VATIS Update Biotechnology . Mar-Apr 2004

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Biotechnology Mar-Apr 2004

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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United Kingdom keen on Indian biotech sector

Academic institutions affiliated to the University of Abertay Dundee (UAD), the United Kingdom, are being encouraged to work with India as it develops a multimillion pound biotechnology industry. The life sciences sector in Scotland, served by 428 organizations, has been growing at around 30 per cent a year. India had 176 biotechnology firms in 2001 and many of these are extremely successful and fuelling a sector worth US$90 million.

The British Council in India is funding a series of visits from UAD to universities and schools in major Indian cities and share its experience in educating young people so that they are ready to fill up employment opportunities that will arise with the sectors success. Prof. John Palfreyman, Head of Abertays School of Contemporary Sciences, has already made a preliminary trip to India where he visited six schools and three universities in Chennai and Delhi. According to him, India is in a similar position to Scotland when biotechnology was in its infancy. A delegation from Abertay, comprising academics from the School of Contemporary Sciences, is scheduled to tour India in August.

Advanced Biotech, February 2004

Marsupial next in line for genome sequencing

In the United States, the Large-scale Sequencing Research Network supported by the National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), will begin sequencing the genomes of more than a dozen new model organisms, including the first marsupial to have its DNA deciphered. This project is part of an effort to further advance understanding of the human genome. According to NHGRI, the ability to compare a wide range of genomes is the best tool currently available to discern the underlying genomic components affecting human health.

The first marsupial selected for sequencing is the gray short-tailed South American opossum (Monodelphis domestica). The opossums position in the evolutionary tree is a major reason for its inclusion in the DNA sequencing programme. Opossums and humans diverged from a common ancestor 130 million years ago, providing a unique mid-point on the evolutionary time-line for comparative studies involving other mammals, like mouse, which separated from humans 75 million years ago and non-mammalian relatives, e.g. birds, which diverged 300-350 million years ago.

Chronicle Pharmabiz, 4 March 2004

Indian institutes join hands with Australia on biotech research

The Indian Institute of Science (Bangalore) India, has entered into a collaborative agreement with the University of Melbourne in Australia for medical biotechnology. The areas of research covered are cancer, infectious diseases, immuno-diagnostics and pharmacogenetics. Another Indian institute, the Manipal Academy of Higher Education, has also teamed up with universities in Australia. A three-day Indo-Australian conference on Biotechnology in Medicine, conducted during 9-11 February 2004 at Bangalore, was the maiden initiative by the two nations to sit together and deliberate on potential research opportunities.

Chronicle Pharmabiz, 19 February 2004

Biotech hub in Malaysia

Bio Valley Malaysia (BVM) is a biotech cluster created recently in Malaysias Selangor state. BVM has three major components comprising a centre of excellence for research and education, a hub for biotechnology and a gateway for bioinformatics. The programme focuses on three major areas genomic and molecular biology, nutraceuticals and pharmaceutical biotechnology, and agricultural biotechnology.

Selangor is the most active place for biotechnology in Malaysia. This state boasts of good universities, and industrial and physical infrastructure. Plans are afoot to make Selangor a model state in the biotech sector. A separate biotechnology programme has been framed by the state to work on further development of the biovalley. A Bio-IT centre has also been proposed, which will house an industrial complex on about 40 acres and a 10 acre bio-innovation complex.

Chronicle Pharmabiz, 12 February 2004


Spectral Geneomics receives licence for nucleic acid arrays

In the United States, Spectral Genomics Inc. (SGI) and Affymetrix have reached an agreement that provides SGI with a worldwide licence to certain Affymetrix patents for manufacturing and selling spotted DNA arrays for use in the diagnostics market, once the essential regulatory approvals have been obtained. SGI develops and manufactures BAC clone arrays that can cover the entire genome representing all the chromosomes at ten times higher resolution than with traditional cytogenetic techniques. The arrays are used in research on pre- and post-natal genetic defects and cancer.

The licence supports SGIs Constitutional Chip, to be introduced in 2004, as well as anticipated speciality arrays to be used in cancer diagnostics. SGI is also seeking regulatory approval for the chips in the diagnostic market. This license would provide additional intellectual property enhancing SGIs proprietary position in BAC clone arrays for research in cytogenetics and molecular biology.


Reagents for GeneChip expression array platform

In the United States, Affymetrix Inc. has launched a new line of GeneChip brand expression reagents that include two cDNA Synthesis Kits, developed together with leading reagent provider Invitrogen Corp. These reagents have been optimized for use with Affymetrixs GeneChip technology, offering a complete, standardized sample preparation system that is easier to use and will help customers produce more robust and consistent array results.

The cDNA kits contain Invitrogens industry-leading SuperScript reverse transcriptase. The one-cycle kit provides all the necessary reagents for standard target labelling, using as little as 1 g of total RNA as starting material, prior to the IVT labelling step. The majority of Affymetrix customers have used this protocol already, but the new kit ensures improved configuration and greater convenience. The two-cycle cDNA kit offers customers a streamlined procedure for preparing samples using a small amount of material, such as biopsy or laser capture dissected samples. It contains all necessary reagents for performing two cycles of cDNA synthesis before IVT Labelling. The entire two-cycle cDNA protocol requires 2 days.

The kits are designed for use with the GeneChip IVT Labelling Kit, employed in standard and small sample target labelling protocol for linear amplification and labelling of targets with biotin. GeneChip IVT Labelling Kit was specifically developed for the GeneChip platform and provides high yield, consistent and uniform labelling efficiency, with a more streamlined protocol and convenient packaging. According to Mr. Alan Dance, Affymetrixs Senior Vice-president of Marketing, by optimizing reagents, instrumentation and software using a systems approach, they are able to offer the best microarray performance available and continue to raise the standard of accuracy and reproducibility in gene expression analysis.


Introgen gets patent for adenoviral formulation technology

In the United States, the Patent and Trademark Office has awarded Patent No. 6,689,600 to Introgen Therapeutics Inc. The patent, titled Formulation of Adenovirus for Gene Therapy, covers Introgens technology for producing long-term storage-stable adenovirus. Such formulations may eventually replace those currently employed in the adenovirus industry by providing conveniences and efficiencies in storage, dispensary and pharmacy handling, etc. Introgens patent addresses the need for formulations that permit long-term storage of adenoviral therapeutics under regular refrigerated conditions.

