PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Galantamine plasma concentration and cognitive response in Alzheimer’s disease
items: A 5-year study (2014–2018) of the relationship between coastal phytoplankton abundance and intertidal barnacle size along the Atlantic Canadian coast
items: The response of cucumber plants (Cucumis sativus L.) to the application of PCB-contaminated sewage sludge and urban sediment
items: Predicting gene expression using DNA methylation in three human populations
items: Anatomy of Rhinochelys pulchriceps (Protostegidae) and marine adaptation during the early evolution of chelonioids
items: Impacts of the invasive shot hole borer (Euwallacea kuroshio) are linked to sewage pollution in southern California: the Enriched Tree Hypothesis
items: ERISNet: deep neural network for Sargassum detection along the coastline of the Mexican Caribbean
items: Manganese affects the growth and metabolism of Ganoderma lucidum based on LC-MS analysis
items: A large scale evaluation of TBProfiler and Mykrobe for antibiotic resistance prediction in Mycobacterium tuberculosis
items: A novel conserved family of Macro-like domains—putative new players in ADP-ribosylation signaling

Galantamine plasma concentration and cognitive response in Alzheimer’s disease
type: item
type: AcademicArticle
description: Background Galantamine has been approved for the treatment of Alzheimer’s disease (AD). However, there are few studies which have reported the association between cognitive responses and galantamine plasma concentration. The aim of this study was to determine the correlation between galantamine plasma concentration and the subsequent cognitive response following treatment in AD patients. Methods AD sufferers who continuously took 8 mg/d galantamine for at least 6 months without previous exposure to other kinds of AChEI such as donepezil, rivastigmine, or memantine were included in this cohort study. The assessments included the Mini Mental Status Examination (MMSE), Clinical Dementia Rating Scale (CDR) and the Cognitive Assessment Screening Instrument (CASI). Each subdomain of the CASI assessment was conducted at baseline and after 6 months of galantamine. The plasma concentrations of galantamine were measured by capillary electrophoresis after 6 months of the treatment. Logistic regression was performed to adjust for age, gender, apolipoprotein E ε4 genotype status, and baseline score to investigate the association between galantamine plasma concentrations and the cognitive response. Results The total sample consisted of 33 clinically diagnosed AD patients taking galantamine 8 mg/d for 6 months. There was no linear correlation between galantamine concentration and cognitive response in patients. However, 22 patients were responsive to the treatment in the long-term memory domain. In CASI subset domain, concentration improved during the 6 months follow up. Conclusions In the limited samples study, galantamine mostly benefitted the cognitive domain of long-term memory. The benefits were not related to the galantamine plasma concentration. Objective intra-individual evaluation of therapeutic response should be encouraged.
format: application/pdf
format: text/html
creator: Yi-Ting Lin
creator: Mei-Chuan Chou
creator: Shyh-Jong Wu
creator: Yuan-Han Yang
subject: Cognitive Disorders
subject: Neurology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6887
publisher: PeerJ Inc.
rights: © 2019 Lin et al.
abstract: Background Galantamine has been approved for the treatment of Alzheimer’s disease (AD). However, there are few studies which have reported the association between cognitive responses and galantamine plasma concentration. The aim of this study was to determine the correlation between galantamine plasma concentration and the subsequent cognitive response following treatment in AD patients. Methods AD sufferers who continuously took 8 mg/d galantamine for at least 6 months without previous exposure to other kinds of AChEI such as donepezil, rivastigmine, or memantine were included in this cohort study. The assessments included the Mini Mental Status Examination (MMSE), Clinical Dementia Rating Scale (CDR) and the Cognitive Assessment Screening Instrument (CASI). Each subdomain of the CASI assessment was conducted at baseline and after 6 months of galantamine. The plasma concentrations of galantamine were measured by capillary electrophoresis after 6 months of the treatment. Logistic regression was performed to adjust for age, gender, apolipoprotein E ε4 genotype status, and baseline score to investigate the association between galantamine plasma concentrations and the cognitive response. Results The total sample consisted of 33 clinically diagnosed AD patients taking galantamine 8 mg/d for 6 months. There was no linear correlation between galantamine concentration and cognitive response in patients. However, 22 patients were responsive to the treatment in the long-term memory domain. In CASI subset domain, concentration improved during the 6 months follow up. Conclusions In the limited samples study, galantamine mostly benefitted the cognitive domain of long-term memory. The benefits were not related to the galantamine plasma concentration. Objective intra-individual evaluation of therapeutic response should be encouraged.
bibliographic citation: Lin et al. (2019) Galantamine plasma concentration and cognitive response in Alzheimer’s disease. PeerJ 7:e6887 https://doi.org/10.7717/peerj.6887
date submitted: 2018-12-18
date accepted: 2019-04-02
issued: 2019-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Yi-Ting
author list: Agent
  family name: Chou
  given name: Mei-Chuan
author list: Agent
  family name: Wu
  given name: Shyh-Jong
author list: Agent
  family name: Yang
  given name: Yuan-Han
doi: 10.7717/peerj.6887
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-02
copyright: ©2019 Lin et al.
attribution name: Lin et al.

