PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Fecal microbiota transplantation mitigates bone loss by improving gut microbiome composition and gut barrier function in aged rats
items: Genome-wide identification and expression analysis of auxin response factors in peanut (Arachis hypogaea L.)
items: Factors related to job burnout among older nurses in Guizhou province, China
items: Sexual and psychological health of couples with azoospermia in the context of the COVID-19 pandemic
items: Spinal malformations in a naturally isolated Neotropical fish population
items: Development of a gene doping detection method to detect overexpressed human follistatin using an adenovirus vector in mice
items: Comparative transcriptome analyses of different Salvia miltiorrhiza varieties during the accumulation of tanshinones
items: Functional analysis of a dihydroflavonol 4-reductase gene in Ophiorrhiza japonica (OjDFR1) reveals its role in the regulation of anthocyanin
items: DNA barcode reference library construction and genetic diversity and structure analysis of Amomum villosum Lour. (Zingiberaceae) populations in Guangdong Province
items: Transcriptomic analysis reveals candidate genes for male sterility in Prunus sibirica

Fecal microbiota transplantation mitigates bone loss by improving gut microbiome composition and gut barrier function in aged rats
type: item
type: AcademicArticle
description: Background Gut microbiota (GM) dysbiosis is closely related to bone loss and the occurrence of osteoporosis in animals and human. However, little is known about the effect and the mechanisms of fecal microbiota transplantation (FMT) on bone in the treatment of senile osteoporosis. Methods Aged female rats were randomly divided into the FMT group and the control group. 3-month-old female rats were used as fecal donors. The rats were sacrificed at 12 and 24 weeks following transplantation and the serum, intestine, bone, and feces were collected for subsequent analyses. Results The bone turnover markers of osteocalcin, procollagen type 1 N-terminal propeptide (P1NP), and carboxy-terminal peptide (CTX) decreased significantly at 12 and 24 weeks following FMT (P < 0.05). At 12 weeks following transplantation, histomorphometric parameters including the bone volume (BV), trabecular bone volume fraction (BV/TV), trabecular number (Tb.N), and trabecular thickness (Tb.Th) of the FMT group were comparable to the control group. However, at 24 weeks following transplantation, these parameters of the FMT group were significantly higher than those of the control group (P < 0.05). Besides, the GM aggregated at 12 and 24 weeks following FMT, and the ecological distance was close between the rats in the FMT group and the donor rats. Alpha diversity, shown by the Shannon index and Simpson index, and the Firmicutes/Bacteroidetes ratio decreased significantly after FMT at 24 weeks. Furthermore, FMT restored the GM composition in aged rats at the phylum and family level, and the intestinal microbiota of the aged rats was similar to that of the donor rats. Correlation network analysis indirectly suggested the causality of FMT on alleviating osteoporosis. FMT improved the intestinal structure and up-regulated the expression of tight junction proteins of occludin, claudin, and ZO-1, which might be associated with the protective effects of FMT on bone. Conclusions GM transplanted from young …
format: application/pdf
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creator: Sicong Ma
creator: Ning Wang
creator: Pu Zhang
creator: Wen Wu
creator: Lingjie Fu
subject: Biochemistry
subject: Microbiology
subject: Molecular Biology
subject: Orthopedics
subject: Histology
description: doi:10.7717/peerj.12293
publisher: PeerJ Inc.
rights: © 2021 Ma et al.
abstract: Background Gut microbiota (GM) dysbiosis is closely related to bone loss and the occurrence of osteoporosis in animals and human. However, little is known about the effect and the mechanisms of fecal microbiota transplantation (FMT) on bone in the treatment of senile osteoporosis. Methods Aged female rats were randomly divided into the FMT group and the control group. 3-month-old female rats were used as fecal donors. The rats were sacrificed at 12 and 24 weeks following transplantation and the serum, intestine, bone, and feces were collected for subsequent analyses. Results The bone turnover markers of osteocalcin, procollagen type 1 N-terminal propeptide (P1NP), and carboxy-terminal peptide (CTX) decreased significantly at 12 and 24 weeks following FMT (P < 0.05). At 12 weeks following transplantation, histomorphometric parameters including the bone volume (BV), trabecular bone volume fraction (BV/TV), trabecular number (Tb.N), and trabecular thickness (Tb.Th) of the FMT group were comparable to the control group. However, at 24 weeks following transplantation, these parameters of the FMT group were significantly higher than those of the control group (P < 0.05). Besides, the GM aggregated at 12 and 24 weeks following FMT, and the ecological distance was close between the rats in the FMT group and the donor rats. Alpha diversity, shown by the Shannon index and Simpson index, and the Firmicutes/Bacteroidetes ratio decreased significantly after FMT at 24 weeks. Furthermore, FMT restored the GM composition in aged rats at the phylum and family level, and the intestinal microbiota of the aged rats was similar to that of the donor rats. Correlation network analysis indirectly suggested the causality of FMT on alleviating osteoporosis. FMT improved the intestinal structure and up-regulated the expression of tight junction proteins of occludin, claudin, and ZO-1, which might be associated with the protective effects of FMT on bone. Conclusions GM transplanted from young …
bibliographic citation: Ma et al. (2021) Fecal microbiota transplantation mitigates bone loss by improving gut microbiome composition and gut barrier function in aged rats. PeerJ 9:e12293 https://doi.org/10.7717/peerj.12293
date submitted: 2021-03-15
date accepted: 2021-09-21
issued: 2021-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Sicong
author list: Agent
  family name: Wang
  given name: Ning
author list: Agent
  family name: Zhang
  given name: Pu
author list: Agent
  family name: Wu
  given name: Wen
author list: Agent
  family name: Fu
  given name: Lingjie
doi: 10.7717/peerj.12293
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-21
copyright: © 2021 Ma et al.
attribution name: Ma et al.

