PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Optimizing the power of human performed audio surveys for monitoring the endangered Houston toad using automated recording devices
items: Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies
items: Genome-wide analysis of the lignin toolbox for morus and the roles of lignin related genes in response to zinc stress
items: The Erlang distribution approximates the age distribution of incidence of childhood and young adulthood cancers
items: Gene selection for studying frugivore-plant interactions: a review and an example using Queensland fruit fly in tomato
items: The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters
items: Congruence between morphology-based species and Barcode Index Numbers (BINs) in Neotropical Eumaeini (Lycaenidae)
items: An efficient sorghum transformation system using embryogenic calli derived from mature seeds
items: Pain and satisfaction: the case of isolated COVID-19 patients of Pakistan
items: Evaluation of structural and ultrastructural changes in thyroid and parathyroid glands after near infrared irradiation: study on an animal model

Optimizing the power of human performed audio surveys for monitoring the endangered Houston toad using automated recording devices
type: item
type: AcademicArticle
description: Knowledge regarding the locations of populations of endangered species is a critical part of recovery and facilitates land use planning that avoids unnecessary impacts. Regulatory agencies often support the development of survey guidelines designed to standardize the methods and maximize the probability of detection, thereby avoiding incorrectly concluding a species is absent from a site. Here, using simulations with data collected using automated recording devices (ARDs) we evaluated the efficacy of the existing U.S. Fish and Wildlife Service’s survey requirements for the endangered Houston Toad (Anaxyrus houstonensis). We explored the effect of (1) increasing survey duration, (2) increasing the number of surveys, and (3) combinations of environmental conditions (e.g., temperature, humidity, rainfall) on the detection probability and the number of surveys needed to be 95% confident of absence. We found that increases in both the duration of the survey and the number of surveys conducted decreased the likelihood of incorrectly concluding the species was absent from the site, and that the number of surveys required to be 95% confident greatly exceeded the existing survey requirements. Targeting specific environmental conditions was also an effective way to decrease the number of surveys required but the infrequency in which these conditions occurred might make application difficult in some years. Overall, we suggest that the survey effort necessary to achieve confidence in the absence of Houston Toads at a site is more practically achievable with the use of ARDs, but this may not be suitable in all monitoring scenarios.
format: application/pdf
format: text/html
creator: Andrew R. MacLaren
creator: Paul S. Crump
creator: Michael R.J. Forstner
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.11935
publisher: PeerJ Inc.
rights: © 2021 MacLaren et al.
abstract: Knowledge regarding the locations of populations of endangered species is a critical part of recovery and facilitates land use planning that avoids unnecessary impacts. Regulatory agencies often support the development of survey guidelines designed to standardize the methods and maximize the probability of detection, thereby avoiding incorrectly concluding a species is absent from a site. Here, using simulations with data collected using automated recording devices (ARDs) we evaluated the efficacy of the existing U.S. Fish and Wildlife Service’s survey requirements for the endangered Houston Toad (Anaxyrus houstonensis). We explored the effect of (1) increasing survey duration, (2) increasing the number of surveys, and (3) combinations of environmental conditions (e.g., temperature, humidity, rainfall) on the detection probability and the number of surveys needed to be 95% confident of absence. We found that increases in both the duration of the survey and the number of surveys conducted decreased the likelihood of incorrectly concluding the species was absent from the site, and that the number of surveys required to be 95% confident greatly exceeded the existing survey requirements. Targeting specific environmental conditions was also an effective way to decrease the number of surveys required but the infrequency in which these conditions occurred might make application difficult in some years. Overall, we suggest that the survey effort necessary to achieve confidence in the absence of Houston Toads at a site is more practically achievable with the use of ARDs, but this may not be suitable in all monitoring scenarios.
bibliographic citation: MacLaren et al. (2021) Optimizing the power of human performed audio surveys for monitoring the endangered Houston toad using automated recording devices. PeerJ 9:e11935 https://doi.org/10.7717/peerj.11935
date submitted: 2021-06-11
date accepted: 2021-07-19
issued: 2021-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: MacLaren
  given name: Andrew R.
author list: Agent
  family name: Crump
  given name: Paul S.
author list: Agent
  family name: Forstner
  given name: Michael R.J.
doi: 10.7717/peerj.11935
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-06
copyright: ©2021 MacLaren et al.
attribution name: MacLaren et al.

Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies
type: item
type: AcademicArticle
description: Background A pangenome is the collection of all genes found in a set of related genomes. For microbes, these genomes are often different strains of the same species, and the pangenome offers a means to compare gene content variation with differences in phenotypes, ecology, and phylogenetic relatedness. Though most frequently applied to bacteria, there is growing interest in adapting pangenome analysis to bacteriophages. However, working with phage genomes presents new challenges. First, most phage families are under-sampled, and homologous genes in related viruses can be difficult to identify. Second, homing endonucleases and intron-like sequences may be present, resulting in fragmented gene calls. Each of these issues can reduce the accuracy of standard pangenome analysis tools. Methods We developed an R pipeline called Rephine.r that takes as input the gene clusters produced by an initial pangenomics workflow. Rephine.r then proceeds in two primary steps. First, it identifies three common causes of fragmented gene calls: (1) indels creating early stop codons and new start codons; (2) interruption by a selfish genetic element; and (3) splitting at the ends of the reported genome. Fragmented genes are then fused to create new sequence alignments. In tandem, Rephine.r searches for distant homologs separated into different gene families using Hidden Markov Models. Significant hits are used to merge families into larger clusters. A final round of fragment identification is then run, and results may be used to infer single-copy core genomes and phylogenetic trees. Results We applied Rephine.r to three well-studied phage groups: the Tevenvirinae (e.g., T4), the Studiervirinae (e.g., T7), and the Pbunaviruses (e.g., PB1). In each case, Rephine.r recovered additional members of the single-copy core genome and increased the overall bootstrap support of the phylogeny. The Rephine.r pipeline is provided through GitHub (https://www.github.com/coevoeco/Rephine.r) as a single sc…
format: application/pdf
format: text/html
creator: Jason W. Shapiro
creator: Catherine Putonti
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.11950
publisher: PeerJ Inc.
rights: © 2021 Shapiro and Putonti
abstract: Background A pangenome is the collection of all genes found in a set of related genomes. For microbes, these genomes are often different strains of the same species, and the pangenome offers a means to compare gene content variation with differences in phenotypes, ecology, and phylogenetic relatedness. Though most frequently applied to bacteria, there is growing interest in adapting pangenome analysis to bacteriophages. However, working with phage genomes presents new challenges. First, most phage families are under-sampled, and homologous genes in related viruses can be difficult to identify. Second, homing endonucleases and intron-like sequences may be present, resulting in fragmented gene calls. Each of these issues can reduce the accuracy of standard pangenome analysis tools. Methods We developed an R pipeline called Rephine.r that takes as input the gene clusters produced by an initial pangenomics workflow. Rephine.r then proceeds in two primary steps. First, it identifies three common causes of fragmented gene calls: (1) indels creating early stop codons and new start codons; (2) interruption by a selfish genetic element; and (3) splitting at the ends of the reported genome. Fragmented genes are then fused to create new sequence alignments. In tandem, Rephine.r searches for distant homologs separated into different gene families using Hidden Markov Models. Significant hits are used to merge families into larger clusters. A final round of fragment identification is then run, and results may be used to infer single-copy core genomes and phylogenetic trees. Results We applied Rephine.r to three well-studied phage groups: the Tevenvirinae (e.g., T4), the Studiervirinae (e.g., T7), and the Pbunaviruses (e.g., PB1). In each case, Rephine.r recovered additional members of the single-copy core genome and increased the overall bootstrap support of the phylogeny. The Rephine.r pipeline is provided through GitHub (https://www.github.com/coevoeco/Rephine.r) as a single sc…
bibliographic citation: Shapiro et al. (2021) Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies. PeerJ 9:e11950 https://doi.org/10.7717/peerj.11950
date submitted: 2021-04-30
date accepted: 2021-07-20
issued: 2021-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shapiro
  given name: Jason W.
author list: Agent
  family name: Putonti
  given name: Catherine
doi: 10.7717/peerj.11950
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-06
copyright: ©2021 Shapiro and Putonti
attribution name: Shapiro and Putonti

Genome-wide analysis of the lignin toolbox for morus and the roles of lignin related genes in response to zinc stress
type: item
type: AcademicArticle
description: Mulberry (Morus, Moraceae) is an important economic plant with nutritional, medicinal, and ecological values. Lignin in mulberry can affect the quality of forage and the saccharification efficiency of mulberry twigs. The availability of the Morus notabilis genome makes it possible to perform a systematic analysis of the genes encoding the 11 protein families specific to the lignin branch of the phenylpropanoid pathway, providing the core genes for the lignin toolbox in mulberry. We performed genome-wide screening, which was combined with de novo transcriptome data for Morus notabilis and Morus alba variety Fengchi, to identify putative members of the lignin gene families followed by phylogenetic and expression profile analyses. We focused on bona fide clade genes and their response to zinc stress were further distinguished based on expression profiles using RNA-seq and RT-qPCR. We finally identified 31 bona fide genes in Morus notabilis and 25 bona fide genes in Fengchi. The putative function of these bona fide genes was proposed, and a lignin toolbox that comprised 19 genes in mulberry was provided, which will be convenient for researchers to explore and modify the monolignol biosynthesis pathway in mulberry. We also observed changes in the expression of some of these lignin biosynthetic genes in response to stress caused by excess zinc in Fengchi and proposed that the enhanced lignin biosynthesis in lignified organs and inhibition of lignin biosynthesis in leaf is an important response to zinc stress in mulberry.
format: application/pdf
format: text/html
creator: Nan Chao
creator: Ting Yu
creator: Chong Hou
creator: Li Liu
creator: Lin Zhang
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11964
publisher: PeerJ Inc.
