‘‘Every drop of human blood contains a history book written in the language of our genes.’’ —Population geneticist Spencer Wells
Eight years ago, an obscure village, nestling among hills and surrounded by paddy fields near Madurai was cause for much excitement for a project team from the US. It was on a mission to trace human roots to a single origin. An unremarkable farmer’s son and the placid Jyotimanickam village shot into the limelight when renowned population geneticist, Spencer Wells, landed on its dusty square.
Wells had hoped to prove that a few descendants of the first humans from Africa, trekking through India to reach Australia, had settled in south India. It took him several days to collect about 700 samples from in and around Madurai and put them through the DNA sequencer. But his search paid off. Virumandi Andi Thevar, an 18-year-old student, now a librarian, whose family had settled in the village for generations, was discovered to have the rare ‘NRYM130’ genetic mutation or ‘marker’ found in the first exodus out of Africa. The same marker was also found in some aborigines in Australia.
This discovery shot Spencer Wells to fame and he convinced the National Geographic Society, IBM and The Ted Waitt Family Foundation to fund a massive global project called Genographic. The project was officially launched in April 2005. The project hopes to unravel the mysteries of what compelled a band of their descendants to leave their home continent and spread across Eurasia. Field scientists will fan out across six continents to gather close to 100,000 samples from interesting and ancient isolated populations of the world. India is a critical link in this project.
Experts in ten regional research centres in Australia, Brazil, China, France, Lebanon, Russia, South Africa, UK, US and India will collate and interpret their findings. In India, the project roped in immunologist, Prof Ramasamy Pitchappan, chairman, School of Biological Science and Head of the Department of Immunology, Madurai Kamaraj University (MKU), and a key contributor to the discovery of the first coastal migration through India 50,000 years ago. Pitchappan had helped Wells in his Madurai project in 1998.
The MKU professor, with a deep fascination for the population structure of India, had been working extensively on immunogenetic basis of tuberculosis and leprosy susceptibility. ‘‘My association with Spencer Wells goes a long way. We knew the answer for the first coastal migration would be found somewhere in south India. Since I am based at Madurai, we performed the sampling here,’’ he recalls.
An MOU will be signed shortly between National Geographic Channel and the Madurai Kamaraj University, says Pitchappan. The Madurai chapter of the project would cost $1 million. Ten laboratories around the world will study 100,000 people across the continents for NRY (Non Recombinant Y chromosome) and mitDNA (Mitochondrial DNA). The Indian chapter will study 10,000-20,000 population samples from the country.
Explains Pitchappan: ‘‘The human genome sequence contains about 30,000 genes and this represents only 5 per cent of our genome. Though most of our sequences are 99 per cent identical, it is the mutations, mostly called single nucleotide polymorphisms, which are responsible for changing a character. Such changes in a gene is responsible for our individual differences, in eye colour or disease risk. Once in an evolutionary blue moon, a random, harmless mutation that occurs in one of these functionless stretches, is passed down to all of that person’s descendants. Generations later, finding that same mutation, or marker, in two people’s DNA indicates that they share the same genes—and perhaps the same ancestor.’’
Such changes are often obscured by the genetic reshuffling that takes place each time a mother and father’s DNA combine to make a child. Luckily some chromosomal regions preserve the telltale variations. One, called the mtDNA is passed down intact from mother to child. Similarly, most of the NRY chromosome, which determines maleness, travels intact from father to son. By comparing the mtDNA and Y chromosomes of people from various populations, geneticists can tell where and when those groups parted ways in the great migrations around the planet.
Pitchappan’s studies on several populations of Tamil Nadu described enormous variations in their genes ascribed to migration and selection. ‘‘I am interested in HLA (human leucocyte antigens, similar to red blood group on white cells) diversity in Indian population, with its various linguistic groups, tribes and caste, each unique in its own way in terms of language, culture, marriage pattern, value system and food habits. These populations are isolated in their gene pool. Though separated by space and culture, each community retains the gene pool,’’ points out Pitchappan.
