PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: Potamopyrgus antipodarum as a potential defender against swimmer’s itch in European recreational water bodies—experimental study
items: Nitrogen addition increases the contents of glomalin-related soil protein and soil organic carbon but retains aggregate stability in a Pinus tabulaeformis forest
items: Specalyzer—an interactive online tool to analyze spectral reflectance measurements
items: Alpha-mangostin inhibits the migration and invasion of A549 lung cancer cells
items: DNA barcoding of marine fish species from Rongcheng Bay, China

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.

Potamopyrgus antipodarum as a potential defender against swimmer’s itch in European recreational water bodies—experimental study
type: item
type: AcademicArticle
description: Swimmer’s itch is a re-emerging human disease caused by bird schistosome cercariae, which can infect bathing or working people in water bodies. Even if cercariae fail after penetrating the human skin, they can cause dangerous symptoms in atypical mammal hosts. One of the natural methods to reduce the presence of cercariae in the environment could lie in the introduction of non–host snail species to the ecosystem, which is known as the “dilution” or “decoy” effect. The caenogastropod Potamopyrgus antipodarum—an alien in Europe—could be a good candidate against swimmer’s itch because of its apparent resistance to invasion by European bird schistosome species and its high population density. As a pilot study on this topic, we have carried out a laboratory experiment on how P. antipodarum influences the infestation of the intermediate host Radix balthica (a native lymnaeid) by the bird schistosome Trichobilharzia regenti. We found that the co–exposure of 200 P. antipodarum individuals per one R. balthica to the T. regenti miracidia under experimental conditions makes the infestation ineffective. Our results show that a non–host snail population has the potential to interfere with the transmission of a trematode via suitable snail hosts.
format: application/pdf
format: text/html
creator: Anna Marszewska
creator: Anna Cichy
creator: Jana Bulantová
creator: Petr Horák
creator: Elżbieta Żbikowska
subject: Ecology
subject: Parasitology
subject: Zoology
subject: Public Health
subject: Freshwater Biology
description: doi:10.7717/peerj.5045
publisher: PeerJ Inc.
rights: © 2018 Marszewska et al.
abstract: Swimmer’s itch is a re-emerging human disease caused by bird schistosome cercariae, which can infect bathing or working people in water bodies. Even if cercariae fail after penetrating the human skin, they can cause dangerous symptoms in atypical mammal hosts. One of the natural methods to reduce the presence of cercariae in the environment could lie in the introduction of non–host snail species to the ecosystem, which is known as the “dilution” or “decoy” effect. The caenogastropod Potamopyrgus antipodarum—an alien in Europe—could be a good candidate against swimmer’s itch because of its apparent resistance to invasion by European bird schistosome species and its high population density. As a pilot study on this topic, we have carried out a laboratory experiment on how P. antipodarum influences the infestation of the intermediate host Radix balthica (a native lymnaeid) by the bird schistosome Trichobilharzia regenti. We found that the co–exposure of 200 P. antipodarum individuals per one R. balthica to the T. regenti miracidia under experimental conditions makes the infestation ineffective. Our results show that a non–host snail population has the potential to interfere with the transmission of a trematode via suitable snail hosts.
bibliographic citation: Marszewska et al. (2018) Potamopyrgus antipodarum as a potential defender against swimmer’s itch in European recreational water bodies—experimental study. PeerJ 6:e5045 https://doi.org/10.7717/peerj.5045
date submitted: 2018-02-28
date accepted: 2018-05-31
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marszewska
  given name: Anna
author list: Agent
  family name: Cichy
  given name: Anna
author list: Agent
  family name: Bulantová
  given name: Jana
author list: Agent
  family name: Horák
  given name: Petr
author list: Agent
  family name: Żbikowska
  given name: Elżbieta
doi: 10.7717/peerj.5045
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: ©2018 Marszewska et al.
attribution name: Marszewska et al.

