PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Endemism and diversity of small mammals along two neighboring Bornean mountains
items: Identification of crucial genes in abdominal aortic aneurysm by WGCNA
items: Bees may drive the reproduction of four sympatric cacti in a vanishing coastal mediterranean-type ecosystem
items: Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China
items: Integrative transcriptome data mining for identification of core lncRNAs in breast cancer
items: CELSR3 mRNA expression is increased in hepatocellular carcinoma and indicates poor prognosis
items: Social Motor Priming: when offline interference facilitates motor execution
items: Validation of COI metabarcoding primers for terrestrial arthropods
items: https://peerj.com/articles/7686
items: Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae

Endemism and diversity of small mammals along two neighboring Bornean mountains
type: item
type: AcademicArticle
description: Mountains offer replicated units with large biotic and abiotic gradients in a reduced spatial scale. This transforms them into well-suited scenarios to evaluate biogeographic theories. Mountain biogeography is a hot topic of research and many theories have been proposed to describe the changes in biodiversity with elevation. Geometric constraints, which predict the highest diversity to occur in mid-elevations, have been a focal part of this discussion. Despite this, there is no general theory to explain these patterns, probably because of the interaction among different predictors with the local effects of historical factors. We characterize the diversity of small non-volant mammals across the elevational gradient on Mount (Mt.) Kinabalu (4,095 m) and Mt. Tambuyukon (2,579 m), two neighboring mountains in Borneo, Malaysia. We documented a decrease in species richness with elevation which deviates from expectations of the geometric constraints and suggests that spatial factors (e.g., larger diversity in larger areas) are important. The lowland small mammal community was replaced in higher elevations (from above ~1,900 m) with montane communities consisting mainly of high elevation Borneo endemics. The positive correlation we find between elevation and endemism is concordant with a hypothesis that predicts higher endemism with topographical isolation. This supports lineage history and geographic history could be important drivers of species diversity in this region.
format: application/pdf
format: text/html
creator: Miguel Camacho-Sanchez
creator: Melissa T.R. Hawkins
creator: Fred Tuh Yit Yu
creator: Jesus E. Maldonado
creator: Jennifer A. Leonard
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.7858
publisher: PeerJ Inc.
rights: © 2019 Camacho-Sanchez et al.
abstract: Mountains offer replicated units with large biotic and abiotic gradients in a reduced spatial scale. This transforms them into well-suited scenarios to evaluate biogeographic theories. Mountain biogeography is a hot topic of research and many theories have been proposed to describe the changes in biodiversity with elevation. Geometric constraints, which predict the highest diversity to occur in mid-elevations, have been a focal part of this discussion. Despite this, there is no general theory to explain these patterns, probably because of the interaction among different predictors with the local effects of historical factors. We characterize the diversity of small non-volant mammals across the elevational gradient on Mount (Mt.) Kinabalu (4,095 m) and Mt. Tambuyukon (2,579 m), two neighboring mountains in Borneo, Malaysia. We documented a decrease in species richness with elevation which deviates from expectations of the geometric constraints and suggests that spatial factors (e.g., larger diversity in larger areas) are important. The lowland small mammal community was replaced in higher elevations (from above ~1,900 m) with montane communities consisting mainly of high elevation Borneo endemics. The positive correlation we find between elevation and endemism is concordant with a hypothesis that predicts higher endemism with topographical isolation. This supports lineage history and geographic history could be important drivers of species diversity in this region.
bibliographic citation: Camacho-Sanchez et al. (2019) Endemism and diversity of small mammals along two neighboring Bornean mountains. PeerJ 7:e7858 https://doi.org/10.7717/peerj.7858
date submitted: 2018-02-14
date accepted: 2019-09-09
issued: 2019-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Camacho-Sanchez
  given name: Miguel
author list: Agent
  family name: Hawkins
  given name: Melissa T.R.
author list: Agent
  family name: Tuh Yit Yu
  given name: Fred
author list: Agent
  family name: Maldonado
  given name: Jesus E.
author list: Agent
  family name: Leonard
  given name: Jennifer A.
doi: 10.7717/peerj.7858
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-08
copyright: © 2019 Camacho-Sanchez et al.
attribution name: Camacho-Sanchez et al.

