PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Annual plankton community metabolism in estuarine and coastal waters in Perth (Western Australia)
items: Synthesis, enzyme inhibitory kinetics mechanism and computational study of N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides as novel therapeutic agents for Alzheimer’s disease
items: A new species of Middle Miocene baleen whale from the Nupinai Group, Hikatagawa Formation of Hokkaido, Japan
items: Hi-MC: a novel method for high-throughput mitochondrial haplogroup classification
items: Forecasting influenza epidemics by integrating internet search queries and traditional surveillance data with the support vector machine regression model in Liaoning, from 2011 to 2015
items: Complex characterization of oat (Avena sativa L.) lines obtained by wide crossing with maize (Zea mays L.)
items: Differing responses of red abalone (Haliotis rufescens) and white abalone (H. sorenseni) to infection with phage-associated Candidatus Xenohaliotis californiensis
items: Dry season diet composition of four-horned antelope Tetracerus quadricornis in tropical dry deciduous forests, Nepal
items: Mulch and groundcover effects on soil temperature and moisture, surface reflectance, grapevine water potential, and vineyard weed management
items: It’s a matter of design—how pitfall trap design affects trap samples and possible predictions

Annual plankton community metabolism in estuarine and coastal waters in Perth (Western Australia)
type: item
type: AcademicArticle
description: The planktonic metabolic balance that is the balance between gross primary production (GPP) and community respiration (CR) was determined in Matilda Bay (estuarine) and Woodman Point (coastal) in Perth, Western Australia. The rates of net community production (NCP = GPP – CR) and the ratio between GPP and CR (P/R) were assessed to evaluate whether the metabolic balance in the two coastal locations tends to be net autotrophic (production exceeding community respiration) or net heterotrophic (respiration exceeding production). We also analyzed environmental variability by measuring temperature, salinity, and nutrients and chlorophyll a concentration. Samples were collected biweekly from March 2014 to March 2015. During the study period the metabolic rates were three times higher in Matilda Bay than in Woodman Point. The predominant metabolism was net autotrophic at both sites with P/R ratios >1 in the majority of the sampling dates. In Matilda Bay, the metabolic rates were negatively correlated with salinity denoting river dynamics influence, and positively with chlorophyll a. In Woodman Point only the GPP was positively correlated with chlorophyll a. The positive correlation between P/R ratio and GPP in Matilda Bay and the positive correlations between the metabolic rates and chlorophyll a suggest that factors controlling autotrophic processes are modulating the planktonic metabolic balance in the coastal marine ecosystem in Perth. Significant correlations were found between CR and GPP-standardized to chlorophyll a and water temperature. The net autotrophic metabolic balance indicates that in both ecosystems planktonic communities are acting as a sink of CO2 and as a source of organic matter and oxygen to the system and are able to export organic matter to other ecosystems.
format: application/pdf
format: text/html
creator: Susana Agusti
creator: Lorena Vigoya
creator: Carlos Manuel Duarte
subject: Ecology
subject: Marine Biology
subject: Biogeochemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.5081
publisher: PeerJ Inc.
rights: © 2018 Agusti et al.
abstract: The planktonic metabolic balance that is the balance between gross primary production (GPP) and community respiration (CR) was determined in Matilda Bay (estuarine) and Woodman Point (coastal) in Perth, Western Australia. The rates of net community production (NCP = GPP – CR) and the ratio between GPP and CR (P/R) were assessed to evaluate whether the metabolic balance in the two coastal locations tends to be net autotrophic (production exceeding community respiration) or net heterotrophic (respiration exceeding production). We also analyzed environmental variability by measuring temperature, salinity, and nutrients and chlorophyll a concentration. Samples were collected biweekly from March 2014 to March 2015. During the study period the metabolic rates were three times higher in Matilda Bay than in Woodman Point. The predominant metabolism was net autotrophic at both sites with P/R ratios >1 in the majority of the sampling dates. In Matilda Bay, the metabolic rates were negatively correlated with salinity denoting river dynamics influence, and positively with chlorophyll a. In Woodman Point only the GPP was positively correlated with chlorophyll a. The positive correlation between P/R ratio and GPP in Matilda Bay and the positive correlations between the metabolic rates and chlorophyll a suggest that factors controlling autotrophic processes are modulating the planktonic metabolic balance in the coastal marine ecosystem in Perth. Significant correlations were found between CR and GPP-standardized to chlorophyll a and water temperature. The net autotrophic metabolic balance indicates that in both ecosystems planktonic communities are acting as a sink of CO2 and as a source of organic matter and oxygen to the system and are able to export organic matter to other ecosystems.
bibliographic citation: Agusti et al. (2018) Annual plankton community metabolism in estuarine and coastal waters in Perth (Western Australia). PeerJ 6:e5081 https://doi.org/10.7717/peerj.5081
date submitted: 2018-02-19
date accepted: 2018-06-04
issued: 2018-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Agusti
  given name: Susana
author list: Agent
  family name: Vigoya
  given name: Lorena
author list: Agent
  family name: Duarte
  given name: Carlos Manuel
doi: 10.7717/peerj.5081
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-26
copyright: ©2018 Agusti et al.
attribution name: Agusti et al.

