VATIS Update Biotechnology . Nov-Dec 2003

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Biotechnology Nov-Dec 2003

ISSN: 0971-5622

VATIS Update Biotechnology is published 4 times a year to keep the readers up to date of most of the relevant and latest technological developments and events in the field of Biotechnology. The Update is tailored to policy-makers, industries and technology transfer intermediaries.

Co-publisher: Biotech Consortium India Ltd
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Johns Hopkins establishes academic division in Singapore

Johns Hopkins Medicine (JHM) of the United States and the Agency for Science, Technology and Research (A*STAR) of Singapore have collaborated to establish the Johns Hopkins Medicine Division of Biomedical Sciences in Singapore. Although JHM began its programmes in Singapore in 1998, this is the first time it has created a full division outside its home base in Baltimore. The new division will include 12 full-time JHM faculty to lead training and research initiatives focused on life science disciplines such as immunology, cancer biology and experimental therapeutics.

Graduate training (Ph.D. programmes) in basic and clinical research will be offered to Singaporeans and other Southeast Asian nationals. The training conducted in Singapore and Baltimore will lead to either a Hopkins Ph.D. or a National University of Singapore Ph.D. degree. The academic division will begin operations in the first quarter of 2004 at the same site as other A*STAR research institutes and industrial companies. Within two years, it plans to build a staff of 150 research professionals. A grant review committee will be set up to assess progress achieved at the new division while a scientific advisory committee comprising renowned scientists from the United States, Singapore and other nations will offer guidance on research priorities.

Contact: Ms. Claudia Costabile. E-mail: ccostab1@jhmi. edu


EU rejects end to biotech ban

The decision to lift a four-year ban imposed on bio-engineered crops in Europe has been postponed by the European Union (EU). This development has incensed EUs trade partners, in particular the United States. The moratorium was ordained in 1999 at the initiative of five countries Denmark, France, Greece, Italy and Luxembourg which were later joined by Austria and Belgium.

Experts handed over to ministers a decision on allowing the import of a form of genetically modified (GM) sweetcorn, Bt-11. Under EU rules, ministers have three months to arrive at a decision. The required majority was not secured on the standing committee for food chain, which gathers scientific representatives from member states. Six countries in the 15 member bloc Britain, Finland, Ireland, the Netherlands, Spain and Sweden voted in favour. The three countries who abstained include Belgium, Germany and Italy, while the following six voted against: Austria, Denmark, France, Portugal, Luxembourg and Greece. The decision is likely to be put to ministers in January by the European Commission, the EUs executive body, and if they fail to agree on action within three months, the file would return to the Commission for a decision.

EU experts concurrence would have lifted a de facto moratorium in place since 1999 against the import and cultivation of GM products in the EU. The decision, against a backdrop of public disquiet in Europe on the issue of Frankenfoods, is being closely watched by its trade partners, notably the United States. However, opponents of GM crops say much more research is necessary to gauge their impact on humans and the environment.


Indo-Swiss initiative

On 10 November 2003, the Swiss President Mr. Pascal Couchepin and Indian Prime Minister Mr. A. B. Vajpayee signed an agreement in New Delhi, India, to strengthen cooperation in science and technology. The agreement puts into place a framework for greater collaboration between the two countries in biotechnology, nanotechnology and information technology. Both governments also committed themselves to open a joint research laboratory in India in the near future, although precise details on what form such an institute would take are yet to be worked out.

It is hoped that the collaboration between Swiss institutes like the ETH Lausanne and Zrich, and Indian Institutes of Technology and Science will bring together some of the very best scientists in these fields. Scientists would be allowed to decide themselves on the topics for collaboration. Both governments have agreed to match each others investment. In a separate agreement, a programme promoting exchanges among students working at two Swiss institutes and eight Indian institutes will also be expanded.


Indo-Syrian cooperation in biotechnology

A joint work plan to boost bilateral cooperation in biotechnology research has been signed between India and Syria. The executive work plan was inked on 15 November 2003 on the occasion of the Indian Prime Minister Mr. A.B. Vajpayees visit to Syria. The agreement heralds a five-year road map for joint research in varied areas of biotechnology. The work plan engineers bilateral cooperation by increasing institutional collaboration for joint research activities as well as exchange of scientists and technical information. Mr. Vajpayee also announced a US$1 million grant for developing Syrias National Biotechnology Centre. After inaugurating the centre, Mr. Vajpayee expressed that the grant would be used to establish a state-of-the-art facility.

Chronicle Pharmabiz, 20 November 2003

NHGRI announces list of sequencing centres

In the United States, the National Human Genome Research Institute (NHGRI) has selected five centres to carry out a new generation of large-scale sequencing projects designed to maximize the promise of the Human Genome Project and dramatically expand the understanding of human health and disease. Over the next three years, the five centres in NHGRIs Large-scale Sequencing Research Network will use high-throughput, robotic technologies to sequence a strategic set of animal genomes totalling as much as 54 billion base pairs or the equivalent of 18 human genomes. For fiscal year (FY) 2004, NHGRI has earmarked US$163 million for the sequencing centres, which were selected through a competitive, peer-reviewed process. Funding levels for FY 2005 and 2006 are planned to be US$163 million and US$133 million, respectively.

The NHGRI-supported large-scale sequencing centres are: Agencourt Bioscience Corporation; Baylor College of Medicine; The Eli and Edythe L. Broad Institute, Massachusetts Institute of Technology; The Institute for Genomic Research, J. Craig Venter Science Foundation Joint Technology Centre; and Washington University School of Medicine. The primary mission of these centres is to produce a publicly available resource of high-quality assembled genome sequences that researchers can use to address human biology and human health. By comparing genome sequences from carefully chosen organisms, researchers are able to identify specific DNA sequences that have been conserved throughout the evolution of different species a strong indicator that these sequences reflect functionally important regions of the genome.


HIV vaccine trial in Thailand ends in failure

Thailands fight against HIV/AIDS received a major setback when trials of a potential vaccine for HIV did not yield good results. VaxGen, a United States-based company that developed the candidate vaccine called AIDSVAX, announced in November 2003 that the vaccine did not prevent HIV infection or slow the progress of the disease. The results follow preliminary findings released in February 2003 that the vaccine did not prevent HIV infection in the United States and Europe, but offered some protection to black and Asian participants. More than 2,500 injecting drug users in Bangkok were involved in the three-year trial. Half of the participants were given injections of the candidate vaccine while placebo was administered to the rest. During the trial, 105 volunteers given the placebo became infected with HIV, compared to 106 volunteers who had received the vaccine.

