PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The Global Museum: natural history collections and the future of evolutionary science and public education
items: ­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae)
items: LINC00844 promotes proliferation and migration of hepatocellular carcinoma by regulating NDRG1 expression
items: Teenage sleep and technology engagement across the week
items: Metabolic response of Scapharca subcrenata to heat stress using GC/MS-based metabolomics
items: Loss of Schlafen3 influences the expression levels of Schlafen family members in ileum, thymus, and spleen tissue
items: Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis
items: Moderation effects of food intake on the relationship between urinary microbiota and urinary interleukin-8 in female type 2 diabetic patients
items: Crypsis and convergence: integrative taxonomic revision of the Gehyra australis group (Squamata: Gekkonidae) from northern Australia
items: Investigating the effects of management practice on mammalian co-occurrence along the West Coast of South Africa

The Global Museum: natural history collections and the future of evolutionary science and public education
type: item
type: AcademicArticle
description: Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then foc…
format: application/pdf
format: text/html
creator: Freek T. Bakker
creator: Alexandre Antonelli
creator: Julia A. Clarke
creator: Joseph A. Cook
creator: Scott V. Edwards
creator: Per G.P. Ericson
creator: Søren Faurby
creator: Nuno Ferrand
creator: Magnus Gelang
creator: Rosemary G. Gillespie
creator: Martin Irestedt
creator: Kennet Lundin
creator: Ellen Larsson
creator: Pável Matos-Maraví
creator: Johannes Müller
creator: Ted von Proschwitz
creator: George K. Roderick
creator: Alexander Schliep
creator: Niklas Wahlberg
creator: John Wiedenhoeft
creator: Mari Källersjö
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
subject: Science Policy
subject: Biosphere Interactions
description: doi:10.7717/peerj.8225
publisher: PeerJ Inc.
rights: © 2020 Bakker et al.
abstract: Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then foc…
bibliographic citation: Bakker et al. (2020) The Global Museum: natural history collections and the future of evolutionary science and public education. PeerJ 8:e8225 https://doi.org/10.7717/peerj.8225
date submitted: 2019-04-18
date accepted: 2019-11-15
issued: 2020-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bakker
  given name: Freek T.
author list: Agent
  family name: Antonelli
  given name: Alexandre
author list: Agent
  family name: Clarke
  given name: Julia A.
author list: Agent
  family name: Cook
  given name: Joseph A.
author list: Agent
  family name: Edwards
  given name: Scott V.
author list: Agent
  family name: Ericson
  given name: Per G.P.
author list: Agent
  family name: Faurby
  given name: Søren
author list: Agent
  family name: Ferrand
  given name: Nuno
author list: Agent
  family name: Gelang
  given name: Magnus
author list: Agent
  family name: Gillespie
  given name: Rosemary G.
author list: Agent
  family name: Irestedt
  given name: Martin
author list: Agent
  family name: Lundin
  given name: Kennet
author list: Agent
  family name: Larsson
  given name: Ellen
author list: Agent
  family name: Matos-Maraví
  given name: Pável
author list: Agent
  family name: Müller
  given name: Johannes
author list: Agent
  family name: von Proschwitz
  given name: Ted
author list: Agent
  family name: Roderick
  given name: George K.
author list: Agent
  family name: Schliep
  given name: Alexander
author list: Agent
  family name: Wahlberg
  given name: Niklas
author list: Agent
  family name: Wiedenhoeft
  given name: John
author list: Agent
  family name: Källersjö
  given name: Mari
doi: 10.7717/peerj.8225
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-28
copyright: ©2020 Bakker et al.
attribution name: Bakker et al.

­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae)
type: item
type: AcademicArticle
description: Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.
format: application/pdf
format: text/html
creator: Janice Valencia-D
creator: José Murillo-A
creator: Clara Inés Orozco
creator: Carlos Parra-O
creator: Kurt M. Neubig
subject: Bioinformatics
subject: Genomics
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.8392
publisher: PeerJ Inc.
rights: © 2020 Valencia-D. et al.
abstract: Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.
bibliographic citation: Valencia-D et al. (2020) ­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae). PeerJ 8:e8392 https://doi.org/10.7717/peerj.8392
date submitted: 2019-07-23
date accepted: 2019-12-13
issued: 2020-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valencia-D
  given name: Janice
author list: Agent
  family name: Murillo-A
  given name: José
author list: Agent
  family name: Orozco
  given name: Clara Inés
author list: Agent
  family name: Parra-O
  given name: Carlos
author list: Agent
  family name: Neubig
  given name: Kurt M.
doi: 10.7717/peerj.8392
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-28
copyright: ©2020 Valencia-D et al.
attribution name: Valencia-D. et al.