Synthesis, enzyme inhibitory kinetics mechanism and computational study of N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides as novel therapeutic agents for Alzheimer’s disease
type: item
type: AcademicArticle
description: The present study comprises the synthesis of a new series of sulfonamides derived from 4-methoxyphenethylamine (1). The synthesis was initiated by the reaction of 1 with 4-methylbenzenesulfonyl chloride (2) in aqueous sodium carbonate solution at pH 9 to yield N-(4-methoxyphenethyl)-4-methylbenzensulfonamide (3).This parent molecule 3 was subsequently treated with various alkyl/aralkyl halides, (4a–j), using N,N-dimethylformamide (DMF) as solvent and LiH as activator to produce a series of new N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides (5a–j). The structural characterization of these derivatives was carried out by spectroscopic techniques like IR, 1H-NMR, and 13C-NMR. The elemental analysis data was also coherent with spectral data of these molecules. The inhibitory effects on acetylcholinesterase and DPPH were evaluated and it was observed that N-(4-Methoxyphenethyl)-4-methyl-N-(2-propyl)benzensulfonamide (5c) showed acetylcholinesterase inhibitory activity 0.075 ± 0.001 (IC50 0.075 ± 0.001 µM) comparable to Neostigmine methylsulfate (IC50 2.038 ± 0.039 µM).The docking studies of synthesized ligands 5a–j were also carried out against acetylcholinesterase (PDBID 4PQE) to compare the binding affinities with IC50 values. The kinetic mechanism analyzed by Lineweaver-Burk plots demonstrated that compound (5c) inhibits the acetylcholinesterase competitively to form an enzyme inhibitor complex. The inhibition constants Ki calculated from Dixon plots for compound (5c) is 2.5 µM. It was also found from kinetic analysis that derivative 5c irreversible enzyme inhibitor complex. It is proposed on the basis of our investigation that title compound 5c may serve as lead structure for the design of more potent acetylcholinesterase inhibitors.
format: application/pdf
format: text/html
creator: Muhammad Athar Abbasi
creator: Mubashir Hassan
creator: Aziz-ur-Rehman
creator: Sabahat Zahra Siddiqui
creator: Syed Adnan Ali Shah
creator: Hussain Raza
creator: Sung Yum Seo
subject: Bioinformatics
subject: Neuroscience
subject: Cognitive Disorders
subject: Drugs and Devices
description: doi:10.7717/peerj.4962
publisher: PeerJ Inc.
rights: © 2018 Abbasi et al.
abstract: The present study comprises the synthesis of a new series of sulfonamides derived from 4-methoxyphenethylamine (1). The synthesis was initiated by the reaction of 1 with 4-methylbenzenesulfonyl chloride (2) in aqueous sodium carbonate solution at pH 9 to yield N-(4-methoxyphenethyl)-4-methylbenzensulfonamide (3).This parent molecule 3 was subsequently treated with various alkyl/aralkyl halides, (4a–j), using N,N-dimethylformamide (DMF) as solvent and LiH as activator to produce a series of new N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides (5a–j). The structural characterization of these derivatives was carried out by spectroscopic techniques like IR, 1H-NMR, and 13C-NMR. The elemental analysis data was also coherent with spectral data of these molecules. The inhibitory effects on acetylcholinesterase and DPPH were evaluated and it was observed that N-(4-Methoxyphenethyl)-4-methyl-N-(2-propyl)benzensulfonamide (5c) showed acetylcholinesterase inhibitory activity 0.075 ± 0.001 (IC50 0.075 ± 0.001 µM) comparable to Neostigmine methylsulfate (IC50 2.038 ± 0.039 µM).The docking studies of synthesized ligands 5a–j were also carried out against acetylcholinesterase (PDBID 4PQE) to compare the binding affinities with IC50 values. The kinetic mechanism analyzed by Lineweaver-Burk plots demonstrated that compound (5c) inhibits the acetylcholinesterase competitively to form an enzyme inhibitor complex. The inhibition constants Ki calculated from Dixon plots for compound (5c) is 2.5 µM. It was also found from kinetic analysis that derivative 5c irreversible enzyme inhibitor complex. It is proposed on the basis of our investigation that title compound 5c may serve as lead structure for the design of more potent acetylcholinesterase inhibitors.
bibliographic citation: Abbasi et al. (2018) Synthesis, enzyme inhibitory kinetics mechanism and computational study of N-(4-methoxyphenethyl)-N-(substituted)-4-methylbenzenesulfonamides as novel therapeutic agents for Alzheimer’s disease. PeerJ 6:e4962 https://doi.org/10.7717/peerj.4962
date submitted: 2018-02-14
date accepted: 2018-05-20
issued: 2018-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abbasi
  given name: Muhammad Athar
author list: Agent
  family name: Hassan
  given name: Mubashir
author list: Agent
  family name: Aziz-ur-Rehman
author list: Agent
  family name: Siddiqui
  given name: Sabahat Zahra
author list: Agent
  family name: Shah
  given name: Syed Adnan Ali
author list: Agent
  family name: Raza
  given name: Hussain
author list: Agent
  family name: Seo
  given name: Sung Yum
doi: 10.7717/peerj.4962
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-26
copyright: ©2018 Abbasi et al.
attribution name: Abbasi et al.

