Pub Date : 2023-01-01DOI: 10.32604/biocell.2023.030191
Xiao-jun Zhou, Yu Tian, Rui Li
Background: Acer griseum Pax is an endangered species endemic to China with both ornamental and economic value. However, the lack of information on its genome size and characteristics hinders further work at the genome level. Methods: This paper applied bioinformatics methods to predict the characteristics and patterns of the A. griseum genome, providing an important basis for formulating its whole-genome sequencing scheme. This study also characterized the simple sequence repeats (SSRs) of A. griseum, laying the foundation for the development and application of genome-wide SSR markers. In this study, PE150 sequencing was performed by the BGI MGISEQ platform, and the sequence files were analyzed by the K-mer method to estimate the characteristic information by GCE software. Results: The genome size was finally determined to be 739.63 Mb, its heterozygosity ratio was 1.33%, and the repetition ratio was 65.68%. A total of 825,960 SSR loci were identified in the assembled genome sequence, and primers were successfully designed for 526,020 loci. To verify the effectiveness of these primers, 100 pairs of primers were randomly selected and synthesized, and 81 pairs successfully amplified the target fragments. Fourteen pairs of primers with good polymorphism were selected for principal component analysis of 31 A. griseum individuals from two populations, showing favorable heterozygosity and PIC values. According to the findings, these SSRs might identify genetic variations based on geographic areas. Conclusion: It is suggested that Illumina + PacBio assembly strategy should be used for whole-genome sequencing due to the high heterozygosity rate and high repetition rate of the genome. In addition, the SSR primers designed in batches in this study laid a foundation for the in-depth study of population structure and population maintenance mechanism of A. griseum, which is helpful for the effective conservation and sustainable utilization of this germplasm resource.
{"title":"The whole-genome survey of Acer griseum, its polymorphic simple sequence repeats development and application","authors":"Xiao-jun Zhou, Yu Tian, Rui Li","doi":"10.32604/biocell.2023.030191","DOIUrl":"https://doi.org/10.32604/biocell.2023.030191","url":null,"abstract":"Background: Acer griseum Pax is an endangered species endemic to China with both ornamental and economic value. However, the lack of information on its genome size and characteristics hinders further work at the genome level. Methods: This paper applied bioinformatics methods to predict the characteristics and patterns of the A. griseum genome, providing an important basis for formulating its whole-genome sequencing scheme. This study also characterized the simple sequence repeats (SSRs) of A. griseum, laying the foundation for the development and application of genome-wide SSR markers. In this study, PE150 sequencing was performed by the BGI MGISEQ platform, and the sequence files were analyzed by the K-mer method to estimate the characteristic information by GCE software. Results: The genome size was finally determined to be 739.63 Mb, its heterozygosity ratio was 1.33%, and the repetition ratio was 65.68%. A total of 825,960 SSR loci were identified in the assembled genome sequence, and primers were successfully designed for 526,020 loci. To verify the effectiveness of these primers, 100 pairs of primers were randomly selected and synthesized, and 81 pairs successfully amplified the target fragments. Fourteen pairs of primers with good polymorphism were selected for principal component analysis of 31 A. griseum individuals from two populations, showing favorable heterozygosity and PIC values. According to the findings, these SSRs might identify genetic variations based on geographic areas. Conclusion: It is suggested that Illumina + PacBio assembly strategy should be used for whole-genome sequencing due to the high heterozygosity rate and high repetition rate of the genome. In addition, the SSR primers designed in batches in this study laid a foundation for the in-depth study of population structure and population maintenance mechanism of A. griseum, which is helpful for the effective conservation and sustainable utilization of this germplasm resource.","PeriodicalId":55384,"journal":{"name":"Biocell","volume":"92 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84522032","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.32604/biocell.2023.024625
Jessica CRISTINA MAR蚇-LLERA, Carlos AMAURY JIM蒒EZ-C罵DENAS, JES赟 CHIMAL-MONROY
{"title":"Control of tendon cell fate in the embryonic limb: A molecular perspective","authors":"Jessica CRISTINA MAR蚇-LLERA, Carlos AMAURY JIM蒒EZ-C罵DENAS, JES赟 CHIMAL-MONROY","doi":"10.32604/biocell.2023.024625","DOIUrl":"https://doi.org/10.32604/biocell.2023.024625","url":null,"abstract":"","PeriodicalId":55384,"journal":{"name":"Biocell","volume":"29 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81637422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.32604/biocell.2023.025677
Kamila Czubak-Prowizor, M. Swiatkowska
{"title":"Junctional adhesion molecule-A (JAM-A) in gynecological cancers: Current state of knowledge","authors":"Kamila Czubak-Prowizor, M. Swiatkowska","doi":"10.32604/biocell.2023.025677","DOIUrl":"https://doi.org/10.32604/biocell.2023.025677","url":null,"abstract":"","PeriodicalId":55384,"journal":{"name":"Biocell","volume":"5 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87807544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.32604/biocell.2023.030796
ZHAOXU YAO, HAIBIN MA, LIN LIU, QIAN ZHAO, LONGCHAO QIN, XUEYAN REN, CHUANJUN WU, KAILI SUN