Mr. Donald Francis, President of VaxGen, said that the outcome of this trial is another reminder of difficulty in combating HIV and how important it is for the international public health community to redouble efforts aimed at developing an effective vaccine. Mr. Kachit Choopanya, the trials chief investigator, opines that despite the disheartening results the study shows Thailands commitment to HIV vaccine development and with the help of volunteers and national and international collaborators, the country has strengthened its research capacity and acquired valuable expertise with which to carry on clinical research. Furthermore, VaxGen and the Thai collaborators have created a model that can be used around the world for advanced clinical research. In October 2003, the Thai government launched a US$25 million programme to provide free anti-retroviral drugs for its 50,000 HIV/AIDS population.


New biosafety law in Brazil

A legislation pertaining to the safety and surveillance of activities involving genetically modified (GM) organisms in Brazil is under scrutiny. Submitted for approval by the National Congress in November 2003, the proposal includes setting up a National Biosafety Council, comprising 12 ministers, to advise on the formulation and implementation of governmental policy and draw up guidelines for other federal organizations. The new measure is expected to harmonize national legislation and ensure the existence of technical-scientific analyses on political decisions on GM organisms.

The proposal includes more civil society representation in the Technical Commission for Biosafety (CTNBio), which will make initial decisions on all demands related to research and commercialization of GM organisms. Only requests considered suitable by CTNBio will be analysed by the National Biosafety Council.  More priority has been given to the need for labelling foods containing GM products, as well as creation of an information system on biosafety to manage information on authorization, registration and monitoring of activities involving GM organisms. Under the proposed legislation, those who harm the environment or humans through their use of GM organisms will be liable for compensation and those who cultivate, transport, commercialize, export, import or store GM organisms, or their derivatives, without permission will be prosecuted and may have to serve a three-year prison term.


UNESCO Exchange of Scientists

UNESCO Exchange of Scientists Scheme invites young research scientists from developing countries of the Network who intend to do research work at laboratories in other countries of the Network to apply for the scheme for 1-3 months. Details on eligibility and application form can be found on the website:

Ms. Duangkaew Chongkachornphong (Gal); National Center for Genetic Engineering and Biotechnology (BIOTEC); 113 Thailand Science Park, Phaholyothin Road, Klong Luang, Pathumthani 12120, Thailand. Tel: (66-2) 5646700; Fax: (66-2) 5646705; Email:


Bharat Biotech to develop oral rotavirus vaccine

Bharat Biotech International Ltd. (BBIL), India, has developed a new vaccine for preventing severe diarrhoea in infants. Expected to reach clinical trials by 2004, BBIL plans to apply for a commercial licence by mid-2005. Normally, there is no direct medication for rotavirus diarrhoea since it is a viral infection. In most instances, oral rehydration or administration of intravenous fluids is advised in order to compensate for the severe loss of water from the body. The body is left to fight the virus on its own. Rotavirus diarrhoea may prove fatal in infants, owing to their weak immune system. BBILs vaccine will help resolve this problem by generating antibodies against the virus. The All India Institute of Medical Sciences at New Delhi will organize and conduct clinical studies and field trials. BBILs venture, which is part of Bill and Melinda Gates Foundations immunization programme for developing countries, is the second initiative to develop a vaccine against diarrhoea.

Chemical Weekly, 2 December 2003

Glowing red GM fish

In the United States, zebra fish that fluoresces bright red will become the first genetically modified (GM) pet to go on sale. Zebra fish are normally black and silver coloured. The new GloFish was produced by injecting zebra fish eggs with the gene of a sea anemone, making it red coloured. Researchers have also produced green fish using a fluorescent marker gene from jellyfish.

GM zebra fish was originally developed by Dr. Gong Zhiyuan et. al. at the National University of Singapore to detect water pollutants by changing colour, in the presence of toxins. Dr. Alan Blake and scientists at Yorktown Technologies LP who developed the GloFish, which especially glows under ultraviolet light, state that the GM fish will be available from January 2004. The fish does not pose any threat to the environment since it cannot survive in non-tropical waters. However, news of the GM pet has sparked some concern among conservationists. Food safety and conservation groups have sent a joint letter to the Food and Drug Administration urging immediate intervention.

To enable the fishes use as pollution detectors, scientists have pinpointed gene promoters which act as on/off switches in the presence of certain triggers. One type of switch is activated by the sex hormone oestrogen, which can contaminate water. Other glow switches can be stress-induced and will respond to the presence of damaging chemicals like heavy metals. According to Dr. Zhiyuan, as many as five colours may be added to zebra fish to light up in the presence of different contaminants. It is believed that the use of glowing fish as ornamental pets should not pose an environmental threat if released into the wild. Glowing fish pets are being sold in Taiwan.


Biotech leads in new employment

In the United States, a survey undertaken by the Commerce Department has revealed that biotech firms have emerged as a leading source of new jobs despite a struggling economy. From 2000 to 2002, biotech companies added roughly 12 per cent more jobs, the fastest growth for any major industry. With a burst of new patent applications and more funds pouring into medical research than ever before, government officials say that biotechnology is poised for a breakthrough. The survey, which polled over 1,000 company representatives, follows a spate of encouraging reports that cite greater access to venture capital, increased sales of drugs and promising new treatments in the pipeline as some of the key factors that may drive the biotech sector to profitability by the end of this decade. The industry employs relatively few technical workers overall; estimates by the Commerce Department puts the total at 34,000 scientists, with the majority of these jobs being located in just six states. Even for cities with a high concentration of biotech companies, such as Boston and San Francisco, the largest firms still rank as minor employers in the region.

The growth of biotech jobs offers increasing options at a time when traditional academic opportunities appear in shorter supply. Although university labs are still teaming with researchers, surveys from the National Science Foundation and others suggest that tenure track positions are not keeping up with demand, leading many Ph.D. graduates to jump the industry. The overall result is that life scientists face an easier time than most in finding work, with an unemployment rate for advanced degree holders hovering at less than 2 per cent. The Commerce Department contends that biotechnology businesses are among the nations most innovative, accounting for nearly 10 per cent of all R&D undertaken in the country last year. These companies also have nearly 32,000 patents awaiting approval, a biological gold mine that could raise intellectual property holdings by 50 per cent.