A new species of Middle Miocene baleen whale from the Nupinai Group, Hikatagawa Formation of Hokkaido, Japan
type: item
type: AcademicArticle
description: A fossil whale from the Hikatagawa Formation (Middle Miocene, 15.2–11.5 Ma) of Hokkaido, Japan is described as a new genus and species Taikicetus inouei and its phylogenetic position is examined. Consistent with the result of Marx, Lambert & de Muizon (2017), the Cetotheriidae form a clade with the Balaenopteroidea, and “a clade comprising Isanacetus, Parietobalaena and related taxa” is located basal to the Balaenopteroidea + Cetotheriidae clade. Taikicetus inouei is placed in the clade with most of members of “Cetotheres” sensu lato comprising Isanacetus, Parietobalaena and related taxa. Taikicetus inouei can be distinguished from the other members of “Cetotheres” sensu lato in having an anteriorly swollen short zygomatic process, high triangular coronoid process, and angular process, which does not reach as far posterior as the mandibular condyle. Taikicetus inouei is only record of “Cetotheres” sensu lato from Hokkaido, Japan and the northern-most records of “Cetotheres” sensu lato in Japan.
format: application/pdf
format: text/html
creator: Yoshihiro Tanaka
creator: Tatsuro Ando
creator: Hiroshi Sawamura
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.4934
publisher: PeerJ Inc.
rights: © 2018 Tanaka et al.
abstract: A fossil whale from the Hikatagawa Formation (Middle Miocene, 15.2–11.5 Ma) of Hokkaido, Japan is described as a new genus and species Taikicetus inouei and its phylogenetic position is examined. Consistent with the result of Marx, Lambert & de Muizon (2017), the Cetotheriidae form a clade with the Balaenopteroidea, and “a clade comprising Isanacetus, Parietobalaena and related taxa” is located basal to the Balaenopteroidea + Cetotheriidae clade. Taikicetus inouei is placed in the clade with most of members of “Cetotheres” sensu lato comprising Isanacetus, Parietobalaena and related taxa. Taikicetus inouei can be distinguished from the other members of “Cetotheres” sensu lato in having an anteriorly swollen short zygomatic process, high triangular coronoid process, and angular process, which does not reach as far posterior as the mandibular condyle. Taikicetus inouei is only record of “Cetotheres” sensu lato from Hokkaido, Japan and the northern-most records of “Cetotheres” sensu lato in Japan.
bibliographic citation: Tanaka et al. (2018) A new species of Middle Miocene baleen whale from the Nupinai Group, Hikatagawa Formation of Hokkaido, Japan. PeerJ 6:e4934 https://doi.org/10.7717/peerj.4934
date submitted: 2018-02-27
date accepted: 2018-05-18
issued: 2018-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tanaka
  given name: Yoshihiro
author list: Agent
  family name: Ando
  given name: Tatsuro
author list: Agent
  family name: Sawamura
  given name: Hiroshi
doi: 10.7717/peerj.4934
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-26
copyright: © 2018 Tanaka et al.
attribution name: Tanaka et al.

Hi-MC: a novel method for high-throughput mitochondrial haplogroup classification
type: item
type: AcademicArticle
description: Effective approaches for assessing mitochondrial DNA (mtDNA) variation are important to multiple scientific disciplines. Mitochondrial haplogroups characterize branch points in the phylogeny of mtDNA. Several tools exist for mitochondrial haplogroup classification. However, most require full or partial mtDNA sequence which is often cost prohibitive for studies with large sample sizes. The purpose of this study was to develop Hi-MC, a high-throughput method for mitochondrial haplogroup classification that is cost effective and applicable to large sample sizes making mitochondrial analysis more accessible in genetic studies. Using rigorous selection criteria, we defined and validated a custom panel of mtDNA single nucleotide polymorphisms that allows for accurate classification of European, African, and Native American mitochondrial haplogroups at broad resolution with minimal genotyping and cost. We demonstrate that Hi-MC performs well in samples of European, African, and Native American ancestries, and that Hi-MC performs comparably to a commonly used classifier. Implementation as a software package in R enables users to download and run the program locally, grants greater flexibility in the number of samples that can be run, and allows for easy expansion in future revisions. Hi-MC is available in the CRAN repository and the source code is freely available at https://github.com/vserch/himc.
format: application/pdf
format: text/html
creator: Sandra Smieszek
creator: Sabrina L. Mitchell
creator: Eric H. Farber-Eger
creator: Olivia J. Veatch
creator: Nicholas R. Wheeler
creator: Robert J. Goodloe
creator: Quinn S. Wells
creator: Deborah G. Murdock
creator: Dana C. Crawford
subject: Bioinformatics
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.5149
publisher: PeerJ Inc.
rights: © 2018 Smieszek et al.
abstract: Effective approaches for assessing mitochondrial DNA (mtDNA) variation are important to multiple scientific disciplines. Mitochondrial haplogroups characterize branch points in the phylogeny of mtDNA. Several tools exist for mitochondrial haplogroup classification. However, most require full or partial mtDNA sequence which is often cost prohibitive for studies with large sample sizes. The purpose of this study was to develop Hi-MC, a high-throughput method for mitochondrial haplogroup classification that is cost effective and applicable to large sample sizes making mitochondrial analysis more accessible in genetic studies. Using rigorous selection criteria, we defined and validated a custom panel of mtDNA single nucleotide polymorphisms that allows for accurate classification of European, African, and Native American mitochondrial haplogroups at broad resolution with minimal genotyping and cost. We demonstrate that Hi-MC performs well in samples of European, African, and Native American ancestries, and that Hi-MC performs comparably to a commonly used classifier. Implementation as a software package in R enables users to download and run the program locally, grants greater flexibility in the number of samples that can be run, and allows for easy expansion in future revisions. Hi-MC is available in the CRAN repository and the source code is freely available at https://github.com/vserch/himc.
