PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Overview of chicken embryo genes related to sex differentiation
items: Endosymbiont and gut bacterial communities of the brown-banded cockroach, Supella longipalpa
items: Beliefs, barriers, and promotion practices of Indian nurses’ regarding healthy eating for cancer survivors in a tertiary care hospital—A cross sectional survey
items: TBX5 genetic variants and SCD-CAD susceptibility: insights from Chinese Han cohorts
items: Biochar’s role in improving pakchoi quality and microbial community structure in rhizosphere soil
items: Anti-ENO1 antibody combined with metformin against tumor resistance: a novel antibody-based platform
items: Integrating single-cell and bulk sequencing data to identify glycosylation-based genes in non-alcoholic fatty liver disease-associated hepatocellular carcinoma
items: Changes in hamstring contractile properties during the competitive season in young football players
items: Deciphering the genomes of motility-deficient mutants of Vibrio alginolyticus 138-2
items: Validation of CDC45 as a novel biomarker for diagnosis and prognosis of gastric cancer

Overview of chicken embryo genes related to sex differentiation
type: item
type: AcademicArticle
description: Sex determination in chickens at an early embryonic stage has been a longstanding challenge in poultry production due to the unique ZZ:ZW sex chromosome system and various influencing factors. This review has summarized the genes related to the sex differentiation of chicken early embryos (mainly Dmrt1, Sox9, Amh, Cyp19a1, Foxl2, Tle4z1, Jun, Hintw, Ube2i, Spin1z, Hmgcs1, Foxd1, Tox3, Ddx4, cHemgn and Serpinb11 in this article), and has found that these contributions enhance our understanding of the genetic basis of sex determination in chickens, while identifying potential gene targets for future research. This knowledge may inform and guide the development of sex screening technologies for hatching eggs and support advancements in gene-editing approaches for chicken embryos. Moreover, these insights offer hope for enhancing animal welfare and promoting conservation efforts in poultry production.
format: application/pdf
format: text/html
creator: Xiaolu Luo
creator: Jiancheng Guo
creator: Jiahang Zhang
creator: Zheng Ma
creator: Hua Li
subject: Biochemistry
subject: Developmental Biology
subject: Genetics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.17072
publisher: PeerJ Inc.
rights: © 2024 Luo et al.
abstract: Sex determination in chickens at an early embryonic stage has been a longstanding challenge in poultry production due to the unique ZZ:ZW sex chromosome system and various influencing factors. This review has summarized the genes related to the sex differentiation of chicken early embryos (mainly Dmrt1, Sox9, Amh, Cyp19a1, Foxl2, Tle4z1, Jun, Hintw, Ube2i, Spin1z, Hmgcs1, Foxd1, Tox3, Ddx4, cHemgn and Serpinb11 in this article), and has found that these contributions enhance our understanding of the genetic basis of sex determination in chickens, while identifying potential gene targets for future research. This knowledge may inform and guide the development of sex screening technologies for hatching eggs and support advancements in gene-editing approaches for chicken embryos. Moreover, these insights offer hope for enhancing animal welfare and promoting conservation efforts in poultry production.
bibliographic citation: Luo et al. (2024) Overview of chicken embryo genes related to sex differentiation. PeerJ 12:e17072 https://doi.org/10.7717/peerj.17072
date submitted: 2023-11-30
date accepted: 2024-02-18
issued: 2024-03-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Xiaolu
author list: Agent
  family name: Guo
  given name: Jiancheng
author list: Agent
  family name: Zhang
  given name: Jiahang
author list: Agent
  family name: Ma
  given name: Zheng
author list: Agent
  family name: Li
  given name: Hua
doi: 10.7717/peerj.17072
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-19
copyright: ©2024 Luo et al.
attribution name: Luo et al.

Endosymbiont and gut bacterial communities of the brown-banded cockroach, Supella longipalpa
type: item
type: AcademicArticle
description: The brown-banded cockroach (Supella longipalpa) is a widespread nuisance and public health pest. Like the German cockroach (Blattella germanica), this species is adapted to the indoor biome and completes the entirety of its life cycle in human-built structures. Recently, understanding the contributions of commensal and symbiotic microbes to the biology of cockroach pests, as well as the applications of targeting these microbes for pest control, have garnered significant scientific interest. However, relative to B. germanica, the biology of S. longipalpa, including its microbial associations, is understudied. Therefore, the goal of the present study was to quantitatively examine and characterize both the endosymbiont and gut bacterial communities of S. longipalpa for the first time. To do so, bacterial 16S rRNA gene amplicon sequencing was conducted on DNA extracts from whole adult females and males, early instar nymphs, and late instar nymphs. The results demonstrate that the gut microbiome is dominated by two genera of bacteria known to have beneficial probiotic effects in other organisms, namely Lactobacillus and Akkermansia. Furthermore, our data show a significant effect of nymphal development on diversity and variation in the gut microbiome. Lastly, we reveal significant negative correlations between the two intracellular endosymbionts, Blattabacterium and Wolbachia, as well as between Blattabacterium and the gut microbiome, suggesting that Blattabacterium endosymbionts could directly or indirectly influence the composition of other bacterial populations. These findings have implications for understanding the adaptation of S. longipalpa to the indoor biome, its divergence from other indoor cockroach pest species such as B. germanica, the development of novel control approaches that target the microbiome, and fundamental insect-microbe interactions more broadly.
