PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development
items: Establishment of a 12-gene expression signature to predict colon cancer prognosis
items: Crucial biological functions of CCL7 in cancer
items: What killed Frame Lake? A precautionary tale for urban planners
items: Population diversity and relatedness in Sugarbirds (Promeropidae: Promerops spp.)
items: Epidemiology of Haemophilus parasuis isolates from pigs in China using serotyping, antimicrobial susceptibility, biofilm formation and ERIC-PCR genotyping
items: Increased chronic kidney disease development and progression in diabetic patients after appendectomy: a population-based cohort study
items: Evaluating the utility of the female-specific mitochondrial f-orf gene for population genetic, phylogeographic and systematic studies in freshwater mussels (Bivalvia: Unionida)
items: Efficient dispersal and substrate acquisition traits in a marine invasive species via transient chimerism and colony mobility
items: Synergistic and antagonistic effects of immunomodulatory drugs on the action of antifungals against Candida glabrata and Saccharomyces cerevisiae

Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development
type: item
type: AcademicArticle
description: Cotton plant architecture, including fruit branch formation and flowering pattern, influences plant light exploitation, cotton yield and planting cost. DNA methylation has been widely observed at different developmental stages in both plants and animals and is associated with regulation of gene expression, chromatin remodelling, genome protection and other functions. Here, we investigated the global epigenetic reprogramming during the development of fruiting branches and floral buds at three developmental stages: the seedling stage, the pre-squaring stage and the squaring stage. We first identified 22 cotton genes which potentially encode DNA methyltransferases and demethylases. Among them, the homologous genes of CMT, DRM2 and MET1 were upregulated at pre-squaring and squaring stages, suggesting that DNA methylation is involved in the development of floral buds and fruit branches. Although the global methylation at all of three developmental stages was not changed, the CHG-type methylation of non-expressed genes was higher than those of expressed genes. In addition, we found that the expression of the homologous genes of the key circadian rhythm regulators, including CRY, LHY and CO, was associated with changes of DNA methylation at three developmental stages.
format: application/pdf
format: text/html
creator: Quan Sun
creator: Jing Qiao
creator: Sai Zhang
creator: Shibin He
creator: Yuzhen Shi
creator: Youlu Yuan
creator: Xiao Zhang
creator: Yingfan Cai
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.4945
publisher: PeerJ Inc.
rights: © 2018 Sun et al.
abstract: Cotton plant architecture, including fruit branch formation and flowering pattern, influences plant light exploitation, cotton yield and planting cost. DNA methylation has been widely observed at different developmental stages in both plants and animals and is associated with regulation of gene expression, chromatin remodelling, genome protection and other functions. Here, we investigated the global epigenetic reprogramming during the development of fruiting branches and floral buds at three developmental stages: the seedling stage, the pre-squaring stage and the squaring stage. We first identified 22 cotton genes which potentially encode DNA methyltransferases and demethylases. Among them, the homologous genes of CMT, DRM2 and MET1 were upregulated at pre-squaring and squaring stages, suggesting that DNA methylation is involved in the development of floral buds and fruit branches. Although the global methylation at all of three developmental stages was not changed, the CHG-type methylation of non-expressed genes was higher than those of expressed genes. In addition, we found that the expression of the homologous genes of the key circadian rhythm regulators, including CRY, LHY and CO, was associated with changes of DNA methylation at three developmental stages.
bibliographic citation: Sun et al. (2018) Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development. PeerJ 6:e4945 https://doi.org/10.7717/peerj.4945
date submitted: 2017-12-29
date accepted: 2018-05-18
issued: 2018-06-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Quan
author list: Agent
  family name: Qiao
  given name: Jing
author list: Agent
  family name: Zhang
  given name: Sai
author list: Agent
  family name: He
  given name: Shibin
author list: Agent
  family name: Shi
  given name: Yuzhen
author list: Agent
  family name: Yuan
  given name: Youlu
author list: Agent
  family name: Zhang
  given name: Xiao
author list: Agent
  family name: Cai
  given name: Yingfan
doi: 10.7717/peerj.4945
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-14
copyright: © 2018 Sun et al.
attribution name: Sun et al.

