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.

Even the hopeful US president jumps on Web2.0 bandwagon

 Barack Obama looks to be diving into this whole “Web 2.0” thing head first, what with his own Facebook profile, Flickr account, and YouTube account. In addition to all this stuff, he also has my.barackobama.com, a social networking type site for his supporters to create profiles, network, and make blogs all about how great Barack Obama is. Meanwhile Former Senator John Edwards is also facing setback in his blogs when two of his former bloggers bloggers Amanda Marcotte and Melissa McEwan are asked to step down for posting blogs that upset the Christian community and Bush supporters

So whats preventing our young scientists from going web2.0 and using blogs, Business networking sites such as Linkedin has given much required value to the business commnity compared to stes like Orkut whch is for the liter side of networking althought even orkut also offers communities too , shouldnt it be time to start one for the scientific community , there are few small steps in this way such as

http://www.cos.com   Community of Science (COS) is the leading global resource for hard-to-find information critical to scientific research and other projects across all disciplines.

http://labcircle.net/  Networking – the new LabCircle.net makes it possible. It is where the global laboratory, analysis, biotech, chemistry and pharma industry meets. Based on the theory of “six degrees of separation”, the club allows members to maintain their personal networks, generate new contacts and actively participate in various forums to exchange information, experiences and opinions.

http://www.scientistsolutions.com/ an international life science forum

http://linkedin.com/  reach a key decision maker and find your colleague or someone working in your field

google video publish your expertise in tackling the problems facing while operating your protolcs or project work , tips and tricks what ever it is all you need is a webcam

James from Research Information Network UK has commented on a previous blog I had published about an article on how researchers fish for information ,

Early in 2006, the Research Information Network commissioned a study as part of its work to promote better arrangements for researchers to find out what information resources relevant to their work are available, where these are, and how they may have access to them. The work has now been concluded, and the report from the study is attached below.

http://www.rin.ac.uk/researchers-discovery-services 

Surprisingly many people still do not know hoe to use the search features of google yet

Microaray and Genomcis consortiums have now started to use more collaborating tools such as wikipedia and wiki pages. few good examples are

https://daphnia.cgb.indiana.edu/83.html and http://en.wikiversity.org/wiki/Portal:Life_Sciences  and http://www.e-biosci.org/

Microarray for Catharanthus Roseus

In the recently concluded Bio-Asia 2007 meeting  Ocimum Biosolutions has entered into an accord with a scientist for developing microarray  on the medicinal plant Catheranthus Roseus. 

 

Catharanthus roseus is known as the common or Madagascar periwinkle, though its name and classification may be contradictory in some literature because this plant was formerly classified as the species Vinca rosea, Lochnera rosea and Ammocallis rosea. Furthermore, lesser periwinkle (Vinca minor) may also be called common periwinkle. Both species are also known as myrtle.

Western researchers finally noticed the plant in the 1950’s when they learned of a tea Jamaicans were drinking to treat diabetes. They discovered the plant contains a motherlode of useful alkaloids (70 in all at last count). Some, such as catharanthine, leurosine sulphate, lochnerine, tetrahydroalstonine, vindoline and vindolinine lower blood sugar levels (thus easing the symptoms of diabetes). Others lower blood pressure, others act as hemostatics (arrest bleeding) and two others, vincristine and vinblastine, have anticancer properties. Periwinkles also contain the alkaloids reserpine and serpentine, which are powerful tranquilizers.

Life Sciences Turning to YouTube- Web2.0 gaining momentum among scientists

I am an ardent follower of all things web2.0 the fact that I have more than 10000 bookmarks catagorized and formatted -big thanks to social bookmarking websites. So its exciting to see more scientists start using web2.0 products such as youtube, google video, social bookmarking sites like furl, stumbleupon , netvouz, del-ic-ious and blogs and wikipedia. The BioIt magazine has published the following article on the trend

Salvatore Salamone January 25, 2007 | Life scientists are eagerly taking advantage of a variety of next-generation “Web 2.0” Internet features to learn, collaborate, and interact more easily.

Wikipedia, for example, has demonstrated how online collaboration can quickly gather a vast amount of information from subject matter experts. Noting Wikipedia’s success, some companies are setting up internal wikis for researchers to share their insights and knowledge. Blogging and specialized social networking sites are also gaining ground among life scientists.

What might not be so obvious is the role another Web 2.0 site – YouTube — is already playing in the life sciences. YouTube allows people to post and easily share videos. Some of the user-generated content is very professional, much of it is appallingly amateurish.

Life science educators, researchers, and even vendors are using the site for a variety of purposes. Some educators have produced short videos illustrating or explaining different scientific concepts. These include molecular visualizations of DNA wrapping and DNA transcription, as well as National Human Genome Research Institute Director Francis Collins talking about advances in personal genomics.

Some researchers have produced short videos that show others how to do certain lab or computer analysis procedures. Examples of these videos includes this demo from the National Center for Biotechnology Information.

