molecular biology

Novel faultless DNA construction method from imperfect oligonucleotides

Attila Csordas — Wed, 14 May 2008 20:00:52 -0700

Description

A novel recursive DNA construction procedure was reported by scientists from the Weizmann Institute of Science, Rehovot, Israel constructing couple of kilobases long DNA molecules. They are claiming that their method "surpasses existing methods for de novo DNA synthesis in speed, precision, amenability to automation, ease of combining synthetic and natural DNA fragments, and ability to construct designer DNA libraries. It thus provides a novel and robust foundation for the design and construction of synthetic biological molecules and organisms."

From the abstract:

"Making faultless complex objects from potentially faulty building blocks is a fundamental challenge in computer engineering, nanotechnology and synthetic biology. Here, we show for the first time how recursion can be used to address this challenge and demonstrate a recursive procedure that constructs error-free DNA molecules and their libraries from error-prone oligonucleotides. Divide and Conquer (D&C), the quintessential recursive problem-solving technique, is applied in silico to divide the target DNA sequence into overlapping oligonucleotides short enough to be synthesized directly, albeit with errors; error-prone oligonucleotides are recursively combined in vitro, forming error-prone DNA molecules; error-free fragments of these molecules are then identified, extracted and used as new, typically longer and more accurate, inputs to another iteration of the recursive construction procedure; the entire process repeats until an error-free target molecule is formed."

Biomedical Sciences and Biotechnology

Source

Gregory Linshiz, Tuval Ben Yehezkel, Shai Kaplan, Ilan Gronau, Sivan Ravid, Rivka Adar & Ehud Shapiro: Recursive construction of perfect DNA molecules from imperfect oligonucleotides
http://www.nature.com/msb/journal/v4/n1/full/msb200826.html
Molecular Systems Biology 4 Article number: 191 doi:10.1038/msb.2008.26
Published online: 6 May 2008
Citation: Molecular Systems Biology 4:191

Redefining biological robustness via rewiring gene networks

Attila Csordas — Mon, 28 Apr 2008 22:27:16 -0700

Description

Network robustness is usually defined somehow with resistance to perturbations and tolerating variations without the loss of functionality. Now Isalan et al used high-throughput assay techniques to systemically rewire the architecture of the genetic network of the bacterium Escherichia coli by introducing new links via recombining the promoters and Open Reading Frame connection of different genes. According to their findings genetic networks in bacteria are much robust to genetic perturbations than previously thought.

Abstract:
"Sequencing DNA from several organisms has revealed that duplication and drift of existing genes have primarily moulded the contents of a given genome. Though the effect of knocking out or overexpressing a particular gene has been studied in many organisms, no study has systematically explored the effect of adding new links in a biological network. To explore network evolvability, we constructed 598 recombinations of promoters (including regulatory regions) with different transcription or sigma-factor genes in Escherichia coli, added over a wild-type genetic background. Here we show that approx95% of new networks are tolerated by the bacteria, that very few alter growth, and that expression level correlates with factor position in the wild-type network hierarchy. Most importantly, we find that certain networks consistently survive over the wild type under various selection pressures. Therefore new links in the network are rarely a barrier for evolution and can even confer a fitness advantage."

Biomedical Sciences and Biotechnology

Source

Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia Garriga-Canut & Luis Serrano: Evolvability and hierarchy in rewired bacterial gene networks Nature 452, 840-845 (17 April 2008) | doi:10.1038/nature06847;http://www.nature.com/nature/journal/v452/n7189/full/nature06847.html
Matthew R. Bennett & Jeff Hasty: Systems biology: Genome rewired Nature 452, 824-825 (17 April 2008) | doi:10.1038/452824a; Published online 16 April 2008 http://www.nature.com/nature/journal/v452/n7189/full/452824a.html

Nanoscale Tool Allows Scientists To Study Membrane Proteins One At A Time

Bartlett Bulkley — Tue, 11 Mar 2008 16:18:37 -0700

Description

Quoted from source text:
"In biology, as in construction, it's all about having tools that fit the job. Researchers at Rockefeller University have now created a tiny tool, more than 10,000 times smaller than the diameter of a human hair, capable of encasing single membrane proteins from living cells. The new system, which resembles a nanoscale sushi roll, will allow investigators to individually stimulate these key proteins with specific molecules and signals in order to precisely define the biological reactions that result."