format: application/pdf
format: text/html
creator: Kylene Guse
creator: Jose E. Pietri
subject: Entomology
subject: Genomics
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.17095
publisher: PeerJ Inc.
rights: © 2024 Guse and Pietri
abstract: The brown-banded cockroach (Supella longipalpa) is a widespread nuisance and public health pest. Like the German cockroach (Blattella germanica), this species is adapted to the indoor biome and completes the entirety of its life cycle in human-built structures. Recently, understanding the contributions of commensal and symbiotic microbes to the biology of cockroach pests, as well as the applications of targeting these microbes for pest control, have garnered significant scientific interest. However, relative to B. germanica, the biology of S. longipalpa, including its microbial associations, is understudied. Therefore, the goal of the present study was to quantitatively examine and characterize both the endosymbiont and gut bacterial communities of S. longipalpa for the first time. To do so, bacterial 16S rRNA gene amplicon sequencing was conducted on DNA extracts from whole adult females and males, early instar nymphs, and late instar nymphs. The results demonstrate that the gut microbiome is dominated by two genera of bacteria known to have beneficial probiotic effects in other organisms, namely Lactobacillus and Akkermansia. Furthermore, our data show a significant effect of nymphal development on diversity and variation in the gut microbiome. Lastly, we reveal significant negative correlations between the two intracellular endosymbionts, Blattabacterium and Wolbachia, as well as between Blattabacterium and the gut microbiome, suggesting that Blattabacterium endosymbionts could directly or indirectly influence the composition of other bacterial populations. These findings have implications for understanding the adaptation of S. longipalpa to the indoor biome, its divergence from other indoor cockroach pest species such as B. germanica, the development of novel control approaches that target the microbiome, and fundamental insect-microbe interactions more broadly.
bibliographic citation: Guse et al. (2024) Endosymbiont and gut bacterial communities of the brown-banded cockroach, Supella longipalpa. PeerJ 12:e17095 https://doi.org/10.7717/peerj.17095
date submitted: 2023-12-22
date accepted: 2024-02-21
issued: 2024-03-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guse
  given name: Kylene
author list: Agent
  family name: Pietri
  given name: Jose E.
doi: 10.7717/peerj.17095
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-19
copyright: © 2024 Guse and Pietri
attribution name: Guse and Pietri

Beliefs, barriers, and promotion practices of Indian nurses’ regarding healthy eating for cancer survivors in a tertiary care hospital—A cross sectional survey
type: item
type: AcademicArticle
description: Purpose To describe the beliefs, barriers and promotion practices of Indian nurses’ regarding healthy eating (HE) behaviours amongst cancer survivors, and to gain insights into whether their educational qualifications might affect the promotion of HE. Methods Data was gathered using a validated questionnaire, 388 of the approached 400 nurses who worked at a tertiary care hospital in India gave informed consent to participate in the study. The Mann-Whitney U test and the Chi square analysis (for continuous and categorical variables respectively) were performed to carry out sub-group comparisons based on the qualification of the nurses i.e., Bachelor of Science in Nursing (BSc) and General Nursing and Midwifery (GNM). Results The nurses believed that dieticians/nutritionists were primarily responsible for educating the cancer survivors regarding HE. HE was promoted by nurses’ relatively equally across multiple treatment stages (“during” treatment 24.4%, “post” treatment 23.1%; and “pre” treatment 22.3%). Nurses’ believed HE practices had numerous benefits, with improved health-related quality of life (HRQoL) (75.7%), and mental health (73.9%) being the most frequent responses. The most frequently cited barriers by the nurses in promoting HE were lack of time (22.2%), and lack of adequate support structure (19.9%). Sub-group comparisons generally revealed no significant difference between the BSc and GNM nurses in their perceptions regarding HE promotion to cancer survivors. Exceptions were how the GNM group had significantly greater beliefs regarding whether HE can “reduce risk of cancer occurrence” (p = 0.004) and “whether or not I promote HE is entirely up to me” (p = 0.002). Conclusion The nurses in India believe in the promotion of HE practices among cancer survivors across various stages of cancer treatments. However, they do face a range of barriers in their attempt to promote HE. Overcoming these barriers might facilitate effective promotion of HE among cancer …
format: application/pdf
format: text/html
creator: Hritika D. Pai
creator: Stephen Rajan Samuel
creator: K. Vijaya Kumar
creator: Charu Eapen
creator: Alicia Olsen
creator: Justin W.L. Keogh
subject: Nursing
subject: Nutrition
subject: Oncology
subject: Palliative Care
subject: Healthcare Services
description: doi:10.7717/peerj.17107
publisher: PeerJ Inc.
rights: © 2024 Pai et al.
