PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Marine amphipods (Parhyale hawaiensis) as an alternative feed for the lined seahorse (Hippocampus erectus, Perri 1810): nutritional value and feeding trial
items: Identification and evaluation of the novel genes for transcript normalization during female gametophyte development in sugarcane
items: Vocal communication in wild chimpanzees: a call rate study
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

Marine amphipods (Parhyale hawaiensis) as an alternative feed for the lined seahorse (Hippocampus erectus, Perri 1810): nutritional value and feeding trial
type: item
type: AcademicArticle
description: Finding new alternatives to traditional live preys such as Artemia and rotifers, which do not always promote optimal fish growth and survival, is required for the successful aquaculture of highly specialized predatory species, including seahorses. The present study assessed the nutritional value of an interesting marine amphipod (Parhyale hawaiensis), and evaluates through a feeding trial its potential use as a natural prey for 10-months lined seahorse, Hippocampus erectus. P. hawaiensis showed high levels of valuable lipids (20.4–26.7% on dry matter basis) and polyunsaturated fatty acids (PUFAs) ( 26.4–41% of total FAs), including the long-chain PUFAs (LC-PUFAs) arachidonic acid (ARA) (2.9–7.7%), eicosapentaenoic acid (EPA) (4.3–6.5%) and docosahexaenoic acid (DHA) (2.1–6.2%). A comparison between wild-captured and cultured amphipods revealed a significant improvement of the amphipod FA profile in terms of DHA%, total omega-3 (n3) FAs and n3/n6 ratio when employing both a conventional amphipod culture based on a commercial shrimp diet, and, to a lesser extent, a large (3,500 L) biofloc system. Seahorses fed with frozen/wild amphipods, either singly or in combination with Artemia enriched with Super Selco® (INVE Aquaculture, Belgium) for 57 days, substantially improved seahorse growth and FA profiles in terms of ARA, EPA and DHA%, including indices associated to marine sources, such as Σn3 and n3/n6, compared to a diet based solely on enriched Artemia. These results support the use of marine amphipods as an alternative food organism for juvenile H. erectus and suggest a potential use for general marine aquaculture.
format: application/pdf
format: text/html
creator: Jorge Arturo Vargas-Abúndez
creator: Gemma Leticia Martínez-Moreno
creator: Nuno Simões
creator: Elsa Noreña-Barroso
creator: Maite Mascaró
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12288
publisher: PeerJ Inc.
rights: © 2021 Vargas-Abúndez et al.
abstract: Finding new alternatives to traditional live preys such as Artemia and rotifers, which do not always promote optimal fish growth and survival, is required for the successful aquaculture of highly specialized predatory species, including seahorses. The present study assessed the nutritional value of an interesting marine amphipod (Parhyale hawaiensis), and evaluates through a feeding trial its potential use as a natural prey for 10-months lined seahorse, Hippocampus erectus. P. hawaiensis showed high levels of valuable lipids (20.4–26.7% on dry matter basis) and polyunsaturated fatty acids (PUFAs) ( 26.4–41% of total FAs), including the long-chain PUFAs (LC-PUFAs) arachidonic acid (ARA) (2.9–7.7%), eicosapentaenoic acid (EPA) (4.3–6.5%) and docosahexaenoic acid (DHA) (2.1–6.2%). A comparison between wild-captured and cultured amphipods revealed a significant improvement of the amphipod FA profile in terms of DHA%, total omega-3 (n3) FAs and n3/n6 ratio when employing both a conventional amphipod culture based on a commercial shrimp diet, and, to a lesser extent, a large (3,500 L) biofloc system. Seahorses fed with frozen/wild amphipods, either singly or in combination with Artemia enriched with Super Selco® (INVE Aquaculture, Belgium) for 57 days, substantially improved seahorse growth and FA profiles in terms of ARA, EPA and DHA%, including indices associated to marine sources, such as Σn3 and n3/n6, compared to a diet based solely on enriched Artemia. These results support the use of marine amphipods as an alternative food organism for juvenile H. erectus and suggest a potential use for general marine aquaculture.
bibliographic citation: Vargas-Abúndez et al. (2021) Marine amphipods (Parhyale hawaiensis) as an alternative feed for the lined seahorse (Hippocampus erectus, Perri 1810): nutritional value and feeding trial. PeerJ 9:e12288 https://doi.org/10.7717/peerj.12288
date submitted: 2021-03-25
date accepted: 2021-09-21
issued: 2021-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vargas-Abúndez
  given name: Jorge Arturo
author list: Agent
  family name: Martínez-Moreno
  given name: Gemma Leticia
author list: Agent
  family name: Simões
  given name: Nuno
author list: Agent
  family name: Noreña-Barroso
  given name: Elsa
author list: Agent
  family name: Mascaró
  given name: Maite
doi: 10.7717/peerj.12288
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-19
copyright: © 2021 Vargas-Abúndez et al.
attribution name: Vargas-Abúndez et al.