Identification of crucial genes in abdominal aortic aneurysm by WGCNA
type: item
type: AcademicArticle
description: Background Abdominal aortic aneurysm (AAA) is the full thickness dilation of the abdominal aorta. However, few effective medical therapies are available. Thus, elucidating the molecular mechanism of AAA pathogenesis and exploring the potential molecular target of medical therapies for AAA is of vital importance. Methods Three expression datasets (GSE7084, GSE47472 and GSE57691) were downloaded from the Gene Expression Omnibus (GEO). These datasets were merged and then normalized using the “sva” R package. Differential expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were conducted. We compared the co-expression patterns between AAA and normal conditions, and hub genes of each functional module were identified. DEGs were mapped to co-expression network under AAA condition and a DEG co-expression network was generated. Crucial genes were identified using molecular complex detection (MCODE) (a plugin in Cytoscape). Results In our study, 6 and 10 gene modules were detected for the AAA and normal conditions, respectively, while 143 DEGs were screened. Compared to the normal condition, genes associated with immune response, inflammation and muscle contraction were clustered in three gene modules respectively under the AAA condition; the hub genes of the three modules were MAP4K1, NFIB and HPK1, respectively. A DEG co-expression network with 102 nodes and 303 edges was identified, and a hub gene cluster with 10 genes from the DEG co-expression network was detected. YIPF6, RABGAP1, ANKRD6, GPD1L, PGRMC2, HIGD1A, GMDS, MGP, SLC25A4 and FAM129A were in the cluster. The expression levels of these 10 genes showed potential diagnostic value. Conclusion Based on WGCNA, we detected 6 modules under the AAA condition and 10 modules in the normal condition. Hub genes of each module and hub gene clusters of the DEG co-expression network were identified. These genes may act as potential targets for medical therapy and diagnostic biomarkers. Further…
format: application/pdf
format: text/html
creator: Siliang Chen
creator: Dan Yang
creator: Chuxiang Lei
creator: Yuan Li
creator: Xiaoning Sun
creator: Mengyin Chen
creator: Xiao Wu
creator: Yuehong Zheng
subject: Bioinformatics
subject: Surgery and Surgical Specialties
subject: Translational Medicine
description: doi:10.7717/peerj.7873
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Background Abdominal aortic aneurysm (AAA) is the full thickness dilation of the abdominal aorta. However, few effective medical therapies are available. Thus, elucidating the molecular mechanism of AAA pathogenesis and exploring the potential molecular target of medical therapies for AAA is of vital importance. Methods Three expression datasets (GSE7084, GSE47472 and GSE57691) were downloaded from the Gene Expression Omnibus (GEO). These datasets were merged and then normalized using the “sva” R package. Differential expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were conducted. We compared the co-expression patterns between AAA and normal conditions, and hub genes of each functional module were identified. DEGs were mapped to co-expression network under AAA condition and a DEG co-expression network was generated. Crucial genes were identified using molecular complex detection (MCODE) (a plugin in Cytoscape). Results In our study, 6 and 10 gene modules were detected for the AAA and normal conditions, respectively, while 143 DEGs were screened. Compared to the normal condition, genes associated with immune response, inflammation and muscle contraction were clustered in three gene modules respectively under the AAA condition; the hub genes of the three modules were MAP4K1, NFIB and HPK1, respectively. A DEG co-expression network with 102 nodes and 303 edges was identified, and a hub gene cluster with 10 genes from the DEG co-expression network was detected. YIPF6, RABGAP1, ANKRD6, GPD1L, PGRMC2, HIGD1A, GMDS, MGP, SLC25A4 and FAM129A were in the cluster. The expression levels of these 10 genes showed potential diagnostic value. Conclusion Based on WGCNA, we detected 6 modules under the AAA condition and 10 modules in the normal condition. Hub genes of each module and hub gene clusters of the DEG co-expression network were identified. These genes may act as potential targets for medical therapy and diagnostic biomarkers. Further…
bibliographic citation: Chen et al. (2019) Identification of crucial genes in abdominal aortic aneurysm by WGCNA. PeerJ 7:e7873 https://doi.org/10.7717/peerj.7873
date submitted: 2019-05-21
date accepted: 2019-09-11
issued: 2019-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Siliang
author list: Agent
  family name: Yang
  given name: Dan
author list: Agent
  family name: Lei
  given name: Chuxiang
author list: Agent
  family name: Li
  given name: Yuan
author list: Agent
  family name: Sun
  given name: Xiaoning
author list: Agent
  family name: Chen
  given name: Mengyin
author list: Agent
  family name: Wu
  given name: Xiao
author list: Agent
  family name: Zheng
  given name: Yuehong
doi: 10.7717/peerj.7873
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-08
copyright: © 2019 Chen et al.
attribution name: Chen et al.

Bees may drive the reproduction of four sympatric cacti in a vanishing coastal mediterranean-type ecosystem
type: item
type: AcademicArticle
description: Background Sympatric congeneric plants might share pollinators, or each species might avoid competition by evolving specialized traits that generate partitions in pollinator assemblages. In both cases, pollen limitation (a decrease in the quality and quantity of compatible reproductive pollen) can occur, driving the plant mating system to autogamy as a mechanism of reproductive assurance. We assessed the relationships between pollinator assemblages and mating systems in a group of sympatric congeneric plants. We attempted to answer the following questions: (i) How similar are pollinator assemblages among sympatric cactus species? (ii) Which mating systems do sympatric cactus species use? Methods We studied sympatric Eriosyce taxa that inhabit a threatened coastal strip in a mediterranean-type ecosystem in central Chile. We performed field observations on four taxa and characterized pollinators during the years 2016 and 2017. We estimated differences in the pollinator assemblages using the Bray–Curtis index. To elucidate the mating systems, we conducted hand-pollination experiments using three treatments: manual cross-pollination, automatic self-pollination, and control (unmanipulated individuals). We tested differences in seed production for statistical significance using Kruskal–Wallis analysis. Results Eriosyce subgibbosa showed a distinctive pollinator assemblage among the sympatric species that we studied (similarity ranged from 0% to 8%); it was visited by small bees and was the only species that was visited by the giant hummingbird Patagona gigas. Pollinator assemblages were similar between E. chilensis (year 2016 = 4 species; 2017 = 8) and E. chilensis var. albidiflora (2016 = 7; 2017 = 4); however, those of E. curvispina var. mutabilis (2016 = 7; 2017 = 6) were less similar to those of the aforementioned species. E. curvispina var. mutabilis showed the highest interannual variation in its pollinator assemblage (18% similarity). Reproduction in E. subgibbosa …
format: application/pdf
format: text/html
creator: Pablo C. Guerrero
creator: Claudia A. Antinao
creator: Beatriz Vergara-Meriño
creator: Cristian A. Villagra
creator: Gastón O. Carvallo
subject: Biodiversity
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.7865
publisher: PeerJ Inc.