bibliographic citation: Smieszek et al. (2018) Hi-MC: a novel method for high-throughput mitochondrial haplogroup classification. PeerJ 6:e5149 https://doi.org/10.7717/peerj.5149
date submitted: 2017-11-20
date accepted: 2018-06-12
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smieszek
  given name: Sandra
author list: Agent
  family name: Mitchell
  given name: Sabrina L.
author list: Agent
  family name: Farber-Eger
  given name: Eric H.
author list: Agent
  family name: Veatch
  given name: Olivia J.
author list: Agent
  family name: Wheeler
  given name: Nicholas R.
author list: Agent
  family name: Goodloe
  given name: Robert J.
author list: Agent
  family name: Wells
  given name: Quinn S.
author list: Agent
  family name: Murdock
  given name: Deborah G.
author list: Agent
  family name: Crawford
  given name: Dana C.
doi: 10.7717/peerj.5149
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: © 2018 Smieszek et al.
attribution name: Smieszek et al.

Forecasting influenza epidemics by integrating internet search queries and traditional surveillance data with the support vector machine regression model in Liaoning, from 2011 to 2015
type: item
type: AcademicArticle
description: Background Influenza epidemics pose significant social and economic challenges in China. Internet search query data have been identified as a valuable source for the detection of emerging influenza epidemics. However, the selection of the search queries and the adoption of prediction methods are crucial challenges when it comes to improving predictions. The purpose of this study was to explore the application of the Support Vector Machine (SVM) regression model in merging search engine query data and traditional influenza data. Methods The official monthly reported number of influenza cases in Liaoning province in China was acquired from the China National Scientific Data Center for Public Health from January 2011 to December 2015. Based on Baidu Index, a publicly available search engine database, search queries potentially related to influenza over the corresponding period were identified. An SVM regression model was built to be used for predictions, and the choice of three parameters (C, γ, ε) in the SVM regression model was determined by leave-one-out cross-validation (LOOCV) during the model construction process. The model’s performance was evaluated by the evaluation metrics including Root Mean Square Error, Root Mean Square Percentage Error and Mean Absolute Percentage Error. Results In total, 17 search queries related to influenza were generated through the initial query selection approach and were adopted to construct the SVM regression model, including nine queries in the same month, three queries at a lag of one month, one query at a lag of two months and four queries at a lag of three months. The SVM model performed well when with the parameters (C = 2, γ = 0.005, ɛ = 0.0001), based on the ensemble data integrating the influenza surveillance data and Baidu search query data. Conclusions The results demonstrated the feasibility of using internet search engine query data as the complementary data source for influenza surveillance and the efficiency of SVM r…
format: application/pdf
format: text/html
creator: Feng Liang
creator: Peng Guan
creator: Wei Wu
creator: Desheng Huang
subject: Health Policy
subject: Infectious Diseases
description: doi:10.7717/peerj.5134
publisher: PeerJ Inc.
rights: © 2018 Liang et al.
abstract: Background Influenza epidemics pose significant social and economic challenges in China. Internet search query data have been identified as a valuable source for the detection of emerging influenza epidemics. However, the selection of the search queries and the adoption of prediction methods are crucial challenges when it comes to improving predictions. The purpose of this study was to explore the application of the Support Vector Machine (SVM) regression model in merging search engine query data and traditional influenza data. Methods The official monthly reported number of influenza cases in Liaoning province in China was acquired from the China National Scientific Data Center for Public Health from January 2011 to December 2015. Based on Baidu Index, a publicly available search engine database, search queries potentially related to influenza over the corresponding period were identified. An SVM regression model was built to be used for predictions, and the choice of three parameters (C, γ, ε) in the SVM regression model was determined by leave-one-out cross-validation (LOOCV) during the model construction process. The model’s performance was evaluated by the evaluation metrics including Root Mean Square Error, Root Mean Square Percentage Error and Mean Absolute Percentage Error. Results In total, 17 search queries related to influenza were generated through the initial query selection approach and were adopted to construct the SVM regression model, including nine queries in the same month, three queries at a lag of one month, one query at a lag of two months and four queries at a lag of three months. The SVM model performed well when with the parameters (C = 2, γ = 0.005, ɛ = 0.0001), based on the ensemble data integrating the influenza surveillance data and Baidu search query data. Conclusions The results demonstrated the feasibility of using internet search engine query data as the complementary data source for influenza surveillance and the efficiency of SVM r…
bibliographic citation: Liang et al. (2018) Forecasting influenza epidemics by integrating internet search queries and traditional surveillance data with the support vector machine regression model in Liaoning, from 2011 to 2015. PeerJ 6:e5134 https://doi.org/10.7717/peerj.5134
date submitted: 2018-04-05
date accepted: 2018-06-08
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Feng
author list: Agent
  family name: Guan
  given name: Peng
author list: Agent
  family name: Wu
  given name: Wei
author list: Agent
  family name: Huang
  given name: Desheng
doi: 10.7717/peerj.5134
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: © 2018 Liang et al.
attribution name: Liang et al.

