PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: LitR directly upregulates autoinducer synthesis and luminescence in Aliivibrio logei
items: LncRNAs specifically overexpressed in endocervical adenocarcinoma are associated with an unfavorable recurrence prognosis and the immune response
items: Mass mortality of pearl oyster (Pinctada fucata (Gould)) in Japan in 2019 and 2020 is caused by an unidentified infectious agent
items: Graft survival of Pinus engelmannii Carr. in relation to two grafting techniques with dormant and sprouting buds
items: Impact of urbanization on functional diversity in macromycete communities along an urban ecosystem in Southwest Mexico
items: Multiomics-based analyses of KPNA2 highlight its multiple potentials in hepatocellular carcinoma
items: Key auxin response factor (ARF) genes constraining wheat tillering of mutant dmc
items: Response of plant diversity and soil physicochemical properties to different gap sizes in a Pinus massoniana plantation
items: Cortinarius subsalor and C. tibeticisalor spp. nov., two new species from the section Delibuti from China
items: The association between serum CD4 T lymphocyte counts and surgical outcomes in HIV/AIDS patients in Guangxi, China: a retrospective cohort study

LitR directly upregulates autoinducer synthesis and luminescence in Aliivibrio logei
type: item
type: AcademicArticle
description: LitR is a master-regulator of transcription in the ainS/R and luxS/PQ quorum sensing (QS) systems of bacteria from Vibrio and Aliivibrio genera. Here, we for the first time directly investigated the influence of LitR on gene expression in the luxI/R QS system of psychrophilic bacteria Aliivibrio logei. Investigated promoters were fused with Photorhabdus luminescens luxCDABE reporter genes cassette in a heterological system of Escherichia coli cells, litR A. logei was introduced into the cells under control of Plac promoter. LitR has been shown to upregulate genes of autoinducer synthase (luxI), luciferase and reductase (luxCDABE), and this effect doesn’t depend on presence of luxR gene. To a much lesser degree, LitR induces luxR1, but not the luxR2 — the main luxI/R regulator. Enhanced litR expression leads to an increase in a LuxI-autoinducer synthesis and a subsequent LuxR-mediated activation of the luxI/R QS system. Effect of LitR on luxI transcription depends on lux-box sequence in luxI promoter even in absence of luxR (lux-box is binding site of LuxR). The last finding indicates a direct interaction of LitR with the promoter in the lux-box region. Investigation of the effect of LitR A. logei on luxI/R QS systems of mesophilic Aliivibrio fischeri and psychrophilic Aliivibrio salmonicida showed direct luxR-independent upregulation of luxI and luxCDABE genes. To a lesser degree, it induces luxR A. fischeri and luxR1 A. salmonicida. Therefore, we assume that the main role of LitR in cross-interaction of these three QS systems is stimulating the expression of luxI.
format: application/pdf
format: text/html
creator: Sergey Bazhenov
creator: Olga Melkina
creator: Vadim Fomin
creator: Ekaterina Scheglova
creator: Pavel Krasnik
creator: Svetlana Khrulnova
creator: Gennadii Zavilgelsky
creator: Ilya Manukhov
subject: Biophysics
subject: Genetics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.12030
publisher: PeerJ Inc.
rights: © 2021 Bazhenov et al.
abstract: LitR is a master-regulator of transcription in the ainS/R and luxS/PQ quorum sensing (QS) systems of bacteria from Vibrio and Aliivibrio genera. Here, we for the first time directly investigated the influence of LitR on gene expression in the luxI/R QS system of psychrophilic bacteria Aliivibrio logei. Investigated promoters were fused with Photorhabdus luminescens luxCDABE reporter genes cassette in a heterological system of Escherichia coli cells, litR A. logei was introduced into the cells under control of Plac promoter. LitR has been shown to upregulate genes of autoinducer synthase (luxI), luciferase and reductase (luxCDABE), and this effect doesn’t depend on presence of luxR gene. To a much lesser degree, LitR induces luxR1, but not the luxR2 — the main luxI/R regulator. Enhanced litR expression leads to an increase in a LuxI-autoinducer synthesis and a subsequent LuxR-mediated activation of the luxI/R QS system. Effect of LitR on luxI transcription depends on lux-box sequence in luxI promoter even in absence of luxR (lux-box is binding site of LuxR). The last finding indicates a direct interaction of LitR with the promoter in the lux-box region. Investigation of the effect of LitR A. logei on luxI/R QS systems of mesophilic Aliivibrio fischeri and psychrophilic Aliivibrio salmonicida showed direct luxR-independent upregulation of luxI and luxCDABE genes. To a lesser degree, it induces luxR A. fischeri and luxR1 A. salmonicida. Therefore, we assume that the main role of LitR in cross-interaction of these three QS systems is stimulating the expression of luxI.
bibliographic citation: Bazhenov et al. (2021) LitR directly upregulates autoinducer synthesis and luminescence in Aliivibrio logei. PeerJ 9:e12030 https://doi.org/10.7717/peerj.12030
date submitted: 2021-04-08
date accepted: 2021-07-30
issued: 2021-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bazhenov
  given name: Sergey
author list: Agent
  family name: Melkina
  given name: Olga
author list: Agent
  family name: Fomin
  given name: Vadim
author list: Agent
  family name: Scheglova
  given name: Ekaterina
author list: Agent
  family name: Krasnik
  given name: Pavel
author list: Agent
  family name: Khrulnova
  given name: Svetlana
author list: Agent
  family name: Zavilgelsky
  given name: Gennadii
author list: Agent
  family name: Manukhov
  given name: Ilya
doi: 10.7717/peerj.12030
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-21
copyright: © 2021 Bazhenov et al.
attribution name: Bazhenov et al.

