New technology could sequence a person''s genome in minutes

Washington, Dec 21 : Researchers at the Imperial College London scientists are developing technology that could lead to ultrafast DNA sequencing tool within ten years.

The new technology could ultimately sequence a person''s genome in mere minutes, at a fraction of the cost of current commercial techniques.

The research has suggested that scientists could eventually sequence an entire genome in a single lab procedure, whereas at present it can only be sequenced after being broken into pieces in a highly complex and time-consuming process.

Fast and inexpensive genome sequencing could allow ordinary people to unlock the secrets of their own DNA, revealing their personal susceptibility to diseases such as Alzheimer''s, diabetes and cancer.

Joshua Edel, one of the authors on the study from the Department of Chemistry at ImperialCollege London, said: "Compared with current technology, this device could lead to much cheaper sequencing: just a few dollars, compared with 1m dollars to sequence an entire genome in 2007. We haven''t tried it on a whole genome yet but our initial experiments suggest that you could theoretically do a complete scan of the 3,165 million bases in the human genome within minutes, providing huge benefits for medical tests, or DNA profiles for police and security work."

In the new study, the researchers demonstrated that it is possible to propel a DNA strand at high speed using an electrical charge.

Tim Albrecht, another author on the study, said, "The next step will be to differentiate between different DNA samples and, ultimately, between individual bases within the DNA strand (ie true sequencing)."

The findings were published in the journal Nano Letters. (ANI)

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Jumping genes may tell why people have varied looks, disease risks

Washington, Feb 5: A Johns Hopkins study has identified ''jumping genes'' in humans that may one day explain why people have such varied physical traits and disease risks.

Using bioinformatics to compare the standard assembly of genetic elements, the team revealed 1,016 new insertions of RIPs, or retrotransposon insertion polymorphisms, thereby expanding the catalog of insertions that are present in some individuals and absent in others.

Retrotransposons are travelling bits of DNA that replicate by copying and pasting themselves at new locations in the genome. Having duplicated themselves and accumulated over evolutionary history, transposable elements now make up about half of the human genome.

"In any individual, only between 80 to 100 retrotransposons are actively copying and inserting into new sites. We''re not only discovering where they are and who has which ones, but also finding out that they insert with a remarkable frequency: On the order of one in every 50 individuals has a brand-new insertion that wasn''t in their parents," said Haig Kazazian of the Johns Hopkins University School of Medicine.

The researchers recognized L1 retrotransposons because these actively jumping genes are human specific and almost exactly the same in sequence from one person to another.

The results appeared in the journal Genome Research. (ANI)

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Scientists sequence two new strains from E. coli outbreak in Germany

Washington, June 12 : Two isolates from the current E. coli (Escherichia coli) outbreak in Germany have been sequenced and analyzed in laboratories.

Both strains are now available from Virginia Bioinformatics Institute''s (VBI''s) Pathosystems Resource Integration Center (PATRIC).

In the rush to save lives, many laboratories are analyzing these genomes and providing data to the research community.

The two genomes have been annotated with Rapid Annotation using Subsystem Technology (RAST), making them consistent with the 184 E. coli genomes and the total 2,865 bacterial genomes available at PATRIC.

The proteins conserved across all E. coli have been used to generate a preliminary phylogenetic tree that is based on 166640 characters across 527 genes in 354 taxa.

This tree shows that the two new strains are most closely related to the pathogenic, enteroaggregative strain 559899, which may give additional insight into its origin.

“The PATRIC team is working around the clock to help the scientific community address this emergency. Analyses such as these provide insights into the origin of highly pathogenic strains and potential response strategies,” said Bruno Sobral, PATRIC''s principal investigator. (ANI)

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Greediness gene dooms dieting

London, Nov 15 - Your dieting resolve can be doomed if you are carrying a 'greediness' gene, a study shows.

Researchers have shown that a rogue gene linked to obesity makes us fat by boosting appetite.

This deep-seated drive to eat could also explain why so many of us succumb to temptation, no matter how strong our initial resolve to lose weight, according to the journal Nature Genetics.

The breakthrough opens the door for drugs that take the edge off appetite, melting away 'muffin tops' and pruning pot bellies, reports the Daily Mail.

Oxford University and the Medical Research Council researchers studied a gene called FTO, which when discovered in 2007, was the first gene to be linked with obesity.

Up to 14 percent of Britons carry two rogue copies of FTO, increasing their risk of obesity by 70 percent and diabetes by 50 percent. These people are, on average, almost half a stone heavier.

The 49 percent who have inherited just one flawed FTO gene are 30 percent more likely to be obese than those with two normal copies of the gene and 25 percent more likely to develop diabetes.

