PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Relationship between catheter related cerebrospinal fluid infections and systemic immune-inflammation index
items: Identification and expression analysis of the small auxin-up RNA (SAUR) gene family in Lycium ruthenicum
items: The evolution of SARS-CoV-2 and the COVID-19 pandemic
items: Head lice: impact of COVID-19 and slow recovery of prevalence in Cambridgeshire, UK
items: Structural and functional brain changes in people with knee osteoarthritis: a scoping review
items: Application of bubble streams to control biofouling on marine infrastructure—pontoon-scale implementation
items: Genetic polymorphisms in the C19orf66 gene influenced HIV-1 infection in a Yunnan population
items: Appendage abnormalities in spiders induced by an alternating temperature protocol in the context of recent advances in molecular spider embryology
items: The current landscape of m6A modification in urological cancers
items: Temporal variation of the relationships between rice yield and climate variables since 1925

Relationship between catheter related cerebrospinal fluid infections and systemic immune-inflammation index
type: item
type: AcademicArticle
description: Background This study investigated the relationship between the systemic immune inflammation index (SII) and catheter-related infections and their effects on prognosis in pediatric patients. Methods A total of 56 pediatric patients diagnosed with ventriculoperitoneal (V-P) shunt infection between January 2017 and October 2019 were included. V-P shunt infection diagnosis was made based on clinical findings. All cerebrospinal fluid (CSF) samples were subjected to direct microscopic examination and culture. Protein, glucose, and sodium levels in CSF, CSF leukocytes, and hematological and biochemical parameters were measured. Results Fifty-six patients with growth in CSF culture were included in this study. 55.4% of the cases were female and 44.6% male. V-P shunt was detected in 82.1% of the cases and external ventricular drainage (EVD) catheter-related infection in 17.9%. The CSF/blood glucose ratio was significantly lower (p = 0.046), and SII was significantly increased (p = 0.002) in non-coagulase-negative staphylococci. Conclusions Early and appropriate antibiotic therapy reduces morbidity and mortality in catheter-related infections. However, it is important to start empirical antibiotherapy until culture results are expected. Therefore, further research on the estimation of possible factors is needed.
format: application/pdf
format: text/html
creator: Sebnem Nergiz
creator: Pinar Aydin Ozturk
subject: Infectious Diseases
subject: Neurology
subject: Pediatrics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.15905
publisher: PeerJ Inc.
rights: © 2023 Nergiz and Aydin Ozturk
abstract: Background This study investigated the relationship between the systemic immune inflammation index (SII) and catheter-related infections and their effects on prognosis in pediatric patients. Methods A total of 56 pediatric patients diagnosed with ventriculoperitoneal (V-P) shunt infection between January 2017 and October 2019 were included. V-P shunt infection diagnosis was made based on clinical findings. All cerebrospinal fluid (CSF) samples were subjected to direct microscopic examination and culture. Protein, glucose, and sodium levels in CSF, CSF leukocytes, and hematological and biochemical parameters were measured. Results Fifty-six patients with growth in CSF culture were included in this study. 55.4% of the cases were female and 44.6% male. V-P shunt was detected in 82.1% of the cases and external ventricular drainage (EVD) catheter-related infection in 17.9%. The CSF/blood glucose ratio was significantly lower (p = 0.046), and SII was significantly increased (p = 0.002) in non-coagulase-negative staphylococci. Conclusions Early and appropriate antibiotic therapy reduces morbidity and mortality in catheter-related infections. However, it is important to start empirical antibiotherapy until culture results are expected. Therefore, further research on the estimation of possible factors is needed.