Chronicle Pharmabiz, 19 February 2004

GeneTech to establish biochem and DNA molecular labs

In India, the Hyderabad-based genetic diagnostic services company GeneTech is planning to set up two research laboratories catering to biochemical and DNA molecular studies. The company will invest about US$0.2 million and is expected to open the labs near its existing premises. According to Dr. Anuradha Udumudi, Founder and Director of GeneTech, the molecular lab would be open for contract research to facilitate pharmaceutical firms. The biochemical lab would enable detection of common metabolic diseases that can be treated. Neonatal screening will help in controlling genetic disorders such as hypothyroidism, PKU and galectosomia in the early stages.

GeneTechs goal is to become a comprehensive genetics diagnostic and counselling centre. It has established links with 23 labs in Andhra Pradesh as well as in neighbouring states under the GeneTech Partnership Programme. The company has also established service linkages with government and missionary-run hospitals, extending services at nominal charges. It has also collaborated with the United Kingdoms University of Leeds, to jointly work and provide advisory and research support for Downs Syndrome screening and infertility related aspects.

Chronicle Pharmabiz, 12 February 2004

Generex gets defence grant for novel vaccine technology

Antigen Express Inc., the United States-based subsidiary of Generex, Canada, has received a US$525,000 Concept Award from the United States Department of Defence for further development of a novel vaccine technology. The Review Group for this Concept Award was charged with identifying applicants with new paradigms in the study of critical problems faced in prostate cancer research. Antigen Express has pioneered and patented novel procedures to enhance antigen-specific immune responses. Such antigens may arise in cancers or virus-infected cells, or can be induced by a DNA vaccine. Antigen Express is focusing on the development of vaccines for HIV, cancer, SARS and bioterrorism agents.

Chronicle Pharmabiz, 5 February 2004

Biocon files insulin DMF, ties up with Bristol-Myers

Indias biotech major Biocon has filed a drug master file (DMF) for recombinant human insulin with the United States Food and Drug Administration, making it the first Indian company to file a DMF for insulin. Biocon has also entered into an agreement with Bristol-Myers Squibb (BMS), the United States, to supply insulin; expected to commence once BMS gets the necessary regulatory approvals. The agreement is non-exclusive in nature, but it is for BMS global operations. Biocon has already completed clinical trials and is awaiting regulatory clearances for the recombinant insulin. It plans to launch the product in India under the brand name Insugen in the first half of 2004.

Chemical Weekly, 9 March 2004

MAHE-HP join hands for pharmacogenomics centre

In India, the Manipal Academy of Higher Education (MAHE) has signed an MoU with Hewlett-Packard India Pvt. Ltd. to support the creation of a Centre of Excellence (CoE) in Pharmacogenomics at MAHEs campus. The CoE would investigate into new pharma and biotech products using the genomics platform. With investments to the tune of about US$1.8 million, the CoE is expected to be complete during the current calendar year. Initially, the CoE would focus on cancer and infectious diseases, with currently one project in asthma and AIDS. It has already received grants for cancer and asthma and has applied for grants from the National Institutes of Health (NIH) in the United States as well as the Indian Council of Medical research (ICMR), based in New Delhi, the Department of Science and Technology and a couple of other universities.

Express Pharma Pulse, 18 March 2004

New osteoporosis drug slated for launch in India

The Indian subsidiary of the United States-based Eli Lilly and Co. is set to launch its recombinant DNA drug for osteoporosis. The new drug, Forteo, would soon be available in India, with the company having already received permission from the Drugs Controller General of India for import and marketing.
Forteo is the active part of parathyroid hormone (PTH), which is naturally found in the body. This drug is given by injection to treat osteoporosis in men and post-menopausal women who are at a high risk of sustaining fractures. Phase III clinical trial data has shown that the drug stimulates new bone formation, lowers the risk of vertebral (spinal) fractures and increases bone mineral density compared with placebo in post-menopausal women with osteoporosis over an average treatment period of 19 months.

Chemical Weekly, 17 February 2004


Stress gene in plants identified

In the United Kingdom, scientists at the universities of Bristol and Oxford, led by Dr. Claire Grierson, have isolated and characterized a gene called OXI1 from thale cress (Arabidopsis thaliana) that helps plants cope with stressful situations like disease or poor environments. OXI1 boosts the plants ability to stop fungal infection from spreading and helps roots to grow despite poor conditions.

Dr. Grierson stressed that this technique was a significant advance from traditional approaches, where investigators have to identify a different gene for each disease or stress they hope to fight. Scientists at Bristol have shown that the new gene is not just important for overcoming disease but is also involved in another type of stress growing in difficult conditions. Studying the OXI1 gene will help understand more about how plants and other organisms deal with stress. As genes similar to OXI1 are likely to be found in many other organisms, in the long term, this work may even provide an insight into medical applications for humans.


Cell fusion: New way to repair organs, deliver cancer vaccines

Researchers led by Dr. Stephen Russell at Mayo Clinic, the United States, have developed a way to biologically fuse living cells through the use of a genetically engineered cell membrane. Named biofusion, this process represents a promising new technological platform for enlisting the natural properties of fused cells to kill cancers, stimulate immune responses or repair damaged tissues.

The key to biological cell fusion is that when two cells come into contact, fusion proteins on the surface of one cell recognise a receptor on the other cell. This act of recognition triggers fusion of their respective outer lipid membranes, just like two bubbles merging into one big bubble. However, when cancer cells fuse with each other, they may grow dramatically, containing up to 1,000 cancer cells, which is unviable and the cancer cells therefore die. The fact that fused cancer cells kill each other has been known for quite some time. However, the missing element has been a way to direct fusion partners to exploit this tendency and use it as a basis for anti-cancer treatment. The ability to target fusion partners is important since if the wrong cells fuse, then healthy cells, instead of the cancerous cells, could be killed.

