microRNA is older than we think

The scientist reports that MicroRNAs control gene expression in a single-celled alga Chlamydomonas reinhardtii the  first single-celled organism in which microRNAs have been discovered. 

The finding suggests that microRNAs evolved earlier than previously thought, according to the authors. The study published in Nature   by researchers David Baulcombe of the Sainsbury Laboratory in UK

Video in Laboratory

I had mentioned earlier a number websites, that offer scientific videos

though many researchers have their own restriants when it comes to using technology whetehr it is open source or peer reviewd journal or blogs itself. Perhaps groups was the only social content driven concept that got off the ground when it comes to science and especially life science

but that certainly doesnt seem to deter more people coming up with new site that offer more web2.0 services to scientists

this time the new kid on the blck is http://www.labaction.com another science video sharing website
for more information on similar services and technology see my earlier posts

Gene splicing, SNP, Jumping genes, Transposons

I was looking for an easy way to explain DNA, Gene splicing, SNP, Jumping genes, Transposons and such to a non biologist without using too much technical jargons. And then I came across a study by University of Cambridge about how human mind reacts and learns written text , JUst see if you can read the following text, They are sure not spelling mistkes but made by rearranging text  in word by retaining the first and last letter in such a way that your mind still can read it

 

*I CAN READ IT! CAN YOU*

 

Cna yuo raed tihs? fi yuo cna raed tihs, yuo hvae a mnid to udrtsand DNA and why it is poisbssle for DNA to Evovle.

 

i cdnuolt blveiee taht I cluod aulaclty uesdnatnrd waht I was rdanieg. The phaonmneal pweor of the hmuan mnid, aoccdrnig to a rscheearch at Cmabrigde inervtisy, it dseno’t mtaetr in waht oerdr the ltteres in a wrod are, the lny iproamtnt tihng is taht the frsit and lsat ltteer be in the rghit pclae. The rset can be a taotl mses and you can sitll raed it whotuit a pboerlm. Tihs is bcuseae the huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe. Azanmig huh? yaeh and I awlyas tghuhot slpeling was ipmorantt! now you can raed tihs

Did you read the text and were you able to understand the meaning and the message it contained, If so think about it if you can read the message even when the order at which it is written is changed, Our DNA is also evolving in a similar fashion,now go on read about Gene splicing, SNP, Jumping genes, Transposons you would understand them better.

I guess perhaps we can use the same to explain to students or non biologists many other features of DNA especially how it is possible for HSP genes to create different proteins from different structural arrangement or how more than one DNA can code for one protein

next generation literature awareness tool

Another science website that seems to be as taking its cues from web2.0 anthology.

Faculty of 1000 Biology is the next generation literature awareness tool. It is a revolutionary new online research service that will comprehensively and systematically highlight and review the most interesting papers published in the biological sciences, based on the recommendations of a faculty of well over 1000 selected leading researchers.

Faculty of 1000 Biology will be run by scientists for scientists, and will provide a rapidly updated consensus map of the important papers and trends across biology.

In the Faculty of 1000 Biology, the entire field of biology is divided into 16 Faculties (subjects), each of which will be run by two to four Heads of Faculty.

Each Faculty is subdivided into 3-12 Sections, each run by two or three Section Heads and comprising between 10 and 50 Faculty Members. Faculty of 1000 Biology aims to invite the best scientists internationally in each field and to involve both experienced and younger investigators.

All in all an excellent website with lots of information which is peer reviewed

from youtube to DNAtube

I would like to introduce you newly found SCIENTIFIC VIDEO site which
is www.DnaTube.com the scientific video site

In this site, you can upload and share your scientific videos, watch videos, experminets, animations and many otherinformation about biology, chemistry.

http://www.dnatube.com

Yahoo answers- Interact with the President of India

Thats not really a big surprise considering he himself is a scientist, Dr. Abdul Kalam Azad the President of India who is also the commander in chief of the Army,Navy and Airforce of India, and is key force for India’s nuclear and Space power and technology uses, yahoo answer so that he can listen and hear from his people, so what about our scientist ! especially in life sciencs and academicians. Recently I had posted about the similar attempts by US presidentail hopeful’s sudden rush to web2.0. and how youtube is helping the science

Dr. Kalam’s His thought provoking question,  has garnered over 28000 answers in just 30 days. wow thats a response rate you could never expect in any other online forum asking for soutions to a scientific question or problem

chekout more visit his profile at http://in.answers.yahoo.com/my/profile?show=1e6b7ca835ee0cc4185b0ab950476c08aa
Some leading Indian figures like Sri Sri Ravishankar, Kiran Bedi, and Leander Paes have posted answers to Dr. Kalam’s question

less than 10% of people build content in an online community — in this case answer questions. The popular thumb-rule for online participation is 1% visitors would be hard-core contributors, 10% mild contributors, and 90% would be beneficiaries

By 2006 end, Yahoo! Answers had gained over 60 million unique users on a monthly basis

http://answers.yahoo.com/question/index?qid=20070112135510AAD7SB8

Cryptography with DNA binary strands

Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The rst approach shows how DNA binary strands can be used for steganography to provide rapid encryption and decryption. It is shown that DNA steganogra- phy based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the rst approach to support encryption.

full article at http://www.cs.mun.ca/~banzhaf/papers/DNA_Crypt_final.pdf

Bioinformatics Techniques for spam detection

Its not a new topic IBM has discovered that it could use many of the pattern detection techniques and analysis used in bioinformatics in other fields as well.

