PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Physical activity and socio-economic status of single and married urban adults: a cross-sectional study
items: Fine-scale plasticity in nest placement can compensate for poor quality junipers as nesting trees for gray vireos
items: Enhanced soluble sugar content in tomato fruit using CRISPR/Cas9-mediated SlINVINH1 and SlVPE5 gene editing
items: Identification of keygenes, miRNAs and miRNA-mRNA regulatory pathways for chemotherapy resistance in ovarian cancer
items: Horsenettle (Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales
items: Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli)
items: Incidence and clinicopathological features of colorectal cancer among multi-ethnic patients in Kuala Lumpur, Malaysia: a hospital-based retrospective analysis over two decades
items: Abundant CpG-sequences in human genomes inhibit KIR3DL2-expressing NK cells
items: Dissection of full-length transcriptome and metabolome of Dichocarpum (Ranunculaceae): implications in evolution of specialized metabolism of Ranunculales medicinal plants
items: Evolutionary history of the vertebrate Piwi gene family

Physical activity and socio-economic status of single and married urban adults: a cross-sectional study
type: item
type: AcademicArticle
description: Background Changing family models have resulted in a large increase in the number of single-person households. This phenomenon has certain implications for society and the economy as single people often exhibit different behaviours, including their engagement in health-related physical activity, than those who are married and living with partners. However, the results of studies on determinants of physical activity in people of different marital status have been inconclusive. The aim of this study was to identify associations between physical activity and socioeconomic status in single and married urban adults. Methods The study material consisted of 4,460 persons (1,828 single and 2,632 married and living with partners). A cross-sectional study was conducted in Wroclaw (Poland). A diagnostic survey-direct interview method was used. Two research tools were applied: the International Physical Activity Questionnaire Short Form (IPAQ-SF) and the Socioeconomic Status Questionnaire (S-ESQ). The level of respondents’ physical activity was assessed following WHO recommendations. The descriptive statistics included the number and frequency of categories of dependent and independent variables as well as measures of association between them, i.e., crude and adjusted odds ratios. Results The odds ratio of meeting the WHO physical activity recommendations was almost 70% higher in single than in married respondents (OR = 1.67; CI [1.46–2.19]), and slightly more than 40% higher after adjusting for sex, age and education (aOR = 1.42; CI [1.21–1.67]). In both groups socioeconomic the respondents’ status revealed a significant and slightly different association with their levels of physical activity. Occupational status and financial savings significantly affected the level of physical activity in single respondents, while net disposable income was a significant modifier of physical activity levels in respondents who were married or lived with their partners. Conclusions Assessment …
format: application/pdf
format: text/html
creator: Daniel Puciato
creator: Michał Rozpara
subject: Anthropology
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.12466
publisher: PeerJ Inc.
rights: © 2021 Puciato and Rozpara
abstract: Background Changing family models have resulted in a large increase in the number of single-person households. This phenomenon has certain implications for society and the economy as single people often exhibit different behaviours, including their engagement in health-related physical activity, than those who are married and living with partners. However, the results of studies on determinants of physical activity in people of different marital status have been inconclusive. The aim of this study was to identify associations between physical activity and socioeconomic status in single and married urban adults. Methods The study material consisted of 4,460 persons (1,828 single and 2,632 married and living with partners). A cross-sectional study was conducted in Wroclaw (Poland). A diagnostic survey-direct interview method was used. Two research tools were applied: the International Physical Activity Questionnaire Short Form (IPAQ-SF) and the Socioeconomic Status Questionnaire (S-ESQ). The level of respondents’ physical activity was assessed following WHO recommendations. The descriptive statistics included the number and frequency of categories of dependent and independent variables as well as measures of association between them, i.e., crude and adjusted odds ratios. Results The odds ratio of meeting the WHO physical activity recommendations was almost 70% higher in single than in married respondents (OR = 1.67; CI [1.46–2.19]), and slightly more than 40% higher after adjusting for sex, age and education (aOR = 1.42; CI [1.21–1.67]). In both groups socioeconomic the respondents’ status revealed a significant and slightly different association with their levels of physical activity. Occupational status and financial savings significantly affected the level of physical activity in single respondents, while net disposable income was a significant modifier of physical activity levels in respondents who were married or lived with their partners. Conclusions Assessment …
bibliographic citation: Puciato et al. (2021) Physical activity and socio-economic status of single and married urban adults: a cross-sectional study. PeerJ 9:e12466 https://doi.org/10.7717/peerj.12466
date submitted: 2021-03-05
date accepted: 2021-10-19
issued: 2021-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Puciato
  given name: Daniel
author list: Agent
  family name: Rozpara
  given name: Michał
doi: 10.7717/peerj.12466
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-09
copyright: © 2021 Puciato and Rozpara
attribution name: Puciato and Rozpara

Fine-scale plasticity in nest placement can compensate for poor quality junipers as nesting trees for gray vireos
type: item
type: AcademicArticle
description: Understanding the interactions between behavior and habitat characteristics can have important implications for species of conservation concern. Gray vireos (Vireo vicinior) are one example of a species of conservation concern that is understudied in terms of nest survival probabilities and the habitat characteristics that influence them. Our objective was to determine if habitat features such as juniper density, juniper foliage density, or tree height influence nest survival probabilities, and if gray vireo nest placement can mitigate habitat risks. Based on previous work, we expected daily nest survival probabilities to be associated with nest height and surrounding vegetation. We monitored 89 nests in central New Mexico from 2016–2018 to estimate daily nest survival probabilities. We compared variation in nest placement, nest tree characteristics, and surrounding vegetation between failed and successful nests using logistic exposure models and Akaike Information Criteria. Daily and cumulative nest survival probability were 0.983 (95% CI [0.973–0.989]) and 0.575 (95% CI [0.444–0.702]), respectively. Top models predicting nest survival included a negative interaction between nest-tree foliage density and the distance of the nest from the edge of the nesting tree. This suggests that gray vireos can mitigate risks associated with low nest concealment by nesting closer to the interior of the nesting tree.
