PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effectiveness of various bioreactors for thraustochytrid culture and production (Aurantiochytruim limacinum BUCHAXM 122)
items: First body of evidence suggesting a role of a tankyrase-binding motif (TBM) of vinculin (VCL) in epithelial cells
items: Identification of key microRNAs and the underlying molecular mechanism in spinal cord ischemia-reperfusion injury in rats
items: Identification of potential gene signatures associated with osteosarcoma by integrated bioinformatics analysis
items: Bracon wasps for ecological pest control–a laboratory experiment
items: https://peerj.com/articles/11291
items: New insight into the divergent responses of plants to warming in the context of root endophytic bacterial and fungal communities
items: https://peerj.com/articles/11417
items: Key circular RNAs identified in male osteoporosis patients by whole transcriptome sequencing
items: Integrative species delimitation based on COI, ITS, and morphological evidence illustrates a unique evolutionary history of the genus Paracercion (Odonata: Coenagrionidae)

Effectiveness of various bioreactors for thraustochytrid culture and production (Aurantiochytruim limacinum BUCHAXM 122)
type: item
type: AcademicArticle
description: This study aimed to develop bioreactors for cultivation of thraustochytrid, Aurantiochytrium limacinum BUCHAXM 122, that are low in cost and simple to operate. Obtaining maximum biomass and fatty acid production was a prerequisite. Three bioreactor designs were used: stirred tank bioreactor (STB), bubble bioreactor (BB) and internal loop airlift bioreactor (ILAB). The bioreactors were evaluated for their influence on oxygen mass transfer coefficient (kLa), using various spargers, mixing speed, and aeration rates. Biomass and DHA production from STB, BB, ILAB were then compared with an incubator shaker, using batch culture experiments. Results showed that a bundle of eight super-fine pore air stones was the best type of aeration sparger for all three bioreactors. Optimal culture conditions in STB were 600 rpm agitation speed and 2 vvm aeration rate, while 2 vvm and 1.5 vvm aeration provided highest biomass productivity in BB and ILAB, respectively. Antifoam agent was needed for all reactor types in order to reduce excessive foaming. Results indicated that with optimized conditions, these bioreactors are capable of thraustochytrid cultivation with a similar efficiency as cultivation using a rotary shaker. STB had the highest kLa and provided the highest biomass of 43.05 ± 0.35 g/L at 48 h. BB was simple in design, had low operating costs and was easy to build, but yielded the lowest biomass (27.50 ± 1.56 g/L). ILAB, on the other hand, had lower kLa than STB, but provided highest fatty acid productivity, of 35.36 ± 2.51% TFA.
format: application/pdf
format: text/html
creator: Khanoksinee Sirirak
creator: Sorawit Powtongsook
creator: Sudarat Suanjit
creator: Somtawin Jaritkhuan
subject: Biotechnology
subject: Cell Biology
subject: Microbiology
description: doi:10.7717/peerj.11405
publisher: PeerJ Inc.
rights: © 2021 Sirirak et al.
abstract: This study aimed to develop bioreactors for cultivation of thraustochytrid, Aurantiochytrium limacinum BUCHAXM 122, that are low in cost and simple to operate. Obtaining maximum biomass and fatty acid production was a prerequisite. Three bioreactor designs were used: stirred tank bioreactor (STB), bubble bioreactor (BB) and internal loop airlift bioreactor (ILAB). The bioreactors were evaluated for their influence on oxygen mass transfer coefficient (kLa), using various spargers, mixing speed, and aeration rates. Biomass and DHA production from STB, BB, ILAB were then compared with an incubator shaker, using batch culture experiments. Results showed that a bundle of eight super-fine pore air stones was the best type of aeration sparger for all three bioreactors. Optimal culture conditions in STB were 600 rpm agitation speed and 2 vvm aeration rate, while 2 vvm and 1.5 vvm aeration provided highest biomass productivity in BB and ILAB, respectively. Antifoam agent was needed for all reactor types in order to reduce excessive foaming. Results indicated that with optimized conditions, these bioreactors are capable of thraustochytrid cultivation with a similar efficiency as cultivation using a rotary shaker. STB had the highest kLa and provided the highest biomass of 43.05 ± 0.35 g/L at 48 h. BB was simple in design, had low operating costs and was easy to build, but yielded the lowest biomass (27.50 ± 1.56 g/L). ILAB, on the other hand, had lower kLa than STB, but provided highest fatty acid productivity, of 35.36 ± 2.51% TFA.
bibliographic citation: Sirirak et al. (2021) Effectiveness of various bioreactors for thraustochytrid culture and production (Aurantiochytruim limacinum BUCHAXM 122). PeerJ 9:e11405 https://doi.org/10.7717/peerj.11405
date submitted: 2020-10-30
date accepted: 2021-04-14
issued: 2021-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sirirak
  given name: Khanoksinee
author list: Agent
  family name: Powtongsook
  given name: Sorawit
author list: Agent
  family name: Suanjit
  given name: Sudarat
author list: Agent
  family name: Jaritkhuan
  given name: Somtawin
doi: 10.7717/peerj.11405
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-27
copyright: © 2021 Sirirak et al.
attribution name: Sirirak et al.

