PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Rapid identification of melioidosis agent by an insulated isothermal PCR on a field–deployable device
items: Effects of temperature on metabolic scaling in black carp
items: Role of echocardiography in screening for portopulmonary hypertension in liver transplant candidates: a meta-analysis
items: Exact integer linear programming solvers outperform simulated annealing for solving conservation planning problems
items: Bioinformatics profiling identifies seven immune-related risk signatures for hepatocellular carcinoma
items: Descriptions of five new species of the salamander genus Chiropterotriton (Caudata: Plethodontidae) from eastern Mexico and the status of three currently recognized taxa
items: Effective connectivity differences in motor network during passive movement of paretic and non-paretic ankles in subacute stroke patients
items: Microbiome analysis of healthy and diseased sponges Lubomirskia baicalensis by using cell cultures of primmorphs
items: Cca-miR398 increases copper sulfate stress sensitivity via the regulation of CSD mRNA transcription levels in transgenic Arabidopsis thaliana
items: The combined effects of light intensity, temperature, and water potential on wall deposition in regulating hypocotyl elongation of Brassica rapa

Rapid identification of melioidosis agent by an insulated isothermal PCR on a field–deployable device
type: item
type: AcademicArticle
description: Background Burkholderia pseudomallei causes melioidosis, a serious illness that can be fatal if untreated or misdiagnosed. Culture from clinical specimens remains the gold standard but has low diagnostic sensitivity. Method In this study, we developed a rapid, sensitive and specific insulated isothermal Polymerase Chain Reaction (iiPCR) targeting bimA gene (Burkholderia Intracellular Motility A; BPSS1492) for the identification of B. pseudomallei. A pair of novel primers: BimA(F) and BimA(R) together with a probe were designed and 121 clinical B. pseudomallei strains obtained from numerous clinical sources and 10 ATCC non-targeted strains were tested with iiPCR and qPCR in parallel. Results All 121 B. pseudomallei isolates were positive for qPCR while 118 isolates were positive for iiPCR, demonstrating satisfactory agreement (97.71%; 95% CI [93.45–99.53%]; k = 0.87). Sensitivity of the bimA iiPCR/POCKIT assay was 97.52% with the lower detection limit of 14 ng/µL of B. pseudomallei DNA. The developed iiPCR assay did not cross-react with 10 types of non-targeted strains, indicating good specificity. Conclusion This bimA iiPCR/POCKIT assay will undoubtedly complement other methodologies used in the clinical laboratory for the rapid identification of this pathogen.
format: application/pdf
format: text/html
creator: Kek Heng Chua
creator: E. Wei Tan
creator: Hwa Chia Chai
creator: SD Puthucheary
creator: Ping Chin Lee
creator: Suat Moi Puah
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.9238
publisher: PeerJ Inc.
rights: © 2020 Chua et al.
abstract: Background Burkholderia pseudomallei causes melioidosis, a serious illness that can be fatal if untreated or misdiagnosed. Culture from clinical specimens remains the gold standard but has low diagnostic sensitivity. Method In this study, we developed a rapid, sensitive and specific insulated isothermal Polymerase Chain Reaction (iiPCR) targeting bimA gene (Burkholderia Intracellular Motility A; BPSS1492) for the identification of B. pseudomallei. A pair of novel primers: BimA(F) and BimA(R) together with a probe were designed and 121 clinical B. pseudomallei strains obtained from numerous clinical sources and 10 ATCC non-targeted strains were tested with iiPCR and qPCR in parallel. Results All 121 B. pseudomallei isolates were positive for qPCR while 118 isolates were positive for iiPCR, demonstrating satisfactory agreement (97.71%; 95% CI [93.45–99.53%]; k = 0.87). Sensitivity of the bimA iiPCR/POCKIT assay was 97.52% with the lower detection limit of 14 ng/µL of B. pseudomallei DNA. The developed iiPCR assay did not cross-react with 10 types of non-targeted strains, indicating good specificity. Conclusion This bimA iiPCR/POCKIT assay will undoubtedly complement other methodologies used in the clinical laboratory for the rapid identification of this pathogen.
bibliographic citation: Chua et al. (2020) Rapid identification of melioidosis agent by an insulated isothermal PCR on a field–deployable device. PeerJ 8:e9238 https://doi.org/10.7717/peerj.9238
date submitted: 2020-02-05
date accepted: 2020-05-05
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chua
  given name: Kek Heng
author list: Agent
  family name: Tan
  given name: E. Wei
author list: Agent
  family name: Chai
  given name: Hwa Chia
author list: Agent
  family name: Puthucheary
  given name: SD
author list: Agent
  family name: Lee
  given name: Ping Chin
author list: Agent
  family name: Puah
  given name: Suat Moi
doi: 10.7717/peerj.9238
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: ©2020 Chua et al.
attribution name: Chua et al.