bibliographic citation: Nergiz et al. (2023) Relationship between catheter related cerebrospinal fluid infections and systemic immune-inflammation index. PeerJ 11:e15905 https://doi.org/10.7717/peerj.15905
date submitted: 2023-05-03
date accepted: 2023-07-25
issued: 2023-09-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nergiz
  given name: Sebnem
author list: Agent
  family name: Aydin Ozturk
  given name: Pinar
doi: 10.7717/peerj.15905
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-07
copyright: ©2023 Nergiz and Aydin Ozturk
attribution name: Nergiz and Aydin Ozturk

Identification and expression analysis of the small auxin-up RNA (SAUR) gene family in Lycium ruthenicum
type: item
type: AcademicArticle
description: The plant hormone auxin regulates numerous aspects of plant growth and development, and small auxin-up RNA (SAUR) is the largest family of early auxin response genes in higher plants. SAUR has been implicated in the regulation of multiple biological processes. However, no comprehensive analysis of SAUR genes has been reported in Lycium ruthenicum. L. ruthenicum is a thorny shrub with very pronounced salt and drought tolerance, and studies have shown that stem thorns are related to drought tolerance in L. ruthenicum. In this study, the identification, phylogenetic analysis, and conserved motif prediction of SAUR genes were extensively explored. Furthermore, the tissue expression patterns of selected SAUR genes were assayed with quantitative real-time polymerase chain reaction (RT-qPCR). A total of 33 putative LrSAURs were identified and divided into three clusters in a phylogenetic tree of L. ruthenicum. MEME analysis identified 10 motifs in L. ruthenicum, and the results suggested that motif 1 and motif 3 were widely distributed. Analyzing the transcriptome data of stem thorns at four developmental stages indicated that LrSAURs were differentially expressed in L. ruthenicum, and could be divided into six expression patterns. The RT-qPCR analysis of 21 genes showed that LrSAUR2, LrSAUR8, LrSAUR9, LrSAUR11, LrSAUR12, and LrSAUR19 were mainly expressed in stems and stem thorns, and may be related to stem thorn development.
format: application/pdf
format: text/html
creator: Jing Hu
creator: Qiushi Yu
creator: Shengxiu Jiang
creator: Xiaoke Hu
creator: Xuemin Li
creator: Zhongchao Liu
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15941
publisher: PeerJ Inc.
rights: © 2023 Hu et al.
abstract: The plant hormone auxin regulates numerous aspects of plant growth and development, and small auxin-up RNA (SAUR) is the largest family of early auxin response genes in higher plants. SAUR has been implicated in the regulation of multiple biological processes. However, no comprehensive analysis of SAUR genes has been reported in Lycium ruthenicum. L. ruthenicum is a thorny shrub with very pronounced salt and drought tolerance, and studies have shown that stem thorns are related to drought tolerance in L. ruthenicum. In this study, the identification, phylogenetic analysis, and conserved motif prediction of SAUR genes were extensively explored. Furthermore, the tissue expression patterns of selected SAUR genes were assayed with quantitative real-time polymerase chain reaction (RT-qPCR). A total of 33 putative LrSAURs were identified and divided into three clusters in a phylogenetic tree of L. ruthenicum. MEME analysis identified 10 motifs in L. ruthenicum, and the results suggested that motif 1 and motif 3 were widely distributed. Analyzing the transcriptome data of stem thorns at four developmental stages indicated that LrSAURs were differentially expressed in L. ruthenicum, and could be divided into six expression patterns. The RT-qPCR analysis of 21 genes showed that LrSAUR2, LrSAUR8, LrSAUR9, LrSAUR11, LrSAUR12, and LrSAUR19 were mainly expressed in stems and stem thorns, and may be related to stem thorn development.
bibliographic citation: Hu et al. (2023) Identification and expression analysis of the small auxin-up RNA (SAUR) gene family in Lycium ruthenicum. PeerJ 11:e15941 https://doi.org/10.7717/peerj.15941
date submitted: 2023-03-29
date accepted: 2023-07-31
issued: 2023-09-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Jing
author list: Agent
  family name: Yu
  given name: Qiushi
author list: Agent
  family name: Jiang
  given name: Shengxiu
author list: Agent
  family name: Hu
  given name: Xiaoke
author list: Agent
  family name: Li
  given name: Xuemin
author list: Agent
  family name: Liu
  given name: Zhongchao
doi: 10.7717/peerj.15941
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-07
copyright: ©2023 Hu et al.
attribution name: Hu et al.

The evolution of SARS-CoV-2 and the COVID-19 pandemic
type: item
type: AcademicArticle
description: Scientists have made great efforts to understand the evolution of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) to provide crucial information to public health experts on strategies to control this viral pathogen. The pandemic of the coronavirus disease that began in 2019, COVID-19, lasted nearly three years, and nearly all countries have set different epidemic prevention policies for this virus. The continuous evolution of SARS-CoV-2 alters its pathogenicity and infectivity in human hosts, thus the policy and treatments have been continually adjusted. Based on our previous study on the dynamics of binding ability prediction between the COVID-19 spike protein and human ACE2, the present study mined over 10 million sequences and epidemiological data of SARS-CoV-2 during 2020-2022 to understand the evolutionary path of SARS-CoV-2. We analyzed and predicted the mutation rates of the whole genome and main proteins of SARS-CoV-2 from different populations to understand the adaptive relationship between humans and COVID-19. Our study identified a correlation of the mutation rates from each protein of SARS-CoV-2 and various human populations. Overall, this analysis provides a scientific basis for developing data-driven strategies to confront human pathogens.
