BIOTECHNOLOGY INFORMATION

Everything a bout The ALlele FREquency Database

2007-04-15T23:20:00.000-07:00

OverviewALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases. Initially, ALFRED contained primarily data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics at Yale, including extensive unpublished data. Data from the published literature are being entered into ALFRED in a systematic way, with a focus on polymorphisms studied in many different populations. (Researchers wishing to have their data entered into ALFRED should contact us. If suitable data can be sent in appropriate electronic format, it will be much easier to include them in ALFRED, see "Criteria" below.) ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation. ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching. ALFRED is a work in progress. The structure and functionality of ALFRED are being revised in an ongoing process as time allows improvements to be implemented. We are also routinely adding new data and links to other databases. Those of us on the ALFRED staff hope these data will be useful to others. We welcome comments on content, structure, and the interfaces available. ALFRED is maintained by the ALFRED Staff. ________________________________________Criteria for Data Entry into ALFREDWe feel that gene frequency data are only meaningful if a population sample is reasonably well defined and large enough for a reasonably accurate frequency estimate and if the polymorphism is sufficiently defined to be replicable. Therefore, not all published gene frequency data will be included in ALFRED. Currently, there is no absolute minimum sample size since samples that are small but come from sparsely represented areas and/or have data on multiple polymorphisms can be very useful. (The Nasioi sample is a specific example of such small sample (22 individuals) studied for multiple markers.) We are only including samples that can be reasonably specified as to ethnicity though this includes some highly heterogeneous groups such as "United States whites", which is the equivalent of "mixed European". Because ALFRED focuses on gene frequency variation among populations, we are generally including frequency estimates only for polymorphisms that have been studied in at least six distinct population samples. Of course, there are exceptions, especially if a sample generally studied for multiple polymorphisms that meet the ">6 populations" criterion also has data on some unique polymorphisms. Similarly, various small sets of data are being entered when we know or expect there are additional data becoming or already available for eventual entry into ALFRED. Our available resources to enter data from the literature are quite limited but if researchers can provide suitable electronic versions of their appropriate data we will be happy to add them to ALFRED. The above criteria for inclusion in ALFRED are subject to change. We welcome comments from the scientific community interested in these data and will attempt to follow any consensus that emerges. ________________________________________Data submission to ALFRED - guidelinesOnly data on well defined population samples that are large enough to yield reasonably accurate frequencies and for polymorphisms sufficiently defined to be replicable can be included in ALFRED. If the submitted data lack any of this information, the data lose much of their value. Therefore, we are looking for the most complete set of information for each population sample. As an aid in your ALFRED submission we have listed below guidelines that you should follow in order to provide the necessary data. In addition to the actual frequencies, we will need further information regarding your publications, samples, loci and sites. Below you will find what type other information we will need to input your data into ALFRED.
PublicationsWe need any citations for publications that contain the allele frequencies that you are submitting.Your data will be linked to these publications. If your data are unpublished the data will be referred to the researcher’s name saying they are unpublished. If they are published in the future, you will need to send us the new citation in order for the data to be linked to the appropriate publication. SampleALFRED distinguishes samples of a population (a particular set of individuals) from the population. This allows future researchers to consider whether differences of whatever sort, shown by different loci, for example, can be attributed to the loci because the same set of individuals was tested for both loci or might be attributed to sampling differences because different sets of individuals were tested. To describe the sample sufficiently, we need to know about certain elements concerning your specific sample. The information you provide will also be used to aid in a complete description of the population from which the sample was collected. The following information is most important:• specific sample information when available (related/unrelated, age, men/women, etc.); • where the sample was collected; • geographic location of sample (city, village, etc.); • precisely who collected the sample (source); • the ethnic make-up of the sample; • the sample size (number of individuals); • any references to articles with published information concerning your particular sample; • language spoken; If the population is not yet described in ALFRED additional information, if available, can also be useful in describing the population. Such information would include: • population name; • subsistence practices; • historical information ; • religion; • any other cultural traditions; • any ethnographic citations. If all of this information is not available, please give the most complete information as possible. Locus: Please provide the official name and symbol for the gene in which the site is located. For the official gene symbol, go to the HGNC website http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl. If you cannot find an official gene symbol for the site, please give us as much information as possible. For intergenic sites it is helpful to have the name of the closest gene and an indication of the distance from the gene 5' or 3'Site (polymorphism): • Specify polymorphism location within the gene if available (e.g. "intron 3"); • Specify nucleotide/amino acid variations if available; • Specify restriction enzyme used to detect this polymorphism if it’s a RFLP; • Give GenBank accession number and/or dbSNP ss# (rs#) if available; • Other additional information used to best describe this site. • Give 10-15 bp flanking sequence on both sides of variant if available. Allele: • For RFLP, use site absent and site present for the two allele names; • For STRP and VNTR, use number of repeats as allele names. If you use fragment size as allele names, please provide typing protocol and specify primer sequences; • For Ins/Del, use insertion and deletion as allele names; • For SNP, use nucleotide variants as allele names. For example, A/G SNP has A and G for the two alleles. Excel Spreadsheet: The excel spreadsheet provided, can be used for sumitting data to the ALFRED Staff at alfred@yale.edu . The information that has be provided in the spreadsheet are as follows: • Sample name: name of sample you used in publication; • Number of chromosomes: number of chromosomes in the population sample; • Locus symbol: official gene symbol; • Site name: site name used in publication; • Allele name: see above; • Frequency: frequency value; • Typed number of chromosomes: number of chromosomes actually typed for that marker in that population sample (may be less than the sample size because of missing data); • Typing method: method used for typing each polymorphism. Sample, locus, and site information can be submitted via a Word file or other comparable word processing file. If you have problems using the excel spreadsheet provided please let us know and we will work with you to come up with a more useful method of submitting your data. If you have any questions, comments or suggestions about any aspect of ALFRED, please feel free to contact us.FOR MORE INFORMATION:http://www.btlogy.blogspot.com/

