PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Transcriptome analysis reveals gene expression differences in Liriomyza trifolii exposed to combined heat and abamectin exposure
items: Investigation of inhibition effect of daidzein on osteosarcoma cells based on experimental validation and systematic pharmacology analysis
items: Hallmarks of glycogene expression and glycosylation pathways in squamous and adenocarcinoma cervical cancer
items: Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins
items: Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives
items: Ciprofloxacin reduces tenocyte viability and proteoglycan synthesis in short-term explant cultures of equine tendon
items: The distribution of benthic amphipod crustaceans in Indonesian seas
items: Wedge-tailed Shearwater (Ardenna pacifica) nesting success in human-dominated coastal environments
items: When size matters: the first comprehensive anatomical study of a species of “Condylocardiidae”, an extremely miniaturized bivalve
items: Anti-clustering in the national SARS-CoV-2 daily infection counts

Transcriptome analysis reveals gene expression differences in Liriomyza trifolii exposed to combined heat and abamectin exposure
type: item
type: AcademicArticle
description: Liriomyza trifolii is an invasive pest of horticultural and vegetable crops that possesses robust competitive advantages that enable it to replace closely-related species. High temperatures often occur concomitantly with insecticide usage during L. trifolii outbreaks. In this study, we compared the transcriptomes of L. trifolii exposed to high temperature (40 °C T40), insecticide (LC50 of technical grade abamectin, I50) and combined high temperature and abamectin exposure (IT5040, I50 followed by T40; and TI4050, T40 followed by I50). RNA-seq generated and revealed 44,633 unigenes with annotation data; these were compared with COG and KEGG databases for functional classification and enrichment analysis. Compared with the I50 treatment, COG classification indicated that ‘post-translational modification, protein turnover, chaperones’ was enriched in the IT5040 treatment. In the TI4050 treatment, ‘carbohydrate transport and metabolism’ was the most abundant group. The most enriched KEGG pathways in the TI4050 and IT5040 treatments were ‘longevity regulating pathway - multiple species’ and ‘protein processing in endoplasmic reticulum’, respectively. Subsequent annotation and enrichment analyses indicated that stress-related genes such as CYP450s and HSPs were differentially expressed in the I50 vs. TI4050 or I50 vs. IT5040 treatment groups. Three commercial insecticide formulations were also used to further verify the expression of selected differentially-expressed genes. This study will be conductive to consider the temperature effect on insecticide tolerance in L. trifolii, and provides a framework for improving the application efficiency of insecticides in hot weather, which will ultimately reduce the overuse of pesticides.
format: application/pdf
format: text/html
creator: Yu-Cheng Wang
creator: Ya-Wen Chang
creator: Yu-Zhou Du
subject: Agricultural Science
subject: Entomology
subject: Molecular Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.12064
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Liriomyza trifolii is an invasive pest of horticultural and vegetable crops that possesses robust competitive advantages that enable it to replace closely-related species. High temperatures often occur concomitantly with insecticide usage during L. trifolii outbreaks. In this study, we compared the transcriptomes of L. trifolii exposed to high temperature (40 °C T40), insecticide (LC50 of technical grade abamectin, I50) and combined high temperature and abamectin exposure (IT5040, I50 followed by T40; and TI4050, T40 followed by I50). RNA-seq generated and revealed 44,633 unigenes with annotation data; these were compared with COG and KEGG databases for functional classification and enrichment analysis. Compared with the I50 treatment, COG classification indicated that ‘post-translational modification, protein turnover, chaperones’ was enriched in the IT5040 treatment. In the TI4050 treatment, ‘carbohydrate transport and metabolism’ was the most abundant group. The most enriched KEGG pathways in the TI4050 and IT5040 treatments were ‘longevity regulating pathway - multiple species’ and ‘protein processing in endoplasmic reticulum’, respectively. Subsequent annotation and enrichment analyses indicated that stress-related genes such as CYP450s and HSPs were differentially expressed in the I50 vs. TI4050 or I50 vs. IT5040 treatment groups. Three commercial insecticide formulations were also used to further verify the expression of selected differentially-expressed genes. This study will be conductive to consider the temperature effect on insecticide tolerance in L. trifolii, and provides a framework for improving the application efficiency of insecticides in hot weather, which will ultimately reduce the overuse of pesticides.