abstract: Purpose To describe the beliefs, barriers and promotion practices of Indian nurses’ regarding healthy eating (HE) behaviours amongst cancer survivors, and to gain insights into whether their educational qualifications might affect the promotion of HE. Methods Data was gathered using a validated questionnaire, 388 of the approached 400 nurses who worked at a tertiary care hospital in India gave informed consent to participate in the study. The Mann-Whitney U test and the Chi square analysis (for continuous and categorical variables respectively) were performed to carry out sub-group comparisons based on the qualification of the nurses i.e., Bachelor of Science in Nursing (BSc) and General Nursing and Midwifery (GNM). Results The nurses believed that dieticians/nutritionists were primarily responsible for educating the cancer survivors regarding HE. HE was promoted by nurses’ relatively equally across multiple treatment stages (“during” treatment 24.4%, “post” treatment 23.1%; and “pre” treatment 22.3%). Nurses’ believed HE practices had numerous benefits, with improved health-related quality of life (HRQoL) (75.7%), and mental health (73.9%) being the most frequent responses. The most frequently cited barriers by the nurses in promoting HE were lack of time (22.2%), and lack of adequate support structure (19.9%). Sub-group comparisons generally revealed no significant difference between the BSc and GNM nurses in their perceptions regarding HE promotion to cancer survivors. Exceptions were how the GNM group had significantly greater beliefs regarding whether HE can “reduce risk of cancer occurrence” (p = 0.004) and “whether or not I promote HE is entirely up to me” (p = 0.002). Conclusion The nurses in India believe in the promotion of HE practices among cancer survivors across various stages of cancer treatments. However, they do face a range of barriers in their attempt to promote HE. Overcoming these barriers might facilitate effective promotion of HE among cancer …
bibliographic citation: Pai et al. (2024) Beliefs, barriers, and promotion practices of Indian nurses’ regarding healthy eating for cancer survivors in a tertiary care hospital—A cross sectional survey. PeerJ 12:e17107 https://doi.org/10.7717/peerj.17107
date submitted: 2023-06-26
date accepted: 2024-02-22
issued: 2024-03-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pai
  given name: Hritika D.
author list: Agent
  family name: Samuel
  given name: Stephen Rajan
author list: Agent
  family name: Kumar
  given name: K. Vijaya
author list: Agent
  family name: Eapen
  given name: Charu
author list: Agent
  family name: Olsen
  given name: Alicia
author list: Agent
  family name: Keogh
  given name: Justin W.L.
doi: 10.7717/peerj.17107
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-19
copyright: ©2024 Pai et al.
attribution name: Pai et al.

TBX5 genetic variants and SCD-CAD susceptibility: insights from Chinese Han cohorts
type: item
type: AcademicArticle
description: Background The prevention and prediction of sudden cardiac death (SCD) present persistent challenges, prompting exploration into common genetic variations for potential insights. T-box 5 (TBX5), a critical cardiac transcription factor, plays a pivotal role in cardiovascular development and function. This study systematically examined variants within the 500-bp region downstream of the TBX5 gene, focusing on their potential impact on susceptibility to SCD associated with coronary artery disease (SCD-CAD) in four different Chinese Han populations. Methods In a comprehensive case-control analysis, we explored the association between rs11278315 and SCD-CAD susceptibility using a cohort of 553 controls and 201 SCD-CAD cases. Dual luciferase reporter assays and genotype-phenotype correlation studies using human cardiac tissue samples as well as integrated in silicon analysis were applied to explore the underlining mechanism. Result Binary logistic regression results underscored a significantly reduced risk of SCD-CAD in individuals harboring the deletion allele (odds ratio = 0.70, 95% CI [0.55–0.88], p = 0.0019). Consistent with the lower transcriptional activity of the deletion allele observed in dual luciferase reporter assays, genotype-phenotype correlation studies on human cardiac tissue samples affirmed lower expression levels associated with the deletion allele at both mRNA and protein levels. Furthermore, our investigation revealed intriguing insights into the role of rs11278315 in TBX5 alternative splicing, which may contribute to alterations in its ultimate functional effects, as suggested by sQTL analysis. Gene ontology analysis and functional annotation further underscored the potential involvement of TBX5 in alternative splicing and cardiac-related transcriptional regulation. Conclusions In summary, our current dataset points to a plausible correlation between rs11278315 and susceptibility to SCD-CAD, emphasizing the potential of rs11278315 as a genetic risk m…
format: application/pdf
format: text/html
creator: Yukun Rui
creator: Ju Zhou
creator: Xiaoyuan Zhen
creator: Jianhua Zhang
creator: Shiquan Liu
creator: Yuzhen Gao
subject: Genetics
subject: Genomics
subject: Cardiology
subject: Public Health
subject: Medical Genetics
description: doi:10.7717/peerj.17139
publisher: PeerJ Inc.
rights: © 2024 Rui et al.
