PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification of areas of very high biodiversity value to achieve the EU Biodiversity Strategy for 2030 key commitments
items: MULTI-DEEP: A novel CAD system for coronavirus (COVID-19) diagnosis from CT images using multiple convolution neural networks
items: The nine ADAMs family members serve as potential biomarkers for immune infiltration in pancreatic adenocarcinoma
items: Morphological and anatomical adaptations to dry, shady environments in Adiantum reniforme var. sinense (Pteridaceae)
items: Explicating anti-amyloidogenic role of curcumin and piperine via amyloid beta (Aβ) explicit pathway: recovery and reversal paradigm effects
items: Identification of fertility-related genes for maize CMS-S via Bulked Segregant RNA-Seq
items: Genetic identification and hybridization in the seagrass genus Halophila (Hydrocharitaceae) in Sri Lankan waters
items: Clinicopathological findings and imaging features of intraductal papillary neoplasms in bile ducts
items: Hyaluronic acid ameliorates the proliferative ability of human amniotic epithelial cells through activation of TGF-β/BMP signaling
items: Global RNA editome landscape discovers reduced RNA editing in glioma: loss of editing of gamma-amino butyric acid receptor alpha subunit 3 (GABRA3) favors glioma migration and invasion

Identification of areas of very high biodiversity value to achieve the EU Biodiversity Strategy for 2030 key commitments
type: item
type: AcademicArticle
description: Background The European Union strives to increase protected areas of the EU terrestrial surface to 30% by year 2030, of which one third should be strictly protected. Designation of the Natura 2000 network, the backbone of nature protection in the EU, was mostly an expert-opinion process with little systematic conservation planning. The designation of the Natura 2000 network in Romania followed the same non-systematic approach, resulting in a suboptimal representation of invertebrates and plants. To help identify areas with very high biodiversity without repeating past planning missteps, we present a reproducible example of spatial prioritization using Romania’s current terrestrial Natura 2000 network and coarse-scale terrestrial species occurrence. Methods We used 371 terrestrial Natura 2000 Sites of Community Importance (Natura 2000 SCI), designated to protect 164 terrestrial species listed under Annex II of Habitats Directive in Romania in our spatial prioritization analyses (marine Natura 2000 sites and species were excluded). Species occurrences in terrestrial Natura 2000 sites were aggregated at a Universal Traverse Mercator spatial resolution of 1 km2. To identify priority terrestrial Natura 2000 sites for species conservation, and to explore if the Romanian Natura 2000 network sufficiently represents species included in Annex II of Habitats Directive, we used Zonation v4, a decision support software tool for spatial conservation planning. We carried out the analyses nationwide (all Natura 2000 sites) as well as separately for each biogeographic region (i.e., Alpine, Continental, Pannonian, Steppic and Black Sea). Results The results of spatial prioritization of terrestrial Natura 2000 vary greatly by planning scenario. The performance of national-level planning of top priorities is minimal. On average, when 33% of the landscape of Natura 2000 sites is protected, only 20% of the distribution of species listed in Annex II of Habitats Directive are protected. As…
format: application/pdf
format: text/html
creator: Iulia V. Miu
creator: Laurentiu Rozylowicz
creator: Viorel D. Popescu
creator: Paulina Anastasiu
subject: Conservation Biology
subject: Ecology
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10067
publisher: PeerJ Inc.
rights: © 2020 Miu et al.
abstract: Background The European Union strives to increase protected areas of the EU terrestrial surface to 30% by year 2030, of which one third should be strictly protected. Designation of the Natura 2000 network, the backbone of nature protection in the EU, was mostly an expert-opinion process with little systematic conservation planning. The designation of the Natura 2000 network in Romania followed the same non-systematic approach, resulting in a suboptimal representation of invertebrates and plants. To help identify areas with very high biodiversity without repeating past planning missteps, we present a reproducible example of spatial prioritization using Romania’s current terrestrial Natura 2000 network and coarse-scale terrestrial species occurrence. Methods We used 371 terrestrial Natura 2000 Sites of Community Importance (Natura 2000 SCI), designated to protect 164 terrestrial species listed under Annex II of Habitats Directive in Romania in our spatial prioritization analyses (marine Natura 2000 sites and species were excluded). Species occurrences in terrestrial Natura 2000 sites were aggregated at a Universal Traverse Mercator spatial resolution of 1 km2. To identify priority terrestrial Natura 2000 sites for species conservation, and to explore if the Romanian Natura 2000 network sufficiently represents species included in Annex II of Habitats Directive, we used Zonation v4, a decision support software tool for spatial conservation planning. We carried out the analyses nationwide (all Natura 2000 sites) as well as separately for each biogeographic region (i.e., Alpine, Continental, Pannonian, Steppic and Black Sea). Results The results of spatial prioritization of terrestrial Natura 2000 vary greatly by planning scenario. The performance of national-level planning of top priorities is minimal. On average, when 33% of the landscape of Natura 2000 sites is protected, only 20% of the distribution of species listed in Annex II of Habitats Directive are protected. As…
bibliographic citation: Miu et al. (2020) Identification of areas of very high biodiversity value to achieve the EU Biodiversity Strategy for 2030 key commitments. PeerJ 8:e10067 https://doi.org/10.7717/peerj.10067
date submitted: 2020-07-14
date accepted: 2020-09-08
issued: 2020-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miu
  given name: Iulia V.
author list: Agent
  family name: Rozylowicz
  given name: Laurentiu
author list: Agent
  family name: Popescu
  given name: Viorel D.
author list: Agent
  family name: Anastasiu
  given name: Paulina
doi: 10.7717/peerj.10067
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-30
copyright: ©2020 Miu et al.
attribution name: Miu et al.