Establishment of a 12-gene expression signature to predict colon cancer prognosis
type: item
type: AcademicArticle
description: A robust and accurate gene expression signature is essential to assist oncologists to determine which subset of patients at similar Tumor-Lymph Node-Metastasis (TNM) stage has high recurrence risk and could benefit from adjuvant therapies. Here we applied a two-step supervised machine-learning method and established a 12-gene expression signature to precisely predict colon adenocarcinoma (COAD) prognosis by using COAD RNA-seq transcriptome data from The Cancer Genome Atlas (TCGA). The predictive performance of the 12-gene signature was validated with two independent gene expression microarray datasets: GSE39582 includes 566 COAD cases for the development of six molecular subtypes with distinct clinical, molecular and survival characteristics; GSE17538 is a dataset containing 232 colon cancer patients for the generation of a metastasis gene expression profile to predict recurrence and death in COAD patients. The signature could effectively separate the poor prognosis patients from good prognosis group (disease specific survival (DSS): Kaplan Meier (KM) Log Rank p = 0.0034; overall survival (OS): KM Log Rank p = 0.0336) in GSE17538. For patients with proficient mismatch repair system (pMMR) in GSE39582, the signature could also effectively distinguish high risk group from low risk group (OS: KM Log Rank p = 0.005; Relapse free survival (RFS): KM Log Rank p = 0.022). Interestingly, advanced stage patients were significantly enriched in high 12-gene score group (Fisher’s exact test p = 0.0003). After stage stratification, the signature could still distinguish poor prognosis patients in GSE17538 from good prognosis within stage II (Log Rank p = 0.01) and stage II & III (Log Rank p = 0.017) in the outcome of DFS. Within stage III or II/III pMMR patients treated with Adjuvant Chemotherapies (ACT) and patients with higher 12-gene score showed poorer prognosis (III, OS: KM Log Rank p = 0.046; III & II, OS: KM Log Rank p = 0.041). Among stage II/III pMMR patients with lower 1…
format: application/pdf
format: text/html
creator: Dalong Sun
creator: Jing Chen
creator: Longzi Liu
creator: Guangxi Zhao
creator: Pingping Dong
creator: Bingrui Wu
creator: Jun Wang
creator: Ling Dong
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.4942
publisher: PeerJ Inc.
rights: © 2018 Sun et al.
abstract: A robust and accurate gene expression signature is essential to assist oncologists to determine which subset of patients at similar Tumor-Lymph Node-Metastasis (TNM) stage has high recurrence risk and could benefit from adjuvant therapies. Here we applied a two-step supervised machine-learning method and established a 12-gene expression signature to precisely predict colon adenocarcinoma (COAD) prognosis by using COAD RNA-seq transcriptome data from The Cancer Genome Atlas (TCGA). The predictive performance of the 12-gene signature was validated with two independent gene expression microarray datasets: GSE39582 includes 566 COAD cases for the development of six molecular subtypes with distinct clinical, molecular and survival characteristics; GSE17538 is a dataset containing 232 colon cancer patients for the generation of a metastasis gene expression profile to predict recurrence and death in COAD patients. The signature could effectively separate the poor prognosis patients from good prognosis group (disease specific survival (DSS): Kaplan Meier (KM) Log Rank p = 0.0034; overall survival (OS): KM Log Rank p = 0.0336) in GSE17538. For patients with proficient mismatch repair system (pMMR) in GSE39582, the signature could also effectively distinguish high risk group from low risk group (OS: KM Log Rank p = 0.005; Relapse free survival (RFS): KM Log Rank p = 0.022). Interestingly, advanced stage patients were significantly enriched in high 12-gene score group (Fisher’s exact test p = 0.0003). After stage stratification, the signature could still distinguish poor prognosis patients in GSE17538 from good prognosis within stage II (Log Rank p = 0.01) and stage II & III (Log Rank p = 0.017) in the outcome of DFS. Within stage III or II/III pMMR patients treated with Adjuvant Chemotherapies (ACT) and patients with higher 12-gene score showed poorer prognosis (III, OS: KM Log Rank p = 0.046; III & II, OS: KM Log Rank p = 0.041). Among stage II/III pMMR patients with lower 1…
bibliographic citation: Sun et al. (2018) Establishment of a 12-gene expression signature to predict colon cancer prognosis. PeerJ 6:e4942 https://doi.org/10.7717/peerj.4942
date submitted: 2018-02-06
date accepted: 2018-05-21
issued: 2018-06-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Dalong
author list: Agent
  family name: Chen
  given name: Jing
author list: Agent
  family name: Liu
  given name: Longzi
author list: Agent
  family name: Zhao
  given name: Guangxi
author list: Agent
  family name: Dong
  given name: Pingping
author list: Agent
  family name: Wu
  given name: Bingrui
author list: Agent
  family name: Wang
  given name: Jun
author list: Agent
  family name: Dong
  given name: Ling
doi: 10.7717/peerj.4942
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-14
copyright: ©2018 Sun et al.
attribution name: Sun et al.

