PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Acoustic monitoring indicates a correlation between calling and spawning in captive spotted seatrout (Cynoscion nebulosus)
items: Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica
items: Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba)
items: Cropping system diversification for food production in Mindanao rubber plantations: a rice cultivar mixture and rice intercropped with mungbean
items: Pull-down combined with proteomic strategy reveals functional diversity of synaptotagmin I
items: Screening of faba bean (Vicia faba L.) accessions to acidity and aluminium stresses
items: Will you swim into my parlour? In situ observations of Atlantic cod (Gadus morhua) interactions with baited pots, with implications for gear design
items: Tracking the virus-like particles of Macrobrachium rosenbergii nodavirus in insect cells
items: Trace elements during primordial plexiform network formation in human cerebral organoids
items: Off the scale: a new species of fish-scale gecko (Squamata: Gekkonidae: Geckolepis) with exceptionally large scales

Acoustic monitoring indicates a correlation between calling and spawning in captive spotted seatrout (Cynoscion nebulosus)
type: item
type: AcademicArticle
description: Background Fish sound production is widespread throughout many families. Territorial displays and courtship are the most common reasons for fish sound production. Yet, there is still some questions on how acoustic signaling and reproduction are correlated in many sound-producing species. In the present study, our aim was to determine if a quantitative relationship exists between calling and egg deposition in captive spotted seatrout (Cynoscion nebulosus). This type of data is essential if passive acoustics is to be used to identify spawning aggregations over large spatial scales and monitor reproductive activity over annual and decadal timeframes. Methods Acoustic recorders (i.e., DSG-Oceans) were placed in three laboratory tanks to record underwater sound over an entire, simulated reproductive season. We enumerated the number of calls, calculated the received sound pressure level, and counted the number of eggs every morning in each tank. Results Spotted seatrout produced three distinct call types characterized as “drums,” “grunts,” and “staccatos.” Spotted seatrout calling increased as the light cycle shifted from 13.5 to 14.5 h of light, and the temperature increased to 27.7 °C. Calling decreased once the temperature fell below 27.7 °C, and the light cycle shifted to 12 h of light. These temperature and light patterns followed the natural reproductive season observed in wild spotted seatrout in the Southeast United States. Spotted seatrout exhibited daily rhythms in calling. Acoustic signaling began once the lights turned off, and calling reached maximum activity approximately 3 h later. Eggs were released only on evenings in which spotted seatrout were calling. In all tanks, spotted seatrout were more likely to spawn when male fish called more frequently. A positive relationship between SPL and the number of eggs collected was found in Tanks 1 and 3. Discussion Our findings indicate that acoustic metrics can predict spawning potential. These findings are importa…
format: application/pdf
format: text/html
creator: Eric W. Montie
creator: Matt Hoover
creator: Christopher Kehrer
creator: Justin Yost
creator: Karl Brenkert
creator: Tim O’Donnell
creator: Michael R. Denson
subject: Animal Behavior
subject: Marine Biology
description: doi:10.7717/peerj.2944
publisher: PeerJ Inc.
rights: © 2017 Montie et al.
abstract: Background Fish sound production is widespread throughout many families. Territorial displays and courtship are the most common reasons for fish sound production. Yet, there is still some questions on how acoustic signaling and reproduction are correlated in many sound-producing species. In the present study, our aim was to determine if a quantitative relationship exists between calling and egg deposition in captive spotted seatrout (Cynoscion nebulosus). This type of data is essential if passive acoustics is to be used to identify spawning aggregations over large spatial scales and monitor reproductive activity over annual and decadal timeframes. Methods Acoustic recorders (i.e., DSG-Oceans) were placed in three laboratory tanks to record underwater sound over an entire, simulated reproductive season. We enumerated the number of calls, calculated the received sound pressure level, and counted the number of eggs every morning in each tank. Results Spotted seatrout produced three distinct call types characterized as “drums,” “grunts,” and “staccatos.” Spotted seatrout calling increased as the light cycle shifted from 13.5 to 14.5 h of light, and the temperature increased to 27.7 °C. Calling decreased once the temperature fell below 27.7 °C, and the light cycle shifted to 12 h of light. These temperature and light patterns followed the natural reproductive season observed in wild spotted seatrout in the Southeast United States. Spotted seatrout exhibited daily rhythms in calling. Acoustic signaling began once the lights turned off, and calling reached maximum activity approximately 3 h later. Eggs were released only on evenings in which spotted seatrout were calling. In all tanks, spotted seatrout were more likely to spawn when male fish called more frequently. A positive relationship between SPL and the number of eggs collected was found in Tanks 1 and 3. Discussion Our findings indicate that acoustic metrics can predict spawning potential. These findings are importa…
bibliographic citation: Montie et al. (2017) Acoustic monitoring indicates a correlation between calling and spawning in captive spotted seatrout (Cynoscion nebulosus). PeerJ 5:e2944 https://doi.org/10.7717/peerj.2944
date submitted: 2016-10-11
date accepted: 2016-12-27
issued: 2017-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Montie
  given name: Eric W.
