PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bacterial communities in the digester bed and liquid effluent of a microflush composting toilet system
items: Modelling of the SDF-1/CXCR4 regulated in vivo homing of therapeutic mesenchymal stem/stromal cells in mice
items: Conservation implications of primate trade in China over 18 years based on web news reports of confiscations
items: Association of urinary activity of MMP-9 with renal impairment in Mexican patients with type 2 diabetes mellitus
items: Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients
items: Diversity of social-genetic relationships in the socially monogamous pied flycatcher (Ficedula hypoleuca) breeding in Western Siberia
items: Urbanization, environmental stabilization and temporal persistence of bird species: a view from Latin America
items: JacLy: a Jacobian-based method for the inference of metabolic interactions from the covariance of steady-state metabolome data
items: An integrative taxonomic approach reveals Octopus insularis as the dominant species in the Veracruz Reef System (southwestern Gulf of Mexico)
items: Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta

Bacterial communities in the digester bed and liquid effluent of a microflush composting toilet system
type: item
type: AcademicArticle
description: Lack of access to clean water and sanitation is a major factor impacting public health in communities worldwide. To address this, the S-Lab at Providence College and the Global Sustainable Aid Project developed a microflush composting toilet system to isolate and treat human waste. Solid waste is composted within a filter-digester bed via an aerobic process involving microbes and invertebrates. Liquid waste may be sanitized by solar disinfection (SODIS) or slow sand filtration (SSF). Here, we used 16S rRNA amplicon sequencing of samples from a scaled-down test version of the system to better understand the bacterial component of the toilet system. Immediately after fecal matter was deposited in the test system, the bacterial community of the filter-digester bed at the site of deposition resembled that of the human gut at both the phylum and genus level, which was expected. Genus-level analysis of filter-digester bed samples collected over the next 30 days from the site of deposition showed reduced or undetectable levels of fecal-associated taxa, with the exception of Clostridium XI, which persisted at low abundance throughout the sampling period. Starting with the sample collected on day 4, the bacterial community of the filter-digester bed at the site of deposition was dominated by bacterial taxa commonly associated with environmental sources, reflecting a major shift in bacterial community composition. These data support the toilet system’s capacity for processing solid human waste. We also analyzed how SODIS and SSF sanitization methods affected the bacterial community composition of liquid effluent collected on day 15 from the test system. Untreated and treated liquid effluent samples were dominated by Proteobacteria. At the genus level, the bacterial community of the untreated effluent included taxa commonly associated with environmental sources. In the SODIS-treated effluent, these genera increased in abundance, whereas in the SSF-treated effluent, they were g…
format: application/pdf
format: text/html
creator: Laura E. Williams
creator: Claire E. Kleinschmidt
creator: Stephen Mecca
subject: Microbiology
subject: Public Health
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6077
publisher: PeerJ Inc.
rights: © 2018 Williams et al.
abstract: Lack of access to clean water and sanitation is a major factor impacting public health in communities worldwide. To address this, the S-Lab at Providence College and the Global Sustainable Aid Project developed a microflush composting toilet system to isolate and treat human waste. Solid waste is composted within a filter-digester bed via an aerobic process involving microbes and invertebrates. Liquid waste may be sanitized by solar disinfection (SODIS) or slow sand filtration (SSF). Here, we used 16S rRNA amplicon sequencing of samples from a scaled-down test version of the system to better understand the bacterial component of the toilet system. Immediately after fecal matter was deposited in the test system, the bacterial community of the filter-digester bed at the site of deposition resembled that of the human gut at both the phylum and genus level, which was expected. Genus-level analysis of filter-digester bed samples collected over the next 30 days from the site of deposition showed reduced or undetectable levels of fecal-associated taxa, with the exception of Clostridium XI, which persisted at low abundance throughout the sampling period. Starting with the sample collected on day 4, the bacterial community of the filter-digester bed at the site of deposition was dominated by bacterial taxa commonly associated with environmental sources, reflecting a major shift in bacterial community composition. These data support the toilet system’s capacity for processing solid human waste. We also analyzed how SODIS and SSF sanitization methods affected the bacterial community composition of liquid effluent collected on day 15 from the test system. Untreated and treated liquid effluent samples were dominated by Proteobacteria. At the genus level, the bacterial community of the untreated effluent included taxa commonly associated with environmental sources. In the SODIS-treated effluent, these genera increased in abundance, whereas in the SSF-treated effluent, they were g…
bibliographic citation: Williams et al. (2018) Bacterial communities in the digester bed and liquid effluent of a microflush composting toilet system. PeerJ 6:e6077 https://doi.org/10.7717/peerj.6077
date submitted: 2018-09-05
date accepted: 2018-11-05
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Williams
  given name: Laura E.
author list: Agent
  family name: Kleinschmidt
  given name: Claire E.
author list: Agent
  family name: Mecca
  given name: Stephen
doi: 10.7717/peerj.6077
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: © 2018 Williams et al.
attribution name: Williams et al.

