PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bacterial diversity and potential risk factors associated with Salmonella contamination of seafood products sold in retail markets in Bangkok, Thailand
items: Quantification of antibiotic resistance genes and mobile genetic in dairy manure
items: A journey through the Corynebacterium pseudotuberculosis proteome promotes insights into its functional genome
items: Rediscovery of Laura’s glassfrog Nymphargus laurae (Anura: Centrolenidae) with new data on its morphology, colouration, phylogenetic position and conservation in Ecuador
items: Identification and molecular characterization of the alternative spliced variants of beta carbonic anhydrase 1 (βCA1) from Arabidopsis thaliana
items: Integrated transcriptomic and proteomic analysis of Tritipyrum provides insights into the molecular basis of salt tolerance
items: Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective
items: ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences
items: Identifying biomarkers for evaluating wound extent and age in the contused muscle of rats using microarray analysis: a pilot study
items: Unique spicules may confound species differentiation: taxonomy and biogeography of Melonanchora Carter, 1874 and two new related genera (Myxillidae: Poecilosclerida) from the Okhotsk Sea

Bacterial diversity and potential risk factors associated with Salmonella contamination of seafood products sold in retail markets in Bangkok, Thailand
type: item
type: AcademicArticle
description: Consumption of contaminated food causes 600 million cases, including 420,000 of fatal infections every year. Estimated cost from food-borne illnesses is USD 110 billion per year, which is an economic burden to low- and middle-income countries. Thailand is a leading producer and consumer of seafood, but little is known about bacterial contamination in seafood. In particular, public health agencies need to know the relationship between Salmonella contamination in seafood and risk factors, as assessed with readily available culture-dependent and bacterial phenotyping methods. To address this, levels of indicator bacteria, Salmonella and Vibrio in various seafood products were determined to identify risk factors associated with Salmonella contamination. A total of 335 samples were collected from October 2018 to July 2019 at seafood markets throughout Bangkok, Thailand; overall sample composition was Pacific white shrimp (n = 85), oysters (n = 82), blood cockles (n = 84), and Asian seabass (n = 84). Prevalence was 100% for fecal coliforms and 85% for E. coli. In contrast, prevalence was 59% for V. parahaemolyticus, 49% for V. cholerae, 19% for V. alginolyticus, 18% for V. vulnificus, and 36% for Salmonella. Highest concentrations of fecal coliforms and E. coli were in oysters. Highest concentrations of Salmonella with Matopeni (31%) being the predominant serotype were in shrimp. Salmonella contamination was significantly associated with type of seafood, sampling location, retail conditions, and the presence of E. coli, V. alginolyticus and V. vulnificus. A cutoff value for E. coli concentration of 1.3 × 104 MPN/g predicted contamination of Salmonella, with a sensitivity of 84% and specificity of 61%. Displaying seafood products on ice, presence of E. coli and Vibrio, and seafood derived from Eastern Thailand were associated with an increased risk of Salmonella contamination.
format: application/pdf
format: text/html
creator: Edward R. Atwill
creator: Saharuetai Jeamsripong
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.12694
publisher: PeerJ Inc.
rights: © 2021 Atwill and Jeamsripong
abstract: Consumption of contaminated food causes 600 million cases, including 420,000 of fatal infections every year. Estimated cost from food-borne illnesses is USD 110 billion per year, which is an economic burden to low- and middle-income countries. Thailand is a leading producer and consumer of seafood, but little is known about bacterial contamination in seafood. In particular, public health agencies need to know the relationship between Salmonella contamination in seafood and risk factors, as assessed with readily available culture-dependent and bacterial phenotyping methods. To address this, levels of indicator bacteria, Salmonella and Vibrio in various seafood products were determined to identify risk factors associated with Salmonella contamination. A total of 335 samples were collected from October 2018 to July 2019 at seafood markets throughout Bangkok, Thailand; overall sample composition was Pacific white shrimp (n = 85), oysters (n = 82), blood cockles (n = 84), and Asian seabass (n = 84). Prevalence was 100% for fecal coliforms and 85% for E. coli. In contrast, prevalence was 59% for V. parahaemolyticus, 49% for V. cholerae, 19% for V. alginolyticus, 18% for V. vulnificus, and 36% for Salmonella. Highest concentrations of fecal coliforms and E. coli were in oysters. Highest concentrations of Salmonella with Matopeni (31%) being the predominant serotype were in shrimp. Salmonella contamination was significantly associated with type of seafood, sampling location, retail conditions, and the presence of E. coli, V. alginolyticus and V. vulnificus. A cutoff value for E. coli concentration of 1.3 × 104 MPN/g predicted contamination of Salmonella, with a sensitivity of 84% and specificity of 61%. Displaying seafood products on ice, presence of E. coli and Vibrio, and seafood derived from Eastern Thailand were associated with an increased risk of Salmonella contamination.
