PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Different roles of urinary light chains and serum light chains as potential biomarkers for monitoring disease activity in systemic lupus erythematosus
items: Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics
items: Genome-wide identification of xyloglucan endotransglucosylase/hydrolase gene family members in peanut and their expression profiles during seed germination
items: Fluoride effect indicators in Phaseolus vulgaris seeds and seedlings
items: A new perleidid neopterygian fish from the Early Triassic (Dienerian, Induan) of South China, with a reassessment of the relationships of Perleidiformes
items: LncRNA OIP5-AS1 modulates the proliferation and apoptosis of Jurkat cells by sponging miR-181c-5p to regulate IL-7 expression in myasthenia gravis
items: Forecasting effects of transport infrastructure on endangered tigers: a tool for conservation planning
items: The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma
items: TFR1 expression in induced sputum is associated with asthma severity
items: The sub-fossil diatom distribution in the Beibu Gulf (northwest South China Sea) and related environmental interpretation

Different roles of urinary light chains and serum light chains as potential biomarkers for monitoring disease activity in systemic lupus erythematosus
type: item
type: AcademicArticle
description: Objective The assessment system for monitoring systemic lupus erythematosus (SLE) disease activity is complex and lacks reliable laboratory indicators. It is necessary to find rapid and noninvasive biomarkers. The aim of this study was to screen and identify the differentially expressed proteins in urine samples between active SLE and stable SLE and to further explore the expression of light chains. Methods First, we used a label-free quantitative proteomics approach to establish the urine protein expression profile of SLE, and then screened differentially expressed proteins. Subsequently, the expression of overall light chains was examined by immunofixation electrophoresis and immunoturbidimetric methods, respectively. Results Mass spectrometry data analysis found a total of 51 light chain peptides in the urinary protein expression spectrum, of which 27 light chain peptides were differentially expressed between the two groups. The largest difference was IGLV5-45 located in the variable region of the immunoglobulin Lambda light chain. The levels of urinary light chains and serum light chains were both significantly elevated in active SLE, and the levels of urinary light chains increased with the severity of disease activity. Conclusions The measurement of light chains would help to monitor SLE disease activity. Serum light chains had better discriminatory capacity than urinary light chains, while urine light chains were closely related to the severity of disease activity and could be used for dynamically monitoring the progress of disease activity.
format: application/pdf
format: text/html
creator: Jun Jiang
creator: Jin Zhao
creator: Dan Liu
creator: Man Zhang
subject: Biochemistry
subject: Bioinformatics
subject: Immunology
subject: Rheumatology
subject: Urology
description: doi:10.7717/peerj.13385
publisher: PeerJ Inc.
rights: © 2022 Jiang et al.
abstract: Objective The assessment system for monitoring systemic lupus erythematosus (SLE) disease activity is complex and lacks reliable laboratory indicators. It is necessary to find rapid and noninvasive biomarkers. The aim of this study was to screen and identify the differentially expressed proteins in urine samples between active SLE and stable SLE and to further explore the expression of light chains. Methods First, we used a label-free quantitative proteomics approach to establish the urine protein expression profile of SLE, and then screened differentially expressed proteins. Subsequently, the expression of overall light chains was examined by immunofixation electrophoresis and immunoturbidimetric methods, respectively. Results Mass spectrometry data analysis found a total of 51 light chain peptides in the urinary protein expression spectrum, of which 27 light chain peptides were differentially expressed between the two groups. The largest difference was IGLV5-45 located in the variable region of the immunoglobulin Lambda light chain. The levels of urinary light chains and serum light chains were both significantly elevated in active SLE, and the levels of urinary light chains increased with the severity of disease activity. Conclusions The measurement of light chains would help to monitor SLE disease activity. Serum light chains had better discriminatory capacity than urinary light chains, while urine light chains were closely related to the severity of disease activity and could be used for dynamically monitoring the progress of disease activity.
bibliographic citation: Jiang et al. (2022) Different roles of urinary light chains and serum light chains as potential biomarkers for monitoring disease activity in systemic lupus erythematosus. PeerJ 10:e13385 https://doi.org/10.7717/peerj.13385
date submitted: 2022-01-04
date accepted: 2022-04-15
issued: 2022-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Jun
author list: Agent
  family name: Zhao
  given name: Jin
author list: Agent
  family name: Liu
  given name: Dan
author list: Agent
  family name: Zhang
  given name: Man
doi: 10.7717/peerj.13385
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-17
copyright: ©2022 Jiang et al.
attribution name: Jiang et al.

Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics
type: item
type: AcademicArticle
description: Classification of beaches into morphodynamic states is a common approach in sandy beach studies, due to the influence of natural variables in ecological patterns and processes. The use of remote sensing for identifying beach type and monitoring changes has been commonly applied through multiple methods, which often involve expensive equipment and software processing of images. A previous study on the South African Coast developed a method to classify beaches using conditional tree inferences, based on beach morphological features estimated from public available satellite images, without the need for remote sensing processing, which allowed for a large-scale characterization. However, since the validation of this method has not been tested in other regions, its potential uses as a trans-scalar tool or dependence from local calibrations has not been evaluated. Here, we tested the validity of this method using a 200-km stretch of the Brazilian coast, encompassing a wide gradient of morphodynamic conditions. We also compared this locally derived model with the results that would be generated using the cut-off values established in the previous study. To this end, 87 beach sites were remotely assessed using an accessible software (i.e., Google Earth) and sampled for an in-situ environmental characterization and beach type classification. These sites were used to derive the predictive model of beach morphodynamics from the remotely assessed metrics, using conditional inference trees. An additional 77 beach sites, with a previously known morphodynamic type, were also remotely evaluated to test the model accuracy. Intertidal width and exposure degree were the only variables selected in the model to classify beach type, with an accuracy higher than 90% through different metrics of model validation. The only limitation was the inability in separating beach types in the reflective end of the morphodynamic continuum. Our results corroborated the usefulness of this method, highl…
format: application/pdf
format: text/html
creator: Helio Herminio Checon
creator: Yasmina Shah Esmaeili
creator: Guilherme N. Corte
creator: Nicole Malinconico
creator: Alexander Turra
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13413
publisher: PeerJ Inc.
