PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: https://peerj.com/articles/11984
items: Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey
items: Living shorelines achieve functional equivalence to natural fringe marshes across multiple ecological metrics
items: Dung beetles as samplers of mammals in Malaysian Borneo—a test of high throughput metabarcoding of iDNA
items: Screening and identification of NOTCH1, CDKN2A, and NOS3 as differentially expressed autophagy-related genes in erectile dysfunction
items: In vitro effect of resin infiltrant on resistance of sound enamel surfaces in permanent teeth to demineralization
items: Regeneration and growth in crowns and rhizome fragments of Japanese knotweed (Reynoutria japonica) and desiccation as a potential control strategy
items: Development of a multiplex qPCR assay for the simultaneous detection of Mycoplasma bovis, Mycoplasma species, and Acholeplasma laidlawii in milk
items: Comparative survival analyses among captive chimpanzees (Pan troglodytes) in America and Japan
items: Quantifying bite force in coexisting tayassuids and feral suids: a comparison between morphometric functional proxies and in vivo measurements

https://peerj.com/articles/11984
type: item
type: AcademicArticle
title: Behavioral phenotyping of cancer pain in domesticated cats with naturally occurring squamous cell carcinoma of the tongue: initial validation studies provide evidence for regional and widespread algoplasticity
description: Feline oral squamous cell carcinoma (FOSCC) is a common and naturally occurring condition that recapitulates many features of human head and neck cancer (HNC). In both species, there is need for improved strategies to reduce pain caused by HNC and its treatment. Research to benefit both species could be conducted using pet cats as a comparative model, but this prospect is limited by lack of validated methods for quantifying FOSCC-associated pain. A prospective non-randomized pilot study was performed for initial validation of: (1) a pet owner administered quality of life questionnaire and visual assessment scoring tool (FORQ/CLIENT); (2) a clinician assessment questionnaire (UFEPS/VET); (3) electronic von Frey testing [EVF]; and (4) Cochet-Bonnet (COBO) aesthesiometry. To assess intra-rater reliability, discriminatory ability, and responsiveness of each assay, 6 cats with sublingual SCC and 16 healthy control cats were enrolled. The intra-rater reliability was moderate-to-good for the clinical metrology instruments and EVF (intraclass correlation coefficient [ICC] ≥ 0.68), but poor for COBO (ICC = 0.21). FORQ/CLIENT scores were higher (worse quality of life) in FOSCC cats vs healthy controls. The internal reliability of FORQ/CLIENT scoring was high (Cronbach α = 0.92); sensitivity and specificity were excellent (100% when using cut-offs determined using receiver operating characteristic [ROC] curves). For the FORQ/CLIENT, there was strong and inverse correlation between scores from the questions and visual assessment (r = − 0.77, r2 = 0.6, P < 0.0001). For the UFEPS/VET, Cronbach’s α was 0.74 (high reliability). Sensitivity and specificity were 100% and 94%, respectively, when using a cut-off score (3.5) based on ROC curves (Youden index of 0.94). Total UFEPS/VET scores were positively correlated with FORQ/CLIENT scores (r2 = 0.72, P < 0.0001). Sensitivity of EVF and COBO ranged from 83 to 100% and specificity ranged from 56 to 94%. Cats with cancer were more sensit…
format: application/pdf
format: text/html
creator: Yen-Hao Erik Lai
creator: B. Duncan X. Lascelles
creator: Michael W. Nolan
subject: Animal Behavior
subject: Neuroscience
subject: Veterinary Medicine
subject: Zoology
subject: Oncology
description: doi:10.7717/peerj.11984
publisher: PeerJ Inc.
rights: © 2021 Lai et al.
abstract: Feline oral squamous cell carcinoma (FOSCC) is a common and naturally occurring condition that recapitulates many features of human head and neck cancer (HNC). In both species, there is need for improved strategies to reduce pain caused by HNC and its treatment. Research to benefit both species could be conducted using pet cats as a comparative model, but this prospect is limited by lack of validated methods for quantifying FOSCC-associated pain. A prospective non-randomized pilot study was performed for initial validation of: (1) a pet owner administered quality of life questionnaire and visual assessment scoring tool (FORQ/CLIENT); (2) a clinician assessment questionnaire (UFEPS/VET); (3) electronic von Frey testing [EVF]; and (4) Cochet-Bonnet (COBO) aesthesiometry. To assess intra-rater reliability, discriminatory ability, and responsiveness of each assay, 6 cats with sublingual SCC and 16 healthy control cats were enrolled. The intra-rater reliability was moderate-to-good for the clinical metrology instruments and EVF (intraclass correlation coefficient [ICC] ≥ 0.68), but poor for COBO (ICC = 0.21). FORQ/CLIENT scores were higher (worse quality of life) in FOSCC cats vs healthy controls. The internal reliability of FORQ/CLIENT scoring was high (Cronbach α = 0.92); sensitivity and specificity were excellent (100% when using cut-offs determined using receiver operating characteristic [ROC] curves). For the FORQ/CLIENT, there was strong and inverse correlation between scores from the questions and visual assessment (r = − 0.77, r2 = 0.6, P < 0.0001). For the UFEPS/VET, Cronbach’s α was 0.74 (high reliability). Sensitivity and specificity were 100% and 94%, respectively, when using a cut-off score (3.5) based on ROC curves (Youden index of 0.94). Total UFEPS/VET scores were positively correlated with FORQ/CLIENT scores (r2 = 0.72, P < 0.0001). Sensitivity of EVF and COBO ranged from 83 to 100% and specificity ranged from 56 to 94%. Cats with cancer were more sensit…
bibliographic citation: Lai et al. (2021) Behavioral phenotyping of cancer pain in domesticated cats with naturally occurring squamous cell carcinoma of the tongue: initial validation studies provide evidence for regional and widespread algoplasticity. PeerJ 9:e11984 https://doi.org/10.7717/peerj.11984
date submitted: 2021-01-05
date accepted: 2021-07-26
issued: 2021-08-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lai
  given name: Yen-Hao Erik
author list: Agent
  family name: Lascelles
  given name: B. Duncan X.
author list: Agent
  family name: Nolan
  given name: Michael W.
doi: 10.7717/peerj.11984
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-16
copyright: ©2021 Lai et al.
attribution name: Lai et al.

Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey
type: item
type: AcademicArticle
description: Studies of the diet, feeding habits and trophic activity of top marine predators are essential for understanding their trophodynamics. The main direct method used for such studies thus far has been morphological inventories of stomach contents. This approach presents limitations such as missing gelatinous prey, which are usually digested too quickly to be detectable. Here, we analysed the stomachs of 48 Atlantic bluefin tuna (Thunnus thynnus, approximately 15 to 60 kg, including juveniles and adult fishes) collected from the Mediterranean Sea through the metabarcoding of two gene regions (cytochrome c oxidase subunit I (COI) and the ribosomal 18S-V1V2 region). The identified prey taxa and their relative read abundances (RRAs) estimated using COI results were in line with the findings of morphologically based inventories simultaneously performed on the same set of tuna samples. In both cases (and with the same rankings), the prey taxa included anchovy (Engraulis encrasicolus, here detected in more than 80% of samples, RRA = 43%), sardine (Sardina pilchardus, also approximately 80%, RRA = 30%), sprat (Sprattus sprattus, approximately 66%, RRA = 8%), mackerel (Scomber colias, approximately 44%, RRA = 7%) and cephalopods (approximately 15%, RRA = 1.4%). Another striking result was the detection, based on 18S (with which vertebrates were detected as the most abundant group, RRA = 61.6%), of a high prevalence and diversity of gelatinous organisms (RRA = 27.1%), including cnidarians (6.7%), salps (11.7%), and ctenophores (8.7%), the latter increasing with the size of the predator. These results thus support the hypothesis of the role of gelatinous prey in the diet of Atlantic bluefin tuna, suggesting that this species is even more generalist and opportunistic than previously thought. This study further confirms that DNA metabarcoding can be a powerful tool for assessing the diet and trophodynamics of top marine predators.
format: application/pdf
format: text/html
creator: Babett Günther
creator: Jean-Marc Fromentin
creator: Luisa Metral
creator: Sophie Arnaud-Haond
subject: Fisheries and Fish Science
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.11757
publisher: PeerJ Inc.
rights: © 2021 Günther et al.
abstract: Studies of the diet, feeding habits and trophic activity of top marine predators are essential for understanding their trophodynamics. The main direct method used for such studies thus far has been morphological inventories of stomach contents. This approach presents limitations such as missing gelatinous prey, which are usually digested too quickly to be detectable. Here, we analysed the stomachs of 48 Atlantic bluefin tuna (Thunnus thynnus, approximately 15 to 60 kg, including juveniles and adult fishes) collected from the Mediterranean Sea through the metabarcoding of two gene regions (cytochrome c oxidase subunit I (COI) and the ribosomal 18S-V1V2 region). The identified prey taxa and their relative read abundances (RRAs) estimated using COI results were in line with the findings of morphologically based inventories simultaneously performed on the same set of tuna samples. In both cases (and with the same rankings), the prey taxa included anchovy (Engraulis encrasicolus, here detected in more than 80% of samples, RRA = 43%), sardine (Sardina pilchardus, also approximately 80%, RRA = 30%), sprat (Sprattus sprattus, approximately 66%, RRA = 8%), mackerel (Scomber colias, approximately 44%, RRA = 7%) and cephalopods (approximately 15%, RRA = 1.4%). Another striking result was the detection, based on 18S (with which vertebrates were detected as the most abundant group, RRA = 61.6%), of a high prevalence and diversity of gelatinous organisms (RRA = 27.1%), including cnidarians (6.7%), salps (11.7%), and ctenophores (8.7%), the latter increasing with the size of the predator. These results thus support the hypothesis of the role of gelatinous prey in the diet of Atlantic bluefin tuna, suggesting that this species is even more generalist and opportunistic than previously thought. This study further confirms that DNA metabarcoding can be a powerful tool for assessing the diet and trophodynamics of top marine predators.
bibliographic citation: Günther et al. (2021) Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey. PeerJ 9:e11757 https://doi.org/10.7717/peerj.11757
date submitted: 2021-01-18
date accepted: 2021-06-21
issued: 2021-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Günther
  given name: Babett
author list: Agent
  family name: Fromentin
  given name: Jean-Marc
author list: Agent
  family name: Metral
  given name: Luisa
author list: Agent
  family name: Arnaud-Haond
  given name: Sophie
doi: 10.7717/peerj.11757
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-13
copyright: ©2021 Günther et al.
attribution name: Günther et al.

