Theoretical Biology and Medical Modelling最新文献_第2页

Numerical simulations of multicomponent ecological models with adaptive methods 多组分生态模型的自适应数值模拟

Theoretical Biology and Medical Modelling Pub Date : 2016-01-08 DOI: 10.1186/s12976-016-0027-4

K. M. Owolabi, K. Patidar

引用次数: 69

A Boolean network model of human gonadal sex determination 人类性腺性别决定的布尔网络模型

Theoretical Biology and Medical Modelling Pub Date : 2015-11-16 DOI: 10.1186/s12976-015-0023-0

O. Ríos, S. Frías, Alfredo Rodríguez, S. Kofman, Horacio Merchant, Leda Torres, Luis Mendoza

引用次数: 32

A measure of regularity for polygonal mosaics in biological systems 生物系统中多边形镶嵌的规律性度量

Theoretical Biology and Medical Modelling Pub Date : 2015-11-16 DOI: 10.1186/s12976-015-0022-1

Gabriela Contreras-Figueroa, L. Hernández-Sandoval, J. Aragón

引用次数: 4

In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour 凤尾草双链断裂修复蛋白MRE11的硅表征及分子建模

Theoretical Biology and Medical Modelling Pub Date : 2015-11-05 DOI: 10.1186/s12976-015-0013-2

I. Rekik, Zayneb Chaâbene, C. Grubb, N. Drira, F. Chéour, A. Elleuch

引用次数: 19

Annual acknowledgement of manuscript reviewers 稿件审稿人的年度确认

Theoretical Biology and Medical Modelling Pub Date : 2015-07-03 DOI: 10.1186/1742-4682-12-4

H. Nishiura, E. Rietman, Rongling Wu

引用次数: 0

Erratum to: improvement of design of a surgical interface using an eye tracking device 更正:使用眼动追踪装置的手术界面设计的改进

Theoretical Biology and Medical Modelling Pub Date : 2014-11-03 DOI: 10.1186/1742-4682-11-48

D. Barkana, Alper Açik, D. G. Duru, A. Duru

引用次数: 6

Molecular docking studies for the identification of novel melatoninergic inhibitors for acetylserotonin-O-methyltransferase using different docking routines. 采用不同对接方法鉴定新型乙酰- 5 -羟色胺- o -甲基转移酶褪黑素能抑制剂的分子对接研究。

Theoretical Biology and Medical Modelling Pub Date : 2013-10-24 DOI: 10.1186/1742-4682-10-63

Syed Sikander Azam, Sumra Wajid Abbasi

{"title":"Molecular docking studies for the identification of novel melatoninergic inhibitors for acetylserotonin-O-methyltransferase using different docking routines.","authors":"Syed Sikander Azam, Sumra Wajid Abbasi","doi":"10.1186/1742-4682-10-63","DOIUrl":"https://doi.org/10.1186/1742-4682-10-63","url":null,"abstract":"Background: N-Acetylserotonin O-methyltransferase (ASMT) is an enzyme which by converting nor-melatonin to melatonin catalyzes the final reaction in melatonin biosynthesis in tryptophan metabolism pathway. High Expression of ASMT gene is evident in PPTs. The presence of abnormally high levels of ASMT in pineal gland could serve as an indication of the existence of pineal parenchymal tumors (PPTs) in the brain (J Neuropathol Exp Neurol 65: 675-684, 2006). Different levels of melatonin are used as a trait marker for prescribing the mood disorders e.g. Seasonal affective disorder, bipolar disorder, or major depressive disorder. In addition, melatonin levels can also be used to calculate the severity of a patient's illness at a given point in time.Methods: Seventy three melatoninergic inhibitors were docked with acetylserotonin-O-methyltransferase in order to identify the potent inhibitor against the enzyme. The chemical nature of the protein and ligands greatly influence the performance of docking routines. Keeping this fact in view, critical evaluation of the performance of four different commonly used docking routines: AutoDock/Vina, GOLD, FlexX and FRED were performed. An evaluation criterion was based on the binding affinities/docking scores and experimental bioactivities.Results and conclusion: Results indicated that both hydrogen bonding and hydrophobic interactions contributed significantly for its ligand binding and the compound selected as potent inhibitor is having minimum binding affinity, maximum GoldScore and minimum FlexX energy. The correlation value of r2 = 0. 66 may be useful in the selection of correct docked complexes based on the energy without having prior knowledge of the active site. This may lead to further understanding of structures, their reliability and Biomolecular activity especially in connection with bipolar disorders.","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"63"},"PeriodicalIF":0.0,"publicationDate":"2013-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-10-63","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40263759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Spatial chaos and complexity in the intracellular space of cancer and normal cells. 癌细胞与正常细胞胞内空间的空间混沌与复杂性。

