PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding
items: Recent advances and challenges on application of tissue engineering for treatment of congenital heart disease
items: Molecular assessment of Pocillopora verrucosa (Scleractinia; Pocilloporidae) distribution along a depth gradient in Ludao, Taiwan
items: Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus
items: Infection and coinfection by human papillomavirus, Epstein–Barr virus and Merkel cell polyomavirus in patients with squamous cell carcinoma of the larynx: a retrospective study
items: Meta-analysis of microarray datasets identify several chromosome segregation-related cancer/testis genes potentially contributing to anaplastic thyroid carcinoma
items: Species diversity of drifting fish eggs in the Yangtze River using molecular identification
items: Integrative analysis of microRNA and mRNA expression profiles in fetal rat model with anorectal malformation
items: Effects of inconsistent reporting, regulation changes and market demand on abundance indices of sharks caught by pelagic longliners off southern Africa
items: Variations in the reproductive strategies of three populations of Phrynocephalus helioscopus in China

Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding
type: item
type: AcademicArticle
description: Sabah is a province of Malaysia located on the northern part of the island of Borneo. Most of the leaf beetle fauna studies from this region conducted over the past 15 years have focussed on the mainland habitats while the leaf beetle fauna from island habitats (ca. 500 islands) have largely been overlooked. This study looks into the leaf beetle fauna of 13 small satellite islands off the west coast of Sabah. All specimens were first sorted into morpho-species operational taxonomic unit (OTU) before being identified to species rank where possible based on morphological characters and species names assigned when the specimens fitted the description of species in the literature. We collected 75 OTUs from 35 genera and five subfamilies according to morphology, 12 of which were identifiable to species level. In addition, the DNA barcode for each OTU was cross checked with records in GenBank and Barcoding of Life Data system (BOLD) to verify their identity. The number of species recorded was reduced from 12 species and 63 OTUs (total 75 OTUs) to 12 species and 56 OTUs (total 68 OTUs) after removal of the colour polymorphic species based on DNA barcode analyses. Pulau Gaya has the highest species richness and Pulau Sulug has the lowest species richness. A total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from the 12 leaf beetle species and 48 OTUs. Based on the DNA barcode analyses, it was possible to confirm several polymorphic OTUs and cryptic species. The mean intraspecific and interspecific genetic divergence were determined as 0.77% and 16.11%, respectively. DNA barcodes of this study show a low similarity with records in GenBank and BOLD, highlighting the lack of representation and the urgency of studying leaf beetles from this region. The study provides the first documentation of leaf beetle fauna from island habitats of Sabah and the first DNA barcoding data for leaf beetles from this part of the world, with the next steps being larger…
format: application/pdf
format: text/html
creator: Kam-Cheng Yeong
creator: Haruo Takizawa
creator: Thor-Seng Liew
subject: Biodiversity
subject: Biogeography
subject: Entomology
subject: Molecular Biology
description: doi:10.7717/peerj.5811
publisher: PeerJ Inc.
rights: © 2018 Yeong et al.
abstract: Sabah is a province of Malaysia located on the northern part of the island of Borneo. Most of the leaf beetle fauna studies from this region conducted over the past 15 years have focussed on the mainland habitats while the leaf beetle fauna from island habitats (ca. 500 islands) have largely been overlooked. This study looks into the leaf beetle fauna of 13 small satellite islands off the west coast of Sabah. All specimens were first sorted into morpho-species operational taxonomic unit (OTU) before being identified to species rank where possible based on morphological characters and species names assigned when the specimens fitted the description of species in the literature. We collected 75 OTUs from 35 genera and five subfamilies according to morphology, 12 of which were identifiable to species level. In addition, the DNA barcode for each OTU was cross checked with records in GenBank and Barcoding of Life Data system (BOLD) to verify their identity. The number of species recorded was reduced from 12 species and 63 OTUs (total 75 OTUs) to 12 species and 56 OTUs (total 68 OTUs) after removal of the colour polymorphic species based on DNA barcode analyses. Pulau Gaya has the highest species richness and Pulau Sulug has the lowest species richness. A total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from the 12 leaf beetle species and 48 OTUs. Based on the DNA barcode analyses, it was possible to confirm several polymorphic OTUs and cryptic species. The mean intraspecific and interspecific genetic divergence were determined as 0.77% and 16.11%, respectively. DNA barcodes of this study show a low similarity with records in GenBank and BOLD, highlighting the lack of representation and the urgency of studying leaf beetles from this region. The study provides the first documentation of leaf beetle fauna from island habitats of Sabah and the first DNA barcoding data for leaf beetles from this part of the world, with the next steps being larger…
bibliographic citation: Yeong et al. (2018) Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding. PeerJ 6:e5811 https://doi.org/10.7717/peerj.5811
date submitted: 2018-03-29
date accepted: 2018-09-23
issued: 2018-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yeong
  given name: Kam-Cheng
author list: Agent
  family name: Takizawa
  given name: Haruo
author list: Agent
  family name: Liew
  given name: Thor-Seng
doi: 10.7717/peerj.5811
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-25
copyright: © 2018 Yeong et al.
attribution name: Yeong et al.