Collaboration on biotech research

In India, an R&D agreement in the area of cancer and inflammation was signed at Anna University in Chennai, between Mumbai-based Nicholas Piramal India Ltd. (NPIL) and the Institute of Genomics and Integrative Biology (IGIB) of New Delhi. The agreement is designed to speed up identification and development of plant extracts in IGIBs repository for treating rheumatoid arthritis and cancer.

NPILs vast collection of natural products (more than 6,000 plant extracts and 18,000 microbial strains) will also be evaluated by IGIB against a variety of established targets. It is starting a new research centre in Chennai with an initial staff strength of 50 scientists, and the company will have exclusive rights to commercialize any product/s fructifying under this collaborative effort.

Chronicle Pharmabiz, 20 November 2003

Lilly, Harvard announce research for multi-drug resistant TB

A new research and training initiative for multi-drug resistant tuberculosis (MDR-TB) in Tomsk, Russia, has been launched by Eli Lilly and Co. along with Brigham and Womens Hospital (BWH), an affiliate of Harvard Medical School in the United States. Tomsk, located in Siberia, is one of the worlds hotspots for this deadly public health threat. As part of the initiative, healthcare workers from Russia and other countries of the former Soviet Union with high burdens of MDR-TB would be trained, while research data obtained will be used globally to improve and potentially develop new treatments.

The Tomsk initiative will have an important global impact in that the initiative will be able to train healthcare workers on best practices in diagnosing, treating and managing the illness. It will also serve as an important repository for new and potentially vital research about the disease that will be shared with both practising physicians and researchers to reach the ultimate goal of eradicating MDR-TB. Led by Dr. Paul Farmer, a Professor at Harvard Medical School and the Division of Social Medicine and Health Inequalities at Brigham and Womens Hospital, the initiative will conduct operational and epidemiological research to support control projects worldwide.

Chronicle Pharmabiz, 20 November 2003

SARS vaccine ready for trials

A vaccine for Severe Acute Respiratory Syndrome (SARS) virus is expected to enter human trials in China. According to Mr. Yin Hongzhang, Head of the Biological Product Section of the State Food and Drug Administration, the agency was expected to approve clinical tests by the end of December 2003. Preclinical trials of the vaccine on monkeys have shown that it is effective against SARS without serious side effects. The flu-like virus emerged in southern China late last year, killing about 350 people in the country and infecting over 5,000. It infected more than 8,000 people worldwide, killing over 800. The vaccines developer, Beijing Kexing Bio-product Co., has produced 1,400 shots of the vaccine and has prepared another 20,000 doses. Scientists have been working on a vaccine since April 2003. The World Health Organization has said a viable SARS vaccine could take at least two years to develop.


Drug discovery centre

The United Kingdom-based GlaxoSmithKline Plc. (GSK) is setting up a new drug discovery centre to focus on biopharmaceuticals, thereby highlighting the growing importance of biotech drugs to major pharmaceutical companies. This unit will be the seventh Centre of Excellence for Drug Discovery (CEDD). GSK established the first six quasi-autonomous centres in a bid to introduce an entrepreneurial culture into drug discovery. The existing CEDDs concentrate on specific disease groupings cardiovascular and urogenital; musculoskeletal and cancer; metabolic and viral; neurological and gastrointestinal; psychiatric; and respiratory and inflammatory.

Chronicle Pharmabiz, 20 November 2003


Smaller chips built using DNA as template

Dr. Erez Braun et. al. at Technion-Israel Institute for Technology, Israel, have created tiny transistors using DNA strands. This breakthrough may provide a practical method for fabricating molecular-size circuits. Dr. Braun states that to construct a circuit, there is a need to invent ways to tell molecules where to go and how to connect with each other. In this regard many scientists have turned to the biologically inspired notion of self-assembly, using molecules like DNA and proteins that can automatically line together in the correct configuration.

The team constructed transistors out of carbon nanotubes, cylindrical molecules about one ten-millionth of an inch in diameter, which resembles rolled-up chicken wire. The new technique takes advantage of a biological process known as recombination, where a segment of DNA is swapped out for an almost identical piece. The cell uses recombination to repair damaged DNA and swap genes. A special protein helps connect the replacement DNA at the desired location. By attaching a nanotube to the protein, the nanotube moves to an exact location along the DNA strand. Scientists then coated the DNA with gold, producing a simple electronic device comprising a nanotube connected to gold wires at each end. Current through the nanotube can be switched on or off by applying an electric field. Earlier, the team had showed that they could stretch DNA across a surface to provide a template to hook together the transistors into a circuit. According to Dr. Braun the next step would be to build the circuit.


New bacteria to combat allergy symptoms

A team of researchers from Kirin Brewerys Central Laboratories for Key Technology have discovered a lactic acid bacteria with potent anti-allergy effects. This bacteria could be used to fight the onset of allergies, e.g. hay fever. Consumer interest in lactic acid bacteria for health benefits is growing with research demonstrating that live bacteria may help digestive functions and boost the immune system. Allergies are on the rise, with incidence of hay fever, food allergies and atopic dermatitis escalating, particularly in developed countries. As conventional medication can only treat the symptoms, scientists continue to seek treatments that could facilitate actual physiological improvement.

Comparative research has been carried out on the effect of more than 100 strains of lactic acid bacteria in balancing lymphocytes, known as Th1 and Th2, in spleen cells from animal models with allergies. An imbalance in the lymphocytes, owing to Th2 dominance, has been associated with allergies. A strain of Lactobacillus paracasei (named Lactobacillus KW) exhibited the greatest ability in improving Th1/Th2 balance, giving expectations that it will be effective against the underlying causes of allergies. Researchers found that Lactobacillus KW improved allergy symptoms in animal models. Further tests with animal models indicated that ingestion of Lactobacillus KW reduces the level of IgE, an indicator of allergic conditions, in blood and improves the Th1/Th2 balance.