Modelling of the SDF-1/CXCR4 regulated in vivo homing of therapeutic mesenchymal stem/stromal cells in mice
type: item
type: AcademicArticle
description: Background Mesenchymal stem/stromal cells (MSCs) are a promising tool for cell-based therapies in the treatment of tissue injury. The stromal cell-derived factor-1 (SDF-1)/CXC chemokine receptor 4 (CXCR4) axis plays a significant role in directing MSC homing to sites of injury. However in vivo MSC distribution following intravenous transplantation remains poorly understood, potentially hampering the precise prediction and evaluation of therapeutic efficacy. Methods A murine model of partial ischemia/reperfusion (I/R) is used to induce liver injury, increase the hepatic levels of SDF-1, and study in vivo MSC distribution. Hypoxia-preconditioning increases the expression of CXCR4 in human bone marrow-derived MSCs. Quantitative assays for human DNA using droplet digital PCR (ddPCR) allow us to examine the in vivo kinetics of intravenously infused human MSCs in mouse blood and liver. A mathematical model-based system is developed to characterize in vivo homing of human MSCs in mouse models with SDF-1 levels in liver and CXCR4 expression on the transfused MSCs. The model is calibrated to experimental data to provide novel estimates of relevant parameter values. Results Images of immunohistochemistry for SDF-1 in the mouse liver with I/R injury show a significantly higher SDF-1 level in the I/R injured liver than that in the control. Correspondingly, the ddPCR results illustrate a higher MSC concentration in the I/R injured liver than the normal liver. CXCR4 is overexpressed in hypoxia-preconditioned MSCs. An increased number of hypoxia-preconditioned MSCs in the I/R injured liver is observed from the ddPCR results. The model simulations align with the experimental data of control and hypoxia-preconditioned human MSC distribution in normal and injured mouse livers, and accurately predict the experimental outcomes with different MSC doses. Discussion The modelling results suggest that SDF-1 in organs is an effective in vivo attractant for MSCs through the SDF-1/CXCR4 axis …
format: application/pdf
format: text/html
creator: Wang Jin
creator: Xiaowen Liang
creator: Anastasia Brooks
creator: Kathryn Futrega
creator: Xin Liu
creator: Michael R. Doran
creator: Matthew J. Simpson
creator: Michael S. Roberts
creator: Haolu Wang
subject: Cell Biology
subject: Mathematical Biology
subject: Drugs and Devices
description: doi:10.7717/peerj.6072
publisher: PeerJ Inc.
rights: © 2018 Jin et al.
abstract: Background Mesenchymal stem/stromal cells (MSCs) are a promising tool for cell-based therapies in the treatment of tissue injury. The stromal cell-derived factor-1 (SDF-1)/CXC chemokine receptor 4 (CXCR4) axis plays a significant role in directing MSC homing to sites of injury. However in vivo MSC distribution following intravenous transplantation remains poorly understood, potentially hampering the precise prediction and evaluation of therapeutic efficacy. Methods A murine model of partial ischemia/reperfusion (I/R) is used to induce liver injury, increase the hepatic levels of SDF-1, and study in vivo MSC distribution. Hypoxia-preconditioning increases the expression of CXCR4 in human bone marrow-derived MSCs. Quantitative assays for human DNA using droplet digital PCR (ddPCR) allow us to examine the in vivo kinetics of intravenously infused human MSCs in mouse blood and liver. A mathematical model-based system is developed to characterize in vivo homing of human MSCs in mouse models with SDF-1 levels in liver and CXCR4 expression on the transfused MSCs. The model is calibrated to experimental data to provide novel estimates of relevant parameter values. Results Images of immunohistochemistry for SDF-1 in the mouse liver with I/R injury show a significantly higher SDF-1 level in the I/R injured liver than that in the control. Correspondingly, the ddPCR results illustrate a higher MSC concentration in the I/R injured liver than the normal liver. CXCR4 is overexpressed in hypoxia-preconditioned MSCs. An increased number of hypoxia-preconditioned MSCs in the I/R injured liver is observed from the ddPCR results. The model simulations align with the experimental data of control and hypoxia-preconditioned human MSC distribution in normal and injured mouse livers, and accurately predict the experimental outcomes with different MSC doses. Discussion The modelling results suggest that SDF-1 in organs is an effective in vivo attractant for MSCs through the SDF-1/CXCR4 axis …
bibliographic citation: Jin et al. (2018) Modelling of the SDF-1/CXCR4 regulated in vivo homing of therapeutic mesenchymal stem/stromal cells in mice. PeerJ 6:e6072 https://doi.org/10.7717/peerj.6072
date submitted: 2018-08-22
date accepted: 2018-11-05
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Wang
author list: Agent
  family name: Liang
  given name: Xiaowen
author list: Agent
  family name: Brooks
  given name: Anastasia
author list: Agent
  family name: Futrega
  given name: Kathryn
author list: Agent
  family name: Liu
  given name: Xin
author list: Agent
  family name: Doran
  given name: Michael R.
author list: Agent
  family name: Simpson
  given name: Matthew J.
author list: Agent
  family name: Roberts
  given name: Michael S.
author list: Agent
  family name: Wang
  given name: Haolu
doi: 10.7717/peerj.6072
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: ©2018 Jin et al.
attribution name: Jin et al.