Complex characterization of oat (Avena sativa L.) lines obtained by wide crossing with maize (Zea mays L.)
type: item
type: AcademicArticle
description: Background The oat × maize addition (OMA) lines are used for mapping of the maize genome, the studies of centromere-specific histone (CENH3), gene expression, meiotic chromosome behavior and also for introducing maize C4 photosynthetic system to oat. The aim of our study was the identification and molecular-cytogenetic characterization of oat × maize hybrids. Methods Oat DH lines and oat × maize hybrids were obtained using the wide crossing of Avena sativa L. with Zea mays L. The plants identified as having a Grande-1 retrotransposon fragment, which produced seeds, were used for genomic in situ hybridization (GISH). Results A total of 138 oat lines obtained by crossing of 2,314 oat plants from 80 genotypes with maize cv. Waza were tested for the presence of maize chromosomes. The presence of maize chromatin was indicated in 66 lines by amplification of the PCR product (500 bp) generated using primers specific for the maize retrotransposon Grande-1. Genomic in situ hybridization (GISH) detected whole maize chromosomes in eight lines (40%). All of the analyzed plants possessed full complement of oat chromosomes. The number of maize chromosomes differed between the OMA lines. Four OMA lines possessed two maize chromosomes similar in size, three OMA—one maize chromosome, and one OMA—four maize chromosomes. In most of the lines, the detected chromosomes were labeled uniformly. The presence of six 45S rDNA loci was detected in oat chromosomes, but none of the added maize chromosomes in any of the lines carried 45S rDNA locus. Twenty of the analyzed lines did not possess whole maize chromosomes, but the introgression of maize chromatin in the oat chromosomes. Five of 66 hybrids were shorter in height, grassy type without panicles. Twenty-seven OMA lines were fertile and produced seeds ranging in number from 1–102 (in total 613). Sixty-three fertile DH lines, out of 72 which did not have an addition of maize chromosomes or chromatin, produced seeds in the range of 1–343 (in…
format: application/pdf
format: text/html
creator: Edyta Skrzypek
creator: Tomasz Warzecha
creator: Angelika Noga
creator: Marzena Warchoł
creator: Ilona Czyczyło-Mysza
creator: Kinga Dziurka
creator: Izabela Marcińska
creator: Kamila Kapłoniak
creator: Agnieszka Sutkowska
creator: Zygmunt Nita
creator: Krystyna Werwińska
creator: Dominika Idziak-Helmcke
creator: Magdalena Rojek
creator: Marta Hosiawa-Barańska
subject: Agricultural Science
subject: Biotechnology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.5107
publisher: PeerJ Inc.
rights: © 2018 Skrzypek et al.
abstract: Background The oat × maize addition (OMA) lines are used for mapping of the maize genome, the studies of centromere-specific histone (CENH3), gene expression, meiotic chromosome behavior and also for introducing maize C4 photosynthetic system to oat. The aim of our study was the identification and molecular-cytogenetic characterization of oat × maize hybrids. Methods Oat DH lines and oat × maize hybrids were obtained using the wide crossing of Avena sativa L. with Zea mays L. The plants identified as having a Grande-1 retrotransposon fragment, which produced seeds, were used for genomic in situ hybridization (GISH). Results A total of 138 oat lines obtained by crossing of 2,314 oat plants from 80 genotypes with maize cv. Waza were tested for the presence of maize chromosomes. The presence of maize chromatin was indicated in 66 lines by amplification of the PCR product (500 bp) generated using primers specific for the maize retrotransposon Grande-1. Genomic in situ hybridization (GISH) detected whole maize chromosomes in eight lines (40%). All of the analyzed plants possessed full complement of oat chromosomes. The number of maize chromosomes differed between the OMA lines. Four OMA lines possessed two maize chromosomes similar in size, three OMA—one maize chromosome, and one OMA—four maize chromosomes. In most of the lines, the detected chromosomes were labeled uniformly. The presence of six 45S rDNA loci was detected in oat chromosomes, but none of the added maize chromosomes in any of the lines carried 45S rDNA locus. Twenty of the analyzed lines did not possess whole maize chromosomes, but the introgression of maize chromatin in the oat chromosomes. Five of 66 hybrids were shorter in height, grassy type without panicles. Twenty-seven OMA lines were fertile and produced seeds ranging in number from 1–102 (in total 613). Sixty-three fertile DH lines, out of 72 which did not have an addition of maize chromosomes or chromatin, produced seeds in the range of 1–343 (in…
bibliographic citation: Skrzypek et al. (2018) Complex characterization of oat (Avena sativa L.) lines obtained by wide crossing with maize (Zea mays L.). PeerJ 6:e5107 https://doi.org/10.7717/peerj.5107
date submitted: 2018-03-24
date accepted: 2018-06-06
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Skrzypek
  given name: Edyta
author list: Agent
  family name: Warzecha
  given name: Tomasz
author list: Agent
  family name: Noga
  given name: Angelika
author list: Agent
  family name: Warchoł
  given name: Marzena
author list: Agent
  family name: Czyczyło-Mysza
  given name: Ilona
author list: Agent
  family name: Dziurka
  given name: Kinga
author list: Agent
  family name: Marcińska
  given name: Izabela
author list: Agent
  family name: Kapłoniak
  given name: Kamila
author list: Agent
  family name: Sutkowska
  given name: Agnieszka
author list: Agent
  family name: Nita
  given name: Zygmunt
author list: Agent
  family name: Werwińska
  given name: Krystyna
author list: Agent
  family name: Idziak-Helmcke
  given name: Dominika
author list: Agent
  family name: Rojek
  given name: Magdalena
author list: Agent
  family name: Hosiawa-Barańska
  given name: Marta
doi: 10.7717/peerj.5107
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: ©2018 Skrzypek et al.
attribution name: Skrzypek et al.