rights: © 2022 Checon et al.
abstract: Classification of beaches into morphodynamic states is a common approach in sandy beach studies, due to the influence of natural variables in ecological patterns and processes. The use of remote sensing for identifying beach type and monitoring changes has been commonly applied through multiple methods, which often involve expensive equipment and software processing of images. A previous study on the South African Coast developed a method to classify beaches using conditional tree inferences, based on beach morphological features estimated from public available satellite images, without the need for remote sensing processing, which allowed for a large-scale characterization. However, since the validation of this method has not been tested in other regions, its potential uses as a trans-scalar tool or dependence from local calibrations has not been evaluated. Here, we tested the validity of this method using a 200-km stretch of the Brazilian coast, encompassing a wide gradient of morphodynamic conditions. We also compared this locally derived model with the results that would be generated using the cut-off values established in the previous study. To this end, 87 beach sites were remotely assessed using an accessible software (i.e., Google Earth) and sampled for an in-situ environmental characterization and beach type classification. These sites were used to derive the predictive model of beach morphodynamics from the remotely assessed metrics, using conditional inference trees. An additional 77 beach sites, with a previously known morphodynamic type, were also remotely evaluated to test the model accuracy. Intertidal width and exposure degree were the only variables selected in the model to classify beach type, with an accuracy higher than 90% through different metrics of model validation. The only limitation was the inability in separating beach types in the reflective end of the morphodynamic continuum. Our results corroborated the usefulness of this method, highl…
bibliographic citation: Checon et al. (2022) Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics. PeerJ 10:e13413 https://doi.org/10.7717/peerj.13413
date submitted: 2022-02-04
date accepted: 2022-04-19
issued: 2022-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Checon
  given name: Helio Herminio
author list: Agent
  family name: Shah Esmaeili
  given name: Yasmina
author list: Agent
  family name: Corte
  given name: Guilherme N.
author list: Agent
  family name: Malinconico
  given name: Nicole
author list: Agent
  family name: Turra
  given name: Alexander
doi: 10.7717/peerj.13413
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-17
copyright: ©2022 Checon et al.
attribution name: Checon et al.

Genome-wide identification of xyloglucan endotransglucosylase/hydrolase gene family members in peanut and their expression profiles during seed germination
type: item
type: AcademicArticle
description: Seed germination marks the beginning of a new plant life cycle. Improving the germination rate of seeds and the consistency of seedling emergence in the field could improve crop yields. Many genes are involved in the regulation of seed germination. Our previous study found that some peanut XTHs (xyloglucan endotransglucosylases/hydrolases) were expressed at higher levels at the newly germinated stage. However, studies of the XTH gene family in peanut have not been reported. In this study, a total of 58 AhXTH genes were identified in the peanut genome. Phylogenetic analysis showed that these AhXTHs, along with 33 AtXTHs from Arabidopsis and 61 GmXTHs from soybean, were classified into three subgroups: the I/II, IIIA and IIIB subclades. All AhXTH genes were unevenly distributed on the 18 peanut chromosomes, with the exception of chr. 07 and 17, and they had relatively conserved exon-intron patterns, most with three to four introns. Through chromosomal distribution pattern and synteny analysis, it was found that the AhXTH family experienced many replication events, including 42 pairs of segmental duplications and 23 pairs of tandem duplications, during genome evolution. Conserved motif analysis indicated that their encoded proteins contained the conserved ExDxE domain and N-linked glycosylation sites and displayed the conserved secondary structural loops 1–3 in members of the same group. Expression profile analysis of freshly harvested seeds, dried seeds, and newly germinated seeds using transcriptome data revealed that 26 AhXTH genes, which account for 45% of the gene family, had relatively higher expression levels at the seed germination stage, implying the important roles of AhXTHs in regulating seed germination. The results of quantitative real-time PCR also confirmed that some AhXTHs were upregulated during seed germination. The results of GUS histochemical staining showed that AhXTH4 was mainly expressed in germinated seeds and etiolated seedlings and had higher …
format: application/pdf
format: text/html
creator: Jieqiong Zhu
creator: Guiying Tang
creator: Pingli Xu
creator: Guowei Li
creator: Changle Ma
creator: Pengxiang Li
creator: Chunyu Jiang
creator: Lei Shan
creator: Shubo Wan
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.13428
publisher: PeerJ Inc.
rights: © 2022 Zhu et al.