bibliographic citation: Atwill et al. (2021) Bacterial diversity and potential risk factors associated with Salmonella contamination of seafood products sold in retail markets in Bangkok, Thailand. PeerJ 9:e12694 https://doi.org/10.7717/peerj.12694
date submitted: 2021-05-14
date accepted: 2021-12-06
issued: 2021-12-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Atwill
  given name: Edward R.
author list: Agent
  family name: Jeamsripong
  given name: Saharuetai
doi: 10.7717/peerj.12694
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-24
copyright: © 2021 Atwill and Jeamsripong
attribution name: Atwill and Jeamsripong

Quantification of antibiotic resistance genes and mobile genetic in dairy manure
type: item
type: AcademicArticle
description: Background Antibiotic resistance genes (ARGs) are considered to be emerging environmental contaminants of concern potentially posing risks to human and animal health, and this research studied the prevalence of antimicrobial resistance in dairy manure. Methods This study is focused on investigating prevalence of ARGs in California dairy farm manure under current common different manure management. A total of 33 manure samples were collected from multiple manure treatment conditions: (1) flushed manure (FM), (2) fresh pile (FP), (3) compost pile (CP), (4) primary lagoon (PL), and (5) secondary lagoon (SL). After DNA extraction, all fecal samples were screened by PCR for the presence of eight ARGs: four sulfonamide ARGs (sulI, sulII, sulIII, sulA), two tetracycline ARGs (tetW, tetO), two macrolide-lincosamide-streptogramin B (MLSB) ARGs (ermB, ermF). Samples were also screened for two mobile genetic elements (MGEs) (intI1, tnpA), which are responsible for dissemination of ARGs. Quantitative PCR was then used to screen all samples for five ARGs (sulII, tetW, ermF, tnpA and intI1). Results Prevalence of genes varied among sample types, but all genes were detectable in different manure types. Results showed that liquid-solid separation, piling, and lagoon conditions had limited effects on reducing ARGs and MGEs, and the effect was only found significant on tetW (p = 0.01). Besides, network analysis indicated that sulII was associated with tnpA (p < 0.05), and Psychrobacter and Pseudomonas as opportunistic human pathogens, were potential ARG/MGE hosts (p < 0.05). This research indicated current different manure management practices in California dairy farms has limited effects on reducing ARGs and MGEs. Improvement of different manure management in dairy farms is thus important to mitigate dissemination of ARGs into the environment.
format: application/pdf
format: text/html
creator: Yi Wang
creator: Pramod Pandey
creator: Colleen Chiu
creator: Richard Jeannotte
creator: Sundaram Kuppu
creator: Ruihong Zhang
creator: Richard Pereira
creator: Bart C. Weimer
creator: Nitin Nitin
creator: Sharif S. Aly
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.12408
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background Antibiotic resistance genes (ARGs) are considered to be emerging environmental contaminants of concern potentially posing risks to human and animal health, and this research studied the prevalence of antimicrobial resistance in dairy manure. Methods This study is focused on investigating prevalence of ARGs in California dairy farm manure under current common different manure management. A total of 33 manure samples were collected from multiple manure treatment conditions: (1) flushed manure (FM), (2) fresh pile (FP), (3) compost pile (CP), (4) primary lagoon (PL), and (5) secondary lagoon (SL). After DNA extraction, all fecal samples were screened by PCR for the presence of eight ARGs: four sulfonamide ARGs (sulI, sulII, sulIII, sulA), two tetracycline ARGs (tetW, tetO), two macrolide-lincosamide-streptogramin B (MLSB) ARGs (ermB, ermF). Samples were also screened for two mobile genetic elements (MGEs) (intI1, tnpA), which are responsible for dissemination of ARGs. Quantitative PCR was then used to screen all samples for five ARGs (sulII, tetW, ermF, tnpA and intI1). Results Prevalence of genes varied among sample types, but all genes were detectable in different manure types. Results showed that liquid-solid separation, piling, and lagoon conditions had limited effects on reducing ARGs and MGEs, and the effect was only found significant on tetW (p = 0.01). Besides, network analysis indicated that sulII was associated with tnpA (p < 0.05), and Psychrobacter and Pseudomonas as opportunistic human pathogens, were potential ARG/MGE hosts (p < 0.05). This research indicated current different manure management practices in California dairy farms has limited effects on reducing ARGs and MGEs. Improvement of different manure management in dairy farms is thus important to mitigate dissemination of ARGs into the environment.
bibliographic citation: Wang et al. (2021) Quantification of antibiotic resistance genes and mobile genetic in dairy manure. PeerJ 9:e12408 https://doi.org/10.7717/peerj.12408
date submitted: 2020-12-23
date accepted: 2021-10-08
issued: 2021-12-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yi
author list: Agent
  family name: Pandey
  given name: Pramod
author list: Agent
  family name: Chiu
  given name: Colleen
author list: Agent
  family name: Jeannotte
  given name: Richard
author list: Agent
  family name: Kuppu
  given name: Sundaram
author list: Agent
  family name: Zhang
  given name: Ruihong
author list: Agent
  family name: Pereira
  given name: Richard
author list: Agent
  family name: Weimer
  given name: Bart C.
author list: Agent
  family name: Nitin
  given name: Nitin
author list: Agent
  family name: Aly
  given name: Sharif S.
doi: 10.7717/peerj.12408
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-23
copyright: © 2021 Wang et al.
attribution name: Wang et al.