Living shorelines achieve functional equivalence to natural fringe marshes across multiple ecological metrics
type: item
type: AcademicArticle
description: Nature-based shoreline protection provides a welcome class of adaptations to promote ecological resilience in the face of climate change. Along coastlines, living shorelines are among the preferred adaptation strategies to both reduce erosion and provide ecological functions. As an alternative to shoreline armoring, living shorelines are viewed favorably among coastal managers and some private property owners, but they have yet to undergo a thorough examination of how their levels of ecosystem functions compare to their closest natural counterpart: fringing marshes. Here, we provide a synthesis of results from a multi-year, large-spatial-scale study in which we compared numerous ecological metrics (including habitat provision for fish, invertebrates, diamondback terrapin, and birds, nutrient and carbon storage, and plant productivity) measured in thirteen pairs of living shorelines and natural fringing marshes throughout coastal Virginia, USA. Living shorelines were composed of marshes created by bank grading, placement of sand fill for proper elevations, and planting of S. alterniflora and S. patens, as well as placement of a stone sill seaward and parallel to the marsh to serve as a wave break. Overall, we found that living shorelines were functionally equivalent to natural marshes in nearly all measured aspects, except for a lag in soil composition due to construction of living shoreline marshes with clean, low-organic sands. These data support the prioritization of living shorelines as a coastal adaptation strategy.
format: application/pdf
format: text/html
creator: Robert E. Isdell
creator: Donna Marie Bilkovic
creator: Amanda G. Guthrie
creator: Molly M. Mitchell
creator: Randolph M. Chambers
creator: Matthias Leu
creator: Carl Hershner
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.11815
publisher: PeerJ Inc.
rights: © 2021 Isdell et al.
abstract: Nature-based shoreline protection provides a welcome class of adaptations to promote ecological resilience in the face of climate change. Along coastlines, living shorelines are among the preferred adaptation strategies to both reduce erosion and provide ecological functions. As an alternative to shoreline armoring, living shorelines are viewed favorably among coastal managers and some private property owners, but they have yet to undergo a thorough examination of how their levels of ecosystem functions compare to their closest natural counterpart: fringing marshes. Here, we provide a synthesis of results from a multi-year, large-spatial-scale study in which we compared numerous ecological metrics (including habitat provision for fish, invertebrates, diamondback terrapin, and birds, nutrient and carbon storage, and plant productivity) measured in thirteen pairs of living shorelines and natural fringing marshes throughout coastal Virginia, USA. Living shorelines were composed of marshes created by bank grading, placement of sand fill for proper elevations, and planting of S. alterniflora and S. patens, as well as placement of a stone sill seaward and parallel to the marsh to serve as a wave break. Overall, we found that living shorelines were functionally equivalent to natural marshes in nearly all measured aspects, except for a lag in soil composition due to construction of living shoreline marshes with clean, low-organic sands. These data support the prioritization of living shorelines as a coastal adaptation strategy.
bibliographic citation: Isdell et al. (2021) Living shorelines achieve functional equivalence to natural fringe marshes across multiple ecological metrics. PeerJ 9:e11815 https://doi.org/10.7717/peerj.11815
date submitted: 2021-04-09
date accepted: 2021-06-28
issued: 2021-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Isdell
  given name: Robert E.
author list: Agent
  family name: Bilkovic
  given name: Donna Marie
author list: Agent
  family name: Guthrie
  given name: Amanda G.
author list: Agent
  family name: Mitchell
  given name: Molly M.
author list: Agent
  family name: Chambers
  given name: Randolph M.
author list: Agent
  family name: Leu
  given name: Matthias
author list: Agent
  family name: Hershner
  given name: Carl
doi: 10.7717/peerj.11815
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-13
copyright: ©2021 Isdell et al.
attribution name: Isdell et al.

Dung beetles as samplers of mammals in Malaysian Borneo—a test of high throughput metabarcoding of iDNA
type: item
type: AcademicArticle
description: Invertebrate-derived DNA (iDNA) sampling in biodiversity surveys is becoming increasingly widespread, with most terrestrial studies relying on DNA derived from the gut contents of blood-feeding invertebrates, such as leeches and mosquitoes. Dung beetles (superfamily Scarabaeoidea) primarily feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps, are globally distributed, and occur in a wide range of habitats. To build on the few existing studies demonstrating the potential of dung beetles as sources of mammalian DNA, we subjected the large-bodied, Bornean dung beetle (Catharsius renaudpauliani) to a controlled feeding experiment. We analysed DNA from gut contents at different times after feeding using qPCR techniques. Here, we first describe the window of DNA persistence within a dung beetle digestive tract. We found that the ability to successfully amplify cattle DNA decayed over relatively short time periods, with DNA copy number decreasing by two orders of magnitude in just 6 h. In addition, we sampled communities of dung beetles from a lowland tropical rainforest in Sabah, Malaysia, in order to test whether it is possible to identify vertebrate sequences from dung beetle iDNA. We sequenced both the gut contents from large dung beetle species, as well as whole communities of smaller beetles. We successfully identified six mammalian species from our samples, including the bearded pig (Sus barbatus) and the sambar deer (Rusa unicolor)—both vulnerable species on the IUCN red list. Our results represent the first use of dung beetle iDNA to sample Southeast Asian vertebrate fauna, and highlight the potential for dung beetle iDNA to be used in future biodiversity monitoring surveys.
format: application/pdf
format: text/html
creator: Rosie Drinkwater
creator: Joseph Williamson
creator: Elizabeth L. Clare
creator: Arthur Y.C. Chung
creator: Stephen J. Rossiter
creator: Eleanor Slade
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.11897
publisher: PeerJ Inc.
rights: © 2021 Drinkwater et al.