Crucial biological functions of CCL7 in cancer
type: item
type: AcademicArticle
description: Chemokine (C-C motif) ligand 7 (CCL7), a CC chemokine, is a chemotactic factor and attractant for various kinds of leukocytes, including monocytes and neutrophils. CCL7 is widely expressed in multiple cell types and can participate in anti-inflammatory responses through binding to its receptors to mediate the recruitment of immune cells. Abnormal CCL7 expression is associated with certain immune diseases. Furthermore, CCL7 plays a pivotal role in tumorigenesis. CCL7 promotes tumor progression by supporting the formation of the tumor microenvironment and facilitating tumor invasion and metastasis, although some studies have suggested that CCL7 has tumor suppressor effects. In this review, we summarize the currently available information regarding the influence of CCL7 on tumors.
format: application/pdf
format: text/html
creator: Yangyang Liu
creator: Yadi Cai
creator: Li Liu
creator: Yudong Wu
creator: Xiangyang Xiong
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.4928
publisher: PeerJ Inc.
rights: © 2018 Liu et al.
abstract: Chemokine (C-C motif) ligand 7 (CCL7), a CC chemokine, is a chemotactic factor and attractant for various kinds of leukocytes, including monocytes and neutrophils. CCL7 is widely expressed in multiple cell types and can participate in anti-inflammatory responses through binding to its receptors to mediate the recruitment of immune cells. Abnormal CCL7 expression is associated with certain immune diseases. Furthermore, CCL7 plays a pivotal role in tumorigenesis. CCL7 promotes tumor progression by supporting the formation of the tumor microenvironment and facilitating tumor invasion and metastasis, although some studies have suggested that CCL7 has tumor suppressor effects. In this review, we summarize the currently available information regarding the influence of CCL7 on tumors.
bibliographic citation: Liu et al. (2018) Crucial biological functions of CCL7 in cancer. PeerJ 6:e4928 https://doi.org/10.7717/peerj.4928
date submitted: 2018-03-19
date accepted: 2018-05-18
issued: 2018-06-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yangyang
author list: Agent
  family name: Cai
  given name: Yadi
author list: Agent
  family name: Liu
  given name: Li
author list: Agent
  family name: Wu
  given name: Yudong
author list: Agent
  family name: Xiong
  given name: Xiangyang
doi: 10.7717/peerj.4928
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-14
copyright: © 2018 Liu et al.
attribution name: Liu et al.

What killed Frame Lake? A precautionary tale for urban planners
type: item
type: AcademicArticle
description: Frame Lake, located within the city of Yellowknife, Northwest Territories, Canada, has been identified as requiring significant remediation due to its steadily declining water quality and inability to support fish by the 1970s. Former gold mining operations and urbanization around the lake have been suspected as probable causes for the decline in water quality. While these land-use activities are well documented, little information is available regarding their impact on the lake itself. For this reason, Arcellinida, a group of shelled protozoans known to be reliable bioindicators of land-use change, were used to develop a hydroecological history of the lake. The purpose of this study was to use Arcellinida to: (1) document the contamination history of the lake, particularly related to arsenic (As) associated with aerial deposition from mine roaster stacks; (2) track the progress of water quality deterioration in Frame Lake related to mining, urbanization and other activities; and (3) identify any evidence of natural remediation within the lake. Arcellinida assemblages were assessed at 1-cm intervals through the upper 30 cm of a freeze core obtained from Frame Lake. The assemblages were statistically compared to geochemical and loss-on-ignition results from the core to document the contamination and degradation of conditions in the lake. The chronology of limnological changes recorded in the lake sediments were derived from 210Pb, 14C dating and known stratigraphic events. The progress of urbanization near the lake was tracked using aerial photography. Using Spearman correlations, the five most significant environmental variables impacting Arcellinida distribution were identified as minerogenics, organics, As, iron and mercury (p < 0.05; n = 30). Based on CONISS and ANOSIM analysis, three Arcellinida assemblages are identified. These include the Baseline Limnological Conditions Assemblage (BLCA), ranging from 17–30 cm and deposited in the early Holocene >7,000 years …
format: application/pdf
format: text/html
creator: Melody J. Gavel
creator: R. Timothy Patterson
creator: Nawaf A. Nasser
creator: Jennifer M. Galloway
creator: Bruce W. Hanna
creator: Peter A. Cott
creator: Helen M. Roe
creator: Hendrik Falck
subject: Ecosystem Science
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.4850
publisher: PeerJ Inc.
rights: © 2018 Gavel et al.
