PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data
items: High microphone signal-to-noise ratio enhances acoustic sampling of wildlife
items: Insect pollination is important in a smallholder bean farming system
items: Isolation and evolutionary analyses of porcine epidemic diarrhea virus in Asia
items: Visual duration bisection in profoundly deaf individuals
items: Polarity and epithelial-mesenchymal transition of retinal pigment epithelial cells in proliferative vitreoretinopathy
items: Mining the potential prognostic value of synaptosomal-associated protein 25 (SNAP25) in colon cancer based on stromal-immune score
items: Craniofacial ontogeny in Tylosaurinae
items: miR-29a-3p directly targets Smad nuclear interacting protein 1 and inhibits the migration and proliferation of cervical cancer HeLa cells
items: Spatiotemporal accumulation of fatal pharyngeal entrapment of flatfish in harbour porpoises (Phocoena phocoena) in the German North Sea

DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data
type: item
type: AcademicArticle
description: For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and, as such, drives proteomics. MS/MS spectra need to be assigned a peptide sequence for which two strategies exist. Either database search or de novo sequencing can be employed to establish peptide spectrum matches. For database search, mzIdentML is the current community standard for data representation. There is no community standard for representing de novo sequencing results, but we previously proposed the de novo markup language (DNML). At the moment, each de novo sequencing solution uses different data representation, complicating downstream data integration, which is crucial since ensemble predictions may be more useful than predictions of a single tool. We here propose the de novo MS Ontology (DNMSO), which can, for example, provide many-to-many mappings between spectra and peptide predictions. Additionally, an application programming interface (API) that supports any file operation necessary for de novo sequencing from spectra input to reading, writing, creating, of the DNMSO format, as well as conversion from many other file formats, has been implemented. This API removes all overhead from the production of de novo sequencing tools and allows developers to concentrate on algorithm development completely. We make the API and formal descriptions of the format freely available at https://github.com/savastakan/dnmso.
format: application/pdf
format: text/html
creator: Savaş Takan
creator: Jens Allmer
subject: Biochemistry
subject: Bioinformatics
subject: Computational Science
description: doi:10.7717/peerj.10216
publisher: PeerJ Inc.
rights: © 2020 Takan and Allmer
abstract: For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and, as such, drives proteomics. MS/MS spectra need to be assigned a peptide sequence for which two strategies exist. Either database search or de novo sequencing can be employed to establish peptide spectrum matches. For database search, mzIdentML is the current community standard for data representation. There is no community standard for representing de novo sequencing results, but we previously proposed the de novo markup language (DNML). At the moment, each de novo sequencing solution uses different data representation, complicating downstream data integration, which is crucial since ensemble predictions may be more useful than predictions of a single tool. We here propose the de novo MS Ontology (DNMSO), which can, for example, provide many-to-many mappings between spectra and peptide predictions. Additionally, an application programming interface (API) that supports any file operation necessary for de novo sequencing from spectra input to reading, writing, creating, of the DNMSO format, as well as conversion from many other file formats, has been implemented. This API removes all overhead from the production of de novo sequencing tools and allows developers to concentrate on algorithm development completely. We make the API and formal descriptions of the format freely available at https://github.com/savastakan/dnmso.
bibliographic citation: Takan et al. (2020) DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data. PeerJ 8:e10216 https://doi.org/10.7717/peerj.10216
date submitted: 2020-03-11
date accepted: 2020-09-28
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Takan
  given name: Savaş
author list: Agent
  family name: Allmer
  given name: Jens
doi: 10.7717/peerj.10216
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Takan and Allmer
attribution name: Takan and Allmer

High microphone signal-to-noise ratio enhances acoustic sampling of wildlife
type: item
type: AcademicArticle
description: Background Automated sound recorders are a popular sampling tool in ecology. However, the microphones themselves received little attention so far, and specifications that determine the recordings’ sound quality are seldom mentioned. Here, we demonstrate the importance of microphone signal-to-noise ratio for sampling sonant animals. Methods We tested 12 different microphone models in the field and measured their signal-to-noise ratios and detection ranges. We also measured the vocalisation activity of birds and bats that they recorded, the bird species richness, the bat call types richness, as well as the performance of automated detection of bird and bat calls. We tested the relationship of each one of these measures with signal-to-noise ratio in statistical models. Results Microphone signal-to-noise ratio positively affects the sound detection space areas, which increased by a factor of 1.7 for audible sound, and 10 for ultrasound, from the lowest to the highest signal-to-noise ratio microphone. Consequently, the sampled vocalisation activity increased by a factor of 1.6 for birds, and 9.7 for bats. Correspondingly, the species pool of birds and bats could not be completely detected by the microphones with lower signal-to-noise ratio. The performance of automated detection of bird and bat calls, as measured by its precision and recall, increased significantly with microphone signal-to-noise ratio. Discussion Microphone signal-to-noise ratio is a crucial characteristic of a sound recording system, positively affecting the acoustic sampling performance of birds and bats. It should be maximised by choosing appropriate microphones, and be quantified independently, especially in the ultrasound range.