abstract: Invertebrate-derived DNA (iDNA) sampling in biodiversity surveys is becoming increasingly widespread, with most terrestrial studies relying on DNA derived from the gut contents of blood-feeding invertebrates, such as leeches and mosquitoes. Dung beetles (superfamily Scarabaeoidea) primarily feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps, are globally distributed, and occur in a wide range of habitats. To build on the few existing studies demonstrating the potential of dung beetles as sources of mammalian DNA, we subjected the large-bodied, Bornean dung beetle (Catharsius renaudpauliani) to a controlled feeding experiment. We analysed DNA from gut contents at different times after feeding using qPCR techniques. Here, we first describe the window of DNA persistence within a dung beetle digestive tract. We found that the ability to successfully amplify cattle DNA decayed over relatively short time periods, with DNA copy number decreasing by two orders of magnitude in just 6 h. In addition, we sampled communities of dung beetles from a lowland tropical rainforest in Sabah, Malaysia, in order to test whether it is possible to identify vertebrate sequences from dung beetle iDNA. We sequenced both the gut contents from large dung beetle species, as well as whole communities of smaller beetles. We successfully identified six mammalian species from our samples, including the bearded pig (Sus barbatus) and the sambar deer (Rusa unicolor)—both vulnerable species on the IUCN red list. Our results represent the first use of dung beetle iDNA to sample Southeast Asian vertebrate fauna, and highlight the potential for dung beetle iDNA to be used in future biodiversity monitoring surveys.
bibliographic citation: Drinkwater et al. (2021) Dung beetles as samplers of mammals in Malaysian Borneo—a test of high throughput metabarcoding of iDNA. PeerJ 9:e11897 https://doi.org/10.7717/peerj.11897
date submitted: 2021-02-17
date accepted: 2021-07-13
issued: 2021-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Drinkwater
  given name: Rosie
author list: Agent
  family name: Williamson
  given name: Joseph
author list: Agent
  family name: Clare
  given name: Elizabeth L.
author list: Agent
  family name: Chung
  given name: Arthur Y.C.
author list: Agent
  family name: Rossiter
  given name: Stephen J.
author list: Agent
  family name: Slade
  given name: Eleanor
doi: 10.7717/peerj.11897
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-13
copyright: © 2021 Drinkwater et al.
attribution name: Drinkwater et al.

Screening and identification of NOTCH1, CDKN2A, and NOS3 as differentially expressed autophagy-related genes in erectile dysfunction
type: item
type: AcademicArticle
description: Background Loss of function of key autophagy genes are associated with a variety of diseases. However specific role of autophagy-related genes in erectile dysfunction ED remains unclear. This study explores the autophagy-related differentially expressed genes (ARGs) profiles and related molecular mechanisms in Corpus Cavernosum endothelial dysfunction, which is a leading cause of ED. Methods The Gene Expression Omnibus (GEO) database was used to identify the key genes and pathways. Differentially expressed genes (DEGs) were mined using the limma package in R language. Next, ARGs were obtained by matching DEGs and autophagy-related genes from GeneCard using Venn diagrams. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of ARGs were described using clusterProfiler and org.Hs.eg.db in R. Moreover, hub ARGs were screened out through protein-protein interaction (PPI), gene-microRNAs, and gene-transcription factors (TFs) networks then visualized using Cytoscape. Of note, the rat model of diabetic ED was established to validate some hub ARGs with qRT-PCR and Western blots. Results Twenty ARGs were identified from four ED samples and eight non-ED samples. GO analysis revealed that molecular functions (MF) of upregulated ARGs were mainly enriched in nuclear receptor activity. Also, MF of downregulated ARGs were mainly enriched in oxidoreductase activity, acting on NAD(P)H and heme proteins as acceptors. Moreover, six hub ARGs were identified by setting high degrees in the network. Additionally, hsa-mir-24-3p and hsa-mir-335-5p might play a central role in several ARGs regulation, and the transcription factors-hub genes network was centered with 13 ARGs. The experimental results further showed that the expression of Notch1, NOS3, and CDKN2A in the diabetic ED group was downregulated compared to the control. Conclusions Our study deepens the autophagy-related mechanistic understanding of endothelial dysfunction of ED. NOTCH1, CDKN2A, and NOS3 are…
format: application/pdf
format: text/html
creator: Chao Luo
creator: Xiongcai Zhou
creator: Li Wang
creator: Qinyu Zeng
creator: Junhong Fan
creator: Shuhua He
creator: Haibo Zhang
creator: Anyang Wei
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Andrology
subject: Histology
description: doi:10.7717/peerj.11986
publisher: PeerJ Inc.
rights: © 2021 Luo et al.