BioCarta

2007-01-19T10:00:00.000-08:00

Proteomics marketplace and resource center
http://www.biocarta.com/

BIOBASE

2007-01-19T09:52:00.000-08:00

Specialized biological databases, mainly from the field of molecular biology, including the TRANSFAC database on transcription factors, their genomic binding sites and their general binding profiles.
BIOBASE is the leading content provider of biological databases, knowledge tools and software for the life science industry. We offer our customers well-structured data, assembled by highly qualified subject-matter experts, organized in an accessible and easily searchable manner that enables researchers to identify connections between disparate pieces of information and to apply that knowledge to their specific topic of interest.

http://www.biobase-international.com/

BIND

2007-01-19T09:45:00.000-08:00

Biomolecular Interaction Network Database
Between 1999-2005 Blueprint developed BIND and other bioinformatics resources at Mount Sinai Hospital in Toronto in the laboratory of Principal Investigator, Christopher Hogue.
In 2006 and beyond Blueprint will continue to engage in cutting-edge research, training and development of bioinformatics products and services.

http://www.blueprint.org/

BGEM

2007-01-19T09:37:00.000-08:00

The St. Jude Brain Gene Expression Map (BGEM) project is managed by Tom Curran, Ph.D., Patricia Jensen, Ph. D., and Susan Magdaleno, Ph. D. in the Department of Developmental Neurobiology at St. Jude Children’s Research Hospital.Technical expertise is provided by Karen Lehman, Andrew Asbury, Tony Cheung, Tommie Cornelius, Diana Batten, and Christopher Eden. Custom primer design for generating riboprobe template for in situ hybridization analysis is performed in part by The National Center for Biotechnology Information (NCBI). The St. Jude BGEM website is built and maintained by software engineers Nileshwar Dosooye, and Sundeep Shakya and the Bioinformatics programs were written by Perdeep Mehta, Ph.D in the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children’s Research Hospital. The BGEM project is part of the Gene Expression Nervous System Atlas (GENSAT) funded by the National Institute for Neurological Disorders and Stroke (NINDS), National Institute of Mental Health (NIMH), and National Institute for Drug Abuse (NIDA) at the NIH and the American Lebanese Syrian Associated Charities (ALSAC) at St. Jude Children's Research Hospital.
http://www.stjudebgem.org