format: application/pdf
format: text/html
creator: Kevin F.A. Darras
creator: Franziska Deppe
creator: Yvonne Fabian
creator: Agus P. Kartono
creator: Andres Angulo
creator: Bjørn Kolbrek
creator: Yeni A. Mulyani
creator: Dewi M. Prawiradilaga
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.9955
publisher: PeerJ Inc.
rights: © 2020 Darras et al.
abstract: Background Automated sound recorders are a popular sampling tool in ecology. However, the microphones themselves received little attention so far, and specifications that determine the recordings’ sound quality are seldom mentioned. Here, we demonstrate the importance of microphone signal-to-noise ratio for sampling sonant animals. Methods We tested 12 different microphone models in the field and measured their signal-to-noise ratios and detection ranges. We also measured the vocalisation activity of birds and bats that they recorded, the bird species richness, the bat call types richness, as well as the performance of automated detection of bird and bat calls. We tested the relationship of each one of these measures with signal-to-noise ratio in statistical models. Results Microphone signal-to-noise ratio positively affects the sound detection space areas, which increased by a factor of 1.7 for audible sound, and 10 for ultrasound, from the lowest to the highest signal-to-noise ratio microphone. Consequently, the sampled vocalisation activity increased by a factor of 1.6 for birds, and 9.7 for bats. Correspondingly, the species pool of birds and bats could not be completely detected by the microphones with lower signal-to-noise ratio. The performance of automated detection of bird and bat calls, as measured by its precision and recall, increased significantly with microphone signal-to-noise ratio. Discussion Microphone signal-to-noise ratio is a crucial characteristic of a sound recording system, positively affecting the acoustic sampling performance of birds and bats. It should be maximised by choosing appropriate microphones, and be quantified independently, especially in the ultrasound range.
bibliographic citation: Darras et al. (2020) High microphone signal-to-noise ratio enhances acoustic sampling of wildlife. PeerJ 8:e9955 https://doi.org/10.7717/peerj.9955
date submitted: 2020-05-06
date accepted: 2020-08-25
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Darras
  given name: Kevin F.A.
author list: Agent
  family name: Deppe
  given name: Franziska
author list: Agent
  family name: Fabian
  given name: Yvonne
author list: Agent
  family name: Kartono
  given name: Agus P.
author list: Agent
  family name: Angulo
  given name: Andres
author list: Agent
  family name: Kolbrek
  given name: Bjørn
author list: Agent
  family name: Mulyani
  given name: Yeni A.
author list: Agent
  family name: Prawiradilaga
  given name: Dewi M.
doi: 10.7717/peerj.9955
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Darras et al.
attribution name: Darras et al.

Insect pollination is important in a smallholder bean farming system
type: item
type: AcademicArticle
description: Background Many crops are dependent on pollination by insects. Habitat management in agricultural landscapes can support pollinator services and even augment crop production. Common bean (Phaseolus vulgaris L.) is an important legume for the livelihoods of smallholder farmers in many low-income countries, particularly so in East Africa. While this crop is autogamous, it is frequently visited by pollinating insects that could improve yields. However, the value of pollination services to common beans (Kariasii) yield is not known. Methods We carried out pollinator-exclusion experiments to determine the contribution of insect pollinators to bean yields. We also carried out a fluorescent-dye experiment to evaluate the role of field margins as refuge for flower-visitors. Results Significantly higher yields, based on pods per plant and seeds per pod, were recorded from open-pollinated and hand-pollinated flowers compared to plants from which pollinators had been excluded indicating that flower visitors contribute significantly to bean yields. Similarly, open and hand-pollinated plants recorded the highest mean seed weight. Extrapolation of yield data to field scale indicated a potential increase per hectare from 681 kg in self-pollinated beans to 1,478 kg in open-pollinated beans indicating that flower visitors contributed significantly to crop yield of beans. Our marking study indicated that flower-visiting insects including bees, flies and lepidopterans moved from the field margin flowers into the bean crop. Overall, these results show that insect pollinators are important for optimising bean yields and an important food security consideration on smallholder farms. Field margin vegetation also provides habitat for flower-visiting insects that pollinate beans. Hence, non-crop habitats merit further research focusing on establishing which field margin species are most important and their capacity to support other ecosystem services such as natural pest regulation or even …
format: application/pdf
format: text/html
creator: Filemon Elisante
creator: Patrick Ndakidemi
creator: Sarah E.J. Arnold
creator: Steven R. Belmain
creator: Geoff M. Gurr
creator: Iain Darbyshire
creator: Gang Xie
creator: Philip C. Stevenson
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Entomology
description: doi:10.7717/peerj.10102
publisher: PeerJ Inc.
rights: © 2020 Elisante et al.