First body of evidence suggesting a role of a tankyrase-binding motif (TBM) of vinculin (VCL) in epithelial cells
type: item
type: AcademicArticle
description: Background Adherens junctions (AJ) are involved in cancer, infections and neurodegeneration. Still, their composition has not been completely disclosed. Poly(ADP-ribose) polymerases (PARPs) catalyze the synthesis of poly(ADP-ribose) (PAR) as a posttranslational modification. Four PARPs synthesize PAR, namely PARP-1/2 and Tankyrase-1/2 (TNKS). In the epithelial belt, AJ are accompanied by a PAR belt and a subcortical F-actin ring. F-actin depolymerization alters the AJ and PAR belts while PARP inhibitors prevent the assembly of the AJ belt and cortical actin. We wondered which PARP synthesizes the belt and which is the PARylation target protein. Vinculin (VCL) participates in the anchorage of F-actin to the AJ, regulating its functions, and colocalized with the PAR belt. TNKS has been formerly involved in the assembly of epithelial cell junctions. Hypothesis TNKS poly(ADP-ribosylates) (PARylates) epithelial belt VCL, affecting its functions in AJ, including cell shape maintenance. Materials and Methods Tankyrase-binding motif (TBM) sequences in hVCL gene were identified and VCL sequences from various vertebrates, Drosophila melanogaster and Caenorhabditis elegans were aligned and compared. Plasma membrane-associated PAR was tested by immunocytofluorescence (ICF) and subcellular fractionation in Vero cells while TNKS role in this structure and cell junction assembly was evaluated using specific inhibitors. The identity of the PARylated proteins was tested by affinity precipitation with PAR-binding reagent followed by western blots. Finally, MCF-7 human breast cancer epithelial cells were subjected to transfection with Tol2-plasmids, carrying a dicistronic expression sequence including Gallus gallus wt VCL (Tol-2-GgVCL), or the same VCL gene with a point mutation in TBM-II (Tol2-GgVCL/*TBM) under the control of a β-actin promoter, plus green fluorescent protein following an internal ribosome entry site (IRES-GFP) to allow the identification of transfected cells without…
format: application/pdf
format: text/html
creator: Salomé Vilchez Larrea
creator: Wanda Mariela Valsecchi
creator: Silvia H. Fernández Villamil
creator: Laura I. Lafon Hughes
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.11442
publisher: PeerJ Inc.
rights: © 2021 Vilchez Larrea et al.
abstract: Background Adherens junctions (AJ) are involved in cancer, infections and neurodegeneration. Still, their composition has not been completely disclosed. Poly(ADP-ribose) polymerases (PARPs) catalyze the synthesis of poly(ADP-ribose) (PAR) as a posttranslational modification. Four PARPs synthesize PAR, namely PARP-1/2 and Tankyrase-1/2 (TNKS). In the epithelial belt, AJ are accompanied by a PAR belt and a subcortical F-actin ring. F-actin depolymerization alters the AJ and PAR belts while PARP inhibitors prevent the assembly of the AJ belt and cortical actin. We wondered which PARP synthesizes the belt and which is the PARylation target protein. Vinculin (VCL) participates in the anchorage of F-actin to the AJ, regulating its functions, and colocalized with the PAR belt. TNKS has been formerly involved in the assembly of epithelial cell junctions. Hypothesis TNKS poly(ADP-ribosylates) (PARylates) epithelial belt VCL, affecting its functions in AJ, including cell shape maintenance. Materials and Methods Tankyrase-binding motif (TBM) sequences in hVCL gene were identified and VCL sequences from various vertebrates, Drosophila melanogaster and Caenorhabditis elegans were aligned and compared. Plasma membrane-associated PAR was tested by immunocytofluorescence (ICF) and subcellular fractionation in Vero cells while TNKS role in this structure and cell junction assembly was evaluated using specific inhibitors. The identity of the PARylated proteins was tested by affinity precipitation with PAR-binding reagent followed by western blots. Finally, MCF-7 human breast cancer epithelial cells were subjected to transfection with Tol2-plasmids, carrying a dicistronic expression sequence including Gallus gallus wt VCL (Tol-2-GgVCL), or the same VCL gene with a point mutation in TBM-II (Tol2-GgVCL/*TBM) under the control of a β-actin promoter, plus green fluorescent protein following an internal ribosome entry site (IRES-GFP) to allow the identification of transfected cells without…
bibliographic citation: Vilchez Larrea et al. (2021) First body of evidence suggesting a role of a tankyrase-binding motif (TBM) of vinculin (VCL) in epithelial cells. PeerJ 9:e11442 https://doi.org/10.7717/peerj.11442
date submitted: 2020-11-23
date accepted: 2021-04-21
issued: 2021-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vilchez Larrea
  given name: Salomé
author list: Agent
  family name: Valsecchi
  given name: Wanda Mariela
author list: Agent
  family name: Fernández Villamil
  given name: Silvia H.
author list: Agent
  family name: Lafon Hughes
  given name: Laura I.
doi: 10.7717/peerj.11442
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-27
copyright: © 2021 Vilchez Larrea et al.
attribution name: Vilchez Larrea et al.