Scientists also investigated anti-allergy effects in people suffering from hay fever. Test subjects were asked to eat yoghurt containing Lactobacillus KW. The yoghurt containing bacteria exhibited twice the effect of conventional yoghurt in improving the Th1/Th2 balance. Reduction in symptoms such as itching, pain and nasal discharge also demonstrated the effectiveness of Lactobacillus KW against hay fever.


Revolutionary tool to fight cancer

The United States-based Cancer Genetics Inc. (CGI) has launched a highly sensitive DNA FISH assay to help diagnose and monitor therapies for chronic myeloid leukaemia (CML) and a subset of acute lymphoblastic leukaemia (ALL). This is the first repeat-free BCR/ABL four-colour fluorescent in situ hybridization (F-FISH) probe. The F-FISH platform is used to simultaneously detect t(9;22) (q34.1;q11.2) translocations, associated deletions, variants and amplifications that occur in CML. The assay is designed to provide improved sensitivity and specificity, eliminating false positive/negative results. F-FISH probe was developed using proprietary Signal Exchange Approach methodology, wherein probes are derived from the regions flanking genes which contain the breakpoints. The company has filed patent applications covering its proprietary signal segregation approach, signal exchange approach and repeat removal technology.

According to Dr. Nallasivam Palanisamy, inventor of the assay, validation studies of the F-FISH assay showed deletions in 20 per cent of known standard translocation cases. Deletions on der(9) chromosome are particularly important, as they are shown to be associated with resistance to treatment and possibly contribute to poor clinical outcomes. Submicroscopic deletions not detectable by conventional G-band analysis can be obtained through the F-FISH assay, which may give physicians a window of opportunity to adjust therapy and treatment regime.


New technology will speed up genome sequencing

Scientists at the Whitehead Institute for Biomedical Research, the United States, will test new technology that could enable faster sequencing of different genomes. Almost 150 different genomes have been sequenced to date, including the human genome, but sequencing needs are growing faster than ever. The success of the growing field of genomic medicine, which promises to deliver better therapies and diagnostics, depends on the speed of the sequencing technology.

BioMEMS 768 Sequencer can sequence the entire human genome in a year, processing up to seven million DNA letters a day, about seven times faster than its nearest rival. Scientists began working on the project in 1999 with a US$7 million National Human Genome Research Institute grant. This technology will eventually help scientists to quickly determine the exact DNA sequence of different organisms and can lead to faster forensic analysis of DNA gathered in criminal cases. At the heart of the BioMEMS machine is a large glass chip etched with tiny microchannels called lanes. It tests 384 lanes of DNA at a time, four times more than existing capillary sequencers. Additionally, each lane can accommodate longer strands of DNA about 850 bases compared to the current 550 bases per lane. It takes about 45 minutes to read the DNA from one of the BioMEMS 768s lanes.



New cancer gene therapy is the first to be approved

A gene therapy-based treatment called Gendicine launched by SiBiono GeneTech of China has been given the go-ahead from regulatory authorities. Chinas medicines authority approved the cancer therapy after it achieved promising results in a clinical trial. The treatment consists of an adenovirus designed to insert a gene called p53, which codes for a protein that triggers cell suicide when cells start to run amok and thus prevents them from becoming cancerous. Many tumours arise after the mutation or inactivation of p53 and in cancers of this type restoration of the protein is believed to be the key to eliminate tumour cells.

SiBiono decided to test the treatment on head and neck squamous cancers, as p53 is known to be mutated in over 60 per cent of these tumours. This form of cancer is also particularly common in China. In the largest clinical trial, 120 patients with nasopharyngeal cancer were given either radiotherapy alone or a combination of Gendicine and radiotherapy. The p53-carrying viruses were injected directly into tumours once a week for eight weeks and most patients were monitored for more than a year afterwards. In 64 per cent of patients given Gendicine there was complete regression of primary tumours, a rate three times more than in the radiotherapy-only group. The only side effect was fever in a third of the patients. No long-term adverse effects are expected because the virus does not integrate into the genome of cells unlike viruses used in the French gene therapy trial that was halted in 2002 after two boys developed leukaemia.


Virus synthesized in a fortnight

Scientists headed by Dr. Craig Venter of Celera Genomics, the United States, have developed a new technique to assemble large pieces of DNA with relative ease and unprecedented speed. This process, which will not be patented, allowed the complete genome of a small virus to be synthesized in just 14 days. Researchers synthesized the genome of a bacteriophage by modifying a common laboratory technique, Polymerase Chain Reaction (PCR), to paste together hundreds of oligonucleotides in one test tube. The molecules then self-assembled into the right sequence. The resulting DNA was placed into bacterial cells where it replicated, creating new infectious viral particles.

The ultimate aim of this project, funded by the Department of Energy, is to create microbes with special properties such as the ability to sequester carbon dioxide or consume toxic waste. The speed of the technique could help accelerate research in which large sections of DNA are used e.g. gene therapy, vaccine research or agricultural biotechnology. But the method equally makes it much simpler to manufacture a deadly virus for use as a biological weapon. The simple precursors needed would be impossible for governments to keep it out of the hands of potential bioterrorists.


Role of obesity gene scrutinized

Researchers from the United Kingdom, France and the United States have been able to discern the functions of a gene, which may explain why some people overeat and become obese. Studies have shown that the gene GAD2 has an appetite stimulating role and that one form of this gene is strongly associated with obese people. Although it is known that obesity is a result of the interactions of many genes and environmental factors, GAD2 is one of the first genes to be strongly touted as a candidate gene for obesity. Located on chromosome 10, the gene acts by speeding up production of a neurotransmitter in the brain called gamma-amino butyric acid (GABA). GABA interacts with another molecule known as neuropeptide Y in the paraventricular nucleus of the hypothalamus, creating the urge to eat. It is believed that people who carry a more active form of GAD2 gene build up larger than normal quantities of GABA in their hypothalamus, enhancing the stimulus to eat more than normal and is thus a basis for explaining why obese people overeat.