rights: © 2021 Chao et al.
abstract: Mulberry (Morus, Moraceae) is an important economic plant with nutritional, medicinal, and ecological values. Lignin in mulberry can affect the quality of forage and the saccharification efficiency of mulberry twigs. The availability of the Morus notabilis genome makes it possible to perform a systematic analysis of the genes encoding the 11 protein families specific to the lignin branch of the phenylpropanoid pathway, providing the core genes for the lignin toolbox in mulberry. We performed genome-wide screening, which was combined with de novo transcriptome data for Morus notabilis and Morus alba variety Fengchi, to identify putative members of the lignin gene families followed by phylogenetic and expression profile analyses. We focused on bona fide clade genes and their response to zinc stress were further distinguished based on expression profiles using RNA-seq and RT-qPCR. We finally identified 31 bona fide genes in Morus notabilis and 25 bona fide genes in Fengchi. The putative function of these bona fide genes was proposed, and a lignin toolbox that comprised 19 genes in mulberry was provided, which will be convenient for researchers to explore and modify the monolignol biosynthesis pathway in mulberry. We also observed changes in the expression of some of these lignin biosynthetic genes in response to stress caused by excess zinc in Fengchi and proposed that the enhanced lignin biosynthesis in lignified organs and inhibition of lignin biosynthesis in leaf is an important response to zinc stress in mulberry.
bibliographic citation: Chao et al. (2021) Genome-wide analysis of the lignin toolbox for morus and the roles of lignin related genes in response to zinc stress. PeerJ 9:e11964 https://doi.org/10.7717/peerj.11964
date submitted: 2020-12-28
date accepted: 2021-07-21
issued: 2021-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chao
  given name: Nan
author list: Agent
  family name: Yu
  given name: Ting
author list: Agent
  family name: Hou
  given name: Chong
author list: Agent
  family name: Liu
  given name: Li
author list: Agent
  family name: Zhang
  given name: Lin
doi: 10.7717/peerj.11964
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-06
copyright: © 2021 Chao et al.
attribution name: Chao et al.

The Erlang distribution approximates the age distribution of incidence of childhood and young adulthood cancers
type: item
type: AcademicArticle
description: Background It is widely believed that cancers develop upon acquiring a particular number of (epi) mutations in driver genes, but the law governing the kinetics of this process is not known. We have previously shown that the age distribution of incidence for the 20 most prevalent cancers of old age is best approximated by the Erlang probability distribution. The Erlang distribution describes the probability of several successive random events occurring by the given time according to the Poisson process, which allows an estimate for the number of critical driver events. Methods Here we employ a computational grid search method to find global parameter optima for five probability distributions on the CDC WONDER dataset of the age distribution of childhood and young adulthood cancer incidence. Results We show that the Erlang distribution is the only classical probability distribution we found that can adequately model the age distribution of incidence for all studied childhood and young adulthood cancers, in addition to cancers of old age. Conclusions This suggests that the Poisson process governs driver accumulation at any age and that the Erlang distribution can be used to determine the number of driver events for any cancer type. The Poisson process implies the fundamentally random timing of driver events and their constant average rate. As waiting times for the occurrence of the required number of driver events are counted in decades, and most cells do not live this long, it suggests that driver mutations accumulate silently in the longest-living dividing cells in the body—the stem cells.
format: application/pdf
format: text/html
creator: Aleksey V. Belikov
creator: Alexey Vyatkin
creator: Sergey V. Leonov
subject: Epidemiology
subject: Oncology
subject: Pediatrics
subject: Statistics
subject: Medical Genetics
description: doi:10.7717/peerj.11976
publisher: PeerJ Inc.
rights: © 2021 Belikov et al.
abstract: Background It is widely believed that cancers develop upon acquiring a particular number of (epi) mutations in driver genes, but the law governing the kinetics of this process is not known. We have previously shown that the age distribution of incidence for the 20 most prevalent cancers of old age is best approximated by the Erlang probability distribution. The Erlang distribution describes the probability of several successive random events occurring by the given time according to the Poisson process, which allows an estimate for the number of critical driver events. Methods Here we employ a computational grid search method to find global parameter optima for five probability distributions on the CDC WONDER dataset of the age distribution of childhood and young adulthood cancer incidence. Results We show that the Erlang distribution is the only classical probability distribution we found that can adequately model the age distribution of incidence for all studied childhood and young adulthood cancers, in addition to cancers of old age. Conclusions This suggests that the Poisson process governs driver accumulation at any age and that the Erlang distribution can be used to determine the number of driver events for any cancer type. The Poisson process implies the fundamentally random timing of driver events and their constant average rate. As waiting times for the occurrence of the required number of driver events are counted in decades, and most cells do not live this long, it suggests that driver mutations accumulate silently in the longest-living dividing cells in the body—the stem cells.
bibliographic citation: Belikov et al. (2021) The Erlang distribution approximates the age distribution of incidence of childhood and young adulthood cancers. PeerJ 9:e11976 https://doi.org/10.7717/peerj.11976
date submitted: 2021-04-07
date accepted: 2021-07-24
issued: 2021-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Belikov
  given name: Aleksey V.
author list: Agent
  family name: Vyatkin
  given name: Alexey
author list: Agent
  family name: Leonov
  given name: Sergey V.
doi: 10.7717/peerj.11976
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-06
copyright: ©2021 Belikov et al.
attribution name: Belikov et al.

