PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: Biometric indices and population parameters of three polynemid fishes from Batang Lassa Estuary of East Malaysia
items: Knowledge and attitudes towards smoking cessation counselling: an Italian cross-sectional survey on tertiary care nursing staff
items: Testis development in the Japanese eel is affected by photic signals through melatonin secretion

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.

Biometric indices and population parameters of three polynemid fishes from Batang Lassa Estuary of East Malaysia
type: item
type: AcademicArticle
description: The length-weight relationships (LWRs), condition factor (Kn), growth, mortality and exploitation status of three polynemid fishes, i.e., Filimanus xanthonema (Valenciennes, 1831), Polynemus melanochir (Valenciennes, 1831) and Polynemus paradiseus (Linnaeus, 1758) from Batang Lassa River estuary were estimated. Fish samples were caught during April 2019 to September 2020 using the ESBN (locally called Gnian) having 1.25 to 4.00 cm mesh size. The total length (TL) and body weight of each individual fish was measured to the nearest 0.1 cm and 0.01 g respectively. The growth coefficients (b) for F. xanthonema, P. melanochir and P. paradiseus, were 2.880, 2.717 and 2.724 with the R2 values 0.956, 0.972 and 0.936 respectively. Estimated growth coefficients indicated a negative allometric growth pattern for all three threadfin fishes. To date, information regarding length-weight relationships for F. xanthonema and P. melanochir is insufficient whereas the information is available for P. paradiseus. About 40–48% of fishes exhibited flat or thin body shape (Kn < 1), 48–50% were rounded or fat (Kn > 1) and only 1–3% of fishes showed proportional body shape (Kn = 1). The growth parameters L∞, K and ϕ’ were estimated at 15.75 cm, 0.95 yr−1 and 2.37 for F. xanthonema; 27.61 cm 0.87 yr−1 and 2.82 for P. melanochir; and 27.30 cm, 0.58 yr−1 and 2.64 for P. paradiseus; respectively. The estimated natural mortality (M) included 2.10, 1.69 and 1.30 yr−1; the fishing mortality (F) 0.57, 0.67 and 0.60 yr−1; and exploitation ratio (E) 0.21, 0.28 and 0.31 for F. xanthonema, P. melanochir and P. paradiseus respectively. The study concluded that the stocks are still under exploitation (E < 0.5) condition. However, the studied Batang Lassa estuary could be a potential nursery ground considering the minimum lengths of 5.0, 3.8 and 4.0 cm for F. xanthonema, P. melanochir and P. paradiseus respectively. Therefore, management initiatives are needed to escape juvenile catches.
format: application/pdf
format: text/html
creator: M. Golam Mustafa
creator: Amy Halimah Rajaee
creator: Hadi Hamli
creator: Khairul Adha A. Rahim
subject: Fisheries and Fish Science
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.12183
publisher: PeerJ Inc.
rights: © 2021 Mustafa et al.
abstract: The length-weight relationships (LWRs), condition factor (Kn), growth, mortality and exploitation status of three polynemid fishes, i.e., Filimanus xanthonema (Valenciennes, 1831), Polynemus melanochir (Valenciennes, 1831) and Polynemus paradiseus (Linnaeus, 1758) from Batang Lassa River estuary were estimated. Fish samples were caught during April 2019 to September 2020 using the ESBN (locally called Gnian) having 1.25 to 4.00 cm mesh size. The total length (TL) and body weight of each individual fish was measured to the nearest 0.1 cm and 0.01 g respectively. The growth coefficients (b) for F. xanthonema, P. melanochir and P. paradiseus, were 2.880, 2.717 and 2.724 with the R2 values 0.956, 0.972 and 0.936 respectively. Estimated growth coefficients indicated a negative allometric growth pattern for all three threadfin fishes. To date, information regarding length-weight relationships for F. xanthonema and P. melanochir is insufficient whereas the information is available for P. paradiseus. About 40–48% of fishes exhibited flat or thin body shape (Kn < 1), 48–50% were rounded or fat (Kn > 1) and only 1–3% of fishes showed proportional body shape (Kn = 1). The growth parameters L∞, K and ϕ’ were estimated at 15.75 cm, 0.95 yr−1 and 2.37 for F. xanthonema; 27.61 cm 0.87 yr−1 and 2.82 for P. melanochir; and 27.30 cm, 0.58 yr−1 and 2.64 for P. paradiseus; respectively. The estimated natural mortality (M) included 2.10, 1.69 and 1.30 yr−1; the fishing mortality (F) 0.57, 0.67 and 0.60 yr−1; and exploitation ratio (E) 0.21, 0.28 and 0.31 for F. xanthonema, P. melanochir and P. paradiseus respectively. The study concluded that the stocks are still under exploitation (E < 0.5) condition. However, the studied Batang Lassa estuary could be a potential nursery ground considering the minimum lengths of 5.0, 3.8 and 4.0 cm for F. xanthonema, P. melanochir and P. paradiseus respectively. Therefore, management initiatives are needed to escape juvenile catches.
bibliographic citation: Mustafa et al. (2021) Biometric indices and population parameters of three polynemid fishes from Batang Lassa Estuary of East Malaysia. PeerJ 9:e12183 https://doi.org/10.7717/peerj.12183
date submitted: 2021-04-13
date accepted: 2021-08-29
issued: 2021-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mustafa
  given name: M. Golam
author list: Agent
  family name: Rajaee
  given name: Amy Halimah
author list: Agent
  family name: Hamli
  given name: Hadi
author list: Agent
  family name: A. Rahim
  given name: Khairul Adha
doi: 10.7717/peerj.12183
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-15
copyright: © 2021 Mustafa et al.
attribution name: Mustafa et al.