MULTI-DEEP: A novel CAD system for coronavirus (COVID-19) diagnosis from CT images using multiple convolution neural networks
type: item
type: AcademicArticle
description: Coronavirus (COVID-19) was first observed in Wuhan, China, and quickly propagated worldwide. It is considered the supreme crisis of the present era and one of the most crucial hazards threatening worldwide health. Therefore, the early detection of COVID-19 is essential. The common way to detect COVID-19 is the reverse transcription-polymerase chain reaction (RT-PCR) test, although it has several drawbacks. Computed tomography (CT) scans can enable the early detection of suspected patients, however, the overlap between patterns of COVID-19 and other types of pneumonia makes it difficult for radiologists to diagnose COVID-19 accurately. On the other hand, deep learning (DL) techniques and especially the convolutional neural network (CNN) can classify COVID-19 and non-COVID-19 cases. In addition, DL techniques that use CT images can deliver an accurate diagnosis faster than the RT-PCR test, which consequently saves time for disease control and provides an efficient computer-aided diagnosis (CAD) system. The shortage of publicly available datasets of CT images, makes the CAD system’s design a challenging task. The CAD systems in the literature are based on either individual CNN or two-fused CNNs; one used for segmentation and the other for classification and diagnosis. In this article, a novel CAD system is proposed for diagnosing COVID-19 based on the fusion of multiple CNNs. First, an end-to-end classification is performed. Afterward, the deep features are extracted from each network individually and classified using a support vector machine (SVM) classifier. Next, principal component analysis is applied to each deep feature set, extracted from each network. Such feature sets are then used to train an SVM classifier individually. Afterward, a selected number of principal components from each deep feature set are fused and compared with the fusion of the deep features extracted from each CNN. The results show that the proposed system is effective and capable of detecti…
format: application/pdf
format: text/html
creator: Omneya Attallah
creator: Dina A. Ragab
creator: Maha Sharkas
subject: Infectious Diseases
subject: Computational Science
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.10086
publisher: PeerJ Inc.
rights: © 2020 Attallah et al.
abstract: Coronavirus (COVID-19) was first observed in Wuhan, China, and quickly propagated worldwide. It is considered the supreme crisis of the present era and one of the most crucial hazards threatening worldwide health. Therefore, the early detection of COVID-19 is essential. The common way to detect COVID-19 is the reverse transcription-polymerase chain reaction (RT-PCR) test, although it has several drawbacks. Computed tomography (CT) scans can enable the early detection of suspected patients, however, the overlap between patterns of COVID-19 and other types of pneumonia makes it difficult for radiologists to diagnose COVID-19 accurately. On the other hand, deep learning (DL) techniques and especially the convolutional neural network (CNN) can classify COVID-19 and non-COVID-19 cases. In addition, DL techniques that use CT images can deliver an accurate diagnosis faster than the RT-PCR test, which consequently saves time for disease control and provides an efficient computer-aided diagnosis (CAD) system. The shortage of publicly available datasets of CT images, makes the CAD system’s design a challenging task. The CAD systems in the literature are based on either individual CNN or two-fused CNNs; one used for segmentation and the other for classification and diagnosis. In this article, a novel CAD system is proposed for diagnosing COVID-19 based on the fusion of multiple CNNs. First, an end-to-end classification is performed. Afterward, the deep features are extracted from each network individually and classified using a support vector machine (SVM) classifier. Next, principal component analysis is applied to each deep feature set, extracted from each network. Such feature sets are then used to train an SVM classifier individually. Afterward, a selected number of principal components from each deep feature set are fused and compared with the fusion of the deep features extracted from each CNN. The results show that the proposed system is effective and capable of detecti…
bibliographic citation: Attallah et al. (2020) MULTI-DEEP: A novel CAD system for coronavirus (COVID-19) diagnosis from CT images using multiple convolution neural networks. PeerJ 8:e10086 https://doi.org/10.7717/peerj.10086
date submitted: 2020-05-15
date accepted: 2020-09-11
issued: 2020-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Attallah
  given name: Omneya
author list: Agent
  family name: Ragab
  given name: Dina A.
author list: Agent
  family name: Sharkas
  given name: Maha
doi: 10.7717/peerj.10086
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-30
copyright: © 2020 Attallah et al.
attribution name: Attallah et al.

The nine ADAMs family members serve as potential biomarkers for immune infiltration in pancreatic adenocarcinoma
type: item
type: AcademicArticle
description: Background The functional significance of ADAMs family members in the immune infiltration of pancreatic adenocarcinoma (PAAD) awaits elucidation. Methods ADAMs family members with significant expression were identified among differentially expressed genes of PAAD based on The Cancer Genome Atlas (TCGA) database followed by a verification based on the Oncomine database. The correlation of ADAMs in PAAD was estimated with the Spearman’s rho value. The pathway enrichment of ADAMs was performed by STRING and GSEALite, respectively. The protein–protein interaction and Gene Ontology analyses of ADAMs and their similar genes were exanimated in STRING and visualized by Cytoscape. Subsequently, the Box-Whisker plot was used to show a correlation between ADAMs and different tumor grade 1/2/3/4 with Student’s t-test. TIMER was applied to estimate a correlation of ADAMs expressions with immune infiltrates and immune checkpoint blockade (ICB) immunotherapy-related molecules. Furthermore, the effect of copy number variation (CNV) of ADAMs genes was assessed on the immune infiltration levels. Result ADAM8/9/10/12/15/19/28/TS2/TS12 were over-expressed in PAAD. Most of the nine ADAMs had a significant correlation. ADAM8/12/15/19 expression was remarkably increased in the comparison between grade 1 and grade 2/3 of PAAD. ADAM8/9/10/12/19/28/TS2/TS12 had a positive correlation with almost five immune infiltrates. ADAM12/19/TS2/TS12 dramatically related with ICB immunotherapy-related molecules. CNV of ADAMs genes potentially influenced the immune infiltration levels. Conclusion Knowledge of the expression level of the ADAMs family could provide a reasonable strategy for improved immunotherapies to PAAD.