format: application/pdf
format: text/html
creator: Yuanfang Si
creator: Weidong Wu
creator: Xia Xue
creator: Xiangdong Sun
creator: Yaping Qin
creator: Ya Li
creator: Chunjing Qiu
creator: Yingying Li
creator: Ziran Zhuo
creator: Yang Mi
creator: Pengyuan Zheng
subject: Bioinformatics
subject: Virology
subject: Global Health
subject: COVID-19
description: doi:10.7717/peerj.15990
publisher: PeerJ Inc.
rights: © 2023 Si et al.
abstract: Scientists have made great efforts to understand the evolution of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) to provide crucial information to public health experts on strategies to control this viral pathogen. The pandemic of the coronavirus disease that began in 2019, COVID-19, lasted nearly three years, and nearly all countries have set different epidemic prevention policies for this virus. The continuous evolution of SARS-CoV-2 alters its pathogenicity and infectivity in human hosts, thus the policy and treatments have been continually adjusted. Based on our previous study on the dynamics of binding ability prediction between the COVID-19 spike protein and human ACE2, the present study mined over 10 million sequences and epidemiological data of SARS-CoV-2 during 2020-2022 to understand the evolutionary path of SARS-CoV-2. We analyzed and predicted the mutation rates of the whole genome and main proteins of SARS-CoV-2 from different populations to understand the adaptive relationship between humans and COVID-19. Our study identified a correlation of the mutation rates from each protein of SARS-CoV-2 and various human populations. Overall, this analysis provides a scientific basis for developing data-driven strategies to confront human pathogens.
bibliographic citation: Si et al. (2023) The evolution of SARS-CoV-2 and the COVID-19 pandemic. PeerJ 11:e15990 https://doi.org/10.7717/peerj.15990
date submitted: 2023-03-21
date accepted: 2023-08-08
issued: 2023-09-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Si
  given name: Yuanfang
author list: Agent
  family name: Wu
  given name: Weidong
author list: Agent
  family name: Xue
  given name: Xia
author list: Agent
  family name: Sun
  given name: Xiangdong
author list: Agent
  family name: Qin
  given name: Yaping
author list: Agent
  family name: Li
  given name: Ya
author list: Agent
  family name: Qiu
  given name: Chunjing
author list: Agent
  family name: Li
  given name: Yingying
author list: Agent
  family name: Zhuo
  given name: Ziran
author list: Agent
  family name: Mi
  given name: Yang
author list: Agent
  family name: Zheng
  given name: Pengyuan
doi: 10.7717/peerj.15990
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-07
copyright: ©2023 Si et al.
attribution name: Si et al.

Head lice: impact of COVID-19 and slow recovery of prevalence in Cambridgeshire, UK
type: item
type: AcademicArticle
description: Following school closures and changes in contact behavior of children and adults a reduced head louse prevalence has been reported from across the globe. In parallel, sales of treatments were observed to fall, partly because of supply problems of some products following the pandemic, but this did not appear to result in more cases of infestation. Surveys of schools in and around Cambridge, UK, found that infestation rates were significantly reduced particularly in city schools compared with similar surveys conducted before the COVID-19 pandemic. Contrary to expectation the number of cases in schools has only risen slowly since schools returned to normal full time working in 2022–2023.
format: application/pdf
format: text/html
creator: Ian F. Burgess
creator: Elizabeth R. Brunton
creator: Mark N. Burgess
subject: Dermatology
subject: Epidemiology
subject: Infectious Diseases
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.16001
publisher: PeerJ Inc.
rights: © 2023 Burgess et al.
abstract: Following school closures and changes in contact behavior of children and adults a reduced head louse prevalence has been reported from across the globe. In parallel, sales of treatments were observed to fall, partly because of supply problems of some products following the pandemic, but this did not appear to result in more cases of infestation. Surveys of schools in and around Cambridge, UK, found that infestation rates were significantly reduced particularly in city schools compared with similar surveys conducted before the COVID-19 pandemic. Contrary to expectation the number of cases in schools has only risen slowly since schools returned to normal full time working in 2022–2023.
bibliographic citation: Burgess et al. (2023) Head lice: impact of COVID-19 and slow recovery of prevalence in Cambridgeshire, UK. PeerJ 11:e16001 https://doi.org/10.7717/peerj.16001
date submitted: 2023-06-28
date accepted: 2023-08-09
issued: 2023-09-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Burgess
  given name: Ian F.
author list: Agent
  family name: Brunton
  given name: Elizabeth R.
author list: Agent
  family name: Burgess
  given name: Mark N.
doi: 10.7717/peerj.16001
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-07
copyright: ©2023 Burgess et al.
attribution name: Burgess et al.