abstract: Background Many crops are dependent on pollination by insects. Habitat management in agricultural landscapes can support pollinator services and even augment crop production. Common bean (Phaseolus vulgaris L.) is an important legume for the livelihoods of smallholder farmers in many low-income countries, particularly so in East Africa. While this crop is autogamous, it is frequently visited by pollinating insects that could improve yields. However, the value of pollination services to common beans (Kariasii) yield is not known. Methods We carried out pollinator-exclusion experiments to determine the contribution of insect pollinators to bean yields. We also carried out a fluorescent-dye experiment to evaluate the role of field margins as refuge for flower-visitors. Results Significantly higher yields, based on pods per plant and seeds per pod, were recorded from open-pollinated and hand-pollinated flowers compared to plants from which pollinators had been excluded indicating that flower visitors contribute significantly to bean yields. Similarly, open and hand-pollinated plants recorded the highest mean seed weight. Extrapolation of yield data to field scale indicated a potential increase per hectare from 681 kg in self-pollinated beans to 1,478 kg in open-pollinated beans indicating that flower visitors contributed significantly to crop yield of beans. Our marking study indicated that flower-visiting insects including bees, flies and lepidopterans moved from the field margin flowers into the bean crop. Overall, these results show that insect pollinators are important for optimising bean yields and an important food security consideration on smallholder farms. Field margin vegetation also provides habitat for flower-visiting insects that pollinate beans. Hence, non-crop habitats merit further research focusing on establishing which field margin species are most important and their capacity to support other ecosystem services such as natural pest regulation or even …
bibliographic citation: Elisante et al. (2020) Insect pollination is important in a smallholder bean farming system. PeerJ 8:e10102 https://doi.org/10.7717/peerj.10102
date submitted: 2020-03-06
date accepted: 2020-09-14
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elisante
  given name: Filemon
author list: Agent
  family name: Ndakidemi
  given name: Patrick
author list: Agent
  family name: Arnold
  given name: Sarah E.J.
author list: Agent
  family name: Belmain
  given name: Steven R.
author list: Agent
  family name: Gurr
  given name: Geoff M.
author list: Agent
  family name: Darbyshire
  given name: Iain
author list: Agent
  family name: Xie
  given name: Gang
author list: Agent
  family name: Stevenson
  given name: Philip C.
doi: 10.7717/peerj.10102
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Elisante et al.
attribution name: Elisante et al.

Isolation and evolutionary analyses of porcine epidemic diarrhea virus in Asia
type: item
type: AcademicArticle
description: Porcine epidemic diarrhea virus (PEDV) is a leading cause of diarrhea in pigs worldwide. Virus isolation and genetic evolutionary analysis allow investigations into the prevalence of epidemic strains and provide data for the clinical diagnosis and vaccine development. In this study, we investigated the genetic characteristics of PEDV circulation in Asia through virus isolation and comparative genomics analysis. APEDV strain designated HB2018 was isolated from a pig in a farm experiencing a diarrhea outbreak. The complete genome sequence of HB2018 was 28,138 bp in length. Phylogenetic analysis of HB2018 and 207 PEDVs in Asia showed that most PEDV strains circulating in Asia after 2010 belong to genotype GII, particularly GII-a. The PEDV vaccine strain CV777 belonged to GI, and thus, unmatched genotypes between CV777 and GII-a variants might partially explain incomplete protection by the CV777-derived vaccine against PEDV variants in China. In addition, we found the S protein of variant strains contained numerous mutations compared to the S protein of CV777, and these mutations occurred in the N-terminal domain of the S protein. These mutations may influence the antigenicity, pathogenicity, and neutralization properties of the variant strains.
format: application/pdf
format: text/html
creator: Wan Liang
creator: Danna Zhou
creator: Chao Geng
creator: Keli Yang
creator: Zhengying Duan
creator: Rui Guo
creator: Wei Liu
creator: Fangyan Yuan
creator: Zewen Liu
creator: Ting Gao
creator: Ling Zhao
creator: Dongwan Yoo
creator: Yongxiang Tian
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
subject: Veterinary Medicine
subject: Epidemiology
description: doi:10.7717/peerj.10114
publisher: PeerJ Inc.
rights: © 2020 Liang et al.
abstract: Porcine epidemic diarrhea virus (PEDV) is a leading cause of diarrhea in pigs worldwide. Virus isolation and genetic evolutionary analysis allow investigations into the prevalence of epidemic strains and provide data for the clinical diagnosis and vaccine development. In this study, we investigated the genetic characteristics of PEDV circulation in Asia through virus isolation and comparative genomics analysis. APEDV strain designated HB2018 was isolated from a pig in a farm experiencing a diarrhea outbreak. The complete genome sequence of HB2018 was 28,138 bp in length. Phylogenetic analysis of HB2018 and 207 PEDVs in Asia showed that most PEDV strains circulating in Asia after 2010 belong to genotype GII, particularly GII-a. The PEDV vaccine strain CV777 belonged to GI, and thus, unmatched genotypes between CV777 and GII-a variants might partially explain incomplete protection by the CV777-derived vaccine against PEDV variants in China. In addition, we found the S protein of variant strains contained numerous mutations compared to the S protein of CV777, and these mutations occurred in the N-terminal domain of the S protein. These mutations may influence the antigenicity, pathogenicity, and neutralization properties of the variant strains.