rights: © 2019 Guerrero et al.
abstract: Background Sympatric congeneric plants might share pollinators, or each species might avoid competition by evolving specialized traits that generate partitions in pollinator assemblages. In both cases, pollen limitation (a decrease in the quality and quantity of compatible reproductive pollen) can occur, driving the plant mating system to autogamy as a mechanism of reproductive assurance. We assessed the relationships between pollinator assemblages and mating systems in a group of sympatric congeneric plants. We attempted to answer the following questions: (i) How similar are pollinator assemblages among sympatric cactus species? (ii) Which mating systems do sympatric cactus species use? Methods We studied sympatric Eriosyce taxa that inhabit a threatened coastal strip in a mediterranean-type ecosystem in central Chile. We performed field observations on four taxa and characterized pollinators during the years 2016 and 2017. We estimated differences in the pollinator assemblages using the Bray–Curtis index. To elucidate the mating systems, we conducted hand-pollination experiments using three treatments: manual cross-pollination, automatic self-pollination, and control (unmanipulated individuals). We tested differences in seed production for statistical significance using Kruskal–Wallis analysis. Results Eriosyce subgibbosa showed a distinctive pollinator assemblage among the sympatric species that we studied (similarity ranged from 0% to 8%); it was visited by small bees and was the only species that was visited by the giant hummingbird Patagona gigas. Pollinator assemblages were similar between E. chilensis (year 2016 = 4 species; 2017 = 8) and E. chilensis var. albidiflora (2016 = 7; 2017 = 4); however, those of E. curvispina var. mutabilis (2016 = 7; 2017 = 6) were less similar to those of the aforementioned species. E. curvispina var. mutabilis showed the highest interannual variation in its pollinator assemblage (18% similarity). Reproduction in E. subgibbosa …
bibliographic citation: Guerrero et al. (2019) Bees may drive the reproduction of four sympatric cacti in a vanishing coastal mediterranean-type ecosystem. PeerJ 7:e7865 https://doi.org/10.7717/peerj.7865
date submitted: 2019-03-18
date accepted: 2019-09-10
issued: 2019-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guerrero
  given name: Pablo C.
author list: Agent
  family name: Antinao
  given name: Claudia A.
author list: Agent
  family name: Vergara-Meriño
  given name: Beatriz
author list: Agent
  family name: Villagra
  given name: Cristian A.
author list: Agent
  family name: Carvallo
  given name: Gastón O.
doi: 10.7717/peerj.7865
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-07
copyright: © 2019 Guerrero et al.
attribution name: Guerrero et al.

Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China
type: item
type: AcademicArticle
description: Labriocimbex sinicus Yan & Wei gen. et sp. nov. of Cimbicidae is described. The new genus is similar to Praia Andre and Trichiosoma Leach. A key to extant Holarctic genera of Cimbicinae is provided. To identify the phylogenetic placement of Cimbicidae, the mitochondrial genome of L. sinicus was annotated and characterized using high-throughput sequencing data. The complete mitochondrial genome of L. sinicus was obtained with a length of 15,405 bp (GenBank: MH136623; SRA: SRR8270383) and a typical set of 37 genes (22 tRNAs, 13 PCGs, and two rRNAs). The results demonstrated that all PCGs were initiated by ATN codon, and ended with TAA or T stop codons. The study reveals that all tRNA genes have a typical clover-leaf secondary structure, except for trnS1. Remarkably, the secondary structures of the rrnS and rrnL of L. sinicus were much different from those of Corynis lateralis. Phylogenetic analyses verified the monophyly and positions of the three Cimbicidae species within the superfamily Tenthredinoidea and demonstrated a relationship as (Tenthredinidae + Cimbicidae) + (Argidae + Pergidae) with strong nodal supports. Furthermore, we found that the generic relationships of Cimbicidae revealed by the phylogenetic analyses based on COI genes agree quite closely with the systematic arrangement of the genera based on the morphological characters. Phylogenetic tree based on two methods shows that L. sinicus is the sister group of Praia with high support values. We suggest that Labriocimbex belongs to the tribe Trichiosomini of Cimbicinae based on adult morphology and molecular data. Besides, we suggest to promote the subgenus Asitrichiosoma to be a valid genus.
format: application/pdf
format: text/html
creator: Yuchen Yan
creator: Gengyun Niu
creator: Yaoyao Zhang
creator: Qianying Ren
creator: Shiyu Du
creator: Bocheng Lan
creator: Meicai Wei
subject: Entomology
subject: Evolutionary Studies
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.7853
publisher: PeerJ Inc.
rights: © 2019 Yan et al.