According to Prof. Philippe Froguel, senior author of the research, the discovery that GAD2 gene plays a role in determining whether someone is likely to overeat could be crucial in understanding the continued rise in obesity rates around the world. Moreover, genetic factors alone cannot explain the rapid rise in obesity rates but they may provide clues to preventive and therapeutic approaches that could ease the health burden associated with obesity. The team compared genome-wide scans of 576 obese and 646 normal weight adults in France and identified two alternative forms, or alleles, of the GAD2 gene. One form of the gene was found to be protective against obesity, while another increased the risk of obesity. In addition to the genome-wide scans, obese patients completed an eating habits questionnaire, measuring dietary restraint, disinhibition and perceived hunger. Results indicate that those carrying the GAD2 allele that increases the risk of obesity were significantly more likely to reveal an inability to control their food intake and perceive high levels of hunger.


New test may better predict breast cancer recurrence

Research carried out by Genomic Health Inc., a United States-based biotech company, has led to the identification of nearly two dozen genes that, taken together, can predict with a high degree of accuracy the likelihood of tumours reoccurring in women whose breast cancer was detected at an early stage. This has led to the development of a first-of-its-kind genetic test that will soon be available to help women with breast cancer make one of their most crucial decisions, whether to undergo the rigours of chemotherapy.

At present, doctors predict the chances of a relapse by looking at the patients age, size and aggressiveness of the tumour. If the chances of recurrence are seen as very low based on the gene test, a woman may opt to not endure chemotherapy. However, if the chances of cancer coming back are high, she may view chemotherapy as the difference between life and death. The companys research was carried out together with the National Surgical Adjuvant Breast and Bowel Project. The test would be available to newly diagnosed cancer patients in early 2004.

The genetic test was developed by analysing tumour samples from nearly 700 women involved in a 1980s cancer study. Genomic Health used its findings to create a point system to express escalating chances of recurrence within 10 years. The sample group included women from their 30s to 70s. All had early-stage breast cancer that had not spread to other parts of the body and all had been treated for at least five years with tamoxifen, a drug that slows or stops the growth of new breast cancer cells. It was found that just over half of the women in its sample group fell into the low-risk category. Their average recurrence rate was about 7 per cent after surgery to remove the tumour, followed by tamoxifen. At the other end of the scale, 27 per cent of the sample were determined to be at high risk of recurrence. About three in every 10 of these patients developed new breast cancer within 10 years of treatment. In the intermediate-risk group, the 10-year recurrence rate averaged about 14 per cent. The error rate in each of the three categories was 2 to 3 percentage points. By using a scoring system, the companys test can give women a more individualized prognosis.


Chromosome 6 sequenced

Scientists at the Wellcome Trust Sanger Institute in the United Kingdom have completed sequencing human chromosome 6, the largest chromosome to be sequenced to date (requiring eight years). The team has corrected most of the previous errors in the DNA sequence, annotated genes on the chromosome and included the latest biological research related to these genes. Chromosome 6 has 1,557 genes and about half of these have no known function. This chromosome carries one of the most important regions in our genome for fighting disease, called the major histocompatibility complex (MHC), which has been linked to over 100 diseases including many autoimmune diseases like multiple sclerosis and type 1 diabetes. Mutations on chromosome 6 are also responsible for a form of childhood Parkinsons, epilepsy and cancers.

Chromosome 6 was compared in the genomes of five other animals mouse, rat, zebra fish and two species of puffer fish. Regions that are conserved between different animals were identified indicating that these may contain important genes or regions that regulate genes. Scientists are already using the DNA sequences for building better tools to screen patients for mutations associated with cancer and other diseases. Chromosome 6 joins 7, 14, 20, 21, 22 and Y among the ranks of essentially complete and published chromosomes.



Stem cells counter tumours in novel gene therapy delivery

Researchers at the University of Texas M. D. Anderson Cancer Centre, the United States, have succeeded in genetically engineering stem cells that can find tumours and then produce biological agents right at the cancer site. This new treatment may offer the first gene therapy delivery system capable of homing in on and then attacking cancer that has metastasized anywhere in a patients body. The stem cells will not be rejected even if they are not derived from the patient. This system has been tested in mice with a variety of human cancers including solid ones such as ovarian, brain and breast cancers, melanoma and even blood-based cancer like leukaemia.

Patent applications have been filed on the system, which uses human mesenchymal progenitor cells (MSC), the bodys natural tissue regenerators. These unspecialized cells can migrate to an injury by responding to signals from the area and there they develop the kind of connective tissue that is needed to repair the wound, and can become any kind of tissue. In their novel delivery system, researchers isolate a small quantity of MSC from bone marrow and greatly expand the quantity of these cells in the lab. They then use a virus to deliver a particular gene into stem cells. When turned on, this gene will produce an anti-cancer effect. When given back to the patient through an intravenous injection, the millions of engineered mesenchymal progenitor cells will engraft where the tumour environment is signalling them and activate the therapeutic gene. According to Dr. Michael Andreeff, the leader for this study, results suggest that gene-modified MSC can inhibit the growth of leukaemias, metastatic tumours of the lungs, and ovarian and brain tumours.


Polio vaccine may spawn disease

A team of scientists led by Dr. Vadim Agol of Moscow State University, Russia, have found that mutated vaccines might seed new bouts of poliomyelitis, even after the disease is stamped out. The common oral polio vaccine (OPV) contains a live virus that can mutate into a disease-causing form and spread. The global vaccination programme has confined the paralysing polio virus to just seven countries in Africa and Asia. Doctors hope to wipe out these pockets as early as next year and certify a polio-free world by 2007. However, the study warns that as vaccination rates drop off the disease may resurface.

Dr. Agols team used archived samples to study the genetic sequence of polio virus circulating in a region of the former Soviet Union, where vaccination was halted from 1963 to 1966. They found nine strains that descended from OPV and are rapidly mutating. Around 37 per cent of unvaccinated children had probably been exposed to these or other vaccine-derived strains. The findings suggest that if countries stop using OPV, mutant virus might spread into the unprotected population from neighbouring regions. Deploying stockpiles of OPV to combat these infections might unleash even more potentially harmful virus.


New strategy to help prevent transplant rejection

In the United Kingdom, researchers from Imperial College, University of Cambridge, University of Edinburgh and Lorantis Ltd. have shown for the first time that it is possible to help prevent organ rejection using a novel strategy that redirects the bodys immune response instead of suppressing it. Researchers used mice to demonstrate that it is possible to alter whether T white blood cells specialize to attack foreign tissue and thus cause rejection, or become part of the bodys peacekeeping force, which patrols the body defending against attacks. Unlike current therapies that leave patients vulnerable to infection by inducing non-specific immunosuppression, this new approach targets a key cellular signal known as Notch, which acts as a gatekeeper by governing how immune cells specialize.