According to Dr. Russell, their biofusion research brings a new level of control to the system so that the right fusion matches are made to serve therapeutic ends. The study offers a biotechnological platform that provides a way to choose and direct the agents of fusion by getting tumour cells to fuse with dendritic cells, a type of cell in the immune system. The result is biofusion that prompts the immune system to attack the tumour. The ability to fuse tumour cells to treat cancers is one application that researchers have envisioned for their biofusion platform. Another possible application involves cancer vaccines that prevent cancer from progressing or developing. Biofusion involves putting genes inside the bodys dendritic cells that will cause them to fuse directly with tumours at multiple sites in the patient.
A third possible application, still in the concept stages, involves stem cells. Research has shown that some of the stem cells repair properties come from their ability to fuse with cells that are naturally resident in the organs they are repairing. The new biofusion technology can be exploited to genetically engineer stem cells so that they fuse quickly and efficiently to a target site and thereby direct the repair process. (Website:

New research provides insights into cell growth

Researchers at the Washington University School of Medicine, the United States, have developed a new probe that allows them to watch protein activity in living cells. In the initial study, which focused on a protein tentatively linked to the spread of cancerous cells, the team showed that their technique works and revealed surprising new details about the proteins activity. Neuronal Wiskott-Aldrich syndrome protein (N-WASP), the protein in this study, is naturally found in every cell in the body and is known to be involved in a wide range of cellular processes. One of its key functions is believed to be guiding cellular growth and movement within the body, including when tumour cells metastasize, or spread, from one organ to another.

In designing the probe, the team took advantage of the fact that N-WASP folds in half when it is inactivated. They latched two fluorescent proteins on to the opposing ends of N-WASP one yellow and the other cyan. When stimulated by a particular wavelength of light, fluorescent proteins normally release energy in the form of light. In the case of yellow and cyan proteins, the light emitted appears either yellow or cyan. Under certain conditions, light energy from the cyan protein can be transferred to the yellow protein as cyan has a higher energy wavelength than yellow and energy naturally jumps from high to low energy states.

Eksigent debuts updated proteomics system

Eksigent Technologies, the United States, has announced several important enhancements to its NanoLC-1D Proteomics System. This is the first high-performance liquid chromatography (HPLC) system to allow nanoscale liquid chromatography mass spectrometry (LC/MS) without flow splitting, at gradient flow rates of 20-1,000 nl/min. It has been modified with several new features that improve the systems throughput and ease of use.

Dr. Karen Hahnenberger, Product Manager, states that their goal is to provide proteomics researchers with a complete solution to nanoscale LC/MS. Software integration of the NanoLC system with Thermos Xcalibur program allows researchers to set up experiments in a single software package, providing integrated control of the LC and mass spectrometer. This complete system integration makes setting up and running proteomics experiments significantly easier.

The NanoLC system now includes a rapid injection capability to load large samples on to trap or analytical columns. While LC/MS experiments are run at 100-200 nl/min, the sample size can often be 10 l or more. At these low flow rates, loading a sample can take hours. However, with the NanoLCs new rapid injection feature large samples can be loaded at a much higher flow rate, usually in a matter of minutes instead of hours. Once sample loading is complete, the system promptly resets to the desired analytical flow rate.

Express Pharma Pulse, 5 February 2004

Single, clonable, adaptable DNA strand

A group of scientists led by Dr. William Shih at the Scripps Research Institute, the United States, has designed, constructed and imaged a single strand of DNA that spontaneously folds into a highly rigid, nanoscale octahedron the size of a small virus or a cellular ribosome. This structure can be amplified with the standard tools of molecular biology and even cloned, replicated, amplified, evolved and adapted for various applications. The process also has the potential to be scaled up so that large amounts of uniform DNA nanomaterials can be produced. These octahedra are potential building blocks for future projects, from new tools for basic biomedical science to the tiny computers of tomorrow.

Dr. Shih and Dr. Joyce built a 1,669-nucleotide strand of DNA with a number of self-complementary regions, which would induce the strand to fold back on itself to form a sturdy octahedron. Folding the DNA into octahedral structures simply required heating and then cooling of solutions containing the DNA, magnesium ions and a few accessory molecules. Researchers used cryoelectron microscopy, in collaboration with research assistant Mr. Joel Quispe, of the Scripps Research Automated Molecular Imaging Group, to take two-dimensional snapshots of the octahedral structures. Significantly, the structures were highly uniform in shape; adequate to allow reconstruction of the three-dimensional structure by computational averaging of the individual particle images.

The DNA octahedron consists of 12 edges, six vertices and eight triangular faces. It is about 22 nm in overall diameter. Since all 12 edges of the octahedral structures have unique sequences, they are versatile molecular building blocks that could be potentially employed to self-assemble complex higher order structures. Potential applications include using these octahedra as artificial compartments into which proteins or other molecules can be inserted. The DNA octahedra could possibly form scaffolds that host proteins for the purposes of X-ray crystallography, which depends on growing well-ordered crystals consisting of arrays of molecules. Another potential application is in the area of electronics and computing. Computers, which depend on the movement and storage of charges, can potentially be built with nanoscale transistors.

Contact: Mr. Keith McKeown, 10550, North Torrey Pines Road, La Jolla, California 92037, United States of America. Tel: +1 (858) 7848 134; Fax: +1 (858) 7848 118



Human embryos yield stem cells

A team of researchers led by Dr. Woo Suk Hwang from Seoul National University, the Republic of Korea, has cloned human embryos and harvested stem cells from one of them. In culture, stem cells went on to form all the three main tissue types that normally appear in the beginning stages of embryonic development. This method may eventually help scientists develop replacement tissues for the treatment of many diseases, including diabetes, stroke and Alzheimers disease.

DNA from cumulus cells, a specialized type of cell that helps nourish developing eggs, was injected into 242 empty eggs, donated by 16 women, to obtain a total of 30 embryos. These embryos had the same DNA as their adult donors, making them clones, and were allowed to divide in culture for just 5-6 days before being terminated. When these cells were grafted into mice, they were able to form muscle, bone, connective and cartilage tissues. Researchers attribute their success to the use of extremely fresh eggs and a new, gentler method for removing DNA from donor cells.