Knowledge and attitudes towards smoking cessation counselling: an Italian cross-sectional survey on tertiary care nursing staff
type: item
type: AcademicArticle
description: Background One of the most effective smoking cessation strategies involves care and advice from nurses due to their role in the front line of treatment. Lack of education on smoking cessation counselling may be detrimental, and adequate smoking cessation training during healthcare studies is needed. Objectives The study aimed to examine nurses’ attitudes, belief, and knowledge of smoking cessation counselling; knowledge of the health risks associated with smoking was also assessed. Design A cross-sectional survey on 77 nurses from the nursing staff of Cardiology, Cardiac Intensive Care and Surgical Oncology Units of two tertiary hospitals. Methods Cronbach’s alpha was calculated to assess the questionnaire’s internal consistency, and three composite indicators were computed to assess the three dimensions of the questionnaire (knowledge, attitude, belief). Furthermore, a stepwise linear regression model was used to predict the attitude to be engaged in smoking cessation counselling, related to demographic and behavioural variables, as well as knowledge and belief indicators. The analysis was stratified by Unit. Results Nurses from three Units had a significantly different attitude score (2.55 ± 0.93 for Cardiology, 2.49 ± 0.72 for Cardiac Intensive Care and 2.09 ± 0.59 for Surgical Oncology Unit) (P-value = 0.0493). Analogously, knowledge of smoking cessation counselling was reported to be higher for Cardiac Intensive Care Unit nurses (3.19 ± 0.70) compared to Surgical Oncology nurses (2.73 ± 0.74) (P-value = 0.021). At the multivariable analysis, attitude towards smoking cessation counselling was significantly related to the nurse’s belief about counselling, for Cardiology staff (coeff = 0.74, 95% CI [0.32–1.16], P-value = 0.002) and for Surgical Oncology staff (coeff = 0.37, 95% CI [0.01–0.72], P-value = 0.042). Conclusions Incorporation of smoking cessation interventions in nurses’ and nursing managers’ education could improve the nursing staff’s attitude, belief,…
format: application/pdf
format: text/html
creator: Laura Maniscalco
creator: Salvatore Barretta
creator: Giuseppe Pizzo
creator: Domenica Matranga
subject: Nursing
subject: Public Health
subject: Science and Medical Education
description: doi:10.7717/peerj.12213
publisher: PeerJ Inc.
rights: © 2021 Maniscalco et al.
abstract: Background One of the most effective smoking cessation strategies involves care and advice from nurses due to their role in the front line of treatment. Lack of education on smoking cessation counselling may be detrimental, and adequate smoking cessation training during healthcare studies is needed. Objectives The study aimed to examine nurses’ attitudes, belief, and knowledge of smoking cessation counselling; knowledge of the health risks associated with smoking was also assessed. Design A cross-sectional survey on 77 nurses from the nursing staff of Cardiology, Cardiac Intensive Care and Surgical Oncology Units of two tertiary hospitals. Methods Cronbach’s alpha was calculated to assess the questionnaire’s internal consistency, and three composite indicators were computed to assess the three dimensions of the questionnaire (knowledge, attitude, belief). Furthermore, a stepwise linear regression model was used to predict the attitude to be engaged in smoking cessation counselling, related to demographic and behavioural variables, as well as knowledge and belief indicators. The analysis was stratified by Unit. Results Nurses from three Units had a significantly different attitude score (2.55 ± 0.93 for Cardiology, 2.49 ± 0.72 for Cardiac Intensive Care and 2.09 ± 0.59 for Surgical Oncology Unit) (P-value = 0.0493). Analogously, knowledge of smoking cessation counselling was reported to be higher for Cardiac Intensive Care Unit nurses (3.19 ± 0.70) compared to Surgical Oncology nurses (2.73 ± 0.74) (P-value = 0.021). At the multivariable analysis, attitude towards smoking cessation counselling was significantly related to the nurse’s belief about counselling, for Cardiology staff (coeff = 0.74, 95% CI [0.32–1.16], P-value = 0.002) and for Surgical Oncology staff (coeff = 0.37, 95% CI [0.01–0.72], P-value = 0.042). Conclusions Incorporation of smoking cessation interventions in nurses’ and nursing managers’ education could improve the nursing staff’s attitude, belief,…
bibliographic citation: Maniscalco et al. (2021) Knowledge and attitudes towards smoking cessation counselling: an Italian cross-sectional survey on tertiary care nursing staff. PeerJ 9:e12213 https://doi.org/10.7717/peerj.12213
date submitted: 2021-06-09
date accepted: 2021-09-05
issued: 2021-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maniscalco
  given name: Laura
author list: Agent
  family name: Barretta
  given name: Salvatore
author list: Agent
  family name: Pizzo
  given name: Giuseppe
author list: Agent
  family name: Matranga
  given name: Domenica
doi: 10.7717/peerj.12213
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-15
copyright: © 2021 Maniscalco et al.
attribution name: Maniscalco et al.