Effects of temperature on metabolic scaling in black carp
type: item
type: AcademicArticle
description: The surface area (SA) of organs and cells may vary with temperature, which changes the SA exchange limitation on metabolic flows as well as the influence of temperature on metabolic scaling. The effect of SA change can intensify (when the effect is the same as that of temperature) or compensate for (when the effect is the opposite of that of temperature) the negative effects of temperature on metabolic scaling, which can result in multiple patterns of metabolic scaling with temperature among species. The present study aimed to examine whether metabolic scaling in black carp changes with temperature and to identify the link between metabolic scaling and SA at the organ and cellular levels at different temperatures. The resting metabolic rate (RMR), gill surface area (GSA) and red blood cell (RBC) size of black carp with different body masses were measured at 10 °C and 25 °C, and the scaling exponents of these parameters were compared. The results showed that both body mass and temperature independently affected the RMR, GSA and RBC size of black carp. A consistent scaling exponent of RMR (0.764, 95% CI [0.718–0.809]) was obtained for both temperatures. The RMR at 25 °C was 2.7 times higher than that at 10 °C. At both temperatures, the GSA scaled consistently with body mass by an exponent of 0.802 (95% CI [0.759–0.846]), while RBC size scaled consistently with body mass by an exponent of 0.042 (95% CI [0.010–0.075]). The constant GSA scaling can explain the constant metabolic scaling as temperature increases, as metabolism may be constrained by fluxes across surfaces. The GSA at 10 °C was 1.2 times higher than that at 25 °C, which suggests that the constraints of GSA on the metabolism of black carp is induced by the higher temperature. The RBC size at 10 °C was 1.1 times higher than that at 25 °C. The smaller RBC size (a larger surface-to-volume ratio) at higher temperature suggests an enhanced oxygen supply and a reduced surface boundary limit on bR, which offset the…
format: application/pdf
format: text/html
creator: Qian Li
creator: Xiaoling Zhu
creator: Wei Xiong
creator: Yanqiu Zhu
creator: Jianghui Zhang
creator: Pathe Karim Djiba
creator: Xiao Lv
creator: Yiping Luo
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.9242
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: The surface area (SA) of organs and cells may vary with temperature, which changes the SA exchange limitation on metabolic flows as well as the influence of temperature on metabolic scaling. The effect of SA change can intensify (when the effect is the same as that of temperature) or compensate for (when the effect is the opposite of that of temperature) the negative effects of temperature on metabolic scaling, which can result in multiple patterns of metabolic scaling with temperature among species. The present study aimed to examine whether metabolic scaling in black carp changes with temperature and to identify the link between metabolic scaling and SA at the organ and cellular levels at different temperatures. The resting metabolic rate (RMR), gill surface area (GSA) and red blood cell (RBC) size of black carp with different body masses were measured at 10 °C and 25 °C, and the scaling exponents of these parameters were compared. The results showed that both body mass and temperature independently affected the RMR, GSA and RBC size of black carp. A consistent scaling exponent of RMR (0.764, 95% CI [0.718–0.809]) was obtained for both temperatures. The RMR at 25 °C was 2.7 times higher than that at 10 °C. At both temperatures, the GSA scaled consistently with body mass by an exponent of 0.802 (95% CI [0.759–0.846]), while RBC size scaled consistently with body mass by an exponent of 0.042 (95% CI [0.010–0.075]). The constant GSA scaling can explain the constant metabolic scaling as temperature increases, as metabolism may be constrained by fluxes across surfaces. The GSA at 10 °C was 1.2 times higher than that at 25 °C, which suggests that the constraints of GSA on the metabolism of black carp is induced by the higher temperature. The RBC size at 10 °C was 1.1 times higher than that at 25 °C. The smaller RBC size (a larger surface-to-volume ratio) at higher temperature suggests an enhanced oxygen supply and a reduced surface boundary limit on bR, which offset the…
bibliographic citation: Li et al. (2020) Effects of temperature on metabolic scaling in black carp. PeerJ 8:e9242 https://doi.org/10.7717/peerj.9242
date submitted: 2020-01-15
date accepted: 2020-05-05
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Qian
author list: Agent
  family name: Zhu
  given name: Xiaoling
author list: Agent
  family name: Xiong
  given name: Wei
author list: Agent
  family name: Zhu
  given name: Yanqiu
author list: Agent
  family name: Zhang
  given name: Jianghui
author list: Agent
  family name: Djiba
  given name: Pathe Karim
author list: Agent
  family name: Lv
  given name: Xiao
author list: Agent
  family name: Luo
  given name: Yiping
doi: 10.7717/peerj.9242
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: © 2020 Li et al.
attribution name: Li et al.

