Good old budding yeast (Wiki Commons)

The Yeast Resource Center Public Image Repository (YRC PIR) is a large database of fluorescence microscopy images of yeast, with a focus on the important model organism Saccharomyces cerevisiae with some attention given to S. pombe.

• 84,270 Experiments
• 530,982 images
• ~450 gigabytes of data

Not bad.

A press release posted at 7th Space offers a short introduction:

There is increasing interest in the development of computational methods to analyze fluorescent microscopy images and enable automated large-scale analysis of the subcellular localization of proteins. Determining the subcellular localization is an integral part of identifying a protein’s function, and the application of bioinformatics to this problem provides a valuable tool for the annotation of proteomes.

NUF2 (Venus tag) and SPC97 (CFP tag) proteins in yeast

The YRC PIR is the work of Trisha Davis and Michael Riffle of the University of Washington and is supported by grant P41 RR11823 from the National Center for Research Resources and grant GM40506 from National Institute of General Medical Sciences at the US National Institutes of Health. Amazingly all the 500,000 + images in the database are from the Davis lab at U of W.

The database is of course online but can also be downloaded for local use. It can be searched using a variety of parameters including fluorescent tag.

For pretty much everything you need to know about this outstanding resource see the YRC PIR FAQ and user guide.

An excerpt: “Sugarcane ethanol producers typically recycle the yeast used in their fermentation process. While yeast recycling can offer a variety of benefits, it can also introduce problems with contamination and shift a plant’s fermentation profile.”

It’s an in-depth article that’s well worth reading.

Wine Yeast

Unique New Zealand Wine Yeasts Discovered comes from the Voxy News Engine. “Scientists from the University of Auckland have discovered a unique group of New Zealand yeasts involved in wine production, and have begun to identify the origins of the local yeast strains – with surprising results. The researchers examined Saccharomyces cerevisiae wine yeast from a spontaneous ferment at Kumeu River winery. ‘We identified almost a hundred different strains in the ferment” says lead researcher Dr Mat Goddard “and many of them were genetically distinct from S. cerevisiae found elsewhere in the world.’ ”

Functional Technologies Corp.: Phyterra(TM) Launches Hydrogen Sulphide-Reducing Yeast Strains. “Phyterra(TM) Yeast, a unit of Functional Technologies Corp. (TSX VENTURE: FEB) today announced the launch of Napa-M, Napa-S, and California Red, the first three strains of its proprietary hydrogen sulphide-reducing wine yeast. These new yeast products prevent the sensory and spoilage issues that often occur from hydrogen sulfide (H2S) through fermentation.”

Fission Yeast DNA Polymerase

BMC Molecular Biology is an Open Access Journal (Good!). Volume 10:82 (August 17) includes research published on a DNA polymerase of the fission yeast Schizosaccharomyces pombe. See Functional mapping of the fission yeast DNA polymerase delta B-subunit Cdc1 by site-directed and random pentapeptide insertion mutagenesis.

Good Old Marmite

Marmite reeks. Or at least a byproduct of its manufacture does. This “interesting” British yeast extract is made from the “surplus yeast from brewing.” I think that means the yeast remaining and filtered out after a large scale brewing operation.

“The yeast slurry arrives in tankers. It takes 50,000 tonnes of yeast a year to make 6,000 tonnes of finished Marmite. Hoses are connected to the tanker and, like petrol, it is pumped into vats. Next, it is stirred and slightly heated and it begins to break down until it becomes a bitter-tasting protein soup. The yeast is pumped through hot centrifuges at 70C, which causes the cell walls in the yeast to separate from the liquid, which is siphoned off to form the basis of Marmite. The separated waste is then pumped off into vats, and it is this material that caused such a stink in the village of Sawley.”

A fun read at Love it, hate it – just don’t you dare spread Marmite’s dark secret by Marcus Dunk.

What’s True for Yeast…

Ever since Leonard Guarente and David Sinclair discovered the sir-2 gene, which affects longevity in yeast, researchers have  hypothesized it might be the key to ultimately extending human lives as well. Both humans and mice (as well as other animals no doubt) have analogous genes that code for proteins called sirtuins. So far it hasn’t worked out. Find out more at Tests Begin on Drugs That May Slow Aging by Nicholas Wade, published at the website of the New York Times.

In northern California, Stumptown Brewery has used a 45-million year old strain Saccharomyces cerevisiae found in a piece of amber dating from the Eocene by Paul Cano. Cano did the original isolation from the gut of an insect over a decade ago. According to Cano’s website, his group’s research on ancient organisms “… includes recovery and growth of amber entombed microorganisms. Yeasts, bacteria, and  actinobacteria have been recovered, as well as DNA from viruses. Our studies focuses on the isolation and characterization of novel natural products (e.g., antibiotics)  from ancient microbes. Other work has included analysis of DNA from tissues of “Iceman” found in the Swiss/Italian Alps.”

More:

Fossil Fuels: Beer Made With 45 Million Year Old Yeast?

The 45 Million Year Old Beer

Amber Ale: Brewing Beer from 45-Million-Year-Old Yeast

According to the company website: “OpenHelix provides convenient and effective online tutorial suites on the most powerful and popular web-based free bioinformatics and genomics resources. The online narrated tutorial, which runs in just about any browser connected to the web, can be viewed from beginning to end or navigated using chapters and forward and backward sliders.”

I viewed the first two parts of the SGD webinar and was impressed. I plan to finish them out and then give SGD a spin to see how effective the training is. I’ll let you know how it works out.