Biotechnology Blog

Genomics & Proteomics facilities @VIMTA Life Sciences, Hyderabad, India.

noreply@blogger.com (Arrayinformatics) — Sat, 31 Mar 2007 08:06:00 +0000

Genomics/Proteomics facilities @VIMTA Life Sciences, Hyderabad, India.

VIMTA is offering multidisciplinary contract research and testing services. Recently VIMTA established Advanced Molecular Biology lab with Affymetrix Microarray platform, Proteomics, DNA sequencing, SEQUENOM platform & Custom peptide synthesis facilities with the main intention to offer contract research services to the scientific community with the latest advancements in Molecular Biology.

VIMTA is having the Affymetrix microarray platform which is the most reliable and reproducible in results when compared to cDNA Microarray. VIMTA is offering both the Expression and SNP Genotyping services using Affymetrix platform.

VIMTA work closely with the clients in a professional and confidential manner. VIMTA's client list includes academic and commercial institutions from around the world. Quality in the work and confidentiality in the results is VIMTA's motto.

For more information regarding the services, please mail to: ravi.chilukoti@vimta.com

or

VIMTA LABS LTD, Life Sciences Facility,
Plot No.5, SP Biotech Park,
Genome Valley,
Shameerpet,Hyderabad-500078
Phone (Off): 040-39 84 84 84 Ext: 4302/4215/4207

Human Genome CGH Oligo Microarray Kit

noreply@blogger.com (Arrayinformatics) — Fri, 04 Feb 2005 07:34:00 +0000

Human Genome CGH Oligo Microarray Kit

Agilent Technologies has introduced its Human Genome CGH Microarray and CGH Analytics software designed to help cancer biologists and cytogeneticists study genomic alterations in cancer. Comparative genomic hybridization (CGH) is used to study the chromosomal changes that frequently occur in cancer....

Human Genome Survey Microarray

noreply@blogger.com (Arrayinformatics) — Fri, 04 Feb 2005 07:27:00 +0000

Applied Biosystems has announced the release of the Human Genome Survey Microarray V2.0 for use with the Applied Biosystems Expression Array System, a component of Applied Biosystems' comprehensive solution for gene expression analysis that allows researchers to easily move from whole-genome analysis to single gene validation.

Nanotechnology: 'Buckypaper' from coaxial nanotubes

noreply@blogger.com (Arrayinformatics) — Fri, 04 Feb 2005 07:19:00 +0000

Genomics/Proteomics facilities @VIMTA Life Sciences, Hyderabad, India.

Please Contact us:
VIMTA LABS LTD, Life Sciences Facility,
Plot No.5, SP Biotech Park,
Genome Valley,
Shameerpet,Hyderabad-500078
Phone (Off): 040-39 84 84 84 Ext: 4302/4215/4207

For more information regarding the services, please mail to: ravi.chilukoti@vimta.com

BRET Technique: Monitoring modification

noreply@blogger.com (Arrayinformatics) — Mon, 17 Jan 2005 04:08:00 +0000

Bioluminescence resonance energy transfer (BRET) is a new technique that can be used to detect in situ changes in protein ubiquitylation.

"Ubiquitylation is a reversible post-translational modification that has important roles in processes such as protein degradation and intracellular signalling. Yet, despite a growing interest in ubiquitylation, a tool for studying the dynamics of this process has been lacking. Now though, in Nature Methods, Bouvier and colleagues describe a technique that can be used to detect in situ changes in protein ubiquitylation. ....."