Conservation implications of primate trade in China over 18 years based on web news reports of confiscations
type: item
type: AcademicArticle
description: Primate species have been increasingly threatened by legal and illegal trade in China, mainly for biomedical research or as pets and traditional medicine, yet most reports on trade from China regard international trade. To assess a proxy for amount of national primate trades, we quantified the number of reports of native primate species featuring in unique web news reports from 2000 to 2017, including accuracy of their identification, location where they were confiscated or rescued, and their condition upon rescue. To measure temporal trends across these categories, the time span was divided into three sections: 2000–2005, 2006–2011 and 2012–2017. A total of 735 individuals of 14 species were reported in 372 news reports, mostly rhesus macaques (n = 165, 22.5%, Macaca mulatta) and two species of slow lorises (n = 487, 66.3%, Nycticebus spp.). During the same period, live individuals of rhesus macaques were recorded 206 times (70,949 individuals) in the Convention on International Trade in Endangered Species of Wild Fauna and Flora Trade Database, whereas slow lorises were only recorded four times (nine individuals), indicating that the species originated illegally from China or were illegally imported into China. Due to their rescued locations in residential areas (n = 211, 56.7%), most primates appeared to be housed privately as pets. A higher proportion of ‘market’ rescues during 2006–2011 (χ2 = 8.485, df = 2, p = 0.014), could be partly attributed to an intensive management on wildlife markets since the outbreak of severe acute respiratory syndrome (SARS) in 2003. More than half (68.3%, 502 individuals) of the primate individuals were unhealthy, injured or dead when rescued. Thus, identification and welfare training and capacity-building should be provided to husbandry and veterinary professionals, as well as education to the public through awareness initiatives. The increase in presence of some species, especially slow lorises, with a declining population in res…
format: application/pdf
format: text/html
creator: Qingyong Ni
creator: Yu Wang
creator: Ariana Weldon
creator: Meng Xie
creator: Huailiang Xu
creator: Yongfang Yao
creator: Mingwang Zhang
creator: Ying Li
creator: Yan Li
creator: Bo Zeng
creator: K.A.I. Nekaris
subject: Biodiversity
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.6069
publisher: PeerJ Inc.
rights: © 2018 Ni et al.
abstract: Primate species have been increasingly threatened by legal and illegal trade in China, mainly for biomedical research or as pets and traditional medicine, yet most reports on trade from China regard international trade. To assess a proxy for amount of national primate trades, we quantified the number of reports of native primate species featuring in unique web news reports from 2000 to 2017, including accuracy of their identification, location where they were confiscated or rescued, and their condition upon rescue. To measure temporal trends across these categories, the time span was divided into three sections: 2000–2005, 2006–2011 and 2012–2017. A total of 735 individuals of 14 species were reported in 372 news reports, mostly rhesus macaques (n = 165, 22.5%, Macaca mulatta) and two species of slow lorises (n = 487, 66.3%, Nycticebus spp.). During the same period, live individuals of rhesus macaques were recorded 206 times (70,949 individuals) in the Convention on International Trade in Endangered Species of Wild Fauna and Flora Trade Database, whereas slow lorises were only recorded four times (nine individuals), indicating that the species originated illegally from China or were illegally imported into China. Due to their rescued locations in residential areas (n = 211, 56.7%), most primates appeared to be housed privately as pets. A higher proportion of ‘market’ rescues during 2006–2011 (χ2 = 8.485, df = 2, p = 0.014), could be partly attributed to an intensive management on wildlife markets since the outbreak of severe acute respiratory syndrome (SARS) in 2003. More than half (68.3%, 502 individuals) of the primate individuals were unhealthy, injured or dead when rescued. Thus, identification and welfare training and capacity-building should be provided to husbandry and veterinary professionals, as well as education to the public through awareness initiatives. The increase in presence of some species, especially slow lorises, with a declining population in res…
bibliographic citation: Ni et al. (2018) Conservation implications of primate trade in China over 18 years based on web news reports of confiscations. PeerJ 6:e6069 https://doi.org/10.7717/peerj.6069
date submitted: 2018-08-20
date accepted: 2018-11-05
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ni
  given name: Qingyong
author list: Agent
  family name: Wang
  given name: Yu
author list: Agent
  family name: Weldon
  given name: Ariana
author list: Agent
  family name: Xie
  given name: Meng
author list: Agent
  family name: Xu
  given name: Huailiang
author list: Agent
  family name: Yao
  given name: Yongfang
author list: Agent
  family name: Zhang
  given name: Mingwang
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: Zeng
  given name: Bo
author list: Agent
  family name: Nekaris
  given name: K.A.I.
doi: 10.7717/peerj.6069
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: © 2018 Ni et al.
attribution name: Ni et al.