Results show that exposing mice to a combination of the Notch signal and material from the donor two weeks in advance of transplantation stimulates an immune response and significantly increases transplant acceptance from 20 to 80 days. The key role that T suppressor cells play in preventing organ rejection is also supported by the observation that depleting their numbers at the time of transplantation reverses pretreatment effects and reduction in the number of T helper cell numbers enhances transplant survival.


Cuba produces synthetic vaccine for children

Scientists at the Synthetic Antigens Laboratory of the University of Havana, Cuba, have developed the first synthetic vaccine against a bacteria that causes pneumonia and meningitis after six years of intense research. The vaccine protects against type b Haemophilus influenzae, a bacteria that causes upper respiratory infections, mainly in children up to five years of age. The disease is a leading cause of meningitis, an infection of the brain and spinal cord coverings that can cause brain damage, deafness or death.

This is the first vaccine for humans made with a chemically produced antigen. Presently available conventional vaccines are made using a difficult and more costly process of growing antigens in a bacterial culture. It is expected that poor nations depending on multinational pharmaceutical firms for the vaccine, which costs about US$3 a dose, will now have a less expensive alternative. Clinical trials conducted in the central Cuban province of Camaguey first on adult volunteers, then on four year olds and finally on babies demonstrated a 99.7 per cent success rate in developing the required antibodies. Technology for the new vaccine was patented in 1999 by the University of Ottawa and University of Havana.


Promising drug for rheumatoid arthritis

Bristol-Myers Squibb Co., the United States, is developing an experimental drug that blindfolds immune system cells that attack the body and is better than conventional care for rheumatoid arthritis (RA). The drug, a protein named CTLA4Ig, prevents T-cells from seeing and going after their targets in joint tissue. Volunteers who took CTLA4Ig in addition to the conventional therapy for RA were nearly twice as likely to experience a 20 per cent reduction in joint pain and swelling, among other symptoms, than those on the usual treatment alone. Those on the drug which prevents T-cells from binding with one of two molecules that activate them were also more likely to exhibit dramatic improvements, though the number of patients who did so was small. While the principal effect of CTLA4Ig is to keep T-cells inactive, the drug also removes inflammation in other ways, such as by preventing immune cells from migrating to sites of inflammation.


SARS corona vaccine tested in animal model

In the United states, researchers have shown that an adenoviral-based vaccine can induce SARS-coronavirus (SARS-CoV)-specific T-cell and virus neutralizing antibody response. The team was led by Dr. Andrea Gambotto from the Departments of Surgery and Medicine, Division of Infectious Diseases and the Molecular Medicine Institute (MMI) at the University of Pittsburgh School of Medicine and the Graduate School of Public Health (GSPH), in collaboration with colleagues at the Centre for Disease Control and Prevention (CDC). This study represents the first published work on the development of a SARS vaccine.

In the study, researchers immunized six rhesus macaques intramuscularly with a combination of three SARS-CoV vectors. Two additional rhesus macaques were immunized with the same amount of empty adenoviral vector, to serve as controls. After a period of 28 days, the animals received a second vaccination. Six weeks later, T-cells and antibodies against SARS were detected in the six immunized animals, but not in either of the control animals. The intensity of the response varied but was generally largest after the booster vaccination. Serum samples from the vaccinated animals, but not from the controls, showed strong neutralizing capacity against SARS-CoV.

It was found that after injection, the vaccine acts as a Trojan horse, first by infecting cells in the body and then stimulating an immune reaction to the delivered SARS antigens, ultimately conferring protection against the disease. Further, the induced immune reaction appears to be broad both antibody and cell-mediated immune responses, equally important for protection from viral infections, were detected in the test animals. The team plans to test the vaccine on ferrets and human clinical trials may be conducted soon.



Database provides window into protein-protein interaction

Scientists led by Dr. Akhilesh Pandey of Johns Hopkins University Medical School in the United States and the Institute of Bioinformatics, India, have compiled a new on-line database, the Human Protein Reference Database (HPRD), which enables biologists to tap into annotated entries on the 3,000 most-studied human proteins and how they interact. Protein-protein interactions are viewed as fundamental to understanding the dynamics of human health and disease. At least 70 databases include information on various aspects of protein-protein and protein-gene interactions. Therefore, rather than putting the existing databases together, Dr. Pandeys team has designed a software that searches by protein name, molecular class, size, localization and functions, modifications that occur in the protein and a range of other characteristics. Each datum is referenced to the experimental literature. Access is free for academic researchers while companies interested in using the database have to pay fees according to licensing criteria being established by Johns Hopkins Licensing and Technology Development.


Latin America gets new bioinformatics network

The Iberoamerican Network for Bioinformatics has been launched in Latin America to boost regional collaboration in bioinformatics. Set up in October 2003, the network is intended to improve training, increase research coordination and encourage student exchanges in the region. It links more than 20 research groups from Argentina, Bolivia, Brazil, Chile, Colombia, Cuba, Mexico, Paraguay, Uruguay and Venezuela, as well as Spain. The Network will receive 50,000 euros/year from the Spanish governments Iberoamerican Programme of Science and Technology for Development. It will collaborate with another initiative, the Latin American and Caribbean Network for Bioinformatics, set up last year to promote training, research and information on bioinformatics.



Researchers design and build first artificial protein

In the United States, researchers led by Dr. David Baker of Howard Hughes Medical Institute and the University of Washington have designed and constructed a novel functional protein that is not found in nature. The protein was created using sophisticated computer algorithms running on standard desktop computers. This achievement will enable researchers to explore larger questions about how proteins evolved and why nature chose certain protein folds over others. The ability to specify and design proteins also opens the way for researchers to engineer artificial protein enzymes for use as medicines or industrial catalysts.

In their design and construction effort, scientists opted for a version of a globular protein of a type called an alpha/beta conformation that was not found in nature. According to Dr. Baker, they chose this conformation because there are many of this type that are currently found in nature, but there are examples of possible folds that have not been seen yet. The computational design approach was iterative in that they specified a starting backbone conformation and identified the lowest energy amino acid sequence for this conformation using the Rosetta Design program developed previously. Researchers then kept the amino acid sequence fixed and used the Rosetta structure prediction methodology successfully used earlier for ab initio protein structure prediction to identify the lowest energy backbone conformation for this sequence. Finally, they fed the results back into the design process to generate a new sequence predicted to fold to the new backbone conformation.


