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 virtual reality on activities of daily living in children with cerebral palsy: a systematic review and meta-analysis
items: Accumulation and transfer of polystyrene microplastics in Solanum nigrum seedlings
items: Evaluation of the correlation of dorsal root ganglia and spinal nerves with clinical symptoms in patients with postherpetic neuralgia using magnetic resonance neurography
items: A multi-sensor array for detecting and analyzing nocturnal avian migration
items: Adrenal SGLT1 or SGLT2 as predictors of atherosclerosis under chronic stress based on a computer algorithm
items: RNA N6-methyladenosine reader IGF2BP3 promotes acute myeloid leukemia progression by controlling stabilization of EPOR mRNA
items: Fishery-based adaption to climate change: the case of migratory species flathead grey mullet (Mugil cephalus L.) in Taiwan Strait, Northwestern Pacific
items: Carboxypeptidase E is a prognostic biomarker co-expressed with osteoblastic genes in osteosarcoma
items: Identification and characterization of novel sesquiterpene synthases TPS9 and TPS12 from Aquilaria sinensis
items: Intestinal GPDH-1 regulates high glucose diet induced lifespan extension in aged worms

Effectiveness of virtual reality on activities of daily living in children with cerebral palsy: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background No meta-analysis has been conducted on the effect of specific virtual reality (VR) treatment modes on activities of daily living (ADL) in children with cerebral palsy (CP). Therefore, this study aimed to confirm whether VR therapy is effective in improving ADL in children with CP according to subgroups. Methodology Literature published in the Cumulated Index to Nursing and Allied Health Literature (CINAHL), Embase, the Physiotherapy Evidence Database (PEDro), and PubMed was reviewed, and Risk of Bias 2.0 (RoB 2) was used to evaluate the quality of the literature. A funnel plot was visually observed to confirm publication bias, supplemented with Egger’s regression test. Data analysis was performed using R version 4.2.1. Subgroup analysis was performed according to the Gross Motor Function Classification System (GMFCS), the Manual Ability Classification System (MACS), treatment minutes per week, treatment period, age, and RoB. Results Eleven of 2,978 studies were included, and the overall effect size was 0.37 (95% confidence interval = 0.17–0.57). Regarding GMFCS, effect sizes of 0.41 and 0.33 was observed for the low- and high-function groups, respectively. For MACS, 0.27 and 0.43 were observed for the low and high-function groups. Regarding treatment minutes per week, the values were 0.22, 0.44, and 0.27 in the 1–100, 101–200, and 201–300 min groups, respectively. In the classification according to age, 0.29 was observed for school-age children and 0.98 for preschool children. Lastly, in the classification according to the RoB, 0.52, −0.01, and 0.23 indicated studies with low risk, some concern, and high risk, respectively. Conclusions The highest effect was observed when VR was applied within 6 weeks of 101-200 per week. Therefore, it is suggested that if the results of this review are applied to children with cerebral palsy in the community, it will be an effective intervention method. Systematic review registration PROPEROS (registration number CRD4202…
format: application/pdf
format: text/html
creator: YongGu Han
creator: SunWook Park
subject: Drugs and Devices
subject: Neurology
subject: Pediatrics
subject: Rehabilitation
description: doi:10.7717/peerj.15964
publisher: PeerJ Inc.
rights: © 2023 Han and Park
abstract: Background No meta-analysis has been conducted on the effect of specific virtual reality (VR) treatment modes on activities of daily living (ADL) in children with cerebral palsy (CP). Therefore, this study aimed to confirm whether VR therapy is effective in improving ADL in children with CP according to subgroups. Methodology Literature published in the Cumulated Index to Nursing and Allied Health Literature (CINAHL), Embase, the Physiotherapy Evidence Database (PEDro), and PubMed was reviewed, and Risk of Bias 2.0 (RoB 2) was used to evaluate the quality of the literature. A funnel plot was visually observed to confirm publication bias, supplemented with Egger’s regression test. Data analysis was performed using R version 4.2.1. Subgroup analysis was performed according to the Gross Motor Function Classification System (GMFCS), the Manual Ability Classification System (MACS), treatment minutes per week, treatment period, age, and RoB. Results Eleven of 2,978 studies were included, and the overall effect size was 0.37 (95% confidence interval = 0.17–0.57). Regarding GMFCS, effect sizes of 0.41 and 0.33 was observed for the low- and high-function groups, respectively. For MACS, 0.27 and 0.43 were observed for the low and high-function groups. Regarding treatment minutes per week, the values were 0.22, 0.44, and 0.27 in the 1–100, 101–200, and 201–300 min groups, respectively. In the classification according to age, 0.29 was observed for school-age children and 0.98 for preschool children. Lastly, in the classification according to the RoB, 0.52, −0.01, and 0.23 indicated studies with low risk, some concern, and high risk, respectively. Conclusions The highest effect was observed when VR was applied within 6 weeks of 101-200 per week. Therefore, it is suggested that if the results of this review are applied to children with cerebral palsy in the community, it will be an effective intervention method. Systematic review registration PROPEROS (registration number CRD4202…