Structural and functional brain changes in people with knee osteoarthritis: a scoping review
type: item
type: AcademicArticle
description: Background Knee osteoarthritis is a highly prevalent disease worldwide that leads to functional disability and chronic pain. It has been shown that not only changes are generated at the joint level in these individuals, but also neuroplastic changes are produced in different brain areas, especially in those areas related to pain perception, therefore, the objective of this research was to identify and compare the structural and functional brain changes in knee OA versus healthy subjects. Methodology Searches in MEDLINE (PubMed), EMBASE, WOS, CINAHL, SCOPUS, Health Source, and Epistemonikos databases were conducted to explore the available evidence on the structural and functional brain changes occurring in people with knee OA. Data were recorded on study characteristics, participant characteristics, and brain assessment techniques. The methodological quality of the studies was analysed with Newcastle Ottawa Scale. Results Sixteen studies met the inclusion criteria. A decrease volume of the gray matter in the insular region, parietal lobe, cingulate cortex, hippocampus, visual cortex, temporal lobe, prefrontal cortex, and basal ganglia was found in people with knee OA. However, the opposite occurred in the frontal lobe, nucleus accumbens, amygdala region and somatosensory cortex, where an increase in the gray matter volume was evidenced. Moreover, a decreased connectivity to the frontal lobe from the insula, cingulate cortex, parietal, and temporal areas, and an increase in connectivity from the insula to the prefrontal cortex, subcallosal area, and temporal lobe was shown. Conclusion All these findings are suggestive of neuroplastic changes affecting the pain matrix in people with knee OA.
format: application/pdf
format: text/html
creator: Joaquín Salazar-Méndez
creator: Iván Cuyul-Vásquez
creator: Nelson Viscay-Sanhueza
creator: Juan Morales-Verdugo
creator: Guillermo Mendez-Rebolledo
creator: Felipe Ponce-Fuentes
creator: Enrique Lluch-Girbés
subject: Anatomy and Physiology
subject: Neurology
subject: Radiology and Medical Imaging
subject: Rheumatology
subject: Rehabilitation
description: doi:10.7717/peerj.16003
publisher: PeerJ Inc.
rights: © 2023 Salazar-Méndez et al.
abstract: Background Knee osteoarthritis is a highly prevalent disease worldwide that leads to functional disability and chronic pain. It has been shown that not only changes are generated at the joint level in these individuals, but also neuroplastic changes are produced in different brain areas, especially in those areas related to pain perception, therefore, the objective of this research was to identify and compare the structural and functional brain changes in knee OA versus healthy subjects. Methodology Searches in MEDLINE (PubMed), EMBASE, WOS, CINAHL, SCOPUS, Health Source, and Epistemonikos databases were conducted to explore the available evidence on the structural and functional brain changes occurring in people with knee OA. Data were recorded on study characteristics, participant characteristics, and brain assessment techniques. The methodological quality of the studies was analysed with Newcastle Ottawa Scale. Results Sixteen studies met the inclusion criteria. A decrease volume of the gray matter in the insular region, parietal lobe, cingulate cortex, hippocampus, visual cortex, temporal lobe, prefrontal cortex, and basal ganglia was found in people with knee OA. However, the opposite occurred in the frontal lobe, nucleus accumbens, amygdala region and somatosensory cortex, where an increase in the gray matter volume was evidenced. Moreover, a decreased connectivity to the frontal lobe from the insula, cingulate cortex, parietal, and temporal areas, and an increase in connectivity from the insula to the prefrontal cortex, subcallosal area, and temporal lobe was shown. Conclusion All these findings are suggestive of neuroplastic changes affecting the pain matrix in people with knee OA.
bibliographic citation: Salazar-Méndez et al. (2023) Structural and functional brain changes in people with knee osteoarthritis: a scoping review. PeerJ 11:e16003 https://doi.org/10.7717/peerj.16003
date submitted: 2023-06-15
date accepted: 2023-08-09
issued: 2023-09-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salazar-Méndez
  given name: Joaquín
author list: Agent
  family name: Cuyul-Vásquez
  given name: Iván
author list: Agent
  family name: Viscay-Sanhueza
  given name: Nelson
author list: Agent
  family name: Morales-Verdugo
  given name: Juan
author list: Agent
  family name: Mendez-Rebolledo
  given name: Guillermo
author list: Agent
  family name: Ponce-Fuentes
  given name: Felipe
author list: Agent
  family name: Lluch-Girbés
  given name: Enrique
doi: 10.7717/peerj.16003
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-07
copyright: ©2023 Salazar-Méndez et al.
attribution name: Salazar-Méndez et al.

