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

DNA computer for diagnostics

REsearchers at columbia university medical centre newyork have developed a DNA-based computer that could lead to faster and more accurate diagnosis of west nile virus and bird flu.

It is the first “medium -scale integrated molecular circuit” it is the most powerful comuting device of its type.

Joanne Macdonald a virologist at columbia’s dapertment of medicine lead the team that developed MAYA-II (molecular arrays of YES and AND logic gates) a computer whose circuits consists of DNA instead of silicon . These computers can be used in fluids such as a a sample of blood in the body and make decisions at the level of single level

 In 2003  Israeli scientists have devised a computer that can perform 330 trillion operations per second, more than 100,000 times the speed of the fastest PC.

Researchers from the Weizmann Institute of Science in Rehovot, Israel, unveiled a programmable molecular computing machine composed of enzymes and DNA molecules instead of silicon microchips,  the single DNA molecule that provides the computer with the input data also provides all the necessary fuel.

Think of DNA as software, and enzymes as hardware. Put them together in a test tube. The way in which these molecules undergo chemical reactions with each other allows simple operations to be performed as a byproduct of the reactions. The scientists tell the devices what to do by controlling the composition of the DNA software molecules. It’s a completely different approach to pushing electrons around a dry circuit in a conventional computer.

To the naked eye, the DNA computer looks like clear water solution in a test tube. There is no mechanical device. A trillion bio-molecular devices could fit into a single drop of water. Instead of showing up on a computer screen, results are analyzed using a technique that allows scientists to see the length of the DNA output molecule.

Notes to a young computational biologist

Bosco Ho a Postdoctoral scholar writes an excellent post about Notes to a young computational biologist   .Bosco puts down his postdoc years of experience into facts  that are relevant to not only those just starting out in computational biology but for other experince people too

his post is published at http://boscoh.com/protein/notes-to-a-young-computational-biologist

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.

Online Data sharing for scientists

Brent Edwards director of the Starkey Hearing Research Center in Berkeley, California, who blogs on innovation in science is writing his blog about an article on Nature magazine on online data sharing. Brent comments about the potential of new online data sharing sites such as Swivel and IBM’s Many Eyes . Accoding to the Nature reprt some scientists are already using these new tools to share sequence and microarray data. The potential value from scientists openly sharing their data is huge, possibly akin to the value provided by open-source software development.

Once data are uploaded to these sites (which are still being tested), people can reanalyse the numbers, mix them with other data and visualize them in different ways. Swivel focuses on letting users combine data sets, with some basic ways to present the results such as scatter graphs and bar charts. Many Eyes allows users to generate more complicated graphs such as network diagrams, which depict nodes and connections within networks, and treemaps, which display data as groups of nested rectangles

Despite the availability of many software solutions at the dispoal of scientists many of them still write their own code for bioinformatics and statistical analysis, perhaps the next frontier that might help the comunity could be the development of Firefox like software, that offers some basic functions free of cost, additional function can be bought or acquired free of cost as add ons form researchers, such a move would benefit researchers and students alike,

There are sure many more data sharing website like http://www.gotomyfiles.com, http://www.xdrive.com, http://www.ibackup.com, but these are more of a data storage sites, and these does not offer the level of document collaboration features required by a life science researcher

Then there is few other sites like microsofts foldershare and others that offer features such as remote PC access gotomyPC VNC and webex are a few exmaple of this stable. some of these also allows to by pass even a firewall such as foldershare and can pose serious security risks to data and pc if handled improperly

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.

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

Microarray based Bio Detection Technologies

DNA microarray detection of antimicrobial resistance genes in diverse bacteria

Study published at http://cat.inist.fr/?aModele=afficheN&cpsidt=17459830
High throughput genotyping is essential for studying the spread of multiple antimicrobial resistance. A test oligonucleotide microarray designed to detect 94 antimicrobial resistance genes was constructed and successfully used to identify antimicrobial resistance genes in control strains. The microarray was then used to assay 51 distantly related bacteria, including Gram-negative and Gram-positive isolates, resulting in the identification of 61 different antimicrobial resistance genes in these bacteria. These results were consistent with their known gene content and resistance phenotypes. Microarray results were confirmed by polymerase chain reaction and Southern blot analysis. These results demonstrate that this approach could be used to construct a microarray to detect all sequenced antimicrobial resistance genes in nearly all bacteria.

