PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Development of droplet digital Polymerase Chain Reaction assays for the detection of long-finned (Anguilla dieffenbachii) and short-finned (Anguilla australis) eels in environmental samples
items: Evaluation of the molluscicidal activities of arylpyrrole on Oncomelania hupensis, the intermediate host of Schistosoma japonicum
items: Effect of control measures on the pattern of COVID-19 Epidemics in Japan
items: Heterogeneity in conservation of multifunctional partner enzymes with meiotic importance, CDK2 kinase and BRCA1 ubiquitin ligase
items: The modeled distribution of corals and sponges surrounding the Salas y Gómez and Nazca ridges with implications for high seas conservation
items: New free-living nematode species and records (Chromadorea: Plectida and Desmodorida) from the edge and axis of Kermadec Trench, Southwest Pacific Ocean
items: Quantitative trait locus mapping analysis of multiple traits when using genotype data with potential errors
items: Bilateral back squat strength is increased during a 3-week undulating resistance training program with and without variable resistance in DIII collegiate football players
items: Novel real-time PCR based assays for differentiating fall armyworm strains using four single nucleotide polymorphisms
items: Efficacy of 4% articaine vs 2% lidocaine in mandibular and maxillary block and infiltration anaesthesia in patients with irreversible pulpitis: a systematic review and meta-analysis

Development of droplet digital Polymerase Chain Reaction assays for the detection of long-finned (Anguilla dieffenbachii) and short-finned (Anguilla australis) eels in environmental samples
type: item
type: AcademicArticle
description: Freshwater eels are ecologically, and culturally important worldwide. The New Zealand long-finned eel (Anguilla dieffenbachii) and short-finned eel (Anguilla australis) are apex predators, playing an important role in ecosystem functioning of rivers and lakes. Recently, there has been a national decline in their populations due to habitat destruction and commercial harvest. The emergence of targeted environmental DNA detection methodologies provides an opportunity to enhance information about their past and present distributions. In this study we successfully developed species-specific droplet digital Polymerase Chain Reaction (ddPCR) assays to detect A. dieffenbachii and A. australis DNA in water and sediment samples. Assays utilized primers and probes designed for regions of the mitochondrial cytochrome b and 16S ribosomal RNA genes in A. dieffenbachii and A. australis, respectively. River water samples (n = 27) were analyzed using metabarcoding of fish taxa and were compared with the ddPCR assays. The presence of A. dieffenbachii and A. australis DNA was detected in a greater number of water samples using ddPCR in comparison to metabarcoding. There was a strong and positive correlation between gene copies (ddPCR analyses) and relative eel sequence reads (metabarcoding analyses) when compared to eel biomass. These ddPCR assays provide a new method for assessing spatial distributions of A. dieffenbachii and A. australis in a range of environments and sample types.
format: application/pdf
format: text/html
creator: Georgia Thomson-Laing
creator: Russleigh Parai
creator: Laura T. Kelly
creator: Xavier Pochon
creator: Rewi Newnham
creator: Marcus J. Vandergoes
creator: Jamie D. Howarth
creator: Susanna A. Wood
subject: Aquaculture, Fisheries and Fish Science
subject: Ecosystem Science
subject: Molecular Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12157
publisher: PeerJ Inc.
rights: © 2021 Thomson-Laing et al.
abstract: Freshwater eels are ecologically, and culturally important worldwide. The New Zealand long-finned eel (Anguilla dieffenbachii) and short-finned eel (Anguilla australis) are apex predators, playing an important role in ecosystem functioning of rivers and lakes. Recently, there has been a national decline in their populations due to habitat destruction and commercial harvest. The emergence of targeted environmental DNA detection methodologies provides an opportunity to enhance information about their past and present distributions. In this study we successfully developed species-specific droplet digital Polymerase Chain Reaction (ddPCR) assays to detect A. dieffenbachii and A. australis DNA in water and sediment samples. Assays utilized primers and probes designed for regions of the mitochondrial cytochrome b and 16S ribosomal RNA genes in A. dieffenbachii and A. australis, respectively. River water samples (n = 27) were analyzed using metabarcoding of fish taxa and were compared with the ddPCR assays. The presence of A. dieffenbachii and A. australis DNA was detected in a greater number of water samples using ddPCR in comparison to metabarcoding. There was a strong and positive correlation between gene copies (ddPCR analyses) and relative eel sequence reads (metabarcoding analyses) when compared to eel biomass. These ddPCR assays provide a new method for assessing spatial distributions of A. dieffenbachii and A. australis in a range of environments and sample types.
bibliographic citation: Thomson-Laing et al. (2021) Development of droplet digital Polymerase Chain Reaction assays for the detection of long-finned (Anguilla dieffenbachii) and short-finned (Anguilla australis) eels in environmental samples. PeerJ 9:e12157 https://doi.org/10.7717/peerj.12157
date submitted: 2021-05-19
date accepted: 2021-08-24
issued: 2021-09-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thomson-Laing
  given name: Georgia
author list: Agent
  family name: Parai
  given name: Russleigh
author list: Agent
  family name: Kelly
  given name: Laura T.
author list: Agent
  family name: Pochon
  given name: Xavier
author list: Agent
  family name: Newnham
  given name: Rewi
author list: Agent
  family name: Vandergoes
  given name: Marcus J.
author list: Agent
  family name: Howarth
  given name: Jamie D.
author list: Agent
  family name: Wood
  given name: Susanna A.
doi: 10.7717/peerj.12157
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-27
copyright: ©2021 Thomson-Laing et al.
attribution name: Thomson-Laing et al.