Gene selection for studying frugivore-plant interactions: a review and an example using Queensland fruit fly in tomato
type: item
type: AcademicArticle
description: Fruit production is negatively affected by a wide range of frugivorous insects, among them tephritid fruit flies are one of the most important. As a replacement for pesticide-based controls, enhancing natural fruit resistance through biotechnology approaches is a poorly researched but promising alternative. The use of quantitative reverse transcription PCR (RT-qPCR) is an approach to studying gene expression which has been widely used in studying plant resistance to pathogens and non-frugivorous insect herbivores, and offers a starting point for fruit fly studies. In this paper, we develop a gene selection pipe-line for known induced-defense genes in tomato fruit, Solanum lycopersicum, and putative detoxification genes in Queensland fruit fly, Bactrocera tryoni, as a basis for future RT-qPCR research. The pipeline started with a literature review on plant/herbivore and plant/pathogen molecular interactions. With respect to the fly, this was then followed by the identification of gene families known to be associated with insect resistance to toxins, and then individual genes through reference to annotated B. tryoni transcriptomes and gene identity matching with related species. In contrast for tomato, a much better studied species, individual defense genes could be identified directly through literature research. For B. tryoni, gene selection was then further refined through gene expression studies. Ultimately 28 putative detoxification genes from cytochrome P450 (P450), carboxylesterase (CarE), glutathione S-transferases (GST), and ATP binding cassette transporters (ABC) gene families were identified for B. tryoni, and 15 induced defense genes from receptor-like kinase (RLK), D-mannose/L-galactose, mitogen-activated protein kinase (MAPK), lipoxygenase (LOX), gamma-aminobutyric acid (GABA) pathways and polyphenol oxidase (PPO), proteinase inhibitors (PI) and resistance (R) gene families were identified from tomato fruit. The developed gene selection process for B. tr…
format: application/pdf
format: text/html
creator: Shirin Roohigohar
creator: Anthony R. Clarke
creator: Peter J. Prentis
subject: Agricultural Science
subject: Ecology
subject: Entomology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.11762
publisher: PeerJ Inc.
rights: © 2021 Roohigohar et al.
abstract: Fruit production is negatively affected by a wide range of frugivorous insects, among them tephritid fruit flies are one of the most important. As a replacement for pesticide-based controls, enhancing natural fruit resistance through biotechnology approaches is a poorly researched but promising alternative. The use of quantitative reverse transcription PCR (RT-qPCR) is an approach to studying gene expression which has been widely used in studying plant resistance to pathogens and non-frugivorous insect herbivores, and offers a starting point for fruit fly studies. In this paper, we develop a gene selection pipe-line for known induced-defense genes in tomato fruit, Solanum lycopersicum, and putative detoxification genes in Queensland fruit fly, Bactrocera tryoni, as a basis for future RT-qPCR research. The pipeline started with a literature review on plant/herbivore and plant/pathogen molecular interactions. With respect to the fly, this was then followed by the identification of gene families known to be associated with insect resistance to toxins, and then individual genes through reference to annotated B. tryoni transcriptomes and gene identity matching with related species. In contrast for tomato, a much better studied species, individual defense genes could be identified directly through literature research. For B. tryoni, gene selection was then further refined through gene expression studies. Ultimately 28 putative detoxification genes from cytochrome P450 (P450), carboxylesterase (CarE), glutathione S-transferases (GST), and ATP binding cassette transporters (ABC) gene families were identified for B. tryoni, and 15 induced defense genes from receptor-like kinase (RLK), D-mannose/L-galactose, mitogen-activated protein kinase (MAPK), lipoxygenase (LOX), gamma-aminobutyric acid (GABA) pathways and polyphenol oxidase (PPO), proteinase inhibitors (PI) and resistance (R) gene families were identified from tomato fruit. The developed gene selection process for B. tr…
bibliographic citation: Roohigohar et al. (2021) Gene selection for studying frugivore-plant interactions: a review and an example using Queensland fruit fly in tomato. PeerJ 9:e11762 https://doi.org/10.7717/peerj.11762
date submitted: 2020-11-12
date accepted: 2021-06-21
issued: 2021-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roohigohar
  given name: Shirin
author list: Agent
  family name: Clarke
  given name: Anthony R.
author list: Agent
  family name: Prentis
  given name: Peter J.
doi: 10.7717/peerj.11762
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-05
copyright: ©2021 Roohigohar et al.
attribution name: Roohigohar et al.