LINC00844 promotes proliferation and migration of hepatocellular carcinoma by regulating NDRG1 expression
type: item
type: AcademicArticle
description: Background Aberrant expression of long noncoding RNAs are implicated in the pathogenesis of human malignancies. LINC00844 expression is dramatically downregulated in prostate cancer, and functional studies have revealed the association between the aberrant expression of LINC00844 and prostate cancer cell invasion and metastasis. However, the function and mechanism of action of LINC00844 in the pathogenesis of hepatocellular carcinoma (HCC) are poorly understood. Methods LINC00844 and N-Myc downstream-regulated 1 (NDRG1) expression in HCC tissues and cell lines was detected with real-time quantitative polymerase chain reaction (RT-qPCR) and western blot analysis. Correlations between LINC00844 expression level and clinicopathological features were investigated using the original data from The Cancer Genome Atlas (TCGA) database. HepG2 and HCCLM9 cell lines were transfected with Lv-LIN00844 virus to obtain LINC00844-overexpressing cell lines. Cell proliferation and cell invasion and migration were examined with the cell counting kit-8 (CCK-8) and transwell assay, respectively. Furthermore, the correlation between LINC00844 and NDRG1 expression was analysed using Pearson’s correlation analysis. Results LINC00844 expression was significantly downregulatedin HCC tissues and cell lines, and a statistical correlation was detected between low LINC00844 expression and sex (Female), advanced American Joint Committee on Cancer (AJCC) stage (III + IV), histological grade (G3 + G4), and vascular invasion (Micro and Macro). In vitro experiments showed that LINC00844 overexpression significantly repressed the proliferation, migration, and invasion of HCC cells. NDRG1 expression was higher in HCC tissues and LINC00844 could partly inhibit the expression of NDRG1.
format: application/pdf
format: text/html
creator: Wei Zhou
creator: Kang Huang
creator: Qiuyan Zhang
creator: Shaojun Ye
creator: Zibiao Zhong
creator: Cheng Zeng
creator: Guizhu Peng
creator: Ling Li
creator: Qifa Ye
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Nephrology
subject: Oncology
description: doi:10.7717/peerj.8394
publisher: PeerJ Inc.
rights: © 2020 Zhou et al.
abstract: Background Aberrant expression of long noncoding RNAs are implicated in the pathogenesis of human malignancies. LINC00844 expression is dramatically downregulated in prostate cancer, and functional studies have revealed the association between the aberrant expression of LINC00844 and prostate cancer cell invasion and metastasis. However, the function and mechanism of action of LINC00844 in the pathogenesis of hepatocellular carcinoma (HCC) are poorly understood. Methods LINC00844 and N-Myc downstream-regulated 1 (NDRG1) expression in HCC tissues and cell lines was detected with real-time quantitative polymerase chain reaction (RT-qPCR) and western blot analysis. Correlations between LINC00844 expression level and clinicopathological features were investigated using the original data from The Cancer Genome Atlas (TCGA) database. HepG2 and HCCLM9 cell lines were transfected with Lv-LIN00844 virus to obtain LINC00844-overexpressing cell lines. Cell proliferation and cell invasion and migration were examined with the cell counting kit-8 (CCK-8) and transwell assay, respectively. Furthermore, the correlation between LINC00844 and NDRG1 expression was analysed using Pearson’s correlation analysis. Results LINC00844 expression was significantly downregulatedin HCC tissues and cell lines, and a statistical correlation was detected between low LINC00844 expression and sex (Female), advanced American Joint Committee on Cancer (AJCC) stage (III + IV), histological grade (G3 + G4), and vascular invasion (Micro and Macro). In vitro experiments showed that LINC00844 overexpression significantly repressed the proliferation, migration, and invasion of HCC cells. NDRG1 expression was higher in HCC tissues and LINC00844 could partly inhibit the expression of NDRG1.
bibliographic citation: Zhou et al. (2020) LINC00844 promotes proliferation and migration of hepatocellular carcinoma by regulating NDRG1 expression. PeerJ 8:e8394 https://doi.org/10.7717/peerj.8394
date submitted: 2019-09-13
date accepted: 2019-12-13
issued: 2020-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Wei
author list: Agent
  family name: Huang
  given name: Kang
author list: Agent
  family name: Zhang
  given name: Qiuyan
author list: Agent
  family name: Ye
  given name: Shaojun
author list: Agent
  family name: Zhong
  given name: Zibiao
author list: Agent
  family name: Zeng
  given name: Cheng
author list: Agent
  family name: Peng
  given name: Guizhu
author list: Agent
  family name: Li
  given name: Ling
author list: Agent
  family name: Ye
  given name: Qifa
doi: 10.7717/peerj.8394
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-28
copyright: ©2020 Zhou et al.
attribution name: Zhou et al.