A 5-year study (2014–2018) of the relationship between coastal phytoplankton abundance and intertidal barnacle size along the Atlantic Canadian coast
type: item
type: AcademicArticle
description: Benthic–pelagic coupling refers to the ecological relationships between benthic and pelagic environments. Studying such links is particularly useful to understand biological variation in intertidal organisms along marine coasts. Filter-feeding invertebrates are ecologically important on marine rocky shores, so they have often been used to investigate benthic–pelagic coupling. Most studies, however, have been conducted on eastern ocean boundaries. To evaluate benthic–pelagic coupling on a western ocean boundary, we conducted a 5-year study spanning 415 km of the Atlantic coast of Nova Scotia (Canada). We hypothesized that the summer size of intertidal barnacles (Semibalanus balanoides) recruited in the preceding spring would be positively related to the nearshore abundance (biomass) of phytoplankton, as phytoplankton constitutes food for the nauplius larvae and benthic stages of barnacles. Every year between 2014 and 2018, we measured summer barnacle size in clearings created before spring recruitment on the rocky substrate at eight wave-exposed locations along this coast. We then examined the annual relationships between barnacle size and chlorophyll-a concentration (Chl-a), a proxy for phytoplankton biomass. For every year and location, we used satellite data to calculate Chl-a averages for a period ranging from the early spring (when most barnacle larvae were in the water) to the summer (when barnacle size was measured after weeks of growth following spring benthic recruitment). The relationships were always positive, Chl-a explaining nearly half, or more, of the variation in barnacle size in four of the five studied years. These are remarkable results because they were based on a relatively limited number of locations (which often curtails statistical power) and point to the relevance of pelagic food supply to explain variation in intertidal barnacle size along this western ocean boundary coast.
format: application/pdf
format: text/html
creator: Ricardo A. Scrosati
creator: Julius A. Ellrich
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6892
publisher: PeerJ Inc.
rights: © 2019 Scrosati and Ellrich
abstract: Benthic–pelagic coupling refers to the ecological relationships between benthic and pelagic environments. Studying such links is particularly useful to understand biological variation in intertidal organisms along marine coasts. Filter-feeding invertebrates are ecologically important on marine rocky shores, so they have often been used to investigate benthic–pelagic coupling. Most studies, however, have been conducted on eastern ocean boundaries. To evaluate benthic–pelagic coupling on a western ocean boundary, we conducted a 5-year study spanning 415 km of the Atlantic coast of Nova Scotia (Canada). We hypothesized that the summer size of intertidal barnacles (Semibalanus balanoides) recruited in the preceding spring would be positively related to the nearshore abundance (biomass) of phytoplankton, as phytoplankton constitutes food for the nauplius larvae and benthic stages of barnacles. Every year between 2014 and 2018, we measured summer barnacle size in clearings created before spring recruitment on the rocky substrate at eight wave-exposed locations along this coast. We then examined the annual relationships between barnacle size and chlorophyll-a concentration (Chl-a), a proxy for phytoplankton biomass. For every year and location, we used satellite data to calculate Chl-a averages for a period ranging from the early spring (when most barnacle larvae were in the water) to the summer (when barnacle size was measured after weeks of growth following spring benthic recruitment). The relationships were always positive, Chl-a explaining nearly half, or more, of the variation in barnacle size in four of the five studied years. These are remarkable results because they were based on a relatively limited number of locations (which often curtails statistical power) and point to the relevance of pelagic food supply to explain variation in intertidal barnacle size along this western ocean boundary coast.
bibliographic citation: Scrosati et al. (2019) A 5-year study (2014–2018) of the relationship between coastal phytoplankton abundance and intertidal barnacle size along the Atlantic Canadian coast. PeerJ 7:e6892 https://doi.org/10.7717/peerj.6892
date submitted: 2019-01-09
date accepted: 2019-04-01
issued: 2019-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scrosati
  given name: Ricardo A.
author list: Agent
  family name: Ellrich
  given name: Julius A.