format: application/pdf
format: text/html
creator: Jonathan Harris
creator: Loren Smith
creator: Scott McMurry
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.12477
publisher: PeerJ Inc.
rights: © 2021 Harris et al.
abstract: Understanding the interactions between behavior and habitat characteristics can have important implications for species of conservation concern. Gray vireos (Vireo vicinior) are one example of a species of conservation concern that is understudied in terms of nest survival probabilities and the habitat characteristics that influence them. Our objective was to determine if habitat features such as juniper density, juniper foliage density, or tree height influence nest survival probabilities, and if gray vireo nest placement can mitigate habitat risks. Based on previous work, we expected daily nest survival probabilities to be associated with nest height and surrounding vegetation. We monitored 89 nests in central New Mexico from 2016–2018 to estimate daily nest survival probabilities. We compared variation in nest placement, nest tree characteristics, and surrounding vegetation between failed and successful nests using logistic exposure models and Akaike Information Criteria. Daily and cumulative nest survival probability were 0.983 (95% CI [0.973–0.989]) and 0.575 (95% CI [0.444–0.702]), respectively. Top models predicting nest survival included a negative interaction between nest-tree foliage density and the distance of the nest from the edge of the nesting tree. This suggests that gray vireos can mitigate risks associated with low nest concealment by nesting closer to the interior of the nesting tree.
bibliographic citation: Harris et al. (2021) Fine-scale plasticity in nest placement can compensate for poor quality junipers as nesting trees for gray vireos. PeerJ 9:e12477 https://doi.org/10.7717/peerj.12477
date submitted: 2021-06-09
date accepted: 2021-10-20
issued: 2021-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harris
  given name: Jonathan
author list: Agent
  family name: Smith
  given name: Loren
author list: Agent
  family name: McMurry
  given name: Scott
doi: 10.7717/peerj.12477
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-09
copyright: © 2021 Harris et al.
attribution name: Harris et al.

Enhanced soluble sugar content in tomato fruit using CRISPR/Cas9-mediated SlINVINH1 and SlVPE5 gene editing
type: item
type: AcademicArticle
description: Soluble sugar is known to improve the sweetness and increase tomato sauce yield. Studies have focused on improving the content of soluble sugar in tomato fruits, usually by promoting functional genes. We studied two genes (SlINVINH1 and SlVPE5) that inhibited the accumulation of soluble sugar in tomato fruits and obtained two genes’ knocked-out lines (CRISPR-invinh1 or CRISPR-vpe5) using CRISPR/Cas9. Aggregated lines with CRISPR-invinh1 and CRISPR-vpe5 were gained by hybridization and self-pollination. Compared to wild-type lines, the glucose, fructose, and total soluble solid (TSS) contents of CRISPR-invinh1 and CRISPR-vpe5 increased significantly. Glucose, fructose, and TSS levels further improved simultaneously with CRISPR-invinh1 and CRISPR-vpe5 than with single gene knock-out lines. This indicates that these genes have a synergistic effect and will increase the soluble sugar content. Thus, the knock-out SlINVINH1 and SlVPE5 may provide a practical basis for improving the sweetness of tomato fruits and their processing quality.
format: application/pdf
format: text/html
creator: Baike Wang
creator: Ning Li
creator: Shaoyong Huang
creator: Jiahui Hu
creator: Qiang Wang
creator: Yaping Tang
creator: Tao Yang
creator: Patiguli Asmutola
creator: Juan Wang
creator: Qinghui Yu
subject: Agricultural Science
subject: Biotechnology
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.12478
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Soluble sugar is known to improve the sweetness and increase tomato sauce yield. Studies have focused on improving the content of soluble sugar in tomato fruits, usually by promoting functional genes. We studied two genes (SlINVINH1 and SlVPE5) that inhibited the accumulation of soluble sugar in tomato fruits and obtained two genes’ knocked-out lines (CRISPR-invinh1 or CRISPR-vpe5) using CRISPR/Cas9. Aggregated lines with CRISPR-invinh1 and CRISPR-vpe5 were gained by hybridization and self-pollination. Compared to wild-type lines, the glucose, fructose, and total soluble solid (TSS) contents of CRISPR-invinh1 and CRISPR-vpe5 increased significantly. Glucose, fructose, and TSS levels further improved simultaneously with CRISPR-invinh1 and CRISPR-vpe5 than with single gene knock-out lines. This indicates that these genes have a synergistic effect and will increase the soluble sugar content. Thus, the knock-out SlINVINH1 and SlVPE5 may provide a practical basis for improving the sweetness of tomato fruits and their processing quality.