A journey through the Corynebacterium pseudotuberculosis proteome promotes insights into its functional genome
type: item
type: AcademicArticle
description: Background Corynebacterium pseudotuberculosis is a Gram-positive facultative intracellular pathogen and the etiologic agent of illnesses like caseous lymphadenitis in small ruminants, mastitis in dairy cattle, ulcerative lymphangitis in equines, and oedematous skin disease in buffalos. With the growing advance in high-throughput technologies, genomic studies have been carried out to explore the molecular basis of its virulence and pathogenicity. However, data large-scale functional genomics studies are necessary to complement genomics data and better understating the molecular basis of a given organism. Here we summarize, MS-based proteomics techniques and bioinformatics tools incorporated in genomic functional studies of C. pseudotuberculosis to discover the different patterns of protein modulation under distinct environmental conditions, and antigenic and drugs targets. Methodology In this study we performed an extensive search in Web of Science of original and relevant articles related to methods, strategy, technology, approaches, and bioinformatics tools focused on the functional study of the genome of C. pseudotuberculosis at the protein level. Results Here, we highlight the use of proteomics for understating several aspects of the physiology and pathogenesis of C. pseudotuberculosis at the protein level. The implementation and use of protocols, strategies, and proteomics approach to characterize the different subcellular fractions of the proteome of this pathogen. In addition, we have discussed the immunoproteomics, immunoinformatics and genetic tools employed to identify targets for immunoassays, drugs, and vaccines against C. pseudotuberculosis infection. Conclusion In this review, we showed that the combination of proteomics and bioinformatics studies is a suitable strategy to elucidate the functional aspects of the C. pseudotuberculosis genome. Together, all information generated from these proteomics studies allowed expanding our knowledge about factors r…
format: application/pdf
format: text/html
creator: Wanderson Marques da Silva
creator: Nubia Seyffert
creator: Artur Silva
creator: Vasco Azevedo
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.12456
publisher: PeerJ Inc.
rights: © 2021 Marques da Silva et al.
abstract: Background Corynebacterium pseudotuberculosis is a Gram-positive facultative intracellular pathogen and the etiologic agent of illnesses like caseous lymphadenitis in small ruminants, mastitis in dairy cattle, ulcerative lymphangitis in equines, and oedematous skin disease in buffalos. With the growing advance in high-throughput technologies, genomic studies have been carried out to explore the molecular basis of its virulence and pathogenicity. However, data large-scale functional genomics studies are necessary to complement genomics data and better understating the molecular basis of a given organism. Here we summarize, MS-based proteomics techniques and bioinformatics tools incorporated in genomic functional studies of C. pseudotuberculosis to discover the different patterns of protein modulation under distinct environmental conditions, and antigenic and drugs targets. Methodology In this study we performed an extensive search in Web of Science of original and relevant articles related to methods, strategy, technology, approaches, and bioinformatics tools focused on the functional study of the genome of C. pseudotuberculosis at the protein level. Results Here, we highlight the use of proteomics for understating several aspects of the physiology and pathogenesis of C. pseudotuberculosis at the protein level. The implementation and use of protocols, strategies, and proteomics approach to characterize the different subcellular fractions of the proteome of this pathogen. In addition, we have discussed the immunoproteomics, immunoinformatics and genetic tools employed to identify targets for immunoassays, drugs, and vaccines against C. pseudotuberculosis infection. Conclusion In this review, we showed that the combination of proteomics and bioinformatics studies is a suitable strategy to elucidate the functional aspects of the C. pseudotuberculosis genome. Together, all information generated from these proteomics studies allowed expanding our knowledge about factors r…
bibliographic citation: Marques da Silva et al. (2021) A journey through the Corynebacterium pseudotuberculosis proteome promotes insights into its functional genome. PeerJ 9:e12456 https://doi.org/10.7717/peerj.12456
date submitted: 2021-05-12
date accepted: 2021-10-18
issued: 2021-12-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marques da Silva
  given name: Wanderson
author list: Agent
  family name: Seyffert
  given name: Nubia
author list: Agent
  family name: Silva
  given name: Artur
author list: Agent
  family name: Azevedo
  given name: Vasco
doi: 10.7717/peerj.12456
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-23
copyright: © 2021 Marques da Silva et al.
attribution name: Marques da Silva et al.

