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Theoretical Biology Forum

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https://www.readbyqxmd.com/read/27167914/the-establishment-of-prezygotic-reproductive-isolation-in-some-simple-models
#1
Franco Spirito
The probability of fixation of a mutant that causes assortative mating according to the 'mass action model' has been studied. A gene of this kind represents one of the simplest hypothetical mechanisms of prezygotic isolation. Computer analysis by Monte Carlo simulations revealed that the fixation of the mutant is very unlikely unless the population is very small in size and/or the degree of partial assortative mating is very low. The introduction into the biological model of pleiotropic effects of the gene on fitness (viability) can facilitate the process of fixation (even to a very large extent in the case of strong selection in favor of the mutant allele)...
2015: Theoretical Biology Forum
https://www.readbyqxmd.com/read/27167913/the-concept-of-plant-life-the-dawn
#2
Sergio Pennazio
An elementary but correct concept of plant life has come to us in writings of Theophrastus who divided the plant life in its three basic stages: generation, sprouting, growth. This image of plants remained practically unchanged until the seventeenth-century, when the scientific method based on experimentation was introduced by Bacon. The invention of the microscope and the change of the traditional alchemy for an embryonic chemistry allowed some penetrating minds to look upon plants as highly complex living structures, to which had to correspond some specific functions...
2015: Theoretical Biology Forum
https://www.readbyqxmd.com/read/27167912/molecular-model-of-cytotoxin-1-from-naja-mossambica-mossambica-venom-in-complex-with-chymotrypsin
#3
Aisha Munawar, Ahmed Akrem, Ashiq Hussain, Patrick Spencer, Christian Betzel
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...
2015: Theoretical Biology Forum
https://www.readbyqxmd.com/read/27167911/impact-of-risk-factor-for-atherosclerosis-on-microvascular-endothelial-function-an-in-vitro-study
#4
Valter Lubrano, Elena Venturi, Silvana Balzan, Simona Baldi, Andrea Natali
It is now widely accepted that the microcirculation plays a role in the complications of atherosclerosis, but the microcirculation response to atherosclerosis risk factors like diabetes, hypercholesterolemia and hypertension, is still unclear. Alterations in the endothelial production of IL6, NO and ET-1 are known to be correlate with these diseases. Simulating the presence of hyperglycemia, hypercholesterolemia and hypertension, this in vitro study investigated the effect of glucose, angiotensin II, and nLDL treatments on IL-6, ET-1 and NO in HMEC-1...
2015: Theoretical Biology Forum
https://www.readbyqxmd.com/read/27167910/molecular-dynamics-simulation-to-elucidate-the-thermostability-of-b-domain-in-cgtase
#5
Yi Fu, Zhiguo Chen, Ji Zhao
Cyclodextrin glycosyltransferase (EC2.4.1.19, CGTase) catalyzes the formation of cyclodextrins from starch. Thermal stability is of great importance for this enzyme. In order to gain better understanding of the thermostability mechanisms of the protein, we herein report structural features of the CGTase B domain at different temperatures. The present study mainly focuses on the contribution of non-covalent intramolecular interaction to protein stability and how they affect the thermal stability of the enzyme...
2015: Theoretical Biology Forum
https://www.readbyqxmd.com/read/27167909/interaction-pattern-of-fullerenes-c20-c180-and-carbon-nanotubes-with-different-forms-of-dna-a-computational-biology-approach
#6
Sumbul Firdaus, Anupam Dhasmana, Shafiul Haque, Snober S Mir, Roshan Jahan, Tasneem Bano, Vandana Srivastava, Saif Khan, Mohtashim Lohani
Recently, the venues of exposure to nanoparticles have increased significantly owing to their increased deliberate production. In this study the interaction of fullerenes with DNA was analyzed along with various factors affecting this interaction like mol. wt. of fullerenes (C20 to C180), the form of DNA i.e., A, B and Z, and sequences of DNA, and was compared with the DNA binding of CNTs. Increase in the molecular weight of the fullerene showed increase in the binding score with A & B-form of DNA, but no regular affect was seen on binding with Z-form of DNA...
2015: Theoretical Biology Forum
https://www.readbyqxmd.com/read/27167908/interleukins-ils-a-fascinating-family-of-cytokines-part-ii-ils-from-il-20-to-il-38
#7
REVIEW
Pieranna Fietta, Elvira Costa, Giovanni Delsante
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...
2015: Theoretical Biology Forum
https://www.readbyqxmd.com/read/27167907/dynamical-systems-on-graphs-from-random-walks-to-transportation-networks
#8
Armando Bazzani
No abstract text is available yet for this article.
2015: Theoretical Biology Forum
https://www.readbyqxmd.com/read/27167906/editorial
#9
EDITORIAL
David Lambert
No abstract text is available yet for this article.
2015: Theoretical Biology Forum
https://www.readbyqxmd.com/read/25936221/dynamics-on-genes-network-structures-an-ago-antagonist-approach
#10
Armando Bazzani, Paolo Freguglia
This paper is a carrying on of the theme examined in (Bazzani, Freguglia 2013) where we discuss a proposal of studying of essential structural aspects of Darwinian Evolution Theory. Also in this case we apply a mathematical ago-antagonist theory inspired by Y. Cherruault's ideas (Cherruault 1998). In the present paper we consider the network structure of genes activity and its dynamics.