Recent advances and challenges on application of tissue engineering for treatment of congenital heart disease
type: item
type: AcademicArticle
description: Congenital heart disease (CHD) affects a considerable number of children and adults worldwide. This implicates not only developmental disorders, high mortality, and reduced quality of life but also, high costs for the healthcare systems. CHD refers to a variety of heart and vascular malformations which could be very challenging to reconstruct the malformed region surgically, especially when the patient is an infant or a child. Advanced technology and research have offered a better mechanistic insight on the impact of CHD in the heart and vascular system of infants, children, and adults and identified potential therapeutic solutions. Many artificial materials and devices have been used for cardiovascular surgery. Surgeons and the medical industry created and evolved the ball valves to the carbon-based leaflet valves and introduced bioprosthesis as an alternative. However, with research further progressing, contracting tissue has been developed in laboratories and tissue engineering (TE) could represent a revolutionary answer for CHD surgery. Development of engineered tissue for cardiac and aortic reconstruction for developing bodies of infants and children can be very challenging. Nevertheless, using acellular scaffolds, allograft, xenografts, and autografts is already very common. Seeding of cells on surface and within scaffold is a key challenging factor for use of the above. The use of different types of stem cells has been investigated and proven to be suitable for tissue engineering. They are the most promising source of cells for heart reconstruction in a developing body, even for adults. Some stem cell types are more effective than others, with some disadvantages which may be eliminated in the future.
format: application/pdf
format: text/html
creator: Antonia Mantakaki
creator: Adegbenro Omotuyi John Fakoya
creator: Fatemeh Sharifpanah
subject: Cell Biology
subject: Developmental Biology
subject: Anatomy and Physiology
subject: Cardiology
subject: Pathology
description: doi:10.7717/peerj.5805
publisher: PeerJ Inc.
rights: © 2018 Mantakaki et al.
abstract: Congenital heart disease (CHD) affects a considerable number of children and adults worldwide. This implicates not only developmental disorders, high mortality, and reduced quality of life but also, high costs for the healthcare systems. CHD refers to a variety of heart and vascular malformations which could be very challenging to reconstruct the malformed region surgically, especially when the patient is an infant or a child. Advanced technology and research have offered a better mechanistic insight on the impact of CHD in the heart and vascular system of infants, children, and adults and identified potential therapeutic solutions. Many artificial materials and devices have been used for cardiovascular surgery. Surgeons and the medical industry created and evolved the ball valves to the carbon-based leaflet valves and introduced bioprosthesis as an alternative. However, with research further progressing, contracting tissue has been developed in laboratories and tissue engineering (TE) could represent a revolutionary answer for CHD surgery. Development of engineered tissue for cardiac and aortic reconstruction for developing bodies of infants and children can be very challenging. Nevertheless, using acellular scaffolds, allograft, xenografts, and autografts is already very common. Seeding of cells on surface and within scaffold is a key challenging factor for use of the above. The use of different types of stem cells has been investigated and proven to be suitable for tissue engineering. They are the most promising source of cells for heart reconstruction in a developing body, even for adults. Some stem cell types are more effective than others, with some disadvantages which may be eliminated in the future.
bibliographic citation: Mantakaki et al. (2018) Recent advances and challenges on application of tissue engineering for treatment of congenital heart disease. PeerJ 6:e5805 https://doi.org/10.7717/peerj.5805
date submitted: 2018-03-13
date accepted: 2018-09-21
issued: 2018-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mantakaki
  given name: Antonia
author list: Agent
  family name: Fakoya
  given name: Adegbenro Omotuyi John
author list: Agent
  family name: Sharifpanah
  given name: Fatemeh
doi: 10.7717/peerj.5805
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-25
copyright: ©2018 Mantakaki et al.
attribution name: Mantakaki et al.

Molecular assessment of Pocillopora verrucosa (Scleractinia; Pocilloporidae) distribution along a depth gradient in Ludao, Taiwan
type: item
type: AcademicArticle
description: It can be challenging to identify scleractinian corals from the genus Pocillopora Lamarck 1816 in the field because of their large range of inter- and intra-specific morphological variation that co-occur with changes in the physical environment. This task is made more arduous in the context of a depth gradient, where light and water current could greatly affect the morphology of the corallum. Pocillopora verrucosa (Ellis & Solander 1786) in Taiwan was previously reported exclusively from shallow waters (<10 m in depth), but a recent observation of this species in the mesophotic zone (>40 m in depth) questions this bathymetric distribution. We used the mitochondrial open reading frame and the histone 3 molecular markers to investigate the vertical and horizontal spatial distribution of P. verrucosa around Ludao (Green Island), Taiwan. We genotyped 101 P. verrucosa-like colonies collected from four depth zones, ranging from 7 to 45 m, at three sites around the island. Of the 101 colonies sampled, 85 were genotyped as P. verrucosa, 15 as P. meandrina, and one specimen as an undescribed Pocillopora species. P. verrucosa was found at all depths, while P. meandrina and the undescribed Pocillopora specimen were limited to 15 m depth. P. verrucosa has a large bathymetric distribution around Ludao and could benefit from the refuge that the mesophotic zone offers. This study illustrates the difficulty of identifying Pocillopora corals in the field and emphasizes the relevance of molecular taxonomy as an important and complementary tool to traditional taxonomy for clarifying vertical and horizontal species distribution. Our results also illustrate the need in conservation biology to target species genetic diversity rather than just species diversity.