Most of these videos are short (1-2 minutes) and, at best, illustrate a simple point. But they do give you an idea about the potential ways such videos might be used in the future. For instance, a new lab technique could be videotaped, posted to YouTube (or a similar site), and a link sent to all researchers who could then view the procedure whenever they needed to learn the methodology.

Some of the slickest YouTube videos, in general and specifically in the life sciences, come from vendors, which are jumping on the highly touted trend of viral marketing trend — the idea that people who view these videos will pass them (or links to them) along to friends. The power of this word-of-mouth marketing was evidenced last November when BBC News reported that a video featuring the so-called Star Wars Kid was viewed 900 million times — more viewers than any TV show or event in history. (In contrast, the highest rated program of all time, the last episode of Mash, had 105 million viewers.)

Vendors in all fields are eager to capitalize on this viral marketing phenomenon. And the life science vendors on YouTube seem to have quickly learned the key to getting their videos passed along. That key: The funnier or more creative the spot, the better, according to a recent article in Inc. Magazine.

For example, a YouTube video called The DNA-ting Game, which is a takeoff on the old Dating Game show complete with campy 70s style décor, humorously plugs the power and benefits of the Caliper Life Sciences LabChip 90 Automated Electrophoresis System.

Similarly, a series of Agilent videos show how a cocky researcher is able to quickly complete experiments using the company’s 2100 Bioanalyzer or its Total RNA Isolation Mini Kit. (Examples of these videos can be found here and here.)

All of these efforts – including those from the educators, researchers, and vendors – are the work of early adopters of the newer technologies incorporated into a site such as YouTube. And all of the examples give a glimpse of the potential use researchers and life science organizations can get out of this technology to quickly produce instructional and training videos that can then easily be shared with colleagues.

Email Salvatore Salamone.

Subscribe to Bio-IT World magazine.

The genetic detective – Pharmacogenomics and personalized medicine

 THe following interesting study was published at  article is from royal society of chemistry website

A selective way to detect genetic variations could help scientists develop personalised medicine.

“[This method] should allow several thousands of single nucleotide variations, at different positions within a person’s genome, to be analysed in parallel.”
– Andreas Marx

Variations in our genetic make-up are responsible for some diseases and are known to be major players in an individual’s predisposition to drug side effects. Convenient and rapid detection of these variations could help doctors to adapt therapies for each patient. This idea has prompted Andreas Marx and colleagues at the University of Konstanz, Germany, to devise a high-throughput technique to detect variations between single nucleotides in genetic sequences. 

Marx’s system uses a microarray of oligonucleotide probes to analyse the DNA. The probes are attached by their 5′ end to a glass surface and treated with an enzyme, a DNA polymerase. The enzyme can add further nucleotides to the unattached ends of the probes. If a probe’s terminal base complements the DNA under investigation, the oligonucleotide chain continues to form; if the base is a mismatch, the chain does not extend further.

A microarray of oligonucleotide probes

Oligonucleotide probes are used to analyse DNA to detect variations between single nucleotides

‘Conventional enzyme-based strategies for detecting single nucleotide variations often lack sufficient selectivity,’ said Marx. The oligonucleotide chain can continue to form even when there is a mismatch. The team was able to increase the selectivity by modifying the terminal nucleotide of the probe with a methoxymethylene group. 

In human DNA, approximately one single nucleotide variation occurs per 1000 bases. This method ‘should allow several thousands of single nucleotide variations, at different positions within a person’s genome, to be analysed in parallel,’ said Marx. ‘This is still a challenging task that none of the present systems is able to achieve reliably.’

Oliver Seitz, an expert in DNA diagnostics at Humboldt University in Berlin, Germany, believes that Marx’s work could have a significant impact in developing diagnostic probes for DNA. ‘The method brings high specificity to the high-throughput format,’ said Seitz. ‘The challenge now is to combine multiplex analysis with specificity and signal amplification in a miniaturised format, to enable point-of-care diagnostics.’

Alison Stoddart

References

Increased single nucleotide discrimination in arrayed primer elongation by 4′C-modified primer probes

J Gaster, G Rangam and A Marx, Chem. Commun., 2007

DNA microarray–based analysis may be useful for assessing the risks and benefits of hormone therapy

Hormone-replacement therapy influences gene expression profiles and is associated with breast-cancer prognosis. The US FDa has apprved use of two new microarrays for clinical decision making. The US Food and Drug Administration (FDA) encourages the development of new technologies such as microarrays which may improve and streamline assessments of safety and the effectiveness of medical products for the benefit of public health. The FDA anticipates that these new technologies may offer the potential for more effective approaches to medical treatment and disease prevention and management. One of the new application for microarrays apart from use in cancer treatment could be in Hormone replacement therapy. A study has been publoished using microarrays to identify modifications in the gene expression profile of the ocular posterior segment in ovariectomized (OVX) mice with and without substitutive estradiol therapy. some of the other studies can be viewd at

http://www.biomedcentral.com/1741-7015/4/16

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1555602

Microarrays for taxonomics studies

The develpment of barcode microarray may be a subject of debate , but it may hel in transgenomic studies, and would help in finding new avenues for use of microarrays

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