Association of urinary activity of MMP-9 with renal impairment in Mexican patients with type 2 diabetes mellitus
type: item
type: AcademicArticle
description: Background Diabetic kidney disease is the most common cause of chronic kidney disease (CKD). An early event in diabetic kidney disease is alteration of the glomerular basement membrane and the mesangial expansion. Matrix metalloproteinases (MMP) are a family of endopeptidases responsible for controlling the pathophysiological remodeling of tissues, including renal tissues. MMP-9 in human urine has been proposed as a marker of diabetic nephropathy and urinary tract infections (UTI). Methods A cross-sectional study was conducted in type 2 diabetes mellitus (T2DM) patients who receive first level medical attention in Mexico. We used ELISA to measure MMP-9 levels in the urine of subjects with T2DM ≥ 18 years of age, who fulfilled the clinical requirements for calculation of glomerular filtration rate (GFR), according to the K/DOQI guide, in an attempt to identify whether MMP-9 levels in T2DM differ in patients with and without renal impairment. Univariate and multivariable analyses were performed in order to identify the association between MMP-9 and renal impairment. Results Included in the study were 34 (45%) subjects with renal impairment and 42 (55%) without. In the group with renal impairment, 10 subjects corresponded to stages 1–2 and 24 subjects corresponded to stage 3, according to their values of GFR and urinary albumin, following that proposed by the K/DOQI. No differences were found relating to sex, age, having or not having a partner, education, being able to read and write a message and duration of T2DM. Moreover, no differences were found between the groups in terms of weight, height, body mass index, waist size in general and frequency of UTI. In contrast, serum creatinine and urinary albumin were higher in the group with renal impairment, while GFR was greater in the group without renal impairment. Levels of MMP-9 were greater in women compared to men. Through univariate analysis in the general population, the presence of MMP-9 and that of its percentile…
format: application/pdf
format: text/html
creator: Alan Uriel García-Tejeda
creator: Clara Luz Sampieri
creator: Irene Suárez-Torres
creator: Jaime Morales-Romero
creator: Verónica Patricia Demeneghi-Marini
creator: Magda Elena Hernández-Hernández
creator: Arturo Rodríguez-Hernández
subject: Biochemistry
subject: Diabetes and Endocrinology
subject: Urology
description: doi:10.7717/peerj.6067
publisher: PeerJ Inc.
rights: © 2018 García-Tejeda et al.
abstract: Background Diabetic kidney disease is the most common cause of chronic kidney disease (CKD). An early event in diabetic kidney disease is alteration of the glomerular basement membrane and the mesangial expansion. Matrix metalloproteinases (MMP) are a family of endopeptidases responsible for controlling the pathophysiological remodeling of tissues, including renal tissues. MMP-9 in human urine has been proposed as a marker of diabetic nephropathy and urinary tract infections (UTI). Methods A cross-sectional study was conducted in type 2 diabetes mellitus (T2DM) patients who receive first level medical attention in Mexico. We used ELISA to measure MMP-9 levels in the urine of subjects with T2DM ≥ 18 years of age, who fulfilled the clinical requirements for calculation of glomerular filtration rate (GFR), according to the K/DOQI guide, in an attempt to identify whether MMP-9 levels in T2DM differ in patients with and without renal impairment. Univariate and multivariable analyses were performed in order to identify the association between MMP-9 and renal impairment. Results Included in the study were 34 (45%) subjects with renal impairment and 42 (55%) without. In the group with renal impairment, 10 subjects corresponded to stages 1–2 and 24 subjects corresponded to stage 3, according to their values of GFR and urinary albumin, following that proposed by the K/DOQI. No differences were found relating to sex, age, having or not having a partner, education, being able to read and write a message and duration of T2DM. Moreover, no differences were found between the groups in terms of weight, height, body mass index, waist size in general and frequency of UTI. In contrast, serum creatinine and urinary albumin were higher in the group with renal impairment, while GFR was greater in the group without renal impairment. Levels of MMP-9 were greater in women compared to men. Through univariate analysis in the general population, the presence of MMP-9 and that of its percentile…
bibliographic citation: García-Tejeda et al. (2018) Association of urinary activity of MMP-9 with renal impairment in Mexican patients with type 2 diabetes mellitus. PeerJ 6:e6067 https://doi.org/10.7717/peerj.6067
date submitted: 2018-06-21
date accepted: 2018-11-04
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Tejeda
  given name: Alan Uriel
author list: Agent
  family name: Sampieri
  given name: Clara Luz
author list: Agent
  family name: Suárez-Torres
  given name: Irene
author list: Agent
  family name: Morales-Romero
  given name: Jaime
author list: Agent
  family name: Demeneghi-Marini
  given name: Verónica Patricia
author list: Agent
  family name: Hernández-Hernández
  given name: Magda Elena
author list: Agent
  family name: Rodríguez-Hernández
  given name: Arturo
doi: 10.7717/peerj.6067
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: © 2018 García-Tejeda et al.
attribution name: García-Tejeda et al.

Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients
type: item
type: AcademicArticle
description: Background Colorectal cancer remains a serious public health problem due to the poor prognosis. In the present study, we attempted to develop and validate a prognostic signature to predict the individual mortality risk in colorectal cancer patients. Materials and Methods The original study datasets were downloaded from The Cancer Genome Atlas database. The present study finally included 424 colorectal cancer patients with wholly gene expression information and overall survival information. Results A nine-lncRNA prognostic signature was built through univariate and multivariate Cox proportional regression model. Time-dependent receiver operating characteristic curves in model cohort demonstrated that the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.768 (95% CI [0.717–0.819]), 0.778 (95% CI [0.727–0.829]) and 0.870 (95% CI [0.819–0.921]) for 1-year, 3-year and 5-year overall survival respectively. In validation cohort, the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.761 (95% CI [0.710–0.812]), 0.801 (95% CI [0.750–0.852]) and 0.883 (95% CI [0.832–0.934]) for 1-year, 3-year and 5-year overall survival respectively. According to the median of nine-lncRNA prognostic signature score in model cohort, 424 CRC patients could be stratified into high risk group (n = 212) and low risk group (n = 212). Kaplan–Meier survival curves showed that the overall survival rate of high risk group was significantly lower than that of low risk group (P < 0.001). Discussion The present study developed and validated a nine-lncRNA prognostic signature for individual mortality risk assessment in colorectal cancer patients. This nine-lncRNA prognostic signature is helpful to evaluate the individual mortality risk and to improve the decision making of individualized treatments in colorectal cancer patients.
format: application/pdf
format: text/html
creator: Zhiqiao Zhang
creator: Qingbo Liu
creator: Peng Wang
creator: Jing Li
creator: Tingshan He
creator: Yanling Ouyang
creator: Yiyan Huang
creator: Weidong Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.6061
publisher: PeerJ Inc.
rights: © 2018 Zhang et al.
abstract: Background Colorectal cancer remains a serious public health problem due to the poor prognosis. In the present study, we attempted to develop and validate a prognostic signature to predict the individual mortality risk in colorectal cancer patients. Materials and Methods The original study datasets were downloaded from The Cancer Genome Atlas database. The present study finally included 424 colorectal cancer patients with wholly gene expression information and overall survival information. Results A nine-lncRNA prognostic signature was built through univariate and multivariate Cox proportional regression model. Time-dependent receiver operating characteristic curves in model cohort demonstrated that the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.768 (95% CI [0.717–0.819]), 0.778 (95% CI [0.727–0.829]) and 0.870 (95% CI [0.819–0.921]) for 1-year, 3-year and 5-year overall survival respectively. In validation cohort, the Harrell’s concordance indexes of nine-lncRNA prognostic signature were 0.761 (95% CI [0.710–0.812]), 0.801 (95% CI [0.750–0.852]) and 0.883 (95% CI [0.832–0.934]) for 1-year, 3-year and 5-year overall survival respectively. According to the median of nine-lncRNA prognostic signature score in model cohort, 424 CRC patients could be stratified into high risk group (n = 212) and low risk group (n = 212). Kaplan–Meier survival curves showed that the overall survival rate of high risk group was significantly lower than that of low risk group (P < 0.001). Discussion The present study developed and validated a nine-lncRNA prognostic signature for individual mortality risk assessment in colorectal cancer patients. This nine-lncRNA prognostic signature is helpful to evaluate the individual mortality risk and to improve the decision making of individualized treatments in colorectal cancer patients.
bibliographic citation: Zhang et al. (2018) Development and internal validation of a nine-lncRNA prognostic signature for prediction of overall survival in colorectal cancer patients. PeerJ 6:e6061 https://doi.org/10.7717/peerj.6061
date submitted: 2018-08-27
date accepted: 2018-11-03
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Zhiqiao
author list: Agent
  family name: Liu
  given name: Qingbo
author list: Agent
  family name: Wang
  given name: Peng
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: He
  given name: Tingshan
author list: Agent
  family name: Ouyang
  given name: Yanling
author list: Agent
  family name: Huang
  given name: Yiyan
author list: Agent
  family name: Wang
  given name: Weidong
doi: 10.7717/peerj.6061
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: ©2018 Zhang et al.
attribution name: Zhang et al.