abstract: Frame Lake, located within the city of Yellowknife, Northwest Territories, Canada, has been identified as requiring significant remediation due to its steadily declining water quality and inability to support fish by the 1970s. Former gold mining operations and urbanization around the lake have been suspected as probable causes for the decline in water quality. While these land-use activities are well documented, little information is available regarding their impact on the lake itself. For this reason, Arcellinida, a group of shelled protozoans known to be reliable bioindicators of land-use change, were used to develop a hydroecological history of the lake. The purpose of this study was to use Arcellinida to: (1) document the contamination history of the lake, particularly related to arsenic (As) associated with aerial deposition from mine roaster stacks; (2) track the progress of water quality deterioration in Frame Lake related to mining, urbanization and other activities; and (3) identify any evidence of natural remediation within the lake. Arcellinida assemblages were assessed at 1-cm intervals through the upper 30 cm of a freeze core obtained from Frame Lake. The assemblages were statistically compared to geochemical and loss-on-ignition results from the core to document the contamination and degradation of conditions in the lake. The chronology of limnological changes recorded in the lake sediments were derived from 210Pb, 14C dating and known stratigraphic events. The progress of urbanization near the lake was tracked using aerial photography. Using Spearman correlations, the five most significant environmental variables impacting Arcellinida distribution were identified as minerogenics, organics, As, iron and mercury (p < 0.05; n = 30). Based on CONISS and ANOSIM analysis, three Arcellinida assemblages are identified. These include the Baseline Limnological Conditions Assemblage (BLCA), ranging from 17–30 cm and deposited in the early Holocene >7,000 years …
bibliographic citation: Gavel et al. (2018) What killed Frame Lake? A precautionary tale for urban planners. PeerJ 6:e4850 https://doi.org/10.7717/peerj.4850
date submitted: 2018-02-08
date accepted: 2018-05-06
issued: 2018-06-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gavel
  given name: Melody J.
author list: Agent
  family name: Patterson
  given name: R. Timothy
author list: Agent
  family name: Nasser
  given name: Nawaf A.
author list: Agent
  family name: Galloway
  given name: Jennifer M.
author list: Agent
  family name: Hanna
  given name: Bruce W.
author list: Agent
  family name: Cott
  given name: Peter A.
author list: Agent
  family name: Roe
  given name: Helen M.
author list: Agent
  family name: Falck
  given name: Hendrik
doi: 10.7717/peerj.4850
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-14
copyright: ©2018 Gavel et al.
attribution name: Gavel et al.

Population diversity and relatedness in Sugarbirds (Promeropidae: Promerops spp.)
type: item
type: AcademicArticle
description: Sugarbirds are a family of two socially-monogamous passerine species endemic to southern Africa. Cape and Gurney’s Sugarbird (Promerops cafer and P. gurneyi) differ in abundance, dispersion across their range and in the degree of sexual dimorphism in tail length, factors that affect breeding systems and potentially genetic diversity. According to recent data, P. gurneyi are in decline and revision of the species’ IUCN conservation status to a threatened category may be warranted. It is therefore necessary to understand genetic diversity and risk of inbreeding in this species. We used six polymorphic microsatellite markers and one mitochondrial gene (ND2) to compare genetic diversity in P. cafer from Helderberg Nature Reserve and P. gurneyi from Golden Gate Highlands National Park, sites at the core of each species distribution. We describe novel universal avian primers which amplify the entire ND2 coding sequence across a broad range of bird orders. We observed high mitochondrial and microsatellite diversity in both sugarbird populations, with no detectable inbreeding and large effective population sizes.
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format: text/html
creator: Evan S. Haworth
creator: Michael J. Cunningham
creator: Kathleen M. Calf Tjorve
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.5000
publisher: PeerJ Inc.
rights: © 2018 Haworth et al.
abstract: Sugarbirds are a family of two socially-monogamous passerine species endemic to southern Africa. Cape and Gurney’s Sugarbird (Promerops cafer and P. gurneyi) differ in abundance, dispersion across their range and in the degree of sexual dimorphism in tail length, factors that affect breeding systems and potentially genetic diversity. According to recent data, P. gurneyi are in decline and revision of the species’ IUCN conservation status to a threatened category may be warranted. It is therefore necessary to understand genetic diversity and risk of inbreeding in this species. We used six polymorphic microsatellite markers and one mitochondrial gene (ND2) to compare genetic diversity in P. cafer from Helderberg Nature Reserve and P. gurneyi from Golden Gate Highlands National Park, sites at the core of each species distribution. We describe novel universal avian primers which amplify the entire ND2 coding sequence across a broad range of bird orders. We observed high mitochondrial and microsatellite diversity in both sugarbird populations, with no detectable inbreeding and large effective population sizes.
bibliographic citation: Haworth et al. (2018) Population diversity and relatedness in Sugarbirds (Promeropidae: Promerops spp.). PeerJ 6:e5000 https://doi.org/10.7717/peerj.5000
date submitted: 2018-03-02
date accepted: 2018-05-29
issued: 2018-06-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Haworth
  given name: Evan S.
author list: Agent
  family name: Cunningham
  given name: Michael J.
author list: Agent
  family name: Calf Tjorve
  given name: Kathleen M.
doi: 10.7717/peerj.5000
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-13
copyright: ©2018 Haworth et al.
attribution name: Haworth et al.

