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.
{"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":null,"pages":null},"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}
In this study, influenza is modeled dynamically under seasonal variables. Seasonal variables made this model geometrically more complicated than without seasonal conditions. This modeling will be done in two cases with vaccination and without vaccination. These two models are solved in similar conditions by using Rung-Kutta method. The resulted data are shown in two diagrams and they are compared. We deduce a model for influenza without seasonal variable and vaccination and we consider its equilibrium points.
{"title":"A dynamical model for influenza under seasonal variables.","authors":"Masomeh Taherian, M. Toomanian, M. Molaei","doi":"10.1400/230161","DOIUrl":"https://doi.org/10.1400/230161","url":null,"abstract":"In this study, influenza is modeled dynamically under seasonal variables. Seasonal variables made this model geometrically more complicated than without seasonal conditions. This modeling will be done in two cases with vaccination and without vaccination. These two models are solved in similar conditions by using Rung-Kutta method. The resulted data are shown in two diagrams and they are compared. We deduce a model for influenza without seasonal variable and vaccination and we consider its equilibrium points.","PeriodicalId":55980,"journal":{"name":"Theoretical Biology Forum","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66622072","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}
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.
{"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":null,"pages":null},"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}
In this paper we introduce the framework for the application of statistical mechanics to network theory, with a particular emphasis to the concept of entropy of network ensembles. This formalism provides novel observables and insights for the analysis of high-throughput transcriptomics data, integrated with apriori biological knowledge, embedded in-to available public databases of protein-protein interaction and cell signaling.
{"title":"Entropy of a network ensemble: definitions and applications to genomic data.","authors":"G. Menichetti, D. Remondini","doi":"10.1400/230154","DOIUrl":"https://doi.org/10.1400/230154","url":null,"abstract":"In this paper we introduce the framework for the application of statistical mechanics to network theory, with a particular emphasis to the concept of entropy of network ensembles. This formalism provides novel observables and insights for the analysis of high-throughput transcriptomics data, integrated with apriori biological knowledge, embedded in-to available public databases of protein-protein interaction and cell signaling.","PeriodicalId":55980,"journal":{"name":"Theoretical Biology Forum","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66621999","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}
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.
{"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":null,"pages":null},"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}
Once considered a passive reservoir for lipid storage and an inert provider of thermal/mechanical insulation, white adipose tissue (WAT) is presently seen as a highly dynamic endocrine organ that actively modulates a variety of physiologic processes, including energy balance, food intake, inflammation, immunity, metabolism, as well as cardio-vascular (CV) and neuroendocrine homeostasis. Actually, other than fatty acids and lipid moieties, WAT secretes a wide range of bioactive factors, considerably different in therms of structure and functions, including cytokines, chemokines, growth factors, complement system molecules, acute phase reactants, and hormones, among which the products predominantly or exclusively synthesized by and released from adipocytes are categorized as "adipokines". The adipokine expression is intimately linked to various parameters of adiposity (such as total body fat, percentage of body fat, and fat distribution), resulting generally (with very few exceptions, such as adiponectin, omentin, and Zinc-alpha2-glycoprotein) in positive correlation with WAT mass. The adipokine profiles undergo opposite changes in WAT excess or deficiency/dystrophy. In obese subjects, the altered adipokine network strikingly contributes to the development of systemic low-grade inflammation, as well as of obesity-related metabolic/CV comorbidities, that collectively define the so called metabolic syndrome. Adipokine dysregulation has been also observed in patients with chronic inflammatory/autoimmune disorders, such as connective tissue diseases, and adipokine pathway targeting has been thought to represent a potential innovative therapeutic perspective. Comprehensive advances in understanding the WAT biology and signaling may provide crucial insights into the physiopathology of the whole body homeostasis.
{"title":"Focus on adipokines.","authors":"P. Fietta, G. Delsante","doi":"10.1400/215770","DOIUrl":"https://doi.org/10.1400/215770","url":null,"abstract":"Once considered a passive reservoir for lipid storage and an inert provider of thermal/mechanical insulation, white adipose tissue (WAT) is presently seen as a highly dynamic endocrine organ that actively modulates a variety of physiologic processes, including energy balance, food intake, inflammation, immunity, metabolism, as well as cardio-vascular (CV) and neuroendocrine homeostasis. Actually, other than fatty acids and lipid moieties, WAT secretes a wide range of bioactive factors, considerably different in therms of structure and functions, including cytokines, chemokines, growth factors, complement system molecules, acute phase reactants, and hormones, among which the products predominantly or exclusively synthesized by and released from adipocytes are categorized as \"adipokines\". The adipokine expression is intimately linked to various parameters of adiposity (such as total body fat, percentage of body fat, and fat distribution), resulting generally (with very few exceptions, such as adiponectin, omentin, and Zinc-alpha2-glycoprotein) in positive correlation with WAT mass. The adipokine profiles undergo opposite changes in WAT excess or deficiency/dystrophy. In obese subjects, the altered adipokine network strikingly contributes to the development of systemic low-grade inflammation, as well as of obesity-related metabolic/CV comorbidities, that collectively define the so called metabolic syndrome. Adipokine dysregulation has been also observed in patients with chronic inflammatory/autoimmune disorders, such as connective tissue diseases, and adipokine pathway targeting has been thought to represent a potential innovative therapeutic perspective. Comprehensive advances in understanding the WAT biology and signaling may provide crucial insights into the physiopathology of the whole body homeostasis.","PeriodicalId":55980,"journal":{"name":"Theoretical Biology Forum","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66616664","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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