• Switzeland aiming for world class in Systems Biology

 Good Systems Biology relies on the successful interaction of scientists from multiple disciplines including Biology, Chemistry, Mathematics, Computer Science, and Engineering.

After careful consideration of all of these issues, Swiss universities and research institutes decided to pool their knowledge and resources in a single research consortium called SystemsX.ch. The Universities of Basle, Berne, Lausanne, Fribourg, Geneva, and Zurich, the Paul Scherrer Institute, Friedrich Miescher Institute, and the Swiss Institute for Bioinformatics teamed up with the two Federal Institutes of Technology in Zurich and Lausanne to support this research initiative. At a press conference in Berne, the State Secretary for Education and Research Charles Kleiber stated that «A cooperation of this magnitude among the universities is of unparalleled personal traits, and on many levels embodies the way projects should be tackled and coordinated among Swiss institutes in the future».

  • Researchers identify 300 new human genes

Cornell researchers have discovered 300 previously unidentified human genes using supercomputers to compare the human genome with those of other mammals. They also found extensions of several hundred known genes.According to researchers, the discovery shows there could be more genes that have not been identified by current biological methods.Using large-scale computer clusters, researchers ran three different algorithms to compare the gene alignments between human, mouse, rat, and chicken in various combinations. The computer created an evolutionary model and searched for potential matches. After eliminating predictions that matched known genes, researchers tested the remainder in the laboratory, proving that many of the genes could in fact be found in samples of human tissue and could code for proteins. 

The research will be published in the December edition of Genome Research... More

  •  Reversing the Signs of Alzheimer's

Scottish scientists are one step further to finding a cure for Alzheimer's, thanks to the development of a compound which reverses signs of the disease. The biologists at the University of St Andrews have developed man-made compounds capable of blocking a nerve cell interaction known to lead to the symptoms of the disease. The researchers have shown that it is possible to reverse some of the signs associated with Alzheimer's.
Dr Frank Gunn-Moore's team, in collaboration with researchers in the US, have successfully reversed a sign for the progression of the disease and prevented the death of brain cells. This subsequently leads to improved memory and learning ability that was already damaged. Read more about this story at ScienceDaily 

  • Computers may replace drugs?

Scientists are predicting an end to the era of human and animal drug testing, saying that computer models will one day become so advanced that they will be able to predict the body's response to various substances. The use of computer models would bring "unprecedented benefits" to medicine, and possibly even dispense with the need for drugs altogether, as doctors discovered ways to prompt the body's own immune system to react to threats, rather than introduce artificial remedies, they said. By building sophisticated computer models which incorporated existing knowledge about an organism, scientists could predict the way the organism would respond to a drug by "switching on and off" various cell functions within the model, and then seeing how the whole system reacted. The whole story can be accessed at TimesOnline.

  • A Gene Biobank on Stroids

The H. Lee Moffitt Cancer Center and Research Institute in Tampa, Florida, is building a gene expression database that will link the molecular profile of cancer tumors with other clinical and historical information about patients in the hope of developing personalized medicines. Currently, response rates to experimental cancer drugs are low — as low as 10% in early phase trials — causing many potentially useful drugs to be prematurely retired. Not all scientists are sold on the promise of molecular profiling but most believe it will be valuable in “matching the right drugs to the right patients. Read  the full story at BioITWorld.com.

  • James Watson is the first to have its genome completely sequenced!

Scientists from Baylor College of Medicine and 454 Life Sciences announced Thursday the complete sequencing of the genome of double helix pioneer James D. Watson (left in the photo). The sequence revealed among other things that Watson carries a mutated version of the BRCA1 breast cancer gene. In the photo, Jonathan Rothberg, founder of 454 Life Sciences (right),
presents James Watson with his genome. Read the full story at http://www.bio-itworld.com/newsitems/2007/may/05-31-07-watson-genome

  •  New source for stem cell line

Scientists have created a new stem cell line from a clinically unusable human egg in a development that could have major implications for research into illnesses such as Alzheimer’s, Parkinson’s, liver disease and diabetes. The breakthrough by Roslin Cells Ltd, a spin out company established in 2006 by Roslin Institute, demonstrates for the first time that eggs which are incapable of becoming viable embryos can be used as a source for stem cells.
The move could help accelerate the development of regenerative medicine, where there is currently an acute shortage of embryos available for stem cell research.
More information on Roslin Cells

  • Autophagy: a new strategy for tackling neurodegenerative diseases?