bibliographic citation: Wang et al. (2021) Enhanced soluble sugar content in tomato fruit using CRISPR/Cas9-mediated SlINVINH1 and SlVPE5 gene editing. PeerJ 9:e12478 https://doi.org/10.7717/peerj.12478
date submitted: 2021-03-11
date accepted: 2021-10-20
issued: 2021-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Baike
author list: Agent
  family name: Li
  given name: Ning
author list: Agent
  family name: Huang
  given name: Shaoyong
author list: Agent
  family name: Hu
  given name: Jiahui
author list: Agent
  family name: Wang
  given name: Qiang
author list: Agent
  family name: Tang
  given name: Yaping
author list: Agent
  family name: Yang
  given name: Tao
author list: Agent
  family name: Asmutola
  given name: Patiguli
author list: Agent
  family name: Wang
  given name: Juan
author list: Agent
  family name: Yu
  given name: Qinghui
doi: 10.7717/peerj.12478
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-09
copyright: © 2021 Wang et al.
attribution name: Wang et al.

Identification of keygenes, miRNAs and miRNA-mRNA regulatory pathways for chemotherapy resistance in ovarian cancer
type: item
type: AcademicArticle
description: Background Chemotherapy resistance, especially platinum resistance, is the main cause of poor prognosis of ovarian cancer. It is of great urgency to find molecular markers and mechanism related to platinum resistance in ovarian cancer. Methods One mRNA dataset (GSE28739) and one miRNA dataset (GSE25202) were acquired from Gene Expression Omnibus (GEO) database. The GEO2R tool was used to screen out differentially expressed genes (DEGs) and differentially expressed miRNAs (DE-miRNAs) between platinum-resistant and platinum-sensitive ovarian cancer patients. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs were performed using the DAVID to present the most visibly enriched pathways. Protein–protein interaction (PPI) of these DEGs was constructed based on the information of the STRING database. Hub genes related to platinum resistance were visualized by Cytoscape software. Then, we chose seven interested hub genes to further validate using qRT-PCR in A2780 ovarian cancer cell lines. And, at last, the TF-miRNA-target genes regulatory network was predicted and constructed using miRNet software. Results A total of 63 upregulated DEGs, 124 downregulated DEGs, four upregulated miRNAs and six downregulated miRNAs were identified. From the PPI network, the top 10 hub genes were identified, which were associated with platinum resistance. Our further qRT-PCR showed that seven hub genes (BUB1, KIF2C, NUP43, NDC80, NUF2, CCNB2 and CENPN) were differentially expressed in platinum-resistant ovarian cancer cells. Furthermore, the upstream transcription factors (TF) for upregulated DE-miRNAs were SMAD4, NFKB1, SMAD3, TP53 and HNF4A. Three overlapping downstream target genes (KIF2C, STAT3 and BUB1) were identified by miRNet, which was regulated by hsa-miR-494. Conclusions The TF-miRNA–mRNA regulatory pairs, that is TF (SMAD4, NFKB1 and SMAD3)-miR-494-target genes (KIF2C, STAT3 and BUB1), were established. In conclusion…
format: application/pdf
format: text/html
creator: Wenwen Wang
creator: Wenwen Zhang
creator: Yuanjing Hu
subject: Bioinformatics
subject: Drugs and Devices
subject: Gynecology and Obstetrics
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.12353
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background Chemotherapy resistance, especially platinum resistance, is the main cause of poor prognosis of ovarian cancer. It is of great urgency to find molecular markers and mechanism related to platinum resistance in ovarian cancer. Methods One mRNA dataset (GSE28739) and one miRNA dataset (GSE25202) were acquired from Gene Expression Omnibus (GEO) database. The GEO2R tool was used to screen out differentially expressed genes (DEGs) and differentially expressed miRNAs (DE-miRNAs) between platinum-resistant and platinum-sensitive ovarian cancer patients. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs were performed using the DAVID to present the most visibly enriched pathways. Protein–protein interaction (PPI) of these DEGs was constructed based on the information of the STRING database. Hub genes related to platinum resistance were visualized by Cytoscape software. Then, we chose seven interested hub genes to further validate using qRT-PCR in A2780 ovarian cancer cell lines. And, at last, the TF-miRNA-target genes regulatory network was predicted and constructed using miRNet software. Results A total of 63 upregulated DEGs, 124 downregulated DEGs, four upregulated miRNAs and six downregulated miRNAs were identified. From the PPI network, the top 10 hub genes were identified, which were associated with platinum resistance. Our further qRT-PCR showed that seven hub genes (BUB1, KIF2C, NUP43, NDC80, NUF2, CCNB2 and CENPN) were differentially expressed in platinum-resistant ovarian cancer cells. Furthermore, the upstream transcription factors (TF) for upregulated DE-miRNAs were SMAD4, NFKB1, SMAD3, TP53 and HNF4A. Three overlapping downstream target genes (KIF2C, STAT3 and BUB1) were identified by miRNet, which was regulated by hsa-miR-494. Conclusions The TF-miRNA–mRNA regulatory pairs, that is TF (SMAD4, NFKB1 and SMAD3)-miR-494-target genes (KIF2C, STAT3 and BUB1), were established. In conclusion…
bibliographic citation: Wang et al. (2021) Identification of keygenes, miRNAs and miRNA-mRNA regulatory pathways for chemotherapy resistance in ovarian cancer. PeerJ 9:e12353 https://doi.org/10.7717/peerj.12353
date submitted: 2021-05-03
date accepted: 2021-09-29
issued: 2021-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Wenwen
author list: Agent
  family name: Zhang
  given name: Wenwen
author list: Agent
  family name: Hu
  given name: Yuanjing
doi: 10.7717/peerj.12353
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-08
copyright: © 2021 Wang et al.
attribution name: Wang et al.

