PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: High expression of MAPK-14 promoting the death of chondrocytes is an important signal of osteoarthritis process
items: Clusters of sub-Saharan African countries based on sociobehavioural characteristics and associated HIV incidence
items: A new caimanine alligatorid from the Middle Eocene of Southwest Texas and implications for spatial and temporal shifts in Paleogene crocodyliform diversity
items: RNA sequencing analysis of FGF2-responsive transcriptome in skin fibroblasts
items: KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models—II: model description, implementation and testing
items: Effective ribosomal RNA depletion for single-cell total RNA-seq by scDASH
items: A preliminary comparative study of percutaneous CT-guided cryoablation with surgical resection for osteoid osteoma
items: Overexpressed PLAU and its potential prognostic value in head and neck squamous cell carcinoma
items: A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera)—patterns of nucleotide misincorporation
items: Identification of a novel association for the WWOX/HIF1A axis with gestational diabetes mellitus (GDM)

High expression of MAPK-14 promoting the death of chondrocytes is an important signal of osteoarthritis process
type: item
type: AcademicArticle
description: Background Osteoarthritis (OA) is one of the most common degenerative diseases worldwide. Many researchers are studying the pathogenesis of OA, however, it is still unclear. Methods Screening and validation of OA relevant hub genes are an important part of exploring their potential molecular mechanism. Therefore, this study aims to explore and verify the mechanisms of hub genes in the OA by bioinformatics, qPCR, fluorescence and propidium iodide staining. Results Microarray datasets GSE43923, GSE55457 and GSE12021 were collected in the Gene Expression Omnibus (GEO), including 45 samples, which divided into 23 osteoarthritis knee joint samples and 22 samples of normal knee joint. Thereafter, 265 differentiallyexpressedgenes (DEGs) were identified in all, which divided into 199 upregulated genes and 66 downregulated genes. The hub genes MAPK-14, PTPRC, PTPN12 were upregulated, while B9D1 was downregulated. In order to further confirm the expression of screening differential genes in human chondrocytes, the human chondrocytes were extracted from a joint replacement surgery and stained with toluidine blue for identification. Compared with normal chondrocytes, OA chondrocytes had high expression of COL I protein and low expression of COL II protein. The expression levels of MAPK-14, PTPRC and PTPN12 in OA chondrocytes were significantly higher than the expression levels of B9D1 in normal chondrocytes. Moreover, the inflammatory necrosis of OA chondrocytes was increased compared with the normal chondrocytes by propidium iodide staining. Conclusions The high expression of MAPK-14 works as a promoter of chondrocytes death and an important signal of the osteoarthritis process.
format: application/pdf
format: text/html
creator: Zhiqin Deng
creator: Xiaotian Hu
creator: Murad Alahdal
creator: Jianquan Liu
creator: Zhe Zhao
creator: Xiaoqiang Chen
creator: Junxiong Xie
creator: Li Duan
creator: Daping Wang
creator: Wencui Li
subject: Bioinformatics
subject: Cell Biology
subject: Orthopedics
subject: Rheumatology
description: doi:10.7717/peerj.10656
publisher: PeerJ Inc.
rights: © 2021 Deng et al.
abstract: Background Osteoarthritis (OA) is one of the most common degenerative diseases worldwide. Many researchers are studying the pathogenesis of OA, however, it is still unclear. Methods Screening and validation of OA relevant hub genes are an important part of exploring their potential molecular mechanism. Therefore, this study aims to explore and verify the mechanisms of hub genes in the OA by bioinformatics, qPCR, fluorescence and propidium iodide staining. Results Microarray datasets GSE43923, GSE55457 and GSE12021 were collected in the Gene Expression Omnibus (GEO), including 45 samples, which divided into 23 osteoarthritis knee joint samples and 22 samples of normal knee joint. Thereafter, 265 differentiallyexpressedgenes (DEGs) were identified in all, which divided into 199 upregulated genes and 66 downregulated genes. The hub genes MAPK-14, PTPRC, PTPN12 were upregulated, while B9D1 was downregulated. In order to further confirm the expression of screening differential genes in human chondrocytes, the human chondrocytes were extracted from a joint replacement surgery and stained with toluidine blue for identification. Compared with normal chondrocytes, OA chondrocytes had high expression of COL I protein and low expression of COL II protein. The expression levels of MAPK-14, PTPRC and PTPN12 in OA chondrocytes were significantly higher than the expression levels of B9D1 in normal chondrocytes. Moreover, the inflammatory necrosis of OA chondrocytes was increased compared with the normal chondrocytes by propidium iodide staining. Conclusions The high expression of MAPK-14 works as a promoter of chondrocytes death and an important signal of the osteoarthritis process.
bibliographic citation: Deng et al. (2021) High expression of MAPK-14 promoting the death of chondrocytes is an important signal of osteoarthritis process. PeerJ 9:e10656 https://doi.org/10.7717/peerj.10656
date submitted: 2020-06-19
date accepted: 2020-12-07
issued: 2021-01-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Zhiqin
author list: Agent
  family name: Hu
  given name: Xiaotian
author list: Agent
  family name: Alahdal
  given name: Murad
author list: Agent
  family name: Liu
  given name: Jianquan
author list: Agent
  family name: Zhao
  given name: Zhe
author list: Agent
  family name: Chen
  given name: Xiaoqiang
author list: Agent
  family name: Xie
  given name: Junxiong
author list: Agent
  family name: Duan
  given name: Li
author list: Agent
  family name: Wang
  given name: Daping
author list: Agent
  family name: Li
  given name: Wencui
doi: 10.7717/peerj.10656
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-15
copyright: ©2021 Deng et al.
attribution name: Deng et al.