The first samples will be collected from the Gond community in Orissa. “They speak the central Dravidian language. There are similarities between them and people from Tamil Nadu. They too celebrate Pongal that we observe here. It will be interesting to find out what the relationship is between two groups of people so far apart,’’ says Pitchappan.
The team will also take up village clusters in Tamil Nadu, which have names similar to those in Madhya Pradesh. ‘‘When people travel, they carry their memories. It will be interesting to study whether there are any cultural similarities and if they are accidental or incidental,’’ he says.
Eventually, India too hopes to have public participation like in the US where individuals can participate in the research effort by purchasing Genographic Project kits for $100 through the National Geographic website. DNA material is collected through cheek swab samples. To ensure participant privacy, the personal results would be included anonymously in the genetic database. Interactive element would give participants an opportunity to follow the progress of their own migratory history and the global research process through their website, providing regular updates on project findings. Presently there is no public participation in India and China, where export of genetic materials requires government approval.
Posted online: Sun Jun 18 2006, 00:00 hrs
THANKS TO MR.Sakthi Sarvanan
Many microarray experiments search for genes with differential expression between a common “reference” group and multiple “test” groups. In such cases currently employed statistical approaches based on t-tests or close derivatives have limited efficacy, mainly because estimation of the standard error is done on only two groups at a time. Alternative approaches based on ANOVA correctly capture within-group variance from all the groups, but then do not confront single test groups with the reference. Ideally, a t-test better suited for this type of data would compare each test group with the reference, but use within-group variance calculated from all the groups.
We implemented an R-Bioconductor package named Mulcom, with a statistical test derived from the Dunnett’s t-test, designed to compare multiple test groups individually against a common reference. Interestingly, the Dunnett’s test uses for the denominator of each comparison a within-group standard error aggregated from all the experimental groups. In addition to the basic Dunnett’s t value, the package includes an optional minimal fold-change threshold, m. Due to the automated, permutation-based estimation of False Discovery Rate (FDR), the package also permits fast optimization of the test, to obtain the maximum number of significant genes at a given FDR value. When applied to a time-course experiment profiled in parallel on two microarray platforms, and compared with two commonly used tests, Mulcom displayed better concordance of significant genes in the two array platforms (39% vs. 26% or 15%), and higher enrichment in functional annotation to categories related to the biology of the experiment (p value < 0.001 in 4 categories vs. 3).
NOTE :IF YOU NEED MORE GO THIS LINK
BIOINFORMATICS APPLICATIONS NOTE
In silico Biochemical Reaction Network Analysis (IBRENA):
a package for simulation and analysis of reaction networks
Gang Liu1 and Sriram Neelamegham1,2,*
Department of Chemical and Biological Engineering, and 2NY State Center for Excellence in Life Science and
Bioinformatics, State University of New York, Buffalo, NY 14260, USA
Received on December 7, 2007; revised on February 11, 2008; accepted on February 12, 2008
Advance Access publication February 28, 2008
Summary: We present In silico Biochemical Reaction Network
Analysis (IBRENA), a software package which facilitates multiple
functions including cellular reaction network simulation and sensi-
tivity analysis (both forward and adjoint methods), coupled with
principal component analysis, singular-value decomposition and
model reduction. The software features a graphical user interface
that aids simulation and plotting of in silico results. While the primary
focus is to aid formulation, testing and reduction of theoretical
biochemical reaction networks, the program can also be used for
analysis of high-throughput genomic and proteomic data.
Availability: The software package, manual and examples are
available at http://www.eng.buffalo.edu/$neel/ibrena
Theoretical Kerr black holes aren’t the only possible cosmic shortcut to the past or future. As made popular by everything from “Star Trek: Deep Space Nine” to “Donnie Darko,” there’s also the equally theoretical Einstein-Rosen bridge to consider. But of course you know this better as a wormhole.