Theoretical Biology and Medical Modelling Pub Date : 2013-10-24 DOI: 10.1186/1742-4682-10-62

Tuan D Pham, Kazuhisa Ichikawa

{"title":"Spatial chaos and complexity in the intracellular space of cancer and normal cells.","authors":"Tuan D Pham, Kazuhisa Ichikawa","doi":"10.1186/1742-4682-10-62","DOIUrl":"https://doi.org/10.1186/1742-4682-10-62","url":null,"abstract":"Background: One of the most challenging problems in biological image analysis is the quantification of the dynamical mechanism and complexity of the intracellular space. This paper investigates potential spatial chaos and complex behavior of the intracellular space of typical cancer and normal cell images whose structural details are revealed by the combination of scanning electron microscopy and focused ion beam systems. Such numerical quantifications have important implications for computer modeling and simulation of diseases.Methods: Cancer cell lines derived from a human head and neck squamous cell carcinoma (SCC-61) and normal mouse embryonic fibroblast (MEF) cells produced by focused ion beam scanning electron microscopes were used in this study. Spatial distributions of the organelles of cancer and normal cells can be analyzed at both short range and long range of the bounded dynamical system of the image space, depending on the orientations of the spatial cell. A procedure was designed for calculating the largest Lyapunov exponent, which is an indicator of the potential chaotic behavior in intracellular images. Furthermore, the sample entropy and regularity dimension were applied to measure the complexity of the intracellular images.Results: Positive values of the largest Lyapunov exponents (LLEs) of the intracellular space of the SCC-61 were obtained in different spatial orientations for both long-range and short-range models, suggesting the chaotic behavior of the cell. The MEF has smaller positive values of LLEs in the long range than those of the SCC-61, and zero vales of the LLEs in the short range analysis, suggesting a non-chaotic behavior. The intracellular space of the SCC-61 is found to be more complex than that of the MEF. The degree of complexity measured in the spatial distribution of the intracellular space in the diagonal direction was found to be approximately twice larger than the complexity measured in the horizontal and vertical directions.Conclusion: Initial findings are promising for characterizing different types of cells and therefore useful for studying cancer cells in the spatial domain using state-of-the-art imaging technology. The measures of the chaotic behavior and complexity of the spatial cell will help computational biologists gain insights into identifying associations between the oscillation patterns and spatial parameters of cells, and appropriate model for simulating cancer cell signaling networks for cancer treatment and new drug discovery.","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"62"},"PeriodicalIF":0.0,"publicationDate":"2013-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-10-62","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40259758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 27

Exploring evolution of brain genes involved in microcephaly through phylogeny and synteny analysis. 通过系统发育和合成分析探讨与小头畸形有关的脑基因的进化。

Theoretical Biology and Medical Modelling Pub Date : 2013-10-22 DOI: 10.1186/1742-4682-10-61