Application of bubble streams to control biofouling on marine infrastructure—pontoon-scale implementation
type: item
type: AcademicArticle
description: There is a lack of cost-effective, environmentally-friendly tools available to manage marine biofouling accumulation on static artificial structures such as drilling rigs, wind turbines, marine farms, and port and marina infrastructure. For there to be uptake and refinement of tools, emerging technologies need to be tested and proven at an operational scale. This study aimed to see whether biofouling accumulation could be suppressed on marine infrastructure under real-world conditions through the delivery of continuous bubble streams. Submerged surfaces of a floating marina pontoon were cleaned in-situ by divers, and the subsequent colonisation by biofouling organisms was monitored on treated (bubbles applied) and untreated sections. Continuous bubble streams proved highly effective (>95%) in controlling macrofouling accumulation on the underside surface of the marina pontoon for the first 2 months after deployment, but efficacy dropped off rapidly once bubble stream delivery was partially obscured due to biofouling accumulation on the diffuser itself. Although extensive macrofouling cover by mussels, bryozoans and hydroids was observed on treated surfaces by 4 months (27.5%, SE = 4.8%), biofouling % cover and diversity was significantly higher on untreated surfaces (79.6%, SE = 2.9%). While this study demonstrates that continuous bubble streams greatly restrict biofouling accumulation over short-to-medium timescales, improved system design, especially the incorporation of diffusers resistant to fouling, is needed for the approach to be considered a viable long-term option for biofouling management on static artificial structures.
format: application/pdf
format: text/html
creator: Grant A. Hopkins
creator: Nicholas Scott
creator: Patrick Cahill
subject: Marine Biology
subject: Zoology
subject: Environmental Impacts
description: doi:10.7717/peerj.16004
publisher: PeerJ Inc.
rights: © 2023 Hopkins et al.
abstract: There is a lack of cost-effective, environmentally-friendly tools available to manage marine biofouling accumulation on static artificial structures such as drilling rigs, wind turbines, marine farms, and port and marina infrastructure. For there to be uptake and refinement of tools, emerging technologies need to be tested and proven at an operational scale. This study aimed to see whether biofouling accumulation could be suppressed on marine infrastructure under real-world conditions through the delivery of continuous bubble streams. Submerged surfaces of a floating marina pontoon were cleaned in-situ by divers, and the subsequent colonisation by biofouling organisms was monitored on treated (bubbles applied) and untreated sections. Continuous bubble streams proved highly effective (>95%) in controlling macrofouling accumulation on the underside surface of the marina pontoon for the first 2 months after deployment, but efficacy dropped off rapidly once bubble stream delivery was partially obscured due to biofouling accumulation on the diffuser itself. Although extensive macrofouling cover by mussels, bryozoans and hydroids was observed on treated surfaces by 4 months (27.5%, SE = 4.8%), biofouling % cover and diversity was significantly higher on untreated surfaces (79.6%, SE = 2.9%). While this study demonstrates that continuous bubble streams greatly restrict biofouling accumulation over short-to-medium timescales, improved system design, especially the incorporation of diffusers resistant to fouling, is needed for the approach to be considered a viable long-term option for biofouling management on static artificial structures.
bibliographic citation: Hopkins et al. (2023) Application of bubble streams to control biofouling on marine infrastructure—pontoon-scale implementation. PeerJ 11:e16004 https://doi.org/10.7717/peerj.16004
date submitted: 2023-06-22
date accepted: 2023-08-09
issued: 2023-09-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hopkins
  given name: Grant A.
author list: Agent
  family name: Scott
  given name: Nicholas
author list: Agent
  family name: Cahill
  given name: Patrick
doi: 10.7717/peerj.16004
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-07
copyright: © 2023 Hopkins et al.
attribution name: Hopkins et al.