format: application/pdf
format: text/html
creator: Bing Qi
creator: Han Liu
creator: Ying Dong
creator: Xueying Shi
creator: Qi Zhou
creator: Fen Zeng
creator: Nabuqi Bao
creator: Qian Li
creator: Yuan Yuan
creator: Lei Yao
creator: Shilin Xia
subject: Bioinformatics
subject: Oncology
description: doi:10.7717/peerj.9736
publisher: PeerJ Inc.
rights: © 2020 Qi et al.
abstract: Background The functional significance of ADAMs family members in the immune infiltration of pancreatic adenocarcinoma (PAAD) awaits elucidation. Methods ADAMs family members with significant expression were identified among differentially expressed genes of PAAD based on The Cancer Genome Atlas (TCGA) database followed by a verification based on the Oncomine database. The correlation of ADAMs in PAAD was estimated with the Spearman’s rho value. The pathway enrichment of ADAMs was performed by STRING and GSEALite, respectively. The protein–protein interaction and Gene Ontology analyses of ADAMs and their similar genes were exanimated in STRING and visualized by Cytoscape. Subsequently, the Box-Whisker plot was used to show a correlation between ADAMs and different tumor grade 1/2/3/4 with Student’s t-test. TIMER was applied to estimate a correlation of ADAMs expressions with immune infiltrates and immune checkpoint blockade (ICB) immunotherapy-related molecules. Furthermore, the effect of copy number variation (CNV) of ADAMs genes was assessed on the immune infiltration levels. Result ADAM8/9/10/12/15/19/28/TS2/TS12 were over-expressed in PAAD. Most of the nine ADAMs had a significant correlation. ADAM8/12/15/19 expression was remarkably increased in the comparison between grade 1 and grade 2/3 of PAAD. ADAM8/9/10/12/19/28/TS2/TS12 had a positive correlation with almost five immune infiltrates. ADAM12/19/TS2/TS12 dramatically related with ICB immunotherapy-related molecules. CNV of ADAMs genes potentially influenced the immune infiltration levels. Conclusion Knowledge of the expression level of the ADAMs family could provide a reasonable strategy for improved immunotherapies to PAAD.
bibliographic citation: Qi et al. (2020) The nine ADAMs family members serve as potential biomarkers for immune infiltration in pancreatic adenocarcinoma. PeerJ 8:e9736 https://doi.org/10.7717/peerj.9736
date submitted: 2020-04-21
date accepted: 2020-07-26
issued: 2020-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Bing
author list: Agent
  family name: Liu
  given name: Han
author list: Agent
  family name: Dong
  given name: Ying
author list: Agent
  family name: Shi
  given name: Xueying
author list: Agent
  family name: Zhou
  given name: Qi
author list: Agent
  family name: Zeng
  given name: Fen
author list: Agent
  family name: Bao
  given name: Nabuqi
author list: Agent
  family name: Li
  given name: Qian
author list: Agent
  family name: Yuan
  given name: Yuan
author list: Agent
  family name: Yao
  given name: Lei
author list: Agent
  family name: Xia
  given name: Shilin
doi: 10.7717/peerj.9736
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-30
copyright: ©2020 Qi et al.
attribution name: Qi et al.

Morphological and anatomical adaptations to dry, shady environments in Adiantum reniforme var. sinense (Pteridaceae)
type: item
type: AcademicArticle
description: The natural distribution of the rare perennial fern Adiantum reniforme var. sinense (Pteridaceae), which is endemic to shady cliff environments, is limited to small areas of Wanzhou County, Chongqing, China. In this study, we used brightfield and epifluorescence microscopy to investigate the anatomical structures and histochemical features that may allow this species to thrive in shady, dry cliff environments. The A. reniforme var. sinense sporophyte had a primary structure and a dictyostele. The plants of this species had an endodermis, sclerenchyma layers and hypodermal sterome, reflecting an adaption to dry cliff environments. Blades had a thin cuticle and isolateral mesophyll, suggesting a tolerance of shady environments. These characteristics are similar to many sciophyte ferns such as Lygodium japonicum and Pteris multifida. Thus, the morphological and anatomical characteristics of A. reniforme var. sinense identified in this study are consistent with adaptations to shady, dry cliff environments.
format: application/pdf
format: text/html
creator: Di Wu
creator: Linbao Li
creator: Xiaobo Ma
creator: Guiyun Huang
creator: Chaodong Yang
subject: Conservation Biology
subject: Plant Science
description: doi:10.7717/peerj.9937
publisher: PeerJ Inc.
rights: © 2020 Wu et al.
