VATIS Update Biotechnology . Mar-Apr 2006

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Biotechnology Mar-Apr 2007

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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Bird flu fight gets US$1.9 billion boost

The global fight against bird flu was given a boost with donors pledging US$1.9 billion. At the international fund-raising conference held recently in Beijing, governments made a joint declaration that national action plans must be guided by political leadership at the highest level. The meeting co-sponsored by China, the European Commission and the World Bank was meant to address the lack of funds that is limiting efforts to contain the spread of bird flu.

Reflecting the international communitys increased sense of urgency and determination, pledges made at the end of the Beijing meeting exceeded the US$1.2 billion anticipated by the World Bank. As part of this, China has agreed to cooperate with other nations and international organizations to develop effective vaccines and drugs against bird flu. The Beijing Declaration, adopted at the meeting by 700 delegates from 100 nations, states that the international community must give long-term support to those countries that are affected or at risk of future bird flu outbreaks.


Application of GM technology in China

China, which attaches great importance to research on genetic modification technology, has conducted studies on genetically modified (GM) timber and flowers species. This focus away from agriculture, the area in which GM technology application is mostly done, is because of the countrys concern for safe application of this technology. According to Mr. Zhuo Rongsheng, Director of the Wildlife Department with the State Forestry Administration, these studies are carried out in strict accordance with biological safety requirements and the research findings are used to cultivate genetically modified timber and flower species instead of producing food. In the meantime, the research findings go through ecological safety tests, to ensure their absolutely reliability. Moreover, in the coming five years, China will carry out a biological technology innovation programme aimed at cultivating improved species and try to minimize the impact they have on forests.


India keen to encourage R&D, innovation in biotechnology

Quality of R&D in the Indian biotechnology sector needs to improve exponentially, particularly in the small and medium biotech industry segments, according to Dr. M.K. Bhan, Secretary, Department of Biotechnology (DBT), Government of India. Government of India has initiated various schemes to boost R&D and innovation like Pharma R&D fund, New Millennium India Leadership Technology Initiative and Technology Development Board which are complementary to each other and is keen to fund and support innovation centres across the country.

On the regulations front, the country has achieved progress both in bio-pharmaceuticals and pharmaceuticals, and creation of a national level Biotech Regulatory Authority is under review. An emphasis is given to human resources development in the biotech sector. The country needs to develop tailor-made human resource for drug discovery and manufacturing in biotechnology. Soon, DBT will be creating a national pool of jobs in biotechnology, and is proposing to establish 20 undergraduate life sciences schools at national level in 20 cities. Dr. Bhan said that DBT is also proposing to create a national working group to scale up clinical trials at a rapid pace. A translational research centre to be set up will be responsible for conceptualization of technologies for development of health and will act as facilitation centre for new product development.

Chronicle Pharmabiz, 16 February 2006

Project Checkmate to focus on infectious disease containment

In the United States, The Scripps Research Institute (TSRI) and IBM have announced a collaborative initiative to conduct advanced research on pandemic viruses, leveraging the industry-leading talent and technology from both organizations. The objective of Project Checkmate is to develop the means to anticipate, manage and contain infectious diseases. The Initiative will capitalize on TSRIs world class research in the areas of biochemical modelling and drug discovery, and IBMs expertise in computational biology bio-patterning and supercomputing.

The joint research team will exploit the use of IBMs Blue Gene supercomputer, the worlds fastest supercomputer technology. This combined team will have access to unparalleled resources from TSRIs network of scientists and to its new state-of-the-art biomedical research facility, Scripps Florida, in Palm Beach County. The team will also tap IBM Researchs depth of expertise in bioinformatics, structural biology, life sciences research, functional genomics, systems biology and medical informatics.

Project Checkmate will create a collaboratory in South Florida, to focus and accelerate the pace of discovery for advanced research of infectious diseases, such as avian influenza. The research team will: define the key areas of research to be pursued for significantly impacting pandemic response at a national and global level; collaborate with leading experts from around the world for the execution of research projects; and see work with government agencies as well as key enterprises to implement the understandings and technologies resulting from the project.

Genetic Engineering News, 16 February 2006

Viet Nam earmarks US$63 million for biotechnology

The Prime Minister of Viet Nam recently approved a VND1 trillion (US$62.9 million) programme to develop and apply biotechnology in agriculture and rural development over the next 15 years. This three-phase programme is designed to help scientists develop genetically modified species of plants, livestock and micro-organisms to bolster agricultural productivity. Funding will be provided for scientific research, trial productions and specialized training for the programme.

In the first phase of the project, which is to run until 2010, scientists are to find ways of applying biotechnology in agricultural production, creating new strains of crops and animal breeds that would allow farmers to operate more efficiently and profitably. Scientists hope to develop eight new strains of rice and two new varieties of maize in the next five years, and develop livestock vaccines by 2015.

Up to 80 doctors and 500 to 1,000 biotechnology technicians specializing in agriculture are to be trained for the project over the next five years, and laboratories are to be upgraded to research institutes to contribute to a future agricultural biotechnology centre. In the second phase, from 2011-15, fifty international co-operation projects will focus on transferring and applying latest technological and scientific achievements and giving Vietnamese scientists access to up-to-date genetic research.

In the following phase, a biotechnology market will be established to promote the production, marketing and trade of key biotechnology products in Viet Nam, with the aim of increasing revenue in the agricultural sector by as much as 20-30 per cent through the application of genetically modified organisms. According to the plan, by 2020, up to half of all cultivated land in Viet Nam will be set aside for genetically modified crops, by which time Viet Nams agricultural biotechnology industry will rank among the most advanced in Southeast Asia.


Plant-made vaccines get registration

Dow AgroSciences, the United States, has received the worlds first regulatory approval for a plant-made vaccine from the USDA Centre for Veterinary Biologics. The Dow AgroSciences ConcertTM Plant-Cell-Produced System represents a new category of plant-made vaccines. This leading edge technology uses plant cells instead of whole plants in a secure, bio-contained environment to produce vaccines. Because of this bio-contained production system, concerns and challenges associated with making vaccines in whole plants or food crops are eliminated. The Concert Plant-Cell-Produced System uses only the necessary parts of the disease-causing agent to stimulate immunity in a manufacturing process that is totally free of animal components.