abstract: Background Loss of function of key autophagy genes are associated with a variety of diseases. However specific role of autophagy-related genes in erectile dysfunction ED remains unclear. This study explores the autophagy-related differentially expressed genes (ARGs) profiles and related molecular mechanisms in Corpus Cavernosum endothelial dysfunction, which is a leading cause of ED. Methods The Gene Expression Omnibus (GEO) database was used to identify the key genes and pathways. Differentially expressed genes (DEGs) were mined using the limma package in R language. Next, ARGs were obtained by matching DEGs and autophagy-related genes from GeneCard using Venn diagrams. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of ARGs were described using clusterProfiler and org.Hs.eg.db in R. Moreover, hub ARGs were screened out through protein-protein interaction (PPI), gene-microRNAs, and gene-transcription factors (TFs) networks then visualized using Cytoscape. Of note, the rat model of diabetic ED was established to validate some hub ARGs with qRT-PCR and Western blots. Results Twenty ARGs were identified from four ED samples and eight non-ED samples. GO analysis revealed that molecular functions (MF) of upregulated ARGs were mainly enriched in nuclear receptor activity. Also, MF of downregulated ARGs were mainly enriched in oxidoreductase activity, acting on NAD(P)H and heme proteins as acceptors. Moreover, six hub ARGs were identified by setting high degrees in the network. Additionally, hsa-mir-24-3p and hsa-mir-335-5p might play a central role in several ARGs regulation, and the transcription factors-hub genes network was centered with 13 ARGs. The experimental results further showed that the expression of Notch1, NOS3, and CDKN2A in the diabetic ED group was downregulated compared to the control. Conclusions Our study deepens the autophagy-related mechanistic understanding of endothelial dysfunction of ED. NOTCH1, CDKN2A, and NOS3 are…
bibliographic citation: Luo et al. (2021) Screening and identification of NOTCH1, CDKN2A, and NOS3 as differentially expressed autophagy-related genes in erectile dysfunction. PeerJ 9:e11986 https://doi.org/10.7717/peerj.11986
date submitted: 2021-04-09
date accepted: 2021-07-26
issued: 2021-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Chao
author list: Agent
  family name: Zhou
  given name: Xiongcai
author list: Agent
  family name: Wang
  given name: Li
author list: Agent
  family name: Zeng
  given name: Qinyu
author list: Agent
  family name: Fan
  given name: Junhong
author list: Agent
  family name: He
  given name: Shuhua
author list: Agent
  family name: Zhang
  given name: Haibo
author list: Agent
  family name: Wei
  given name: Anyang
doi: 10.7717/peerj.11986
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-13
copyright: ©2021 Luo et al.
attribution name: Luo et al.

In vitro effect of resin infiltrant on resistance of sound enamel surfaces in permanent teeth to demineralization
type: item
type: AcademicArticle
description: Objective To investigate the effect of resin infiltrant on resistance of sound permanent enamel surfaces to demineralization. Method Eighty healthy premolars were sectioned to obtain enamel blocks from the buccal surface. Specimens with baseline surface microhardness values of 320–370 were selected. The experimental group were treated with resin infiltrant, while the control group was not. Specimens from each group were artificially demineralized and the surface microhardness values were measured again. Confocal laser scanning microscopy was used to measure the depth of demineralization and detect the penetration ability of the resin infiltrant. The specimens were subjected to a simulated toothbrushing abrasion test. Scanning electron microscopy was used to observe changes in the surface morphology of specimens after each of these procedures. Results No significant differences between the experimental and control groups were observed in the baseline microhardness values or in the experimental group after resin infiltration compared with the baseline conditions. After artificial demineralization, the microhardness value in the control group was significantly lower than that in the experimental group (266.0 (±34.5) compared with 304.0 (±13.0), P = 0.017). Confocal laser scanning microscopy results showed that the demineralization depth in the control group was significantly deeper than that in the experimental group (97.9 (±22.8) µm vs. 50.4 (±14.3) µm, P < 0.001), and that resin infiltrant completely penetrated the acid-etched demineralized area of the tooth enamel with a mean penetration depth of 31.6 (±9.0) µm. Scanning electron microscopy showed that the surface morphology was more uniform and smoother after simulated toothbrushing. The enamel surface structure was more severely destroyed in the control group after artificial demineralization compared with that of the experimental group. Conclusion Resin infiltrant can completely penetrate an acid-etched demineral…
format: application/pdf
format: text/html
creator: Meng Li
creator: Zhengyan Yang
creator: Yajing Huang
creator: Yueheng Li
creator: Zhi Zhou
subject: Dentistry
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.12008
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Objective To investigate the effect of resin infiltrant on resistance of sound permanent enamel surfaces to demineralization. Method Eighty healthy premolars were sectioned to obtain enamel blocks from the buccal surface. Specimens with baseline surface microhardness values of 320–370 were selected. The experimental group were treated with resin infiltrant, while the control group was not. Specimens from each group were artificially demineralized and the surface microhardness values were measured again. Confocal laser scanning microscopy was used to measure the depth of demineralization and detect the penetration ability of the resin infiltrant. The specimens were subjected to a simulated toothbrushing abrasion test. Scanning electron microscopy was used to observe changes in the surface morphology of specimens after each of these procedures. Results No significant differences between the experimental and control groups were observed in the baseline microhardness values or in the experimental group after resin infiltration compared with the baseline conditions. After artificial demineralization, the microhardness value in the control group was significantly lower than that in the experimental group (266.0 (±34.5) compared with 304.0 (±13.0), P = 0.017). Confocal laser scanning microscopy results showed that the demineralization depth in the control group was significantly deeper than that in the experimental group (97.9 (±22.8) µm vs. 50.4 (±14.3) µm, P < 0.001), and that resin infiltrant completely penetrated the acid-etched demineralized area of the tooth enamel with a mean penetration depth of 31.6 (±9.0) µm. Scanning electron microscopy showed that the surface morphology was more uniform and smoother after simulated toothbrushing. The enamel surface structure was more severely destroyed in the control group after artificial demineralization compared with that of the experimental group. Conclusion Resin infiltrant can completely penetrate an acid-etched demineral…
bibliographic citation: Li et al. (2021) In vitro effect of resin infiltrant on resistance of sound enamel surfaces in permanent teeth to demineralization. PeerJ 9:e12008 https://doi.org/10.7717/peerj.12008
date submitted: 2020-11-27
date accepted: 2021-07-27
issued: 2021-08-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Meng
author list: Agent
  family name: Yang
  given name: Zhengyan
author list: Agent
  family name: Huang
  given name: Yajing
author list: Agent
  family name: Li
  given name: Yueheng
author list: Agent
  family name: Zhou
  given name: Zhi
doi: 10.7717/peerj.12008
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-13
copyright: ©2021 Li et al.
attribution name: Li et al.