Nitrogen addition increases the contents of glomalin-related soil protein and soil organic carbon but retains aggregate stability in a Pinus tabulaeformis forest
type: item
type: AcademicArticle
description: Background Glomalin-related soil protein (GRSP) and soil organic carbon (SOC) contribute to the formation and stability of soil aggregates, but the mechanism by which global atmospheric nitrogen (N) deposition changes soil aggregate stability by altering the distribution of GRSP and SOC in different aggregate fractions remains unknown. Methods We used a gradient N addition (0–9 g N m−2 y−1) in Pinus tabulaeformis forest for two years in northeast China and then examined the changes in SOC contents, total GRSP (T-GRSP), and easily extractable GRSP (EE-GRSP) contents in three soil aggregate fractions (macro-aggregate: >250 μm, micro-aggregate: 250–53 μm, and fine material: <53 μm) and their relationship with aggregate stability. Results (1) The soil was dominated by macro-aggregates. Short term N addition had no significant effect on mean weight diameter (MWD) and geometric mean diameter (GMD). (2) GRSP varied among aggregate fractions, and N addition had different effects on the distribution of GRSP in aggregate fractions. The EE-GRSP content in the macro-aggregates increased initially and then decreased with increasing N addition levels, having a peak value of 0.480 mg g−1 at 6 g N m−2 y−1. The micro-aggregates had the lowest EE-GRSP content (0.148 mg g−1) at 6 g N m−2 y−1. Furthermore, the T-GRSP content significantly increased in the aggregate fractions with the N addition levels. (3) The macro-aggregate had the highest SOC content, followed by the micro-aggregate and the fine material had the lowest SOC content. N addition significantly increased the SOC content in all the aggregate fractions. (4) GRSP and SOC contents were not significantly correlated with MWD. Conclusion Glomalin-related soil protein and SOC contents increased by N addition, but this increase did not enhance aggregate stability in short term, and the improvement of stability might depend on binding agents and incubation time.
format: application/pdf
format: text/html
creator: Lipeng Sun
creator: Hang Jing
creator: Guoliang Wang
creator: Guobin Liu
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.5039
publisher: PeerJ Inc.
rights: © 2018 Sun et al.
abstract: Background Glomalin-related soil protein (GRSP) and soil organic carbon (SOC) contribute to the formation and stability of soil aggregates, but the mechanism by which global atmospheric nitrogen (N) deposition changes soil aggregate stability by altering the distribution of GRSP and SOC in different aggregate fractions remains unknown. Methods We used a gradient N addition (0–9 g N m−2 y−1) in Pinus tabulaeformis forest for two years in northeast China and then examined the changes in SOC contents, total GRSP (T-GRSP), and easily extractable GRSP (EE-GRSP) contents in three soil aggregate fractions (macro-aggregate: >250 μm, micro-aggregate: 250–53 μm, and fine material: <53 μm) and their relationship with aggregate stability. Results (1) The soil was dominated by macro-aggregates. Short term N addition had no significant effect on mean weight diameter (MWD) and geometric mean diameter (GMD). (2) GRSP varied among aggregate fractions, and N addition had different effects on the distribution of GRSP in aggregate fractions. The EE-GRSP content in the macro-aggregates increased initially and then decreased with increasing N addition levels, having a peak value of 0.480 mg g−1 at 6 g N m−2 y−1. The micro-aggregates had the lowest EE-GRSP content (0.148 mg g−1) at 6 g N m−2 y−1. Furthermore, the T-GRSP content significantly increased in the aggregate fractions with the N addition levels. (3) The macro-aggregate had the highest SOC content, followed by the micro-aggregate and the fine material had the lowest SOC content. N addition significantly increased the SOC content in all the aggregate fractions. (4) GRSP and SOC contents were not significantly correlated with MWD. Conclusion Glomalin-related soil protein and SOC contents increased by N addition, but this increase did not enhance aggregate stability in short term, and the improvement of stability might depend on binding agents and incubation time.
bibliographic citation: Sun et al. (2018) Nitrogen addition increases the contents of glomalin-related soil protein and soil organic carbon but retains aggregate stability in a Pinus tabulaeformis forest. PeerJ 6:e5039 https://doi.org/10.7717/peerj.5039
date submitted: 2018-03-07
date accepted: 2018-05-31
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Lipeng
author list: Agent
  family name: Jing
  given name: Hang
author list: Agent
  family name: Wang
  given name: Guoliang
author list: Agent
  family name: Liu
  given name: Guobin
doi: 10.7717/peerj.5039
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: © 2018 Sun et al.
attribution name: Sun et al.