Genetic polymorphisms in the C19orf66 gene influenced HIV-1 infection in a Yunnan population
type: item
type: AcademicArticle
description: Background Due to the deficiencies of vaccines and effective medicine, the human immunodeficiency virus (HIV) infection mechanism should be studied. The C19orf66 gene, one of the interferon-stimulated genes (ISGs), expresses broad-spectra anti-viral activity, including inhibiting HIV replication. Methods In this study, we collect 421 HIV-1 infected patients and 448 controls to genotype three SNPs in the C19orf66 gene. Then, the association between SNPs and biochemical indices/ HIV-1 subtypes are analyzed. Results Genotypes CC and CT of rs12611087 show statistically lower and higher frequencies in HIV-1 infected patients than in controls, respectively. Alleles C and T of rs12611087 play protective and risk roles in Yunnan HIV population, respectively. Biochemical indices analysis shows that HIV-1 infected persons carried genotype TT of rs77076061 express significantly lower CD3+/CD45+ ratio level and higher IBIL level. The epidemic subtypes of HIV-1 patients in this study are CRF 07_BC and CRF 08_BC. Moreover, subtype CRF 08_BC tends to infect persons with genotype CC of rs12611087. Conclusion The genetic polymorphisms of the C19orf66 gene are firstly studied and reported to associate with HIV-1 infection and biochemical indices of patients in Yunnan. Furthermore, subtype CRF 08_BC infection could be influenced by genotypes of SNP in the C19orf66 gene.
format: application/pdf
format: text/html
creator: Yaxiang Zhang
creator: Yue Feng
creator: Yang Liu
creator: Li Liu
creator: Xueshan Xia
creator: A-Mei Zhang
subject: Molecular Biology
subject: HIV
subject: Immunology
subject: Medical Genetics
description: doi:10.7717/peerj.16005
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Background Due to the deficiencies of vaccines and effective medicine, the human immunodeficiency virus (HIV) infection mechanism should be studied. The C19orf66 gene, one of the interferon-stimulated genes (ISGs), expresses broad-spectra anti-viral activity, including inhibiting HIV replication. Methods In this study, we collect 421 HIV-1 infected patients and 448 controls to genotype three SNPs in the C19orf66 gene. Then, the association between SNPs and biochemical indices/ HIV-1 subtypes are analyzed. Results Genotypes CC and CT of rs12611087 show statistically lower and higher frequencies in HIV-1 infected patients than in controls, respectively. Alleles C and T of rs12611087 play protective and risk roles in Yunnan HIV population, respectively. Biochemical indices analysis shows that HIV-1 infected persons carried genotype TT of rs77076061 express significantly lower CD3+/CD45+ ratio level and higher IBIL level. The epidemic subtypes of HIV-1 patients in this study are CRF 07_BC and CRF 08_BC. Moreover, subtype CRF 08_BC tends to infect persons with genotype CC of rs12611087. Conclusion The genetic polymorphisms of the C19orf66 gene are firstly studied and reported to associate with HIV-1 infection and biochemical indices of patients in Yunnan. Furthermore, subtype CRF 08_BC infection could be influenced by genotypes of SNP in the C19orf66 gene.
bibliographic citation: Zhang et al. (2023) Genetic polymorphisms in the C19orf66 gene influenced HIV-1 infection in a Yunnan population. PeerJ 11:e16005 https://doi.org/10.7717/peerj.16005
date submitted: 2023-03-22
date accepted: 2023-08-09
issued: 2023-09-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yaxiang
author list: Agent
  family name: Feng
  given name: Yue
author list: Agent
  family name: Liu
  given name: Yang
author list: Agent
  family name: Liu
  given name: Li
author list: Agent
  family name: Xia
  given name: Xueshan
author list: Agent
  family name: Zhang
  given name: A-Mei
doi: 10.7717/peerj.16005
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-07
copyright: ©2023 Zhang et al.
attribution name: Zhang et al.