abstract: Seed germination marks the beginning of a new plant life cycle. Improving the germination rate of seeds and the consistency of seedling emergence in the field could improve crop yields. Many genes are involved in the regulation of seed germination. Our previous study found that some peanut XTHs (xyloglucan endotransglucosylases/hydrolases) were expressed at higher levels at the newly germinated stage. However, studies of the XTH gene family in peanut have not been reported. In this study, a total of 58 AhXTH genes were identified in the peanut genome. Phylogenetic analysis showed that these AhXTHs, along with 33 AtXTHs from Arabidopsis and 61 GmXTHs from soybean, were classified into three subgroups: the I/II, IIIA and IIIB subclades. All AhXTH genes were unevenly distributed on the 18 peanut chromosomes, with the exception of chr. 07 and 17, and they had relatively conserved exon-intron patterns, most with three to four introns. Through chromosomal distribution pattern and synteny analysis, it was found that the AhXTH family experienced many replication events, including 42 pairs of segmental duplications and 23 pairs of tandem duplications, during genome evolution. Conserved motif analysis indicated that their encoded proteins contained the conserved ExDxE domain and N-linked glycosylation sites and displayed the conserved secondary structural loops 1–3 in members of the same group. Expression profile analysis of freshly harvested seeds, dried seeds, and newly germinated seeds using transcriptome data revealed that 26 AhXTH genes, which account for 45% of the gene family, had relatively higher expression levels at the seed germination stage, implying the important roles of AhXTHs in regulating seed germination. The results of quantitative real-time PCR also confirmed that some AhXTHs were upregulated during seed germination. The results of GUS histochemical staining showed that AhXTH4 was mainly expressed in germinated seeds and etiolated seedlings and had higher …
bibliographic citation: Zhu et al. (2022) Genome-wide identification of xyloglucan endotransglucosylase/hydrolase gene family members in peanut and their expression profiles during seed germination. PeerJ 10:e13428 https://doi.org/10.7717/peerj.13428
date submitted: 2021-01-08
date accepted: 2022-04-21
issued: 2022-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Jieqiong
author list: Agent
  family name: Tang
  given name: Guiying
author list: Agent
  family name: Xu
  given name: Pingli
author list: Agent
  family name: Li
  given name: Guowei
author list: Agent
  family name: Ma
  given name: Changle
author list: Agent
  family name: Li
  given name: Pengxiang
author list: Agent
  family name: Jiang
  given name: Chunyu
author list: Agent
  family name: Shan
  given name: Lei
author list: Agent
  family name: Wan
  given name: Shubo
doi: 10.7717/peerj.13428
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-17
copyright: © 2022 Zhu et al.
attribution name: Zhu et al.

Fluoride effect indicators in Phaseolus vulgaris seeds and seedlings
type: item
type: AcademicArticle
description: Background Fluoride (F) is one of the main environmental pollutants, and high concentrations are commonly detected in the air and in both surface and groundwater. However, the effects of this pollutant on seed germination and on the initial growth of crop seedlings are still poorly understood. In this context, the aim of this study was to assess morphoanatomical, physiological and biochemical fluoride effect indicators in Phaseolus vulgaris L. seeds and seedlings. Methods P. vulgaris seeds were exposed to a liquid potassium fluoride solution (KF, pH 6.0) at concentrations of 0 (control), 10, 20, 30 mg L−1 for 7 days. A completely randomized experimental design was applied, consisting of four treatments with four replications each. During the experimental period, physiological (7 days) anatomical and histochemical (2 days), biochemical and chemical (4 days) assessments. An analysis of variance was performed followed by Dunnett’s test. to determine significant differences between the KF-exposed groups and control seeds; and a multivariate analysis was performed. Results The germination parameters, and anatomical, morphological, physiological, biochemical and nutritional characteristics of the seedlings did not show negative effects from exposure to KF at the lowest doses evaluated. On the other hand, treatment with the highest dose of KF (30 mg L−1) resulted in a lower germination rate index and increase in abnormal seedlings, and higher electrical conductivity. A lower root length, magnesium content and photochemical efficiency were also observed. The exposure of P. vulgaris to KF, regardless the dose did not affect seeds anatomy and the accumulation of starch and proteins, in relation to the control group. Conclusions Our findings demonstrated that P. vulgaris seedlings were tolerant to KF solutions up to 20 mg L−1, and sensitive when exposed to 30 mg KF L−1.
format: application/pdf
format: text/html
creator: Ingrid Maressa Hungria de Lima e Silva
creator: Arthur Almeida Rodrigues
creator: Juliana de Fátima Sales
creator: Douglas Almeida Rodrigues
creator: Sebastião Carvalho Vasconcelos Filho
creator: Cássia Lino Rodrigues
creator: Priscila Ferreira Batista
creator: Alan Carlos Costa
creator: Marisa Domingos
creator: Caroline Müller
creator: Adinan Alves da Silva
subject: Agricultural Science
subject: Plant Science
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.13434
publisher: PeerJ Inc.
rights: © 2022 Maressa Hungria de Lima e Silva et al.
abstract: Background Fluoride (F) is one of the main environmental pollutants, and high concentrations are commonly detected in the air and in both surface and groundwater. However, the effects of this pollutant on seed germination and on the initial growth of crop seedlings are still poorly understood. In this context, the aim of this study was to assess morphoanatomical, physiological and biochemical fluoride effect indicators in Phaseolus vulgaris L. seeds and seedlings. Methods P. vulgaris seeds were exposed to a liquid potassium fluoride solution (KF, pH 6.0) at concentrations of 0 (control), 10, 20, 30 mg L−1 for 7 days. A completely randomized experimental design was applied, consisting of four treatments with four replications each. During the experimental period, physiological (7 days) anatomical and histochemical (2 days), biochemical and chemical (4 days) assessments. An analysis of variance was performed followed by Dunnett’s test. to determine significant differences between the KF-exposed groups and control seeds; and a multivariate analysis was performed. Results The germination parameters, and anatomical, morphological, physiological, biochemical and nutritional characteristics of the seedlings did not show negative effects from exposure to KF at the lowest doses evaluated. On the other hand, treatment with the highest dose of KF (30 mg L−1) resulted in a lower germination rate index and increase in abnormal seedlings, and higher electrical conductivity. A lower root length, magnesium content and photochemical efficiency were also observed. The exposure of P. vulgaris to KF, regardless the dose did not affect seeds anatomy and the accumulation of starch and proteins, in relation to the control group. Conclusions Our findings demonstrated that P. vulgaris seedlings were tolerant to KF solutions up to 20 mg L−1, and sensitive when exposed to 30 mg KF L−1.