abstract: Labriocimbex sinicus Yan & Wei gen. et sp. nov. of Cimbicidae is described. The new genus is similar to Praia Andre and Trichiosoma Leach. A key to extant Holarctic genera of Cimbicinae is provided. To identify the phylogenetic placement of Cimbicidae, the mitochondrial genome of L. sinicus was annotated and characterized using high-throughput sequencing data. The complete mitochondrial genome of L. sinicus was obtained with a length of 15,405 bp (GenBank: MH136623; SRA: SRR8270383) and a typical set of 37 genes (22 tRNAs, 13 PCGs, and two rRNAs). The results demonstrated that all PCGs were initiated by ATN codon, and ended with TAA or T stop codons. The study reveals that all tRNA genes have a typical clover-leaf secondary structure, except for trnS1. Remarkably, the secondary structures of the rrnS and rrnL of L. sinicus were much different from those of Corynis lateralis. Phylogenetic analyses verified the monophyly and positions of the three Cimbicidae species within the superfamily Tenthredinoidea and demonstrated a relationship as (Tenthredinidae + Cimbicidae) + (Argidae + Pergidae) with strong nodal supports. Furthermore, we found that the generic relationships of Cimbicidae revealed by the phylogenetic analyses based on COI genes agree quite closely with the systematic arrangement of the genera based on the morphological characters. Phylogenetic tree based on two methods shows that L. sinicus is the sister group of Praia with high support values. We suggest that Labriocimbex belongs to the tribe Trichiosomini of Cimbicinae based on adult morphology and molecular data. Besides, we suggest to promote the subgenus Asitrichiosoma to be a valid genus.
bibliographic citation: Yan et al. (2019) Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China. PeerJ 7:e7853 https://doi.org/10.7717/peerj.7853
date submitted: 2019-02-13
date accepted: 2019-09-08
issued: 2019-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Yuchen
author list: Agent
  family name: Niu
  given name: Gengyun
author list: Agent
  family name: Zhang
  given name: Yaoyao
author list: Agent
  family name: Ren
  given name: Qianying
author list: Agent
  family name: Du
  given name: Shiyu
author list: Agent
  family name: Lan
  given name: Bocheng
author list: Agent
  family name: Wei
  given name: Meicai
doi: 10.7717/peerj.7853
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-07
copyright: ©2019 Yan et al.
attribution name: Yan et al.

Integrative transcriptome data mining for identification of core lncRNAs in breast cancer
type: item
type: AcademicArticle
description: Background Cumulative evidence suggests that long non-coding RNAs (lncRNAs) play an important role in tumorigenesis. This study aims to identify lncRNAs that can serve as new biomarkers for breast cancer diagnosis or screening. Methods First, the linear fitting method was used to identify differentially expressed genes from the breast cancer RNA expression profiles in The Cancer Genome Atlas (TCGA). Next, the diagnostic value of all differentially expressed lncRNAs was evaluated using a receiver operating characteristic (ROC) curve. Then, the top ten lncRNAs with the highest diagnostic value were selected as core genes for clinical characteristics and prognosis analysis. Furthermore, core lncRNA-mRNA co-expression networks based on weighted gene co-expression network analysis (WGCNA) were constructed, and functional enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The differential expression level and diagnostic value of core lncRNAs were further evaluated by using independent data set from Gene Expression Omnibus (GEO). Finally, the expression status and prognostic value of core lncRNAs in various tumors were analyzed based on Gene Expression Profiling Interactive Analysis (GEPIA). Results Seven core lncRNAs (LINC00478, PGM5-AS1, AL035610.1, MIR143HG, RP11-175K6.1, AC005550.4, and MIR497HG) have good single-factor diagnostic value for breast cancer. AC093850.2 has a prognostic value for breast cancer. AC005550.4 and MIR497HG can better distinguish breast cancer patients in early-stage from the advanced-stage. Low expression of MAGI2-AS3, LINC00478, AL035610.1, MIR143HG, and MIR145 may be associated with lymph node metastasis in breast cancer. Conclusion Our study provides candidate biomarkers for the diagnosis and prognosis of breast cancer, as well as a bioinformatics basis for the further elucidation of the molecular pathological mechanism of breast cancer.
format: application/pdf
format: text/html
creator: Xiaoming Zhang
creator: Jing Zhuang
creator: Lijuan Liu
creator: Zhengguo He
creator: Cun Liu
creator: Xiaoran Ma
creator: Jie Li
creator: Xia Ding
creator: Changgang Sun
subject: Bioinformatics
subject: Oncology
description: doi:10.7717/peerj.7821
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background Cumulative evidence suggests that long non-coding RNAs (lncRNAs) play an important role in tumorigenesis. This study aims to identify lncRNAs that can serve as new biomarkers for breast cancer diagnosis or screening. Methods First, the linear fitting method was used to identify differentially expressed genes from the breast cancer RNA expression profiles in The Cancer Genome Atlas (TCGA). Next, the diagnostic value of all differentially expressed lncRNAs was evaluated using a receiver operating characteristic (ROC) curve. Then, the top ten lncRNAs with the highest diagnostic value were selected as core genes for clinical characteristics and prognosis analysis. Furthermore, core lncRNA-mRNA co-expression networks based on weighted gene co-expression network analysis (WGCNA) were constructed, and functional enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The differential expression level and diagnostic value of core lncRNAs were further evaluated by using independent data set from Gene Expression Omnibus (GEO). Finally, the expression status and prognostic value of core lncRNAs in various tumors were analyzed based on Gene Expression Profiling Interactive Analysis (GEPIA). Results Seven core lncRNAs (LINC00478, PGM5-AS1, AL035610.1, MIR143HG, RP11-175K6.1, AC005550.4, and MIR497HG) have good single-factor diagnostic value for breast cancer. AC093850.2 has a prognostic value for breast cancer. AC005550.4 and MIR497HG can better distinguish breast cancer patients in early-stage from the advanced-stage. Low expression of MAGI2-AS3, LINC00478, AL035610.1, MIR143HG, and MIR145 may be associated with lymph node metastasis in breast cancer. Conclusion Our study provides candidate biomarkers for the diagnosis and prognosis of breast cancer, as well as a bioinformatics basis for the further elucidation of the molecular pathological mechanism of breast cancer.