Epidemiology of Haemophilus parasuis isolates from pigs in China using serotyping, antimicrobial susceptibility, biofilm formation and ERIC-PCR genotyping
type: item
type: AcademicArticle
description: Background Haemophilus parasuis is a commensal organism of the upper respiratory tract of healthy pigs and causes high morbidity and mortality in piglets. The aim of this study was to investigate the epidemiology of H. parasuis in China from 2014 to 2017. Methods We characterized 143 H. parasuis isolates by serotyping, antimicrobial susceptibility, biofilm formation and with enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) assays. Results Serotyping revealed serovar 5 as the most prevalent (26.6%) followed by serovars 4 (22.4%), 7 (9.1 %), 13 (6.3%), 12 (5.6 %), and non-typeable (8.4%). In a panel of 23 antimicrobials, the minimum inhibitory concentration 50% (MIC50) were in the range of 0.25–16 μg/mL and MIC90 were 2–>512 μg/mL. A total of 99 isolates of H. parasuis (69.2%) were able to form biofilms and 59.6% (59/99) performed weak biofilm-forming ability. ERIC-PCR revealed a very heterogeneous pattern with 87 clusters. Discussion These H. parasuis isolates showed a high serovar and genotypic lineage diversity, different abilities to form biofilms and a high degree of genetic diversity. Biofilm formation was related to antimicrobial susceptibility but there were no statistically significant associations between the antimicrobial susceptibility and either the serovars or the ERIC-PCR clusters. This study showed a high prevalence of high-MIC H. parasuis strains and suggests the need for a continuous surveillance of clinical isolates of H. parasuis.
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format: text/html
creator: Yongda Zhao
creator: Qin Wang
creator: Jie Li
creator: Xiaohuan Lin
creator: Xianhui Huang
creator: Binghu Fang
subject: Microbiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.5040
publisher: PeerJ Inc.
rights: © 2018 Zhao et al.
abstract: Background Haemophilus parasuis is a commensal organism of the upper respiratory tract of healthy pigs and causes high morbidity and mortality in piglets. The aim of this study was to investigate the epidemiology of H. parasuis in China from 2014 to 2017. Methods We characterized 143 H. parasuis isolates by serotyping, antimicrobial susceptibility, biofilm formation and with enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) assays. Results Serotyping revealed serovar 5 as the most prevalent (26.6%) followed by serovars 4 (22.4%), 7 (9.1 %), 13 (6.3%), 12 (5.6 %), and non-typeable (8.4%). In a panel of 23 antimicrobials, the minimum inhibitory concentration 50% (MIC50) were in the range of 0.25–16 μg/mL and MIC90 were 2–>512 μg/mL. A total of 99 isolates of H. parasuis (69.2%) were able to form biofilms and 59.6% (59/99) performed weak biofilm-forming ability. ERIC-PCR revealed a very heterogeneous pattern with 87 clusters. Discussion These H. parasuis isolates showed a high serovar and genotypic lineage diversity, different abilities to form biofilms and a high degree of genetic diversity. Biofilm formation was related to antimicrobial susceptibility but there were no statistically significant associations between the antimicrobial susceptibility and either the serovars or the ERIC-PCR clusters. This study showed a high prevalence of high-MIC H. parasuis strains and suggests the need for a continuous surveillance of clinical isolates of H. parasuis.
bibliographic citation: Zhao et al. (2018) Epidemiology of Haemophilus parasuis isolates from pigs in China using serotyping, antimicrobial susceptibility, biofilm formation and ERIC-PCR genotyping. PeerJ 6:e5040 https://doi.org/10.7717/peerj.5040
date submitted: 2018-03-29
date accepted: 2018-06-01
issued: 2018-06-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yongda
author list: Agent
  family name: Wang
  given name: Qin
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Lin
  given name: Xiaohuan
author list: Agent
  family name: Huang
  given name: Xianhui
author list: Agent
  family name: Fang
  given name: Binghu
doi: 10.7717/peerj.5040
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-13
copyright: © 2018 Zhao et al.
attribution name: Zhao et al.

Increased chronic kidney disease development and progression in diabetic patients after appendectomy: a population-based cohort study
type: item
type: AcademicArticle
description: Background The vermiform appendix serves as a “safe house” for maintaining normal gut bacteria and appendectomy may impair the intestinal microbiota. Appendectomy is expected to profoundly alter the immune system and modulate the pathogenic inflammatory immune responses of the gut. Recent studies have shown that a dysbiotic gut increases the risk of cardiovascular disease and chronic kidney disease (CKD). Therefore, we hypothesized that appendectomy would increase the risk of CKD. Methods This nationwide, population-based, propensity-score-matched cohort study included 10,383 patients who underwent appendectomy and 41,532 propensity-score-matched controls. Data were collected by the National Health Insurance Research Database of Taiwan from 2000 to 2013. We examined the associations between appendectomy and CKD and end-stage renal disease (ESRD). The major outcome was a new diagnosis of CKD based on an outpatient diagnosis made at least three times or hospital discharge diagnosis made once during the follow-up period. ESRD was defined as undergoing dialysis therapy for at least 90 days, as in previous studies. Results The incidence rates of CKD and ESRD were higher in the appendectomy group than in the control cohort (CKD: 6.52 vs. 5.93 per 1,000 person-years, respectively; ESRD: 0.49 vs. 0.31 per 1,000 person-years, respectively). Appendectomy patients also had a higher risk of developing CKD (adjusted hazard ratio [aHR] 1.13; 95% CI [1.01–1.26]; P = 0.037) and ESRD (aHR 1.59; 95% CI [1.06–2.37]; P = 0.024) than control group patients. Subgroup analysis showed that appendectomy patients with concomitant diabetes mellitus (aHR 2.08; P = 0.004) were at higher risk of incident ESRD than those without diabetes mellitus. The interaction effects of appendectomy and diabetes mellitus were significant for ESRD risk (P = 0.022); no interaction effect was found for CKD risk (P = 0.555). Conclusions Appendectomy increases the risk of developing CKD and ESRD, especially in dia…
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creator: Chin-Hua Chang
creator: Chew-Teng Kor
creator: Chia-Lin Wu
creator: Ping-Fang Chiu
creator: Jhao-Rong Li
creator: Chun-Chieh Tsai
creator: Teng-Hsiang Chang
creator: Chia-Chu Chang
subject: Microbiology
subject: Diabetes and Endocrinology
subject: Internal Medicine
subject: Nephrology
description: doi:10.7717/peerj.5019
publisher: PeerJ Inc.
