Applied Bimatics - An Informatics & eHealth Blog

I am a clinician with a passion for informatics. This blog is about my eHealth journey exploring interoperability in Electronic Medical Records (EMR/EHR), Patient Safety, Pharmacovigilance, Data Analytics, Clinical Research and Bioinformatics in a clinical context. Comparing Canadian, Indian and Middle Eastern healthcare systems and services. Join our open facebook group here: https://www.facebook.com/groups/clinical.bioinformaticians/


Good Clinical Practice GCP

Good Clinical Practice (GCP) guidelines

GCP has two important goals: protection of the subject, and protection of the data which is possible only through adequate training of all concerned staff. An independent audit is needed to ensure compliance to the standards. US FDA acts as enforcement officers. As they are less flexible unconventional approaches have no scope. European agencies are more flexible but they need to be convinced.

The Declaration of Helsinki issued by world medical association insists that all research subjects must be fully informed about the nature and risks of a clinical trial. Protocol design is a responsibility of the investigator and need to be assessed by the concerned ethical committee. The principal investigator has an overall responsibility over the entire project.

Informed consent which includes signing a consent form and a recruiting interview preferably by the physician is extremely important. Though not absolutely necessary it is a good practice to define and describe in writing how all aspects of clinical research are to be conducted. These standard operating procedures (SOPs) must be followed during the execution of the research.

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Translation


Translation

Today I learnt few concepts in protein expression which I found very interesting. As we all know, because of the redundancy of the triplet code, it is possible to preserve aminoacid sequence coding while varying the nucleic acid code. This can even happen as a silent mutation. However the availability of corresponding tRNA for each triplet varies from species to species. The translational efficiency of each code may be different (some times to a very great extend) though all may code for the same product. All silent mutations may not be silent after all.
Few codon pairs exist in relative abundance which may act as translation pause sites and slow down translational process. The tRNAs that bind during the translation of such a biased pair appear somehow incompatible. These codon pairs vary from species to species.
These points need to be considered while designing a gene for expression systems. Designing and implementing an algorithm to optimize the gene with respect to the above points can be a good bioinformatics project.

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Gain-of-function mutation


Gain-of-function mutation

Today I learned about a concept (new to me) called gain of function mutation. A mutation in Loricin gene (LOR 730insG) leads to a frame-shift and delayed termination, thus elongating the protein by 22 amino acids. And changing the Gly/Lys-rich domain into an Arg/Leu-rich terminal domain. Instead of being incorporated into the cell envelope, the mutant loricin is translocated into the neucleus as the mutant C-terminus acquires a new function of a nuclear targeting sequence.

The authors have named the resulting phenotype as honeycomb palmoplantar keratoderma with ichthyosis with occasional features like pseudoainhums, prominent knuckle pads and collodion baby. This is however different from Vohwinkel syndrome (hearing impairment but no ichthyosis) and Olmsted syndrome (severe mutilation and periorificial keratotic plaques). The chapter on hereditary PPKs is already a nightmare for dermatology post graduates with umpteen syndromes. The recent advances make it no better.

M.M. Gedicke et al. Palmoplantar keratoderma with mutation in loricin. Brit Journal of Dermatol 2006;154:167-171

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About Me

As a Dermatologist and Informatician my research mainly involves application of bioinformatics techniques and tools in dermatological conditions. However my research interests are varied and I have publications in areas ranging from artificial intelligence, sequence analysis, systems biology, ontology development, microarray analysis, immunology, computational biology and clinical dermatology. I am also interested in eHealth, Health Informatics and Health Policy.

Address

Bell Raj Eapen
Hamilton, ON
Canada