Differing responses of red abalone (Haliotis rufescens) and white abalone (H. sorenseni) to infection with phage-associated Candidatus Xenohaliotis californiensis
type: item
type: AcademicArticle
description: The Rickettsiales-like prokaryote and causative agent of Withering Syndrome (WS)—Candidatus Xenohaliotis californiensis (Ca. Xc)—decimated black abalone populations along the Pacific coast of North America. White abalone—Haliotis sorenseni—are also susceptible to WS and have become nearly extinct in the wild due to overfishing in the 1970s. Candidatus Xenohaliotis californiensis proliferates within epithelial cells of the abalone gastrointestinal tract and causes clinical signs of starvation. In 2012, evidence of a putative bacteriophage associated with Ca. Xc in red abalone—Haliotis rufescens—was described. Recently, histologic examination of animals with Ca. Xc infection in California abalone populations universally appear to have the phage-containing inclusions. In this study, we investigated the current virulence of Ca. Xc in red abalone and white abalone at different environmental temperatures. Using a comparative experimental design, we observed differences over time between the two abalone species in mortality, body condition, and bacterial load by quantitative real time PCR (qPCR). By day 251, all white abalone exposed to the current variant of Ca. Xc held in the warm water (18.5 °C) treatment died, while red abalone exposed to the same conditions had a mortality rate of only 10%, despite a relatively heavy bacterial burden as determined by qPCR of posterior esophagus tissue and histological assessment at the termination of the experiment. These data support the current status of Ca. Xc as less virulent in red abalone, and may provide correlative evidence of a protective phage interaction. However, white abalone appear to remain highly susceptible to this disease. These findings have important implications for implementation of a white abalone recovery program, particularly with respect to the thermal regimes of locations where captively-reared individuals will be outplanted.
format: application/pdf
format: text/html
creator: Ashley Vater
creator: Barbara A. Byrne
creator: Blythe C. Marshman
creator: Lauren W. Ashlock
creator: James D. Moore
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Microbiology
subject: Virology
subject: Natural Resource Management
description: doi:10.7717/peerj.5104
publisher: PeerJ Inc.
rights: © 2018 Vater et al.
abstract: The Rickettsiales-like prokaryote and causative agent of Withering Syndrome (WS)—Candidatus Xenohaliotis californiensis (Ca. Xc)—decimated black abalone populations along the Pacific coast of North America. White abalone—Haliotis sorenseni—are also susceptible to WS and have become nearly extinct in the wild due to overfishing in the 1970s. Candidatus Xenohaliotis californiensis proliferates within epithelial cells of the abalone gastrointestinal tract and causes clinical signs of starvation. In 2012, evidence of a putative bacteriophage associated with Ca. Xc in red abalone—Haliotis rufescens—was described. Recently, histologic examination of animals with Ca. Xc infection in California abalone populations universally appear to have the phage-containing inclusions. In this study, we investigated the current virulence of Ca. Xc in red abalone and white abalone at different environmental temperatures. Using a comparative experimental design, we observed differences over time between the two abalone species in mortality, body condition, and bacterial load by quantitative real time PCR (qPCR). By day 251, all white abalone exposed to the current variant of Ca. Xc held in the warm water (18.5 °C) treatment died, while red abalone exposed to the same conditions had a mortality rate of only 10%, despite a relatively heavy bacterial burden as determined by qPCR of posterior esophagus tissue and histological assessment at the termination of the experiment. These data support the current status of Ca. Xc as less virulent in red abalone, and may provide correlative evidence of a protective phage interaction. However, white abalone appear to remain highly susceptible to this disease. These findings have important implications for implementation of a white abalone recovery program, particularly with respect to the thermal regimes of locations where captively-reared individuals will be outplanted.
bibliographic citation: Vater et al. (2018) Differing responses of red abalone (Haliotis rufescens) and white abalone (H. sorenseni) to infection with phage-associated Candidatus Xenohaliotis californiensis. PeerJ 6:e5104 https://doi.org/10.7717/peerj.5104
date submitted: 2018-01-26
date accepted: 2018-06-05
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vater
  given name: Ashley
author list: Agent
  family name: Byrne
  given name: Barbara A.
author list: Agent
  family name: Marshman
  given name: Blythe C.
author list: Agent
  family name: Ashlock
  given name: Lauren W.
author list: Agent
  family name: Moore
  given name: James D.
doi: 10.7717/peerj.5104
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: ©2018 Vater et al.
attribution name: Vater et al.