Berkeley Drosophila Genome Project

2007-01-19T09:32:00.000-08:00

Berkeley Drosophila Genome Project

http://www.fruitfly.org/

BCM Search Launcher

2007-01-19T09:29:00.000-08:00

Baylor Human Genome Center

BCM Search Launcher
The Baylor College of Medicine Search Launcher is an on-going project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters).

http://searchlauncher.bcm.tmc.edu/

Base4 Bioinformatics

2007-01-19T09:21:00.000-08:00

Integrated systems solutions for biotechnology and pharmaceutical development.

http://www.opentext.com/

Bacterial Names with Standing in Nomenclature

2007-01-19T08:59:00.000-08:00

List of Prokaryotic names with Standing in Nomenclature Formerly List of Bacterial names with Standing in Nomenclature (LBSN)

http://www.bacterio.cict.fr/

AtlasInfo

2007-01-19T08:52:00.000-08:00

Clontech Laboratories, Inc.
Clontech Laboratories provides kits, reagents, and services that help researchers explore questions about gene discovery, regulation, and function. As the newest member of the Takara Bio Group, Clontech joins a company that holds a leadership position in the global market and is committed to improving the human condition through biotechnology. Clontech’s mission is to develop high-quality innovative tools and services to accelerate discovery.

http://atlasinfo.clontech.com/

Atlas of Side-Chain and Main-Chain Hydrogen Bonding is available for biomolecular modellers

2007-01-19T08:35:00.000-08:00

University College London was early to recognise the importance of Biochemistry as a scientific discipline. Even during the last quarter of the nineteenth century the study of Physiological Chemistry was being actively pursued within the UCL Department of Physiology. The appointment of the eminent nutritionist Sir Jack Drummond as UCL's first Professor of Biochemistry in 1922 began the process that eventually led to the founding of a separate department of Biochemistry in 1946 and the recognition at UCL of Biochemistry as a distinct and important scientific discipline. Initially the new department only admitted postgraduate students but by 1953 was one of the first departments in the UK to offer a BSc programme in Biochemistry. Emeritus Professor Peter Campbell has compiled a detailed history of the department since its establishment.

http://www.biochem.ucl.ac.uk/

ATCC

2007-01-19T08:23:00.000-08:00

ATCC is a global nonprofit bioresource center that provides biological products, technical services and educational programs to private industry, government and academic organizations around the world. Our mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement, validation and application of scientific knowledge.
http://www.atcc.org/

ARP

2007-01-19T08:10:00.000-08:00

Antibody Resources Page

http://www.antibodyresource.com/

Anti-Cancer Maps

2007-01-19T08:01:00.000-08:00

Public database with viewing tools (NCI).

http://spheroid.ncifcrf.gov/

ANGIS

2007-01-19T03:14:00.000-08:00

Australian National Genomic Information Service provides access for biologists to a comprehensive system of bioinformatics software, databases, documentation, training and support, on a subscription basis.
http://www.angis.org.au/

ALFRED

2007-01-19T02:53:00.000-08:00

Allele frequency database from the Kidd Lab at Yale Univ.

http://alfred.med.yale.edu/alfred/

addgene

2007-01-19T02:46:00.000-08:00

A non-profit organization dedicated to promoting sharing of plasmid constructs described in published literature. Addgene stores original plasmid samples submitted by scientists and distributes them for use in advancing life science research.

http://www.addgene.org/pgvec1

2007-01-18T10:27:00.000-08:00

Short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI and from sites belonging to its collaborators.

http://www.ebi.ac.uk/2can/home.html

BIOTECHNOLOGY IN AUSTRALIA

2006-12-24T09:17:00.000-08:00

Biotechnology Australia, a multi-departmental Government agency, was established in 1999.
We are responsible for managing the National Biotechnology Strategy and for coordinating non-regulatory biotechnology issues for the Australian Government.
We also provide balanced and factual information on biotechnology to the Australian community, including through our Biotechnology Online school resource.
Our five partner agencies are:
Department of Agriculture, Fisheries and Forestry
Department of Education, Science and Training
Department of Health and Ageing
Department of Industry, Tourism and Resources
Department of Environment and Heritage