Regeneration and growth in crowns and rhizome fragments of Japanese knotweed (Reynoutria japonica) and desiccation as a potential control strategy
type: item
type: AcademicArticle
description: Reynoutria japonica (Japanese knotweed) is a problematic invasive plant found in many areas of Europe and North America. Notably, in the UK, the species can cause issues with mortgage acquisition. Control of R. japonica is complicated by its ability to regenerate from small fragments of plant material; however, there remains uncertainty about how much (in terms of mass) rhizome is required for successful regeneration. This study investigated the ability of crowns and rhizomes with different numbers of nodes to regenerate successfully from three sites in the north of England, UK. Two of the sites had been subject to herbicide treatment for two years prior to sampling and the third site had no history of herbicide treatment. No significant differences were observed in regenerated stem diameter, maximum height of stem and maximum growth increments among crowns. All traits measured from the planted crowns were significantly greater than those of the planted rhizome fragments and at least one node was necessary for successful regeneration of rhizomes. The smallest initial fragment weight to regenerate and survive the experiment was 0.5 g. Subjecting all plant material to desiccation for 38 days resulted in no regrowth (emergence or regeneration) after replanting. These findings suggest that desiccation could be a valuable management strategy for small to medium scale infestations common in urban settings.
format: application/pdf
format: text/html
creator: Jacob W. Lawson
creator: Mark Fennell
creator: Mark W. Smith
creator: Karen L. Bacon
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.11783
publisher: PeerJ Inc.
rights: © 2021 Lawson et al.
abstract: Reynoutria japonica (Japanese knotweed) is a problematic invasive plant found in many areas of Europe and North America. Notably, in the UK, the species can cause issues with mortgage acquisition. Control of R. japonica is complicated by its ability to regenerate from small fragments of plant material; however, there remains uncertainty about how much (in terms of mass) rhizome is required for successful regeneration. This study investigated the ability of crowns and rhizomes with different numbers of nodes to regenerate successfully from three sites in the north of England, UK. Two of the sites had been subject to herbicide treatment for two years prior to sampling and the third site had no history of herbicide treatment. No significant differences were observed in regenerated stem diameter, maximum height of stem and maximum growth increments among crowns. All traits measured from the planted crowns were significantly greater than those of the planted rhizome fragments and at least one node was necessary for successful regeneration of rhizomes. The smallest initial fragment weight to regenerate and survive the experiment was 0.5 g. Subjecting all plant material to desiccation for 38 days resulted in no regrowth (emergence or regeneration) after replanting. These findings suggest that desiccation could be a valuable management strategy for small to medium scale infestations common in urban settings.
bibliographic citation: Lawson et al. (2021) Regeneration and growth in crowns and rhizome fragments of Japanese knotweed (Reynoutria japonica) and desiccation as a potential control strategy. PeerJ 9:e11783 https://doi.org/10.7717/peerj.11783
date submitted: 2020-10-27
date accepted: 2021-06-24
issued: 2021-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lawson
  given name: Jacob W.
author list: Agent
  family name: Fennell
  given name: Mark
author list: Agent
  family name: Smith
  given name: Mark W.
author list: Agent
  family name: Bacon
  given name: Karen L.
doi: 10.7717/peerj.11783
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-12
copyright: ©2021 Lawson et al.
attribution name: Lawson et al.

Development of a multiplex qPCR assay for the simultaneous detection of Mycoplasma bovis, Mycoplasma species, and Acholeplasma laidlawii in milk
type: item
type: AcademicArticle
description: Contagious bovine mastitis caused by Mycoplasma bovis and other Mycoplasma species including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma canadense is an economical obstacle affecting many dairy herds throughout California and elsewhere. Routine bacteriological culture-based assays for the pathogens are slow and subject to false-positive results due to the presence of the related, non-pathogenic species Acholeplasma laidlawii. To address the need for rapid and accurate detection methods, a new TaqMan multiplex, quantitative real-time PCR (qPCR) assay was developed that targets the 16S rRNA gene of Mycoplasma, rpoB gene of M. bovis, and the 16S to 23S rRNA intergenic transcribed spacer (ITS) region of A. laidlawii. qPCR amplification efficiency and range of detection were similar for individual assays in multiplex as when performed separately. The multiplex assay was able to distinguish between M. bovis and A. laidlawii as well as detect Mycoplasma spp. collectively, including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma canadense, Mycoplasma arginini and Mycoplasma alkalescens. In milk, the lower limit of detection of M. bovis, M. californicum, and A. laidlawii with the multiplex assay was between 120 to 250 colony forming units (CFU) per mL. The assay was also able to simultaneously detect both M. bovis and A. laidlawii in milk when present in moderate (103 to 104 CFU/mL) to high (106 to 107 CFU/mL) quantities. Compared to laboratory culture-based methods, the multiplex qPCR diagnostic specificity (Sp) was 100% (95% CI [86.8–100]; n = 26) and diagnostic sensitivity (Se) was 92.3% (95% CI [74.9–99.1]; n = 26) for Mycoplasma species in milk samples collected from California dairy farms. Similarly, the Sp was 100% (95% CI [90.5–100]; n = 37) and Se was 93.3% (95% CI [68.1–99.8]; n = 15) for M. bovis. Our assay can detect and distinguish among M. bovis, other prevalent Mycoplasma spp.,…
format: application/pdf
format: text/html
creator: Kanika Chauhan
creator: Sharif S. Aly
creator: Terry W. Lehenbauer
creator: Karen H. Tonooka
creator: Kathy Glenn
creator: Paul Rossitto
creator: Maria L. Marco
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.11881
publisher: PeerJ Inc.