abstract: Background The prevention and prediction of sudden cardiac death (SCD) present persistent challenges, prompting exploration into common genetic variations for potential insights. T-box 5 (TBX5), a critical cardiac transcription factor, plays a pivotal role in cardiovascular development and function. This study systematically examined variants within the 500-bp region downstream of the TBX5 gene, focusing on their potential impact on susceptibility to SCD associated with coronary artery disease (SCD-CAD) in four different Chinese Han populations. Methods In a comprehensive case-control analysis, we explored the association between rs11278315 and SCD-CAD susceptibility using a cohort of 553 controls and 201 SCD-CAD cases. Dual luciferase reporter assays and genotype-phenotype correlation studies using human cardiac tissue samples as well as integrated in silicon analysis were applied to explore the underlining mechanism. Result Binary logistic regression results underscored a significantly reduced risk of SCD-CAD in individuals harboring the deletion allele (odds ratio = 0.70, 95% CI [0.55–0.88], p = 0.0019). Consistent with the lower transcriptional activity of the deletion allele observed in dual luciferase reporter assays, genotype-phenotype correlation studies on human cardiac tissue samples affirmed lower expression levels associated with the deletion allele at both mRNA and protein levels. Furthermore, our investigation revealed intriguing insights into the role of rs11278315 in TBX5 alternative splicing, which may contribute to alterations in its ultimate functional effects, as suggested by sQTL analysis. Gene ontology analysis and functional annotation further underscored the potential involvement of TBX5 in alternative splicing and cardiac-related transcriptional regulation. Conclusions In summary, our current dataset points to a plausible correlation between rs11278315 and susceptibility to SCD-CAD, emphasizing the potential of rs11278315 as a genetic risk m…
bibliographic citation: Rui et al. (2024) TBX5 genetic variants and SCD-CAD susceptibility: insights from Chinese Han cohorts. PeerJ 12:e17139 https://doi.org/10.7717/peerj.17139
date submitted: 2024-01-22
date accepted: 2024-02-28
issued: 2024-03-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rui
  given name: Yukun
author list: Agent
  family name: Zhou
  given name: Ju
author list: Agent
  family name: Zhen
  given name: Xiaoyuan
author list: Agent
  family name: Zhang
  given name: Jianhua
author list: Agent
  family name: Liu
  given name: Shiquan
author list: Agent
  family name: Gao
  given name: Yuzhen
doi: 10.7717/peerj.17139
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-19
copyright: ©2024 Rui et al.
attribution name: Rui et al.

Biochar’s role in improving pakchoi quality and microbial community structure in rhizosphere soil
type: item
type: AcademicArticle
description: Background Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi (Brassica campestris L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes. Methods The soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq. Results The results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, Gemmatimonadetes, Anaerolineae, Deltaproteobacteria and Verrucomicrobiae were reduced, and Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, and Acidimicrobiia relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of Gemmatimonas and increased the relative abundances of Ilumatobacter, Luteolibacter, Lysobacter, Arthrobacter, and Mesorhizobium. The nitrate content was positively correlated with the abundance of Gemmatimonadetes, and the nitrate content was significant…
format: application/pdf
format: text/html
creator: Xia Wu
creator: Fengjun Yang
creator: Jili Zhang
creator: Feng Gao
creator: Yi Chen Hu
creator: Kejun Yang
creator: Peng Wang
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.16733
publisher: PeerJ Inc.
rights: © 2024 Wu et al.
abstract: Background Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi (Brassica campestris L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes. Methods The soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq. Results The results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, Gemmatimonadetes, Anaerolineae, Deltaproteobacteria and Verrucomicrobiae were reduced, and Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, and Acidimicrobiia relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of Gemmatimonas and increased the relative abundances of Ilumatobacter, Luteolibacter, Lysobacter, Arthrobacter, and Mesorhizobium. The nitrate content was positively correlated with the abundance of Gemmatimonadetes, and the nitrate content was significant…
bibliographic citation: Wu et al. (2024) Biochar’s role in improving pakchoi quality and microbial community structure in rhizosphere soil. PeerJ 12:e16733 https://doi.org/10.7717/peerj.16733
date submitted: 2023-05-01
date accepted: 2023-12-07
issued: 2024-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Xia
author list: Agent
  family name: Yang
  given name: Fengjun
author list: Agent
  family name: Zhang
  given name: Jili
author list: Agent
  family name: Gao
  given name: Feng
author list: Agent
  family name: Hu
  given name: Yi Chen
author list: Agent
  family name: Yang
  given name: Kejun
author list: Agent
  family name: Wang
  given name: Peng
doi: 10.7717/peerj.16733
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-18
copyright: ©2024 Wu et al.
attribution name: Wu et al.

Anti-ENO1 antibody combined with metformin against tumor resistance: a novel antibody-based platform
type: item
type: AcademicArticle
description: Background Antibody-based platforms (i.e., ADC) have emerged as one of the most encouraging tools for the cancer resistance caused by cancer stem cells (CSCs) enrichment. Our study might provide a promising therapeutic direction against drug resistance and serve as a potential precursor platform for screening ADC. Methods The cell migration, invasion, drug resistance, and self-renewal were assessed by the cell invasion and migration assay, wound healing assay, CCK-8 assay, colony formation assay, and sphere formation assay, respectively. The expression profiles of CSCs (ALDH+ and CD44+) subpopulations were screened by flow cytometry. The western blot and cell immunofluorescence assay were used to evaluate pathway-related protein expression in both anti-ENO1 antibody, MET combined with DPP/CTX-treated CSCs. Results In the present study, western blot and flow cytometry verified that anti-ENO1 antibody target the CD44+ subpopulation by inhibiting the PI3K/AKT pathway, while metformin might target the ALDH+ subpopulation through activation of the AMPK pathway and thus reverse drug resistance to varying degrees. Subsequently, in vitro investigation indicated that anti-ENO1 antibody, metformin combined with cisplatin/cetuximab could simultaneously target ALDH+ and CD44+ subpopulations. The combination also inhibited the CSCs proliferation, migration, invasion, and sphere formation; which may result in overcoming the drug resistance. Then, molecular mechanism exploration verified that the anti-ENO1 antibody, metformin combined with cisplatin/cetuximab inhibited the Wnt/β-catenin signaling. Conclusions The study preliminarily revealed anti-ENO1 antibody combined with metformin could overcome drug resistance against CSCs by inhibiting the Wnt//β-catenin pathway and might serve as a potential precursor platform for screening ADC. More importantly, it is reasonably believed that antibody-based drug combination therapy might function as an encouraging tool for oncotherapy.