Evaluation of the molluscicidal activities of arylpyrrole on Oncomelania hupensis, the intermediate host of Schistosoma japonicum
type: item
type: AcademicArticle
description: The snail Oncomelania hupensis is the only intermediate host of the highly invasive parasite Schistosoma japonicum. Molluscicide is often used to curb transmission of S. japonicum. Niclosamide, the only World Health Organization (WHO) recognized molluscicide, presents major drawbacks, including high cost and toxicity towards aquatic animals. In the present study, a number of aryl pyrrole derivatives (ADs) were synthesized to serve as potential molluscicides and were tested on O. hupensis. To uncover the underlying mechanisms, adenosine triphosphate (ATP) and adenosine diphosphate (ADP) levels were assessed in the soft body of ADs-exposed O. hupensis, using high performance liquid chromatography (HPLC). The effect of C6 on key points of energy metabolism (the activities of complexes I, III, IV and the membrane potential) was determined. We demonstrated that the Compound 6 (C6, 4-bromo-1-(bromomethyl)-2-(4-chlorophenyl)-5-(trifluoromethyl)-1H-pyrrole-3-carbonitrile) exerted the strongest molluscicidal activity against adult O. hupensis at LC50 of 0.27, 0.19, and 0.13 mg/L for 24, 48, and 72 h respectively. Moreover, we found that the bromide on the pyrrole ring of C6 was essential for molluscicidal activity. Furthermore, the ATP content reduced from 194.46 to 139.75 μg/g after exposure to 1/2 LC50, and reduced to 93.06 μg/g after exposure to LC50. ADP, on the other hand, remained the same level before and after C6 exposure. We found that C6, at 1/2 LC50, reduced the membrane potential of O. hupensis, while no significant changes were observed in the activities of complexes I, III, and IV. C6 was identified with excellent activities on O. hupensis. The obtained structure−activity relationship and action mechanism study results should be useful for further compound design and development.
format: application/pdf
format: text/html
creator: Yuntian Xing
creator: Jiakai Yao
creator: Guoli Qu
creator: Jianrong Dai
creator: Bainian Feng
subject: Biochemistry
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.12209
publisher: PeerJ Inc.
rights: © 2021 Xing et al.
abstract: The snail Oncomelania hupensis is the only intermediate host of the highly invasive parasite Schistosoma japonicum. Molluscicide is often used to curb transmission of S. japonicum. Niclosamide, the only World Health Organization (WHO) recognized molluscicide, presents major drawbacks, including high cost and toxicity towards aquatic animals. In the present study, a number of aryl pyrrole derivatives (ADs) were synthesized to serve as potential molluscicides and were tested on O. hupensis. To uncover the underlying mechanisms, adenosine triphosphate (ATP) and adenosine diphosphate (ADP) levels were assessed in the soft body of ADs-exposed O. hupensis, using high performance liquid chromatography (HPLC). The effect of C6 on key points of energy metabolism (the activities of complexes I, III, IV and the membrane potential) was determined. We demonstrated that the Compound 6 (C6, 4-bromo-1-(bromomethyl)-2-(4-chlorophenyl)-5-(trifluoromethyl)-1H-pyrrole-3-carbonitrile) exerted the strongest molluscicidal activity against adult O. hupensis at LC50 of 0.27, 0.19, and 0.13 mg/L for 24, 48, and 72 h respectively. Moreover, we found that the bromide on the pyrrole ring of C6 was essential for molluscicidal activity. Furthermore, the ATP content reduced from 194.46 to 139.75 μg/g after exposure to 1/2 LC50, and reduced to 93.06 μg/g after exposure to LC50. ADP, on the other hand, remained the same level before and after C6 exposure. We found that C6, at 1/2 LC50, reduced the membrane potential of O. hupensis, while no significant changes were observed in the activities of complexes I, III, and IV. C6 was identified with excellent activities on O. hupensis. The obtained structure−activity relationship and action mechanism study results should be useful for further compound design and development.
bibliographic citation: Xing et al. (2021) Evaluation of the molluscicidal activities of arylpyrrole on Oncomelania hupensis, the intermediate host of Schistosoma japonicum. PeerJ 9:e12209 https://doi.org/10.7717/peerj.12209
date submitted: 2021-06-24
date accepted: 2021-09-05
issued: 2021-09-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xing
  given name: Yuntian
author list: Agent
  family name: Yao
  given name: Jiakai
author list: Agent
  family name: Qu
  given name: Guoli
author list: Agent
  family name: Dai
  given name: Jianrong
author list: Agent
  family name: Feng
  given name: Bainian
doi: 10.7717/peerj.12209
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-27
copyright: © 2021 Xing et al.
attribution name: Xing et al.