Rediscovery of Laura’s glassfrog Nymphargus laurae (Anura: Centrolenidae) with new data on its morphology, colouration, phylogenetic position and conservation in Ecuador
type: item
type: AcademicArticle
description: We report the rediscovery of Laura’s Glassfrog, Nymphargus laurae Cisneros-Heredia & McDiarmid, 2007, based on two specimens collected at the Colonso-Chalupas Biological Reserve, province of Napo, Ecuador. The species was described and known from a single male specimen collected in 1955 at Loreto, north-eastern Andean foothills of Ecuador. Limited information was available about the colouration, systematics, ecology, and biogeography of N. laurae. We provide new data on the external morphology, colouration, distribution and comment on its conservation status and extinction risk. We discuss the phylogenetic relationships of N. laurae, which forms a clade together with N. siren and N. humboldti. The importance of research in unexplored areas must be a national priority to document the biodiversity associated, especially in protected areas.
format: application/pdf
format: text/html
creator: María José Sánchez-Carvajal
creator: Grace C. Reyes-Ortega
creator: Diego F. Cisneros-Heredia
creator: H. Mauricio Ortega-Andrade
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12644
publisher: PeerJ Inc.
rights: © 2021 Sánchez-Carvajal et al.
abstract: We report the rediscovery of Laura’s Glassfrog, Nymphargus laurae Cisneros-Heredia & McDiarmid, 2007, based on two specimens collected at the Colonso-Chalupas Biological Reserve, province of Napo, Ecuador. The species was described and known from a single male specimen collected in 1955 at Loreto, north-eastern Andean foothills of Ecuador. Limited information was available about the colouration, systematics, ecology, and biogeography of N. laurae. We provide new data on the external morphology, colouration, distribution and comment on its conservation status and extinction risk. We discuss the phylogenetic relationships of N. laurae, which forms a clade together with N. siren and N. humboldti. The importance of research in unexplored areas must be a national priority to document the biodiversity associated, especially in protected areas.
bibliographic citation: Sánchez-Carvajal et al. (2021) Rediscovery of Laura’s glassfrog Nymphargus laurae (Anura: Centrolenidae) with new data on its morphology, colouration, phylogenetic position and conservation in Ecuador. PeerJ 9:e12644 https://doi.org/10.7717/peerj.12644
date submitted: 2021-10-15
date accepted: 2021-11-26
issued: 2021-12-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sánchez-Carvajal
  given name: María José
author list: Agent
  family name: Reyes-Ortega
  given name: Grace C.
author list: Agent
  family name: Cisneros-Heredia
  given name: Diego F.
author list: Agent
  family name: Ortega-Andrade
  given name: H. Mauricio
doi: 10.7717/peerj.12644
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-23
copyright: © 2021 Sánchez-Carvajal et al.
attribution name: Sánchez-Carvajal et al.

Identification and molecular characterization of the alternative spliced variants of beta carbonic anhydrase 1 (βCA1) from Arabidopsis thaliana
type: item
type: AcademicArticle
description: Carbonic anhydrases (CAs) are ubiquitous zinc metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. Higher plants mainly contain the three evolutionarily distinct CA families αCA, βCA, and γCA, with each represented by multiple isoforms. Alternative splicing (AS) of the CA transcripts is common. However, there is little information on the spliced variants of individual CA isoforms. In this study, we focused on the characterization of spliced variants of βCA1 from Arabidopsis. The expression patterns and subcellular localization of the individual spliced variants of βCA1 were examined. The results showed that the spliced variants of βCA1 possessed different subcellular and tissue distributions and responded differently to environmental stimuli. Additionally, we addressed the physiological role of βCA1 in heat stress response and its protein-protein interaction (PPI) network. Our results showed that βCA1 was regulated by heat stresses, and βca1 mutant was hypersensitive to heat stress, indicating a role for βCA1 in heat stress response. Furthermore, PPI network analysis revealed that βCA1 interacts with multiple proteins involved in several processes, including photosynthesis, metabolism, and the stress response, and these will provide new avenues for future investigations of βCA1.
format: application/pdf
format: text/html
creator: Jinyu Shen
creator: Zhiyong Li
creator: Yajuan Fu
creator: Jiansheng Liang
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12673
publisher: PeerJ Inc.
rights: © 2021 Shen et al.
abstract: Carbonic anhydrases (CAs) are ubiquitous zinc metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. Higher plants mainly contain the three evolutionarily distinct CA families αCA, βCA, and γCA, with each represented by multiple isoforms. Alternative splicing (AS) of the CA transcripts is common. However, there is little information on the spliced variants of individual CA isoforms. In this study, we focused on the characterization of spliced variants of βCA1 from Arabidopsis. The expression patterns and subcellular localization of the individual spliced variants of βCA1 were examined. The results showed that the spliced variants of βCA1 possessed different subcellular and tissue distributions and responded differently to environmental stimuli. Additionally, we addressed the physiological role of βCA1 in heat stress response and its protein-protein interaction (PPI) network. Our results showed that βCA1 was regulated by heat stresses, and βca1 mutant was hypersensitive to heat stress, indicating a role for βCA1 in heat stress response. Furthermore, PPI network analysis revealed that βCA1 interacts with multiple proteins involved in several processes, including photosynthesis, metabolism, and the stress response, and these will provide new avenues for future investigations of βCA1.