LncRNAs specifically overexpressed in endocervical adenocarcinoma are associated with an unfavorable recurrence prognosis and the immune response
type: item
type: AcademicArticle
description: Background Cervical cancer is the fourth most common gynecological tumor in terms of both the incidence and mortality of females worldwide. Cervical squamous cell carcinoma (CSCC) accounts for 70–80% of cervical cancers, and endocervical adenocarcinoma (EAC) accounts for 20–25%. Unlike CSCC, EAC has worse clinical outcomes and prognosis. In this study, we explored the relationship between various types of long noncoding RNAs (lncRNAs) and pathological types of cervical cancer. Methods RNA sequencing (RNA-Seq) and clinical data from The Cancer Genome Atlas (TCGA) were used in this study. A single-sample gene set enrichment analysis (ssGSEA) and the ESTIMATE package were used to assess lncRNA activity and immune responses, respectively. RT-qPCR was performed to verify our findings. Results We explored the relationship between various types of lncRNAs and pathological types of cervical cancer. A series of long intergenic noncoding RNAs (lincRNAs) and antisense RNAs, which are the major types of lncRNAs, were identified to be specifically expressed in EAC and associated with a poor recurrence prognosis in patients with cervical cancer, suggesting that they might serve as independent prognostic markers of recurrence in patients with cervical cancer. RT-qPCR was performed to verify the 10 EAC-specific lncRNAs in cervical cancer samples we collected. Furthermore, the overexpression of these lncRNAs was positively correlated with EAC pathology levels but negatively correlated with immune responses in the microenvironment of cervical cancer. Conclusions These lncRNAs potentially represent new biomarkers for the prediction of the recurrence prognosis and help obtain deeper insights into potential immunotherapeutic approaches for treating cervical cancer.
format: application/pdf
format: text/html
creator: Yong Song
creator: Long Nie
creator: Yu-Ting Zhang
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.12116
publisher: PeerJ Inc.
rights: © 2021 Song et al.
abstract: Background Cervical cancer is the fourth most common gynecological tumor in terms of both the incidence and mortality of females worldwide. Cervical squamous cell carcinoma (CSCC) accounts for 70–80% of cervical cancers, and endocervical adenocarcinoma (EAC) accounts for 20–25%. Unlike CSCC, EAC has worse clinical outcomes and prognosis. In this study, we explored the relationship between various types of long noncoding RNAs (lncRNAs) and pathological types of cervical cancer. Methods RNA sequencing (RNA-Seq) and clinical data from The Cancer Genome Atlas (TCGA) were used in this study. A single-sample gene set enrichment analysis (ssGSEA) and the ESTIMATE package were used to assess lncRNA activity and immune responses, respectively. RT-qPCR was performed to verify our findings. Results We explored the relationship between various types of lncRNAs and pathological types of cervical cancer. A series of long intergenic noncoding RNAs (lincRNAs) and antisense RNAs, which are the major types of lncRNAs, were identified to be specifically expressed in EAC and associated with a poor recurrence prognosis in patients with cervical cancer, suggesting that they might serve as independent prognostic markers of recurrence in patients with cervical cancer. RT-qPCR was performed to verify the 10 EAC-specific lncRNAs in cervical cancer samples we collected. Furthermore, the overexpression of these lncRNAs was positively correlated with EAC pathology levels but negatively correlated with immune responses in the microenvironment of cervical cancer. Conclusions These lncRNAs potentially represent new biomarkers for the prediction of the recurrence prognosis and help obtain deeper insights into potential immunotherapeutic approaches for treating cervical cancer.
bibliographic citation: Song et al. (2021) LncRNAs specifically overexpressed in endocervical adenocarcinoma are associated with an unfavorable recurrence prognosis and the immune response. PeerJ 9:e12116 https://doi.org/10.7717/peerj.12116
date submitted: 2021-02-26
date accepted: 2021-08-15
issued: 2021-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Yong
author list: Agent
  family name: Nie
  given name: Long
author list: Agent
  family name: Zhang
  given name: Yu-Ting
doi: 10.7717/peerj.12116
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-21
copyright: © 2021 Song et al.
attribution name: Song et al.

Mass mortality of pearl oyster (Pinctada fucata (Gould)) in Japan in 2019 and 2020 is caused by an unidentified infectious agent
type: item
type: AcademicArticle
description: Mass mortality of 0-year-old pearl oysters, Pinctada fucata (Gould), and anomalies in adults were observed in Japan’s major pearl farming areas in the summer of 2019 and 2020. Although adult oyster mortality was low, both adult and juvenile oysters underwent atrophy of the soft body, detachment of the mantle from nacre (the shiny inner surface of the valves), deposition of brownish material on the nacre, and loss of nacre luster. Infection trials were conducted to verify the involvement of pathogens in this phenomenon. Healthy adult pearl oysters were obtained from areas where this disease had not occurred to use as the recipients. The sources of infection were either affected adult oysters with atrophied soft bodies or batches of juveniles in which mortality had reached conspicuous levels. Transmission of the disease to the healthy oysters were tested either by cohabitation with affected oysters or by injections of the hemolymph of affected animals. The injection infection test examined the effects of filtration and chloroform exposure on the pathogen. Occurrence of the disease was confirmed by the appearance of brown deposits on the nacre and loss of nacre luster. The abnormalities of nacre were clearly reproduced in recipient shells in three out of four cohabitation trials with affected oysters. The disease was also reproduced in six out of six injection trails either with hemolymph filtered through 100 nm filter or with hemolymph treated with chloroform. In a serial passage with hemolymph injections, the disease was successfully transmitted through eight passages. These results suggest that the etiology of the disease is a non-enveloped virus with a diameter ≤100 nm.