bibliographic citation: Liang et al. (2020) Isolation and evolutionary analyses of porcine epidemic diarrhea virus in Asia. PeerJ 8:e10114 https://doi.org/10.7717/peerj.10114
date submitted: 2020-03-26
date accepted: 2020-09-16
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Wan
author list: Agent
  family name: Zhou
  given name: Danna
author list: Agent
  family name: Geng
  given name: Chao
author list: Agent
  family name: Yang
  given name: Keli
author list: Agent
  family name: Duan
  given name: Zhengying
author list: Agent
  family name: Guo
  given name: Rui
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Yuan
  given name: Fangyan
author list: Agent
  family name: Liu
  given name: Zewen
author list: Agent
  family name: Gao
  given name: Ting
author list: Agent
  family name: Zhao
  given name: Ling
author list: Agent
  family name: Yoo
  given name: Dongwan
author list: Agent
  family name: Tian
  given name: Yongxiang
doi: 10.7717/peerj.10114
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Liang et al.
attribution name: Liang et al.

Visual duration bisection in profoundly deaf individuals
type: item
type: AcademicArticle
description: Background Previous research has been designed to study the effect of hearing loss on supra-second duration estimation in the visual channel and position effect of visual abilities among deaf populations. The current study aimed to investigate the sub-second duration perception of different visual fields in profoundly deaf individuals. Methods A total of 16 profoundly deaf undergraduates and 16 hearing undergraduates completed a visual duration bisection task in which participants made judgments about whether a series of probe durations that were linearly spaced from 200 ms to 800 ms at 100 ms intervals were more similar to a standard short duration (200 ms) or a standard long duration (800 ms). The probe stimuli were presented in the center, left, or right of the screen. A repeated measure analysis of variance (ANOVA) with a between-participants factor of group and a within-participants factor of position, and a one-sample t-test were conducted. Results The Weber ratio (WR) values of deaf participants were significantly higher than those of hearing participants, regardless of the presented positions of the visual stimulus. The bisection point (BP) value of deaf participants was significantly lower than 500 ms (average mean of 200/800 ms) and the BP value of hearing participants did not significantly differ from 500 ms, although the overall difference of BP values between the deaf group and hearing group did not reach significance. For deaf participants, the BP value in the center condition was significantly lower than 500 ms; however, the difference between the BP value in the left condition and 500 ms did not reach significance, indicating that their duration discrimination accuracy in the left visual field was better than that in the center visual field. Conclusions Hearing loss impaired visual sub-second duration perception, and deaf individuals showed a left visual field advantage of duration discrimination accuracy during the visual duration bisection task.
format: application/pdf
format: text/html
creator: Feng Zhang
creator: Kaige Jin
creator: Sainan Zhang
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.10133
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Background Previous research has been designed to study the effect of hearing loss on supra-second duration estimation in the visual channel and position effect of visual abilities among deaf populations. The current study aimed to investigate the sub-second duration perception of different visual fields in profoundly deaf individuals. Methods A total of 16 profoundly deaf undergraduates and 16 hearing undergraduates completed a visual duration bisection task in which participants made judgments about whether a series of probe durations that were linearly spaced from 200 ms to 800 ms at 100 ms intervals were more similar to a standard short duration (200 ms) or a standard long duration (800 ms). The probe stimuli were presented in the center, left, or right of the screen. A repeated measure analysis of variance (ANOVA) with a between-participants factor of group and a within-participants factor of position, and a one-sample t-test were conducted. Results The Weber ratio (WR) values of deaf participants were significantly higher than those of hearing participants, regardless of the presented positions of the visual stimulus. The bisection point (BP) value of deaf participants was significantly lower than 500 ms (average mean of 200/800 ms) and the BP value of hearing participants did not significantly differ from 500 ms, although the overall difference of BP values between the deaf group and hearing group did not reach significance. For deaf participants, the BP value in the center condition was significantly lower than 500 ms; however, the difference between the BP value in the left condition and 500 ms did not reach significance, indicating that their duration discrimination accuracy in the left visual field was better than that in the center visual field. Conclusions Hearing loss impaired visual sub-second duration perception, and deaf individuals showed a left visual field advantage of duration discrimination accuracy during the visual duration bisection task.
bibliographic citation: Zhang et al. (2020) Visual duration bisection in profoundly deaf individuals. PeerJ 8:e10133 https://doi.org/10.7717/peerj.10133
date submitted: 2020-05-28
date accepted: 2020-09-18
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Feng
author list: Agent
  family name: Jin
  given name: Kaige
author list: Agent
  family name: Zhang
  given name: Sainan
doi: 10.7717/peerj.10133
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: © 2020 Zhang et al.
attribution name: Zhang et al.