bibliographic citation: Han et al. (2023) Effectiveness of virtual reality on activities of daily living in children with cerebral palsy: a systematic review and meta-analysis. PeerJ 11:e15964 https://doi.org/10.7717/peerj.15964
date submitted: 2023-04-20
date accepted: 2023-08-04
issued: 2023-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: YongGu
author list: Agent
  family name: Park
  given name: SunWook
doi: 10.7717/peerj.15964
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-31
copyright: ©2023 Han and Park
attribution name: Han and Park

Accumulation and transfer of polystyrene microplastics in Solanum nigrum seedlings
type: item
type: AcademicArticle
description: Microplastic (MP) pollution is lately receiving increasing attention owing to its harmful impact on terrestrial ecosystems. In this microcosm study, we assessed the uptake and transfer of MPs in Solanum nigrum seedlings exposed to 50 mg L–1 of 0.2-µm polystyrene (PS) beads for 30 d. Confocal laser scanning micrographs helped detect highly intense red fluorescence signals from PS-MP beads in S. nigrum root compared with the controls. Confocal images revealed that the PS beads were primarily distributed in the epidermis and xylem of roots and vascular systems of stems and leaves. Scanning electron microscopy showed that PS beads were scattered on the cell walls of the root xylem and leaf vascular system. Few PS beads were transferred from roots to stems and leaves via the vascular system following the transpiration stream. In conclusion, our findings showed that PS beads accumulated in S. nigrum roots and were transferred from the roots to the aerial parts.
format: application/pdf
format: text/html
creator: JuKui Zhang
creator: Lian Cao
creator: Xiaoyan Zhu
creator: Hanbo Li
creator: Gang Duan
creator: Ying Wang
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Toxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.15967
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Microplastic (MP) pollution is lately receiving increasing attention owing to its harmful impact on terrestrial ecosystems. In this microcosm study, we assessed the uptake and transfer of MPs in Solanum nigrum seedlings exposed to 50 mg L–1 of 0.2-µm polystyrene (PS) beads for 30 d. Confocal laser scanning micrographs helped detect highly intense red fluorescence signals from PS-MP beads in S. nigrum root compared with the controls. Confocal images revealed that the PS beads were primarily distributed in the epidermis and xylem of roots and vascular systems of stems and leaves. Scanning electron microscopy showed that PS beads were scattered on the cell walls of the root xylem and leaf vascular system. Few PS beads were transferred from roots to stems and leaves via the vascular system following the transpiration stream. In conclusion, our findings showed that PS beads accumulated in S. nigrum roots and were transferred from the roots to the aerial parts.
bibliographic citation: Zhang et al. (2023) Accumulation and transfer of polystyrene microplastics in Solanum nigrum seedlings. PeerJ 11:e15967 https://doi.org/10.7717/peerj.15967
date submitted: 2023-03-07
date accepted: 2023-08-04
issued: 2023-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: JuKui
author list: Agent
  family name: Cao
  given name: Lian
author list: Agent
  family name: Zhu
  given name: Xiaoyan
author list: Agent
  family name: Li
  given name: Hanbo
author list: Agent
  family name: Duan
  given name: Gang
author list: Agent
  family name: Wang
  given name: Ying
doi: 10.7717/peerj.15967
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-31
copyright: ©2023 Zhang et al.
attribution name: Zhang et al.

Evaluation of the correlation of dorsal root ganglia and spinal nerves with clinical symptoms in patients with postherpetic neuralgia using magnetic resonance neurography
type: item
type: AcademicArticle
description: Purpose To assess changes of dorsal root ganglia (DRG) and spinal nerves in patients with postherpetic neuralgia (PHN), and investigate the correlation between DRG morphology and clinical symptoms in PHN patients using magnetic resonance neurography (MRN). Methods In this case-control study, forty-nine lesioned DRG in 30 patients and 49 normal DRG in 30 well-matched (age, sex, height, weight) healthy controls were assessed. Clinical symptoms of patients (pain, allodynia, itching, and numbness) were assessed. MRN features (DRG volume (VDRG), the largest diameter (Dmax) of spinal nerves, signal intensity of DRG and spinal nerves (M-value)) were measured in all participants. Multilinear regression analysis was used to evaluate the relationship between the DRG morphology and clinical symptoms in patients. Results The volume and relative M-value of lesioned DRG in patients were significantly higher than those on the same side of healthy controls (p = 0.013, p < 0.001, respectively). The mean Dmax and relative M-value of spinal nerves on the lesioned side were significantly higher than those on the contralateral and same side of healthy controls (p < 0.0001, p = 0.0001, p = 0.0011, p = 0.0053, respectively). No difference was found between the mean VDRG of the lesioned and contralateral sides. Multiple linear regression analysis revealed that disease duration was independent risk factor for the maximum rate of VDRG differences (p = 0.013). Conclusions DRG and spinal nerves on the lesioned side are swollen during PHN. Disease duration is an independent risk factor for morphological differences in the lesioned DRG of PHN patients. This study provides important guidance for individualized treatments of PHN.