Source

http://www.sciencedaily.com/releases/2008/03/080307085536.htm
Rockefeller University (2008, March 11). Nanoscale Tool Allows Scientists To Study Membrane Proteins One At A Time.

Stem Cell Solution? A company claims to have made safer reprogrammed stem cells

Matt Daniels — Mon, 10 Mar 2008 09:31:34 -0700

Description

Stem-Cell Solution?
A company claims to have made safer reprogrammed stem cells
Thursday, February 28, 2008
(Emily Singer, MIT Technology Review)

PrimeGen, a small biotech company based in Irvine, CA, says that it has solved one of the major hurdles in using reprogrammed stem cells for human therapies. Last year, scientists announced that they had successfully created embryonic-like stem cells from adult cells, circumventing the ethical and technical hurdles associated with embryonic stem cells. But the method used viruses to deliver genes, raising concerns over cancer risk.

According to an article in Forbes,

PrimeGen claimed Tuesday it had circumvented this problem. Instead of genes, it uses unspecified carbon-based "delivery particles" to insert four proteins into cells to stimulate the reprogramming process. This caused some of the cells to revert to being much like embryonic stem cells, PrimeGen said. PrimeGen said it has done the experiment with retinal, skin and testicular cells.

"Our goals are ambitious--we believe with this therapy, we can be in clinic in 2010," said PrimeGen president John Sundsmo in an interview. He said he couldn't release details on what the delivery particles are until the company finalizes an agreement with a corporate partner.

However, some scientists are skeptical. Rather than being published in a peer-reviewed scientific journal, the findings were released during a brief presentation at a stem-cell industry conference in New York.

According to Forbes,

Many outside scientists said they weren't familiar with the work and weren't quite sure what to think. "Until the work goes through [peer-review], it would be difficult to evaluate," says James Thomson, the researcher at University of Wisconsin, Madison, who created the first embryonic stem cells in 1998. George Daley, of Harvard University, said he was "pretty suspicious of publication by press release."

Nonetheless, "if this is real it really is a significant step," says Arnold Kriegstein, director of the Institute for Regenerative Medicine at U.C.-San Francisco. "They could be on to something."

Source

Therapeutic and Research Uses of RNA Interference

Alex Soojung-Kim Pang — Tue, 23 Oct 2007 11:10:30 -0700

Description

New discoveries by cell biologists regarding the role of RNA in gene regulation have provided researchers with a powerful tool that will likely have wide-ranging impact. These discoveries have also spurred the formation of biotechnology companies aiming to develop RNA-based therapies.

"Research on RNA, the intermediary messenger molecule between DNA and protein synthesis, has long been of secondary interest compared to DNA. Discoveries in the last decade, however, have shown RNA to have a complex role in gene regulation. An especially significant discovery is that some kinds of RNA can interfere with gene expression after translation from DNA. This phenomenon of RNA interference causing 'gene silencing' is leading to a fundamental revision of the understanding of the role of RNA. In the next decade, researchers will continue to sort out the function of RNA. The research is likely to have a significant impact on models of the cell and theories about genetic regulation and inheritance, specifically by challenging the notion of the exclusive power of DNA. Researchers hypothesize that the newly discovered property of what is now called small interfering RNA (siRNA) may be to protect the cell from viruses and provide a way of achieving genomic stability. The molecule may also play a role in development, perhaps offering a way to better understand stem cells. Of perhaps even greater consequence is that scientists have already learned to harness this natural genetic machinery to experimentally 'silence' the expression of specific genes.

The implications of this biological tool for new therapeutic strategies, as well as new genetically modified organisms, are being explored by the biotechnology industry with intense interest. Some new biotechnology companies have formed primarily around the concept of developing RNA-based therapies. Notwithstanding the industry investments, some critics believe that effective clinical applications of this new discovery may be decades away at best and point to past clinical disappointments with antisense RNA therapies, which were meant to treat genetic disorders by deactivating messenger RNA from a particular gene. Furthermore, the potential therapeutic benefits are likely to be costly and difficult to administer, suggesting wealthy countries and individuals stand to benefit the most initially."