Though therapeutic stem cell treatments are a long way off, this study sheds light on how adult human DNA could be reprogrammed into an embryonic state. According to Dr. Hwang, this approach would open the door for the use of specially developed cells in transplantation medicine. Researchers hope to produce stem cells for individual patients by injecting the patients DNA into an egg to obtain a clone. Stem cells from the clone would then be harvested and injected into the patient, where they may be able to repair and replace the damaged tissue. Since the cells are an exact tissue match, researchers opine that they will not be rejected.



CCMB develops capability for gene silencing

A team of scientists led by Dr. Utpal Bhadra and Dr. Manika Pal Bhadra at the Centre for Cellular and Molecular Biology (CCMB), India, has for the first time provided evidence for the role of small interfering RNA (RNAi) in gene silencing during the conversion of euchromatin to heterochromatin. The team demonstrated that disruption of RNAi interference mechanism in the living cell eventually affects specific chromosome regions.

Regulation of gene activity is controlled by several mechanisms in the cell. When the gene expression is completely stopped, or reduced dramatically, the phenomenon is known as gene silencing. One way by which genes are silenced in plants and animals is by interfering with the activity of the gene through RNA, a relatively small molecule, and this process is known as RNA interference. These small 21-25 nucleotide fragments called SiRNAs are also found to degrade the mRNA, which carries information for making proteins.

In transgenic plants and animals, multiple copies of transgenes introduced into the host genome become inactive because of such interactions; simultaneously, even some of the host genes get silenced. This creates a major obstacle for biotechnologists engaged in creating transgenic organisms with new traits for crop improvements and animal husbandry or doctors who look forward to use gene therapy to treat diseases. Although RNA interaction was being investigated in many biological systems, CCMB scientists are the ones who succeded in finding a way to overcome this obstacle.

Chronicle Pharmabiz, 26 February 2004

Scientists report sequencing of microbial community genome

In the United States, researchers have for the first time sequenced the genomes of the most abundant members of a community of microbes. The whole microbial community was sequenced at once, a technique called community genomics. The team took a simple community of organisms from a pink slick on the floor of Richmond mine in Iron Mountain, California, ground them up and shotgun sequenced the lot. As they put the pieces of DNA back together, the snippets fell easily into five distinct genomes, four of them unknown till now. The team was led by Dr. Jillian F. Banfield at the University of California-Berkeleys Department of Environmental Science, Policy and Management, in collaboration with the Joint Genome Institute.

Researchers reassembled the genomes, each containing about 2,000 genes, using different software programs to arrive at composite genomes. Two of the draft genomes, Leptospirillum group II bacterium and Ferroplasma type II microbe from the ancient group known as Archaea, are now about 97 per cent complete, with a few gaps. The genome of one of the six microbes in the community, Ferroplasma acidarmanus (a type I Ferroplasma), had been sequenced earlier by the team and was a good control during the sequencing and assembly process. The other genomes were highly fragmented but identifiable as microbes from Leptospirillum group III, Ferroplasma type I and a G-plasma microbe.

Once researchers had the five new genomes, they compared the genes in each with a database of known genes to identify their functions. For the two microbes with the most complete draft genomes, researchers were able to reconstruct nearly the entire metabolic cycle. Scientists determined how the microbes shared tasks in the isolated microbial community. The Leptospirillum group II bacteria fixed carbon and manufactured the biofilm that protected them and kept them afloat, while a minor member of the community, Leptospirillum group III bacteria, fixed both carbon and nitrogen. The iron is probably munched by all the members.


Steroids used in gene therapy

Researchers led by Dr. Scott Diamond at the University of Pennsylvania, the United States, have created a more effective gene delivery system by coating DNA with a common topical steroid. Researchers have shown that wrapping DNA in a common steroid not only allows the gene to be taken up into a cell more easily, but the steroid itself prevents the sort of inflammatory immune response seen in gene transfer therapy.

The team attached a steroid to DNA to suppress inflammatory cytokines created by the immune system after gene delivery. To counter the DNAs negative charge, they modified a common steroid, dexamethasone, for the job by adding nitrogen-rich, positively charged tail that glues the steroid to the naked DNA. According to studies in cell cultures and animals, the steroid-coated DNA caused greater gene expression and less inflammation. Cells also seemed more able to use foreign DNA effectively.

Dr. Diamond states that a steroid coating would greatly enhance the chances of successful gene transfer in humans, especially in inflammatory diseases. As an alternative, this coating technique could be used to tailor therapies by choosing drugs that would amplify the benefit of a particular therapeutic gene.


New genomics tool boosts diabetes research

A research team led by Dr. Richard Young at the Whitehead Institute for Biomedical Research, the United States, has devised a method for scanning the entire human genome to successfully map the location of key gene regulators, mutated forms of which are known to cause type II diabetes. This research marks the first time that human organs, pancreas and liver, have been analysed in this way and opens the door to similar studies of other organ systems and diseases. This work could lead to new approaches for developing medications and assessing a persons genetic risk to the disease.

Researchers developed an efficient gene-scanning technology for mapping genome binding sites for many transcription factors, proteins that bind to specific areas of the genome and act to switch genes on and off, in a human organ. This allowed them to identify the sets of genes where transcription factors adhered and acted as switches and to learn how defects in these switches might cause the disease. Application of the new technology to several transcription factors residing in the pancreas and liver, known to be associated with type II diabetes, revealed that one of the transcription factors, called HNF4, controls about half of all the genes needed to make the pancreas and liver. This suggests that without HNF4, these organs could not function normally, which is particularly relevant to diabetes because insulin is produced by the pancreas and loss of insulin production causes diabetes. The new evidence also explains why defects in the HNF4 transcription factor lead to diabetes. Even a small loss of HNF4 function could affect the health of the pancreas because this regulator is associated with so many important genes in the organ. Development of medications that modify the activities of mutated forms of HNF4 could possibly prevent diabetes in some at-risk individuals.

These findings go beyond diabetes and offer a whole new way of approaching research on many diseases like cancer, hypertension and immunological and neurological disorders. Discovering how transcription factors regulate genes in various human organs could provide clues to the causes of diseases and offer new approaches for therapy.