Specalyzer—an interactive online tool to analyze spectral reflectance measurements
type: item
type: AcademicArticle
description: Low-cost phenotyping using proximal sensors is increasingly becoming popular in plant breeding. As these techniques generate a large amount of data, analysis pipelines that do not require expertise in computer programming can benefit a broader user base. In this work, a new online tool Specalyzer is presented that allows interactive analysis of the spectral reflectance data generated by proximal spectroradiometers. Specalyzer can be operated from any web browser allowing data uploading, analysis, interactive plots and exporting by point and click using a simple graphical user interface. Specalyzer is evaluated with case study data from a winter wheat fertilizer trial with two fertilizer treatments. Specalyzer can be accessed online at http://www.specalyzer.org.
format: application/pdf
format: text/html
creator: Alexander Koc
creator: Tina Henriksson
creator: Aakash Chawade
subject: Agricultural Science
subject: Bioinformatics
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.5031
publisher: PeerJ Inc.
rights: © 2018 Koc et al.
abstract: Low-cost phenotyping using proximal sensors is increasingly becoming popular in plant breeding. As these techniques generate a large amount of data, analysis pipelines that do not require expertise in computer programming can benefit a broader user base. In this work, a new online tool Specalyzer is presented that allows interactive analysis of the spectral reflectance data generated by proximal spectroradiometers. Specalyzer can be operated from any web browser allowing data uploading, analysis, interactive plots and exporting by point and click using a simple graphical user interface. Specalyzer is evaluated with case study data from a winter wheat fertilizer trial with two fertilizer treatments. Specalyzer can be accessed online at http://www.specalyzer.org.
bibliographic citation: Koc et al. (2018) Specalyzer—an interactive online tool to analyze spectral reflectance measurements. PeerJ 6:e5031 https://doi.org/10.7717/peerj.5031
date submitted: 2018-03-03
date accepted: 2018-05-31
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koc
  given name: Alexander
author list: Agent
  family name: Henriksson
  given name: Tina
author list: Agent
  family name: Chawade
  given name: Aakash
doi: 10.7717/peerj.5031
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: ©2018 Koc et al.
attribution name: Koc et al.

Alpha-mangostin inhibits the migration and invasion of A549 lung cancer cells
type: item
type: AcademicArticle
description: Several studies have indicated that α-mangostin exerts anti-metastasis and anti-subsistence effects on several types of cancer cells. Especially, the anti-metastatic effect of α-mangostin on cancer cells is a prospective function in cancer treatment. However, the metastasis process is complicated, and includes migration, invasion, intravasation, and extravasation; thus, the main target of anti-metastatic effect of α-mangostin is not known. In this study, we investigated the effects of α-mangostin on the invasion, subsistence, and migration of lung cancer cells under co-culture conditions with normal cells and regular mono-culture conditions. We found that α-mangostin killed the lung cancer and normal cells in a dose-dependent manner. Furthermore, the alteration in the surface mechanical properties of cells was examined by using atomic force microscopy. Although the α-mangostin concentrations of 5 and 10 µM did not affect the short-term cell viability, they considerably decreased the Young’s modulus of lung cancer cells implying a decline in cell surface actin cytoskeletal properties. Additionally, these concentrations of α-mangostin inhibited the migration of lung cancer cells. In co-culture conditions (cancer cells with normal cells), the invasive activities of cancer cells on normal cells were discernibly observed, and was inhibited after treatment with 5 and 10 µM of α-mangostin. Taken together, α-mangostin suppressed the subsistence of lung cancer cells and displayed anti-metastatic activities by inhibiting the migration and invasion, and reducing the actin cytoskeleton of cancer cells. Our findings suggest that α-mangostin could be a potential therapeutic agent for cancer treatment.
format: application/pdf
format: text/html
creator: Thi Kieu Trang Phan
creator: Fahimeh Shahbazzadeh
creator: Thi Thu Huong Pham
creator: Takanori Kihara
subject: Biotechnology
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.5027
publisher: PeerJ Inc.
rights: © 2018 Phan et al.
abstract: Several studies have indicated that α-mangostin exerts anti-metastasis and anti-subsistence effects on several types of cancer cells. Especially, the anti-metastatic effect of α-mangostin on cancer cells is a prospective function in cancer treatment. However, the metastasis process is complicated, and includes migration, invasion, intravasation, and extravasation; thus, the main target of anti-metastatic effect of α-mangostin is not known. In this study, we investigated the effects of α-mangostin on the invasion, subsistence, and migration of lung cancer cells under co-culture conditions with normal cells and regular mono-culture conditions. We found that α-mangostin killed the lung cancer and normal cells in a dose-dependent manner. Furthermore, the alteration in the surface mechanical properties of cells was examined by using atomic force microscopy. Although the α-mangostin concentrations of 5 and 10 µM did not affect the short-term cell viability, they considerably decreased the Young’s modulus of lung cancer cells implying a decline in cell surface actin cytoskeletal properties. Additionally, these concentrations of α-mangostin inhibited the migration of lung cancer cells. In co-culture conditions (cancer cells with normal cells), the invasive activities of cancer cells on normal cells were discernibly observed, and was inhibited after treatment with 5 and 10 µM of α-mangostin. Taken together, α-mangostin suppressed the subsistence of lung cancer cells and displayed anti-metastatic activities by inhibiting the migration and invasion, and reducing the actin cytoskeleton of cancer cells. Our findings suggest that α-mangostin could be a potential therapeutic agent for cancer treatment.
bibliographic citation: Phan et al. (2018) Alpha-mangostin inhibits the migration and invasion of A549 lung cancer cells. PeerJ 6:e5027 https://doi.org/10.7717/peerj.5027
date submitted: 2018-03-01
date accepted: 2018-05-31
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Phan
  given name: Thi Kieu Trang
author list: Agent
  family name: Shahbazzadeh
  given name: Fahimeh
author list: Agent
  family name: Pham
  given name: Thi Thu Huong
author list: Agent
  family name: Kihara
  given name: Takanori
doi: 10.7717/peerj.5027
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: ©2018 Phan et al.
attribution name: Phan et al.

