Theoretical Biology Forum最新文献_第4页

Mathematical Modeling for Genes to Collective Cell Dynamics 基因对集体细胞动力学的数学建模

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2021-01-01 DOI: 10.1007/978-981-16-7132-6

引用次数: 0

Potential Applications and Challenges 潜在的应用和挑战

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2019-01-01 DOI: 10.1007/978-981-15-1731-0_5

A. Kamimura, T. Ohira

引用次数: 4

Chases and Escapes 追逐和逃跑

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2019-01-01 DOI: 10.1007/978-981-15-1731-0_2

A. Kamimura, T. Ohira

引用次数: 4

MOLECULAR MODEL OF CYTOTOXIN-1 FROM NAJA MOSSAMBICA MOSSAMBICA VENOM IN COMPLEX WITH CHYMOTRYPSIN. 莫桑舌鱼毒液中细胞毒素-1与凝乳胰蛋白酶复合物的分子模型。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2015-01-01 DOI: 10.1400/240197

A. Munawar, A. Akrem, A. Hussain, P. Spencer, C. Betzel

{"title":"MOLECULAR MODEL OF CYTOTOXIN-1 FROM NAJA MOSSAMBICA MOSSAMBICA VENOM IN COMPLEX WITH CHYMOTRYPSIN.","authors":"A. Munawar, A. Akrem, A. Hussain, P. Spencer, C. Betzel","doi":"10.1400/240197","DOIUrl":"https://doi.org/10.1400/240197","url":null,"abstract":"Snake venom is a myriad of biologically active proteins and peptides. Three finger toxins are highly conserved in their molecular structure, but interestingly possess diverse biological functions. During the course of evolution the introduction of subtle mutations in loop regions and slight variations in the three dimensional structure, has resulted in their functional versatility. Cytotoxin-1 (UniProt ID: P01467), isolated from Naja mossambica mossambica, showed the potential to inhibit chymotrypsin and the chymotryptic activity of the 20S proteasome. In the present work we describe a molecular model of cytotoxin-1 in complex with chymotrypsin, prepared by the online server ClusPro. Analysis of the molecular model shows that Cytotoxin-1 (P01467) binds to chymotrypsin through its loop I located near the N-terminus. The concave side of loop I of the toxin fits well in the substrate binding pocket of the protease. We propose Phe10 as the dedicated P1 site of the ligand. Being a potent inhibitor of the 20S proteasome, cytotoxin-1 (P01467) can serve as a potential antitumor agent. Already snake venom cytotoxins have been investigated for their ability as an anticancer agent. The molecular model of cytotoxin-1 in complex with chymotrypsin provides important information towards understanding the complex formation.","PeriodicalId":55980,"journal":{"name":"Theoretical Biology Forum","volume":"108 1-2 1","pages":"89-99"},"PeriodicalIF":1.5,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66623680","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}

引用次数: 3

DYNAMICAL SYSTEMS ON GRAPHS: FROM RANDOM WALKS TO TRANSPORTATION NETWORKS. 图上的动态系统:从随机漫步到交通网络。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2015-01-01 DOI: 10.1400/240192

A. Bazzani

引用次数: 1

Interleukins (ILs), a fascinating family of cytokines. Part I: ILs from IL-1 to IL-19. 白细胞介素(il)，一个令人着迷的细胞因子家族。第一部分:IL-1到IL-19的il。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2014-01-01 DOI: 10.1400/230151

P. Fietta, E. Costa, G. Delsante

{"title":"Interleukins (ILs), a fascinating family of cytokines. Part I: ILs from IL-1 to IL-19.","authors":"P. Fietta, E. Costa, G. Delsante","doi":"10.1400/230151","DOIUrl":"https://doi.org/10.1400/230151","url":null,"abstract":"Every nucleated cell can produce and respond to cytokines, extracellular proteic/glycoproteic mediators that constitute a complex, interconnected, and flexible signaling network, addressed to modulate cell behavior and homeostasis through the interaction with high-affinity surface receptors. These messenger molecules, whose main characteristics are potency, pleiotropism, and redundancy, primarily act in autocrine, paracrine, and juxtacrine way, but can also display systemic activity in endocrine-like modality. They are generally classified according to their cellular sources, three-dimensional structure, or biological functions. Among cytokines, interleukins (ILs) represent a fascinating and multifunctional group of immunomodulators that primarily mediate the leukocyte cross-talk (hence the name), and mainly regulate the immune cell proliferation, differentiation, growth, survival, activation, and functions. Up to 38 ILs have been so far identified, numbered according to the order of discovery, and grouped in different subsets, based on distinguishing structural/functional features. Due to their crucial role in regulating inflammation and immune response, ILs are known to be involved in the pathogenesis of human inflammatory/autoimmune diseases. Therefore, they have increasingly attracted great interest as effective or promising therapeutic targets. The biology and functions of the hitherto identified human ILs are reviewed and discussed: in this first section of the article, ILs from IL-1 to IL-19 are presented.","PeriodicalId":55980,"journal":{"name":"Theoretical Biology Forum","volume":"107 1-2 1","pages":"13-45"},"PeriodicalIF":1.5,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66621988","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}