Identification of key microRNAs and the underlying molecular mechanism in spinal cord ischemia-reperfusion injury in rats
type: item
type: AcademicArticle
description: Spinal cord ischemia-reperfusion injury (SCII) is a pathological process with severe complications such as paraplegia and paralysis. Aberrant miRNA expression is involved in the development of SCII. Differences in the experimenters, filtering conditions, control selection, and sequencing platform may lead to different miRNA expression results. This study systematically analyzes the available SCII miRNA expression data to explore the key differently expressed miRNAs (DEmiRNAs) and the underlying molecular mechanism in SCII. A systematic bioinformatics analysis was performed on 23 representative rat SCII miRNA datasets from PubMed. The target genes of key DEmiRNAs were predicted on miRDB. The DAVID and TFactS databases were utilized for functional enrichment and transcription factor binding analyses. In this study, 19 key DEmiRNAs involved in SCII were identified, 9 of which were upregulated (miR-144-3p, miR-3568, miR-204, miR-30c, miR-34c-3p, miR-155-3p, miR-200b, miR-463, and miR-760-5p) and 10 downregulated (miR-28-5p, miR-21-5p, miR-702-3p, miR-291a-3p, miR-199a-3p, miR-352, miR-743b-3p, miR-125b-2-3p, miR-129-1-3p, and miR-136). KEGG enrichment analysis on the target genes of the upregulated DEmiRNAs revealed that the involved pathways were mainly the cGMP-PKG and cAMP signaling pathways. KEGG enrichment analysis on the target genes of the downregulated DEmiRNAs revealed that the involved pathways were mainly the Chemokine and MAPK signaling pathways. GO enrichment analysis indicated that the target genes of the upregulated DEmiRNAs were markedly enriched in biological processes such as brain development and the positive regulation of transcription from RNA polymerase II promoter. Target genes of the downregulated DEmiRNAs were mainly enriched in biological processes such as intracellular signal transduction and negative regulation of cell proliferation. According to the transcription factor analysis, the four transcription factors, including SP1, GLI1, GLI2, and…
format: application/pdf
format: text/html
creator: Fengshou Chen
creator: Jie Han
creator: Dan Wang
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Neuroscience
subject: Neurology
description: doi:10.7717/peerj.11454
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Spinal cord ischemia-reperfusion injury (SCII) is a pathological process with severe complications such as paraplegia and paralysis. Aberrant miRNA expression is involved in the development of SCII. Differences in the experimenters, filtering conditions, control selection, and sequencing platform may lead to different miRNA expression results. This study systematically analyzes the available SCII miRNA expression data to explore the key differently expressed miRNAs (DEmiRNAs) and the underlying molecular mechanism in SCII. A systematic bioinformatics analysis was performed on 23 representative rat SCII miRNA datasets from PubMed. The target genes of key DEmiRNAs were predicted on miRDB. The DAVID and TFactS databases were utilized for functional enrichment and transcription factor binding analyses. In this study, 19 key DEmiRNAs involved in SCII were identified, 9 of which were upregulated (miR-144-3p, miR-3568, miR-204, miR-30c, miR-34c-3p, miR-155-3p, miR-200b, miR-463, and miR-760-5p) and 10 downregulated (miR-28-5p, miR-21-5p, miR-702-3p, miR-291a-3p, miR-199a-3p, miR-352, miR-743b-3p, miR-125b-2-3p, miR-129-1-3p, and miR-136). KEGG enrichment analysis on the target genes of the upregulated DEmiRNAs revealed that the involved pathways were mainly the cGMP-PKG and cAMP signaling pathways. KEGG enrichment analysis on the target genes of the downregulated DEmiRNAs revealed that the involved pathways were mainly the Chemokine and MAPK signaling pathways. GO enrichment analysis indicated that the target genes of the upregulated DEmiRNAs were markedly enriched in biological processes such as brain development and the positive regulation of transcription from RNA polymerase II promoter. Target genes of the downregulated DEmiRNAs were mainly enriched in biological processes such as intracellular signal transduction and negative regulation of cell proliferation. According to the transcription factor analysis, the four transcription factors, including SP1, GLI1, GLI2, and…
bibliographic citation: Chen et al. (2021) Identification of key microRNAs and the underlying molecular mechanism in spinal cord ischemia-reperfusion injury in rats. PeerJ 9:e11454 https://doi.org/10.7717/peerj.11454
date submitted: 2020-11-17
date accepted: 2021-04-23
issued: 2021-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Fengshou
author list: Agent
  family name: Han
  given name: Jie
author list: Agent
  family name: Wang
  given name: Dan
doi: 10.7717/peerj.11454
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-27
copyright: © 2021 Chen et al.
attribution name: Chen et al.

Identification of potential gene signatures associated with osteosarcoma by integrated bioinformatics analysis
type: item
type: AcademicArticle
description: Background Osteosarcoma (OS) is the most primary malignant bone cancer in children and adolescents with a high mortality rate. This work aims to screen novel potential gene signatures associated with OS by integrated microarray analysis of the Gene Expression Omnibus (GEO) database. Material and Methods The OS microarray datasets were searched and downloaded from GEO database to identify differentially expressed genes (DEGs) between OS and normal samples. Afterwards, the functional enrichment analysis, protein–protein interaction (PPI) network analysis and transcription factor (TF)-target gene regulatory network were applied to uncover the biological function of DEGs. Finally, two published OS datasets (GSE39262 and GSE126209) were obtained from GEO database for evaluating the expression level and diagnostic values of key genes. Results In total 1,059 DEGs (569 up-regulated DEGs and 490 down-regulated DEGs) between OS and normal samples were screened. Functional analysis showed that these DEGs were markedly enriched in 214 GO terms and 54 KEGG pathways such as pathways in cancer. Five genes (CAMP, METTL7A, TCN1, LTF and CXCL12) acted as hub genes in PPI network. Besides, METTL7A, CYP4F3, TCN1, LTF and NETO2 were key genes in TF-gene network. Moreover, Pax-6 regulated four key genes (TCN1, CYP4F3, NETO2 and CXCL12). The expression levels of four genes (METTL7A, TCN1, CXCL12 and NETO2) in GSE39262 set were consistent with our integration analysis. The expression levels of two genes (CXCL12 and NETO2) in GSE126209 set were consistent with our integration analysis. ROC analysis of GSE39262 set revealed that CYP4F3, CXCL12, METTL7A, TCN1 and NETO2 had good diagnostic values for OS patients. ROC analysis of GSE126209 set revealed that CXCL12, METTL7A, TCN1 and NETO2 had good diagnostic values for OS patients.