bibliographic citation: Maressa Hungria de Lima e Silva et al. (2022) Fluoride effect indicators in Phaseolus vulgaris seeds and seedlings. PeerJ 10:e13434 https://doi.org/10.7717/peerj.13434
date submitted: 2021-11-12
date accepted: 2022-04-22
issued: 2022-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maressa Hungria de Lima e Silva
  given name: Ingrid
author list: Agent
  family name: Almeida Rodrigues
  given name: Arthur
author list: Agent
  family name: de Fátima Sales
  given name: Juliana
author list: Agent
  family name: Almeida Rodrigues
  given name: Douglas
author list: Agent
  family name: Carvalho Vasconcelos Filho
  given name: Sebastião
author list: Agent
  family name: Lino Rodrigues
  given name: Cássia
author list: Agent
  family name: Ferreira Batista
  given name: Priscila
author list: Agent
  family name: Carlos Costa
  given name: Alan
author list: Agent
  family name: Domingos
  given name: Marisa
author list: Agent
  family name: Müller
  given name: Caroline
author list: Agent
  family name: Alves da Silva
  given name: Adinan
doi: 10.7717/peerj.13434
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-17
copyright: ©2022 Maressa Hungria de Lima e Silva et al.
attribution name: Maressa Hungria de Lima e Silva et al.

A new perleidid neopterygian fish from the Early Triassic (Dienerian, Induan) of South China, with a reassessment of the relationships of Perleidiformes
type: item
type: AcademicArticle
description: Neopterygii is the largest clade of ray-finned fishes, including Teleostei, Holostei, and their closely related fossil taxa. This clade was first documented in the Early Carboniferous and underwent rapid evolutionary radiation during the Early to Middle Triassic. This article describes a new perleidid neopterygian species, Teffichthys elegans sp. nov., based on 13 well-preserved specimens from the lower Daye Formation (Dienerian, Induan) in Guizhou, China. The new species documents one of the oldest perleidids, providing insights into the early diversification of this family. The results of a phylogenetic analysis recover Teffichthys elegans sp. nov. as the sister taxon to Teffichthys madagascariensis within the Perleididae. T. elegans sp. nov. shares three derived features of Perleididae: the length of the anteroventral margin of the dermohyal nearly half the length of the anterodorsal margin of the preopercle; the anteroventral margin of the preopercle nearly equal to the anterior margin of the subopercle in length; and the anteroventral margin of the preopercle one to two times as long as the anterodorsal margin of the preopercle. It possesses diagnostic features of Teffichthys but differs from T. madagascariensis by the following features: presence of three supraorbitals; six pairs of branchiostegal rays; relatively deep anterodorsal process of subopercle; absence of spine on the posterior margin of the jugal; and pterygial formula of D26/P14, A22, C36/T39-41. The Perleidiformes are restricted to include only the Perleididae, and other previously alleged ‘perleidiform’ families (e.g., Hydropessidae and Gabanellidae) are excluded to maintain the monophyly of the order. Similar to many other perleidids, T. elegans sp. nov. was likely a durophagous predator with dentition combining grasping and crushing morphologies. The new finding also may indicate a relatively complex trophic structure of the Early Triassic marine ecosystem in South China.
format: application/pdf
format: text/html
creator: Zhiwei Yuan
creator: Guang-Hui Xu
creator: Xu Dai
creator: Fengyu Wang
creator: Xiaokang Liu
creator: Enhao Jia
creator: Luyi Miao
creator: Haijun Song
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13448
publisher: PeerJ Inc.
rights: © 2022 Yuan et al.
abstract: Neopterygii is the largest clade of ray-finned fishes, including Teleostei, Holostei, and their closely related fossil taxa. This clade was first documented in the Early Carboniferous and underwent rapid evolutionary radiation during the Early to Middle Triassic. This article describes a new perleidid neopterygian species, Teffichthys elegans sp. nov., based on 13 well-preserved specimens from the lower Daye Formation (Dienerian, Induan) in Guizhou, China. The new species documents one of the oldest perleidids, providing insights into the early diversification of this family. The results of a phylogenetic analysis recover Teffichthys elegans sp. nov. as the sister taxon to Teffichthys madagascariensis within the Perleididae. T. elegans sp. nov. shares three derived features of Perleididae: the length of the anteroventral margin of the dermohyal nearly half the length of the anterodorsal margin of the preopercle; the anteroventral margin of the preopercle nearly equal to the anterior margin of the subopercle in length; and the anteroventral margin of the preopercle one to two times as long as the anterodorsal margin of the preopercle. It possesses diagnostic features of Teffichthys but differs from T. madagascariensis by the following features: presence of three supraorbitals; six pairs of branchiostegal rays; relatively deep anterodorsal process of subopercle; absence of spine on the posterior margin of the jugal; and pterygial formula of D26/P14, A22, C36/T39-41. The Perleidiformes are restricted to include only the Perleididae, and other previously alleged ‘perleidiform’ families (e.g., Hydropessidae and Gabanellidae) are excluded to maintain the monophyly of the order. Similar to many other perleidids, T. elegans sp. nov. was likely a durophagous predator with dentition combining grasping and crushing morphologies. The new finding also may indicate a relatively complex trophic structure of the Early Triassic marine ecosystem in South China.
bibliographic citation: Yuan et al. (2022) A new perleidid neopterygian fish from the Early Triassic (Dienerian, Induan) of South China, with a reassessment of the relationships of Perleidiformes. PeerJ 10:e13448 https://doi.org/10.7717/peerj.13448
date submitted: 2021-12-08
date accepted: 2022-04-26
issued: 2022-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Zhiwei
author list: Agent
  family name: Xu
  given name: Guang-Hui
author list: Agent
  family name: Dai
  given name: Xu
author list: Agent
  family name: Wang
  given name: Fengyu
author list: Agent
  family name: Liu
  given name: Xiaokang
author list: Agent
  family name: Jia
  given name: Enhao
author list: Agent
  family name: Miao
  given name: Luyi
author list: Agent
  family name: Song
  given name: Haijun
doi: 10.7717/peerj.13448
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-17
copyright: © 2022 Yuan et al.
attribution name: Yuan et al.

