PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Testis development in the Japanese eel is affected by photic signals through melatonin secretion
items: The beneficial effect of physical activity on cognitive function in community-dwelling older persons with locomotive syndrome
items: The role of zinc transporter proteins as predictive and prognostic biomarkers of hepatocellular cancer
items: HLA alleles measured from COVID-19 patient transcriptomes reveal associations with disease prognosis in a New York cohort
items: Seasonal trends of the polyp expansion and nutritional condition of Alcyonium acaule (Octocorallia, Alcyonacea)
items: Changes in diversity and composition of rhizosphere bacterial community during natural restoration stages in antimony mine
items: A novel pyroptosis-associated gene signature for immune status and prognosis of cutaneous melanoma
items: https://peerj.com/articles/12321
items: Characteristics and factors influencing the natural regeneration of Larix principis-rupprechtii seedlings in northern China
items: A docked mutation phenocopies dumpy oblique alleles via altered vesicle trafficking

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

The beneficial effect of physical activity on cognitive function in community-dwelling older persons with locomotive syndrome
type: item
type: AcademicArticle
description: Background Cognitive decline is closely related to motor decline. Locomotive syndrome (LS) is defined as a state associated with a high risk of requiring support because of locomotive organ disorders, and can be evaluated using a questionnaire. This study aimed to clarify the effectiveness of daily goal-targeted exercise on cognitive function in two different populations classified by scores on the Locomo 25 questionnaire. Methods Seventy community-dwelling older people who participated in a 13-week health class were divided into two populations based on Locomo 25 scores: <7 (non-LS) and ≥7 (LS). Participants were presented with a daily target steps and worked towards that goal. Cognitive function was evaluated using the Japanese version of Addenbrooke’s Cognitive Examination-Revised (ACE-R). Average daily physical activity (exercise [Ex]) for 13 weeks was measured using a portable activity meter. Depression status was assessed using the Geriatric Depression Scale (GDS-15). Results No significant differences were observed in age, years of education, body mass index, smooth muscle mass index, GDS-15 scores, or ACE-R scores between the non-LS and LS populations. Multiple logistic regression analysis showed that Ex (odds ratio = 5.01, p = 0.002) for 13 weeks was significantly associated with increased cognitive function in the LS population. The Ex threshold for the increase in cognitive function based on receiver operating curve analysis was 2.29 metabolic equivalents of task (METs) × h (METs · h/day) (p = 0.047) in the LS population. After 13 weeks, ACE-R scores were significantly higher in the Ex ≥ 2.29 than in the Ex < 2.29 METs · h/day group (p = 0.024, ηp2 = 0.241) in the LS population based on two-way analysis of covariance. Furthermore, a significant increase in the ACE-R memory domain was seen in the Ex ≥ 2.29 group (p = 0.035, ηp2 = 0.213). Conclusions These results suggest that Ex ≥ 2.29 METs · h/day is important for improving cognitive function in LS popula…
format: application/pdf
format: text/html
creator: Misa Nakamura
creator: Masakazu Imaoka
creator: Hiroshi Hashizume
creator: Fumie Tazaki
creator: Mitsumasa Hida
creator: Hidetoshi Nakao
creator: Tomoko Omizu
creator: Hideki Kanemoto
creator: Masatoshi Takeda
subject: Cognitive Disorders
subject: Geriatrics
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.12292
publisher: PeerJ Inc.
rights: © 2021 Nakamura et al.
abstract: Background Cognitive decline is closely related to motor decline. Locomotive syndrome (LS) is defined as a state associated with a high risk of requiring support because of locomotive organ disorders, and can be evaluated using a questionnaire. This study aimed to clarify the effectiveness of daily goal-targeted exercise on cognitive function in two different populations classified by scores on the Locomo 25 questionnaire. Methods Seventy community-dwelling older people who participated in a 13-week health class were divided into two populations based on Locomo 25 scores: <7 (non-LS) and ≥7 (LS). Participants were presented with a daily target steps and worked towards that goal. Cognitive function was evaluated using the Japanese version of Addenbrooke’s Cognitive Examination-Revised (ACE-R). Average daily physical activity (exercise [Ex]) for 13 weeks was measured using a portable activity meter. Depression status was assessed using the Geriatric Depression Scale (GDS-15). Results No significant differences were observed in age, years of education, body mass index, smooth muscle mass index, GDS-15 scores, or ACE-R scores between the non-LS and LS populations. Multiple logistic regression analysis showed that Ex (odds ratio = 5.01, p = 0.002) for 13 weeks was significantly associated with increased cognitive function in the LS population. The Ex threshold for the increase in cognitive function based on receiver operating curve analysis was 2.29 metabolic equivalents of task (METs) × h (METs · h/day) (p = 0.047) in the LS population. After 13 weeks, ACE-R scores were significantly higher in the Ex ≥ 2.29 than in the Ex < 2.29 METs · h/day group (p = 0.024, ηp2 = 0.241) in the LS population based on two-way analysis of covariance. Furthermore, a significant increase in the ACE-R memory domain was seen in the Ex ≥ 2.29 group (p = 0.035, ηp2 = 0.213). Conclusions These results suggest that Ex ≥ 2.29 METs · h/day is important for improving cognitive function in LS popula…
bibliographic citation: Nakamura et al. (2021) The beneficial effect of physical activity on cognitive function in community-dwelling older persons with locomotive syndrome. PeerJ 9:e12292 https://doi.org/10.7717/peerj.12292
date submitted: 2020-12-04
date accepted: 2021-09-21
issued: 2021-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nakamura
  given name: Misa
author list: Agent
  family name: Imaoka
  given name: Masakazu
author list: Agent
  family name: Hashizume
  given name: Hiroshi
author list: Agent
  family name: Tazaki
  given name: Fumie
author list: Agent
  family name: Hida
  given name: Mitsumasa
author list: Agent
  family name: Nakao
  given name: Hidetoshi
author list: Agent
  family name: Omizu
  given name: Tomoko
author list: Agent
  family name: Kanemoto
  given name: Hideki
author list: Agent
  family name: Takeda
  given name: Masatoshi
doi: 10.7717/peerj.12292
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-15
copyright: © 2021 Nakamura et al.