Worlds first proteomics map of multicellular organism

The worlds first comprehensive protein interaction map for a multicellular organism, Drosophila melanogaster, was completed recently in the United States. This effort was undertaken by CuraGen, a genomics-pharmaceutical firm, in collaboration with researchers at the Johns Hopkins University, Wayne State University School of Medicine and Yale University School of Medicine. The research utilized yeast two-hybrid protocol in a high throughput mode to capture a significant fraction of the organisms protein-protein interactions. The map tracked over 20,000 (unique) interactions involving approximately 7,000 genes in D. melanogaster.

Mathematical modelling of the interactions between apparently disconnected proteins revealed both local and global connections among and within various protein complexes. It is expected that the vast amount of important new information reported will provide researchers around the globe with productive avenues to pursue for years to come. Since much of the understanding of the complex biochemical pathways that underlie human disease has been derived from the study of D. melanogaster, having the opportunity to integrate the new huge proteomic dataset with prior knowledge of this well-studied organism will be a boon to the understanding of normal biology, as well as human disease.


International collaborators to form worldwide protein data bank

A joint effort between the Research Collaboratory for Structural Bioinformatics (RCSB) of the United States, the Macromolecular Structure Database at the EMBL-European Bioinformatics Institute (MSD-EBI) and Protein Data Bank Japan (PDBj) has led to the formation of the Worldwide Protein Data Bank (wwPDB). This venture reflects the growing international and interdisciplinary nature of scientific research and formalizes the global character of the Protein Data Bank (PDB), which has been used as an international resource for the collection and sharing of three-dimensional information on proteins and other large molecules since its inception 32 years ago. Formation of the wwPDB will be transparent to users and ensure overall quality and consistency of data available directly through PDB.

Dr. Helen Berman, Director of RCSB PDB, states that by providing a formal mechanism for standardizing the presentation of PDB data, software developers and users of the data will be assured of consistent data. At the same time, it is hoped that wwPDB will allow for individual creativity on how data is presented and made available. PDB is the single archive of biological macromolecular structure data, which is made freely and publicly available to researchers, educators and students. Worldwide, the PDB receives over 60 million hits per year. As of 28 October 2003, it listed 22,984 structures, a number that has been growing exponentially. According to a 10-year agreement signed by the three founding members of the wwPDB, responsibilities relating to data deposition, data processing and distribution would be shared. An international advisory board will be formed to support the collaboration.


Cell dividing protein key to cell growth

In the United States, scientists at the University of Texas M.D. Anderson Cancer Centre have found that a single protein known as ARF helps coordinate both growth and division within a cell functions that are often disrupted in cancer development. Although many proteins have been found in cancer research that are associated with either errant cell division or uncontrolled growth, ARF is the first master molecule that seems to be involved in both crucial aspects of the cell cycle. According to team leader Dr. Yanping Zhang, this work helps explain why so many human cancers, more than 40 per cent, are found to have altered ARF proteins. The picture of molecular cell processes now painted by investigators also suggests that drugs might be developed that could mimic normal ARF function.

Cells that grow often divide and ARF has a known function in regulating this aspect of the cell cycle. ARF works in conjunction with the p53 protein, a tumour suppressor that blocks the cell cycle if the cell starts to grow erratically. Abnormally high levels of molecules that signal this kind of growth activates ARF, which in turn facilitates p53 to accumulate in the cell to halt the growth. As such, ARF and the proteins it has power over are major players in cancer development. ARF is the second most frequently altered protein in cancer development. This study shows that ARF also controls a protein known as B23, found in abnormally high levels in almost every tumour cell.

Contact: Ms. Heather Russell, University of Texas M. D. Anderson Cancer Centre, the United States. Tel: +1 (713) 7920 655.




Bayer gets exclusive rights to plant-parasite patent

The European Patent Office has issued a patent for a technology that is the basis for all genetically modified plant production. The patented method is based on the plant parasite agrobacterium, which can cause tumour development in plants. This brings to an end the longest-running patent battle in the history of plant biotechnology between the German firm Bayer AG and the United States company Monsanto.

Bayer was awarded exclusive patent rights on a plant parasite technology developed by the Max Planck Society of Germany. This technology allows researchers to exploit the natural genetic engineering capacities of bacteria and turn these into a basic tool for the production of transgenic plants. Though Monsanto developed a similar technology, the United States Patent Office recently decided that Monsantos patent interfered with that of the Max Planck Society. The Max Planck Society invented the technology 20 years ago, but the European Patent Office only issued a patent on November 2003, a fact that highlights the controversy surrounding the technology and Europes hesitation to accept such research developments. The new patent will now be the dominant patent in relation to the production of transgenic plants.


Pyramided treatment for insect resistance

Dr. Jian-Zhou Zhao and colleagues at Cornell University, the United States, have reported an evaluation of methods used for determining the efficacy in delaying insect resistance in a model system. The development of transgenic crops bearing insecticidal genes can benefit the environment by decreasing the use of insecticides, but evolution of resistance to genetically engineered toxins in the target insects could threaten such benefits. Reducing acquisition of resistance by insects can be achieved by the use of two different transgenic plants grown sequentially in mosaics, or by mixing genetically engineered seeds, or by the use of crops bearing two different toxin genes in the same plant (pyramiding). Scientists show that by far the most efficient method is pyramiding. These results have implications for the current use of single transgene plants as well as for growing strategies in the future.

Dr. Zhaos team developed and tested a model greenhouse system using an artificial population of four strains of the diamondback moth Plutella xylostella and broccoli plants bearing either or both transgenic toxins Cry1Ac and Cry1C from Bacillus thuringiensis (Bt). The team tested plant and insect combinations that included moths carrying genetic resistant to one, other or both toxins and broccoli grown sequentially, in mosaic or alone as double transgene plants. Numbers of surviving larvae and pupae were followed over 24 generations and analysed for resistance. Researchers found that Cry1C resistance evolved more slowly than Cry1Ac resistance, attributing this to multigene control of resistance for Cry1C as opposed to single autosomal inheritance for Cry1Ac. Survival of larvae and pupae on plants grown in mosaic or with Cry1Ac as first in sequence was significantly greater (more than 70 per cent after 18-24 generations) than those on double transgene plants, demonstrating the mosaic strategy to be clearly inferior. For two-gene plants, insect survival was almost zero.