Watch saturated fats and calories too

2006-12-22T21:07:00.000-08:00

Boston -- In December, New York City passed a law to phase out the use of trans fat in restaurants. Other cities, including Boston and Chicago, might follow suit. According to Alice H. Lichtenstein, DSc, Gershoff professor of nutrition science and policy at the Friedman School of Nutrition Science and Policy at Tufts University, the ban is a step in the right direction, but restaurateurs need to replace partially hydrogenated fat with unsaturated fat. If they choose saturated fat it would diminish the health benefits of this new initiative. Another new regulation that requires some restaurants to provide calorie information as prominently as price might be even more important, notes Lichtenstein.
"There is no biological need for trans fat and intake is associated with adverse health outcomes. However, the media attention on the trans fat announcement to the exclusion of the calorie labeling is unfortunate. Two-thirds of Americans are overweight or obese. The New York City Department of Health and Mental Hygiene has proposed that the calorie content of food items be displayed as prominently as the price, at the point of purchase," says Lichtenstein, also director of the Cardiovascular Nutrition Laboratory at the Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts.
"That means," Lichtenstein continues, "that if you are wavering between placing an order for a small versus a medium order of French fries, both the price and the number of calories per serving will be displayed. People will become more aware of the caloric cost of the foods they order, and the next step on a public health level would be to educate the consumer on the amount of calories their body needs per day. This way, they will be able to put the numbers they see on the board or menu into perspective. Because the amount of food and beverages we eat that is prepared outside the home is so large, even if this regulation just covers a fraction of food service establishments, it can have a tremendous impact on caloric intake."
"Trans fat," says Lichtenstein, "is a double whammy, because like saturated fat, it raises levels of LDL or 'bad cholesterol,' but it also lowers levels of HDL or 'good' cholesterol." Most of the trans fats we eat are formed during the partial hydrogenation of oils used in fried foods and commercial baked goods. Partially hydrogenated oils provide processed foods with longer shelf lives and therefore greater economic profitability.
"But, trans fat is just one part of the diet. In general, people are still eating far more saturated fat than trans fat, and both need to be reduced in order to maintain optimal cholesterol levels and promote heart health," says Lichtenstein. "And the big giant – total calories – is always looming in the background."
In one study to assess the effects of consuming different types of oils on cholesterol levels, led by Lichtenstein and published earlier this year, fifteen adult volunteers with moderately high LDL cholesterol were fed each of four diets with a different source of primary fat, including partially hydrogenated soybean oil (trans fat), palm oil (50 percent saturated fat), non-hydrogenated soybean oil (only 16 percent saturated fat), and canola oil (only 7 percent saturated fat).
The results, published in the American Journal of Clinical Nutrition (AJCN), reported that after a trial of 35 days on each diet, participants consuming the partially hydrogenated soybean oil and palm oil diets had levels of LDL cholesterol that were 12 and 14 percent higher, respectively, than when consuming the non-hydrogenated soybean oil diet. An even greater difference was observed when the partially hydrogenated soybean oil and palm oil diets were compared to the canola oil diet. While participants were on the partially hydrogenated soybean oil and palm oil diets their LDL levels were 16 and 18 percent higher, respectively, than when on the canola oil diet.
"On the basis of this and other work, it's clear that phasing out partially hydrogenated oils (trans fats) will improve diet in some ways, "says Lichtenstein, corresponding author on the AJCN study. "However, just decreasing trans fat intake without changing other dietary habits, such as minimizing saturated fat intake and controlling total calorie intake, will result in some real disappointments with respect to both heart health and obesity."
Lichtenstein recommends that other cities monitor the successes and challenges of the trans fat ban in New York City before implementing their own regulations, and also advises that the focus on the new regulations shift to the mandate to display calorie labeling in food service establishments, and educating people about their total daily caloric requirements.
###
Vega-Lopez S, Ausman LM, Jalbert SM, Erkkila AT, Lichtenstein AH. "Palm and partially hydrogenated soybean oils adversely alter lipoprotein profiles compared with soybean and canola oils in moderately hyperlipidemic subjects." American Journal of Clinical Nutrition. 2006 (July);84(1):54-62.
If you are interested in learning more about this topic, or speaking with a faculty member at the Friedman School of Nutrition Science and Policy at Tufts University, or another Tufts health sciences researcher, please contact Siobhan Gallagher at 617-636-6586.
The Gerald J. and Dorothy R. Friedman School of Nutrition Science and Policy at Tufts University is the only independent school of nutrition in the United States. The school's eight centers, which focus on questions relating to famine, hunger, poverty, and communications, are renowned for the application of scientific research to national and international policy. For two decades, the Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University has studied the relationship between good nutrition and good health in aging populations. Tufts research scientists work with federal agencies to establish the USDA Dietary Guidelines, the Dietary Reference Intakes, and other significant public policies