bibliographic citation: Wang et al. (2021) Transcriptome analysis reveals gene expression differences in Liriomyza trifolii exposed to combined heat and abamectin exposure. PeerJ 9:e12064 https://doi.org/10.7717/peerj.12064
date submitted: 2021-04-21
date accepted: 2021-08-04
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wang
  given name: Yu-Cheng
author list: Agent
  family name: Chang
  given name: Ya-Wen
author list: Agent
  family name: Du
  given name: Yu-Zhou
doi: 10.7717/peerj.12064
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Investigation of inhibition effect of daidzein on osteosarcoma cells based on experimental validation and systematic pharmacology analysis
type: item
type: AcademicArticle
description: Objective This study aims to explore the effect of daidzein, which is a natural isoflavone compound mainly extracted from soybeans, on osteosarcoma and the potential molecular mechanism. Material and Methods 143B and U2OS osteosarcoma cells were treated with gradient concentrations of daidzein, and MTT assay was used to determine the cell proliferation capacity and IC50. Hoechst 33342 staining and Annexin V-FITC/PI detection were used to determine apoptosis. Cell cycle was analyzed by flow cytometry, and migration ability were detected by transwell assays and scratch wound assay. An osteosarcoma xenograft mice model was applied to investigate the effect of daidzein on osteosarcoma in vivo. Systematic pharmacology and molecular modeling analysis were applied to predict the target of daidzein to osteosarcoma, and the target Src was verified by western blotting. We also observed the effect of daidzein on cell proliferation and apoptosis of Src-overexpressing osteosarcoma cells. Results In vitro, daidzein significantly inhibited 143B and U2OS osteosarcoma cell proliferation and migration, and induced cell cycle arrest. In vivo, daidzein exerts antitumor effects in osteosarcoma xenograft mice. After systematic screening and analysis, Src-MAPK signaling pathway was predicted as the highest-ranked pathway. Western blot demonstrated that daidzein inhibited phosphorylation of the Src-ERK pathway in osteosarcoma cells. Also, overexpression of Src could partially reverse the inhibitory effects of daidzein on osteosarcoma cell proliferation. Conclusion Daidzein exerts an antitumor effect on osteosarcoma, and the mechanism may be through the Src-ERK pathway.
format: application/pdf
format: text/html
creator: Yufan Zhu
creator: Zhiqiang Yang
creator: Yuanlong Xie
creator: Min Yang
creator: Yufeng Zhang
creator: Zhouming Deng
creator: Lin Cai
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Toxicology
description: doi:10.7717/peerj.12072
publisher: PeerJ Inc.
rights: © 2021 Zhu et al.
abstract: Objective This study aims to explore the effect of daidzein, which is a natural isoflavone compound mainly extracted from soybeans, on osteosarcoma and the potential molecular mechanism. Material and Methods 143B and U2OS osteosarcoma cells were treated with gradient concentrations of daidzein, and MTT assay was used to determine the cell proliferation capacity and IC50. Hoechst 33342 staining and Annexin V-FITC/PI detection were used to determine apoptosis. Cell cycle was analyzed by flow cytometry, and migration ability were detected by transwell assays and scratch wound assay. An osteosarcoma xenograft mice model was applied to investigate the effect of daidzein on osteosarcoma in vivo. Systematic pharmacology and molecular modeling analysis were applied to predict the target of daidzein to osteosarcoma, and the target Src was verified by western blotting. We also observed the effect of daidzein on cell proliferation and apoptosis of Src-overexpressing osteosarcoma cells. Results In vitro, daidzein significantly inhibited 143B and U2OS osteosarcoma cell proliferation and migration, and induced cell cycle arrest. In vivo, daidzein exerts antitumor effects in osteosarcoma xenograft mice. After systematic screening and analysis, Src-MAPK signaling pathway was predicted as the highest-ranked pathway. Western blot demonstrated that daidzein inhibited phosphorylation of the Src-ERK pathway in osteosarcoma cells. Also, overexpression of Src could partially reverse the inhibitory effects of daidzein on osteosarcoma cell proliferation. Conclusion Daidzein exerts an antitumor effect on osteosarcoma, and the mechanism may be through the Src-ERK pathway.
bibliographic citation: Zhu et al. (2021) Investigation of inhibition effect of daidzein on osteosarcoma cells based on experimental validation and systematic pharmacology analysis. PeerJ 9:e12072 https://doi.org/10.7717/peerj.12072
date submitted: 2021-04-07
date accepted: 2021-08-05
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Yufan
author list: Agent
  family name: Yang
  given name: Zhiqiang
author list: Agent
  family name: Xie
  given name: Yuanlong
author list: Agent
  family name: Yang
  given name: Min
author list: Agent
  family name: Zhang
  given name: Yufeng
author list: Agent
  family name: Deng
  given name: Zhouming
author list: Agent
  family name: Cai
  given name: Lin
doi: 10.7717/peerj.12072
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: ©2021 Zhu et al.
attribution name: Zhu et al.