An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis

noreply@blogger.com (Arrayinformatics) — Mon, 10 Jan 2005 06:12:00 +0000

An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis

Interesting article on cross-species gene-expression in NATURE. Using advanced gene targeting methods, generating mouse models of cancer that accurately reproduce the genetic alterations present in human tumors is now relatively straightforward. The challenge is to determine to what extent such models faithfully mimic human disease with respect to the underlying molecular mechanisms that accompany tumor progression. Here we describe a method for comparing mouse models of cancer with human tumors using gene-expression profiling. We applied this method to the analysis of a model of Kras2-mediated lung cancer and found a good relationship to human lung adenocarcinoma, thereby validating the model. Furthermore, we found that whereas a gene-expression signature of KRAS2 activation was not identifiable when analyzing human tumors with known KRAS2 mutation status alone, integrating mouse and human data uncovered a gene-expression signature of KRAS2 mutation in human lung cancer. We confirmed the importance of this signature by gene-expression analysis of short hairpin RNA−mediated inhibition of oncogenic Kras2. These experiments identified both a pattern of gene expression indicative of KRAS2 mutation and potential effectors of oncogenic KRAS2 activity in human cancer. This approach provides a strategy for using genomic analysis of animal models to probe human disease.

A gene highly expressed in tumor cells encodes novel structure proteins

noreply@blogger.com (Arrayinformatics) — Tue, 04 Jan 2005 10:34:00 +0000

"We isolated several related but distinct cDNA clones encoding novel structure proteins (NSP) when screening a cDNA library. Analysis revealed that these cDNAs and several similar ESTs in the public databases are derived from a single gene of 17 exons that span a minimum of 227-kb region. ...."

Cross-species comparisons of cancer signaling

noreply@blogger.com (Arrayinformatics) — Wed, 29 Dec 2004 05:45:00 +0000

"Modeling of human cancer in genetically engineered mice and genome-wide measurements of mRNA expression have now been combined to accelerate the search for new molecularly targeted therapies against cancer. Looking forward, we propose a community-wide systematic effort to model and characterize an array of different cancer-related aberrant signaling pathways in several mouse models of cancer...."

PHD Studentship

noreply@blogger.com (Arrayinformatics) — Tue, 28 Dec 2004 06:59:00 +0000

University of Sussex PHD STUDENTSHIP

"University of Sussex PHD STUDENTSHIP

Genome Damage and Stability Centre

The Genome Damage and Stability Centre is an internationally renowned Institute carrying out research on the response of cells to DNA damage, genome instability and its relationship to human disease. We are seeking motivated individuals to fill the posts and studentships described below. We provide a stimulating and supportive environment and our expertise covers a range of experimental systems. Further information about our research can be obtained from our website at http://www.sussex.ac.uk/gdsc/

PHD STUDENTSHIPS FUNDED FOR 3 YEARS......"

TECHNOLOGY FEATURE

noreply@blogger.com (Arrayinformatics) — Tue, 28 Dec 2004 06:48:00 +0000

Western blot analysis with quantum dot fluorescence technology: a sensitive and quantitative method for multiplexed proteomics
"Western or immunoblotting analysis of protein expression in cells and tissues has been the major analytical tool for assessing molecular biological functions in basic cell biological research, pathology and drug discovery and development. With the rapid growth of our understanding of gene and protein expression pathways and limited supplies of tissue, there is an ever-increasing need for more sensitive, quantitative methods capable of multiplex detection of proteins or protein states from a single western blot. Quantum Dot Corporation's (QDC) new western blot detection kits harness the high brightness, extreme stability and multiple colors of the Qdot Secondary Antibody Conjugates to quantitatively detect several proteins in a single gel. When used in combination with existing user-defined primary antibodies, the kit combines ease of use with sensitivity to picogram levels of protein using several existing gel imaging systems. ....."