format: application/pdf
format: text/html
creator: Yutao Jia
creator: Yang Liu
creator: Zhihua Han
creator: Rong Tian
subject: Bioinformatics
subject: Oncology
subject: Orthopedics
subject: Rheumatology
subject: Medical Genetics
description: doi:10.7717/peerj.11496
publisher: PeerJ Inc.
rights: © 2021 Jia et al.
abstract: Background Osteosarcoma (OS) is the most primary malignant bone cancer in children and adolescents with a high mortality rate. This work aims to screen novel potential gene signatures associated with OS by integrated microarray analysis of the Gene Expression Omnibus (GEO) database. Material and Methods The OS microarray datasets were searched and downloaded from GEO database to identify differentially expressed genes (DEGs) between OS and normal samples. Afterwards, the functional enrichment analysis, protein–protein interaction (PPI) network analysis and transcription factor (TF)-target gene regulatory network were applied to uncover the biological function of DEGs. Finally, two published OS datasets (GSE39262 and GSE126209) were obtained from GEO database for evaluating the expression level and diagnostic values of key genes. Results In total 1,059 DEGs (569 up-regulated DEGs and 490 down-regulated DEGs) between OS and normal samples were screened. Functional analysis showed that these DEGs were markedly enriched in 214 GO terms and 54 KEGG pathways such as pathways in cancer. Five genes (CAMP, METTL7A, TCN1, LTF and CXCL12) acted as hub genes in PPI network. Besides, METTL7A, CYP4F3, TCN1, LTF and NETO2 were key genes in TF-gene network. Moreover, Pax-6 regulated four key genes (TCN1, CYP4F3, NETO2 and CXCL12). The expression levels of four genes (METTL7A, TCN1, CXCL12 and NETO2) in GSE39262 set were consistent with our integration analysis. The expression levels of two genes (CXCL12 and NETO2) in GSE126209 set were consistent with our integration analysis. ROC analysis of GSE39262 set revealed that CYP4F3, CXCL12, METTL7A, TCN1 and NETO2 had good diagnostic values for OS patients. ROC analysis of GSE126209 set revealed that CXCL12, METTL7A, TCN1 and NETO2 had good diagnostic values for OS patients.
bibliographic citation: Jia et al. (2021) Identification of potential gene signatures associated with osteosarcoma by integrated bioinformatics analysis. PeerJ 9:e11496 https://doi.org/10.7717/peerj.11496
date submitted: 2020-07-01
date accepted: 2021-04-30
issued: 2021-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jia
  given name: Yutao
author list: Agent
  family name: Liu
  given name: Yang
author list: Agent
  family name: Han
  given name: Zhihua
author list: Agent
  family name: Tian
  given name: Rong
doi: 10.7717/peerj.11496
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-27
copyright: ©2021 Jia et al.
attribution name: Jia et al.

Bracon wasps for ecological pest control–a laboratory experiment
type: item
type: AcademicArticle
description: Biological control of pest insects by natural enemies may be an effective, cheap and environmentally friendly alternative to synthetic pesticides. The cosmopolitan parasitoid wasp species Bracon brevicornis Wesmael and B. hebetor Say (Hymenoptera: Braconidae) use lepidopteran species as hosts, including insect pests like Ephestia kuehniella or Ostrinia nubilalis. Here, we compare the reproductive success of both Bracon species on E. kuehniella in a laboratory experiment. We asked (1) how the reproductive success on a single host larva changes with temperature, (2) how it changes with temperature when more host larvae are present and (3) how temperature and availability of host larvae influence the efficacy of Bracon species as biological control agents. In general, differences between B. brevicornis and B. hebetor have been small. For rearing both Bracon species in the laboratory on one host larva, a temperature between 20–27 °C seems appropriate to obtain the highest number of offspring with a female-biased sex ratio. Rearing the braconid wasps on more than one host larva revealed a higher number of total offspring but less offspring per host larva on average. Again, highest numbers of offspring hatched at 27 °C and the sex ratio was independent from temperature. Although no parasitoids hatched at 12 °C and only few at 36 °C, host larvae were still paralyzed. The efficacy of B. brevicornis was higher than 80% at all numbers of host larvae presented at all temperatures while the efficacy of B. hebetor was less than 80% at 12 °C and 27 °C at low numbers of host larvae presented. In conclusion, practitioners can use either B. brevicornis or B. hebetor at low and high temperatures and at varying host densities to achieve high pest control efficacy.
format: application/pdf
format: text/html
creator: Jessica Lettmann
creator: Karsten Mody
creator: Tore-Aliocha Kursch-Metz
creator: Nico Blüthgen
creator: Katja Wehner
subject: Agricultural Science
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.11540
publisher: PeerJ Inc.
rights: © 2021 Lettmann et al.
abstract: Biological control of pest insects by natural enemies may be an effective, cheap and environmentally friendly alternative to synthetic pesticides. The cosmopolitan parasitoid wasp species Bracon brevicornis Wesmael and B. hebetor Say (Hymenoptera: Braconidae) use lepidopteran species as hosts, including insect pests like Ephestia kuehniella or Ostrinia nubilalis. Here, we compare the reproductive success of both Bracon species on E. kuehniella in a laboratory experiment. We asked (1) how the reproductive success on a single host larva changes with temperature, (2) how it changes with temperature when more host larvae are present and (3) how temperature and availability of host larvae influence the efficacy of Bracon species as biological control agents. In general, differences between B. brevicornis and B. hebetor have been small. For rearing both Bracon species in the laboratory on one host larva, a temperature between 20–27 °C seems appropriate to obtain the highest number of offspring with a female-biased sex ratio. Rearing the braconid wasps on more than one host larva revealed a higher number of total offspring but less offspring per host larva on average. Again, highest numbers of offspring hatched at 27 °C and the sex ratio was independent from temperature. Although no parasitoids hatched at 12 °C and only few at 36 °C, host larvae were still paralyzed. The efficacy of B. brevicornis was higher than 80% at all numbers of host larvae presented at all temperatures while the efficacy of B. hebetor was less than 80% at 12 °C and 27 °C at low numbers of host larvae presented. In conclusion, practitioners can use either B. brevicornis or B. hebetor at low and high temperatures and at varying host densities to achieve high pest control efficacy.