Hallmarks of glycogene expression and glycosylation pathways in squamous and adenocarcinoma cervical cancer
type: item
type: AcademicArticle
description: Background Dysregulation of glycogene expression in cancer can lead to aberrant glycan expression, which can promote tumorigenesis. Cervical cancer (CC) displays an increased expression of glycogenes involved in sialylation and sialylated glycans. Here, we show a comprehensive analysis of glycogene expression in CC to identify glycogene expression signatures and the possible glycosylation pathways altered. Methods First, we performed a microarray expression assay to compare glycogene expression changes between normal and cervical cancer tissues. Second, we used 401 glycogenes to analyze glycogene expression in adenocarcinoma and squamous carcinoma from RNA-seq data at the cBioPortal for Cancer Genomics. Results The analysis of the microarray expression assay indicated that CC displayed an increase in glycogenes related to GPI-anchored biosynthesis and a decrease in genes associated with chondroitin and dermatan sulfate with respect to normal tissue. Also, the glycogene analysis of CC samples by the RNA-seq showed that the glycogenes involved in the chondroitin and dermatan sulfate pathway were downregulated. Interestingly the adenocarcinoma tumors displayed a unique glycogene expression signature compared to squamous cancer that shows heterogeneous glycogene expression divided into six types. Squamous carcinoma type 5 (SCC-5) showed increased expression of genes implicated in keratan and heparan sulfate synthesis, glycosaminoglycan degradation, ganglio, and globo glycosphingolipid synthesis was related to poorly differentiated tumors and poor survival. Squamous carcinoma type 6 (SCC-6) displayed an increased expression of genes involved in chondroitin/dermatan sulfate synthesis and lacto and neolacto glycosphingolipid synthesis and was associated with nonkeratinizing squamous cancer and good survival. In summary, our study showed that CC tumors are not a uniform entity, and their glycome signatures could be related to different clinicopathological characteristics.
format: application/pdf
format: text/html
creator: Patricia Martinez-Morales
creator: Irene Morán Cruz
creator: Lorena Roa-de la Cruz
creator: Paola Maycotte
creator: Juan Salvador Reyes Salinas
creator: Victor Javier Vazquez Zamora
creator: Claudia Teresita Gutierrez Quiroz
creator: Alvaro Jose Montiel-Jarquin
creator: Verónica Vallejo-Ruiz
subject: Biochemistry
subject: Molecular Biology
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.12081
publisher: PeerJ Inc.
rights: © 2021 Martinez-Morales et al.
abstract: Background Dysregulation of glycogene expression in cancer can lead to aberrant glycan expression, which can promote tumorigenesis. Cervical cancer (CC) displays an increased expression of glycogenes involved in sialylation and sialylated glycans. Here, we show a comprehensive analysis of glycogene expression in CC to identify glycogene expression signatures and the possible glycosylation pathways altered. Methods First, we performed a microarray expression assay to compare glycogene expression changes between normal and cervical cancer tissues. Second, we used 401 glycogenes to analyze glycogene expression in adenocarcinoma and squamous carcinoma from RNA-seq data at the cBioPortal for Cancer Genomics. Results The analysis of the microarray expression assay indicated that CC displayed an increase in glycogenes related to GPI-anchored biosynthesis and a decrease in genes associated with chondroitin and dermatan sulfate with respect to normal tissue. Also, the glycogene analysis of CC samples by the RNA-seq showed that the glycogenes involved in the chondroitin and dermatan sulfate pathway were downregulated. Interestingly the adenocarcinoma tumors displayed a unique glycogene expression signature compared to squamous cancer that shows heterogeneous glycogene expression divided into six types. Squamous carcinoma type 5 (SCC-5) showed increased expression of genes implicated in keratan and heparan sulfate synthesis, glycosaminoglycan degradation, ganglio, and globo glycosphingolipid synthesis was related to poorly differentiated tumors and poor survival. Squamous carcinoma type 6 (SCC-6) displayed an increased expression of genes involved in chondroitin/dermatan sulfate synthesis and lacto and neolacto glycosphingolipid synthesis and was associated with nonkeratinizing squamous cancer and good survival. In summary, our study showed that CC tumors are not a uniform entity, and their glycome signatures could be related to different clinicopathological characteristics.