Diversity of social-genetic relationships in the socially monogamous pied flycatcher (Ficedula hypoleuca) breeding in Western Siberia
type: item
type: AcademicArticle
description: We explored the genetic background of social interactions in two breeding metapopulations of the pied flycatcher (Ficedula hypoleuca) in Western Siberia. In 2005, we sampled blood from birds breeding in study areas located in the city of Tomsk and in a natural forest 13 km southward of Tomsk (Western Siberia, Russia). We sampled 30 males, 46 females, 268 nestlings (46 nests) in the urban settlement of pied flycatcher, and 232 males, 250 females, 1,485 nestlings (250 nests) in the woodland plot. DNA fingerprinting was carried out using eight microsatellite loci, which were amplified by two multiplex-PCRs and analyzed by capillary electrophoresis. About 50–58% of all couples were socially and genetically monogamous in both study plots. However, almost all possible social and genetic interactions were detected for non-monogamous couples: polygamy, polyandry, helping, adoption, and egg dumping. Differences in the rate of polygyny and the rate of extra-pair paternity between both study sites could be explained by differences in environmental heterogeneity and breeding density. Our findings suggest that egg dumping, adoption, polygamy, extra pair copulation, and other types of social-genetic interactions are modifications of the monogamous social system caused by patchy environment, breeding density, and birds’ breeding status.
format: application/pdf
format: text/html
creator: Vladimir G. Grinkov
creator: Andreas Bauer
creator: Sergey I. Gashkov
creator: Helmut Sternberg
creator: Michael Wink
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.6059
publisher: PeerJ Inc.
rights: © 2018 Grinkov et al.
abstract: We explored the genetic background of social interactions in two breeding metapopulations of the pied flycatcher (Ficedula hypoleuca) in Western Siberia. In 2005, we sampled blood from birds breeding in study areas located in the city of Tomsk and in a natural forest 13 km southward of Tomsk (Western Siberia, Russia). We sampled 30 males, 46 females, 268 nestlings (46 nests) in the urban settlement of pied flycatcher, and 232 males, 250 females, 1,485 nestlings (250 nests) in the woodland plot. DNA fingerprinting was carried out using eight microsatellite loci, which were amplified by two multiplex-PCRs and analyzed by capillary electrophoresis. About 50–58% of all couples were socially and genetically monogamous in both study plots. However, almost all possible social and genetic interactions were detected for non-monogamous couples: polygamy, polyandry, helping, adoption, and egg dumping. Differences in the rate of polygyny and the rate of extra-pair paternity between both study sites could be explained by differences in environmental heterogeneity and breeding density. Our findings suggest that egg dumping, adoption, polygamy, extra pair copulation, and other types of social-genetic interactions are modifications of the monogamous social system caused by patchy environment, breeding density, and birds’ breeding status.
bibliographic citation: Grinkov et al. (2018) Diversity of social-genetic relationships in the socially monogamous pied flycatcher (Ficedula hypoleuca) breeding in Western Siberia. PeerJ 6:e6059 https://doi.org/10.7717/peerj.6059
date submitted: 2018-03-13
date accepted: 2018-11-04
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grinkov
  given name: Vladimir G.
author list: Agent
  family name: Bauer
  given name: Andreas
author list: Agent
  family name: Gashkov
  given name: Sergey I.
author list: Agent
  family name: Sternberg
  given name: Helmut
author list: Agent
  family name: Wink
  given name: Michael
doi: 10.7717/peerj.6059
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: © 2018 Grinkov et al.
attribution name: Grinkov et al.

Urbanization, environmental stabilization and temporal persistence of bird species: a view from Latin America
type: item
type: AcademicArticle
description: Background A scarcely studied consequence of urbanization is the effect of temporal stabilization of the environment on bird communities. This alteration is thought to dampen environmental variations between day and night, seasons and years, promoting a temporal persistence of bird composition in urban areas. The aim of this study was to review current evidence of temporal stabilization of biotic and abiotic factors in urban environments and the potential effects of such stabilization on temporal variation of bird species presence at different temporal scales. Methods I selected the literature by searching published articles and book chapters using Scopus and Google scholar. I only included articles that compared the temporal variation of bird composition or resources between different levels of urbanization. Results In general, there is evidence of temporal stabilization of abiotic and biotic factors at the three time scales considered. At the diurnal scale, the main factor considered was artificial light in the context of light pollution. At the seasonal and interannual scales, several case studies found a smaller temporal variation of primary productivity in urban than in natural and rural areas. Bird species composition showed more stabilization in urban environments at the three temporal scales: (1) several case studies reported bird activity at night, associated with artificial light; (2) studies in urban parks and along urbanization gradients showed smaller seasonal variation of bird composition in the more urbanized areas; and (3) in general, case studies along urbanization gradients showed smaller interannual variation of bird composition in the more urbanized areas, although some studies showed no relationships or opposite trends than expected. Discussion The published evidence suggests that urban areas dampen the natural cycles at several temporal scales. The stabilization of biotic and abiotic factors, such as light, temperature, food and habitat structu…
format: application/pdf
format: text/html
creator: Lucas Matías Leveau
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.6056
publisher: PeerJ Inc.