2014: Theoretical Biology Forum
https://www.readbyqxmd.com/read/25936220/a-dynamical-model-for-influenza-under-seasonal-variables
#11
Masomeh Taherian, Megerdich Toomanian, Mohammadreza Molaei
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...
2014: Theoretical Biology Forum
https://www.readbyqxmd.com/read/25936219/conscience-dilemma-to-become-a-bioengineer-or-to-survive-as-a-biologist
#12
Sureyya Mert Selimoglu
Bioengineering is the consideration of biological problems from modern engineering, therefore money-oriented, perspective. Today, grant-giving bodies always favor bioengineering projects rather than pure biology projects (like those in ecology, entomology, etc.). Therefore, today's biologist is forced to be on the horns of a dilemma. They have to either submit a very powerful and valid reason for the proposal of their project, or change the project to one having a potential of money-based outcome. On the other hand, because of dealing with the living components of nature, conducting a research in pure biology is like a kind of worship...
2014: Theoretical Biology Forum
https://www.readbyqxmd.com/read/25936218/demography-and-conservation-of-the-mediterranean-fin-whale-balaenoptera-physalus-what-clues-can-be-obtained-from-photo-identification-data
#13
Alessia Rossi, Simone Panigada, Massimo Arrigoni, Margherita Zanardelli, Cristina Cimmino, Luigi Marangi, Piero Manfredi, Giovanni Santangelo
Long-lived and slow reproducing species, such as cetaceans, are among the most critical conservation units: a demographic approach can be very useful for their management and conservation. In the present work, we examined, by demographic tools, the most exhaustive photo-identification database available for the Mediterranean fin whale (Balaenoptera physalus) population, recorded by Tethys Research Institute between 1990 and 2007 in the Western Ligurian Sea. A total of 31,782 km were covered and 548 fin whale sightings were recorded...
2014: Theoretical Biology Forum
https://www.readbyqxmd.com/read/25936217/fractal-analysis-of-dendrite-morphology-of-rotated-neuronal-pictures-the-modified-box-counting-method
#14
Dušan Ristanović, Bratislav D Stefanović, Nela Puškaš
The fractal dimension of a non-stellate neuron changes continuously with rotation of the neuronal picture. For a stellate neuron such changes cannot be noticed. During preprocessing for the box counting, non-stellate neurons should be arranged so that the major diameters of their dendrite fields are parallel. It was shown that a non-stellate neuronal picture had the smallest box dimension when the angle between the horizontal or vertical axis and its major diameter was about 45 degrees. The box counting method which uses ImageJ software does not consider the position of a picture on the computer's screen...
2014: Theoretical Biology Forum
https://www.readbyqxmd.com/read/25936216/elements-of-plant-physiology-in-theophrastus-botany
#15
Sergio Pennazio
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...
2014: Theoretical Biology Forum
https://www.readbyqxmd.com/read/25936215/on-the-dinucleotide-circular-codes-of-maximum-cardinality
#16
Marco Pellegrini, Giuseppe Pirillo
In a recent paper, Michel and Pirillo prove that there are 24 dinucleotide circular codes of maximum cardinality over an alphabet of cardinality 4. In this paper we find the exact number of dinucleotide circular codes of maximum cardinality for any given (finite) cardinality of the alphabet. Moreover, we describe the structure of these codes.
2014: Theoretical Biology Forum
https://www.readbyqxmd.com/read/25936214/entropy-of-a-network-ensemble-definitions-and-applications-to-genomic-data
#17
Giulia Menichetti, Daniel Remondini
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.
2014: Theoretical Biology Forum
https://www.readbyqxmd.com/read/25936213/modeling-ant-battles-by-means-of-a-diffusion-limited-gillespie-algorithm
#18
Gianluca Martelloni, Santarlasci Alisa, Franco Bagnoli, Giacomo Santini
We propose two modeling approaches to describe the dynamics of ant battles, starting from laboratory experiments on the behavior of two ant species, the invasive Lasius neglectus and the authocthonus Lasius paralienus. This work is mainly motivated by the need to have realistic models to predict the interaction dynamics of invasive species. The two considered species exhibit different fighting strategies. In order to describe the observed battle dynamics, we start by building a chemical model considering the ants and the fighting groups (for instance two ants of a species and one of the other one) as a chemical species...
2014: Theoretical Biology Forum
https://www.readbyqxmd.com/read/25936212/modelling-ecological-complexity-for-marine-species-conservation-the-effect-of-variable-connectivity-on-species-spatial-distribution-and-age-structure
#19
Katell Guizien, Lorenzo Bramanti
Connectivity is currently emphasized as a key factor in conservation for its role in enhancing biodiversity of an area and giving benefit to the adjacent areas. For most marine species, connectivity is synonomous of larval dispersal. We applied a spatially explicit meta-population model to test the hypothesis that larval dispersal can affect local demographical features, consequently misleading conservation practice in the marine environment. Simulations were carried out in the Gulf of Lions where coastal circulation displays highly variable temporal and spatial submeso-scale structures...
2014: Theoretical Biology Forum
https://www.readbyqxmd.com/read/25936211/interleukins-ils-a-fascinating-family-of-cytokines-part-i-ils-from-il-1-to-il-19
#20
REVIEW
Pieranna Fietta, Elvira Costa, Giovanni Delsante
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...
2014: Theoretical Biology Forum
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