Role of echocardiography in screening for portopulmonary hypertension in liver transplant candidates: a meta-analysis
type: item
type: AcademicArticle
description: Objectives To demonstrate the screening value of echocardiography for portopulmonary hypertension (POPH) in liver transplant candidates. Design Systematic review and meta-analysis. Background POPH is a complication of end-stage liver disease that adversely affects the outcome of orthotopic liver transplant. There are no specific symptoms in the early stage of POPH. POPH reduce the survival rate of patients with end-stage liver disease specially if they are not diagnosed. Therefore, early detection may improve prognosis. The objective of this study is to explore the screening value of echocardiography on liver transplant candidates for screening of POPH compared to right heart catheterization (RHC). Method PubMed, EMBASE and the Cochrane Library were searched by two independent reviewers for potentially eligible studies published up to 30 June 2019 to retrieve data based on per-patient analysis. STATA, Meta-DiSc, and RevMan were applied to perform this meta-analysis. Results Our search yielded 1576 studies, of which 11 satisfied the inclusion criteria. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and area under the summary receiver operating characteristic (SROC) curve (AUC) of echocardiography for POPH were 0.85 (95% CI [0.65–0.94]), 0.83 (95% CI [0.73–0.90]), 4.99 (95% CI [3.03–8.21]), 0.19 (95% CI [0.07–0.46]), and 0.91 (95% CI [0.88–0.93]), respectively. Deeks’ funnel plot did not indicate the existence of publication bias (P = 0.66). Conclusions Echocardiography, a noninvasive modality, provides superior screening for POPH, but the diagnosis of POPH still requires RHC. PROSPERO registration number CRD42019144589.
format: application/pdf
format: text/html
creator: Xin Yin
creator: Yueming Shao
creator: Yu Zhang
creator: Hui Gao
creator: Tingting Qin
creator: Xiaoyu Wen
creator: Chen Yang
subject: Gastroenterology and Hepatology
subject: Internal Medicine
description: doi:10.7717/peerj.9243
publisher: PeerJ Inc.
rights: © 2020 Yin et al.
abstract: Objectives To demonstrate the screening value of echocardiography for portopulmonary hypertension (POPH) in liver transplant candidates. Design Systematic review and meta-analysis. Background POPH is a complication of end-stage liver disease that adversely affects the outcome of orthotopic liver transplant. There are no specific symptoms in the early stage of POPH. POPH reduce the survival rate of patients with end-stage liver disease specially if they are not diagnosed. Therefore, early detection may improve prognosis. The objective of this study is to explore the screening value of echocardiography on liver transplant candidates for screening of POPH compared to right heart catheterization (RHC). Method PubMed, EMBASE and the Cochrane Library were searched by two independent reviewers for potentially eligible studies published up to 30 June 2019 to retrieve data based on per-patient analysis. STATA, Meta-DiSc, and RevMan were applied to perform this meta-analysis. Results Our search yielded 1576 studies, of which 11 satisfied the inclusion criteria. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and area under the summary receiver operating characteristic (SROC) curve (AUC) of echocardiography for POPH were 0.85 (95% CI [0.65–0.94]), 0.83 (95% CI [0.73–0.90]), 4.99 (95% CI [3.03–8.21]), 0.19 (95% CI [0.07–0.46]), and 0.91 (95% CI [0.88–0.93]), respectively. Deeks’ funnel plot did not indicate the existence of publication bias (P = 0.66). Conclusions Echocardiography, a noninvasive modality, provides superior screening for POPH, but the diagnosis of POPH still requires RHC. PROSPERO registration number CRD42019144589.
bibliographic citation: Yin et al. (2020) Role of echocardiography in screening for portopulmonary hypertension in liver transplant candidates: a meta-analysis. PeerJ 8:e9243 https://doi.org/10.7717/peerj.9243
date submitted: 2020-01-02
date accepted: 2020-05-06
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Xin
author list: Agent
  family name: Shao
  given name: Yueming
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Gao
  given name: Hui
author list: Agent
  family name: Qin
  given name: Tingting
author list: Agent
  family name: Wen
  given name: Xiaoyu
author list: Agent
  family name: Yang
  given name: Chen
doi: 10.7717/peerj.9243
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: ©2020 Yin et al.
attribution name: Yin et al.

Exact integer linear programming solvers outperform simulated annealing for solving conservation planning problems
type: item
type: AcademicArticle
description: The resources available for conserving biodiversity are limited, and so protected areas need to be established in places that will achieve objectives for minimal cost. Two of the main algorithms for solving systematic conservation planning problems are Simulated Annealing (SA) and exact integer linear programing (EILP) solvers. Using a case study in BC, Canada, we compare the cost-effectiveness and processing times of SA used in Marxan versus EILP using both commercial and open-source algorithms. Plans for expanding protected area systems based on EILP algorithms were 12–30% cheaper than plans using SA, due to EILP’s ability to find optimal solutions as opposed to approximations. The best EILP solver we examined was on average 1,071 times faster than the SA algorithm tested. The performance advantages of EILP solvers were also observed when we aimed for spatially compact solutions by including a boundary penalty. One practical advantage of using EILP over SA is that the analysis does not require calibration, saving even more time. Given the performance of EILP solvers, they can be used to generate conservation plans in real-time during stakeholder meetings and can facilitate rapid sensitivity analysis, and contribute to a more transparent, inclusive, and defensible decision-making process.
format: application/pdf
format: text/html
creator: Richard Schuster
creator: Jeffrey O. Hanson
creator: Matthew Strimas-Mackey
creator: Joseph R. Bennett
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9258
publisher: PeerJ Inc.
rights: © 2020 Schuster et al.