Autophagy is believed to prevent Huntington's disease by removing aggregation-prone proteins. Researchers have found a way of identifying small molecules capable of inducing autophagy without the side effects seen with rapamycin. They  have shown that stimulating autophagy in the cells—in other words, encouraging the cells to eat the malformed huntingtin proteins—can be an effective way of preventing them from building up. This appears to stall the onset of Huntington's-like symptoms in fruit fly and mice, and we hope it will do the same in humans. Full story can be obtained from Nature Chemical Biology.

  • Central German information platform on open access launched

Researchers in Germany can now go to a single DFG-supported website to find information on open access-related issues, ranging from publication strategies and legal aspects to the relevant policies of research institutions such as Max Planck Society and Helmholtz Association. Read more at http://openaccess-germany.de/de/startseite/

  • PlantIGB: visualization of plant genomic data

This tool is mainly useful for in-depth analyses of large genomic regions, or when you need to look carefully at a lot of genes in a short period of time. For example, if you are doing a project involving analyses of many different splice variants, this tool will likely be very useful. This tool is also good for visualizing  genome-scale data sets, such as tiling array or ChIP-chip data. You can download a copy and run it on your computer by visiting this link: http://www.bioviz.org/plant_igb

  • The World’s First Division of Pathway Medicine

University of Edinburgh forms a new interdisciplinary team of investigators to explore the fundamental molecular mechanisms of human disease. Pathway Medicine is a pioneering new discipline that takes a systems level approach to the interplay between biological pathways within and between cells. Following the completion of the sequencing of the human genome in 2001, a grand challenge of biomedical research lies in understanding how genes and molecules interact at a physiological level. The Division of Pathway Medicine, a research centre within the College of Medicine and Veterinary Medicine at the University of Edinburgh was officially launched on 1st March 2007. This trail-blazing new division is uniquely focused on exploring how post genomics-based research techniques can be applied to clinical research by mapping ‘pathways’ of molecular interactions relevant to human disease.

  • Rhesus Monkey Genome Uncovers Genetic Differences with Humans, Chimps

International consortium of researchers has published the genome sequence of the rhesus macaque monkey and aligned it with the chimpanzee and human genomes. Published April 13 in a special section of the journal "Science", the analysis reveals that the three primate species share about 93 percent of their DNA, yet have some significant differences among their genes. In addition to comparing the rhesus with the chimp and human genomes, the group also studied genetic variation in macaque populations, and developed a set of 'single nucleotide polymorphisms' or SNPs (single base DNA differences) that can be used for future analysis of inheritance of biomedically important traits in rhesus. This advance in macaque genetics will enhance the use of macaques for the study of genetic diseases of man.

  • Microsoft Supports Synthetic Biology

Microsoft is adding synthetic biology to its universe. Today, the software giant announced $570,000 in grants to six teams of academic researchers exploring new ways to meld biology with computer science, math, and engineering.

"The reason we're in this area is there is a lot of potential," said Microsoft official Simon Mercer earlier this year in an interview with Science. "We may never be a biotech company, but ... we want to see growth of a set of tools that support synthetic biology activities." Synthetic biology uses mathematical modeling and other computational tools to devise new biological functions.  The scientists are involved in building the next generation of cloning methods and creating computer code to help them fold DNA into more complex shapes.

  • An Attractive Target for Antibacterial Drugs

Science Volume 315, Number 5817, Issue of 09 March 2007

The bacterial cell wall is built by glycosyltransferase (GT) and transpeptidase (TP) enzymes. Penicillin and related antibiotics act on TP enzymes, but bacterial resistance is developing against these antibiotics. GT enzymes are an attractive target for new drugs because they are essential and are membrane bound and thus accessible. Lovering et al.  have determined the crystal structure of penicillin-binding protein 2, a bifunctional enzyme from Staphylococcus aureus that contains both a GT and a TP domain. Structures with and without the inhibitor moenomycin bound in the GT domain provide insight into the mechanism of cell-wall biosynthesis and provide a starting point for structure-based design of antibacterials.

  • New Molecular Screening Approach

 Science Volume 315, Number 5817, Issue of 09 March 2007

Ideally, molecular screening should allow for the simultaneous analysis of many molecular targets. Pregibon et al.  used microfluidics and lithographic masks to create flat particles with lateral dimensions of ~100 micrometers and thicknesses of about 30 micrometers. One half of each particle bears a distinct fluorescent barcode (out of more than 1 million possible codes); the other half bears a probe for target binding. After incubation with a sample, a flow-based analysis system then scans each particle via single-wavelength fluorescence for its code and evidence of bound target. Fluorescently labeled DNA targets could be detected at the 500-attomole level.