Dry season diet composition of four-horned antelope Tetracerus quadricornis in tropical dry deciduous forests, Nepal
type: item
type: AcademicArticle
description: It is essential to assess the feeding strategies of threatened species during resource-scarce seasons to understand their dietary niche breadth and inform appropriate habitat management measures. In this study, we examined the diet composition of four-horned antelope (FHA) Tetracerus and quadricornis, one of the least studied ungulate species, in Banke National Park, Nepal. A total of 53 fresh pellet groups were collected between December 2015 and January 2016 and analyzed using micro-histological fecal analysis technique. First, we prepared 133 micro-histological photographs of different parts of 64 reference plant species. Then we compared 1,590 fragments of 53 fecal samples with photographs of reference plants to assess the percentage of occurrence of different plant species in FHA diet. A total of 30 plant species belonging to 18 different families were identified in fecal samples. Chi-square goodness of fit tests showed that FHA appeared not to feed all plant uniformly. Out of 1,520 identified fragments in fecal samples, 1,300 were browse species and 220 were grass species. Browse represented 85.5% of the identified plant fragments, suggesting that FHA might be adopting a browser strategy at least during winter when grasses are low in abundance and their nutritive quality is poor. Tree species had the highest contribution in the diet (46.55%) followed by shrubs (24.52%). The family Gramineae was consumed in the highest proportion (27.68%) followed by Euphorbiaceae (11.95%). Overall, our results suggest that FHA has the feeding plasticity to adapt to resource fluctuation. Based on the findings of this study, we recommend that dicot plant species—particularly fruit trees and shrubs, which are the major source of nutrients for FHA during resource-lean, dry season—be conserved and natural regeneration of these taxa be promoted.
format: application/pdf
format: text/html
creator: Chet Bahadur Oli
creator: Saroj Panthi
creator: Naresh Subedi
creator: Gagan Ale
creator: Ganesh Pant
creator: Gopal Khanal
creator: Suman Bhattarai
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.5102
publisher: PeerJ Inc.
rights: © 2018 Oli et al.
abstract: It is essential to assess the feeding strategies of threatened species during resource-scarce seasons to understand their dietary niche breadth and inform appropriate habitat management measures. In this study, we examined the diet composition of four-horned antelope (FHA) Tetracerus and quadricornis, one of the least studied ungulate species, in Banke National Park, Nepal. A total of 53 fresh pellet groups were collected between December 2015 and January 2016 and analyzed using micro-histological fecal analysis technique. First, we prepared 133 micro-histological photographs of different parts of 64 reference plant species. Then we compared 1,590 fragments of 53 fecal samples with photographs of reference plants to assess the percentage of occurrence of different plant species in FHA diet. A total of 30 plant species belonging to 18 different families were identified in fecal samples. Chi-square goodness of fit tests showed that FHA appeared not to feed all plant uniformly. Out of 1,520 identified fragments in fecal samples, 1,300 were browse species and 220 were grass species. Browse represented 85.5% of the identified plant fragments, suggesting that FHA might be adopting a browser strategy at least during winter when grasses are low in abundance and their nutritive quality is poor. Tree species had the highest contribution in the diet (46.55%) followed by shrubs (24.52%). The family Gramineae was consumed in the highest proportion (27.68%) followed by Euphorbiaceae (11.95%). Overall, our results suggest that FHA has the feeding plasticity to adapt to resource fluctuation. Based on the findings of this study, we recommend that dicot plant species—particularly fruit trees and shrubs, which are the major source of nutrients for FHA during resource-lean, dry season—be conserved and natural regeneration of these taxa be promoted.
bibliographic citation: Oli et al. (2018) Dry season diet composition of four-horned antelope Tetracerus quadricornis in tropical dry deciduous forests, Nepal. PeerJ 6:e5102 https://doi.org/10.7717/peerj.5102
date submitted: 2017-11-01
date accepted: 2018-06-05
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oli
  given name: Chet Bahadur
author list: Agent
  family name: Panthi
  given name: Saroj
author list: Agent
  family name: Subedi
  given name: Naresh
author list: Agent
  family name: Ale
  given name: Gagan
author list: Agent
  family name: Pant
  given name: Ganesh
author list: Agent
  family name: Khanal
  given name: Gopal
author list: Agent
  family name: Bhattarai
  given name: Suman
doi: 10.7717/peerj.5102
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: ©2018 Oli et al.
attribution name: Oli et al.

Mulch and groundcover effects on soil temperature and moisture, surface reflectance, grapevine water potential, and vineyard weed management
type: item
type: AcademicArticle
description: The objectives of this research were to identify alternatives to glyphosate for intra-row (under-trellis) vineyard floor management and to evaluate the potential for intra-row and inter-row (alleyway) groundcovers to reduce vegetative vigor of ‘Marquette’ grapevines (Vitis spp.) in a southeast Nebraska vineyard. The experiment was a randomized factorial design with five intra-row treatments (crushed glass mulch [CG], distillers’ grain mulch [DG], creeping red fescue [CRF], non-sprayed control [NSC], and glyphosate [GLY]) and three inter-row treatments (creeping red fescue [CRF], Kentucky bluegrass [KB], and resident vegetation [RV]). Treatments were established in 2010–2011 and measurements were conducted during 2012 and 2013 on 5- and 6-year-old vines. Soil temperatures were mostly higher under mulches and lower under intra-row groundcovers, compared to GLY. Weed cover in CG, DG, and CRF treatments was the same or less than GLY. At most sampling dates, inter-row soil moisture was lowest under KB. Intra-row soil moisture was highest under DG mulch and lowest under CRF and NSC; CG had the same or lower soil moisture than GLY. Surprisingly, we did not detect differences in mid-day photosynthetically active radiation (PAR) reflectance, despite visual differences among the intra-row treatments. Mid-day vine water potential did not differ among treatments. We concluded it is not necessary to maintain a bare soil strip under established vines in this region, where soil fertility and moisture are non-limiting.