rights: © 2018 Chang et al.
abstract: Background The vermiform appendix serves as a “safe house” for maintaining normal gut bacteria and appendectomy may impair the intestinal microbiota. Appendectomy is expected to profoundly alter the immune system and modulate the pathogenic inflammatory immune responses of the gut. Recent studies have shown that a dysbiotic gut increases the risk of cardiovascular disease and chronic kidney disease (CKD). Therefore, we hypothesized that appendectomy would increase the risk of CKD. Methods This nationwide, population-based, propensity-score-matched cohort study included 10,383 patients who underwent appendectomy and 41,532 propensity-score-matched controls. Data were collected by the National Health Insurance Research Database of Taiwan from 2000 to 2013. We examined the associations between appendectomy and CKD and end-stage renal disease (ESRD). The major outcome was a new diagnosis of CKD based on an outpatient diagnosis made at least three times or hospital discharge diagnosis made once during the follow-up period. ESRD was defined as undergoing dialysis therapy for at least 90 days, as in previous studies. Results The incidence rates of CKD and ESRD were higher in the appendectomy group than in the control cohort (CKD: 6.52 vs. 5.93 per 1,000 person-years, respectively; ESRD: 0.49 vs. 0.31 per 1,000 person-years, respectively). Appendectomy patients also had a higher risk of developing CKD (adjusted hazard ratio [aHR] 1.13; 95% CI [1.01–1.26]; P = 0.037) and ESRD (aHR 1.59; 95% CI [1.06–2.37]; P = 0.024) than control group patients. Subgroup analysis showed that appendectomy patients with concomitant diabetes mellitus (aHR 2.08; P = 0.004) were at higher risk of incident ESRD than those without diabetes mellitus. The interaction effects of appendectomy and diabetes mellitus were significant for ESRD risk (P = 0.022); no interaction effect was found for CKD risk (P = 0.555). Conclusions Appendectomy increases the risk of developing CKD and ESRD, especially in dia…
bibliographic citation: Chang et al. (2018) Increased chronic kidney disease development and progression in diabetic patients after appendectomy: a population-based cohort study. PeerJ 6:e5019 https://doi.org/10.7717/peerj.5019
date submitted: 2018-02-14
date accepted: 2018-05-30
issued: 2018-06-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chang
  given name: Chin-Hua
author list: Agent
  family name: Kor
  given name: Chew-Teng
author list: Agent
  family name: Wu
  given name: Chia-Lin
author list: Agent
  family name: Chiu
  given name: Ping-Fang
author list: Agent
  family name: Li
  given name: Jhao-Rong
author list: Agent
  family name: Tsai
  given name: Chun-Chieh
author list: Agent
  family name: Chang
  given name: Teng-Hsiang
author list: Agent
  family name: Chang
  given name: Chia-Chu
doi: 10.7717/peerj.5019
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-13
copyright: ©2018 Chang et al.
attribution name: Chang et al.

Evaluating the utility of the female-specific mitochondrial f-orf gene for population genetic, phylogeographic and systematic studies in freshwater mussels (Bivalvia: Unionida)
type: item
type: AcademicArticle
description: Freshwater mussels (order: Unionida) represent one of the most critically imperilled groups of animals; consequently, there exists a need to establish a variety of molecular markers for population genetics and systematic studies in this group. Recently, two novel mitochondrial protein-coding genes were described in unionoids with doubly uniparental inheritance of mtDNA. These genes are the f-orf in female-transmitted mtDNA and the m-orf in male-transmitted mtDNA. In this study, whole F-type mitochondrial genome sequences of two morphologically similar Lampsilis spp. were compared to identify the most divergent protein-coding regions, including the f-orf gene, and evaluate its utility for population genetic and phylogeographic studies in the subfamily Ambleminae. We also tested whether the f-orf gene is phylogenetically informative at the species level. Our preliminary results indicated that the f-orf gene could represent a viable molecular marker for population- and species-level studies in freshwater mussels.