Clusters of sub-Saharan African countries based on sociobehavioural characteristics and associated HIV incidence
type: item
type: AcademicArticle
description: Introduction HIV incidence varies widely between sub-Saharan African (SSA) countries. This variation coincides with a substantial sociobehavioural heterogeneity, which complicates the design of effective interventions. In this study, we investigated how sociobehavioural heterogeneity in sub-Saharan Africa could account for the variance of HIV incidence between countries. Methods We analysed aggregated data, at the national-level, from the most recent Demographic and Health Surveys of 29 SSA countries (2010–2017), which included 594,644 persons (183,310 men and 411,334 women). We preselected 48 demographic, socio-economic, behavioural and HIV-related attributes to describe each country. We used Principal Component Analysis to visualize sociobehavioural similarity between countries, and to identify the variables that accounted for most sociobehavioural variance in SSA. We used hierarchical clustering to identify groups of countries with similar sociobehavioural profiles, and we compared the distribution of HIV incidence (estimates from UNAIDS) and sociobehavioural variables within each cluster. Results The most important characteristics, which explained 69% of sociobehavioural variance across SSA among the variables we assessed were: religion; male circumcision; number of sexual partners; literacy; uptake of HIV testing; women’s empowerment; accepting attitude toward people living with HIV/AIDS; rurality; ART coverage; and, knowledge about AIDS. Our model revealed three groups of countries, each with characteristic sociobehavioural profiles. HIV incidence was mostly similar within each cluster and different between clusters (median (IQR); 0.5/1000 (0.6/1000), 1.8/1000 (1.3/1000) and 5.0/1000 (4.2/1000)). Conclusions Our findings suggest that the combination of sociobehavioural factors play a key role in determining the course of the HIV epidemic, and that similar techniques can help to predict the effects of behavioural change on the HIV epidemic and to design targete…
format: application/pdf
format: text/html
creator: Aziza Merzouki
creator: Janne Estill
creator: Erol Orel
creator: Kali Tal
creator: Olivia Keiser
subject: HIV
subject: Infectious Diseases
subject: Computational Science
description: doi:10.7717/peerj.10660
publisher: PeerJ Inc.
rights: © 2021 Merzouki et al.
abstract: Introduction HIV incidence varies widely between sub-Saharan African (SSA) countries. This variation coincides with a substantial sociobehavioural heterogeneity, which complicates the design of effective interventions. In this study, we investigated how sociobehavioural heterogeneity in sub-Saharan Africa could account for the variance of HIV incidence between countries. Methods We analysed aggregated data, at the national-level, from the most recent Demographic and Health Surveys of 29 SSA countries (2010–2017), which included 594,644 persons (183,310 men and 411,334 women). We preselected 48 demographic, socio-economic, behavioural and HIV-related attributes to describe each country. We used Principal Component Analysis to visualize sociobehavioural similarity between countries, and to identify the variables that accounted for most sociobehavioural variance in SSA. We used hierarchical clustering to identify groups of countries with similar sociobehavioural profiles, and we compared the distribution of HIV incidence (estimates from UNAIDS) and sociobehavioural variables within each cluster. Results The most important characteristics, which explained 69% of sociobehavioural variance across SSA among the variables we assessed were: religion; male circumcision; number of sexual partners; literacy; uptake of HIV testing; women’s empowerment; accepting attitude toward people living with HIV/AIDS; rurality; ART coverage; and, knowledge about AIDS. Our model revealed three groups of countries, each with characteristic sociobehavioural profiles. HIV incidence was mostly similar within each cluster and different between clusters (median (IQR); 0.5/1000 (0.6/1000), 1.8/1000 (1.3/1000) and 5.0/1000 (4.2/1000)). Conclusions Our findings suggest that the combination of sociobehavioural factors play a key role in determining the course of the HIV epidemic, and that similar techniques can help to predict the effects of behavioural change on the HIV epidemic and to design targete…
bibliographic citation: Merzouki et al. (2021) Clusters of sub-Saharan African countries based on sociobehavioural characteristics and associated HIV incidence. PeerJ 9:e10660 https://doi.org/10.7717/peerj.10660
date submitted: 2020-04-24
date accepted: 2020-12-07
issued: 2021-01-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Merzouki
  given name: Aziza
author list: Agent
  family name: Estill
  given name: Janne
author list: Agent
  family name: Orel
  given name: Erol
author list: Agent
  family name: Tal
  given name: Kali
author list: Agent
  family name: Keiser
  given name: Olivia
doi: 10.7717/peerj.10660
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-15
copyright: ©2021 Merzouki et al.
attribution name: Merzouki et al.

A new caimanine alligatorid from the Middle Eocene of Southwest Texas and implications for spatial and temporal shifts in Paleogene crocodyliform diversity
type: item
type: AcademicArticle
description: Dramatic early Cenozoic climatic shifts resulted in faunal reorganization on a global scale. Among vertebrates, multiple groups of mammals (e.g., adapiform and omomyiform primates, mesonychids, taeniodonts, dichobunid artiodactyls) are well known from the Western Interior of North America in the warm, greenhouse conditions of the early Eocene, but a dramatic drop in the diversity of these groups, along with the introduction of more dry-tolerant taxa, occurred near the Eocene–Oligocene boundary. Crocodyliforms underwent a striking loss of diversity at this time as well. Pre-Uintan crocodyliform assemblages in the central Western Interior are characterized by multiple taxa, whereas Chadronian assemblages are depauperate with only Alligator prenasalis previously known. Crocodyliform diversity through the intervening Uintan and Duchesnean is not well understood. The middle Eocene Devil’s Graveyard Formation (DGF) of southwest Texas provides new data from southern latitudes during that crucial period. A new specimen from the middle member of the DGF (late Uintan–Duchesnean) is the most complete cranial material of an alligatorid known from Paleogene deposits outside the Western Interior. We identify this specimen as a caimanine based on notched descending laminae of the pterygoids posterior to the choanae and long descending processes of the exoccipitals that are in contact with the basioccipital tubera. Unlike Eocaiman cavernensis, the anterior palatine process is rounded rather than quadrangular. The relationships and age of this new taxon support the hypothesis that the modern distribution of caimanines represents a contraction of a more expansive early Cenozoic distribution. We hypothesize that the range of caimanines tracked shifting warm, humid climatic conditions that contracted latitudinally toward the hothouse-icehouse transition later in the Eocene.