format: application/pdf
format: text/html
creator: Xiong Shu
creator: Hui Wen Zhang
creator: Shi Ya Liu
creator: Li Xin Sun
creator: Tao Zhang
creator: Yu Liang Ran
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.16817
publisher: PeerJ Inc.
rights: © 2024 Shu et al.
abstract: Background Antibody-based platforms (i.e., ADC) have emerged as one of the most encouraging tools for the cancer resistance caused by cancer stem cells (CSCs) enrichment. Our study might provide a promising therapeutic direction against drug resistance and serve as a potential precursor platform for screening ADC. Methods The cell migration, invasion, drug resistance, and self-renewal were assessed by the cell invasion and migration assay, wound healing assay, CCK-8 assay, colony formation assay, and sphere formation assay, respectively. The expression profiles of CSCs (ALDH+ and CD44+) subpopulations were screened by flow cytometry. The western blot and cell immunofluorescence assay were used to evaluate pathway-related protein expression in both anti-ENO1 antibody, MET combined with DPP/CTX-treated CSCs. Results In the present study, western blot and flow cytometry verified that anti-ENO1 antibody target the CD44+ subpopulation by inhibiting the PI3K/AKT pathway, while metformin might target the ALDH+ subpopulation through activation of the AMPK pathway and thus reverse drug resistance to varying degrees. Subsequently, in vitro investigation indicated that anti-ENO1 antibody, metformin combined with cisplatin/cetuximab could simultaneously target ALDH+ and CD44+ subpopulations. The combination also inhibited the CSCs proliferation, migration, invasion, and sphere formation; which may result in overcoming the drug resistance. Then, molecular mechanism exploration verified that the anti-ENO1 antibody, metformin combined with cisplatin/cetuximab inhibited the Wnt/β-catenin signaling. Conclusions The study preliminarily revealed anti-ENO1 antibody combined with metformin could overcome drug resistance against CSCs by inhibiting the Wnt//β-catenin pathway and might serve as a potential precursor platform for screening ADC. More importantly, it is reasonably believed that antibody-based drug combination therapy might function as an encouraging tool for oncotherapy.
bibliographic citation: Shu et al. (2024) Anti-ENO1 antibody combined with metformin against tumor resistance: a novel antibody-based platform. PeerJ 12:e16817 https://doi.org/10.7717/peerj.16817
date submitted: 2023-03-31
date accepted: 2023-12-30
issued: 2024-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shu
  given name: Xiong
author list: Agent
  family name: Zhang
  given name: Hui Wen
author list: Agent
  family name: Liu
  given name: Shi Ya
author list: Agent
  family name: Sun
  given name: Li Xin
author list: Agent
  family name: Zhang
  given name: Tao
author list: Agent
  family name: Ran
  given name: Yu Liang
doi: 10.7717/peerj.16817
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-18
copyright: © 2024 Shu et al.
attribution name: Shu et al.

Integrating single-cell and bulk sequencing data to identify glycosylation-based genes in non-alcoholic fatty liver disease-associated hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background The incidence of non-alcoholic fatty liver disease (NAFLD) associated hepatocellular carcinoma (HCC) has been increasing. However, the role of glycosylation, an important modification that alters cellular differentiation and immune regulation, in the progression of NAFLD to HCC is rare. Methods We used the NAFLD-HCC single-cell dataset to identify variation in the expression of glycosylation patterns between different cells and used the HCC bulk dataset to establish a link between these variations and the prognosis of HCC patients. Then, machine learning algorithms were used to identify those glycosylation-related signatures with prognostic significance and to construct a model for predicting the prognosis of HCC patients. Moreover, it was validated in high-fat diet-induced mice and clinical cohorts. Results The NAFLD-HCC Glycogene Risk Model (NHGRM) signature included the following genes: SPP1, SOCS2, SAPCD2, S100A9, RAMP3, and CSAD. The higher NHGRM scores were associated with a poorer prognosis, stronger immune-related features, immune cell infiltration and immunity scores. Animal experiments, external and clinical cohorts confirmed the expression of these genes. Conclusion The genetic signature we identified may serve as a potential indicator of survival in patients with NAFLD-HCC and provide new perspectives for elucidating the role of glycosylation-related signatures in this pathologic process.
