PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird
items: Molecular and morphological congruence of three new cryptic Neopetrosia spp. in the Caribbean
items: Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis
items: Motor expertise modulates unconscious rather than conscious executive control
items: Fruit availability for migratory birds: a GIS approach
items: Evaluation of DESS as a storage medium for microbial community analysis
items: LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics
items: Methods of body temperature assessment in Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid
items: Effects of particle size on physicochemical and functional properties of superfine black kidney bean (Phaseolus vulgaris L.) powder
items: Density dependent attributes of fish aggregative behaviour

Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird
type: item
type: AcademicArticle
description: The Hoatzin (Opisthocomus hoazin) is the only extant member of the order Opisthocomiformes. This unique South American bird lives in the riparian lowland vegetation characteristic of the Amazon and Orinoco basins. Hoatzins nest in communal social units close to water bodies; they are strictly folivores being the only bird with pregastric fermentation in the crop. Because of the complex logistics involved in capturing this bird, there is a knowledge gap on its parasites. This study documents two distant lineages of haemosporidian parasites (Plasmodium spp.) in a juvenile and two adults sampled in the Cojedes state, Venezuela. Although negative by microscopy, the parasite identification was possible by using molecular methods. We estimated the phylogenetic relationships on the parasite cytochrome b (cytb, 480 bp) gene and the mitochondrial DNA. We found one of the parasites lineages in two individuals (nestling and adult), and the corresponding fragment of cytb was identical to a one found in Wood Stork (Mycteria americana) from Brazil. The other lineage, found in an adult, has an identity of 469 out of 478 bp (98%) with Plasmodium sp. GAL-2012 (isolate THAMB08) from Brazil. Although a morphological description of these parasites was not possible, this is the first molecular study focusing on Hoatzin haemosporidian parasites and the first documentation of Plasmodium infections in the Hoatzin from Venezuela. Furthermore, we reported microfilaria in two adults as well as hematological parameters for six individuals. Information on hematological parameters could contribute to establishing the necessary baseline to detect underlying conditions, such as infections, in this bird species.
format: application/pdf
format: text/html
creator: M. Andreína Pacheco
creator: M. Alexandra García-Amado
creator: Jaime Manzano
creator: Nubia E. Matta
creator: Ananias A. Escalante
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.6361
publisher: PeerJ Inc.
rights: © 2019 Pacheco et al.
abstract: The Hoatzin (Opisthocomus hoazin) is the only extant member of the order Opisthocomiformes. This unique South American bird lives in the riparian lowland vegetation characteristic of the Amazon and Orinoco basins. Hoatzins nest in communal social units close to water bodies; they are strictly folivores being the only bird with pregastric fermentation in the crop. Because of the complex logistics involved in capturing this bird, there is a knowledge gap on its parasites. This study documents two distant lineages of haemosporidian parasites (Plasmodium spp.) in a juvenile and two adults sampled in the Cojedes state, Venezuela. Although negative by microscopy, the parasite identification was possible by using molecular methods. We estimated the phylogenetic relationships on the parasite cytochrome b (cytb, 480 bp) gene and the mitochondrial DNA. We found one of the parasites lineages in two individuals (nestling and adult), and the corresponding fragment of cytb was identical to a one found in Wood Stork (Mycteria americana) from Brazil. The other lineage, found in an adult, has an identity of 469 out of 478 bp (98%) with Plasmodium sp. GAL-2012 (isolate THAMB08) from Brazil. Although a morphological description of these parasites was not possible, this is the first molecular study focusing on Hoatzin haemosporidian parasites and the first documentation of Plasmodium infections in the Hoatzin from Venezuela. Furthermore, we reported microfilaria in two adults as well as hematological parameters for six individuals. Information on hematological parameters could contribute to establishing the necessary baseline to detect underlying conditions, such as infections, in this bird species.
bibliographic citation: Pacheco et al. (2019) Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird. PeerJ 7:e6361 https://doi.org/10.7717/peerj.6361
date submitted: 2018-09-07
date accepted: 2018-12-30
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pacheco
  given name: M. Andreína
author list: Agent
  family name: García-Amado
  given name: M. Alexandra
author list: Agent
  family name: Manzano
  given name: Jaime
author list: Agent
  family name: Matta
  given name: Nubia E.
author list: Agent
  family name: Escalante
  given name: Ananias A.
doi: 10.7717/peerj.6361
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: ©2019 Pacheco et al.
attribution name: Pacheco et al.