Identification and evaluation of the novel genes for transcript normalization during female gametophyte development in sugarcane
type: item
type: AcademicArticle
description: Background Sugarcane (Saccharum spontaneum L.), the major sugar and biofuel feedstock crop, is cultivated mainly by vegetative propagation worldwide due to the infertility of female reproductive organs resulting in the reduction of quality and output of sugar. Deciphering the gene expression profile during ovule development will improve our understanding of the complications underlying sexual reproduction in sugarcane. Optimal reference genes are essential for elucidating the expression pattern of a given gene by quantitative real-time PCR (qRT-PCR). Method In this study, based on transcriptome data obtained from sugarcane ovule, eighteen candidate reference genes were identified, cloned, and their expression levels were evaluated across five developmental stages ovule (AC, MMC, Meiosis, Mitosis, and Mature). Results Our results indicated that FAB2 and MOR1 were the most stably expressed genes during sugarcane female gametophyte development. Moreover, two genes, cell cycle-related genes REC8 and CDK, were selected, and their feasibility was validated. This study provides important insights into the female gametophyte development of sugarcane and reports novel reference genes for gene expression research on sugarcane sexual reproduction.
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format: text/html
creator: Maokai Yan
creator: Xingyue Jin
creator: Yanhui Liu
creator: Huihuang Chen
creator: Tao Ye
creator: Zhimin Hou
creator: Zhenxia Su
creator: Yingzhi Chen
creator: Mohammad Aslam
creator: Yuan Qin
creator: Xiaoping Niu
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12298
publisher: PeerJ Inc.
rights: © 2021 Yan et al.
abstract: Background Sugarcane (Saccharum spontaneum L.), the major sugar and biofuel feedstock crop, is cultivated mainly by vegetative propagation worldwide due to the infertility of female reproductive organs resulting in the reduction of quality and output of sugar. Deciphering the gene expression profile during ovule development will improve our understanding of the complications underlying sexual reproduction in sugarcane. Optimal reference genes are essential for elucidating the expression pattern of a given gene by quantitative real-time PCR (qRT-PCR). Method In this study, based on transcriptome data obtained from sugarcane ovule, eighteen candidate reference genes were identified, cloned, and their expression levels were evaluated across five developmental stages ovule (AC, MMC, Meiosis, Mitosis, and Mature). Results Our results indicated that FAB2 and MOR1 were the most stably expressed genes during sugarcane female gametophyte development. Moreover, two genes, cell cycle-related genes REC8 and CDK, were selected, and their feasibility was validated. This study provides important insights into the female gametophyte development of sugarcane and reports novel reference genes for gene expression research on sugarcane sexual reproduction.
bibliographic citation: Yan et al. (2021) Identification and evaluation of the novel genes for transcript normalization during female gametophyte development in sugarcane. PeerJ 9:e12298 https://doi.org/10.7717/peerj.12298
date submitted: 2021-04-12
date accepted: 2021-09-21
issued: 2021-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Maokai
author list: Agent
  family name: Jin
  given name: Xingyue
author list: Agent
  family name: Liu
  given name: Yanhui
author list: Agent
  family name: Chen
  given name: Huihuang
author list: Agent
  family name: Ye
  given name: Tao
author list: Agent
  family name: Hou
  given name: Zhimin
author list: Agent
  family name: Su
  given name: Zhenxia
author list: Agent
  family name: Chen
  given name: Yingzhi
author list: Agent
  family name: Aslam
  given name: Mohammad
author list: Agent
  family name: Qin
  given name: Yuan
author list: Agent
  family name: Niu
  given name: Xiaoping
doi: 10.7717/peerj.12298
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-19
copyright: © 2021 Yan et al.
attribution name: Yan et al.