Teenage sleep and technology engagement across the week
type: item
type: AcademicArticle
description: Background Throughout the developed world, adolescents are growing up with increased access to and engagement with a range of screen-based technologies, allowing them to encounter ideas and people on a global scale from the intimacy of their bedroom. The concerns about digital technologies negatively influencing sleep are therefore especially noteworthy, as sleep has been proven to greatly affect both cognitive and emotional well-being. The associations between digital engagement and adolescent sleep should therefore be carefully investigated in research adhering to the highest methodological standards. This understood, studies published to date have not often done so and have instead focused mainly on data derived from general retrospective self-report questionnaires. The value of this work has been called into question by recent research showing that retrospective questionnaires might fail to accurately measure these variables of interest. Novel and diverse approaches to measurement are therefore necessary for academic study to progress. Methods This study analyses data from 11,884 adolescents included in the UK Millennium Cohort Study to examine the association between digital engagement and adolescent sleep, comparing the relative effects of retrospective self-report vs. time-use diary measures of technology use. By doing so, it provides an empirical lens to understand the effects of digital engagement both throughout the day and before bedtime and adds nuance to a research area primarily relying on retrospective self-report. Results The study finds that there is a small negative association relating digital engagement to adolescent sleep both on weekdays and weekend days (median standardized association βweekday = −0.06 and βweekend = −0.03). There is a more negative association between digital engagement and total sleep time on weekdays compared to weekend days (median standardized βweekday = −0.08, median standardized βweekend = −0.02), while there is no such…
format: application/pdf
format: text/html
creator: Amy Orben
creator: Andrew K. Przybylski
subject: Psychiatry and Psychology
subject: Public Health
subject: Human-Computer Interaction
description: doi:10.7717/peerj.8427
publisher: PeerJ Inc.
rights: © 2020 Orben and Przybylski
abstract: Background Throughout the developed world, adolescents are growing up with increased access to and engagement with a range of screen-based technologies, allowing them to encounter ideas and people on a global scale from the intimacy of their bedroom. The concerns about digital technologies negatively influencing sleep are therefore especially noteworthy, as sleep has been proven to greatly affect both cognitive and emotional well-being. The associations between digital engagement and adolescent sleep should therefore be carefully investigated in research adhering to the highest methodological standards. This understood, studies published to date have not often done so and have instead focused mainly on data derived from general retrospective self-report questionnaires. The value of this work has been called into question by recent research showing that retrospective questionnaires might fail to accurately measure these variables of interest. Novel and diverse approaches to measurement are therefore necessary for academic study to progress. Methods This study analyses data from 11,884 adolescents included in the UK Millennium Cohort Study to examine the association between digital engagement and adolescent sleep, comparing the relative effects of retrospective self-report vs. time-use diary measures of technology use. By doing so, it provides an empirical lens to understand the effects of digital engagement both throughout the day and before bedtime and adds nuance to a research area primarily relying on retrospective self-report. Results The study finds that there is a small negative association relating digital engagement to adolescent sleep both on weekdays and weekend days (median standardized association βweekday = −0.06 and βweekend = −0.03). There is a more negative association between digital engagement and total sleep time on weekdays compared to weekend days (median standardized βweekday = −0.08, median standardized βweekend = −0.02), while there is no such…
bibliographic citation: Orben et al. (2020) Teenage sleep and technology engagement across the week. PeerJ 8:e8427 https://doi.org/10.7717/peerj.8427
date submitted: 2019-08-05
date accepted: 2019-12-18
issued: 2020-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Orben
  given name: Amy
author list: Agent
  family name: Przybylski
  given name: Andrew K.