Genome-wide identification and expression analysis of auxin response factors in peanut (Arachis hypogaea L.)
type: item
type: AcademicArticle
description: Auxin response factors (ARFs) are transcription factors that regulate the expression of auxin response genes, and have important functions in plant growth and development. In this study, available genome data for peanut (Arachis hypogaea L.) were used to identify AhARF genes. In total, 61 AhARFs and 23 AtARFs were divided into six groups (I–VI). Molecular structural analysis revealed that the protein members of AhARF contain at least two domains, the B3 domain and the Auxin-resp domain, and that some have a C-terminal dimerisation domain. Screening of the transcriptome data of 22 tissues of A. hypogaea cv. Tifrunner in a public database showed high expression levels of AhARF2 and AhARF6. AhARF6 was expressed more highly in the stem and branch than in the root and leaf of the wild species Arachis monticola (A. mon) and cultivated species H103. After treatment with exogenous auxin (NAA), the expression of AhARF6 was inhibited, and this inhibition was greater in A. mon than in H103. The transcriptome map revealed that the expression of AhARF6 was higher in the larger pods of H8107 and ZP06 than in the medium pods of H103 and small pods of A. mon. Moreover, AhARF6-5 was proven to be localised in the nucleus, consistent with the location of AtARF6. These results suggest that AhARF6 may play an important role in pod development in peanut.
format: application/pdf
format: text/html
creator: Peipei Li
creator: Qian Ma
creator: Chengxin Qu
creator: Shuliang Zhu
creator: Kunkun Zhao
creator: Xingli Ma
creator: Zhongfeng Li
creator: Xingguo Zhang
creator: Fangping Gong
creator: Dongmei Yin
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12319
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Auxin response factors (ARFs) are transcription factors that regulate the expression of auxin response genes, and have important functions in plant growth and development. In this study, available genome data for peanut (Arachis hypogaea L.) were used to identify AhARF genes. In total, 61 AhARFs and 23 AtARFs were divided into six groups (I–VI). Molecular structural analysis revealed that the protein members of AhARF contain at least two domains, the B3 domain and the Auxin-resp domain, and that some have a C-terminal dimerisation domain. Screening of the transcriptome data of 22 tissues of A. hypogaea cv. Tifrunner in a public database showed high expression levels of AhARF2 and AhARF6. AhARF6 was expressed more highly in the stem and branch than in the root and leaf of the wild species Arachis monticola (A. mon) and cultivated species H103. After treatment with exogenous auxin (NAA), the expression of AhARF6 was inhibited, and this inhibition was greater in A. mon than in H103. The transcriptome map revealed that the expression of AhARF6 was higher in the larger pods of H8107 and ZP06 than in the medium pods of H103 and small pods of A. mon. Moreover, AhARF6-5 was proven to be localised in the nucleus, consistent with the location of AtARF6. These results suggest that AhARF6 may play an important role in pod development in peanut.
bibliographic citation: Li et al. (2021) Genome-wide identification and expression analysis of auxin response factors in peanut (Arachis hypogaea L.). PeerJ 9:e12319 https://doi.org/10.7717/peerj.12319
date submitted: 2021-01-28
date accepted: 2021-09-25
issued: 2021-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Peipei
author list: Agent
  family name: Ma
  given name: Qian
author list: Agent
  family name: Qu
  given name: Chengxin
author list: Agent
  family name: Zhu
  given name: Shuliang
author list: Agent
  family name: Zhao
  given name: Kunkun
author list: Agent
  family name: Ma
  given name: Xingli
author list: Agent
  family name: Li
  given name: Zhongfeng
author list: Agent
  family name: Zhang
  given name: Xingguo
author list: Agent
  family name: Gong
  given name: Fangping
author list: Agent
  family name: Yin
  given name: Dongmei
doi: 10.7717/peerj.12319
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-21
copyright: © 2021 Li et al.
attribution name: Li et al.

Factors related to job burnout among older nurses in Guizhou province, China
type: item
type: AcademicArticle
description: Background The nursing workforce shortage has long been a global concern, and with the aging of nurses, this problem has become more prominent. Nursing is recognized as a high-stress occupation, and nurses experience high levels of job burnout, which reduces their professional identity. Older nurses are an indispensable talent force for nursing teams and are extremely important for the stability of nursing teams and improvement in nursing quality. Exploring the mental health and influencing factors of older nurses is very beneficial for the stability and development of nurse teams and patients’ clinical outcomes. Purpose This study aimed to investigate the level of job burnout and its influencing factors among older nurses in Guizhou Province, China and confirm the correlations among job burnout, professional identity and stress level. Methods From July to August 2019, 520 registered nurses aged over 40 years in Guizhou Province, China were surveyed through the Questionnaire Star platform. The questionnaire contained the following four parts: a general information questionnaire, the Maslach Burnout Inventory (MBI), a professional identity scale, and a job stressors scale. Results The results showed that the job burnout score of the 520 older nurses was 55.44 ± 18.62, which was moderate. The level of job burnout was positively correlated with the level of nurse stress and negatively correlated with the level of professional identity, which was influenced by various personal and social factors. Conclusions This study not only revealed that job burnout was still at a moderate level, but also revealed its current status and influencing factors among older nurses in China.