format: application/pdf
format: text/html
creator: Michelle R. Stocker
creator: Christopher A. Brochu
creator: E. Christopher Kirk
subject: Biodiversity
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10665
publisher: PeerJ Inc.
rights: © 2021 Stocker et al.
abstract: Dramatic early Cenozoic climatic shifts resulted in faunal reorganization on a global scale. Among vertebrates, multiple groups of mammals (e.g., adapiform and omomyiform primates, mesonychids, taeniodonts, dichobunid artiodactyls) are well known from the Western Interior of North America in the warm, greenhouse conditions of the early Eocene, but a dramatic drop in the diversity of these groups, along with the introduction of more dry-tolerant taxa, occurred near the Eocene–Oligocene boundary. Crocodyliforms underwent a striking loss of diversity at this time as well. Pre-Uintan crocodyliform assemblages in the central Western Interior are characterized by multiple taxa, whereas Chadronian assemblages are depauperate with only Alligator prenasalis previously known. Crocodyliform diversity through the intervening Uintan and Duchesnean is not well understood. The middle Eocene Devil’s Graveyard Formation (DGF) of southwest Texas provides new data from southern latitudes during that crucial period. A new specimen from the middle member of the DGF (late Uintan–Duchesnean) is the most complete cranial material of an alligatorid known from Paleogene deposits outside the Western Interior. We identify this specimen as a caimanine based on notched descending laminae of the pterygoids posterior to the choanae and long descending processes of the exoccipitals that are in contact with the basioccipital tubera. Unlike Eocaiman cavernensis, the anterior palatine process is rounded rather than quadrangular. The relationships and age of this new taxon support the hypothesis that the modern distribution of caimanines represents a contraction of a more expansive early Cenozoic distribution. We hypothesize that the range of caimanines tracked shifting warm, humid climatic conditions that contracted latitudinally toward the hothouse-icehouse transition later in the Eocene.
bibliographic citation: Stocker et al. (2021) A new caimanine alligatorid from the Middle Eocene of Southwest Texas and implications for spatial and temporal shifts in Paleogene crocodyliform diversity. PeerJ 9:e10665 https://doi.org/10.7717/peerj.10665
date submitted: 2020-07-15
date accepted: 2020-12-08
issued: 2021-01-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stocker
  given name: Michelle R.
author list: Agent
  family name: Brochu
  given name: Christopher A.
author list: Agent
  family name: Kirk
  given name: E. Christopher
doi: 10.7717/peerj.10665
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-15
copyright: © 2021 Stocker et al.
attribution name: Stocker et al.

RNA sequencing analysis of FGF2-responsive transcriptome in skin fibroblasts
type: item
type: AcademicArticle
description: Background Fibroblast growth factor 2 (FGF2) is a highly pleiotropic cytokine with antifibrotic activity in wound healing. During the process of wound healing and fibrosis, fibroblasts are the key players. Although accumulating evidence has suggested the antagonistic effects of FGF2 in the activation process of fibroblasts, the mechanisms by which FGF2 hinders the fibroblast activation remains incompletely understood. This study aimed to identify the key genes and their regulatory networks in skin fibroblasts treated with FGF2. Methods RNA-seq was performed to identify the differentially expressed mRNA (DEGs) and lncRNA between FGF2-treated fibroblasts and control. DEGs were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Furthermore, the networks between mRNAs and lncRNAs were constructed by Pearson correlation analysis and the networkanalyst website. Finally, hub genes were validated by real time-PCR. Results Between FGF2-treated fibroblasts and control fibroblasts, a total of 1475 DEGs was obtained. These DEGs were mainly enriched in functions such as the ECM organization, cell adhesion, and cell migration. They were mainly involved in ECM-receptor interaction, PI3K-Akt signaling, and the Hippo pathway. The hub DEGs included COL3A1, COL4A1, LOX, PDGFA, TGFBI, and ITGA10. Subsequent real-time PCR, as well as bioinformatics analysis, consistently demonstrated that the expression of ITGA10 was significantly upregulated while the other five DEGs (COL3A1, COL4A1, LOX, PDGFA, TGFBI) were downregulated in FGF2-treated fibroblasts. Meanwhile, 213 differentially expressed lncRNAs were identified and three key lncRNAs (HOXA-AS2, H19, and SNHG8) were highlighted in FGF2-treated fibroblasts. Conclusion The current study comprehensively analyzed the FGF2-responsive transcriptional profile and provided candidate mechanisms that may account for FGF2-mediated wound healing.
format: application/pdf
format: text/html
creator: Baojin Wu
creator: Xinjie Tang
creator: Zhaoping Zhou
creator: Honglin Ke
creator: Shao Tang
creator: Ronghu Ke
subject: Bioinformatics
subject: Molecular Biology
subject: Dermatology
subject: Medical Genetics
description: doi:10.7717/peerj.10671
publisher: PeerJ Inc.
rights: © 2021 Wu et al.