rights: © 2018 Leveau
abstract: Background A scarcely studied consequence of urbanization is the effect of temporal stabilization of the environment on bird communities. This alteration is thought to dampen environmental variations between day and night, seasons and years, promoting a temporal persistence of bird composition in urban areas. The aim of this study was to review current evidence of temporal stabilization of biotic and abiotic factors in urban environments and the potential effects of such stabilization on temporal variation of bird species presence at different temporal scales. Methods I selected the literature by searching published articles and book chapters using Scopus and Google scholar. I only included articles that compared the temporal variation of bird composition or resources between different levels of urbanization. Results In general, there is evidence of temporal stabilization of abiotic and biotic factors at the three time scales considered. At the diurnal scale, the main factor considered was artificial light in the context of light pollution. At the seasonal and interannual scales, several case studies found a smaller temporal variation of primary productivity in urban than in natural and rural areas. Bird species composition showed more stabilization in urban environments at the three temporal scales: (1) several case studies reported bird activity at night, associated with artificial light; (2) studies in urban parks and along urbanization gradients showed smaller seasonal variation of bird composition in the more urbanized areas; and (3) in general, case studies along urbanization gradients showed smaller interannual variation of bird composition in the more urbanized areas, although some studies showed no relationships or opposite trends than expected. Discussion The published evidence suggests that urban areas dampen the natural cycles at several temporal scales. The stabilization of biotic and abiotic factors, such as light, temperature, food and habitat structu…
bibliographic citation: Leveau (2018) Urbanization, environmental stabilization and temporal persistence of bird species: a view from Latin America. PeerJ 6:e6056 https://doi.org/10.7717/peerj.6056
date submitted: 2018-02-08
date accepted: 2018-11-01
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leveau
  given name: Lucas Matías
doi: 10.7717/peerj.6056
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: ©2018 Leveau
attribution name: Leveau

JacLy: a Jacobian-based method for the inference of metabolic interactions from the covariance of steady-state metabolome data
type: item
type: AcademicArticle
description: Reverse engineering metabolome data to infer metabolic interactions is a challenging research topic. Here we introduce JacLy, a Jacobian-based method to infer metabolic interactions of small networks (<20 metabolites) from the covariance of steady-state metabolome data. The approach was applied to two different in silico small-scale metabolome datasets. The power of JacLy lies on the use of steady-state metabolome data to predict the Jacobian matrix of the system, which is a source of information on structure and dynamic characteristics of the system. Besides its advantage of inferring directed interactions, its superiority over correlation-based network inference was especially clear in terms of the required number of replicates and the effect of the use of priori knowledge in the inference. Additionally, we showed the use of standard deviation of the replicate data as a suitable approximation for the magnitudes of metabolite fluctuations inherent in the system.
format: application/pdf
format: text/html
creator: Mohammad Jafar Khatibipour
creator: Furkan Kurtoğlu
creator: Tunahan Çakır
subject: Bioengineering
subject: Bioinformatics
subject: Biotechnology
subject: Computational Biology
subject: Computational Science
description: doi:10.7717/peerj.6034
publisher: PeerJ Inc.
rights: © 2018 Khatibipour et al.
abstract: Reverse engineering metabolome data to infer metabolic interactions is a challenging research topic. Here we introduce JacLy, a Jacobian-based method to infer metabolic interactions of small networks (<20 metabolites) from the covariance of steady-state metabolome data. The approach was applied to two different in silico small-scale metabolome datasets. The power of JacLy lies on the use of steady-state metabolome data to predict the Jacobian matrix of the system, which is a source of information on structure and dynamic characteristics of the system. Besides its advantage of inferring directed interactions, its superiority over correlation-based network inference was especially clear in terms of the required number of replicates and the effect of the use of priori knowledge in the inference. Additionally, we showed the use of standard deviation of the replicate data as a suitable approximation for the magnitudes of metabolite fluctuations inherent in the system.
bibliographic citation: Khatibipour et al. (2018) JacLy: a Jacobian-based method for the inference of metabolic interactions from the covariance of steady-state metabolome data. PeerJ 6:e6034 https://doi.org/10.7717/peerj.6034
date submitted: 2018-03-23
date accepted: 2018-10-30
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khatibipour
  given name: Mohammad Jafar
author list: Agent
  family name: Kurtoğlu
  given name: Furkan
author list: Agent
  family name: Çakır
  given name: Tunahan
doi: 10.7717/peerj.6034
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: ©2018 Khatibipour et al.
attribution name: Khatibipour et al.

