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 Nanoparticle Exposure Can Awaken Dormant Viruses in the Lungs
16.01.2017 | Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt

nachricht Cholera bacteria infect more effectively with a simple twist of shape
13.01.2017 | Princeton University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Designing Architecture with Solar Building Envelopes

Among the general public, solar thermal energy is currently associated with dark blue, rectangular collectors on building roofs. Technologies are needed for aesthetically high quality architecture which offer the architect more room for manoeuvre when it comes to low- and plus-energy buildings. With the “ArKol” project, researchers at Fraunhofer ISE together with partners are currently developing two façade collectors for solar thermal energy generation, which permit a high degree of design flexibility: a strip collector for opaque façade sections and a solar thermal blind for transparent sections. The current state of the two developments will be presented at the BAU 2017 trade fair.

As part of the “ArKol – development of architecturally highly integrated façade collectors with heat pipes” project, Fraunhofer ISE together with its partners...

Im Focus: How to inflate a hardened concrete shell with a weight of 80 t

At TU Wien, an alternative for resource intensive formwork for the construction of concrete domes was developed. It is now used in a test dome for the Austrian Federal Railways Infrastructure (ÖBB Infrastruktur).

Concrete shells are efficient structures, but not very resource efficient. The formwork for the construction of concrete domes alone requires a high amount of...

Im Focus: Bacterial Pac Man molecule snaps at sugar

Many pathogens use certain sugar compounds from their host to help conceal themselves against the immune system. Scientists at the University of Bonn have now, in cooperation with researchers at the University of York in the United Kingdom, analyzed the dynamics of a bacterial molecule that is involved in this process. They demonstrate that the protein grabs onto the sugar molecule with a Pac Man-like chewing motion and holds it until it can be used. Their results could help design therapeutics that could make the protein poorer at grabbing and holding and hence compromise the pathogen in the host. The study has now been published in “Biophysical Journal”.

The cells of the mouth, nose and intestinal mucosa produce large quantities of a chemical called sialic acid. Many bacteria possess a special transport system...

Im Focus: Newly proposed reference datasets improve weather satellite data quality

UMD, NOAA collaboration demonstrates suitability of in-orbit datasets for weather satellite calibration

"Traffic and weather, together on the hour!" blasts your local radio station, while your smartphone knows the weather halfway across the world. A network of...

Im Focus: Repairing defects in fiber-reinforced plastics more efficiently

Fiber-reinforced plastics (FRP) are frequently used in the aeronautic and automobile industry. However, the repair of workpieces made of these composite materials is often less profitable than exchanging the part. In order to increase the lifetime of FRP parts and to make them more eco-efficient, the Laser Zentrum Hannover e.V. (LZH) and the Apodius GmbH want to combine a new measuring device for fiber layer orientation with an innovative laser-based repair process.

Defects in FRP pieces may be production or operation-related. Whether or not repair is cost-effective depends on the geometry of the defective area, the tools...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

12V, 48V, high-voltage – trends in E/E automotive architecture

10.01.2017 | Event News

2nd Conference on Non-Textual Information on 10 and 11 May 2017 in Hannover

09.01.2017 | Event News

Nothing will happen without batteries making it happen!

05.01.2017 | Event News

 
Latest News

Solar Collectors from Ultra-High Performance Concrete Combine Energy Efficiency and Aesthetics

16.01.2017 | Trade Fair News

3D scans for the automotive industry

16.01.2017 | Automotive Engineering

Nanoparticle Exposure Can Awaken Dormant Viruses in the Lungs

16.01.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>