doi: 10.7717/peerj.6892
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-02
copyright: ©2019 Scrosati and Ellrich
attribution name: Scrosati and Ellrich

The response of cucumber plants (Cucumis sativus L.) to the application of PCB-contaminated sewage sludge and urban sediment
type: item
type: AcademicArticle
description: Background The increasing production of sewage sludge (SS) engenders the problem of its responsible utilization and disposal. Likewise, urban sediments (SED) are deposited at the bottom of urban reservoirs and sedimentation ponds, and these require periodical dredging and utilization. However, while the SS and SED deposits often contain nutrients such as nitrogen and phosphorus; however, they also contain a variety of hazardous compounds including heavy metals, Persistent Organic Pollutants (POPs) and microbial pollutants. Fortunately, some species of Cucurbitaceae can accumulate high levels of POPs, such as polychlorinated dibenzo-p-dioxins (PCDD), polychlorinated dibenzofurans (PCDF) and polychlorinated biphenyls (PCB), in their tissues. Methods SS was collected from the Lodz Municipal Wastewater Treatment Plant and SED from the Sokołówka Sequential Biofiltration System. The SS and SED samples were added to soil in flower pots at three concentrations (1.8 g, 5.4 g and 10.8 g per flower pot), and one pot was left as an unamended control (C). Soil PCB concentrations were determined before cucumber planting, and after five weeks of growth. Also, total soluble protein, total chlorophyll content, chlorophyll a/b ratio and degree of lipid peroxidation (TBARS) were examined in the leaves of the cucumber plants (Cucumis sativus L.) cv. Cezar after five weeks. Antioxidative response was assessed by ascorbate peroxidase (APx) and catalase (CAT) assay. Results The initial PCB concentration in soil after application of SS or SED was dependent on the applied dose. After five weeks, PCB concentration fell significantly for all samples and confirmed that the dose of SS/SED had a strong effect. Soil remediation was found to be more effective after SS application. Total soluble protein content in the cucumber leaf tissues was dependent on both the type and the dose of the applied amendments, and increased with greater SS doses in the soil. The total chlorophyll content remained un…
format: application/pdf
format: text/html
creator: Anna Wyrwicka
creator: Magdalena Urbaniak
creator: Mirosław Przybylski
subject: Agricultural Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6743
publisher: PeerJ Inc.
rights: © 2019 Wyrwicka et al.
abstract: Background The increasing production of sewage sludge (SS) engenders the problem of its responsible utilization and disposal. Likewise, urban sediments (SED) are deposited at the bottom of urban reservoirs and sedimentation ponds, and these require periodical dredging and utilization. However, while the SS and SED deposits often contain nutrients such as nitrogen and phosphorus; however, they also contain a variety of hazardous compounds including heavy metals, Persistent Organic Pollutants (POPs) and microbial pollutants. Fortunately, some species of Cucurbitaceae can accumulate high levels of POPs, such as polychlorinated dibenzo-p-dioxins (PCDD), polychlorinated dibenzofurans (PCDF) and polychlorinated biphenyls (PCB), in their tissues. Methods SS was collected from the Lodz Municipal Wastewater Treatment Plant and SED from the Sokołówka Sequential Biofiltration System. The SS and SED samples were added to soil in flower pots at three concentrations (1.8 g, 5.4 g and 10.8 g per flower pot), and one pot was left as an unamended control (C). Soil PCB concentrations were determined before cucumber planting, and after five weeks of growth. Also, total soluble protein, total chlorophyll content, chlorophyll a/b ratio and degree of lipid peroxidation (TBARS) were examined in the leaves of the cucumber plants (Cucumis sativus L.) cv. Cezar after five weeks. Antioxidative response was assessed by ascorbate peroxidase (APx) and catalase (CAT) assay. Results The initial PCB concentration in soil after application of SS or SED was dependent on the applied dose. After five weeks, PCB concentration fell significantly for all samples and confirmed that the dose of SS/SED had a strong effect. Soil remediation was found to be more effective after SS application. Total soluble protein content in the cucumber leaf tissues was dependent on both the type and the dose of the applied amendments, and increased with greater SS doses in the soil. The total chlorophyll content remained un…
bibliographic citation: Wyrwicka et al. (2019) The response of cucumber plants (Cucumis sativus L.) to the application of PCB-contaminated sewage sludge and urban sediment. PeerJ 7:e6743 https://doi.org/10.7717/peerj.6743
date submitted: 2018-07-19
date accepted: 2019-03-06
issued: 2019-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wyrwicka
  given name: Anna
author list: Agent
  family name: Urbaniak
  given name: Magdalena
author list: Agent
  family name: Przybylski
  given name: Mirosław
doi: 10.7717/peerj.6743
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-01
copyright: ©2019 Wyrwicka et al.
attribution name: Wyrwicka et al.

Predicting gene expression using DNA methylation in three human populations
type: item
type: AcademicArticle
description: Background DNA methylation, an important epigenetic mark, is well known for its regulatory role in gene expression, especially the negative correlation in the promoter region. However, its correlation with gene expression across genome at human population level has not been well studied. In particular, it is unclear if genome-wide DNA methylation profile of an individual can predict her/his gene expression profile. Previous studies were mostly limited to association analyses between single CpG site methylation and gene expression. It is not known whether DNA methylation of a gene has enough prediction power to serve as a surrogate for gene expression in existing human study cohorts with DNA samples other than RNA samples. Results We examined DNA methylation in the gene region for predicting gene expression across individuals in non-cancer tissues of three human population datasets, adipose tissue of the Multiple Tissue Human Expression Resource Projects (MuTHER), peripheral blood mononuclear cell (PBMC) from Asthma and normal control study participates, and lymphoblastoid cell lines (LCL) from healthy individuals. Three prediction models were investigated, single linear regression, multiple linear regression, and least absolute shrinkage and selection operator (LASSO) penalized regression. Our results showed that LASSO regression has superior performance among these methods. However, the prediction power is generally low and varies across datasets. Only 30 and 42 genes were found to have cross-validation R2 greater than 0.3 in the PBMC and Adipose datasets, respectively. A substantially larger number of genes (258) were identified in the LCL dataset, which was generated from a more homogeneous cell line sample source. We also demonstrated that it gives better prediction power not to exclude any CpG probe due to cross hybridization or SNP effect. Conclusion In our three population analyses DNA methylation of CpG sites at gene region have limited prediction power for …
format: application/pdf
format: text/html
creator: Huan Zhong
creator: Soyeon Kim
creator: Degui Zhi
creator: Xiangqin Cui
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Epidemiology
subject: Statistics
description: doi:10.7717/peerj.6757
publisher: PeerJ Inc.