bibliographic citation: Martinez-Morales et al. (2021) Hallmarks of glycogene expression and glycosylation pathways in squamous and adenocarcinoma cervical cancer. PeerJ 9:e12081 https://doi.org/10.7717/peerj.12081
date submitted: 2021-05-14
date accepted: 2021-08-06
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martinez-Morales
  given name: Patricia
author list: Agent
  family name: Morán Cruz
  given name: Irene
author list: Agent
  family name: Roa-de la Cruz
  given name: Lorena
author list: Agent
  family name: Maycotte
  given name: Paola
author list: Agent
  family name: Reyes Salinas
  given name: Juan Salvador
author list: Agent
  family name: Vazquez Zamora
  given name: Victor Javier
author list: Agent
  family name: Gutierrez Quiroz
  given name: Claudia Teresita
author list: Agent
  family name: Montiel-Jarquin
  given name: Alvaro Jose
author list: Agent
  family name: Vallejo-Ruiz
  given name: Verónica
doi: 10.7717/peerj.12081
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: © 2021 Martinez-Morales et al.
attribution name: Martinez-Morales et al.

Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins
type: item
type: AcademicArticle
description: Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species’ guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent.
format: application/pdf
format: text/html
creator: Ruber Rodríguez-Barreras
creator: Eduardo L. Tosado-Rodríguez
creator: Filipa Godoy-Vitorino
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Zoology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.12084
publisher: PeerJ Inc.
rights: © 2021 Rodríguez-Barreras et al.
abstract: Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species’ guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent.
bibliographic citation: Rodríguez-Barreras et al. (2021) Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins. PeerJ 9:e12084 https://doi.org/10.7717/peerj.12084
date submitted: 2021-03-24
date accepted: 2021-08-07
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodríguez-Barreras
  given name: Ruber
author list: Agent
  family name: Tosado-Rodríguez
  given name: Eduardo L.
author list: Agent
  family name: Godoy-Vitorino
  given name: Filipa
doi: 10.7717/peerj.12084
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: ©2021 Rodríguez-Barreras et al.
attribution name: Rodríguez-Barreras et al.

Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives
type: item
type: AcademicArticle
description: The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.
format: application/pdf
format: text/html
creator: Mikhail I. Schelkunov
creator: Maxim S. Nuraliev
creator: Maria D. Logacheva
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.12106
publisher: PeerJ Inc.
rights: © 2021 Schelkunov et al.
abstract: The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.
bibliographic citation: Schelkunov et al. (2021) Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives. PeerJ 9:e12106 https://doi.org/10.7717/peerj.12106
date submitted: 2020-10-07
date accepted: 2021-08-11
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schelkunov
  given name: Mikhail I.
author list: Agent
  family name: Nuraliev
  given name: Maxim S.
author list: Agent
  family name: Logacheva
  given name: Maria D.
doi: 10.7717/peerj.12106
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: © 2021 Schelkunov et al.
attribution name: Schelkunov et al.

Ciprofloxacin reduces tenocyte viability and proteoglycan synthesis in short-term explant cultures of equine tendon
type: item
type: AcademicArticle
description: Fluoroquinolones are an effective, broad-spectrum antibiotic used to treat an array of bacterial infections. However, they are associated with an increased risk of tendinopathy and tendon rupture even after discontinuation of treatment. This condition is known as fluoroquinolone-associated tendinopathy, the underlying mechanisms of which are poorly understood. While many factors may be involved in the pathophysiology of tendinopathies in general, changes in tenocyte metabolism and viability, as well as alteration of proteoglycan metabolism are prominent findings in the scientific literature. This study investigated the effects of ciprofloxacin, a common fluoroquinolone, on cell viability, proteoglycan synthesis, and proteoglycan mRNA expression in equine superficial digital flexor tendon explants after 96 h treatment with between 1–300 µg/mL ciprofloxacin, and again after 8 days discontinuation of treatment. Ciprofloxacin caused significant reductions in cell viability by between 25–33% at all dosages except 10 µg/mL, and viability decreased further after 8 days discontinuation of treatment. Proteoglycan synthesis significantly decreased by approximately 50% in explants treated with 100 µg/mL and 300 µg/mL, however this effect reversed after 8 days in the absence of treatment. No significant mRNA expression changes were observed after the treatment period with the exception of versican which was down-regulated at the highest concentration of ciprofloxacin. After the recovery period, aggrecan, biglycan and versican genes were all significantly downregulated in explants initially treated with 1–100 µg/mL. Results from this study corroborate previously reported findings of reduced cell viability and proteoglycan synthesis in a whole tissue explant model and provide further insight into the mechanisms underlying fluoroquinolone-associated tendinopathy and rupture. This study further demonstrates that certain ciprofloxacin induced cellular changes are not rapidly reverse…
format: application/pdf
format: text/html
creator: Stuart James
creator: Johannes Schuijers
creator: John Daffy
creator: Jill Cook
creator: Tom Samiric
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.12003
publisher: PeerJ Inc.