abstract: The resources available for conserving biodiversity are limited, and so protected areas need to be established in places that will achieve objectives for minimal cost. Two of the main algorithms for solving systematic conservation planning problems are Simulated Annealing (SA) and exact integer linear programing (EILP) solvers. Using a case study in BC, Canada, we compare the cost-effectiveness and processing times of SA used in Marxan versus EILP using both commercial and open-source algorithms. Plans for expanding protected area systems based on EILP algorithms were 12–30% cheaper than plans using SA, due to EILP’s ability to find optimal solutions as opposed to approximations. The best EILP solver we examined was on average 1,071 times faster than the SA algorithm tested. The performance advantages of EILP solvers were also observed when we aimed for spatially compact solutions by including a boundary penalty. One practical advantage of using EILP over SA is that the analysis does not require calibration, saving even more time. Given the performance of EILP solvers, they can be used to generate conservation plans in real-time during stakeholder meetings and can facilitate rapid sensitivity analysis, and contribute to a more transparent, inclusive, and defensible decision-making process.
bibliographic citation: Schuster et al. (2020) Exact integer linear programming solvers outperform simulated annealing for solving conservation planning problems. PeerJ 8:e9258 https://doi.org/10.7717/peerj.9258
date submitted: 2020-01-16
date accepted: 2020-05-08
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schuster
  given name: Richard
author list: Agent
  family name: Hanson
  given name: Jeffrey O.
author list: Agent
  family name: Strimas-Mackey
  given name: Matthew
author list: Agent
  family name: Bennett
  given name: Joseph R.
doi: 10.7717/peerj.9258
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: © 2020 Schuster et al.
attribution name: Schuster et al.

Bioinformatics profiling identifies seven immune-related risk signatures for hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Density of tumor infiltrating lymphocytes (TIL) and expressions of certain immune-related genes have prognostic and predictive values in hepatocellular carcinoma (HCC); however, factors determining the immunophenotype of HCC patients are still unclear. In the current study, the transcript sequencing data of liver cancer were systematically analyzed to determine an immune gene marker for the prediction of clinical outcome of HCC. Methods RNASeq data and clinical follow-up information were downloaded from The Cancer Genome Atlas (TCGA), and the samples were assigned into high-stage and low-stage groups. Immune pathway-related genes were screened from the Molecular Signatures Database v4.0 (MsigDB) database. LASSO regression analysis was performed to identify robust immune-related biomarkers in predicting HCC clinical outcomes. Moreover, an immune gene-related prognostic model was established and validated by test sets and Gene Expression Omnibus (GEO) external validation sets. Results We obtained 319 immune genes from MsigDB, and the genes have different expression profiles in high-stage and low-stage of HCC. Univariate survival analysis found that 17 genes had a significant effect on HCC prognosis, among them, 13 (76.5%) genes were prognostically protective factors. Further lasso regression analysis identified seven potential prognostic markers (IL27, CD1D, NCOA6, CTSE, FCGRT, CFHR1, and APOA2) of robustness, most of which are related to tumor development. Cox regression analysis was further performed to establish a seven immune gene signature, which could stratify the risk of samples in training set, test set and external verification set (p < 0.01), and the AUC in both training set and test set was greater than 0.85, which also greater compared with previous studies. Conclusion This study constructed a 7-immunogenic marker as novel prognostic markers for predicting survival of HCC patients.
format: application/pdf
format: text/html
creator: Feng Xue
creator: Lixue Yang
creator: Binghua Dai
creator: Hui Xue
creator: Lei Zhang
creator: Ruiliang Ge
creator: Yanfu Sun
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.8301
publisher: PeerJ Inc.
rights: © 2020 Xue et al.
abstract: Background Density of tumor infiltrating lymphocytes (TIL) and expressions of certain immune-related genes have prognostic and predictive values in hepatocellular carcinoma (HCC); however, factors determining the immunophenotype of HCC patients are still unclear. In the current study, the transcript sequencing data of liver cancer were systematically analyzed to determine an immune gene marker for the prediction of clinical outcome of HCC. Methods RNASeq data and clinical follow-up information were downloaded from The Cancer Genome Atlas (TCGA), and the samples were assigned into high-stage and low-stage groups. Immune pathway-related genes were screened from the Molecular Signatures Database v4.0 (MsigDB) database. LASSO regression analysis was performed to identify robust immune-related biomarkers in predicting HCC clinical outcomes. Moreover, an immune gene-related prognostic model was established and validated by test sets and Gene Expression Omnibus (GEO) external validation sets. Results We obtained 319 immune genes from MsigDB, and the genes have different expression profiles in high-stage and low-stage of HCC. Univariate survival analysis found that 17 genes had a significant effect on HCC prognosis, among them, 13 (76.5%) genes were prognostically protective factors. Further lasso regression analysis identified seven potential prognostic markers (IL27, CD1D, NCOA6, CTSE, FCGRT, CFHR1, and APOA2) of robustness, most of which are related to tumor development. Cox regression analysis was further performed to establish a seven immune gene signature, which could stratify the risk of samples in training set, test set and external verification set (p < 0.01), and the AUC in both training set and test set was greater than 0.85, which also greater compared with previous studies. Conclusion This study constructed a 7-immunogenic marker as novel prognostic markers for predicting survival of HCC patients.
bibliographic citation: Xue et al. (2020) Bioinformatics profiling identifies seven immune-related risk signatures for hepatocellular carcinoma. PeerJ 8:e8301 https://doi.org/10.7717/peerj.8301
date submitted: 2019-07-12
date accepted: 2019-11-26
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xue
  given name: Feng
author list: Agent
  family name: Yang
  given name: Lixue
author list: Agent
  family name: Dai
  given name: Binghua
author list: Agent
  family name: Xue
  given name: Hui
author list: Agent
  family name: Zhang
  given name: Lei
author list: Agent
  family name: Ge
  given name: Ruiliang
author list: Agent
  family name: Sun
  given name: Yanfu
doi: 10.7717/peerj.8301
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: ©2020 Xue et al.
attribution name: Xue et al.