  • MIT Researchers Uncover New Class of RNAs in Worms

Dec 21 2006,GEN News Highlights

Researchers from MIT have uncovered a new class of small, noncoding RNAs in worms. "This discovery further emphasizes the point that we have not completely reached the depths of RNA function, and we are excited to see how this develops," comments Michael Egholm, Ph.D., vp, molecular biology, 454 Life Sciences.

Using 454 Life Sciences’ parallel sequencing technology, David Bartel, a Howard Hughes Medical Institute Investigator at MIT, and colleagues sequenced some 400,000 small RNAs from Caenorhabditis elegans, identifying 18 new microRNA genes and more than 5,000 other RNAs of a type that had not been previously reported.

The study, entitled, “Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans” appeared in the December 15 issue of the journal Cell.

  • NYU Chemists Create First DNA Array Containing a Nano Device 

 Dec 7 2006,GEN News Highlights

New York University scientists report the first time that a functional nanotechnology device within a DNA array has been developed. Nadrian C. Seeman, Ph.D., professor in the chemistry department and graduate student Baoquan Ding developed a DNA cassette through which a nanomechanical device can be inserted and function within a DNA array, allowing for the motion of a nanorobotic arm. "It is crucial for nanorobotics to be able to insert controllable devices into a particular site within an array, thereby leading to a diversity of structural states,” explains Dr. Seeman. “Here we have demonstrated that a single device has been inserted and converted at a specific site.” The results pave the way for creating nanoscale assembly lines in which more complex maneuvers could be executed, adds Dr. Seeman. The invention has the potential to develop new synthetic fibers, advance the encryption of information, and improve DNA-based computation. 

  • The Pathway Interaction Database - Now Launched!

Nov 30 2006,Nature alert

Explore human cell signalling pathways with the new Pathway Interactions Database, a collaboration between the National Cancer Institute and Nature Publishing Group. The database, aimed at biologists and bioinformaticians, is up-to-date, reviewed by experts and curated.
Access the Pathway Interaction Database FREE online and sign up for your free email alert.

  • New Gene-Based Test for Prostate Cancer Introduced in Europe

Nov 22 2006,GEN News Highlights

Gen-Probe launched its PCA3 assay, a new prostate cancer-specific molecular diagnostic test in Europe.

The PCA3 gene-based test detects the overexpression of PCA3 mRNA in urine. Studies have shown that, in greater than 95% of prostate cancer cases, PCA3 is 60- to 100-fold over-expressed in prostate cancer cells compared to normal cells, indicating that PCA3 may be a useful biomarker for prostate cancer.

Preliminary data show that the PCA3 assay is more specific to prostate cancer than the traditional serum prostate specific antigen (PSA) test, thus decreasing the likelihood of false positive results. PSA is produced by both cancerous and noncancerous prostate cells. Noncancerous conditions, such as BPH, can therefore cause elevated serum PSA levels that must be investigated, resulting in unnecessary medical procedures and patient anxiety.

  • Korea invests 14 billion dollar in biotech-related sciences:

Korea plans to invest $14.3 billion in biotechnology research and industrialization over the next 10 years to create a $60 billion market by 2016. This market will push the nation to No. 7 worldwide, from its current ranking of No. 14. The ministry’s ``Bio-Vision 2016’’ plan puts priority on the acquisition of core technologies and the establishment of infrastructure that will help them in the applied industry, a ministry spokesman said. The detailed plan calls for the integration of bio-technology with related areas such as post-genome studies, gene-to-life research, information technology and nano-technology.

 

  • Sea urchin and human genomes are similar:

An international team of scientists has analyzed the newly sequenced genome of the sea urchin and found it has so much in common with the human genome that new drugs could be developed that aid immune system ailments.

    "The sea urchin is surprisingly similar to humans," said George Weinstock of Baylor College of Medicine, co-director of the sea urchin sequencing project. "Sea urchins don't look any more like humans than fruit flies, but about 70 percent of sea urchin genes have a human counterpart whereas only about 40 percent of fruit fly genes do."

    This similarity means sea urchins can serve as a model for understanding how the group of animals that includes humans split off and evolved different traits. Scientists used DNA from the sperm of a male California purple sea urchin, a species found along North America's west coast from Baja to Alaska for the genome project.

    Analysis of the sea urchin genome revealed a surprisingly unique immune system more complex than humans, which could explain their lengthy life spans of up to 100 years.

    Humans have an acquired immune system and our body must learn how to attack and destroy invaders once they enter the body, sea urchins are hard-wired to detect foreign bacteria and viruses and begin an attack.

    Researchers said sea urchin genes could lead to new drugs for combating infectious diseases. In fact, sea urchins carry genes associated with many human diseases, including muscular dystrophy and Huntington's disease.