ENCODE consortium: forming background of why 3 billions bp are required for a human to survive not just the set of genes.

ENCODE consortium today published one in nature and 28 papers in genome research involving 35 groups from 80 organizations around the world, which promise to reshape our understanding of how the human genome functions. The findings totally challenge the tidy collection of independent genes , but sees as a complex networking system, along with regulatory elements and other types of DNA sequences that do not code for proteins, interact in overlapping ways not yet fully understood.

“This impressive effort has uncovered many exciting surprises and blazed the way for future efforts to explore the functional landscape of the entire human genome,” said NHGRI Director Francis S. Collins, M.D., Ph.D. “Because of the hard work and keen insights of the ENCODE consortium, the scientific community will need to rethink some long-held views about what genes are and what they do, as well as how the genome’s functional elements have evolved. This could have significant implications for efforts to identify the DNA sequences involved in many human diseases.”

Loads to come out of this …. few days back in nature cell biology there was a article stating small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA in an eukaryote…

Future of High Throughput Genome Sequencing

In Bangalore Bio 2007 LabIndia has introduced  SOLiD: Sequencing by Oligonucleotide Ligation and Detection which is the Future of High Throughput Sequencing.

“This is useful for those who want to do full genome sequencing. Whole genome projects will be more cost effective with this new instrument than they are today,” said Dr. Anupama Gaur, Team Leader Application Support, Labindia Instruments, Pvt. Ltd.

HistoGenetics has come up with Sequence Based Typing which has many advantages such as identifying many rare and new alleles. “Nearly 2000 alleles have been identified so far and it has been launched in the US and UK as of now” said Dr. Cereb Nezih, M.D., President and co-founder, Histogenetics, Inc.

Gene Expression is affected when cells are cultured in petri dish

When trying to figure out how different respond to drugs and other environemnts in the body scientists turn to cells. The cultured cells are grown in petri dishes now with the onset of tissue microarrays the process is getting more advanced

A new Brown University study shows that nerve cells grown in three-dimensional cultures use 1,766 genes differently compared to cells grown in standard two-dimensional petri dishes.

The research shows that culture techniques can significantly affect cell growth and function. cells grown in a laboratory in 3-D environments are more like cells grown in the ultimate 3-D environment – the human body.

“More and more, we’re seeing evidence that cells cultured in three dimensions look and behave more like cells in your body,” said Diane Hoffman-Kim, the University of Brown bioengineer who spearheaded the new study,

The study is published in the May edition of Tissue Engineering,

Indian genetic database offers R&D advances

Imagine a diabetic patient from NewYork being put on a drug regimen distinct from a patient London. Personalized medicine allows tratement to decided on the genetic make up of the individual. Genetically europeans and asians and others have different ways of responding to same treatment genetically

FortunatelyIf Indian researchers have their way, such customised medication based on genetic differences could be a possibility for a range of illnesses.

A consortium of Indian scientists recently completed a genetic database for India, home to one of the world’s most ethnically diverse populations that will allow researchers to understand the genetic predisposition of ethnic groups to diseases. Icelanders are considered for Human genome project because of very less number such diversity

The genetic map will enable global and Indian pharma companies to enhance research on predictive medicine and targeted drugs. Research firm TCG Life Sciences is about to become the first private player to use the database.

The consortium collected data on the genetic codes of over a 1,000 genes from among 15,000 individuals belonging to Indian sub-populations

Another user of the data is the clinical diabetics’ consortium, which aims to identify if there are specific genetic reasons for a particular ethnic group to be predisposed to the disease. It is already known that some cultures are pre disposed to certain diseases so Indian are more prone to heart attack and diabetes and such

The Indian Genome Variation Consortium, a public-private partnership that networks six Council of Indian Scientific and Industrial Research labs and some private software firms, undertook the genetic variation mapping.

UK is appealing for volunteers to help worlds biggest medical experiment project- to understand impact of Genetics and life style in illness and medical treatment

 UK is appealing for volunteers to help worlds biggest medical experiment project- to understand impact of Genetics and lifestyle in health and medical treatment

The  BBC reports about a medical experiment aiming to be the biggest in the world is appealing for volunteers to help end Scotland’s reputation as the “sick man of Europe”.

The project named as  UK Biobank will be the world’s biggest resource for the study of the role of nature and nurture in health and disease.

Funded and guided under the supervision of leading scientists from the UK and around the world. Funded by the  Wellcome Trust, the UK’s largest independent medical research charity, the  Medical Research Council, the Department of Health, the Scottish Executive and the Northwest Regional Development Agency. and many other major medical research charities, including the British Heart Foundation and Cancer Research UK. The project is also supported by the National Health Service.

claiming to help not just the volunteer, but for the future generation to come the £61m UK Biobank project will track the health of thousands of people for up to 30 years.