bibliographic citation: Lettmann et al. (2021) Bracon wasps for ecological pest control–a laboratory experiment. PeerJ 9:e11540 https://doi.org/10.7717/peerj.11540
date submitted: 2021-02-01
date accepted: 2021-05-10
issued: 2021-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lettmann
  given name: Jessica
author list: Agent
  family name: Mody
  given name: Karsten
author list: Agent
  family name: Kursch-Metz
  given name: Tore-Aliocha
author list: Agent
  family name: Blüthgen
  given name: Nico
author list: Agent
  family name: Wehner
  given name: Katja
doi: 10.7717/peerj.11540
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-27
copyright: © 2021 Lettmann et al.
attribution name: Lettmann et al.

https://peerj.com/articles/11291
type: item
type: AcademicArticle
title: The effect of a brown-rice diets on glycemic control and metabolic parameters in prediabetes and type 2 diabetes mellitus: a meta-analysis of randomized controlled trials and controlled clinical trials
description: Background Brown rice is a whole-grain food that is often assumed to have a lower glycemic index compared to white rice. A few studies have objectively confirmed the effect of a brown-rice diet on glycemic control and metabolic parameters compared to a white-rice diet. The purpose of this study is to determine the effect of brown rice on improving glycemic control and metabolic parameters in prediabetes and type 2 diabetes. The researchers conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) and controlled clinical trials. Methods PRISMA guidelines were used as the basis of this systematic review. Relevant studies were identified by searching the following databases: Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE (PubMed), as well as Epistemonikos for randomized controlled trials (RCTs) and controlled clinical trials published not later than January 2021 involving adults with prediabetes and diabetes mellitus who were consuming brown rice compared to those consuming white rice. The primary outcomes measured were glycated hemoglobin (HbA1c) and fasting blood glucose (FBG) levels. The secondary outcomes were body weight, waist circumference, systolic and diastolic blood pressure levels, LDL and HDL-cholesterol levels. The mean differences (MDs) with 95% confidence intervals (CIs) between brown and white-rice-diet groups were calculated using a random-effects model. Results Seven trials involving 417 adults with prediabetes or type 2 diabetes were included in this study. Brown-rice diet did not improve the glycemic control because it had no effect on the HbA1c level (p = 0.15) and the FBG level (p = 0.95) compared to white-rice diet. Brown-rice diet reduced body weight (p < 0.00001; MD −2.2 kg; 95% CI [−3.13 to −1.26]; I2 = 0%). However, it had no effect on the waist circumference (p = 0.09), systolic blood pressure (p = 0.60) and diastolic blood pressure level (p = 0.40). HDL-cholesterol level is increased in brown-…
format: application/pdf
format: text/html
creator: Anis Farhanah Abdul Rahim
creator: Mohd Noor Norhayati
creator: Aida Maziha Zainudin
subject: Clinical Trials
subject: Diabetes and Endocrinology
subject: Nutrition
description: doi:10.7717/peerj.11291
publisher: PeerJ Inc.
rights: © 2021 Abdul Rahim et al.
abstract: Background Brown rice is a whole-grain food that is often assumed to have a lower glycemic index compared to white rice. A few studies have objectively confirmed the effect of a brown-rice diet on glycemic control and metabolic parameters compared to a white-rice diet. The purpose of this study is to determine the effect of brown rice on improving glycemic control and metabolic parameters in prediabetes and type 2 diabetes. The researchers conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) and controlled clinical trials. Methods PRISMA guidelines were used as the basis of this systematic review. Relevant studies were identified by searching the following databases: Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE (PubMed), as well as Epistemonikos for randomized controlled trials (RCTs) and controlled clinical trials published not later than January 2021 involving adults with prediabetes and diabetes mellitus who were consuming brown rice compared to those consuming white rice. The primary outcomes measured were glycated hemoglobin (HbA1c) and fasting blood glucose (FBG) levels. The secondary outcomes were body weight, waist circumference, systolic and diastolic blood pressure levels, LDL and HDL-cholesterol levels. The mean differences (MDs) with 95% confidence intervals (CIs) between brown and white-rice-diet groups were calculated using a random-effects model. Results Seven trials involving 417 adults with prediabetes or type 2 diabetes were included in this study. Brown-rice diet did not improve the glycemic control because it had no effect on the HbA1c level (p = 0.15) and the FBG level (p = 0.95) compared to white-rice diet. Brown-rice diet reduced body weight (p < 0.00001; MD −2.2 kg; 95% CI [−3.13 to −1.26]; I2 = 0%). However, it had no effect on the waist circumference (p = 0.09), systolic blood pressure (p = 0.60) and diastolic blood pressure level (p = 0.40). HDL-cholesterol level is increased in brown-…
bibliographic citation: Abdul Rahim et al. (2021) The effect of a brown-rice diets on glycemic control and metabolic parameters in prediabetes and type 2 diabetes mellitus: a meta-analysis of randomized controlled trials and controlled clinical trials. PeerJ 9:e11291 https://doi.org/10.7717/peerj.11291
date submitted: 2020-09-22
date accepted: 2021-03-26
issued: 2021-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdul Rahim
  given name: Anis Farhanah
author list: Agent
  family name: Norhayati
  given name: Mohd Noor
author list: Agent
  family name: Zainudin
  given name: Aida Maziha
doi: 10.7717/peerj.11291
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-26
copyright: ©2021 Abdul Rahim et al.
attribution name: Abdul Rahim et al.