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creator: Hu Jiang
creator: Nanqu Huang
creator: Xue Jiang
creator: Jianghong Yu
creator: Yehong Zhou
creator: Hengping Pu
subject: Nursing
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12333
publisher: PeerJ Inc.
rights: © 2021 Jiang et al.
abstract: Background The nursing workforce shortage has long been a global concern, and with the aging of nurses, this problem has become more prominent. Nursing is recognized as a high-stress occupation, and nurses experience high levels of job burnout, which reduces their professional identity. Older nurses are an indispensable talent force for nursing teams and are extremely important for the stability of nursing teams and improvement in nursing quality. Exploring the mental health and influencing factors of older nurses is very beneficial for the stability and development of nurse teams and patients’ clinical outcomes. Purpose This study aimed to investigate the level of job burnout and its influencing factors among older nurses in Guizhou Province, China and confirm the correlations among job burnout, professional identity and stress level. Methods From July to August 2019, 520 registered nurses aged over 40 years in Guizhou Province, China were surveyed through the Questionnaire Star platform. The questionnaire contained the following four parts: a general information questionnaire, the Maslach Burnout Inventory (MBI), a professional identity scale, and a job stressors scale. Results The results showed that the job burnout score of the 520 older nurses was 55.44 ± 18.62, which was moderate. The level of job burnout was positively correlated with the level of nurse stress and negatively correlated with the level of professional identity, which was influenced by various personal and social factors. Conclusions This study not only revealed that job burnout was still at a moderate level, but also revealed its current status and influencing factors among older nurses in China.
bibliographic citation: Jiang et al. (2021) Factors related to job burnout among older nurses in Guizhou province, China. PeerJ 9:e12333 https://doi.org/10.7717/peerj.12333
date submitted: 2021-04-26
date accepted: 2021-09-27
issued: 2021-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Hu
author list: Agent
  family name: Huang
  given name: Nanqu
author list: Agent
  family name: Jiang
  given name: Xue
author list: Agent
  family name: Yu
  given name: Jianghong
author list: Agent
  family name: Zhou
  given name: Yehong
author list: Agent
  family name: Pu
  given name: Hengping
doi: 10.7717/peerj.12333
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-21
copyright: ©2021 Jiang et al.
attribution name: Jiang et al.

Sexual and psychological health of couples with azoospermia in the context of the COVID-19 pandemic
type: item
type: AcademicArticle
description: Background To date, there have been no reports on the sexual and psychological health of patients with azoospermia during the coronavirus disease 2019 (COVID-19) pandemic. Previous studies on the sexual health of couples with azoospermia are limited and are especially lacking in data on the wives of azoospermic men. Methods We conducted a case–control cross-sectional study between 1 July 2020 and 20 December 2020. In total, 100 couples with azoospermia comprised the experimental group and 100 couples with normozoospermia comprised the control group. The couples’ sexual health was measured using standardised sexual function questionnaires (male: International Index of Erectile Function-15 [IIEF-15] and Premature Ejaculation Diagnostic Tool [PEDT]; female: Female Sexual Function Index [FSFI]) and a self-designed questionnaire to evaluate changes in sexual behaviours (sexual satisfaction, desire, frequency of sexual activity, masturbation, and pornography use) during lockdown. The couples’ psychological health was measured using the 7-item Generalized Anxiety Disorder (GAD-7) scale and 9-item Patient Health Questionnaire (PHQ-9). The Actor–Partner Interdependence Model (APIM) was used to analyse the associations between sexual health and psychological health. Results The IIEF-15 scores (53.07 ± 11.11 vs. 57.52 ± 8.57, t = − 3.17, p = 0.00) were lower and the PEDT scores (6.58 ± 3.13 vs. 5.17 ± 2.22, t = 3.67, p = 0.00) and incidence of premature ejaculation (χ2 = 14.73, p = 0.00) were higher for men with azoospermia than for men with normozoospermia. Compared with those of wives of men with normozoospermia, the total FSFI scores (25.12 ± 5.56 vs. 26.75 ± 4.82, t = − 2.22, p = 0.03) of wives of men with azoospermia were lower. The chi-square test showed that the perceived changes in sexual satisfaction (χ2 = 7.22, p = 0.03), frequency of masturbation (χ2 = 21.96, p = 0.00), and pornography use (χ2 = 10.90, p = 0.01) were significantly different between the female groups…
format: application/pdf
format: text/html
creator: Meng Dong
creator: Yanqiang Tao
creator: Shanshan Wu
creator: Zhengtao Li
creator: Xiaobin Wang
creator: Jichun Tan
subject: Andrology
subject: Psychiatry and Psychology
subject: Women’s Health
description: doi:10.7717/peerj.12162
publisher: PeerJ Inc.
rights: © 2021 Dong et al.