rights: © 2021 James et al.
abstract: Fluoroquinolones are an effective, broad-spectrum antibiotic used to treat an array of bacterial infections. However, they are associated with an increased risk of tendinopathy and tendon rupture even after discontinuation of treatment. This condition is known as fluoroquinolone-associated tendinopathy, the underlying mechanisms of which are poorly understood. While many factors may be involved in the pathophysiology of tendinopathies in general, changes in tenocyte metabolism and viability, as well as alteration of proteoglycan metabolism are prominent findings in the scientific literature. This study investigated the effects of ciprofloxacin, a common fluoroquinolone, on cell viability, proteoglycan synthesis, and proteoglycan mRNA expression in equine superficial digital flexor tendon explants after 96 h treatment with between 1–300 µg/mL ciprofloxacin, and again after 8 days discontinuation of treatment. Ciprofloxacin caused significant reductions in cell viability by between 25–33% at all dosages except 10 µg/mL, and viability decreased further after 8 days discontinuation of treatment. Proteoglycan synthesis significantly decreased by approximately 50% in explants treated with 100 µg/mL and 300 µg/mL, however this effect reversed after 8 days in the absence of treatment. No significant mRNA expression changes were observed after the treatment period with the exception of versican which was down-regulated at the highest concentration of ciprofloxacin. After the recovery period, aggrecan, biglycan and versican genes were all significantly downregulated in explants initially treated with 1–100 µg/mL. Results from this study corroborate previously reported findings of reduced cell viability and proteoglycan synthesis in a whole tissue explant model and provide further insight into the mechanisms underlying fluoroquinolone-associated tendinopathy and rupture. This study further demonstrates that certain ciprofloxacin induced cellular changes are not rapidly reverse…
bibliographic citation: James et al. (2021) Ciprofloxacin reduces tenocyte viability and proteoglycan synthesis in short-term explant cultures of equine tendon. PeerJ 9:e12003 https://doi.org/10.7717/peerj.12003
date submitted: 2021-03-17
date accepted: 2021-07-27
issued: 2021-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: James
  given name: Stuart
author list: Agent
  family name: Schuijers
  given name: Johannes
author list: Agent
  family name: Daffy
  given name: John
author list: Agent
  family name: Cook
  given name: Jill
author list: Agent
  family name: Samiric
  given name: Tom
doi: 10.7717/peerj.12003
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-30
copyright: © 2021 James et al.
attribution name: James et al.

The distribution of benthic amphipod crustaceans in Indonesian seas
type: item
type: AcademicArticle
description: Amphipod crustaceans are an essential component of tropical marine biodiversity. However, their distribution and biogeography have not been analysed in one of the world’s largest tropical countries nested in the Coral Triangle, Indonesia. We collected and identified amphipod crustaceans from eight sites in Indonesian waters and combined the results with data from 32 additional sites in the literature. We analysed the geographic distribution of 147 benthic amphipod crustaceans using cluster analysis and the ‘Bioregions Infomaps’ neural network method of biogeographic discrimination. We found five groups of benthic amphipod crustaceans which show relationships with sampling methods, depth, and substrata. Neural network biogeographic analysis indicated there was only one biogeographic region that matched with the global amphipod regions and marine biogeographic realms defined for all marine taxa. There was no support for Wallaces or other lines being marine biogeographic boundaries in the region. Species richness was lower than expected considering the region is within the Coral Triangle. We hypothesise that this low richness might be due to the intense fish predation which may have limited amphipod diversification. The results indicated that habitat rather than biogeography determines amphipod distribution in Indonesia. Therefore, future research needs to sample more habitats, and consider habitat in conservation planning.
format: application/pdf
format: text/html
creator: Tri Arfianti
creator: Mark John Costello
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12054
publisher: PeerJ Inc.