Horsenettle (Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales
type: item
type: AcademicArticle
description: Fruit house microbial communities that are unique from the rest of the plant. While symbiotic microbial communities complete important functions for their hosts, the fruit microbiome is often understudied compared to other plant organs. Fruits are reproductive tissues that house, protect, and facilitate the dispersal of seeds, and thus they are directly tied to plant fitness. Fruit microbial communities may, therefore, also impact plant fitness. In this study, we assessed how bacterial communities associated with fruit of Solanum carolinense, a native herbaceous perennial weed, vary at fine spatial scales (<0.5 km). A majority of the studies conducted on plant microbial communities have been done at large spatial scales and have observed microbial community variation across these large spatial scales. However, both the environment and pollinators play a role in shaping plant microbial communities and likely have impacts on the plant microbiome at fine scales. We collected fruit samples from eight sampling locations, ranging from 2 to 450 m apart, and assessed the fruit bacterial communities using 16S rRNA gene amplicon sequencing. Overall, we found no differences in observed richness or microbial community composition among sampling locations. Bacterial community structure of fruits collected near one another were not more different than those that were farther apart at the scales we examined. These fine spatial scales are important to obligate out-crossing plant species such as S. carolinense because they are ecologically relevant to pollinators. Thus, our results could imply that pollinators serve to homogenize fruit bacterial communities across these smaller scales.
format: application/pdf
format: text/html
creator: Ariel R. Heminger
creator: Lisa K. Belden
creator: Jacob N. Barney
creator: Brian D. Badgley
creator: David C. Haak
subject: Bioinformatics
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12359
publisher: PeerJ Inc.
rights: © 2021 Heminger et al.
abstract: Fruit house microbial communities that are unique from the rest of the plant. While symbiotic microbial communities complete important functions for their hosts, the fruit microbiome is often understudied compared to other plant organs. Fruits are reproductive tissues that house, protect, and facilitate the dispersal of seeds, and thus they are directly tied to plant fitness. Fruit microbial communities may, therefore, also impact plant fitness. In this study, we assessed how bacterial communities associated with fruit of Solanum carolinense, a native herbaceous perennial weed, vary at fine spatial scales (<0.5 km). A majority of the studies conducted on plant microbial communities have been done at large spatial scales and have observed microbial community variation across these large spatial scales. However, both the environment and pollinators play a role in shaping plant microbial communities and likely have impacts on the plant microbiome at fine scales. We collected fruit samples from eight sampling locations, ranging from 2 to 450 m apart, and assessed the fruit bacterial communities using 16S rRNA gene amplicon sequencing. Overall, we found no differences in observed richness or microbial community composition among sampling locations. Bacterial community structure of fruits collected near one another were not more different than those that were farther apart at the scales we examined. These fine spatial scales are important to obligate out-crossing plant species such as S. carolinense because they are ecologically relevant to pollinators. Thus, our results could imply that pollinators serve to homogenize fruit bacterial communities across these smaller scales.
bibliographic citation: Heminger et al. (2021) Horsenettle (Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales. PeerJ 9:e12359 https://doi.org/10.7717/peerj.12359
date submitted: 2021-06-14
date accepted: 2021-09-30
issued: 2021-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heminger
  given name: Ariel R.
author list: Agent
  family name: Belden
  given name: Lisa K.
author list: Agent
  family name: Barney
  given name: Jacob N.
author list: Agent
  family name: Badgley
  given name: Brian D.
author list: Agent
  family name: Haak
  given name: David C.
doi: 10.7717/peerj.12359
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-08
copyright: ©2021 Heminger et al.
attribution name: Heminger et al.

Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli)
type: item
type: AcademicArticle
description: The phylogenetic relationships of most Paleozoic tetrapod clades remain poorly resolved, which is variably attributed to a lack of study, the limitations of inference from phenotypic data, and constant revision of best practices. While refinement of phylogenetic methods continues to be important, any phylogenetic analysis is inherently constrained by the underlying dataset that it analyzes. Therefore, it becomes equally important to assess the accuracy of these datasets, especially when a select few are repeatedly propagated. While repeat analyses of these datasets may appear to constitute a working consensus, they are not in fact independent, and it becomes especially important to evaluate the accuracy of these datasets in order to assess whether a seeming consensus is robust. Here I address the phylogeny of the Dissorophidae, a speciose clade of Paleozoic temnospondyls. This group is an ideal case study among temnospondyls for exploring phylogenetic methods and datasets because it has been extensively studied (eight phylogenetic studies to date) but with most (six studies) using a single matrix that has been propagated with very little modification. In spite of the conserved nature of the matrix, dissorophid studies have produced anything but a conserved topology. Therefore, I analyzed an independently designed matrix, which recovered less resolution and some disparate nodes compared to previous studies. In order to reconcile these differences, I carefully examined previous matrices and analyses. While some differences are a matter of personal preference (e.g., analytical software), others relate to discrepancies with respect to what are currently considered as best practices. The most concerning discovery was the identification of pervasive dubious scorings that extend back to the origins of the widely propagated matrix. These include scores for skeletal features that are entirely unknown in a given taxon (e.g., postcrania in Cacops woehri) and characters for whi…
format: application/pdf
format: text/html
creator: Bryan M. Gee
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.12423
publisher: PeerJ Inc.