引用次数: 15

A dynamical model for influenza under seasonal variables. 季节性变量下的流感动力学模型。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2014-01-01 DOI: 10.1400/230161

Masomeh Taherian, M. Toomanian, M. Molaei

引用次数: 1

Elements of plant physiology in theophrastus' botany. 山芋植物学中的植物生理要素。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2014-01-01 DOI: 10.1400/230157

S. Pennazio

{"title":"Elements of plant physiology in theophrastus' botany.","authors":"S. Pennazio","doi":"10.1400/230157","DOIUrl":"https://doi.org/10.1400/230157","url":null,"abstract":"For thousands of years the plants were considered only as a source of food and medicine, and as ornamental objects. Only from the fifth century BC, some philosophers of Ancient Greece realized that the plants were living organisms but, unfortunately, their works have come to us as fragments that we often know from the biological works of Aristotle. This eminent philosopher and man of science, however, did not give us a complete work on the plants, which he often promised to write. From scattered fragments of his conspicuous biological work, it emerges a concept of nutritive soul that, in the presence of heat and moisture, allows plants to grow and reproduce. The task of writing a comprehensive botanical work was delegated to his first pupil, Theophrastus, who left us two treatises over time translated into the various languages up to the current versions (Enquiry into plants, On the causes of plants). The plant life is described and interpreted on the basis of highly accurate observations. The physiological part of his botany is essentially the nutrition: According to Theophrastus, plants get matter and moisture from the soil through root uptake and process the absorbed substances transforming them into food, thanks to the heat. The processing (pepsis, coction) of matter into the food represents an extraordinary physiological intuition because individual organs of a plant appear to perform its specific transformation. Despite that Theophrastus did not do scientific experiments or use special methods other than the sharpness of his observations, he can be considered the forerunner of a plant physiology that would take rebirth only after two millennia.","PeriodicalId":55980,"journal":{"name":"Theoretical Biology Forum","volume":"107 1-2 1","pages":"97-108"},"PeriodicalIF":1.5,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66622011","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}

引用次数: 1

Entropy of a network ensemble: definitions and applications to genomic data. 网络集成的熵:基因组数据的定义和应用。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2014-01-01 DOI: 10.1400/230154

G. Menichetti, D. Remondini

引用次数: 5

Fractal analysis of dendrites morphology using modified Richardson's and box counting method. 用改进的理查德森和箱形计数法进行枝晶形态的分形分析。

IF 1.5 4区生物学

Theoretical Biology Forum Pub Date : 2013-01-01 DOI: 10.1400/215773

D. Ristanovic, B. Stefanovic, N. Puškaš

{"title":"Fractal analysis of dendrites morphology using modified Richardson's and box counting method.","authors":"D. Ristanovic, B. Stefanovic, N. Puškaš","doi":"10.1400/215773","DOIUrl":"https://doi.org/10.1400/215773","url":null,"abstract":"Fractal analysis has proven to be a useful tool in analysis of various phenomena in numerous naturel sciences including biology and medicine. It has been widely used in quantitative morphologic studies mainly in calculating the fractal dimension of objects. The fractal dimension describes an object's complexity: it is higher if the object is more complex, that is, its border more rugged, its linear structure more winding, or its space more filled. We use a manual version of Richardson's (ruler-based) method and a most popular computer-based box-counting method applying to the problem of measuring the fractal dimension of dendritic arborization in neurons. We also compare how these methods work with skeletonized vs. unskeletonized binary images. We show that for dendrite arborization, the mean box dimension of unskeletonized images is significantly larger than that of skeletonized images. We also show that the box-counting method is sensitive to an object's orientation, whereas the ruler-based dimension is unaffected by skeletonizing and orientation. We show that the mean fractal dimension measured using the ruler-based method is significantly smaller than that measured using the box-counting method. Whereas the box-counting method requires defined usage that limits its utility for analyzing dendritic arborization, the ruler-based method based on Richardson's model presented here can be used more liberally. Although this method is rather tedious to use manually, an accessible computer-based implementation for the neuroscientist has not yet been made available.","PeriodicalId":55980,"journal":{"name":"Theoretical Biology Forum","volume":"106 1-2 1","pages":"157-68"},"PeriodicalIF":1.5,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66616697","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}

引用次数: 7