abstract: Background To date, there have been no reports on the sexual and psychological health of patients with azoospermia during the coronavirus disease 2019 (COVID-19) pandemic. Previous studies on the sexual health of couples with azoospermia are limited and are especially lacking in data on the wives of azoospermic men. Methods We conducted a case–control cross-sectional study between 1 July 2020 and 20 December 2020. In total, 100 couples with azoospermia comprised the experimental group and 100 couples with normozoospermia comprised the control group. The couples’ sexual health was measured using standardised sexual function questionnaires (male: International Index of Erectile Function-15 [IIEF-15] and Premature Ejaculation Diagnostic Tool [PEDT]; female: Female Sexual Function Index [FSFI]) and a self-designed questionnaire to evaluate changes in sexual behaviours (sexual satisfaction, desire, frequency of sexual activity, masturbation, and pornography use) during lockdown. The couples’ psychological health was measured using the 7-item Generalized Anxiety Disorder (GAD-7) scale and 9-item Patient Health Questionnaire (PHQ-9). The Actor–Partner Interdependence Model (APIM) was used to analyse the associations between sexual health and psychological health. Results The IIEF-15 scores (53.07 ± 11.11 vs. 57.52 ± 8.57, t = − 3.17, p = 0.00) were lower and the PEDT scores (6.58 ± 3.13 vs. 5.17 ± 2.22, t = 3.67, p = 0.00) and incidence of premature ejaculation (χ2 = 14.73, p = 0.00) were higher for men with azoospermia than for men with normozoospermia. Compared with those of wives of men with normozoospermia, the total FSFI scores (25.12 ± 5.56 vs. 26.75 ± 4.82, t = − 2.22, p = 0.03) of wives of men with azoospermia were lower. The chi-square test showed that the perceived changes in sexual satisfaction (χ2 = 7.22, p = 0.03), frequency of masturbation (χ2 = 21.96, p = 0.00), and pornography use (χ2 = 10.90, p = 0.01) were significantly different between the female groups…
bibliographic citation: Dong et al. (2021) Sexual and psychological health of couples with azoospermia in the context of the COVID-19 pandemic. PeerJ 9:e12162 https://doi.org/10.7717/peerj.12162
date submitted: 2021-05-11
date accepted: 2021-08-25
issued: 2021-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Meng
author list: Agent
  family name: Tao
  given name: Yanqiang
author list: Agent
  family name: Wu
  given name: Shanshan
author list: Agent
  family name: Li
  given name: Zhengtao
author list: Agent
  family name: Wang
  given name: Xiaobin
author list: Agent
  family name: Tan
  given name: Jichun
doi: 10.7717/peerj.12162
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-20
copyright: ©2021 Dong et al.
attribution name: Dong et al.

Spinal malformations in a naturally isolated Neotropical fish population
type: item
type: AcademicArticle
description: Fish populations that reside in completely isolated freshwater ecosystems are rare worldwide. The Vila Velha State Park (VVSP), located in southern Brazil, is recognized for its arenitic formations called sinkholes (furnas), which are completely isolated. Fish populations within, such as those of Psalidodon aff. fasciatus, often develop vertebral malformations due to this isolation from other conspecifics and other species. In this study, we analyzed geometric morphology in digital radiographs to identify congenital deformations of Psalidodon aff. fasciatus in Furna 2 of VVSP. We found many fish with spinal deformities, including wide variation in the number of caudal vertebrae and corporal deformations related to a flattened body and spinal curvature. Females were more affected than males. We also demonstrated that these deformations reflect inbreeding and an absence of gene flow in the population. In conclusion, isolated populations such as fish species in furnas are potential models for evo-devo research.
format: application/pdf
format: text/html
creator: Franciele Fernanda Kerniske
creator: Jonathan Pena Castro
creator: Luz Elena De la Ossa-Guerra
creator: Bruna Angelina Mayer
creator: Vinícius Abilhoa
creator: Igor de Paiva Affonso
creator: Roberto Ferreira Artoni
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Ecology
subject: Evolutionary Studies
subject: Freshwater Biology
description: doi:10.7717/peerj.12239
publisher: PeerJ Inc.
rights: © 2021 Kerniske et al.
abstract: Fish populations that reside in completely isolated freshwater ecosystems are rare worldwide. The Vila Velha State Park (VVSP), located in southern Brazil, is recognized for its arenitic formations called sinkholes (furnas), which are completely isolated. Fish populations within, such as those of Psalidodon aff. fasciatus, often develop vertebral malformations due to this isolation from other conspecifics and other species. In this study, we analyzed geometric morphology in digital radiographs to identify congenital deformations of Psalidodon aff. fasciatus in Furna 2 of VVSP. We found many fish with spinal deformities, including wide variation in the number of caudal vertebrae and corporal deformations related to a flattened body and spinal curvature. Females were more affected than males. We also demonstrated that these deformations reflect inbreeding and an absence of gene flow in the population. In conclusion, isolated populations such as fish species in furnas are potential models for evo-devo research.
bibliographic citation: Kerniske et al. (2021) Spinal malformations in a naturally isolated Neotropical fish population. PeerJ 9:e12239 https://doi.org/10.7717/peerj.12239
date submitted: 2021-05-06
date accepted: 2021-09-10
issued: 2021-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kerniske
  given name: Franciele Fernanda
author list: Agent
  family name: Pena Castro
  given name: Jonathan
author list: Agent
  family name: De la Ossa-Guerra
  given name: Luz Elena
author list: Agent
  family name: Mayer
  given name: Bruna Angelina
author list: Agent
  family name: Abilhoa
  given name: Vinícius
author list: Agent
  family name: de Paiva Affonso
  given name: Igor
author list: Agent
  family name: Ferreira Artoni
  given name: Roberto
doi: 10.7717/peerj.12239
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-20
copyright: © 2021 Kerniske et al.
attribution name: Kerniske et al.

