Gene Logic sells in genomics division

It hardly a week I have wrote about acquisition and mergers , it seems the rain is noit going to stop any time soon, the latest one , to give away the home plate is Genelogic agreeing to sell its genomics division to India HQ Ocimum Biosolutions subject to the authorization of the transaction at a special meeting of shareholders of Gene Logic.

This is a transforming event of significant strategic proportion,” said Charles L. Dimmler, III, President and Chief Executive Officer of Gene Logic.

Genelogic bought its preclinical division from TherImmune, a Gaithersburg company, in April 2003 for $51 million which was sold to Bridge Pharmaceuticals for $15 Million,

Gene Logic Inc said it agreed to sell its Genomics assets to Ocimum Biosolutions Ltd for $10 million in cash. Under the terms of the Ocimum sale agreement, Gene Logic retains full rights in perpetuity to utilize the existing information data bases of its former Genomics business as key elements in building its emerging drug repositioning and development business. Furthermore, the Company will retain specified assets related to molecular diagnostics and will continue to explore strategic alternatives for these assets

The sale is part of the Genelogic new strategy to focus on to build drug repositioning and development business which was decided last year.

Ocium will assume certain liabilities associated with the Genomics assets and business and will pay Gene Logic $7 million at closing and $3 million payable in a promissory note due 18 months from closing.

The purchase includes Gene Logic’s Knowledge Products business including the The BioExpress® System a continually growing genomic database of gene expression data and associated clinical information from over 18,000 human and animal tissues and cell line samples. ToxExpress® a toxicogenomics reference database.

Ocimum will continue to operate the business out of the current state-of-the-art laboratory facility of Gene Logic in Gaithersburg, Maryland.

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Toxicogenomics can change face of clinical trials

“Genomics is only the start. Proteomics has been around for years and metabonomics is an up and coming important technology, both of which are complimentary to genomics. But still I think that genomics will be the most successful and most predictive of all these technologies.” Dr Phil Hewitt  Head of Toxicogenomics at Merck.

Meanwhile Gene Logic Provides the FDA with Access to Toxicogenomics Data and Analysis Systems for Reviewing Voluntary Genomic Data Submissions, and Iconix Released On-Line Version of World’s Largest Toxicogenomic Reference Database ,

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 clinical diagnostics in hand-foot-and-mouth disease

The following study was published in journal of clinical microbiology,

Combining Multiplex Reverse Transcription-PCR and a Diagnostic Microarray To Detect and Differentiate Enterovirus 71 and Coxsackievirus A16

Tsan-Chi Chen,1,2 Guang-Wu Chen,3 Chao Agnes Hsiung,4 Jyh-Yuan Yang,5 Shin-Ru Shih,6 Yiu-Kay Lai,2 and Jyh-Lyh Juang1* Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan,1 Department of Life Science and Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan,2 Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan,3 Biostatistics and Bioinformatics, National Health Research Institutes, Miaoli, Taiwan,4 Center for Disease Control, Department of Health, Taipei, Taiwan,5 Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan6

Received 18 November 2005/ Returned for modification 16 January 2006/ Accepted 7 April 2006

Cluster A enteroviruses, including enterovirus 71 (EV71) and coxsackievirus A16 (CA16), are known to cause hand-foot-and-mouth disease (HFMD). Despite the close genetic relationship between these two viruses, EV71 is generally known to be a more perpetuating pathogen involved in severe clinical manifestations and deaths. While the serotyping of enteroviruses is mostly done by conventional immunological methods, many clinical isolates remain unclassifiable due to the limited number of antibodies against enterovirus surface proteins. Array-based assays are able to detect several serotypes with high accuracy. We combined an enterovirus microarray with multiplex reverse transcription-PCR to try to develop a method of sensitively and accurately detecting and differentiating EV71 and CA16. In an effort to design serotype-specific probes for detection of the virus, we first did an elaborate bioinformatic analysis of the sequence database derived from different enterovirus serotypes. We then constructed a microarray using 60-mer degenerate oligonucleotide probes covalently bound to array slides. Using this enterovirus microarray to study 144 clinical specimens from patients infected with HFMD or suspected to have HFMD, we found that it had a diagnostic accuracy of 92.0% for EV71 and 95.8% for CA16. Diagnostic accuracy for other enteroviruses (non-EV71 or -CA16) was 92.0%. All specimens were analyzed in parallel by real-time PCR and subsequently confirmed by neutralization tests. This highly sensitive array-based assay may become a useful alternative in clinical diagnostics of EV71 and CA16.


* Corresponding author. Mailing address: Division of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 350, Taiwan. Phone: 886-37-246-166, ext. 35308. Fax: 886-37-586-459. E-mail: juang@nhri.org.tw.