format: application/pdf
format: text/html
creator: Tomomasa Matsuyama
creator: Satoshi Miwa
creator: Tohru Mekata
creator: Yuta Matsuura
creator: Tomokazu Takano
creator: Chihaya Nakayasu
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12180
publisher: PeerJ Inc.
rights: © 2021 Matsuyama et al.
abstract: Mass mortality of 0-year-old pearl oysters, Pinctada fucata (Gould), and anomalies in adults were observed in Japan’s major pearl farming areas in the summer of 2019 and 2020. Although adult oyster mortality was low, both adult and juvenile oysters underwent atrophy of the soft body, detachment of the mantle from nacre (the shiny inner surface of the valves), deposition of brownish material on the nacre, and loss of nacre luster. Infection trials were conducted to verify the involvement of pathogens in this phenomenon. Healthy adult pearl oysters were obtained from areas where this disease had not occurred to use as the recipients. The sources of infection were either affected adult oysters with atrophied soft bodies or batches of juveniles in which mortality had reached conspicuous levels. Transmission of the disease to the healthy oysters were tested either by cohabitation with affected oysters or by injections of the hemolymph of affected animals. The injection infection test examined the effects of filtration and chloroform exposure on the pathogen. Occurrence of the disease was confirmed by the appearance of brown deposits on the nacre and loss of nacre luster. The abnormalities of nacre were clearly reproduced in recipient shells in three out of four cohabitation trials with affected oysters. The disease was also reproduced in six out of six injection trails either with hemolymph filtered through 100 nm filter or with hemolymph treated with chloroform. In a serial passage with hemolymph injections, the disease was successfully transmitted through eight passages. These results suggest that the etiology of the disease is a non-enveloped virus with a diameter ≤100 nm.
bibliographic citation: Matsuyama et al. (2021) Mass mortality of pearl oyster (Pinctada fucata (Gould)) in Japan in 2019 and 2020 is caused by an unidentified infectious agent. PeerJ 9:e12180 https://doi.org/10.7717/peerj.12180
date submitted: 2021-06-03
date accepted: 2021-08-29
issued: 2021-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matsuyama
  given name: Tomomasa
author list: Agent
  family name: Miwa
  given name: Satoshi
author list: Agent
  family name: Mekata
  given name: Tohru
author list: Agent
  family name: Matsuura
  given name: Yuta
author list: Agent
  family name: Takano
  given name: Tomokazu
author list: Agent
  family name: Nakayasu
  given name: Chihaya
doi: 10.7717/peerj.12180
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-21
copyright: © 2021 Matsuyama et al.
attribution name: Matsuyama et al.

Graft survival of Pinus engelmannii Carr. in relation to two grafting techniques with dormant and sprouting buds
type: item
type: AcademicArticle
description: Developing methods for successfully grafting forest species will be helpful for establishing asexual seed orchards and increasing the success of forest genetic improvement programs in Mexico. In this study we investigated the effects of two grafting techniques (side veneer and top cleft) and two phenological stages of the scion buds (end of latency and beginning of sprouting), in combination with other seven grafting variables, on the sprouting and survival of 120 intraspecific grafts of Pinus engelmannii Carr. The scions used for grafting were taken from a 5.5-year-old commercial forest plantation. The first grafting was performed on January 18 (buds at the end of dormancy) and the second on February 21 (buds at the beginning of sprouting). The data were examined by analysis of variance and a test of means and were fitted to two survival models (the Weibull’s accelerated failure time and the Cox’s proportional hazards model) and the respective hazard ratios were calculated. Survival was higher in the top cleft grafts made with buds at the end of latency, with 80% sprouting and an estimated average survival time of between 164 and 457 days after the end of the 6-month evaluation period. Four variables (grafting technique, phenological stage of the scion buds, scion diameter and rootstock height) significantly affected the risk of graft death in both survival models. Use of top cleft grafts with buds at the end of the latency stage, combined with scion diameters smaller than 11.4 mm and rootstock heights greater than 58.5 cm, was associated with a lower risk of death.
format: application/pdf
format: text/html
creator: Alberto Pérez-Luna
creator: José Ciro Hernández-Díaz
creator: Christian Wehenkel
creator: Sergio Leonel Simental-Rodríguez
creator: Javier Hernández-Velasco
creator: José Ángel Prieto-Ruíz
subject: Genetics
subject: Plant Science
subject: Statistics
subject: Forestry
description: doi:10.7717/peerj.12182
publisher: PeerJ Inc.
rights: © 2021 Pérez-Luna et al.
abstract: Developing methods for successfully grafting forest species will be helpful for establishing asexual seed orchards and increasing the success of forest genetic improvement programs in Mexico. In this study we investigated the effects of two grafting techniques (side veneer and top cleft) and two phenological stages of the scion buds (end of latency and beginning of sprouting), in combination with other seven grafting variables, on the sprouting and survival of 120 intraspecific grafts of Pinus engelmannii Carr. The scions used for grafting were taken from a 5.5-year-old commercial forest plantation. The first grafting was performed on January 18 (buds at the end of dormancy) and the second on February 21 (buds at the beginning of sprouting). The data were examined by analysis of variance and a test of means and were fitted to two survival models (the Weibull’s accelerated failure time and the Cox’s proportional hazards model) and the respective hazard ratios were calculated. Survival was higher in the top cleft grafts made with buds at the end of latency, with 80% sprouting and an estimated average survival time of between 164 and 457 days after the end of the 6-month evaluation period. Four variables (grafting technique, phenological stage of the scion buds, scion diameter and rootstock height) significantly affected the risk of graft death in both survival models. Use of top cleft grafts with buds at the end of the latency stage, combined with scion diameters smaller than 11.4 mm and rootstock heights greater than 58.5 cm, was associated with a lower risk of death.
