Transplant Patients Could Live Free of Anti-Rejection Drugs

Scientists from the Lucile Packard Children’s Hospital and the Stanford University School of Medicine have identified a pattern of gene expression shared by a small group of patients who beat the odds and remained healthy for years without medication, after undergoing Organ transplant.

The findings made by Minnie Sarwal, MD, PhD, a pediatric nephrologist at Packard Children’s is a major advantage in organ transplantation treatment. Transplant recipients who share the same pattern of genes but are still on conventional medication may be able to reduce or eliminate their lifelong dependence on immunosuppressive drugs. The study may also help physicians determine how best to induce acceptance, or tolerance, of donor organs in all transplant patients, regardless of their gene expression profiles.

Although the anti-rejection medications, known as immunosuppressants, tamp down the immune system enough to permit lifesaving organ transplants, their benefits come at a price. They also quash the body’s natural response to dangerous invaders, such as bacteria and viruses, and to rogue cancer cells. Transplant physicians prescribing immunosuppressants to their patients walk a fine line between avoiding organ rejection and increasing the risk of infection and cancer

The researchers used microarray, or gene chip, technology to compare gene expression patterns in blood samples from 16 healthy volunteers with those from three groups of adult kidney transplant recipients from the United States, Canada and France

IS Microarray facing the DOOM….Invading microarray turf……….

ChIP-sequencing (ChIPSeq) – a combination of chromatin immunoprecipitation and next-generation, or parallel, sequencing. The feat was performed “with a speed and precision that goes beyond what has been achieved with previous technologies,” comments University of Washington geneticist Stanley Fields, in an accompanying essay in Science.

hIP is a well-established lab technique to identify those specific sites where proteins latch onto the DNA. Cells are treated with a chemical to fossilize the links between DNA and protein, the chromatin is then isolated, the DNA broken up, and the attached proteins immunoprecipitated. Finally, the DNA stuck to the protein can be released and analyzed. Until now, the most high-throughput application of this technique involved using microarrays containing thousands of gene spots able to identify binding sites for transcription factors and the like.

Next-Generation Sequencing Invades Microarray Turf By Kevin Davies June 14, 2007 | Two new papers unveil a new dimension to commercial next-generation sequencing applications – one that could potentiallypose a threat to more-established microarray technologies. Using theGenome Analyzer from Illumina/Solexa, two groups working independentlyhave been able to map the locations across the genome where a specific
DNA-binding protein latches onto the DNA.

ChIPSeq is a cost-effective alternative to microarray methods, with a significant upside. “Other ultrahigh-throughput sequencing platforms, such as the one from 454 LifeSciences, could also be used to assay ChIP products, but whatever sequencing platform is used, our results indicate that read numbercapacity and input ChIP DNA size are key parameters,” Johnson et al. writes.ChIPSeq might be an order of magnitude cheaper than microarray alternatives, with the eight flow cell lanes in theGenome Analyzer offering excellent design flexibility. Fewer materialsare required, and the method can be applied to any organism – it is not restricted to available gene arrays.

Changing ChIPs
The advantages of ChIPSeq over ChIP-chip include the ability to interrogate the entire genome rather than just the genesrepresented on a microarray. (For example, Johnson et al. point out thata similar experiment using Affymetrix-style microarrays would requireroughly 1 billion features per array.) There is also the benefit of
sidestepping known hybridization complications with microarrayplatforms. “Perhaps most usefully,” writes Fields, “ChIPSeq canimmediately be applied to any of those [available] genomes, rather thanonly those for which microarrays are available.”

New horizons ahead

Its been two years since I have been with Ocimum Biosolutions ,the India HQ company serving bioinformatics and microarray market in US with office in Indianapolis and another lab in netherlands, I have been working in the business development of the company’s microarray arm in US which was acquired from MWG biotech, we had tasted success,

I have been busy lately as I have resigned from the company now that explains the absence of any new posts for few weeks now. Ocimum is one of the unique bioinformatics oraganization to make its mark in this industry, because unlike many new companies .  it was started by people with no biological background but has been selected as one of fastest growing life science company in India and Asia many times by Deloitte ranking and many other independent agencies. apart from winning awards from government and even a funding fro world bank. So what makes them so sucessful

Ocimum offers services in bioinformatics oligo microarray and R&D but its the presence of its labs near to its customers and the company’s software development division housed at Hyderabad India that makes the difference. Coupled with India’s cost efficiency, it has many advantages

Bioinformatics industry is going through a face of consolidation, marketed in India in its infancy as a glamorous field to work many who jumped into the fray has burned their hands. and industry analysis in 2000 predicted the industry to become a 100 billion worth by 2004, yet even in 2007, majority of the biologists are yet to warm upto the industry in a way predicted by the software pundits

Research and Markets (http://www.researchandmarkets.com/reports/c59429) has announced the addition of “Biomed Outsourcing Report: An Overview of the Life Sciences and Outsourcing Landscape in India: Spotlight on Bangalore” to their offering.

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

Genographic Project

National geographic has got some very good presentations to  overview of genetics, a good presentation called genographic project  i came across it while writing my article on transposons and the new sequencing project of opposum

Search Engine for Life science Data

NextBio is a web-based scientific data search engine that offers instant access, search and collaboration across a vast repository of life sciences information

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

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

i-Kode to take control of your scientific mail and email.

 Practicallly I use the Foward feature of GMAIL to send my mails to the my corporate email address this I can make sure that no has my Id but also When I leave the company I still get to have acess to all the newsletters i received and I can even forward it to the new email address if need to

but I still thought or writing about www.i-kode.com as its a new service and has a lot features too and obviosly its freee and you can even win price too, UMM sound too good ha

you can select from a list available scientific newsletters and search for new one or add your own new

The i-kode.com™ service lets you take control of your scientific mail and emails journals and online magazines in one place.

Get the mail you want
• Don’t get the mail you don’t want
• Add yourself to mail lists
• Remove yourself from mail lists
• Find Vendors of key products and services
• Manage your contact with Academic Societies and Journals
• When you move, update them all in less than a minute

You can read an article about i-kode.com and see what other scientists think of our service here or you can read our latest press release.

Latest! Online File Storage and Spam-free Secure Email Inbox.

You can store files online in your own secure Document Store or receive Spam-free Email without interference from spam filters.

And ofcourse Rewards when you refer colleagues

Read an article on OBBEC magazine http://www.obbec.com/lscbio/

Moleculare Frontiers Intiative for researchers of future

Molecular Frontiers is a global effort to promote the understanding and appreciation of molecular science in society

THe initiative offers an arena for budding biologists and life science researchers of the future. Wish them all the best. Some of the interesting aspects are

Catalytic Forum

think tank to discuss and analyze current scientific developments with researchers from all over the world.

MoleClues

A web site where young people are invited to explore the realm of molecular science.

 

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

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 22^nd 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.