Journal of Clinical Microbiology, June 2006, p. 2212-2219, Vol. 44, No. 6
0095-1137/06/$08.00+0     doi:10.1128/JCM.02393-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Rapid genotyping of methicillin-resistant Staphylococcus aureus (MRSA) using OLigonucleotide microarrays

Published by 

1Institute for Medical Microbiology and Hygiene, Faculty of Medicine ‘Carl Gustav Carus’, Technical University of Dresden, Dresden and 2Clondiag Chip Technologies GmbH, Jena, Germany
ABSTRACT
This study evaluated a DNA oligonucleotide array that recognised 38 different Staphylococcus aureus targets, including all relevant resistance determinants and some toxins and species-specific controls. A new method for labelling sample DNA, based on a linear multiplex amplification that incorporated biotin-labelled dUTP into the amplicon, was established, and allowed detection of hybridisation of the amplicons to the array with an enzymic precipitation reaction. The whole assay was validated by hybridisations with a panel of reference strains and cloned specific PCR products of all targets. To
evaluate performance under routine conditions, the assay was used to test 100 methicillin-resistant S. aureus (MRSA) isolates collected from a university hospital in Saxony, Germany. The results showed a high correlation with conventional susceptibility data. The ermA and ermC macrolide resistance genes were found in 40% and 32% of the isolates, respectively. The most prevalent aminoglycoside resistance gene was aphA3 (57% of the isolates), followed by aacA–aphD (29%) and aadD (29%); tet genes, mupR
and dfrA were rare. There were no isolates with van genes or genes involved in resistance to quinupristin–dalfopristin. Enterotoxins were detected in 27% of the isolates. Genes encoding Panton– Valentine leukocidin, toxic shock syndrome toxin and exfoliative toxins were not found. The DNA array facilitated rapid and reliable detection of resistance determinants and toxins under conditions used in a routine laboratory and has the potential to be used for array-based high-throughput screening.

complete article at http://www.clondiag.com/pub/CMI-2005_Genotyping%20of%20MRSA.pdf

Similar studies are also published at

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1393086

Microarray for Clinical Diagnostics- For detecting sepsis

http://www.biologynews.net/archives/2006/12/19/gene_chip_technology_shows_potential_for_identifying_lifethreatening_blood_infection.html

Right now there’s no rapid way to diagnose sepsis, a fast-moving blood infection that is a leading cause of death in hospital intensive care units. The illness unleashes a powerful inflammatory response that can quickly overwhelm the body, causing organ failure and death, often within days.

New research now suggests that doctors one day could quickly distinguish sepsis from widespread non-infectious inflammation based on genetic profiles of patients’ blood. Testing this method in mice, researchers at Washington University School of Medicine in St. Louis found the profiles could accurately discriminate between the two conditions 94 percent of the time. The molecular profiles measure differences in patterns of gene expression that are unique to sepsis vs. non-infectious inflammation.

The researchers used microarrays, also called gene chips, to analyze patterns of gene expression in the mice. The same technology is already used by doctors to diagnose breast cancer and predict a patient’s response to various chemotherapy drugs, but this is the first time researchers have attempted to use gene chips to distinguish sepsis from non-infectious inflammation.

DNA Analysis Could Boost Accuracy Of Thyroid Tests

Source: http://www.medicalnewstoday.com/sections/genetics/

By fine-tuning “fine-needle aspiration” biopsies with a super-fast genetic microarray technology, a team of surgeons from NewYork-Presbyterian Hospital/Weill Cornell Medical Center in New York City says they can greatly enhance the accuracy of these tests.

“For patients with worrisome thyroid nodules, this means better information on whether the nodule is malignant or benign. That should help them and their doctors make better decisions as to what treatment they’d like to pursue,” explains senior researcher Dr. Thomas J. Fahey III, associate professor of surgery and Frank Glenn Faculty Scholar in Surgery at Weill Cornell Medical College, and associate attending surgeon at NewYork-Presbyterian Hospital/Weill Cornell Medial Center in New York City.

In the study, the team created microarray-generated “gene expression profiles” from fine-needle aspirates by comparing the expression of thousands of genes from both cancerous and benign thyroid tissues. This process ended in a grouping of 25 differently expressed genes that helped distinguish malignant from benign growths.

“We next tested the accuracy of these patterns using 22 fine-needle aspirate samples from benign or malignant thyroid nodules,” Dr. Lubitz explained.

“In all but one case, the microarray test agreed completely with the results of extensive histological analysis in the lab,” she said.

According to the researchers, a move from histological to microarray analysis of thyroid aspirates could impact anywhere from 5 to 25 percent of patients undergoing this kind of diagnosis — giving them a better grasp of whether they might require surgery, for example.

Cost remains a factor, with a single microarray screen currently totaling about $500. “We anticipate, however, that as this technology becomes more widespread and improves, the price per test will fall much lower,” Dr. Fahey says.

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