With this approval, Dow AgroSciences has shown that using this revolutionary technology for human diseases is a real possibility. This milestone achievement by Dow AgroSciences was the result of effective collaborations with many organizations and institutions including Washington University, and Boyce Thompson Institute for Plant Research.


India and Ireland sign biotechnology pact

The Irish Bio-Industry Association (IBIA) and its Indian counterpart, Association of Biotechnology-led Enterprises (ABLE), have signed a memorandum of understanding (MoU) as part of the recent Ireland trade mission to India. The MoU lays the foundation for research and commercial collaboration between the growing biotechnology sectors of the two countries.
The agreement was signed at the headquarters of Biocon Ltd. In Bangalore, in the presence of the Ireland Prime Minister, Mr. Bertie Ahern, and the visiting Minister for Enterprise, Trade and Employment, Mr. Micheal Martin. The President of ABLE and the CMD of Biocon Limited, Dr. Kiran Mazumdar Shaw, and the Chairman of IBIA and the CEO of Biotrin International, Dr. Cormac Kilty, signed the MoU.

Chemical Weekly, 24 January 2006

Coordinated research on plant and microbial genomics

The United States Department of Agriculture (USDA) and the Department Energy (DoE) have announced that they will share resources and coordinate the study of plant and microbial genomics. USDA and DoE will establish a framework to cooperate and coordinate agency-relevant plant and microbial genome sequencing and bioinformatics that can serve the needs of the broader scientific community and solve problems that are key to each agencys mission. This agreement could help speed up the deployment of emerging technologies, such as improved methods of gene identification and sequence assembly.

The DoE Joint Genome Institute (DoE JGI) will sequence the genome of the soybean Glycine Max, the worlds most valuable legume crop. The soybean genome is about 1.1 billion base pairs in size, less than half the size of the maize or human genomes. According to Dr. Eddy Rubin, DOE JGI Director, the soybean represents an excellent example of DOEs key role in translational genomics, that is, applying the tools of DNA sequencing and molecular biology to contributing to the development of new avenues for clean energy generation and crop improvement.



Dow Agro sciences, Monsanto reach global agreement

In the United States, Dow AgroSciences LLC, a subsidiary of the Dow Chemical Company, and Monsanto Company have announced a global business agreement that establishes cooperative arrangements that are claimed to give farmers new technology options and more choice in the products to meet their needs. According to Dr. Hugh Grant, Monsantos President and CEO, the key to this agreement was that the companies were able to deliver an outcome that would provide farmers with greater access to new technology offerings and trait combinations with the industrys leading weed control system in Roundup Ready.

Under the agreement, Dow received a commercial licence to certain Monsanto seed stock and biotechnology traits for corn and soybeans. Dow also receives royalty-bearing rights to create and license finished hybrids, which combine Monsantos Roundup Ready Corn 2 technology with Dows Herculex I and Herculex XTRA technologies, to licensees of Monsantos Roundup Ready Corn 2. Dow and Monsanto also established cross-licences of cotton technologies on a non-exclusive basis. Dows licence includes Monsantos patent estate for cotton transformation. Monsantos licence includes the patent estate for glyphosate tolerant cotton of Mycogen Plant Sciences Inc., an affiliate of Dow AgroSciences. Dow receives the intellectual property licences for the commercialization of its WideStrikeTM insect protection technology.

Monsanto receives the intellectual property licenses related to its Bollgard, Bollgard II, Roundup Ready and Roundup Ready Flex technologies, besides a commercial licence for WideStrike technology in South America and Mexico.

The agreement also covers non-exclusive cross licences of certain enabling technologies. Dows licence includes Monsantos patent estate for synthetic Bt technology. Monsantos licence includes the patent estate for Bt in plants owned by Mycogen. As part of the agreement, Monsanto and Dow have agreed to settle outstanding patent-related legal disputes among them.


Abbotts real-time PCR test for ST pathogens gets certification

Abbotts highly sensitive new test for the simultaneous detection of Chlamydia trachomatis (CT) and Neissera gonorrhoea (NG) pathogens which cause the two most common sexually transmitted diseases in the world has received CE Mark certification, allowing it to be marketed in the European Union. The test is designed for use on the Abbott m2000, an automated instrument using magnetic particle and real-time polymerase chain reaction (PCR) technology.

The Abbott RealTime CT/NG assay combined with the automated Abbott m2000 system gives European laboratories an important new option for delivering highly reliable test results to patients quickly and efficiently. Amplified nucleic acid tests for detection of Chlamydia and gonorrhoea are accurate and, unlike conventional methods, can be performed non-invasively on urine samples. The m2000 automates all critical steps of the process, from sample preparation to data analysis, allowing laboratories to process molecular tests efficiently and accurately.

The Abbott RealTime CT/NG test will be offered in Europe by Abbott as part of its alliance with Celera Diagnostics. To provide additional testing flexibility for laboratories, the companies will also offer the Abbott RealTime CT assay, a real-time PCR test for the sole detection of Chlamydia trachomatis. Offered along with the tests will be the Abbott multi-Collect Specimen Collection Kit, a unique laboratory tool for the collection and room-temperature transportation of urine specimens and endocervical, male urethral and vaginal swab specimens. The new CE certification further expands the menu of tests available on the Abbott m2000 system, which also includes real-time PCR tests for HIV-1 and hepatitis C virus.


Locus Pharma enters research agreement with Eli Lilly

In the United States, Locus Pharmaceuticals Inc., a computational drug design and development company, has entered into a research agreement with Eli Lilly & Company, a pharmaceutical major. Under the agreement, Locus will apply its proprietary computational technologies to design small molecule compounds having activity against a protein kinase target identified by Lilly.

According to Dr. Jeffrey S. Wiseman, Vice President for Technology and Information at Locus, the company views its working with Eli Lilly as a major additional validation of their virtual fragment design approach and Locus expanding core competence in kinases. Locus core technology is fragment-based computational drug design, which it has combined with highly integrated medicinal chemistry and biology capabilities. Starting with a protein crystal structure, an in silico collection of 40,000 molecular fragments and one of the worlds largest privately owned Linux-based super computer clusters, Locus identifies optimum ligand binding sites on protein targets and computes the binding affinity of molecular fragments on these sites. The fragments are assembled computationally into drug candidates.