Molecular and morphological congruence of three new cryptic Neopetrosia spp. in the Caribbean
type: item
type: AcademicArticle
description: Neopetrosia proxima (Porifera: Demospongiae: Haplosclerida) is described as a morphologically variable sponge common on shallow reefs of the Caribbean. However, the range of morphological and reproductive variation within putative N. proxima led us to hypothesize that such variability may be indicative of cryptic species rather than plasticity. Using DNA sequences and morphological characters we confirmed the presence of three previously undescribed species of Neopetrosia. Morphological differences of each new congener were best resolved by partial gene sequences of the mitochondrial cytochrome oxidase subunit 1 over nuclear ones (18S rRNA and 28S rRNA). Several new characters for Neopetrosia were revealed by each new species. For example, N. dendrocrevacea sp. nov. and N. cristata sp. nov. showed the presence of grooves on the surface of the sponge body that converge at the oscula, and a more disorganized skeleton than previously defined for the genus. N. sigmafera sp. nov. adds the (1) presence of sigma microscleres, (2) significantly wider/longer oxeas (>200 μm), and (3) the presence of parenchymella larvae. Sampling of conspecifics throughout several locations in the Caribbean revealed larger spicules in habitats closer to the continental shelf than those in remote island locations. Our study highlights the importance of integrating molecular and morphological systematics for the discrimination of new Neopetrosia spp. despite belonging to one of several polyphyletic groups (families, genera) within the current definition of the order Haplosclerida.
format: application/pdf
format: text/html
creator: Jan Vicente
creator: Jaime Andrés Ríos
creator: Sven Zea
creator: Robert J. Toonen
subject: Biodiversity
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6371
publisher: PeerJ Inc.
rights: © 2019 Vicente et al.
abstract: Neopetrosia proxima (Porifera: Demospongiae: Haplosclerida) is described as a morphologically variable sponge common on shallow reefs of the Caribbean. However, the range of morphological and reproductive variation within putative N. proxima led us to hypothesize that such variability may be indicative of cryptic species rather than plasticity. Using DNA sequences and morphological characters we confirmed the presence of three previously undescribed species of Neopetrosia. Morphological differences of each new congener were best resolved by partial gene sequences of the mitochondrial cytochrome oxidase subunit 1 over nuclear ones (18S rRNA and 28S rRNA). Several new characters for Neopetrosia were revealed by each new species. For example, N. dendrocrevacea sp. nov. and N. cristata sp. nov. showed the presence of grooves on the surface of the sponge body that converge at the oscula, and a more disorganized skeleton than previously defined for the genus. N. sigmafera sp. nov. adds the (1) presence of sigma microscleres, (2) significantly wider/longer oxeas (>200 μm), and (3) the presence of parenchymella larvae. Sampling of conspecifics throughout several locations in the Caribbean revealed larger spicules in habitats closer to the continental shelf than those in remote island locations. Our study highlights the importance of integrating molecular and morphological systematics for the discrimination of new Neopetrosia spp. despite belonging to one of several polyphyletic groups (families, genera) within the current definition of the order Haplosclerida.
bibliographic citation: Vicente et al. (2019) Molecular and morphological congruence of three new cryptic Neopetrosia spp. in the Caribbean. PeerJ 7:e6371 https://doi.org/10.7717/peerj.6371
date submitted: 2018-10-25
date accepted: 2018-12-28
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vicente
  given name: Jan
author list: Agent
  family name: Ríos
  given name: Jaime Andrés
author list: Agent
  family name: Zea
  given name: Sven
author list: Agent
  family name: Toonen
  given name: Robert J.
doi: 10.7717/peerj.6371
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: © 2019 Vicente et al.
attribution name: Vicente et al.

Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis
type: item
type: AcademicArticle
description: Genotype-specific contributions to the environmental tolerance and disease susceptibility of corals are widely accepted. Yet our understanding of how host genotype influences the composition and stability of the coral microbiome subjected to environmental fluctuations is limited. To gain insight into the community dynamics and environmental stability of microbiomes associated with distinct coral genotypes, we assessed the microbial community associated with Acropora tenuis under single and cumulative pressure experiments. Experimental treatments comprised either a single pulse of reduced salinity (minimum of 28 psu) or exposure to the cumulative pressures of reduced salinity (minimum of 28 psu), elevated seawater temperature (+2 °C), elevated pCO2 (900 ppm), and the presence of macroalgae. Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment. On average, 48% of the A. tenuis microbiome was dominated by Endozoicomonas. Amplicon sequence variants (ASVs) belonging to this genus were significantly different between host individuals. Although no signs of stress were evident in the coral holobiont and the vast majority of ASVs remained stable across treatments, a microbial indicator approach identified 26 ASVs belonging to Vibrionaceae, Rhodobacteraceae, Hahellaceae, Planctomycetes, Phylobacteriaceae, Flavobacteriaceae, and Cryomorphaceae that were significantly enriched in corals exposed to single and cumulative stressors. While several recent studies have highlighted the efficacy of microbial indicators as sensitive markers for environmental disturbance, the high host-genotype specificity of coral microbiomes may limit their utility and we therefore recommend meticulous control of host-genotype effects in coral microbiome research.
format: application/pdf
format: text/html
creator: Bettina Glasl
creator: Caitlin E. Smith
creator: David G. Bourne
creator: Nicole S. Webster
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.6377
publisher: PeerJ Inc.
rights: © 2019 Glasl et al.
abstract: Genotype-specific contributions to the environmental tolerance and disease susceptibility of corals are widely accepted. Yet our understanding of how host genotype influences the composition and stability of the coral microbiome subjected to environmental fluctuations is limited. To gain insight into the community dynamics and environmental stability of microbiomes associated with distinct coral genotypes, we assessed the microbial community associated with Acropora tenuis under single and cumulative pressure experiments. Experimental treatments comprised either a single pulse of reduced salinity (minimum of 28 psu) or exposure to the cumulative pressures of reduced salinity (minimum of 28 psu), elevated seawater temperature (+2 °C), elevated pCO2 (900 ppm), and the presence of macroalgae. Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment. On average, 48% of the A. tenuis microbiome was dominated by Endozoicomonas. Amplicon sequence variants (ASVs) belonging to this genus were significantly different between host individuals. Although no signs of stress were evident in the coral holobiont and the vast majority of ASVs remained stable across treatments, a microbial indicator approach identified 26 ASVs belonging to Vibrionaceae, Rhodobacteraceae, Hahellaceae, Planctomycetes, Phylobacteriaceae, Flavobacteriaceae, and Cryomorphaceae that were significantly enriched in corals exposed to single and cumulative stressors. While several recent studies have highlighted the efficacy of microbial indicators as sensitive markers for environmental disturbance, the high host-genotype specificity of coral microbiomes may limit their utility and we therefore recommend meticulous control of host-genotype effects in coral microbiome research.
bibliographic citation: Glasl et al. (2019) Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis. PeerJ 7:e6377 https://doi.org/10.7717/peerj.6377
date submitted: 2018-11-05
date accepted: 2018-12-30
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Glasl
  given name: Bettina
author list: Agent
  family name: Smith
  given name: Caitlin E.
author list: Agent
  family name: Bourne
  given name: David G.
author list: Agent
  family name: Webster
  given name: Nicole S.
doi: 10.7717/peerj.6377
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: © 2019 Glasl et al.
attribution name: Glasl et al.