This will be enabled by:

Dissemination of research protocols to expand the use of RNA interference as a research tool
Investment from biotechnology companies to expand the range of potential clinical applications

Early indicators include:

The journal Science's naming of the discovery of RNA interference as 'breakthrough of the year' in 2002
Acuity Pharmaceutical's filing with the US Food and Drug Administration in August 2004 of a new investigational drug application involving the therapeutic use of RNA interference

What to watch:

Commercial 'gene silencing' kits for research become available.
Results of long-term clinical trials show the efficacy of RNA-based therapies for age-related macular degeneration.
A Nobel Prize is awarded for research on the mechanics of RNA interference and downgrading of DNA as the 'master molecule'.

Signals

Promising Applications of Computational Biology

Alex Soojung-Kim Pang — Tue, 23 Oct 2007 11:10:30 -0700

Description

The tools of computational biology may be applied at an increasing rate to pharmaceutical innovation in the next 20 to 50 years, resulting in a faster, less costly, and more tailored approach to drug development.

Computer science and molecular biology have made some of the most significant contributions to science over the past 20 years, and computational biology (also known as bioinformatics) seeks to organize the multitude of activities that are emerging from new collaborations between the two fields. Computational biology makes use of advances in computing power, modelling, visualisation, genomics, protein chemistry, and information science, among others, to find relationships among biomarkers, genetics, pharmaceutical responses, normal responses, and diseases. For example, a computational biologist might search the human genome for particular patterns, analyse gene expression data for biologically relevant molecules, or develop models for visualising the interaction of DNA with other molecules. A loosely shared goal of computational biology is to bring the predictive power of mathematics and computer modelling to modern molecular biology and reign in the enormous amount of information produced by genomic sequencing.

Computational biology is showing preliminary signs of successful of applications. The applied subfields generating some of the greatest interest because of their potential impact on biomedicine are biosimulation and pharmacogenomics, and further research progress will come in these areas in the next 3 to 10 years.

Biosimulation is the computer modelling of biological processes and has the character of what some have called a 'laptop lab'. One hope is to use knowledge of the human genome and pharmaceutical chemistry to design new or more effective drugs that could then be 'tested' in computer models before attempting costly clinical trials, although this potential development is still years away.
Pharmacogenomics is the science of inherited variations in drug responses and promises better biomedicine through a personalized approach. The idea is that a patient's genome could be profiled to predict in advance the effectiveness of a particular drug or treatment. One of the few instances in which this approach has been demonstrated is with the cytochrome P450 (CYP) family of liver enzymes, which are involved in the metabolism of more than 30 different classes of drugs. Genetics tests have been developed to screen for variations and avoid drug overdoses. Another enzyme, thiopurine methyltransferase, has been shown to negatively influence chemotherapy treatments for childhood leukaemia in the rare patient who has a defective variant.

A new industry has developed around applications of computational biology in the last decade. Initial hopes have been tempered, however, and ethical concerns about privacy and property rights to genetic information have arisen. Nonetheless, many new computer applications to aid the drug development process are expected in the next decade. The larger goal of creating a fully predictive biomedicine with tailored treatments is still 20 to 50 years out."

This will be enabled by:

"Training of a new generation of scientists in computer science and biology
Continued investment by governments seeking to remain competitive in scientific research, especially biomedicine
New collaborations between the pharmaceutical industry and the biotechnology industry"

Early indicators include:

"Passage by Iceland in 1998 of the Health Sector Database Act, giving the DeCode exclusive rights to databases of genetic and medical information for the country's 270,00 citizens
Consideration by other countries, including the UK, of 'biobanks' or population databases
Issuance in 1999 by the Biomedical Information Science and Technology Initiative (BITSI) of the US National Institutes of Health of a report stating that the NIH should create between 5 and 20 National Programs of Excellence in Biomedical Computing and should develop a national computer infrastructure
Opening of research facilities related to the State of California's new initiative, the California Institute for Quantitative Biomedical Research, beginning in 2005
Choice by the Public Library of Science, a new open-access publisher of scientific and medical research, of Computational Biology to be its third journal and publication of the first issue in June 2005"

What to watch:

"New publicly and privately funded centres for biomedical computing open.
Life science research in universities reorganizes under the banner computational biology and bioinformatics.
Debates are waged over the merits of computer models verus clinical trials in providing evidence of toxicity or pharmacological efficacy.
A computer of model of a cell, perhaps a liver cell, is developed.