format: application/pdf
format: text/html
creator: Zhijia Zhou
creator: Yanan Gao
creator: Longxin Deng
creator: Xiaole Lu
creator: Yancheng Lai
creator: Jieke Wu
creator: Shaodong Chen
creator: Chengzhong Li
creator: Huiqing Liang
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Histology
description: doi:10.7717/peerj.17002
publisher: PeerJ Inc.
rights: © 2024 Zhou et al.
abstract: Background The incidence of non-alcoholic fatty liver disease (NAFLD) associated hepatocellular carcinoma (HCC) has been increasing. However, the role of glycosylation, an important modification that alters cellular differentiation and immune regulation, in the progression of NAFLD to HCC is rare. Methods We used the NAFLD-HCC single-cell dataset to identify variation in the expression of glycosylation patterns between different cells and used the HCC bulk dataset to establish a link between these variations and the prognosis of HCC patients. Then, machine learning algorithms were used to identify those glycosylation-related signatures with prognostic significance and to construct a model for predicting the prognosis of HCC patients. Moreover, it was validated in high-fat diet-induced mice and clinical cohorts. Results The NAFLD-HCC Glycogene Risk Model (NHGRM) signature included the following genes: SPP1, SOCS2, SAPCD2, S100A9, RAMP3, and CSAD. The higher NHGRM scores were associated with a poorer prognosis, stronger immune-related features, immune cell infiltration and immunity scores. Animal experiments, external and clinical cohorts confirmed the expression of these genes. Conclusion The genetic signature we identified may serve as a potential indicator of survival in patients with NAFLD-HCC and provide new perspectives for elucidating the role of glycosylation-related signatures in this pathologic process.
bibliographic citation: Zhou et al. (2024) Integrating single-cell and bulk sequencing data to identify glycosylation-based genes in non-alcoholic fatty liver disease-associated hepatocellular carcinoma. PeerJ 12:e17002 https://doi.org/10.7717/peerj.17002
date submitted: 2023-07-28
date accepted: 2024-02-05
issued: 2024-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Zhijia
author list: Agent
  family name: Gao
  given name: Yanan
author list: Agent
  family name: Deng
  given name: Longxin
author list: Agent
  family name: Lu
  given name: Xiaole
author list: Agent
  family name: Lai
  given name: Yancheng
author list: Agent
  family name: Wu
  given name: Jieke
author list: Agent
  family name: Chen
  given name: Shaodong
author list: Agent
  family name: Li
  given name: Chengzhong
author list: Agent
  family name: Liang
  given name: Huiqing
doi: 10.7717/peerj.17002
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-18
copyright: ©2024 Zhou et al.
attribution name: Zhou et al.

Changes in hamstring contractile properties during the competitive season in young football players
type: item
type: AcademicArticle
description: Background The study aimed to examine alterations and imbalances in hamstring muscle contractile properties among young football players throughout their competitive season, and to understand how these changes might contribute to the risk of muscle injuries. Hamstring injuries are particularly common in football, yet the underlying causes and effective prevention methods remain unclear. Methods The research involved 74 young footballers who were assessed before the season (pre-test) and after 12 weeks of training (post-test). To evaluate changes in hamstring muscle contractile properties, specifically the left and right biceps femoris (BF) and semitendinosus (ST), tensiomyography (TMG) parameters were utilized. Results In comparison to the BF muscle, significant differences in time delay (Td) between the left and right sides in the post-test (p = 0.0193), and maximal displacement (Dm) between the left and right sides at the pre-test (p = 0.0395). However, significant differences in Dm were observed only in the left ST muscle between the pre- and post-tests (p = 0.0081). Regarding lateral symmetry, BF registered measurements of 79.7 ± 13.43 (pre-test) and 77.4 ± 14.82 (post-test), whereas ST showed measurements of 87.0 ± 9.79 (pre-test) and 87.5 ± 9.60 (post-test). Conclusions These assessments provided TMG reference data for hamstring muscles in young footballers, both before the season and after 12 weeks of in-season training. The observed changes in the contractile properties and decrease in lateral symmetry of the BF in both tests suggest an increased risk of injury.
format: application/pdf
format: text/html
creator: Paweł Pakosz
creator: Mariusz Konieczny
creator: Przemysław Domaszewski
creator: Tomasz Dybek
creator: Mariusz Gnoiński
creator: Elżbieta Skorupska
subject: Anatomy and Physiology
subject: Kinesiology
subject: Biomechanics
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.17049
publisher: PeerJ Inc.
rights: © 2024 Pakosz et al.
abstract: Background The study aimed to examine alterations and imbalances in hamstring muscle contractile properties among young football players throughout their competitive season, and to understand how these changes might contribute to the risk of muscle injuries. Hamstring injuries are particularly common in football, yet the underlying causes and effective prevention methods remain unclear. Methods The research involved 74 young footballers who were assessed before the season (pre-test) and after 12 weeks of training (post-test). To evaluate changes in hamstring muscle contractile properties, specifically the left and right biceps femoris (BF) and semitendinosus (ST), tensiomyography (TMG) parameters were utilized. Results In comparison to the BF muscle, significant differences in time delay (Td) between the left and right sides in the post-test (p = 0.0193), and maximal displacement (Dm) between the left and right sides at the pre-test (p = 0.0395). However, significant differences in Dm were observed only in the left ST muscle between the pre- and post-tests (p = 0.0081). Regarding lateral symmetry, BF registered measurements of 79.7 ± 13.43 (pre-test) and 77.4 ± 14.82 (post-test), whereas ST showed measurements of 87.0 ± 9.79 (pre-test) and 87.5 ± 9.60 (post-test). Conclusions These assessments provided TMG reference data for hamstring muscles in young footballers, both before the season and after 12 weeks of in-season training. The observed changes in the contractile properties and decrease in lateral symmetry of the BF in both tests suggest an increased risk of injury.