Effect of control measures on the pattern of COVID-19 Epidemics in Japan
type: item
type: AcademicArticle
description: Background COVID-19 has spread worldwide since its emergence in 2019. In contrast to many other countries with epidemics, Japan differed in that it avoided lockdowns and instead asked people for self-control. A travel campaign was conducted with a sizable budget, but the number of PCR tests was severely limited. These choices may have influenced the course of the epidemic. Methods The increase or decrease in the classes of SARS-CoV-2 variants was estimated by analyzing the published sequences with an objective multivariate analysis. This approach observes the samples in multiple directions, digesting complex differences into simpler forms. The results were compared over time with the number of confirmed cases, PCR tests, and overseas visitors. The kinetics of infection were analyzed using the logarithmic growth rate. Results The declared states of emergency failed to alter the movement of the growth rate. Three epidemic peaks were caused by domestically mutated variants. In other countries, there are few cases in which multiple variants have peaked. However, due to the relaxation of immigration restrictions, several infective variants have been imported from abroad and are currently competing for expansion, creating the fourth peak. By April 2021, these foreign variants exceeded 80%. The chaotic situation in Japan will continue for some time, in part because no effort has been made to identify asymptomatic carriers, and details of the vaccination program are undecided.
format: application/pdf
format: text/html
creator: Tomokazu Konishi
subject: Bioinformatics
subject: Virology
subject: Epidemiology
subject: Infectious Diseases
subject: Data Science
description: doi:10.7717/peerj.12215
publisher: PeerJ Inc.
rights: © 2021 Konishi
abstract: Background COVID-19 has spread worldwide since its emergence in 2019. In contrast to many other countries with epidemics, Japan differed in that it avoided lockdowns and instead asked people for self-control. A travel campaign was conducted with a sizable budget, but the number of PCR tests was severely limited. These choices may have influenced the course of the epidemic. Methods The increase or decrease in the classes of SARS-CoV-2 variants was estimated by analyzing the published sequences with an objective multivariate analysis. This approach observes the samples in multiple directions, digesting complex differences into simpler forms. The results were compared over time with the number of confirmed cases, PCR tests, and overseas visitors. The kinetics of infection were analyzed using the logarithmic growth rate. Results The declared states of emergency failed to alter the movement of the growth rate. Three epidemic peaks were caused by domestically mutated variants. In other countries, there are few cases in which multiple variants have peaked. However, due to the relaxation of immigration restrictions, several infective variants have been imported from abroad and are currently competing for expansion, creating the fourth peak. By April 2021, these foreign variants exceeded 80%. The chaotic situation in Japan will continue for some time, in part because no effort has been made to identify asymptomatic carriers, and details of the vaccination program are undecided.
bibliographic citation: Konishi (2021) Effect of control measures on the pattern of COVID-19 Epidemics in Japan. PeerJ 9:e12215 https://doi.org/10.7717/peerj.12215
date submitted: 2021-03-12
date accepted: 2021-09-06
issued: 2021-09-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Konishi
  given name: Tomokazu
doi: 10.7717/peerj.12215
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-27
copyright: © 2021 Konishi
attribution name: Konishi

Heterogeneity in conservation of multifunctional partner enzymes with meiotic importance, CDK2 kinase and BRCA1 ubiquitin ligase
type: item
type: AcademicArticle
description: The evolution of proteins can be accompanied by changes not only to their amino acid sequences, but also their structural and spatial molecular organization. Comparison of the protein conservation within different taxonomic groups (multifunctional, or highly specific) allows to clarify their specificity and the direction of evolution. Two multifunctional enzymes, cyclin-dependent kinase 2 (CDK2) and BRCA1 ubiquitin ligase, that are partners in some mitotic and meiotic processes were investigated in the present work. Two research methods, bioinformatics and immunocytochemical, were combined to examine the conservation levels of the two enzymes. It has been established that CDK2 is a highly conserved protein in different taxonomic lineages of the eukaryotic tree. Immunocytochemically, a conserved CDK2 pattern was revealed in the meiotic autosomes of five rodent species and partially in domestic turkey and clawed frog. Nevertheless, variable CDK2 distribution was detected at the unsynapsed segments of the rodent X chromosomes. BRCA1 was shown to be highly conserved only within certain mammalian taxa. It was also noted that in those rodent nuclei, where BRCA1 specifically binds to antigens, asynaptic regions of sex chromosomes were positive. BRCA1 staining was not always accompanied by specific binding, and a high nonspecificity in the nucleoplasm was observed. Thus, the studies revealed different conservation of the two enzymes at the level of protein structure as well as at the level of chromosome behavior. This suggests variable rates of evolution due to both size and configuration of the protein molecules and their multifunctionality.
format: application/pdf
format: text/html
creator: Sergey Matveevsky
creator: Tatiana Grishaeva
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.12231
publisher: PeerJ Inc.