Objective: Through integrated bioinformatics analysis, the goal of this work was to find new, characterised N7-methylguanosine modification-related long non-coding RNAs (m7G-lncRNAs) that might be used to predict the prognosis of laryngeal squamous cell carcinoma (LSCC). Methods: The clinical data and LSCC gene expression data for the current investigation were initially retrieved from the TCGA database & sanitised. Then, using co-expression analysis of m7G-associated mRNAs & lncRNAs & differential expression analysis (DEA) among LSCC & normal sample categories, we discovered lncRNAs that were connected to m7G. The prognosis prediction model was built for the training category using univariate & multivariate COX regression & LASSO regression analyses, & the model’s efficacy was checked against the test category data. In addition, we conducted DEA of prognostic m7G-lncRNAs among LSCC & normal sample categories & compiled a list of co-expression networks & the structure of prognosis m7G-lncRNAs. To compare the prognoses for individuals with LSCC in the high- & low-risk categories in the prognosis prediction model, survival and risk assessments were also carried out. Finally, we created a nomogram to accurately forecast the outcomes of LSCC patients & created receiver operating characteristic (ROC) curves to assess the prognosis prediction model’s predictive capability. Results: Using co-expression network analysis & differential expression analysis, we discovered 774 m7G-lncRNAs and 551 DEm7G-lncRNAs, respectively. We then constructed a prognosis prediction model for six m7G-lncRNAs (FLG−AS1, RHOA−IT1, AC020913.3, AC027307.2, AC010973.2 and AC010789.1), identified 32 DEPm7G-lncRNAs, analyzed the correlation between 32 DEPm7G-lncRNAs and 13 DEPm7G-mRNAs, and performed survival analyses and risk analyses of the prognosis prediction model to assess the prognostic performance of LSCC patients. By displaying ROC curves and a nomogram, we finally checked the prognosis prediction model's accuracy. Conclusion: By creating novel predictive lncRNA signatures for clinical diagnosis & therapy, our findings will contribute to understanding the pathogenetic process of LSCC.
{"title":"Novel defined N7-methylguanosine modification-related lncRNAs for predicting the prognosis of laryngeal squamous cell carcinoma","authors":"ZHAOXU YAO, HAIBIN MA, LIN LIU, QIAN ZHAO, LONGCHAO QIN, XUEYAN REN, CHUANJUN WU, KAILI SUN","doi":"10.32604/biocell.2023.030796","DOIUrl":"https://doi.org/10.32604/biocell.2023.030796","url":null,"abstract":"<b>Objective:</b> Through integrated bioinformatics analysis, the goal of this work was to find new, characterised N7-methylguanosine modification-related long non-coding RNAs (m7G-lncRNAs) that might be used to predict the prognosis of laryngeal squamous cell carcinoma (LSCC). <b>Methods:</b> The clinical data and LSCC gene expression data for the current investigation were initially retrieved from the TCGA database & sanitised. Then, using co-expression analysis of m7G-associated mRNAs & lncRNAs & differential expression analysis (DEA) among LSCC & normal sample categories, we discovered lncRNAs that were connected to m7G. The prognosis prediction model was built for the training category using univariate & multivariate COX regression & LASSO regression analyses, & the model’s efficacy was checked against the test category data. In addition, we conducted DEA of prognostic m7G-lncRNAs among LSCC & normal sample categories & compiled a list of co-expression networks & the structure of prognosis m7G-lncRNAs. To compare the prognoses for individuals with LSCC in the high- & low-risk categories in the prognosis prediction model, survival and risk assessments were also carried out. Finally, we created a nomogram to accurately forecast the outcomes of LSCC patients & created receiver operating characteristic (ROC) curves to assess the prognosis prediction model’s predictive capability. <b>Results:</b> Using co-expression network analysis & differential expression analysis, we discovered 774 m7G-lncRNAs and 551 DEm7G-lncRNAs, respectively. We then constructed a prognosis prediction model for six m7G-lncRNAs (<i>FLG−AS1</i>, <i>RHOA−IT1</i>, <i>AC020913.3</i>, <i>AC027307.2</i>, <i>AC010973.2</i> and <i>AC010789.1</i>), identified 32 DEPm7G-lncRNAs, analyzed the correlation between 32 DEPm7G-lncRNAs and 13 DEPm7G-mRNAs, and performed survival analyses and risk analyses of the prognosis prediction model to assess the prognostic performance of LSCC patients. By displaying ROC curves and a nomogram, we finally checked the prognosis prediction model's accuracy. <b>Conclusion:</b> By creating novel predictive lncRNA signatures for clinical diagnosis & therapy, our findings will contribute to understanding the pathogenetic process of LSCC.","PeriodicalId":55384,"journal":{"name":"Biocell","volume":"354 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135755380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Exosomes are extracellular vesicles with a 30–150 nm diameter originating from endosomes. In recent years, scientists have regarded exosomes as an ideal small molecule carrier for the targeted treatment of Alzheimer’s disease (AD) across the blood-brain barrier due to their nanoscale size and low immunogenicity. A large amount of evidence shows that exosomes are rich in biomarkers, and it has been found that the changes in biomarker content in blood, cerebrospinal fluid, and urine are often associated with the onset of AD patients. In this paper, some recent advances in the use of exosomes in the treatment of AD are reviewed, and various exosome markers and some latest detection methods are summarized to provide some evidence for the detection or treatment of AD by exosomes.