attribution name: Nakamura et al.

The role of zinc transporter proteins as predictive and prognostic biomarkers of hepatocellular cancer
type: item
type: AcademicArticle
description: Identification of the key processes involved in the tumor progression, malignancy and the molecular factors which are responsible for the transition of the cirrhotic cells to the tumor cells, contribute to the detection of biomarkers for diagnosis of hepatocellular carcinoma (HCC) at an early stage. According to clinical data, HCC is mostly characterized by a significant decrease in zinc levels. It is strongly implied that zinc deficiency is the major event required in the early stages of tumor formation and development of malignancy. Due to this reason, the definition of the molecular players which have a role in zinc homeostasis and cellular zinc level could give us a clue about the transition state of the cirrhosis to hepatic tumor formation. Despite the well-known implications of zinc in the development of HCCthe correlation of the expression of zinc transporter proteins with tumor progression and malignancy remain largely unknown. In the present study, we evaluated in detail the relationship of zinc deficiency on the prognosis of early HCC patients. In this study, we aimed to test the potential zinc transporters which contribute tothe transformation of cirrhosis to HCCand the progression of HCC. Among the 24 zinc transporter proteins, the proteins to be examined were chosen by using Gene Expression Profiling Interactive Analysis (GEPIA) webpage and RNA-seq analysis using TCGA database. ZIP14 and ZIP5 transporters were found as common differentially expressed genes from both bioinformatic analyses. ZnT1, ZnT7 and ZIP7 transporters have been associated with tumor progression. Relative abundance of ZnT1, ZIP5 and ZIP14 protein level was determined by immunohistochemistry (IHC) in surgically resected liver specimens from 16 HCC patients at different stages. IHC staining intensity was analyzed by using ImageJ software and scored with the histological scoring (H-score) method. The staining of ZnT1 was significantly higher in Grade III comparing to Grade II and Grade …
format: application/pdf
format: text/html
creator: Ceylan V. Bitirim
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.12314
publisher: PeerJ Inc.
rights: © 2021 Bitirim
abstract: Identification of the key processes involved in the tumor progression, malignancy and the molecular factors which are responsible for the transition of the cirrhotic cells to the tumor cells, contribute to the detection of biomarkers for diagnosis of hepatocellular carcinoma (HCC) at an early stage. According to clinical data, HCC is mostly characterized by a significant decrease in zinc levels. It is strongly implied that zinc deficiency is the major event required in the early stages of tumor formation and development of malignancy. Due to this reason, the definition of the molecular players which have a role in zinc homeostasis and cellular zinc level could give us a clue about the transition state of the cirrhosis to hepatic tumor formation. Despite the well-known implications of zinc in the development of HCCthe correlation of the expression of zinc transporter proteins with tumor progression and malignancy remain largely unknown. In the present study, we evaluated in detail the relationship of zinc deficiency on the prognosis of early HCC patients. In this study, we aimed to test the potential zinc transporters which contribute tothe transformation of cirrhosis to HCCand the progression of HCC. Among the 24 zinc transporter proteins, the proteins to be examined were chosen by using Gene Expression Profiling Interactive Analysis (GEPIA) webpage and RNA-seq analysis using TCGA database. ZIP14 and ZIP5 transporters were found as common differentially expressed genes from both bioinformatic analyses. ZnT1, ZnT7 and ZIP7 transporters have been associated with tumor progression. Relative abundance of ZnT1, ZIP5 and ZIP14 protein level was determined by immunohistochemistry (IHC) in surgically resected liver specimens from 16 HCC patients at different stages. IHC staining intensity was analyzed by using ImageJ software and scored with the histological scoring (H-score) method. The staining of ZnT1 was significantly higher in Grade III comparing to Grade II and Grade …
bibliographic citation: Bitirim (2021) The role of zinc transporter proteins as predictive and prognostic biomarkers of hepatocellular cancer. PeerJ 9:e12314 https://doi.org/10.7717/peerj.12314
date submitted: 2021-08-04
date accepted: 2021-09-24
issued: 2021-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bitirim
  given name: Ceylan V.