Appendage abnormalities in spiders induced by an alternating temperature protocol in the context of recent advances in molecular spider embryology
type: item
type: AcademicArticle
description: In the literature there are numerous reports of developmental deformities in arthropods collected in their natural habitat. Since such teratogenically affected individuals are found purely by chance, the causes of their defects are unknown. Numerous potential physical, mechanical, chemical, and biological teratogens have been considered and tested in the laboratory. Thermal shocks, frequently used in teratological research on the spider Eratigena atrica, have led to deformities on both the prosoma and the opisthosoma. In the 2020/2021 breeding season, by applying alternating temperatures (14 °C and 32 °C, changed every 12 h) for the first 10 days of embryonic development, we obtained 212 postembryos (out of 3,007) with the following anomalies: oligomely, heterosymely, bicephaly, schistomely, symely, polymely, complex anomalies, and others. From these we selected six spiders with defects on the prosoma and two with short appendages on the pedicel for further consideration. The latter cases seem particularly interesting because appendages do not normally develop on this body part, viewed as the first segment of the opisthosoma, and appear to represent examples of atavism. In view of the ongoing development of molecular techniques and recent research on developmental mechanisms in spiders, we believe the observed phenotypes may result, at least in part, from the erroneous suppression or expression of segmentation or appendage patterning genes. We consider “knockdown” experiments described in the literature as a means for generating hypotheses about the sources of temperature-induced body abnormalities in E. atrica.
format: application/pdf
format: text/html
creator: Teresa Napiórkowska
creator: Julita Templin
creator: Paweł Napiórkowski
creator: Mark A. Townley
subject: Developmental Biology
subject: Entomology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.16011
publisher: PeerJ Inc.
rights: © 2023 Napiórkowska et al.
abstract: In the literature there are numerous reports of developmental deformities in arthropods collected in their natural habitat. Since such teratogenically affected individuals are found purely by chance, the causes of their defects are unknown. Numerous potential physical, mechanical, chemical, and biological teratogens have been considered and tested in the laboratory. Thermal shocks, frequently used in teratological research on the spider Eratigena atrica, have led to deformities on both the prosoma and the opisthosoma. In the 2020/2021 breeding season, by applying alternating temperatures (14 °C and 32 °C, changed every 12 h) for the first 10 days of embryonic development, we obtained 212 postembryos (out of 3,007) with the following anomalies: oligomely, heterosymely, bicephaly, schistomely, symely, polymely, complex anomalies, and others. From these we selected six spiders with defects on the prosoma and two with short appendages on the pedicel for further consideration. The latter cases seem particularly interesting because appendages do not normally develop on this body part, viewed as the first segment of the opisthosoma, and appear to represent examples of atavism. In view of the ongoing development of molecular techniques and recent research on developmental mechanisms in spiders, we believe the observed phenotypes may result, at least in part, from the erroneous suppression or expression of segmentation or appendage patterning genes. We consider “knockdown” experiments described in the literature as a means for generating hypotheses about the sources of temperature-induced body abnormalities in E. atrica.
bibliographic citation: Napiórkowska et al. (2023) Appendage abnormalities in spiders induced by an alternating temperature protocol in the context of recent advances in molecular spider embryology. PeerJ 11:e16011 https://doi.org/10.7717/peerj.16011
date submitted: 2023-01-24
date accepted: 2023-08-10
issued: 2023-09-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Napiórkowska
  given name: Teresa
author list: Agent
  family name: Templin
  given name: Julita
author list: Agent
  family name: Napiórkowski
  given name: Paweł
author list: Agent
  family name: Townley
  given name: Mark A.
doi: 10.7717/peerj.16011
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-07
copyright: © 2023 Napiórkowska et al.
attribution name: Napiórkowska et al.

The current landscape of m6A modification in urological cancers
type: item
type: AcademicArticle
description: N6-methyladenosine (m6A) methylation is a dynamic and reversible procession of epigenetic modifications. It is increasingly recognized that m6A modification has been involved in the tumorigenesis, development, and progression of urological tumors. Emerging research explored the role of m6A modification in urological cancer. In this review, we will summarize the relationship between m6A modification, renal cell carcinoma, bladder cancer, and prostate cancer, and discover the biological function of m6A regulators in tumor cells. We will also discuss the possible mechanism and future application value used as a potential biomarker or therapeutic target to benefit patients with urological cancers.
format: application/pdf
format: text/html
creator: Yaohui Zeng
creator: Cai Lv
creator: Bangbei Wan
creator: Binghao Gong
subject: Genetics
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.16023
publisher: PeerJ Inc.
rights: © 2023 Zeng et al.
abstract: N6-methyladenosine (m6A) methylation is a dynamic and reversible procession of epigenetic modifications. It is increasingly recognized that m6A modification has been involved in the tumorigenesis, development, and progression of urological tumors. Emerging research explored the role of m6A modification in urological cancer. In this review, we will summarize the relationship between m6A modification, renal cell carcinoma, bladder cancer, and prostate cancer, and discover the biological function of m6A regulators in tumor cells. We will also discuss the possible mechanism and future application value used as a potential biomarker or therapeutic target to benefit patients with urological cancers.
bibliographic citation: Zeng et al. (2023) The current landscape of m6A modification in urological cancers. PeerJ 11:e16023 https://doi.org/10.7717/peerj.16023
date submitted: 2023-04-11
date accepted: 2023-08-11
issued: 2023-09-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeng
  given name: Yaohui
author list: Agent
  family name: Lv
  given name: Cai
author list: Agent
  family name: Wan
  given name: Bangbei
author list: Agent
  family name: Gong
  given name: Binghao
doi: 10.7717/peerj.16023
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-07
copyright: ©2023 Zeng et al.
attribution name: Zeng et al.