DNA barcoding of marine fish species from Rongcheng Bay, China
type: item
type: AcademicArticle
description: Rongcheng Bay is a coastal bay of the Northern Yellow Sea, China. To investigate and monitor the fish resources in Rongcheng Bay, 187 specimens from 41 different species belonging to 28 families in nine orders were DNA-barcoded using the mitochondrial cytochrome c oxidase subunit I gene (COI). Most of the fish species could be discriminated using this COI sequence with the exception of Cynoglossus joyneri and Cynoglossus lighti. The average GC% content of the 41 fish species was 47.3%. The average Kimura 2-parameter genetic distances within the species, genera, families, and orders were 0.21%, 5.28%, 21.30%, and 23.63%, respectively. Our results confirmed that the use of combined morphological and DNA barcoding identification methods facilitated fish species identification in Rongcheng Bay, and also established a reliable DNA barcode reference library for these fish. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in this area.
format: application/pdf
format: text/html
creator: Lijuan Wang
creator: Zhihao Wu
creator: Mengxia Liu
creator: Wei Liu
creator: Wenxi Zhao
creator: Hongjun Liu
creator: Feng You
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.5013
publisher: PeerJ Inc.
rights: © 2018 Wang et al.
abstract: Rongcheng Bay is a coastal bay of the Northern Yellow Sea, China. To investigate and monitor the fish resources in Rongcheng Bay, 187 specimens from 41 different species belonging to 28 families in nine orders were DNA-barcoded using the mitochondrial cytochrome c oxidase subunit I gene (COI). Most of the fish species could be discriminated using this COI sequence with the exception of Cynoglossus joyneri and Cynoglossus lighti. The average GC% content of the 41 fish species was 47.3%. The average Kimura 2-parameter genetic distances within the species, genera, families, and orders were 0.21%, 5.28%, 21.30%, and 23.63%, respectively. Our results confirmed that the use of combined morphological and DNA barcoding identification methods facilitated fish species identification in Rongcheng Bay, and also established a reliable DNA barcode reference library for these fish. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in this area.
bibliographic citation: Wang et al. (2018) DNA barcoding of marine fish species from Rongcheng Bay, China. PeerJ 6:e5013 https://doi.org/10.7717/peerj.5013
date submitted: 2018-02-22
date accepted: 2018-05-29
issued: 2018-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lijuan
author list: Agent
  family name: Wu
  given name: Zhihao
author list: Agent
  family name: Liu
  given name: Mengxia
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Zhao
  given name: Wenxi
author list: Agent
  family name: Liu
  given name: Hongjun
author list: Agent
  family name: You
  given name: Feng
doi: 10.7717/peerj.5013
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-25
copyright: ©2018 Wang et al.
attribution name: Wang et al.

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