doi: 10.7717/peerj.8427
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-28
copyright: © 2020 Orben and Przybylski
attribution name: Orben and Przybylski

Metabolic response of Scapharca subcrenata to heat stress using GC/MS-based metabolomics
type: item
type: AcademicArticle
description: Marine mollusks are commonly subjected to heat stress. To evaluate the effects of heat stress on the physiological metabolism of the ark shell Scapharca subcrenata, clams were exposed to different high temperatures (24, 28 and 32 °C) for 72 h. The oxygen consumption and ammonia excretion rates were measured at 2, 12, 24, 48 and 72 h. The results indicated that the metabolic rates of the ark shell significantly increased with increasing heat stress, accompanied by mortalities in response to prolonged exposure. A metabolomics approach based on gas chromatography coupled with mass spectrometry was further applied to assess the changes of metabolites in the mantle of the ark shell at 32 °C. Moreover, multivariate and pathway analyses were conducted for the different metabolites. The results showed that the heat stress caused changes in energy metabolism, amino acid metabolism, osmotic regulation, carbohydrate metabolism and lipid metabolism through different metabolic pathways. These results are consistent with the significant changes of oxygen consumption rate and ammonia excretion rate. The present study contributes to the understanding of the impacts of heat stress on intertidal bivalves and elucidates the relationship between individual-level responses and underlying molecular metabolic dynamics.
format: application/pdf
format: text/html
creator: Yazhou Jiang
creator: Haifeng Jiao
creator: Peng Sun
creator: Fei Yin
creator: Baojun Tang
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.8445
publisher: PeerJ Inc.
rights: © 2020 Jiang et al.
abstract: Marine mollusks are commonly subjected to heat stress. To evaluate the effects of heat stress on the physiological metabolism of the ark shell Scapharca subcrenata, clams were exposed to different high temperatures (24, 28 and 32 °C) for 72 h. The oxygen consumption and ammonia excretion rates were measured at 2, 12, 24, 48 and 72 h. The results indicated that the metabolic rates of the ark shell significantly increased with increasing heat stress, accompanied by mortalities in response to prolonged exposure. A metabolomics approach based on gas chromatography coupled with mass spectrometry was further applied to assess the changes of metabolites in the mantle of the ark shell at 32 °C. Moreover, multivariate and pathway analyses were conducted for the different metabolites. The results showed that the heat stress caused changes in energy metabolism, amino acid metabolism, osmotic regulation, carbohydrate metabolism and lipid metabolism through different metabolic pathways. These results are consistent with the significant changes of oxygen consumption rate and ammonia excretion rate. The present study contributes to the understanding of the impacts of heat stress on intertidal bivalves and elucidates the relationship between individual-level responses and underlying molecular metabolic dynamics.
bibliographic citation: Jiang et al. (2020) Metabolic response of Scapharca subcrenata to heat stress using GC/MS-based metabolomics. PeerJ 8:e8445 https://doi.org/10.7717/peerj.8445
date submitted: 2019-09-05
date accepted: 2019-12-20
issued: 2020-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Yazhou
author list: Agent
  family name: Jiao
  given name: Haifeng
author list: Agent
  family name: Sun
  given name: Peng
author list: Agent
  family name: Yin
  given name: Fei
author list: Agent
  family name: Tang
  given name: Baojun
doi: 10.7717/peerj.8445
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-28
copyright: © 2020 Jiang et al.
attribution name: Jiang et al.

Loss of Schlafen3 influences the expression levels of Schlafen family members in ileum, thymus, and spleen tissue
type: item
type: AcademicArticle
description: Background The Schlafen (Slfn) family proteins are important for regulation of cell growth, cell differentiation and cell cycle progression. We sought to distinguish Slfn family expression in Slfn3 knockout (KO) mice after RNA sequencing analysis of Slfn3KO vs. wildtype (WT) mice revealed varying expressions of Slfn family in ileal mucosa. Methods Quantitative PCR analysis of Slfn members was evaluated in ileal mucosa, thymus and spleen tissue since Slfn family members have roles in differentiating intestinal and immune cells. Results Ileal mucosa of Slfn3KO mice displayed a decrease in Slfn3, 4, 8 and 9 while Slfn1 and 5 increased in mRNA expression vs. WT mice. Thymic tissue had a Slfn9 increase and a Slfn4 decrease while splenic tissue had a Slfn8 and Slfn9 increase in Slfn3KO mice vs. WT mice. These differential expressions of Slfn members could indicate a feedback regulatory mechanism within the Slfn family. Indeed, MATCH™ tool from geneXplain predicted that all Slfn members have regions in their promoters for the Kruppel-like factor-6 transcription factor. In addition, NFAT related factors, ING4, ZNF333 and KLF4 are also predicted to bind in up to 6 of the 8 Slfn promoters. This study further describes a possible autoregulatory mechanism amongst the Slfn family members which could be important in how they regulate the differentiation of various cell types.