author list: Agent
  family name: Hoover
  given name: Matt
author list: Agent
  family name: Kehrer
  given name: Christopher
author list: Agent
  family name: Yost
  given name: Justin
author list: Agent
  family name: Brenkert
  given name: Karl
author list: Agent
  family name: O’Donnell
  given name: Tim
author list: Agent
  family name: Denson
  given name: Michael R.
doi: 10.7717/peerj.2944
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-09
copyright: ©2017 Montie et al.
attribution name: Montie et al.

Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica
type: item
type: AcademicArticle
description: We estimated the genetic diversity of 50 Jatropha curcas samples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values for J. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f = − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of the Jatropha curcas germplasm bank in Costa Rica.
format: application/pdf
format: text/html
creator: Marcela Vásquez-Mayorga
creator: Eric J. Fuchs
creator: Eduardo J. Hernández
creator: Franklin Herrera
creator: Jesús Hernández
creator: Ileana Moreira
creator: Elizabeth Arnáez
creator: Natalia M. Barboza
subject: Biodiversity
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.2931
publisher: PeerJ Inc.
rights: © 2017 Vásquez-Mayorga et al.
abstract: We estimated the genetic diversity of 50 Jatropha curcas samples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values for J. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f = − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of the Jatropha curcas germplasm bank in Costa Rica.
bibliographic citation: Vásquez-Mayorga et al. (2017) Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica. PeerJ 5:e2931 https://doi.org/10.7717/peerj.2931
date submitted: 2016-09-20
date accepted: 2016-12-21
issued: 2017-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vásquez-Mayorga
  given name: Marcela
author list: Agent
  family name: Fuchs
  given name: Eric J.
author list: Agent
  family name: Hernández
  given name: Eduardo J.
author list: Agent
  family name: Herrera
  given name: Franklin
author list: Agent
  family name: Hernández
  given name: Jesús
author list: Agent
  family name: Moreira
  given name: Ileana
author list: Agent
  family name: Arnáez
  given name: Elizabeth
author list: Agent
  family name: Barboza
  given name: Natalia M.
doi: 10.7717/peerj.2931
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-09
copyright: ©2017 Vásquez-Mayorga et al.
attribution name: Vásquez-Mayorga et al.

Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba)
type: item
type: AcademicArticle
description: Background The endemic Australian freshwater prawn, Macrobrachium koombooloomba, provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively few Macrobrachium species that can complete its entire life cycle in freshwater. Methods The present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation by M. koombooloomba using a transcriptomics approach. De novo assembly of 75 bp paired end 227,564,643 high quality Illumina raw reads from 6 different cDNA libraries revealed 125,917 contigs of variable lengths (200–18,050 bp) with an N50 value of 1597. Results In total, 31,272 (24.83%) of the assembled contigs received significant blast hits, of which 27,686 and 22,560 contigs were mapped and functionally annotated, respectively. CEGMA (Core Eukaryotic Genes Mapping Approach) based transcriptome quality assessment revealed 96.37% completeness. We identified 43 different potential genes that are likely to be involved with freshwater adaptation in M. koombooloomba. Identified candidate genes included: 25 genes for osmoregulation, five for cell volume regulation, seven for stress tolerance, three for body fluid (haemolymph) maintenance, eight for epithelial permeability and water channel regulation, nine for egg size control and three for larval development. RSEM (RNA-Seq Expectation Maximization) based abundance estimation revealed that 6,253, 5,753 and 3,795 transcripts were expressed (at TPM value ≥10) in post larvae, juveniles and adults, respectively. Differential gene expression (DGE) analysis showed that 15 genes were expressed differentially in different individuals but these genes apparently were not involved with freshwater adaptation but rather were involved in growth, development and reproductive maturation. Discussion The genomic resources developed here will be useful for better understanding the molecular basis of freshwater adaptation in Macrobr…
format: application/pdf
format: text/html
creator: Md Lifat Rahi
creator: Shorash Amin
creator: Peter B. Mather
creator: David A. Hurwood
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Freshwater Biology
subject: Genomics
subject: Marine Biology
description: doi:10.7717/peerj.2977
publisher: PeerJ Inc.
rights: © 2017 Rahi et al.
