PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality
items: According, against, and above dietary norms: a key to understanding the relationship between personality style and taste preferences
items: In vitro histomorphometric comparison of dental pulp tissue in different teeth
items: VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs
items: Critical multi-stranded approach for determining the ecological values of diatoms in unique aquatic ecosystems of anthropogenic origin
items: Design and preliminary application of affinity peptide based on the structure of the porcine circovirus type II Capsid (PCV2 Cap)
items: Bleaching and post-bleaching mortality of Acropora corals on a heat-susceptible reef in 2016
items: TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
items: A high latitude Devonian lungfish, from the Famennian of South Africa
items: Rediscovery of Osteocephalus vilarsi (Anura: Hylidae): an overlooked but widespread Amazonian spiny-backed treefrog

Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality
type: item
type: AcademicArticle
description: Environmental DNA (eDNA) is a powerful tool for monitoring the distribution of aquatic macro-organisms. However, environmental factors, including the water temperature and water quality, can affect the inhibition and/or degradation of eDNA, which complicates accurate estimations of eDNA concentrations and the detection of the presence/absence of species in natural habitats. Further very few eDNA studies have been conducted for reptiles, especially with respect to estimating their biomass and/or abundances. Here we examined the relationship between the visually-observed number of red-eared sliders (Trachemys scripta elegans) and eDNA concentrations across 100 ponds. Additionally, we evaluated the effect of water quality on red-eared slider eDNA concentration in these ponds. We found that there was a significant positive correlation between the observed number of red-eared sliders and the eDNA concentration in the ponds. On comparing various water quality indicators, including dissolved nitrogen, dissolved phosphorous, organic matter, and chlorophyll a (Chl. a), we found that only Chl. a had a negative correlation with the red-eared slider eDNA concentration, while we did not find any inhibition in the quantitative PCR. We conclude that concentrations of eDNA can potentially be used for estimating the abundance of the red-eared slider. Additionally, Chl. a might indirectly influence the degradation of eDNA through the microorganisms bonded to the phytoplankton in the ponds, as microbial activity is thought to decrease eDNA persistence.
format: application/pdf
format: text/html
creator: Aozora Kakuda
creator: Hideyuki Doi
creator: Rio Souma
creator: Mariko Nagano
creator: Toshifumi Minamoto
creator: Izumi Katano
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.8155
publisher: PeerJ Inc.
rights: © 2019 Kakuda et al.
abstract: Environmental DNA (eDNA) is a powerful tool for monitoring the distribution of aquatic macro-organisms. However, environmental factors, including the water temperature and water quality, can affect the inhibition and/or degradation of eDNA, which complicates accurate estimations of eDNA concentrations and the detection of the presence/absence of species in natural habitats. Further very few eDNA studies have been conducted for reptiles, especially with respect to estimating their biomass and/or abundances. Here we examined the relationship between the visually-observed number of red-eared sliders (Trachemys scripta elegans) and eDNA concentrations across 100 ponds. Additionally, we evaluated the effect of water quality on red-eared slider eDNA concentration in these ponds. We found that there was a significant positive correlation between the observed number of red-eared sliders and the eDNA concentration in the ponds. On comparing various water quality indicators, including dissolved nitrogen, dissolved phosphorous, organic matter, and chlorophyll a (Chl. a), we found that only Chl. a had a negative correlation with the red-eared slider eDNA concentration, while we did not find any inhibition in the quantitative PCR. We conclude that concentrations of eDNA can potentially be used for estimating the abundance of the red-eared slider. Additionally, Chl. a might indirectly influence the degradation of eDNA through the microorganisms bonded to the phytoplankton in the ponds, as microbial activity is thought to decrease eDNA persistence.
bibliographic citation: Kakuda et al. (2019) Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality. PeerJ 7:e8155 https://doi.org/10.7717/peerj.8155
date submitted: 2019-01-29
date accepted: 2019-11-04
issued: 2019-12-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kakuda
  given name: Aozora
author list: Agent
  family name: Doi
  given name: Hideyuki
author list: Agent
  family name: Souma
  given name: Rio
author list: Agent
  family name: Nagano
  given name: Mariko
author list: Agent
  family name: Minamoto
  given name: Toshifumi
author list: Agent
  family name: Katano
  given name: Izumi
doi: 10.7717/peerj.8155
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-06
copyright: ©2019 Kakuda et al.
attribution name: Kakuda et al.