Motor expertise modulates unconscious rather than conscious executive control
type: item
type: AcademicArticle
description: Background Executive control, the ability to regulate the execution of a goal-directed task, is an important element in an athlete’s skill set. Although previous studies have shown that executive control in athletes is better than that in non-athletes, those studies were mainly confined to conscious executive control. Many recent studies have suggested that executive control can be triggered by the presentation of visual stimuli without participant’s conscious awareness. However, few studies have examined unconscious executive control in sports. Thus, the present study investigated whether, similar to conscious executive control, unconscious executive control in table tennis athletes is superior to that in non-athletes. Methods In total, 42 age-matched undergraduate students were recruited for this study; 22 nonathletic students lacking practical athletic experience comprised one group, and 20 table tennis athletes with many years of training in this sport comprised a second group. Each participant first completed an unconscious response priming task, the unconscious processing of visual-spatial information, and then completed a conscious version of this same response priming task. Results Table tennis athletes showed a significant response priming effect, whereas non-athletes did not, when participants were unable to consciously perceive the visual-spatial priming stimuli. In addition, the number of years the table tennis athletes had trained in this sport (a measure of their motor expertise) was positively correlated with the strength of the unconscious response priming effect. However, both table tennis athletes and non-athletes showed a response priming effect when the primes were unmasked and the participants were able to consciously perceive the visual-spatial priming stimuli. Conclusion Our results suggest that motor expertise modulates unconscious, rather than conscious, executive control and that motor expertise is positively correlated with unconscious exe…
format: application/pdf
format: text/html
creator: Fanying Meng
creator: Anmin Li
creator: Yihong You
creator: Chun Xie
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6387
publisher: PeerJ Inc.
rights: © 2019 Meng et al.
abstract: Background Executive control, the ability to regulate the execution of a goal-directed task, is an important element in an athlete’s skill set. Although previous studies have shown that executive control in athletes is better than that in non-athletes, those studies were mainly confined to conscious executive control. Many recent studies have suggested that executive control can be triggered by the presentation of visual stimuli without participant’s conscious awareness. However, few studies have examined unconscious executive control in sports. Thus, the present study investigated whether, similar to conscious executive control, unconscious executive control in table tennis athletes is superior to that in non-athletes. Methods In total, 42 age-matched undergraduate students were recruited for this study; 22 nonathletic students lacking practical athletic experience comprised one group, and 20 table tennis athletes with many years of training in this sport comprised a second group. Each participant first completed an unconscious response priming task, the unconscious processing of visual-spatial information, and then completed a conscious version of this same response priming task. Results Table tennis athletes showed a significant response priming effect, whereas non-athletes did not, when participants were unable to consciously perceive the visual-spatial priming stimuli. In addition, the number of years the table tennis athletes had trained in this sport (a measure of their motor expertise) was positively correlated with the strength of the unconscious response priming effect. However, both table tennis athletes and non-athletes showed a response priming effect when the primes were unmasked and the participants were able to consciously perceive the visual-spatial priming stimuli. Conclusion Our results suggest that motor expertise modulates unconscious, rather than conscious, executive control and that motor expertise is positively correlated with unconscious exe…
bibliographic citation: Meng et al. (2019) Motor expertise modulates unconscious rather than conscious executive control. PeerJ 7:e6387 https://doi.org/10.7717/peerj.6387
date submitted: 2018-08-20
date accepted: 2019-01-03
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Fanying
author list: Agent
  family name: Li
  given name: Anmin
author list: Agent
  family name: You
  given name: Yihong
author list: Agent
  family name: Xie
  given name: Chun
doi: 10.7717/peerj.6387
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: ©2019 Meng et al.
attribution name: Meng et al.