abstract: Background The endemic Australian freshwater prawn, Macrobrachium koombooloomba, provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively few Macrobrachium species that can complete its entire life cycle in freshwater. Methods The present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation by M. koombooloomba using a transcriptomics approach. De novo assembly of 75 bp paired end 227,564,643 high quality Illumina raw reads from 6 different cDNA libraries revealed 125,917 contigs of variable lengths (200–18,050 bp) with an N50 value of 1597. Results In total, 31,272 (24.83%) of the assembled contigs received significant blast hits, of which 27,686 and 22,560 contigs were mapped and functionally annotated, respectively. CEGMA (Core Eukaryotic Genes Mapping Approach) based transcriptome quality assessment revealed 96.37% completeness. We identified 43 different potential genes that are likely to be involved with freshwater adaptation in M. koombooloomba. Identified candidate genes included: 25 genes for osmoregulation, five for cell volume regulation, seven for stress tolerance, three for body fluid (haemolymph) maintenance, eight for epithelial permeability and water channel regulation, nine for egg size control and three for larval development. RSEM (RNA-Seq Expectation Maximization) based abundance estimation revealed that 6,253, 5,753 and 3,795 transcripts were expressed (at TPM value ≥10) in post larvae, juveniles and adults, respectively. Differential gene expression (DGE) analysis showed that 15 genes were expressed differentially in different individuals but these genes apparently were not involved with freshwater adaptation but rather were involved in growth, development and reproductive maturation. Discussion The genomic resources developed here will be useful for better understanding the molecular basis of freshwater adaptation in Macrobr…
bibliographic citation: Rahi et al. (2017) Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba). PeerJ 5:e2977 https://doi.org/10.7717/peerj.2977
date submitted: 2016-09-28
date accepted: 2017-01-10
issued: 2017-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rahi
  given name: Md Lifat
author list: Agent
  family name: Amin
  given name: Shorash
author list: Agent
  family name: Mather
  given name: Peter B.
author list: Agent
  family name: Hurwood
  given name: David A.
doi: 10.7717/peerj.2977
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-08
copyright: ©2017 Rahi et al.
attribution name: Rahi et al.

Cropping system diversification for food production in Mindanao rubber plantations: a rice cultivar mixture and rice intercropped with mungbean
type: item
type: AcademicArticle
description: Including food production in non-food systems, such as rubber plantations and biofuel or bioenergy crops, may contribute to household food security. We evaluated the potential for planting rice, mungbean, rice cultivar mixtures, and rice intercropped with mungbean in young rubber plantations in experiments in the Arakan Valley of Mindanao in the Philippines. Rice mixtures consisted of two- or three-row strips of cultivar Dinorado, a cultivar with higher value but lower yield, and high-yielding cultivar UPL Ri-5. Rice and mungbean intercropping treatments consisted of different combinations of two- or three-row strips of rice and mungbean. We used generalized linear mixed models to evaluate the yield of each crop alone and in the mixture or intercropping treatments. We also evaluated a land equivalent ratio for yield, along with weed biomass (where Ageratum conyzoides was particularly abundant), the severity of disease caused by Magnaporthe oryzae and Cochliobolus miyabeanus, and rice bug (Leptocorisa acuta) abundance. We analyzed the yield ranking of each cropping system across site-year combinations to determine mean relative performance and yield stability. When weighted by their relative economic value, UPL Ri-5 had the highest mean performance, but with decreasing performance in low-yielding environments. A rice and mungbean intercropping system had the second highest performance, tied with high-value Dinorado but without decreasing relative performance in low-yielding environments. Rice and mungbean intercropped with rubber have been adopted by farmers in the Arakan Valley.
format: application/pdf
format: text/html
creator: Rosa Fe Hondrade
creator: Edwin Hondrade
creator: Lianqing Zheng
creator: Francisco Elazegui
creator: Jo-Anne Lynne Joy E. Duque
creator: Christopher C. Mundt
creator: Casiana M. Vera Cruz
creator: Karen A. Garrett
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.2975
publisher: PeerJ Inc.
rights: © 2017 Hondrade et al.
abstract: Including food production in non-food systems, such as rubber plantations and biofuel or bioenergy crops, may contribute to household food security. We evaluated the potential for planting rice, mungbean, rice cultivar mixtures, and rice intercropped with mungbean in young rubber plantations in experiments in the Arakan Valley of Mindanao in the Philippines. Rice mixtures consisted of two- or three-row strips of cultivar Dinorado, a cultivar with higher value but lower yield, and high-yielding cultivar UPL Ri-5. Rice and mungbean intercropping treatments consisted of different combinations of two- or three-row strips of rice and mungbean. We used generalized linear mixed models to evaluate the yield of each crop alone and in the mixture or intercropping treatments. We also evaluated a land equivalent ratio for yield, along with weed biomass (where Ageratum conyzoides was particularly abundant), the severity of disease caused by Magnaporthe oryzae and Cochliobolus miyabeanus, and rice bug (Leptocorisa acuta) abundance. We analyzed the yield ranking of each cropping system across site-year combinations to determine mean relative performance and yield stability. When weighted by their relative economic value, UPL Ri-5 had the highest mean performance, but with decreasing performance in low-yielding environments. A rice and mungbean intercropping system had the second highest performance, tied with high-value Dinorado but without decreasing relative performance in low-yielding environments. Rice and mungbean intercropped with rubber have been adopted by farmers in the Arakan Valley.