Classic Protocol-Two-dimensional gel electrophoresis of proteins

noreply@blogger.com (Arrayinformatics) — Tue, 28 Dec 2004 06:37:00 +0000

Two-dimensional gel electrophoresis of proteins

"Two-dimensional polyacrylamide gel electrophoresis (PAGE) is used for separation of complex protein mixtures by the independent parameters of isoelectric point and molecular weight. Isoelectric focusing (IEF) separates proteins in a pH gradient. Each protein is 'focused' because it moves under the influence of the electric field until it reaches its isoelectric point, the pH at which it has no net charge. After IEF in the presence of urea and a nonionic detergent, the IEF gel is equilibrated in sodium dodecyl sulfate (SDS) to prepare the proteins for SDS-PAGE. The method described here1 uses carrier ampholytes to form a pH gradient in a long, thin (1.2-mm) focusing gel composed of a low percentage (2.7%) of acrylamide and containing 9.5 M urea and 2% Nonidet P-40 to maintain protein solubility. After IEF, the gel is briefly equilibrated in SDS and placed directly onto the top edge of a second-dimension slab gel. Because the time between the end of IEF and the start of SDS-PAGE is only a few minutes (thereby minimizing diffusion), the spots are highly resolved and nearly round in shape.
....."

Brain imaging could spot liars

noreply@blogger.com (Arrayinformatics) — Tue, 07 Dec 2004 07:40:00 +0000

Tests reveals patches in the brain that light up during a lie.

"Lying activates tell-tale areas of the brain that can be tracked using functional magnetic resonance imaging (fMRI), according to scientists who believe the technique could replace traditional lie detectors....."

Opportunity: First 90 days on Mars

noreply@blogger.com (Arrayinformatics) — Tue, 07 Dec 2004 07:37:00 +0000

As the rover's groundbreaking results are published, http://www.nature.com/news/2004/041129/full/041129-10.html looks at the key moments of discovery.

Does shampoo pose risk to pregnant women?

noreply@blogger.com (Arrayinformatics) — Tue, 07 Dec 2004 07:26:00 +0000

Experts contest claim that cosmetic preservative could harm fetuses.

"A preservative commonly found in cosmetics such as shampoo and moisturizers harms developing nerve cells, according to a controversial study.But claims that the compound may therefore pose a risk to unborn babies have provoked concern from other scientists, who are worried that such assertions may create unnecessary panic....."

Focus on Kinases in Cancer

noreply@blogger.com (Arrayinformatics) — Mon, 06 Dec 2004 11:14:00 +0000

"Mutations that induce kinase activation are a frequent occurrence in human cancers, thus elevating kinases to the second most important class of drug targets. Nature Reviews Cancer and Nature Reviews Drug Discovery present a FREE Web Focus that examines the role of kinase signaling in cancer and the potential for developing effective therapies that can modulate various kinase pathways."

http://www.nature.com/reviews/focus/kinases/index.html

noreply@blogger.com (dnamicro) — Sat, 27 Nov 2004 08:53:00 +0000

Researchers find potential new Alzheimer's treatment target
Pharmaceutical Business Review Online: "Scientists have identified a new, longer species of amyloid beta-peptide that has the potential to be a new target for the treatment of Alzheimer's disease, according to research published in the Journal of Biological Chemistry, an American Society for Biochemistry and Molecular Biology journal. (webmaster@datamonitor.com (Datamonitor))"

noreply@blogger.com (dnamicro) — Sat, 27 Nov 2004 08:49:00 +0000

Emerging Technologies in Lab-on-a-Chip
Biohealthmatics.com: "The microarray industry has evolved very rapidly from providing highly specialized techniques for a few genetic researchers to becoming a laboratory standard in molecular biology and clinical research. (Digital Silence, PA)"

RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells

noreply@blogger.com (Arrayinformatics) — Sat, 27 Nov 2004 04:54:00 +0000

Developmental biology paper in Nature methods.

http://info.nature.com/cgi-bin24/DM/y/hRIt0BfkCp0BtI0UTk0AN

RNA interference (RNAi)-mediated loss-of-function screening in Drosophila melanogaster tissue culture cells is a powerful method for identifying the genes underlying cell biological functions and for annotating the fly genome. Here we describe the development of living-cell microarrays for screening large collections of RNAi-inducing double-stranded RNAs (dsRNAs) in Drosophila cells. The features of the microarrays consist of clusters of cells 200 m in diameter, each with an RNAi-mediated depletion of a specific gene product. Because of the small size of the features, thousands of distinct dsRNAs can be screened on a single chip. The microarrays are suitable for quantitative and high-content cellular phenotyping and, in combination screens, for the identification of genetic suppressors, enhancers and synthetic lethal interactions. We used a prototype cell microarray with 384 different dsRNAs to identify previously unknown genes that affect cell proliferation and morphology, and, in a combination screen, that regulate dAkt/dPKB phosphorylation in the absence of dPTEN expression.