rights: © 2021 Arfianti and Costello
abstract: Amphipod crustaceans are an essential component of tropical marine biodiversity. However, their distribution and biogeography have not been analysed in one of the world’s largest tropical countries nested in the Coral Triangle, Indonesia. We collected and identified amphipod crustaceans from eight sites in Indonesian waters and combined the results with data from 32 additional sites in the literature. We analysed the geographic distribution of 147 benthic amphipod crustaceans using cluster analysis and the ‘Bioregions Infomaps’ neural network method of biogeographic discrimination. We found five groups of benthic amphipod crustaceans which show relationships with sampling methods, depth, and substrata. Neural network biogeographic analysis indicated there was only one biogeographic region that matched with the global amphipod regions and marine biogeographic realms defined for all marine taxa. There was no support for Wallaces or other lines being marine biogeographic boundaries in the region. Species richness was lower than expected considering the region is within the Coral Triangle. We hypothesise that this low richness might be due to the intense fish predation which may have limited amphipod diversification. The results indicated that habitat rather than biogeography determines amphipod distribution in Indonesia. Therefore, future research needs to sample more habitats, and consider habitat in conservation planning.
bibliographic citation: Arfianti et al. (2021) The distribution of benthic amphipod crustaceans in Indonesian seas. PeerJ 9:e12054 https://doi.org/10.7717/peerj.12054
date submitted: 2021-04-27
date accepted: 2021-08-04
issued: 2021-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arfianti
  given name: Tri
author list: Agent
  family name: Costello
  given name: Mark John
doi: 10.7717/peerj.12054
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-30
copyright: ©2021 Arfianti and Costello
attribution name: Arfianti and Costello

Wedge-tailed Shearwater (Ardenna pacifica) nesting success in human-dominated coastal environments
type: item
type: AcademicArticle
description: Many seabird populations are declining globally, but successful conservation efforts have led to population expansion of some species into human-dominated landscapes. Thus, there is an increased potential for direct human and seabird interactions for certain species in human-occupied areas, with nest-site characteristics potentially affecting the susceptibility of nests to human disturbance. We assessed the effect of human activity and nest-site characteristics on Wedge-tailed Shearwater (Ardenna pacifica, ʻuaʻu kani) nesting success at two breeding colonies, one with human exposure and one without, located in Kailua, Oʻahu, Hawaiʻi. Human activity was measured by recording the frequency of people who entered a 5 m buffer around each nest. Nests were checked every two to three days to monitor nest success. The effect of human activity and nest-site characteristics on nesting success was determined using a variety of combinations of variables within binomial logistic regression models and AICc model selection. Nest-site characteristics among nests at both sites and human activity at the human-exposed site did not show a significant effect on nesting success. Our results suggest Wedge-tailed Shearwaters may experience some tolerance of human activity immediately around their nests—as long as burrow collapse does not occur. Given the small sample sizes and a single season of data collection, additional studies are needed to better understand the effect of human disturbance on Wedge-tailed Shearwaters. Infrastructure, such as fencing and signage, may be effective at reducing human-caused nest failure and may allow humans and disturbance-tolerant seabird species to coexist in shared coastal environments.
format: application/pdf
format: text/html
creator: Jessica L. Idle
creator: Chad J. Wilhite
creator: Kristen C. Harmon
creator: Brooke Friswold
creator: Melissa R. Price
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.12096
publisher: PeerJ Inc.
rights: © 2021 Idle et al.
abstract: Many seabird populations are declining globally, but successful conservation efforts have led to population expansion of some species into human-dominated landscapes. Thus, there is an increased potential for direct human and seabird interactions for certain species in human-occupied areas, with nest-site characteristics potentially affecting the susceptibility of nests to human disturbance. We assessed the effect of human activity and nest-site characteristics on Wedge-tailed Shearwater (Ardenna pacifica, ʻuaʻu kani) nesting success at two breeding colonies, one with human exposure and one without, located in Kailua, Oʻahu, Hawaiʻi. Human activity was measured by recording the frequency of people who entered a 5 m buffer around each nest. Nests were checked every two to three days to monitor nest success. The effect of human activity and nest-site characteristics on nesting success was determined using a variety of combinations of variables within binomial logistic regression models and AICc model selection. Nest-site characteristics among nests at both sites and human activity at the human-exposed site did not show a significant effect on nesting success. Our results suggest Wedge-tailed Shearwaters may experience some tolerance of human activity immediately around their nests—as long as burrow collapse does not occur. Given the small sample sizes and a single season of data collection, additional studies are needed to better understand the effect of human disturbance on Wedge-tailed Shearwaters. Infrastructure, such as fencing and signage, may be effective at reducing human-caused nest failure and may allow humans and disturbance-tolerant seabird species to coexist in shared coastal environments.
bibliographic citation: Idle et al. (2021) Wedge-tailed Shearwater (Ardenna pacifica) nesting success in human-dominated coastal environments. PeerJ 9:e12096 https://doi.org/10.7717/peerj.12096
date submitted: 2020-09-14
date accepted: 2021-08-10
issued: 2021-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Idle
  given name: Jessica L.
author list: Agent
  family name: Wilhite
  given name: Chad J.
author list: Agent
  family name: Harmon
  given name: Kristen C.
author list: Agent
  family name: Friswold
  given name: Brooke
author list: Agent
  family name: Price
  given name: Melissa R.
doi: 10.7717/peerj.12096
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-30
copyright: ©2021 Idle et al.
attribution name: Idle et al.