format: application/pdf
format: text/html
creator: Stéphane De Palmas
creator: Derek Soto
creator: Vianney Denis
creator: Ming-Jay Ho
creator: Chaolun Allen Chen
subject: Biodiversity
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.5797
publisher: PeerJ Inc.
rights: © 2018 De Palmas et al.
abstract: It can be challenging to identify scleractinian corals from the genus Pocillopora Lamarck 1816 in the field because of their large range of inter- and intra-specific morphological variation that co-occur with changes in the physical environment. This task is made more arduous in the context of a depth gradient, where light and water current could greatly affect the morphology of the corallum. Pocillopora verrucosa (Ellis & Solander 1786) in Taiwan was previously reported exclusively from shallow waters (<10 m in depth), but a recent observation of this species in the mesophotic zone (>40 m in depth) questions this bathymetric distribution. We used the mitochondrial open reading frame and the histone 3 molecular markers to investigate the vertical and horizontal spatial distribution of P. verrucosa around Ludao (Green Island), Taiwan. We genotyped 101 P. verrucosa-like colonies collected from four depth zones, ranging from 7 to 45 m, at three sites around the island. Of the 101 colonies sampled, 85 were genotyped as P. verrucosa, 15 as P. meandrina, and one specimen as an undescribed Pocillopora species. P. verrucosa was found at all depths, while P. meandrina and the undescribed Pocillopora specimen were limited to 15 m depth. P. verrucosa has a large bathymetric distribution around Ludao and could benefit from the refuge that the mesophotic zone offers. This study illustrates the difficulty of identifying Pocillopora corals in the field and emphasizes the relevance of molecular taxonomy as an important and complementary tool to traditional taxonomy for clarifying vertical and horizontal species distribution. Our results also illustrate the need in conservation biology to target species genetic diversity rather than just species diversity.
bibliographic citation: De Palmas et al. (2018) Molecular assessment of Pocillopora verrucosa (Scleractinia; Pocilloporidae) distribution along a depth gradient in Ludao, Taiwan. PeerJ 6:e5797 https://doi.org/10.7717/peerj.5797
date submitted: 2018-08-07
date accepted: 2018-09-20
issued: 2018-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Palmas
  given name: Stéphane
author list: Agent
  family name: Soto
  given name: Derek
author list: Agent
  family name: Denis
  given name: Vianney
author list: Agent
  family name: Ho
  given name: Ming-Jay
author list: Agent
  family name: Chen
  given name: Chaolun Allen
doi: 10.7717/peerj.5797
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-25
copyright: © 2018 De Palmas et al.
attribution name: De Palmas et al.

Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus
type: item
type: AcademicArticle
description: Although genome sequencing has become a very promising approach to conduct microbial taxonomy, few labs have the resources to afford this especially when dealing with data sets of hundreds to thousands of isolates. The goal of this study was to identify the most adequate loci for inferring the phylogeny of the species within the genus Staphylococcus; with the idea that those who cannot afford whole genome sequencing can use these loci to carry out species assignation confidently. We retrieved 177 orthologous groups (OGs) by using a genome-based phylogeny and an average nucleotide identity analysis. The top 26 OGs showed topologies similar to the species tree and the concatenation of them yielded a topology almost identical to that of the species tree. Furthermore, a phylogeny of just the top seven OGs could be used for species assignment. We sequenced four staphylococcus isolates to test the 26 OGs and found that these OGs were far superior to commonly used markers for this genus. On the whole, our procedure allowed identification of the most adequate markers for inferring the phylogeny within the genus Staphylococcus. We anticipate that this approach will be employed for the identification of the most suitable markers for other bacterial genera and can be very helpful to sort out poorly classified genera.
format: application/pdf
format: text/html
creator: Lucia Graña-Miraglia
creator: César Arreguín-Pérez
creator: Gamaliel López-Leal
creator: Alan Muñoz
creator: Angeles Pérez-Oseguera
creator: Estefan Miranda-Miranda
creator: Raquel Cossío-Bayúgar
creator: Santiago Castillo-Ramírez
subject: Ecology
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.5839
publisher: PeerJ Inc.
rights: © 2018 Graña-Miraglia et al.
abstract: Although genome sequencing has become a very promising approach to conduct microbial taxonomy, few labs have the resources to afford this especially when dealing with data sets of hundreds to thousands of isolates. The goal of this study was to identify the most adequate loci for inferring the phylogeny of the species within the genus Staphylococcus; with the idea that those who cannot afford whole genome sequencing can use these loci to carry out species assignation confidently. We retrieved 177 orthologous groups (OGs) by using a genome-based phylogeny and an average nucleotide identity analysis. The top 26 OGs showed topologies similar to the species tree and the concatenation of them yielded a topology almost identical to that of the species tree. Furthermore, a phylogeny of just the top seven OGs could be used for species assignment. We sequenced four staphylococcus isolates to test the 26 OGs and found that these OGs were far superior to commonly used markers for this genus. On the whole, our procedure allowed identification of the most adequate markers for inferring the phylogeny within the genus Staphylococcus. We anticipate that this approach will be employed for the identification of the most suitable markers for other bacterial genera and can be very helpful to sort out poorly classified genera.