bibliographic citation: Shen et al. (2021) Identification and molecular characterization of the alternative spliced variants of beta carbonic anhydrase 1 (βCA1) from Arabidopsis thaliana. PeerJ 9:e12673 https://doi.org/10.7717/peerj.12673
date submitted: 2021-05-14
date accepted: 2021-12-02
issued: 2021-12-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shen
  given name: Jinyu
author list: Agent
  family name: Li
  given name: Zhiyong
author list: Agent
  family name: Fu
  given name: Yajuan
author list: Agent
  family name: Liang
  given name: Jiansheng
doi: 10.7717/peerj.12673
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-23
copyright: © 2021 Shen et al.
attribution name: Shen et al.

Integrated transcriptomic and proteomic analysis of Tritipyrum provides insights into the molecular basis of salt tolerance
type: item
type: AcademicArticle
description: Background Soil salinity is a major environmental stress that restricts crop growth and yield. Methods Here, crucial proteins and biological pathways were investigated under salt-stress and recovery conditions in Tritipyrum ‘Y1805’ using the data-independent acquisition proteomics techniques to explore its salt-tolerance mechanism. Results In total, 44 and 102 differentially expressed proteins (DEPs) were identified in ‘Y1805’ under salt-stress and recovery conditions, respectively. A proteome-transcriptome-associated analysis revealed that the expression patterns of 13 and 25 DEPs were the same under salt-stress and recovery conditions, respectively. ‘Response to stimulus’, ‘antioxidant activity’, ‘carbohydrate metabolism’, ‘amino acid metabolism’, ‘signal transduction’, ‘transport and catabolism’ and ‘biosynthesis of other secondary metabolites’ were present under both conditions in ‘Y1805’. In addition, ‘energy metabolism’ and ‘lipid metabolism’ were recovery-specific pathways, while ‘antioxidant activity’, and ‘molecular function regulator’ under salt-stress conditions, and ‘virion’ and ‘virion part’ during recovery, were ‘Y1805’-specific compared with the salt-sensitive wheat ‘Chinese Spring’. ‘Y1805’ contained eight specific DEPs related to salt-stress responses. The strong salt tolerance of ‘Y1805’ could be attributed to the strengthened cell walls, reactive oxygen species scavenging, osmoregulation, phytohormone regulation, transient growth arrest, enhanced respiration, transcriptional regulation and error information processing. These data will facilitate an understanding of the molecular mechanisms of salt tolerance and aid in the breeding of salt-tolerant wheat.
format: application/pdf
format: text/html
creator: Rui Yang
creator: Zhifen Yang
creator: Ze Peng
creator: Fang He
creator: Luxi Shi
creator: Yabing Dong
creator: Mingjian Ren
creator: Qingqin Zhang
creator: Guangdong Geng
creator: Suqin Zhang
subject: Agricultural Science
subject: Food Science and Technology
subject: Molecular Biology
description: doi:10.7717/peerj.12683
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Background Soil salinity is a major environmental stress that restricts crop growth and yield. Methods Here, crucial proteins and biological pathways were investigated under salt-stress and recovery conditions in Tritipyrum ‘Y1805’ using the data-independent acquisition proteomics techniques to explore its salt-tolerance mechanism. Results In total, 44 and 102 differentially expressed proteins (DEPs) were identified in ‘Y1805’ under salt-stress and recovery conditions, respectively. A proteome-transcriptome-associated analysis revealed that the expression patterns of 13 and 25 DEPs were the same under salt-stress and recovery conditions, respectively. ‘Response to stimulus’, ‘antioxidant activity’, ‘carbohydrate metabolism’, ‘amino acid metabolism’, ‘signal transduction’, ‘transport and catabolism’ and ‘biosynthesis of other secondary metabolites’ were present under both conditions in ‘Y1805’. In addition, ‘energy metabolism’ and ‘lipid metabolism’ were recovery-specific pathways, while ‘antioxidant activity’, and ‘molecular function regulator’ under salt-stress conditions, and ‘virion’ and ‘virion part’ during recovery, were ‘Y1805’-specific compared with the salt-sensitive wheat ‘Chinese Spring’. ‘Y1805’ contained eight specific DEPs related to salt-stress responses. The strong salt tolerance of ‘Y1805’ could be attributed to the strengthened cell walls, reactive oxygen species scavenging, osmoregulation, phytohormone regulation, transient growth arrest, enhanced respiration, transcriptional regulation and error information processing. These data will facilitate an understanding of the molecular mechanisms of salt tolerance and aid in the breeding of salt-tolerant wheat.
bibliographic citation: Yang et al. (2021) Integrated transcriptomic and proteomic analysis of Tritipyrum provides insights into the molecular basis of salt tolerance. PeerJ 9:e12683 https://doi.org/10.7717/peerj.12683
date submitted: 2021-06-22
date accepted: 2021-12-02
issued: 2021-12-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Rui
author list: Agent
  family name: Yang
  given name: Zhifen
author list: Agent
  family name: Peng
  given name: Ze
author list: Agent
  family name: He
  given name: Fang
author list: Agent
  family name: Shi
  given name: Luxi
author list: Agent
  family name: Dong
  given name: Yabing
author list: Agent
  family name: Ren
  given name: Mingjian
author list: Agent
  family name: Zhang
  given name: Qingqin
author list: Agent
  family name: Geng
  given name: Guangdong
author list: Agent
  family name: Zhang
  given name: Suqin
doi: 10.7717/peerj.12683
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-23
copyright: © 2021 Yang et al.
attribution name: Yang et al.

Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective
type: item
type: AcademicArticle
description: Background There have been extensive debates on the interrelationships among the four major classes of Myriapoda—Chilopoda, Symphyla, Diplopoda, and Pauropoda. The core controversy is the position of Pauropoda; that is, whether it should be grouped with Symphyla or Diplopoda as a sister group. Two recent phylogenomic studies separately investigated transcriptomic data from 14 and 29 Myriapoda species covering all four groups along with outgroups, and proposed two different topologies of phylogenetic relationships. Methods Building on these studies, we extended the taxon sampling by investigating 39 myriapods and integrating the previously available data with three new transcriptomic datasets generated in this study. Our analyses present the phylogenetic relationships among the four major classes of Myriapoda with a more abundant taxon sampling and provide a new perspective to investigate the above-mentioned question, where visual genes’ identification were conducted. We compared the appearance pattern of genes, grouping them according to their classes and the visual pathways involved. Positive selection was detected for all identified visual genes between every pair of 39 myriapods, and 14 genes showed positive selection among 27 pairs. Results From the results of phylogenomic analyses, we propose that Symphyla is a sister group of Pauropoda. This stance has also received strong support from tree inference and topology tests.
format: application/pdf
format: text/html
creator: Jiajia Wang
creator: Yu Bai
creator: Haifeng Zhao
creator: Ruinan Mu
creator: Yan Dong
subject: Biodiversity
subject: Bioinformatics
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12691
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background There have been extensive debates on the interrelationships among the four major classes of Myriapoda—Chilopoda, Symphyla, Diplopoda, and Pauropoda. The core controversy is the position of Pauropoda; that is, whether it should be grouped with Symphyla or Diplopoda as a sister group. Two recent phylogenomic studies separately investigated transcriptomic data from 14 and 29 Myriapoda species covering all four groups along with outgroups, and proposed two different topologies of phylogenetic relationships. Methods Building on these studies, we extended the taxon sampling by investigating 39 myriapods and integrating the previously available data with three new transcriptomic datasets generated in this study. Our analyses present the phylogenetic relationships among the four major classes of Myriapoda with a more abundant taxon sampling and provide a new perspective to investigate the above-mentioned question, where visual genes’ identification were conducted. We compared the appearance pattern of genes, grouping them according to their classes and the visual pathways involved. Positive selection was detected for all identified visual genes between every pair of 39 myriapods, and 14 genes showed positive selection among 27 pairs. Results From the results of phylogenomic analyses, we propose that Symphyla is a sister group of Pauropoda. This stance has also received strong support from tree inference and topology tests.
bibliographic citation: Wang et al. (2021) Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective. PeerJ 9:e12691 https://doi.org/10.7717/peerj.12691
date submitted: 2021-09-02
date accepted: 2021-12-05
issued: 2021-12-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jiajia
author list: Agent
  family name: Bai
  given name: Yu
author list: Agent
  family name: Zhao
  given name: Haifeng
author list: Agent
  family name: Mu
  given name: Ruinan
author list: Agent
  family name: Dong
  given name: Yan
doi: 10.7717/peerj.12691
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-23
copyright: ©2021 Wang et al.
attribution name: Wang et al.

ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences
type: item
type: AcademicArticle
description: The massively parallel nature of next-generation sequencing technologies has contributed to the generation of massive sequence data in the last two decades. Deciphering the meaning of each generated sequence requires multiple analysis tools, at all stages of analysis, from the reads stage all the way up to the whole-genome level. Homology-based approaches based on related reference sequences are usually the preferred option for gene and transcript prediction in newly sequenced genomes, resulting in the popularity of a variety of BLAST and BLAST-based tools. For organelle genomes, a single-reference–based gene finding tool that uses grouping parameters for BLAST results has been implemented in the Genome Search Plotter (GSP). However, this tool does not accept multiple and user-customized reference sequences required for a broad homology search. Here, we present multiple Reference–based Gene Search and Plot (ReGSP), a simple and convenient web tool that accepts multiple reference sequences for homology-based gene search. The tool incorporates cPlot, a novel dot plot tool, for illustrating nucleotide sequence similarity between the query and the reference sequences. ReGSP has an easy-to-use web interface and is freely accessible at https://ds.mju.ac.kr/regsp.