bibliographic citation: Zhang et al. (2019) Integrative transcriptome data mining for identification of core lncRNAs in breast cancer. PeerJ 7:e7821 https://doi.org/10.7717/peerj.7821
date submitted: 2019-05-03
date accepted: 2019-09-03
issued: 2019-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhang
  given name: Xiaoming
author list: Agent
  family name: Zhuang
  given name: Jing
author list: Agent
  family name: Liu
  given name: Lijuan
author list: Agent
  family name: He
  given name: Zhengguo
author list: Agent
  family name: Liu
  given name: Cun
author list: Agent
  family name: Ma
  given name: Xiaoran
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Ding
  given name: Xia
author list: Agent
  family name: Sun
  given name: Changgang
doi: 10.7717/peerj.7821
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-07
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

CELSR3 mRNA expression is increased in hepatocellular carcinoma and indicates poor prognosis
type: item
type: AcademicArticle
description: Objective Hepatocellular carcinoma (HCC) is a disease that is associated with high mortality; currently, there is no curative and reliable treatment. Cadherin EGF LAG seven-pass G-type receptor 3 (CELSR3) is the key signaling molecule in the wingless and INT-1/planar cell polarity (WNT/PCP) pathway. This study aimed to elucidate the prognostic significance of CELSR3 in HCC patients. Methods The Cancer Genome Atlas (TCGA) database, the Cancer Cell Line Encyclopedia (CCLE) database and the Gene Expression Omnibus (GEO) database were used to analyze the expression of CELSR3 mRNA in HCC samples and cells. The relationship between CELSR3 mRNA and clinical features was assessed by the chi-square test. the diagnostic and predictive value of CELSR3 mRNA expression were analyzed using the receiver operating characteristic (ROC) curve. Kaplan–Meier curve and Cox regression analyses were performed to assess the prognostic value of CELSR3 mRNA in HCC patients. Finally, all three cohorts database was used for gene set enrichment analysis(GSEA) and the identification of CELSR3-related signal transduction pathways. Results The expression of CELSR3 mRNA was upregulated in HCC, and its expression was correlated with age (P = 0.025), tumor status (P = 0.022), clinical stage (P = 0.003), T classification (P = 0.010), vital status (P = 0.001), and relapse (P = 0.005). The ROC curve assessment indicated that CELSR3 mRNA expression has high diagnostic value in HCC and in the subgroup analysis of stage. In addition, the Kaplan-Meier curve and Cox analyses suggested that patients with high CELSR3 mRNA expression have a poor prognosis, indicating that CELSR3 mRNA is an independent prognostic factor for the overall survival of HCC patients. GSEA showed that GO somatic diversification of immune receptors, GO endonuclease activity, GO DNA repair complex and GO somatic cell DNA recombination, were differentially enriched in the meta-GEO cohort, the HCC cell line cohort and the TCGA cohort of th…
format: application/pdf
format: text/html
creator: Xuefeng Gu
creator: Hongbo Li
creator: Ling Sha
creator: Yuan Mao
creator: Chuanbing Shi
creator: Wei Zhao
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.7816
publisher: PeerJ Inc.
rights: © 2019 Gu et al.
abstract: Objective Hepatocellular carcinoma (HCC) is a disease that is associated with high mortality; currently, there is no curative and reliable treatment. Cadherin EGF LAG seven-pass G-type receptor 3 (CELSR3) is the key signaling molecule in the wingless and INT-1/planar cell polarity (WNT/PCP) pathway. This study aimed to elucidate the prognostic significance of CELSR3 in HCC patients. Methods The Cancer Genome Atlas (TCGA) database, the Cancer Cell Line Encyclopedia (CCLE) database and the Gene Expression Omnibus (GEO) database were used to analyze the expression of CELSR3 mRNA in HCC samples and cells. The relationship between CELSR3 mRNA and clinical features was assessed by the chi-square test. the diagnostic and predictive value of CELSR3 mRNA expression were analyzed using the receiver operating characteristic (ROC) curve. Kaplan–Meier curve and Cox regression analyses were performed to assess the prognostic value of CELSR3 mRNA in HCC patients. Finally, all three cohorts database was used for gene set enrichment analysis(GSEA) and the identification of CELSR3-related signal transduction pathways. Results The expression of CELSR3 mRNA was upregulated in HCC, and its expression was correlated with age (P = 0.025), tumor status (P = 0.022), clinical stage (P = 0.003), T classification (P = 0.010), vital status (P = 0.001), and relapse (P = 0.005). The ROC curve assessment indicated that CELSR3 mRNA expression has high diagnostic value in HCC and in the subgroup analysis of stage. In addition, the Kaplan-Meier curve and Cox analyses suggested that patients with high CELSR3 mRNA expression have a poor prognosis, indicating that CELSR3 mRNA is an independent prognostic factor for the overall survival of HCC patients. GSEA showed that GO somatic diversification of immune receptors, GO endonuclease activity, GO DNA repair complex and GO somatic cell DNA recombination, were differentially enriched in the meta-GEO cohort, the HCC cell line cohort and the TCGA cohort of th…
bibliographic citation: Gu et al. (2019) CELSR3 mRNA expression is increased in hepatocellular carcinoma and indicates poor prognosis. PeerJ 7:e7816 https://doi.org/10.7717/peerj.7816
date submitted: 2019-06-03
date accepted: 2019-09-02
issued: 2019-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gu
  given name: Xuefeng
author list: Agent
  family name: Li
  given name: Hongbo
author list: Agent
  family name: Sha
  given name: Ling
author list: Agent
  family name: Mao
  given name: Yuan
author list: Agent
  family name: Shi
  given name: Chuanbing
author list: Agent
  family name: Zhao
  given name: Wei
doi: 10.7717/peerj.7816
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-07
copyright: ©2019 Gu et al.
attribution name: Gu et al.