bibliographic citation: Pérez-Luna et al. (2021) Graft survival of Pinus engelmannii Carr. in relation to two grafting techniques with dormant and sprouting buds. PeerJ 9:e12182 https://doi.org/10.7717/peerj.12182
date submitted: 2021-02-09
date accepted: 2021-08-29
issued: 2021-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pérez-Luna
  given name: Alberto
author list: Agent
  family name: Hernández-Díaz
  given name: José Ciro
author list: Agent
  family name: Wehenkel
  given name: Christian
author list: Agent
  family name: Simental-Rodríguez
  given name: Sergio Leonel
author list: Agent
  family name: Hernández-Velasco
  given name: Javier
author list: Agent
  family name: Prieto-Ruíz
  given name: José Ángel
doi: 10.7717/peerj.12182
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-21
copyright: © 2021 Pérez-Luna et al.
attribution name: Pérez-Luna et al.

Impact of urbanization on functional diversity in macromycete communities along an urban ecosystem in Southwest Mexico
type: item
type: AcademicArticle
description: Macromycetes are a group of fungi characterized by the production of fruit bodies and are highly relevant in most terrestrial ecosystems as pathogens, mutualists, and organic matter decomposers. Habitat transformation can drastically alter macromycete communities and diminish the contribution of these organisms to ecosystem functioning; however, knowledge on the effect of urbanization on macrofungal communities is scarce. Diversity metrics based on functional traits of macromycete species have shown to be valuable tools to predict how species contribute to ecosystem functionality since traits determine the performance of species in ecosystems. The aim of this study was to assess patterns of species richness, functional diversity, and composition of macrofungi in an urban ecosystem in Southwest Mexico, and to identify microclimatic, environmental, and urban factors related to these patterns in order to infer the effect of urbanization on macromycete communities. We selected four oak forests along an urbanization gradient and established a permanent sampling area of 0.1 ha at each site. Macromycete sampling was carried out every week from June to October 2017. The indices used to measure functional diversity were functional richness (FRic), functional divergence (FDig), and functional evenness (FEve). The metric used to assess variation of macrofungal ecological function along the study area was the functional value. We recorded a total of 134 macromycete species and 223 individuals. Our results indicated a decline of species richness with increased urbanization level related mainly to microclimatic variables, and a high turnover of species composition among study sites, which appears to be related to microclimatic and urbanization variables. FRic decreased with urbanization level, indicating that some of the available resources in the niche space within the most urbanized sites are not being utilized. FDig increased with urbanization, which suggests a high degree of …
format: application/pdf
format: text/html
creator: Marko Gómez-Hernández
creator: Emily Avendaño-Villegas
creator: María Toledo-Garibaldi
creator: Etelvina Gándara
subject: Biodiversity
subject: Ecology
subject: Mycology
description: doi:10.7717/peerj.12191
publisher: PeerJ Inc.
rights: © 2021 Gómez-Hernández et al.
abstract: Macromycetes are a group of fungi characterized by the production of fruit bodies and are highly relevant in most terrestrial ecosystems as pathogens, mutualists, and organic matter decomposers. Habitat transformation can drastically alter macromycete communities and diminish the contribution of these organisms to ecosystem functioning; however, knowledge on the effect of urbanization on macrofungal communities is scarce. Diversity metrics based on functional traits of macromycete species have shown to be valuable tools to predict how species contribute to ecosystem functionality since traits determine the performance of species in ecosystems. The aim of this study was to assess patterns of species richness, functional diversity, and composition of macrofungi in an urban ecosystem in Southwest Mexico, and to identify microclimatic, environmental, and urban factors related to these patterns in order to infer the effect of urbanization on macromycete communities. We selected four oak forests along an urbanization gradient and established a permanent sampling area of 0.1 ha at each site. Macromycete sampling was carried out every week from June to October 2017. The indices used to measure functional diversity were functional richness (FRic), functional divergence (FDig), and functional evenness (FEve). The metric used to assess variation of macrofungal ecological function along the study area was the functional value. We recorded a total of 134 macromycete species and 223 individuals. Our results indicated a decline of species richness with increased urbanization level related mainly to microclimatic variables, and a high turnover of species composition among study sites, which appears to be related to microclimatic and urbanization variables. FRic decreased with urbanization level, indicating that some of the available resources in the niche space within the most urbanized sites are not being utilized. FDig increased with urbanization, which suggests a high degree of …
bibliographic citation: Gómez-Hernández et al. (2021) Impact of urbanization on functional diversity in macromycete communities along an urban ecosystem in Southwest Mexico. PeerJ 9:e12191 https://doi.org/10.7717/peerj.12191
date submitted: 2021-03-29
date accepted: 2021-08-30
issued: 2021-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gómez-Hernández
  given name: Marko
author list: Agent
  family name: Avendaño-Villegas
  given name: Emily
author list: Agent
  family name: Toledo-Garibaldi
  given name: María
author list: Agent
  family name: Gándara
  given name: Etelvina
doi: 10.7717/peerj.12191
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-21
copyright: © 2021 Gómez-Hernández et al.
attribution name: Gómez-Hernández et al.