bibliographic citation: Hondrade et al. (2017) Cropping system diversification for food production in Mindanao rubber plantations: a rice cultivar mixture and rice intercropped with mungbean. PeerJ 5:e2975 https://doi.org/10.7717/peerj.2975
date submitted: 2016-10-06
date accepted: 2017-01-10
issued: 2017-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hondrade
  given name: Rosa Fe
author list: Agent
  family name: Hondrade
  given name: Edwin
author list: Agent
  family name: Zheng
  given name: Lianqing
author list: Agent
  family name: Elazegui
  given name: Francisco
author list: Agent
  family name: Duque
  given name: Jo-Anne Lynne Joy E.
author list: Agent
  family name: Mundt
  given name: Christopher C.
author list: Agent
  family name: Vera Cruz
  given name: Casiana M.
author list: Agent
  family name: Garrett
  given name: Karen A.
doi: 10.7717/peerj.2975
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-08
copyright: ©2017 Hondrade et al.
attribution name: Hondrade et al.

Pull-down combined with proteomic strategy reveals functional diversity of synaptotagmin I
type: item
type: AcademicArticle
description: Synaptotagmin I (Syt I) is most abundant in the brain and is involved in multiple cellular processes. Its two C2 domains, C2A and C2B, are the main functional regions. Our present study employed a pull-down combined with proteomic strategy to identify the C2 domain-interacting proteins to comprehensively understand the biological roles of the C2 domains and thus the functional diversity of Syt I. A total of 135 non-redundant proteins interacting with the C2 domains of Syt I were identified. Out of them, 32 and 64 proteins only bound to C2A or C2B domains, respectively, and 39 proteins bound to both of them. Compared with C2A, C2B could bind to many more proteins particularly those involved in synaptic transmission and metabolic regulation. Functional analysis indicated that Syt I may exert impacts by interacting with other proteins on multiple cellular processes, including vesicular membrane trafficking, synaptic transmission, metabolic regulation, catalysis, transmembrane transport and structure formation, etc. These results demonstrate that the functional diversity of Syt I is higher than previously expected, that its two domains may mediate the same and different cellular processes cooperatively or independently, and that C2B domain may play even more important roles than C2A in the functioning of Syt I. This work not only further deepened our understanding of the functional diversity of Syt I and the functional differences between its two C2 domains, but also provided important clues for the further related researches.
format: application/pdf
format: text/html
creator: Tianyao Guo
creator: Zhigui Duan
creator: Jia Chen
creator: Chunliang Xie
creator: Ying Wang
creator: Ping Chen
creator: Xianchun Wang
subject: Biochemistry
subject: Molecular Biology
subject: Neuroscience
description: doi:10.7717/peerj.2973
publisher: PeerJ Inc.
rights: © 2017 Guo et al.
abstract: Synaptotagmin I (Syt I) is most abundant in the brain and is involved in multiple cellular processes. Its two C2 domains, C2A and C2B, are the main functional regions. Our present study employed a pull-down combined with proteomic strategy to identify the C2 domain-interacting proteins to comprehensively understand the biological roles of the C2 domains and thus the functional diversity of Syt I. A total of 135 non-redundant proteins interacting with the C2 domains of Syt I were identified. Out of them, 32 and 64 proteins only bound to C2A or C2B domains, respectively, and 39 proteins bound to both of them. Compared with C2A, C2B could bind to many more proteins particularly those involved in synaptic transmission and metabolic regulation. Functional analysis indicated that Syt I may exert impacts by interacting with other proteins on multiple cellular processes, including vesicular membrane trafficking, synaptic transmission, metabolic regulation, catalysis, transmembrane transport and structure formation, etc. These results demonstrate that the functional diversity of Syt I is higher than previously expected, that its two domains may mediate the same and different cellular processes cooperatively or independently, and that C2B domain may play even more important roles than C2A in the functioning of Syt I. This work not only further deepened our understanding of the functional diversity of Syt I and the functional differences between its two C2 domains, but also provided important clues for the further related researches.
bibliographic citation: Guo et al. (2017) Pull-down combined with proteomic strategy reveals functional diversity of synaptotagmin I. PeerJ 5:e2973 https://doi.org/10.7717/peerj.2973
date submitted: 2016-10-18
date accepted: 2017-01-10
issued: 2017-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Tianyao
author list: Agent
  family name: Duan
  given name: Zhigui
author list: Agent
  family name: Chen
  given name: Jia
author list: Agent
  family name: Xie
  given name: Chunliang
author list: Agent
  family name: Wang
  given name: Ying
author list: Agent
  family name: Chen
  given name: Ping
author list: Agent
  family name: Wang
  given name: Xianchun
doi: 10.7717/peerj.2973
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-08
copyright: ©2017 Guo et al.
attribution name: Guo et al.