According, against, and above dietary norms: a key to understanding the relationship between personality style and taste preferences
type: item
type: AcademicArticle
description: Background Understanding individual food preferences is critical for creating tailored strategies that promote healthy individual eating behaviors. Individual sensory liking appears to be an essential determinant of dietary intake. Taste preferences influence satisfaction and satiety, and may consequently influence weight status and psychological adjustment. The purpose of this study was to identify the association between taste preferences (sweet, salty, sweet & fatty, salty & fatty) and personality features. Methods The Millon Clinical Multiaxial Inventory-III (MCMI-III) was used for the assessment of personality traits and PrefQuest (PQ) was used for measuring recalled food preferences. A total of 137 participants were included in the study. The relationship between compulsive and antisocial features and taste preferences was assessed by hierarchical multiple linear regression, while controlling for age, gender, BMI, marital status, and educational level. Results The antisocial personality traits were a negative explanatory variable for sweet & fatty taste preference, R2 = .15, t(132) = − 2.40, p = .018, 95% [−.57, −.06] and salty & fatty taste preference, R2 = .16, t(133) = − 2.38, p = .019, 95% [−.07, −.01], while controlling for anthropological factors. In addition, men showed a higher preference than women for sweet & fatty food, such as chocolate or desserts, rsp = .19, p = .021, and for the salty & fatty food, rsp = .30, p < .001. BMI was not found to moderate the relationship between personality and taste preference. No significant association was found between compulsive personality traits and food preference, as assessed by sensory liking. Conclusions The findings can bring a much better understanding of the relationship between the compulsive or antisocial personality and taste preferences. In addition, it may help build psychotherapeutic and nutritional strategies that promote healthy eating behaviors, tailored to a particular personality style.
format: application/pdf
format: text/html
creator: Ligiana Mihaela Petre
creator: Bianca Nicoleta Vatasescu
subject: Global Health
subject: Nutrition
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8198
publisher: PeerJ Inc.
rights: © 2019 Petre and Vatasescu
abstract: Background Understanding individual food preferences is critical for creating tailored strategies that promote healthy individual eating behaviors. Individual sensory liking appears to be an essential determinant of dietary intake. Taste preferences influence satisfaction and satiety, and may consequently influence weight status and psychological adjustment. The purpose of this study was to identify the association between taste preferences (sweet, salty, sweet & fatty, salty & fatty) and personality features. Methods The Millon Clinical Multiaxial Inventory-III (MCMI-III) was used for the assessment of personality traits and PrefQuest (PQ) was used for measuring recalled food preferences. A total of 137 participants were included in the study. The relationship between compulsive and antisocial features and taste preferences was assessed by hierarchical multiple linear regression, while controlling for age, gender, BMI, marital status, and educational level. Results The antisocial personality traits were a negative explanatory variable for sweet & fatty taste preference, R2 = .15, t(132) = − 2.40, p = .018, 95% [−.57, −.06] and salty & fatty taste preference, R2 = .16, t(133) = − 2.38, p = .019, 95% [−.07, −.01], while controlling for anthropological factors. In addition, men showed a higher preference than women for sweet & fatty food, such as chocolate or desserts, rsp = .19, p = .021, and for the salty & fatty food, rsp = .30, p < .001. BMI was not found to moderate the relationship between personality and taste preference. No significant association was found between compulsive personality traits and food preference, as assessed by sensory liking. Conclusions The findings can bring a much better understanding of the relationship between the compulsive or antisocial personality and taste preferences. In addition, it may help build psychotherapeutic and nutritional strategies that promote healthy eating behaviors, tailored to a particular personality style.
bibliographic citation: Petre et al. (2019) According, against, and above dietary norms: a key to understanding the relationship between personality style and taste preferences. PeerJ 7:e8198 https://doi.org/10.7717/peerj.8198
date submitted: 2019-01-25
date accepted: 2019-11-13
issued: 2019-12-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Petre
  given name: Ligiana Mihaela
author list: Agent
  family name: Vatasescu
  given name: Bianca Nicoleta
doi: 10.7717/peerj.8198
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-06
copyright: ©2019 Petre and Vatasescu
attribution name: Petre and Vatasescu

In vitro histomorphometric comparison of dental pulp tissue in different teeth
type: item
type: AcademicArticle
description: Background Dental pulp (DP) represents an accessible and valuable source promising of stem cells for clinical application. However, there are some disadvantages associated with the isolation of dental pulp stem cells (DPSCs), which include the size and weight of the pulp tissue needed to yield sufficient cells for culturing in vitro. Therefore, the objective of this study was to compare in vitro histomorphometry of DP from permanent (premolars, third molar), supernumerary and deciduous teeth of patients between 5 and 25 years old with regards to weight, length, width and the cell density in the four regions of the DP in order to obtain quantitative parameters in a tissue that represents a valuable source of stem cells. Methods DPs were obtained from 10 central incisors deciduous, 20 permanent teeth (10 premolars, 10 third molars) and 10 supernumeraries (six mesiodents and four inferior premolar shapes). The pulps were carefully removed, and the entire tissue was weighed. The pulp length and the width were measured with a digital Vernier caliper. The cellular density analysis was performed according to the four regions of the DP (coronal, cervical, medial and apical) in histological slides using photography and the ImageJ® program for quantification. Results The Pearson correlation test revealed that DP weight among different types of teeth is correlated with age in male patients. A significant positive correlation was noted between length and width of the DP with age in both genders. The mean DP weight for supernumerary and third molar teeth was greater than deciduous and premolar teeth. Finally, the histological analysis showed that the coronal and apical portions of DP in supernumerary and premolar teeth have the highest cell density. Conclusions The DP of supernumerary teeth has quantitatively the best morphometric parameters and cell density comparable with the quality of DP obtained from deciduous teeth.