Nature Biotechnology

2006-12-13T23:56:00.000-08:00

Home page: http://www.nature.com/nbt/
Table of contents: http://www.nature.com/nbt/current_issue/
Publisher: http://www.nature.com/
Field: Biotechnology

Engineered yeast speeds ethanol production

2006-12-08T23:39:00.000-08:00

Currently used as a fuel additive to improve gasoline combustibility, ethanol is often touted as a potential solution to the growing oil-driven energy crisis. But there are significant obstacles to producing ethanol: One is that high ethanol levels are toxic to the yeast that ferments corn and other plant material into ethanol. By manipulating the yeast genome, the researchers have engineered a new strain of yeast that can tolerate elevated levels of both ethanol and glucose, while producing ethanol faster than un-engineered yeast. The work will be reported in the Dec. 8 issue of Science.Fuels such as E85, which is 85 percent ethanol, are becoming common in states where corn is plentiful; however, their use is mainly confined to the Midwest because corn supplies are limited and ethanol production technology is not yet efficient enough.Boosting efficiency has been an elusive goal, but the MIT researchers, led by Hal Alper, a postdoctoral associate in the laboratories of Professor Gregory Stephanopoulos of chemical engineering and Professor Gerald Fink of the Whitehead Institute, took a new approach.The key to the MIT strategy is manipulating the genes encoding proteins responsible for regulating gene transcription and, in turn, controlling the repertoire of genes expressed in a particular cell. These types of transcription factors bind to DNA and turn genes on or off, essentially controlling what traits a cell expresses.The traditional way to genetically alter a trait, or phenotype, of an organism is to alter the expression of genes that affect the phenotype. But for traits influenced by many genes, it is difficult to change the phenotype by altering each of those genes, one at a time.Targeting the transcription factors instead can be a more efficient way to produce desirable traits. "It is the makeup of the transcripts that determines how a cell is going to behave and this is controlled by the transcription factors in the cell," according to Stephanopoulos, a co-author on the paper.The MIT researchers are the first to use this new approach, which is akin to altering the central processor of a computer (transcription factors) rather than individual software applications (genes), says Fink, an MIT professor of biology and a co-author on the paper.In this case, the researchers targeted two different transcription factors. They got their best results with a factor known as a TATA-binding protein, which when altered in three specific locations caused the over-expression overexpresion of at least a dozen genes, all of which were found to be necessary to elicit an improved ethanol tolerance, thus allowing that strain of yeast to survive high ethanol concentrations.Because so many genes are involved, engineering high ethanol tolerance by the traditional method of overexpressing individual genes would have been impossible, says Alper. Furthermore, the identification of the complete set of such genes would have been a very difficult task, Stephanopoulos adds.The high-ethanol-tolerance yeast also proved to be more rapid fermenters: The new strain produced 50 percent more ethanol during a 21-hour period than normal yeast.The prospect of using this approach to engineer similar tolerance traits in industrial yeast could dramatically impact industrial ethanol production, a multi-step process in which yeast plays a crucial role. First, cornstarch or another polymer of glucose is broken down into single sugar (glucose) molecules by enzymes, then yeast ferments the glucose into ethanol and carbon dioxide.Last year, four billion gallons of ethanol were produced from 1.43 billion bushels of corn grain (including kernels, stalks, leaves, cobs, husks) in the United States, according to the Department of Energy. In comparison, the United States consumed about 140 billion gallons of gasoline. Other co-authors on the Science paper are Joel Moxley, an MIT graduate student in chemical engineering, and Elke Nevoigt of the Berlin University of Technology.The research was funded by the DuPont-MIT Alliance, the Singapore-MIT Alliance, the National Institutes of Health and the U.S. Department of Energy.

