Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Powerful ’toolkit’ developed for functional profiling of yeast genes

05.11.2004


Because 60 percent of yeast genes have at least one clearly identifiable human counterpart, the advance, described in the Nov. 5 issue of Molecular Cell, should speed advances in understanding human gene and protein functions, as well as improve the reliability of what scientists think they know about this extremely useful microorganism. Eventually the work with yeast could reveal particular gene interactions that could become targets for therapies to fight cancers or fungal infections, say the researchers.



The toolkit, a combination of techniques developed by the Hopkins researchers and others, starts with a collection of almost 6,000 yeast strains, each missing a different gene, and allows researchers to identify genes whose coupled elimination kills the yeast. Many laboratories are already using the "single knock-out" yeast collections, but postdoctoral fellow Xuewen Pan, Ph.D., found a way to protect the genetic integrity of the collection so that repeated experiments will provide the same results, regardless of when and where the experiments are conducted.

"Everyone in the yeast community has been using their own batch of yeast mutants, but the slow-growing mutants gradually accumulate extra genetic changes so they can grow faster," says Jef Boeke, Ph.D., professor of molecular biology and genetics and director of the HighThroughput Biology (HiT) Center in Hopkins’ Institute for Basic Biomedical Sciences. "This potential for genetic impurity means that one person’s batch of yeast is no longer exactly the same as someone else’s. We went back to the original stocks of yeast mutants, in certain cases, so we know exactly what we have."


Human cells, with the exception of egg and sperm, have two copies of each gene, but yeast are content with either two copies of each gene or just one. Libraries of the almost 6,000 yeast mutants have just one copy of each gene, so there’s no back-up for a missing gene that leads to slow growth.

Pan’s mutant yeast are protected from collecting genetic impurities because he’s added a second copy of all the genes, a cloak that temporarily obscures the effects of whatever gene is missing. He then uses a laboratory trick developed by researchers at the University of Toronto to get rid of the extra set of genes at just the right time.

A second advantage of the Hopkins "toolkit," Boeke says, is that all the yeast mutants are mixed together and studied simultaneously, an advance reported a year ago in Nature Genetics by then-graduate student Siew-Loon Ooi, Boeke, and Stanford University’s Dan Shoemaker. At the end of an experiment, each mutant in the mix is identified by a genetic "barcode" -- created by Shoemaker -- embedded in its genome. The researchers then use special microarrays to find out how much of each mutant is present. An improved barcode microarray, designed by research associate Daniel Yuan, replaces the original in the new toolkit. "Much like barcodes identify your purchases at the grocery store, these genetic barcodes identify each of the yeast mutants," says Boeke. "So we can mix the mutants together, challenge them to survive removal of a particular gene, nurture the ones that make it and use microarrays to see quickly which ones are missing."

The researchers dubbed the combined technique dSLAM, for diploid-based synthetic lethality analysis on microarrays. "Diploid" reflects the second set of genes added to the yeast mutants, and "synthetic lethality" refers to genes that only kill the yeast if missing in combination. dSLAM is easier to use than the earlier version, so it’s more likely to be widely adopted by the yeast research community, Boeke says.

To test the new method, Pan and the team applied it to synthetic lethality experiments already tested by other methods. Their analysis, conducted with Forrest Spencer, Ph.D., an associate professor in the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins, revealed that the new technique missed fewer of the known gene interactions and provided more consistent results than older techniques. "No technique is going to give 100 percent, so the question becomes, How many can you miss and still be happy with the results?" says Boeke. "We think our numbers are sufficient to get the big picture of how genes interact, and the technique has better potential to scale to the whole genome than other techniques."

In one set of experiments, the new technique identified 116 genes that were synthetic lethal with a gene called cin8 and confirmed their involvement. Of these genes, 73 had not been identified by other techniques. The new technique missed just 16 genes previously identified and confirmed by the older techniques.

Boeke’s goal is to use the new technique to build detailed maps of yeast genes’ interactions, an ambitious project being done with Joel Bader, Ph.D., an assistant professor of biomedical engineering in the Whiting School of Engineering at Johns Hopkins and a computational biologist in the HiT Center, among others.

Joanna Downer | EurekAlert!
Further information:
http://www.jhmi.edu

More articles from Life Sciences:

nachricht Transport of molecular motors into cilia
28.03.2017 | Aarhus University

nachricht Asian dust providing key nutrients for California's giant sequoias
28.03.2017 | University of California - Riverside

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: A Challenging European Research Project to Develop New Tiny Microscopes

The Institute of Semiconductor Technology and the Institute of Physical and Theoretical Chemistry, both members of the Laboratory for Emerging Nanometrology (LENA), at Technische Universität Braunschweig are partners in a new European research project entitled ChipScope, which aims to develop a completely new and extremely small optical microscope capable of observing the interior of living cells in real time. A consortium of 7 partners from 5 countries will tackle this issue with very ambitious objectives during a four-year research program.

To demonstrate the usefulness of this new scientific tool, at the end of the project the developed chip-sized microscope will be used to observe in real-time...

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

Transport of molecular motors into cilia

28.03.2017 | Life Sciences

A novel hybrid UAV that may change the way people operate drones

28.03.2017 | Information Technology

NASA spacecraft investigate clues in radiation belts

28.03.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>