abstract: Background Fibroblast growth factor 2 (FGF2) is a highly pleiotropic cytokine with antifibrotic activity in wound healing. During the process of wound healing and fibrosis, fibroblasts are the key players. Although accumulating evidence has suggested the antagonistic effects of FGF2 in the activation process of fibroblasts, the mechanisms by which FGF2 hinders the fibroblast activation remains incompletely understood. This study aimed to identify the key genes and their regulatory networks in skin fibroblasts treated with FGF2. Methods RNA-seq was performed to identify the differentially expressed mRNA (DEGs) and lncRNA between FGF2-treated fibroblasts and control. DEGs were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Furthermore, the networks between mRNAs and lncRNAs were constructed by Pearson correlation analysis and the networkanalyst website. Finally, hub genes were validated by real time-PCR. Results Between FGF2-treated fibroblasts and control fibroblasts, a total of 1475 DEGs was obtained. These DEGs were mainly enriched in functions such as the ECM organization, cell adhesion, and cell migration. They were mainly involved in ECM-receptor interaction, PI3K-Akt signaling, and the Hippo pathway. The hub DEGs included COL3A1, COL4A1, LOX, PDGFA, TGFBI, and ITGA10. Subsequent real-time PCR, as well as bioinformatics analysis, consistently demonstrated that the expression of ITGA10 was significantly upregulated while the other five DEGs (COL3A1, COL4A1, LOX, PDGFA, TGFBI) were downregulated in FGF2-treated fibroblasts. Meanwhile, 213 differentially expressed lncRNAs were identified and three key lncRNAs (HOXA-AS2, H19, and SNHG8) were highlighted in FGF2-treated fibroblasts. Conclusion The current study comprehensively analyzed the FGF2-responsive transcriptional profile and provided candidate mechanisms that may account for FGF2-mediated wound healing.
bibliographic citation: Wu et al. (2021) RNA sequencing analysis of FGF2-responsive transcriptome in skin fibroblasts. PeerJ 9:e10671 https://doi.org/10.7717/peerj.10671
date submitted: 2020-07-03
date accepted: 2020-12-08
issued: 2021-01-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Baojin
author list: Agent
  family name: Tang
  given name: Xinjie
author list: Agent
  family name: Zhou
  given name: Zhaoping
author list: Agent
  family name: Ke
  given name: Honglin
author list: Agent
  family name: Tang
  given name: Shao
author list: Agent
  family name: Ke
  given name: Ronghu
doi: 10.7717/peerj.10671
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-15
copyright: ©2021 Wu et al.
attribution name: Wu et al.

KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models—II: model description, implementation and testing
type: item
type: AcademicArticle
description: New knowledge on soil structure highlights its importance for hydrology and soil organic matter (SOM) stabilization, which however remains neglected in many wide used models. We present here a new model, KEYLINK, in which soil structure is integrated with the existing concepts on SOM pools, and elements from food web models, that is, those from direct trophic interactions among soil organisms. KEYLINK is, therefore, an attempt to integrate soil functional diversity and food webs in predictions of soil carbon (C) and soil water balances. We present a selection of equations that can be used for most models as well as basic parameter intervals, for example, key pools, functional groups’ biomasses and growth rates. Parameter distributions can be determined with Bayesian calibration, and here an example is presented for food web growth rate parameters for a pine forest in Belgium. We show how these added equations can improve the functioning of the model in describing known phenomena. For this, five test cases are given as simulation examples: changing the input litter quality (recalcitrance and carbon to nitrogen ratio), excluding predators, increasing pH and changing initial soil porosity. These results overall show how KEYLINK is able to simulate the known effects of these parameters and can simulate the linked effects of biopore formation, hydrology and aggregation on soil functioning. Furthermore, the results show an important trophic cascade effect of predation on the complete C cycle with repercussions on the soil structure as ecosystem engineers are predated, and on SOM turnover when predation on fungivore and bacterivore populations are reduced. In summary, KEYLINK shows how soil functional diversity and trophic organization and their role in C and water cycling in soils should be considered in order to improve our predictions on C sequestration and C emissions from soils.
format: application/pdf
format: text/html
creator: Omar Flores
creator: Gaby Deckmyn
creator: Jorge Curiel Yuste
creator: Mathieu Javaux
creator: Alexei Uvarov
creator: Sietse van der Linde
creator: Bruno De Vos
creator: Harry Vereecken
creator: Juan Jiménez
creator: Olga Vinduskova
creator: Andrea Schnepf
subject: Computational Biology
subject: Ecology
subject: Ecosystem Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.10707
publisher: PeerJ Inc.
rights: © 2021 Flores et al.
abstract: New knowledge on soil structure highlights its importance for hydrology and soil organic matter (SOM) stabilization, which however remains neglected in many wide used models. We present here a new model, KEYLINK, in which soil structure is integrated with the existing concepts on SOM pools, and elements from food web models, that is, those from direct trophic interactions among soil organisms. KEYLINK is, therefore, an attempt to integrate soil functional diversity and food webs in predictions of soil carbon (C) and soil water balances. We present a selection of equations that can be used for most models as well as basic parameter intervals, for example, key pools, functional groups’ biomasses and growth rates. Parameter distributions can be determined with Bayesian calibration, and here an example is presented for food web growth rate parameters for a pine forest in Belgium. We show how these added equations can improve the functioning of the model in describing known phenomena. For this, five test cases are given as simulation examples: changing the input litter quality (recalcitrance and carbon to nitrogen ratio), excluding predators, increasing pH and changing initial soil porosity. These results overall show how KEYLINK is able to simulate the known effects of these parameters and can simulate the linked effects of biopore formation, hydrology and aggregation on soil functioning. Furthermore, the results show an important trophic cascade effect of predation on the complete C cycle with repercussions on the soil structure as ecosystem engineers are predated, and on SOM turnover when predation on fungivore and bacterivore populations are reduced. In summary, KEYLINK shows how soil functional diversity and trophic organization and their role in C and water cycling in soils should be considered in order to improve our predictions on C sequestration and C emissions from soils.