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Source: EurekAlert Press Release

Biomass research center pursued

2006-12-08T23:38:00.000-08:00

There are prominent pieces of the puzzle located in Massachusetts and in my congressional district," said Delahunt, a Democrat who represents the area along the coast from Quincy to Provincetown. "I can't imagine a more suitable location for a center."Delahunt is part of a team that includes representatives from Harvard University, the Massachusetts Institute of Technology, the Romney administration, and state business leaders crafting a formal proposal for winning one of two $125 million centers.Each center will receive $25 million in startup money plus $25 million a year for four years to study new ways to convert biomass -- stems, leaves, grasses, and other plant products -- to ethanol or similar materials that could be used in place of petroleum products.The center would not only bring high-paying jobs but would also place the region on the leading edge of a technology that could spawn new industry by attracting biofuel manufacturing facilities.Delahunt and his team are facing stiff competition from other parts of the country. Researchers, government officials, and politicians from several other regions are also pursuing the federal research center award."I think this will be very competitive," said Ann Marie Sastry, professor of mechanical engineering at the University of Michigan and a leader of an effort to win a center in her state. "These centers offer enormous opportunities to a region."Delahunt said he did not know where on the South Shore the center would be built, but he and others involved in the Massachusetts bid are eyeing the Fore River basin, where Quincy, Braintree, and Weymouth converge.Twin Rivers Technologies, a firm that produces biodiesel fuel for trucks and other heavy equipment, is headquartered on the Fore River in Quincy. Twin Rivers produces biodiesel from soybean products at facilities in Ohio. Its Quincy manufacturing plant processes imported tropical oils for use in soap and cosmetics.It is one of two prominent area companies in US bioenergy development. The other is Bioenergy International LLC in Norwell. Bioenergy International is developing ethanol production facilities in Louisiana and Pennsylvania. At its Norwell location, the company conducts research and development, and manages its operations elsewhere in the country.Officials from the companies are part of the team preparing a bid to win the federal research center, and both would like to expand on the South Shore, according to their top executives.Twin Rivers' president, Paul Angelico, said the company wants to build a biodiesel manufacturing plant in Quincy. The company has only one undeveloped acre on its Fore River site and would need access to other land nearby.Stephen Gatto, chief executive officer of Bioenergy International, said the company is considering several sites on the South Shore for a $17 million research and pilot manufacturing facility.Proposals for the federal research centers are due Feb. 1, and the US Energy Department expects to make its selections in June. The money would be awarded by September."What we would like to see is a consortium of universities and research institutions and businesses coming together with a proposal," said Craig Stevens, a department spokesman.He acknowledged the stiff national competition. While declining to speculate on Boston's proposal, he said, "There is no question Boston brings together a lot of intellectual and investment capital."The Energy Policy Act of 2005, adopted by Congress and signed by President Bush after the oil shocks of last year, spurred planning for the new research centers. Policymakers want to find new and cleaner sources of fuel and also lessen US dependence on foreign oil. Secretary of Energy Samuel W. Bodman has set a goal of replacing 30 percent of current transportation fuel demand with biofuels by 2030.Converting biomass to energy is one of the oldest technologies, which humans first used when they burned wood to keep warm. But converting plants and plant-based products into fuels that can power automobiles has proven to be a difficult challenge.After the oil crisis of the 1970s, the federal government launched a major initiative for production of ethanol, known then as "gasohol," using corn and other agricultural products to produce fuel. The program foundered, in part, because of the large amount of energy needed to make the fuel.Recent research has focused on finding more efficient ways to convert plant products to fuel. And researchers are seeking to use different types of plant-based products, from corn husks to scrap wood to animal waste.Both Gatto of Bioenergy International and Angelico of Twin Rivers said the Fore River basin could make a good site for a research center. The area has a deep-water port and a connection to the East Coast rail network, they noted."I think we are well-prepared to have that center here," Angelico said. Most available sites in the Fore River area are privately owned, and deals with owners would need to be completed. The largest parcel is the approximately 110-acre former Quincy Shipyard, now owned by South Shore automobile dealer Dan Quirk.Quirk is planning a mixed-use development on the site with mostly housing and stores. John Dobie, planning director for Quirk, said he knew very little about the bioenergy proposals. While Quirk's preliminary master plan for the Quincy Shipyard does not include a site for research facilities, the property is large enough that it might be able to accommodate a research center.Jay Cashman, a prominent Boston contractor, owns a 12-acre parcel on the Fore River waterfront. Cashman had tried unsuccessfully to acquire the entire Quincy Shipyard, and he sued in an unsuccessful attempt to block Quirk's purchase of the property.Delahunt said he believes bioenergy development in the Fore River area would benefit all parties."These are business people," Delahunt said. "I'm certain the stakeholders can sit down and have a conversation. Let's see what happens."© Copyright 2006 Globe Newspaper Company