Fruit availability for migratory birds: a GIS approach
type: item
type: AcademicArticle
description: Bird migration is a widely studied phenomenon, however many factors that influence migratory flows remain unknown or poorly understood. Food availability en route is particularly important for many species and can affect their migration success, pattern and timing but this relationship has not been addressed at a wide scale due to the lack of spatial models of food availability on the terrain. This work presents a GIS-database approach that combines spatial and non-spatial ecological information in order to map fruit availability from vegetation over time in the SE Alps, an important node of European migratory routes. We created a unique database that contains information on the presence and periods of fructification of 52 wild plants carrying berries and a series of original cartographic themes. The presence and coverage of the plant species was modelled with the geo-statistical method of the Gaussian Kernel, which was validated against the ground truth of field sampling data with a correct classification power above 80% in most cases. The highest fruit availability in the study area during September and October co-occurs with the peak of captures of berry eating birds. The maps created and distributed along this work can be useful to address more detailed studies about stopover sites as well as the spatial ecology of other fruit eating animals.
format: application/pdf
format: text/html
creator: Clara Tattoni
creator: Erica Soardi
creator: Filippo Prosser
creator: Maurizio Odasso
creator: Paolo Zatelli
creator: Marco Ciolli
subject: Biodiversity
subject: Ecology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6394
publisher: PeerJ Inc.
rights: © 2019 Tattoni et al.
abstract: Bird migration is a widely studied phenomenon, however many factors that influence migratory flows remain unknown or poorly understood. Food availability en route is particularly important for many species and can affect their migration success, pattern and timing but this relationship has not been addressed at a wide scale due to the lack of spatial models of food availability on the terrain. This work presents a GIS-database approach that combines spatial and non-spatial ecological information in order to map fruit availability from vegetation over time in the SE Alps, an important node of European migratory routes. We created a unique database that contains information on the presence and periods of fructification of 52 wild plants carrying berries and a series of original cartographic themes. The presence and coverage of the plant species was modelled with the geo-statistical method of the Gaussian Kernel, which was validated against the ground truth of field sampling data with a correct classification power above 80% in most cases. The highest fruit availability in the study area during September and October co-occurs with the peak of captures of berry eating birds. The maps created and distributed along this work can be useful to address more detailed studies about stopover sites as well as the spatial ecology of other fruit eating animals.
bibliographic citation: Tattoni et al. (2019) Fruit availability for migratory birds: a GIS approach. PeerJ 7:e6394 https://doi.org/10.7717/peerj.6394
date submitted: 2018-02-24
date accepted: 2019-01-04
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tattoni
  given name: Clara
author list: Agent
  family name: Soardi
  given name: Erica
author list: Agent
  family name: Prosser
  given name: Filippo
author list: Agent
  family name: Odasso
  given name: Maurizio
author list: Agent
  family name: Zatelli
  given name: Paolo
author list: Agent
  family name: Ciolli
  given name: Marco
doi: 10.7717/peerj.6394
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: ©2019 Tattoni et al.
attribution name: Tattoni et al.

Evaluation of DESS as a storage medium for microbial community analysis
type: item
type: AcademicArticle
description: Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated dimethyl sulfoxide, ethylenediamine tetraacetic acid, saturated salt (DESS) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test their impact on the fungus garden microbial community. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.
format: application/pdf
format: text/html
creator: Kevin M. Lee
creator: Madison Adams
creator: Jonathan L. Klassen
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.6414
publisher: PeerJ Inc.
rights: © 2019 Lee et al.
abstract: Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated dimethyl sulfoxide, ethylenediamine tetraacetic acid, saturated salt (DESS) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test their impact on the fungus garden microbial community. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.
bibliographic citation: Lee et al. (2019) Evaluation of DESS as a storage medium for microbial community analysis. PeerJ 7:e6414 https://doi.org/10.7717/peerj.6414
date submitted: 2018-07-12
date accepted: 2018-12-24
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Kevin M.
author list: Agent
  family name: Adams
  given name: Madison
author list: Agent
  family name: Klassen
  given name: Jonathan L.
doi: 10.7717/peerj.6414
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: © 2019 Lee et al.
attribution name: Lee et al.

LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics
type: item
type: AcademicArticle
description: Protocols for preparing RNA sequencing (RNA-seq) libraries, most prominently “Smart-seq” variations, introduce global biases that can have a significant impact on the quantification of gene expression levels. This global bias can lead to drastic over- or under-representation of RNA in non-linear length-dependent fashion due to enzymatic reactions during cDNA production. It is currently not corrected by any RNA-seq software, which mostly focus on local bias in coverage along RNAs. This paper describes LiBiNorm, a simple command line program that mimics the popular htseq-count software and allows diagnostics, quantification, and global bias removal. LiBiNorm outputs gene expression data that has been normalized to correct for global bias introduced by the Smart-seq2 protocol. In addition, it produces data and several plots that allow insights into the experimental history underlying library preparation. The LiBiNorm package includes an R script that allows visualization of the main results. LiBiNorm is the first software application to correct for the global bias that is introduced by the Smart-seq2 protocol. It is freely downloadable at http://www2.warwick.ac.uk/fac/sci/lifesci/research/libinorm.
format: application/pdf
format: text/html
creator: Nigel P. Dyer
creator: Vahid Shahrezaei
creator: Daniel Hebenstreit
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Computational Science
description: doi:10.7717/peerj.6222
publisher: PeerJ Inc.
rights: © 2019 Dyer et al.
abstract: Protocols for preparing RNA sequencing (RNA-seq) libraries, most prominently “Smart-seq” variations, introduce global biases that can have a significant impact on the quantification of gene expression levels. This global bias can lead to drastic over- or under-representation of RNA in non-linear length-dependent fashion due to enzymatic reactions during cDNA production. It is currently not corrected by any RNA-seq software, which mostly focus on local bias in coverage along RNAs. This paper describes LiBiNorm, a simple command line program that mimics the popular htseq-count software and allows diagnostics, quantification, and global bias removal. LiBiNorm outputs gene expression data that has been normalized to correct for global bias introduced by the Smart-seq2 protocol. In addition, it produces data and several plots that allow insights into the experimental history underlying library preparation. The LiBiNorm package includes an R script that allows visualization of the main results. LiBiNorm is the first software application to correct for the global bias that is introduced by the Smart-seq2 protocol. It is freely downloadable at http://www2.warwick.ac.uk/fac/sci/lifesci/research/libinorm.
bibliographic citation: Dyer et al. (2019) LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics. PeerJ 7:e6222 https://doi.org/10.7717/peerj.6222
date submitted: 2018-09-11
date accepted: 2018-12-05
issued: 2019-02-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dyer
  given name: Nigel P.
author list: Agent
  family name: Shahrezaei
  given name: Vahid
author list: Agent
  family name: Hebenstreit
  given name: Daniel
doi: 10.7717/peerj.6222
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-04
copyright: © 2019 Dyer et al.
attribution name: Dyer et al.

Methods of body temperature assessment in Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid
type: item
type: AcademicArticle
description: Since cardiovascular, respiratory, and metabolic systems of reptiles are affected by temperature, accurate measurements are of great importance in both captive husbandry and research. Ectothermic animals generally have core body temperatures close to ambient temperature but can differ from the immediate environment if they are using sunlight to thermoregulate. Many zoological facilities and exotic pet caregivers have begun using infrared temperature guns to assess ambient temperatures of reptile enclosures but there are currently few studies assessing the efficacy of these devices for measuring the body temperatures of reptiles. Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid are robust land iguanas endemic to the Galápagos archipelago. By comparing the infrared body temperature measurements of land iguanas against virtual simultaneous collection of cloacal temperatures obtained using a thermocouple thermometer, we sought to assess the efficacy of this non-invasive method. We found that internal body temperature can be predicted with a high level of accuracy from three external body temperature sites, providing a good non-invasive method that avoids the capture of animals.
format: application/pdf
format: text/html
creator: Carlos A. Valle
creator: Colon J. Grijalva
creator: Paul P. Calle
creator: Juan Pablo Muñoz-Pérez
creator: Galo Quezada
creator: Carlos A. Vera
creator: Gregory A. Lewbart
subject: Ecology
subject: Ecosystem Science
subject: Veterinary Medicine
subject: Zoology
subject: Anatomy and Physiology
description: doi:10.7717/peerj.6291
publisher: PeerJ Inc.
rights: © 2019 Valle et al.