format: application/pdf
format: text/html
creator: Marytere Guerrero-Jiménez
creator: Geovanny I. Nic-Can
creator: Nelly Castro-Linares
creator: Fernando Javier Aguilar-Ayala
creator: Michel Canul-Chan
creator: Rafael A. Rojas-Herrera
creator: Ricardo Peñaloza-Cuevas
creator: Beatriz A. Rodas-Junco
subject: Cell Biology
subject: Dentistry
description: doi:10.7717/peerj.8212
publisher: PeerJ Inc.
rights: © 2019 Guerrero-Jiménez et al.
abstract: Background Dental pulp (DP) represents an accessible and valuable source promising of stem cells for clinical application. However, there are some disadvantages associated with the isolation of dental pulp stem cells (DPSCs), which include the size and weight of the pulp tissue needed to yield sufficient cells for culturing in vitro. Therefore, the objective of this study was to compare in vitro histomorphometry of DP from permanent (premolars, third molar), supernumerary and deciduous teeth of patients between 5 and 25 years old with regards to weight, length, width and the cell density in the four regions of the DP in order to obtain quantitative parameters in a tissue that represents a valuable source of stem cells. Methods DPs were obtained from 10 central incisors deciduous, 20 permanent teeth (10 premolars, 10 third molars) and 10 supernumeraries (six mesiodents and four inferior premolar shapes). The pulps were carefully removed, and the entire tissue was weighed. The pulp length and the width were measured with a digital Vernier caliper. The cellular density analysis was performed according to the four regions of the DP (coronal, cervical, medial and apical) in histological slides using photography and the ImageJ® program for quantification. Results The Pearson correlation test revealed that DP weight among different types of teeth is correlated with age in male patients. A significant positive correlation was noted between length and width of the DP with age in both genders. The mean DP weight for supernumerary and third molar teeth was greater than deciduous and premolar teeth. Finally, the histological analysis showed that the coronal and apical portions of DP in supernumerary and premolar teeth have the highest cell density. Conclusions The DP of supernumerary teeth has quantitatively the best morphometric parameters and cell density comparable with the quality of DP obtained from deciduous teeth.
bibliographic citation: Guerrero-Jiménez et al. (2019) In vitro histomorphometric comparison of dental pulp tissue in different teeth. PeerJ 7:e8212 https://doi.org/10.7717/peerj.8212
date submitted: 2019-05-08
date accepted: 2019-11-14
issued: 2019-12-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guerrero-Jiménez
  given name: Marytere
author list: Agent
  family name: Nic-Can
  given name: Geovanny I.
author list: Agent
  family name: Castro-Linares
  given name: Nelly
author list: Agent
  family name: Aguilar-Ayala
  given name: Fernando Javier
author list: Agent
  family name: Canul-Chan
  given name: Michel
author list: Agent
  family name: Rojas-Herrera
  given name: Rafael A.
author list: Agent
  family name: Peñaloza-Cuevas
  given name: Ricardo
author list: Agent
  family name: Rodas-Junco
  given name: Beatriz A.
doi: 10.7717/peerj.8212
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-06
copyright: © 2019 Guerrero-Jiménez et al.
attribution name: Guerrero-Jiménez et al.

VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs
type: item
type: AcademicArticle
description: In the past decades a number of software programs have been developed to infer phylogenetic relationships between populations. However, most of these programs typically use alignments of sequences from genes to build phylogeny. Recently, many standalone or web applications have been developed to handle large-scale whole genome data, but they are either computationally intensive, dependent on third party software or required significant time and resource of a web server. In the post-genomic era, researchers are able to obtain bioinformatically processed high-quality publication-ready whole genome data for many individuals in a population from next generation sequencing companies due to the reduction in the cost of sequencing and analysis. Such genotype data is typically presented in the Variant Call Format (VCF) and there is no simple software available that directly uses this data format to construct the phylogeny of populations in a short time. To address this limitation, we have developed a user-friendly software, VCF2PopTree that uses genome-wide SNPs to construct and display phylogenetic trees in seconds to minutes. For example, it reads a VCF file containing 4 million SNPs and draws a tree in less than 30 seconds. VCF2PopTree accepts genotype data from a local machine, constructs a tree using UPGMA and Neighbour-Joining algorithms and displays it on a web-browser. It also produces pairwise-diversity matrix in MEGA and PHYLIP file formats as well as trees in the Newick format which could be directly used by other popular phylogenetic software programs. The software including the source code, a test VCF file and a documentation are available at: https://github.com/sansubs/vcf2pop.
format: application/pdf
format: text/html
creator: Sankar Subramanian
creator: Umayal Ramasamy
creator: David Chen
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Population Biology
description: doi:10.7717/peerj.8213
publisher: PeerJ Inc.
rights: © 2019 Subramanian et al.
abstract: In the past decades a number of software programs have been developed to infer phylogenetic relationships between populations. However, most of these programs typically use alignments of sequences from genes to build phylogeny. Recently, many standalone or web applications have been developed to handle large-scale whole genome data, but they are either computationally intensive, dependent on third party software or required significant time and resource of a web server. In the post-genomic era, researchers are able to obtain bioinformatically processed high-quality publication-ready whole genome data for many individuals in a population from next generation sequencing companies due to the reduction in the cost of sequencing and analysis. Such genotype data is typically presented in the Variant Call Format (VCF) and there is no simple software available that directly uses this data format to construct the phylogeny of populations in a short time. To address this limitation, we have developed a user-friendly software, VCF2PopTree that uses genome-wide SNPs to construct and display phylogenetic trees in seconds to minutes. For example, it reads a VCF file containing 4 million SNPs and draws a tree in less than 30 seconds. VCF2PopTree accepts genotype data from a local machine, constructs a tree using UPGMA and Neighbour-Joining algorithms and displays it on a web-browser. It also produces pairwise-diversity matrix in MEGA and PHYLIP file formats as well as trees in the Newick format which could be directly used by other popular phylogenetic software programs. The software including the source code, a test VCF file and a documentation are available at: https://github.com/sansubs/vcf2pop.
bibliographic citation: Subramanian et al. (2019) VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs. PeerJ 7:e8213 https://doi.org/10.7717/peerj.8213
date submitted: 2019-06-21
date accepted: 2019-11-14
issued: 2019-12-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Subramanian
  given name: Sankar
author list: Agent
  family name: Ramasamy
  given name: Umayal
author list: Agent
  family name: Chen
  given name: David
doi: 10.7717/peerj.8213
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-06
copyright: ©2019 Subramanian et al.
attribution name: Subramanian et al.

Critical multi-stranded approach for determining the ecological values of diatoms in unique aquatic ecosystems of anthropogenic origin
type: item
type: AcademicArticle
description: Background The ecological state of surface waters is typically assessed by a multi-aspect approach based on a determination of its chemical and physical parameters, by hydromorphology and the use of indicator organisms such as benthic diatoms. By assigning ecological indicator values, it is possible to create diatom indices which serve as the basic tool in assessing the ecological status of surface waters. These ecological indicator values are set according to classification systems, such as the Van Dam, Mertens & Sinkeldam (1994) system, which classifies species of diatoms according to seven different ecological factors. However, recent studies on the autecology of diatoms have shown the need to verify and establish new ecological indicator values. To this end, aquatic ecosystems are good environments to observe the range of tolerance of benthic diatoms to environmental conditions due to their unique physical and chemical parameters. The aim of the present study was to propose the establishment of new, or altered, ecological indicator values, according to the Van Dam, Mertens & Sinkeldam (1994) classification, of species of diatoms characteristic of three post-mining aquatic ecosystems. Methods In total, 36 species were identified that were characteristic of three waterbodies: a salt aquatic complex (water outflow, a drainage ditch and a pond), mined iron ore reservoirs and a mined lignite reservoir. Their ecological indicator values were specified using OMNIDIA software, and the environmental conditions prevailing in the studied ecosystems were determined. Of the 36 characteristic species, 16 lacking at least one assigned ecological indicator value were analyzed further. The analysis identified three groups of selected characteristic species which showed a correlation, or lack of such, to the tested physical and chemical parameters. Results Based on this multistage study of the autecology of characteristic diatoms, comprising an analysis of environmental condition…
format: application/pdf
format: text/html
creator: Rafał M. Olszyński
creator: Ewelina Szczepocka
creator: Joanna Żelazna-Wieczorek
subject: Aquaculture, Fisheries and Fish Science
subject: Freshwater Biology
subject: Ecohydrology
description: doi:10.7717/peerj.8117
publisher: PeerJ Inc.