doi: 10.7717/peerj.12314
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-15
copyright: ©2021 Bitirim
attribution name: Bitirim

HLA alleles measured from COVID-19 patient transcriptomes reveal associations with disease prognosis in a New York cohort
type: item
type: AcademicArticle
description: Background The Human Leukocyte Antigen (HLA) gene locus plays a fundamental role in human immunity, and it is established that certain HLA alleles are disease determinants. Previously, we have identified prevalent HLA class I and class II alleles, including DPA1*02:02, in two small patient cohorts at the COVID-19 pandemic onset. Methods We have since analyzed a larger public patient cohort data (n = 126 patients) with controls, associated demographic and clinical data. By combining the predictive power of multiple in silico HLA predictors, we report on HLA-I and HLA-II alleles, along with their associated risk significance. Results We observe HLA-II DPA1*02:02 at a higher frequency in the COVID-19 positive cohort (29%) when compared to the COVID-negative control group (Fisher’s exact test [FET] p = 0.0174). Having this allele, however, does not appear to put this cohort’s patients at an increased risk of hospitalization. Inspection of COVID-19 disease severity outcomes, including admission to intensive care, reveal nominally significant risk associations with A*11:01 (FET p = 0.0078) and C*04:01 (FET p = 0.0087). The association with severe disease outcome is especially evident for patients with C*04:01, where disease prognosis measured by mechanical ventilation-free days was statistically significant after multiple hypothesis correction (Bonferroni p = 0.0323). While prevalence of some of these alleles falls below statistical significance after Bonferroni correction, COVID-19 patients with HLA-I C*04:01 tend to fare worse overall. This HLA allele may hold potential clinical value.
format: application/pdf
format: text/html
creator: René L. Warren
creator: Inanc Birol
subject: Bioinformatics
subject: Genomics
subject: Immunology
subject: Public Health
subject: Medical Genetics
description: doi:10.7717/peerj.12368
publisher: PeerJ Inc.
rights: © 2021 Warren and Birol
abstract: Background The Human Leukocyte Antigen (HLA) gene locus plays a fundamental role in human immunity, and it is established that certain HLA alleles are disease determinants. Previously, we have identified prevalent HLA class I and class II alleles, including DPA1*02:02, in two small patient cohorts at the COVID-19 pandemic onset. Methods We have since analyzed a larger public patient cohort data (n = 126 patients) with controls, associated demographic and clinical data. By combining the predictive power of multiple in silico HLA predictors, we report on HLA-I and HLA-II alleles, along with their associated risk significance. Results We observe HLA-II DPA1*02:02 at a higher frequency in the COVID-19 positive cohort (29%) when compared to the COVID-negative control group (Fisher’s exact test [FET] p = 0.0174). Having this allele, however, does not appear to put this cohort’s patients at an increased risk of hospitalization. Inspection of COVID-19 disease severity outcomes, including admission to intensive care, reveal nominally significant risk associations with A*11:01 (FET p = 0.0078) and C*04:01 (FET p = 0.0087). The association with severe disease outcome is especially evident for patients with C*04:01, where disease prognosis measured by mechanical ventilation-free days was statistically significant after multiple hypothesis correction (Bonferroni p = 0.0323). While prevalence of some of these alleles falls below statistical significance after Bonferroni correction, COVID-19 patients with HLA-I C*04:01 tend to fare worse overall. This HLA allele may hold potential clinical value.
bibliographic citation: Warren et al. (2021) HLA alleles measured from COVID-19 patient transcriptomes reveal associations with disease prognosis in a New York cohort. PeerJ 9:e12368 https://doi.org/10.7717/peerj.12368
date submitted: 2021-06-03
date accepted: 2021-10-01
issued: 2021-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Warren
  given name: René L.