Temporal variation of the relationships between rice yield and climate variables since 1925
type: item
type: AcademicArticle
description: Background Long-term time-series datasets of crop yield and climate variables are necessary to study the temporal variation of climate effects on crops. The aim of this study was to broadly assess assessment of the effects of climate on rice, and the associated temporal variations of the effects during the long-term period. Methods We conducted field experiments in Taiwan from 1925 to 2019 to collect and analyze rice yield data and evaluate the impacts of changes in average temperature, diurnal temperature range (DTR), rainfall, and sunshine duration on rice yield during cool and warm cropping seasons. We then estimated the relationships between annual grain yield and the climate variables using the time series of their first difference values. We also computed the total relative and annual actual yield changes using regression coefficients for each climate variable for the intervals 1925–1944, 1945–1983, and 1996–2019 to reveal the impacts of climate change on yields and the associated temporal variations during the overall experimental period. Results The annual daily average temperature calculated from the trend of the regression lines increased by 0.94–1.03 °C during the 95-year period. The maximum temperature remained steady while the minimum temperature increased, leading to decreased DTR. The total annual rainfall decreased by 237–352 mm and the annual total sunshine duration decreased by 93.9–238.9 h during the experimental period. We observed that during the cool cropping season, yield response to temperature change decreased, while that to DTR and rainfall changes increased. During the warm cropping season, all the yield responses to temperature, DTR, and rainfall changes were negative throughout the experimental period. In recent years (1996–2019) the estimated annual actual rice yield changes during the cool cropping season were negatively affected by climate variables (except for sunshine duration), and slightly positively affected (except for temperatu…
format: application/pdf
format: text/html
creator: Hungyen Chen
creator: Yi-Chien Wu
creator: Chih-Yung Teng
subject: Agricultural Science
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.16045
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Background Long-term time-series datasets of crop yield and climate variables are necessary to study the temporal variation of climate effects on crops. The aim of this study was to broadly assess assessment of the effects of climate on rice, and the associated temporal variations of the effects during the long-term period. Methods We conducted field experiments in Taiwan from 1925 to 2019 to collect and analyze rice yield data and evaluate the impacts of changes in average temperature, diurnal temperature range (DTR), rainfall, and sunshine duration on rice yield during cool and warm cropping seasons. We then estimated the relationships between annual grain yield and the climate variables using the time series of their first difference values. We also computed the total relative and annual actual yield changes using regression coefficients for each climate variable for the intervals 1925–1944, 1945–1983, and 1996–2019 to reveal the impacts of climate change on yields and the associated temporal variations during the overall experimental period. Results The annual daily average temperature calculated from the trend of the regression lines increased by 0.94–1.03 °C during the 95-year period. The maximum temperature remained steady while the minimum temperature increased, leading to decreased DTR. The total annual rainfall decreased by 237–352 mm and the annual total sunshine duration decreased by 93.9–238.9 h during the experimental period. We observed that during the cool cropping season, yield response to temperature change decreased, while that to DTR and rainfall changes increased. During the warm cropping season, all the yield responses to temperature, DTR, and rainfall changes were negative throughout the experimental period. In recent years (1996–2019) the estimated annual actual rice yield changes during the cool cropping season were negatively affected by climate variables (except for sunshine duration), and slightly positively affected (except for temperatu…
bibliographic citation: Chen et al. (2023) Temporal variation of the relationships between rice yield and climate variables since 1925. PeerJ 11:e16045 https://doi.org/10.7717/peerj.16045
date submitted: 2023-05-04
date accepted: 2023-08-15
issued: 2023-09-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Hungyen
author list: Agent
  family name: Wu
  given name: Yi-Chien
author list: Agent
  family name: Teng
  given name: Chih-Yung
doi: 10.7717/peerj.16045
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-07
copyright: © 2023 Chen et al.
attribution name: Chen et al.

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