rights: © 2021 Gee
abstract: The phylogenetic relationships of most Paleozoic tetrapod clades remain poorly resolved, which is variably attributed to a lack of study, the limitations of inference from phenotypic data, and constant revision of best practices. While refinement of phylogenetic methods continues to be important, any phylogenetic analysis is inherently constrained by the underlying dataset that it analyzes. Therefore, it becomes equally important to assess the accuracy of these datasets, especially when a select few are repeatedly propagated. While repeat analyses of these datasets may appear to constitute a working consensus, they are not in fact independent, and it becomes especially important to evaluate the accuracy of these datasets in order to assess whether a seeming consensus is robust. Here I address the phylogeny of the Dissorophidae, a speciose clade of Paleozoic temnospondyls. This group is an ideal case study among temnospondyls for exploring phylogenetic methods and datasets because it has been extensively studied (eight phylogenetic studies to date) but with most (six studies) using a single matrix that has been propagated with very little modification. In spite of the conserved nature of the matrix, dissorophid studies have produced anything but a conserved topology. Therefore, I analyzed an independently designed matrix, which recovered less resolution and some disparate nodes compared to previous studies. In order to reconcile these differences, I carefully examined previous matrices and analyses. While some differences are a matter of personal preference (e.g., analytical software), others relate to discrepancies with respect to what are currently considered as best practices. The most concerning discovery was the identification of pervasive dubious scorings that extend back to the origins of the widely propagated matrix. These include scores for skeletal features that are entirely unknown in a given taxon (e.g., postcrania in Cacops woehri) and characters for whi…
bibliographic citation: Gee (2021) Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli). PeerJ 9:e12423 https://doi.org/10.7717/peerj.12423
date submitted: 2021-03-24
date accepted: 2021-10-11
issued: 2021-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gee
  given name: Bryan M.
doi: 10.7717/peerj.12423
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-08
copyright: © 2021 Gee
attribution name: Gee

Incidence and clinicopathological features of colorectal cancer among multi-ethnic patients in Kuala Lumpur, Malaysia: a hospital-based retrospective analysis over two decades
type: item
type: AcademicArticle
description: Background The incidence rate of colorectal cancer (CRC) in Asian countries is increasing. Furthermore, recent studies have shown a concerning rise in the incidence of CRC among younger patients aged less than 50 years. This study aimed to analyze the incidence trends and clinicopathological features in patients with early-onset CRC (EOCRC) and later-onset CRC (at age ≥ 50 years). Methods A retrospective analysis was performed on 946 patients with CRC diagnosed from 1997 to 2017 at Universiti Kebangsaan Malaysia Medical Centre. The time trend was assessed by dividing the two decades into four 5-year periods. The mean age-standardized and age-specific incidence rates were calculated by using the 5-year cumulative population of Kuala Lumpur and World Health Organization standard population. The mean incidence was expressed per 100,000 person-years. Results After a stable (all age groups) CRC incidence rate during the first decade (3.00 per 100,000 and 3.85 per 100,000), it sharply increased to 6.12 per 100,000 in the 2008–2012 period before decreasing to 4.54 per 100,000 in the 2013–2017 period. The CRC incidence trend in later-onset CRC showed a decrease in the 2013–2017 period. Contrariwise, for age groups of 40–44 and 45–49 years, the trends showed an increase in the latter 15 years of the study period (40–44 years: 1.44 to 1.92 to 2.3 per 100,000; 45–49 years: 2.87 to 2.94 to 4.01 per 100,000). Malays’ EOCRC incidence rate increased from 2008–2012 to 2013–2017 for both the age groups 40–44 years (1.46 to 2.89 per 100,000) and 45–49 years (2.73 to 6.51 per 100,000). Nearly one-fifth of EOCRC cases were diagnosed at an advanced stage (Dukes D: 19.9%), and the majority of them had rectal cancer (72.8%). Conclusion The incidence of EOCRC increased over the period 1997–2017; the patients were predominantly Malays, diagnosed at a later stage, and with cancer commonly localized in the rectal region. All the relevant stakeholders need to work on the management and prevent…
format: application/pdf
format: text/html
creator: Khairul Najmi Muhammad Nawawi
creator: Norfilza M. Mokhtar
creator: Zhiqin Wong
creator: Zairul Azwan Mohd Azman
creator: Deborah Chia Hsin Chew
creator: Rasyidah Rehir
creator: Jocelyn Leong
creator: Fuad Ismail
creator: Isa Mohamed Rose
creator: Yazmin Yaacob
creator: Hamzaini Abdul Hamid
creator: Ismail Sagap
creator: Raja Affendi Raja Ali
subject: Epidemiology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Public Health
description: doi:10.7717/peerj.12425
publisher: PeerJ Inc.
rights: © 2021 Muhammad Nawawi et al.