format: application/pdf
format: text/html
creator: Brent M. Robicheau
creator: Emily E. Chase
creator: Walter R. Hoeh
creator: John L. Harris
creator: Donald T. Stewart
creator: Sophie Breton
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.5007
publisher: PeerJ Inc.
rights: © 2018 Robicheau et al.
abstract: Freshwater mussels (order: Unionida) represent one of the most critically imperilled groups of animals; consequently, there exists a need to establish a variety of molecular markers for population genetics and systematic studies in this group. Recently, two novel mitochondrial protein-coding genes were described in unionoids with doubly uniparental inheritance of mtDNA. These genes are the f-orf in female-transmitted mtDNA and the m-orf in male-transmitted mtDNA. In this study, whole F-type mitochondrial genome sequences of two morphologically similar Lampsilis spp. were compared to identify the most divergent protein-coding regions, including the f-orf gene, and evaluate its utility for population genetic and phylogeographic studies in the subfamily Ambleminae. We also tested whether the f-orf gene is phylogenetically informative at the species level. Our preliminary results indicated that the f-orf gene could represent a viable molecular marker for population- and species-level studies in freshwater mussels.
bibliographic citation: Robicheau et al. (2018) Evaluating the utility of the female-specific mitochondrial f-orf gene for population genetic, phylogeographic and systematic studies in freshwater mussels (Bivalvia: Unionida). PeerJ 6:e5007 https://doi.org/10.7717/peerj.5007
date submitted: 2018-02-17
date accepted: 2018-05-29
issued: 2018-06-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Robicheau
  given name: Brent M.
author list: Agent
  family name: Chase
  given name: Emily E.
author list: Agent
  family name: Hoeh
  given name: Walter R.
author list: Agent
  family name: Harris
  given name: John L.
author list: Agent
  family name: Stewart
  given name: Donald T.
author list: Agent
  family name: Breton
  given name: Sophie
doi: 10.7717/peerj.5007
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-13
copyright: ©2018 Robicheau et al.
attribution name: Robicheau et al.

Efficient dispersal and substrate acquisition traits in a marine invasive species via transient chimerism and colony mobility
type: item
type: AcademicArticle
description: Over the past three decades the colonial ascidian Didemnum vexillum has been expanding its global range, significantly impacting marine habitats and aquaculture facilities. What biological features make D. vexillum so highly invasive? Here, we show that juxtaposed allogeneic D. vexillum colony fragments (‘ramets’) may, initially, form chimeric entities. Subsequently, zooids of the differing genotypes within such chimeras coordinately retreat away from fusion zones. A few days following such post-fusion retreat movements there is further ramet fission and the formation of zooid-depauperate tunic zones. Using polymorphic microsatellite loci to distinguish between genotypes, we found that they were sectorial at the fusion zones and the subsequent ramet movements resulted in further spatial separation of the paired-genotypes indicating that the fusion events observed did not lead to formation of long-term, stable chimeras. Thus, movements of D. vexillum colony ramets from initial fusion zones lead to progressive segregation of genotypes probably minimizing potential somatic/germ-cell competition/parasitism. We speculate that relatively fast (≤10 mm/day) movement of D. vexillum colonies on substrates along with frequent, and perhaps unrestrained, transient allogeneic fusions play significant roles in this species’ striking invasiveness and capacity to colonize new substrates.
format: application/pdf
format: text/html
creator: Andrew E. Fidler
creator: Aurelie Bacq-Labreuil
creator: Elad Rachmilovitz
creator: Baruch Rinkevich
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.5006
publisher: PeerJ Inc.
rights: © 2018 Fidler et al.
abstract: Over the past three decades the colonial ascidian Didemnum vexillum has been expanding its global range, significantly impacting marine habitats and aquaculture facilities. What biological features make D. vexillum so highly invasive? Here, we show that juxtaposed allogeneic D. vexillum colony fragments (‘ramets’) may, initially, form chimeric entities. Subsequently, zooids of the differing genotypes within such chimeras coordinately retreat away from fusion zones. A few days following such post-fusion retreat movements there is further ramet fission and the formation of zooid-depauperate tunic zones. Using polymorphic microsatellite loci to distinguish between genotypes, we found that they were sectorial at the fusion zones and the subsequent ramet movements resulted in further spatial separation of the paired-genotypes indicating that the fusion events observed did not lead to formation of long-term, stable chimeras. Thus, movements of D. vexillum colony ramets from initial fusion zones lead to progressive segregation of genotypes probably minimizing potential somatic/germ-cell competition/parasitism. We speculate that relatively fast (≤10 mm/day) movement of D. vexillum colonies on substrates along with frequent, and perhaps unrestrained, transient allogeneic fusions play significant roles in this species’ striking invasiveness and capacity to colonize new substrates.