Chronicle Pharmabiz, 9 February 2006

Scynexis Europe becomes Selcia

Scynexis Europe is to operate under the name Selcia Limited after Scynexis Inc. sold the subsidiary to its management in the United Kingdom in a move that allows Selcia to provide custom radio labelling, chemistry and analytics services to a broader customer base. The move will also allow Scynexis to concentrate on its core business and partners enhancing its growing presence in the global pharmaceutical marketplace and continue to build discovery collaborations with major companies.

Scynexis, a chemistry-focused drug discovery and development company, has made a name in the industry by providing services in the form of research teams in the field of computational chemists, medicinal chemists, analytical chemists and bioanalytical scientists to work on with customers. The company has a number of agreements set in place with businesses such as Merck and Co., Roche and Teijin Pharma.

Selcia already provides custom radio labelling, analytical technologies and their integration with synthetic chemistry. The company also produces radio labelled versions of pharmaceutical and agricultural drug candidates by GMP principles. The products are suitable for use in human trials.



Missing steps of jumping-gene replication discovered

Researchers led by Dr. Haig H. Kazazian at the University of Pennsylvania School of Medicine, California, the United States, have discovered the remaining steps in the complicated process of how the largest class of jumping genes or transposons replicates and inserts themselves within the human genome.

Jumping genes are sequences of DNA that can move or jump to different areas of the genome within the same cell. They are a rare cause of several genetic diseases. Retrotransposons are one class of jumping genes, with the L1 family being the most abundant in the human genome. They move by having their DNA sequence transcribed or copied to RNA and then having it copied back to DNA by the retrotransposons own enzyme called reverse transcriptase. This DNA is then inserted back into the genome.

In order to learn about the effects of L1 retrotransposon insertions into the human genome, the researchers made a transgenic mouse in which human L1 retrotransposons could replicate. They injected several copies of a human L1 retrotransposon to create the transgenic mouse. In subsequent generations, the retrotransposons moved within the offsprings genomes and the investigators could detect each new insertion.

The researchers characterized 51 new jumps of L1, finding that insertions landed in random genomic regions. Several L1 insertions included small pieces of extra DNA.

While tracing the origin of this extra DNA, the scientists came up with the missing steps in the mechanism of retrotransposon replication. It was known previously that the enzyme endonuclease cleaves one of the strands of cellular DNA and then the retrotransposon inserts by binding to that cleaved DNA strand and copying itself onto that strand. How the retrotransposon finally integrated and pasted itself back together was unknown, until this study. What the research team saw in the insertions hinted at the possibility that reverse transcriptase actually jumps onto the second DNA strand and continues the synthesis, and this is how the second part of the element integrates into the genome. If this mechanism proves to be correct, it would bring scientists much closer to knowing how more than half a million retrotransposons have accumulated in the human genome.

Continuous jumping by retrotransposons eventually expands the size of the human genome and may cause shuffling of genome content. By knowing the final steps in retrotransposon replication and being able to follow and map new insertions in animals, the researchers will be able to more fully understand how L1 retrotransposons are able to invade the human genome.


First large-scale bird flu genome study conducted

A group of scientists led by Dr. Robert Webster at St. Jude Childrens Research Hospital, Memphis, the United States, has completed the first large-scale study of bird flu virus (H5N1) genomes, thereby doubling the amount of genetic information available on the genes and proteins of these viruses. According to Dr. Webster, these studies provide the first fundamental insight into the evolution of influenza viruses in nature the source of all influenza viruses that affect humans, domestic animals and birds.

The project produced 70 million bases of sequence information leading to DNA sequences for 2,196 genes and 169 complete bird flu genomes from the St. Jude collection, including representatives of all known sub-types of the virus including H5 bird flu. Preliminary analysis of these data and development of new analysis software have led to the discovery of new forms of bird flu genes, how these viruses evolve through time and the identification of genes that travel together through evolution. The St. Jude research also made an intriguing discovery that avian influenza viruses have a particular molecular feature that human influenza viruses do not have, which may cause them to be more toxic when infecting human cells.


Genome-wide map of miRNA-mRNA interactions

In the United States, researchers at New York Universitys Centre for Comparative Functional Genomics, New York, and the University of California, Berkeley, have used computational analyses to predict a genome-wide map of microRNA, or miRNA, targets in the animal model organism Caenorhabditis elegans. In a specific section called 3'UTR, miRNA bind to and regulate messenger RNA (mRNA). Parts of the predicted map were confirmed through the development of a novel in vivo method that asked whether the 3'UTR part of mRNAs was driving regulation during development in a living organism. Using PicTar, an algorithm developed at New York University (NYU), the researchers predicted miRNA functions of C. elegans genes. The researchers found that one-third of C. elegans miRNAs target gene sets have related functions. That is, it appears that miRNAs can control groups of genes that work in a specific biological process. At least 10 per cent of C. elegans genes are predicted miRNA targets.

To test the computational predictions, the NYU team developed a new in vivo analysis system comparing the expression of a reporter green fluorescent protein (GFP) carrying target 3UTRs with controls that did not carry the target 3UTRs. The laboratory results confirmed the role of specific 3'UTRs in suppressing gene expression even more widely than predicted by the computational analysis, suggesting that 3'UTRs contain a largely unexplored universe for gene regulation.


Researchers identify ataxia gene

Dr. Laura Ranum and co-researchers at the University of Minnesota Medical School, the United States, have discovered the gene responsible for a type of ataxia, an incurable degenerative brain disease affecting movement and coordination. This is the first neurodegenerative disease shown to be caused by mutations in spectrin, the protein that plays an important role in maintaining the health of nerve cells. This discovery provides a genetic test that will lead to improved patient diagnoses and gives new insight into the effects of this abnormal protein, which provides internal structure to cells, said Dr. Ranum.

Spinocerebellar ataxia type 5 (SCA5) is a dominant gene disorder; if a parent has the disease, each of their children has a 50 per cent chance of inheriting the mutation and developing ataxia sometime during their lifetime. The onset of SCA5 usually occurs between the ages of 30 and 50, but can appear earlier or later in life. Now that researchers have identified the specific mutation that causes SCA5, testing of patients at risk of developing this disease is possible before any symptoms appear. The availability of predictive testing allows people with a family history of the disease to determine whether they will develop the disease and whether their children are at risk of inheriting the mutation. In addition, the prognoses of the different types of ataxias vary greatly, so identifying the specific type of ataxia provides patients with a more accurate picture of what the future holds.