rights: © 2021 Matveevsky and Grishaeva
abstract: The evolution of proteins can be accompanied by changes not only to their amino acid sequences, but also their structural and spatial molecular organization. Comparison of the protein conservation within different taxonomic groups (multifunctional, or highly specific) allows to clarify their specificity and the direction of evolution. Two multifunctional enzymes, cyclin-dependent kinase 2 (CDK2) and BRCA1 ubiquitin ligase, that are partners in some mitotic and meiotic processes were investigated in the present work. Two research methods, bioinformatics and immunocytochemical, were combined to examine the conservation levels of the two enzymes. It has been established that CDK2 is a highly conserved protein in different taxonomic lineages of the eukaryotic tree. Immunocytochemically, a conserved CDK2 pattern was revealed in the meiotic autosomes of five rodent species and partially in domestic turkey and clawed frog. Nevertheless, variable CDK2 distribution was detected at the unsynapsed segments of the rodent X chromosomes. BRCA1 was shown to be highly conserved only within certain mammalian taxa. It was also noted that in those rodent nuclei, where BRCA1 specifically binds to antigens, asynaptic regions of sex chromosomes were positive. BRCA1 staining was not always accompanied by specific binding, and a high nonspecificity in the nucleoplasm was observed. Thus, the studies revealed different conservation of the two enzymes at the level of protein structure as well as at the level of chromosome behavior. This suggests variable rates of evolution due to both size and configuration of the protein molecules and their multifunctionality.
bibliographic citation: Matveevsky et al. (2021) Heterogeneity in conservation of multifunctional partner enzymes with meiotic importance, CDK2 kinase and BRCA1 ubiquitin ligase. PeerJ 9:e12231 https://doi.org/10.7717/peerj.12231
date submitted: 2021-05-07
date accepted: 2021-09-09
issued: 2021-09-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matveevsky
  given name: Sergey
author list: Agent
  family name: Grishaeva
  given name: Tatiana
doi: 10.7717/peerj.12231
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-27
copyright: ©2021 Matveevsky and Grishaeva
attribution name: Matveevsky and Grishaeva

The modeled distribution of corals and sponges surrounding the Salas y Gómez and Nazca ridges with implications for high seas conservation
type: item
type: AcademicArticle
description: The Salas y Gómez and Nazca ridges are two adjacent seamount chains off the west coast of South America that collectively contain more than 110 seamounts. The ridges support an exceptionally rich diversity of benthic and pelagic communities, with the highest level of endemism found in any marine environment. Despite some historical fishing in the region, the seamounts are relatively pristine and represent an excellent conservation opportunity to protect a global biodiversity hotspot before it is degraded. One obstacle to effective spatial management of the ridges is the scarcity of direct observations in deeper waters throughout the region and an accompanying understanding of the distribution of key taxa. Species distribution models are increasingly used tools to quantify the distributions of species in data-poor environments. Here, we focused on modeling the distribution of demosponges, glass sponges, and stony corals, three foundation taxa that support large assemblages of associated fauna through the creation of complex habitat structures. Models were constructed at a 1 km2 resolution using presence and pseudoabsence data, dissolved oxygen, nitrate, phosphate, silicate, aragonite saturation state, and several measures of seafloor topography. Highly suitable habitat for each taxa was predicted to occur throughout the Salas y Gómez and Nazca ridges, with the most suitable habitat occurring in small patches on large terrain features such as seamounts, guyots, ridges, and escarpments. Determining the spatial distribution of these three taxa is a critical first step towards supporting the improved spatial management of the region. While the total area of highly suitable habitat was small, our results showed that nearly all of the seamounts in this region provide suitable habitats for deep-water corals and sponges and should therefore be protected from exploitation using the best available conservation measures.
format: application/pdf
format: text/html
creator: Samuel Georgian
creator: Lance Morgan
creator: Daniel Wagner
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.11972
publisher: PeerJ Inc.
rights: © 2021 Georgian et al.
abstract: The Salas y Gómez and Nazca ridges are two adjacent seamount chains off the west coast of South America that collectively contain more than 110 seamounts. The ridges support an exceptionally rich diversity of benthic and pelagic communities, with the highest level of endemism found in any marine environment. Despite some historical fishing in the region, the seamounts are relatively pristine and represent an excellent conservation opportunity to protect a global biodiversity hotspot before it is degraded. One obstacle to effective spatial management of the ridges is the scarcity of direct observations in deeper waters throughout the region and an accompanying understanding of the distribution of key taxa. Species distribution models are increasingly used tools to quantify the distributions of species in data-poor environments. Here, we focused on modeling the distribution of demosponges, glass sponges, and stony corals, three foundation taxa that support large assemblages of associated fauna through the creation of complex habitat structures. Models were constructed at a 1 km2 resolution using presence and pseudoabsence data, dissolved oxygen, nitrate, phosphate, silicate, aragonite saturation state, and several measures of seafloor topography. Highly suitable habitat for each taxa was predicted to occur throughout the Salas y Gómez and Nazca ridges, with the most suitable habitat occurring in small patches on large terrain features such as seamounts, guyots, ridges, and escarpments. Determining the spatial distribution of these three taxa is a critical first step towards supporting the improved spatial management of the region. While the total area of highly suitable habitat was small, our results showed that nearly all of the seamounts in this region provide suitable habitats for deep-water corals and sponges and should therefore be protected from exploitation using the best available conservation measures.
bibliographic citation: Georgian et al. (2021) The modeled distribution of corals and sponges surrounding the Salas y Gómez and Nazca ridges with implications for high seas conservation. PeerJ 9:e11972 https://doi.org/10.7717/peerj.11972
date submitted: 2021-02-23
date accepted: 2021-07-23
issued: 2021-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Georgian
  given name: Samuel
author list: Agent
  family name: Morgan
  given name: Lance
author list: Agent
  family name: Wagner
  given name: Daniel
doi: 10.7717/peerj.11972
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-24
copyright: © 2021 Georgian et al.
attribution name: Georgian et al.