format: application/pdf
format: text/html
creator: Christina M. Bavougian
creator: Paul E. Read
subject: Agricultural Science
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.5082
publisher: PeerJ Inc.
rights: © 2018 Bavougian and Read
abstract: The objectives of this research were to identify alternatives to glyphosate for intra-row (under-trellis) vineyard floor management and to evaluate the potential for intra-row and inter-row (alleyway) groundcovers to reduce vegetative vigor of ‘Marquette’ grapevines (Vitis spp.) in a southeast Nebraska vineyard. The experiment was a randomized factorial design with five intra-row treatments (crushed glass mulch [CG], distillers’ grain mulch [DG], creeping red fescue [CRF], non-sprayed control [NSC], and glyphosate [GLY]) and three inter-row treatments (creeping red fescue [CRF], Kentucky bluegrass [KB], and resident vegetation [RV]). Treatments were established in 2010–2011 and measurements were conducted during 2012 and 2013 on 5- and 6-year-old vines. Soil temperatures were mostly higher under mulches and lower under intra-row groundcovers, compared to GLY. Weed cover in CG, DG, and CRF treatments was the same or less than GLY. At most sampling dates, inter-row soil moisture was lowest under KB. Intra-row soil moisture was highest under DG mulch and lowest under CRF and NSC; CG had the same or lower soil moisture than GLY. Surprisingly, we did not detect differences in mid-day photosynthetically active radiation (PAR) reflectance, despite visual differences among the intra-row treatments. Mid-day vine water potential did not differ among treatments. We concluded it is not necessary to maintain a bare soil strip under established vines in this region, where soil fertility and moisture are non-limiting.
bibliographic citation: Bavougian et al. (2018) Mulch and groundcover effects on soil temperature and moisture, surface reflectance, grapevine water potential, and vineyard weed management. PeerJ 6:e5082 https://doi.org/10.7717/peerj.5082
date submitted: 2018-01-04
date accepted: 2018-06-03
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bavougian
  given name: Christina M.
author list: Agent
  family name: Read
  given name: Paul E.
doi: 10.7717/peerj.5082
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: ©2018 Bavougian and Read
attribution name: Bavougian and Read

It’s a matter of design—how pitfall trap design affects trap samples and possible predictions
type: item
type: AcademicArticle
description: Background Pitfall traps are commonly used to assess ground dwelling arthropod communities. The effects of different pitfall trap designs on the trapping outcome are poorly investigated however they might affect conclusions drawn from pitfall trap data greatly. Methods We tested four pitfall trap types which have been used in previous studies for their effectiveness: a simple type, a faster exchangeable type with an extended plastic rim plate and two types with guidance barriers (V- and X-shaped). About 20 traps were active for 10 weeks and emptied biweekly resulting in 100 trap samples. Results Pitfall traps with guidance barriers were up to five times more effective than simple pitfall traps and trap samples resulted in more similar assemblage approximations. Pitfall traps with extended plastic rim plates did not only perform poorly but also resulted in distinct carabid assemblages with less individuals of small species and a larger variation. Discussion Due to the obvious trait filtering and resulting altered assemblages, we suggest not to use pitfall traps with extended plastic rim plates. In comprehensive biodiversity inventories, a smaller number of pitfall traps with guidance barriers and a larger number of spatial replicates is of advantage, while due to comparability reasons, the use of simple pitfall traps will be recommended in most other cases.
format: application/pdf
format: text/html
creator: Fabian A. Boetzl
creator: Elena Ries
creator: Gudrun Schneider
creator: Jochen Krauss
subject: Agricultural Science
subject: Conservation Biology
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.5078
publisher: PeerJ Inc.
rights: © 2018 Boetzl et al.
abstract: Background Pitfall traps are commonly used to assess ground dwelling arthropod communities. The effects of different pitfall trap designs on the trapping outcome are poorly investigated however they might affect conclusions drawn from pitfall trap data greatly. Methods We tested four pitfall trap types which have been used in previous studies for their effectiveness: a simple type, a faster exchangeable type with an extended plastic rim plate and two types with guidance barriers (V- and X-shaped). About 20 traps were active for 10 weeks and emptied biweekly resulting in 100 trap samples. Results Pitfall traps with guidance barriers were up to five times more effective than simple pitfall traps and trap samples resulted in more similar assemblage approximations. Pitfall traps with extended plastic rim plates did not only perform poorly but also resulted in distinct carabid assemblages with less individuals of small species and a larger variation. Discussion Due to the obvious trait filtering and resulting altered assemblages, we suggest not to use pitfall traps with extended plastic rim plates. In comprehensive biodiversity inventories, a smaller number of pitfall traps with guidance barriers and a larger number of spatial replicates is of advantage, while due to comparability reasons, the use of simple pitfall traps will be recommended in most other cases.
bibliographic citation: Boetzl et al. (2018) It’s a matter of design—how pitfall trap design affects trap samples and possible predictions. PeerJ 6:e5078 https://doi.org/10.7717/peerj.5078
date submitted: 2018-03-24
date accepted: 2018-06-04
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boetzl
  given name: Fabian A.
author list: Agent
  family name: Ries
  given name: Elena
author list: Agent
  family name: Schneider
  given name: Gudrun
author list: Agent
  family name: Krauss
  given name: Jochen
doi: 10.7717/peerj.5078
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: © 2018 Boetzl et al.
attribution name: Boetzl et al.

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