Researchers design chip that can improve citrus varieties

Researchers at the University of California Riverside (UCR) in the United States, in partnership with Affymetrix Inc., California, the United States, have designed a chip the GeneChip Citrus Genome Array that can improve citrus varieties and suggest ways to better manage them. By helping to determine which genes are turned on in a tissue of citrus for example, genes that are associated with taste, acidic content and disease the GeneChip provides information useful to researchers for rectifying existing problems and making improvements to the fruit.

The citrus array will be used to develop new diagnostic tools for citrus agriculture improvement and post-harvest fruit handling, and to understand mechanisms underlying citrus diseases. Scientists will study traits pertinent to the citrus industry such as eas of peeling, absence of seeds, flavour components, pest and disease resistance, nutritional features and reproductive development.

According to Dr. Mikeal Roose, a professor of genetics in the Department of Botany and Plant Sciences at UCR, the citrus array helps to quickly examine a certain trait in citrus. For a problem trait, such as an undesirable flavour, the genes associated with that trait can be identified and targeted for correction. Besides helping to address citrus diseases by assisting scientists to see what happens in cells when a citrus plant is under attack from a virus, the chip also helps scientists to better understand what happens at the cellular level when oranges are in cold storage.

The array, manufactured by Affymetrix, is made up of a glass wafer on to which nearly one million different pieces of citrus DNA are deposited on a grid or microarray using methods similar to those used to produce computer chips. The glass wafer is encased in a plastic container somewhat smaller than the size of a credit card. To use the chip, researchers purify total RNA from plant tissue, make a copy of these molecules with a chemical tag added, and then wash the chip with the RNA sample. If a gene is being expressed in the tissue, its corresponding RNA will be present and bind to the complementary DNA sequences on the chip. The locations of the bound RNA have a visible signal that helps analysis.


Scientists identify key factor in fruit fly colour receptor cells

Scientists led by Dr. Claude Desplan in New York Universitys Centre for Developmental Genetics, the United States, have identified a key factor that enables photoreceptor cells to decide their colour sensitivity. The researchers used the fruit fly Drosophila as a genetic model system to study stochastic events like colour sensitivity in photoreceptor cells. The eye of the fly contains some 800 optical units, called ommatidia, each containing six outer and two inner photoreceptors (R7 and R8). The inner receptors detect colour, like cone cells in human eyes. About 30 per cent of the ommatidia named pale have sensitivity to blue light, while 70 per cent called yellow are sensitive to green light.

The key question Dr. Desplans team explored was how each individual R7 and R8 receptor decides to be either pale or yellow and how this decision contributes to the stochastic distribution of each type in the mosaic of colour photoreceptors in the fruit flys eyes. In this study, the team identified a transcription factor gene nicknamed spineless as the key regulator for establishing the retinal mosaic when expressed during the fruit flys mid-pupation stage. Fruit flies in which the spineless gene could not be expressed, all of the R7 photoreceptors and most R8 receptors were pale; flies in which spineless was over-expressed, all photoreceptors were yellow. Moreover, the researchers found that the colour photoreceptor cells made their decision without the influence of other nearby cells.



Targeting pancreatic cancer

Dr. Johanna Joyce at the Memorial Sloan Kettering Cancer Centre and Dr. Douglas Hanahan of University of California, San Francisco, the United States, have found how broad-spectrum cysteine cathepsin inhibitors combat pancreatic cancer. Results of their study provide new data to help refine the design of more precisely targeted anti-cathepsin therapies and may help guide the design of clinical trials aimed to assess cathepsin inhibitors as cancer therapies.

To determine how the loss of individual cathepsin genes affects tumorigenesis, the researchers engineered the pancreatic cancer-prone mice to also lack one of four cathepsin genes: cathepsin B, C, L or S. They found that cathepsin B-, L-, or S-deficient transgenic mice displayed reduced tumour formation, but cathepsin C-deficient mice did not. They were then able to identify the stage-specific roles of cathepsins B, L and S in tumour development, as well as a key target that mediates the tumorigenic roles of these three cathepsins.

The researchers found that E-cadherin (a known inhibitor of tumour invasion) is a target substrate of cathepsins B, L and S; but not cathepsin C. Their evidence suggests that cathepsins B, L and S promote pancreatic tumour invasion by cleaving, and thereby inactivating, E-cadherin. Interestingly, the researchers also found increased levels of cathepsins B and L in some human pancreatic tumour samples. According to Dr. Joyce, using the powerful approach of mouse genetics, scientists have been able to identify distinct, stage-specific roles for various members of the cysteine cathepsin family.


Study unearths mutant gene behind heart drug inaction

A research team led by Dr. Li Jin has indicated that about 30-50 per cent of East Asians might carry a genetic trait that blocks the bodys ability to process the heart drug, nitroglycerin, rendering it useless. In the normal run, the human body converts nitroglycerin to nitric oxide, which relaxes and expands the smooth muscles of blood vessels. This improves blood flow and the heart has to pump less forcefully to keep blood circulating. Nitroglycerin has since been used in pill form and in a pump spray to provide quick relief, and as a patch worn for continuous improvement to blood flow. However, the exact mechanism of action of nitroglycerin was not known till 2002, when the researchers discovered that the enzyme ALDH-2 helps the body convert nitroglycerin into nitric oxide.

Significantly the gene that produces ALDH-2 has an unusual expression in Asians, especially the East Asians. Dr. Li Jin along with colleagues conducted their study with 111 Han Chinese patients who all had coronary heart disease and dosed themselves with a nitroglycerin tablet under the tongue during acute angina attacks. While 80 people in the study reported relief within 10 minutes of taking nitroglycerin, the other 31 people said they experienced no pain relief at all. Tests showed that most of these non-responders carried the mutant gene. However, the researchers note other genes and environmental factors might also be in play, as this one genetic trait could not explain the lack of response in all the patients who felt no relief.

Biospectrum, March 2006

Scientists develop avian flu vaccine

At University of Pittsburgh, Pennsylvania, the United States, researchers led by Dr. Andrea Gambotto have announced the genetic engineering of an avian flu vaccine, from the critical components of the deadly H5N1 virus, which completely protected mice and chickens from infection. As this vaccine contains a live virus, it may be more immune-activating than avian flu vaccines prepared by traditional methods. Since it is grown in cells, it can be produced much more quickly than traditional vaccines.