Development of a gene doping detection method to detect overexpressed human follistatin using an adenovirus vector in mice
type: item
type: AcademicArticle
description: Background Gene doping is the misuse of genome editing and gene therapy technologies for the purpose of manipulating specific genes or gene functions in order to improve athletic performance. However, a non-invasive detection method for gene doping using recombinant adenoviral (rAdV) vectors containing human follistatin (hFST) genes (rAdV<hFST>) has not yet been developed. Therefore, the aim of this study was to develop a method to detect gene doping using rAdV<hFST>. Methods First, we generated rAdV<hFST> and evaluated the overexpression of the hFST gene, FST protein, and muscle protein synthesis signaling using cell lines. Next, rAdV<hFST> was injected intravenously or intramuscularly into mice, and whole blood was collected, and hFST and cytomegalovirus promoter (CMVp) gene fragments were detected using TaqMan-quantitative polymerase chain reaction (qPCR). Finally, to confirm the specificity of the primers and the TaqMan probes, samples from each experiment were pooled, amplified using TaqMan-qPCR, and sequenced using the Sanger sequencing. Results The expression of hFST and FST proteins and muscle protein synthesis signaling significantly increased in C2C12 cells. In long-term, transgene fragments could be detected until 4 days after intravenous injection and 3 days after intramuscular injection. Finally, the Sanger sequencing confirmed that the primers and TaqMan probe specifically amplified the gene sequence of interest. Conclusions These results indicate the possibility of detecting gene doping using rAdV<hFST> using TaqMan-qPCR in blood samples. This study may contribute to the development of detection methods for gene doping using rAdV<hFST>.
format: application/pdf
format: text/html
creator: Koki Yanazawa
creator: Takehito Sugasawa
creator: Kai Aoki
creator: Takuro Nakano
creator: Yasushi Kawakami
creator: Kazuhiro Takekoshi
subject: Biochemistry
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.12285
publisher: PeerJ Inc.
rights: © 2021 Yanazawa et al.
abstract: Background Gene doping is the misuse of genome editing and gene therapy technologies for the purpose of manipulating specific genes or gene functions in order to improve athletic performance. However, a non-invasive detection method for gene doping using recombinant adenoviral (rAdV) vectors containing human follistatin (hFST) genes (rAdV<hFST>) has not yet been developed. Therefore, the aim of this study was to develop a method to detect gene doping using rAdV<hFST>. Methods First, we generated rAdV<hFST> and evaluated the overexpression of the hFST gene, FST protein, and muscle protein synthesis signaling using cell lines. Next, rAdV<hFST> was injected intravenously or intramuscularly into mice, and whole blood was collected, and hFST and cytomegalovirus promoter (CMVp) gene fragments were detected using TaqMan-quantitative polymerase chain reaction (qPCR). Finally, to confirm the specificity of the primers and the TaqMan probes, samples from each experiment were pooled, amplified using TaqMan-qPCR, and sequenced using the Sanger sequencing. Results The expression of hFST and FST proteins and muscle protein synthesis signaling significantly increased in C2C12 cells. In long-term, transgene fragments could be detected until 4 days after intravenous injection and 3 days after intramuscular injection. Finally, the Sanger sequencing confirmed that the primers and TaqMan probe specifically amplified the gene sequence of interest. Conclusions These results indicate the possibility of detecting gene doping using rAdV<hFST> using TaqMan-qPCR in blood samples. This study may contribute to the development of detection methods for gene doping using rAdV<hFST>.
bibliographic citation: Yanazawa et al. (2021) Development of a gene doping detection method to detect overexpressed human follistatin using an adenovirus vector in mice. PeerJ 9:e12285 https://doi.org/10.7717/peerj.12285
date submitted: 2021-04-17
date accepted: 2021-09-20
issued: 2021-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yanazawa
  given name: Koki
author list: Agent
  family name: Sugasawa
  given name: Takehito
author list: Agent
  family name: Aoki
  given name: Kai
author list: Agent
  family name: Nakano
  given name: Takuro
author list: Agent
  family name: Kawakami
  given name: Yasushi
author list: Agent
  family name: Takekoshi
  given name: Kazuhiro
doi: 10.7717/peerj.12285
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-20
copyright: © 2021 Yanazawa et al.
attribution name: Yanazawa et al.

Comparative transcriptome analyses of different Salvia miltiorrhiza varieties during the accumulation of tanshinones
type: item
type: AcademicArticle
description: Salvia miltiorrhiza (Labiatae) is an important medicinal plant in traditional Chinese medicine. Tanshinones are one of the main active components of S. miltiorrhiza. It has been found that the intraspecific variation of S. miltiorrhiza is relatively large and the content of tanshinones in its roots of different varieties is also relatively different. To investigate the molecular mechanisms that responsible for the differences among these varieties, the tanshinones content was determined and comparative transcriptomics analysis was carried out during the tanshinones accumulation stage. A total of 52,216 unigenes were obtained from the transcriptome by RNA sequencing among which 23,369 genes were differentially expressed among different varieties, and 2,016 genes including 18 diterpenoid biosynthesis-related genes were differentially expressed during the tanshinones accumulation stage. Functional categorization of the differentially expressed genes (DEGs) among these varieties revealed that the pathway related to photosynthesis, oxidative phosphorylation, secondary metabolite biosynthesis, diterpenoid biosynthesis, terpenoid backbone biosynthesis, sesquiterpenoid and triterpenoid biosynthesis are the most differentially regulated processes in these varieties. The six tanshinone components in these varieties showed different dynamic changes in tanshinone accumulation stage. In addition, combined with the analysis of the dynamic changes, 277 DEGs (including one dehydrogenase, three CYP450 and 24 transcription factors belonging to 12 transcription factor families) related to the accumulation of tanshinones components were obtained. Furthermore, the KEGG pathway enrichment analysis of these 277 DEGs suggested that there might be an interconnection between the primary metabolic processes, signaling processes and the accumulation of tanshinones components. This study expands the vision of intraspecific variation and gene regulation mechanism of secondary metabolite biosynth…
format: application/pdf
format: text/html
creator: Jingwen Zhou
creator: Rui Liu
creator: Min Shuai
creator: Zhu-Yun Yan
creator: Xin Chen
subject: Biodiversity
subject: Bioinformatics
subject: Ecology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.12300
publisher: PeerJ Inc.