rights: © 2019 Olszyński et al.
abstract: Background The ecological state of surface waters is typically assessed by a multi-aspect approach based on a determination of its chemical and physical parameters, by hydromorphology and the use of indicator organisms such as benthic diatoms. By assigning ecological indicator values, it is possible to create diatom indices which serve as the basic tool in assessing the ecological status of surface waters. These ecological indicator values are set according to classification systems, such as the Van Dam, Mertens & Sinkeldam (1994) system, which classifies species of diatoms according to seven different ecological factors. However, recent studies on the autecology of diatoms have shown the need to verify and establish new ecological indicator values. To this end, aquatic ecosystems are good environments to observe the range of tolerance of benthic diatoms to environmental conditions due to their unique physical and chemical parameters. The aim of the present study was to propose the establishment of new, or altered, ecological indicator values, according to the Van Dam, Mertens & Sinkeldam (1994) classification, of species of diatoms characteristic of three post-mining aquatic ecosystems. Methods In total, 36 species were identified that were characteristic of three waterbodies: a salt aquatic complex (water outflow, a drainage ditch and a pond), mined iron ore reservoirs and a mined lignite reservoir. Their ecological indicator values were specified using OMNIDIA software, and the environmental conditions prevailing in the studied ecosystems were determined. Of the 36 characteristic species, 16 lacking at least one assigned ecological indicator value were analyzed further. The analysis identified three groups of selected characteristic species which showed a correlation, or lack of such, to the tested physical and chemical parameters. Results Based on this multistage study of the autecology of characteristic diatoms, comprising an analysis of environmental condition…
bibliographic citation: Olszyński et al. (2019) Critical multi-stranded approach for determining the ecological values of diatoms in unique aquatic ecosystems of anthropogenic origin. PeerJ 7:e8117 https://doi.org/10.7717/peerj.8117
date submitted: 2019-05-15
date accepted: 2019-10-29
issued: 2019-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olszyński
  given name: Rafał M.
author list: Agent
  family name: Szczepocka
  given name: Ewelina
author list: Agent
  family name: Żelazna-Wieczorek
  given name: Joanna
doi: 10.7717/peerj.8117
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-05
copyright: © 2019 Olszyński et al.
attribution name: Olszyński et al.

Design and preliminary application of affinity peptide based on the structure of the porcine circovirus type II Capsid (PCV2 Cap)
type: item
type: AcademicArticle
description: Background Affinity peptides, as a core part of affinity chromatography, play an important role in the purification of target molecules. Methods Here we describe the use of molecular docking technology for virtual screening of affinity peptides that specifically recognize the PCV2 Cap protein for the first time. Thirteen candidate peptides with high scores were obtained and then further characterized. Experimentally, the affinity and sensitivity of the peptides studied were identified by ELISA and LSPR, respectively. In order to investigate the purification effect of a selected peptide (L11) for the recombinant PCV2 Cap protein, it was coupled to NHS agarose magnetic beads as an affinity adsorbent (NaMB-L11); and the ligand density of the affinity adsorbent and pH value in the purification of the recombinant PCV2 Cap protein were optimized. Results Our data showed that the peptide L11- DYWWQSWE has the smallest KD = 103 nM with higher specificity for PCV2 Cap protein recognition. The NaMB-L11 affinity adsorbent yielded a purified Cap sample with 98% purity at 90% recovery in a single step. Conclusion Based on the structure, we obtained a high affinity peptide L11 binding to the PCV2 Cap protein by molecular docking technology. It not only provides a theoretical basis for the design of PCV2 Cap affinity peptide, but a new method for the purification of the PCV2 Cap protein.
format: application/pdf
format: text/html
creator: Junfang Hao
creator: Fangyu Wang
creator: Guangxu Xing
creator: Yunchao Liu
creator: Ruiguang Deng
creator: Hao Zhang
creator: Anchun Cheng
creator: Gaiping Zhang
subject: Agricultural Science
subject: Biochemistry
subject: Biotechnology
description: doi:10.7717/peerj.8132
publisher: PeerJ Inc.
rights: © 2019 Hao et al.