When size matters: the first comprehensive anatomical study of a species of “Condylocardiidae”, an extremely miniaturized bivalve
type: item
type: AcademicArticle
description: ‘Miniaturization’ is a widespread phenomenon among the Metazoa. In the molluscan class Bivalvia, records of miniaturization are numerous. Among the Archiheterodonta, Warrana besnardi (Klappenbach, 1963) has attracted attention for its tiny size, which does not exceed 1.5 mm in shell length, and because it belongs to a group with limited anatomical information and often-debated status, the “Condylocardiidae” (which recent molecular studies place deeply nested within the family Carditidae). All species of Warrana Laseron, 1953 are small-bodied, and so miniaturization presumably occurred from a large-bodied ancestor within the Carditidae sensu lato. South American W. besnardi is here studied in detail. Its small size and the enlargement of the anterodorsal region during growth, reflects (and likely led) to infaunal habit, living as a burrowing bivalve that passively feeds on deposit particles entering the pallial cavity anteriorly. Mantle glands, previously reported as a common feature of other archiheterodonts, are missing in W. besnardi, but spongiform tissue in the antero-ventral portion of the mantle lobes presumably represents a blood sinus that might compensate for the great reduction of the ctenidia. Lecithotrophy is reported, with yolky oocytes bearing a thick non-cellular capsule layer; brooding was not observed, and it is here hypothesized that the extreme miniaturization, with the great reduction of ctenidia, is responsible for a shift in the reproductive mode of condylocardiids, contrasting with the commonly reported ovoviviparity of the carditids.
format: application/pdf
format: text/html
creator: Flávio Dias Passos
creator: Alan Rodrigo Batistão
creator: Rüdiger Bieler
subject: Biodiversity
subject: Marine Biology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.12108
publisher: PeerJ Inc.
rights: © 2021 Passos et al.
abstract: ‘Miniaturization’ is a widespread phenomenon among the Metazoa. In the molluscan class Bivalvia, records of miniaturization are numerous. Among the Archiheterodonta, Warrana besnardi (Klappenbach, 1963) has attracted attention for its tiny size, which does not exceed 1.5 mm in shell length, and because it belongs to a group with limited anatomical information and often-debated status, the “Condylocardiidae” (which recent molecular studies place deeply nested within the family Carditidae). All species of Warrana Laseron, 1953 are small-bodied, and so miniaturization presumably occurred from a large-bodied ancestor within the Carditidae sensu lato. South American W. besnardi is here studied in detail. Its small size and the enlargement of the anterodorsal region during growth, reflects (and likely led) to infaunal habit, living as a burrowing bivalve that passively feeds on deposit particles entering the pallial cavity anteriorly. Mantle glands, previously reported as a common feature of other archiheterodonts, are missing in W. besnardi, but spongiform tissue in the antero-ventral portion of the mantle lobes presumably represents a blood sinus that might compensate for the great reduction of the ctenidia. Lecithotrophy is reported, with yolky oocytes bearing a thick non-cellular capsule layer; brooding was not observed, and it is here hypothesized that the extreme miniaturization, with the great reduction of ctenidia, is responsible for a shift in the reproductive mode of condylocardiids, contrasting with the commonly reported ovoviviparity of the carditids.
bibliographic citation: Passos et al. (2021) When size matters: the first comprehensive anatomical study of a species of “Condylocardiidae”, an extremely miniaturized bivalve. PeerJ 9:e12108 https://doi.org/10.7717/peerj.12108
date submitted: 2021-03-29
date accepted: 2021-08-12
issued: 2021-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Passos
  given name: Flávio Dias
author list: Agent
  family name: Batistão
  given name: Alan Rodrigo
author list: Agent
  family name: Bieler
  given name: Rüdiger
doi: 10.7717/peerj.12108
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-30
copyright: © 2021 Passos et al.
attribution name: Passos et al.