Multiomics-based analyses of KPNA2 highlight its multiple potentials in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Dysregulation and prognostic roles of Karyopherin α2 (KPNA2) were reported in many malignancies including hepatocellular carcinoma (HCC). A multi-omics analysis of KPNA2 is needed to gain a deeper understanding of its multilevel molecular characteristics and provide novel clues for HCC diagnosis, prognosis, and target therapy. Herein multi-omic alterations of KPNA2 were analyzed at genetic, epigenetic, transcript, and protein levels with evaluation of their relevance with clinicopathological features of HCC by integrative analyses. The significant correlations of KPNA2 expression with its gene copy number variation (CNV) and methylation status were shown through Spearman correlation analyses. With Cox regression, Kaplan-Meier survival, and receiver operating characteristic (ROC) analyses, based on the factors of KPNA2 CNV, methylation, expression, and tumor stage, risk models for HCC overall survival (OS) and disease-free survival (DFS) were constructed which could discriminate the 1-year, 3-year, and 5-year OS/DFS status effectively. With Microenvironment Cell Populations-counter (MCP-counter), the immune infiltrations of HCC samples were evaluated and their associations with KPNA2 were shown. KPNA2 expression in liver was found to be influenced by low fat diet and presented significant correlations with fatty acid metabolism and fatty acid synthase activity in HCC. KPNA2 was detected lowered in HCC patient’s plasma by enzyme linked immunosorbent assay (ELISA), consistent with its translocation to nuclei of HCC cells. In conclusion, KPNA2 multilevel dysregulation in HCC and its correlations with immune infiltration and the fatty acid metabolism pathway indicated its multiple roles in HCC. The clinicopathological significance of KPNA2 was highlighted through the in-depth analyses at multilevels.
format: application/pdf
format: text/html
creator: Jinzhong Zhang
creator: Xiuzhi Zhang
creator: Lingxiao Wang
creator: Chunyan Kang
creator: Ningning Li
creator: Zhefeng Xiao
creator: Liping Dai
subject: Bioinformatics
subject: Genomics
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.12197
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Dysregulation and prognostic roles of Karyopherin α2 (KPNA2) were reported in many malignancies including hepatocellular carcinoma (HCC). A multi-omics analysis of KPNA2 is needed to gain a deeper understanding of its multilevel molecular characteristics and provide novel clues for HCC diagnosis, prognosis, and target therapy. Herein multi-omic alterations of KPNA2 were analyzed at genetic, epigenetic, transcript, and protein levels with evaluation of their relevance with clinicopathological features of HCC by integrative analyses. The significant correlations of KPNA2 expression with its gene copy number variation (CNV) and methylation status were shown through Spearman correlation analyses. With Cox regression, Kaplan-Meier survival, and receiver operating characteristic (ROC) analyses, based on the factors of KPNA2 CNV, methylation, expression, and tumor stage, risk models for HCC overall survival (OS) and disease-free survival (DFS) were constructed which could discriminate the 1-year, 3-year, and 5-year OS/DFS status effectively. With Microenvironment Cell Populations-counter (MCP-counter), the immune infiltrations of HCC samples were evaluated and their associations with KPNA2 were shown. KPNA2 expression in liver was found to be influenced by low fat diet and presented significant correlations with fatty acid metabolism and fatty acid synthase activity in HCC. KPNA2 was detected lowered in HCC patient’s plasma by enzyme linked immunosorbent assay (ELISA), consistent with its translocation to nuclei of HCC cells. In conclusion, KPNA2 multilevel dysregulation in HCC and its correlations with immune infiltration and the fatty acid metabolism pathway indicated its multiple roles in HCC. The clinicopathological significance of KPNA2 was highlighted through the in-depth analyses at multilevels.
bibliographic citation: Zhang et al. (2021) Multiomics-based analyses of KPNA2 highlight its multiple potentials in hepatocellular carcinoma. PeerJ 9:e12197 https://doi.org/10.7717/peerj.12197
date submitted: 2021-06-02
date accepted: 2021-08-31
issued: 2021-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Jinzhong
author list: Agent
  family name: Zhang
  given name: Xiuzhi
author list: Agent
  family name: Wang
  given name: Lingxiao
author list: Agent
  family name: Kang
  given name: Chunyan
author list: Agent
  family name: Li
  given name: Ningning
author list: Agent
  family name: Xiao
  given name: Zhefeng
author list: Agent
  family name: Dai
  given name: Liping
doi: 10.7717/peerj.12197
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-21
copyright: ©2021 Zhang et al.
attribution name: Zhang et al.