LncRNA OIP5-AS1 modulates the proliferation and apoptosis of Jurkat cells by sponging miR-181c-5p to regulate IL-7 expression in myasthenia gravis
type: item
type: AcademicArticle
description: Background Myasthenia gravis (MG) is an antibody-mediated autoimmune disease. In recent years, accumulating evidence has indicated that long non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs), contributing to the progression of various autoimmune diseases. Nevertheless, the regulatory roles of ceRNAs in MG pathogenesis remain unclear. In this study, we aimed to elucidate the role of lncRNA OIP5-AS1 as a ceRNA associated with MG progression. Methods Real-time PCR was used to detect OIP5-AS1 levels in peripheral blood mononuclear cells (PBMCs) from patients with MG. Luciferase reporter assays were performed to validate the relationship between OIP5-AS1 and miR-181c-5p. CCK-8 and flow cytometry were performed to test the proliferation and apoptotic abilities of OIP5-AS1 in Jurkat cells. Furthermore, real-time PCR and Western blot assays were performed to explore the interactions between OIP5-AS1, miR-181c-5p, and IL-7. Results The expression of OIP5-AS1 was up-regulated in patients with MG. Luciferase reporter assay indicated that OIP5-AS1 targeted the miR-181c-5p. Functional assays showed that OIP5-AS1 suppressed Jurkat cell apoptosis and promoted cell proliferation by sponging miR-181c-5p. Mechanistically, knockdown of OIP5-AS1 inhibited IL-7 expression at both the mRNA and protein levels in Jurkat cells, whereas the miR-181c-5p inhibitor blocked the reduction of IL-7 expression induced by OIP5-AS1 suppression. Conclusions We confirmed that OIP5-AS1 serves as an endogenous sponge for miR-181c-5p to regulate the expression of IL-7. Our findings provide novel insights into MG processes and suggests potential therapeutic targets for patients with MG.
format: application/pdf
format: text/html
creator: Xu Wang
creator: Huixue Zhang
creator: Xiaoyu Lu
creator: Shuang Li
creator: Xiaotong Kong
creator: Li Liu
creator: Lifang Li
creator: Si Xu
creator: Tianfeng Wang
creator: Jianjian Wang
creator: Lihua Wang
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13454
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Myasthenia gravis (MG) is an antibody-mediated autoimmune disease. In recent years, accumulating evidence has indicated that long non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs), contributing to the progression of various autoimmune diseases. Nevertheless, the regulatory roles of ceRNAs in MG pathogenesis remain unclear. In this study, we aimed to elucidate the role of lncRNA OIP5-AS1 as a ceRNA associated with MG progression. Methods Real-time PCR was used to detect OIP5-AS1 levels in peripheral blood mononuclear cells (PBMCs) from patients with MG. Luciferase reporter assays were performed to validate the relationship between OIP5-AS1 and miR-181c-5p. CCK-8 and flow cytometry were performed to test the proliferation and apoptotic abilities of OIP5-AS1 in Jurkat cells. Furthermore, real-time PCR and Western blot assays were performed to explore the interactions between OIP5-AS1, miR-181c-5p, and IL-7. Results The expression of OIP5-AS1 was up-regulated in patients with MG. Luciferase reporter assay indicated that OIP5-AS1 targeted the miR-181c-5p. Functional assays showed that OIP5-AS1 suppressed Jurkat cell apoptosis and promoted cell proliferation by sponging miR-181c-5p. Mechanistically, knockdown of OIP5-AS1 inhibited IL-7 expression at both the mRNA and protein levels in Jurkat cells, whereas the miR-181c-5p inhibitor blocked the reduction of IL-7 expression induced by OIP5-AS1 suppression. Conclusions We confirmed that OIP5-AS1 serves as an endogenous sponge for miR-181c-5p to regulate the expression of IL-7. Our findings provide novel insights into MG processes and suggests potential therapeutic targets for patients with MG.