abstract: The natural distribution of the rare perennial fern Adiantum reniforme var. sinense (Pteridaceae), which is endemic to shady cliff environments, is limited to small areas of Wanzhou County, Chongqing, China. In this study, we used brightfield and epifluorescence microscopy to investigate the anatomical structures and histochemical features that may allow this species to thrive in shady, dry cliff environments. The A. reniforme var. sinense sporophyte had a primary structure and a dictyostele. The plants of this species had an endodermis, sclerenchyma layers and hypodermal sterome, reflecting an adaption to dry cliff environments. Blades had a thin cuticle and isolateral mesophyll, suggesting a tolerance of shady environments. These characteristics are similar to many sciophyte ferns such as Lygodium japonicum and Pteris multifida. Thus, the morphological and anatomical characteristics of A. reniforme var. sinense identified in this study are consistent with adaptations to shady, dry cliff environments.
bibliographic citation: Wu et al. (2020) Morphological and anatomical adaptations to dry, shady environments in Adiantum reniforme var. sinense (Pteridaceae). PeerJ 8:e9937 https://doi.org/10.7717/peerj.9937
date submitted: 2020-04-14
date accepted: 2020-08-24
issued: 2020-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Di
author list: Agent
  family name: Li
  given name: Linbao
author list: Agent
  family name: Ma
  given name: Xiaobo
author list: Agent
  family name: Huang
  given name: Guiyun
author list: Agent
  family name: Yang
  given name: Chaodong
doi: 10.7717/peerj.9937
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-30
copyright: © 2020 Wu et al.
attribution name: Wu et al.

Explicating anti-amyloidogenic role of curcumin and piperine via amyloid beta (Aβ) explicit pathway: recovery and reversal paradigm effects
type: item
type: AcademicArticle
description: Previously, we reported the synergistic effects of curcumin and piperine in cell cultures as potential anti-cholinesterase and anti-amyloidogenic agents. Due to limited findings on the enrolment of these compounds on epigenetic events in AD, we aimed at elucidating the expression profiles of Aβ42-induced SH-SY5Y cells using microarray profiling. In this study, an optimized concentration of 35 µM of curcumin and piperine in combination was used to treat Aβ42 fibril and high-throughput microarray profiling was performed on the extracted RNA. This was then compared to curcumin and piperine used singularly at 49.11 µM and 25 µM, respectively. Our results demonstrated that in the curcumin treated group, from the top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ −2), there were five upregulated and three downregulated genes involved in the amyloidogenic pathway. While from top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ − 2) in the piperine treated group, there were four upregulated and three downregulated genes involved in the same pathway, whereas there were five upregulated and two downregulated genes involved (p < 0.05; fold change ≥ 2 or ≤ − 2) in the curcumin-piperine combined group. Four genes namely GABARAPL1, CTSB, RAB5 and AK5 were expressed significantly in all groups. Other genes such as ITPR1, GSK3B, PPP3CC, ERN1, APH1A, CYCS and CALM2 were novel putative genes that are involved in the pathogenesis of AD. We revealed that curcumin and piperine have displayed their actions against Aβ via the modulation of various mechanistic pathways. Alterations in expression profiles of genes in the neuronal cell model may explain Aβ pathology post-treatment and provide new insights for remedial approaches of a combined treatment using curcumin and piperine.
format: application/pdf
format: text/html
creator: Aimi Syamima Abdul Manap
creator: Priya Madhavan
creator: Shantini Vijayabalan
creator: Adeline Chia
creator: Koji Fukui
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
description: doi:10.7717/peerj.10003
publisher: PeerJ Inc.
rights: © 2020 Abdul Manap et al.
abstract: Previously, we reported the synergistic effects of curcumin and piperine in cell cultures as potential anti-cholinesterase and anti-amyloidogenic agents. Due to limited findings on the enrolment of these compounds on epigenetic events in AD, we aimed at elucidating the expression profiles of Aβ42-induced SH-SY5Y cells using microarray profiling. In this study, an optimized concentration of 35 µM of curcumin and piperine in combination was used to treat Aβ42 fibril and high-throughput microarray profiling was performed on the extracted RNA. This was then compared to curcumin and piperine used singularly at 49.11 µM and 25 µM, respectively. Our results demonstrated that in the curcumin treated group, from the top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ −2), there were five upregulated and three downregulated genes involved in the amyloidogenic pathway. While from top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ − 2) in the piperine treated group, there were four upregulated and three downregulated genes involved in the same pathway, whereas there were five upregulated and two downregulated genes involved (p < 0.05; fold change ≥ 2 or ≤ − 2) in the curcumin-piperine combined group. Four genes namely GABARAPL1, CTSB, RAB5 and AK5 were expressed significantly in all groups. Other genes such as ITPR1, GSK3B, PPP3CC, ERN1, APH1A, CYCS and CALM2 were novel putative genes that are involved in the pathogenesis of AD. We revealed that curcumin and piperine have displayed their actions against Aβ via the modulation of various mechanistic pathways. Alterations in expression profiles of genes in the neuronal cell model may explain Aβ pathology post-treatment and provide new insights for remedial approaches of a combined treatment using curcumin and piperine.
bibliographic citation: Abdul Manap et al. (2020) Explicating anti-amyloidogenic role of curcumin and piperine via amyloid beta (Aβ) explicit pathway: recovery and reversal paradigm effects. PeerJ 8:e10003 https://doi.org/10.7717/peerj.10003
date submitted: 2020-03-10
date accepted: 2020-08-30
issued: 2020-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdul Manap
  given name: Aimi Syamima
author list: Agent
  family name: Madhavan
  given name: Priya
author list: Agent
  family name: Vijayabalan
  given name: Shantini
author list: Agent
  family name: Chia
  given name: Adeline
author list: Agent
  family name: Fukui
  given name: Koji
doi: 10.7717/peerj.10003
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-30
copyright: ©2020 Abdul Manap et al.
attribution name: Abdul Manap et al.