Social Motor Priming: when offline interference facilitates motor execution
type: item
type: AcademicArticle
description: Many daily activities involve synchronizing with other people’s actions. Previous literature has revealed that a slowdown of performance occurs whenever the action to be carried out is different to the one observed (i.e., visuomotor interference). However, action execution can be facilitated by observing a different action if it calls for an interactive gesture (i.e., social motor priming). The aim of this study is to investigate the costs and benefits of spontaneously processing a social response and then executing the same or a different action. Participants performed two different types of grips, which could be either congruent or not with the socially appropriate response and with the observed action. In particular, participants performed a precision grip (PG; thumb-index fingers opposition) or a whole-hand grasp (WHG; fingers-palm opposition) after observing videos showing an actor performing a PG and addressing them (interactive condition) or not (non-interactive condition). Crucially, in the interactive condition, the most appropriate response was a WHG, but in 50 percent of trials participants were asked to perform a PG. This procedure allowed us to measure both the facilitator effect of performing an action appropriate to the social context (WHG)—but different with respect to the observed one (PG)—and the cost of inhibiting it. These effects were measured by means of 3-D kinematical analysis of movement. Results show that, in terms of reaction time and movement time, the interactive request facilitated (i.e., speeded) the socially appropriate action (WHG), whereas interfered with (i.e., delayed) a different action (PG), although observed actions were always PGs. This interference also manifested with an increase of maximum grip aperture, which seemingly reflects the concurrent representation of the socially appropriate response. Overall, these findings extend previous research by revealing that physically incongruent action representations can be integrated…
format: application/pdf
format: text/html
creator: Sonia Betti
creator: Eris Chinellato
creator: Silvia Guerra
creator: Umberto Castiello
creator: Luisa Sartori
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.7796
publisher: PeerJ Inc.
rights: © 2019 Betti et al.
abstract: Many daily activities involve synchronizing with other people’s actions. Previous literature has revealed that a slowdown of performance occurs whenever the action to be carried out is different to the one observed (i.e., visuomotor interference). However, action execution can be facilitated by observing a different action if it calls for an interactive gesture (i.e., social motor priming). The aim of this study is to investigate the costs and benefits of spontaneously processing a social response and then executing the same or a different action. Participants performed two different types of grips, which could be either congruent or not with the socially appropriate response and with the observed action. In particular, participants performed a precision grip (PG; thumb-index fingers opposition) or a whole-hand grasp (WHG; fingers-palm opposition) after observing videos showing an actor performing a PG and addressing them (interactive condition) or not (non-interactive condition). Crucially, in the interactive condition, the most appropriate response was a WHG, but in 50 percent of trials participants were asked to perform a PG. This procedure allowed us to measure both the facilitator effect of performing an action appropriate to the social context (WHG)—but different with respect to the observed one (PG)—and the cost of inhibiting it. These effects were measured by means of 3-D kinematical analysis of movement. Results show that, in terms of reaction time and movement time, the interactive request facilitated (i.e., speeded) the socially appropriate action (WHG), whereas interfered with (i.e., delayed) a different action (PG), although observed actions were always PGs. This interference also manifested with an increase of maximum grip aperture, which seemingly reflects the concurrent representation of the socially appropriate response. Overall, these findings extend previous research by revealing that physically incongruent action representations can be integrated…
bibliographic citation: Betti et al. (2019) Social Motor Priming: when offline interference facilitates motor execution. PeerJ 7:e7796 https://doi.org/10.7717/peerj.7796
date submitted: 2019-05-04
date accepted: 2019-08-29
issued: 2019-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Betti
  given name: Sonia
author list: Agent
  family name: Chinellato
  given name: Eris
author list: Agent
  family name: Guerra
  given name: Silvia
author list: Agent
  family name: Castiello
  given name: Umberto
author list: Agent
  family name: Sartori
  given name: Luisa
doi: 10.7717/peerj.7796
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-07
copyright: ©2019 Betti et al.
attribution name: Betti et al.

Validation of COI metabarcoding primers for terrestrial arthropods
type: item
type: AcademicArticle
description: Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. This study tests the performance of 36 primer sets on a mock community containing 374 insect species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets were also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from both mock community and Malaise trap sample metabarcoding were used to select four primer sets for additional evaluation at different annealing temperatures (40–60 °C) using the mock community. The effect of temperature varied by primer pair but overall it only had a minor effect on taxon recovery. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrates that certain primer sets can recover most taxa in a diverse species assemblage. Thus, based our experimental set up, there is no need to employ several primer sets targeting the same gene region. We identify several suitable primer sets for arthropod metabarcoding, and specifically recommend BF3 + BR2, as it is not affected by primer slippage and provides maximal taxonomic resolution. The fwhF2 + fwhR2n primer set amplifies a shorter fragment and is therefore ideal when targeting degraded DNA (e.g., from gut contents).
format: application/pdf
format: text/html
creator: Vasco Elbrecht
creator: Thomas W.A. Braukmann
creator: Natalia V. Ivanova
creator: Sean W.J. Prosser
creator: Mehrdad Hajibabaei
creator: Michael Wright
creator: Evgeny V. Zakharov
creator: Paul D.N. Hebert
creator: Dirk Steinke
subject: Ecology
subject: Ecosystem Science
subject: Entomology
subject: Molecular Biology
subject: Forestry
description: doi:10.7717/peerj.7745
publisher: PeerJ Inc.