Descriptions of five new species of the salamander genus Chiropterotriton (Caudata: Plethodontidae) from eastern Mexico and the status of three currently recognized taxa
type: item
type: AcademicArticle
description: The genus Chiropterotriton is endemic to Mexico with a geographical distribution along the Sierra Madre Oriental, the Trans Mexican Volcanic Belt and the Sierra de Juárez. The recent use of molecular tools has shown that Mexico’s amphibian diversity is highly underestimated, including a large number of cryptic, unnamed species. Chiropterotriton has 18 described species including terrestrial, arboreal and cave-dwelling species. In previous molecular studies, the presence of multiple undescribed species was evident. We present a phylogenetic hypothesis based on mitochondrial data, which includes all described species and six undescribed taxa. Based on the morphological analyses and, when available, combined with molecular data, we describe five new species of the genus; Chiropterotriton casasi sp. nov., C. ceronorum sp. nov., C. melipona sp. nov., C. perotensis sp. nov. and C. totonacus sp. nov. In addition, we redescribe two others: Chiropterotriton chiropterus and C. orculus, and provide a comparable account of one additional sympatric congener. This increases the number of species in the genus to 23, which represent a considerable component of Mexican plethodontid richness.
format: application/pdf
format: text/html
creator: Gabriela Parra Olea
creator: Mirna G. Garcia-Castillo
creator: Sean M. Rovito
creator: Jessica A. Maisano
creator: James Hanken
creator: David B. Wake
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.8800
publisher: PeerJ Inc.
rights: © 2020 Parra Olea et al.
abstract: The genus Chiropterotriton is endemic to Mexico with a geographical distribution along the Sierra Madre Oriental, the Trans Mexican Volcanic Belt and the Sierra de Juárez. The recent use of molecular tools has shown that Mexico’s amphibian diversity is highly underestimated, including a large number of cryptic, unnamed species. Chiropterotriton has 18 described species including terrestrial, arboreal and cave-dwelling species. In previous molecular studies, the presence of multiple undescribed species was evident. We present a phylogenetic hypothesis based on mitochondrial data, which includes all described species and six undescribed taxa. Based on the morphological analyses and, when available, combined with molecular data, we describe five new species of the genus; Chiropterotriton casasi sp. nov., C. ceronorum sp. nov., C. melipona sp. nov., C. perotensis sp. nov. and C. totonacus sp. nov. In addition, we redescribe two others: Chiropterotriton chiropterus and C. orculus, and provide a comparable account of one additional sympatric congener. This increases the number of species in the genus to 23, which represent a considerable component of Mexican plethodontid richness.
bibliographic citation: Parra Olea et al. (2020) Descriptions of five new species of the salamander genus Chiropterotriton (Caudata: Plethodontidae) from eastern Mexico and the status of three currently recognized taxa. PeerJ 8:e8800 https://doi.org/10.7717/peerj.8800
date submitted: 2019-12-06
date accepted: 2020-02-25
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Parra Olea
  given name: Gabriela
author list: Agent
  family name: Garcia-Castillo
  given name: Mirna G.
author list: Agent
  family name: Rovito
  given name: Sean M.
author list: Agent
  family name: Maisano
  given name: Jessica A.
author list: Agent
  family name: Hanken
  given name: James
author list: Agent
  family name: Wake
  given name: David B.
doi: 10.7717/peerj.8800
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: © 2020 Parra Olea et al.
attribution name: Parra Olea et al.