Identification of fertility-related genes for maize CMS-S via Bulked Segregant RNA-Seq
type: item
type: AcademicArticle
description: Cytoplasmic male sterility (CMS) is extensively used in maize hybrid production, and identification of genes related to fertility restoration for CMS is important for hybrid breeding. The fertility restoration of S type CMS is governed by several loci with major and minor effects, while the mechanism of fertility restoration for CMS-S is still unknown. In this study, BSR-Seq was conducted with two backcrossing populations with the fertility restoration genes, Rf3 and Rf10, respectively. Genetic mapping via BSR-Seq verified the positions of the two loci. A total of 353 and 176 differentially expressed genes (DEGs) between the male fertility and male sterile pools were identified in the populations with Rf3 and Rf10, respectively. In total, 265 DEGs were co-expressed in the two populations, which were up-regulated in the fertile plants, and they might be related to male fertility involving in anther or pollen development. Moreover, 35 and seven DEGs were specifically up-regulated in the fertile plants of the population with Rf3 and Rf10, respectively. Function analysis of these DEGs revealed that jasmonic acid (JA) signal pathway might be involved in the Rf3 mediated fertility restoration for CMS-S, while the small ubiquitin-related modifier system could play a role in the fertility restoration of Rf10.
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creator: Xiner Qin
creator: Wenliang Zhang
creator: Xue Dong
creator: Shike Tian
creator: Panpan Zhang
creator: Yanxin Zhao
creator: Yi Wang
creator: Jianbing Yan
creator: Bing Yue
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.10015
publisher: PeerJ Inc.
rights: © 2020 Qin et al.
abstract: Cytoplasmic male sterility (CMS) is extensively used in maize hybrid production, and identification of genes related to fertility restoration for CMS is important for hybrid breeding. The fertility restoration of S type CMS is governed by several loci with major and minor effects, while the mechanism of fertility restoration for CMS-S is still unknown. In this study, BSR-Seq was conducted with two backcrossing populations with the fertility restoration genes, Rf3 and Rf10, respectively. Genetic mapping via BSR-Seq verified the positions of the two loci. A total of 353 and 176 differentially expressed genes (DEGs) between the male fertility and male sterile pools were identified in the populations with Rf3 and Rf10, respectively. In total, 265 DEGs were co-expressed in the two populations, which were up-regulated in the fertile plants, and they might be related to male fertility involving in anther or pollen development. Moreover, 35 and seven DEGs were specifically up-regulated in the fertile plants of the population with Rf3 and Rf10, respectively. Function analysis of these DEGs revealed that jasmonic acid (JA) signal pathway might be involved in the Rf3 mediated fertility restoration for CMS-S, while the small ubiquitin-related modifier system could play a role in the fertility restoration of Rf10.
bibliographic citation: Qin et al. (2020) Identification of fertility-related genes for maize CMS-S via Bulked Segregant RNA-Seq. PeerJ 8:e10015 https://doi.org/10.7717/peerj.10015
date submitted: 2020-02-20
date accepted: 2020-09-01
issued: 2020-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qin
  given name: Xiner
author list: Agent
  family name: Zhang
  given name: Wenliang
author list: Agent
  family name: Dong
  given name: Xue
author list: Agent
  family name: Tian
  given name: Shike
author list: Agent
  family name: Zhang
  given name: Panpan
author list: Agent
  family name: Zhao
  given name: Yanxin
author list: Agent
  family name: Wang
  given name: Yi
author list: Agent
  family name: Yan
  given name: Jianbing
author list: Agent
  family name: Yue
  given name: Bing
doi: 10.7717/peerj.10015
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-30
copyright: ©2020 Qin et al.
attribution name: Qin et al.

Genetic identification and hybridization in the seagrass genus Halophila (Hydrocharitaceae) in Sri Lankan waters
type: item
type: AcademicArticle
description: Seagrasses, as marine angiosperms, play important roles in coastal ecosystems. With increasing anthropogenic impacts, they are facing dramatic declines on a global scale. Halophila is well-known as a complex taxonomic challenge mainly due to high morphological plasticity. By using only a morphological approach, the genus could be over-split or similar species could be erroneously lumped, thus masking its true biodiversity. In the present study, we incorporated genetic identification with morphological examination to reveal the identity of Halophila plants in southern and northwestern Sri Lankan waters. The nuclear ribosomal internal transcribed spacer (ITS) region and chloroplast ribulose-bisphosphate carboxylase gene (rbcL) were used to identify plants collected from the Gulf of Mannar, Puttalam Lagoon, and Matara, Sri Lanka. Based on genetic identification, H. major (Zoll.) Miquel is reported for the first time from Sri Lanka, which might have been misidentified as H. ovalis in previous literature based on morphology alone. We also observed a first hybridization case of Halophila cross between H. ovalis and H. major. Two potential cryptic species were found, herein designated Halophila sp. 1 (allied to H. minor) and Halophila sp. 2 (closely related to H. decipiens). In order to clarify taxonomic ambiguity caused by morphological plasticity and the low resolution of genetic markers, further comparative phylogenomic approaches might be needed to solve species boundary issues in this genus.