rights: © 2019 Zhong et al.
abstract: Background DNA methylation, an important epigenetic mark, is well known for its regulatory role in gene expression, especially the negative correlation in the promoter region. However, its correlation with gene expression across genome at human population level has not been well studied. In particular, it is unclear if genome-wide DNA methylation profile of an individual can predict her/his gene expression profile. Previous studies were mostly limited to association analyses between single CpG site methylation and gene expression. It is not known whether DNA methylation of a gene has enough prediction power to serve as a surrogate for gene expression in existing human study cohorts with DNA samples other than RNA samples. Results We examined DNA methylation in the gene region for predicting gene expression across individuals in non-cancer tissues of three human population datasets, adipose tissue of the Multiple Tissue Human Expression Resource Projects (MuTHER), peripheral blood mononuclear cell (PBMC) from Asthma and normal control study participates, and lymphoblastoid cell lines (LCL) from healthy individuals. Three prediction models were investigated, single linear regression, multiple linear regression, and least absolute shrinkage and selection operator (LASSO) penalized regression. Our results showed that LASSO regression has superior performance among these methods. However, the prediction power is generally low and varies across datasets. Only 30 and 42 genes were found to have cross-validation R2 greater than 0.3 in the PBMC and Adipose datasets, respectively. A substantially larger number of genes (258) were identified in the LCL dataset, which was generated from a more homogeneous cell line sample source. We also demonstrated that it gives better prediction power not to exclude any CpG probe due to cross hybridization or SNP effect. Conclusion In our three population analyses DNA methylation of CpG sites at gene region have limited prediction power for …
bibliographic citation: Zhong et al. (2019) Predicting gene expression using DNA methylation in three human populations. PeerJ 7:e6757 https://doi.org/10.7717/peerj.6757
date submitted: 2018-07-19
date accepted: 2019-03-10
issued: 2019-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Huan
author list: Agent
  family name: Kim
  given name: Soyeon
author list: Agent
  family name: Zhi
  given name: Degui
author list: Agent
  family name: Cui
  given name: Xiangqin
doi: 10.7717/peerj.6757
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-01
copyright: ©2019 Zhong et al.
attribution name: Zhong et al.

Anatomy of Rhinochelys pulchriceps (Protostegidae) and marine adaptation during the early evolution of chelonioids
type: item
type: AcademicArticle
description: Knowledge of the early evolution of sea turtles (Chelonioidea) has been limited by conflicting phylogenetic hypotheses resulting from sparse taxon sampling and a superficial understanding of the morphology of key taxa. This limits our understanding of evolutionary adaptation to marine life in turtles, and in amniotes more broadly. One problematic group are the protostegids, Early–Late Cretaceous marine turtles that have been hypothesised to be either stem-cryptodires, stem-chelonioids, or crown-chelonioids. Different phylogenetic hypotheses for protostegids suggest different answers to key questions, including (1) the number of transitions to marine life in turtles, (2) the age of the chelonioid crown-group, and (3) patterns of skeletal evolution during marine adaptation. We present a detailed anatomical study of one of the earliest protostegids, Rhinochelys pulchriceps from the early Late Cretaceous of Europe, using high-resolution μCT. We synonymise all previously named European species and document the variation seen among them. A phylogeny of turtles with increased chelonioid taxon sampling and revised postcranial characters is provided, recovering protostegids as stem-chelonioids. Our results imply a mid Early Cretaceous origin of total-group chelonioids and an early Late Cretaceous age for crown-chelonioids, which may inform molecular clock analyses in future. Specialisations of the chelonioid flipper evolved in a stepwise-fashion, with innovations clustered into pulses at the origin of total-group chelonioids, and subsequently among dermochelyids, crown-cheloniids, and gigantic protostegids from the Late Cretaceous.
format: application/pdf
format: text/html
creator: Serjoscha W. Evers
creator: Paul M. Barrett
creator: Roger B. J. Benson
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6811
publisher: PeerJ Inc.
rights: © 2019 Evers et al.