rights: © 2021 Zhou et al.
abstract: Salvia miltiorrhiza (Labiatae) is an important medicinal plant in traditional Chinese medicine. Tanshinones are one of the main active components of S. miltiorrhiza. It has been found that the intraspecific variation of S. miltiorrhiza is relatively large and the content of tanshinones in its roots of different varieties is also relatively different. To investigate the molecular mechanisms that responsible for the differences among these varieties, the tanshinones content was determined and comparative transcriptomics analysis was carried out during the tanshinones accumulation stage. A total of 52,216 unigenes were obtained from the transcriptome by RNA sequencing among which 23,369 genes were differentially expressed among different varieties, and 2,016 genes including 18 diterpenoid biosynthesis-related genes were differentially expressed during the tanshinones accumulation stage. Functional categorization of the differentially expressed genes (DEGs) among these varieties revealed that the pathway related to photosynthesis, oxidative phosphorylation, secondary metabolite biosynthesis, diterpenoid biosynthesis, terpenoid backbone biosynthesis, sesquiterpenoid and triterpenoid biosynthesis are the most differentially regulated processes in these varieties. The six tanshinone components in these varieties showed different dynamic changes in tanshinone accumulation stage. In addition, combined with the analysis of the dynamic changes, 277 DEGs (including one dehydrogenase, three CYP450 and 24 transcription factors belonging to 12 transcription factor families) related to the accumulation of tanshinones components were obtained. Furthermore, the KEGG pathway enrichment analysis of these 277 DEGs suggested that there might be an interconnection between the primary metabolic processes, signaling processes and the accumulation of tanshinones components. This study expands the vision of intraspecific variation and gene regulation mechanism of secondary metabolite biosynth…
bibliographic citation: Zhou et al. (2021) Comparative transcriptome analyses of different Salvia miltiorrhiza varieties during the accumulation of tanshinones. PeerJ 9:e12300 https://doi.org/10.7717/peerj.12300
date submitted: 2021-03-26
date accepted: 2021-09-22
issued: 2021-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Jingwen
author list: Agent
  family name: Liu
  given name: Rui
author list: Agent
  family name: Shuai
  given name: Min
author list: Agent
  family name: Yan
  given name: Zhu-Yun
author list: Agent
  family name: Chen
  given name: Xin
doi: 10.7717/peerj.12300
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-20
copyright: © 2021 Zhou et al.
attribution name: Zhou et al.

Functional analysis of a dihydroflavonol 4-reductase gene in Ophiorrhiza japonica (OjDFR1) reveals its role in the regulation of anthocyanin
type: item
type: AcademicArticle
description: Dihydroflavonol 4-reductase (DFR), a key regulatory enzyme, participated in the biosynthesis of anthocyanins, proanthocyanidins and other flavonoids that essential for plant survival and human health. However, the role of this enzyme in Ophiorrhiza japonica is still unknown. Here, three putative DFR-like genes were firstly isolated from O. japonica. Phylogenetic analysis indicated that OjDFR1 was classified into DFR subgroup, while the rest two were clustered into other NADPH-dependent reductases. Then, functions of the three genes were further characterized. Expression analysis showed that OjDFR1 transcripts had strong correlations with the accumulation pattern of anthocyanin during the flower developmental, whereas other two were not, this suggested the potential roles of OjDFR1 in anthocyanin biosynthesis. Subsequently, all three clones were functionally expressed in Escherichia coli, but confirming that only OjDFR1 encode active DFR proteins that catalyzed the reduction of dihydroflavonols to leucoanthocyanidin. Consistant with the biochemical assay results, overexpressing OjDFR1 in Arabidopsis tt3-1 mutant successfully restored the deficiency of anthocyanin and proanthocyanidin, hinting its function as DFR in planta. Additionally, heterologous expression of OjDFR1 in transgenic tobacco contributed to darker flower color via up-regulating the expressions of endogenous NtANS and NtUFGT, which suggested that OjDFR1 was involved in flower color development. In summary, this study validates the functions of OjDFR1 and expands our understanding of anthocyanin biosynthesis in O. japonica.
format: application/pdf
format: text/html
creator: Wei Sun
creator: Nana Zhou
creator: Cai Feng
creator: Shiyu Sun
creator: Ming Tang
creator: Xiaoxin Tang
creator: Zhigang Ju
creator: Yin Yi
subject: Biochemistry
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12323
publisher: PeerJ Inc.
rights: © 2021 Sun et al.