bibliographic citation: Fidler et al. (2018) Efficient dispersal and substrate acquisition traits in a marine invasive species via transient chimerism and colony mobility. PeerJ 6:e5006 https://doi.org/10.7717/peerj.5006
date submitted: 2018-03-08
date accepted: 2018-05-29
issued: 2018-06-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fidler
  given name: Andrew E.
author list: Agent
  family name: Bacq-Labreuil
  given name: Aurelie
author list: Agent
  family name: Rachmilovitz
  given name: Elad
author list: Agent
  family name: Rinkevich
  given name: Baruch
doi: 10.7717/peerj.5006
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-13
copyright: ©2018 Fidler et al.
attribution name: Fidler et al.

Synergistic and antagonistic effects of immunomodulatory drugs on the action of antifungals against Candida glabrata and Saccharomyces cerevisiae
type: item
type: AcademicArticle
description: Candidemia and other forms of invasive fungal infections caused by Candida glabrata and to a lesser extent Saccharomyces cerevisiae are a serious health problem, especially if their steadily rising resistance to the limited range of antifungal drugs is taken into consideration. Various drug combinations are an attractive solution to the resistance problem, and some drug combinations are already common in the clinical environment due to the nature of diseases or therapies. We tested a few of the common antifungal-immunomodulatory drug combinations and evaluated their effect on selected strains of C. glabrata and S. cerevisiae. The combinations were performed using the checkerboard microdilution assay and interpreted using the Loewe additivity model and a model based on the Bliss independence criterion. A synergistic interaction was confirmed between calcineurin inhibitors (Fk506 and cyclosporine A) and antifungals (fluconazole, itraconazole, and amphotericin B). A new antagonistic interaction between mycophenolic acid (MPA) and azole antifungals was discovered in non-resistant strains. A possible mechanism that explains this is induction of the Cdr1 efflux pump by MPA in C. glabrata ATCC 2001. The Pdr1 regulatory cascade plays a role in overall resistance to fluconazole, but it is not essential for the antagonistic interaction. This was confirmed by the Cgpdr1Δ mutant still displaying the antagonistic interaction between the drugs, although at lower concentrations of fluconazole. This antagonism calls into question the use of simultaneous therapy with MPA and azoles in the clinical environment.
format: application/pdf
format: text/html
creator: Miha Tome
creator: Jure Zupan
creator: Zorica Tomičić
creator: Tadeja Matos
creator: Peter Raspor
subject: Microbiology
subject: Drugs and Devices
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.4999
publisher: PeerJ Inc.
rights: © 2018 Tome et al.
abstract: Candidemia and other forms of invasive fungal infections caused by Candida glabrata and to a lesser extent Saccharomyces cerevisiae are a serious health problem, especially if their steadily rising resistance to the limited range of antifungal drugs is taken into consideration. Various drug combinations are an attractive solution to the resistance problem, and some drug combinations are already common in the clinical environment due to the nature of diseases or therapies. We tested a few of the common antifungal-immunomodulatory drug combinations and evaluated their effect on selected strains of C. glabrata and S. cerevisiae. The combinations were performed using the checkerboard microdilution assay and interpreted using the Loewe additivity model and a model based on the Bliss independence criterion. A synergistic interaction was confirmed between calcineurin inhibitors (Fk506 and cyclosporine A) and antifungals (fluconazole, itraconazole, and amphotericin B). A new antagonistic interaction between mycophenolic acid (MPA) and azole antifungals was discovered in non-resistant strains. A possible mechanism that explains this is induction of the Cdr1 efflux pump by MPA in C. glabrata ATCC 2001. The Pdr1 regulatory cascade plays a role in overall resistance to fluconazole, but it is not essential for the antagonistic interaction. This was confirmed by the Cgpdr1Δ mutant still displaying the antagonistic interaction between the drugs, although at lower concentrations of fluconazole. This antagonism calls into question the use of simultaneous therapy with MPA and azoles in the clinical environment.
bibliographic citation: Tome et al. (2018) Synergistic and antagonistic effects of immunomodulatory drugs on the action of antifungals against Candida glabrata and Saccharomyces cerevisiae. PeerJ 6:e4999 https://doi.org/10.7717/peerj.4999
date submitted: 2018-02-13
date accepted: 2018-05-29
issued: 2018-06-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tome
  given name: Miha
author list: Agent
  family name: Zupan
  given name: Jure
author list: Agent
  family name: Tomičić
  given name: Zorica
author list: Agent
  family name: Matos
  given name: Tadeja
author list: Agent
  family name: Raspor
  given name: Peter
doi: 10.7717/peerj.4999
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-13
copyright: ©2018 Tome et al.
attribution name: Tome et al.

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