New insight into the divergent responses of plants to warming in the context of root endophytic bacterial and fungal communities
type: item
type: AcademicArticle
description: Plant adaptation under climate changes is critical to the maintenance of terrestrial ecosystem structure and function. Studying the response of the endophytic community to climate warming is a novel way to reveal the mechanism of host environmental adaptability because of the prominent role endophytes play in host nutrient acquisition and stress tolerance. However, host performance was generally neglected in previous relevant research, which limits our understanding of the relationships between the endophytic community and host responses to climate warming. The present study selected two plants with different responses to climate warming. Elymus nutans is more suitable for growing in warm environments at low altitude compared to Kobresia pygmaea. K. pygmaea and E. nutans were sampled along an altitude gradient in the natural grassland of Qinghai-Tibet Plateau, China. Root endophytic bacterial and fungal communities were analyzed using high throughput sequencing. The results revealed that hosts growing in more suitable habitats held higher endophytic fungal diversity. Elevation and host identity significantly affected the composition of the root endophytic bacterial and fungal community. 16S rRNA functional prediction demonstrated that hosts that adapted to lower temperatures recruited endophytic communities with higher abundance of genes related to cold resistance. Hosts that were more suitable for warmer and drier environments recruited endophytes with higher abundance of genes associated with nutrient absorption and oxidation resistance. We associated changes in the endophytic community with hosts adaptability to climate warming and suggested a synchronism of endophytic communities and hosts in environmental adaptation.
format: application/pdf
format: text/html
creator: Xiaoting Wei
creator: Fengyan Jiang
creator: Bing Han
creator: Hui Zhang
creator: Ding Huang
creator: Xinqing Shao
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.11340
publisher: PeerJ Inc.
rights: © 2021 Wei et al.
abstract: Plant adaptation under climate changes is critical to the maintenance of terrestrial ecosystem structure and function. Studying the response of the endophytic community to climate warming is a novel way to reveal the mechanism of host environmental adaptability because of the prominent role endophytes play in host nutrient acquisition and stress tolerance. However, host performance was generally neglected in previous relevant research, which limits our understanding of the relationships between the endophytic community and host responses to climate warming. The present study selected two plants with different responses to climate warming. Elymus nutans is more suitable for growing in warm environments at low altitude compared to Kobresia pygmaea. K. pygmaea and E. nutans were sampled along an altitude gradient in the natural grassland of Qinghai-Tibet Plateau, China. Root endophytic bacterial and fungal communities were analyzed using high throughput sequencing. The results revealed that hosts growing in more suitable habitats held higher endophytic fungal diversity. Elevation and host identity significantly affected the composition of the root endophytic bacterial and fungal community. 16S rRNA functional prediction demonstrated that hosts that adapted to lower temperatures recruited endophytic communities with higher abundance of genes related to cold resistance. Hosts that were more suitable for warmer and drier environments recruited endophytes with higher abundance of genes associated with nutrient absorption and oxidation resistance. We associated changes in the endophytic community with hosts adaptability to climate warming and suggested a synchronism of endophytic communities and hosts in environmental adaptation.
bibliographic citation: Wei et al. (2021) New insight into the divergent responses of plants to warming in the context of root endophytic bacterial and fungal communities. PeerJ 9:e11340 https://doi.org/10.7717/peerj.11340
date submitted: 2021-01-06
date accepted: 2021-04-03
issued: 2021-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Xiaoting
author list: Agent
  family name: Jiang
  given name: Fengyan
author list: Agent
  family name: Han
  given name: Bing
author list: Agent
  family name: Zhang
  given name: Hui
author list: Agent
  family name: Huang
  given name: Ding
author list: Agent
  family name: Shao
  given name: Xinqing
doi: 10.7717/peerj.11340
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-26
copyright: ©2021 Wei et al.
attribution name: Wei et al.

https://peerj.com/articles/11417
type: item
type: AcademicArticle
title: Only two out of five articles by New Zealand researchers are free-to-access: a multiple API study of access, citations, cost of Article Processing Charges (APC), and the potential to increase the proportion of open access
description: We studied journal articles published by researchers at all eight New Zealand universities in 2017 to determine how many were freely accessible on the web. We wrote software code to harvest data from multiple sources, code that we now share to enable others to reproduce our work on their own sample set. In May 2019, we ran our code to determine which of the 2017 articles were open at that time and by what method; where those articles would have incurred an Article Processing Charge (APC) we calculated the cost if those charges had been paid. Where articles were not freely available we determined whether the policies of publishers in each case would have allowed deposit in a non-commercial repository (Green open access). We also examined citation rates for different types of access. We found that, of our 2017 sample set, about two out of every five articles were freely accessible without payment or subscription (41%). Where research was explicitly said to be funded by New Zealand’s major research funding agencies, the proportion was slightly higher at 45%. Where open articles would have incurred an APC we estimated an average cost per article of USD1,682 (for publications where all articles require an APC, that is, Gold open access) and USD2,558 (where APC payment is optional, Hybrid open access) at a total estimated cost of USD1.45m. Of the paid options, Gold is by far more common for New Zealand researchers (82% Gold, 18% Hybrid). In terms of citations, our analysis aligned with previous studies that suggest a correlation between publications being freely accessible and, on balance, slightly higher rates of citation. This is not seen across all types of open access, however, with Diamond OA achieving the lowest rates. Where articles were not freely accessible we found that a very large majority of them (88% or 3089 publications) could have been legally deposited in an institutional repository. Similarly, only in a very small number of cases had a version deposited …
format: application/pdf
format: text/html
creator: Richard K.A. White
creator: Anton Angelo
creator: Deborah Fitchett
creator: Moira Fraser
creator: Luqman Hayes
creator: Jessica Howie
creator: Emma Richardson
creator: Bruce White
subject: Legal Issues
subject: Science Policy
subject: Computational Science
description: doi:10.7717/peerj.11417
publisher: PeerJ Inc.