According to scientists, although the population sizes were much smaller than those occurring in nature, the selection response to Cry1Ac in the pyramided treatments showed that their experiments had initial resistance frequencies sufficiently high to generate the effects expected in the field, i.e. resistance can still evolve to pyramids. However, scientists caution that although Bt cotton with the pyramided two Bt genes is now in commercial use, total replacement of Cry1Ac gene varieties with two Bt gene varieties is not expected to occur for many years.


Biotech corn can boost yields to meet growing world demand

A report from the International Service for the Acquisition of Agri-biotech Applications (ISAAA) has indicated that wider global adoption of the first generation of biotech corn or maize could produce an additional 35 million tonnes of corn, more than a 5 per cent increase globally. This would enable developing countries to meet the rising demand for corn which, by 2020, will surpass wheat and rice as the worlds No. 1 crop. The report said rising incomes in the developing regions of Asia and Latin America are triggering a shift towards more meat consumption, which will cause a dramatic increase in demand for corn-based animal feeds.

Bt corn can reduce by half the estimated 9 per cent loss of the global corn harvest to insect pests. The pest-resistant corn also can make food and feed safer by minimizing insect damage that causes incidence of harmful mycotoxins, according to the report. In addition, wider adoption of Bt corn could halve pesticide spraying. The report said average yield gains for Bt corn over traditional varieties were an average of 5 per cent higher in the United States, 6 per cent more in Spain and about 10 per cent greater in Argentina and South Africa. In Spain, the only country in the European Union to grow a significant area of the biotech crop, growers realized gains of 170 euros/ha due to increased productivity and insecticide savings. In field trials, Bt corn yields were 24 per cent higher in Brazil, up to 41 per cent more in the Philippines and 9- 23 per cent greater in China. Second-generation biotech corn will yield even more gains with US$1 billion in annual benefits accruing to the United States alone.


Biotech companies muscle in on rice research

With the sequencing of the rice genome, biotech companies are entering into rice research as donor funds for studies. According to officials at the International Rice Research Institute (IRRI) in the Philippines, there are large untapped commercial possibilities of the tiny cereal giving rise to potential intellectual property rights altercations between governments and corporate entities.

The advent of biotechnology has caused a spurt in patents on gene products associated with rice. However, compared with wheat or maize rice patents comprise a very small percentage among the cereals. Held in deep freeze at a laboratory near Manila, IRRI holds in trust for humanity an invaluable gene bank of more than 100,000 rice varieties. It distributes the seeds globally for research on the condition that the users do not take out patents on them.


Photosynthesis resolved

In France, Dr. David Stroebel and colleagues at the National Centre for Scientific Research/Universit Paris have resolved the X-ray structure of the major pigment-containing protein complexes involved in photosynthesis. This breakthrough has enabled identification of the properties of a key protein complex of the photosynthetic electron transfer chain, cytochrome b6f, and describe important features that refine the understanding of the photosynthetic pathway. It provides new insights into this most fundamental of biochemical processes.

In oxygen-producing photosynthetic organisms, light energy is captured by the reaction centres photosystem II (PS-II) and photosystem I (PS-I) both large membrane-embedded protein complexes and used to extract electrons from water molecules. These electrons then pass through a long chain of redox co-factors until they reach nicotinamide-adenine dinucleotide phosphate (NADPH), transforming it into the reducing agent NADPH, which is required for the synthesis of sugars. Cytochrome b6f plays a crucial role in this process, shuttling electrons from PS-II to PS-I and pumping protons across the photosynthetic membrane. This transmembrane proton gradient is ultimately used to generate adenosine triphosphate (ATP), which fuels cellular metabolism. A characteristic of cytochrome b6f is its ability to switch to a cyclic mode of electron transfer around PS-I, that boosts ATP synthesis but stops the production of NADPH by diverting electrons from their original linear flow.

Dr. Stroebel and colleagues determined the 3.1 structure of the cytochrome b6f complex purified from chloroplasts of the unicellular alga Chlamydomonas reinhardtii. Cytochrome b6f comprises several membrane-spanning proteins with a range of pigments attached, including chlorophyll and -carotene. Overall, the structure resembles that of the mitochondrial cytochrome bc1 complex, which has electron transfer and proton translocation functions similar to those of b6f. In particular, the core of the two complexes shares a common organization, with two b-type haems involved in electron transfer. Outside the core, however, the b6f design in unique. Scientists also identified a third haem bound to a hydrophobic cavity of cytochrome b6f.



Biotechnology: The Making of a Global Controversy

Biotechnology is one of the fastest growing areas of scientific, technical and industrial innovation, and one of the most controversial. New developments have made public debates more heated and grave concerns expressed about access to genetic data, labelling, etc. This book provides results of a unique cross-national and cross-disciplinary study of the relationship between the development of new biotechnology and public perception, media coverage and policy formulation. It outlines a new conceptual framework for understanding these issues and contains several empirical studies, including studies of the international controversies surrounding the cloning of the sheep Dolly and GM soya.

Contact: Cambridge University Press, the United Kingdom. Tel: +44 (01223) 326 050; Fax: +44 (01223) 326 111.

Biotechnology: Present Position and Future Developments

This book examines current trends in biotechnology worldwide, public concerns and the potential in a wide range of sectors. It focuses on the applications of biotechnology, various technologies, explains the progress made to-date and outlines the future of the technology for each application. Key areas covered are crop production, animal biotechnology, environment, industrial biotechnology and animal and human health. Other topics covered include developments in new platform technologies like genomics, proteomics and bioinformatics, imaging and optical biology, biosensors, bioelectronics and bionetworks, etc. The publication also discusses the major contributions biotechnology can make to medicine and healthcare by facilitating improved approaches to diagnosis, treatment and prevention of diseases.

Contact: Teagasc, 19, Sandymount Avenue, Ballsbridge, Dublin 7, Ireland. Tel: +353 (1) 6376 000; Fax: +353 (1) 6688 023.


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