Key auxin response factor (ARF) genes constraining wheat tillering of mutant dmc
type: item
type: AcademicArticle
description: Tillering ability is a key agronomy trait for wheat (Triticum aestivum L.) production. Studies on a dwarf monoculm wheat mutant (dmc) showed that ARF11 played an important role in tillering of wheat. In this study, a total of 67 ARF family members were identified and clustered to two main classes with four subgroups based on their protein structures. The promoter regions of T. aestivum ARF (TaARF) genes contain a large number of cis-acting elements closely related to plant growth and development, and hormone response. The segmental duplication events occurred commonly and played a major role in the expansion of TaARFs. The gene collinearity degrees of the ARFs between wheat and other grasses, rice and maize, were significantly high. The evolution distances among TaARFs determine their expression profiles, such as homoeologous genes have similar expression profiles, like TaARF4-3A-1, TaARF4-3A-2 and their homoeologous genes. The expression profiles of TaARFs in various tissues or organs indicated TaARF3, TaARF4, TaARF9 and TaARF22 and their homoeologous genes played basic roles during wheat development. TaARF4, TaARF9, TaARF12, TaARF15, TaARF17, TaARF21, TaARF25 and their homoeologous genes probably played basic roles in tiller development. qRT-PCR analyses of 20 representative TaARF genes revealed that the abnormal expressions of TaARF11 and TaARF14 were major causes constraining the tillering of dmc. Indole-3-acetic acid (IAA) contents in dmc were significantly less than that in Guomai 301 at key tillering stages. Exogenous IAA application significantly promoted wheat tillering, and affected the transcriptions of TaARFs. These data suggested that TaARFs as well as IAA signaling were involved in controlling wheat tillering. This study provided valuable clues for functional characterization of ARFs in wheat.
format: application/pdf
format: text/html
creator: Junchang Li
creator: Yumei Jiang
creator: Jing Zhang
creator: Yongjing Ni
creator: Zhixin Jiao
creator: Huijuan Li
creator: Ting Wang
creator: Peipei Zhang
creator: Wenlong Guo
creator: Lei Li
creator: Hongjie Liu
creator: Hairong Zhang
creator: Qiaoyun Li
creator: Jishan Niu
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12221
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Tillering ability is a key agronomy trait for wheat (Triticum aestivum L.) production. Studies on a dwarf monoculm wheat mutant (dmc) showed that ARF11 played an important role in tillering of wheat. In this study, a total of 67 ARF family members were identified and clustered to two main classes with four subgroups based on their protein structures. The promoter regions of T. aestivum ARF (TaARF) genes contain a large number of cis-acting elements closely related to plant growth and development, and hormone response. The segmental duplication events occurred commonly and played a major role in the expansion of TaARFs. The gene collinearity degrees of the ARFs between wheat and other grasses, rice and maize, were significantly high. The evolution distances among TaARFs determine their expression profiles, such as homoeologous genes have similar expression profiles, like TaARF4-3A-1, TaARF4-3A-2 and their homoeologous genes. The expression profiles of TaARFs in various tissues or organs indicated TaARF3, TaARF4, TaARF9 and TaARF22 and their homoeologous genes played basic roles during wheat development. TaARF4, TaARF9, TaARF12, TaARF15, TaARF17, TaARF21, TaARF25 and their homoeologous genes probably played basic roles in tiller development. qRT-PCR analyses of 20 representative TaARF genes revealed that the abnormal expressions of TaARF11 and TaARF14 were major causes constraining the tillering of dmc. Indole-3-acetic acid (IAA) contents in dmc were significantly less than that in Guomai 301 at key tillering stages. Exogenous IAA application significantly promoted wheat tillering, and affected the transcriptions of TaARFs. These data suggested that TaARFs as well as IAA signaling were involved in controlling wheat tillering. This study provided valuable clues for functional characterization of ARFs in wheat.
bibliographic citation: Li et al. (2021) Key auxin response factor (ARF) genes constraining wheat tillering of mutant dmc. PeerJ 9:e12221 https://doi.org/10.7717/peerj.12221
date submitted: 2021-06-26
date accepted: 2021-09-06
issued: 2021-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Junchang
author list: Agent
  family name: Jiang
  given name: Yumei
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Ni
  given name: Yongjing
author list: Agent
  family name: Jiao
  given name: Zhixin
author list: Agent
  family name: Li
  given name: Huijuan
author list: Agent
  family name: Wang
  given name: Ting
author list: Agent
  family name: Zhang
  given name: Peipei
author list: Agent
  family name: Guo
  given name: Wenlong
author list: Agent
  family name: Li
  given name: Lei
author list: Agent
  family name: Liu
  given name: Hongjie
author list: Agent
  family name: Zhang
  given name: Hairong
author list: Agent
  family name: Li
  given name: Qiaoyun
author list: Agent
  family name: Niu
  given name: Jishan
doi: 10.7717/peerj.12221
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-21
copyright: ©2021 Li et al.
attribution name: Li et al.

Response of plant diversity and soil physicochemical properties to different gap sizes in a Pinus massoniana plantation
type: item
type: AcademicArticle
description: As one means of close-to-nature management, forest gaps have an important impact on the ecological service function of plantations. To improve the current situation of P. massoniana plantations, three different sizes of forest gaps (large gaps, medium gaps and small gaps) were established to observe whether gap setting can improve the soil fertility and plant diversity of forest plantations. The results showed that compared with the control, the soil organic matter content of different soil layers increased significantly in the medium forest gap and large forest gap. The content of soil organic matter in the surface layer of the middle gap had the largest increase (80.64%). Compared with the control, the content of soil-available potassium between different soil layers decreased significantly by 15.93% to 25.80%. The soil hydrolysable nitrogen reached its maximum under the medium gap. Soil moisture showed significant changes among different gap treatments, different soil layers and their interaction, decreasing significantly in large gaps and small gaps but increasing significantly in medium gaps. The soil bulk density decreased significantly compared with the control, and the surface soil reached the minimum in the medium gap. There were different plant species in forest gaps of different sizes, and shrub layer plants were more sensitive to gap size differences than herb layer plants. The plant diversity indices of the shrub layer increased significantly and showed a maximum under the medium gap. The plant diversity of the herb layer showed the opposite trend, and the Shannon-Wiener index, Simpson index and Pielou index were significantly lower than those of the control. RDA showed that different gap treatments had significant effects on the distribution of plants under the forest. Soil available potassium, soil moisture and soil bulk density affected the distribution and diversity of plants under the forest, serving as the limiting factors of plant growth. In fore…
format: application/pdf
format: text/html
creator: Qian Lyu
creator: Jiangli Liu
creator: Junjie Liu
creator: Yan Luo
creator: Luman Chen
creator: Gang Chen
creator: Kuangji Zhao
creator: Yuqin Chen
creator: Chuan Fan
creator: Xianwei Li
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.12222
publisher: PeerJ Inc.