format: application/pdf
format: text/html
creator: Shang Yin Vanson Liu
creator: Terney Pradeep Kumara
creator: Chi-Hsuan Hsu
subject: Biodiversity
subject: Genetics
subject: Marine Biology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.10027
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: Seagrasses, as marine angiosperms, play important roles in coastal ecosystems. With increasing anthropogenic impacts, they are facing dramatic declines on a global scale. Halophila is well-known as a complex taxonomic challenge mainly due to high morphological plasticity. By using only a morphological approach, the genus could be over-split or similar species could be erroneously lumped, thus masking its true biodiversity. In the present study, we incorporated genetic identification with morphological examination to reveal the identity of Halophila plants in southern and northwestern Sri Lankan waters. The nuclear ribosomal internal transcribed spacer (ITS) region and chloroplast ribulose-bisphosphate carboxylase gene (rbcL) were used to identify plants collected from the Gulf of Mannar, Puttalam Lagoon, and Matara, Sri Lanka. Based on genetic identification, H. major (Zoll.) Miquel is reported for the first time from Sri Lanka, which might have been misidentified as H. ovalis in previous literature based on morphology alone. We also observed a first hybridization case of Halophila cross between H. ovalis and H. major. Two potential cryptic species were found, herein designated Halophila sp. 1 (allied to H. minor) and Halophila sp. 2 (closely related to H. decipiens). In order to clarify taxonomic ambiguity caused by morphological plasticity and the low resolution of genetic markers, further comparative phylogenomic approaches might be needed to solve species boundary issues in this genus.
bibliographic citation: Liu et al. (2020) Genetic identification and hybridization in the seagrass genus Halophila (Hydrocharitaceae) in Sri Lankan waters. PeerJ 8:e10027 https://doi.org/10.7717/peerj.10027
date submitted: 2020-04-20
date accepted: 2020-09-02
issued: 2020-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Shang Yin Vanson
author list: Agent
  family name: Kumara
  given name: Terney Pradeep
author list: Agent
  family name: Hsu
  given name: Chi-Hsuan
doi: 10.7717/peerj.10027
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-30
copyright: ©2020 Liu et al.
attribution name: Liu et al.

Clinicopathological findings and imaging features of intraductal papillary neoplasms in bile ducts
type: item
type: AcademicArticle
description: Background Intraductal papillary mucinous neoplasm of the bile duct (IPMN-B) is considered an uncommon tumor, and there is limited understanding of IPMN-B. This study aimed to investigate the prognosis and influential factors of the IPMN-B from 58 cases. Methods The clinical data of 58 patients with pathologically confirmed IPMN-B admitted to our hospital from January 1, 2012 to August 2017 were collected and analyzed. The patients were followed up by outpatient or telephone until January 1, 2019. SPSS 19.0 software was applied for data analysis. Survival analysis was performed using Kaplan-Meier method and parallel Log-rank test. Prognostic factors were analyzed by univariate analysis and multiple Cox regression model. Results Among of all the patients, 26 cases were benign tumors and 32 cases were malignant tumors. The preoperative tumor markers CA242 and CEA of malignant IPNM-B patients were significantly higher than those in benign tumors (P < 0.05). Survival analysis showed that patients with malignant tumors had a worse prognosis. The median survival time of malignant IPMN-B patients was 40.6 ± 3.0 months, yet median survival time of benign IPMN-B patients was not reached (P = 0.19). The one-year survival rate and three-year survival rate of benign IPMN-B were 84% and 74% respectively. The one-year survival rate and three-year survival rate of malignant IPMN-B were 88% and 64% respectively. Univariate analysis showed that combined lymph node metastasis, surgical method, and differentiation degree could affect patients’ prognosis (P < 0.05). Multivariate analysis showed differentiation degree was an independent risk factor affecting prognosis (OR = 0.06, 95% confidence interval: 0.007∼0.486, P < 0.05). Conclusion The levels of CEA and CA242 were helpful to identify benign and malignant of IPNM-B. Moreover, radical surgical resection could prolong patients’ survival. Finally, differentiation degree was an independent risk factor affecting malignant IPNM-B progno…
format: application/pdf
format: text/html
creator: Honghui Zhang
creator: Zhendong Zhong
creator: Gaoyin Kong
creator: Junaid Khan
creator: Lianhong Zou
creator: Yu Jiang
creator: Xiehong Liu
creator: Yixun Tang
creator: Bo Jiang
creator: Chuang Peng
creator: Yinghui Song
creator: Sulai Liu
subject: Evidence Based Medicine
subject: Oncology
description: doi:10.7717/peerj.10040
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Background Intraductal papillary mucinous neoplasm of the bile duct (IPMN-B) is considered an uncommon tumor, and there is limited understanding of IPMN-B. This study aimed to investigate the prognosis and influential factors of the IPMN-B from 58 cases. Methods The clinical data of 58 patients with pathologically confirmed IPMN-B admitted to our hospital from January 1, 2012 to August 2017 were collected and analyzed. The patients were followed up by outpatient or telephone until January 1, 2019. SPSS 19.0 software was applied for data analysis. Survival analysis was performed using Kaplan-Meier method and parallel Log-rank test. Prognostic factors were analyzed by univariate analysis and multiple Cox regression model. Results Among of all the patients, 26 cases were benign tumors and 32 cases were malignant tumors. The preoperative tumor markers CA242 and CEA of malignant IPNM-B patients were significantly higher than those in benign tumors (P < 0.05). Survival analysis showed that patients with malignant tumors had a worse prognosis. The median survival time of malignant IPMN-B patients was 40.6 ± 3.0 months, yet median survival time of benign IPMN-B patients was not reached (P = 0.19). The one-year survival rate and three-year survival rate of benign IPMN-B were 84% and 74% respectively. The one-year survival rate and three-year survival rate of malignant IPMN-B were 88% and 64% respectively. Univariate analysis showed that combined lymph node metastasis, surgical method, and differentiation degree could affect patients’ prognosis (P < 0.05). Multivariate analysis showed differentiation degree was an independent risk factor affecting prognosis (OR = 0.06, 95% confidence interval: 0.007∼0.486, P < 0.05). Conclusion The levels of CEA and CA242 were helpful to identify benign and malignant of IPNM-B. Moreover, radical surgical resection could prolong patients’ survival. Finally, differentiation degree was an independent risk factor affecting malignant IPNM-B progno…