author list: Agent
  family name: Birol
  given name: Inanc
doi: 10.7717/peerj.12368
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-15
copyright: ©2021 Warren and Birol
attribution name: Warren and Birol

Seasonal trends of the polyp expansion and nutritional condition of Alcyonium acaule (Octocorallia, Alcyonacea)
type: item
type: AcademicArticle
description: The ecological physiology of anthozoans, as well as their resistance to stressors, are strongly influenced by environmental factors and the availability of resources. The energy budget of anthozoans can vary seasonally in order to find an equilibrium between the available resources and respiration, polyp activity, growth, and reproduction processes. The variation in the biochemical composition of the animal tissues in these organisms results from a combination of the productivity processes of the water column coupled with the reproductive effort and potential starvation periods of the anthozoans. Here, the seasonal variation in the polyp activity of a slow-growing passive suspension feeder, the octocoral Alcyonium acaule, as well as their carbohydrate, protein and lipid contents, was investigated in a warm temperate environment using in-situ observations and biochemical analyses. Polyp activity exhibited a significant variability that was moderately dependent on season, while an aestivation phenomenon in A. acaule (i.e., a resting period in which the anthozoan is not capable of any polyp activity) during the warmer months is clearly observed. Carbohydrate concentrations in the coral species showed a significant increase in the late winter and spring seasons, and the lipid content increased during the spring. A higher abundance of lipids and carbohydrates coincided with a higher primary productivity in the water column, as well as with the octocoral reproduction period. In late autumn, there was a depletion of these biomolecules, with protein levels exhibiting great variability across sampling times. Complex alterations driven by climate change could affect the energy fluxes that depend on the dead or alive particles that are intercepted by marine animal forests. The obtained findings show a food shortage in late summer and autumn of the benthic suspension feeder A. acaule through the integrative descriptors of the ecophysiology of these anthozoans. This research con…
format: application/pdf
format: text/html
creator: Lucia Rizzo
creator: Ida Fiorillo
creator: Sergio Rossi
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12032
publisher: PeerJ Inc.
rights: © 2021 Rizzo et al.
abstract: The ecological physiology of anthozoans, as well as their resistance to stressors, are strongly influenced by environmental factors and the availability of resources. The energy budget of anthozoans can vary seasonally in order to find an equilibrium between the available resources and respiration, polyp activity, growth, and reproduction processes. The variation in the biochemical composition of the animal tissues in these organisms results from a combination of the productivity processes of the water column coupled with the reproductive effort and potential starvation periods of the anthozoans. Here, the seasonal variation in the polyp activity of a slow-growing passive suspension feeder, the octocoral Alcyonium acaule, as well as their carbohydrate, protein and lipid contents, was investigated in a warm temperate environment using in-situ observations and biochemical analyses. Polyp activity exhibited a significant variability that was moderately dependent on season, while an aestivation phenomenon in A. acaule (i.e., a resting period in which the anthozoan is not capable of any polyp activity) during the warmer months is clearly observed. Carbohydrate concentrations in the coral species showed a significant increase in the late winter and spring seasons, and the lipid content increased during the spring. A higher abundance of lipids and carbohydrates coincided with a higher primary productivity in the water column, as well as with the octocoral reproduction period. In late autumn, there was a depletion of these biomolecules, with protein levels exhibiting great variability across sampling times. Complex alterations driven by climate change could affect the energy fluxes that depend on the dead or alive particles that are intercepted by marine animal forests. The obtained findings show a food shortage in late summer and autumn of the benthic suspension feeder A. acaule through the integrative descriptors of the ecophysiology of these anthozoans. This research con…
bibliographic citation: Rizzo et al. (2021) Seasonal trends of the polyp expansion and nutritional condition of Alcyonium acaule (Octocorallia, Alcyonacea). PeerJ 9:e12032 https://doi.org/10.7717/peerj.12032
date submitted: 2021-04-28
date accepted: 2021-07-30
issued: 2021-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rizzo
  given name: Lucia
author list: Agent
  family name: Fiorillo
  given name: Ida
author list: Agent
  family name: Rossi
  given name: Sergio
doi: 10.7717/peerj.12032
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-14
copyright: © 2021 Rizzo et al.
attribution name: Rizzo et al.

Changes in diversity and composition of rhizosphere bacterial community during natural restoration stages in antimony mine
type: item
type: AcademicArticle
description: Background Open pit antimony (Sb) mining causes serious soil pollution, and phytoremediation is a low-cost approach to remediate heavy metal contaminated soil. Rhizosphere bacteria play an important role in ecological restoration in mining areas. There is a knowledge gap on how to find suitable rhizosphere microorganisms to improve the phytoremediation effect. Understanding the differences of rhizosphere bacterial diversity in different restoration stages is helpful to find suitable bacteria for ecological restoration. Methods A method of the substitution of “space” for “time” was used to study the effect of natural restoration on rhizosphere bacterial community. According to the dominant vegetation types (herb, shrub, and tree) in the natural restoration area of Sb mining, the early restoration (ER), middle restoration (MR), and later restoration (LR) from the largest Sb mine (Xikuangshan mine) in the world were selected to evaluate the differences in the composition and diversity of rhizosphere bacteria during three natural restoration stages. Each restoration stage had five samples. To determine the relationship between restoration stages and bacterial diversity in the rhizosphere, high throughput sequencing of PCR amplified were used. Results Alpha diversity, as assessed by Chao indices, appeared lowest in ER but this trend was not seen with other diversity metrics, including the Simpson and Shannon. Beta diversity analysis suggested there were differences in rhizobacterial community structure associate with restoration stage. At the phylum level, natural restoration led to a significant increase in the relative abundance of Actinobacteria in the MR, and a significant decrease in the relative abundance of Patescibacteria in the LR. Additionally, Calditrichaeota, Deferribacteres and Epsilonbacteraeota were only found in ER. At the genus level, the relative abundance of RB41 and Haliangium were highest in LR plots, while that of Bacillus and Gaiella were highest i…
format: application/pdf
format: text/html
creator: Renyan Duan
creator: Yuxiang Lin
creator: Jianing Zhang
creator: Minyi Huang
creator: Yihuan Du
creator: Li Yang
creator: Jing Bai
creator: Guohong Xiang
creator: Zhigao Wang
creator: Yaqi Zhang
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.12302
publisher: PeerJ Inc.