Polarity and epithelial-mesenchymal transition of retinal pigment epithelial cells in proliferative vitreoretinopathy
type: item
type: AcademicArticle
description: Under physiological conditions, retinal pigment epithelium (RPE) is a cellular monolayer composed of mitotically quiescent cells. Tight junctions and adherens junctions maintain the polarity of RPE cells, and are required for cellular functions. In proliferative vitreoretinopathy (PVR), upon retinal tear, RPE cells lose cell-cell contact, undergo epithelial-mesenchymal transition (EMT), and ultimately transform into myofibroblasts, leading to the formation of fibrocellular membranes on both surfaces of the detached retina and on the posterior hyaloids, which causes tractional retinal detachment. In PVR, RPE cells are crucial contributors, and multiple signaling pathways, including the SMAD-dependent pathway, Rho pathway, MAPK pathways, Jagged/Notch pathway, and the Wnt/β-catenin pathway are activated. These pathways mediate the EMT of RPE cells, which play a key role in the pathogenesis of PVR. This review summarizes the current body of knowledge on the polarized phenotype of RPE, the role of cell-cell contact, and the molecular mechanisms underlying the RPE EMT in PVR, emphasizing key insights into potential approaches to prevent PVR.
format: application/pdf
format: text/html
creator: Hui Zou
creator: Chenli Shan
creator: Linlin Ma
creator: Jia Liu
creator: Ning Yang
creator: Jinsong Zhao
subject: Cell Biology
subject: Molecular Biology
subject: Ophthalmology
description: doi:10.7717/peerj.10136
publisher: PeerJ Inc.
rights: © 2020 Zou et al.
abstract: Under physiological conditions, retinal pigment epithelium (RPE) is a cellular monolayer composed of mitotically quiescent cells. Tight junctions and adherens junctions maintain the polarity of RPE cells, and are required for cellular functions. In proliferative vitreoretinopathy (PVR), upon retinal tear, RPE cells lose cell-cell contact, undergo epithelial-mesenchymal transition (EMT), and ultimately transform into myofibroblasts, leading to the formation of fibrocellular membranes on both surfaces of the detached retina and on the posterior hyaloids, which causes tractional retinal detachment. In PVR, RPE cells are crucial contributors, and multiple signaling pathways, including the SMAD-dependent pathway, Rho pathway, MAPK pathways, Jagged/Notch pathway, and the Wnt/β-catenin pathway are activated. These pathways mediate the EMT of RPE cells, which play a key role in the pathogenesis of PVR. This review summarizes the current body of knowledge on the polarized phenotype of RPE, the role of cell-cell contact, and the molecular mechanisms underlying the RPE EMT in PVR, emphasizing key insights into potential approaches to prevent PVR.
bibliographic citation: Zou et al. (2020) Polarity and epithelial-mesenchymal transition of retinal pigment epithelial cells in proliferative vitreoretinopathy. PeerJ 8:e10136 https://doi.org/10.7717/peerj.10136
date submitted: 2020-06-10
date accepted: 2020-09-18
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zou
  given name: Hui
author list: Agent
  family name: Shan
  given name: Chenli
author list: Agent
  family name: Ma
  given name: Linlin
author list: Agent
  family name: Liu
  given name: Jia
author list: Agent
  family name: Yang
  given name: Ning
author list: Agent
  family name: Zhao
  given name: Jinsong
doi: 10.7717/peerj.10136
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Zou et al.
attribution name: Zou et al.

Mining the potential prognostic value of synaptosomal-associated protein 25 (SNAP25) in colon cancer based on stromal-immune score
type: item
type: AcademicArticle
description: Background Colon cancer is one of the deadliest tumors worldwide. Stromal cells and immune cells play important roles in cancer biology and microenvironment across different types of cancer. This study aimed to identify the prognostic value of stromal/immune cell-associated genes for colon cancer in The Cancer Genome Atlas (TCGA) database using bioinformatic technology. Methods The gene expression data and corresponding clinical information of colon cancer were downloaded from TCGA database. Stromal and immune scores were estimated based on the ESTIMATE algorithm. Sanger software was used to identify the differentially expressed genes (DEGs) and prognostic DEGs based on stromal and immune scores. External validation of prognostic biomarkers was conducted in Gene Expression Omnibus (GEO) database. Gene ontology (GO) analysis, pathway enrichment analysis, and gene set enrichment analysis (GSEA) were used for functional analysis. STRING and Cytoscape were used to assess the protein-protein interaction (PPI) network and screen hub genes. Quantitative real-time PCR (qRT-PCR) was used to validate the expression of hub genes in clinical tissues. Synaptosomal-associated protein 25 (SNAP25) was selected for analyzing its correlations with tumor-immune system in the TISIDB database. Results Worse overall survivals of colon cancer patients were found in high stromal score group (2963 vs. 1930 days, log-rank test P = 0.038) and high immune score group (2894 vs. 2230 days, log-rank test P = 0.076). 563 up-regulated and 9 down-regulated genes were identified as stromal-immune score-related DEGs. 70 up-regulated DEGs associated with poor outcomes were identified by COX proportional hazard regression model, and 15 hub genes were selected later. Then, we verified aquaporin 4 (AQP4) and SNAP25 as prognostic biomarkers in GEO database. qRT-PCR results revealed that AQP4 and SNAP25 were significantly elevated in colon cancer tissues compared with adjacent normal tissues (P = 0.003, 0.0…
format: application/pdf
format: text/html
creator: Jinyan Zou
creator: Darong Duan
creator: Changfa Yu
creator: Jie Pan
creator: Jinwei Xia
creator: Zaixing Yang
creator: Shasha Cai
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.10142
publisher: PeerJ Inc.