abstract: Knowledge of the early evolution of sea turtles (Chelonioidea) has been limited by conflicting phylogenetic hypotheses resulting from sparse taxon sampling and a superficial understanding of the morphology of key taxa. This limits our understanding of evolutionary adaptation to marine life in turtles, and in amniotes more broadly. One problematic group are the protostegids, Early–Late Cretaceous marine turtles that have been hypothesised to be either stem-cryptodires, stem-chelonioids, or crown-chelonioids. Different phylogenetic hypotheses for protostegids suggest different answers to key questions, including (1) the number of transitions to marine life in turtles, (2) the age of the chelonioid crown-group, and (3) patterns of skeletal evolution during marine adaptation. We present a detailed anatomical study of one of the earliest protostegids, Rhinochelys pulchriceps from the early Late Cretaceous of Europe, using high-resolution μCT. We synonymise all previously named European species and document the variation seen among them. A phylogeny of turtles with increased chelonioid taxon sampling and revised postcranial characters is provided, recovering protostegids as stem-chelonioids. Our results imply a mid Early Cretaceous origin of total-group chelonioids and an early Late Cretaceous age for crown-chelonioids, which may inform molecular clock analyses in future. Specialisations of the chelonioid flipper evolved in a stepwise-fashion, with innovations clustered into pulses at the origin of total-group chelonioids, and subsequently among dermochelyids, crown-cheloniids, and gigantic protostegids from the Late Cretaceous.
bibliographic citation: Evers et al. (2019) Anatomy of Rhinochelys pulchriceps (Protostegidae) and marine adaptation during the early evolution of chelonioids. PeerJ 7:e6811 https://doi.org/10.7717/peerj.6811
date submitted: 2018-10-23
date accepted: 2019-03-19
issued: 2019-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Evers
  given name: Serjoscha W.
author list: Agent
  family name: Barrett
  given name: Paul M.
author list: Agent
  family name: Benson
  given name: Roger B. J.
doi: 10.7717/peerj.6811
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-01
copyright: © 2019 Evers et al.
attribution name: Evers et al.

Impacts of the invasive shot hole borer (Euwallacea kuroshio) are linked to sewage pollution in southern California: the Enriched Tree Hypothesis
type: item
type: AcademicArticle
description: The Kuroshio Shot Hole Borer (KSHB, Euwallacea kuroshio) and the Polyphagous Shot Hole Borer (E. whitfordiodendrus; Coleoptera: Curculionidae: Scolytinae) have recently invaded southern California and are attacking live trees in commercial agriculture groves, urban parks and native riparian forests. Among native forests the worst impacts observed to date have been in the Tijuana River Valley in south San Diego County, where approximately 30% of the native willows (Salix spp.), or 120,000 trees, have died as a result of a KSHB infestation. This paper examines wood densities, wood moisture contents, KSHB infestation rates, and KSHB-induced mortality rates in two willow species (Salix lasiolepis and S. gooddingii) at sites near and far from sewage input. Comparisons were made on two spatial scales: broadly among sites within San Diego County; and locally among sites within the Tijuana River Valley. The results showed that, on average, willow trees growing closest to sewage pollution had significantly lower wood density, higher wood moisture content, higher KSHB infestation rates, and higher KSHB-induced willow mortality rates than those growing farther away. We present the Enriched Tree Hypothesis to explain the link between sewage pollution and KSHB impacts; it is as follows: (A) Riparian trees subject to nutrient enrichment from frequent sewage pollution grow quickly, and their fast growth results in wood of low density and high moisture content. If attacked by the KSHB, the trunks and branches of these nutrient-enriched trees provide an environment conducive to the fast growth of the symbiotic fungi upon which the KSHB feeds. With an abundant food supply, the KSHB population increases rapidly and the trees are heavily damaged by thousands of KSHB galleries in their trunks and branches. (B) Riparian trees not subject to frequent sewage pollution grow more slowly and have denser, drier wood. Conditions in their trunks and branches are not conducive to the fast growth …
format: application/pdf
format: text/html
creator: John M. Boland
creator: Deborah L. Woodward
subject: Ecology
subject: Entomology
subject: Environmental Impacts
subject: Forestry
subject: Plant Science
description: doi:10.7717/peerj.6812
publisher: PeerJ Inc.