rights: © 2021 Duan et al.
abstract: Background Open pit antimony (Sb) mining causes serious soil pollution, and phytoremediation is a low-cost approach to remediate heavy metal contaminated soil. Rhizosphere bacteria play an important role in ecological restoration in mining areas. There is a knowledge gap on how to find suitable rhizosphere microorganisms to improve the phytoremediation effect. Understanding the differences of rhizosphere bacterial diversity in different restoration stages is helpful to find suitable bacteria for ecological restoration. Methods A method of the substitution of “space” for “time” was used to study the effect of natural restoration on rhizosphere bacterial community. According to the dominant vegetation types (herb, shrub, and tree) in the natural restoration area of Sb mining, the early restoration (ER), middle restoration (MR), and later restoration (LR) from the largest Sb mine (Xikuangshan mine) in the world were selected to evaluate the differences in the composition and diversity of rhizosphere bacteria during three natural restoration stages. Each restoration stage had five samples. To determine the relationship between restoration stages and bacterial diversity in the rhizosphere, high throughput sequencing of PCR amplified were used. Results Alpha diversity, as assessed by Chao indices, appeared lowest in ER but this trend was not seen with other diversity metrics, including the Simpson and Shannon. Beta diversity analysis suggested there were differences in rhizobacterial community structure associate with restoration stage. At the phylum level, natural restoration led to a significant increase in the relative abundance of Actinobacteria in the MR, and a significant decrease in the relative abundance of Patescibacteria in the LR. Additionally, Calditrichaeota, Deferribacteres and Epsilonbacteraeota were only found in ER. At the genus level, the relative abundance of RB41 and Haliangium were highest in LR plots, while that of Bacillus and Gaiella were highest i…
bibliographic citation: Duan et al. (2021) Changes in diversity and composition of rhizosphere bacterial community during natural restoration stages in antimony mine. PeerJ 9:e12302 https://doi.org/10.7717/peerj.12302
date submitted: 2021-07-06
date accepted: 2021-09-22
issued: 2021-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duan
  given name: Renyan
author list: Agent
  family name: Lin
  given name: Yuxiang
author list: Agent
  family name: Zhang
  given name: Jianing
author list: Agent
  family name: Huang
  given name: Minyi
author list: Agent
  family name: Du
  given name: Yihuan
author list: Agent
  family name: Yang
  given name: Li
author list: Agent
  family name: Bai
  given name: Jing
author list: Agent
  family name: Xiang
  given name: Guohong
author list: Agent
  family name: Wang
  given name: Zhigao
author list: Agent
  family name: Zhang
  given name: Yaqi
doi: 10.7717/peerj.12302
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-14
copyright: © 2021 Duan et al.
attribution name: Duan et al.

A novel pyroptosis-associated gene signature for immune status and prognosis of cutaneous melanoma
type: item
type: AcademicArticle
description: Background Cutaneous melanoma (CM) is a life-threatening destructive malignancy. Pyroptosis significantly correlates with programmed tumor cell death and its microenvironment through active host-tumor crosstalk. However, the prognostic value of pyroptosis-associated gene signatures in CM remains unclear. Methods Gene profiles and clinical data of patients with CM were downloaded from The Cancer Genome Atlas (TCGA) to identify differentially expressed genes associated with pyroptosis and overall survival (OS). We constructed a prognostic gene signature using LASSO analysis, then applied immune cell infiltration scores and Kaplan-Meier, Cox, and pathway enrichment analyses to determine the roles of the gene signature in CM. A validation cohort was collected from the Gene Expression Omnibus (GEO) database. Results Four pyroptosis-associated genes were identified and incorporated into a prognostic gene signature. Integrated bioinformatics findings showed that the signature correlated with patient survival and was associated with tumor growth and metastasis. The results of Gene Set Enrichment Analysis of a risk signature indicated that several enriched pathways are associated with cancer and immunity. The risk signature for immune status significantly correlated with tumor stem cells, the immune microenvironment, immune cell infiltration and immune subtypes. The expression of four pyroptosis genes significantly correlated with the OS of patients with CM and was related to the sensitivity of cancer cells to several antitumor drugs. A signature comprising four genes associated with pyroptosis offers a novel approach to the prognosis and survival of patients with CM and will facilitate the development of individualized therapy.