format: application/pdf
format: text/html
creator: Emilie E. Vomhof-DeKrey
creator: Josey Umthun
creator: Marc D. Basson
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.8461
publisher: PeerJ Inc.
rights: © 2020 Vomhof-DeKrey et al.
abstract: Background The Schlafen (Slfn) family proteins are important for regulation of cell growth, cell differentiation and cell cycle progression. We sought to distinguish Slfn family expression in Slfn3 knockout (KO) mice after RNA sequencing analysis of Slfn3KO vs. wildtype (WT) mice revealed varying expressions of Slfn family in ileal mucosa. Methods Quantitative PCR analysis of Slfn members was evaluated in ileal mucosa, thymus and spleen tissue since Slfn family members have roles in differentiating intestinal and immune cells. Results Ileal mucosa of Slfn3KO mice displayed a decrease in Slfn3, 4, 8 and 9 while Slfn1 and 5 increased in mRNA expression vs. WT mice. Thymic tissue had a Slfn9 increase and a Slfn4 decrease while splenic tissue had a Slfn8 and Slfn9 increase in Slfn3KO mice vs. WT mice. These differential expressions of Slfn members could indicate a feedback regulatory mechanism within the Slfn family. Indeed, MATCH™ tool from geneXplain predicted that all Slfn members have regions in their promoters for the Kruppel-like factor-6 transcription factor. In addition, NFAT related factors, ING4, ZNF333 and KLF4 are also predicted to bind in up to 6 of the 8 Slfn promoters. This study further describes a possible autoregulatory mechanism amongst the Slfn family members which could be important in how they regulate the differentiation of various cell types.
bibliographic citation: Vomhof-DeKrey et al. (2020) Loss of Schlafen3 influences the expression levels of Schlafen family members in ileum, thymus, and spleen tissue. PeerJ 8:e8461 https://doi.org/10.7717/peerj.8461
date submitted: 2019-10-02
date accepted: 2019-12-26
issued: 2020-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vomhof-DeKrey
  given name: Emilie E.
author list: Agent
  family name: Umthun
  given name: Josey
author list: Agent
  family name: Basson
  given name: Marc D.
doi: 10.7717/peerj.8461
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-28
copyright: © 2020 Vomhof-DeKrey et al.
attribution name: Vomhof-DeKrey et al.

Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis
type: item
type: AcademicArticle
description: The Lhc (light-harvesting chlorophyll a/b-binding protein) superfamily represents a class of antennae proteins that play indispensable roles in capture of solar energy as well as photoprotection under stress conditions. Despite their importance, little information has been available beyond model plants. In this study, we presents a first genome-wide analysis of Lhc superfamily genes in jatropha (Jatropha curcas L., Euphorbiaceae), an oil-bearing plant for biodiesel purpose. A total of 27 members were identified from the jatropha genome, which were shown to distribute over nine out of the 11 chromosomes. The superfamily number is comparable to 28 present in castor (Ricinus communis, Euphorbiaceae), but relatively less than 35 in cassava (Manihot esculenta, Euphorbiaceae) and 34 in arabidopsis (Arabidopsis thaliana) that experienced one or two recent whole-genome duplications (WGDs), respectively. In contrast to a high number of paralogs present in cassava and arabidopsis, few duplicates were found in jatropha as observed in castor, corresponding to no recent WGD occurred in these two species. Nevertheless, 26 orthologous groups representing four defined families were found in jatropha, and nearly one-to-one orthologous relationship was observed between jatropha and castor. By contrast, a novel group named SEP6 was shown to have been lost in arabidopsis. Global transcriptome profiling revealed a predominant expression pattern of most JcLhc superfamily genes in green tissues, reflecting their key roles in photosynthesis. Moreover, their expression profiles upon hormones, drought, and salt stresses were also investigated. These findings not only improve our knowledge on species-specific evolution of the Lhc supergene family, but also provide valuable information for further studies in jatropha.
format: application/pdf
format: text/html
creator: Yongguo Zhao
creator: Hua Kong
creator: Yunling Guo
creator: Zhi Zou
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.8465
publisher: PeerJ Inc.
rights: © 2020 Zhao et al.