Screening of faba bean (Vicia faba L.) accessions to acidity and aluminium stresses
type: item
type: AcademicArticle
description: Background Faba bean is an important starch-based protein crop produced worldwide. Soil acidity and aluminium toxicity are major abiotic stresses affecting its production, so in regions where soil acidity is a problem, there is a gap between the potential and actual productivity of the crop. Hence, we set out to evaluate acidity and aluminium tolerance in a range of faba bean germplasm using solution culture and pot experiments. Methods A set of 30 accessions was collected from regions where acidity and aluminium are or are not problems. The accessions were grown in solution culture and a subset of 10 was grown first in peat and later in perlite potting media. In solution culture, morphological parameters including taproot length, root regrowth and root tolerance index were measured, and in the pot experiments the key measurements were taproot length, plant biomass, chlorophyll concentration and stomatal conductance. Result Responses to acidity and aluminium were apparently independent. Accessions Dosha and NC 58 were tolerant to both stress. Kassa and GLA 1103 were tolerant to acidity showing less than 3% reduction in taproot length. Aurora and Messay were tolerant to aluminium. Babylon was sensitive to both, with up to 40% reduction in taproot length from acidity and no detectable recovery from Al3+ challenge. Discussion The apparent independence of the responses to acidity and aluminium is in agreement with the previous research findings, suggesting that crop accessions separately adapt to H+ and Al3+ toxicity as a result of the difference in the nature of soil parent materials where the accession originated. Differences in rankings between experiments were minor and attributable to heterogeneity of seed materials and the specific responses of accessions to the rooting media. Use of perlite as a potting medium offers an ideal combination of throughput, inertness of support medium, access to leaves for detection of their stress responses, and harvest of clean root…
format: application/pdf
format: text/html
creator: Kiflemariam Y. Belachew
creator: Frederick L. Stoddard
subject: Agricultural Science
subject: Ecotoxicology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.2963
publisher: PeerJ Inc.
rights: © 2017 Belachew and Stoddard
abstract: Background Faba bean is an important starch-based protein crop produced worldwide. Soil acidity and aluminium toxicity are major abiotic stresses affecting its production, so in regions where soil acidity is a problem, there is a gap between the potential and actual productivity of the crop. Hence, we set out to evaluate acidity and aluminium tolerance in a range of faba bean germplasm using solution culture and pot experiments. Methods A set of 30 accessions was collected from regions where acidity and aluminium are or are not problems. The accessions were grown in solution culture and a subset of 10 was grown first in peat and later in perlite potting media. In solution culture, morphological parameters including taproot length, root regrowth and root tolerance index were measured, and in the pot experiments the key measurements were taproot length, plant biomass, chlorophyll concentration and stomatal conductance. Result Responses to acidity and aluminium were apparently independent. Accessions Dosha and NC 58 were tolerant to both stress. Kassa and GLA 1103 were tolerant to acidity showing less than 3% reduction in taproot length. Aurora and Messay were tolerant to aluminium. Babylon was sensitive to both, with up to 40% reduction in taproot length from acidity and no detectable recovery from Al3+ challenge. Discussion The apparent independence of the responses to acidity and aluminium is in agreement with the previous research findings, suggesting that crop accessions separately adapt to H+ and Al3+ toxicity as a result of the difference in the nature of soil parent materials where the accession originated. Differences in rankings between experiments were minor and attributable to heterogeneity of seed materials and the specific responses of accessions to the rooting media. Use of perlite as a potting medium offers an ideal combination of throughput, inertness of support medium, access to leaves for detection of their stress responses, and harvest of clean root…
bibliographic citation: Belachew et al. (2017) Screening of faba bean (Vicia faba L.) accessions to acidity and aluminium stresses. PeerJ 5:e2963 https://doi.org/10.7717/peerj.2963
date submitted: 2016-10-24
date accepted: 2017-01-05
issued: 2017-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Belachew
  given name: Kiflemariam Y.
author list: Agent
  family name: Stoddard
  given name: Frederick L.