bibliographic citation: Flores et al. (2021) KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models—II: model description, implementation and testing. PeerJ 9:e10707 https://doi.org/10.7717/peerj.10707
date submitted: 2020-04-07
date accepted: 2020-12-14
issued: 2021-01-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Flores
  given name: Omar
author list: Agent
  family name: Deckmyn
  given name: Gaby
author list: Agent
  family name: Curiel Yuste
  given name: Jorge
author list: Agent
  family name: Javaux
  given name: Mathieu
author list: Agent
  family name: Uvarov
  given name: Alexei
author list: Agent
  family name: van der Linde
  given name: Sietse
author list: Agent
  family name: De Vos
  given name: Bruno
author list: Agent
  family name: Vereecken
  given name: Harry
author list: Agent
  family name: Jiménez
  given name: Juan
author list: Agent
  family name: Vinduskova
  given name: Olga
author list: Agent
  family name: Schnepf
  given name: Andrea
doi: 10.7717/peerj.10707
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-15
copyright: © 2021 Flores et al.
attribution name: Flores et al.

Effective ribosomal RNA depletion for single-cell total RNA-seq by scDASH
type: item
type: AcademicArticle
description: A decade since its invention, single-cell RNA sequencing (scRNA-seq) has become a mainstay technology for profiling transcriptional heterogeneity in individual cells. Yet, most existing scRNA-seq methods capture only polyadenylated mRNA to avoid the cost of sequencing non-messenger transcripts, such as ribosomal RNA (rRNA), that are usually not of-interest. Hence, there are not very many protocols that enable single-cell analysis of total RNA. We adapted a method called DASH (Depletion of Abundant Sequences by Hybridisation) to make it suitable for depleting rRNA sequences from single-cell total RNA-seq libraries. Our analyses show that our single-cell DASH (scDASH) method can effectively deplete rRNAs from sequencing libraries with minimal off-target non-specificity. Importantly, as a result of depleting the rRNA, the rest of the transcriptome is significantly enriched for detection.
format: application/pdf
format: text/html
creator: Danson S.C. Loi
creator: Lei Yu
creator: Angela R. Wu
subject: Bioengineering
subject: Bioinformatics
subject: Biotechnology
subject: Genomics
description: doi:10.7717/peerj.10717
publisher: PeerJ Inc.
rights: © 2021 Loi et al.
abstract: A decade since its invention, single-cell RNA sequencing (scRNA-seq) has become a mainstay technology for profiling transcriptional heterogeneity in individual cells. Yet, most existing scRNA-seq methods capture only polyadenylated mRNA to avoid the cost of sequencing non-messenger transcripts, such as ribosomal RNA (rRNA), that are usually not of-interest. Hence, there are not very many protocols that enable single-cell analysis of total RNA. We adapted a method called DASH (Depletion of Abundant Sequences by Hybridisation) to make it suitable for depleting rRNA sequences from single-cell total RNA-seq libraries. Our analyses show that our single-cell DASH (scDASH) method can effectively deplete rRNAs from sequencing libraries with minimal off-target non-specificity. Importantly, as a result of depleting the rRNA, the rest of the transcriptome is significantly enriched for detection.
bibliographic citation: Loi et al. (2021) Effective ribosomal RNA depletion for single-cell total RNA-seq by scDASH. PeerJ 9:e10717 https://doi.org/10.7717/peerj.10717
date submitted: 2020-09-01
date accepted: 2020-12-15
issued: 2021-01-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Loi
  given name: Danson S.C.
author list: Agent
  family name: Yu
  given name: Lei
author list: Agent
  family name: Wu
  given name: Angela R.
doi: 10.7717/peerj.10717
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-15
copyright: ©2021 Loi et al.
attribution name: Loi et al.

A preliminary comparative study of percutaneous CT-guided cryoablation with surgical resection for osteoid osteoma
type: item
type: AcademicArticle
description: Background The traditional treatment for osteoid osteoma is the nidus’ surgical resection, which was difficult to eradicate with more invasive and complications because of osteosclerosis surrounding the nidus. This study aimed to analyze the efficacy and safety of percutaneous CT-guided cryoablation of osteoid osteoma at different sites (especially refractory sites such as the spine). Methods Fifteen patients with osteoid osteoma who underwent cryoablation at our institution were analyzed retrospectively on their imaging data and clinical visual analog scale (VAS) pain scores before and after the procedure. Fifty-three patients underwent surgical resection during the period were also included in this study as a control group. Treatment efficacy was assessed primarily by comparing the differences in VAS scores at different time points in each group of patients by paired-sample t-test. Differences in length of hospital stay and complications between the two groups were also compared. Results The technical success rate was 100% in both the cryoablation and surgical resection group. Cryoablation had a significantly shorter hospitalization time than surgery (p = 0.001). Clinically, the post-operative VAS scores were all significantly improved compared to the pre-operative period, and the clinical cure was achieved in both groups. Surgical operations had more complications than cryoablation, although there was no significant difference. In the group of cryoablation, only one patient had mild numbness of the left lower extremity, which relieved itself; two patients had mild post-operative pain. No patients in the cryoablation group experienced recurrence during the follow-up period. In the surgery group, three of the patients experienced massive bleeding (>500 ml), and two underwent transfusion therapy. Only one patient in the surgical resection group experienced a recurrence at 29 months postoperatively and underwent a second resection. All patients had local scars on the…
format: application/pdf
format: text/html
creator: Liangliang Meng
creator: Xiao Zhang
creator: Ruijiang Xu
creator: Bin Wu
creator: Xiaobo Zhang
creator: Yingtian Wei
creator: Jing Li
creator: Husheng Shan
creator: Yueyong Xiao
subject: Oncology
subject: Orthopedics
subject: Pediatrics
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.10724
publisher: PeerJ Inc.