format: application/pdf
format: text/html
creator: Xueqin Cao
creator: Bo Jiao
creator: Donglin Wen
creator: Guangyou Duan
creator: Mi Zhang
creator: Caixia Zhang
creator: Gang Wu
creator: Xianwei Zhang
subject: Anesthesiology and Pain Management
subject: Anatomy and Physiology
subject: Dermatology
subject: Nephrology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.15998
publisher: PeerJ Inc.
rights: © 2023 Cao et al.
abstract: Purpose To assess changes of dorsal root ganglia (DRG) and spinal nerves in patients with postherpetic neuralgia (PHN), and investigate the correlation between DRG morphology and clinical symptoms in PHN patients using magnetic resonance neurography (MRN). Methods In this case-control study, forty-nine lesioned DRG in 30 patients and 49 normal DRG in 30 well-matched (age, sex, height, weight) healthy controls were assessed. Clinical symptoms of patients (pain, allodynia, itching, and numbness) were assessed. MRN features (DRG volume (VDRG), the largest diameter (Dmax) of spinal nerves, signal intensity of DRG and spinal nerves (M-value)) were measured in all participants. Multilinear regression analysis was used to evaluate the relationship between the DRG morphology and clinical symptoms in patients. Results The volume and relative M-value of lesioned DRG in patients were significantly higher than those on the same side of healthy controls (p = 0.013, p < 0.001, respectively). The mean Dmax and relative M-value of spinal nerves on the lesioned side were significantly higher than those on the contralateral and same side of healthy controls (p < 0.0001, p = 0.0001, p = 0.0011, p = 0.0053, respectively). No difference was found between the mean VDRG of the lesioned and contralateral sides. Multiple linear regression analysis revealed that disease duration was independent risk factor for the maximum rate of VDRG differences (p = 0.013). Conclusions DRG and spinal nerves on the lesioned side are swollen during PHN. Disease duration is an independent risk factor for morphological differences in the lesioned DRG of PHN patients. This study provides important guidance for individualized treatments of PHN.
bibliographic citation: Cao et al. (2023) Evaluation of the correlation of dorsal root ganglia and spinal nerves with clinical symptoms in patients with postherpetic neuralgia using magnetic resonance neurography. PeerJ 11:e15998 https://doi.org/10.7717/peerj.15998
date submitted: 2023-04-28
date accepted: 2023-08-08
issued: 2023-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Xueqin
author list: Agent
  family name: Jiao
  given name: Bo
author list: Agent
  family name: Wen
  given name: Donglin
author list: Agent
  family name: Duan
  given name: Guangyou
author list: Agent
  family name: Zhang
  given name: Mi
author list: Agent
  family name: Zhang
  given name: Caixia
author list: Agent
  family name: Wu
  given name: Gang
author list: Agent
  family name: Zhang
  given name: Xianwei
doi: 10.7717/peerj.15998
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-31
copyright: © 2023 Cao et al.
attribution name: Cao et al.

A multi-sensor array for detecting and analyzing nocturnal avian migration
type: item
type: AcademicArticle
description: Avian migration has fascinated humans for centuries. Insights into the lives of migrant birds are often elusive; however, recent, standalone technological innovations have revolutionized our understanding of this complex biological phenomenon. A future challenge for following these highly mobile animals is the necessity of bringing multiple technologies together to capture a more complete understanding of their movements. Here, we designed a proof-of-concept multi-sensor array consisting of two weather surveillance radars (WSRs), one local and one regional, an autonomous moon-watching sensor capable of detecting birds flying in front of the moon, and an autonomous recording unit (ARU) capable of recording avian nocturnal flight calls. We deployed this array at a field site in central Oklahoma on select nights in March, April, and May of 2021 and integrated data from this array with wind data corresponding to this site to examine the influence of wind on the movements of spring migrants aloft across these spring nights. We found that regional avian migration intensity is statistically significantly negatively correlated with wind velocity, in line with previous research. Furthermore, we found evidence suggesting that when faced with strong, southerly winds, migrants take advantage of these conditions by adjusting their flight direction by drifting. Importantly, we found that most of the migration intensities detected by the sensors were intercorrelated, except when this correlation could not be ascertained because we lacked the sample size to do so. This study demonstrates the potential for multi-sensor arrays to reveal the detailed ways in which avian migrants move in response to changing atmospheric conditions while in flight.
format: application/pdf
format: text/html
creator: Alva I. Strand
creator: Eli S. Bridge
creator: Jeffrey F. Kelly
creator: Phillip M. Stepanian
creator: David J. Bodine
creator: James R. Soto
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Data Science
subject: Biosphere Interactions
description: doi:10.7717/peerj.15622
publisher: PeerJ Inc.
rights: © 2023 Strand et al.