abstract: Since cardiovascular, respiratory, and metabolic systems of reptiles are affected by temperature, accurate measurements are of great importance in both captive husbandry and research. Ectothermic animals generally have core body temperatures close to ambient temperature but can differ from the immediate environment if they are using sunlight to thermoregulate. Many zoological facilities and exotic pet caregivers have begun using infrared temperature guns to assess ambient temperatures of reptile enclosures but there are currently few studies assessing the efficacy of these devices for measuring the body temperatures of reptiles. Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid are robust land iguanas endemic to the Galápagos archipelago. By comparing the infrared body temperature measurements of land iguanas against virtual simultaneous collection of cloacal temperatures obtained using a thermocouple thermometer, we sought to assess the efficacy of this non-invasive method. We found that internal body temperature can be predicted with a high level of accuracy from three external body temperature sites, providing a good non-invasive method that avoids the capture of animals.
bibliographic citation: Valle et al. (2019) Methods of body temperature assessment in Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid. PeerJ 7:e6291 https://doi.org/10.7717/peerj.6291
date submitted: 2018-10-02
date accepted: 2018-12-11
issued: 2019-02-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valle
  given name: Carlos A.
author list: Agent
  family name: Grijalva
  given name: Colon J.
author list: Agent
  family name: Calle
  given name: Paul P.
author list: Agent
  family name: Muñoz-Pérez
  given name: Juan Pablo
author list: Agent
  family name: Quezada
  given name: Galo
author list: Agent
  family name: Vera
  given name: Carlos A.
author list: Agent
  family name: Lewbart
  given name: Gregory A.
doi: 10.7717/peerj.6291
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-04
copyright: © 2019 Valle et al.
attribution name: Valle et al.

Effects of particle size on physicochemical and functional properties of superfine black kidney bean (Phaseolus vulgaris L.) powder
type: item
type: AcademicArticle
description: Black kidney bean (Phaseolus vulgaris L.) powder (BKBP) with particle sizes of 250–180, 180–125, 125–75, 75–38, and <38 μm was prepared by using coarse and eccentric vibratory milling, respectively. Physicochemical properties, cholesterol adsorption, and antioxidant activities of powders were investigated. Size and scanning electron microscopy analyses showed that particle size of BKBP could be effectively decreased after the superfine grinding treatment, and the specific surface area was increased. Flow properties, hydration properties, thermal stability, and cholesterol adsorption efficiency significantly improved with the reducing of particle size. The superfine powder with sizes of 75–38 or <38 μm exhibited higher antioxidant activity via 2,2-diphenyl-1-picryhydrazyl, hydroxyl radical-scavenging, and ferrous ion-chelating assays. The results indicated that the BKBP with a size of <38 μm could serve as a better potential biological resource for food additives, and could be applied for the development of low-cholesterol products.
format: application/pdf
format: text/html
creator: Xianbao Sun
creator: Yuwei Zhang
creator: Jing Li
creator: Nayab Aslam
creator: Hanju Sun
creator: Jinlong Zhao
creator: Zeyu Wu
creator: Shudong He
subject: Bioengineering
subject: Food Science and Technology
description: doi:10.7717/peerj.6369
publisher: PeerJ Inc.
rights: © 2019 Sun et al.
abstract: Black kidney bean (Phaseolus vulgaris L.) powder (BKBP) with particle sizes of 250–180, 180–125, 125–75, 75–38, and <38 μm was prepared by using coarse and eccentric vibratory milling, respectively. Physicochemical properties, cholesterol adsorption, and antioxidant activities of powders were investigated. Size and scanning electron microscopy analyses showed that particle size of BKBP could be effectively decreased after the superfine grinding treatment, and the specific surface area was increased. Flow properties, hydration properties, thermal stability, and cholesterol adsorption efficiency significantly improved with the reducing of particle size. The superfine powder with sizes of 75–38 or <38 μm exhibited higher antioxidant activity via 2,2-diphenyl-1-picryhydrazyl, hydroxyl radical-scavenging, and ferrous ion-chelating assays. The results indicated that the BKBP with a size of <38 μm could serve as a better potential biological resource for food additives, and could be applied for the development of low-cholesterol products.