Effective connectivity differences in motor network during passive movement of paretic and non-paretic ankles in subacute stroke patients
type: item
type: AcademicArticle
description: Background A better understanding of the neural changes associated with paresis in stroke patients could have important implications for therapeutic approaches. Dynamic Causal Modeling (DCM) for functional magnetic resonance imaging (fMRI) is commonly used for analyzing effective connectivity patterns of brain networks due to its significant property of modeling neural states behind fMRI signals. We applied this technique to analyze the differences between motor networks (MNW) activated by continuous passive movement (CPM) of paretic and non-paretic ankles in subacute stroke patients. This study aimed to identify CPM induced connectivity characteristics of the primary sensory area (S1) and the differences in extrinsic directed connections of the MNW and to explain the hemodynamic differences of brain regions of MNW. Methods For the network analysis, we used ten stroke patients’ task fMRI data collected under CPMs of both ankles. Regions for the MNW, the primary motor cortex (M1), the premotor cortex (PM), the supplementary motor area (SMA) and the S1 were defined in a data-driven way, by independent component analysis. For the network analysis of both CPMs, we compared twelve models organized into two model-families, depending on the S1 connections and input stimulus modeling. Using DCM, we evaluated the extrinsic connectivity strengths and hemodynamic parameters of both stimulations of all patients. Results After a statistical comparison of the extrinsic connections and their modulations of the “best model”, we concluded that three contralateral self-inhibitions (cM1, cS1 and cSMA), one contralateral inter-regional connection (cSMA→cM1), and one interhemispheric connection (cM1→iM1) were significantly different. Our research shows that hemodynamic parameters can be estimated with the Balloon model using DCM but the parameters do not change with stroke. Conclusions Our results confirm that the DCM-based connectivity analyses combined with Bayesian model selection ma…
format: application/pdf
format: text/html
creator: Marianna Nagy
creator: Csaba Aranyi
creator: Gábor Opposits
creator: Tamás Papp
creator: Levente Lánczi
creator: Ervin Berényi
creator: Csilla Vér
creator: László Csiba
creator: Péter Katona
creator: Tamás Spisák
creator: Miklós Emri
subject: Neuroscience
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.8942
publisher: PeerJ Inc.
rights: © 2020 Nagy et al.
abstract: Background A better understanding of the neural changes associated with paresis in stroke patients could have important implications for therapeutic approaches. Dynamic Causal Modeling (DCM) for functional magnetic resonance imaging (fMRI) is commonly used for analyzing effective connectivity patterns of brain networks due to its significant property of modeling neural states behind fMRI signals. We applied this technique to analyze the differences between motor networks (MNW) activated by continuous passive movement (CPM) of paretic and non-paretic ankles in subacute stroke patients. This study aimed to identify CPM induced connectivity characteristics of the primary sensory area (S1) and the differences in extrinsic directed connections of the MNW and to explain the hemodynamic differences of brain regions of MNW. Methods For the network analysis, we used ten stroke patients’ task fMRI data collected under CPMs of both ankles. Regions for the MNW, the primary motor cortex (M1), the premotor cortex (PM), the supplementary motor area (SMA) and the S1 were defined in a data-driven way, by independent component analysis. For the network analysis of both CPMs, we compared twelve models organized into two model-families, depending on the S1 connections and input stimulus modeling. Using DCM, we evaluated the extrinsic connectivity strengths and hemodynamic parameters of both stimulations of all patients. Results After a statistical comparison of the extrinsic connections and their modulations of the “best model”, we concluded that three contralateral self-inhibitions (cM1, cS1 and cSMA), one contralateral inter-regional connection (cSMA→cM1), and one interhemispheric connection (cM1→iM1) were significantly different. Our research shows that hemodynamic parameters can be estimated with the Balloon model using DCM but the parameters do not change with stroke. Conclusions Our results confirm that the DCM-based connectivity analyses combined with Bayesian model selection ma…
bibliographic citation: Nagy et al. (2020) Effective connectivity differences in motor network during passive movement of paretic and non-paretic ankles in subacute stroke patients. PeerJ 8:e8942 https://doi.org/10.7717/peerj.8942
date submitted: 2019-12-03
date accepted: 2020-03-18
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nagy
  given name: Marianna
author list: Agent
  family name: Aranyi
  given name: Csaba
author list: Agent
  family name: Opposits
  given name: Gábor
author list: Agent
  family name: Papp
  given name: Tamás
author list: Agent
  family name: Lánczi
  given name: Levente
author list: Agent
  family name: Berényi
  given name: Ervin
author list: Agent
  family name: Vér
  given name: Csilla
author list: Agent
  family name: Csiba
  given name: László
author list: Agent
  family name: Katona
  given name: Péter
author list: Agent
  family name: Spisák
  given name: Tamás
author list: Agent
  family name: Emri
  given name: Miklós
doi: 10.7717/peerj.8942
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: © 2020 Nagy et al.
attribution name: Nagy et al.

Microbiome analysis of healthy and diseased sponges Lubomirskia baicalensis by using cell cultures of primmorphs
type: item
type: AcademicArticle
description: Endemic sponges (Demosponges, Lubomirskiidae) dominate the fauna of the littoral zone of Lake Baikal. These freshwater sponges live in symbiosis with diverse eukaryotes and prokaryotes, including chlorophyll-containing microalgae. Within the last 5 years, the incidence of sponge disease and mortality events in Lake Baikal has increased. The etiology and ecology of these events remain unknown, in part because of the lack of models to study sponge-microbe interactions. In this work, we tested the use of primmorph cell cultures of Lubomirskia baicalensis as a tool for investigating the microbiomes of sponges. We infected primmorphs, cultured in vitro, with samples from diseased sponges and observed, by microscopy, disease symptoms, including loss of green symbionts, associated with mass die-off events. Subsequent sequencing of 16S rRNA gene fragments revealed that the microbiome community of healthy sponge and primmorphs formed a group separate from the community of diseased sponges and infected primmorphs. This confirms the suitability of the primmorph cell culture as a model sponge system. We also discovered mass mortality of green symbionts (Chlorophyta) was associated with a shift in the microbial communities of sponges/primmorphs. Microbes in diseased sponges, and infected primmorphs, belonged mainly to the phyla Bacteroidetes and Proteobacteria and these families Flavobacteriaceae, Burkholderiaceae, and Moraxellaceae. Primmorphs cell culture may provide a model to study interactions between these bacteria and their host and elucidate the cause of mass mortality events.