The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters
type: item
type: AcademicArticle
description: The geoemydid turtles of the Eocoene Messel Pit Quarry of Hesse, Germany, are part of a rich Western European fossil record of testudinoids. Originally referred to as “Ocadia” kehreri and “Ocadia” messeliana, their systematic relationships remain unclear. A previous study proposed that a majority of the Western European geoemydids, including the Messel geoemydids, are closely related to the Recent European representatives of the clade Mauremys. Another study hypothesised that the Western European geoemydid fauna is more phylogenetically diverse, and that the Messel geoemydids are closely related to the East Asian turtles Orlitia and Malayemys. Here we present the first quantitative analyses to date that investigate this question. We use continuous characters in the form of ratios to estimate the placement of the Messel geoemydids in a reference tree that was estimated from molecular data. We explore the placement error obtained from that data with maximum likelihood and Bayesian methods, as well as linear parsimony in combination with discrete characters. We find good overall performance with Bayesian and parsimony analyses. Parsimony performs even better when we also incorporated discrete characters. Yet, we cannot pin down the position of the Messel geoemydids with high confidence. Depending on how intraspecific variation of the ratio characters is treated, parsimony favours a placement of the Messel fossils sister to Orlitia borneensis or sister to Geoemyda spengleri, with weak bootstrap support. The latter placement is suspect because G. spengleri is a phylogenetically problematic species with molecular and morphological data. There is even less support for placements within the Mauremys clade.
format: application/pdf
format: text/html
creator: Eduardo Ascarrunz
creator: Julien Claude
creator: Walter G. Joyce
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11805
publisher: PeerJ Inc.
rights: © 2021 Ascarrunz et al.
abstract: The geoemydid turtles of the Eocoene Messel Pit Quarry of Hesse, Germany, are part of a rich Western European fossil record of testudinoids. Originally referred to as “Ocadia” kehreri and “Ocadia” messeliana, their systematic relationships remain unclear. A previous study proposed that a majority of the Western European geoemydids, including the Messel geoemydids, are closely related to the Recent European representatives of the clade Mauremys. Another study hypothesised that the Western European geoemydid fauna is more phylogenetically diverse, and that the Messel geoemydids are closely related to the East Asian turtles Orlitia and Malayemys. Here we present the first quantitative analyses to date that investigate this question. We use continuous characters in the form of ratios to estimate the placement of the Messel geoemydids in a reference tree that was estimated from molecular data. We explore the placement error obtained from that data with maximum likelihood and Bayesian methods, as well as linear parsimony in combination with discrete characters. We find good overall performance with Bayesian and parsimony analyses. Parsimony performs even better when we also incorporated discrete characters. Yet, we cannot pin down the position of the Messel geoemydids with high confidence. Depending on how intraspecific variation of the ratio characters is treated, parsimony favours a placement of the Messel fossils sister to Orlitia borneensis or sister to Geoemyda spengleri, with weak bootstrap support. The latter placement is suspect because G. spengleri is a phylogenetically problematic species with molecular and morphological data. There is even less support for placements within the Mauremys clade.
bibliographic citation: Ascarrunz et al. (2021) The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters. PeerJ 9:e11805 https://doi.org/10.7717/peerj.11805
date submitted: 2021-04-08
date accepted: 2021-06-27
issued: 2021-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ascarrunz
  given name: Eduardo
author list: Agent
  family name: Claude
  given name: Julien
author list: Agent
  family name: Joyce
  given name: Walter G.
doi: 10.7717/peerj.11805
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-05
copyright: © 2021 Ascarrunz et al.
attribution name: Ascarrunz et al.

Congruence between morphology-based species and Barcode Index Numbers (BINs) in Neotropical Eumaeini (Lycaenidae)
type: item
type: AcademicArticle
description: Background With about 1,000 species in the Neotropics, the Eumaeini (Theclinae) are one of the most diverse butterfly tribes. Correct morphology-based identifications are challenging in many genera due to relatively little interspecific differences in wing patterns. Geographic infraspecific variation is sometimes more substantial than variation between species. In this paper we present a large DNA barcode dataset of South American Lycaenidae. We analyze how well DNA barcode BINs match morphologically delimited species. Methods We compare morphology-based species identifications with the clustering of molecular operational taxonomic units (MOTUs) delimitated by the RESL algorithm in BOLD, which assigns Barcode Index Numbers (BINs). We examine intra- and interspecific divergences for genera represented by at least four morphospecies. We discuss the existence of local barcode gaps in a genus by genus analysis. We also note differences in the percentage of species with barcode gaps in groups of lowland and high mountain genera. Results We identified 2,213 specimens and obtained 1,839 sequences of 512 species in 90 genera. Overall, the mean intraspecific divergence value of CO1 sequences was 1.20%, while the mean interspecific divergence between nearest congeneric neighbors was 4.89%, demonstrating the presence of a barcode gap. However, the gap seemed to disappear from the entire set when comparing the maximum intraspecific distance (8.40%) with the minimum interspecific distance (0.40%). Clear barcode gaps are present in many genera but absent in others. From the set of specimens that yielded COI fragment lengths of at least 650 bp, 75% of the a priori morphology-based identifications were unambiguously assigned to a single Barcode Index Number (BIN). However, after a taxonomic a posteriori review, the percentage of matched identifications rose to 85%. BIN splitting was observed for 17% of the species and BIN sharing for 9%. We found that genera that contain primarily …
format: application/pdf
format: text/html
creator: Carlos Prieto
creator: Christophe Faynel
creator: Robert Robbins
creator: Axel Hausmann
subject: Biodiversity
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11843
publisher: PeerJ Inc.