rights: © 2021 Lyu et al.
abstract: As one means of close-to-nature management, forest gaps have an important impact on the ecological service function of plantations. To improve the current situation of P. massoniana plantations, three different sizes of forest gaps (large gaps, medium gaps and small gaps) were established to observe whether gap setting can improve the soil fertility and plant diversity of forest plantations. The results showed that compared with the control, the soil organic matter content of different soil layers increased significantly in the medium forest gap and large forest gap. The content of soil organic matter in the surface layer of the middle gap had the largest increase (80.64%). Compared with the control, the content of soil-available potassium between different soil layers decreased significantly by 15.93% to 25.80%. The soil hydrolysable nitrogen reached its maximum under the medium gap. Soil moisture showed significant changes among different gap treatments, different soil layers and their interaction, decreasing significantly in large gaps and small gaps but increasing significantly in medium gaps. The soil bulk density decreased significantly compared with the control, and the surface soil reached the minimum in the medium gap. There were different plant species in forest gaps of different sizes, and shrub layer plants were more sensitive to gap size differences than herb layer plants. The plant diversity indices of the shrub layer increased significantly and showed a maximum under the medium gap. The plant diversity of the herb layer showed the opposite trend, and the Shannon-Wiener index, Simpson index and Pielou index were significantly lower than those of the control. RDA showed that different gap treatments had significant effects on the distribution of plants under the forest. Soil available potassium, soil moisture and soil bulk density affected the distribution and diversity of plants under the forest, serving as the limiting factors of plant growth. In fore…
bibliographic citation: Lyu et al. (2021) Response of plant diversity and soil physicochemical properties to different gap sizes in a Pinus massoniana plantation. PeerJ 9:e12222 https://doi.org/10.7717/peerj.12222
date submitted: 2021-06-01
date accepted: 2021-09-06
issued: 2021-09-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lyu
  given name: Qian
author list: Agent
  family name: Liu
  given name: Jiangli
author list: Agent
  family name: Liu
  given name: Junjie
author list: Agent
  family name: Luo
  given name: Yan
author list: Agent
  family name: Chen
  given name: Luman
author list: Agent
  family name: Chen
  given name: Gang
author list: Agent
  family name: Zhao
  given name: Kuangji
author list: Agent
  family name: Chen
  given name: Yuqin
author list: Agent
  family name: Fan
  given name: Chuan
author list: Agent
  family name: Li
  given name: Xianwei
doi: 10.7717/peerj.12222
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-21
copyright: ©2021 Lyu et al.
attribution name: Lyu et al.

Cortinarius subsalor and C. tibeticisalor spp. nov., two new species from the section Delibuti from China
type: item
type: AcademicArticle
description: Cortinarius subsalor and C. tibeticisalor, belonging to the section Delibuti, are described from China as new to science. Cortinarius subsalor has been found to be associated with Lithocarpus trees in subtropical China and resembling C. salor, but it differs from the later by having slender basidiomata and the narrower basidiospores. Cortinarius tibeticisalor was collected from eastern Tibetan Plateau, associated with Abies. It differs from other species within sect. Delibuti by having olive tinge of mature or dried basidiomata and bigger basidiospores. The molecular data also support C. subsalor and C. tibeticisalor as new species. The phylogenetic analyses and biogeography of sect. Delibuti are discussed and a key to the species of this section currently known in the world is provided.
format: application/pdf
format: text/html
creator: Meng-Le Xie
creator: Jun-Liang Chen
creator: Chayanard Phukhamsakda
creator: Bálint Dima
creator: Yong-Ping Fu
creator: Rui-Qing Ji
creator: Ke Wang
creator: Tie-Zheng Wei
creator: Yu Li
subject: Biodiversity
subject: Molecular Biology
subject: Mycology
subject: Taxonomy
description: doi:10.7717/peerj.11982
publisher: PeerJ Inc.
rights: © 2021 Xie et al.
abstract: Cortinarius subsalor and C. tibeticisalor, belonging to the section Delibuti, are described from China as new to science. Cortinarius subsalor has been found to be associated with Lithocarpus trees in subtropical China and resembling C. salor, but it differs from the later by having slender basidiomata and the narrower basidiospores. Cortinarius tibeticisalor was collected from eastern Tibetan Plateau, associated with Abies. It differs from other species within sect. Delibuti by having olive tinge of mature or dried basidiomata and bigger basidiospores. The molecular data also support C. subsalor and C. tibeticisalor as new species. The phylogenetic analyses and biogeography of sect. Delibuti are discussed and a key to the species of this section currently known in the world is provided.
bibliographic citation: Xie et al. (2021) Cortinarius subsalor and C. tibeticisalor spp. nov., two new species from the section Delibuti from China. PeerJ 9:e11982 https://doi.org/10.7717/peerj.11982
date submitted: 2021-05-20
date accepted: 2021-07-26
issued: 2021-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Meng-Le
author list: Agent
  family name: Chen
  given name: Jun-Liang
author list: Agent
  family name: Phukhamsakda
  given name: Chayanard
author list: Agent
  family name: Dima
  given name: Bálint
author list: Agent
  family name: Fu
  given name: Yong-Ping
author list: Agent
  family name: Ji
  given name: Rui-Qing
author list: Agent
  family name: Wang
  given name: Ke
author list: Agent
  family name: Wei
  given name: Tie-Zheng
author list: Agent
  family name: Li
  given name: Yu
doi: 10.7717/peerj.11982
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-20
copyright: © 2021 Xie et al.
attribution name: Xie et al.