{"title":"Exploring exosomes to provide evidence for the treatment and prediction of Alzheimer’s disease","authors":"XIANGYU QUAN, XUETING MA, GUODONG LI, XUEQI FU, JIANGTAO LI, LINLIN ZENG","doi":"10.32604/biocell.2023.031226","DOIUrl":"https://doi.org/10.32604/biocell.2023.031226","url":null,"abstract":"Exosomes are extracellular vesicles with a 30–150 nm diameter originating from endosomes. In recent years, scientists have regarded exosomes as an ideal small molecule carrier for the targeted treatment of Alzheimer’s disease (AD) across the blood-brain barrier due to their nanoscale size and low immunogenicity. A large amount of evidence shows that exosomes are rich in biomarkers, and it has been found that the changes in biomarker content in blood, cerebrospinal fluid, and urine are often associated with the onset of AD patients. In this paper, some recent advances in the use of exosomes in the treatment of AD are reviewed, and various exosome markers and some latest detection methods are summarized to provide some evidence for the detection or treatment of AD by exosomes.","PeriodicalId":55384,"journal":{"name":"Biocell","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135504583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.32604/biocell.2023.025880
Yuanyuan Huang, Hongmei Wu, Ruyuan Liu, Song Jin, Weilai Xiang, Chang Yang, Li Xu, Xiaonian Zhu
{"title":"Research progress of TRIMs protein family in tumors","authors":"Yuanyuan Huang, Hongmei Wu, Ruyuan Liu, Song Jin, Weilai Xiang, Chang Yang, Li Xu, Xiaonian Zhu","doi":"10.32604/biocell.2023.025880","DOIUrl":"https://doi.org/10.32604/biocell.2023.025880","url":null,"abstract":"","PeriodicalId":55384,"journal":{"name":"Biocell","volume":"34 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77803263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.32604/biocell.2023.024738
Linshen Xie, Qiaolan Wang, Jingxuan Ma, Ye Zeng
Fibrosis is the end-stage change of damaged tissues in various human diseases, which can lead to permanent scarring or organ malfunction. Hypoxia leads to oxidative stress, mitochondrial dysfunction, and inflammation in dysfunctional organs and tissues. Oxidative stress resulting from the overproduction of reactive oxygen species plays a central role in the fibrosis of injured organs. This review addresses the updated knowledge of the relationship between hypoxia and tissue fibrosis mediated by the reactive oxygen species pathway. Moreover, novel anti-fibrotic strategies are discussed, which may suppress reactive oxygen species and organ fibrosis.
{"title":"Hypoxia-induced reactive oxygen species in organ and tissue fibrosis","authors":"Linshen Xie, Qiaolan Wang, Jingxuan Ma, Ye Zeng","doi":"10.32604/biocell.2023.024738","DOIUrl":"https://doi.org/10.32604/biocell.2023.024738","url":null,"abstract":"Fibrosis is the end-stage change of damaged tissues in various human diseases, which can lead to permanent scarring or organ malfunction. Hypoxia leads to oxidative stress, mitochondrial dysfunction, and inflammation in dysfunctional organs and tissues. Oxidative stress resulting from the overproduction of reactive oxygen species plays a central role in the fibrosis of injured organs. This review addresses the updated knowledge of the relationship between hypoxia and tissue fibrosis mediated by the reactive oxygen species pathway. Moreover, novel anti-fibrotic strategies are discussed, which may suppress reactive oxygen species and organ fibrosis.","PeriodicalId":55384,"journal":{"name":"Biocell","volume":"2 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86868506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.32604/biocell.2023.028035
Haiying Chen, Yuqing Wu, Baojian Huang, Lei Han
{"title":"Recent progress in microbial cell surface display systems and their application on biosensors","authors":"Haiying Chen, Yuqing Wu, Baojian Huang, Lei Han","doi":"10.32604/biocell.2023.028035","DOIUrl":"https://doi.org/10.32604/biocell.2023.028035","url":null,"abstract":"","PeriodicalId":55384,"journal":{"name":"Biocell","volume":"74 1","pages":""},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74566854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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