Did you know?? Omega-3 Kills Cancer Cells

Docosahexanoic acid (DHA), an omega-3 fatty acid found in fish oils, has been shown to reduce the size of tumours and enhance the positive effects of the chemotherapy drug cisplatin, while limiting its harmful side effects. The rat experiments provide some support for the plethora of health benefits often ascribed to omega-3 acids.

DHA is an omega-3 fatty acid that is commonly found in cold-water fish oil, and some vegetable oils. It is a major component of brain gray matter and of the retina in most mammalian species and is considered essential for normal neurological and cellular developments. According to the authors, "While DHA has been tentatively linked with protection against cardiovascular, neurological and neoplastic diseases, there exists a paucity of research information, in particular regarding its interactions with existing chemotherapy drugs". The researchers found that, at the molecular level, DHA acts by reducing leukocytosis (white blood cell accumulation), systemic inflammation, and oxidative stress – all processes that have been linked with tumour growth.

El-Mowafy and his colleagues have called for greater deployment of omega-3 in the fight against cancer. They write, "Our results suggest a new, fruitful drug regimen in the management of solid tumors based on combining cisplatin, and possibly other chemotherapeutics, with DHA".

Numerous Undiscovered Gene Alterations In Pancreatic And Brain Cancers Detected

HHMI investigators have detected a multitude of broken, missing, and overactive genes in pancreatic and brain tumors, in the most detailed genetic survey yet of any human tumor. Some of these genetic changes were previously unknown and could provide new leads for improved diagnosis and therapy for these devastating cancers.

The discoveries, described in two reports published September 4, 2008, in Science Express, which provides early electronic publication of selected Science papers, emerged from the sequencing of nearly all the known protein-making genes in pancreatic cancers and in the most common form of brain tumors, glioblastomas. The study adds numerous items to the known "parts list" of these cancers, though further research is needed to determine which gene changes actually trigger development or spread of the disease.

HHMI investigator Bert Vogelstein and colleagues at the Johns Hopkins Kimmel Cancer Center, in collaboration with investigators at Duke University and elsewhere, sequenced 20,661 genes in cells from 24 patients with pancreatic cancer and 22 patients with glioblastoma. The team identified hundreds of gene mutations associated with the cancers.

The researchers also found numerous cases where tumor cells had extra or too few copies of a gene. The typical pancreatic cancer contained 63 genetic alterations, while the average brain tumor contained 60. Using "next generation" sequencing, the researchers also comprehensively assessed changes in levels of gene activity.

Taken together, the two studies suggest that a small number of commonly mutated genes - or "mountains" - and a much larger number of rarer, low-frequency gene changes - "hills" - cause these cancers, said the researchers.

The authors said their results demonstrate that "genome-wide genetic analyses…can identify the precise genetic alterations that are likely to be responsible for pathway disregulation in each patient's tumor." They found that each individual tumor had its own particular assortment of gene changes. "If you have 100 patients, you have 100 different diseases," said Vogelstein, who is a co-corresponding author of the Science paper with Johns Hopkins researchers Victor E. Velculescu and Kenneth W. Kinzler. "But this will not surprise clinical oncologists, because they see how different every patient is" in the way their tumor behaves and responds to treatment.

Cancer biologist Tyler Jacks, a Howard Hughes Medical Institute investigator at the Massachusetts Institute of Technology who was not involved in the studies, said he was not surprised by the large number of infrequent gene mutations — primarily because Vogelstein and his colleagues reported in 2007 that they had found breast and colon cancers to be similarly complex genetically. "But if you had asked me three years ago, I would have given a different answer," Jacks said.

Vogelstein said the sheer number and variability of genetic changes in the tumors pose a challenge to one of the main goals of "personalized medicine" — identifying as many cancer-causing mutations as possible and developing an array of targeted drugs, each designed to strike a specific mutation.

Jacks agreed that cancer researchers would have preferred that tumors' mutational landscapes be dominated by the high-frequency "mountains," as these make attractive targets for the design of new drugs. With conventional DNA sequencing technologies, these prominent mountains were the mutations most readily linked to cancer, he said. But as new methods make it feasible to sequence nearly all the genes in a tumor sample, researchers are beginning to recognize that "the landscape is crowded with changes, mostly occurring at low frequency."

"It's suggesting that maybe we shouldn't even be focusing so much on the individual genes that are mutated," Vogelstein said. "Instead, we should be thinking about the functional pathways in which these genes operate. This is a different way of looking at how cancer develops."

Indeed, many of the gene abnormalities could be grouped into functional units. For example, when they analyzed the DNA in 24 pancreatic cancers, the scientists identified 12 core signaling pathways that were each abnormal in the great majority of tumors. Some of those pathways regulate apoptosis - the programmed death of abnormal cells - or repair of damaged DNA. Other altered pathways control the rate of cell division, influence how tightly cells stick together, or determine their ability to invade nearby tissues.