The research team constructed the vaccine by genetically engineering adenovirus, a common cold virus, to express either all or parts of an avian influenza protein called hemagglutinin (HA) on its surface. Found on the surface of all influenza viruses, HA allows the virus to attach to the cell that is being infected and is, therefore, critical to the influenza virus ability to cause illness and death. The team constructed several adenovirus vectors, containing either the full genetic sequence of the HA protein or sequences for only parts, or subunits, of HA. They also constructed a vector containing sequences for a portion of the HA protein from the H5N1 Hong Kong strain.

Dr. Gambottos team tested the ability of their vaccines to protect mice from infection by wild-type H5N1 by comparing its performance to an adenovirus vector containing no H5N1 genes, or an empty vector. The investigators observed that all of the mice immunized with the empty vector vaccine experienced substantial weight loss beginning about three days after exposure to wild type H5N1, and all were dead within six to nine days of avian flu exposure. In sharp contrast, most of the mice immunized with the adenovirus containing either the whole or part of the HA protein showed only mild short-lived weight loss and survived H5N1 infection. Dr. Gambotto and his colleagues suggest that rather than replacing traditional inactivated influenza vaccines, their adenovirus-based vaccine could be important complement to them.

Biospectrum, March 2006

RNA interference tackles a sexually transmitted disease

In the United States, a group of researchers from CBR Institute for Biomedical Research, Boston, and Department of Paediatrics, Minneapolis, has reported that small interfering RNA (siRNA) can be used to prevent vaginal transmission of herpes simplex virus-2 (HSV-2) in a rodent model. This study, led by Dr. Deborah Palliser of CBR Institute, is the first to show that vaginal administration of a siRNA therapeutic can be used as prophylactic against a sexually transmitted viral infection, both pre- and post-exposure.

The team showed that mice can be protected from HSV-2 infection by application of siRNA on vaginal epithelium, targeting two viral genes: UL29, encoding a DNA-binding protein; and UL27, encoding envelope glycoprotein B. The products of these genes are necessary for productive viral infections: UL29 codes for the protein ICP8 required for DNA replication, while UL27 codes for glycoprotein B that attaches the viron to the host cell surface. The team treated mice with antiviral or control siRNA 2 hours before and 4 hours after vaginal virus challenge and monitored disease severity and survival for 15 days. Although all control mice shed virus on day 6, no virus was detected in 70 per cent of the mice treated with UL29 siRNA and 50 per cent of the mice treated with UL27-siRNA. The investigators also found that a combination of UL 27 and UL 29 siRNA protected animals from HSV-2 infection 3 and 6 hours after vaginal virus challenge. The work shows the enormous potential of siRNA in the prevention and control of viral infections.

Nature Biotechnology, January 2006

Bone marrow cells useful in stem cell transplants for cancer

Scientists led by Dr. Doug Engel at the University of Michigan Medical School, the United States, and Dr. Norio Suzuki at the University of Tsukuba, Japan, have discovered blood stem cells hiding out in the edges of bone marrow. They invented a technique that makes it possible to see a stem cell alive in bone marrow and could help ease life-saving stem cell transplants for diseases such as cancer.

Stem cells are not clustered throughout the bone marrow, but live alongside bone forming cells on the edges of the marrow. Currently, doctors must remove large amounts of bone marrow from a donor and separate stem cells for infusion into a sick patient. Dr. Suzuki and colleagues spliced a green fluorescent protein gene from jellyfish into two genes one called Gata-2 and another called IS that helps control Gata-2 uniquely used by the blood stem cells. They then developed a mouse that would express green fluorescent protein controlled by the Gata-2 gene promoter, and took time-lapse movies of frozen sections from mouse leg bone under a fluorescent microscope. The movies clearly showed individual, isolated bone marrow stem cellsat the edge of the bone marrow.

Express Pharma Pulse, 16-28 February 2006

Key factor for survival of human embryonic stem cells

Human embryonic stem cells (hES) offer great hope for the treatment of some devastating diseases, but finding a way to keep enough of these cells usable and healthy for transplantation in patients has been a problem. In the United States, scientists led by Dr. Peter Donovan and Dr. Leslie Lock at University of California Irvine, along with Dr. April Pyle of Johns Hopkins University, have discovered a way to keep large quantities of these cells alive.

Although stem cells have the ability to self-renew and to differentiate into any cell in the body, it has been a challenge to keep them alive as single cells in an undifferentiated state. This has restricted their production in quantities useful for therapy and their genetic manipulation before transplantation. In their laboratory, Dr. Donovan and Dr. Lock added neurotrophins, which normally aid the survival of tissue in the nervous system, to hES cells to see the effect they would have on cell survival. When three members of the family of neurotrophin growth factors brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT-3), and neurotrophin 4 (NT-4) were added to hES cells in culture, the cells survival increased 36-fold.
The finding could potentially lead to mass production of hES cells at lower cost for therapeutic use.

Understanding the role that neurotrophins play in stem cell survival could also help scientists with another major problem they face in using hES cells for therapy. Undifferentiated stem cells transplanted into the body often form tumours, particularly in areas where neurotrophins are present such as the spinal cord as neurotrophins that help the growth of tissues could help form tumours instead of treating the disease. By treating stem cells in culture with chemicals that block the action of neurotrophins on hES cells, and thus killing the undifferentiated stem cells before they are implanted into the body, the current work provides a potential solution to this problem.


Researchers identify gene that marks the fate of embryonic cells

At Missouri-Columbia University, the United States, Dr. R. Michael Roberts and co-researchers have marked the formation of an embryo and a placenta before implantation, which could explain the frequent failure of cloning in farm and laboratory animals. This could have large implications for in vitro fertilization techniques widely used in human fertility procedures. They found that when a mouse egg is fertilized and begins its cell division process, the first two cells are not created equal. One of the cells expresses a protein known as Cdx2 and will create other cells that form the placenta. The other cell, which does not express the protein, will form the foetus. The researchers predicted that any disruption of the Cdx2 expression may lead to an improperly formed placenta or a pregnancy failure. Disruption can occur when material is either injected or replaced in the cells, such as in cloning and in vitro fertilization procedures.