format: application/pdf
format: text/html
creator: Zhengyuan Wu
creator: Leilei Chen
creator: Chaojie Jin
creator: Jing Xu
creator: Xingqun Zhang
creator: Yi Yao
subject: Bioinformatics
subject: Dermatology
subject: Immunology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.12304
publisher: PeerJ Inc.
rights: © 2021 Wu et al.
abstract: Background Cutaneous melanoma (CM) is a life-threatening destructive malignancy. Pyroptosis significantly correlates with programmed tumor cell death and its microenvironment through active host-tumor crosstalk. However, the prognostic value of pyroptosis-associated gene signatures in CM remains unclear. Methods Gene profiles and clinical data of patients with CM were downloaded from The Cancer Genome Atlas (TCGA) to identify differentially expressed genes associated with pyroptosis and overall survival (OS). We constructed a prognostic gene signature using LASSO analysis, then applied immune cell infiltration scores and Kaplan-Meier, Cox, and pathway enrichment analyses to determine the roles of the gene signature in CM. A validation cohort was collected from the Gene Expression Omnibus (GEO) database. Results Four pyroptosis-associated genes were identified and incorporated into a prognostic gene signature. Integrated bioinformatics findings showed that the signature correlated with patient survival and was associated with tumor growth and metastasis. The results of Gene Set Enrichment Analysis of a risk signature indicated that several enriched pathways are associated with cancer and immunity. The risk signature for immune status significantly correlated with tumor stem cells, the immune microenvironment, immune cell infiltration and immune subtypes. The expression of four pyroptosis genes significantly correlated with the OS of patients with CM and was related to the sensitivity of cancer cells to several antitumor drugs. A signature comprising four genes associated with pyroptosis offers a novel approach to the prognosis and survival of patients with CM and will facilitate the development of individualized therapy.
bibliographic citation: Wu et al. (2021) A novel pyroptosis-associated gene signature for immune status and prognosis of cutaneous melanoma. PeerJ 9:e12304 https://doi.org/10.7717/peerj.12304
date submitted: 2021-07-15
date accepted: 2021-09-22
issued: 2021-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Zhengyuan
author list: Agent
  family name: Chen
  given name: Leilei
author list: Agent
  family name: Jin
  given name: Chaojie
author list: Agent
  family name: Xu
  given name: Jing
author list: Agent
  family name: Zhang
  given name: Xingqun
author list: Agent
  family name: Yao
  given name: Yi
doi: 10.7717/peerj.12304
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-14
copyright: © 2021 Wu et al.
attribution name: Wu et al.

https://peerj.com/articles/12321
type: item
type: AcademicArticle
title: Betulinic acid decreases lipid accumulation in adipogenesis-induced human mesenchymal stem cells with upregulation of PGC-1α and UCP-1 and post-transcriptional downregulation of adiponectin and leptin secretion
description: Background Controlling cellular functions, including stem cell growth and differentiation, can be the key for the treatment of metabolic disorders, such as type II diabetes mellitus (T2DM). Previously identified as peroxisome proliferator-activated receptor gamma (PPARγ) antagonist, betulinic acid (BA) may have the capability to control stem cell homeostasis, benefiting T2DM treatment. In this study, the effects of BA on osteogenesis and adipogenesis mechanisms of human mesenchymal stem cells (hMSCs) were investigated. Results We observed that BA increased hMSC osteogenesis by enhancing the alkaline phosphatase activity, calcium deposition, and mRNA expressions of osteogenic markers, namely, runt-related transcription factor 2, osteocalcin, and osteopontin. In addition, BA decreased hMSC adipogenesis with the decrease in glycerol-3-phosphate dehydrogenase activity, reduced intracellular lipid accumulations, down-regulated CCAAT-enhancer-binding protein alpha, and suppressed post-transcriptional adiponectin and leptin secretion. BA increased the brown adipocyte characteristics with the increase in the ratio of small lipid droplets and glucose uptake. Furthermore, the mRNA expressions of brown adipocyte markers, namely, PPARγ coactivator one alpha, uncoupling protein 1, and interleukin-6 increased. Conclusions Our results uncovered the mechanisms of how BA improved glucose and lipid metabolisms by decreasing white adipogenesis and increasing brown adipogenesis. Altogether, BA may be used for balancing glucose metabolisms without the potential side effects on bone loss or weight gain.
format: application/pdf
format: text/html
creator: Sasithon Senamontree
creator: Thitiporn Lakthan
creator: Pornsri Charoenpanich
creator: Chanpen Chanchao
creator: Adisri Charoenpanich
subject: Cell Biology
subject: Developmental Biology
subject: Molecular Biology
description: doi:10.7717/peerj.12321
publisher: PeerJ Inc.
