Theoretical biology is a field of academic study and research that involves the use of quantitative tools in biology.

Many separate areas of biology fall under the concept of theoretical biology, according to the way they are studied. Some of these areas include: animal behaviour (ethology), biomechanics, biorhythms, cell biology, complexity of biological systems, ecology, enzyme kinetics, evolutionary biology, genetics, immunology, membrane transport, microbiology, molecular structures, morphogenesis, physiological mechanisms, systems biology and the origin of life. Neurobiology is an example of a subdiscipline of biology which already has a theoretical version of its own, theoretical or computational neuroscience.

The ultimate goal of the theoretical biologist is to explain the biological world using mainly mathematical and computational tools, though not necessarily. Though it is ultimately based on observations and experimental results, the theoretical biologist's product is a model or theory, and it is this that chiefly distinguishes the theoretical biologist from other biologists. Over recent years the theoretical biologist has become nearly obsolete, as tests prove the impossibility of accurate results where the environment of the observations is not homogeneous.

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Theoretical Biology and Medical Modelling - Latest Articles

Formal kinetics of H1N1 epidemic
Konstantin Gurevich Tue, 15 Sep 2009 00:00:00 -0000
Background: The formal kinetics of the H1N1 epidemic seems to take the form of an exponential curve. There is a good correlation between this theoretical model and epidemiological data on the number of H1N1-infected people. But this formal model leads to paradoxes about the dates when everyone becomes infected: in Mexico this will happen after one year, then in the rest of the world.Further implications of the formal modelThe general limitations of this formal kinetics model are discussed. More detailed modeling is examined and the implications are examined in the light of currently available data. The evidence indicates that not more than 10% of the population is initially resistant to the H1N1 virus. Conclusion: We are probably only at the initial stage of development of the H1N1 epidemic. Increasing the number of H1N1-resistant people in future (e.g. due to vaccination) may influence the dynamics of epidemic development. At present, the development of the epidemic depends only on the number of people in the population who are initially resistant to the virus.
Comparative modeling of DNA and RNA polymerases from Moniliophthora perniciosa mitochondrial plasmid
Bruno AndradeAlex TarantoAristoteles Goes-NetoAngelo Duarte Thu, 10 Sep 2009 00:00:00 -0000
Background: The filamentous fungus Moniliophthora perniciosa (Stahel) Aime & Phillips-Mora is a hemibiotrophic Basidiomycota that causes witches' broom disease of cocoa (Theobroma cacao L.). This disease has resulted in a severe decrease in Brazilian cocoa production, which changed the position of Brazil in the market from the second largest cocoa exporter to a cocoa importer. Fungal mitochondrial plasmids are usually invertrons encoding DNA and RNA polymerases. Plasmid insertions into host mitochondrial genomes are probably associated with modifications in host generation time, which can be involved in fungal aging. This association suggests activity of polymerases, and these can be used as new targets for drugs against mitochondrial activity of fungi, more specifically against witches' broom disease. Sequencing and modeling: DNA and RNA polymerases of M. perniciosa mitochondrial plasmid were completely sequenced and their models were carried out by Comparative Homology approach. The sequences of DNA and RNA polymerase showed 25% of identity to 1XHX and 1ARO (pdb code) using BLASTp, which were used as templates. The models were constructed using Swiss PDB-Viewer and refined with a set of Molecular Mechanics (MM) and Molecular Dynamics (MD) in water carried out with AMBER 8.0, both working under the ff99 force fields, respectively. Ramachandran plots were generated by Procheck 3.0 and exhibited models with 97% and 98% for DNA and RNA polymerases, respectively. MD simulations in water showed models with thermodynamic stability after 2000 ps and 300 K of simulation. Conclusion: This work contributes to the development of new alternatives for controlling the fungal agent of witches' broom disease.
Homeostatic mechanisms in dopamine synthesis and release: a mathematical model
Janet BestH. NijhoutMichael Reed Thu, 10 Sep 2009 00:00:00 -0000
Background: Dopamine is a catecholamine that is used as a neurotransmitter both in the periphery and in the central nervous system. Dysfunction in various dopaminergic systems is known to be associated with various disorders, including schizophrenia, Parkinson's disease, and Tourette's syndrome. Furthermore, microdialysis studies have shown that addictive drugs increase extracellular dopamine and brain imaging has shown a correlation between euphoria and psycho-stimulant-induced increases in extracellular dopamine 1. These consequences of dopamine dysfunction indicate the importance of maintaining dopamine functionality through homeostatic mechanisms that have been attributed to the delicate balance between synthesis, storage, release, metabolism, and reuptake. Methods: We construct a mathematical model of dopamine synthesis, release, and reuptake and use it to study homeostasis in single dopaminergic neuron terminals. We investigate the substrate inhibition of tyrosine hydroxylase by tyrosine, the consequences of the rapid uptake of extracellular dopamine by the dopamine transporters, and the effects of the autoreceoptors on dopaminergic function. The main focus is to understand the regulation and control of synthesis and release and to explicate and interpret experimental findings. Results: We show that the substrate inhibition of tyrosine hydroxylase by tyrosine stabilizes cytosolic and vesicular dopamine against changes in tyrosine availability due to meals. We find that the autoreceptors dampen the fluctuations in extracellular dopamine caused by changes in tyrosine hydroxylase expression and changes in the rate of firing. We show that short bursts of action potentials create significant dopamine signals against the background of tonic firing. We explain the observed time courses of extracellular dopamine responses to stimulation in wild type mice and mice that have genetically altered dopamine transporter densities and the observed half-lives of extracellular dopamine under various treatment protocols. Conclusion: Dopaminergic systems must respond robustly to important biological signals such as bursts, while at the same time maintaining homeostasis in the face of normal biological fluctuations in inputs, expression levels, and firing rates. This is accomplished through the cooperative effect of many different homeostatic mechanisms including special properties of tyrosine hydroxylase, the dopamine transporters, and the dopamine autoreceptors.

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