abstract: Avian migration has fascinated humans for centuries. Insights into the lives of migrant birds are often elusive; however, recent, standalone technological innovations have revolutionized our understanding of this complex biological phenomenon. A future challenge for following these highly mobile animals is the necessity of bringing multiple technologies together to capture a more complete understanding of their movements. Here, we designed a proof-of-concept multi-sensor array consisting of two weather surveillance radars (WSRs), one local and one regional, an autonomous moon-watching sensor capable of detecting birds flying in front of the moon, and an autonomous recording unit (ARU) capable of recording avian nocturnal flight calls. We deployed this array at a field site in central Oklahoma on select nights in March, April, and May of 2021 and integrated data from this array with wind data corresponding to this site to examine the influence of wind on the movements of spring migrants aloft across these spring nights. We found that regional avian migration intensity is statistically significantly negatively correlated with wind velocity, in line with previous research. Furthermore, we found evidence suggesting that when faced with strong, southerly winds, migrants take advantage of these conditions by adjusting their flight direction by drifting. Importantly, we found that most of the migration intensities detected by the sensors were intercorrelated, except when this correlation could not be ascertained because we lacked the sample size to do so. This study demonstrates the potential for multi-sensor arrays to reveal the detailed ways in which avian migrants move in response to changing atmospheric conditions while in flight.
bibliographic citation: Strand et al. (2023) A multi-sensor array for detecting and analyzing nocturnal avian migration. PeerJ 11:e15622 https://doi.org/10.7717/peerj.15622
date submitted: 2022-08-15
date accepted: 2023-06-01
issued: 2023-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Strand
  given name: Alva I.
author list: Agent
  family name: Bridge
  given name: Eli S.
author list: Agent
  family name: Kelly
  given name: Jeffrey F.
author list: Agent
  family name: Stepanian
  given name: Phillip M.
author list: Agent
  family name: Bodine
  given name: David J.
author list: Agent
  family name: Soto
  given name: James R.
doi: 10.7717/peerj.15622
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-30
copyright: © 2023 Strand et al.
attribution name: Strand et al.

Adrenal SGLT1 or SGLT2 as predictors of atherosclerosis under chronic stress based on a computer algorithm
type: item
type: AcademicArticle
description: Background Chronic stress promotes the development of atherosclerosis, causing disruptions in the body’s hormone levels and changes in the structural function of organs. Objective The purpose of this study was to investigate the pathological changes in the adrenal gland in a model of atherosclerosis under chronic stress and to verify the expression levels of Sodium-glucose cotransporter (SGLT) 1 and SGLT2 in the adrenal gland and their significance in the changes of adrenal gland. Methods The model mice were constructed by chronic unpredictable stress, high-fat diet, and Apoe-/- knockout, and they were tested behaviorally at 0, 4, 8 and 12 weeks. The state of the abdominal artery was examined by ultrasound, and the pathological changes of the aorta and adrenal glands were observed by histological methods, and the expression levels and distribution of SGLT1 and SGLT2 in the adrenal gland were observed and analyzed by immunofluorescence and immunohistochemistry. The predictive value of SGLT1 and SGLT2 expression levels on intima-media thickness, internal diameter and adrenal abnormalities were verified by receiver operating characteristic (ROC) curves, support vector machine (SVM) and back-propagation (BP) neural network. Results The results showed that chronic stress mice had elevated expression levels of SGLT1 and SGLT2. The model mice developed thickening intima-media and smaller internal diameter in the aorta, and edema, reticular fiber rupture, increased adrenal glycogen content in the adrenal glands. More importantly, analysis of ROC, SVM and BP showed that SGLT1 and SGLT2 expression levels in the adrenal glands could predict the above changes in the aorta and were also sensitive and specific predictors of adrenal abnormalities. Conclusion SGLT1 and SGLT2 could be potential biomarkers of adrenal injury in atherosclerosis under chronic stress.
format: application/pdf
format: text/html
creator: Jianyi Li
creator: Lingbing Meng
creator: Dishan Wu
creator: Hongxuan Xu
creator: Xing Hu
creator: Gaifeng Hu
creator: Yuhui Chen
creator: Jiapei Xu
creator: Tao Gong
creator: Deping Liu
subject: Biochemistry
subject: Computational Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.15647
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background Chronic stress promotes the development of atherosclerosis, causing disruptions in the body’s hormone levels and changes in the structural function of organs. Objective The purpose of this study was to investigate the pathological changes in the adrenal gland in a model of atherosclerosis under chronic stress and to verify the expression levels of Sodium-glucose cotransporter (SGLT) 1 and SGLT2 in the adrenal gland and their significance in the changes of adrenal gland. Methods The model mice were constructed by chronic unpredictable stress, high-fat diet, and Apoe-/- knockout, and they were tested behaviorally at 0, 4, 8 and 12 weeks. The state of the abdominal artery was examined by ultrasound, and the pathological changes of the aorta and adrenal glands were observed by histological methods, and the expression levels and distribution of SGLT1 and SGLT2 in the adrenal gland were observed and analyzed by immunofluorescence and immunohistochemistry. The predictive value of SGLT1 and SGLT2 expression levels on intima-media thickness, internal diameter and adrenal abnormalities were verified by receiver operating characteristic (ROC) curves, support vector machine (SVM) and back-propagation (BP) neural network. Results The results showed that chronic stress mice had elevated expression levels of SGLT1 and SGLT2. The model mice developed thickening intima-media and smaller internal diameter in the aorta, and edema, reticular fiber rupture, increased adrenal glycogen content in the adrenal glands. More importantly, analysis of ROC, SVM and BP showed that SGLT1 and SGLT2 expression levels in the adrenal glands could predict the above changes in the aorta and were also sensitive and specific predictors of adrenal abnormalities. Conclusion SGLT1 and SGLT2 could be potential biomarkers of adrenal injury in atherosclerosis under chronic stress.