rights: © 2021 Senamontree et al.
abstract: Background Controlling cellular functions, including stem cell growth and differentiation, can be the key for the treatment of metabolic disorders, such as type II diabetes mellitus (T2DM). Previously identified as peroxisome proliferator-activated receptor gamma (PPARγ) antagonist, betulinic acid (BA) may have the capability to control stem cell homeostasis, benefiting T2DM treatment. In this study, the effects of BA on osteogenesis and adipogenesis mechanisms of human mesenchymal stem cells (hMSCs) were investigated. Results We observed that BA increased hMSC osteogenesis by enhancing the alkaline phosphatase activity, calcium deposition, and mRNA expressions of osteogenic markers, namely, runt-related transcription factor 2, osteocalcin, and osteopontin. In addition, BA decreased hMSC adipogenesis with the decrease in glycerol-3-phosphate dehydrogenase activity, reduced intracellular lipid accumulations, down-regulated CCAAT-enhancer-binding protein alpha, and suppressed post-transcriptional adiponectin and leptin secretion. BA increased the brown adipocyte characteristics with the increase in the ratio of small lipid droplets and glucose uptake. Furthermore, the mRNA expressions of brown adipocyte markers, namely, PPARγ coactivator one alpha, uncoupling protein 1, and interleukin-6 increased. Conclusions Our results uncovered the mechanisms of how BA improved glucose and lipid metabolisms by decreasing white adipogenesis and increasing brown adipogenesis. Altogether, BA may be used for balancing glucose metabolisms without the potential side effects on bone loss or weight gain.
bibliographic citation: Senamontree et al. (2021) Betulinic acid decreases lipid accumulation in adipogenesis-induced human mesenchymal stem cells with upregulation of PGC-1α and UCP-1 and post-transcriptional downregulation of adiponectin and leptin secretion. PeerJ 9:e12321 https://doi.org/10.7717/peerj.12321
date submitted: 2021-07-26
date accepted: 2021-09-25
issued: 2021-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Senamontree
  given name: Sasithon
author list: Agent
  family name: Lakthan
  given name: Thitiporn
author list: Agent
  family name: Charoenpanich
  given name: Pornsri
author list: Agent
  family name: Chanchao
  given name: Chanpen
author list: Agent
  family name: Charoenpanich
  given name: Adisri
doi: 10.7717/peerj.12321
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-14
copyright: © 2021 Senamontree et al.
attribution name: Senamontree et al.

Characteristics and factors influencing the natural regeneration of Larix principis-rupprechtii seedlings in northern China
type: item
type: AcademicArticle
description: Larix principis-rupprechtii is an important and widely distributed species in the mountains of northern China. However, it has inefficient natural regeneration in many stands and difficulty recruiting seedlings and saplings. In this study, we selected six plots with improved naturally-regenerated L. principis-rupprechtii seedlings. A point pattern analysis (pair-correlation function) was applied to identify the spatial distribution pattern and correlation between adult trees and regenerated seedlings mapped through X/Y coordinates. Several possible influencing factors of L. principis-rupprechtii seedlings’ natural regeneration were also investigated. The results showed that the spatial distribution patterns of Larix principis-rupprechtii seedlings were concentrated 0–5 m around adult trees when considering the main univariate distribution type of regeneration. There was a positive correlation at a scale of 1.5–4 m between seedlings and adult trees according to bivariate analyses. When the scale was increased, these relationships were no longer significant. Generally, adult trees raised regenerated L. principis-rupprechtii seedlings at a scale of 1.5–4 m. Principal component analysis showed that the understory herb diversity and litter layer had a negative correlation with the number of regenerated seedlings. There was also a weak relationship between regenerated numbers and canopy density. This study demonstrated that the main factors promoting natural regeneration were litter thickness, herb diversity, and the distance between adult trees and regenerated seedlings. Additionally, these findings will provide a basis for the late-stage and practical management of natural regeneration in northern China’s mountain ranges.
format: application/pdf
format: text/html
creator: Weiwen Zhao
creator: Wenjun Liang
creator: Youzhi Han
creator: Xi Wei
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.12327
publisher: PeerJ Inc.
rights: © 2021 Zhao et al.