rights: © 2019 Elbrecht et al.
abstract: Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. This study tests the performance of 36 primer sets on a mock community containing 374 insect species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets were also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from both mock community and Malaise trap sample metabarcoding were used to select four primer sets for additional evaluation at different annealing temperatures (40–60 °C) using the mock community. The effect of temperature varied by primer pair but overall it only had a minor effect on taxon recovery. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrates that certain primer sets can recover most taxa in a diverse species assemblage. Thus, based our experimental set up, there is no need to employ several primer sets targeting the same gene region. We identify several suitable primer sets for arthropod metabarcoding, and specifically recommend BF3 + BR2, as it is not affected by primer slippage and provides maximal taxonomic resolution. The fwhF2 + fwhR2n primer set amplifies a shorter fragment and is therefore ideal when targeting degraded DNA (e.g., from gut contents).
bibliographic citation: Elbrecht et al. (2019) Validation of COI metabarcoding primers for terrestrial arthropods. PeerJ 7:e7745 https://doi.org/10.7717/peerj.7745
date submitted: 2019-07-23
date accepted: 2019-08-25
issued: 2019-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elbrecht
  given name: Vasco
author list: Agent
  family name: Braukmann
  given name: Thomas W.A.
author list: Agent
  family name: Ivanova
  given name: Natalia V.
author list: Agent
  family name: Prosser
  given name: Sean W.J.
author list: Agent
  family name: Hajibabaei
  given name: Mehrdad
author list: Agent
  family name: Wright
  given name: Michael
author list: Agent
  family name: Zakharov
  given name: Evgeny V.
author list: Agent
  family name: Hebert
  given name: Paul D.N.
author list: Agent
  family name: Steinke
  given name: Dirk
doi: 10.7717/peerj.7745
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-07
copyright: ©2019 Elbrecht et al.
attribution name: Elbrecht et al.

https://peerj.com/articles/7686
type: item
type: AcademicArticle
title: In vivo acute toxicity evaluation and in vitro molecular mechanism study of antiproliferative activity of a novel indole Schiff base β-diiminato manganeseIII complex in hormone-dependent and triple negative breast cancer cells
description: Breast cancer is the most frequently diagnosed cancer among women worldwide. Recently, increasing attention has been paid to the anticancer effects of transition metal complexes of indole Schiff bases. β-diiminato ManganeseIII complex has shown promising cell cycle arrest and apoptosis induction against MCF-7 and MDA-MB-231 breast cancer cells. In this study, time- and dose- dependent inhibitory activity were evaluated using MTT assay after 48 h and 72 h exposure time. In addition, median effect analysis was conducted according to Chou–Talalay method to investigate whether MnIII complex has synergistic effect in combination with chemotherapeutic drugs on inhibiting breast cancer cell growth. The molecular mechanisms underlying its potent antiproliferative effect was determined through bioluminescent caspase-3/7, -8 and -9 activity assays and quantitative expression analysis of cell cycle- and apoptosis-related genes. Furthermore, safety evaluation of MnIII complex was assessed through the acute oral toxicity test in in vivo model. The MTT assay results revealed that it potently reduced the viability of MCF-7 (IC50 of 0.63 ± 0.07 µg/mL for 48 h and 0.39 ± 0.08 µg/mL for 72 h) and MDA-MB-231 (1.17 ± 0.06 µg/mL for 48 h, 1.03 ± 0.15 µg/mL for 72 h) cells in dose- and time-dependent manner. Combination treatment also enhanced the cytotoxic effects of doxorubicin but not tamoxifen on inhibiting breast cancer cell growth. The involvement of intrinsic and extrinsic pathway in apoptosis induction was exhibited through the increased activity of caspase-9 and caspase-8, respectively, leading to enhanced downstream executioner caspase-3/7 activity in treated MCF-7 and MDA-MB-231 cells. In addition, gene expression analysis revealed that MnIII complex exerts its antiproliferative effect via up-and down-regulation of p21 and cyclin D1, respectively, along with increased expression of Bax/Bcl-2 ratio, TNF-α, initiator caspase-8 and -10 and effector caspase-3 in MCF-7 and MDA-MB-2…
format: application/pdf
format: text/html
creator: Reyhaneh Farghadani
creator: Maryam Seifaddinipour
creator: Jayakumar Rajarajeswaran
creator: Mahmood Ameen Abdulla
creator: Najihah Binti Mohd Hashim
creator: Si Lay Khaing
creator: Nur’ain Binti Salehen
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.7686
publisher: PeerJ Inc.
rights: © 2019 Farghadani et al.
