Mathematical Biology and Bioinformatics最新文献

On The Thermalization of One-Dimensional Lattices. I. Microcanonical Ensemble 论一维晶格的热化。I. 微卡农合集

Mathematical Biology and Bioinformatics Pub Date : 2024-07-08 DOI: 10.17537/2024.19.248

G.A. Vinogradov, V.D. Lakhno

引用次数: 0

Trajectories of Solitons Movement in the Potential Field of pPF1 Plasmid with Non-Zero Initial Velocity 质粒 pPF1 在非零初始速度势场中的孤子运动轨迹

Mathematical Biology and Bioinformatics Pub Date : 2024-07-02 DOI: 10.17537/2024.19.232

L. Yakushevich, L. Krasnobaeva

{"title":"Trajectories of Solitons Movement in the Potential Field of pPF1 Plasmid with Non-Zero Initial Velocity","authors":"L. Yakushevich, L. Krasnobaeva","doi":"10.17537/2024.19.232","DOIUrl":"https://doi.org/10.17537/2024.19.232","url":null,"abstract":"\u0000Nonlinear conformational distortions, such as, for example, locally unwound regions of the DNA double helix, named open states, are considered in this work as solitons moving in the potential field of this molecule. It is believed that open states play an important role in the processes of transcription, replication, denaturation, as well as in the transmission of structural changes and information along the DNA molecule. This work examines the problem of the movement of kink-like solitons (kinks) in the potential field of the pPF1 plasmid, the sequence of which includes the genes of the fluorescent proteins Egfp and mCherry, separated by a small intermediate region. The results of calculations of energy profiles of the main and complementary sequences of the plasmid, as well as 2D and 3D trajectories of kinks with a non-zero initial velocity are presented. It has been shown that two types of kinks can be activated in the pPF1 plasmid, which can be considered as two types of quasiparticles that have their own energy, mass, velocity and move in the potential field of the plasmid. It was found that the lowest energy required to form these kinks is observed in the intermediate region located between the fluorescent protein genes. It was shown that the nature of the motion of kinks does not depend on the value of their initial velocity. It was shown that there are threshold values of the torsion field, upon reaching which the behavior of kinks changes sharply: from damped oscillations within the intermediate region to forward motion and penetration into neighboring regions. These values have been calculated. It turned out that for the first kink moving in the main sequence potential field, the threshold value is 4.95×10–22 J, and for the second kink – 4.20 × 10–22 J.\u0000","PeriodicalId":509888,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"317 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141686679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Bioinformatics Analysis for Unveiling Novel Long Non-Coding RNAs and their Regulatory Impact on Key Genes Associated with Vitiligo 生物信息学分析揭示新型长非编码 RNA 及其对白癜风相关关键基因的调控影响

Mathematical Biology and Bioinformatics Pub Date : 2024-05-01 DOI: 10.17537/2024.19.155

Safa Sadeq Fayez, Ahmed AbdulJabbar Suleiman

{"title":"A Bioinformatics Analysis for Unveiling Novel Long Non-Coding RNAs and their Regulatory Impact on Key Genes Associated with Vitiligo","authors":"Safa Sadeq Fayez, Ahmed AbdulJabbar Suleiman","doi":"10.17537/2024.19.155","DOIUrl":"https://doi.org/10.17537/2024.19.155","url":null,"abstract":"\u0000 Vitiligo involves the gradual disappearance of melanocytes, causing skin depigmentation. Long noncoding RNAs (lncRNAs), a type of noncoding RNA, are important for regulating inflammation and immunity. Despite this significance, there needs to be more published research on how lncRNAs are expressed in vitiligo cases and their potential roles in the biology of this skin condition. This study aims to elucidate the molecular landscape of vitiligo by analyzing gene expression profiles of vitiligo skin and normal skin. Two datasets, RNA-seq and microarray, were thoroughly investigated to identify differentially expressed (DE) genes and lncRNAs associated with vitiligo development. Functional enrichment analysis revealed biological processes and pathways influenced by dysregulated genes, highlighting intricate processes such as melanin biosynthesis and melanogenesis, shedding light on the complex regulatory networks involved in pigmentation and immune responses. Protein-protein interaction analysis highlighted significantly downregulated hub genes, including TYRP1, MLANA, MC1R, SLC45A2, PAX3, TYR, DCT, OCA2, PMEL, and SOX10, revealing significant functional relationships among identified hub genes within the network. RNA-seq data analysis uncovered DE-lncRNAs, emphasizing the regulatory role of lncRNAs in vitiligo. Moreover, the correlation analysis between the expression of lncRNAs and key genes associated with melanogenesis (OCA2, TYRP1, and PMEL) unveiled novel upregulated lncRNAs such as CRTC3-AS1, LCMT1-AS1, LINC02178 contributing to vitiligo development. Additionally, lncRNA-gene networks constructed based on key melanocyte-related genes provided insights into the molecular relationships relevant to vitiligo. Overall, this study offers a comprehensive understanding of vitiligo pathogenesis, identifying potential therapeutic targets and laying the foundation for future research in this critical area.\u0000","PeriodicalId":509888,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141053937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mathematical Modeling Of the Spread of COVID-19, Taking Into Account the Distribution of Asymptomatic Cases between Actually Asymptomatic and Pre-Symptomatic Cases 考虑到无症状病例在实际无症状病例和无症状前病例之间的分布情况，建立 COVID-19 传播的数学模型

Mathematical Biology and Bioinformatics Pub Date : 2024-03-21 DOI: 10.17537/2024.19.52

I. Kolesin, E. Zhitkova

引用次数: 0

GENIS – methodological approach for in silico genotyping (validation on Sus scrofa sequencing) GENIS - 硅基因分型方法（在鲭鱼测序上进行验证）

Mathematical Biology and Bioinformatics Pub Date : 2024-03-02 DOI: 10.17537/2024.19.36

V.N. Kipen, E. V. Snytkov

引用次数: 0