Promoter prediction analysis on the whole human genome

noreply@blogger.com (Arrayinformatics) — Fri, 26 Nov 2004 09:31:00 +0000

Paper on Promoter prediction programs (PPPs):

http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n11/abs/nbt1032.html

Abstract:

Promoter prediction programs (PPPs) are important for in silico gene discovery without support from expressed sequence tag (EST)/cDNA/mRNA sequences, in the analysis of gene regulation and in genome annotation. Contrary to previous expectations, a comprehensive analysis of PPPs reveals that no program simultaneously achieves sensitivity and a positive predictive value >65%. PPP performances deduced from a limited number of chromosomes or smaller data sets do not hold when evaluated at the level of the whole genome, with serious inaccuracy of predictions for non-CpG-island-related promoters. Some PPPs even perform worse than, or close to, pure random guessing.

Overexpression of SPARC in Gastric Cancer

noreply@blogger.com (Arrayinformatics) — Fri, 26 Nov 2004 09:18:00 +0000

I found a paper in BJC regarding SPARC and its relation to gastric cancer. The link is:

http://www.nature.com/cgi-taf/DynaPage.taf?file=/bjc/journal/v91/n11/full/6602213a.html&filetype=pdf

Abstract:

Gastric cancer is the second most common cancer in the world and the fifth leading cause of cancer-related death in Taiwan. To improve the survival of gastric cancer patients, biomarkers for early detection and effective anticancer therapy are required. An essential first step is to profile gene expression in gastric cancer and identify genes that are aberrantly expressed, and to do this cDNA microarrays were performed. The clinic-pathologic correlation and prognostic significance of the aberrantly expressed genes were evaluated to identify novel biomarkers of gastric cancer. Fresh surgical samples of tumour tissue and matching noncancerous mucosa were obtained immediately after gastric resection in 43 patients. Secreted Protein, Acidic and Rich in Cysteine (SPARC) (Osteonectins), one of the most highly expressed genes in both intestinal and diffuse gastric cancers in our microarray results, was selected for further study. The overexpression of SPARC was verified using real-time quantitative-reverse transcription-polymerase chain reaction (Q-RT-PCR), Northern blot and immunohistochemical staining. The expression of SPARC in tumour tissues was, on average, 4.27-fold increased (95% CI 2.68-5.85) compared to adjacent noncancerous mucosa (P<0.001). The expression of SPARC was higher in advanced (T2, T3 and T4) cancer compared to the early (T1) cancer (P=0.048) with regard to depth of wall invasion. Higher expression of SPARC was significantly associated with lymph node metastasis (P<0.001), lymphatic invasion (P=0.004) and perineural invasion (P=0.047). Expression of SPARC in patients in stage II and above was significantly higher than those in stage I (P=0.017). The 3-year survival of patients with lower expression of SPARC was significantly better than those with a higher expression (log rank P=0.047). These data indicate the potential of SPARC as a prognostic marker for gastric cancer.

Keywords: gastric cancer; SPARC; real-time RT-PCR; microarray

noreply@blogger.com (Arrayinformatics) — Thu, 25 Nov 2004 13:56:00 +0000

International research team identifies gene that promotes prostate ...
research News: "innovations report,?Germany?-... NIH) in the United States, the research was continued in Finland at VTT in the Medical Biotechnology Department, in collaboration with a research team at the ...::"