Information and DNA gathered from volunteers will be used by researchers to help tackle serious diseases.

Volunteers will be asked to attend an assessment centre where they will fill out a lifestyle questionnaire, have body measurements such as bone density, blood pressure, height and weight recorded, and donate a small sample of blood and urine for long-term storage as a resource for researchers in the future.

Researchers will study the relationship between our genes, our lifestyles and our current health to find out why some people develop certain illnesses and others do not.

It is hoped the project will eventually include 500,000 volunteers from across Britain, making it the biggest study of its type ever undertaken.

The Biobank will run alongside the complementary Generation Scotland project, which focuses on how genes inherited from our parents affect the likelihood of developing diseases.

Data collected by the two projects will be used to help prevent and develop new treatments for cancer, heart disease, diabetes, Parkinson’s, Alzheimer’s, mental health illnesses, osteoporosis and arthritis.

Free DNA Paternity Test for Father’s Day

I am not promoting anything here but I thought it was an intersting news aswell as nothing short of odd considering the recent and ongoing news pages spend on discussing hollywood and famous fatherhood battles inside and out of court this is  one kind of an offer that Chromosomal Laboratories, Inc. a leading DNA testing laboratory, has announced that it will repeat its  offer of five free paternity tests, a $2000 value, to fathers and alleged fathers as a special promotion to celebrate the upcoming Father’s Day holiday. Interested parties should contact Chromosomal Laboratories by June 14th to be entered into the drawing. Five fathers will be chosen at random to receive a free home paternity test kit.

source webwire

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State law protects DNA of Minnesota wild rice

ST. PAUL — The DNA of Minnesota wild rice gets special protection under a new state law adopted this year with the backing of Indian tribes.

Genetic modifications to wild rice will be watched more closely, with environmental impact statements required and permits controlled by the Minnesota Environmental Quality Board.

DNA DATABASE TO HELP IDENTIFY DISAPPEARED

(May 23, 2007) The head of Chile’s Medical Legal Service (SML), Patricio Bustos, announced this week that his organization would create a DNA database that will be used to help identify the remains of those who were disappeared and murdered during the military regime led by Gen. Augusto Pinochet.

Source Santigao times

Errors in DNA database

The exciting news of google or its benefactor investing in genomics companya and google founders earlier enthusiasm to offer its billion dollar power for genomics indutsry, has produced a mixed responses. I agree with Hsiens post that we should welcome the move

I guess its worthwhile to know why its better if google does so , The UK’s national DNA database, which houses 4.1 million records pertaining to evidence of crimes collected by police, has been found to have upwards of 100,000 incorrect records. 

According to theregister.co.uk, the complex relationship between the country’s police force, its National DNA Database Unit and the forensic service along with a lack of checks and balances has left its DNA database with the large amount of corrupted records, causing 26,200 load problems alone

“There’s in the order of 100,000 unreconciled records now,” claims The Register’s source.

Realated posts

GeneticsandHealth

ScienceDirect

NEWS

DNA file on 100,000 innocent children

Microarrays in daily life

Accurate assessment of a calf’s future performance may soon be possible by using microarrays.

By 2010, less than three years away,
Australia’s largest integrated beef research program, the Beef Cooperative Research Centre (CRC) anticipates cattle breeders may be able to get an accurate assessment of a bull or a dam’s future performance within a few months of its birth

Professor John Gibson, Beef CRC Adaptation and Cattle Welfare Research Leader, says microarray technology has enabled the entire 23,000-odd separate genes of the bovine genome to be printed on one microarray plate the size of a microscope slide. 

“Research overseas indicates that how an animal expresses its genes in early life provides an accurate picture of its gene expression at breeding age.” 

This leads to the prospect of microarrays being printed that carry genes of commercial interest, which could be then used to predict the breeding performance of young animals well before they reach breeding age.

 Prof. Gibson observes that this would help breeders quickly eliminate genetically dud bulls and cows early in their life, without the costs of feeding and progeny testing now required to determine the duds. 

Genes add up risk of autoimmune disease

Geneticists have identified a link between the number of copies of a specific gene an individual has and their susceptibility to autoimmune diseases like lupus.

The research by Professor Tim Aitman of the Medical Research Council Clinical Sciences Centre at Imperial College London, and colleagues, is published in Nature Genetics.

From Medical News 

New approach to study microbiaL GENOTYPING

Over 99% of the Earth’s microorganisms cannot be cultivated in laboratory, making their ecological roles, biochemistry and potential practical applications an unresolved mystery. The cutting-edge approach to tackle this enigma, originally developed for the human genome sequencing project, has been sequencing large quantities of short sections of DNA from the extracts of entire microbial communities, and then assembling these sections back into individual genomes by computational means.