Vocal communication in wild chimpanzees: a call rate study
type: item
type: AcademicArticle
description: Background Patterns of vocal communication have implications for species conservation: a change in calling behaviour can, for instance, reflect a disturbed habitat. More importantly, call rate is a parameter that allows conservation planners to convert call density into animal density, when detecting calls with a passive acoustic monitoring system (PAM). Methods We investigated chimpanzee (Pan troglodytes schweinfurthii) call rate during the late dry season in the Issa Valley, western Tanzania by conducting focal follows. We examined the socio-ecological factors that influence call production rate of savanna woodland chimpanzees. Results We found that sex, proportion of time spent in a vegetation type, proportion of time spent travelling, time of the day, party size and swollen parous female presence had a significant effect on the call rate. Call rate differed among the different demographic classes with subadult and adult males vocalising twice as often as the subadult and adult females and three times as often as the juveniles. Applications The use of PAM and recent statistical developments to estimate animal density is promising but relies on our knowing individual call rate, often not available for many species. With the improvement in automatic call detection, we anticipate that PAM will increasingly be broadly applied to primates but also across taxa, for conservation.
format: application/pdf
format: text/html
creator: Anne-Sophie Crunchant
creator: Fiona A. Stewart
creator: Alex K. Piel
subject: Animal Behavior
subject: Anthropology
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.12326
publisher: PeerJ Inc.
rights: © 2021 Crunchant et al.
abstract: Background Patterns of vocal communication have implications for species conservation: a change in calling behaviour can, for instance, reflect a disturbed habitat. More importantly, call rate is a parameter that allows conservation planners to convert call density into animal density, when detecting calls with a passive acoustic monitoring system (PAM). Methods We investigated chimpanzee (Pan troglodytes schweinfurthii) call rate during the late dry season in the Issa Valley, western Tanzania by conducting focal follows. We examined the socio-ecological factors that influence call production rate of savanna woodland chimpanzees. Results We found that sex, proportion of time spent in a vegetation type, proportion of time spent travelling, time of the day, party size and swollen parous female presence had a significant effect on the call rate. Call rate differed among the different demographic classes with subadult and adult males vocalising twice as often as the subadult and adult females and three times as often as the juveniles. Applications The use of PAM and recent statistical developments to estimate animal density is promising but relies on our knowing individual call rate, often not available for many species. With the improvement in automatic call detection, we anticipate that PAM will increasingly be broadly applied to primates but also across taxa, for conservation.
bibliographic citation: Crunchant et al. (2021) Vocal communication in wild chimpanzees: a call rate study. PeerJ 9:e12326 https://doi.org/10.7717/peerj.12326
date submitted: 2020-10-12
date accepted: 2021-09-27
issued: 2021-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Crunchant
  given name: Anne-Sophie
author list: Agent
  family name: Stewart
  given name: Fiona A.
author list: Agent
  family name: Piel
  given name: Alex K.
doi: 10.7717/peerj.12326
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-19
copyright: ©2021 Crunchant et al.
attribution name: Crunchant et al.

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.

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