New free-living nematode species and records (Chromadorea: Plectida and Desmodorida) from the edge and axis of Kermadec Trench, Southwest Pacific Ocean
type: item
type: AcademicArticle
description: One new nematode species is described and two new species records are provided from the edge (6,080 m depth) and axis (7,132 m) of Kermadec Trench, Southwest Pacific. Leptolaimus hadalis sp. nov. is characterised by medium body 587–741 μm long, labial region not offset from body contour, inconspicuous labial sensilla, amphid located 12–19 μm from anterior end, female without supplements, male with four tubular precloacal supplements (alveolar supplements absent), tubular supplements almost straight with dentate tip, arcuate spicules and weakly cuticularized dorsal gubernacular apophyses strongly bent distally. In a previously published ecological survey of Kermadec Trench, L. hadalis sp. nov. was the most abundant species in a core obtained at 8,079 m water depth and third most abundant species in a core obtained at 7,132 m, while only one individual was found at 6,096 m depth, and none at 9,175 m depth (Leduc & Rowden, 2018). Alaimella aff. cincta and Desmodora aff. pilosa are recorded for the first time from the Southwest Pacific region. Prior to the present study, Alaimella had only been recorded from coastal locations and from the Weddell sea to a depth of 2,000 m. The record of Desmodora aff. pilosa at 6,080 m depth is the deepest record of a Desmodora species to date, although unidentified Desmodora specimens have been found as deep as 6,300 m in the South Sandwich Trench. The morphology of the Kermadec Trench Alaimella aff. cincta and Desmodora aff. pilosa specimens bear a strong resemblance to their respective type populations from the Northern Hemisphere, but further morphological and molecular data are required to ascertain whether they in fact represent distinct species.
format: application/pdf
format: text/html
creator: Daniel Leduc
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12037
publisher: PeerJ Inc.
rights: © 2021 Leduc
abstract: One new nematode species is described and two new species records are provided from the edge (6,080 m depth) and axis (7,132 m) of Kermadec Trench, Southwest Pacific. Leptolaimus hadalis sp. nov. is characterised by medium body 587–741 μm long, labial region not offset from body contour, inconspicuous labial sensilla, amphid located 12–19 μm from anterior end, female without supplements, male with four tubular precloacal supplements (alveolar supplements absent), tubular supplements almost straight with dentate tip, arcuate spicules and weakly cuticularized dorsal gubernacular apophyses strongly bent distally. In a previously published ecological survey of Kermadec Trench, L. hadalis sp. nov. was the most abundant species in a core obtained at 8,079 m water depth and third most abundant species in a core obtained at 7,132 m, while only one individual was found at 6,096 m depth, and none at 9,175 m depth (Leduc & Rowden, 2018). Alaimella aff. cincta and Desmodora aff. pilosa are recorded for the first time from the Southwest Pacific region. Prior to the present study, Alaimella had only been recorded from coastal locations and from the Weddell sea to a depth of 2,000 m. The record of Desmodora aff. pilosa at 6,080 m depth is the deepest record of a Desmodora species to date, although unidentified Desmodora specimens have been found as deep as 6,300 m in the South Sandwich Trench. The morphology of the Kermadec Trench Alaimella aff. cincta and Desmodora aff. pilosa specimens bear a strong resemblance to their respective type populations from the Northern Hemisphere, but further morphological and molecular data are required to ascertain whether they in fact represent distinct species.
bibliographic citation: Leduc (2021) New free-living nematode species and records (Chromadorea: Plectida and Desmodorida) from the edge and axis of Kermadec Trench, Southwest Pacific Ocean. PeerJ 9:e12037 https://doi.org/10.7717/peerj.12037
date submitted: 2021-06-28
date accepted: 2021-08-02
issued: 2021-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leduc
  given name: Daniel
doi: 10.7717/peerj.12037
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-24
copyright: © 2021 Leduc
attribution name: Leduc

Quantitative trait locus mapping analysis of multiple traits when using genotype data with potential errors
type: item
type: AcademicArticle
description: Background Quantitative trait locus (QTL) analysis aims to locate and estimate the effects of the genes influencing quantitative traits and infer the relationship between gene variants and changes in phenotypic characteristics using statistical methods. Some methods have been developed to map QTLs of multiple traits in the case of no genotype error in a given dataset. However, practical genetic data that people use may contain some potential errors because of the limitations of biotechnology. Common genetic data correction methods can only reduce errors, but cannot calculate the degree of error. In this paper, we propose a QTL mapping strategy for multiple traits in the presence of genotype errors. Methods The additive effect, dominant effect, recombination rate, error rate, and other parameters of QTLs can be simultaneously obtained using this new method in the framework of multiple-interval mapping. Results Our simulation results show that the accuracy of parameter estimation can be improved by considering the errors of marker genotypes during the analysis of genetic data. Real data analysis also shows that the new method proposed in this paper can map the QTLs of multiple traits more accurately.