abstract: Background Affinity peptides, as a core part of affinity chromatography, play an important role in the purification of target molecules. Methods Here we describe the use of molecular docking technology for virtual screening of affinity peptides that specifically recognize the PCV2 Cap protein for the first time. Thirteen candidate peptides with high scores were obtained and then further characterized. Experimentally, the affinity and sensitivity of the peptides studied were identified by ELISA and LSPR, respectively. In order to investigate the purification effect of a selected peptide (L11) for the recombinant PCV2 Cap protein, it was coupled to NHS agarose magnetic beads as an affinity adsorbent (NaMB-L11); and the ligand density of the affinity adsorbent and pH value in the purification of the recombinant PCV2 Cap protein were optimized. Results Our data showed that the peptide L11- DYWWQSWE has the smallest KD = 103 nM with higher specificity for PCV2 Cap protein recognition. The NaMB-L11 affinity adsorbent yielded a purified Cap sample with 98% purity at 90% recovery in a single step. Conclusion Based on the structure, we obtained a high affinity peptide L11 binding to the PCV2 Cap protein by molecular docking technology. It not only provides a theoretical basis for the design of PCV2 Cap affinity peptide, but a new method for the purification of the PCV2 Cap protein.
bibliographic citation: Hao et al. (2019) Design and preliminary application of affinity peptide based on the structure of the porcine circovirus type II Capsid (PCV2 Cap). PeerJ 7:e8132 https://doi.org/10.7717/peerj.8132
date submitted: 2019-07-19
date accepted: 2019-10-31
issued: 2019-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Junfang
author list: Agent
  family name: Wang
  given name: Fangyu
author list: Agent
  family name: Xing
  given name: Guangxu
author list: Agent
  family name: Liu
  given name: Yunchao
author list: Agent
  family name: Deng
  given name: Ruiguang
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: Cheng
  given name: Anchun
author list: Agent
  family name: Zhang
  given name: Gaiping
doi: 10.7717/peerj.8132
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-05
copyright: ©2019 Hao et al.
attribution name: Hao et al.

Bleaching and post-bleaching mortality of Acropora corals on a heat-susceptible reef in 2016
type: item
type: AcademicArticle
description: In 2016, global temperatures were the highest on record, and mass coral bleaching occurred world-wide. However, around Sesoko Island, Okinawa, southwestern Japan, the heat stress assessed by degree heating week (DHW) based on local temperature measurements was moderate in 2016; in 1998, DHW was three times higher than in 2016 (10.6 vs. 3.3 in September in respective years). On a reef flat of Sesoko Island where the effect of severe coral bleaching on coral assemblage was monitored in 1998, significant coral bleaching occurred in 2016. Bleaching of the heat stress sensitive Acropora corals began in July 2016 on the reef flat as seawater temperature rose. We observed the bleaching and post-bleaching mortality status of individual colonies of Acropora spp. in 2016 in fixed plots on the reef flat. In total, 123 Acropora colonies were followed for six months after seawater temperature became normal by multiple surveys. At the beginning of September 2016, 99.2% of colonies, were either completely (92.7%) or partially (6.5%) bleached. Of those, the dominant species or species groups were A. gemmifera (Ag), A. digitifera (Ad), and tabular Acropora (tA). For all Acropora colonies, the overall whole and partial mortality was 41.5% and 11.4%, respectively. Whole mortality rate differed significantly among species; 72.5%, 17.9%, and 27.8% in Ag, Ad, and tA, respectively. Mortality rates at the end of the surveys were similar in smaller (≤10 cm in diameter) and larger Ag, but the former suffered mortality earlier than the latter. Higher survival of smaller colonies was observed only in tA (100%), which may be associated with large morphological differences between smaller and larger colonies. Some of the dominant Acropora colonies had survived without partial mortality including 15.0% survival of the most vulnerable Ag at the end of the surveys. These results suggest that moderate heat stress may have a potential for selecting heat-tolerant genotypes. A longer period of mortalit…
format: application/pdf
format: text/html
creator: Kazuhiko Sakai
creator: Tanya Singh
creator: Akira Iguchi
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.8138
publisher: PeerJ Inc.
rights: © 2019 Sakai et al.