bibliographic citation: Graña-Miraglia et al. (2018) Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus. PeerJ 6:e5839 https://doi.org/10.7717/peerj.5839
date submitted: 2018-06-04
date accepted: 2018-09-28
issued: 2018-10-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Graña-Miraglia
  given name: Lucia
author list: Agent
  family name: Arreguín-Pérez
  given name: César
author list: Agent
  family name: López-Leal
  given name: Gamaliel
author list: Agent
  family name: Muñoz
  given name: Alan
author list: Agent
  family name: Pérez-Oseguera
  given name: Angeles
author list: Agent
  family name: Miranda-Miranda
  given name: Estefan
author list: Agent
  family name: Cossío-Bayúgar
  given name: Raquel
author list: Agent
  family name: Castillo-Ramírez
  given name: Santiago
doi: 10.7717/peerj.5839
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-24
copyright: ©2018 Graña-Miraglia et al.
attribution name: Graña-Miraglia et al.

Infection and coinfection by human papillomavirus, Epstein–Barr virus and Merkel cell polyomavirus in patients with squamous cell carcinoma of the larynx: a retrospective study
type: item
type: AcademicArticle
description: Background Human papillomavirus (HPV) is recognized as an important risk factor for laryngeal carcinogenesis. Although HPV-16 and 18 have been strongly implicated, the presence of other high-risk HPV (HR-HPV) genotypes or the coinfection with Epstein-Barr virus (EBV) or Merkel cell polyomavirus (MCPV) may increase the risk, but their etiological association has not been definitively established. Methods We characterized the genotype-specific HPV and the frequency of EBV and MCPV infections through the detection of their DNA in 195 laryngeal specimens of squamous cell carcinoma (SCC) histologically confirmed. Results HPV DNA was detected in 93 (47.7%) specimens. HPV-11 was the most frequent with 68 cases (73.1%), and HPV-52 was the most frequently HR-HPV found with 51 cases, which corresponds to 54.8% of all HPV-positive specimens. EBV DNA was detected in 54 (27.7%) tumor tissue specimens of which 25 (46.3%) were in coinfection with HPV. MCPV DNA was detected only in 11 (5.6%) cases of which 5 (45.4%) were in coinfection with an HR-HPV. No association between the presence of DNA of the three examined viruses and the patient smoking habits, alcohol consumption, age, the keratinization status, differentiation grade, or localization of the tumor in the larynx were found. Discussion HPV-52 was the most prevalent HR-HPV, which may suggest that this and other genotypes in addition to HPV-16 and 18 could be considered for prophylaxis. However, further studies including non-cancer larynx cases and the evaluation of other molecular markers and viral co-infection mechanisms are needed to determine the role of the different HR-HPV genotypes, EBV, and MCPV in the etiology of SCC of the larynx.
format: application/pdf
format: text/html
creator: Jose Manuel Vazquez-Guillen
creator: Gerardo C. Palacios-Saucedo
creator: Lydia Guadalupe Rivera-Morales
creator: Monica Valeria Alonzo-Morado
creator: Saira Berenice Burciaga-Bernal
creator: Maribel Montufar-Martinez
creator: Rocio Ortiz-Lopez
creator: Vianey Gonzalez-Villasana
creator: Ana Carolina Martinez-Torres
creator: Julio Cesar Serna-Hernandez
creator: Silvia Judith Hernandez-Martinez
creator: Edmundo Erbey Castelan-Maldonado
creator: Angel Zavala-Pompa
creator: Martha Socorro Montalvo-Bañuelos
creator: Ricardo Garcia-Cabello
creator: Ethel Corinthia Sanchez-Fresno
creator: Cristina Rodriguez-Padilla
subject: Virology
subject: Oncology
subject: Otorhinolaryngology
subject: Respiratory Medicine
description: doi:10.7717/peerj.5834
publisher: PeerJ Inc.
rights: © 2018 Vazquez-Guillen et al.
abstract: Background Human papillomavirus (HPV) is recognized as an important risk factor for laryngeal carcinogenesis. Although HPV-16 and 18 have been strongly implicated, the presence of other high-risk HPV (HR-HPV) genotypes or the coinfection with Epstein-Barr virus (EBV) or Merkel cell polyomavirus (MCPV) may increase the risk, but their etiological association has not been definitively established. Methods We characterized the genotype-specific HPV and the frequency of EBV and MCPV infections through the detection of their DNA in 195 laryngeal specimens of squamous cell carcinoma (SCC) histologically confirmed. Results HPV DNA was detected in 93 (47.7%) specimens. HPV-11 was the most frequent with 68 cases (73.1%), and HPV-52 was the most frequently HR-HPV found with 51 cases, which corresponds to 54.8% of all HPV-positive specimens. EBV DNA was detected in 54 (27.7%) tumor tissue specimens of which 25 (46.3%) were in coinfection with HPV. MCPV DNA was detected only in 11 (5.6%) cases of which 5 (45.4%) were in coinfection with an HR-HPV. No association between the presence of DNA of the three examined viruses and the patient smoking habits, alcohol consumption, age, the keratinization status, differentiation grade, or localization of the tumor in the larynx were found. Discussion HPV-52 was the most prevalent HR-HPV, which may suggest that this and other genotypes in addition to HPV-16 and 18 could be considered for prophylaxis. However, further studies including non-cancer larynx cases and the evaluation of other molecular markers and viral co-infection mechanisms are needed to determine the role of the different HR-HPV genotypes, EBV, and MCPV in the etiology of SCC of the larynx.