rights: © 2021 Chauhan et al.
abstract: Contagious bovine mastitis caused by Mycoplasma bovis and other Mycoplasma species including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma canadense is an economical obstacle affecting many dairy herds throughout California and elsewhere. Routine bacteriological culture-based assays for the pathogens are slow and subject to false-positive results due to the presence of the related, non-pathogenic species Acholeplasma laidlawii. To address the need for rapid and accurate detection methods, a new TaqMan multiplex, quantitative real-time PCR (qPCR) assay was developed that targets the 16S rRNA gene of Mycoplasma, rpoB gene of M. bovis, and the 16S to 23S rRNA intergenic transcribed spacer (ITS) region of A. laidlawii. qPCR amplification efficiency and range of detection were similar for individual assays in multiplex as when performed separately. The multiplex assay was able to distinguish between M. bovis and A. laidlawii as well as detect Mycoplasma spp. collectively, including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma canadense, Mycoplasma arginini and Mycoplasma alkalescens. In milk, the lower limit of detection of M. bovis, M. californicum, and A. laidlawii with the multiplex assay was between 120 to 250 colony forming units (CFU) per mL. The assay was also able to simultaneously detect both M. bovis and A. laidlawii in milk when present in moderate (103 to 104 CFU/mL) to high (106 to 107 CFU/mL) quantities. Compared to laboratory culture-based methods, the multiplex qPCR diagnostic specificity (Sp) was 100% (95% CI [86.8–100]; n = 26) and diagnostic sensitivity (Se) was 92.3% (95% CI [74.9–99.1]; n = 26) for Mycoplasma species in milk samples collected from California dairy farms. Similarly, the Sp was 100% (95% CI [90.5–100]; n = 37) and Se was 93.3% (95% CI [68.1–99.8]; n = 15) for M. bovis. Our assay can detect and distinguish among M. bovis, other prevalent Mycoplasma spp.,…
bibliographic citation: Chauhan et al. (2021) Development of a multiplex qPCR assay for the simultaneous detection of Mycoplasma bovis, Mycoplasma species, and Acholeplasma laidlawii in milk. PeerJ 9:e11881 https://doi.org/10.7717/peerj.11881
date submitted: 2021-03-22
date accepted: 2021-07-07
issued: 2021-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chauhan
  given name: Kanika
author list: Agent
  family name: Aly
  given name: Sharif S.
author list: Agent
  family name: Lehenbauer
  given name: Terry W.
author list: Agent
  family name: Tonooka
  given name: Karen H.
author list: Agent
  family name: Glenn
  given name: Kathy
author list: Agent
  family name: Rossitto
  given name: Paul
author list: Agent
  family name: Marco
  given name: Maria L.
doi: 10.7717/peerj.11881
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-12
copyright: © 2021 Chauhan et al.
attribution name: Chauhan et al.

Comparative survival analyses among captive chimpanzees (Pan troglodytes) in America and Japan
type: item
type: AcademicArticle
description: Detailed, long-term datasets on the life histories of long-lived species such as great apes are necessary to understand their survival patterns but are relatively rare. Such information requires prolonged and consistent record-keeping over many generations, so for chimpanzees (Pan troglodytes), this equates to many decades of input. As life history variables can be altered by differences in environmental influences (whether natural or artificial), there is substantial value to being able to compare across populations. Here, we present the first comparative analysis of life history data for two ex situ chimpanzee populations residing in North America (1975–2020; n = 730) and Japan (1980–2020; n = 660). Overall, survival patterns were similar between regions, and the median life expectancy from birth is estimated at 35.7 (95% CI = [32.4–40.0]) years for females and 30.1 (27.3–34.3) years for males across both populations. Females who survive to their first birthday are estimated to survive 42.4 (40.0–46.3) years and males 35.5 (32.6–38.0) years. We found that birth type (wild-born or captive-born) did not influence survival patterns in either population, but there were differential effects of sex on longevity. In the America population, males had higher mortality rates than females, whereas in the Japan population we found no differences between the sexes. First year mortality did not differ between populations for males (18–20%), but for females it was lower in America (15%) compared to Japan (25%). Survival patterns of chimpanzees in the present study will be useful for future investigation into potential causes of regional differences and cross-species comparisons.
format: application/pdf
format: text/html
creator: Judy Che-Castaldo
creator: Kristin Havercamp
creator: Koshiro Watanuki
creator: Tetsuro Matsuzawa
creator: Satoshi Hirata
creator: Stephen R. Ross
subject: Evolutionary Studies
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.11913
publisher: PeerJ Inc.
rights: © 2021 Che-Castaldo et al.
abstract: Detailed, long-term datasets on the life histories of long-lived species such as great apes are necessary to understand their survival patterns but are relatively rare. Such information requires prolonged and consistent record-keeping over many generations, so for chimpanzees (Pan troglodytes), this equates to many decades of input. As life history variables can be altered by differences in environmental influences (whether natural or artificial), there is substantial value to being able to compare across populations. Here, we present the first comparative analysis of life history data for two ex situ chimpanzee populations residing in North America (1975–2020; n = 730) and Japan (1980–2020; n = 660). Overall, survival patterns were similar between regions, and the median life expectancy from birth is estimated at 35.7 (95% CI = [32.4–40.0]) years for females and 30.1 (27.3–34.3) years for males across both populations. Females who survive to their first birthday are estimated to survive 42.4 (40.0–46.3) years and males 35.5 (32.6–38.0) years. We found that birth type (wild-born or captive-born) did not influence survival patterns in either population, but there were differential effects of sex on longevity. In the America population, males had higher mortality rates than females, whereas in the Japan population we found no differences between the sexes. First year mortality did not differ between populations for males (18–20%), but for females it was lower in America (15%) compared to Japan (25%). Survival patterns of chimpanzees in the present study will be useful for future investigation into potential causes of regional differences and cross-species comparisons.