format: application/pdf
format: text/html
creator: Lubov Chernogor
creator: Elizaveta Klimenko
creator: Igor Khanaev
creator: Sergei Belikov
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.9080
publisher: PeerJ Inc.
rights: © 2020 Chernogor et al.
abstract: Endemic sponges (Demosponges, Lubomirskiidae) dominate the fauna of the littoral zone of Lake Baikal. These freshwater sponges live in symbiosis with diverse eukaryotes and prokaryotes, including chlorophyll-containing microalgae. Within the last 5 years, the incidence of sponge disease and mortality events in Lake Baikal has increased. The etiology and ecology of these events remain unknown, in part because of the lack of models to study sponge-microbe interactions. In this work, we tested the use of primmorph cell cultures of Lubomirskia baicalensis as a tool for investigating the microbiomes of sponges. We infected primmorphs, cultured in vitro, with samples from diseased sponges and observed, by microscopy, disease symptoms, including loss of green symbionts, associated with mass die-off events. Subsequent sequencing of 16S rRNA gene fragments revealed that the microbiome community of healthy sponge and primmorphs formed a group separate from the community of diseased sponges and infected primmorphs. This confirms the suitability of the primmorph cell culture as a model sponge system. We also discovered mass mortality of green symbionts (Chlorophyta) was associated with a shift in the microbial communities of sponges/primmorphs. Microbes in diseased sponges, and infected primmorphs, belonged mainly to the phyla Bacteroidetes and Proteobacteria and these families Flavobacteriaceae, Burkholderiaceae, and Moraxellaceae. Primmorphs cell culture may provide a model to study interactions between these bacteria and their host and elucidate the cause of mass mortality events.
bibliographic citation: Chernogor et al. (2020) Microbiome analysis of healthy and diseased sponges Lubomirskia baicalensis by using cell cultures of primmorphs. PeerJ 8:e9080 https://doi.org/10.7717/peerj.9080
date submitted: 2019-02-18
date accepted: 2020-04-07
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chernogor
  given name: Lubov
author list: Agent
  family name: Klimenko
  given name: Elizaveta
author list: Agent
  family name: Khanaev
  given name: Igor
author list: Agent
  family name: Belikov
  given name: Sergei
doi: 10.7717/peerj.9080
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: ©2020 Chernogor et al.
attribution name: Chernogor et al.

Cca-miR398 increases copper sulfate stress sensitivity via the regulation of CSD mRNA transcription levels in transgenic Arabidopsis thaliana
type: item
type: AcademicArticle
description: MicroRNAs play crucial roles during the process of plant development under stress conditions. Copper is an essential micronutrient for most organisms and serves as an important redox-active cofactor for various functional proteins. In the present study, we investigated the effects of copper sulfate stress on hickory (Carya cathayensis) root development. We identified that hickory cca-miR398 was related to copper sulfate stress response, targeting Copper/Zinc superoxide dismutases (cytosolic (CSD1) and chloroplastic (CSD2)) and a 5b subunit of mitochondrial cytochrome C oxidase (COX5b.1) that are linked directly to stress regulatory networks. The sequence of hickory cca-miR398 is highly similar to that of Arabidopsis miR398b and miR398c, regardless of one nucleotide variation. Therefore, target genes of cca-miR398 were investigated by using 5′-Rapid-amplification of cDNA ends. An overexpression of cca-miR398 in Arabidopsis caused a reduction not only in root length and cotyledon greening, but also in the CSD1, CSD2, and CSD3 transcription levels. These reductions had greater significance in transgenic Arabidopsis than in wild-type Arabidopsis under copper sulfate stress. The level of physiological indicators also changed in transgenic Arabidopsis. In addition, the expressions of copper-responsive microRNAs, such as miR397 and miR408, were affected by the copper sulfate stress. These results showed that CSD possesses the ability to enhance copper sulfate stress response in both transgenic Arabidopsis and hickory roots by increasing the production of superoxide dismutase. Our results also demonstrated that cca-miR398 weakens hickory tolerance to copper sulfate by regulating CSD targets.
format: application/pdf
format: text/html
creator: Zhichao Sun
creator: Lilu Shu
creator: Wei Zhang
creator: Zhengjia Wang
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
subject: Ecotoxicology
description: doi:10.7717/peerj.9105
publisher: PeerJ Inc.
rights: © 2020 Sun et al.