rights: © 2019 Boland and Woodward
abstract: The Kuroshio Shot Hole Borer (KSHB, Euwallacea kuroshio) and the Polyphagous Shot Hole Borer (E. whitfordiodendrus; Coleoptera: Curculionidae: Scolytinae) have recently invaded southern California and are attacking live trees in commercial agriculture groves, urban parks and native riparian forests. Among native forests the worst impacts observed to date have been in the Tijuana River Valley in south San Diego County, where approximately 30% of the native willows (Salix spp.), or 120,000 trees, have died as a result of a KSHB infestation. This paper examines wood densities, wood moisture contents, KSHB infestation rates, and KSHB-induced mortality rates in two willow species (Salix lasiolepis and S. gooddingii) at sites near and far from sewage input. Comparisons were made on two spatial scales: broadly among sites within San Diego County; and locally among sites within the Tijuana River Valley. The results showed that, on average, willow trees growing closest to sewage pollution had significantly lower wood density, higher wood moisture content, higher KSHB infestation rates, and higher KSHB-induced willow mortality rates than those growing farther away. We present the Enriched Tree Hypothesis to explain the link between sewage pollution and KSHB impacts; it is as follows: (A) Riparian trees subject to nutrient enrichment from frequent sewage pollution grow quickly, and their fast growth results in wood of low density and high moisture content. If attacked by the KSHB, the trunks and branches of these nutrient-enriched trees provide an environment conducive to the fast growth of the symbiotic fungi upon which the KSHB feeds. With an abundant food supply, the KSHB population increases rapidly and the trees are heavily damaged by thousands of KSHB galleries in their trunks and branches. (B) Riparian trees not subject to frequent sewage pollution grow more slowly and have denser, drier wood. Conditions in their trunks and branches are not conducive to the fast growth …
bibliographic citation: Boland et al. (2019) Impacts of the invasive shot hole borer (Euwallacea kuroshio) are linked to sewage pollution in southern California: the Enriched Tree Hypothesis. PeerJ 7:e6812 https://doi.org/10.7717/peerj.6812
date submitted: 2018-11-21
date accepted: 2019-03-19
issued: 2019-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boland
  given name: John M.
author list: Agent
  family name: Woodward
  given name: Deborah L.
doi: 10.7717/peerj.6812
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-01
copyright: © 2019 Boland and Woodward
attribution name: Boland and Woodward

ERISNet: deep neural network for Sargassum detection along the coastline of the Mexican Caribbean
type: item
type: AcademicArticle
description: Recently, Caribbean coasts have experienced atypical massive arrivals of pelagic Sargassum with negative consequences both ecologically and economically. Based on deep learning techniques, this study proposes a novel algorithm for floating and accumulated pelagic Sargassum detection along the coastline of Quintana Roo, Mexico. Using convolutional and recurrent neural networks architectures, a deep neural network (named ERISNet) was designed specifically to detect these macroalgae along the coastline through remote sensing support. A new dataset which includes pixel values with and without Sargassum was built to train and test ERISNet. Aqua-MODIS imagery was used to build the dataset. After the learning process, the designed algorithm achieves a 90% of probability in its classification skills. ERISNet provides a novel insight to detect accurately algal blooms arrivals.
format: application/pdf
format: text/html
creator: Javier Arellano-Verdejo
creator: Hugo E. Lazcano-Hernandez
creator: Nancy Cabanillas-Terán
subject: Computational Science
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6842
publisher: PeerJ Inc.
rights: © 2019 Arellano-Verdejo et al.
abstract: Recently, Caribbean coasts have experienced atypical massive arrivals of pelagic Sargassum with negative consequences both ecologically and economically. Based on deep learning techniques, this study proposes a novel algorithm for floating and accumulated pelagic Sargassum detection along the coastline of Quintana Roo, Mexico. Using convolutional and recurrent neural networks architectures, a deep neural network (named ERISNet) was designed specifically to detect these macroalgae along the coastline through remote sensing support. A new dataset which includes pixel values with and without Sargassum was built to train and test ERISNet. Aqua-MODIS imagery was used to build the dataset. After the learning process, the designed algorithm achieves a 90% of probability in its classification skills. ERISNet provides a novel insight to detect accurately algal blooms arrivals.
bibliographic citation: Arellano-Verdejo et al. (2019) ERISNet: deep neural network for Sargassum detection along the coastline of the Mexican Caribbean. PeerJ 7:e6842 https://doi.org/10.7717/peerj.6842
date submitted: 2018-12-22
date accepted: 2019-03-25
issued: 2019-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arellano-Verdejo
  given name: Javier
author list: Agent
  family name: Lazcano-Hernandez
  given name: Hugo E.
author list: Agent
  family name: Cabanillas-Terán
  given name: Nancy
doi: 10.7717/peerj.6842
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-01
copyright: ©2019 Arellano-Verdejo et al.
attribution name: Arellano-Verdejo et al.

Manganese affects the growth and metabolism of Ganoderma lucidum based on LC-MS analysis
type: item
type: AcademicArticle
description: Background As a metal-enriched edible fungus, Ganoderma lucidum is capable of adsorbing manganese effectively. And the manganese ion is demonstrated to play an important role in the synthesis of manganese peroxidase (Mnp) and other physiological activities during G. lucidum growth. Recently, the influence of manganese on the metabolites of G. lucidum fruiting bodies can be revealed through metabonomics technique. Methods In this study, we uncovered the changes between the control and 200 mg/kg Mn-treated fruiting bodies with liquid chromatography coupled to mass spectrometry (LC-MS). Results The mycelial growth rate, dry yield, Mnp activity , total polysaccharide content, triterpenoid content, and total manganese content in the mature fruiting bodies of G. lucidum changed between the control and different Mn-treated groups. Based on LC-MS method, a total of 16 significantly different metabolites were obtained and identified, among which, five presented significantly down-regulated and 11 up-regulated in Mn-treated samples. The metabolites chavicol and palmitoylethanolamide were particularly significantly up-regulated, and were found the strong promotion relationship. Dependent on the MetPA database, four KEGG pathways were detected and glycerophospholipid metabolism was most impacted, in which, choline was involved in. Discussion The added manganese ion in the substrate enhanced Mnp activities, and consequently promoted the mycelial growth, yield , metabolites in the fruiting bodies including triterpenoids, total manganese, chavicol, etc. Our finding can provide a theoretical reference to regulation of manganese on the physiological metabolism of G. lucidum.