abstract: Dihydroflavonol 4-reductase (DFR), a key regulatory enzyme, participated in the biosynthesis of anthocyanins, proanthocyanidins and other flavonoids that essential for plant survival and human health. However, the role of this enzyme in Ophiorrhiza japonica is still unknown. Here, three putative DFR-like genes were firstly isolated from O. japonica. Phylogenetic analysis indicated that OjDFR1 was classified into DFR subgroup, while the rest two were clustered into other NADPH-dependent reductases. Then, functions of the three genes were further characterized. Expression analysis showed that OjDFR1 transcripts had strong correlations with the accumulation pattern of anthocyanin during the flower developmental, whereas other two were not, this suggested the potential roles of OjDFR1 in anthocyanin biosynthesis. Subsequently, all three clones were functionally expressed in Escherichia coli, but confirming that only OjDFR1 encode active DFR proteins that catalyzed the reduction of dihydroflavonols to leucoanthocyanidin. Consistant with the biochemical assay results, overexpressing OjDFR1 in Arabidopsis tt3-1 mutant successfully restored the deficiency of anthocyanin and proanthocyanidin, hinting its function as DFR in planta. Additionally, heterologous expression of OjDFR1 in transgenic tobacco contributed to darker flower color via up-regulating the expressions of endogenous NtANS and NtUFGT, which suggested that OjDFR1 was involved in flower color development. In summary, this study validates the functions of OjDFR1 and expands our understanding of anthocyanin biosynthesis in O. japonica.
bibliographic citation: Sun et al. (2021) Functional analysis of a dihydroflavonol 4-reductase gene in Ophiorrhiza japonica (OjDFR1) reveals its role in the regulation of anthocyanin. PeerJ 9:e12323 https://doi.org/10.7717/peerj.12323
date submitted: 2021-07-29
date accepted: 2021-09-26
issued: 2021-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Wei
author list: Agent
  family name: Zhou
  given name: Nana
author list: Agent
  family name: Feng
  given name: Cai
author list: Agent
  family name: Sun
  given name: Shiyu
author list: Agent
  family name: Tang
  given name: Ming
author list: Agent
  family name: Tang
  given name: Xiaoxin
author list: Agent
  family name: Ju
  given name: Zhigang
author list: Agent
  family name: Yi
  given name: Yin
doi: 10.7717/peerj.12323
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-20
copyright: © 2021 Sun et al.
attribution name: Sun et al.

DNA barcode reference library construction and genetic diversity and structure analysis of Amomum villosum Lour. (Zingiberaceae) populations in Guangdong Province
type: item
type: AcademicArticle
description: Background Amomum villosum Lour. is the plant that produces the famous traditional Chinese medicine Amomi Fructus. Frequent habitat destruction seriously threatens A. villosum germplasm resources. Genetic diversity is very important to the optimization of germplasm resources and population protection, but the range of inherited traits within A. villosum is unclear. In this study, we analyzed the genetic diversity and genetic structures of A. villosum populations in Guangdong and constructed a local reference DNA barcode library as a resource for conservation efforts. Methods DNA barcoding and Inter-Simple Sequence Repeat (ISSR) markers were used to investigate the population genetics of A. villosum. Five universal DNA barcodes were amplified and used in the construction of a DNA barcode reference library. Parameters including percentage of polymorphic sites (PPB), number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity index (H), and Shannon’s polymorphism information index (I) were calculated for the assessment of genetic diversity. Genetic structure was revealed by measuring Nei’s gene differentiation coefficient (Gst), total population genetic diversity (Ht), intra-group genetic diversity (Hs), and gene flow (Nm). Analysis of molecular variance (AMOVA), Mantel tests, unweighted pair-group method with arithmetic mean (UPGMA) dendrogram, and principal co-ordinates (PCoA) analysis were used to elucidate the genetic differentiation and relationship among populations. Results A total of 531 sequences were obtained from the five DNA barcodes with no variable sites from any of the barcode sequences. A total of 66 ISSR bands were generated from A. villosum populations using the selected six ISSR primers; 56 bands, 84.85% for all the seven A. villosum populations were polymorphic. The A. villosum populations showed high genetic diversity (H = 0.3281, I = 0.4895), whereas the gene flow was weak (Nm = 0.6143). Gst (0.4487) and AMOVA analysis indicated…
format: application/pdf
format: text/html
creator: Lu Gong
creator: Danchun Zhang
creator: Xiaoxia Ding
creator: Juan Huang
creator: Wan Guan
creator: Xiaohui Qiu
creator: Zhihai Huang
subject: Biodiversity
subject: Molecular Biology
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.12325
publisher: PeerJ Inc.
rights: © 2021 Gong et al.
abstract: Background Amomum villosum Lour. is the plant that produces the famous traditional Chinese medicine Amomi Fructus. Frequent habitat destruction seriously threatens A. villosum germplasm resources. Genetic diversity is very important to the optimization of germplasm resources and population protection, but the range of inherited traits within A. villosum is unclear. In this study, we analyzed the genetic diversity and genetic structures of A. villosum populations in Guangdong and constructed a local reference DNA barcode library as a resource for conservation efforts. Methods DNA barcoding and Inter-Simple Sequence Repeat (ISSR) markers were used to investigate the population genetics of A. villosum. Five universal DNA barcodes were amplified and used in the construction of a DNA barcode reference library. Parameters including percentage of polymorphic sites (PPB), number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity index (H), and Shannon’s polymorphism information index (I) were calculated for the assessment of genetic diversity. Genetic structure was revealed by measuring Nei’s gene differentiation coefficient (Gst), total population genetic diversity (Ht), intra-group genetic diversity (Hs), and gene flow (Nm). Analysis of molecular variance (AMOVA), Mantel tests, unweighted pair-group method with arithmetic mean (UPGMA) dendrogram, and principal co-ordinates (PCoA) analysis were used to elucidate the genetic differentiation and relationship among populations. Results A total of 531 sequences were obtained from the five DNA barcodes with no variable sites from any of the barcode sequences. A total of 66 ISSR bands were generated from A. villosum populations using the selected six ISSR primers; 56 bands, 84.85% for all the seven A. villosum populations were polymorphic. The A. villosum populations showed high genetic diversity (H = 0.3281, I = 0.4895), whereas the gene flow was weak (Nm = 0.6143). Gst (0.4487) and AMOVA analysis indicated…
bibliographic citation: Gong et al. (2021) DNA barcode reference library construction and genetic diversity and structure analysis of Amomum villosum Lour. (Zingiberaceae) populations in Guangdong Province. PeerJ 9:e12325 https://doi.org/10.7717/peerj.12325
date submitted: 2021-06-08
date accepted: 2021-09-27
issued: 2021-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gong
  given name: Lu
author list: Agent
  family name: Zhang
  given name: Danchun
author list: Agent
  family name: Ding
  given name: Xiaoxia
author list: Agent
  family name: Huang
  given name: Juan
author list: Agent
  family name: Guan
  given name: Wan
author list: Agent
  family name: Qiu
  given name: Xiaohui
author list: Agent
  family name: Huang
  given name: Zhihai
doi: 10.7717/peerj.12325
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-20
copyright: ©2021 Gong et al.