According to Dr. Roberts, they have learned how normal development might be accidentally impaired by cloning and in vitro fertilization. Further, some artificial reproduction technologies may also be inherently damaging and convert a good egg into a poor quality embryo.


Small molecules can help fight drug resistance in cancers

A team of researchers led by Dr. Brent Stockwell from Columbia University, the United States, has identified compounds and mechanisms that can overcome a specific type of resistance to chemotherapeutic-induced apoptosis in the treatment of human cancer. The findings may have application for treatment of cancers that are linked to the human papilloma virus (HPV) oncoprotein E6, such as cervical cancer.

Certain viral oncoproteins, including HPV E6, are known to interfere with the function of a protein called p53, a key tumour suppressor involved in apoptosis. Loss of p53 is linked to uncontrolled cell proliferation, the hallmark of cancer, and is known to increase the resistance of tumour cells to some drugs. The researchers looked for small molecules that can overcome E6-induced drug resistance. They screened for compounds that potentiate chemotherapeutic effectiveness of the agent doxorubicin in E6-expressing colon cancer cells that normally have resistance to the drug.

The scientists identified several groups of compounds that potentiate doxorubicins lethality in E6-expressing tumour cells, thus overcoming E6-induced drug resistance. Indoxins, one group of compounds, proved dual-action agents driving two distinct cell cycle-related mechanisms: activation of both mechanisms simultaneously contributed substantially to doxorubicin sensitivity.



A cancer-promoting protein shows up in cell

Dr. Mark Philips and co-researchers at New York University School of Medicine, the United States, have discovered a protein widely known to cause the out-of-control growth of cells but can actually be manipulated to induce those cells to commit suicide. They reported a new mechanism that regulates the action of K-Ras, a cellular protein that plays an important role in many human cancers, providing a novel target for the development of anti-cancer drugs.

Of the three Ras oncogenes, K-Ras is the most important in terms of its impact on human cancer. K-Ras acts like as a molecular switch and can be turned on and off in its normal form to control pathways that regulate cell growth. However, the mutated form is locked in on position, causing cells to grow uncontrollably and turning off apoptosis, the process that tells a cell when it is time to die. The result is cancer.

K-Ras was thought to function only at the cell membrane, where it is permanently anchored in place by lipid molecules and electrostatic forces. Scientists then discovered that the position of K-Ras in membranes is not permanent and can be regulated by a signalling enzyme called protein kinase C (PKC). The current study showed that PKC causes a phosphate molecule to be added to K-Ras, a process that weakens the electrostatic bonds that anchor the protein, allowing it to dislodge from the plasma membrane.

Based on prior work, the researchers expected that the dislodged K-Ras would attach to the membrane of organelles in the cell, such as the endoplasmic reticulum and the Golgi body. But they were surprised to find that dislodged K-Ras also goes to the surface of the mitochondria the powerhouse of the cell, and one of the organelles that is much involved in regulating apoptosis. When phosphorylated K-Ras was introduced into cells grown in culture, it turned out to be highly toxic. The toxicity was due to the promotion of apoptosis. That was very surprising because Ras is usually thought of as an oncogene. Oncogenes generally promote uncontrolled growth and block cell death, but here Ras was promoting cell death. According to Dr. Philips, the study identified a potential new mode of suppressing tumours that are K-Ras dependent.


Groovy protein essential for promoting cancer development

At the University of Colorado, the United States, Dr. Thomas R. Cech and colleagues have determined the detailed structure of an essential piece of the telomerase enzyme, an enzyme whose excessive activity contributes to the unchecked growth of about 90 per cent of human tumours. Understanding the physical shape of telomerase should help scientists, who have long sought a way to subdue the enzyme, to design broadly effective cancer drugs.

The enzyme is vital for rapidly dividing cells where it extends telomeres, the regions of highly repetitive DNA found at the ends of chromosomes. In most healthy adult cells, telomerase is shut off and telomeres slowly shrink during cell division. Getting telomeres replicated again is an essential step in the development of cancer, and that is of interest therapeutically because it is a target that could impact a wide variety of cancers.

The researchers, in a new approach, engineered bacteria to produce fragments of the telomerase enzyme fused to a protein that emits green fluorescent light. They then randomly screened tens of thousands of fragments of the enzyme for one that would lend itself to successful structural analysis. Since telomerase fragments that clustered together would drag along and quench their associated fluorescent protein, any bright green bacterial colonies would be producing protein fragments that remained free. Those rare colonies would be the best candidates for further analysis.

Dr. Cech and team found that the experiments worked only on a fragment of the telomerase from the non-pathogenic ciliate protozoa Tetrahymena. They named the protein fragment telomerase essential N-terminal (TEN) domain, which they crystallized and analysed using X-ray diffraction to obtain an extremely detailed three-dimensional map, elucidating the position of each individual atom within the TEN domain. The studies revealed that TEN was characterized by a deep groove on its surface. The TEN domain was able to grip telomeric DNA in a test tube. When the researchers made a series of single amino acids changes within the domain, they found that three of these severely affected the binding of the chromosome end. They turned out to be lined up right within the groove. These same mutations abolished telomerases ability to extend telomeres, demonstrating that the groove was important for active telomerase.


Shuttling protein is possible key to resilience of cancer cells

In the United States, a group of researchers led by Dr. Chang-Deng Hu at Purdue University and an investigator at the Walther Cancer Institute in Indianapolis have discovered a molecular mechanism, which may play a crucial role in cancers ability to resist chemotherapy and radiation treatment and may also be involved in Alzheimers and heart disease. The scientists have learned that a protein previously believed to be confined to the nucleus of healthy cells actually shuttles between the nucleus and cytoplasm.

The experiments were done using a line of teratocarcinoma malignant tumour cells, considered to be cancer stem cells, from mice called F9. If these cells prove to be critical to cancers resistance to treatment, new medications might be developed to target cancer stem cells. The study focused on two proteins called c-Jun and ATF2, which are key components of a protein complex called activating protein-1 (AP-1). AP-1 is a major transcription factor that binds to The proteins that make up AP-1 often join together in the nucleus, forming either homodimers (when two of the same proteins join) or heterodimers (when two different proteins come together).