abstract: The Lhc (light-harvesting chlorophyll a/b-binding protein) superfamily represents a class of antennae proteins that play indispensable roles in capture of solar energy as well as photoprotection under stress conditions. Despite their importance, little information has been available beyond model plants. In this study, we presents a first genome-wide analysis of Lhc superfamily genes in jatropha (Jatropha curcas L., Euphorbiaceae), an oil-bearing plant for biodiesel purpose. A total of 27 members were identified from the jatropha genome, which were shown to distribute over nine out of the 11 chromosomes. The superfamily number is comparable to 28 present in castor (Ricinus communis, Euphorbiaceae), but relatively less than 35 in cassava (Manihot esculenta, Euphorbiaceae) and 34 in arabidopsis (Arabidopsis thaliana) that experienced one or two recent whole-genome duplications (WGDs), respectively. In contrast to a high number of paralogs present in cassava and arabidopsis, few duplicates were found in jatropha as observed in castor, corresponding to no recent WGD occurred in these two species. Nevertheless, 26 orthologous groups representing four defined families were found in jatropha, and nearly one-to-one orthologous relationship was observed between jatropha and castor. By contrast, a novel group named SEP6 was shown to have been lost in arabidopsis. Global transcriptome profiling revealed a predominant expression pattern of most JcLhc superfamily genes in green tissues, reflecting their key roles in photosynthesis. Moreover, their expression profiles upon hormones, drought, and salt stresses were also investigated. These findings not only improve our knowledge on species-specific evolution of the Lhc supergene family, but also provide valuable information for further studies in jatropha.
bibliographic citation: Zhao et al. (2020) Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis. PeerJ 8:e8465 https://doi.org/10.7717/peerj.8465
date submitted: 2019-08-22
date accepted: 2019-12-27
issued: 2020-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yongguo
author list: Agent
  family name: Kong
  given name: Hua
author list: Agent
  family name: Guo
  given name: Yunling
author list: Agent
  family name: Zou
  given name: Zhi
doi: 10.7717/peerj.8465
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-28
copyright: ©2020 Zhao et al.
attribution name: Zhao et al.

Moderation effects of food intake on the relationship between urinary microbiota and urinary interleukin-8 in female type 2 diabetic patients
type: item
type: AcademicArticle
description: Background Our previous study demonstrated that the composition of the urinary microbiota in female patients with type 2 diabetes mellitus (T2DM) was correlated with the concentration of urinary interleukin (IL)-8. As the composition of urine is mainly determined by diet, diet might mediate the correlation. Methods Seventy female T2DM patients and 70 healthy controls (HCs) were recruited. Midstream urine was used for the urine specimens. Urinary IL-8 was determined by enzyme-linked immunosorbent assay. A Chinese Food Frequency Questionnaire was used to collect food intake data. The independent variables in the hierarchical regression analysis were the relative abundances of the bacterial genera and species that were significantly different between the T2DM and HCs and between the T2DM patients with and without detectable urinary IL-8, and the bacterial genera associated with IL-8 concentration in the multiple regression model reported in our previous research. IL-8 concentration was the dependent variable, and nutrient intakes were moderator variables. Results Fiber and vitamin B3 and E intake exerted enhancing effects, and water intake exerted a buffering effect, on the positive relationship between the relative abundance of Ruminococcus and IL-8 concentration (p < 0.05). Cholesterol and magnesium intake exerted enhancing effects on the positive relationship between the relative abundance of Comamonas and IL-8 concentration (p < 0.05). Conclusion Modulating T2DM patients’ dietary patterns may prevent bladder inflammation.
format: application/pdf
format: text/html
creator: Fengping Liu
creator: Zongxin Ling
creator: Chulei Tang
creator: Fendi Yi
creator: Yong Q. Chen
subject: Microbiology
subject: Diabetes and Endocrinology
subject: Nutrition
subject: Translational Medicine
subject: Urology
description: doi:10.7717/peerj.8481
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: Background Our previous study demonstrated that the composition of the urinary microbiota in female patients with type 2 diabetes mellitus (T2DM) was correlated with the concentration of urinary interleukin (IL)-8. As the composition of urine is mainly determined by diet, diet might mediate the correlation. Methods Seventy female T2DM patients and 70 healthy controls (HCs) were recruited. Midstream urine was used for the urine specimens. Urinary IL-8 was determined by enzyme-linked immunosorbent assay. A Chinese Food Frequency Questionnaire was used to collect food intake data. The independent variables in the hierarchical regression analysis were the relative abundances of the bacterial genera and species that were significantly different between the T2DM and HCs and between the T2DM patients with and without detectable urinary IL-8, and the bacterial genera associated with IL-8 concentration in the multiple regression model reported in our previous research. IL-8 concentration was the dependent variable, and nutrient intakes were moderator variables. Results Fiber and vitamin B3 and E intake exerted enhancing effects, and water intake exerted a buffering effect, on the positive relationship between the relative abundance of Ruminococcus and IL-8 concentration (p < 0.05). Cholesterol and magnesium intake exerted enhancing effects on the positive relationship between the relative abundance of Comamonas and IL-8 concentration (p < 0.05). Conclusion Modulating T2DM patients’ dietary patterns may prevent bladder inflammation.