abstract: In 2016, global temperatures were the highest on record, and mass coral bleaching occurred world-wide. However, around Sesoko Island, Okinawa, southwestern Japan, the heat stress assessed by degree heating week (DHW) based on local temperature measurements was moderate in 2016; in 1998, DHW was three times higher than in 2016 (10.6 vs. 3.3 in September in respective years). On a reef flat of Sesoko Island where the effect of severe coral bleaching on coral assemblage was monitored in 1998, significant coral bleaching occurred in 2016. Bleaching of the heat stress sensitive Acropora corals began in July 2016 on the reef flat as seawater temperature rose. We observed the bleaching and post-bleaching mortality status of individual colonies of Acropora spp. in 2016 in fixed plots on the reef flat. In total, 123 Acropora colonies were followed for six months after seawater temperature became normal by multiple surveys. At the beginning of September 2016, 99.2% of colonies, were either completely (92.7%) or partially (6.5%) bleached. Of those, the dominant species or species groups were A. gemmifera (Ag), A. digitifera (Ad), and tabular Acropora (tA). For all Acropora colonies, the overall whole and partial mortality was 41.5% and 11.4%, respectively. Whole mortality rate differed significantly among species; 72.5%, 17.9%, and 27.8% in Ag, Ad, and tA, respectively. Mortality rates at the end of the surveys were similar in smaller (≤10 cm in diameter) and larger Ag, but the former suffered mortality earlier than the latter. Higher survival of smaller colonies was observed only in tA (100%), which may be associated with large morphological differences between smaller and larger colonies. Some of the dominant Acropora colonies had survived without partial mortality including 15.0% survival of the most vulnerable Ag at the end of the surveys. These results suggest that moderate heat stress may have a potential for selecting heat-tolerant genotypes. A longer period of mortalit…
bibliographic citation: Sakai et al. (2019) Bleaching and post-bleaching mortality of Acropora corals on a heat-susceptible reef in 2016. PeerJ 7:e8138 https://doi.org/10.7717/peerj.8138
date submitted: 2019-05-14
date accepted: 2019-11-01
issued: 2019-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sakai
  given name: Kazuhiko
author list: Agent
  family name: Singh
  given name: Tanya
author list: Agent
  family name: Iguchi
  given name: Akira
doi: 10.7717/peerj.8138
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-05
copyright: ©2019 Sakai et al.
attribution name: Sakai et al.

TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
type: item
type: AcademicArticle
description: Introduction Recent studies highlight the crucial regulatory roles of transposable elements (TEs) on proximal gene expression in distinct biological contexts such as disease and development. However, computational tools extracting potential TE –proximal gene expression associations from RNA-sequencing data are still missing. Implementation Herein, we developed a novel R package, using a linear regression model, for studying the potential influence of TE species on proximal gene expression from a given RNA-sequencing data set. Our R package, namely TEffectR, makes use of publicly available RepeatMasker TE and Ensembl gene annotations as well as several functions of other R-packages. It calculates total read counts of TEs from sorted and indexed genome aligned BAM files provided by the user, and determines statistically significant relations between TE expression and the transcription of nearby genes under diverse biological conditions. Availability TEffectR is freely available at https://github.com/karakulahg/TEffectR along with a handy tutorial as exemplified by the analysis of RNA-sequencing data including normal and tumour tissue specimens obtained from breast cancer patients.
format: application/pdf
format: text/html
creator: Gökhan Karakülah
creator: Nazmiye Arslan
creator: Cihangir Yandım
creator: Aslı Suner
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.8192
publisher: PeerJ Inc.
rights: © 2019 Karakülah et al.
abstract: Introduction Recent studies highlight the crucial regulatory roles of transposable elements (TEs) on proximal gene expression in distinct biological contexts such as disease and development. However, computational tools extracting potential TE –proximal gene expression associations from RNA-sequencing data are still missing. Implementation Herein, we developed a novel R package, using a linear regression model, for studying the potential influence of TE species on proximal gene expression from a given RNA-sequencing data set. Our R package, namely TEffectR, makes use of publicly available RepeatMasker TE and Ensembl gene annotations as well as several functions of other R-packages. It calculates total read counts of TEs from sorted and indexed genome aligned BAM files provided by the user, and determines statistically significant relations between TE expression and the transcription of nearby genes under diverse biological conditions. Availability TEffectR is freely available at https://github.com/karakulahg/TEffectR along with a handy tutorial as exemplified by the analysis of RNA-sequencing data including normal and tumour tissue specimens obtained from breast cancer patients.
bibliographic citation: Karakülah et al. (2019) TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model. PeerJ 7:e8192 https://doi.org/10.7717/peerj.8192
date submitted: 2019-08-15
date accepted: 2019-11-11
issued: 2019-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karakülah
  given name: Gökhan
author list: Agent
  family name: Arslan
  given name: Nazmiye
author list: Agent
  family name: Yandım
  given name: Cihangir
author list: Agent
  family name: Suner
  given name: Aslı
doi: 10.7717/peerj.8192
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-05
copyright: ©2019 Karakülah et al.
attribution name: Karakülah et al.

