enriched diets on critical determinants of health and immune function in Africanized Apis mellifera
type: item
type: AcademicArticle
description: Nutrition is vital for health and immune function in honey bees (Apis mellifera). The effect of diets enriched with bee-associated yeasts and essential oils of Mexican oregano (Lippia graveolens) was tested on survival, food intake, accumulated fat body tissue, and gene expression of vitellogenin (Vg), prophenoloxidase (proPO) and glucose oxidase (GOx) in newly emerged worker bees. The enriched diets were provided to bees under the premise that supplementation with yeasts or essential oils can enhance health variables and the expression of genes related to immune function in worker bees. Based on a standard pollen substitute, used as a control diet, enriched diets were formulated, five with added bee-associated yeasts (Starmerella bombicola, Starmerella etchellsii, Starmerella bombicola 2, Zygosaccharomyces mellis, and the brewers’ yeast Saccharomyces cerevisiae) and three with added essential oils from L. graveolens (carvacrol, thymol, and sesquiterpenes). Groups of bees were fed one of the diets for 9 or 12 days. Survival probability was similar in the yeast and essential oils treatments in relation to the control, but median survival was lower in the carvacrol and sesquiterpenes treatments. Food intake was higher in all the yeast treatments than in the control. Fat body percentage in individual bees was slightly lower in all treatments than in the control, with significant decreases in the thymol and carvacrol treatments. Expression of the genes Vg, proPO, and GOx was minimally affected by the yeast treatments but was adversely affected by the carvacrol and thymol treatments.
format: application/pdf
format: text/html
creator: César Canché-Collí
creator: Humberto Estrella-Maldonado
creator: Luis A. Medina-Medina
creator: Humberto Moo-Valle
creator: Luz Maria Calvo-Irabien
creator: Elisa Chan-Vivas
creator: Rosalina Rodríguez
creator: Azucena Canto
subject: Entomology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.12164
publisher: PeerJ Inc.
rights: © 2021 Canché-Collí et al.
abstract: Nutrition is vital for health and immune function in honey bees (Apis mellifera). The effect of diets enriched with bee-associated yeasts and essential oils of Mexican oregano (Lippia graveolens) was tested on survival, food intake, accumulated fat body tissue, and gene expression of vitellogenin (Vg), prophenoloxidase (proPO) and glucose oxidase (GOx) in newly emerged worker bees. The enriched diets were provided to bees under the premise that supplementation with yeasts or essential oils can enhance health variables and the expression of genes related to immune function in worker bees. Based on a standard pollen substitute, used as a control diet, enriched diets were formulated, five with added bee-associated yeasts (Starmerella bombicola, Starmerella etchellsii, Starmerella bombicola 2, Zygosaccharomyces mellis, and the brewers’ yeast Saccharomyces cerevisiae) and three with added essential oils from L. graveolens (carvacrol, thymol, and sesquiterpenes). Groups of bees were fed one of the diets for 9 or 12 days. Survival probability was similar in the yeast and essential oils treatments in relation to the control, but median survival was lower in the carvacrol and sesquiterpenes treatments. Food intake was higher in all the yeast treatments than in the control. Fat body percentage in individual bees was slightly lower in all treatments than in the control, with significant decreases in the thymol and carvacrol treatments. Expression of the genes Vg, proPO, and GOx was minimally affected by the yeast treatments but was adversely affected by the carvacrol and thymol treatments.
bibliographic citation: Canché-Collí et al. (2021) Effect of yeast and essential oil-enriched diets on critical determinants of health and immune function in Africanized Apis mellifera. PeerJ 9:e12164 https://doi.org/10.7717/peerj.12164
date submitted: 2020-11-30
date accepted: 2021-08-25
issued: 2021-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Canché-Collí
  given name: César
author list: Agent
  family name: Estrella-Maldonado
  given name: Humberto
author list: Agent
  family name: Medina-Medina
  given name: Luis A.
author list: Agent
  family name: Moo-Valle
  given name: Humberto
author list: Agent
  family name: Calvo-Irabien
  given name: Luz Maria
author list: Agent
  family name: Chan-Vivas
  given name: Elisa
author list: Agent
  family name: Rodríguez
  given name: Rosalina
author list: Agent
  family name: Canto
  given name: Azucena
doi: 10.7717/peerj.12164
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-15
copyright: ©2021 Canché-Collí et al.
attribution name: Canché-Collí et al.

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