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Source: Boston Globe

MAF admits that it has made a mistake with regional boundaries

2006-12-08T23:37:00.000-08:00

Their original statement was that there were 147 hectares of suspect corn in the Gisborne district — however 90.1 hectares of that was being grown in Wairoa."We made an incorrect assumption that Wairoa was in the Gisborne district," said MAF spokesman Brett Sangster.Much of the Wairoa corn is being grown for Gisborne-based processor Cedenco Foods, which faces a potentially disrupted sweetcorn-processing season.If the offending corn had to be removed, the company now had little opportunity to replant it, said Cedenco New Zealand operations manager Richard Thorp.Time was of essence, with the region now well into its finite optimum growing season.The issue now was one of compensation, with estimates that the Government might face a bill of up to $1 million to clean up the border bungle.Mr Sangster said MAF was seeking legal advice on liability and compensation."Once we have clarity on that, we will be having discussions with affected growers and seed importing companies," he said.Imports of a total of 4420kg of sweetcorn seed is being being investigated for possible GE contamination. About two-thirds of the sweetcorn seed — 3067.5kg — was planted in Hawke’s Bay, Gisborne, and Ashburton, on about 373ha spread over 25 properties."The bill the Crown faces for cleanup of the latest incident is understood to be in the vicinity of $1 million," Sustainability Council executive director Simon Terry said yesterday.Two years ago, the council had proposed to the Ministry of Agriculture and Forestry low-cost and no-cost biosecurity measures to significantly boost chances of detecting seed contamination and avoiding expensive cleanup bills. These included trebling the quantity of seeds sampled to raise the ability to detect low concentrations, and encouraging importers to track and screen seeds for GE content from origin to delivery. Such quality assurance procedures would have aided MAF’s stated objective of ensuring New Zealand’s GE-free status was maintained.Mr Terry said MAF had put aside the council’s proposals, to be reviewed at some later date. But they would have boosted the chance of detecting GE seeds in the latest shipments, even if the paperwork had not been read correctly at the border.Copyright 2006 Gisborne Herald

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Source: Gisborne Herald

GM canola shipment contaminated: AQIS

2006-12-08T23:29:00.000-08:00

The shipment arrived at the Port of Newcastle this week.It will be processed in Newcastle into protein meal and vegetable oil, and sold to the food and biodiesel industries.National manager for Plant Programs at AQIS Peter Liehne says it is common for bulk commodities to contain other material."In this case we found that there are some seeds present in the shipment which have sufficient concern for us to look at the management of the product to ensure there is no risk to the environment resulting from these weed seeds," he said. "I understand that there is a little bit of barley present in the product and possibly some other seeds, as well as some other weed species that are normally found in grain production areas."© 2006 ABC

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Source: Australian Broadcasting Company

The Government may face a hill of up to $1 million to clean up the latest border bungle - allowing genetically-engineered (GE)