Anti-clustering in the national SARS-CoV-2 daily infection counts
type: item
type: AcademicArticle
description: The noise in daily infection counts of an epidemic should be super-Poissonian due to intrinsic epidemiological and administrative clustering. Here, we use this clustering to classify the official national SARS-CoV-2 daily infection counts and check for infection counts that are unusually anti-clustered. We adopt a one-parameter model of $\phi _i^{\prime}$ϕi′ infections per cluster, dividing any daily count ni into $n_i/ _i^{\prime}$ni/ϕi′ ‘clusters’, for ‘country’ i. We assume that ${n_i}/\phi _i^{\prime}$ni/ϕi′ on a given day j is drawn from a Poisson distribution whose mean is robustly estimated from the four neighbouring days, and calculate the inferred Poisson probability $P_{ij}^{\prime}$Pij′ of the observation. The $P_{ij}^{\prime}$Pij′ values should be uniformly distributed. We find the value $\phi_i$ϕi that minimises the Kolmogorov–Smirnov distance from a uniform distribution. We investigate the (ϕi, Ni) distribution, for total infection count Ni. We consider consecutive count sequences above a threshold of 50 daily infections. We find that most of the daily infection count sequences are inconsistent with a Poissonian model. Most are found to be consistent with the ϕi model. The 28-, 14- and 7-day least noisy sequences for several countries are best modelled as sub-Poissonian, suggesting a distinct epidemiological family. The 28-day least noisy sequence of Algeria has a preferred model that is strongly sub-Poissonian, with $\phi _i^{28} < 0.1$ϕi28<0.1 . Tajikistan, Turkey, Russia, Belarus, Albania, United Arab Emirates and Nicaragua have preferred models that are also sub-Poissonian, with $\phi _i^{28} < 0.5$ϕi28<0.5 . A statistically significant (Pτ < 0.05) correlation was found between the lack of media freedom in a country, as represented by a high Reporters sans frontieres Press Freedom Index (PFI2020), and the lack of statistical noise in the country’s daily counts. The ϕi model appears to be an effective detector of suspiciously low statistical noise i…
format: application/pdf
format: text/html
creator: Boudewijn F. Roukema
subject: Epidemiology
subject: Infectious Diseases
subject: Statistics
subject: Data Science
description: doi:10.7717/peerj.11856
publisher: PeerJ Inc.
rights: © 2021 Roukema
abstract: The noise in daily infection counts of an epidemic should be super-Poissonian due to intrinsic epidemiological and administrative clustering. Here, we use this clustering to classify the official national SARS-CoV-2 daily infection counts and check for infection counts that are unusually anti-clustered. We adopt a one-parameter model of $\phi _i^{\prime}$ϕi′ infections per cluster, dividing any daily count ni into $n_i/ _i^{\prime}$ni/ϕi′ ‘clusters’, for ‘country’ i. We assume that ${n_i}/\phi _i^{\prime}$ni/ϕi′ on a given day j is drawn from a Poisson distribution whose mean is robustly estimated from the four neighbouring days, and calculate the inferred Poisson probability $P_{ij}^{\prime}$Pij′ of the observation. The $P_{ij}^{\prime}$Pij′ values should be uniformly distributed. We find the value $\phi_i$ϕi that minimises the Kolmogorov–Smirnov distance from a uniform distribution. We investigate the (ϕi, Ni) distribution, for total infection count Ni. We consider consecutive count sequences above a threshold of 50 daily infections. We find that most of the daily infection count sequences are inconsistent with a Poissonian model. Most are found to be consistent with the ϕi model. The 28-, 14- and 7-day least noisy sequences for several countries are best modelled as sub-Poissonian, suggesting a distinct epidemiological family. The 28-day least noisy sequence of Algeria has a preferred model that is strongly sub-Poissonian, with $\phi _i^{28} < 0.1$ϕi28<0.1 . Tajikistan, Turkey, Russia, Belarus, Albania, United Arab Emirates and Nicaragua have preferred models that are also sub-Poissonian, with $\phi _i^{28} < 0.5$ϕi28<0.5 . A statistically significant (Pτ < 0.05) correlation was found between the lack of media freedom in a country, as represented by a high Reporters sans frontieres Press Freedom Index (PFI2020), and the lack of statistical noise in the country’s daily counts. The ϕi model appears to be an effective detector of suspiciously low statistical noise i…
bibliographic citation: Roukema (2021) Anti-clustering in the national SARS-CoV-2 daily infection counts. PeerJ 9:e11856 https://doi.org/10.7717/peerj.11856
date submitted: 2021-01-26
date accepted: 2021-07-04
issued: 2021-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roukema
  given name: Boudewijn F.
doi: 10.7717/peerj.11856
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-27
copyright: © 2021 Roukema
attribution name: Roukema

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