Bell Eapen

Physician | HealthIT Developer | Digital Health Consultant

Best peptides for women

In continuation with my previous posts here and in skin deep, let me add few more things I found recently.

Peptide Synthesis Deprotection
Peptide Synthesis Deprotection (Photo credit: Beige Alert)

The article titled “Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks “ published recently in PLOS Biology ( full text at : http://dx.plos.org/10.1371/journal.pbio.0030405 ) describes the signalling by short peptide segments. Short peptide segments interact with globular protein domains that share a common sequence pattern (e.g., SH3 binding to PxxP). They also point out that sequence comparison experiments are unlikely to discover the optimum short motif. They recommend using data from genome-scale interaction studies. So the methodology adopted by the designers of peptide-21 may not be robust.

OK, now I am going to do something here that I rarely ever do on my blogs: I am going to shamelessly self promote me without actually giving away much information. My plan is to get noticed by the cosmetic tycoons and make some money out of this incessant babbling about beauty peptides 🙂

English: Example of mechanism of direct penetr...
English: Example of mechanism of direct penetrating peptide (Photo credit: Wikipedia)

I used a newly published algorithm (not mine) for bioinformatics analysis and found some interesting information.

The most commonly occurring tetra peptide in collagen is in fact GXXG and PXXP the commonest being GPPG.

The commonest tetra peptide repeats were GERG, GEKG, GFPG, GENG, GPRG, GHRG.

This is what terapeptide-21 is based on and there is nothing new till here.

But here comes the most surprising part!

The highest scoring short peptide of probable biological (signal) function does not belong to the above list!!

Hey, Do I hear my phone ringing?????

Lignin and Plant tissue utilization

PLOS Computational Biology: Functional Analysis of Metabolic Channeling and Regulation in Lignin Biosynthesis: A Computational Approach:

The growing energy needs of our burgeoning population can only be tackled by advances in biotechnology. Lignin is a plant cell wall protein that reduces forage digestibility, pulping efficiency, and sugar release. Any improvement in lignin digestibility could have enormous impact on the utilization of grains like corn and is an area of active research. This article explains a novel computational approach to decipher the intricacies of lignin biosynthesis.

Structure of a typical plant cell
Structure of a typical plant cell (Photo credit: Wikipedia)

Potential ways of improving energy utilization include reduction in the indigestible cell-wall fraction, improvement in the digestibility of cell wall, reduction in the rate of GI passage and increased rate of absorption. Lignin reduction has been achieved using anti-sense genes to limit production of key enzymes on the lignin biosynthesis pathway. A genome wide comparative survey of various grain crops might identify genes that can be targeted by an anti-sense approach. Unfortunately Bt corn that has been genetically modified to express the Cry1Ab protein of Bacillus thuringiensis to kill lepidopteran pests, has a higher lignin content than non-Bt corn.

Breaking down cellulose strands by Lyocell process and cellulase activity inducers like Sophorose could improve the digestibility of cell wall. I wonder whether we could employ any of the tricks we cosmetic dermatologists use to create nanoparticles for increasing the absorption!

‘via Blog this’

The 4th Virtual Training Workshop on Bioinformatics in 2010, organized by Asian Bioinformatics Research and Education Network (ABREN) was a great success, drawing 1,869 participants from 76 countries. Now they are planning to hold the 5th Workshop for two months starting from December, 2011. The registration will start on Nov. 4th.

Workshop and registration site: http://www.abren.net/workshop/

The art of taking online help:

I am not a big time researcher with lots of international experience. However I would like to make an attempt to suggest few guidelines for the young Indian bioinformatician, seeking online help for project or showcasing their profile online.

How to address a researcher online? Generally in research community, people are not bothered much about show of respect. Hence sir, respected sir, the most adorable etc can be translated to lack of confidence or to too much submissiveness. Hence it is appropriate to address anybody by the second name adding the appropriate title. Just using the first name is also OK. However title is often taken seriously and addressing a Dr/Prof as Mr is a cardinal sin even if you add a liberal dose of sir/almighty to that.

Career guidance is often done face to face or over the phone or through forums specifically dedicated for that. However before posting career guidance questions to forums search the forum for similar questions unless your profile is unique. Questions like I am going to finish my Kinder Garden What should I do next to become a successful bioinformatician is unlikely to fetch many answers. If you dont have enough time to search the forum, dont expect anybody else to send a personal two page letter to you.

The same applies to very broad, open ended questions. Questions like How is bioinformatics important for clinical medicine? is unlikely to get much attention. Be as specific as possible. Do not expect others to provide complete answers in a platter. Answers will be mostly very short, incomplete and often cryptic (because you may not know what the other person is talking about). Be ready to do some background research on the answer rather than asking for more information.

Posting your profile in online forums is also an art. Bioinformatics is a very broad field and employers look for certain specific skills which you may not always have. I often see sequence analysis, genomics, proteiomics, computer programming, PERL, RUBY, EMERALD, systems biology, drug designing, structural and molecular biology, talking, reading and sleeping in the skill set, everyone competing to make the complete list. In reality, no body can be a complete bioinformatician and it is better to showcase your core competency which needs to be substantiated by your projects or publications.

Please post your comments / criticisms / suggestions here.

Bioinformatics Projects

I feel bioinformatics projects broadly fall into three categories.

  1. Academic project as part of UG or PG course.
  2. Professional projects for biotech/drug companies
  3. Hobbyist/personal projects

When you do an academic project it is important to achieve a preset target within a limited time frame. Hence you have to adopt a bottom up approach wherein you know what your final result is going to be and work your way up. It is always better to keep it simple. You always have time to do more complicated things later on.

Professional projects also have a predefined goal. However it has a wider scope but often has the backing of a team. Funding is also available. This is what most of us aspire to do once we become full fledged professionals.

The third type of projects is for people who are not primarily bioinformaticians, but try to explore this nascent specialty, keeping their field as the initial entry point. They often try a top down approach and may not be always successful!

Let me suggest the following topics, categorized based on your area of expertise.

  • IT Prepare a database (organism, disease, or any other) and deploy it online
  • Microbiology Select an organism and do a comparative genomic study
  • Biochemistry Model a pathway using systems biology tools and discuss its clinical significance.
  • Pharmacology Docking studies and study of the targets of existing drugs.
  • Clinicians Expression profile study of any disease of interest.
  • Vet / Agri Functional genomic study of any chosen gene.