format: application/pdf
format: text/html
creator: Liang Tong
creator: Ying Zhou
creator: Yixing Guo
creator: Hui Ding
creator: Donghai Ji
subject: Bioinformatics
subject: Genetics
subject: Statistics
description: doi:10.7717/peerj.12187
publisher: PeerJ Inc.
rights: © 2021 Tong et al.
abstract: Background Quantitative trait locus (QTL) analysis aims to locate and estimate the effects of the genes influencing quantitative traits and infer the relationship between gene variants and changes in phenotypic characteristics using statistical methods. Some methods have been developed to map QTLs of multiple traits in the case of no genotype error in a given dataset. However, practical genetic data that people use may contain some potential errors because of the limitations of biotechnology. Common genetic data correction methods can only reduce errors, but cannot calculate the degree of error. In this paper, we propose a QTL mapping strategy for multiple traits in the presence of genotype errors. Methods The additive effect, dominant effect, recombination rate, error rate, and other parameters of QTLs can be simultaneously obtained using this new method in the framework of multiple-interval mapping. Results Our simulation results show that the accuracy of parameter estimation can be improved by considering the errors of marker genotypes during the analysis of genetic data. Real data analysis also shows that the new method proposed in this paper can map the QTLs of multiple traits more accurately.
bibliographic citation: Tong et al. (2021) Quantitative trait locus mapping analysis of multiple traits when using genotype data with potential errors. PeerJ 9:e12187 https://doi.org/10.7717/peerj.12187
date submitted: 2021-06-10
date accepted: 2021-08-30
issued: 2021-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tong
  given name: Liang
author list: Agent
  family name: Zhou
  given name: Ying
author list: Agent
  family name: Guo
  given name: Yixing
author list: Agent
  family name: Ding
  given name: Hui
author list: Agent
  family name: Ji
  given name: Donghai
doi: 10.7717/peerj.12187
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-24
copyright: © 2021 Tong et al.
attribution name: Tong et al.

Bilateral back squat strength is increased during a 3-week undulating resistance training program with and without variable resistance in DIII collegiate football players
type: item
type: AcademicArticle
description: Background Optimizing training adaptations is of the utmost importance for the strength and conditioning professional. The pre-season of any sport is particularly important to ensure preparedness of the athletes. In DIII Collegiate Football pre-season consists of approximately 3 weeks. The abbreviated time of the pre-season increases the importance of optimizing training using safe methods, including alternative loading strategies. The purpose of the current study was to determine if a 3-week variable resistance training VRT during an undulating (UL) resistance training program elicited a greater increase in back squat strength compared to traditional loading methods. Methods and Materials Forty DIII Football players (age range: 18–25 years) participated in a 3-week UL bilateral back squat (BBS) program. Both groups performed the BBS 3 times per week with a minimum of 24 hours between exercise sessions. The control group (C) (n = 20) (height = 182.3 + 5.1 cm, body mass: pre = 102.8 ± 17.7 kg, post = 104.1 ± 17.8 kg) used traditional loading methods (i.e., Olympic weights only) and the experimental group (E) (n = 20) (height = 180.7 ± 8.0 cm, body mass: pre = 100.3 ± 27.1 kg, post = 101.0 ± 27.7 kg) used traditional loading methods and variable resistance (i.e., resistance bands). The variable resistance accounted for approximately 20% of the total resistance while 80% of the resistance was supplied by traditional loading methods. Results When all data was pooled, subjects had a significant increase (p < 0.05) in 1-RM BBS from pre (154.2 + 26.1 kg) to post (166.8 + 26.2 kg), with a percent increase of 8.13% at the completion of the 3-week training program. There was no significant difference (p > 0.05) between the C and E groups for muscular strength, muscular power, or vertical jump. Volume-loads were not significantly (p > 0.05) different between groups for any of the weeks (C: Week 1 = 858.1 + 101.3, Week 2 = 588.6 + 69.2, Week 3 = 332.5 + 38.9, Total = 1179.2 + 2…
format: application/pdf
format: text/html
creator: Jason Sawyer
creator: Paul Higgins
creator: Paul A. Cacolice
creator: Troy Doming
subject: Cardiology
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.12189
publisher: PeerJ Inc.
rights: © 2021 Sawyer et al.