doi: 10.7717/peerj.2963
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-08
copyright: ©2017 Belachew and Stoddard
attribution name: Belachew and Stoddard

Will you swim into my parlour? In situ observations of Atlantic cod (Gadus morhua) interactions with baited pots, with implications for gear design
type: item
type: AcademicArticle
description: Pots (also known as traps) are baited fishing gears widely used in commercial fisheries, and are being considered as a tool for harvesting Atlantic cod (Gadus morhua) in Newfoundland and Labrador, Canada. Pots produce lower environmental impacts than many other fishing gears, but they will only be a viable fishing strategy if they are efficient and selective at catching their target species. To study the behaviour of cod in and around pots, and how those behaviours affect pot efficiency, we used long-duration underwater video cameras to assess two models of cod pot deployed in the nearshore waters of Fogo Island, NL. We examined the number of cod that approached the pot, the number and proportion that successfully completed entries into the pot openings, and the number that exited, and related these factors to the direction of water movement. We observed very few entry attempts relative to the number of approaches by cod, and only 22% of all entry attempts were successful. We observed that 50% of approaches, 70% of entry attempts, and 73% of successful entrances occurred against the current, and 25% of cod were able to exit the pot following capture. Based on our observations, we suggest that future cod pots should have a greater number of entrances, or a mechanism to ensure that entrances rotate in line with the current, in order to maximize their catch efficiency for cod.
format: application/pdf
format: text/html
creator: Phillip Meintzer
creator: Philip Walsh
creator: Brett Favaro
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.2953
publisher: PeerJ Inc.
rights: © 2017 Meintzer et al.
abstract: Pots (also known as traps) are baited fishing gears widely used in commercial fisheries, and are being considered as a tool for harvesting Atlantic cod (Gadus morhua) in Newfoundland and Labrador, Canada. Pots produce lower environmental impacts than many other fishing gears, but they will only be a viable fishing strategy if they are efficient and selective at catching their target species. To study the behaviour of cod in and around pots, and how those behaviours affect pot efficiency, we used long-duration underwater video cameras to assess two models of cod pot deployed in the nearshore waters of Fogo Island, NL. We examined the number of cod that approached the pot, the number and proportion that successfully completed entries into the pot openings, and the number that exited, and related these factors to the direction of water movement. We observed very few entry attempts relative to the number of approaches by cod, and only 22% of all entry attempts were successful. We observed that 50% of approaches, 70% of entry attempts, and 73% of successful entrances occurred against the current, and 25% of cod were able to exit the pot following capture. Based on our observations, we suggest that future cod pots should have a greater number of entrances, or a mechanism to ensure that entrances rotate in line with the current, in order to maximize their catch efficiency for cod.
bibliographic citation: Meintzer et al. (2017) Will you swim into my parlour? In situ observations of Atlantic cod (Gadus morhua) interactions with baited pots, with implications for gear design. PeerJ 5:e2953 https://doi.org/10.7717/peerj.2953
date submitted: 2016-10-17
date accepted: 2016-12-31
issued: 2017-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meintzer
  given name: Phillip
author list: Agent
  family name: Walsh
  given name: Philip
author list: Agent
  family name: Favaro
  given name: Brett
doi: 10.7717/peerj.2953
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-08
copyright: ©2017 Meintzer et al.
attribution name: Meintzer et al.

Tracking the virus-like particles of Macrobrachium rosenbergii nodavirus in insect cells
type: item
type: AcademicArticle
description: Macrobrachium rosenbergii nodavirus (MrNv) poses a major threat to the prawn industry. Currently, no effective vaccine and treatment are available to prevent the spread of MrNv. Its infection mechanism and localisation in a host cell are also not well characterised. The MrNv capsid protein (MrNvc) produced in Escherichia coli self-assembled into virus-like particles (VLPs) resembling the native virus. Thus, fluorescein labelled MrNvc VLPs were employed as a model to study the virus entry and localisation in Spodoptera frugiperda, Sf9 cells. Through fluorescence microscopy and sub-cellular fractionation, the MrNvc was shown to enter Sf9 cells, and eventually arrived at the nucleus. The presence of MrNvc within the cytoplasm and nucleus of Sf9 cells was further confirmed by the Z-stack imaging. The presence of ammonium chloride (NH4Cl), genistein, methyl-β-cyclodextrin or chlorpromazine (CPZ) inhibited the entry of MrNvc into Sf9 cells, but cytochalasin D did not inhibit this process. This suggests that the internalisation of MrNvc VLPs is facilitated by caveolae- and clathrin-mediated endocytosis. The whole internalisation process of MrNvc VLPs into a Sf9 cell was recorded with live cell imaging. We have also identified a potential nuclear localisation signal (NLS) of MrNvc through deletion mutagenesis and verified by classical-NLS mapping. Overall, this study provides an insight into the journey of MrNvc VLPs in insect cells.
format: application/pdf
format: text/html
creator: Ummi Fairuz Hanapi
creator: Chean Yeah Yong
creator: Zee Hong Goh
creator: Noorjahan Banu Alitheen
creator: Swee Keong Yeap
creator: Wen Siang Tan
subject: Biotechnology
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.2947
publisher: PeerJ Inc.
rights: © 2017 Hanapi et al.