First avian genome available worldwide

A team of researchers led by Dr. Richard Wilson from the Washington University School of Medicine, the United States, has successfully assembled the genome of the Red Jungle Fowl, Gallus gallus, the ancestor of domestic chickens. Comprising about one billion DNA base pairs, this is the first avian genome to be sequenced. Researchers have deposited the initial assembly, which is based on seven-fold sequence coverage of the chicken genome, into the GenBank public database .To facilitate comparative genomic analysis, researchers have also aligned the draft version of the chicken sequence with the human sequence. The alignments can be scanned using the University of California, Santa Cruzs Genome Browser, 

An international team led by the Beijing Genomics Institute in China, supported by the Wellcome Trust in the United Kingdom, has created a map of genetic variation for three different strains of domestic chickens using the Gallus gallus genome sequence as a reference framework. The chicken strains are a broiler strain from the United Kingdom, a layer strain from Sweden and a Silkie strain from China. To make the map, researchers identified and analysed about two million genetic variation sites, mostly single nucleotide polymorphisms (SNPs).

From an evolutionary standpoint, chicken is well-positioned to provide an intermediate perspective between mammals, e.g. humans, and lower vertebrates like fish. By comparing the human genome with that of other organisms, researchers can identify regions of similarity and difference. This information can help scientists better understand the structure and function of genes and thereby develop new strategies to combat diseases.


Researchers decode genome of rabbit fever pathogen

The complete genomes of separate strains of Francisella tularensis (rabbit fever bacterium) have been sequenced by scientists at the United States Department of Energys Lawrence Livermore National Laboratory (LLNL) and Uppsala University in Sweden. F. tularensis Live Vaccine Strain (LVS) sequence, consisting of about 1.9 million base pairs, is being published on LLNLs website ( while the F. tularensis SchuS4 sequence is available at www.artedi.ebc. Once the genomes are fully annotated, both sequences will be submitted to GenBank to facilitate access by scientists around the world.

The intracellular pathogen invades human body cells, shuts down their normal immune response and then multiplies within the body. It can enter the body through open wounds, inhalation, ingestion or bites from ticks and deerflies. The bacteria causes a rare but serious disease called Tularaemia. While seldom fatal, and treatable with antibiotics, the disease causes severe, long-lasting pneumonia-like symptoms and a variety of glandular as well as intestinal disorders. As few as 10 organisms entering the body can cause fever, making tularaemia one of the most infectious of all diseases.

While the virulent SchuS4 strain sequenced by the Uppsala University is found primarily in North America, the microbe sequenced by LLNL is more widespread yet less virulent and is found in North America, Europe and North-east and Central Asia. In addition to being found naturally in the environment, F. tularensis is considered a potential biothreat agent. Prompt treatment with antibiotics can head off the worst symptoms of tularaemia, which is currently fatal in about 2 per cent of reported cases.



Gene expression assays predict responsiveness to drugs

Scientists at DeCode Genetics, Iceland, have developed gene expression assays capable of predicting a patients responsiveness to common drugs given for asthma and hypertension, including corticosteroids, angiotensin II inhibitors, leukotriene inhibitors, calcium channel blockers and ACE inhibitors. Encode, DeCodes pharmacogenomics and clinical trials subsidiary, states that assays developed through the companys DNA diagnostics alliance with Roche, Switzerland, are based on fewer than a dozen genes, the expression of which provides an 85 per cent accurate prediction of responsiveness to such drugs. DeCode is now working with Roche to validate these findings, with a view to developing novel diagnostic tests that will help clinicians select individualized treatment options for patients.

Genetic Engineering News, 15 January 2004

Genechip aids treatment of breast cancer

Researches led by Dr. Alane Koki at Ipsogen, France, have developed a genechip that will help guide breast cancer treatment choices based on an individuals genetic make-up. Expected to be available soon, the Breast Cancer ProfileChip uses DNA microarray technology to analyse the genetic characteristics of a persons tumour.

According to Dr. Koki, understanding differences in gene expression can help both patients and clinicians to decide what treatment would be most effective and appropriate. Tumours have different genetic signatures that can be read using DNA microarrays glass or plastic wafers, similar to computer chips, lined with pieces of DNA that act as probes to determine the activity of genes in a biological sample. Most existing procedures of diagnosing genetic signatures require samples to be sent to a lab. However, the Breast Cancer ProfileChip will be available to patients in clinics. It will concurrently measure expressions of more than 900 important genes to augment conventional methods for clinically assessing breast cancer. The genechip would also provide useful information to deliver a more personalized approach to patient care by providing both patients and physicians with reliable information to make informed, intelligent treatment decisions.


Designer mice yield heart-friendly nutrients

Geneticists led by Dr. Jing Kang of Harvard Medical School, the United States, have engineered a mouse strain to produce omega-3 fatty acids, compounds known to help prevent heart diseases in humans. If this feat can be replicated in livestock animals, they could be made to produce healthier milk, eggs and meat. In their study, mice were engineered to use a gene called fat-1, from the roundworm Caenorhabditis elegans, for converting omega-6 fatty acids into the healthier omega-3 version. According to Dr. Kang, mammals cannot ordinarily do this but if farm animals can make these compounds themselves, it may provide a way to increase peoples omega-3 intake without a lifestyle overhaul.

Many farmers already feed their chickens with ground-up fish to create omega-3-rich designer eggs, but this is costly and time-consuming. Dr. Kangs transgenic method could offer a simpler route to the same goal. Some researchers strongly feel that Dr. Kangs team should make sure the mice do not suffer long-term health problems before attempting to transfer the technology to any other species; but the idea shows promise and the team insists that transgenic mice are healthy.


First TB vaccine trial starts in the United States

The first phase of human safety testing of a recombinant tuberculosis (TB) vaccine, made with several proteins from the bacterium that causes TB, would soon be conducted in the United States by Seattle-based biotechnology company Corixa and GlaxoSmithKline Biologicals, a vaccine manufacturer headquartered in Belgium. The National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), has supported research on the candidate vaccine from its earliest stages.