rights: © 2021 Prieto et al.
abstract: Background With about 1,000 species in the Neotropics, the Eumaeini (Theclinae) are one of the most diverse butterfly tribes. Correct morphology-based identifications are challenging in many genera due to relatively little interspecific differences in wing patterns. Geographic infraspecific variation is sometimes more substantial than variation between species. In this paper we present a large DNA barcode dataset of South American Lycaenidae. We analyze how well DNA barcode BINs match morphologically delimited species. Methods We compare morphology-based species identifications with the clustering of molecular operational taxonomic units (MOTUs) delimitated by the RESL algorithm in BOLD, which assigns Barcode Index Numbers (BINs). We examine intra- and interspecific divergences for genera represented by at least four morphospecies. We discuss the existence of local barcode gaps in a genus by genus analysis. We also note differences in the percentage of species with barcode gaps in groups of lowland and high mountain genera. Results We identified 2,213 specimens and obtained 1,839 sequences of 512 species in 90 genera. Overall, the mean intraspecific divergence value of CO1 sequences was 1.20%, while the mean interspecific divergence between nearest congeneric neighbors was 4.89%, demonstrating the presence of a barcode gap. However, the gap seemed to disappear from the entire set when comparing the maximum intraspecific distance (8.40%) with the minimum interspecific distance (0.40%). Clear barcode gaps are present in many genera but absent in others. From the set of specimens that yielded COI fragment lengths of at least 650 bp, 75% of the a priori morphology-based identifications were unambiguously assigned to a single Barcode Index Number (BIN). However, after a taxonomic a posteriori review, the percentage of matched identifications rose to 85%. BIN splitting was observed for 17% of the species and BIN sharing for 9%. We found that genera that contain primarily …
bibliographic citation: Prieto et al. (2021) Congruence between morphology-based species and Barcode Index Numbers (BINs) in Neotropical Eumaeini (Lycaenidae). PeerJ 9:e11843 https://doi.org/10.7717/peerj.11843
date submitted: 2021-02-09
date accepted: 2021-07-01
issued: 2021-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prieto
  given name: Carlos
author list: Agent
  family name: Faynel
  given name: Christophe
author list: Agent
  family name: Robbins
  given name: Robert
author list: Agent
  family name: Hausmann
  given name: Axel
doi: 10.7717/peerj.11843
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-05
copyright: © 2021 Prieto et al.
attribution name: Prieto et al.

An efficient sorghum transformation system using embryogenic calli derived from mature seeds
type: item
type: AcademicArticle
description: Significant progress has been made on sorghum transformation in the last decades; however, the transformation process has been constrained by the availability of immature embryos because most of the researchers have utilized immature embryos as favorable explants. Although immature embryos have been proven to be optimal for tissue culture and transformation, isolation of immature embryos is time-consuming, labor-intensive, and limited by warm weather. In this study, we developed an efficient genetic transformation system using mature seeds as explants. The nptII and gus gene, used as the selective marker and report gene respectively, have been co-transformed by particle bombardment. After optimization of tissue culture, the G418 concentration, and transgenic, the average transformation frequency at 13.33% was achieved routinely. The transgenic events and transgene copy numbers were determined by PCR and RT-PCR, respectively. The geneticin selection and GUS staining on T1 seedlings confirmed that the transgenic plants were heritable. Our results demonstrated that the efficient sorghum transformation system has been established using mature seeds as explants. This transformation system will promote sorghum research on genetic engineering and genome editing without seasonal weather conditions restriction and explant resources restriction.
format: application/pdf
format: text/html
creator: Lihua Wang
creator: Li Gao
creator: Guoquan Liu
creator: Ruirui Meng
creator: Yanlong Liu
creator: Jieqin Li
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11849
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Significant progress has been made on sorghum transformation in the last decades; however, the transformation process has been constrained by the availability of immature embryos because most of the researchers have utilized immature embryos as favorable explants. Although immature embryos have been proven to be optimal for tissue culture and transformation, isolation of immature embryos is time-consuming, labor-intensive, and limited by warm weather. In this study, we developed an efficient genetic transformation system using mature seeds as explants. The nptII and gus gene, used as the selective marker and report gene respectively, have been co-transformed by particle bombardment. After optimization of tissue culture, the G418 concentration, and transgenic, the average transformation frequency at 13.33% was achieved routinely. The transgenic events and transgene copy numbers were determined by PCR and RT-PCR, respectively. The geneticin selection and GUS staining on T1 seedlings confirmed that the transgenic plants were heritable. Our results demonstrated that the efficient sorghum transformation system has been established using mature seeds as explants. This transformation system will promote sorghum research on genetic engineering and genome editing without seasonal weather conditions restriction and explant resources restriction.