format: application/pdf
format: text/html
creator: Girum Fitihamlak Ejigu
creator: Gangman Yi
creator: Jong Im Kim
creator: Jaehee Jung
subject: Bioinformatics
subject: Computational Biology
subject: Genetics
description: doi:10.7717/peerj.12707
publisher: PeerJ Inc.
rights: © 2021 Ejigu et al.
abstract: The massively parallel nature of next-generation sequencing technologies has contributed to the generation of massive sequence data in the last two decades. Deciphering the meaning of each generated sequence requires multiple analysis tools, at all stages of analysis, from the reads stage all the way up to the whole-genome level. Homology-based approaches based on related reference sequences are usually the preferred option for gene and transcript prediction in newly sequenced genomes, resulting in the popularity of a variety of BLAST and BLAST-based tools. For organelle genomes, a single-reference–based gene finding tool that uses grouping parameters for BLAST results has been implemented in the Genome Search Plotter (GSP). However, this tool does not accept multiple and user-customized reference sequences required for a broad homology search. Here, we present multiple Reference–based Gene Search and Plot (ReGSP), a simple and convenient web tool that accepts multiple reference sequences for homology-based gene search. The tool incorporates cPlot, a novel dot plot tool, for illustrating nucleotide sequence similarity between the query and the reference sequences. ReGSP has an easy-to-use web interface and is freely accessible at https://ds.mju.ac.kr/regsp.
bibliographic citation: Ejigu et al. (2021) ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences. PeerJ 9:e12707 https://doi.org/10.7717/peerj.12707
date submitted: 2021-10-07
date accepted: 2021-12-07
issued: 2021-12-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ejigu
  given name: Girum Fitihamlak
author list: Agent
  family name: Yi
  given name: Gangman
author list: Agent
  family name: Kim
  given name: Jong Im
author list: Agent
  family name: Jung
  given name: Jaehee
doi: 10.7717/peerj.12707
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-23
copyright: ©2021 Ejigu et al.
attribution name: Ejigu et al.

Identifying biomarkers for evaluating wound extent and age in the contused muscle of rats using microarray analysis: a pilot study
type: item
type: AcademicArticle
description: Wound age estimation is still one of the most important and significant challenges in forensic practice. The extent of wound damage greatly affects the accuracy and reliability of wound age estimation, so it is important to find effective biomarkers to help diagnose wound degree and wound age. In the present study, the gene expression profiles of both mild and severe injuries in 33 rats were assayed at 0, 1, 3, 24, 48, and 168 hours using the Affymetrix microarray system to provide biomarkers for the evaluation of wound age and the extent of the wound. After obtaining thousands of differentially expressed genes, a principal component analysis, the least absolute shrinkage and selection operator, and a time-series analysis were used to select the most predictive prognostic genes. Finally, 15 genes were screened for evaluating the extent of wound damage, and the top 60 genes were also screened for wound age estimation in mild and severe injury. Selected indicators showed good diagnostic performance for identifying the extent of the wound and wound age in a Fisher discriminant analysis. A function analysis showed that the candidate genes were mainly related to cell proliferation and the inflammatory response, primarily IL-17 and the Hematopoietic cell lineage signalling pathway. The results revealed that these genes play an essential role in wound-healing and yield helpful and valuable potential biomarkers for further targeted studies.
format: application/pdf
format: text/html
creator: Na Li
creator: Chun Li
creator: Dan Li
creator: Li-hong Dang
creator: Kang Ren
creator: Qiu-xiang Du
creator: Jie Cao
creator: Qian-qian Jin
creator: Ying-yuan Wang
creator: Ru-feng Bai
creator: Jun-hong Sun
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
description: doi:10.7717/peerj.12709
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Wound age estimation is still one of the most important and significant challenges in forensic practice. The extent of wound damage greatly affects the accuracy and reliability of wound age estimation, so it is important to find effective biomarkers to help diagnose wound degree and wound age. In the present study, the gene expression profiles of both mild and severe injuries in 33 rats were assayed at 0, 1, 3, 24, 48, and 168 hours using the Affymetrix microarray system to provide biomarkers for the evaluation of wound age and the extent of the wound. After obtaining thousands of differentially expressed genes, a principal component analysis, the least absolute shrinkage and selection operator, and a time-series analysis were used to select the most predictive prognostic genes. Finally, 15 genes were screened for evaluating the extent of wound damage, and the top 60 genes were also screened for wound age estimation in mild and severe injury. Selected indicators showed good diagnostic performance for identifying the extent of the wound and wound age in a Fisher discriminant analysis. A function analysis showed that the candidate genes were mainly related to cell proliferation and the inflammatory response, primarily IL-17 and the Hematopoietic cell lineage signalling pathway. The results revealed that these genes play an essential role in wound-healing and yield helpful and valuable potential biomarkers for further targeted studies.