rights: © 2021 Meng et al.
abstract: Background The traditional treatment for osteoid osteoma is the nidus’ surgical resection, which was difficult to eradicate with more invasive and complications because of osteosclerosis surrounding the nidus. This study aimed to analyze the efficacy and safety of percutaneous CT-guided cryoablation of osteoid osteoma at different sites (especially refractory sites such as the spine). Methods Fifteen patients with osteoid osteoma who underwent cryoablation at our institution were analyzed retrospectively on their imaging data and clinical visual analog scale (VAS) pain scores before and after the procedure. Fifty-three patients underwent surgical resection during the period were also included in this study as a control group. Treatment efficacy was assessed primarily by comparing the differences in VAS scores at different time points in each group of patients by paired-sample t-test. Differences in length of hospital stay and complications between the two groups were also compared. Results The technical success rate was 100% in both the cryoablation and surgical resection group. Cryoablation had a significantly shorter hospitalization time than surgery (p = 0.001). Clinically, the post-operative VAS scores were all significantly improved compared to the pre-operative period, and the clinical cure was achieved in both groups. Surgical operations had more complications than cryoablation, although there was no significant difference. In the group of cryoablation, only one patient had mild numbness of the left lower extremity, which relieved itself; two patients had mild post-operative pain. No patients in the cryoablation group experienced recurrence during the follow-up period. In the surgery group, three of the patients experienced massive bleeding (>500 ml), and two underwent transfusion therapy. Only one patient in the surgical resection group experienced a recurrence at 29 months postoperatively and underwent a second resection. All patients had local scars on the…
bibliographic citation: Meng et al. (2021) A preliminary comparative study of percutaneous CT-guided cryoablation with surgical resection for osteoid osteoma. PeerJ 9:e10724 https://doi.org/10.7717/peerj.10724
date submitted: 2020-08-28
date accepted: 2020-12-16
issued: 2021-01-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Liangliang
author list: Agent
  family name: Zhang
  given name: Xiao
author list: Agent
  family name: Xu
  given name: Ruijiang
author list: Agent
  family name: Wu
  given name: Bin
author list: Agent
  family name: Zhang
  given name: Xiaobo
author list: Agent
  family name: Wei
  given name: Yingtian
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Shan
  given name: Husheng
author list: Agent
  family name: Xiao
  given name: Yueyong
doi: 10.7717/peerj.10724
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-15
copyright: ©2021 Meng et al.
attribution name: Meng et al.

Overexpressed PLAU and its potential prognostic value in head and neck squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Metastasis is a major event for survival and prognosis in patients with head and neck squamous cell carcinomas (HNSCC). A primary cause of metastasis is the proteolytic degradation of the extracellular matrix (ECM). The plasminogen activator urokinase (PLAU) is involved in the transformation of plasminogen to plasmin leading to hydrolyzation of ECM-related proteins. However, the role of PLAU expression in HNSCC is unclear and the worth being investigated. Methods PLAU expression profiles and clinical parameters from multiple HNSCC datasets were used to investigate the relationship of PLAU expression and HNSCC survival. GO and PPI network were established on PLAU-related downstream molecular. The stroma score was deconvoluted for analysis of PLAU’s association with the immune environment. ROC analysis was applied to show the performance of PLAU in predicting HNSCC prognosis. Results PLAU mRNA was significantly elevated, as opposed to its methylation, in HNSCC tumor samples over normal specimens (all p < 0.01). Univariate and multivariate cox analysis showed PLAU could be an independent indicator for HNSCC prognosis. Combining with neck lymph node status, the AUC of PLAU in predicting 5-years overall survival reached to 0.862. GO enrichment analysis showed the major biological process (extracellular matrix organization and the P13K-Akt signaling pathway) may involve to the possible mechanism of PLAU’s function on HNSCC prognosis. Furthermore, PLAU expression was positively correlated with stroma cell score, M1 type macrophages, and negatively associated with CD4 + T cell, Tregs cell, and follicular helper T cell. Conclusions PLAU might be an independent biomarker for predicting outcomes of HNSCC patients. The elevated expression of PLAU was associated with HPV positivity and neck node status. The PI3K-Akt pathway and aberrant proportions of immune cells might underly the mechanism of PLAU’s oncogene role in HNSCC.
format: application/pdf
format: text/html
creator: Zhexuan Li
creator: Changhan Chen
creator: Juncheng Wang
creator: Ming Wei
creator: Guancheng Liu
creator: Yuexiang Qin
creator: Li She
creator: Yong Liu
creator: Donghai Huang
creator: Yongquan Tian
creator: Gangcai Zhu
creator: Xin Zhang
subject: Bioinformatics
subject: Oncology
subject: Otorhinolaryngology
description: doi:10.7717/peerj.10746
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Background Metastasis is a major event for survival and prognosis in patients with head and neck squamous cell carcinomas (HNSCC). A primary cause of metastasis is the proteolytic degradation of the extracellular matrix (ECM). The plasminogen activator urokinase (PLAU) is involved in the transformation of plasminogen to plasmin leading to hydrolyzation of ECM-related proteins. However, the role of PLAU expression in HNSCC is unclear and the worth being investigated. Methods PLAU expression profiles and clinical parameters from multiple HNSCC datasets were used to investigate the relationship of PLAU expression and HNSCC survival. GO and PPI network were established on PLAU-related downstream molecular. The stroma score was deconvoluted for analysis of PLAU’s association with the immune environment. ROC analysis was applied to show the performance of PLAU in predicting HNSCC prognosis. Results PLAU mRNA was significantly elevated, as opposed to its methylation, in HNSCC tumor samples over normal specimens (all p < 0.01). Univariate and multivariate cox analysis showed PLAU could be an independent indicator for HNSCC prognosis. Combining with neck lymph node status, the AUC of PLAU in predicting 5-years overall survival reached to 0.862. GO enrichment analysis showed the major biological process (extracellular matrix organization and the P13K-Akt signaling pathway) may involve to the possible mechanism of PLAU’s function on HNSCC prognosis. Furthermore, PLAU expression was positively correlated with stroma cell score, M1 type macrophages, and negatively associated with CD4 + T cell, Tregs cell, and follicular helper T cell. Conclusions PLAU might be an independent biomarker for predicting outcomes of HNSCC patients. The elevated expression of PLAU was associated with HPV positivity and neck node status. The PI3K-Akt pathway and aberrant proportions of immune cells might underly the mechanism of PLAU’s oncogene role in HNSCC.