abstract: Background The incidence rate of colorectal cancer (CRC) in Asian countries is increasing. Furthermore, recent studies have shown a concerning rise in the incidence of CRC among younger patients aged less than 50 years. This study aimed to analyze the incidence trends and clinicopathological features in patients with early-onset CRC (EOCRC) and later-onset CRC (at age ≥ 50 years). Methods A retrospective analysis was performed on 946 patients with CRC diagnosed from 1997 to 2017 at Universiti Kebangsaan Malaysia Medical Centre. The time trend was assessed by dividing the two decades into four 5-year periods. The mean age-standardized and age-specific incidence rates were calculated by using the 5-year cumulative population of Kuala Lumpur and World Health Organization standard population. The mean incidence was expressed per 100,000 person-years. Results After a stable (all age groups) CRC incidence rate during the first decade (3.00 per 100,000 and 3.85 per 100,000), it sharply increased to 6.12 per 100,000 in the 2008–2012 period before decreasing to 4.54 per 100,000 in the 2013–2017 period. The CRC incidence trend in later-onset CRC showed a decrease in the 2013–2017 period. Contrariwise, for age groups of 40–44 and 45–49 years, the trends showed an increase in the latter 15 years of the study period (40–44 years: 1.44 to 1.92 to 2.3 per 100,000; 45–49 years: 2.87 to 2.94 to 4.01 per 100,000). Malays’ EOCRC incidence rate increased from 2008–2012 to 2013–2017 for both the age groups 40–44 years (1.46 to 2.89 per 100,000) and 45–49 years (2.73 to 6.51 per 100,000). Nearly one-fifth of EOCRC cases were diagnosed at an advanced stage (Dukes D: 19.9%), and the majority of them had rectal cancer (72.8%). Conclusion The incidence of EOCRC increased over the period 1997–2017; the patients were predominantly Malays, diagnosed at a later stage, and with cancer commonly localized in the rectal region. All the relevant stakeholders need to work on the management and prevent…
bibliographic citation: Muhammad Nawawi et al. (2021) Incidence and clinicopathological features of colorectal cancer among multi-ethnic patients in Kuala Lumpur, Malaysia: a hospital-based retrospective analysis over two decades. PeerJ 9:e12425 https://doi.org/10.7717/peerj.12425
date submitted: 2021-06-01
date accepted: 2021-10-11
issued: 2021-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Muhammad Nawawi
  given name: Khairul Najmi
author list: Agent
  family name: Mokhtar
  given name: Norfilza M.
author list: Agent
  family name: Wong
  given name: Zhiqin
author list: Agent
  family name: Mohd Azman
  given name: Zairul Azwan
author list: Agent
  family name: Hsin Chew
  given name: Deborah Chia
author list: Agent
  family name: Rehir
  given name: Rasyidah
author list: Agent
  family name: Leong
  given name: Jocelyn
author list: Agent
  family name: Ismail
  given name: Fuad
author list: Agent
  family name: Mohamed Rose
  given name: Isa
author list: Agent
  family name: Yaacob
  given name: Yazmin
author list: Agent
  family name: Abdul Hamid
  given name: Hamzaini
author list: Agent
  family name: Sagap
  given name: Ismail
author list: Agent
  family name: Raja Ali
  given name: Raja Affendi
doi: 10.7717/peerj.12425
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-08
copyright: ©2021 Muhammad Nawawi et al.
attribution name: Muhammad Nawawi et al.

Abundant CpG-sequences in human genomes inhibit KIR3DL2-expressing NK cells
type: item
type: AcademicArticle
description: Killer Immunoglobulin-like Receptors (KIR) comprise a diverse, highly polymorphic family of cell-surface glycoproteins that are principally expressed by Natural Killer (NK) cells. These innate immune lymphocytes fulfill vital functions in human reproduction and immune responses to viral infection. KIR3DL2 is an inhibitory NK cell receptor that recognizes a common epitope of the HLA-A3 and HLA-A11 class I glycoproteins of the major histocompatibility complex. KIR3DL2 also binds exogenous DNA containing the CpG motif. This interaction causes internalization of the KIR-DNA. Exogenous CpG-DNA typically activates NK cells, but the specificity of KIR3DL2-DNA binding and internalization is unclear. We hypothesized that KIR3DL2 binds exogenous DNA in a sequence-specific manner that differentiates pathogen DNA from self-DNA. In testing this hypothesis, we surveyed octameric CpG-DNA sequences in the human genome, and in reference genomes of all bacteria, fungi, viruses, and parasites, with focus on medically relevant species. Among all pathogens, the nucleotides flanking CpG motifs in the genomes of parasitic worms that infect humans are most divergent from those in the human genome. We cultured KIR3DL2+NKL cells with the commonest CpG-DNA sequences in either human or pathogen genomes. DNA uptake was negatively correlated with the most common CpG-DNA sequences in the human genome. These CpG-DNA sequences induced inhibitory signaling in KIR3DL2+NKL cells. In contrast, KIR3DL2+NKL cells lysed more malignant targets and produced more IFNγ after culture with CpG-DNA sequences prevalent in parasitic worms. By applying functional immunology to evolutionary genomics, we conclude that KIR3DL2 allows NK cells to differentiate self-DNA from pathogen DNA.
format: application/pdf
format: text/html
creator: Jason Pugh
creator: Lisbeth Guethlein
creator: Peter Parham
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.12258
publisher: PeerJ Inc.