bibliographic citation: Pakosz et al. (2024) Changes in hamstring contractile properties during the competitive season in young football players. PeerJ 12:e17049 https://doi.org/10.7717/peerj.17049
date submitted: 2023-10-06
date accepted: 2024-02-13
issued: 2024-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pakosz
  given name: Paweł
author list: Agent
  family name: Konieczny
  given name: Mariusz
author list: Agent
  family name: Domaszewski
  given name: Przemysław
author list: Agent
  family name: Dybek
  given name: Tomasz
author list: Agent
  family name: Gnoiński
  given name: Mariusz
author list: Agent
  family name: Skorupska
  given name: Elżbieta
doi: 10.7717/peerj.17049
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-18
copyright: © 2024 Pakosz et al.
attribution name: Pakosz et al.

Deciphering the genomes of motility-deficient mutants of Vibrio alginolyticus 138-2
type: item
type: AcademicArticle
description: The motility of Vibrio species plays a pivotal role in their survival and adaptation to diverse environments and is intricately associated with pathogenicity in both humans and aquatic animals. Numerous mutant strains of Vibrio alginolyticus have been generated using UV or EMS mutagenesis to probe flagellar motility using molecular genetic approaches. Identifying these mutations promises to yield valuable insights into motility at the protein structural physiology level. In this study, we determined the complete genomic structure of 4 reference specimens of laboratory V. alginolyticus strains: a precursor strain, V. alginolyticus 138-2, two strains showing defects in the lateral flagellum (VIO5 and YM4), and one strain showing defects in the polar flagellum (YM19). Subsequently, we meticulously ascertained the specific mutation sites within the 18 motility-deficient strains related to the polar flagellum (they fall into three categories: flagellar-deficient, multi-flagellar, and chemotaxis-deficient strains) by whole genome sequencing and mapping to the complete genome of parental strains VIO5 or YM4. The mutant strains had an average of 20.6 (±12.7) mutations, most of which were randomly distributed throughout the genome. However, at least two or more different mutations in six flagellar-related genes were detected in 18 mutants specifically selected as chemotaxis-deficient mutants. Genomic analysis using a large number of mutant strains is a very effective tool to comprehensively identify genes associated with specific phenotypes using forward genetics.
format: application/pdf
format: text/html
creator: Kazuma Uesaka
creator: Keita Inaba
creator: Noriko Nishioka
creator: Seiji Kojima
creator: Michio Homma
creator: Kunio Ihara
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.17126
publisher: PeerJ Inc.
rights: © 2024 Uesaka et al.
abstract: The motility of Vibrio species plays a pivotal role in their survival and adaptation to diverse environments and is intricately associated with pathogenicity in both humans and aquatic animals. Numerous mutant strains of Vibrio alginolyticus have been generated using UV or EMS mutagenesis to probe flagellar motility using molecular genetic approaches. Identifying these mutations promises to yield valuable insights into motility at the protein structural physiology level. In this study, we determined the complete genomic structure of 4 reference specimens of laboratory V. alginolyticus strains: a precursor strain, V. alginolyticus 138-2, two strains showing defects in the lateral flagellum (VIO5 and YM4), and one strain showing defects in the polar flagellum (YM19). Subsequently, we meticulously ascertained the specific mutation sites within the 18 motility-deficient strains related to the polar flagellum (they fall into three categories: flagellar-deficient, multi-flagellar, and chemotaxis-deficient strains) by whole genome sequencing and mapping to the complete genome of parental strains VIO5 or YM4. The mutant strains had an average of 20.6 (±12.7) mutations, most of which were randomly distributed throughout the genome. However, at least two or more different mutations in six flagellar-related genes were detected in 18 mutants specifically selected as chemotaxis-deficient mutants. Genomic analysis using a large number of mutant strains is a very effective tool to comprehensively identify genes associated with specific phenotypes using forward genetics.
bibliographic citation: Uesaka et al. (2024) Deciphering the genomes of motility-deficient mutants of Vibrio alginolyticus 138-2. PeerJ 12:e17126 https://doi.org/10.7717/peerj.17126
date submitted: 2023-12-08
date accepted: 2024-02-27
issued: 2024-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Uesaka
  given name: Kazuma
author list: Agent
  family name: Inaba
  given name: Keita
author list: Agent
  family name: Nishioka
  given name: Noriko
author list: Agent
  family name: Kojima
  given name: Seiji
author list: Agent
  family name: Homma
  given name: Michio
author list: Agent
  family name: Ihara
  given name: Kunio
doi: 10.7717/peerj.17126
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-18
copyright: © 2024 Uesaka et al.
attribution name: Uesaka et al.