Genetically Guided Treatment For Cancer

Two critical characteristics of breast cancer that are important to treatment can be identified by measuring gene expression in the tumor, a research team led by scientists at The University of Texas M. D. Anderson Cancer Center reports in Lancet Oncology online.

Researchers developed and validated a new genomic microarray test that identifies whether a tumor’s growth is fueled by the female hormone estrogen and the role of a growth factor receptor known as HER-2 that makes a tumor vulnerable to a specific drug.

“This is one important step towards personalized diagnosis and treatment planning based on an integrated genomic test of an individual tumor,” said senior author W. Fraser Symmans, M.D., associate professor in the M. D. Anderson Department of Pathology.

The Lancet Oncology paper results are the latest in an effort by the research team to develop a single test to quickly and efficiently determine the characteristics and vulnerabilities of a patient’s breast cancer and ultimately to guide treatment.

About 70 percent of breast cancers are estrogen-receptor positive and another 15 to 25 percent are human epidermal growth factor receptor-2 (HER-2) positive. Each receptor status requires different types of treatment.

“This moves us closer to developing an integrated single genomic test that could estimate the risk of cancer relapse after surgery, determine the ER and HER2 receptor status, and also gauge the sensitivity of the tumor to hormone therapy and chemotherapy,” says Lajos Pusztai, M.D., Ph.D., associate professor in the M. D. Anderson Department of Breast Medical Oncology, and team leader with Symmans.

Last fall, the group published a study showing that a genomic microarray test can also predict a patient’s response to chemotherapy. They also presented a paper in December showing that another genomic index predicts how an ER-positive patient will respond to hormonal therapy.

The study was funded by the National Cancer Institute, the Breast Cancer Research Foundation and the Goodwin Foundation.

Co-authors with Symmans and Pusztai are: first author Yun Gong, M.D., and Nour Sneige, M.D., of the M. D. Anderson Department of Pathology; Kai Yan, Keith Anderson, and Kenneth Hess, of the M. D. Anderson Department of Biostatistics; Feng Lin, M.D., Vicente Valero, M.D., Daniel Booser, M.D., Jaime Mejia, M.D., and Gabriel Hortobagyi, M.D., of the M. D. Anderson Department of Breast Medical Oncology; Christos Sotiriou, M.D., Ph.D., Institut Jules Bordet, Brussels, Belgium; Fabrice Andre, M.D., of Institut Gustave Roussy, Villejuif, France; Frankie Holmes, M.D., John Pippen Jr., M.D., and Svetislava Vukelja, M.D., of U.S. Oncology-Texas Oncology; Henry Gomez, M.D., of the Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru; and Luis Barajas, M.D., Departmento de Ginecologia Oncologica, Instituto Mexicano del Seguro Social, Guadalajara, Mexico.

Contact: Scott Merville
University of Texas M. D. Anderson Cancer Center

The Insider -Code inside Codes : Scientists Discover Parallel Codes in Genes

Researchers from The Weizmann Institute of Science report the discovery of two new properties of the genetic code. Their work, which appears online in Genome Research, shows that the genetic code—used by organisms as diverse as reef coral, termites, and humans—is nearly optimal for encoding signals of any length in parallel to sequences that code for proteins. In addition, they report that the genetic code is organized so efficiently that when the cellular machinery misses a beat during protein synthesis, the process is promptly halted before energy and resources are wasted.

DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.

“Our findings open the possibility that genes can carry additional, currently unknown codes,” explains Dr. Uri Alon, principal investigator on the project. “These findings point at possible selection forces that may have shaped the universal genetic code.”

The genetic code consists of 61 codons—tri-nucleotide sequences of DNA—that encode 20 amino acids, the building blocks of proteins. In addition, three codons signal the cellular machinery to stop protein synthesis after a full-length protein is built.

While the best-known function of genes is to code for proteins, the DNA sequences of genes also harbor signals for folding, organization, regulation, and splicing. These DNA sequences are typically a bit longer: from four to 150 or more nucleotides in length.

 

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