The new vaccine combines two TB proteins known to stimulate strong immune responses in humans. These proteins were initially identified by screening blood taken from volunteers who never became ill with TB despite long-term infection with Mycobacterium tuberculosis. Using recombinant DNA technology, the TB proteins were fused and then combined with adjuvants, substances that further boost the immune systems response to the vaccine. Different versions of the candidate vaccine were tested in animals at Colorado State University.

Express Pharma Pulse, 5 February 2004

Scientists grow neurons using nanostructures

Scientists at North-western University, the United States, have designed synthetic molecules that promote neuron growth, a promising development that could lead to the reversal of paralysis resulting from spinal cord injury. New materials have been created that, because of their chemical structure, interact with cells of the central nervous system in ways that may help prevent formation of the scar that is often linked with paralysis after spinal cord injury.

The team has successfully grown nerve cells using an artificial 3-D network of nanofibres, an important technique in regenerative medicine. The innovative scaffold is made up of nanofibres formed by peptide amphiphile molecules. A key breakthrough in this development was designing the peptide amphiphiles so that when they self-assembled into the scaffold, a specific sequence of five amino acids known to promote neuron growth was presented in enormous density on the outer surfaces.

Express Pharma Pulse, 5 February 2004

Kissing RNA and HIV-1: Unravelling the details

In the United States, scientists at the National Institute of Standards and Technology (NIST) and the University of Maryland, working at the Centre for Advanced Research in Biotechnology (CARB), have identified a subtle structural change that may play a role in the molecular machinery for making HIV-1, a virus that causes AIDS. If confirmed in living cells, this mechanism might provide a new target for antiviral drugs.

RNA provides the genetic blueprint for retroviruses like HIV-1. CARB scientists developed a model system to track the changes in an RNA structural element involved in forming HIV-1 viral particles. As new HIV-1 viruses form and mature into infectious particles, two strands of RNA interact through a transient structure called a molecular kiss. This structure is then packaged into new virus particles, which undergo further maturation after being released from the infected cell. CARB scientists found that specific sites in the kissing structure acquire a proton at a pH close to that of living cells. The protons presence alters the RNA structure and accelerates its refolding by a protein associated with viral maturation. Taken together, these observations suggested that such a mechanism might be at work during viral infection.


Study on breast cancer vaccine

Researchers led by Dr. Robert Vonderheide at the Abramson Cancer Centre of the University of Pennsylvania, the United States, have commenced phase I clinical trials to evaluate the effectiveness of a telomerase peptide as a possible vaccine against breast cancer. The study would measure potential tumour cell shrinkage in patients after an immune response has been triggered to an antigen, the telomerase peptide, found in over 90 per cent of breast cancer tumours. The study has been made possible through a unique US$500,000 grant from the Avon-NCI Progress for Patients Awards programme a special private-public partnership between Avon Foundation Inc. and the National Cancer Institute (NCI) dedicated to accelerating early phase clinical research into promising therapies.

Dr. Vonderheide states that this is the first clinical study to use a telomerase peptide as a possible vaccine for breast cancer. Twenty-eight patients with metastatic breast cancer would be enrolled in the study, expected to be completed in two years. Patients will be injected with one of three escalating doses of the telomerase antigen in combination with adjuvant therapies (GM-CSF) over a period of seven months. Immune and tumour responses to the telomerase-based vaccine will be monitored over the duration of the study and compared with a control response to an injection of cytomegalovirus peptide.

Express Pharma Pulse, 19 February 2004


CDFD and Sun Microsystems to establish bioinformatics centre

In India, the Centre for DNA Fingerprinting (CDFD) and the Government of Andhra Pradesh have signed a memorandum of understanding (MoU) with Sun Microsystems, the United States, for setting up a US$6 million Centre of Excellence (CoE) in bioinformatics. This project, to be located at CDFDs new site at Gandipet near Hyderabad, will focus on medical bioinformatics. The facility is expected to start its operations by the end of 2004. State-of-the-art computing architecture from Sun Microsystems and software provided by TCS would enable the premier research centre to cater to the needs of the regional biological community in a user-friendly manner.

The CoE would also function as the national node for the Asia-Pacific Bioinformatics Network to promote bioinformatics education in the state. It is the regional node for the Department of Biotechnologys India Bio-Grid. CDFD is also becoming the only national node for the European Molecular Biology Network outside Europe. Co-development of new hybrid varieties of silk worms and development of novel diagnostic approaches for certain eye disorders are some of the major achievements of CDFD.

Chronicle Pharmabiz, 19 February 2004

India and Malaysia join hands in bioinformatics

Based on the protocol of cooperation between the Ministry of Science and Technology (S&T), India, and Malaysias Ministry of Science and Technology and the Environment, a joint work-plan for major collaborative initiatives in the field of bioinformatics will be announced by both the countries. This would be an attempt to identify R&D activities in bioinformatics, which are of mutual interest for the future of Indo-Malaysian cooperation.

According to the S&T Ministry, both nations would soon host a common website to showcase Indo-Malaysian cooperation in bioinformatics. Resources such as databases and software tools in the public domain would be shared and also hosted on the website. The Bio-Grid node at the Centre for DNA Fingerprinting and Diagnostics, India, will bring out a e-newsletter that will be hosted on the website.

Joint research programmes and exploratory visits of Malaysian delegations to premier institutions in India, and vice versa, to identify new areas in biotechnology for future cooperation have also been decided. Exchange visits of scientists as course facilitators for technical courses/seminars and short-term attachment with institutions for specific training in bioinformatics have been agreed upon. The expense of these attachments would be as per the agreed programme of cooperation signed by the Malaysia-India joint S&T committee. Technical meeting of scientists in the collaborative projects would be undertaken to evaluate progress and future direction of the programme.

Chronicle Pharmabiz, 12 February 2004

Indian university develops virus identification software

Biotechnologists and researchers led by Dr. Ashok Kolaskar, Vice Chancellor, University of Pune, India, have developed a virus identification software program. VirGen software is the first of its kind in the world to provide the complete genome sequence of viruses. At present, no genome resources are available for viruses. VirGen imparts detailed information of viral genomes in a sequence space and structured fashion.