abstract: Macrobrachium rosenbergii nodavirus (MrNv) poses a major threat to the prawn industry. Currently, no effective vaccine and treatment are available to prevent the spread of MrNv. Its infection mechanism and localisation in a host cell are also not well characterised. The MrNv capsid protein (MrNvc) produced in Escherichia coli self-assembled into virus-like particles (VLPs) resembling the native virus. Thus, fluorescein labelled MrNvc VLPs were employed as a model to study the virus entry and localisation in Spodoptera frugiperda, Sf9 cells. Through fluorescence microscopy and sub-cellular fractionation, the MrNvc was shown to enter Sf9 cells, and eventually arrived at the nucleus. The presence of MrNvc within the cytoplasm and nucleus of Sf9 cells was further confirmed by the Z-stack imaging. The presence of ammonium chloride (NH4Cl), genistein, methyl-β-cyclodextrin or chlorpromazine (CPZ) inhibited the entry of MrNvc into Sf9 cells, but cytochalasin D did not inhibit this process. This suggests that the internalisation of MrNvc VLPs is facilitated by caveolae- and clathrin-mediated endocytosis. The whole internalisation process of MrNvc VLPs into a Sf9 cell was recorded with live cell imaging. We have also identified a potential nuclear localisation signal (NLS) of MrNvc through deletion mutagenesis and verified by classical-NLS mapping. Overall, this study provides an insight into the journey of MrNvc VLPs in insect cells.
bibliographic citation: Hanapi et al. (2017) Tracking the virus-like particles of Macrobrachium rosenbergii nodavirus in insect cells. PeerJ 5:e2947 https://doi.org/10.7717/peerj.2947
date submitted: 2016-04-30
date accepted: 2016-12-30
issued: 2017-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hanapi
  given name: Ummi Fairuz
author list: Agent
  family name: Yong
  given name: Chean Yeah
author list: Agent
  family name: Goh
  given name: Zee Hong
author list: Agent
  family name: Alitheen
  given name: Noorjahan Banu
author list: Agent
  family name: Yeap
  given name: Swee Keong
author list: Agent
  family name: Tan
  given name: Wen Siang
doi: 10.7717/peerj.2947
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-08
copyright: ©2017 Hanapi et al.
attribution name: Hanapi et al.

Trace elements during primordial plexiform network formation in human cerebral organoids
type: item
type: AcademicArticle
description: Systematic studies of micronutrients during brain formation are hindered by restrictions to animal models and adult post-mortem tissues. Recently, advances in stem cell biology have enabled recapitulation of the early stages of human telencephalon development in vitro. In the present work, we analyzed cerebral organoids derived from human pluripotent stem cells by synchrotron radiation X-ray fluorescence in order to measure biologically valuable micronutrients incorporated and distributed into the exogenously developing brain. Our findings indicate that elemental inclusion in organoids is consistent with human brain tissue and involves P, S, K, Ca, Fe and Zn. Occurrence of different concentration gradients also suggests active regulation of elemental transmembrane transport. Finally, the analysis of pairs of elements shows interesting elemental interaction patterns that change from 30 to 45 days of development, suggesting short- or long-term associations, such as storage in similar compartments or relevance for time-dependent biological processes. These findings shed light on which trace elements are important during human brain development and will support studies aimed to unravel the consequences of disrupted metal homeostasis for neurodevelopmental diseases, including those manifested in adulthood.
format: application/pdf
format: text/html
creator: Rafaela C. Sartore
creator: Simone C. Cardoso
creator: Yury V.M. Lages
creator: Julia M. Paraguassu
creator: Mariana P. Stelling
creator: Rodrigo F. Madeiro da Costa
creator: Marilia Z. Guimaraes
creator: Carlos A. Pérez
creator: Stevens K. Rehen
subject: Cell Biology
subject: Developmental Biology
subject: Neuroscience
description: doi:10.7717/peerj.2927
publisher: PeerJ Inc.
rights: © 2017 Sartore et al.
abstract: Systematic studies of micronutrients during brain formation are hindered by restrictions to animal models and adult post-mortem tissues. Recently, advances in stem cell biology have enabled recapitulation of the early stages of human telencephalon development in vitro. In the present work, we analyzed cerebral organoids derived from human pluripotent stem cells by synchrotron radiation X-ray fluorescence in order to measure biologically valuable micronutrients incorporated and distributed into the exogenously developing brain. Our findings indicate that elemental inclusion in organoids is consistent with human brain tissue and involves P, S, K, Ca, Fe and Zn. Occurrence of different concentration gradients also suggests active regulation of elemental transmembrane transport. Finally, the analysis of pairs of elements shows interesting elemental interaction patterns that change from 30 to 45 days of development, suggesting short- or long-term associations, such as storage in similar compartments or relevance for time-dependent biological processes. These findings shed light on which trace elements are important during human brain development and will support studies aimed to unravel the consequences of disrupted metal homeostasis for neurodevelopmental diseases, including those manifested in adulthood.