attribution name: Gong et al.

Transcriptomic analysis reveals candidate genes for male sterility in Prunus sibirica
type: item
type: AcademicArticle
description: Background The phenomenon of male sterility widely occurs in Prunus sibirica and has a serious negative impact on yield. We identified the key stage and cause of male sterility and found differentially expressed genes related to male sterility in Prunus sibirica, and we analyzed the expression pattern of these genes. This work aimed to provide valuable reference and theoretical basis for the study of reproductive development and the mechanisms of male sterility in Prunus sibirica. Method The microstructures of male sterile flower buds and male fertile flower buds were observed by paraffin section. Transcriptome sequencing was used to screen genes related to male sterility in Prunus sibirica. Quantitative real-time PCR analysis was performed to verify the transcriptome data. Results Anther development was divided into the sporogenous cell stage, tetrad stage, microspore stage, and pollen maturity stage. Compared with male fertile flower buds, in the microspore stage, the pollen sac wall tissue in the male sterile flower buds showed no signs of degeneration. In the pollen maturity stage, the tapetum and middle layer were not fully degraded, and anther development stopped. Therefore, the microspore stage was the key stage for anther abortion , and the pollen maturity stage was the post stage for anther abortion. A total of 4,108 differentially expressed genes were identified by transcriptome analysis. Among them, 1,899 were up-regulated, and 2,209 were down-regulated in the transcriptome of male sterile flower buds. We found that “protein kinase activity”, “apoptosis process”, “calcium binding”, “cell death”, “cytochrome c oxidase activity”, “aspartate peptidase activity”, “cysteine peptidase activity” and other biological pathways such as “starch and sucrose metabolism” and “proteasome” were closely related to male sterility in Prunus sibirica. A total of 331 key genes were preliminarily screened. Conclusion The occurrence of male sterility in Prunus sibirica involved…
format: application/pdf
format: text/html
creator: Jianhua Chen
creator: Hao Xu
creator: Jian Zhang
creator: Shengjun Dong
creator: Quangang Liu
creator: Ruoxi Wang
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.12349
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Background The phenomenon of male sterility widely occurs in Prunus sibirica and has a serious negative impact on yield. We identified the key stage and cause of male sterility and found differentially expressed genes related to male sterility in Prunus sibirica, and we analyzed the expression pattern of these genes. This work aimed to provide valuable reference and theoretical basis for the study of reproductive development and the mechanisms of male sterility in Prunus sibirica. Method The microstructures of male sterile flower buds and male fertile flower buds were observed by paraffin section. Transcriptome sequencing was used to screen genes related to male sterility in Prunus sibirica. Quantitative real-time PCR analysis was performed to verify the transcriptome data. Results Anther development was divided into the sporogenous cell stage, tetrad stage, microspore stage, and pollen maturity stage. Compared with male fertile flower buds, in the microspore stage, the pollen sac wall tissue in the male sterile flower buds showed no signs of degeneration. In the pollen maturity stage, the tapetum and middle layer were not fully degraded, and anther development stopped. Therefore, the microspore stage was the key stage for anther abortion , and the pollen maturity stage was the post stage for anther abortion. A total of 4,108 differentially expressed genes were identified by transcriptome analysis. Among them, 1,899 were up-regulated, and 2,209 were down-regulated in the transcriptome of male sterile flower buds. We found that “protein kinase activity”, “apoptosis process”, “calcium binding”, “cell death”, “cytochrome c oxidase activity”, “aspartate peptidase activity”, “cysteine peptidase activity” and other biological pathways such as “starch and sucrose metabolism” and “proteasome” were closely related to male sterility in Prunus sibirica. A total of 331 key genes were preliminarily screened. Conclusion The occurrence of male sterility in Prunus sibirica involved…
bibliographic citation: Chen et al. (2021) Transcriptomic analysis reveals candidate genes for male sterility in Prunus sibirica. PeerJ 9:e12349 https://doi.org/10.7717/peerj.12349
date submitted: 2021-03-23
date accepted: 2021-09-29
issued: 2021-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jianhua
author list: Agent
  family name: Xu
  given name: Hao
author list: Agent
  family name: Zhang
  given name: Jian
author list: Agent
  family name: Dong
  given name: Shengjun
author list: Agent
  family name: Liu
  given name: Quangang
author list: Agent
  family name: Wang
  given name: Ruoxi
doi: 10.7717/peerj.12349
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-20
copyright: ©2021 Chen et al.
attribution name: Chen et al.

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