The database of viral genome resource has been developed with the objective of serving a complete genome sequence of viruses with value-addition derived data and data mining tools. The software program offers details of approximately 1,450 viral genomes. It constantly archives the results of comparisons of genomes, proteomes and individual proteins within and between different viral species. VirGen is the first resource database that curates viral genomes for alternate names of proteins and then archives the results of whole genome phylogeny. It displays an exhaustive phylogenetic tree of every single viral species computed using the whole genome sequence data. A unique feature of VirGen is that the software also attempts to link the viral genome to its respective family history and available antiviral drugs and vaccines, if any. The software has been patented in the United States.

Chronicle Pharmabiz, 4 March 2004


Researchers publish structure of Flt-3 kinase in molecular cell

Researchers led by Dr. James Griffith from Vertex Pharmaceuticals Inc., the United States, have published the first crystal structure of Flt-3, a member of the receptor tyrosine kinase family that is implicated in the development and progression of leukaemia. The study provides direct insights into the mechanism by which mutated forms of the Flt-3 receptor can activate themselves and trigger uncontrolled proliferation of immature blood cells, a common feature of several types of leukaemia.

Based on an analysis of the crystal structure, the team hypothesised that specific mutations cause Flt-3s juxta-membrane domain to adopt a conformation that enables the receptor to phosphorylate itself, causing uncontrolled cellular proliferation. According to Dr. Griffith, given the genetic and structural homology among the receptor tyrosine kinase family, and overactivation of these receptor kinases in many tumour types, it is speculated that the mechanism would have broad implications in developing small molecule cancer therapies.


Protein reveals the way gene expression is controlled

In the United States, Dr. Maria A. Martinez-Yamout and her team at Scripps Research Institute, together with Dr. Brian P. Hudson of Rutgers University, have solved the structure of a protein that regulates the expression of genes by controlling the stability of mRNA, an intermediate form of genetic information between DNA genes and proteins. According to Dr. Peter Wright at Scripps Institute, gene expression can be controlled at many levels, and one of them is at the level of the message.

The structure of the tandem zinc finger domain of the regulatory protein TIS11d was solved in complex with a strand of mRNA. This is the first such structure to be solved and provides insights into the process of gene regulation at the atomic level. It has been called the tandem zinc finger because it contains two finger-like domains that bind to zinc to fold into its active form. These tandem zinc fingers are very common motif in mammalian genes and hundreds of genes in the human genome contain some version of them. This discovery perhaps indicate the capability of tandem zinc finger proteins to specifically recognise a large number of different RNA sequence motifs.

Express Pharma Pulse, 11 March 2004

Enzymes stitch together non-standard DNA

In the United States, Dr. Floyd Romesberg and co-workers at Scripps Research Institute have harnessed the principles of evolution to find an enzyme capable of assembling non-standard DNA. All natural DNA are made up of just four bases. However, researchers have created unnatural bases which can be used to make forms of DNA that are robust and will not break apart when exposed to high temperatures. The tricky part is stitching these artificial bases into a chain and getting the chains to replicate as natural DNA does. DNA polymerase enzyme, which does the job in nature, cannot stitch the artificial DNA bases. By systematically tinkering with the structure of DNA polymerase at one or two specific locations, researchers have made enzymes that work with the artificial bases. However, this technique, called rational design, is tedious and unpredictable.

Dr. Romesberg and colleagues tried an approach called directed evolution. Mutant polymerases capable of stitching together non-standard bases were obtained by randomly scrambling part of the natural enzymes chemical structure. The mutants were further mutated until one of them was able to copy the sequence of a template molecule into the modified form of DNA as efficiently and faithfully as DNA polymerase working with natural bases. However, the mutant polymerase stopped working after adding five artificial bases to a growing chain.

In another study at the University of Florida, Mr. Steven Benner and colleagues used an enzyme made by HIV virus to achieve the same objective. This enzyme can even make multiple copies of unnatural DNA, opening up the possibility that the code could eventually evolve on its own. The team started with a different enzyme altogether, a reverse transcriptase (RT) made by HIV-1.



Plant designed to yield potential anti-carcinogen

Scientists headed by Dr. David Salt at Purdue University, the United States, have successfully engineered plants that may not only lead to the production of anti-carcinogenic nutritional supplements, but may also be used to remove excess selenium from agricultural fields. The team inserted a gene responsible for converting selenium taken up from soil into a non-toxic form called methylselenocysteine (MSC) into Arabidopsis thaliana, a model lab plant that does not tolerate selenium, and produced plant strains that not only thrive in a selenium-rich environment but also amass high levels of selenium-containing MSC in their tissues.

This study provided researchers with a genetic means to manipulate the amount of MSC produced in plants. Other studies have shown MSC to be effective in reducing cancer risk in animal models, making it an attractive prospect for eventual use in a nutritional supplement. According to Dr. Salt, plants that naturally hyper-accumulate selenium may not be good candidates for use as a supplement since they often produce other compounds which may have an adverse effect on humans.


New discovery could raise key food ingredient availability

In the United States, a team of researchers led by Dr. Kanwarpal Dhugga from Pioneer Hi-Bred International Inc., a subsidiary of DuPont, recently achieved a scientific breakthrough by identifying a gene found in guar and carob plants that produces gum, a key food additive. The team successfully transferred the gene to soya bean plants, enabling them to manufacture a component of gum. The team identified and isolated the molecular components for galactomannan, the gum, in the seeds of guar and carob plants.

Gums are commonly used in the food industry as additives that provide texture, prevent ice crystal formation, maintain crispiness and retain moisture. They also have commercial uses in several other industries, including cosmetics, healthcare, textile and paper. The ability to produce gums in high-yielding commercial crops like soya beans could provide benefits for manufacturers by stabilizing the supply of this important food ingredient. At present, prices for gums derived from guar and carob fluctuate because of seasonal variations in crop performance.

Chemical Weekly, 17 February 2004

India develops pest-proof rice

In India, scientists at the Centre for Cellular and Molecular Biology (CCMB) and the Directorate of Rice Research (DRR) have jointly developed a new variety of rice resistant to bacterial leaf blight (BLB). Researchers tracked genes that were resistant to the bacteria and introduced them into the popular rice variety Samba Masuri (bpt5204) and another variety Triguna, using molecular breeding techniques. In greenhouse experiments and limited field trials, the new rice lines exhibited good resistance to both pest and disease, without compromising on yields.