abstract: Background Optimizing training adaptations is of the utmost importance for the strength and conditioning professional. The pre-season of any sport is particularly important to ensure preparedness of the athletes. In DIII Collegiate Football pre-season consists of approximately 3 weeks. The abbreviated time of the pre-season increases the importance of optimizing training using safe methods, including alternative loading strategies. The purpose of the current study was to determine if a 3-week variable resistance training VRT during an undulating (UL) resistance training program elicited a greater increase in back squat strength compared to traditional loading methods. Methods and Materials Forty DIII Football players (age range: 18–25 years) participated in a 3-week UL bilateral back squat (BBS) program. Both groups performed the BBS 3 times per week with a minimum of 24 hours between exercise sessions. The control group (C) (n = 20) (height = 182.3 + 5.1 cm, body mass: pre = 102.8 ± 17.7 kg, post = 104.1 ± 17.8 kg) used traditional loading methods (i.e., Olympic weights only) and the experimental group (E) (n = 20) (height = 180.7 ± 8.0 cm, body mass: pre = 100.3 ± 27.1 kg, post = 101.0 ± 27.7 kg) used traditional loading methods and variable resistance (i.e., resistance bands). The variable resistance accounted for approximately 20% of the total resistance while 80% of the resistance was supplied by traditional loading methods. Results When all data was pooled, subjects had a significant increase (p < 0.05) in 1-RM BBS from pre (154.2 + 26.1 kg) to post (166.8 + 26.2 kg), with a percent increase of 8.13% at the completion of the 3-week training program. There was no significant difference (p > 0.05) between the C and E groups for muscular strength, muscular power, or vertical jump. Volume-loads were not significantly (p > 0.05) different between groups for any of the weeks (C: Week 1 = 858.1 + 101.3, Week 2 = 588.6 + 69.2, Week 3 = 332.5 + 38.9, Total = 1179.2 + 2…
bibliographic citation: Sawyer et al. (2021) Bilateral back squat strength is increased during a 3-week undulating resistance training program with and without variable resistance in DIII collegiate football players. PeerJ 9:e12189 https://doi.org/10.7717/peerj.12189
date submitted: 2021-03-30
date accepted: 2021-08-30
issued: 2021-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sawyer
  given name: Jason
author list: Agent
  family name: Higgins
  given name: Paul
author list: Agent
  family name: Cacolice
  given name: Paul A.
author list: Agent
  family name: Doming
  given name: Troy
doi: 10.7717/peerj.12189
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-24
copyright: ©2021 Sawyer et al.
attribution name: Sawyer et al.

Novel real-time PCR based assays for differentiating fall armyworm strains using four single nucleotide polymorphisms
type: item
type: AcademicArticle
description: The fall armyworm, Spodoptera frugiperda, is a polyphagous global pest with a preference for gramineous crops such as corn, sorghum and pasture grasses. This species is comprised of two morphologically identical but genetically distinct host strains known as the corn and rice strains, which can complicate pest management approaches. Two molecular markers are commonly used to differentiate between strains, however, discordance between these markers can lead to inconclusive strain identification. Here, we used double digest restriction site associated DNA sequencing to identify diagnostic single nucleotide polymorphisms (SNPs) with alleles unique to each strain. We then used these strain-specific SNPs to develop four real-time PCR based TaqMan assays to rapidly and reliably differentiate between strains and interstrain hybrids. These assays provide a new tool for differentiating between strains in field-collected samples, facilitating future studies on strain population dynamics and interstrain hybridization rates. Understanding the basic ecology of S. frugiperda strains is necessary to inform future management strategies.
format: application/pdf
format: text/html
creator: Ashley E. Tessnow
creator: Todd M. Gilligan
creator: Eric Burkness
creator: Caroline Placidi De Bortoli
creator: Juan Luis Jurat-Fuentes
creator: Patrick Porter
creator: Danielle Sekula
creator: Gregory A. Sword
subject: Agricultural Science
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.12195
publisher: PeerJ Inc.
rights: © 2021 Tessnow et al.
abstract: The fall armyworm, Spodoptera frugiperda, is a polyphagous global pest with a preference for gramineous crops such as corn, sorghum and pasture grasses. This species is comprised of two morphologically identical but genetically distinct host strains known as the corn and rice strains, which can complicate pest management approaches. Two molecular markers are commonly used to differentiate between strains, however, discordance between these markers can lead to inconclusive strain identification. Here, we used double digest restriction site associated DNA sequencing to identify diagnostic single nucleotide polymorphisms (SNPs) with alleles unique to each strain. We then used these strain-specific SNPs to develop four real-time PCR based TaqMan assays to rapidly and reliably differentiate between strains and interstrain hybrids. These assays provide a new tool for differentiating between strains in field-collected samples, facilitating future studies on strain population dynamics and interstrain hybridization rates. Understanding the basic ecology of S. frugiperda strains is necessary to inform future management strategies.
bibliographic citation: Tessnow et al. (2021) Novel real-time PCR based assays for differentiating fall armyworm strains using four single nucleotide polymorphisms. PeerJ 9:e12195 https://doi.org/10.7717/peerj.12195
date submitted: 2021-05-06
date accepted: 2021-08-31
issued: 2021-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tessnow
  given name: Ashley E.
author list: Agent
  family name: Gilligan
  given name: Todd M.
author list: Agent
  family name: Burkness
  given name: Eric
author list: Agent
  family name: Placidi De Bortoli
  given name: Caroline
author list: Agent
  family name: Jurat-Fuentes
  given name: Juan Luis
author list: Agent
  family name: Porter
  given name: Patrick
author list: Agent
  family name: Sekula
  given name: Danielle
author list: Agent
  family name: Sword
  given name: Gregory A.
doi: 10.7717/peerj.12195
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-24
copyright: ©2021 Tessnow et al.
attribution name: Tessnow et al.