Scientists found that mice bred to have extra copies of the rogue gene were healthy, but ate more and became heavier than normal rodents.

Researcher Chris Church said: "For the first time, we have provided convincing proof that the FTO gene causes obesity."

Prof Frances Ashcroft, one of the research leaders, said: "Too much activity of this gene canlead to putting on weight by overeating." (IANS)

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Targeting malaria’s ‘sticky’ proteins could put an end to the disease

Washington, July 10 : A team of Australian researchers have identified a key mechanism that enables malaria-infected red blood cells to stick to the walls of blood vessels and avoid being destroyed by the body''''s immune system.

The discovery highlights an important potential new target for anti-malarial drugs.

Malaria is caused by the malaria parasite, which is injected into the bloodstream from the salivary glands of infected mosquitoes.

There are a number of different species of parasite, but the deadliest is the Plasmodiumfalciparum parasite.

The malaria parasite infects healthy red blood cells, where it reproduces, producing up to thirty-two new daughter parasites.

The parasite secretes a ‘glue’, known as PfEMP1, which travels to the surface of the infected red blood cells, leading to the formation of the knobs on the surface of the cells.

The cells become sticky and adhere to the walls of the blood vessels.

This prevents the cells being flushed through the spleen, where the parasites would be destroyed by the body''''s immune system, but also restricts blood supply to vital organs.

Now, researchers, led by Professor Alan Cowman from the Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia, have identified eight new proteins that transport the P. falciparum parasite''''s ‘glue’ to the surface of the infected red blood cells.

They have shown that removing just one of these proteins prevents the infected red blood cells from sticking to the walls of the blood vessels.

"These findings greatly enhance our understanding of how the malaria parasite commandeers the red blood cell for its own survival and avoids our immune defences," Cowman said.

"They also suggest that a drug that targets the ''''stickiness'''' proteins could be an effective treatment for malaria," he added.

The study is published in the journal Cell. (ANI)

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Rare genetic disease mutation protects against malaria

London, Apr 17: The mutation that causes the raregenetic disease pyruvate kinase deficiency protects against malaria, states a new study.

Approximately 1 in 20,000 people have two copies of a genetic mutation that prevents red blood cells from producing energy and causes anaemia.

And patients with the condition often die young.

But, according to Philippe Gros, a geneticist at McGill University in Montreal who led the new study, people with one mutated pyruvate kinase (PK) gene might be spared from the malaria parasite Plasmodium falciparum.

"These guys are absolutely normal; they don't know that they have one copy of the mutation," New Scientist quoted him, as saying.

The research team is currently collecting blood samples in areas rife with malaria to determine whether the mutation offers some resistance in people with one mutation.

"In one or two years max we'll have the answer," Gros said.

Another disease, sickle cell anaemia, protects against malaria in a similar way. Patients with a single mutation in a gene for the blood protein haemoglobin have partial resistance to malaria, while two copies spell disease.

For this, the research team tracked down several patients and collected blood from them.

When the researchers tried infecting the red blood cells with P. falciparum, the sickly cells were virtually impervious to the parasite.

Some parasites managed to invade, but those cells proved easier targets for the immunesystem. White blood cells destroyed the infected cells in a Petri dish.

Gros' team performed the same tests in cells of people who had only one mutation in the PK gene.

Their red blood cells easily succumbed to the malaria parasite. However, white blood cells made easy work of the infected cells. This suggests that people with PK mutations – but no disease – might get some protection from malaria, Gros said.

The study is published in The New England Journal of Medicine.

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The Potential of Bioinformatics

The potential of Bioinformatics in the identification of useful genes leading to the development of new gene products, drug discovery and drug development has led to a paradigm shift in biology and biotechnology-these fields are becoming more & more computationally intensive. The new paradigm, now emerging, is that all the genes will be known "in the sense of being resident in database available electronically", and the starting point of biological investigation will be theoretical and a scientist will begin with a theoretical conjecture and only then turning to experiment to follow or test the hypothesis. With a much deep understanding of the biological processes at the molecular level, the Bioinformatics scientist have developed new techniques to analyse genes on an industrial scale resulting in a new area of science known as 'Genomics'.

The shift from gene biology has resulted in the development of strategies-from lab techniques to computer programmes to analyse whole batch of genes at once. Genomics is revolutionizing drug development, gene therapy, and our entire approach to health care and human medicine.

