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.

In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour
Conclusions: A model structure of DnMRE11 was constructed and validated with various bioinformatics programs which suggested the predicted model to be satisfactory. Further validation studies were conducted by COACH analysis for active site ligand prediction, and revealed the presence of six ligands binding sites and two ligands (2 Mn 2+ and dAMP). (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - November 5, 2015 Category: Biomedical Science Authors: Imen RekikZayneb ChaabeneC. GrubbNoureddine DriraFoued CheourAmine Elleuch Source Type: research

Bioelectric memory: modeling resting potential bistability in amphibian embryos and mammalian cells
Conclusion: Our results reveal conditions under which cells can stably maintain one of several resting voltage potential values. These models suggest testable predictions for experiments in developmental bioelectricity, and illustrate how cells can be used as versatile physiological memory elements in synthetic biology, and unconventional computation contexts. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - October 15, 2015 Category: Biomedical Science Authors: Robert LawMichael Levin Source Type: research

Deconvolution of the vestibular evoked myogenic potential using the power spectrum of the electromyogram
Conclusions: The approach is suited, for example, to estimate the duration of the inhibition causing the VEMP or to disentangle a VEMP consisting of more than one component. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - October 6, 2015 Category: Biomedical Science Authors: Bernd Lütkenhöner Source Type: research

PDON: Parkinson’s disease ontology for representation and modeling of the Parkinson’s disease knowledge domain
Conclusions: Parkinson’s disease ontology delivers the knowledge domain of Parkinson’s disease in a compact, computer-readable form, which can be further edited and enriched by the scientific community and also to be used to construct, represent and automatically extend Parkinson’s-related computable models. A practical version of the Parkinson’s disease ontology for browsing and editing can be publicly accessed at http://bioportal.bioontology.org/ontologies/PDON. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - September 22, 2015 Category: Biomedical Science Authors: Erfan YounesiAshutosh MalhotraMichaela GündelPhil ScordisAlpha KodamullilMatt PageBernd MüllerStephan SpringstubbeUllrich WüllnerDieter SchellerMartin Hofmann-Apitius Source Type: research

Fanconi anemia cells with unrepaired DNA damage activate components of the checkpoint recovery process
Conclusions: Our results show that FA cells, despite extensive DNA damage, do not loss the capacity to express the transcriptional and protein components of checkpoint recovery that might eventually allow their division with unrepaired DNA damage. This might allow cell survival but increases the genomic instability inherent to FA individuals and promotes cancer. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - September 18, 2015 Category: Biomedical Science Authors: Alfredo RodríguezLeda TorresUlises JuárezDavid SosaEugenio AzpeitiaBenilde TeresaEdith CortésRocío OrtízAna SalazarPatricia Ostrosky-WegmanLuis MendozaSara Frías Source Type: research

The waiting time problem in a model hominin population
Conclusion: We show that the waiting time problem is a significant constraint on the macroevolution of the classic hominin population. Routine establishment of specific beneficial strings of two or more nucleotides becomes very problematic. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - September 17, 2015 Category: Biomedical Science Authors: John SanfordWesley BrewerFranzine SmithJohn Baumgardner Source Type: research

Modeling the energetic cost of cancer as a result of altered energy metabolism: implications for cachexia
Conclusions: Quantifying the energetic cost of cancer may benefit an understanding of the tumor’s causation of cachexia. Our estimates of the range of tumor cost include values that are higher than prior estimates and suggest that in metastatic disease the tumor cost could be expected to eclipse attempts to stabilize energy balance through nutrition support or by drug therapies. Tumor mass and the percentage of anaerobic metabolism in the tumor contribute to the cost of the tumor on the body and potentially lead directly to negative energy balance and increased muscle wasting. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - September 15, 2015 Category: Biomedical Science Authors: Douglas FriesenVickie BaracosJack Tuszynski Source Type: research

Mechanistic-enriched models: integrating transcription factor networks and metabolic deregulation in cancer
Conclusion: After analyzing the way we studied the coupling of metabolic and transcriptional deregulation in breast cancer, we have concluded that one plausible strategy to integrate data driven and hypothesis driven approaches is by means of resorting to fundamental and well established laws of physics and chemistry since these provide a solid ground for assessment. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - September 9, 2015 Category: Biomedical Science Authors: Enrique Hernández-LemusJ. Siqueiros-García Source Type: research