rights: © 2020 Zou et al.
abstract: Background Colon cancer is one of the deadliest tumors worldwide. Stromal cells and immune cells play important roles in cancer biology and microenvironment across different types of cancer. This study aimed to identify the prognostic value of stromal/immune cell-associated genes for colon cancer in The Cancer Genome Atlas (TCGA) database using bioinformatic technology. Methods The gene expression data and corresponding clinical information of colon cancer were downloaded from TCGA database. Stromal and immune scores were estimated based on the ESTIMATE algorithm. Sanger software was used to identify the differentially expressed genes (DEGs) and prognostic DEGs based on stromal and immune scores. External validation of prognostic biomarkers was conducted in Gene Expression Omnibus (GEO) database. Gene ontology (GO) analysis, pathway enrichment analysis, and gene set enrichment analysis (GSEA) were used for functional analysis. STRING and Cytoscape were used to assess the protein-protein interaction (PPI) network and screen hub genes. Quantitative real-time PCR (qRT-PCR) was used to validate the expression of hub genes in clinical tissues. Synaptosomal-associated protein 25 (SNAP25) was selected for analyzing its correlations with tumor-immune system in the TISIDB database. Results Worse overall survivals of colon cancer patients were found in high stromal score group (2963 vs. 1930 days, log-rank test P = 0.038) and high immune score group (2894 vs. 2230 days, log-rank test P = 0.076). 563 up-regulated and 9 down-regulated genes were identified as stromal-immune score-related DEGs. 70 up-regulated DEGs associated with poor outcomes were identified by COX proportional hazard regression model, and 15 hub genes were selected later. Then, we verified aquaporin 4 (AQP4) and SNAP25 as prognostic biomarkers in GEO database. qRT-PCR results revealed that AQP4 and SNAP25 were significantly elevated in colon cancer tissues compared with adjacent normal tissues (P = 0.003, 0.0…
bibliographic citation: Zou et al. (2020) Mining the potential prognostic value of synaptosomal-associated protein 25 (SNAP25) in colon cancer based on stromal-immune score. PeerJ 8:e10142 https://doi.org/10.7717/peerj.10142
date submitted: 2020-06-25
date accepted: 2020-09-19
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zou
  given name: Jinyan
author list: Agent
  family name: Duan
  given name: Darong
author list: Agent
  family name: Yu
  given name: Changfa
author list: Agent
  family name: Pan
  given name: Jie
author list: Agent
  family name: Xia
  given name: Jinwei
author list: Agent
  family name: Yang
  given name: Zaixing
author list: Agent
  family name: Cai
  given name: Shasha
doi: 10.7717/peerj.10142
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Zou et al.
attribution name: Zou et al.

Craniofacial ontogeny in Tylosaurinae
type: item
type: AcademicArticle
description: Mosasaurs were large, globally distributed aquatic lizards that lived during the Late Cretaceous. Despite numerous specimens of varying maturity, a detailed growth series has not been proposed for any mosasaur taxon. Two taxa—Tylosaurus proriger and T. kansasensis/nepaeolicus—have robust fossil records with specimens spanning a wide range of sizes and are thus ideal for studying mosasaur ontogeny. Tylosaurus is a genus of particularly large mosasaurs with long, edentulous anterior extensions of the premaxilla and dentary that lived in Europe and North America during the Late Cretaceous. An analysis of growth in Tylosaurus provides an opportunity to test hypotheses of the synonymy of T. kansasensis with T. nepaeolicus, sexual dimorphism, anagenesis, and heterochrony. Fifty-nine hypothetical growth characters were identified, including size-dependent, size-independent, and phylogenetic characters, and quantitative cladistic analysis was used to recover growth series for the two taxa. The results supported the synonymy of T. kansasensis with T. nepaeolicus and that T. kansasensis represent juveniles of T. nepaeolicus. A Spearman rank-order correlation test resulted in a significant correlation between two measures of size (total skull length and quadrate height) and maturity. Eleven growth changes were shared across both species, neither of the ontogram topologies showed evidence of skeletal sexual dimorphism, and a previous hypothesis of paedomorphy in T. proriger was not rejected. Finally, a novel hypothesis of anagenesis in Western Interior Seaway Tylosaurus species, driven by peramorphy, is proposed here.
format: application/pdf
format: text/html
creator: Amelia R. Zietlow
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10145
publisher: PeerJ Inc.