Validation of CDC45 as a novel biomarker for diagnosis and prognosis of gastric cancer
type: item
type: AcademicArticle
description: Background Cell division cycle protein 45 (CDC45) has been demonstrated to play vital roles in the progression of various malignancies. However, the clinical significance of CDC45 in gastric cancer (GC) remains unreported. Method In this study, we employed the TCGA database and the TCGA & GTEx dataset to compare the mRNA expression levels of CDC45 between gastric cancer tissues and adjacent or normal tissues (p < 0.05 was considered statistically significant), which was further validated in multiple datasets including GSE13911, GSE29272, GSE118916, GSE66229, as well as RT-qPCR. Furthermore, we harnessed the Human Protein Atlas (HPA) to evaluate the protein expression of CDC45, which was subsequently verified through immunohistochemistry (IHC). To ascertain the diagnostic utility of CDC45, receiver operating characteristic (ROC) curves and the area under the ROC curve (AUC) were calculated in TCGA database, and further validated it in TCGA & GTEx and GSE66229 datasets. The Kaplan–Meier method was used to reveal the prognostic importance of CDC45 in The Cancer Genome Atlas (TCGA) database and authenticated through the GSE66229, GSE84433, and GSE84437 datasets. Through cBioPortal, we identified co-expressed genes of CDC45, and pursued enrichment analysis. Additionally, we availed gene set enrichment analysis (GSEA) to annotate the biological functions of CDC45. Results Differential expression analysis revealed that CDC45 was significantly upregulated at both the mRNA and protein levels in GC (all p < 0.05). Remarkably, CDC45 emerged as a promising prognostic indicator and a novel diagnostic biomarker for GC. In a comprehensive the drug susceptibility analysis, we found that patients with high expression of CDC45 had high sensitivity to various chemotherapeutic agents, among which 5-fluorouracil, docetaxel, cisplatin, and elesclomol were most evident. Furthermore, our findings suggested a plausible association between CDC45 and immune cell infiltration. Enrichment analy…
format: application/pdf
format: text/html
creator: Lihua Wu
creator: Gan Gao
creator: Hui Mi
creator: Zhou Luo
creator: Zheng Wang
creator: Yongdong Liu
creator: Liangyan Wu
creator: Haihua Long
creator: Yongqi Shen
subject: Computational Biology
subject: Genomics
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.17130
publisher: PeerJ Inc.
rights: © 2024 Wu et al.
abstract: Background Cell division cycle protein 45 (CDC45) has been demonstrated to play vital roles in the progression of various malignancies. However, the clinical significance of CDC45 in gastric cancer (GC) remains unreported. Method In this study, we employed the TCGA database and the TCGA & GTEx dataset to compare the mRNA expression levels of CDC45 between gastric cancer tissues and adjacent or normal tissues (p < 0.05 was considered statistically significant), which was further validated in multiple datasets including GSE13911, GSE29272, GSE118916, GSE66229, as well as RT-qPCR. Furthermore, we harnessed the Human Protein Atlas (HPA) to evaluate the protein expression of CDC45, which was subsequently verified through immunohistochemistry (IHC). To ascertain the diagnostic utility of CDC45, receiver operating characteristic (ROC) curves and the area under the ROC curve (AUC) were calculated in TCGA database, and further validated it in TCGA & GTEx and GSE66229 datasets. The Kaplan–Meier method was used to reveal the prognostic importance of CDC45 in The Cancer Genome Atlas (TCGA) database and authenticated through the GSE66229, GSE84433, and GSE84437 datasets. Through cBioPortal, we identified co-expressed genes of CDC45, and pursued enrichment analysis. Additionally, we availed gene set enrichment analysis (GSEA) to annotate the biological functions of CDC45. Results Differential expression analysis revealed that CDC45 was significantly upregulated at both the mRNA and protein levels in GC (all p < 0.05). Remarkably, CDC45 emerged as a promising prognostic indicator and a novel diagnostic biomarker for GC. In a comprehensive the drug susceptibility analysis, we found that patients with high expression of CDC45 had high sensitivity to various chemotherapeutic agents, among which 5-fluorouracil, docetaxel, cisplatin, and elesclomol were most evident. Furthermore, our findings suggested a plausible association between CDC45 and immune cell infiltration. Enrichment analy…
bibliographic citation: Wu et al. (2024) Validation of CDC45 as a novel biomarker for diagnosis and prognosis of gastric cancer. PeerJ 12:e17130 https://doi.org/10.7717/peerj.17130
date submitted: 2023-10-25
date accepted: 2024-02-27
issued: 2024-03-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Lihua
author list: Agent
  family name: Gao
  given name: Gan
author list: Agent
  family name: Mi
  given name: Hui
author list: Agent
  family name: Luo
  given name: Zhou
author list: Agent
  family name: Wang
  given name: Zheng
author list: Agent
  family name: Liu
  given name: Yongdong
author list: Agent
  family name: Wu
  given name: Liangyan
author list: Agent
  family name: Long
  given name: Haihua
author list: Agent
  family name: Shen
  given name: Yongqi
doi: 10.7717/peerj.17130
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-03-18
copyright: © 2024 Wu et al.
attribution name: Wu et al.

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