Scientists took the resistant genes from SS1113 and back-crossed it with Samba Masuri to hasten the process of development. The new varieties of Samba Masuri and Triguna promise farmers with fine quality and disease resistance without lowering the yield. According to Dr. B.B. Mishra, Director of DRR, the lines will be nominated for evaluation under the All India Coordinated Rice Testing Programme and are expected to enter the commercial domain in three years.

Chemical Weekly, 16 March 2004

Canola plants with mini-chromosomes

Chromatin, the United States, has entered into separate partnerships with Canada-based National Research Councils Plant Biotechnology Institute and Cibus Genetics, the United States, to generate canola plants containing mini-chromosomes. The collaborations are among the first projects to introduce mini-chromosomes into a commercially significant plant. Chromatins mini-chromosome technology is designed to allow simultaneous introduction of multiple genes into plants without disruption of the plants own chromosomes. This technology enables stacking of genes to produce such phenotypes as improved product quality, increased yield and resistance to herbicides, insects and pathogens.

Genetic Engineering News, 15 February 2004

GM soya developed in Brazil

Scientists at Embrapa, Brazils crop research agency, have developed a genetically modified (GM) soya bean. The new soya works in a similar way as Roundup Ready soya, patented by the United States biotech seed giant Monsanto Co. and is the only GM soya used in Brazil. Embrapas soya variety is resistant to imidazolinone-based herbicides, which could kill other soya beans not having a certain enzyme altered genetically. Dr. Carlos Arias, genetic researcher at Embrapa, states that the new soya was adapted to various types of Brazilian soya and performed very well in early tests.


Newly cloned gene key to global adaptation of wheat

A team of researchers led by Dr. Jorge Dubcovsky at the University of California-Davis, the United States, has pieced together a clearer picture of how wheat has been able to adapt to such a wide range of climates and become one of the worlds staple food grains. The team accomplished their goal by isolating and cloning the VRN2 gene in wheat, that controls vernalization a cold-weather requirement for triggering flowering. The study has practical implications for improving wheat varieties through manipulation of flowering times.

The team, which last year cloned the first wheat vernalization gene VRN1, discovered VRN2 gene by using detailed genetic and physical maps. They determined that VRN2 was a new type of gene involved in the regulation of other flowering genes. In winter wheat varieties, the VRN2 gene prevented the plant from developing flowers. However, on exposure to cold weather during vernalization, the gene got down-regulated, thus allowing the plant to proceed with flower formation.

The team found that experimental down-regulation of the VRN2 gene accelerated flowering time in genetically modified wheat plants by over a month. They further showed that loss-of-function mutations in either of the genes, VRN1 and VRN2, resulted in spring wheat varieties that did not require cold weather to initiate flowering. These varieties could be planted in spring to grow throughout the warmer months of the year. Results of the study also indicated that unlike the VRN1 gene, the VRN2 is distinctly different than a gene in Arabidopsis that had a similar function suggesting that as they evolved, Arabidopsis and the temperate grasses developed different vernalization pathways, including both similar and very different genes.


Red wine gene produces healthier tomato

Researchers led by Mr. Jim Myers at the United States-based Oregon State University have created purple tomatoes containing the health-promoting antioxidant pigments of red wine that are thought to prevent heart diseases. Domestic varieties grown and consumed do not normally produce fruits containing the antioxidants, called anthocyanins. These are phytochemicals disease-preventing chemicals found in plants that give blueberries, raspberries and grapes their colour. They are powerful antioxidants that protect the human body from the oxidative damage thought to contribute to heart disease, cancer and ageing. According to Mr. Myers, boosting the nutritional value of tomatoes could benefit a large part of the population, as tomatoes are second only to potato in terms of top vegetable consumed in the world.

Researchers created the new purple tomato by crossing a tomato plant with a wild anthocyanin-containing relative. The team then grew the seeds of their new crossbreed in a greenhouse for two generations, and discovered that anthocyanin was transmitted in tomatoes by a single, dominant gene called Aft. Researchers are now conducting preliminary studies on humans to see how the new tomatoes are metabolized and which strains provide the most phytochemicals.



Peptide Nucleic Acids: Protocols and Applications

This second edition has been extensively revised, updated and enlarged to include new material covering the most recent topics and applications in this fast-moving field. The book contains state-of-the-art protocols and applications on all aspects of peptide nucleic acids (PNA). It describes the theory and history of PNA and is a key reference text and lab manual for all molecular biologists.

DNA Amplification: Current Technologies and Applications

DNA amplification is the cornerstone of modern biotechnology and also an important procedure in numerous basic studies involving DNA and other biomolecules. Polymerase chain reaction (PCR) is still the most popular amplification process. However, alternatives to PCR have successfully invaded the area and dramatically improved the technological abilities of basic as well as applied researchers in various fields of life sciences.

This book presents a wide range of methods to amplify DNA with an emphasis on their diverse applications. It covers both well-established and recently developed protocols, including ligation-based thermocycling approaches, real-time PCR and other new PCR developments, plus several powerful non-PCR isothermal DNA amplification techniques. An entire section has been devoted to a group of enzymes, both natural and engineered, that are employed for DNA amplification and related purposes. In addition, the use of DNA amplification in the detection of non-DNA analytes is presented. This publication serves as a practical tool and an invaluable reference guidebook for academic researchers and industry biotechnologists who use DNA amplification techniques.

For the above publications, contact: Horizon Bioscience, Horizon Scientific Press, 32, Hewitts Lane, Wymondham NR18 0JA, United Kingdom. Fax: +44 (1953) 603 068.

Biotechnology: Applications and Career

The book addresses the young aspirants willing to make their careers in this upcoming area of science. Brief treatments of different branches of biotechnology including plant, animal, medicine, marine, bioinformatics, environment and industrial are provided for guidance, together with exhaustive lists of institutes, references and websites.

Contact: Mr. Vinod Vasishtha, Viva Books Pvt. Ltd., 4262/3, Ansari Road, Daryaganj, New Delhi 110 002, India. E-mail:


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