bibliographic citation: Li et al. (2023) Adrenal SGLT1 or SGLT2 as predictors of atherosclerosis under chronic stress based on a computer algorithm. PeerJ 11:e15647 https://doi.org/10.7717/peerj.15647
date submitted: 2023-03-23
date accepted: 2023-06-06
issued: 2023-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jianyi
author list: Agent
  family name: Meng
  given name: Lingbing
author list: Agent
  family name: Wu
  given name: Dishan
author list: Agent
  family name: Xu
  given name: Hongxuan
author list: Agent
  family name: Hu
  given name: Xing
author list: Agent
  family name: Hu
  given name: Gaifeng
author list: Agent
  family name: Chen
  given name: Yuhui
author list: Agent
  family name: Xu
  given name: Jiapei
author list: Agent
  family name: Gong
  given name: Tao
author list: Agent
  family name: Liu
  given name: Deping
doi: 10.7717/peerj.15647
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-30
copyright: ©2023 Li et al.
attribution name: Li et al.

RNA N6-methyladenosine reader IGF2BP3 promotes acute myeloid leukemia progression by controlling stabilization of EPOR mRNA
type: item
type: AcademicArticle
description: Background N6-methyladenosine (m6A) methylation epigenetically regulates normal hematopoiesis and plays a role in the pathogenesis of acute myeloid leukemia (AML). However, its potential value for prognosis remains elusive. Methods Analysis of the datasets downloaded from The Cancer Genome Atlas and Genotype Tissue Expression databases revealed that the expression level of 20 regulators related to m6A RNA methylation differ between patients with AML and normal individuals. A prognostic risk model with three genes (YTHDF3, IGF2BP3, and HNRNPA2B1) was developed using univariate Cox regression and the least absolute shrinkage and selection operator Cox regression methods. Results This established signature demonstrated good predictive efficacy with an area under the curve of 0.892 and 0.731 in the training cohort and the validation cohort, respectively. Patients with AML and an increased level of Insulin growth factor 2 mRNA binding protein 3 (IGF2BP3) expression exhibited a poor prognosis. IGF2BP3 knockdown significantly induced G0/G1 phase arrest and inhibited cell proliferation, apoptosis, and/or differentiation. Further, the JAK/STAT pathway may be involved in the regulation of EPOR expression by IGF2BP3-mediated m6A RNA methylation. Conclusion These findings indicate that IGF2BP3 plays a carcinogenic role in AML, implying that it can predict patient survival and could be an effective strategy for AML therapy.
format: application/pdf
format: text/html
creator: Jin Fan
creator: Mengqi Zhuang
creator: Wei Fan
creator: Ming Hou
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Hematology
subject: Oncology
description: doi:10.7717/peerj.15706
publisher: PeerJ Inc.
rights: © 2023 Fan et al.
abstract: Background N6-methyladenosine (m6A) methylation epigenetically regulates normal hematopoiesis and plays a role in the pathogenesis of acute myeloid leukemia (AML). However, its potential value for prognosis remains elusive. Methods Analysis of the datasets downloaded from The Cancer Genome Atlas and Genotype Tissue Expression databases revealed that the expression level of 20 regulators related to m6A RNA methylation differ between patients with AML and normal individuals. A prognostic risk model with three genes (YTHDF3, IGF2BP3, and HNRNPA2B1) was developed using univariate Cox regression and the least absolute shrinkage and selection operator Cox regression methods. Results This established signature demonstrated good predictive efficacy with an area under the curve of 0.892 and 0.731 in the training cohort and the validation cohort, respectively. Patients with AML and an increased level of Insulin growth factor 2 mRNA binding protein 3 (IGF2BP3) expression exhibited a poor prognosis. IGF2BP3 knockdown significantly induced G0/G1 phase arrest and inhibited cell proliferation, apoptosis, and/or differentiation. Further, the JAK/STAT pathway may be involved in the regulation of EPOR expression by IGF2BP3-mediated m6A RNA methylation. Conclusion These findings indicate that IGF2BP3 plays a carcinogenic role in AML, implying that it can predict patient survival and could be an effective strategy for AML therapy.
bibliographic citation: Fan et al. (2023) RNA N6-methyladenosine reader IGF2BP3 promotes acute myeloid leukemia progression by controlling stabilization of EPOR mRNA. PeerJ 11:e15706 https://doi.org/10.7717/peerj.15706
date submitted: 2023-03-03
date accepted: 2023-06-15
issued: 2023-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Jin
author list: Agent
  family name: Zhuang
  given name: Mengqi
author list: Agent
  family name: Fan
  given name: Wei
author list: Agent
  family name: Hou
  given name: Ming
doi: 10.7717/peerj.15706
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-30
copyright: © 2023 Fan et al.
attribution name: Fan et al.