rights: © 2021 White et al.
abstract: We studied journal articles published by researchers at all eight New Zealand universities in 2017 to determine how many were freely accessible on the web. We wrote software code to harvest data from multiple sources, code that we now share to enable others to reproduce our work on their own sample set. In May 2019, we ran our code to determine which of the 2017 articles were open at that time and by what method; where those articles would have incurred an Article Processing Charge (APC) we calculated the cost if those charges had been paid. Where articles were not freely available we determined whether the policies of publishers in each case would have allowed deposit in a non-commercial repository (Green open access). We also examined citation rates for different types of access. We found that, of our 2017 sample set, about two out of every five articles were freely accessible without payment or subscription (41%). Where research was explicitly said to be funded by New Zealand’s major research funding agencies, the proportion was slightly higher at 45%. Where open articles would have incurred an APC we estimated an average cost per article of USD1,682 (for publications where all articles require an APC, that is, Gold open access) and USD2,558 (where APC payment is optional, Hybrid open access) at a total estimated cost of USD1.45m. Of the paid options, Gold is by far more common for New Zealand researchers (82% Gold, 18% Hybrid). In terms of citations, our analysis aligned with previous studies that suggest a correlation between publications being freely accessible and, on balance, slightly higher rates of citation. This is not seen across all types of open access, however, with Diamond OA achieving the lowest rates. Where articles were not freely accessible we found that a very large majority of them (88% or 3089 publications) could have been legally deposited in an institutional repository. Similarly, only in a very small number of cases had a version deposited …
bibliographic citation: White et al. (2021) Only two out of five articles by New Zealand researchers are free-to-access: a multiple API study of access, citations, cost of Article Processing Charges (APC), and the potential to increase the proportion of open access. PeerJ 9:e11417 https://doi.org/10.7717/peerj.11417
date submitted: 2020-08-04
date accepted: 2021-04-16
issued: 2021-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: White
  given name: Richard K.A.
author list: Agent
  family name: Angelo
  given name: Anton
author list: Agent
  family name: Fitchett
  given name: Deborah
author list: Agent
  family name: Fraser
  given name: Moira
author list: Agent
  family name: Hayes
  given name: Luqman
author list: Agent
  family name: Howie
  given name: Jessica
author list: Agent
  family name: Richardson
  given name: Emma
author list: Agent
  family name: White
  given name: Bruce
doi: 10.7717/peerj.11417
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-26
copyright: ©2021 White et al.
attribution name: White et al.

Key circular RNAs identified in male osteoporosis patients by whole transcriptome sequencing
type: item
type: AcademicArticle
description: Background Osteoporosis (OP) is a systemic disease with bone loss and microstructural deterioration. Numerous noncoding RNAs (ncRNAs) have been proved to participate in various diseases, especially circular RNAs (circRNAs). However, the expression profile and mechanisms underlying circRNAs in male osteoporosis have not yet been explored. Methods The whole transcriptome expression profile and differences in mRNAs, circRNAs, and microRNAs (miRNAs) were investigated in peripheral blood samples of patients with osteoporosis and healthy controls consisting of males ≥ 60-years-old. Results A total of 398 circRNAs, 51 miRNAs, and 642 mRNAs were significantly and differentially expressed in osteoporosis compared to healthy controls. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the host genes of significantly differentially expressed circRNAs were mainly enriched in the regulation of cell cycle process: biological process (BP), organelle part cellular components (CC), protein binding molecular function (MF), Toll-like receptor signaling pathway, tumor necrosis factor (TNF) signaling pathway, and thyroid hormone signaling pathway. circRNA-miRNA-mRNA regulatory network was constructed using the differentially expressed RNAs. Moreover, key circRNAs (hsa_circ_0042409) in osteoporosis were discovered and validated by qPCR. Conclusions The key cicrRNAs plays a major role in the pathogenesis of osteoporosis and could be used as potential biomarkers or targets in the diagnosis and treatment of osteoporosis.