rights: © 2020 Zietlow
abstract: Mosasaurs were large, globally distributed aquatic lizards that lived during the Late Cretaceous. Despite numerous specimens of varying maturity, a detailed growth series has not been proposed for any mosasaur taxon. Two taxa—Tylosaurus proriger and T. kansasensis/nepaeolicus—have robust fossil records with specimens spanning a wide range of sizes and are thus ideal for studying mosasaur ontogeny. Tylosaurus is a genus of particularly large mosasaurs with long, edentulous anterior extensions of the premaxilla and dentary that lived in Europe and North America during the Late Cretaceous. An analysis of growth in Tylosaurus provides an opportunity to test hypotheses of the synonymy of T. kansasensis with T. nepaeolicus, sexual dimorphism, anagenesis, and heterochrony. Fifty-nine hypothetical growth characters were identified, including size-dependent, size-independent, and phylogenetic characters, and quantitative cladistic analysis was used to recover growth series for the two taxa. The results supported the synonymy of T. kansasensis with T. nepaeolicus and that T. kansasensis represent juveniles of T. nepaeolicus. A Spearman rank-order correlation test resulted in a significant correlation between two measures of size (total skull length and quadrate height) and maturity. Eleven growth changes were shared across both species, neither of the ontogram topologies showed evidence of skeletal sexual dimorphism, and a previous hypothesis of paedomorphy in T. proriger was not rejected. Finally, a novel hypothesis of anagenesis in Western Interior Seaway Tylosaurus species, driven by peramorphy, is proposed here.
bibliographic citation: Zietlow (2020) Craniofacial ontogeny in Tylosaurinae. PeerJ 8:e10145 https://doi.org/10.7717/peerj.10145
date submitted: 2020-06-09
date accepted: 2020-09-21
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zietlow
  given name: Amelia R.
doi: 10.7717/peerj.10145
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: © 2020 Zietlow
attribution name: Zietlow

miR-29a-3p directly targets Smad nuclear interacting protein 1 and inhibits the migration and proliferation of cervical cancer HeLa cells
type: item
type: AcademicArticle
description: Smad nuclear interacting protein 1 (SNIP1) is a nuclear protein and involved in essential biological processes. MicroRNAs are effective regulators of tumorigenesis and cancer progression via targeting multiple genes. In present study, we aimed to investigate the function of SNIP1 and identify novel miRNA-SNIP1 axis in the development of cervical cancer. The results showed for the first time that silencing of the SNIP1 gene inhibited the migration and proliferation in HeLa cells significantly. Bioinformatics analysis and dual luciferase reporter assay demonstrated that miR-29a-3p could target 3′ UTR of SNIP1 directly. The mRNA and protein expression levels of SNIP1 were negative regulated by miR-29a-3p according to the RT-qPCR and Western blot analysis, respectively. Furthermore, functional studies showed that over-expression of miR-29a-3p restrained HeLa cells migration and proliferation, and the mRNA expression of SNIP1 downstream genes (HSP27, c-Myc, and cyclin D1) were down-regulated by miR-29a-3p. Together, we concluded that miR-29a-3p suppressed the migration and proliferation in HeLa cells by directly targeting SNIP1. The newly identified miR-29a-3p/SNIP1 axis could provide new insight into the development of cervical cancer.
format: application/pdf
format: text/html
creator: Ying Chen
creator: Weiji Zhang
creator: Lijun Yan
creator: Peng Zheng
creator: Jin Li
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.10148
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Smad nuclear interacting protein 1 (SNIP1) is a nuclear protein and involved in essential biological processes. MicroRNAs are effective regulators of tumorigenesis and cancer progression via targeting multiple genes. In present study, we aimed to investigate the function of SNIP1 and identify novel miRNA-SNIP1 axis in the development of cervical cancer. The results showed for the first time that silencing of the SNIP1 gene inhibited the migration and proliferation in HeLa cells significantly. Bioinformatics analysis and dual luciferase reporter assay demonstrated that miR-29a-3p could target 3′ UTR of SNIP1 directly. The mRNA and protein expression levels of SNIP1 were negative regulated by miR-29a-3p according to the RT-qPCR and Western blot analysis, respectively. Furthermore, functional studies showed that over-expression of miR-29a-3p restrained HeLa cells migration and proliferation, and the mRNA expression of SNIP1 downstream genes (HSP27, c-Myc, and cyclin D1) were down-regulated by miR-29a-3p. Together, we concluded that miR-29a-3p suppressed the migration and proliferation in HeLa cells by directly targeting SNIP1. The newly identified miR-29a-3p/SNIP1 axis could provide new insight into the development of cervical cancer.
bibliographic citation: Chen et al. (2020) miR-29a-3p directly targets Smad nuclear interacting protein 1 and inhibits the migration and proliferation of cervical cancer HeLa cells. PeerJ 8:e10148 https://doi.org/10.7717/peerj.10148
date submitted: 2020-07-06
date accepted: 2020-09-21
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Ying
author list: Agent
  family name: Zhang
  given name: Weiji
author list: Agent
  family name: Yan
  given name: Lijun
author list: Agent
  family name: Zheng
  given name: Peng
author list: Agent
  family name: Li
  given name: Jin
doi: 10.7717/peerj.10148
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Chen et al.
attribution name: Chen et al.