bibliographic citation: Zhang et al. (2020) Clinicopathological findings and imaging features of intraductal papillary neoplasms in bile ducts. PeerJ 8:e10040 https://doi.org/10.7717/peerj.10040
date submitted: 2020-04-06
date accepted: 2020-09-04
issued: 2020-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Honghui
author list: Agent
  family name: Zhong
  given name: Zhendong
author list: Agent
  family name: Kong
  given name: Gaoyin
author list: Agent
  family name: Khan
  given name: Junaid
author list: Agent
  family name: Zou
  given name: Lianhong
author list: Agent
  family name: Jiang
  given name: Yu
author list: Agent
  family name: Liu
  given name: Xiehong
author list: Agent
  family name: Tang
  given name: Yixun
author list: Agent
  family name: Jiang
  given name: Bo
author list: Agent
  family name: Peng
  given name: Chuang
author list: Agent
  family name: Song
  given name: Yinghui
author list: Agent
  family name: Liu
  given name: Sulai
doi: 10.7717/peerj.10040
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-30
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

Hyaluronic acid ameliorates the proliferative ability of human amniotic epithelial cells through activation of TGF-β/BMP signaling
type: item
type: AcademicArticle
description: Human amniotic epithelial cells (hAECs) are a useful and noncontroversial source of stem cells for cell therapy and regenerative medicine, but their limited proliferative ability hinders the acquisition of adequate quantities of cells for clinical use due to not expressing telomerase in hAECs. Our previous study showed that hyaluronic acid (HA), an important component of the extracellular matrix, promoted the proliferation of human amniotic mesenchymal stem cells. Herein, we hypothesize that HA might improve the proliferative capability of hAECs. In the present study, the role of HA on the proliferation of human amniotic epithelial cells (hAECs) in vitro was investigated for the first time. HA at molecular weight of 300 kDa showed an obvious pro-proliferation effect on hAECs. Furthermore, HA not only kept phenotypic characteristics and differentiation capabilities of hAECs, but significantly promoted the secretion of the anti-inflammatory factors such as IL-10 and TGF-β1, and the expression of stem cell pluripotent factors such as Oct4 and Nanog. Analysis of PCR microarray data and RT-qPCR validation showed that TGF-β/BMP signaling was activated in the presence of HA. Further study showed that SB431542, an inhibitor of the TGF-β/BMP signaling, significantly suppressed the mRNA expression of TGFBR3, BMP4, BMP7, BMPR1B, SMAD3, SMAD4, and the pro-proliferative effect of HA on hAECs. These data suggest that HA is a safe and effective enhancer for in vitro expansion of hAECs, whose regulatory mechanism involves the TGF-β/BMP signaling.
format: application/pdf
format: text/html
creator: Ya-Bing Tian
creator: Nuo-Xin Wang
creator: Yan Xu
creator: Chang-Yin Yu
creator: Ru-Ming Liu
creator: Yi Luo
creator: Jian-Hui Xiao
subject: Cell Biology
subject: Translational Medicine
description: doi:10.7717/peerj.10104
publisher: PeerJ Inc.
rights: © 2020 Tian et al.
abstract: Human amniotic epithelial cells (hAECs) are a useful and noncontroversial source of stem cells for cell therapy and regenerative medicine, but their limited proliferative ability hinders the acquisition of adequate quantities of cells for clinical use due to not expressing telomerase in hAECs. Our previous study showed that hyaluronic acid (HA), an important component of the extracellular matrix, promoted the proliferation of human amniotic mesenchymal stem cells. Herein, we hypothesize that HA might improve the proliferative capability of hAECs. In the present study, the role of HA on the proliferation of human amniotic epithelial cells (hAECs) in vitro was investigated for the first time. HA at molecular weight of 300 kDa showed an obvious pro-proliferation effect on hAECs. Furthermore, HA not only kept phenotypic characteristics and differentiation capabilities of hAECs, but significantly promoted the secretion of the anti-inflammatory factors such as IL-10 and TGF-β1, and the expression of stem cell pluripotent factors such as Oct4 and Nanog. Analysis of PCR microarray data and RT-qPCR validation showed that TGF-β/BMP signaling was activated in the presence of HA. Further study showed that SB431542, an inhibitor of the TGF-β/BMP signaling, significantly suppressed the mRNA expression of TGFBR3, BMP4, BMP7, BMPR1B, SMAD3, SMAD4, and the pro-proliferative effect of HA on hAECs. These data suggest that HA is a safe and effective enhancer for in vitro expansion of hAECs, whose regulatory mechanism involves the TGF-β/BMP signaling.
bibliographic citation: Tian et al. (2020) Hyaluronic acid ameliorates the proliferative ability of human amniotic epithelial cells through activation of TGF-β/BMP signaling. PeerJ 8:e10104 https://doi.org/10.7717/peerj.10104
date submitted: 2020-02-05
date accepted: 2020-09-15
issued: 2020-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tian
  given name: Ya-Bing
author list: Agent
  family name: Wang
  given name: Nuo-Xin
author list: Agent
  family name: Xu
  given name: Yan
author list: Agent
  family name: Yu
  given name: Chang-Yin
author list: Agent
  family name: Liu
  given name: Ru-Ming
author list: Agent
  family name: Luo
  given name: Yi
author list: Agent
  family name: Xiao
  given name: Jian-Hui
doi: 10.7717/peerj.10104
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-30
copyright: ©2020 Tian et al.
attribution name: Tian et al.