Fishery-based adaption to climate change: the case of migratory species flathead grey mullet (Mugil cephalus L.) in Taiwan Strait, Northwestern Pacific
type: item
type: AcademicArticle
description: The flathead gray mullet (Mugil cephalus L.) is a cosmopolitan fish that lives in warm and temperate zones over 42°N–42°S. It is a key fish species for industrial fishing off coastal Taiwan. Gray mullets enter the coastal waters of the southeastern Taiwan Strait (22°N–25°N) to spawn in winter and feed in the coastal and tidal waters of China (25°N–30°N). From 1986 to 2010, the annual catch of gray mullet decreased substantially and remained low. Although the Pacific Decadal Oscillation and El Niño–Southern Oscillation are recognized to affect gray mullet migration, the increase in sea surface temperature may be the main cause of the aforementioned decrease. We explored how weather changes affect fishing conditions and patterns at the gray mullet fishing grounds in Taiwan’s coastal areas. Because of the decrease in gray mullet catches, the most common method for catching gray mullet in Taiwan’s coastal areas between 1990 and 2010 was the use of drift or trawl nets instead of two-boat purse-seiner fleets. Since 2012, purse-seiner fleets have become the most common method for catching gray mullet. This trend indicates that the local fishing industry is adapting to changing environmental conditions.
format: application/pdf
format: text/html
creator: Ming An Lee
creator: Sandipan Mondal
creator: Sheng-Yuan Teng
creator: Manh-Linh Nguyen
creator: Platinasoka Lin
creator: Jun-Hong Wu
creator: Biraj Kanti Mondal
subject: Aquaculture
subject: Fisheries and Fish Science
subject: Marine Biology
subject: Natural Resource Management
subject: Biological Oceanography
description: doi:10.7717/peerj.15788
publisher: PeerJ Inc.
rights: © 2023 Lee et al.
abstract: The flathead gray mullet (Mugil cephalus L.) is a cosmopolitan fish that lives in warm and temperate zones over 42°N–42°S. It is a key fish species for industrial fishing off coastal Taiwan. Gray mullets enter the coastal waters of the southeastern Taiwan Strait (22°N–25°N) to spawn in winter and feed in the coastal and tidal waters of China (25°N–30°N). From 1986 to 2010, the annual catch of gray mullet decreased substantially and remained low. Although the Pacific Decadal Oscillation and El Niño–Southern Oscillation are recognized to affect gray mullet migration, the increase in sea surface temperature may be the main cause of the aforementioned decrease. We explored how weather changes affect fishing conditions and patterns at the gray mullet fishing grounds in Taiwan’s coastal areas. Because of the decrease in gray mullet catches, the most common method for catching gray mullet in Taiwan’s coastal areas between 1990 and 2010 was the use of drift or trawl nets instead of two-boat purse-seiner fleets. Since 2012, purse-seiner fleets have become the most common method for catching gray mullet. This trend indicates that the local fishing industry is adapting to changing environmental conditions.
bibliographic citation: Lee et al. (2023) Fishery-based adaption to climate change: the case of migratory species flathead grey mullet (Mugil cephalus L.) in Taiwan Strait, Northwestern Pacific. PeerJ 11:e15788 https://doi.org/10.7717/peerj.15788
date submitted: 2023-02-02
date accepted: 2023-07-04
issued: 2023-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Ming An
author list: Agent
  family name: Mondal
  given name: Sandipan
author list: Agent
  family name: Teng
  given name: Sheng-Yuan
author list: Agent
  family name: Nguyen
  given name: Manh-Linh
author list: Agent
  family name: Lin
  given name: Platinasoka
author list: Agent
  family name: Wu
  given name: Jun-Hong
author list: Agent
  family name: Mondal
  given name: Biraj Kanti
doi: 10.7717/peerj.15788
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-30
copyright: © 2023 Lee et al.
attribution name: Lee et al.