An integrative taxonomic approach reveals Octopus insularis as the dominant species in the Veracruz Reef System (southwestern Gulf of Mexico)
type: item
type: AcademicArticle
description: The common octopus of the Veracruz Reef System (VRS, southwestern Gulf of Mexico) has historically been considered as Octopus vulgaris, and yet, to date, no study including both morphological and genetic data has tested that assumption. To assess this matter, 52 octopuses were sampled in different reefs within the VRS to determine the taxonomic identity of this commercially valuable species using an integrative taxonomic approach through both morphological and genetic analyses. Morphological and genetic data confirmed that the common octopus of the VRS is not O. vulgaris and determined that it is, in fact, the recently described O. insularis. Morphological measurements, counts, indices, and other characteristics such as specific colour patterns, closely matched what had been reported for O. insularis in Brazil. In addition, sequences from cytochrome oxidase I (COI) and 16S ribosomal RNA (r16S) mitochondrial genes confirmed that the common octopus from the VRS is in the same highly supported clade as O. insularis from Brazil. Genetic distances of both mitochondrial genes as well as of cytochrome oxidase subunit III (COIII) and novel nuclear rhodopsin sequences for the species, also confirmed this finding (0–0.8%). We discuss our findings in the light of the recent reports of octopus species misidentifications involving the members of the ‘O. vulgaris species complex’ and underscore the need for more morphological studies regarding this group to properly address the management of these commercially valuable and similar taxa.
format: application/pdf
format: text/html
creator: Roberto González-Gómez
creator: Irene de los Angeles Barriga-Sosa
creator: Ricardo Pliego-Cárdenas
creator: Lourdes Jiménez-Badillo
creator: Unai Markaida
creator: César Meiners-Mandujano
creator: Piedad S. Morillo-Velarde
subject: Biodiversity
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.6015
publisher: PeerJ Inc.
rights: © 2018 González-Gómez et al.
abstract: The common octopus of the Veracruz Reef System (VRS, southwestern Gulf of Mexico) has historically been considered as Octopus vulgaris, and yet, to date, no study including both morphological and genetic data has tested that assumption. To assess this matter, 52 octopuses were sampled in different reefs within the VRS to determine the taxonomic identity of this commercially valuable species using an integrative taxonomic approach through both morphological and genetic analyses. Morphological and genetic data confirmed that the common octopus of the VRS is not O. vulgaris and determined that it is, in fact, the recently described O. insularis. Morphological measurements, counts, indices, and other characteristics such as specific colour patterns, closely matched what had been reported for O. insularis in Brazil. In addition, sequences from cytochrome oxidase I (COI) and 16S ribosomal RNA (r16S) mitochondrial genes confirmed that the common octopus from the VRS is in the same highly supported clade as O. insularis from Brazil. Genetic distances of both mitochondrial genes as well as of cytochrome oxidase subunit III (COIII) and novel nuclear rhodopsin sequences for the species, also confirmed this finding (0–0.8%). We discuss our findings in the light of the recent reports of octopus species misidentifications involving the members of the ‘O. vulgaris species complex’ and underscore the need for more morphological studies regarding this group to properly address the management of these commercially valuable and similar taxa.
bibliographic citation: González-Gómez et al. (2018) An integrative taxonomic approach reveals Octopus insularis as the dominant species in the Veracruz Reef System (southwestern Gulf of Mexico). PeerJ 6:e6015 https://doi.org/10.7717/peerj.6015
date submitted: 2018-09-04
date accepted: 2018-10-26
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: González-Gómez
  given name: Roberto
author list: Agent
  family name: Barriga-Sosa
  given name: Irene de los Angeles
author list: Agent
  family name: Pliego-Cárdenas
  given name: Ricardo
author list: Agent
  family name: Jiménez-Badillo
  given name: Lourdes
author list: Agent
  family name: Markaida
  given name: Unai
author list: Agent
  family name: Meiners-Mandujano
  given name: César
author list: Agent
  family name: Morillo-Velarde
  given name: Piedad S.
doi: 10.7717/peerj.6015
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: © 2018 González-Gómez et al.
attribution name: González-Gómez et al.

Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta
type: item
type: AcademicArticle
description: Coptoformica Müller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta.
format: application/pdf
format: text/html
creator: Sanja Maria Hakala
creator: Perttu Seppä
creator: Maria Heikkilä
creator: Pekka Punttila
creator: Jouni Sorvari
creator: Heikki Helanterä
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
description: doi:10.7717/peerj.6013
publisher: PeerJ Inc.
rights: © 2018 Hakala et al.
abstract: Coptoformica Müller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta.
bibliographic citation: Hakala et al. (2018) Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta. PeerJ 6:e6013 https://doi.org/10.7717/peerj.6013
date submitted: 2018-07-27
date accepted: 2018-10-27
issued: 2018-12-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hakala
  given name: Sanja Maria
author list: Agent
  family name: Seppä
  given name: Perttu
author list: Agent
  family name: Heikkilä
  given name: Maria
author list: Agent
  family name: Punttila
  given name: Pekka
author list: Agent
  family name: Sorvari
  given name: Jouni
author list: Agent
  family name: Helanterä
  given name: Heikki
doi: 10.7717/peerj.6013
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-06
copyright: ©2018 Hakala et al.
attribution name: Hakala et al.

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