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6

Your sugar substrate was sucrose. Yeast cells metabolise this by secreting an enzyme, invertase, which splits the disaccharide into glucose and fructose both of which can be fermented by yeast to produce CO2. According to this site Equal Original (blue packaging)  is a zero calorie sweetener that contains aspartame and acesulfame potassium as its ...


6

I went to the Yeastbank website at Weihenstephan for some info. The keyword here is "Stamm," which is German for stem, clade, clan, or strain. So, I would take this to mean that the 34/70 is an isolate (#70) of strain 34. Two of 34/70's strengths, according to the link above are it makes clean beer and gives a pleasant taste profile due to its low yeast-like ...


5

A dependable protocol for yeast DNA extraction I used to use was broadly similar to the protocols you cite but included an ethanol precipitation before and after the P:C extractions. The only expensive material was time. The general outline was: Alkaline lysis Ethanol precipitation RNase A treatment of resuspended DNA for 15 minutes Phenol:chloroform ...


3

Not well, they need dextrose. Use YBT: 20 g Casein Peptone Tpe-M 10 g Yeast Extract 20 g Dextrose 17 g Agar q.s. to 975 mls in di-water. pH to 6.2 w 5M NaOH q.s. to 1L with di-water. Autoclave for 45 min at 121C Aseptically dispense in Petri dishes. Store at 4C for up to 12 weeks. If you want to grow Co-culture do so in LB supplemented with 20g/L ...


3

I am not sure why you say there is no information... a quick Google search returned a few interesting pages... In this paper: Progress in Metabolic Engineering of Saccharomyces cerevisiae - Nevoigt, Microbiol Mol Biol Rev. 2008 the author says: The identification of the entire genomic sequence of a commonly used lager brewer's yeast strain, i.e., ...


3

I'd take that computational angle and run the sequence data through tRNAscan-SE (Lowe & Eddy, Nucl Acids Res 25: 955-964). Ideally, you'd install this locally. This tool is what the UCSC folks use and it has been the best known, most widely used tRNA predictor for years. It's what we all used on Arabidopsis thaliana genome annotation back in the late ...


3

It depends upon exactly what you have done. The standard way of using a yeast intergrating plasmid (YIp) is for it to integrate into the genome by recombination between a piece of yeast DNA that the YIp carries and the same DNA in the genome. This is often, but not necessarily, the selectable marker. So for example a YIp carrying the URA3 gene as its only ...


2

Yeast integrating plasmids are known to be stable, even in absence of a selective medium but can revert like most homologous recombination plasmids. Quoting from the book Yeast Gene Analysis (pg476): YIps are generally more stable than YRp or YEp plasmids. As a result it is safe to grow most YIp-bearing strains in rich media, although it is good ...


2

I think that you could try a similar approach to GSFS: use transduction in proteins (if you don't know star code, then you must use 3 strings for each gene) use a basic tool (a stand alone like UNIPROT tools) to identify the proteic domain type (chain alpha, ..) divide the genes by proteic domain type (pdt): which contains which pdt and the pdt order ...


2

http://www.protocol-online.org/biology-forums/posts/26634.html I found this link - it says 'we don't really know'. It says PEG binds DNA, I assume shielding the membrane from its negative charge and allowing internalization to happen. I would guess that the amphipathic nature of PEG, being partly hydrophobic, also helps soften up the membrane. ...


2

I would use an RNA microarray to look at those difference instead of sequencing. To delicately amplify your tRNAs in an unbiased manner would be a tricky molecular biology endeavor. I wouldn't be surprised if there were detectable and significant differences. Those experiments will be able to confirm your hypotheses regarding codon usage bias.


2

I've successfully used the Zymoprep kit, but only for smaller plasmids in 2-hybrid experiments. So their cell lysis enzyme/buffer system works well, but I'd guess that your 42kb plasmid is precipitating out with the genomic DNA. The standard Qiagen midi columns are capable of capturing large constructs. This has worked wonders for me when I was purifying ...


2

I've published a paper comparing different measures of specificity, if that is of any help. But if you plan to have, e.g., measures of performance on carbon sources, pH, and temperature, then you'll have three measures of specificity (i.e. one for each). Also, worth to have a look at Graham Bell's inconsistency and responsiveness, as used by Venail et al. ...


2

The Saccharomyces Genome Database has a list of sources here. One of them is the Japanese Yeast Genetic Stock Center: I checked their site out and found that they charge ¥390 per strain which is around USD4. There is also a USD5 fee on all orders. I searched for a couple of standard strains, and these were in the catalogue, so it looks like a good ...


1

Browsing around GEO, I see 13 experiments focusing on microtubule disruption in yeast. This CHIP-CHP experiment actually uses nocodazole. This is a microarray experiment with benomyl treatment. The rest focus on specific mutants that try to perturb the microtubules in specific ways. What's more if you broaden the search there is an extensive body of ...


1

Here is my list, in no particular order. Methods in Yeast Genetics Some other yeast books at CSHL Fred Sherman's primer, available free at various sites including here. The Freiburg manual here The timeless classics (link to volume 3 but see all volumes) The YeastBook is an attempt to build a current encyclopaedia to replace the previous item on my ...


1

Equal is marketed as a "zero calorie" sweetener, with respect to human digestion. The sweetening agents are aspartame (Asp-Phe; a dipeptide) and acesulfame K. The maltodextrin and dextrose are probably bulking agents to give the product a free-flowing, poweder consistence. The "fermentables" in question are: Dextrose. This is another name of glucose, and ...


1

I don't have a definitive answer to this, but a little over a decade ago I was in an undergraduate lab that had a similar thing happen - a small amount of metabolism of a "control" group of bacteria fed artificial, sugar/calorie free sweeteners instead of sugar. Our running theories at the time were: Contamination. Always a problem in laboratory ...


1

ATCC is the place I would go to, just like purchasing cell lines or bacterial lines. The reference ATCC catalog numbers are also listed with each of the common strains you have linked. Depending on the purpose, you could just go to your local grocery store for baker's yeast.


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You could try Paracoccus denitrificans. Here is a study where acetate is used as the growth-limiting substrate: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.320.1692&rep=rep1&type=pdf Here's the details of its version of acetate kinase: http://www.uniprot.org/uniprot/A1B9S8 I'd be happy to collaborate with you further on this.


1

Although this information doesn't provide a direct answer to your question, I hope that it sets the scene for what is achievable in metabolic engineering from IPP. It should also provide a jumping off point for further literature research. This is a fairly recent review of metabolic engineering of relevant pathways in various microbial systems, including ...


1

According to this site, for yeast (I assume this means Saccharomyces cerevisiae) you should use 50 µg/ml to 200 µg/ml; for fungi (!) use 100 µg/ml to 300 µg/ml. The site also stresses the importance of the pH of the medium. I think that, unless a Hansenula expert comes along, you will have to try an initial experiment to measure the sensitivity of ...



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