Carboxypeptidase E is a prognostic biomarker co-expressed with osteoblastic genes in osteosarcoma
type: item
type: AcademicArticle
description: Osteosarcoma (OS) is a rare primary malignant bone tumor in adolescents and children with a poor prognosis. The identification of prognostic genes lags far behind advancements in treatment. In this study, we identified differential genes using mRNA microarray analysis of five paired OS tissues. Hub genes, gene set enrichment analysis, and pathway analysis were performed to gain insight into the pathway alterations of OS. Prognostic genes were screened using the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) dataset, then overlapped with the differential gene dataset. The carboxypeptidase E (CPE) gene, found to be an independent risk factor, was further validated using RT-PCR and Gene Expression Omnibus (GEO) datasets. Additionally, we explored the specific expression of CPE in OS tissues by reanalyzing single-cell genomics. Interestingly, CPE was found to be co-expressed with osteoblast lineage cell clusters that expressed RUNX2, SP7, SPP1, and IBSP marker genes in OS. These results suggest that CPE could serve as a prognostic factor in osteoblastic OS and should be further investigated as a potential therapeutic target.
format: application/pdf
format: text/html
creator: Dafu Chen
creator: Ben Wan
creator: Yuning Cheng
creator: Yuwen Luo
creator: Xueshan Bai
creator: Jianxun Guo
creator: Guangping Li
creator: Tao Jin
creator: Jingjun Nie
creator: Weifeng Liu
creator: Renxian Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Orthopedics
subject: Medical Genetics
description: doi:10.7717/peerj.15814
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Osteosarcoma (OS) is a rare primary malignant bone tumor in adolescents and children with a poor prognosis. The identification of prognostic genes lags far behind advancements in treatment. In this study, we identified differential genes using mRNA microarray analysis of five paired OS tissues. Hub genes, gene set enrichment analysis, and pathway analysis were performed to gain insight into the pathway alterations of OS. Prognostic genes were screened using the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) dataset, then overlapped with the differential gene dataset. The carboxypeptidase E (CPE) gene, found to be an independent risk factor, was further validated using RT-PCR and Gene Expression Omnibus (GEO) datasets. Additionally, we explored the specific expression of CPE in OS tissues by reanalyzing single-cell genomics. Interestingly, CPE was found to be co-expressed with osteoblast lineage cell clusters that expressed RUNX2, SP7, SPP1, and IBSP marker genes in OS. These results suggest that CPE could serve as a prognostic factor in osteoblastic OS and should be further investigated as a potential therapeutic target.
bibliographic citation: Chen et al. (2023) Carboxypeptidase E is a prognostic biomarker co-expressed with osteoblastic genes in osteosarcoma. PeerJ 11:e15814 https://doi.org/10.7717/peerj.15814
date submitted: 2023-03-30
date accepted: 2023-07-10
issued: 2023-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Dafu
author list: Agent
  family name: Wan
  given name: Ben
author list: Agent
  family name: Cheng
  given name: Yuning
author list: Agent
  family name: Luo
  given name: Yuwen
author list: Agent
  family name: Bai
  given name: Xueshan
author list: Agent
  family name: Guo
  given name: Jianxun
author list: Agent
  family name: Li
  given name: Guangping
author list: Agent
  family name: Jin
  given name: Tao
author list: Agent
  family name: Nie
  given name: Jingjun
author list: Agent
  family name: Liu
  given name: Weifeng
author list: Agent
  family name: Wang
  given name: Renxian
doi: 10.7717/peerj.15814
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-30
copyright: © 2023 Chen et al.
attribution name: Chen et al.

Identification and characterization of novel sesquiterpene synthases TPS9 and TPS12 from Aquilaria sinensis
type: item
type: AcademicArticle
description: Sesquiterpenes are characteristic components and important quality criterions for agarwood. Although sesquiterpenes are well-known to be biosynthesized by sesquiterpene synthases (TPSs), to date, only a few TPS genes involved in agarwood formation have been reported. Here, two new TPS genes, namely, TPS9 and TPS12, were isolated from Aquilaria sinensis (Lour.) Gilg, and their functions were examined in Escherichia coli BL21(DE3), with farnesyl pyrophosphate (FPP) and geranyl pyrophosphate (GPP) as the substrate of the corresponding enzyme activities. They were both identified as a multiproduct enzymes. After incubation with FPP, TPS9 liberated β-farnesene and cis-sesquisabinene hydrate as main products, with cedrol and another unidentified sesquiterpene as minor products. TPS12 catalyzes the formation of β-farnesene, nerolidol, γ-eudesmol, and hinesol. After incubation with GPP, TPS9 generated citronellol and geraniol as main products, with seven minor products. TPS12 converted GPP into four monoterpenes, with citral as the main product, and three minor products. Both TPS9 and TPS12 showed much higher expression in the two major tissues emitting floral volatiles: flowers and agarwood. Further, RT-PCR analysis showed TPS9 and TPS12 are typical genes mainly expressed during later stages of stress response, which is better known than that of chromone derivatives. This study will advance our understanding of agarwood formation and provide a solid theoretical foundation for clarifying its mechanism in A. sinensis.
format: application/pdf
format: text/html
creator: Cuicui Yu
creator: Shixi Gao
creator: Mei Rong
creator: Mengjun Xiao
creator: Yanhong Xu
creator: Jianhe Wei
subject: Agricultural Science
subject: Biodiversity
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15818
publisher: PeerJ Inc.
rights: © 2023 Yu et al.