bibliographic citation: Wang et al. (2022) LncRNA OIP5-AS1 modulates the proliferation and apoptosis of Jurkat cells by sponging miR-181c-5p to regulate IL-7 expression in myasthenia gravis. PeerJ 10:e13454 https://doi.org/10.7717/peerj.13454
date submitted: 2021-12-01
date accepted: 2022-04-27
issued: 2022-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xu
author list: Agent
  family name: Zhang
  given name: Huixue
author list: Agent
  family name: Lu
  given name: Xiaoyu
author list: Agent
  family name: Li
  given name: Shuang
author list: Agent
  family name: Kong
  given name: Xiaotong
author list: Agent
  family name: Liu
  given name: Li
author list: Agent
  family name: Li
  given name: Lifang
author list: Agent
  family name: Xu
  given name: Si
author list: Agent
  family name: Wang
  given name: Tianfeng
author list: Agent
  family name: Wang
  given name: Jianjian
author list: Agent
  family name: Wang
  given name: Lihua
doi: 10.7717/peerj.13454
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-17
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Forecasting effects of transport infrastructure on endangered tigers: a tool for conservation planning
type: item
type: AcademicArticle
description: The rapid development of transport infrastructure is a major threat to endangered species worldwide. Roads and railways can increase animal mortality, fragment habitats, and exacerbate other threats to biodiversity. Predictive models that forecast the future impacts to endangered species can guide land-use planning in ways that proactively reduce the negative effects of transport infrastructure. Agent-based models are well suited for predictive scenario testing, yet their application to endangered species conservation is rare. Here, we developed a spatially explicit, agent-based model to forecast the effects of transport infrastructure on an isolated tiger (Panthera tigris) population in Nepal’s Chitwan National Park—a global biodiversity hotspot. Specifically, our model evaluated the independent and interactive effects of two mechanisms by which transport infrastructure may affect tigers: (a) increasing tiger mortality, e.g., via collisions with vehicles, and (b) depleting prey near infrastructure. We projected potential impacts on tiger population dynamics based on the: (i) existing transportation network in and near the park, and (ii) the inclusion of a proposed railway intersecting through the park’s buffer zone. Our model predicted that existing roads would kill 46 tigers over 20 years via increased mortality, and reduced the adult tiger population by 39% (133 to 81). Adding the proposed railway directly killed 10 more tigers over those 20 years; deaths that reduced the overall tiger population by 30 more individuals (81 to 51). Road-induced mortality also decreased the proportion of time a tiger occupied a given site by 5 years in the 20-year simulation. Interestingly, we found that transportation-induced depletion of prey decreased tiger occupancy by nearly 20% in sites close to roads and the railway, thereby reducing tiger exposure to transportation-induced mortality. The results of our model constitute a strong argument for taking into account prey distribu…
format: application/pdf
format: text/html
creator: Neil H. Carter
creator: Narendra Pradhan
creator: Krishna Hengaju
creator: Chinmay Sonawane
creator: Abigail H. Sage
creator: Volker Grimm
subject: Conservation Biology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13472
publisher: PeerJ Inc.
rights: © 2022 Carter et al.
abstract: The rapid development of transport infrastructure is a major threat to endangered species worldwide. Roads and railways can increase animal mortality, fragment habitats, and exacerbate other threats to biodiversity. Predictive models that forecast the future impacts to endangered species can guide land-use planning in ways that proactively reduce the negative effects of transport infrastructure. Agent-based models are well suited for predictive scenario testing, yet their application to endangered species conservation is rare. Here, we developed a spatially explicit, agent-based model to forecast the effects of transport infrastructure on an isolated tiger (Panthera tigris) population in Nepal’s Chitwan National Park—a global biodiversity hotspot. Specifically, our model evaluated the independent and interactive effects of two mechanisms by which transport infrastructure may affect tigers: (a) increasing tiger mortality, e.g., via collisions with vehicles, and (b) depleting prey near infrastructure. We projected potential impacts on tiger population dynamics based on the: (i) existing transportation network in and near the park, and (ii) the inclusion of a proposed railway intersecting through the park’s buffer zone. Our model predicted that existing roads would kill 46 tigers over 20 years via increased mortality, and reduced the adult tiger population by 39% (133 to 81). Adding the proposed railway directly killed 10 more tigers over those 20 years; deaths that reduced the overall tiger population by 30 more individuals (81 to 51). Road-induced mortality also decreased the proportion of time a tiger occupied a given site by 5 years in the 20-year simulation. Interestingly, we found that transportation-induced depletion of prey decreased tiger occupancy by nearly 20% in sites close to roads and the railway, thereby reducing tiger exposure to transportation-induced mortality. The results of our model constitute a strong argument for taking into account prey distribu…
bibliographic citation: Carter et al. (2022) Forecasting effects of transport infrastructure on endangered tigers: a tool for conservation planning. PeerJ 10:e13472 https://doi.org/10.7717/peerj.13472
date submitted: 2021-12-15
date accepted: 2022-04-29
issued: 2022-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carter
  given name: Neil H.
author list: Agent
  family name: Pradhan
  given name: Narendra
author list: Agent
  family name: Hengaju
  given name: Krishna
author list: Agent
  family name: Sonawane
  given name: Chinmay
author list: Agent
  family name: Sage
  given name: Abigail H.
author list: Agent
  family name: Grimm
  given name: Volker
doi: 10.7717/peerj.13472
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-17
copyright: ©2022 Carter et al.
attribution name: Carter et al.

The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background The genome map of hepatocellular carcinoma (HCC) is complex. In order to explore whether circulating tumor cell DNA (ctDNA) can be used as the basis for sequencing and use ctDNA to find tumor related biomarkers, we analyzed the mutant genes of ctDNA in patients with liver cancer by sequencing. Methods We used next-generation targeted sequencing technology to identify mutations in patients with liver cancer. The ctDNA from 10 patients with hepatocellular carcinoma (including eight cases of primary hepatocellular carcinoma and two cases of secondary hepatocellular carcinoma) was sequenced. We used SAMtools to detect and screen single nucleotide polymorphisms (SNPs) and insertion deletion mutations (INDELs) and ANNOVAR to annotate the structure and function of the detected mutations. Screening of pathogenic and possible pathogenic genes was performed using American College of Medical Genetics and Genomics (ACMG) guidelines. GO analysis and KEGG analysis of pathogenic and possible pathogenic genes were performed using the DAVID database, and protein–protein interaction network analysis of pathogenic and possible pathogenic genes was performed using the STRING database. Then, the Kaplan–Meier plotter database, GEPIA database and HPA database were used to analyse the relationship between pathogenic and possible pathogenic genes and patients with liver cancer. Results Targeted capture and deep sequencing of 560 cancer-related genes in 10 liver cancer ctDNA samples revealed 8,950 single nucleotide variation (SNV) mutations and 70 INDELS. The most commonly mutated gene was PDE4DIP, followed by SYNE1, KMT2C, PKHD1 and FN1. We compared these results to the COSMIC database and determined that ctDNA could be used for sequencing. According to the ACMG guidelines, we identified 54 pathogenic and possible pathogenic mutations in 39 genes in exons and splice regions of 10 HCC patients and performed GO analysis, KEGG analysis, and PPI network analysis. Through further anal…
format: application/pdf
format: text/html
creator: Yubo Ding
creator: Jingwei Yao
creator: Meiling Wen
creator: Xiong Liu
creator: Jialu Huang
creator: Minghui Zhang
creator: Yu Zhang
creator: Yufan Lv
creator: Zhuoyi Xie
creator: JianHong Zuo
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.13473
publisher: PeerJ Inc.