Efficacy of 4% articaine vs 2% lidocaine in mandibular and maxillary block and infiltration anaesthesia in patients with irreversible pulpitis: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective The goal of this systematic review and meta-analysis is to determine the performance of 4% Articaine vs. 2% Lidocaine for mandibular and maxillary block and infiltration anaesthesia in patients with irreversible pulpitis (IP). Methods PubMed/MEDLINE, Cochrane Central Register of Controlled Trials, Web of Science, Google Scholar, and Open Gray were used to conduct a thorough literature search. A manual search of the reference lists of the publications found was also carried out. Two reviewers critically evaluated the papers for inclusion and exclusion criteria, and data extraction was done on the selected publications. The Cochrane Collaboration Tool and the Minors checklist were used to assess the quality of the selected studies for randomised controlled trials (RCTs) and non-randomised studies, respectively. The RevMan software was used to perform a meta-analysis of the pooled data and subgroups according to the technique of anaesthetic solution delivery, as well as a sensitivity analysis (P < 0.05). Results A total of twenty-six papers were included in the qualitative synthesis, with twenty-two of them being included in the meta-analysis. There were fifteen studies with a low potential for bias, three with a moderate potential for bias, and seven with a high potential for bias. The combined results of the 19 trials in the tooth level unit revealed that 4% articaine had a success rate 1.37 times greater than 2% lidocaine for mandibular teeth (RR, 1.37; 95% CI [1.17–1.62]; P = 0.0002). For the maxillary buccal infiltration method, the combined results from the three trials revealed that 4% articaine resulted in a success rate 1.06 times greater than 2% lidocaine (RR, 1.06; 95% CI [0.95–1.2]; P = 0.3). Excluding subgroups with a single study in sensitivity analysis for mandibular teeth revealed a substantial improvement in the success rate of the articaine group in treating IP when compared to the lidocaine group. Conclusion The findings of this meta-analys…
format: application/pdf
format: text/html
creator: Sanjay Miglani
creator: Irfan Ansari
creator: Swadheena Patro
creator: Ankita Mohanty
creator: Shahnaz Mansoori
creator: Bhoomika Ahuja
creator: Mohmed Isaqali Karobari
creator: Krishna Prasad Shetty
creator: Musab Hamed Saeed
creator: Alexander Maniangat Luke
creator: Ajinkya M. Pawar
subject: Dentistry
description: doi:10.7717/peerj.12214
publisher: PeerJ Inc.
rights: © 2021 Miglani et al.
abstract: Objective The goal of this systematic review and meta-analysis is to determine the performance of 4% Articaine vs. 2% Lidocaine for mandibular and maxillary block and infiltration anaesthesia in patients with irreversible pulpitis (IP). Methods PubMed/MEDLINE, Cochrane Central Register of Controlled Trials, Web of Science, Google Scholar, and Open Gray were used to conduct a thorough literature search. A manual search of the reference lists of the publications found was also carried out. Two reviewers critically evaluated the papers for inclusion and exclusion criteria, and data extraction was done on the selected publications. The Cochrane Collaboration Tool and the Minors checklist were used to assess the quality of the selected studies for randomised controlled trials (RCTs) and non-randomised studies, respectively. The RevMan software was used to perform a meta-analysis of the pooled data and subgroups according to the technique of anaesthetic solution delivery, as well as a sensitivity analysis (P < 0.05). Results A total of twenty-six papers were included in the qualitative synthesis, with twenty-two of them being included in the meta-analysis. There were fifteen studies with a low potential for bias, three with a moderate potential for bias, and seven with a high potential for bias. The combined results of the 19 trials in the tooth level unit revealed that 4% articaine had a success rate 1.37 times greater than 2% lidocaine for mandibular teeth (RR, 1.37; 95% CI [1.17–1.62]; P = 0.0002). For the maxillary buccal infiltration method, the combined results from the three trials revealed that 4% articaine resulted in a success rate 1.06 times greater than 2% lidocaine (RR, 1.06; 95% CI [0.95–1.2]; P = 0.3). Excluding subgroups with a single study in sensitivity analysis for mandibular teeth revealed a substantial improvement in the success rate of the articaine group in treating IP when compared to the lidocaine group. Conclusion The findings of this meta-analys…
bibliographic citation: Miglani et al. (2021) Efficacy of 4% articaine vs 2% lidocaine in mandibular and maxillary block and infiltration anaesthesia in patients with irreversible pulpitis: a systematic review and meta-analysis. PeerJ 9:e12214 https://doi.org/10.7717/peerj.12214
date submitted: 2021-05-12
date accepted: 2021-09-05
issued: 2021-09-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miglani
  given name: Sanjay
author list: Agent
  family name: Ansari
  given name: Irfan
author list: Agent
  family name: Patro
  given name: Swadheena
author list: Agent
  family name: Mohanty
  given name: Ankita
author list: Agent
  family name: Mansoori
  given name: Shahnaz
author list: Agent
  family name: Ahuja
  given name: Bhoomika
author list: Agent
  family name: Karobari
  given name: Mohmed Isaqali
author list: Agent
  family name: Shetty
  given name: Krishna Prasad
author list: Agent
  family name: Saeed
  given name: Musab Hamed
author list: Agent
  family name: Luke
  given name: Alexander Maniangat
author list: Agent
  family name: Pawar
  given name: Ajinkya M.
doi: 10.7717/peerj.12214
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-24
copyright: ©2021 Miglani et al.
attribution name: Miglani et al.

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