abstract: Sesquiterpenes are characteristic components and important quality criterions for agarwood. Although sesquiterpenes are well-known to be biosynthesized by sesquiterpene synthases (TPSs), to date, only a few TPS genes involved in agarwood formation have been reported. Here, two new TPS genes, namely, TPS9 and TPS12, were isolated from Aquilaria sinensis (Lour.) Gilg, and their functions were examined in Escherichia coli BL21(DE3), with farnesyl pyrophosphate (FPP) and geranyl pyrophosphate (GPP) as the substrate of the corresponding enzyme activities. They were both identified as a multiproduct enzymes. After incubation with FPP, TPS9 liberated β-farnesene and cis-sesquisabinene hydrate as main products, with cedrol and another unidentified sesquiterpene as minor products. TPS12 catalyzes the formation of β-farnesene, nerolidol, γ-eudesmol, and hinesol. After incubation with GPP, TPS9 generated citronellol and geraniol as main products, with seven minor products. TPS12 converted GPP into four monoterpenes, with citral as the main product, and three minor products. Both TPS9 and TPS12 showed much higher expression in the two major tissues emitting floral volatiles: flowers and agarwood. Further, RT-PCR analysis showed TPS9 and TPS12 are typical genes mainly expressed during later stages of stress response, which is better known than that of chromone derivatives. This study will advance our understanding of agarwood formation and provide a solid theoretical foundation for clarifying its mechanism in A. sinensis.
bibliographic citation: Yu et al. (2023) Identification and characterization of novel sesquiterpene synthases TPS9 and TPS12 from Aquilaria sinensis. PeerJ 11:e15818 https://doi.org/10.7717/peerj.15818
date submitted: 2022-04-22
date accepted: 2023-07-10
issued: 2023-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Cuicui
author list: Agent
  family name: Gao
  given name: Shixi
author list: Agent
  family name: Rong
  given name: Mei
author list: Agent
  family name: Xiao
  given name: Mengjun
author list: Agent
  family name: Xu
  given name: Yanhong
author list: Agent
  family name: Wei
  given name: Jianhe
doi: 10.7717/peerj.15818
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-30
copyright: ©2023 Yu et al.
attribution name: Yu et al.

Intestinal GPDH-1 regulates high glucose diet induced lifespan extension in aged worms
type: item
type: AcademicArticle
description: A high glucose diet (HGD) is associated with many metabolic diseases including type 2 diabetes, and cardiovascular diseases. Additionally, a HGD increases the oxidative stress resistance of young animals but shortens their lifespan. To investigate the role of HGD feeding on the aging of aged animals, we tested for oxidative stress resistance and changes in lifespan using C. elegans. We showed that a HGD extends the lifespan of aged worms that are dependent on oxidative stress resistance. Furthermore, we measured the lifespan of oxidative stress responding genes of HGD-fed worms. We found that gpdh-1 and col-92 are highly expressed in HGD and paraquat (PQ) treated worms. Further experiments indicated that intestinal gpdh-1 is essential for the HGD induced lifespan extension of aged worms. Our studies provide new insights into understanding the correlation between glucose metabolism, oxidative stress resistance, and aging.
format: application/pdf
format: text/html
creator: Jihao Mo
creator: Zhenzhen Zhang
creator: Xiaowei Wang
creator: Miaomiao Wang
creator: Ning Sun
creator: Lei Wang
creator: Meimei Wang
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.15845
publisher: PeerJ Inc.
rights: © 2023 Mo et al.
abstract: A high glucose diet (HGD) is associated with many metabolic diseases including type 2 diabetes, and cardiovascular diseases. Additionally, a HGD increases the oxidative stress resistance of young animals but shortens their lifespan. To investigate the role of HGD feeding on the aging of aged animals, we tested for oxidative stress resistance and changes in lifespan using C. elegans. We showed that a HGD extends the lifespan of aged worms that are dependent on oxidative stress resistance. Furthermore, we measured the lifespan of oxidative stress responding genes of HGD-fed worms. We found that gpdh-1 and col-92 are highly expressed in HGD and paraquat (PQ) treated worms. Further experiments indicated that intestinal gpdh-1 is essential for the HGD induced lifespan extension of aged worms. Our studies provide new insights into understanding the correlation between glucose metabolism, oxidative stress resistance, and aging.
bibliographic citation: Mo et al. (2023) Intestinal GPDH-1 regulates high glucose diet induced lifespan extension in aged worms. PeerJ 11:e15845 https://doi.org/10.7717/peerj.15845
date submitted: 2023-03-08
date accepted: 2023-07-14
issued: 2023-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mo
  given name: Jihao
author list: Agent
  family name: Zhang
  given name: Zhenzhen
author list: Agent
  family name: Wang
  given name: Xiaowei
author list: Agent
  family name: Wang
  given name: Miaomiao
author list: Agent
  family name: Sun
  given name: Ning
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Wang
  given name: Meimei
doi: 10.7717/peerj.15845
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-30
copyright: © 2023 Mo et al.
attribution name: Mo et al.

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