rights: © 2021 Pugh et al.
abstract: Killer Immunoglobulin-like Receptors (KIR) comprise a diverse, highly polymorphic family of cell-surface glycoproteins that are principally expressed by Natural Killer (NK) cells. These innate immune lymphocytes fulfill vital functions in human reproduction and immune responses to viral infection. KIR3DL2 is an inhibitory NK cell receptor that recognizes a common epitope of the HLA-A3 and HLA-A11 class I glycoproteins of the major histocompatibility complex. KIR3DL2 also binds exogenous DNA containing the CpG motif. This interaction causes internalization of the KIR-DNA. Exogenous CpG-DNA typically activates NK cells, but the specificity of KIR3DL2-DNA binding and internalization is unclear. We hypothesized that KIR3DL2 binds exogenous DNA in a sequence-specific manner that differentiates pathogen DNA from self-DNA. In testing this hypothesis, we surveyed octameric CpG-DNA sequences in the human genome, and in reference genomes of all bacteria, fungi, viruses, and parasites, with focus on medically relevant species. Among all pathogens, the nucleotides flanking CpG motifs in the genomes of parasitic worms that infect humans are most divergent from those in the human genome. We cultured KIR3DL2+NKL cells with the commonest CpG-DNA sequences in either human or pathogen genomes. DNA uptake was negatively correlated with the most common CpG-DNA sequences in the human genome. These CpG-DNA sequences induced inhibitory signaling in KIR3DL2+NKL cells. In contrast, KIR3DL2+NKL cells lysed more malignant targets and produced more IFNγ after culture with CpG-DNA sequences prevalent in parasitic worms. By applying functional immunology to evolutionary genomics, we conclude that KIR3DL2 allows NK cells to differentiate self-DNA from pathogen DNA.
bibliographic citation: Pugh et al. (2021) Abundant CpG-sequences in human genomes inhibit KIR3DL2-expressing NK cells. PeerJ 9:e12258 https://doi.org/10.7717/peerj.12258
date submitted: 2021-07-25
date accepted: 2021-09-15
issued: 2021-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pugh
  given name: Jason
author list: Agent
  family name: Guethlein
  given name: Lisbeth
author list: Agent
  family name: Parham
  given name: Peter
doi: 10.7717/peerj.12258
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-05
copyright: © 2021 Pugh et al.
attribution name: Pugh et al.

Dissection of full-length transcriptome and metabolome of Dichocarpum (Ranunculaceae): implications in evolution of specialized metabolism of Ranunculales medicinal plants
type: item
type: AcademicArticle
description: Several main families of Ranunculales are rich in alkaloids and other medicinal compounds; many species of these families are used in traditional and folk medicine. Dichocarpum is a representative medicinal genus of Ranunculaceae, but the genetic basis of its metabolic phenotype has not been investigated, which hinders its sustainable conservation and utilization. We use the third-generation high-throughput sequencing and metabolomic techniques to decipher the full-length transcriptomes and metabolomes of five Dichocarpum species endemic in China, and 71,598 non-redundant full-length transcripts were obtained, many of which are involved in defense, stress response and immunity, especially those participating in the biosynthesis of specialized metabolites such as benzylisoquinoline alkaloids (BIAs). Twenty-seven orthologs extracted from trancriptome datasets were concatenated to reconstruct the phylogenetic tree, which was verified by the clustering analysis based on the metabolomic profile and agreed with the Pearson correlation between gene expression patterns of Dichocarpum species. The phylogenomic analysis of phytometabolite biosynthesis genes, e.g., (S)-norcoclaurine synthase, methyltransferases, cytochrome p450 monooxygenases, berberine bridge enzyme and (S)-tetrahydroprotoberberine oxidase, revealed the evolutionary trajectories leading to the chemodiversity, especially that of protoberberine type, aporphine type and bis-BIA abundant in Dichocarpum and related genera. The biosynthesis pathways of these BIAs are proposed based on full-length transcriptomes and metabolomes of Dichocarpum. Within Ranunculales, the gene duplications are common, and a unique whole genome duplication is possible in Dichocarpum. The extensive correlations between metabolite content and gene expression support the co-evolution of various genes essential for the production of different specialized metabolites. Our study provides insights into the transcriptomic and metabolomic landsca…
format: application/pdf
format: text/html
creator: Da-Cheng Hao
creator: Pei Li
creator: Pei-Gen Xiao
creator: Chun-Nian He
subject: Biochemistry
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12428
publisher: PeerJ Inc.
rights: © 2021 Hao et al.