Spatiotemporal accumulation of fatal pharyngeal entrapment of flatfish in harbour porpoises (Phocoena phocoena) in the German North Sea
type: item
type: AcademicArticle
description: The evolution of a permanent separation of the upper respiratory and digestive tract is one of the adaptions cetaceans evolved for their aquatic life. Generally, it prevents odontocetes from choking on either saltwater or foreign bodies during ingestion under water. Nevertheless, several sporadic single case reports from different parts of the world show that this separation can be reversed especially by overly large items of prey. This incident can have a fatal outcome for the odontocetes. The German federal state of Schleswig-Holstein has a year-round, permanent and systematic stranding network that retrieves stranded marine mammals from its shorelines and constantly enables post-mortem examinations. In 2016, with nine affected animals, a high incidence of fatal pharyngeal entrapment of flatfish in harbour porpoises (Phocoena phocoena) occurred during spring and early summer on the German North Sea island of Sylt. All flatfish were identified as common sole (Solea solea). A retrospective post-mortem data analysis over a 30-year period from the North and Baltic Sea revealed similar yearly and seasonally case accumulations on the same island in the 1990s as well as several single case events over the whole timespan. All cases except one were caused by flatfish. When flatfish speciation was performed, only common sole was identified. From 1990 to 2019, of all examined harbour porpoises, 0.3% (2/713) from the Baltic Sea and 5.5% (45/820) from the North Sea died due to fish entrapped in the pharynx. On the North Sea coast, the occurrence of fatal obstruction shows high yearly variations from 0 to 33.3%. Years that stand out are especially 1990 to 1992, 1995, as well as 2016. The majority of all cases generally occurred between April and July, indicating also a seasonality of cases. This study evaluates the occurrence of fatal pharyngeal entrapment of fish in two geographically separated harbour porpoise populations. Additionally, common sole is clearly identified as a …
format: application/pdf
format: text/html
creator: Stephanie Gross
creator: Marco Roller
creator: Holger Haslob
creator: Miguel Grilo
creator: Jan Lakemeyer
creator: Anja Reckendorf
creator: Peter Wohlsein
creator: Ursula Siebert
subject: Animal Behavior
subject: Marine Biology
subject: Veterinary Medicine
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.10160
publisher: PeerJ Inc.
rights: © 2020 Gross et al.
abstract: The evolution of a permanent separation of the upper respiratory and digestive tract is one of the adaptions cetaceans evolved for their aquatic life. Generally, it prevents odontocetes from choking on either saltwater or foreign bodies during ingestion under water. Nevertheless, several sporadic single case reports from different parts of the world show that this separation can be reversed especially by overly large items of prey. This incident can have a fatal outcome for the odontocetes. The German federal state of Schleswig-Holstein has a year-round, permanent and systematic stranding network that retrieves stranded marine mammals from its shorelines and constantly enables post-mortem examinations. In 2016, with nine affected animals, a high incidence of fatal pharyngeal entrapment of flatfish in harbour porpoises (Phocoena phocoena) occurred during spring and early summer on the German North Sea island of Sylt. All flatfish were identified as common sole (Solea solea). A retrospective post-mortem data analysis over a 30-year period from the North and Baltic Sea revealed similar yearly and seasonally case accumulations on the same island in the 1990s as well as several single case events over the whole timespan. All cases except one were caused by flatfish. When flatfish speciation was performed, only common sole was identified. From 1990 to 2019, of all examined harbour porpoises, 0.3% (2/713) from the Baltic Sea and 5.5% (45/820) from the North Sea died due to fish entrapped in the pharynx. On the North Sea coast, the occurrence of fatal obstruction shows high yearly variations from 0 to 33.3%. Years that stand out are especially 1990 to 1992, 1995, as well as 2016. The majority of all cases generally occurred between April and July, indicating also a seasonality of cases. This study evaluates the occurrence of fatal pharyngeal entrapment of fish in two geographically separated harbour porpoise populations. Additionally, common sole is clearly identified as a …
bibliographic citation: Gross et al. (2020) Spatiotemporal accumulation of fatal pharyngeal entrapment of flatfish in harbour porpoises (Phocoena phocoena) in the German North Sea. PeerJ 8:e10160 https://doi.org/10.7717/peerj.10160
date submitted: 2020-06-25
date accepted: 2020-09-21
issued: 2020-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gross
  given name: Stephanie
author list: Agent
  family name: Roller
  given name: Marco
author list: Agent
  family name: Haslob
  given name: Holger
author list: Agent
  family name: Grilo
  given name: Miguel
author list: Agent
  family name: Lakemeyer
  given name: Jan
author list: Agent
  family name: Reckendorf
  given name: Anja
author list: Agent
  family name: Wohlsein
  given name: Peter
author list: Agent
  family name: Siebert
  given name: Ursula
doi: 10.7717/peerj.10160
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-20
copyright: ©2020 Gross et al.
attribution name: Gross et al.

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