Current thinking is that all of these AP-1 proteins in healthy cells are localized to the nucleus. But in this work the researchers found that ATF2 possesses nuclear export and nuclear localization signals, which enable it to travel from nucleus to cytoplasm and back into the nucleus, respectively. They also found that if ATF2 attaches to c-Jun in the nucleus, forming a heterodimer, the nuclear export signal is blocked, preventing ATF2 from travelling from the nucleus to the cytoplasm.

The researchers found that over-expressed ATF2 is predominantly located in the cytoplasm because of an inadequate amount of c-Jun in the nucleus, suggesting that over-expressed ATF2 also may be localized in the cytoplasm in cancer cells. They not only discovered that ATF2 is localized in the cytoplasm of the mouse cancer stem cells, but also that exposing the cells to ultraviolet light induced more production of c-Jun protein in the nucleus, causing the ATF2 to bind with c-Jun, stopping the shuttling process and causing cell death. Because ATF2 overexpression causes the resistance of cancer cells to chemotherapy and radiation, the ATF2 shuttling might play a key role in the ability of cancer cells to resist cancer treatments, and preventing the ATF2 from moving into the cytoplasm might improve the effectiveness of anticancer treatments.


Prediction of a prokaryotic RNA-silencing system

A group of researchers led by Dr. Kira Makarova and Dr. Eugene Koonin, from the National Institutes of Health, Bethesda, the United States, carried out a comparative genomic analysis of Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and CRISPR-associated (Cas) genes in archaeal and bacterial genome sequences. The researchers used computational methods to predict what could be a prokaryotic RNA-silencing mechanism similar to the eukaryotic RNA-interference (RNAi) system.

The mechanism provides the first strong evidence that the CRISPR a type of tandem repeats found in archaea and bacteria might act in conjunction with the Cas family of genes as a defence mechanism against phage and plasmid RNA. A number of Cas proteins contain domains that suggest a functional similarity to eukaryotic proteins involved in the eukaryotic RNAi system.

The team identified several Cas genes that are located close to CRISPR clusters and encode proteins potentially involved in RNA-processing mechanisms such as unwinding and cleaving. It has been shown that a proportion of inserts in CRISPR units are similar to fragments of viral or plasmid genomes. The researchers propose that all CRISPR inserts are derived from viruses or plasmids but this is not immediately obvious, as most of these agents are unknown. They speculate that the inserts are transcribed and silence phage or plasmid sequences via the formation of a duplex, which is then cleaved by Cas proteins to destroy the foreign RNA.


Longevity modulated without disrupting life-sustaining function

Dr. Andrew Dillin and colleagues at the Molecular and Cell Biology Laboratory at The Salk Institute for Biological Studies, the United States, have identified a protein that functions specifically to extend lifespan and youthfulness without disrupting fertility, immunity or the organisms response to stress. The Salk scientists discovered the protein in studies with worms. As this signalling cascade, including the newly identified protein, is conserved across many species including humans, these findings raise the possibility to medically tweaking this pathway to slow aging and improve the quality of life without harmful consequences to the body.

This signalling cascade the insulin/IGF-1 pathway is prompted by insulin and the closely related insulin-like growth factor-1 (IGF-1). Both have key regulatory functions in the human body. In worms, however, the chain of signals is set in motion when a single receptor on the cell surface is matched to an insulin-like signal. When this pathway called DAF-2 was clipped in worms, they lived longer than normal but their larval development and reproduction were disrupted. The issue was whether one element of the pathway could be genetically manipulated without disrupting its other functions.

The researchers identified a protein in the worm Caenorhabditis elegans that is encoded by the Smk-1 gene, which is the first known gene that regulates longevity without affecting other vital functions of the insulin signalling pathway. Under favourable conditions, a still unidentified molecule binds to DAF-2. A cascade of signalling molecules relays the information to the cell protein DAF-16, which encodes a DNA-binding protein that turns on other genes. If the worms are having a good day in a favourable environment, but for some reason DAF-2 signalling gets turned off, the worms benefit with increased stress resistance and doubled lifespan, from 20 to 40 days, though with fewer progeny and a tendency to enter a dormant, hibernation stage.



GM potato is no threat to health

BASF Plant Sciences genetically modified (GM) potato EH92-527-1, which has a higher amylopectin:amylose ratio, poses no threat to human health, according to European Food Safety Authority panel ruling.

Amylopectin starch potatoes, used mainly for the production of starch for industrial purposes, is derived from the cultivar Prevalent. Using agrobacterium-mediated gene transfer technology, potato leaf discs were transformed to inhibit the expression of granule-bound starch synthase protein responsible for amylose biosynthesis. As a result, the starch produced has little or no amylose and consists of amylopectin (branched starch), which modifies the physical properties of the starch. A gene conferring kanamycin resistance (nptII) was used as a selectable marker.

The scientific assessment included examination of the DNA inserted into potato EH92-527-1, the nature and safety of the modification in protein expression in the plants with respect to toxicology and allergenicity. Furthermore, a comparative analysis of agronomic traits, composition and safety of the food/feed was made, and both nutritional and environmental risk assessments were undertaken. Molecular analysis showed potato EH92-527-1 as containing two partial copies of the DNA fragment the insert, including the flanking region, was duplicated in reverse orientation and joined tail-to-tail. This is present at a single locus in the nuclear genome of the GM plant. The GMO Panel is of the opinion that bioinformatic analysis of the DNA insert and flanking regions indicates no cause for concern, and that sufficient evidence for the stability of the insert structure was provided.


Increased plant enzyme efficiency may hold key to global warming

A team of researchers led by Dr. Monal R. Parikh and Dr. Ichiro Matsumura at Emory University School of Medicine, the United States, has discovered a mutant enzyme that could enable plants to use and convert carbon dioxide (CO2) more quickly, effectively removing more greenhouse gases from the atmosphere. Scientists have long known that photosynthesis relies on the enzyme rubulose 1,5-bisphosphate carboxylase/oxygenase, also called RuBisCO. While RuBisCO is the most abundant enzyme in the world, it is also one of the least efficient.

The present study used a process called directed evolution, which involved isolating and randomly mutating genes, and then inserting the mutated genes into bacteria (in this case Escherichia coli). The resulting mutant proteins were then screened for the fastest and most efficient enzymes. Dr. Matsumuras team added the genes encoding RuBisCO and a helper enzyme to E. coli, thus enabling it to change CO2 into consumable energy.