format: application/pdf
format: text/html
creator: Bo Zhang
creator: Jie Zhou
creator: Qiang Li
creator: Bingcheng Gan
creator: Weihong Peng
creator: Xiaoping Zhang
creator: Wei Tan
creator: Lin Jiang
creator: Xiaolin Li
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Mycology
description: doi:10.7717/peerj.6846
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background As a metal-enriched edible fungus, Ganoderma lucidum is capable of adsorbing manganese effectively. And the manganese ion is demonstrated to play an important role in the synthesis of manganese peroxidase (Mnp) and other physiological activities during G. lucidum growth. Recently, the influence of manganese on the metabolites of G. lucidum fruiting bodies can be revealed through metabonomics technique. Methods In this study, we uncovered the changes between the control and 200 mg/kg Mn-treated fruiting bodies with liquid chromatography coupled to mass spectrometry (LC-MS). Results The mycelial growth rate, dry yield, Mnp activity , total polysaccharide content, triterpenoid content, and total manganese content in the mature fruiting bodies of G. lucidum changed between the control and different Mn-treated groups. Based on LC-MS method, a total of 16 significantly different metabolites were obtained and identified, among which, five presented significantly down-regulated and 11 up-regulated in Mn-treated samples. The metabolites chavicol and palmitoylethanolamide were particularly significantly up-regulated, and were found the strong promotion relationship. Dependent on the MetPA database, four KEGG pathways were detected and glycerophospholipid metabolism was most impacted, in which, choline was involved in. Discussion The added manganese ion in the substrate enhanced Mnp activities, and consequently promoted the mycelial growth, yield , metabolites in the fruiting bodies including triterpenoids, total manganese, chavicol, etc. Our finding can provide a theoretical reference to regulation of manganese on the physiological metabolism of G. lucidum.
bibliographic citation: Zhang et al. (2019) Manganese affects the growth and metabolism of Ganoderma lucidum based on LC-MS analysis. PeerJ 7:e6846 https://doi.org/10.7717/peerj.6846
date submitted: 2018-11-15
date accepted: 2019-03-19
issued: 2019-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Bo
author list: Agent
  family name: Zhou
  given name: Jie
author list: Agent
  family name: Li
  given name: Qiang
author list: Agent
  family name: Gan
  given name: Bingcheng
author list: Agent
  family name: Peng
  given name: Weihong
author list: Agent
  family name: Zhang
  given name: Xiaoping
author list: Agent
  family name: Tan
  given name: Wei
author list: Agent
  family name: Jiang
  given name: Lin
author list: Agent
  family name: Li
  given name: Xiaolin
doi: 10.7717/peerj.6846
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-01
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

A large scale evaluation of TBProfiler and Mykrobe for antibiotic resistance prediction in Mycobacterium tuberculosis
type: item
type: AcademicArticle
description: Recent years saw a growing interest in predicting antibiotic resistance from whole-genome sequencing data, with promising results obtained for Staphylococcus aureus and Mycobacterium tuberculosis. In this work, we gathered 6,574 sequencing read datasets of M. tuberculosis public genomes with associated antibiotic resistance profiles for both first and second-line antibiotics. We performed a systematic evaluation of TBProfiler and Mykrobe, two widely recognized softwares allowing to predict resistance in M. tuberculosis. The size of the dataset allowed us to obtain confident estimations of their overall predictive performance, to assess precisely the individual predictive power of the markers they rely on, and to study in addition how these softwares behave across the major M. tuberculosis lineages. While this study confirmed the overall good performance of these tools, it revealed that an important fraction of the catalog of mutations they embed is of limited predictive power. It also revealed that these tools offer different sensitivity/specificity trade-offs, which is mainly due to the different sets of mutation they embed but also to their underlying genotyping pipelines. More importantly, it showed that their level of predictive performance varies greatly across lineages for some antibiotics, therefore suggesting that the predictions made by these softwares should be deemed more or less confident depending on the lineage inferred and the predictive performance of the marker(s) actually detected. Finally, we evaluated the relevance of machine learning approaches operating from the set of markers detected by these softwares and show that they present an attractive alternative strategy, allowing to reach better performance for several drugs while significantly reducing the number of candidate mutations to consider.
format: application/pdf
format: text/html
creator: Pierre Mahé
creator: Meriem El Azami
creator: Philippine Barlas
creator: Maud Tournoud
subject: Bioinformatics
subject: Infectious Diseases
subject: Public Health
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6857
publisher: PeerJ Inc.
rights: © 2019 Mahé et al.