rights: © 2022 Ding et al.
abstract: Background The genome map of hepatocellular carcinoma (HCC) is complex. In order to explore whether circulating tumor cell DNA (ctDNA) can be used as the basis for sequencing and use ctDNA to find tumor related biomarkers, we analyzed the mutant genes of ctDNA in patients with liver cancer by sequencing. Methods We used next-generation targeted sequencing technology to identify mutations in patients with liver cancer. The ctDNA from 10 patients with hepatocellular carcinoma (including eight cases of primary hepatocellular carcinoma and two cases of secondary hepatocellular carcinoma) was sequenced. We used SAMtools to detect and screen single nucleotide polymorphisms (SNPs) and insertion deletion mutations (INDELs) and ANNOVAR to annotate the structure and function of the detected mutations. Screening of pathogenic and possible pathogenic genes was performed using American College of Medical Genetics and Genomics (ACMG) guidelines. GO analysis and KEGG analysis of pathogenic and possible pathogenic genes were performed using the DAVID database, and protein–protein interaction network analysis of pathogenic and possible pathogenic genes was performed using the STRING database. Then, the Kaplan–Meier plotter database, GEPIA database and HPA database were used to analyse the relationship between pathogenic and possible pathogenic genes and patients with liver cancer. Results Targeted capture and deep sequencing of 560 cancer-related genes in 10 liver cancer ctDNA samples revealed 8,950 single nucleotide variation (SNV) mutations and 70 INDELS. The most commonly mutated gene was PDE4DIP, followed by SYNE1, KMT2C, PKHD1 and FN1. We compared these results to the COSMIC database and determined that ctDNA could be used for sequencing. According to the ACMG guidelines, we identified 54 pathogenic and possible pathogenic mutations in 39 genes in exons and splice regions of 10 HCC patients and performed GO analysis, KEGG analysis, and PPI network analysis. Through further anal…
bibliographic citation: Ding et al. (2022) The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma. PeerJ 10:e13473 https://doi.org/10.7717/peerj.13473
date submitted: 2021-10-21
date accepted: 2022-04-29
issued: 2022-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ding
  given name: Yubo
author list: Agent
  family name: Yao
  given name: Jingwei
author list: Agent
  family name: Wen
  given name: Meiling
author list: Agent
  family name: Liu
  given name: Xiong
author list: Agent
  family name: Huang
  given name: Jialu
author list: Agent
  family name: Zhang
  given name: Minghui
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Lv
  given name: Yufan
author list: Agent
  family name: Xie
  given name: Zhuoyi
author list: Agent
  family name: Zuo
  given name: JianHong
doi: 10.7717/peerj.13473
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-17
copyright: ©2022 Ding et al.
attribution name: Ding et al.

TFR1 expression in induced sputum is associated with asthma severity
type: item
type: AcademicArticle
description: Background Asthma is characterized as a chronic inflammatory airway disease. Iron accumulation is related to asthma pathogenesis. Transferrin receptor 1(TFR1) expression is associated with intracellular iron overload in macrophages. In our study, we explored the association among TFR1 expression, the inflammatory macrophage phenotype, and asthma severity. Methods Induced sputum was collected from 50 asthma patients. Real-time PCR was used to evaluate mRNA expression. The status of inflammatory macrophage phenotype was assessed using flow cytometry. Results TFR1 levels were inversely correlated with forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) and FEV1/vital capacity (VC). Among inflammatory cytokines, TFR1 expression was positively correlated with IL-1β, TNF-α, IL-6, IFN-γ, and IL-17A mRNA expression in induced sputum. Moreover, TFR1 expression was positively correlated with the number of proinflammatory M1 macrophages and iNOS expression in induced sputum. Neutrophil counts in induced sputum were significantly and positively related to TFR1 expression. Furthermore, TFR1 expression showed an increasing trend in asthma patients with no family history. Our findings indicated that TFR1 expression was consistent with the asthma severity index, especially the proinflammatory M1 macrophage phenotype. TFR1 expression may be a good marker to indicate asthma severity.
format: application/pdf
format: text/html
creator: Yang Wang
creator: li Feng Gu
creator: Xincheng Zhao
creator: Chengping Hu
creator: Qiong Chen
subject: Allergy and Clinical Immunology
subject: Internal Medicine
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.13474
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Asthma is characterized as a chronic inflammatory airway disease. Iron accumulation is related to asthma pathogenesis. Transferrin receptor 1(TFR1) expression is associated with intracellular iron overload in macrophages. In our study, we explored the association among TFR1 expression, the inflammatory macrophage phenotype, and asthma severity. Methods Induced sputum was collected from 50 asthma patients. Real-time PCR was used to evaluate mRNA expression. The status of inflammatory macrophage phenotype was assessed using flow cytometry. Results TFR1 levels were inversely correlated with forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) and FEV1/vital capacity (VC). Among inflammatory cytokines, TFR1 expression was positively correlated with IL-1β, TNF-α, IL-6, IFN-γ, and IL-17A mRNA expression in induced sputum. Moreover, TFR1 expression was positively correlated with the number of proinflammatory M1 macrophages and iNOS expression in induced sputum. Neutrophil counts in induced sputum were significantly and positively related to TFR1 expression. Furthermore, TFR1 expression showed an increasing trend in asthma patients with no family history. Our findings indicated that TFR1 expression was consistent with the asthma severity index, especially the proinflammatory M1 macrophage phenotype. TFR1 expression may be a good marker to indicate asthma severity.