In the brain tumor samples, the survey found that the mutated genes could be grouped into similar pathways, such as those controlling growth and apoptosis. However, some of the newly found mutations occurred in pathways involved in nervous system signaling processes not previously known to be altered in any form of cancer. The scientists speculate that this pathway may be specific for glial cell tumorigenesis.

Similarly, one particular genetic change netted by the survey was found exclusively in brain tumors. That mutation was particularly intriguing because of its potential near-term clinical importance. Specific mutations in the isocitrate dehydrogenase gene IDH1 were found in 12 percent of the brain tumors. They were found in almost all cases of secondary glioblastomas - developing from lower-grade tumors - but rarely in primary high-grade glioblastomas. They also tended to affect younger patients (average age 33 compared to age 53 for patients without the mutations). Patients whose brain tumors had the IDH1mutation lived significantly longer with their cancer than those who did not.

Although it is not known how the IDH1 mutation contributes to cancer, Vogelstein said that it could help single out individuals who are likely to have better outcomes. With further research, it is conceivable that the mutation could have relevance for therapy, he said.

Like the Vogelstein group's 2007 findings on breast and colon cancer, the new study suggests that many these diseases are caused not by a few major genetic kingpins, but instead by a large cast of minor culprits. How this multiplicity of cancer triggers can best be confronted is uncertain, but the authors of the two papers say it may force a shift in drug development emphasis. The best hope for new therapies, they wrote, "may lie in the discovery of agents that target the physiologic effects of the altered pathways and processes, rather than their individual genetic components."

Microsoft Announces Synthetic Biology Grants

Microsoft Research (MSR) has announced the six winners of its inaugural grants in synthetic biology. The company issued a request for proposals a few months ago, seeking to identify outstanding research projects aimed at tackling the computational challenges in two areas of synthetic biology:

• The re-engineering of natural biological pathways to produce interoperable, composed, biological parts; and
• The development of tools and information repositories relating to the use of DNA in the fabrication of nanostructures and nanodevices

The company said that 49 proposals were submitted from 11 countries, including many leading researchers and labs in the field. Following external peer review, six proposals were chosen. They are as follows:

• Computational Interchange Standards for Synthetic Biology -- Herbert Sauro, University of Washington
• Design and Synthesis of Minimal and Persistent Protein Complexes -- David Green and Steven Skiena, Stony Brook University
• BioStudio: A Collaborative Editing and Revision Control Environment for Synthetic Genomes -- Joel Bader and Jef Boeke, Johns Hopkins University School of Medicine
• Identification of Standard Gene Regulatory Sequences for Synthetic Biology -- Robert Holt, University of British Columbia, Canada
• Using programmable stacking bonds to combine DNA origami into larger, more complex, reconfigurable structures -- Paul Rothemund and Erik Winfree, California Institute of Technology
• Noise Suppression and Next-Generation Cloning Vectors -- Johan Paulsson, Harvard University

Summaries of the six selected research abstracts can be found here.

In announcing the program in December, MSR Bioinformatics Program Manager Simon Mercer said the challenges faced by scientists today will be faced by business tomorrow and eventually by everyone. “Encouraging and participating in basic research helps us to better understand these problems and their potential solutions.” Synthetic biology is a particularly interesting field, Mercer said, because it has “the potential to provide insights into living systems, transform biotechnology and perhaps generate entirely new industries.”

Synthetic biology: new engineering rules for an emerging discipline

I came across this very informative article...it's really long, but very good..

Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.

Read the rest of the article here

Synthetic Biology is 'Extreme Genetic Engineering' and Far More Dangerous

A new report by the ETC Group concludes that the social,
environmental and bio-weapons threats of synthetic biology surpass
the possible dangers and abuses of biotech. The full text of the 70-
page report, Extreme Genetic Engineering: An Introduction to
Synthetic Biology, is available for downloading free-of-charge on the
ETC Group website: www.etcgroup.org

"Genetic engineering is passe," said Pat Mooney, Executive Director
of ETC Group. "Today, scientists aren't just mapping genomes and
manipulating genes, they're building life from scratch - and they're
doing it in the absence of societal debate and regulatory oversight,"
said Mooney.

Synbio - dubbed "genetic engineering on steroids" - is inspired by
the convergence of nano-scale biology, computing and engineering.
Using a laptop computer, published gene sequence information and mail-
order synthetic DNA, just about anyone has the potential to construct
genes or entire genomes from scratch (including those of lethal
pathogens). Scientists predict that within 2-5 years it will be
possible to synthesise any virus; the first de novo bacterium will
likely make its debut in 2007; in 5-10 years simple bacterial genomes
will be synthesised routinely and it will become no big deal to
cobble together a designer genome, insert it into an empty bacterial
cell and - voila - give birth to a living, self-replicating organism.
Other synthetic biologists hope to reconfigure the genetic pathways
of existing organisms to perform new functions - such as
manufacturing high-value drugs or chemicals.