Sobiah Rauf, Asif Mir

{"title":"Exploring evolution of brain genes involved in microcephaly through phylogeny and synteny analysis.","authors":"Sobiah Rauf, Asif Mir","doi":"10.1186/1742-4682-10-61","DOIUrl":"https://doi.org/10.1186/1742-4682-10-61","url":null,"abstract":"Background: Human brain development is a complicated process. When normal growth and development of brain or central nervous system is impaired, it leads to neurodevelopemental disorders (NDDs). Autosomal Recessive Primary Microcephaly (MCPH) is one of those, for which seven loci (MCPH1-MCPH7) with the corresponding genes (MCPH1, WDR62, CDK5RAP2, CEP152, ASPM, CENPJ, and STIL) have been reported so far. An important field of study is to find out diversity among organisms due to evolution. How species are related to each other can be inferred through finding evolutionary relationship between organisms in the form of ancestors and descendents.Methods: MEGA5 was used for phylogenetic tree reconstruction. Pair-wise and multiple alignment was built through ClustalW algorithm. Neighbor joining (NJ) and maximum parsimony (MP) methods were used for tree reconstruction. Bootstrap analysis was done to check the reliability of trees. Synteny analysis was performed using Ensemble synteny view in ensemble database and genome synteny viewer (GSV).Results: Evolutionary time for single gene trees showed that CENPJ (0.02) evolving rapidly while CDK5RAP2 (0.1) evolving with least rate as compare to other genes. All trees were reconciling the species divergence time. Chimpanzee was inferred as closest specie of Human. In MCPH combined tree, five duplications were observed. Four duplications were before and one was after vertebrate and invertebrate divergence. Two genes MCPH1 and WDR62 were closely related with each other. Synteny analysis indicated that maximum conservation of Human was with Chimpanzee. Highly conserved synteny was observed for Human and Chimpanzee in case of CENPJ with no deletion.Conclusion: It has been hypothesized that due to having closest relationship, mutations can affect Chimpanzee likewise as these affect Human. Conservation shows that apart from sequence similarity, function of MCPH genes in closely related species is also same and this function disrupts as a result of mutation and hence leads to the diseased state. Huge genomic and proteomic data is available today which enables us to perform In Silico analysis. Our cost and time effective analysis has opened many insights into disease understanding and it will definitely provide a way towards accurate diagnosis.","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"61"},"PeriodicalIF":0.0,"publicationDate":"2013-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-10-61","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40258091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Agent-based modeling of competence phenotype switching in Bacillus subtilis. 枯草芽孢杆菌能力表型转换的agent建模。

Theoretical Biology and Medical Modelling Pub Date : 2013-04-03 DOI: 10.1186/1742-4682-10-23

Suzy M Stiegelmeyer, Morgan C Giddings

{"title":"Agent-based modeling of competence phenotype switching in Bacillus subtilis.","authors":"Suzy M Stiegelmeyer, Morgan C Giddings","doi":"10.1186/1742-4682-10-23","DOIUrl":"https://doi.org/10.1186/1742-4682-10-23","url":null,"abstract":"Background: It is a fascinating phenomenon that in genetically identical bacteria populations of Bacillus subtilis, a distinct DNA uptake phenotype called the competence phenotype may emerge in 10-20% of the population. Many aspects of the phenomenon are believed to be due to the variable expression of critical genes: a stochastic occurrence termed \"noise\" which has made the phenomenon difficult to examine directly by lab experimentation.Methods: To capture and model noise in this system and further understand the emergence of competence both at the intracellular and culture levels in B. subtilis, we developed a novel multi-scale, agent-based model. At the intracellular level, our model recreates the regulatory network involved in the competence phenotype. At the culture level, we simulated growth conditions, with our multi-scale model providing feedback between the two levels.Results: Our model predicted three potential sources of genetic \"noise\". First, the random spatial arrangement of molecules may influence the manifestation of the competence phenotype. In addition, the evidence suggests that there may be a type of epigenetic heritability to the emergence of competence, influenced by the molecular concentrations of key competence molecules inherited through cell division. Finally, the emergence of competence during the stationary phase may in part be due to the dilution effect of cell division upon protein concentrations.Conclusions: The competence phenotype was easily translated into an agent-based model - one with the ability to illuminate complex cell behavior. Models such as the one described in this paper can simulate cell behavior that is otherwise unobservable in vivo, highlighting their potential usefulness as research tools.","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"23"},"PeriodicalIF":0.0,"publicationDate":"2013-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-10-23","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40225266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11