Unfortunately, the diversity of natural microbial communities proved so incredibly high, that very few genomes could be assembled from even the largest metagenomic studies, consisting of millions of DNA sequences.

In a paper published this month in the Proceedings of the National Academy of Sciences, Drs. Stepanauskas and Sieracki from Bigelow Laboratory for Ocean Sciences  propose an alternative to the metagenomic research.

The new method is based on fluorescence-activated sorting, whole genome amplification, and multi-locus DNA sequencing of single cells. This allows us to sequence any number of genes in each cell, including those that reveal cell’s identity and those that tell us what biochemical reactions the cell is capable of performing”, said Dr. Stepanauskas.

The publication “Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time,” is a result of the researchers’ collaboration, 

The paper is available online at: PNAS

There is no ET in Human DNA

Well after all the hulllaba about the presence of extraterrestrial DNA in human genome and lots of blogs and articles later inlcuding the ones from mine which talked about the unusual presence and shift in genetic codon makeup in human DNA. More plausible evidence has started to emerge for what can be termed as ET DNA  in Human genome, triggered  by the completion of the genome sequencing of the marsupial opposum

An international team, led by researchers at the Broad Institute of MIT and Harvard, and supported by the National Institutes of Health (NIH), have announced the publication of the first genome of a marsupial, belonging to a South American species of opossum (Monodelphis domestica ). In a comparison of the marsupial genome to genomes of non-marsupials, including human, published in the journal Nature, the team found that most innovations leading to the human genome sequence lie not in protein-coding genes, but in areas that until recently were referred to as “junk” DNA. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences the study helps to explain the evolutionary origins of human DNA and the role played by transposons,  

The study reveals a surprising role in human evolution for “jumping genes”

So how does the marsupial genome sequencing explains what has been refered as the presence of extraterrestrial gene or well of course we dont have any ET DNA

In the words of  Broad Institute director Eric Lander “Evolution is tinkering much more with the controls than it is with the genes themselves,”. “Almost all of the new innovation … is in the regulatory controls. In fact, marsupial mammals and placental mammals have largely the same set of protein-coding genes. But by contrast, 20 percent of the regulatory instructions in the human genome were invented after we parted ways with the marsupial.”

It showed that an important source of genetic innovation comes from bits of DNA, called transposons, that make up roughly half of our genome and that were previously thought to be genetic “junk.”

The research shows that this so-called junk DNA is anything but, and that it instead can help drive evolution by moving between chromosomes, turning genes on and off in new ways.

 “The official textbook picture of how genes work really didn’t appear to be right,” Lander said. “There was much more of the genome standing around shouting instructions than actually producing proteins.”

That raised a question of how evolution actually works on the genome, Lander said. With so much of the genome devoted to regulation, it became apparent that evolution could work by simply changing the instructions rather than changing the protein-coding genes themselves.

Now that perhaps explain all the articles you may have come across about the discovery of extraterrestrial genes in human DNA

Thus, the mobile elements that are typically thought of as “junk DNA” have played a creative role in genome evolution – spreading key genetic innovations involved in the control of gene expression across the genome.

 

A tiny opossum’s genome has shed light on how evolution creates new creatures from old, showing that change primarily comes by finding new ways of turning existing genes on and off

whats in your beef- is Genetically Engineered Food a Hazard?!

Do you share the same concern if you are in EU then relax the rules stipulates that GM food should carry the label to distinguish them from the rest of the crowd. But what if that is not enough.

The website http://www.psrast.org/ gives a list that should worry any spokesperson for GM . well I am certainly concerned and not at all against GM food and GMO studies especially if it can create cheaper medicines or study drug resistance in microbes

According to Charles Saunders, chairman of the British Medical Association’s public health committee

”We simply do not have enough reliable scientific evidence on their safety to be able to make a valid decision as to whether there are potential health effects or not.

Already, an estimated 1 to 2 percent of Americans are allergic to some food, and their reactions can be serious or even fatal.

food allergies Food allergies are caused by proteins which are made by genes. Indeed, the whole purpose of genetic engineering is to force a plant or animal to make new proteins.

In one of the few pieces of hard evidence about the health dangers of genetic engineering, Stephen Taylor, who studies food allergies at the University of Nebraska, found that moving a gene indeed made a new food allergenic.

The regulatory part of the genome was two to three times larger than the portion that actually held the instructions for individual proteins.

With so much of the genome devoted to regulation, it became apparent that evolution could work by simply changing the instructions rather than changing the protein-coding genes themselves.