bibliographic citation: Liu et al. (2020) Moderation effects of food intake on the relationship between urinary microbiota and urinary interleukin-8 in female type 2 diabetic patients. PeerJ 8:e8481 https://doi.org/10.7717/peerj.8481
date submitted: 2019-08-22
date accepted: 2019-12-27
issued: 2020-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Fengping
author list: Agent
  family name: Ling
  given name: Zongxin
author list: Agent
  family name: Tang
  given name: Chulei
author list: Agent
  family name: Yi
  given name: Fendi
author list: Agent
  family name: Chen
  given name: Yong Q.
doi: 10.7717/peerj.8481
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-28
copyright: © 2020 Liu et al.
attribution name: Liu et al.

Crypsis and convergence: integrative taxonomic revision of the Gehyra australis group (Squamata: Gekkonidae) from northern Australia
type: item
type: AcademicArticle
description: For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of lineages, but occasionally do not. In recent years it has become increasingly possible to survey geographic variation by sequencing thousands of loci, enabling more rigorous assessment of species boundaries across morphologically similar lineages. Here we take this approach, adding new, geographically extensive SNP data to existing mtDNA and exon capture datasets for the Gehyra australis and G. koira species complexes of gecko from northern Australia. The combination of exon-based phylogenetics with dense spatial sampling of mitochondrial DNA sequencing, SNP-based tests for introgression at lineage boundaries and newly-collected morphological evidence supports the recognition of nine species, six of which are newly described here. Detection of discrete genetic clusters using new SNP data was especially convincing where candidate taxa were continuously sampled across their distributions up to and across geographic boundaries with analyses revealing no admixture. Some species defined herein appear to be truly cryptic, showing little, if any, diagnostic morphological variation. As these SNP-based approaches are progressively applied, and with all due conservatism, we can expect to see a substantial improvement in our ability to delineate and name cryptic species, especially in taxa for which previous approaches have struggled to resolve taxonomic boundaries.
format: application/pdf
format: text/html
creator: Paul M. Oliver
creator: Audrey Miranda Prasetya
creator: Leonardo G. Tedeschi
creator: Jessica Fenker
creator: Ryan J. Ellis
creator: Paul Doughty
creator: Craig Moritz
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7971
publisher: PeerJ Inc.
rights: © 2020 Oliver et al.
abstract: For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of lineages, but occasionally do not. In recent years it has become increasingly possible to survey geographic variation by sequencing thousands of loci, enabling more rigorous assessment of species boundaries across morphologically similar lineages. Here we take this approach, adding new, geographically extensive SNP data to existing mtDNA and exon capture datasets for the Gehyra australis and G. koira species complexes of gecko from northern Australia. The combination of exon-based phylogenetics with dense spatial sampling of mitochondrial DNA sequencing, SNP-based tests for introgression at lineage boundaries and newly-collected morphological evidence supports the recognition of nine species, six of which are newly described here. Detection of discrete genetic clusters using new SNP data was especially convincing where candidate taxa were continuously sampled across their distributions up to and across geographic boundaries with analyses revealing no admixture. Some species defined herein appear to be truly cryptic, showing little, if any, diagnostic morphological variation. As these SNP-based approaches are progressively applied, and with all due conservatism, we can expect to see a substantial improvement in our ability to delineate and name cryptic species, especially in taxa for which previous approaches have struggled to resolve taxonomic boundaries.
bibliographic citation: Oliver et al. (2020) Crypsis and convergence: integrative taxonomic revision of the Gehyra australis group (Squamata: Gekkonidae) from northern Australia. PeerJ 8:e7971 https://doi.org/10.7717/peerj.7971
date submitted: 2019-05-27
date accepted: 2019-10-01
issued: 2020-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oliver
  given name: Paul M.
author list: Agent
  family name: Prasetya
  given name: Audrey Miranda
author list: Agent
  family name: Tedeschi
  given name: Leonardo G.
author list: Agent
  family name: Fenker
  given name: Jessica
author list: Agent
  family name: Ellis
  given name: Ryan J.
author list: Agent
  family name: Doughty
  given name: Paul
author list: Agent
  family name: Moritz
  given name: Craig
doi: 10.7717/peerj.7971
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-27
copyright: © 2020 Oliver et al.
attribution name: Oliver et al.