bibliographic citation: Vazquez-Guillen et al. (2018) Infection and coinfection by human papillomavirus, Epstein–Barr virus and Merkel cell polyomavirus in patients with squamous cell carcinoma of the larynx: a retrospective study. PeerJ 6:e5834 https://doi.org/10.7717/peerj.5834
date submitted: 2018-03-21
date accepted: 2018-09-27
issued: 2018-10-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vazquez-Guillen
  given name: Jose Manuel
author list: Agent
  family name: Palacios-Saucedo
  given name: Gerardo C.
author list: Agent
  family name: Rivera-Morales
  given name: Lydia Guadalupe
author list: Agent
  family name: Alonzo-Morado
  given name: Monica Valeria
author list: Agent
  family name: Burciaga-Bernal
  given name: Saira Berenice
author list: Agent
  family name: Montufar-Martinez
  given name: Maribel
author list: Agent
  family name: Ortiz-Lopez
  given name: Rocio
author list: Agent
  family name: Gonzalez-Villasana
  given name: Vianey
author list: Agent
  family name: Martinez-Torres
  given name: Ana Carolina
author list: Agent
  family name: Serna-Hernandez
  given name: Julio Cesar
author list: Agent
  family name: Hernandez-Martinez
  given name: Silvia Judith
author list: Agent
  family name: Castelan-Maldonado
  given name: Edmundo Erbey
author list: Agent
  family name: Zavala-Pompa
  given name: Angel
author list: Agent
  family name: Montalvo-Bañuelos
  given name: Martha Socorro
author list: Agent
  family name: Garcia-Cabello
  given name: Ricardo
author list: Agent
  family name: Sanchez-Fresno
  given name: Ethel Corinthia
author list: Agent
  family name: Rodriguez-Padilla
  given name: Cristina
doi: 10.7717/peerj.5834
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-24
copyright: ©2018 Vazquez-Guillen et al.
attribution name: Vazquez-Guillen et al.

Meta-analysis of microarray datasets identify several chromosome segregation-related cancer/testis genes potentially contributing to anaplastic thyroid carcinoma
type: item
type: AcademicArticle
description: Aim Anaplastic thyroid carcinoma (ATC) is the most lethal thyroid malignancy. Identification of novel drug targets is urgently needed. Materials & Methods We re-analyzed several GEO datasets by systematic retrieval and data merging. Differentially expressed genes (DEGs) were filtered out. We also performed pathway enrichment analysis to interpret the data. We predicted key genes based on protein–protein interaction networks, weighted gene co-expression network analysis and genes’ cancer/testis expression pattern. We also further characterized these genes using data from the Cancer Genome Atlas (TCGA) project and gene ontology annotation. Results Cell cycle-related pathways were significantly enriched in upregulated genes in ATC. We identified TRIP13, DLGAP5, HJURP, CDKN3, NEK2, KIF15, TTK, KIF2C, AURKA and TPX2 as cell cycle-related key genes with cancer/testis expression pattern. We further uncovered that most of these putative key genes were critical components during chromosome segregation. Conclusion We predicted several key genes harboring potential therapeutic value in ATC. Cell cycle-related processes, especially chromosome segregation, may be the key to tumorigenesis and treatment of ATC.
format: application/pdf
format: text/html
creator: Mu Liu
creator: Yu-lu Qiu
creator: Tong Jin
creator: Yin Zhou
creator: Zhi-yuan Mao
creator: Yong-jie Zhang
subject: Genetics
subject: Diabetes and Endocrinology
subject: Oncology
description: doi:10.7717/peerj.5822
publisher: PeerJ Inc.
rights: © 2018 Liu et al.
abstract: Aim Anaplastic thyroid carcinoma (ATC) is the most lethal thyroid malignancy. Identification of novel drug targets is urgently needed. Materials & Methods We re-analyzed several GEO datasets by systematic retrieval and data merging. Differentially expressed genes (DEGs) were filtered out. We also performed pathway enrichment analysis to interpret the data. We predicted key genes based on protein–protein interaction networks, weighted gene co-expression network analysis and genes’ cancer/testis expression pattern. We also further characterized these genes using data from the Cancer Genome Atlas (TCGA) project and gene ontology annotation. Results Cell cycle-related pathways were significantly enriched in upregulated genes in ATC. We identified TRIP13, DLGAP5, HJURP, CDKN3, NEK2, KIF15, TTK, KIF2C, AURKA and TPX2 as cell cycle-related key genes with cancer/testis expression pattern. We further uncovered that most of these putative key genes were critical components during chromosome segregation. Conclusion We predicted several key genes harboring potential therapeutic value in ATC. Cell cycle-related processes, especially chromosome segregation, may be the key to tumorigenesis and treatment of ATC.