bibliographic citation: Sun et al. (2019) Effects of particle size on physicochemical and functional properties of superfine black kidney bean (Phaseolus vulgaris L.) powder. PeerJ 7:e6369 https://doi.org/10.7717/peerj.6369
date submitted: 2018-07-05
date accepted: 2018-12-29
issued: 2019-02-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Xianbao
author list: Agent
  family name: Zhang
  given name: Yuwei
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Aslam
  given name: Nayab
author list: Agent
  family name: Sun
  given name: Hanju
author list: Agent
  family name: Zhao
  given name: Jinlong
author list: Agent
  family name: Wu
  given name: Zeyu
author list: Agent
  family name: He
  given name: Shudong
doi: 10.7717/peerj.6369
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-04
copyright: © 2019 Sun et al.
attribution name: Sun et al.

Density dependent attributes of fish aggregative behaviour
type: item
type: AcademicArticle
description: Grouping behaviour, as fascinating as it is unclear, has lately drawn the attention of numerous researchers. While most of the authors focused their work on a mechanistic approach to the matter of schooling, this study explores the issue from a population point of view. Present camera observation study on the fish community carried out in the epipelagic habitat of a European temperate reservoir in the Czech Republic explored the relationship between density and aggregative features of predominantly cyprinid fish stock. Results demonstrated that schooling behaviour is triggered by the ‘critical density’ of fish in the habitat. School size as well as counts of schools and proportion of schooling individuals increased with the density of fish. Counts of clusters (observed units in time, including singletons, pairs and schools) and cluster size, on the other hand, showed a slowing tendency to increase. The slower increase implies the tendency of fish for not being frequent but rather to create larger groups. Altogether, our findings suggest that fish density is a triggering factor in the formation of large fish schools. As the tendency of cyprinid species for school formation could be an evolutional advantage responsible for dominance in later succession phases of water bodies, we suggest that more in situ studies should be encouraged for the proper understanding of the ecological interactions that drive the structure of aquatic ecosystems and for ensuring unbiased assessment.
format: application/pdf
format: text/html
creator: Michaela Holubová
creator: Martin Čech
creator: Mojmír Vašek
creator: Jiří Peterka
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.6378
publisher: PeerJ Inc.
rights: © 2019 Holubová et al.
abstract: Grouping behaviour, as fascinating as it is unclear, has lately drawn the attention of numerous researchers. While most of the authors focused their work on a mechanistic approach to the matter of schooling, this study explores the issue from a population point of view. Present camera observation study on the fish community carried out in the epipelagic habitat of a European temperate reservoir in the Czech Republic explored the relationship between density and aggregative features of predominantly cyprinid fish stock. Results demonstrated that schooling behaviour is triggered by the ‘critical density’ of fish in the habitat. School size as well as counts of schools and proportion of schooling individuals increased with the density of fish. Counts of clusters (observed units in time, including singletons, pairs and schools) and cluster size, on the other hand, showed a slowing tendency to increase. The slower increase implies the tendency of fish for not being frequent but rather to create larger groups. Altogether, our findings suggest that fish density is a triggering factor in the formation of large fish schools. As the tendency of cyprinid species for school formation could be an evolutional advantage responsible for dominance in later succession phases of water bodies, we suggest that more in situ studies should be encouraged for the proper understanding of the ecological interactions that drive the structure of aquatic ecosystems and for ensuring unbiased assessment.
bibliographic citation: Holubová et al. (2019) Density dependent attributes of fish aggregative behaviour. PeerJ 7:e6378 https://doi.org/10.7717/peerj.6378
date submitted: 2018-08-30
date accepted: 2018-12-28
issued: 2019-02-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holubová
  given name: Michaela
author list: Agent
  family name: Čech
  given name: Martin
author list: Agent
  family name: Vašek
  given name: Mojmír
author list: Agent
  family name: Peterka
  given name: Jiří
doi: 10.7717/peerj.6378
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-04
copyright: © 2019 Holubová et al.
attribution name: Holubová et al.

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