Investigating the effects of management practice on mammalian co-occurrence along the West Coast of South Africa
type: item
type: AcademicArticle
description: The subtle and cascading effects (e.g., altered interspecific interactions) that anthropogenic stressors have on local ecological assemblages often go unnoticed but are concerning given their importance in ecosystem function. For example, elimination of buffalo from the Serengeti National Park is suggested to have driven increased abundance of smaller antelope as a result of release from competition. The perceived low abundance of small antelope in the contractual Postberg section of the West Coast National Park (the park) has been an ongoing management concern which has been anecdotally attributed to predation by a mesopredator (the caracal, Caracal caracal). However, we hypothesized that the historical overstocking, and consequent overgrazing by larger-bodied managed ungulates would influence small antelope abundance. Using camera traps, we investigated species co-occurrence and temporal activity between small antelope, managed ungulates and caracals in Postberg as well as another part of the park (Langebaan) and a farm outside of the park. Results suggest that small antelope and managed ungulates have a high degree of temporal overlap (Δ = 0.74, 0.79 and 0.86 for the farm, Langebaan and Postberg respectively), while temporal partitioning between small antelope and caracal is apparent (Δ = 0.59). Further, small antelope and managed ungulates appear to occur independently of one another (SIF = 0.91–1 across areas). Managed ungulates were detected almost three times more frequently on fallow lands when compared to the more vegetated sites within the park suggesting that segregated food/cover resources allow for independent occurrence. Small antelope had a much higher probability of occurrence outside of the protected area (e.g., ψ = 0.192 and 0.486 for steenbok at Postberg, Langebaan compared to 0.841 on the farm), likely due to less variable (more intact) habitat outside of the protected area. There is not sufficient evidence to currently warrant management interve…
format: application/pdf
format: text/html
creator: Deborah Jean Winterton
creator: Nicola J. van Wilgen
creator: Jan A. Venter
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.8184
publisher: PeerJ Inc.
rights: © 2020 Winterton et al.
abstract: The subtle and cascading effects (e.g., altered interspecific interactions) that anthropogenic stressors have on local ecological assemblages often go unnoticed but are concerning given their importance in ecosystem function. For example, elimination of buffalo from the Serengeti National Park is suggested to have driven increased abundance of smaller antelope as a result of release from competition. The perceived low abundance of small antelope in the contractual Postberg section of the West Coast National Park (the park) has been an ongoing management concern which has been anecdotally attributed to predation by a mesopredator (the caracal, Caracal caracal). However, we hypothesized that the historical overstocking, and consequent overgrazing by larger-bodied managed ungulates would influence small antelope abundance. Using camera traps, we investigated species co-occurrence and temporal activity between small antelope, managed ungulates and caracals in Postberg as well as another part of the park (Langebaan) and a farm outside of the park. Results suggest that small antelope and managed ungulates have a high degree of temporal overlap (Δ = 0.74, 0.79 and 0.86 for the farm, Langebaan and Postberg respectively), while temporal partitioning between small antelope and caracal is apparent (Δ = 0.59). Further, small antelope and managed ungulates appear to occur independently of one another (SIF = 0.91–1 across areas). Managed ungulates were detected almost three times more frequently on fallow lands when compared to the more vegetated sites within the park suggesting that segregated food/cover resources allow for independent occurrence. Small antelope had a much higher probability of occurrence outside of the protected area (e.g., ψ = 0.192 and 0.486 for steenbok at Postberg, Langebaan compared to 0.841 on the farm), likely due to less variable (more intact) habitat outside of the protected area. There is not sufficient evidence to currently warrant management interve…
bibliographic citation: Winterton et al. (2020) Investigating the effects of management practice on mammalian co-occurrence along the West Coast of South Africa. PeerJ 8:e8184 https://doi.org/10.7717/peerj.8184
date submitted: 2019-08-15
date accepted: 2019-11-10
issued: 2020-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Winterton
  given name: Deborah Jean
author list: Agent
  family name: van Wilgen
  given name: Nicola J.
author list: Agent
  family name: Venter
  given name: Jan A.
doi: 10.7717/peerj.8184
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-01-27
copyright: ©2020 Winterton et al.
attribution name: Winterton et al.

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