bibliographic citation: Liu et al. (2018) Meta-analysis of microarray datasets identify several chromosome segregation-related cancer/testis genes potentially contributing to anaplastic thyroid carcinoma. PeerJ 6:e5822 https://doi.org/10.7717/peerj.5822
date submitted: 2018-05-11
date accepted: 2018-09-25
issued: 2018-10-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Mu
author list: Agent
  family name: Qiu
  given name: Yu-lu
author list: Agent
  family name: Jin
  given name: Tong
author list: Agent
  family name: Zhou
  given name: Yin
author list: Agent
  family name: Mao
  given name: Zhi-yuan
author list: Agent
  family name: Zhang
  given name: Yong-jie
doi: 10.7717/peerj.5822
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-24
copyright: ©2018 Liu et al.
attribution name: Liu et al.

Species diversity of drifting fish eggs in the Yangtze River using molecular identification
type: item
type: AcademicArticle
description: The dam constructions greatly changed the hydrologic conditions in the Yangtze River, and then significantly affected the spawning activities of indigenous river fish. Monitoring the species composition of drifting eggs during spawning season is important for protection issues. In this study, we have sampled drifting fish eggs in nine locations from 2014 to 2016. Eggs were identified using the mitochondrial cyt b gene sequence. A total of 7,933 fish eggs were sequenced successfully and blasted into the NCBI database. Thirty-nine fish species were identified, and were assigned to four families and two orders. Approximately 64% of the species identified, and 67% of the eggs, were classified in the Family Cyprinidae. Abundance and Shannon–Wiener diversity index of species were higher in the main river than in tributaries of the river. However, tributaries may be important spawning grounds for some fish species. The Jaccard’s similarity index and river-way distances among sampled stations were negatively correlated suggesting the environment shapes species composition in the sampled spawning grounds. These results showed that mitochondrial DNA sequence is a powerful and effective tool for fish egg identification in Yangtze River and these data are useful for conservation efforts.
format: application/pdf
format: text/html
creator: Mingdian Liu
creator: Dengqiang Wang
creator: Lei Gao
creator: Huiwu Tian
creator: Shaoping Liu
creator: Daqing Chen
creator: Xinbin Duan
subject: Aquaculture, Fisheries and Fish Science
subject: Freshwater Biology
description: doi:10.7717/peerj.5807
publisher: PeerJ Inc.
rights: © 2018 Liu et al.
abstract: The dam constructions greatly changed the hydrologic conditions in the Yangtze River, and then significantly affected the spawning activities of indigenous river fish. Monitoring the species composition of drifting eggs during spawning season is important for protection issues. In this study, we have sampled drifting fish eggs in nine locations from 2014 to 2016. Eggs were identified using the mitochondrial cyt b gene sequence. A total of 7,933 fish eggs were sequenced successfully and blasted into the NCBI database. Thirty-nine fish species were identified, and were assigned to four families and two orders. Approximately 64% of the species identified, and 67% of the eggs, were classified in the Family Cyprinidae. Abundance and Shannon–Wiener diversity index of species were higher in the main river than in tributaries of the river. However, tributaries may be important spawning grounds for some fish species. The Jaccard’s similarity index and river-way distances among sampled stations were negatively correlated suggesting the environment shapes species composition in the sampled spawning grounds. These results showed that mitochondrial DNA sequence is a powerful and effective tool for fish egg identification in Yangtze River and these data are useful for conservation efforts.
bibliographic citation: Liu et al. (2018) Species diversity of drifting fish eggs in the Yangtze River using molecular identification. PeerJ 6:e5807 https://doi.org/10.7717/peerj.5807
date submitted: 2018-04-23
date accepted: 2018-09-21
issued: 2018-10-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Mingdian
author list: Agent
  family name: Wang
  given name: Dengqiang
author list: Agent
  family name: Gao
  given name: Lei
author list: Agent
  family name: Tian
  given name: Huiwu
author list: Agent
  family name: Liu
  given name: Shaoping
author list: Agent
  family name: Chen
  given name: Daqing
author list: Agent
  family name: Duan
  given name: Xinbin
doi: 10.7717/peerj.5807
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-24
copyright: ©2018 Liu et al.
attribution name: Liu et al.

Integrative analysis of microRNA and mRNA expression profiles in fetal rat model with anorectal malformation
type: item
type: AcademicArticle
description: Background Anorectal malformations (ARMs) are the most common congenital malformation of the gut, and regulated by multiple signal transduction pathways. The microRNA (miRNA) expression profiles and their biologial functions in anorectal malformations (ARMs) remain unclear. The aim of our study was to evaluate miRNA and mRNA expression profiles in the ARM rats. Methods and Materials ARM was induced with ethylenethiourea (ETU) on gestational day 10. Cesarean deliveries were performed to harvest the embryos on gestional day 20. For the extraction of total RNA, 1 cm terminal hindgut samples were obtained from three fetal rats that had similar weights. The microarrays and quantitative RT-PCR analysis were conducted to evaluate the miRNA and mRNA expression profiles in normal fetal rats (n = 3) and ARM fetal rats (n = 3). Results In total, 33 miRNAs and 772 mRNAs were significantly and differentially expressed in terminal hindgut tissues of ARM group versus control group. Functional annotation was performed to understand the functions and pathways of differentially expressed mRNAs. Also, we constructed a miRNA-target gene regulatory network including 25 differentially expressed miRNAs and 76 mRNAs. Furthermore, the credibility of the microarray-based results were validated by using qRT-PCR. Conclusion The miRNA and mRNA expression in terminal hindgut tissue of ARM fetal rats might provide a basis for further research on the pathogenesis of ARMs.
