Theoretical Biology and Medical Modelling This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Development of global consensus sequence of HCV glycoproteins involved in viral entry
Conclusion: This study was designed to perform conservation and variability analysis of HCV glycoproteins and to find potentially conserved peptides among genotypes 3a and 1a (the most prevalent genotypes in Pakistan) that could serve as useful targets in the development of novel inhibitory compounds, thus reducing the threat of HCV infection in Pakistan. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - April 10, 2013 Category: Biomedical Science Authors: Sobia IdreesUsman AshfaqNatasha Idrees Source Type: research

Structural mimicry between SLA/LP and Rickettsia surface antigens as a driver of autoimmune hepatitis: insights from an in silico study
Conclusions: These findings strongly support the notion that a molecular mimicry mechanism can trigger AIH onset. CD4+ T cells recognizing peptides of SLA/LP could indeed cross-react with foreign Rickettsia spp. antigens. Finally, the same analysis suggests a molecular explanation for the importance of position 71 in conferring the susceptibility of the allele HLA-DRB1*03:01 to AIH. The lack of a positive charge at such position could prevent HLA alleles from binding the foreign peptides and triggering the molecular mimicry event. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - April 10, 2013 Category: Biomedical Science Authors: Alessandro PaiardiniStefano Pascarella Source Type: research

Is it possible to stabilize a thermophilic protein further using sequences and structures of mesophilic proteins: a theoretical case study concerning DgAS
Incorporating structural elements of thermostable homologs can greatly improve the thermostability of a mesophilic protein. Despite the effectiveness of this method, applying it is often hampered. First, it requires alignment of the target mesophilic protein sequence with those of thermophilic homologs, but not every mesophilic protein has a thermophilic homolog. Second, not all favorable features of a thermophilic protein can be incorporated into the structure of a mesophilic protein. Furthermore, even the most stable native protein is not sufficiently stable for industrial applications. Therefore, creating an industriall...
Source: Theoretical Biology and Medical Modelling - April 10, 2013 Category: Biomedical Science Authors: Ming LiuHongqiu HeJiguo Su Source Type: research

Agent-based modeling of competence phenotype switching in Bacillus subtilis
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. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - April 3, 2013 Category: Biomedical Science Authors: Suzy StiegelmeyerMorgan Giddings Source Type: research

Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 beta-lactamase
Background: blaVEB-1 is an integron-located extended-spectrum beta-lactamase gene initially detected in Escherichia coli and Pseudomonas aeruginosa strains from south-east Asia. Several recent studies have reported that VEB-1-positive strains are highly resistant to ceftazidime, cefotaxime and aztreonam antibiotics. One strategy to overcome resistance involves administering antibiotics together with beta-lactamase inhibitors during the treatment of infectious diseases. During this study, four VEB-1 beta-lactamase inhibitors were identified using computer-aided drug design. Methods: The SWISS-MODEL tool was utilized to gene...
Source: Theoretical Biology and Medical Modelling - April 2, 2013 Category: Biomedical Science Authors: Abdelmonaem MessaoudiHatem BelguithJeannette Ben Hamida Source Type: research

Experimental designs for a Benign Paroxysmal Positional Vertigo model
Conclusions: A biomechanical model was derived to provide a quantitative basis for the detection of BPPV. The robustness study for the D-optimal design, with respect to the choice of the nominal values of the parameters, shows high efficiencies for small variations and provides a guide to the researcher.Furthermore, c-optimal designs give valuable assistance to check how efficient the D-optimal design is for the estimation of each of the parameters. The experimental designs provided in this paper allow the physician to validate the model. The authors of the paper have held consultations with an ENT consultant in order to...
Source: Theoretical Biology and Medical Modelling - March 19, 2013 Category: Biomedical Science Authors: Santiago Campos-BarreiroJesús López-Fidalgo Source Type: research

Effect of blood protein concentrations on drug-dosing regimes: practical guidance
In this article the importance of blood proteins for drug dosing regimes is discussed. A simple mathematical model is presented for estimating recommended drug doses when the concentration of blood proteins is decreased. Practical guidance for drug dosing regimes is discussed and given in the form of a figure. It is demonstrated that correction of drug dosing regimes is needed only for when there is a high level of drug conjugation with blood proteins and a high degree of hypoalbuminaemia. An example of the use of this model is given. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - March 18, 2013 Category: Biomedical Science Authors: Konstantin Gurevich Source Type: research