bibliographic citation: Li et al. (2021) Identifying biomarkers for evaluating wound extent and age in the contused muscle of rats using microarray analysis: a pilot study. PeerJ 9:e12709 https://doi.org/10.7717/peerj.12709
date submitted: 2021-09-06
date accepted: 2021-12-08
issued: 2021-12-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Li
  given name: Chun
author list: Agent
  family name: Li
  given name: Dan
author list: Agent
  family name: Dang
  given name: Li-hong
author list: Agent
  family name: Ren
  given name: Kang
author list: Agent
  family name: Du
  given name: Qiu-xiang
author list: Agent
  family name: Cao
  given name: Jie
author list: Agent
  family name: Jin
  given name: Qian-qian
author list: Agent
  family name: Wang
  given name: Ying-yuan
author list: Agent
  family name: Bai
  given name: Ru-feng
author list: Agent
  family name: Sun
  given name: Jun-hong
doi: 10.7717/peerj.12709
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-23
copyright: ©2021 Li et al.
attribution name: Li et al.

Unique spicules may confound species differentiation: taxonomy and biogeography of Melonanchora Carter, 1874 and two new related genera (Myxillidae: Poecilosclerida) from the Okhotsk Sea
type: item
type: AcademicArticle
description: Sponges are amongst the most difficult benthic taxa to properly identify, which has led to a prevalence of cryptic species in several sponge genera, especially in those with simple skeletons. This is particularly true for sponges living in remote or hardly accessible environments, such as the deep-sea, as the inaccessibility of their habitat and the lack of accurate descriptions usually leads to misclassifications. However, species can also remain hidden even when they belong to genera that have particularly characteristic features. In these cases, researchers inevitably pay attention to these peculiar features, sometimes disregarding small differences in the other “typical” spicules. The genus Melonanchora Carter, 1874, is among those well suited for a revision, as their representatives possess a unique type of spicule (spherancorae). After a thorough review of the material available for this genus from several institutions, four new species of Melonanchora, M. tumultuosa sp. nov., M. insulsa sp. nov., M. intermedia sp. nov. and M. maeli sp. nov. are formally described from different localities across the Atlanto-Mediterranean region. Additionally, all Melonanchora from the Okhotsk Sea and nearby areas are reassigned to other genera; Melonanchora kobjakovae is transferred to Myxilla (Burtonanchora) while two new genera, Hanstoreia gen. nov. and Arhythmata gen. nov. are created to accommodate Melonanchora globogilva and Melonanchora tetradedritifera, respectively. Hanstoreia gen. nov. is closest to Melonanchora, whereas Arhythmata gen. nov., is closer to Stelodoryx, which is most likely polyphyletic and in need of revision.
format: application/pdf
format: text/html
creator: Andreu Santín
creator: María-Jesús Uriz
creator: Javier Cristobo
creator: Joana R. Xavier
creator: Pilar Ríos
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12515
publisher: PeerJ Inc.
rights: © 2021 Santín et al.
abstract: Sponges are amongst the most difficult benthic taxa to properly identify, which has led to a prevalence of cryptic species in several sponge genera, especially in those with simple skeletons. This is particularly true for sponges living in remote or hardly accessible environments, such as the deep-sea, as the inaccessibility of their habitat and the lack of accurate descriptions usually leads to misclassifications. However, species can also remain hidden even when they belong to genera that have particularly characteristic features. In these cases, researchers inevitably pay attention to these peculiar features, sometimes disregarding small differences in the other “typical” spicules. The genus Melonanchora Carter, 1874, is among those well suited for a revision, as their representatives possess a unique type of spicule (spherancorae). After a thorough review of the material available for this genus from several institutions, four new species of Melonanchora, M. tumultuosa sp. nov., M. insulsa sp. nov., M. intermedia sp. nov. and M. maeli sp. nov. are formally described from different localities across the Atlanto-Mediterranean region. Additionally, all Melonanchora from the Okhotsk Sea and nearby areas are reassigned to other genera; Melonanchora kobjakovae is transferred to Myxilla (Burtonanchora) while two new genera, Hanstoreia gen. nov. and Arhythmata gen. nov. are created to accommodate Melonanchora globogilva and Melonanchora tetradedritifera, respectively. Hanstoreia gen. nov. is closest to Melonanchora, whereas Arhythmata gen. nov., is closer to Stelodoryx, which is most likely polyphyletic and in need of revision.
bibliographic citation: Santín et al. (2021) Unique spicules may confound species differentiation: taxonomy and biogeography of Melonanchora Carter, 1874 and two new related genera (Myxillidae: Poecilosclerida) from the Okhotsk Sea. PeerJ 9:e12515 https://doi.org/10.7717/peerj.12515
date submitted: 2021-08-05
date accepted: 2021-10-27
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santín
  given name: Andreu
author list: Agent
  family name: Uriz
  given name: María-Jesús
author list: Agent
  family name: Cristobo
  given name: Javier
author list: Agent
  family name: Xavier
  given name: Joana R.
author list: Agent
  family name: Ríos
  given name: Pilar
doi: 10.7717/peerj.12515
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: © 2021 Santín et al.
attribution name: Santín et al.

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