bibliographic citation: Li et al. (2021) Overexpressed PLAU and its potential prognostic value in head and neck squamous cell carcinoma. PeerJ 9:e10746 https://doi.org/10.7717/peerj.10746
date submitted: 2020-07-27
date accepted: 2020-12-18
issued: 2021-01-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhexuan
author list: Agent
  family name: Chen
  given name: Changhan
author list: Agent
  family name: Wang
  given name: Juncheng
author list: Agent
  family name: Wei
  given name: Ming
author list: Agent
  family name: Liu
  given name: Guancheng
author list: Agent
  family name: Qin
  given name: Yuexiang
author list: Agent
  family name: She
  given name: Li
author list: Agent
  family name: Liu
  given name: Yong
author list: Agent
  family name: Huang
  given name: Donghai
author list: Agent
  family name: Tian
  given name: Yongquan
author list: Agent
  family name: Zhu
  given name: Gangcai
author list: Agent
  family name: Zhang
  given name: Xin
doi: 10.7717/peerj.10746
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-15
copyright: ©2021 Li et al.
attribution name: Li et al.

A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera)—patterns of nucleotide misincorporation
type: item
type: AcademicArticle
description: Natural history collections are a valuable resource for molecular taxonomic studies and for examining patterns of evolutionary diversification, particularly in the case of rare or extinct species. However, the recovery of sequence information is often complicated by DNA degradation. This article describes use of the Sequel platform (Pacific Biosciences) to recover the 658 bp barcode region of the mitochondrial cytochrome c oxidase I (COI) gene from 380 butterflies with an average age of 50 years. Nested multiplex PCR was employed for library preparation to facilitate sequence recovery from extracts with low concentrations of highly degraded DNA. By employing circular consensus sequencing (CCS) of short amplicons (circa 150 bp), full-length barcodes could be assembled without a reference sequence, an important advance from earlier protocols which required reference sequences to guide contig assembly. The Sequel protocol recovered COI sequences (499 bp on average) from 318 of 380 specimens (84%), much higher than for Sanger sequencing (26%). Because each read derives from a single molecule, it was also possible to quantify the incidence of substitutions arising from DNA damage. In agreement with past work on sequence changes induced by DNA degradation, the transition C/G → T/A was the most prevalent category of change, but its rate of occurrence (4.58E−4) was so low that it did not impede the recovery of reliable sequences. Because the current protocol recovers COI sequence from most museum specimens, and because sequence fidelity is unaffected by nucleotide misincorporations, large-scale sequence characterization of museum specimens is feasible.
format: application/pdf
format: text/html
creator: Jacopo D’Ercole
creator: Sean W.J. Prosser
creator: Paul D.N. Hebert
subject: Biodiversity
subject: Bioinformatics
subject: Evolutionary Studies
subject: Molecular Biology
description: doi:10.7717/peerj.10420
publisher: PeerJ Inc.
rights: © 2021 D’Ercole et al.
abstract: Natural history collections are a valuable resource for molecular taxonomic studies and for examining patterns of evolutionary diversification, particularly in the case of rare or extinct species. However, the recovery of sequence information is often complicated by DNA degradation. This article describes use of the Sequel platform (Pacific Biosciences) to recover the 658 bp barcode region of the mitochondrial cytochrome c oxidase I (COI) gene from 380 butterflies with an average age of 50 years. Nested multiplex PCR was employed for library preparation to facilitate sequence recovery from extracts with low concentrations of highly degraded DNA. By employing circular consensus sequencing (CCS) of short amplicons (circa 150 bp), full-length barcodes could be assembled without a reference sequence, an important advance from earlier protocols which required reference sequences to guide contig assembly. The Sequel protocol recovered COI sequences (499 bp on average) from 318 of 380 specimens (84%), much higher than for Sanger sequencing (26%). Because each read derives from a single molecule, it was also possible to quantify the incidence of substitutions arising from DNA damage. In agreement with past work on sequence changes induced by DNA degradation, the transition C/G → T/A was the most prevalent category of change, but its rate of occurrence (4.58E−4) was so low that it did not impede the recovery of reliable sequences. Because the current protocol recovers COI sequence from most museum specimens, and because sequence fidelity is unaffected by nucleotide misincorporations, large-scale sequence characterization of museum specimens is feasible.
bibliographic citation: D’Ercole et al. (2021) A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera)—patterns of nucleotide misincorporation. PeerJ 9:e10420 https://doi.org/10.7717/peerj.10420
date submitted: 2019-12-19
date accepted: 2020-11-02
issued: 2021-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: D’Ercole
  given name: Jacopo
author list: Agent
  family name: Prosser
  given name: Sean W.J.
author list: Agent
  family name: Hebert
  given name: Paul D.N.
doi: 10.7717/peerj.10420
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-14
copyright: © 2021 D’Ercole et al.
attribution name: D’Ercole et al.