abstract: Recent years saw a growing interest in predicting antibiotic resistance from whole-genome sequencing data, with promising results obtained for Staphylococcus aureus and Mycobacterium tuberculosis. In this work, we gathered 6,574 sequencing read datasets of M. tuberculosis public genomes with associated antibiotic resistance profiles for both first and second-line antibiotics. We performed a systematic evaluation of TBProfiler and Mykrobe, two widely recognized softwares allowing to predict resistance in M. tuberculosis. The size of the dataset allowed us to obtain confident estimations of their overall predictive performance, to assess precisely the individual predictive power of the markers they rely on, and to study in addition how these softwares behave across the major M. tuberculosis lineages. While this study confirmed the overall good performance of these tools, it revealed that an important fraction of the catalog of mutations they embed is of limited predictive power. It also revealed that these tools offer different sensitivity/specificity trade-offs, which is mainly due to the different sets of mutation they embed but also to their underlying genotyping pipelines. More importantly, it showed that their level of predictive performance varies greatly across lineages for some antibiotics, therefore suggesting that the predictions made by these softwares should be deemed more or less confident depending on the lineage inferred and the predictive performance of the marker(s) actually detected. Finally, we evaluated the relevance of machine learning approaches operating from the set of markers detected by these softwares and show that they present an attractive alternative strategy, allowing to reach better performance for several drugs while significantly reducing the number of candidate mutations to consider.
bibliographic citation: Mahé et al. (2019) A large scale evaluation of TBProfiler and Mykrobe for antibiotic resistance prediction in Mycobacterium tuberculosis. PeerJ 7:e6857 https://doi.org/10.7717/peerj.6857
date submitted: 2018-12-06
date accepted: 2019-03-25
issued: 2019-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mahé
  given name: Pierre
author list: Agent
  family name: El Azami
  given name: Meriem
author list: Agent
  family name: Barlas
  given name: Philippine
author list: Agent
  family name: Tournoud
  given name: Maud
doi: 10.7717/peerj.6857
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-01
copyright: © 2019 Mahé et al.
attribution name: Mahé et al.

A novel conserved family of Macro-like domains—putative new players in ADP-ribosylation signaling
type: item
type: AcademicArticle
description: The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers a full understanding of the functioning of living cells. One such example is the human protein C12ORF4, which belongs to the DUF2362 family, present in many eukaryotic lineages and conserved in metazoans. The only functional information available on C12ORF4 (Chromosome 12 Open Reading Frame 4) is its involvement in mast cell degranulation and its being a genetic cause of autosomal intellectual disability. Bioinformatics analysis of the DUF2362 family provides strong evidence that it is a novel member of the Macro clan/superfamily. Sequence similarity analysis versus other representatives of the Macro superfamily of ADP-ribose-binding proteins and mapping sequence conservation on predicted three-dimensional structure provides hypotheses regarding the molecular function for members of the DUF2362 family. For example, the available functional data suggest a possible role for C12ORF4 in ADP-ribosylation signaling in asthma and related inflammatory diseases. This novel family appears to be a likely novel ADP-ribosylation “reader” and “eraser,” a previously unnoticed putative new player in cell signaling by this emerging post-translational modification.
format: application/pdf
format: text/html
creator: Małgorzata Dudkiewicz
creator: Krzysztof Pawłowski
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
description: doi:10.7717/peerj.6863
publisher: PeerJ Inc.
rights: © 2019 Dudkiewicz and Pawłowski
abstract: The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers a full understanding of the functioning of living cells. One such example is the human protein C12ORF4, which belongs to the DUF2362 family, present in many eukaryotic lineages and conserved in metazoans. The only functional information available on C12ORF4 (Chromosome 12 Open Reading Frame 4) is its involvement in mast cell degranulation and its being a genetic cause of autosomal intellectual disability. Bioinformatics analysis of the DUF2362 family provides strong evidence that it is a novel member of the Macro clan/superfamily. Sequence similarity analysis versus other representatives of the Macro superfamily of ADP-ribose-binding proteins and mapping sequence conservation on predicted three-dimensional structure provides hypotheses regarding the molecular function for members of the DUF2362 family. For example, the available functional data suggest a possible role for C12ORF4 in ADP-ribosylation signaling in asthma and related inflammatory diseases. This novel family appears to be a likely novel ADP-ribosylation “reader” and “eraser,” a previously unnoticed putative new player in cell signaling by this emerging post-translational modification.
bibliographic citation: Dudkiewicz et al. (2019) A novel conserved family of Macro-like domains—putative new players in ADP-ribosylation signaling. PeerJ 7:e6863 https://doi.org/10.7717/peerj.6863
date submitted: 2019-02-18
date accepted: 2019-03-28
issued: 2019-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dudkiewicz
  given name: Małgorzata
author list: Agent
  family name: Pawłowski
  given name: Krzysztof
doi: 10.7717/peerj.6863
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-01
copyright: © 2019 Dudkiewicz and Pawłowski
attribution name: Dudkiewicz and Pawłowski

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