General overview on structure prediction of twilight-zone proteins
Protein structure prediction from amino acid sequence has been one of the most challenging aspects in computational structural biology despite significant progress in recent years showed by critical assessment of protein structure prediction (CASP) experiments. When experimentally determined structures are unavailable, the predictive structures may serve as starting points to study a protein. If the target protein consists of homologous region, high-resolution (typically (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - September 4, 2015 Category: Biomedical Science Authors: Bee KhorGee TyeTheam LimYee Choong Source Type: research

Annual acknowledgement of manuscript reviewers
Contributing reviewersThe Editors of Theoretical Biology and Medical Modelling would like to thank all the Reviewers who have contributed to the journal in Volume 11 (2014). (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - July 3, 2015 Category: Biomedical Science Authors: Hiroshi Nishiura Source Type: research

Proposal of a hybrid approach for tumor progression and tumor-induced angiogenesis
One of the main challenges in cancer modelling is to improve the knowledge of tumor progression in areas related to tumor growth, tumor-induced angiogenesis and targeted therapies efficacy. For this purpose, incorporate the expertise from applied mathematicians, biologists and physicians is highly desirable. Despite the existence of a very wide range of models, involving many stages in cancer progression, few models have been proposed to take into account all relevant processes in tumor progression, in particular the effect of systemic treatments and angiogenesis. Composite biological experiments, both in vitro and in vivo...
Source: Theoretical Biology and Medical Modelling - July 2, 2015 Category: Biomedical Science Authors: Patricio CumsilleAníbal CoronelCarlos ConcaCristóbal QuiñinaoCarlos Escudero Source Type: research

Enhancing dendritic cell immunotherapy for melanoma using a simple mathematical model
Conclusion: By using this mathematical model it is possible to simulate the growth of the tumor cells with or without immunotherapy using the infusion protocol of the UNAM researchers, to obtain a good approximation of the biological trials data.It is worth mentioning that by manipulating the different parameters of the model the effectiveness of the immunotherapy may increase. This last suggests that different protocols could be implemented by the Immunotherapy Laboratory of UNAM in order to improve their results. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - June 9, 2015 Category: Biomedical Science Authors: E. Castillo-MontielJ. Chimal-EguíaJ. TelloG. Piñon-ZaráteM. Herrera-EnríquezAE. Castell-Rodríguez Source Type: research

Cell cycle progression is regulated by intertwined redox oscillators
The different phases of the eukaryotic cell cycle are exceptionally well-preserved phenomena. DNA decompaction, RNA and protein synthesis (in late G1 phase) followed by DNA replication (in S phase) and lipid synthesis (in G2 phase) occur after resting cells (in G0) are committed to proliferate. The G1 phase of the cell cycle is characterized by an increase in the glycolytic metabolism, sustained by high NAD+/NADH ratio. A transient cytosolic acidification occurs, probably due to lactic acid synthesis or ATP hydrolysis, followed by cytosolic alkalinization. A hyperpolarized transmembrane potential is also observed, as resul...
Source: Theoretical Biology and Medical Modelling - May 29, 2015 Category: Biomedical Science Authors: Jorgelindo MoreiraSabine PeresJean-Marc SteyaertErwan BiganLoïc PaulevéMarcel NogeiraLaurent Schwartz Source Type: research

A control system analysis of the dynamic response of N-methyl-D-aspartate glutamate receptors to alcoholism and alcohol withdrawal
Conclusions: The negative feedback control system produced characteristic behaviors of NMDAR populations in response to simulations of alcohol dependence and abrupt withdrawal. The model can also predict the severity of excitotoxic withdrawal following various alcohol consumption and/or withdrawal patterns in order to generate testable hypotheses regarding ameliorating withdrawal. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - May 16, 2015 Category: Biomedical Science Authors: Carlos GutierrezMary Staehle Source Type: research

CT brush and CancerZap!: two video games for computed tomography dose minimization
Conclusions: We anticipate that human computing games like these, analyzed by methods similar to those used to understand eye tracking, will lead to new object dependent CT algorithms that will require significantly less dose than object independent nonlinear and compressive sensing algorithms that depend on sprayed photons. Preliminary results suggest substantial dose reduction is achievable. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - May 12, 2015 Category: Biomedical Science Authors: Graham AlvareRichard Gordon Source Type: research