bibliographic citation: Che-Castaldo et al. (2021) Comparative survival analyses among captive chimpanzees (Pan troglodytes) in America and Japan. PeerJ 9:e11913 https://doi.org/10.7717/peerj.11913
date submitted: 2021-03-26
date accepted: 2021-07-14
issued: 2021-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Che-Castaldo
  given name: Judy
author list: Agent
  family name: Havercamp
  given name: Kristin
author list: Agent
  family name: Watanuki
  given name: Koshiro
author list: Agent
  family name: Matsuzawa
  given name: Tetsuro
author list: Agent
  family name: Hirata
  given name: Satoshi
author list: Agent
  family name: Ross
  given name: Stephen R.
doi: 10.7717/peerj.11913
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-12
copyright: © 2021 Che-Castaldo et al.
attribution name: Che-Castaldo et al.

Quantifying bite force in coexisting tayassuids and feral suids: a comparison between morphometric functional proxies and in vivo measurements
type: item
type: AcademicArticle
description: Background Measuring mammals’ bite force in laboratory conditions is not a simple task, let alone on wild medium-sized mammals in the field. Thus, morphometric-proxies are usually used to infer morphofunctional properties of musculoskeletal features. For instance, the study of bite force-indexes suggests that different capacities to crack food items reduce the competition between coexistent collared and white-lipped peccaries (Pecari tajacu and Tayassu pecari). The presence of exotic feral hogs (Sus scrofa) in peccaries’ endemic areas gives rise to new ecological interactions between them. An example is the Brazilian Pantanal wetland, where ecomorphological mechanisms may play a role in their ecological relations. Taking this scenario as a case of study, we aimed to verify if the morphometric-proxies are de facto reliable tools, by comparing bite forces-indexes with the in vivo bite forces of these species. Methods We captured 21 collared and white-lipped peccaries and feral hogs in the Brazilian Pantanal to assess their bite force at first molar. The Bite Force Measuring Tube (BiTu) is a robust and simple mechanical device designed to be used in field conditions. Only 11 individuals successfully bit the BiTu before being released. Their body measurements were compared and correlated with their bite force. The in vivo bite forces were compared with bite force-indexes of two papers based on independent morphometric methods and datasets: Sicuro & Oliveira (2002) used classic morphometrics to infer the bite forces of these three species in the Brazilian Pantanal, and Hendges et al. (2019) used geometric morphometrics to compare bite forces-indexes and feeding habits of the extant peccary species. The results of all species were standardized (Z-curves) according to each method. Doing so, we obtained comparable dimensionless comparable values but maintaining the differences between them. Results The morphometric-proxies-based studies presented similar results: collared p…
format: application/pdf
format: text/html
creator: Fernando L. Sicuro
creator: Luiz Flamarion B. Oliveira
creator: Carla D. Hendges
creator: Carlos Fonseca
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.11948
publisher: PeerJ Inc.
rights: © 2021 Sicuro et al.
abstract: Background Measuring mammals’ bite force in laboratory conditions is not a simple task, let alone on wild medium-sized mammals in the field. Thus, morphometric-proxies are usually used to infer morphofunctional properties of musculoskeletal features. For instance, the study of bite force-indexes suggests that different capacities to crack food items reduce the competition between coexistent collared and white-lipped peccaries (Pecari tajacu and Tayassu pecari). The presence of exotic feral hogs (Sus scrofa) in peccaries’ endemic areas gives rise to new ecological interactions between them. An example is the Brazilian Pantanal wetland, where ecomorphological mechanisms may play a role in their ecological relations. Taking this scenario as a case of study, we aimed to verify if the morphometric-proxies are de facto reliable tools, by comparing bite forces-indexes with the in vivo bite forces of these species. Methods We captured 21 collared and white-lipped peccaries and feral hogs in the Brazilian Pantanal to assess their bite force at first molar. The Bite Force Measuring Tube (BiTu) is a robust and simple mechanical device designed to be used in field conditions. Only 11 individuals successfully bit the BiTu before being released. Their body measurements were compared and correlated with their bite force. The in vivo bite forces were compared with bite force-indexes of two papers based on independent morphometric methods and datasets: Sicuro & Oliveira (2002) used classic morphometrics to infer the bite forces of these three species in the Brazilian Pantanal, and Hendges et al. (2019) used geometric morphometrics to compare bite forces-indexes and feeding habits of the extant peccary species. The results of all species were standardized (Z-curves) according to each method. Doing so, we obtained comparable dimensionless comparable values but maintaining the differences between them. Results The morphometric-proxies-based studies presented similar results: collared p…
bibliographic citation: Sicuro et al. (2021) Quantifying bite force in coexisting tayassuids and feral suids: a comparison between morphometric functional proxies and in vivo measurements. PeerJ 9:e11948 https://doi.org/10.7717/peerj.11948
date submitted: 2021-04-20
date accepted: 2021-07-20
issued: 2021-08-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sicuro
  given name: Fernando L.
author list: Agent
  family name: Oliveira
  given name: Luiz Flamarion B.
author list: Agent
  family name: Hendges
  given name: Carla D.
author list: Agent
  family name: Fonseca
  given name: Carlos
doi: 10.7717/peerj.11948
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-12
copyright: ©2021 Sicuro et al.
attribution name: Sicuro et al.

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