A tiny opossum’s genome has shed light on how evolution creates new creatures from old, showing that change primarily comes by finding new ways of turning existing genes on and off

 

 

Does the finding prove that transgenic foods are inherently dangerous? Not really

 

 

 

 

Whole Genome microarray @ 99 USD

Ocimum Biosolutions is offering whole genome microarrays at 99 USD as part of its 6th year celebration, The limited period marketing offer is available for many cataloge whole genome microarrays at 99 USD irrespective of the number of microarrays ordered.

The company now offers one of the best cost effective microarray prices in the market

To get more information on microarray price please contact Ocimum Biosolutions web  http://www.ocimumbio.com/web/promo/array99.asp


 

 

‘Personalized Medicine’ Goal of Human Genetics Initiative

Oregon Health & Science University effort, launched 25-April 2007 during National DNA Day, will meld genetics and clinical care

OHSU today is launching the Human Genetics Initiative (HGI), an effort that brings together the university’s vast array of genetics research resources and brainpower, and applies them in a health care setting. It will allow the university to seek new ways of understanding the role of genetics in common disorders like obesity, hypertension, osteoporosis and diabetes.

The goal of HGI is to accelerate the translation of scientific knowledge to patient care by recruiting new geneticists, building a campuswide bank of advanced technology, developing new educational programs for the next generation of health care providers, and, eventually, establishing a novel delivery model for genetics health care.

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

Theranostics-Genetics Testing for Clinical Diagnostics for Personalized Medicine

Theranostics is the term used to describe the proposed process of diagnostic therapy for individual patients – to test them for possible reaction to taking a new medication and to tailor a treatment for them based on the test results or in plain english Personalized Medicine.

Personalized medicine is the use of detailed information about a patient’s genotype or level of gene expression and a patient’s clinical data in order to select a medication, therapy or preventative measure that is particularly suited to that patient at the time of administration

The test results are used to tailor treatment, usually with a drug that targets a particular gene or protein.

Seen the movie Gattaca it shows glipses of the what to come.

This method is looked as the possible end result of new advances made in Pharmacogenomics, Drug Discovery using Genetics, Molecular Biology and Microarray chips technology

The technology is set to grow by leaps as new companies are introducing new microarray chip which are getting cheaper day by day

Already there are microarraychips approved by FDA for clinical diagnostics

Defra funds team to build microarray biochip to detect disease outbreaks

A single test for more than 600 deadly viruses is being developed by a group of Defra-funded scientists, offering the possibility of spotting a disease outbreak in hours rather than days.

The microarray, which is being led by the Central Science Laboratory near York, with £1.5m funding from Defra, will detect viruses that affect humans, animals, plants, fish and bees including avian influenza, rabies and foot and mouth.

Animal and plant researchers will be able to use the same test to identify many viruses, saving time and resources in the event of an outbreak It will also help to quickly identify when a virus has jumped from one species to another and when new strains of existing disease emerge in the future.

its not so much of junk DNA- University of Oxford Scientists discoveres Cancer cure with it

 Junk DNA is not junk after all

Recently, scientists at the University of Oxford have discovered that ‘junk’ genetic material can switch off cancer tumours, preventing them from growing.

By using RNA to switch off a gene involved in controlling cell division, Oxford University scientists may have found a role for RNA in developing new cancer therapies. RNA is the mirror image of DNA, and is used to pass on instructions to the cell to build the proteins that run every body function.

The Human Genome Project found that human DNA carries approximately 34,000 genes that produce proteins. The remaining majority of the genome constituted what was considered to be junk DNA as it had no obvious function. However, this is set to change.

‘‘There has been a quiet revolution taking place in biology in past few years,’’ said Dr Alexandre Akoulitchev, a Senior Research Fellow at Oxford. ‘‘Scientists have begun to see ‘junk’ DNA as having an important function. The variety of RNA types produced from this so called ‘junk’ is staggering and the functional implications are huge.”

Akoulitchev studied the RNA that regulates a gene called DHFR. This gene produces an enzyme that controls the production of molecules called tetrahydrofolate and thymine that cells need to divide rapidly.

“Switching off the DHFR gene could help prevent ordinary cells from developing into cancerous tumour cells, by slowing down their replication. In fact, one of the first anti-cancer drugs, Methotrexate, acts by binding and inhibiting the enzyme produced by this gene. Targeting the gene itself would cut the enzyme out of the picture altogether. Understanding how we can use RNA to switch off or inhibit DHFR and other genes may have important therapeutic implications for developing new anti-cancer treatments.”

This research was funded by The Wellcome Trust and the Medical Research Council.

Original paper: Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript was published in Nature on 22nd January 2006.

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