format: application/pdf
format: text/html
creator: Hui Xiao
creator: Rui Huang
creator: Mei Diao
creator: Long Li
creator: XiaoDai Cui
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Pediatrics
description: doi:10.7717/peerj.5774
publisher: PeerJ Inc.
rights: © 2018 Xiao et al.
abstract: Background Anorectal malformations (ARMs) are the most common congenital malformation of the gut, and regulated by multiple signal transduction pathways. The microRNA (miRNA) expression profiles and their biologial functions in anorectal malformations (ARMs) remain unclear. The aim of our study was to evaluate miRNA and mRNA expression profiles in the ARM rats. Methods and Materials ARM was induced with ethylenethiourea (ETU) on gestational day 10. Cesarean deliveries were performed to harvest the embryos on gestional day 20. For the extraction of total RNA, 1 cm terminal hindgut samples were obtained from three fetal rats that had similar weights. The microarrays and quantitative RT-PCR analysis were conducted to evaluate the miRNA and mRNA expression profiles in normal fetal rats (n = 3) and ARM fetal rats (n = 3). Results In total, 33 miRNAs and 772 mRNAs were significantly and differentially expressed in terminal hindgut tissues of ARM group versus control group. Functional annotation was performed to understand the functions and pathways of differentially expressed mRNAs. Also, we constructed a miRNA-target gene regulatory network including 25 differentially expressed miRNAs and 76 mRNAs. Furthermore, the credibility of the microarray-based results were validated by using qRT-PCR. Conclusion The miRNA and mRNA expression in terminal hindgut tissue of ARM fetal rats might provide a basis for further research on the pathogenesis of ARMs.
bibliographic citation: Xiao et al. (2018) Integrative analysis of microRNA and mRNA expression profiles in fetal rat model with anorectal malformation. PeerJ 6:e5774 https://doi.org/10.7717/peerj.5774
date submitted: 2018-06-04
date accepted: 2018-09-14
issued: 2018-10-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Hui
author list: Agent
  family name: Huang
  given name: Rui
author list: Agent
  family name: Diao
  given name: Mei
author list: Agent
  family name: Li
  given name: Long
author list: Agent
  family name: Cui
  given name: XiaoDai
doi: 10.7717/peerj.5774
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-24
copyright: ©2018 Xiao et al.
attribution name: Xiao et al.

Effects of inconsistent reporting, regulation changes and market demand on abundance indices of sharks caught by pelagic longliners off southern Africa
type: item
type: AcademicArticle
description: The assumption of a proportional relationship between catch-per-unit-effort (CPUE) and the abundance of sharks caught by pelagic longliners is tenuous when based on fisher logbooks that report only retained specimens. Nevertheless, commercial logbooks and landings statistics are often the only data available for stock status assessments. Logbook data collected from local and foreign pelagic longline vessels operating in four areas off southern Africa between 2000 and 2015 were used to construct standardized CPUE indices for blue sharks Prionace glauca and shortfin makos Isurus oxyrinchus. Generalized linear mixed models were used to explore the effects of year, month, vessel, fleet and presence of an observer on blue shark and shortfin mako variability. Landing statistics and auxiliary information on the history of the fishery, regulation changes, and market factors were superimposed on the CPUE indices, to test hypotheses that they would influence CPUE trends. Indices in the West and Southwest (Atlantic) areas were elevated for both species, compared to the South and East (Indian Ocean). The scale of year-on-year CPUE increments, up to an order of magnitude for blue sharks, reflected occasional targeting and retention, interspersed with periods where blue sharks were not caught, or discarded and not reported. Increments were smaller for higher value shortfin makos, suggesting that indices were less affected by unreported discarding. CPUE indices and landings of both shark species have increased in recent years, suggesting increased importance as target species. Analysis of logbook data resulted in unreliable indicators of shark abundance, but when trends were interpreted in conjunction with landings data, disaggregated by area and month, and with hindsight of market demand and regulation changes, anomalies could be explained.
format: application/pdf
format: text/html
creator: Gareth L. Jordaan
creator: Jorge Santos
creator: Johan C. Groeneveld
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.5726
publisher: PeerJ Inc.
rights: © 2018 Jordaan et al.