Identification of a novel association for the WWOX/HIF1A axis with gestational diabetes mellitus (GDM)
type: item
type: AcademicArticle
description: Background Although the WW-domain-containing oxidoreductase (WWOX)/Hypoxia-inducible factor 1 (HIF1) pathway is a well-known regulator of cellular glucose and energy metabolism in pathophysiological processes, its role in gestational diabetes mellitus (GDM), remains elusive. We undertook this study to determine the effect of WWOX/HIF1A signaling on the expression of glucose metabolism genes in GDM patients. Methods Leukocytes were obtained from 135 pregnant women with (n = 98) or without (n = 37) GDM and, in turn, 3 months (n = 8) and 1 year (n = 12) postpartum. Quantitative RT-PCR was performed to determine gene expression profiles of the WWOX/HIF1A-related genes, including those involved in glucose transport (SLC2A1, SLC2A4), glycolytic pathway (HK2, PKM2, PFK, LDHA), Wnt pathway (DVL2, CTNNB1), and inflammatory response (NFKB1). Results GDM patients displayed a significant downregulation of WWOX with simultaneous upregulation of HIF1A which resulted in approximately six times reduction in WWOX/HIF1A ratio. As a consequence, HIF1A induced genes (SLC2A1, HK2, PFK, PKM) were found to be overexpressed in GDM compared to normal pregnancy and negative correlate with WWOX/HIF1A ratio. The postpartum WWOX expression was higher than during GDM, but its level was comparable to that observed in normal pregnancy. Conclusions The obtained results suggest a significant contribution of the WWOX gene to glucose metabolism in patients with gestational diabetes. Decreased WWOX expression in GDM compared to normal pregnancy, and in particular reduction of WWOX/HIF1A ratio, indicate that WWOX modulates HIF1α activity in normal tissues as described in the tumor. The effect of HIF1α excessive activation is to increase the expression of genes encoding proteins directly involved in the glycolysis which may lead to pathological changes in glucose metabolism observed in gestational diabetes.
format: application/pdf
format: text/html
creator: Izabela Baryla
creator: Elzbieta Pluciennik
creator: Katarzyna Kośla
creator: Marzena Wojcik
creator: Andrzej Zieleniak
creator: Monika Zurawska-Klis
creator: Katarzyna Cypryk
creator: Lucyna Alicja Wozniak
creator: Andrzej K Bednarek
subject: Molecular Biology
subject: Diabetes and Endocrinology
subject: Women’s Health
description: doi:10.7717/peerj.10604
publisher: PeerJ Inc.
rights: © 2021 Baryla et al.
abstract: Background Although the WW-domain-containing oxidoreductase (WWOX)/Hypoxia-inducible factor 1 (HIF1) pathway is a well-known regulator of cellular glucose and energy metabolism in pathophysiological processes, its role in gestational diabetes mellitus (GDM), remains elusive. We undertook this study to determine the effect of WWOX/HIF1A signaling on the expression of glucose metabolism genes in GDM patients. Methods Leukocytes were obtained from 135 pregnant women with (n = 98) or without (n = 37) GDM and, in turn, 3 months (n = 8) and 1 year (n = 12) postpartum. Quantitative RT-PCR was performed to determine gene expression profiles of the WWOX/HIF1A-related genes, including those involved in glucose transport (SLC2A1, SLC2A4), glycolytic pathway (HK2, PKM2, PFK, LDHA), Wnt pathway (DVL2, CTNNB1), and inflammatory response (NFKB1). Results GDM patients displayed a significant downregulation of WWOX with simultaneous upregulation of HIF1A which resulted in approximately six times reduction in WWOX/HIF1A ratio. As a consequence, HIF1A induced genes (SLC2A1, HK2, PFK, PKM) were found to be overexpressed in GDM compared to normal pregnancy and negative correlate with WWOX/HIF1A ratio. The postpartum WWOX expression was higher than during GDM, but its level was comparable to that observed in normal pregnancy. Conclusions The obtained results suggest a significant contribution of the WWOX gene to glucose metabolism in patients with gestational diabetes. Decreased WWOX expression in GDM compared to normal pregnancy, and in particular reduction of WWOX/HIF1A ratio, indicate that WWOX modulates HIF1α activity in normal tissues as described in the tumor. The effect of HIF1α excessive activation is to increase the expression of genes encoding proteins directly involved in the glycolysis which may lead to pathological changes in glucose metabolism observed in gestational diabetes.
bibliographic citation: Baryla et al. (2021) Identification of a novel association for the WWOX/HIF1A axis with gestational diabetes mellitus (GDM). PeerJ 9:e10604 https://doi.org/10.7717/peerj.10604
date submitted: 2020-07-17
date accepted: 2020-11-28
issued: 2021-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baryla
  given name: Izabela
author list: Agent
  family name: Pluciennik
  given name: Elzbieta
author list: Agent
  family name: Kośla
  given name: Katarzyna
author list: Agent
  family name: Wojcik
  given name: Marzena
author list: Agent
  family name: Zieleniak
  given name: Andrzej
author list: Agent
  family name: Zurawska-Klis
  given name: Monika
author list: Agent
  family name: Cypryk
  given name: Katarzyna
author list: Agent
  family name: Wozniak
  given name: Lucyna Alicja
author list: Agent
  family name: Bednarek
  given name: Andrzej K
doi: 10.7717/peerj.10604
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-14
copyright: ©2021 Baryla et al.
attribution name: Baryla et al.

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