bibliographic citation: Sartore et al. (2017) Trace elements during primordial plexiform network formation in human cerebral organoids. PeerJ 5:e2927 https://doi.org/10.7717/peerj.2927
date submitted: 2016-07-25
date accepted: 2016-12-20
issued: 2017-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sartore
  given name: Rafaela C.
author list: Agent
  family name: Cardoso
  given name: Simone C.
author list: Agent
  family name: Lages
  given name: Yury V.M.
author list: Agent
  family name: Paraguassu
  given name: Julia M.
author list: Agent
  family name: Stelling
  given name: Mariana P.
author list: Agent
  family name: Madeiro da Costa
  given name: Rodrigo F.
author list: Agent
  family name: Guimaraes
  given name: Marilia Z.
author list: Agent
  family name: Pérez
  given name: Carlos A.
author list: Agent
  family name: Rehen
  given name: Stevens K.
doi: 10.7717/peerj.2927
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-08
copyright: ©2017 Sartore et al.
attribution name: Sartore et al.

Off the scale: a new species of fish-scale gecko (Squamata: Gekkonidae: Geckolepis) with exceptionally large scales
type: item
type: AcademicArticle
description: The gecko genus Geckolepis, endemic to Madagascar and the Comoro archipelago, is taxonomically challenging. One reason is its members ability to autotomize a large portion of their scales when grasped or touched, most likely to escape predation. Based on an integrative taxonomic approach including external morphology, morphometrics, genetics, pholidosis, and osteology, we here describe the first new species from this genus in 75 years: Geckolepis megalepis sp. nov. from the limestone karst of Ankarana in northern Madagascar. The new species has the largest known body scales of any gecko (both relatively and absolutely), which come off with exceptional ease. We provide a detailed description of the skeleton of the genus Geckolepis based on micro-Computed Tomography (micro-CT) analysis of the new species, the holotype of G. maculata, the recently resurrected G. humbloti, and a specimen belonging to an operational taxonomic unit (OTU) recently suggested to represent G. maculata. Geckolepis is characterized by highly mineralized, imbricated scales, paired frontals, and unfused subolfactory processes of the frontals, among other features. We identify diagnostic characters in the osteology of these geckos that help define our new species and show that the OTU assigned to G. maculata is probably not conspecific with it, leaving the taxonomic identity of this species unclear. We discuss possible reasons for the extremely enlarged scales of G. megalepis in the context of an anti-predator defence mechanism, and the future of Geckolepis taxonomy.
format: application/pdf
format: text/html
creator: Mark D. Scherz
creator: Juan D. Daza
creator: Jörn Köhler
creator: Miguel Vences
creator: Frank Glaw
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2955
publisher: PeerJ Inc.
rights: © 2017 Scherz et al.
abstract: The gecko genus Geckolepis, endemic to Madagascar and the Comoro archipelago, is taxonomically challenging. One reason is its members ability to autotomize a large portion of their scales when grasped or touched, most likely to escape predation. Based on an integrative taxonomic approach including external morphology, morphometrics, genetics, pholidosis, and osteology, we here describe the first new species from this genus in 75 years: Geckolepis megalepis sp. nov. from the limestone karst of Ankarana in northern Madagascar. The new species has the largest known body scales of any gecko (both relatively and absolutely), which come off with exceptional ease. We provide a detailed description of the skeleton of the genus Geckolepis based on micro-Computed Tomography (micro-CT) analysis of the new species, the holotype of G. maculata, the recently resurrected G. humbloti, and a specimen belonging to an operational taxonomic unit (OTU) recently suggested to represent G. maculata. Geckolepis is characterized by highly mineralized, imbricated scales, paired frontals, and unfused subolfactory processes of the frontals, among other features. We identify diagnostic characters in the osteology of these geckos that help define our new species and show that the OTU assigned to G. maculata is probably not conspecific with it, leaving the taxonomic identity of this species unclear. We discuss possible reasons for the extremely enlarged scales of G. megalepis in the context of an anti-predator defence mechanism, and the future of Geckolepis taxonomy.
bibliographic citation: Scherz et al. (2017) Off the scale: a new species of fish-scale gecko (Squamata: Gekkonidae: Geckolepis) with exceptionally large scales. PeerJ 5:e2955 https://doi.org/10.7717/peerj.2955
date submitted: 2016-10-26
date accepted: 2017-01-03
issued: 2017-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scherz
  given name: Mark D.
author list: Agent
  family name: Daza
  given name: Juan D.
author list: Agent
  family name: Köhler
  given name: Jörn
author list: Agent
  family name: Vences
  given name: Miguel
author list: Agent
  family name: Glaw
  given name: Frank
doi: 10.7717/peerj.2955
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-07
copyright: ©2017 Scherz et al.
attribution name: Scherz et al.

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