Toll-like receptor 9 interaction with CpG ODN - An in silico analysis approach
Conclusion: In this study, we present two structural models for the human and mouse TLR9 ECD in a complex with CpG ODN. Some features predicted by this model are consistent with previously reported experimental data. This complex model may lead to a better understanding of the function of TLR9 and its interaction with CpG ODN and will improve our understanding of TLR9-ligand interaction in general. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - March 14, 2013 Category: Biomedical Science Authors: Wei ZhouYan LiXichun PanYuan GaoBeiping LiZhengliang QiuLong LiangHong ZhouJunjie Yue Source Type: research

Stochastic time-concentration activity models for in vitro neurotoxicity
In vitro aggregating brain cell cultures containing all types of brain cells have been shown to be useful for neurotoxicological investigations. The cultures are used for the detection of nervous system specific effects of compounds by measuring multiple endpoints including changes of enzyme activities. Concentration-dependent neurotoxicity is determined at several time points.A Markov model is set up to describe dynamics of brain cell populations exposed to potentially neurotoxic compounds. Brain cells are assumed to be either in a healthy or stressed state and only stressed cells are susceptible to cell death. Cells may ...
Source: Theoretical Biology and Medical Modelling - March 14, 2013 Category: Biomedical Science Authors: Maria RennerMarie-Gabrielle ZurichAnnette Kopp-Schneider Source Type: research

Modeling the obesity epidemic: social contagion and its implications for control
Conclusions: The optimality of intervention programs depends on the contagiousness of obesity. Filling associated data gaps of obesity transmission would help systematically understand the epidemiological dynamics and consider required control programs. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - March 9, 2013 Category: Biomedical Science Authors: Keisuke EjimaKazuyuki AiharaHiroshi Nishiura Source Type: research

Molecular docking between the RNA polymerase of the Moniliophthora perniciosa mitochondrial plasmid and Rifampicin produces a highly stable complex
Conclusions: The results indicate that Rifampicin could be a good inhibitor for testing in vitro and in vivo against M. perniciosa. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - February 26, 2013 Category: Biomedical Science Authors: Bruno AndradeCatiane SouzaAristóteles Góes-Neto Source Type: research

IMGT/Collier-de-Perles: A two-dimensional visualization tool for amino acid domain sequences
IMGT/Collier-de-Perles is a tool that allows the user to analyze and draw two-dimensional graphical representations (or IMGT Collier de Perles) of protein domains (e.g., hydropathy plots). The IMGT/Collier-de-Perles specializes in the area of immunoglobulins (IG) or antibodies, T cell receptors (TR) and major histocompatibility (MH) of human and other vertebrate species as well as other proteins of the immunoglobulin superfamily (IgSF) and of the major histocompatibility superfamily (MhSF) and related proteins of the immune system of vertebrates and invertebrates. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - February 21, 2013 Category: Biomedical Science Authors: Dimitrios VlachakisChristos FeidakisVasileios MegalooikonomouSophia Kossida Source Type: research

A new kink in an old theory of carcinogenesis
According to Berenblum's two-stage hypothesis, the first stage in carcinogenesis is the production of benign premalignant lesions. Between this initiation stage and the formation of a malignant tumor there is often a long lag phase. We propose that this lag is caused by the delay in the formation of a new and rare tumor-specific antigen, which induces an immune response that stimulates tumor growth. Such tumor-specific antigens could arise as a result of a mutator-like phenotype, which is supposedly present in the benign initial stage of carcinogenesis. According to this hypothesis, the first stage lesion provides a weakly...
Source: Theoretical Biology and Medical Modelling - February 18, 2013 Category: Biomedical Science Authors: Richmond PrehnLiisa Prehn Source Type: research

A clinical study of the effects of lead poisoning on the intelligence and neurobehavioral abilities of children
Conclusion: Lead poisoning has adverse effects on the behavior and mental development of 2--4-year-old children, prescribing positive and effective precautionary measures. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - February 18, 2013 Category: Biomedical Science Authors: Shuangxing HouLianfang YuanPengpeng JinBojun DingNa QinLi LiXuedong LiuZhongliang WuGang ZhaoYanchun Deng Source Type: research

A statistical thin-tail test of predicting regulatory regions in the Drosophila genome
Conclusions: The novel thin-tail test provides an efficient and effective means for distinguishing CRMs from NCNRs based on the specific statistical properties of CRMs and can guide future experiments aimed at finding new CRMs in the post-genome time. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - February 14, 2013 Category: Biomedical Science Authors: Jian-Jun ShuYajing Li Source Type: research