abstract: Several main families of Ranunculales are rich in alkaloids and other medicinal compounds; many species of these families are used in traditional and folk medicine. Dichocarpum is a representative medicinal genus of Ranunculaceae, but the genetic basis of its metabolic phenotype has not been investigated, which hinders its sustainable conservation and utilization. We use the third-generation high-throughput sequencing and metabolomic techniques to decipher the full-length transcriptomes and metabolomes of five Dichocarpum species endemic in China, and 71,598 non-redundant full-length transcripts were obtained, many of which are involved in defense, stress response and immunity, especially those participating in the biosynthesis of specialized metabolites such as benzylisoquinoline alkaloids (BIAs). Twenty-seven orthologs extracted from trancriptome datasets were concatenated to reconstruct the phylogenetic tree, which was verified by the clustering analysis based on the metabolomic profile and agreed with the Pearson correlation between gene expression patterns of Dichocarpum species. The phylogenomic analysis of phytometabolite biosynthesis genes, e.g., (S)-norcoclaurine synthase, methyltransferases, cytochrome p450 monooxygenases, berberine bridge enzyme and (S)-tetrahydroprotoberberine oxidase, revealed the evolutionary trajectories leading to the chemodiversity, especially that of protoberberine type, aporphine type and bis-BIA abundant in Dichocarpum and related genera. The biosynthesis pathways of these BIAs are proposed based on full-length transcriptomes and metabolomes of Dichocarpum. Within Ranunculales, the gene duplications are common, and a unique whole genome duplication is possible in Dichocarpum. The extensive correlations between metabolite content and gene expression support the co-evolution of various genes essential for the production of different specialized metabolites. Our study provides insights into the transcriptomic and metabolomic landsca…
bibliographic citation: Hao et al. (2021) Dissection of full-length transcriptome and metabolome of Dichocarpum (Ranunculaceae): implications in evolution of specialized metabolism of Ranunculales medicinal plants. PeerJ 9:e12428 https://doi.org/10.7717/peerj.12428
date submitted: 2021-06-17
date accepted: 2021-10-12
issued: 2021-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0/
author list: Agent
  family name: Hao
  given name: Da-Cheng
author list: Agent
  family name: Li
  given name: Pei
author list: Agent
  family name: Xiao
  given name: Pei-Gen
author list: Agent
  family name: He
  given name: Chun-Nian
doi: 10.7717/peerj.12428
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-05
copyright: ©2021 Hao et al.
attribution name: Hao et al.

Evolutionary history of the vertebrate Piwi gene family
type: item
type: AcademicArticle
description: PIWIs are regulatory proteins that belong to the Argonaute family. Piwis are primarily expressed in gonads and protect the germline against the mobilization and propagation of transposable elements (TEs) through transcriptional gene silencing. Vertebrate genomes encode up to four Piwi genes: Piwil1, Piwil2, Piwil3 and Piwil4, but their duplication history is unresolved. We leveraged phylogenetics, synteny and expression analyses to address this void. Our phylogenetic analysis suggests Piwil1 and Piwil2 were retained in all vertebrate members. Piwil4 was the result of Piwil1 duplication in the ancestor of gnathostomes, but was independently lost in ray-finned fishes and birds. Further, Piwil3 was derived from a tandem Piwil1 duplication in the common ancestor of marsupial and placental mammals, but was secondarily lost in Atlantogenata (Xenarthra and Afrotheria) and some rodents. The evolutionary rate of Piwil3 is considerably faster than any Piwi among all lineages, but an explanation is lacking. Our expression analyses suggest Piwi expression has mostly been constrained to gonads throughout vertebrate evolution. Vertebrate evolution is marked by two early rounds of whole genome duplication and many multigene families are linked to these events. However, our analyses suggest Piwi expansion was independent of whole genome duplications.
format: application/pdf
format: text/html
creator: Javier Gutierrez
creator: Roy Platt
creator: Juan C. Opazo
creator: David A. Ray
creator: Federico Hoffmann
creator: Michael Vandewege
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.12451
publisher: PeerJ Inc.
rights: © 2021 Gutierrez et al.
abstract: PIWIs are regulatory proteins that belong to the Argonaute family. Piwis are primarily expressed in gonads and protect the germline against the mobilization and propagation of transposable elements (TEs) through transcriptional gene silencing. Vertebrate genomes encode up to four Piwi genes: Piwil1, Piwil2, Piwil3 and Piwil4, but their duplication history is unresolved. We leveraged phylogenetics, synteny and expression analyses to address this void. Our phylogenetic analysis suggests Piwil1 and Piwil2 were retained in all vertebrate members. Piwil4 was the result of Piwil1 duplication in the ancestor of gnathostomes, but was independently lost in ray-finned fishes and birds. Further, Piwil3 was derived from a tandem Piwil1 duplication in the common ancestor of marsupial and placental mammals, but was secondarily lost in Atlantogenata (Xenarthra and Afrotheria) and some rodents. The evolutionary rate of Piwil3 is considerably faster than any Piwi among all lineages, but an explanation is lacking. Our expression analyses suggest Piwi expression has mostly been constrained to gonads throughout vertebrate evolution. Vertebrate evolution is marked by two early rounds of whole genome duplication and many multigene families are linked to these events. However, our analyses suggest Piwi expansion was independent of whole genome duplications.
bibliographic citation: Gutierrez et al. (2021) Evolutionary history of the vertebrate Piwi gene family. PeerJ 9:e12451 https://doi.org/10.7717/peerj.12451
date submitted: 2021-06-07
date accepted: 2021-10-18
issued: 2021-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gutierrez
  given name: Javier
author list: Agent
  family name: Platt
  given name: Roy
author list: Agent
  family name: Opazo
  given name: Juan C.
author list: Agent
  family name: Ray
  given name: David A.
author list: Agent
  family name: Hoffmann
  given name: Federico
author list: Agent
  family name: Vandewege
  given name: Michael
doi: 10.7717/peerj.12451
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-05
copyright: ©2021 Gutierrez et al.
attribution name: Gutierrez et al.

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