bibliographic citation: Wang et al. (2021) An efficient sorghum transformation system using embryogenic calli derived from mature seeds. PeerJ 9:e11849 https://doi.org/10.7717/peerj.11849
date submitted: 2021-03-12
date accepted: 2021-07-02
issued: 2021-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lihua
author list: Agent
  family name: Gao
  given name: Li
author list: Agent
  family name: Liu
  given name: Guoquan
author list: Agent
  family name: Meng
  given name: Ruirui
author list: Agent
  family name: Liu
  given name: Yanlong
author list: Agent
  family name: Li
  given name: Jieqin
doi: 10.7717/peerj.11849
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-05
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Pain and satisfaction: the case of isolated COVID-19 patients of Pakistan
type: item
type: AcademicArticle
description: Background Over 3 million people lost their lives across the globe due to the COVID-19 related pandemic. The unprecedented restrictions on mobility have imposed in the form of isolation, quarantines, and lockdowns to curb the profound effects of the pandemic and retain physical health. This study examined the relationship between various pain levels, demographic variables and patient satisfaction with COVID-19 during isolation. Methods The primary data in this study were collected from isolated patients during their isolation and treatment in a public hospital. We obtained information from patients with COVID-19 (N = 100) about their demographic characteristics, varying levels of pain, and satisfaction with the services provided during the isolation period. We computed the descriptive statistics to explain the profile of participants, ANOVA was used to find out the difference between various groups on patient satisfaction, and structural equation modeling was performed to examine the link between pain levels, demographic factors, and patient satisfaction. This analysis was performed with STATA and SmartPLS-3. Results The findings of this study ascertained that respondent’s education (Beta, β = 2.961, p = 0.003), assets such as possession of a house (β = 4.563, p = 0.000), perception of income adequacy during the lockdown (=2.299, p = 0.022), and negligence in prevention (β = 1.975, p = 0.049) significantly affects patient satisfaction during the isolation period. Moreover, satisfaction with life, physicians and medicine, income adequacy, and fear of the participants was significantly linked to the pain level (Model F-stat = 86.323, p = 0.0001). Patients who were satisfied with their treatment had significantly lower odds of having pain (OR 0.023, 95% CI [0.001–0.0452]). Patients who had enough income to meet their basic necessities were found to have significantly lower odds of having pain (OR 0.155, 95% CI [0.032–0.740]. Discussion and Conclusion We conclude that a…
format: application/pdf
format: text/html
creator: Wajiha Haq
creator: Siddrah Irfan
creator: Syed Hassan Raza
creator: Waqar Ahmed
creator: Mian Alam
creator: Samia Wasif
creator: Muhammad Wasif Malik
creator: Saeed Ahmad
subject: Anesthesiology and Pain Management
subject: Global Health
subject: Infectious Diseases
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11859
publisher: PeerJ Inc.
rights: © 2021 Haq et al.
abstract: Background Over 3 million people lost their lives across the globe due to the COVID-19 related pandemic. The unprecedented restrictions on mobility have imposed in the form of isolation, quarantines, and lockdowns to curb the profound effects of the pandemic and retain physical health. This study examined the relationship between various pain levels, demographic variables and patient satisfaction with COVID-19 during isolation. Methods The primary data in this study were collected from isolated patients during their isolation and treatment in a public hospital. We obtained information from patients with COVID-19 (N = 100) about their demographic characteristics, varying levels of pain, and satisfaction with the services provided during the isolation period. We computed the descriptive statistics to explain the profile of participants, ANOVA was used to find out the difference between various groups on patient satisfaction, and structural equation modeling was performed to examine the link between pain levels, demographic factors, and patient satisfaction. This analysis was performed with STATA and SmartPLS-3. Results The findings of this study ascertained that respondent’s education (Beta, β = 2.961, p = 0.003), assets such as possession of a house (β = 4.563, p = 0.000), perception of income adequacy during the lockdown (=2.299, p = 0.022), and negligence in prevention (β = 1.975, p = 0.049) significantly affects patient satisfaction during the isolation period. Moreover, satisfaction with life, physicians and medicine, income adequacy, and fear of the participants was significantly linked to the pain level (Model F-stat = 86.323, p = 0.0001). Patients who were satisfied with their treatment had significantly lower odds of having pain (OR 0.023, 95% CI [0.001–0.0452]). Patients who had enough income to meet their basic necessities were found to have significantly lower odds of having pain (OR 0.155, 95% CI [0.032–0.740]. Discussion and Conclusion We conclude that a…
bibliographic citation: Haq et al. (2021) Pain and satisfaction: the case of isolated COVID-19 patients of Pakistan. PeerJ 9:e11859 https://doi.org/10.7717/peerj.11859
date submitted: 2021-02-08
date accepted: 2021-07-05
issued: 2021-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Haq
  given name: Wajiha
author list: Agent
  family name: Irfan
  given name: Siddrah
author list: Agent
  family name: Raza
  given name: Syed Hassan
author list: Agent
  family name: Ahmed
  given name: Waqar
author list: Agent
  family name: Alam
  given name: Mian
author list: Agent
  family name: Wasif
  given name: Samia
author list: Agent
  family name: Malik
  given name: Muhammad Wasif
author list: Agent
  family name: Ahmad
  given name: Saeed
doi: 10.7717/peerj.11859
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-05
copyright: ©2021 Haq et al.
attribution name: Haq et al.