Einstein’s general theory of relativity allows for the existence of wormholes since it states that any mass curves space-time. To understand this curvature, think about two people holding a bedsheet up and stretching it tight. If one person were to place a baseball on the bedsheet, the weight of the baseball would roll to the middle of the sheet and cause the sheet to curve at that point. Now, if a marble were placed on the edge of the same bedsheet it would travel toward the baseball because of the curve.
In this simplified example, space is depicted as a two-dimensional plane rather than a four-dimensional one. Imagine that this sheet is folded over, leaving a space between the top and bottom. Placing the baseball on the top side will cause a curvature to form. If an equal mass were placed on the bottom part of the sheet at a point that corresponds with the location of the baseball on the top, the second mass would eventually meet with the baseball. This is similar to how wormholes might develop.
In space, masses that place pressure on different parts of the universe could combine eventually to create a kind of tunnel. This tunnel would, in theory, join two separate times and allow passage between them. Of course, it’s also possible that some unforeseen physical or quantum property prevents such a wormhole from occurring. And even if they do exist, they may be incredibly unstable.
According to astrophysicist Stephen Hawking, wormholes may exist in quantum foam, the smallest environment in the universe. Here, tiny tunnels constantly blink in and out of existence, momentarily linking separate places and time like an ever-changing game of “Chutes and Ladders.”
Wormholes such as these might prove too small and too brief for human time travel, but might we one day learn to capture, stabilize and enlarge them? Certainly, says Hawking, provided you’re prepared for some feedback. If we were to artificially prolong the life of a tunnel through folded space-time, a radiation feedback loop might occur, destroying the time tunnel in the same way audio feedback can wreck a speaker.
தமிழ் மறந்த நான்…!!
என்றும் நானிருந்தேன் நலமாய்…
கற்பனை வானில் வெள்ளி ரத உலா வரும்
தேயாத வெண்ணிலவாய் நான்..!
தனித்திரிந்தும் உணர்ந்ததில்லை தனிமையை
காரணம் என்னுள் வாழும் தமிழ் ரசனை;
பார்ப்பவை எல்லாம் அழகாய்
தமிழ் கொண்டு செல்லும் பணிவாய்;
கடலலைகளிலும் இசை கண்டேன்;
உலகம் முழுதும் எனதென ரசித்திருந்தேன்;
அனைத்தையும் என் தமிழில் இசைத்திருந்தேன்!
தமிழ் எனக்கு மறந்ததில்லை!
இவ்வில்லை எல்லாம் இல்லாமல் போக
உண்டென்ற ஒரு நிலை இன்றோ..?
மனதில் சலனித்த நீரோட்டம்
எண்ணங்கள் கொள்ளவில்லை தோற்றம்
கவிதைகளில் ஏனோ ஏமாற்றம்!
தேடலில் திரை நிற்க
மௌனத்தில் மனம் இருக்க
மாற்றங்களை மாற்றிட எதை நான் கற்க..?
தமிழ் மறந்து திரிவேனோ..?
உயிர் மறந்து உலவுவேனோ..
இதயம் அழுவதாய் ஒரு உருகண்டு
சட்டென கண் திறந்தேன்..
ஆஹா..!! தமிழ் மறந்து தவித்ததும்
என் கற்பனையின் தீவிரமோ..?
கற்பனைகள் கடலலையாய் என்றதால் ,…,.,…,..
Bioinformatics is the application of computer technology to the management of biological information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied to gene-based drug discovery and development. The need for Bioinformatics capabilities has been precipitated by the explosion of publicly available genomic information resulting from the Human Genome Project. The goal of this project – determination of the sequence of the entire human genome (approximately three billion base pairs) – will be reached by the year 2002. The science of Bioinformatics, which is the melding of molecular biology with computer science, is essential to the use of genomic information in understanding human diseases and in the identification of new molecular targets for drug discovery. In recognition of this, many universities, government institutions and pharmaceutical firms have formed bioinformatics groups, consisting of computational biologists and bioinformatics computer scientists. Such groups will be key to unraveling the mass of information generated by large scale sequencing efforts underway in laboratories around the world.