Testis development in the Japanese eel is affected by photic signals through melatonin secretion
type: item
type: AcademicArticle
description: Objective According to reported spawning characteristics of Japanese eel, Anguilla japonica, which exhibit spawning and migration patterns that are synchronized with lunar cycles and photoperiod, we hypothesized that a close association exists between specific photic signals (daylight, daylength, and moonlight) and endocrinological regulation. Given the photic control in melatonin secretion, this hypothesis was tested by investigating whether melatonin signals act as mediators relaying photic signals during testis development in the eel. Methods We examined changes in melatonin-secretion patterns using time-resolved fluorescence immunoassays in sexually immature and mature male Japanese eels under the condition of a new moon (NM) and a full moon (FM). Results The eye and plasma melatonin levels exhibited a nocturnal pattern under a 12-h light: dark cycle (12L12D) or under constant darkness (DD), but not with constant light (LL). Eye melatonin levels were similar under the 12L12D and short-day (9L15D) conditions. In the long-day condition (15L9D), secreted plasma melatonin levels were stable, whereas short-day melatonin secretion began when darkness commenced. Sexual maturation began at 8 weeks following intraperitoneal injection of human chorionic gonadotropin (hCG), and NM exposure led to significantly higher eye and plasma melatonin levels compared with those detected under FM exposure.
format: application/pdf
format: text/html
creator: Ji-Yeon Hyeon
creator: Jun-Hwan Byun
creator: Eun-Su Kim
creator: Yoon-Seong Heo
creator: Kodai Fukunaga
creator: Shin-Kwon Kim
creator: Satoshi Imamura
creator: Se-Jae Kim
creator: Akihiro Takemura
creator: Sung-Pyo Hur
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12289
publisher: PeerJ Inc.
rights: © 2021 Hyeon et al.
abstract: Objective According to reported spawning characteristics of Japanese eel, Anguilla japonica, which exhibit spawning and migration patterns that are synchronized with lunar cycles and photoperiod, we hypothesized that a close association exists between specific photic signals (daylight, daylength, and moonlight) and endocrinological regulation. Given the photic control in melatonin secretion, this hypothesis was tested by investigating whether melatonin signals act as mediators relaying photic signals during testis development in the eel. Methods We examined changes in melatonin-secretion patterns using time-resolved fluorescence immunoassays in sexually immature and mature male Japanese eels under the condition of a new moon (NM) and a full moon (FM). Results The eye and plasma melatonin levels exhibited a nocturnal pattern under a 12-h light: dark cycle (12L12D) or under constant darkness (DD), but not with constant light (LL). Eye melatonin levels were similar under the 12L12D and short-day (9L15D) conditions. In the long-day condition (15L9D), secreted plasma melatonin levels were stable, whereas short-day melatonin secretion began when darkness commenced. Sexual maturation began at 8 weeks following intraperitoneal injection of human chorionic gonadotropin (hCG), and NM exposure led to significantly higher eye and plasma melatonin levels compared with those detected under FM exposure.
bibliographic citation: Hyeon et al. (2021) Testis development in the Japanese eel is affected by photic signals through melatonin secretion. PeerJ 9:e12289 https://doi.org/10.7717/peerj.12289
date submitted: 2020-11-26
date accepted: 2021-09-21
issued: 2021-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hyeon
  given name: Ji-Yeon
author list: Agent
  family name: Byun
  given name: Jun-Hwan
author list: Agent
  family name: Kim
  given name: Eun-Su
author list: Agent
  family name: Heo
  given name: Yoon-Seong
author list: Agent
  family name: Fukunaga
  given name: Kodai
author list: Agent
  family name: Kim
  given name: Shin-Kwon
author list: Agent
  family name: Imamura
  given name: Satoshi
author list: Agent
  family name: Kim
  given name: Se-Jae
author list: Agent
  family name: Takemura
  given name: Akihiro
author list: Agent
  family name: Hur
  given name: Sung-Pyo
doi: 10.7717/peerj.12289
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-15
copyright: ©2021 Hyeon et al.
attribution name: Hyeon et al.

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