2006-12-07T23:25:00.000-08:00

Imports of a total of 4420kg of sweetcorn seed is being being investigated for possible GE contamination. About two-thirds of the sweetcorn seed -- 3067.5kg -- was planted in Hawke's Bay, Gisborne, and Ashburton, on about 373ha spread over 25 properties. The bill the Crown faces for cleanup of the latest incident is understood to be in the vicinity of $1 million," Sustainability Council executive director Simon Terry said today.He said the council had proposed to the Ministry of Agriculture and Forestry (MAF) two years ago low-cost and no-cost biosecurity measures to significantly boost chances of detecting seed contamination and avoiding expensive cleanup bills.These included trebling the quantity of seeds sampled, to raise the ability to detect low concentrations, and encouraging importers to track and screen seeds for GE content from origin to delivery.Such quality assurance procedures would aid MAF's stated objective of ensuring New Zealand's GE-free status was maintained. Mr Terry said MAF had put aside the council's proposals, to be reviewed at some later date.But they would have boosted the chance of detecting GE seeds in the latest shipments, even if the paperwork had not been read correctly at the border.Green Party co-leader Jeanette Fitizsimons said tonight that efforts by Biosecurity NZ, an agency within MAF, to go back to the US suppliers ofthe seeds, Syngenta, seemed pointless."These four consignments came through with documentation that showed GE contamination," she said. "Even if Syngenta provides 100 more documents, it will not change the fact that several tonnes of contaminated seeds have been illegally imported and planted."Ms Fitzsimons said that for MAF or biosecurity officials to consider letting the corn mature and be harvested, on the condition that it was then exported would send a dangerous signal to markets that expected NZ to be GE-free.Mr Terry said trying to contain the GE seeds in that way would raise questions about how committed NZ was to the policy of "zero tolerance" of illicit GE seed. "No level of GE contamination is acceptable for the buyers who seek out New Zealand producers because of this country’s GE-free reputation," he said.
Copyright New Zealand Press Association

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Source: New Zealand Press Association

CAPE TOWN - South Africa wants biofuels to contribute up to 75% of renewable energy needs by 2013 under a R6bn programme

2006-12-07T23:24:00.000-08:00

The strategy, which would not require "excessive support" nor hit food security, comes as volatile oil prices combined with a global drive to limit greenhouse gases forces governments to look at alternative energy sources. South Africa, an economic giant on the African continent, envisages that biofuels would create jobs, particularly in the agriculture sector which is under pressure as it comes to grips with post-apartheid liberalisation and global competition. "The biofuels industry has the potential to create 55 000 agricultural jobs and will contribute to reducing greenhouse gases and promote a cleaner environment," government spokesperson Themba Maseko told a news briefing. "The required capital investment will be approximately R6bn which will come from both public and private sectors." Maseko said a team will review the strategy before it is submitted for finalisation in May 2007. The proposed strategy will see South Africa, which produces a surfeit of sugar and maize crops, use the excess to manufacture bio-ethanol for possible use in cars. Already Brazil, a strategic partner in trade relations with South Africa, is being touted as an example to follow because of its successful biofuels industry. Plants have also emerged in the United States and in Europe as countries look for cheaper and more environmentally friendly alternatives to conventional fuels.
Copyright Fin24

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Source: Fin24

Queensland localities could be used by sugar industry research arm BSES to trial a genetically modified (GM) cane variety

2006-12-07T23:20:00.000-08:00

The Gene Technology Regulator needs to approve the trial before plantings can begin.BSES spokesman Ross Gilmore says the trial will take place either on the Sunshine Coast, Bundaberg or near Cairns and will involve fewer than 18 hectares of sugar cane.He says the proposed three-year trial is part of an ongoing program to improve sugar cane varieties."The purpose of this particular trial is to evaluate two things - the first is the methods we are using to genetically transform the cane and the second aspect of it is to evaluate certain traits that we have inserted into the sugar cane varieties," he said.The public has until late January to comment on a planned trial.But Gene Ethics director Bob Phelps says it is too early to bring the sugar cane out of the laboratory.He says the cane would include genes that cause antibiotic resistance in humans."If there is a plan to ultimately commercialise these crops, then it's our view that these would not be acceptable," he said. "We would certainly be arguing very strenuously against them, because of the antibiotic resistance problem."© 2006 ABC

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Source: Australian Broadcasting Company