A clutch of entrepreneurial scientists, including the gene maverick
J. Craig Venter, is setting up synthetic biology companies backed by
government funding and venture capital. They aim to commercialise new
biological parts, devices and systems that don't exist in the natural
world - some of which are designed for environmental release.
Advocates insist that synthetic biology is the key to cheap biofuels,
a cure for malaria, and climate change remediation - media-friendly
goals that aim to mollify public concerns about a dangerous and
controversial technology. Ultimately synthetic biology means cheaper
and widely accessible tools to build bioweapons, virulent pathogens
and artificial organisms that could pose grave threats to people and
the planet. The danger is not just bio-terror, but "bio-error," warns
ETC Group.

Despite calls for open source biology, corporate and academic
scientists are winning exclusive monopoly patents on the products and
processes of synthetic genetics. Like biotech, the power to make
synthetic life could be concentrated in the hands of major
multinational firms. As gene synthesis becomes cheaper and faster, it
will become easier to synthesise a microbe than to find it in nature
or retrieve it from a gene bank. Biological samples, sequenced and
stored in digital form, will move instantaneously across the globe
and be resurrected in corporate labs thousands of miles away - a
practice that could erode future support for genetic conservation and
create new challenges for international negotiations on biodiversity.

"Last year, 38 civil society organizations rejected proposals for
self-regulation of synthetic biology put forth by a small group of
synthetic biologists," said Kathy Jo Wetter of ETC Group. "Widespread
debate on the social, economic and ethical implications of synbio
must come first - and it must not be limited to biosecurity and
biosafety issues," said Wetter.

The tools for synthesising genes and genomes are widely accessible
and advancing at break-neck pace. ETC Group's new report concludes
that it is not enough to regulate synthetic biology on the national
level. Decisions must be considered in a global context, with broad
participation from civil society and social movements. In keeping
with the Precautionary Principle, ETC Group asserts that - at a
minimum - there must be an immediate ban on environmental release of
de novo synthetic organisms until wide societal debate and strong
governance are in place.

The Dangers of Synthetic Biology

Nobel Prize winner David Baltimore explains why building smallpox from scratch is a key safety concern in synthetic biology.

The emerging field of synthetic biology -- the quest to design and build new life forms that can perform useful functions -- brings exciting promise and potentially dangerous capabilities. Scientists have the ability to synthesize entire strings of DNA and put together complicated molecular machinery. But that power has raised some troubling questions. Could terrorists recreate viruses such as smallpox? Or engineer a virus even more deadly than avian flu? (see "The Knowledge").

In the 1970s, scientists faced a similar dilemma. The advent of recombinant DNA technology meant biologists could manipulate DNA as they never could before. Concerned about the potential perils of this new tool, a prominent group of scientists held the now-famous Asilomar Conference in 1975 (formally titled the "International Congress on Recombinant DNA Molecules") to determine how to proceed safely.

Thirty years later, at the Synthetic Biology 2.0 meeting at the University of California, Berkeley this month, scientists met to discuss not only new developments in the field, but also how the community should deal with the growing safety concerns surrounding synthetic biology.

David Baltimore, a winner of the 1975 Nobel Prize in physiology or medicine, and president of the California Institute of Technology, was one of the organizers of the Asilomar Conference. At the Synthetic Biology conference last week, he reflected on changes in the field over the last 30 years. Baltimore talks here with Technology Review about what scientists have learned since 1975 and the specific dangers we should be most worried about.

Technology Review: What were you were most concerned about 30 years ago?

David Baltimore: The Asilomar Conference was convened in a very different context than we have today. We were marveling at a wholly new world of experimentation -- we literally had no experience with moving DNA around. But people were also concerned, and rightly so, about issues of intrinsic safety. They were worried, for example, that we could create organisms that we didn't know how to control.

At the conference, we decided to focus purely on safety, rather than ethics or biowarfare. We believed, somewhat naively, that there was a treaty that everyone held to prohibiting use of technology to make biological weapons. In retrospect, the U.S.S.R. had a huge clandestine program. We also didn't have the situation we have today, where terrorist organizations cross boundaries and are not held by treaties. So we clearly have an unfinished agenda from Asilomar on biowarfare.

TR: What issues are you most worried about today?

DB: The real danger today is from organisms that already exist. The idea of synthesizing something worse than that, of taking bits of Ebola and other viruses to create something more deadly, underestimates how hard it is to survive in the natural world.

Adapting to the human lifestyle is very complicated, so I would guess that we would fail if we tried to engineer a dangerous organism. Ebola, for example, is very pathogenic. It infects families and health workers, but it never spreads widely because it is too lethal -- it isn't in the community long enough to spread. Bird flu is not likely to spread widely until it mutates to become less pathogenic.

Read the full interview here

Synthetic Biology 3.0

oiy! it's almost wierd that everything is being tagged as a number, web 2.0, synthetic bio 2.0, blog 2.0, whew! what next???

yep.. Synthetic Biology 3.0!!

The conference is gonna be held on the 24th to 27th June 2007, at Zurich Switzerland (did i spell that right??) anyway, stay tuned as we have more of this coming up...

http://www.syntheticbiology.ethz.ch/conf_2007

Cheers!