abstract: The assumption of a proportional relationship between catch-per-unit-effort (CPUE) and the abundance of sharks caught by pelagic longliners is tenuous when based on fisher logbooks that report only retained specimens. Nevertheless, commercial logbooks and landings statistics are often the only data available for stock status assessments. Logbook data collected from local and foreign pelagic longline vessels operating in four areas off southern Africa between 2000 and 2015 were used to construct standardized CPUE indices for blue sharks Prionace glauca and shortfin makos Isurus oxyrinchus. Generalized linear mixed models were used to explore the effects of year, month, vessel, fleet and presence of an observer on blue shark and shortfin mako variability. Landing statistics and auxiliary information on the history of the fishery, regulation changes, and market factors were superimposed on the CPUE indices, to test hypotheses that they would influence CPUE trends. Indices in the West and Southwest (Atlantic) areas were elevated for both species, compared to the South and East (Indian Ocean). The scale of year-on-year CPUE increments, up to an order of magnitude for blue sharks, reflected occasional targeting and retention, interspersed with periods where blue sharks were not caught, or discarded and not reported. Increments were smaller for higher value shortfin makos, suggesting that indices were less affected by unreported discarding. CPUE indices and landings of both shark species have increased in recent years, suggesting increased importance as target species. Analysis of logbook data resulted in unreliable indicators of shark abundance, but when trends were interpreted in conjunction with landings data, disaggregated by area and month, and with hindsight of market demand and regulation changes, anomalies could be explained.
bibliographic citation: Jordaan et al. (2018) Effects of inconsistent reporting, regulation changes and market demand on abundance indices of sharks caught by pelagic longliners off southern Africa. PeerJ 6:e5726 https://doi.org/10.7717/peerj.5726
date submitted: 2017-11-16
date accepted: 2018-09-07
issued: 2018-10-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jordaan
  given name: Gareth L.
author list: Agent
  family name: Santos
  given name: Jorge
author list: Agent
  family name: Groeneveld
  given name: Johan C.
doi: 10.7717/peerj.5726
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-24
copyright: ©2018 Jordaan et al.
attribution name: Jordaan et al.

Variations in the reproductive strategies of three populations of Phrynocephalus helioscopus in China
type: item
type: AcademicArticle
description: Background Egg size and clutch size are key life history traits. During the breeding period, it is possible for females to increase their reproductive output either by increasing the number of eggs if the optimal egg size (OES) is maintained, or by increasing the allocation of energy to each egg. However, the strategies adopted are often influenced by animals’ morphology and environment. Methods Here, we examined variation in female morphological and reproductive traits, tested for trade-offs between egg size and clutch size, and evaluated the relationship between egg size and female morphology in three populations of Phrynocephalus helioscopus. Results Female body size, egg size, and clutch size were larger in the Yi Ning (YN) and Fu Yun (FY) populations than in the Bei Tun (BT) population (the FY and YN populations laid more, and rounder eggs). Egg size was independent of female body size in two populations (BT and FY), even though both populations had an egg-size/clutch size trade-off. In the YN population, egg size and clutch size were independent, but egg size was correlated with female body size, consistent with the hypothesis of morphological constraint. Conclusions Our study found geographical variation in body size and reproductive strategies of P. helioscopus. Egg size was correlated with morphology in the larger-bodied females of the YN population, but not in the smaller-bodied females of the BT population, illustrating that constraints on female body size and egg size are not consistent between populations.
format: application/pdf
format: text/html
creator: Tao Liang
creator: Lu Zhou
creator: Wenfeng He
creator: Lirong Xiao
creator: Lei Shi
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.5705
publisher: PeerJ Inc.
rights: © 2018 Liang et al.
abstract: Background Egg size and clutch size are key life history traits. During the breeding period, it is possible for females to increase their reproductive output either by increasing the number of eggs if the optimal egg size (OES) is maintained, or by increasing the allocation of energy to each egg. However, the strategies adopted are often influenced by animals’ morphology and environment. Methods Here, we examined variation in female morphological and reproductive traits, tested for trade-offs between egg size and clutch size, and evaluated the relationship between egg size and female morphology in three populations of Phrynocephalus helioscopus. Results Female body size, egg size, and clutch size were larger in the Yi Ning (YN) and Fu Yun (FY) populations than in the Bei Tun (BT) population (the FY and YN populations laid more, and rounder eggs). Egg size was independent of female body size in two populations (BT and FY), even though both populations had an egg-size/clutch size trade-off. In the YN population, egg size and clutch size were independent, but egg size was correlated with female body size, consistent with the hypothesis of morphological constraint. Conclusions Our study found geographical variation in body size and reproductive strategies of P. helioscopus. Egg size was correlated with morphology in the larger-bodied females of the YN population, but not in the smaller-bodied females of the BT population, illustrating that constraints on female body size and egg size are not consistent between populations.
bibliographic citation: Liang et al. (2018) Variations in the reproductive strategies of three populations of Phrynocephalus helioscopus in China. PeerJ 6:e5705 https://doi.org/10.7717/peerj.5705
date submitted: 2018-04-13
date accepted: 2018-09-06
issued: 2018-10-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Tao
author list: Agent
  family name: Zhou
  given name: Lu
author list: Agent
  family name: He
  given name: Wenfeng
author list: Agent
  family name: Xiao
  given name: Lirong
author list: Agent
  family name: Shi
  given name: Lei
doi: 10.7717/peerj.5705
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-24
copyright: ©2018 Liang et al.
attribution name: Liang et al.

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