bibliographic citation: Wang et al. (2022) TFR1 expression in induced sputum is associated with asthma severity. PeerJ 10:e13474 https://doi.org/10.7717/peerj.13474
date submitted: 2022-01-27
date accepted: 2022-04-29
issued: 2022-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yang
author list: Agent
  family name: Gu
  given name: li Feng
author list: Agent
  family name: Zhao
  given name: Xincheng
author list: Agent
  family name: Hu
  given name: Chengping
author list: Agent
  family name: Chen
  given name: Qiong
doi: 10.7717/peerj.13474
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-17
copyright: ©2022 Wang et al.
attribution name: Wang et al.

The sub-fossil diatom distribution in the Beibu Gulf (northwest South China Sea) and related environmental interpretation
type: item
type: AcademicArticle
description: Located in northwestern South China Sea (SCS), the Beibu Gulf constitutes an environmentally sensitive region shaped by land-ocean-atmosphere interactions in Asia between the western Pacific and eastern Indian Oceans. This study aims to provide a comprehensive view of the sub-fossil diatom biogeography, distribution pattern and oceanographic environmental controls with support of multivariate methods based on Beibu Gulf core-top samples. Cluster analysis of diatom assemblages divides the distribution pattern into four subclusters. Sea surface salinity (SSS), temperature (SST), trophic state (chlorophyll a concentration in this study) and water depth constrain the diatom distribution pattern through canonical redundancy analysis although only partly support an interpretation of the relationship between these various variables. Chlorophyll a has a strong correlation to diatom distribution, and responds to Paralia sulcata occurrence, while SSS and SST also have significant influence and indicate warm water invasion from the open SCS. Water depth is a subordinate factor in terms of Beibu Gulf diatom distribution. The ca. 25 m water-depth marks the upper extent of Paralia sulcata dominance in the northern Beibu Gulf. A strong mixing area with a complex diatom distribution exists below this water depth in the middle of Beibu Gulf. Coastal currents from north of SCS invade Beibu Gulf through Qiongzhou Strait and south of Hainan Island, as recorded by higher percentages of Paralia sulcata and Cyclotella striata at these sites. Our results provide a selection of evaluation method for a marine ecological red-line definition for sustainable development. This study highlights the perspective relationships between the spatial distribution of sub-fossil diatom assemblages in surface sediments and oceanographic variables, which could serve as a model for paleoenvironmental and paleoclimatic reconstruction in future marginal sea geoscience research for the Beibu Gulf, northwestern …
format: application/pdf
format: text/html
creator: Jinpeng Zhang
creator: Andrzej Witkowski
creator: Michał Tomczak
creator: Chao Li
creator: Kevin McCartney
creator: Zhen Xia
subject: Ecology
subject: Marine Biology
subject: Mathematical Biology
subject: Paleontology
description: doi:10.7717/peerj.13115
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Located in northwestern South China Sea (SCS), the Beibu Gulf constitutes an environmentally sensitive region shaped by land-ocean-atmosphere interactions in Asia between the western Pacific and eastern Indian Oceans. This study aims to provide a comprehensive view of the sub-fossil diatom biogeography, distribution pattern and oceanographic environmental controls with support of multivariate methods based on Beibu Gulf core-top samples. Cluster analysis of diatom assemblages divides the distribution pattern into four subclusters. Sea surface salinity (SSS), temperature (SST), trophic state (chlorophyll a concentration in this study) and water depth constrain the diatom distribution pattern through canonical redundancy analysis although only partly support an interpretation of the relationship between these various variables. Chlorophyll a has a strong correlation to diatom distribution, and responds to Paralia sulcata occurrence, while SSS and SST also have significant influence and indicate warm water invasion from the open SCS. Water depth is a subordinate factor in terms of Beibu Gulf diatom distribution. The ca. 25 m water-depth marks the upper extent of Paralia sulcata dominance in the northern Beibu Gulf. A strong mixing area with a complex diatom distribution exists below this water depth in the middle of Beibu Gulf. Coastal currents from north of SCS invade Beibu Gulf through Qiongzhou Strait and south of Hainan Island, as recorded by higher percentages of Paralia sulcata and Cyclotella striata at these sites. Our results provide a selection of evaluation method for a marine ecological red-line definition for sustainable development. This study highlights the perspective relationships between the spatial distribution of sub-fossil diatom assemblages in surface sediments and oceanographic variables, which could serve as a model for paleoenvironmental and paleoclimatic reconstruction in future marginal sea geoscience research for the Beibu Gulf, northwestern …
bibliographic citation: Zhang et al. (2022) The sub-fossil diatom distribution in the Beibu Gulf (northwest South China Sea) and related environmental interpretation. PeerJ 10:e13115 https://doi.org/10.7717/peerj.13115
date submitted: 2021-05-17
date accepted: 2022-02-23
issued: 2022-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Jinpeng
author list: Agent
  family name: Witkowski
  given name: Andrzej
author list: Agent
  family name: Tomczak
  given name: Michał
author list: Agent
  family name: Li
  given name: Chao
author list: Agent
  family name: McCartney
  given name: Kevin
author list: Agent
  family name: Xia
  given name: Zhen
doi: 10.7717/peerj.13115
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-05-16
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

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