The genomic discoveries are getting translated in to practical biomedical results through Bioinformatics applications. Work on proteomics and genomics will continue using highly sophisticated software tools and data networks that can carry multimedia databases. Thus, the research will be in the development of multimedia databases in various areas of life sciences and biotechnology. There will be an urgent need for development of software tools for datamining, analysis and modelling, and downstream processing. Security of data, data transfer and data compression, auto checks on data accuracy and correctness will also be major research area of bioinformatics. The use of virtual Reality in drug design, metabolic pathway design, and unicellular organism design, paving the way to design and modification of muticellular organisms, will be the challenges challenges which Bioinformatics scientist and specialist have to tackle. It has now been universally recognized that Bioinformatics is the key to the new grand data-intensive molecular biology that will take us into 21 century.

Bioinformatics - Industry Overview The Bioinformatics industry has grown to keep up with the information explosion, growing at 25-50% a year. In 2000, the US market Research company estimated that the value of the Bioinformatics industry would touch $2 billion. Now it s demand for individuals capable of doing bioinformatics is soaring. Industry's demand for scientists with skills in Bioinformatics far exceeds the supply of qualified specialists in the field, Seems likely that this figure will be reached within the coming year. Therefore, companies are developing methods of spotting potential Bioinformatics experts and then training them on the job.

Bioinformatics and computational biology Bioinformatics and computational biology each maintain close interactions with life sciences to realize their full potential. Bioinformatics applies principles of information sciences and technologies to make the vast, diverse, and complex life sciences data more understandable and useful. Computational biology uses mathematical and computational approaches to address theoretical and experimental questions in biology. Although bioinformatics and computational biology are distinct, there is also significant overlap and activity at their interface.

Biocomputing Biocomputing is often used as a catch-all term covering all this area at the intersection of Biology and Computation , although many other terms are used to name the same area. We can distinguish in to (non-disjoint) sub-fields:

• Bioinformatics - this includes management of biological databases, data mining and data modeling, as well as IT-tools for data visualization
• Computational Biology - this includes efforts to solve biological problems with computational tools (such as modeling, algorithms, heuristics)
• DNA computing and nano-engineering - this includes models and experiments to use DNA (and other) molecules to perform computations
• Computations in living organisms - this is concerned with constructing computational components in living cells, as well as with studying computational processes taking place daily in living organisms

Computational Biology Computational Biology is application of core technology of computer science (eg. algorithms, artificial intelligence, databases etc) to problems arising from biology. Computational biology is particularly exciting today because the problems are large enough to motivate the efficient algorithms and moreover the demand of biology on computational science is increasing.

The most pressing tasks in bioinformatics involve the analysis of sequence information. Computational Biology is the name given to this process, and it involves the following:

• Finding the genes in the DNA sequences of various organisms
• Developing methods to predict the structure and/or function of newly discovered proteins and structural RNA sequences.
• Clustering protein sequences into families of related sequences and the development of protein models.
• Aligning similar proteins and generating phylogenetic trees to examine evolutionary relationships.

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Bioinformatics and its scope

Bioinformatics uses advances in the area of computer science, information science, computer and information technology, communication technology to solve complex problems in life sciences and particularly in biotechnology. Data capture, data warehousing and data mining have become major issues for biotechnologists and biological scientists due to sudden growth in quantitative data in biology such as complete genomes of biological species including human genome, protein sequences, protein 3-D structures, metabolic pathways databases, cell line & hybridoma information, biodiversity related information. Advancements in information technology, particularly the Internet, are being used to gather and access ever-increasing information in biology and biotechnology. Functional genomics, proteomics, discovery of new drugs and vaccines, molecular diagnostic kits and pharmacogenomics are some of the areas in which bioinformatics has become an integral part of Research & Development. The knowledge of multimedia databases, tools to carry out data analysis and modeling of molecules and biological systems on computer workstations as well as in a network environment has become essential for any student of Bioinformatics. Bioinformatics, the multidisciplinary area, has grown so much that one divides it into molecular bioinformatics, organal bioinformatics and species bioinformatics. Issues related to biodiversity and environment, cloning of higher animals such as Dolly and Polly, tissue culture and cloning of plants have brought out that Bioinformatics is not only a support branch of science but is also a subject that directs future course of research in biotechnology and life sciences. The importance and usefulness of Bioinformatics isrealized in last few years by many industries. Therefore, large Bioinformatics R & D divisions are being established in many pharmaceutical companies, biotechnology companies and even in other conventional industry dealing with biological. Bioinformatics is thus rated as number one career in the field of biosciences.

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Genome Map

What is Genome?