abstract: Breast cancer is the most frequently diagnosed cancer among women worldwide. Recently, increasing attention has been paid to the anticancer effects of transition metal complexes of indole Schiff bases. β-diiminato ManganeseIII complex has shown promising cell cycle arrest and apoptosis induction against MCF-7 and MDA-MB-231 breast cancer cells. In this study, time- and dose- dependent inhibitory activity were evaluated using MTT assay after 48 h and 72 h exposure time. In addition, median effect analysis was conducted according to Chou–Talalay method to investigate whether MnIII complex has synergistic effect in combination with chemotherapeutic drugs on inhibiting breast cancer cell growth. The molecular mechanisms underlying its potent antiproliferative effect was determined through bioluminescent caspase-3/7, -8 and -9 activity assays and quantitative expression analysis of cell cycle- and apoptosis-related genes. Furthermore, safety evaluation of MnIII complex was assessed through the acute oral toxicity test in in vivo model. The MTT assay results revealed that it potently reduced the viability of MCF-7 (IC50 of 0.63 ± 0.07 µg/mL for 48 h and 0.39 ± 0.08 µg/mL for 72 h) and MDA-MB-231 (1.17 ± 0.06 µg/mL for 48 h, 1.03 ± 0.15 µg/mL for 72 h) cells in dose- and time-dependent manner. Combination treatment also enhanced the cytotoxic effects of doxorubicin but not tamoxifen on inhibiting breast cancer cell growth. The involvement of intrinsic and extrinsic pathway in apoptosis induction was exhibited through the increased activity of caspase-9 and caspase-8, respectively, leading to enhanced downstream executioner caspase-3/7 activity in treated MCF-7 and MDA-MB-231 cells. In addition, gene expression analysis revealed that MnIII complex exerts its antiproliferative effect via up-and down-regulation of p21 and cyclin D1, respectively, along with increased expression of Bax/Bcl-2 ratio, TNF-α, initiator caspase-8 and -10 and effector caspase-3 in MCF-7 and MDA-MB-2…
bibliographic citation: Farghadani et al. (2019) In vivo acute toxicity evaluation and in vitro molecular mechanism study of antiproliferative activity of a novel indole Schiff base β-diiminato manganeseIII complex in hormone-dependent and triple negative breast cancer cells. PeerJ 7:e7686 https://doi.org/10.7717/peerj.7686
date submitted: 2019-03-26
date accepted: 2019-08-19
issued: 2019-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Farghadani
  given name: Reyhaneh
author list: Agent
  family name: Seifaddinipour
  given name: Maryam
author list: Agent
  family name: Rajarajeswaran
  given name: Jayakumar
author list: Agent
  family name: Abdulla
  given name: Mahmood Ameen
author list: Agent
  family name: Mohd Hashim
  given name: Najihah Binti
author list: Agent
  family name: Khaing
  given name: Si Lay
author list: Agent
  family name: Salehen
  given name: Nur’ain Binti
doi: 10.7717/peerj.7686
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-07
copyright: ©2019 Farghadani et al.
attribution name: Farghadani et al.

Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae
type: item
type: AcademicArticle
description: Lindera is a genus (c. 100 spp.) of trees belonging to the “core Laureae” group in the family Lauraceae. It is often confused with Litsea, and the systematics of the genus is unclear. Here, total 10 complete plastomes from nine trinerved Lindera species and another species Lindera obtusiloba (sect. Palminerviae Meissn.) were sequenced. Nine highly variable regions, trnH-GUG/psbA, psbM/trnD-GUC, petA/psbL, ndhF, trnL-UAG/ndhD, and ycf1, were identified among the 10 Lindera species. In addition, a total of 1,836 mutation events including six micro-inversions, 156 indels, and 1,674 substitutions, were also summarized. Comparing our sequences with other available plastomes in the “core Laureae,” we put forward that six hypervariable loci, trnH-GUG/psbA, ndhF, ndhF/rpl32, trl32/trnL-UAG, ndhD, and ycf1, could potentially be used as plastid barcode candidates for species identification. Further phylogenetic analyses were conducted using 49 complete Lauraceae plastomes. The results supported a close relationship among trinerved Lindera species and suggested an improved trinerved group comprising species of trinerved Lindera species and Iteadaphne caudate.
format: application/pdf
format: text/html
creator: Xiangyu Tian
creator: Junwei Ye
creator: Yu Song
subject: Bioinformatics
subject: Conservation Biology
subject: Genetics
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.7662
publisher: PeerJ Inc.
rights: © 2019 Tian et al.
abstract: Lindera is a genus (c. 100 spp.) of trees belonging to the “core Laureae” group in the family Lauraceae. It is often confused with Litsea, and the systematics of the genus is unclear. Here, total 10 complete plastomes from nine trinerved Lindera species and another species Lindera obtusiloba (sect. Palminerviae Meissn.) were sequenced. Nine highly variable regions, trnH-GUG/psbA, psbM/trnD-GUC, petA/psbL, ndhF, trnL-UAG/ndhD, and ycf1, were identified among the 10 Lindera species. In addition, a total of 1,836 mutation events including six micro-inversions, 156 indels, and 1,674 substitutions, were also summarized. Comparing our sequences with other available plastomes in the “core Laureae,” we put forward that six hypervariable loci, trnH-GUG/psbA, ndhF, ndhF/rpl32, trl32/trnL-UAG, ndhD, and ycf1, could potentially be used as plastid barcode candidates for species identification. Further phylogenetic analyses were conducted using 49 complete Lauraceae plastomes. The results supported a close relationship among trinerved Lindera species and suggested an improved trinerved group comprising species of trinerved Lindera species and Iteadaphne caudate.
bibliographic citation: Tian et al. (2019) Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae. PeerJ 7:e7662 https://doi.org/10.7717/peerj.7662
date submitted: 2018-10-02
date accepted: 2019-08-12
issued: 2019-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tian
  given name: Xiangyu
author list: Agent
  family name: Ye
  given name: Junwei
author list: Agent
  family name: Song
  given name: Yu
doi: 10.7717/peerj.7662
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-07
copyright: © 2019 Tian et al.
attribution name: Tian et al.

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