Evaluation of structural and ultrastructural changes in thyroid and parathyroid glands after near infrared irradiation: study on an animal model
type: item
type: AcademicArticle
description: Intraoperative identification of parathyroid glands is a tough task for surgeons performing thyroid or parathyroid surgery, because the small size, color and shape of these glands hinder their discrimination from other cervical tissues. In 2011, Paras described the autofluorescence of parathyroid glands, a property that could facilitate their intraoperative identification. Parathyroid glands submitted to a 785 nm laser beam emit fluorescence in the near infrared range, with a peak at 822 nm. As the intrinsic properties of secretory tissues may be affected by the exposure to the near infrared light, a situation that could preclude their intraoperative utilization, the authors compared the structural and ultra-structural patterns of rat’s thyroid and parathyroid glands submitted to irradiation replicating the conditions that allow their intraoperative identification, with those of non irradiated animals. Twenty-four Wistar rats were divided into six groups: animals of Groups 1, 3 and 5 were submitted under general anesthesia to direct irradiation of the cervical area with a 780 nm LED light for 3 minutes through a cervical incision, and animals of Groups 2, 4 and 6 were submitted to cervical dissection without irradiation. Animals of were euthanized immediately (Groups 1 and 2), at Day 30 (Groups 3 and 4) at and at Day 60 (Groups 5 and 6) and thyroid and parathyroid glands were removed: one lobe was prepared for conventional pathological examination and the other lobe for electron microscopy observed by three experienced pathological experts. Twenty-four samples were prepared for conventional histology and there were no alterations reported in any group. Due to technical problems, only 21 samples were observed by electron microscopy and there were no differences in the ultrastructure of parathyroid and thyroid glands, namely the nuclear pattern, mitochondria, endoplasmic reticulum or secretory granules, in any of the groups. These results confirm the innocuity of near…
format: application/pdf
format: text/html
creator: Carlos Serra
creator: Luis Silveira
subject: Biochemistry
subject: Drugs and Devices
subject: Surgery and Surgical Specialties
subject: Histology
description: doi:10.7717/peerj.11891
publisher: PeerJ Inc.
rights: © 2021 Serra and Silveira
abstract: Intraoperative identification of parathyroid glands is a tough task for surgeons performing thyroid or parathyroid surgery, because the small size, color and shape of these glands hinder their discrimination from other cervical tissues. In 2011, Paras described the autofluorescence of parathyroid glands, a property that could facilitate their intraoperative identification. Parathyroid glands submitted to a 785 nm laser beam emit fluorescence in the near infrared range, with a peak at 822 nm. As the intrinsic properties of secretory tissues may be affected by the exposure to the near infrared light, a situation that could preclude their intraoperative utilization, the authors compared the structural and ultra-structural patterns of rat’s thyroid and parathyroid glands submitted to irradiation replicating the conditions that allow their intraoperative identification, with those of non irradiated animals. Twenty-four Wistar rats were divided into six groups: animals of Groups 1, 3 and 5 were submitted under general anesthesia to direct irradiation of the cervical area with a 780 nm LED light for 3 minutes through a cervical incision, and animals of Groups 2, 4 and 6 were submitted to cervical dissection without irradiation. Animals of were euthanized immediately (Groups 1 and 2), at Day 30 (Groups 3 and 4) at and at Day 60 (Groups 5 and 6) and thyroid and parathyroid glands were removed: one lobe was prepared for conventional pathological examination and the other lobe for electron microscopy observed by three experienced pathological experts. Twenty-four samples were prepared for conventional histology and there were no alterations reported in any group. Due to technical problems, only 21 samples were observed by electron microscopy and there were no differences in the ultrastructure of parathyroid and thyroid glands, namely the nuclear pattern, mitochondria, endoplasmic reticulum or secretory granules, in any of the groups. These results confirm the innocuity of near…
bibliographic citation: Serra et al. (2021) Evaluation of structural and ultrastructural changes in thyroid and parathyroid glands after near infrared irradiation: study on an animal model. PeerJ 9:e11891 https://doi.org/10.7717/peerj.11891
date submitted: 2021-04-15
date accepted: 2021-07-10
issued: 2021-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Serra
  given name: Carlos
author list: Agent
  family name: Silveira
  given name: Luis
doi: 10.7717/peerj.11891
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-05
copyright: ©2021 Serra and Silveira
attribution name: Serra and Silveira

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