format: application/pdf
format: text/html
creator: Haijin Zhang
creator: Xue Song
creator: Zongyan Teng
creator: Sujun Cheng
creator: Weigang Yu
creator: Xiaoyi Yao
creator: Zhiqiang Song
creator: Yina Zhang
subject: Molecular Biology
subject: Andrology
subject: Geriatrics
subject: Orthopedics
description: doi:10.7717/peerj.11420
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Background Osteoporosis (OP) is a systemic disease with bone loss and microstructural deterioration. Numerous noncoding RNAs (ncRNAs) have been proved to participate in various diseases, especially circular RNAs (circRNAs). However, the expression profile and mechanisms underlying circRNAs in male osteoporosis have not yet been explored. Methods The whole transcriptome expression profile and differences in mRNAs, circRNAs, and microRNAs (miRNAs) were investigated in peripheral blood samples of patients with osteoporosis and healthy controls consisting of males ≥ 60-years-old. Results A total of 398 circRNAs, 51 miRNAs, and 642 mRNAs were significantly and differentially expressed in osteoporosis compared to healthy controls. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the host genes of significantly differentially expressed circRNAs were mainly enriched in the regulation of cell cycle process: biological process (BP), organelle part cellular components (CC), protein binding molecular function (MF), Toll-like receptor signaling pathway, tumor necrosis factor (TNF) signaling pathway, and thyroid hormone signaling pathway. circRNA-miRNA-mRNA regulatory network was constructed using the differentially expressed RNAs. Moreover, key circRNAs (hsa_circ_0042409) in osteoporosis were discovered and validated by qPCR. Conclusions The key cicrRNAs plays a major role in the pathogenesis of osteoporosis and could be used as potential biomarkers or targets in the diagnosis and treatment of osteoporosis.
bibliographic citation: Zhang et al. (2021) Key circular RNAs identified in male osteoporosis patients by whole transcriptome sequencing. PeerJ 9:e11420 https://doi.org/10.7717/peerj.11420
date submitted: 2020-10-13
date accepted: 2021-04-16
issued: 2021-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Haijin
author list: Agent
  family name: Song
  given name: Xue
author list: Agent
  family name: Teng
  given name: Zongyan
author list: Agent
  family name: Cheng
  given name: Sujun
author list: Agent
  family name: Yu
  given name: Weigang
author list: Agent
  family name: Yao
  given name: Xiaoyi
author list: Agent
  family name: Song
  given name: Zhiqiang
author list: Agent
  family name: Zhang
  given name: Yina
doi: 10.7717/peerj.11420
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-26
copyright: ©2021 Zhang et al.
attribution name: Zhang et al.

Integrative species delimitation based on COI, ITS, and morphological evidence illustrates a unique evolutionary history of the genus Paracercion (Odonata: Coenagrionidae)
type: item
type: AcademicArticle
description: Paracercion are common ‘blue and black’ colored damselflies. We explore the species boundaries of Paracercion (Odonata: Coenagrionidae) using ABGD, bPTP, GMYC and Distance-based clustering. We finally got the molecular data of all nine species of Paracercion. P. hieroglyphicum and P. melanotum were combined into one putative species based on cytochrome c oxidase I (COI). However, they were separated into two putative species based on the nuclear segment including ITS1-5.8S-ITS2 (ITS). This suggests the introgression of mtDNA in Paracercion. Paracercion barbatum and Paracercion melanotum can be separated into two species based on COI, whereas they were combined into one putative species based on ITS, which suggests a hybridization event between them. The lower interspecific divergence (COI: 0.49%) between P. barbatum and Paracercion v-nigrum indicates a recent speciation event in Paracercion. Paracercion sieboldii and P. v-nigrum can be separated into two putative species based on COI, while they were frequently merged into the same putative species based on ITS. This can be explained by incomplete lineage sorting in nDNA. Besides, P. pendulum and P. malayanum were synonymized as junior synonyms of P. melanotum. P. luzonicum was confirmed not to belong to Paracercion. The possibility of introgression, hybridization, recent speciation and incomplete lineage sorting makes species delimitation, based on molecular data, difficult and complicates understanding of the evolutionary history of Paracercion. The discordance in COI and ITS also indicates the value of using markers from different sources in species delimitation studies.
format: application/pdf
format: text/html
creator: Haiguang Zhang
creator: Xin Ning
creator: Xin Yu
creator: Wen-Jun Bu
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.11459
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Paracercion are common ‘blue and black’ colored damselflies. We explore the species boundaries of Paracercion (Odonata: Coenagrionidae) using ABGD, bPTP, GMYC and Distance-based clustering. We finally got the molecular data of all nine species of Paracercion. P. hieroglyphicum and P. melanotum were combined into one putative species based on cytochrome c oxidase I (COI). However, they were separated into two putative species based on the nuclear segment including ITS1-5.8S-ITS2 (ITS). This suggests the introgression of mtDNA in Paracercion. Paracercion barbatum and Paracercion melanotum can be separated into two species based on COI, whereas they were combined into one putative species based on ITS, which suggests a hybridization event between them. The lower interspecific divergence (COI: 0.49%) between P. barbatum and Paracercion v-nigrum indicates a recent speciation event in Paracercion. Paracercion sieboldii and P. v-nigrum can be separated into two putative species based on COI, while they were frequently merged into the same putative species based on ITS. This can be explained by incomplete lineage sorting in nDNA. Besides, P. pendulum and P. malayanum were synonymized as junior synonyms of P. melanotum. P. luzonicum was confirmed not to belong to Paracercion. The possibility of introgression, hybridization, recent speciation and incomplete lineage sorting makes species delimitation, based on molecular data, difficult and complicates understanding of the evolutionary history of Paracercion. The discordance in COI and ITS also indicates the value of using markers from different sources in species delimitation studies.
bibliographic citation: Zhang et al. (2021) Integrative species delimitation based on COI, ITS, and morphological evidence illustrates a unique evolutionary history of the genus Paracercion (Odonata: Coenagrionidae). PeerJ 9:e11459 https://doi.org/10.7717/peerj.11459
date submitted: 2020-12-15
date accepted: 2021-04-25
issued: 2021-05-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Haiguang
author list: Agent
  family name: Ning
  given name: Xin
author list: Agent
  family name: Yu
  given name: Xin
author list: Agent
  family name: Bu
  given name: Wen-Jun
doi: 10.7717/peerj.11459
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-26
copyright: © 2021 Zhang et al.
attribution name: Zhang et al.

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