Global RNA editome landscape discovers reduced RNA editing in glioma: loss of editing of gamma-amino butyric acid receptor alpha subunit 3 (GABRA3) favors glioma migration and invasion
type: item
type: AcademicArticle
description: Background Gliomas are the most common and lethal type of intracranial tumors. With the current treatment regime, the median survival of patients with grade IV glioma (glioblastoma/GBM) remains at 14–16 months. RNA editing modifies the function and regulation of transcripts. The development of glial tumors may be caused by altered RNA editing events. Methods In this study, we uncover the global RNA editome landscape of glioma patients from RNA-seq data of control, lower grade glioma (LGG) and GBM samples (n = 1,083). Results A-to-I editing events were found to comprise 80% of the total editing events of which 96% were located in the Alu regions. The total RNA editing events were found to be reduced in glioma compared to control samples. More specifically, we found Gamma-aminobutyric acid type A receptor alpha3 (GABRA3) to be edited (c.1026 A-to-G; pI343M) in 73% (editing ratio 0.8) of control samples compared to LGG (28.96%; 0.47) and GBM (5.2%; 0.53) samples. GABRA3 transcript level was found to be downregulated in glioma compared to control in a grade-specific manner with GBMs having the lowest level of the transcript. Further, GABRA3 transcripts were observed to be higher in edited compared to unedited glioma samples. The transcript and protein levels of exogenously expressed gene were found to be higher for edited compared to unedited GABRA3 in glioma cells. Further, exogenously expressed edited GABRA3 inhibited migration and invasion of glioma cells efficiently but not the unedited GABRA3. Conclusion Collectively, our study discovered a reduction in RNA editing during glioma development. We further demonstrate that elevated RNA editing maintains a high level of GABRA3 RNA and protein in normal glial cells which provides a less migratory environment for the normal functioning of the brain. In contrast, the reduction in GABRA3 protein levels, due to lower stability of unedited RNA, results in the loss of function which confers an aggressive phenotype to GBM tumor…
format: application/pdf
format: text/html
creator: Vikas Patil
creator: Jagriti Pal
creator: Kulandaivelu Mahalingam
creator: Kumaravel Somasundaram
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Neurology
subject: Oncology
description: doi:10.7717/peerj.9755
publisher: PeerJ Inc.
rights: © 2020 Patil et al.
abstract: Background Gliomas are the most common and lethal type of intracranial tumors. With the current treatment regime, the median survival of patients with grade IV glioma (glioblastoma/GBM) remains at 14–16 months. RNA editing modifies the function and regulation of transcripts. The development of glial tumors may be caused by altered RNA editing events. Methods In this study, we uncover the global RNA editome landscape of glioma patients from RNA-seq data of control, lower grade glioma (LGG) and GBM samples (n = 1,083). Results A-to-I editing events were found to comprise 80% of the total editing events of which 96% were located in the Alu regions. The total RNA editing events were found to be reduced in glioma compared to control samples. More specifically, we found Gamma-aminobutyric acid type A receptor alpha3 (GABRA3) to be edited (c.1026 A-to-G; pI343M) in 73% (editing ratio 0.8) of control samples compared to LGG (28.96%; 0.47) and GBM (5.2%; 0.53) samples. GABRA3 transcript level was found to be downregulated in glioma compared to control in a grade-specific manner with GBMs having the lowest level of the transcript. Further, GABRA3 transcripts were observed to be higher in edited compared to unedited glioma samples. The transcript and protein levels of exogenously expressed gene were found to be higher for edited compared to unedited GABRA3 in glioma cells. Further, exogenously expressed edited GABRA3 inhibited migration and invasion of glioma cells efficiently but not the unedited GABRA3. Conclusion Collectively, our study discovered a reduction in RNA editing during glioma development. We further demonstrate that elevated RNA editing maintains a high level of GABRA3 RNA and protein in normal glial cells which provides a less migratory environment for the normal functioning of the brain. In contrast, the reduction in GABRA3 protein levels, due to lower stability of unedited RNA, results in the loss of function which confers an aggressive phenotype to GBM tumor…
bibliographic citation: Patil et al. (2020) Global RNA editome landscape discovers reduced RNA editing in glioma: loss of editing of gamma-amino butyric acid receptor alpha subunit 3 (GABRA3) favors glioma migration and invasion. PeerJ 8:e9755 https://doi.org/10.7717/peerj.9755
date submitted: 2019-01-15
date accepted: 2020-07-28
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Patil
  given name: Vikas
author list: Agent
  family name: Pal
  given name: Jagriti
author list: Agent
  family name: Mahalingam
  given name: Kulandaivelu
author list: Agent
  family name: Somasundaram
  given name: Kumaravel
doi: 10.7717/peerj.9755
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: © 2020 Patil et al.
attribution name: Patil et al.

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