A high latitude Devonian lungfish, from the Famennian of South Africa
type: item
type: AcademicArticle
description: New fossil lungfish remains comprising two parasphenoids, tooth plates and scales from the Famennian Witpoort Formation of South Africa are described. From the parasphenoid material, which bears similarity to Oervigia and Sagenodus but is nevertheless unique, a new genus, Isityumzi mlomomde gen. et sp. nov. is erected. Tooth plates and scales from the same locality may be conspecific but are not yet assigned until further material becomes available. The tooth plates closely resemble those of some taxa in the Carboniferous genus Ctenodus. The new taxon is significant as only the second Devonian lungfish described from the African continent, and for hailing from the high-latitude (polar) Waterloo Farm environment situated close to 70° south during the Famennian.
format: application/pdf
format: text/html
creator: Robert W. Gess
creator: Alice M. Clement
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.8073
publisher: PeerJ Inc.
rights: © 2019 Gess and Clement
abstract: New fossil lungfish remains comprising two parasphenoids, tooth plates and scales from the Famennian Witpoort Formation of South Africa are described. From the parasphenoid material, which bears similarity to Oervigia and Sagenodus but is nevertheless unique, a new genus, Isityumzi mlomomde gen. et sp. nov. is erected. Tooth plates and scales from the same locality may be conspecific but are not yet assigned until further material becomes available. The tooth plates closely resemble those of some taxa in the Carboniferous genus Ctenodus. The new taxon is significant as only the second Devonian lungfish described from the African continent, and for hailing from the high-latitude (polar) Waterloo Farm environment situated close to 70° south during the Famennian.
bibliographic citation: Gess et al. (2019) A high latitude Devonian lungfish, from the Famennian of South Africa. PeerJ 7:e8073 https://doi.org/10.7717/peerj.8073
date submitted: 2019-07-30
date accepted: 2019-10-21
issued: 2019-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gess
  given name: Robert W.
author list: Agent
  family name: Clement
  given name: Alice M.
doi: 10.7717/peerj.8073
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-04
copyright: © 2019 Gess and Clement
attribution name: Gess and Clement

Rediscovery of Osteocephalus vilarsi (Anura: Hylidae): an overlooked but widespread Amazonian spiny-backed treefrog
type: item
type: AcademicArticle
description: Osteocephalus vilarsi (Melin, 1941) is an Amazonian treefrog species known for over 75 years from its holotype only. Due to a lack of published data on its morphological diagnostic characters and their variations, as well as the absence of molecular, acoustic and ecological data supporting its identity, a highly dynamic taxonomic history has led this species to be confused and even synonymised with other Osteocephalus species from distinct species groups. The molecular phylogenetic relationships of O. vilarsi were investigated based on recently collected specimens from eight Northwestern Brazilian localities in the state of Amazonas, leading to its removal from the Osteocephalus taurinus species group and placement in the Osteocephalus planiceps species group. Furthermore, detailed data on morphology and colour variation are provided, as well as advertisement call and tadpole descriptions. Finally, the currently known geographic range of O. vilarsi is considerably extended, first data on the natural history of the species are provided, and the possible ecological preference of O. vilarsi for Amazonian white-sand forests is discussed.
format: application/pdf
format: text/html
creator: Miquéias Ferrão
creator: Jiří Moravec
creator: Leandro J.C.L. Moraes
creator: Vinicius T. de Carvalho
creator: Marcelo Gordo
creator: Albertina P. Lima
subject: Ecology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.8160
publisher: PeerJ Inc.
rights: © 2019 Ferrão et al.
abstract: Osteocephalus vilarsi (Melin, 1941) is an Amazonian treefrog species known for over 75 years from its holotype only. Due to a lack of published data on its morphological diagnostic characters and their variations, as well as the absence of molecular, acoustic and ecological data supporting its identity, a highly dynamic taxonomic history has led this species to be confused and even synonymised with other Osteocephalus species from distinct species groups. The molecular phylogenetic relationships of O. vilarsi were investigated based on recently collected specimens from eight Northwestern Brazilian localities in the state of Amazonas, leading to its removal from the Osteocephalus taurinus species group and placement in the Osteocephalus planiceps species group. Furthermore, detailed data on morphology and colour variation are provided, as well as advertisement call and tadpole descriptions. Finally, the currently known geographic range of O. vilarsi is considerably extended, first data on the natural history of the species are provided, and the possible ecological preference of O. vilarsi for Amazonian white-sand forests is discussed.
bibliographic citation: Ferrão et al. (2019) Rediscovery of Osteocephalus vilarsi (Anura: Hylidae): an overlooked but widespread Amazonian spiny-backed treefrog. PeerJ 7:e8160 https://doi.org/10.7717/peerj.8160
date submitted: 2019-08-08
date accepted: 2019-11-04
issued: 2019-12-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferrão
  given name: Miquéias
author list: Agent
  family name: Moravec
  given name: Jiří
author list: Agent
  family name: Moraes
  given name: Leandro J.C.L.
author list: Agent
  family name: de Carvalho
  given name: Vinicius T.
author list: Agent
  family name: Gordo
  given name: Marcelo
author list: Agent
  family name: Lima
  given name: Albertina P.
doi: 10.7717/peerj.8160
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-04
copyright: © 2019 Ferrão et al.
attribution name: Ferrão et al.

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