abstract: MicroRNAs play crucial roles during the process of plant development under stress conditions. Copper is an essential micronutrient for most organisms and serves as an important redox-active cofactor for various functional proteins. In the present study, we investigated the effects of copper sulfate stress on hickory (Carya cathayensis) root development. We identified that hickory cca-miR398 was related to copper sulfate stress response, targeting Copper/Zinc superoxide dismutases (cytosolic (CSD1) and chloroplastic (CSD2)) and a 5b subunit of mitochondrial cytochrome C oxidase (COX5b.1) that are linked directly to stress regulatory networks. The sequence of hickory cca-miR398 is highly similar to that of Arabidopsis miR398b and miR398c, regardless of one nucleotide variation. Therefore, target genes of cca-miR398 were investigated by using 5′-Rapid-amplification of cDNA ends. An overexpression of cca-miR398 in Arabidopsis caused a reduction not only in root length and cotyledon greening, but also in the CSD1, CSD2, and CSD3 transcription levels. These reductions had greater significance in transgenic Arabidopsis than in wild-type Arabidopsis under copper sulfate stress. The level of physiological indicators also changed in transgenic Arabidopsis. In addition, the expressions of copper-responsive microRNAs, such as miR397 and miR408, were affected by the copper sulfate stress. These results showed that CSD possesses the ability to enhance copper sulfate stress response in both transgenic Arabidopsis and hickory roots by increasing the production of superoxide dismutase. Our results also demonstrated that cca-miR398 weakens hickory tolerance to copper sulfate by regulating CSD targets.
bibliographic citation: Sun et al. (2020) Cca-miR398 increases copper sulfate stress sensitivity via the regulation of CSD mRNA transcription levels in transgenic Arabidopsis thaliana. PeerJ 8:e9105 https://doi.org/10.7717/peerj.9105
date submitted: 2019-10-21
date accepted: 2020-04-10
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Zhichao
author list: Agent
  family name: Shu
  given name: Lilu
author list: Agent
  family name: Zhang
  given name: Wei
author list: Agent
  family name: Wang
  given name: Zhengjia
doi: 10.7717/peerj.9105
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: ©2020 Sun et al.
attribution name: Sun et al.

The combined effects of light intensity, temperature, and water potential on wall deposition in regulating hypocotyl elongation of Brassica rapa
type: item
type: AcademicArticle
description: Hypocotyl elongation is a critical sign of seed germination and seedling growth, and it is regulated by multi-environmental factors. Light, temperature, and water potential are the major environmental stimuli, and their regulatory mechanism on hypocotyl growth has been extensively studied at molecular level. However, the converged point in signaling process of light, temperature, and water potential on modulating hypocotyl elongation is still unclear. In the present study, we found cell wall was the co-target of the three environmental factors in regulating hypocotyl elongation by analyzing the extension kinetics of hypocotyl and the changes in hypocotyl cell wall of Brassica rapa under the combined effects of light intensity, temperature, and water potential. The three environmental factors regulated hypocotyl cell elongation both in isolation and in combination. Cell walls thickened, maintained, or thinned depending on growth conditions and developmental stages during hypocotyl elongation. Further analysis revealed that the imbalance in wall deposition and hypocotyl elongation led to dynamic changes in wall thickness. Low light repressed wall deposition by influencing the accumulation of cellulose, hemicellulose, and pectin; high temperature and high water potential had significant effects on pectin accumulation overall. It was concluded that wall deposition was tightly controlled during hypocotyl elongation, and low light, high temperature, and high water potential promoted hypocotyl elongation by repressing wall deposition, especially the deposition of pectin.
format: application/pdf
format: text/html
creator: Hongfei Wang
creator: Qingmao Shang
subject: Agricultural Science
subject: Developmental Biology
subject: Plant Science
description: doi:10.7717/peerj.9106
publisher: PeerJ Inc.
rights: © 2020 Wang and Shang
abstract: Hypocotyl elongation is a critical sign of seed germination and seedling growth, and it is regulated by multi-environmental factors. Light, temperature, and water potential are the major environmental stimuli, and their regulatory mechanism on hypocotyl growth has been extensively studied at molecular level. However, the converged point in signaling process of light, temperature, and water potential on modulating hypocotyl elongation is still unclear. In the present study, we found cell wall was the co-target of the three environmental factors in regulating hypocotyl elongation by analyzing the extension kinetics of hypocotyl and the changes in hypocotyl cell wall of Brassica rapa under the combined effects of light intensity, temperature, and water potential. The three environmental factors regulated hypocotyl cell elongation both in isolation and in combination. Cell walls thickened, maintained, or thinned depending on growth conditions and developmental stages during hypocotyl elongation. Further analysis revealed that the imbalance in wall deposition and hypocotyl elongation led to dynamic changes in wall thickness. Low light repressed wall deposition by influencing the accumulation of cellulose, hemicellulose, and pectin; high temperature and high water potential had significant effects on pectin accumulation overall. It was concluded that wall deposition was tightly controlled during hypocotyl elongation, and low light, high temperature, and high water potential promoted hypocotyl elongation by repressing wall deposition, especially the deposition of pectin.
bibliographic citation: Wang et al. (2020) The combined effects of light intensity, temperature, and water potential on wall deposition in regulating hypocotyl elongation of Brassica rapa. PeerJ 8:e9106 https://doi.org/10.7717/peerj.9106
date submitted: 2019-08-20
date accepted: 2020-04-10
issued: 2020-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hongfei
author list: Agent
  family name: Shang
  given name: Qingmao
doi: 10.7717/peerj.9106
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-26
copyright: ©2020 Wang and Shang
attribution name: Wang and Shang

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