The association between serum CD4 T lymphocyte counts and surgical outcomes in HIV/AIDS patients in Guangxi, China: a retrospective cohort study
type: item
type: AcademicArticle
description: Background HIV/AIDS is a chronic disease leading to complications in infected individuals that often require surgical intervention. These patients’ serum CD4 T lymphocyte (CD4) counts represent one of the most important indicators of their ability to tolerate surgical treatment. Previous studies have demonstrated that CD4 cell count (CD4-CC) < 200 cells/μl may increase the risk of surgical complications in these patients, limiting their ability to undergo surgery, which may negatively affect their quality of life. Further investigation into the surgical outcomes of patients with CD4-CC < 200 cells/μl should provide guidance in making appropriate clinical decisions for the optimal healthcare of this patient demographic. Methods All enrolled patients were selected from 14 prefecture-level general hospitals in Guangxi, China, and were referred to AIDS outpost hospitals for inpatient surgical therapy. A total cohort of 168 adult patients was retrospectively analyzed. Multifactorial and stratified analyses were performed to evaluate the in surgical outcome differences for patients with CD4-CC < 200 cells/μl (N = 43), using those with CD4-CC ≥ 200 cells/μl (N = 125) as controls. Results Poor incisional healing was used as the primary outcome indicator, and postoperative complications were used as the secondary outcome indicator. In the patient group with CD4-CC < 200 cells/μl, the risk of surgical complications was significantly increased (OR 2.379; 95% CI [1.049–5.394]) after adjustment. Adjusted stratified analysis of the CD4-CC < 200 cells/μl group revealed that individuals over 60 years (OR 27.504; 95% CI [2.297–329.317]) with erythrocyte counts below 4.00/ml for males or 3.50/ml for females (OR 3.353; 95% CI [1.079–10.419]) had a significantly higher risk of postoperative complications; this finding was statistically different from the control (CD4 ≥ 200 cells/μl) group. However, there was no significant difference between the two groups regarding the risk of poorly …
format: application/pdf
format: text/html
creator: Aimei Liu
creator: Cunxu Liu
creator: Xiaojun Deng
creator: Yongbao Huang
creator: Linchu Liao
creator: Zhihao Meng
creator: Minfu He
creator: Junli Huang
subject: Epidemiology
subject: Hematology
subject: HIV
subject: Immunology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.12023
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background HIV/AIDS is a chronic disease leading to complications in infected individuals that often require surgical intervention. These patients’ serum CD4 T lymphocyte (CD4) counts represent one of the most important indicators of their ability to tolerate surgical treatment. Previous studies have demonstrated that CD4 cell count (CD4-CC) < 200 cells/μl may increase the risk of surgical complications in these patients, limiting their ability to undergo surgery, which may negatively affect their quality of life. Further investigation into the surgical outcomes of patients with CD4-CC < 200 cells/μl should provide guidance in making appropriate clinical decisions for the optimal healthcare of this patient demographic. Methods All enrolled patients were selected from 14 prefecture-level general hospitals in Guangxi, China, and were referred to AIDS outpost hospitals for inpatient surgical therapy. A total cohort of 168 adult patients was retrospectively analyzed. Multifactorial and stratified analyses were performed to evaluate the in surgical outcome differences for patients with CD4-CC < 200 cells/μl (N = 43), using those with CD4-CC ≥ 200 cells/μl (N = 125) as controls. Results Poor incisional healing was used as the primary outcome indicator, and postoperative complications were used as the secondary outcome indicator. In the patient group with CD4-CC < 200 cells/μl, the risk of surgical complications was significantly increased (OR 2.379; 95% CI [1.049–5.394]) after adjustment. Adjusted stratified analysis of the CD4-CC < 200 cells/μl group revealed that individuals over 60 years (OR 27.504; 95% CI [2.297–329.317]) with erythrocyte counts below 4.00/ml for males or 3.50/ml for females (OR 3.353; 95% CI [1.079–10.419]) had a significantly higher risk of postoperative complications; this finding was statistically different from the control (CD4 ≥ 200 cells/μl) group. However, there was no significant difference between the two groups regarding the risk of poorly …
bibliographic citation: Liu et al. (2021) The association between serum CD4 T lymphocyte counts and surgical outcomes in HIV/AIDS patients in Guangxi, China: a retrospective cohort study. PeerJ 9:e12023 https://doi.org/10.7717/peerj.12023
date submitted: 2021-01-25
date accepted: 2021-07-29
issued: 2021-09-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Aimei
author list: Agent
  family name: Liu
  given name: Cunxu
author list: Agent
  family name: Deng
  given name: Xiaojun
author list: Agent
  family name: Huang
  given name: Yongbao
author list: Agent
  family name: Liao
  given name: Linchu
author list: Agent
  family name: Meng
  given name: Zhihao
author list: Agent
  family name: He
  given name: Minfu
author list: Agent
  family name: Huang
  given name: Junli
doi: 10.7717/peerj.12023
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-20
copyright: © 2021 Liu et al.
attribution name: Liu et al.

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