Other nutrients were withheld from this genetically modified organism so that it would need RuBisCO and CO2 to survive. They then randomly mutated the RuBisCO gene, and added these mutant genes to the modified E. coli. The fastest growing strains carried mutated RuBisCO genes that produced a larger quantity of the enzyme, leading to faster CO2 assimilation. These mutations caused a 500 per cent increase in RuBisCO expression.

According to Dr. Matsumura, all life pretty much depends on the function on this enzyme. It has had billions of years to improve, but remains about a thousand times slower than most other enzymes. Plants have to make tonnes of it just to stay alive. Therefore, scientists decided to do what nature does, but at a much faster pace. Essentially they were using evolution as a tool to engineer the protein. Scientists are excited that the enzyme is evolving in their laboratory in the same way that it did in nature.


Genetically modified plants used as pollution pumps

Researchers led by Dr. Neil Bruce from the Centre for Novel Agricultural Products, University of New York, the United States, used micro-organisms found in soil to turn plants into highly effective pollution-busters. It is a new development in the field of bioremediation in which the plants have been genetically altered by scientists to act as giant pumps, sucking pollutants from the soil.

The researchers identified a naturally occurring micro-organism in the soil which breaks down explosives to use the nitrogen to grow, but found it was not degrading the RDX fast enough to prevent contamination. To solve this problem, the team isolated the enzyme in the bacteria that was breaking down the toxic explosive and genetically inserted it into plants, which can do the job much quicker. According to Dr. Bruce, this is a sustainable, low-maintenance and low-cost process that has the potential to clean up large areas of land in military training ranges or industrial sites. A tree, for instance, is effectively a big pump. If the scientists can redeploy the enzyme, it would combine the capabilities of soil bacteria with the high biomass and uptake properties in plants to biodegrade the RDX fast. The team is hopeful that the technique can also be used to modify plants to absorb other organic pollutants.


New method enables gene disruption in fungal pathogen

In the United States, a research team from the Virginia Bioinformatics Institute at Virginia Tech, Colorado State University, and Duke University Medical Centre, North Carolina, has developed a new method to determine gene function on a genome-wide scale in the fungal pathogen Alternaria brassicicola. The fungus causes black spot disease, leading to considerable leaf loss in economically important crops such as canola, cabbage and broccoli.

According to Dr. Christopher Lawrence, the team leader, the new method takes advantage of a novel linear DNA construct that greatly improves the efficiency of targeted gene disruption. The DNA construct includes an antibiotic-resistance marker gene, which allows for easy selection of the new mutants, and a short partial target gene that disrupts genes in the pathogens genome.

The scientists looked at over 20 genes and were able to produce transformants and inactivated genes or knock-outs in each experiment. In most cases, the efficiency of gene disruption was 100 per cent, which represents a considerable improvement over previously reported methods and makes large-scale functional analysis of individual genes feasible. It is expected that the high throughput system described in this study would allow for the systematic analysis of large sets of candidate genes in A. brassicicola such as those encoding cell-wall-degrading enzymes and other genes of interest in pathogen-plant interactions.


Plants eavesdrop for their own protection

Insect-damaged sagebrush has a novel way of broadcasting to nearby plants that a predator is in the area. It releases a bouquet of airborne odours and perfumes. If wild tobacco is growing nearby, it will eavesdrop on these chemical signals and fortify its defences against such pests. These are the findings of a research team led by Dr. Andre Kessler, at Cornell University, the United States.

The researchers have found that the release of volatile organic compounds from a wounded sagebrush (Artemisia tridentata) primes the defences of wild tobacco (Nicotiana attenuata) to prepare itself for herbivore attacks. But the tobacco plant holds off actually creating its defences until it is attacked. Most of the proteins and compounds used for defence contain nitrogen and carbon, which are needed to produce seeds. Because of this cost, the defences are advantageous to the plant only if a herbivore actually attacks. According to Dr. Kessler, by priming its defence response the plant is not investing resources before it is actually attacked and this could be a crucial plant- plant communication mechanism.

In both greenhouse and field experiments, the researchers spread sagebrush clippings with their perfumes and odours around wild tobacco plants. Each experiment included an isolated tobacco plant as a control, a tobacco plant exposed to clipped sagebrush, a tobacco plant loaded with tobacco hornworms (hawkmoth caterpillar) that feed on tobacco, and a plant exposed to both sagebrush and hornworms. The damage and compounds from the hornworms saliva trigger plants to produce defensive proteins called trypsin proteinase inhibitors (TPI), which make it difficult for caterpillars to digest proteins. They found that the controls showed little difference from the plants exposed only to sagebrush. But plants that were exposed to both hornworms and sagebrush clippings produced more TPIs earlier than plants just damaged by hornworms, indicating that exposure to sagebrush gave the tobacco a head start in defending itself.



Environmental Exposure and Health (EEH 2005)

This book provides current environmental management policies aimed to achieve a harmonious balance between the development of economic resources and the preservation of the environment with the ultimate goal of reaching sustainability while improving the health, safety and prosperity of the population. This approach involves taking acceptable risks in terms of the environment, human health and the economy, an interdisciplinary activity that requires close cooperation between several scientific and engineering fields.

This volume features contributions from health specialists, social and physical scientists and engineers. The papers included cover areas such as: air exposure modelling and assessment; indoor air quality and exposure; emerging water contaminants: environmental fate and health effects; exposure-dose reconstruction; biomarkers in exposure studies; chemical mixtures and exposure; health risk analysis; environmental impact and exposure; and communication and social issues in environmental exposure.

Contacts: Witt Press, Ashurst Lodge, Ashurst, Southamption, SO40 7AA, United Kingdom. Tel: +44 (2380) 293 223; Fax: +44 (2380) 292 853


Cell Cycle in the Central Nervous System

This book focuses on: cell cycle during the development of the mammalian central nervous system; post-natal development of neurons and glia; control of cell cycle and apoptosis in glia; adult neurogenesis a mechanism for brain repair? cell cycle re-entry a mechanism of brain disease? the biology of gliomas; and future directions.

Contact: Humana Press, 999 Riverview Drive, Suite 208, Totowa, NJ 07512, United States. Tel: +1 (973) 256 1699; Fax: +1 (973) 256 8341



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