I thought of adding this as bioinformatics is and microarrays are growing in popularity and decided to give few bytes such articles as wel.

Many of these studies are based on the homology detection. Perhaps going forward the techniques used in SNP detection in SNP microarrays might also find use in other fields notably in spam detection and share market analysis or trends analysis

I find some of the presentation onthe web andd from IBm on using the famous Teiresias algorithm, for spam detection

Chung-Kwei applies advanced pattern matching algorithms developed in IBM’s bioinformatics group to spam detection. This new classification algorithm can detect complex patterns in messages that go beyond the simple word or word phrases used in most algorithms.

A technique originally designed to analyse DNA sequences is the latest weapon in the war against spam. An algorithm named Chung-Kwei (after a feng-shui talisman that protects the home against evil spirits) can catch nearly 97 per cent of spam.

Chung-Kwei is based on the Teiresias algorithm, developed by the bioinformatics research group at IBM’s Thomas J Watson Research Center in New York, US. Teiresias was designed to search different DNA and amino acid sequences for recurring patterns, which often indicate genetic structures
that have an important role.

Instead of chains of characters representing DNA sequences, the research group fed the algorithm 65,000 examples of known spam. Each email was treated as a long, DNA-like chain of characters. Teiresias identified six million recurring patterns in this collection, such as “Viagra”.

Each pattern represented a common sequence of letters and numbers that had appeared in more than one unsolicited message. The researchers then ran a collection of known non-spam (dubbed “ham”) through the same process, and removed the patterns that occurred in both groups.

Genuine email Incoming email was given a score based on how many spam patterns it had. A long email that only had a few spammy sentences would get a relatively low score; but one with many patterns spread across the length of the message would score much higher. The Chung-Kwei correctly identified 64,665 of 66,697 test messages as being spam or 96.56 per cent. More importantly, its rate of misidentifying genuine email as spam was just 1 in 6000 messages. Losing a single email in a torrent of spam is a greater failing in a filter than letting the occasional spam email through.

Chung-Kwei deals with common spammer strategies to dodge pattern-recognition schemes, such as replacing the s with a $, as in “increa$e your $ex power” using its built-in tolerance for different, but
functionally equivalent, DNA sequences. Just as in genetic analysis, Teiresias could be taught that CCC and CCU codons both produce the same amino acid, proline, the anti-spam system an be trained to accept $ and s as identical.

IBM intends to include Chung-Kwei in its commercial product, SpamGuru. Justin Mason, who developed SpamAssassin, one of the most popular open-source anti-spam filters, says that Chung-Kwei looks promising.

 

 

 

A little bit of fun- I did a PhD and did NOT go mad by Richard Butterworth from university of Middlesex.

I did a PhD and did NOT go mad

Before reading these wise words advising you how to do a PhD (inspired by three years of the author carefully and diligently banging his head on a table) you are requested to read and digest the following irony…

To say that I enjoyed doing my PhD would be a lie, not just an ordinary lie mind you. More the sort of lie one would normally associate with Tory party conferences. A big wobbly lie with a dusting of sugar on top. At times I hated my PhD, so why do I have any authority to give advice on doing a PhD? Well, I don’t claim to have any — other than the fact that I completed and passed the thing, so I must have done somthing right.

Read on at http://www.cs.mdx.ac.uk/staffpages/richardb/PhDtalk.html

 

standardization in microarray analysis software industry

scouting for the right software for the microarray analysis software , kept me thinkng why despite these software being used by scores or scientists no one has come forward to create what can be called as a standard for such software, the confusion rains in this field as one company’s software data do not work with another one and vice versa, For an industry like biology and drug discovery  that is trying to benefit from the knowledge of mathematics statitics and chemistry physics inability to port data across platform is a serious roadblock. there are standards such as MIAMe and MAGE but these are just data standards, not for softwares, I believe ther should be  something similar to ISO standards, SEI CMI etc.

majority of the newsgroup and forums are used by graduate and at times senor researchers to find out which is the best software to be used, I thought of starting a wiki page where researchers can post their comments and rate the products and compare the features against each other,

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