The word genome refers to all DNA present in an organism. The DNA is the “Genetic Blueprint” that determines the genotypic make-up of each organism. DNA consists of two strings of nucleotides, or bases (abbreviated A, C, G, and T), wound around each other. The bases composing DNA have specific binding capabilities: A always binds to T, and C always binds to G. These binding capabilities are useful for scientists to understand since, if the nucleotide sequence of one DNA strand is determined, complementary binding allows the sequence of other strand to be deduced.

In humans, DNA is organized into 24 structural units called chromosomes. Each chromosome consists of compacted coils of DNA. While much of this DNA has no known function (these stretches of DNA are conveniently referred to as spacer DNA or junk DNA), a significant portion of the DNA codes for genes.

Each gene provides the information necessary to produce a protein, which is responsible for carrying out cellular functions. The complement of proteins in an organism is very important, with diseases often manifesting when a protein does not function properly.

Why Sequence Genomes?  Why do we sequence non-human genomes?

One of the interesting things about biological organisms is their remarkable similarity at the molecular level, despite their obvious outward differences.

Many genes are found in morphologically different organisms despite the phylogenetic distance between them. Not only are these genes very similar in their DNA sequence composition; they also tend to perform the same functions.

By understanding the function of a gene in one organism, scientists can get an idea of what function that gene may perform in a more complex organism such as humans. The knowledge gained can then be applied to various fields such as medicine, biological engineering and forensics.

To understand how DNA is sequenced, you must first understand a little about the structure of DNA:

A segment of DNA, which is ordinarily double stranded, has a specific orientation, as it has a 5′ (read as “5 prime”) and a 3′ (”3 prime”) end. This can be simply thought of as a front and tail end to the DNA segment.
When DNA is synthesized in the lab, the two strands are separated and new bases are added to the 3′ end-thus DNA is assembled from the 5′ to 3′ end.

DNA cannot be synthesized from scratch. A short piece of DNA, called a primer, is required for the reaction to begin.
Primers are designed such that they are able to bind to the target DNA, the binding of which is the initiator for DNA synthesis.

DNA sequencing is accomplished by the Fredrick Sanger method (see the above diagram), for which he won his second Nobel Prize in 1980.
 

Below is a diagram of a non human DNA sequencing.. .the sequence of a cave bear:

The Human Genome Project

The HGP or Human Genome Project was a 13-year project by the U.S. Department of Energy and the National Institutes of Health. During.  The goals were to identify all the approximately 20,000-25,000 genes in human DNA, determine the sequences of the 3 billion chemical base pairs that make up human DNA, store this information in a genome databases, improve tools for data analysis, transfer related technologies to the private sector, and address the ethical, legal, and social issues that may arise from these type of projects.

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Meet my genome: 10 people release their DNA on the Web

Ten people today allowed their genetic maps to be publicly displayed on the Web in the name of research. The effort is part of Harvard Medical School's Personal Genome Project (PGP), which aims to create a large public database of human DNA to aid researchers in their quest to find the causes and cures for genetic maladies.   

The first 10 volunteers, dubbed the PGP-10, include project director and Harvard Medical School geneticist George Church; Harvard psychologist Steven Pinker; technology writer Esther Dyson; Duke University science editor Misha Angrist; Keith Batchelder, CEO of Genomic Healthcare Strategies in Charlestown, Mass.; Rosalynn Gill, founder of personalized health company Sciona in Aurora, Colo.; John Halamka, technology dean at Harvard Medical School; Stanley Lapidus, chairman and CEO of Helicos BioSciences Corp. in Cambridge, Mass.; Kirk Maxey, founder of the research biochemical company Cayman Chemical based in Ann Arbor, Mich.; and James Shirley, senior scientist at the Boston Biomedical Research Institute.The reason they signed up? "It wasn't so much a curiosity about my genome as a desire to be part of a group that is engaging a public dialogue about the issue of genetic privacy," volunteer Lapidus said during a press conference held at Harvard yesterday to announce the launch. 

Although all of the participants agreed to be identified, their genomes are not labeled by name. The data was published anonymously on the Personal Genome Project website. Info on their medical history, ancestry, and current meds was already available but not linked to specific participants. The researchers used blood or tissue samples to screen for genes related to diseases, such as Alzheimer's and breast cancer.Church explains in this Scientific American article how relatively inexpensive DNA sequencing technology works and why he believes this project has the potential to change the face of medical research.Dyson argues in Scientific American that privacy issues may be a concern but that it's overshadowed by the fear that insurance companies will refuse to provide coverage or will charge sky-high rates if aware that someone has a pre-existing genetic condition or risk of developing a certain disease. Interested in having your health history and genes published online for the benefit of science?  The project got approval this spring to expand the project to 100,000 people, and they're looking for volunteers.

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