abstract: Larix principis-rupprechtii is an important and widely distributed species in the mountains of northern China. However, it has inefficient natural regeneration in many stands and difficulty recruiting seedlings and saplings. In this study, we selected six plots with improved naturally-regenerated L. principis-rupprechtii seedlings. A point pattern analysis (pair-correlation function) was applied to identify the spatial distribution pattern and correlation between adult trees and regenerated seedlings mapped through X/Y coordinates. Several possible influencing factors of L. principis-rupprechtii seedlings’ natural regeneration were also investigated. The results showed that the spatial distribution patterns of Larix principis-rupprechtii seedlings were concentrated 0–5 m around adult trees when considering the main univariate distribution type of regeneration. There was a positive correlation at a scale of 1.5–4 m between seedlings and adult trees according to bivariate analyses. When the scale was increased, these relationships were no longer significant. Generally, adult trees raised regenerated L. principis-rupprechtii seedlings at a scale of 1.5–4 m. Principal component analysis showed that the understory herb diversity and litter layer had a negative correlation with the number of regenerated seedlings. There was also a weak relationship between regenerated numbers and canopy density. This study demonstrated that the main factors promoting natural regeneration were litter thickness, herb diversity, and the distance between adult trees and regenerated seedlings. Additionally, these findings will provide a basis for the late-stage and practical management of natural regeneration in northern China’s mountain ranges.
bibliographic citation: Zhao et al. (2021) Characteristics and factors influencing the natural regeneration of Larix principis-rupprechtii seedlings in northern China. PeerJ 9:e12327 https://doi.org/10.7717/peerj.12327
date submitted: 2021-04-27
date accepted: 2021-09-27
issued: 2021-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Weiwen
author list: Agent
  family name: Liang
  given name: Wenjun
author list: Agent
  family name: Han
  given name: Youzhi
author list: Agent
  family name: Wei
  given name: Xi
doi: 10.7717/peerj.12327
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-14
copyright: ©2021 Zhao et al.
attribution name: Zhao et al.

A docked mutation phenocopies dumpy oblique alleles via altered vesicle trafficking
type: item
type: AcademicArticle
description: The Drosophila extracellular matrix protein Dumpy (Dpy) is one of the largest proteins encoded by any animal. One class of dpy mutations produces a characteristic shortening of the wing blade known as oblique (dpyo), due to altered tension in the developing wing. We describe here the characterization of docked (doc), a gene originally named because of an allele producing a truncated wing. We show that doc corresponds to the gene model CG5484, which encodes a homolog of the yeast protein Yif1 and plays a key role in ER to Golgi vesicle transport. Genetic analysis is consistent with a similar role for Doc in vesicle trafficking: docked alleles interact not only with genes encoding the COPII core proteins sec23 and sec13, but also with the SNARE proteins synaptobrevin and syntaxin. Further, we demonstrate that the strong similarity between the doc1 and dpyo wing phenotypes reflects a functional connection between the two genes; we found that various dpy alleles are sensitive to changes in dosage of genes encoding other vesicle transport components such as sec13 and sar1. Doc’s effects on trafficking are not limited to Dpy; for example, reduced doc dosage disturbed Notch pathway signaling during wing blade and vein development. These results suggest a model in which the oblique wing phenotype in doc1 results from reduced transport of wild-type Dumpy protein; by extension, an additional implication is that the dpyo alleles can themselves be explained as hypomorphs.
format: application/pdf
format: text/html
creator: Suresh Kandasamy
creator: Kiley Couto
creator: Justin Thackeray
subject: Cell Biology
subject: Genetics
description: doi:10.7717/peerj.12175
publisher: PeerJ Inc.
rights: © 2021 Kandasamy et al.
abstract: The Drosophila extracellular matrix protein Dumpy (Dpy) is one of the largest proteins encoded by any animal. One class of dpy mutations produces a characteristic shortening of the wing blade known as oblique (dpyo), due to altered tension in the developing wing. We describe here the characterization of docked (doc), a gene originally named because of an allele producing a truncated wing. We show that doc corresponds to the gene model CG5484, which encodes a homolog of the yeast protein Yif1 and plays a key role in ER to Golgi vesicle transport. Genetic analysis is consistent with a similar role for Doc in vesicle trafficking: docked alleles interact not only with genes encoding the COPII core proteins sec23 and sec13, but also with the SNARE proteins synaptobrevin and syntaxin. Further, we demonstrate that the strong similarity between the doc1 and dpyo wing phenotypes reflects a functional connection between the two genes; we found that various dpy alleles are sensitive to changes in dosage of genes encoding other vesicle transport components such as sec13 and sar1. Doc’s effects on trafficking are not limited to Dpy; for example, reduced doc dosage disturbed Notch pathway signaling during wing blade and vein development. These results suggest a model in which the oblique wing phenotype in doc1 results from reduced transport of wild-type Dumpy protein; by extension, an additional implication is that the dpyo alleles can themselves be explained as hypomorphs.
bibliographic citation: Kandasamy et al. (2021) A docked mutation phenocopies dumpy oblique alleles via altered vesicle trafficking. PeerJ 9:e12175 https://doi.org/10.7717/peerj.12175
date submitted: 2020-05-28
date accepted: 2021-08-27
issued: 2021-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kandasamy
  given name: Suresh
author list: Agent
  family name: Couto
  given name: Kiley
author list: Agent
  family name: Thackeray
  given name: Justin
doi: 10.7717/peerj.12175
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-13
copyright: © 2021 Kandasamy et al.
attribution name: Kandasamy et al.

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