Off topic discussions and journal club for LG11's thread

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Ferment_It
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Off topic discussions and journal club for LG11's thread

Post by Ferment_It » Fri Dec 05, 2014 8:10 am

I made this thread as an effort to keep LG11's "More than you ever wanted to know about yeast" thread free from my drivel and ramblings, as well as having a place to discuss and post primary literature relating to the topic at hand.

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HDNB
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Re: Off topic discussions and journal club for LG11's thread

Post by HDNB » Fri Dec 05, 2014 6:29 pm

good idea. be nice to keep that thread free of ramblings...i've got a lot to learn and and clutter...clutters things up.
I finally quit drinking for good.

now i drink for evil.

Ferment_It
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Re: Off topic discussions and journal club for LG11's thread

Post by Ferment_It » Sat Dec 06, 2014 8:35 am

We've all got a lot to learn, there are no laws in the field of biology so no one is absolutely certain or knows everything there is to know about any particular subject, which in our case is yeast biology.
Knowing everything is impossible, learning how to coax the best.drop out of our yeast is very possible.

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Re: Off topic discussions and journal club for LG11's thread

Post by Ferment_It » Sat Dec 06, 2014 9:09 am

Galeoturpis wrote:These are old studies but hopefully answer your questions. my old flat-mate did a pHd in micro and someone sad to him "Hey, you seem smart enough to work on eukaryotes!"
http://www.sciencedirect.com/science/ar ... 2704000220" onclick="window.open(this.href);return false;" rel="nofollow
http://www.pnas.org/content/106/7/2136.long" onclick="window.open(this.href);return false;" rel="nofollow
http://www.biomedcentral.com/1471-2164/4/45" onclick="window.open(this.href);return false;" rel="nofollow
There are plenty of genomes published of yeasts , especially S. cerevisiae. There are genetically modified S.cerevisiae which produce omega 3s but I have not seen it in wild types. I don't think that they're auxotrophic; they probably never had the capacity (just like animals!) All minerals and vitamins are considered vital but people don't immediately die from scurvy, rickets, vitamin A blindness, pernicious anaemia or iron deficiency.
So many things....
Oklets work out way down from the top. I am on my phone and this is a pain to type so please excuse the brevity.
I don't understand what your flatmate has to do with this but as someone getting their PhD in micro working with prokaryotes, I am not entertained.
Paper 1. Didn't see anything about yeast or ethanol stress. This paper argues omega 3 and other FAs are generally important in biological systems.
Paper 2. Yeast lipidome. What am I supposed to find here? Did they see the lipids you say yeast need but can't make? In general I don't consider contributed works to be good citations. We can talk about that later tho.
Paper3. I can't get it to open. Once I get to my computer I will comment further.
The yeast genome is incomplete. About 20% of the genome is uncharacterized or dubious as of Dec. 2014. http://www.yeastgenome.org/cache/genomeSnapshot.html" onclick="window.open(this.href);return false;" rel="nofollow

That's what auxotrophic means- Need something that you cannot make. Sorry, I speak in jargon sometimes
I don't follow the rest of your post. Not everything is "vital" if you have a source cite it please.
Everything that follows seems like a "straw man" argument.

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Re: Off topic discussions and journal club for LG11's thread

Post by LG11 » Sat Dec 06, 2014 2:20 pm

Hi
The yeast genome is complete, several pathways are a problem. All genes are identified however several so far elude conclusive evidence as to what function is primary.
There is a great deal of the genome not in the public domain yet, I have no personal connection with the program myself however, the lab next to mine is active in this region. From over coffee chats I have had with them, I dont think much progress is going to be made anytime soon as to the purpose of the genes identified but the pathway unknown.
Just to be clear I am talking about the actual genome and genes there in. I have a complete copy on my desk, what I and no one else has is a map of function that is complete. Next year is a big year, from a quick count round the office I am aware of 26 papers gene related due to be published, 11 papers awaiting review and 6 papers that near completion. Most of the work was done this year, however because some of the papers mark major progress the choice of journal to publish in has meant a delay, as with one of my own papers, being accepted by NATURE is a great honor, the downside however is they have the pick of the crop when it comes to publishing. So you end up with work sitting in a cue waiting for a publishing slot. The Journal of applied microbial studies is much quicker to publish in but still dosnt carry the punch needed with high end new work.
As with most science disciplines its a case not only of publish or perish, but with little research cash around knowing where to publish can have an impact. This is where the company I work for does really well, we are not under pressure to publish. Most of our R&D is industry paid for, OR because the company also manufactures a number and range of products they can also afford to fund a couple of Blue sky R&D labs. I am lucky enough to work in one of them the downside as always is your place is only guaranteed for as long as you can come up with the goodies. Its one reason's that over the years I have built my own small lab. I also have the advantage that I actually live on site! I am going o sort the cell wall part of my thread first, then come back and discuss some of the points raised here as they are linked.

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Re: Off topic discussions and journal club for LG11's thread

Post by Galeoturpis » Sun Dec 07, 2014 12:51 am

My flatmate was very smart but thought it amusing that a cancer"eukaryotic" researcher arrogantly thought that their field was of a much higher standing and more prestigious.  
Prokaryotes and eukaryotes share the genetic code, many similar biochemical pathways and if something like omega 3 fatty acids are retained, they have to be reasonably important. That was paper 1 and paper 2 didn't have omega 3 being coded by yeast but elsewhere I have seen omega 3s in yeast.  I don't know how important they are for yeast, that's why I asked the question. It could be really important or something like vanadium deficiency which might take fifty years to kill you if at all!
I agree that the other 2 papers I sourced are low quality but "PNAS" - that's the only publication that got my flatmate excited (even more than nature or science.) It has a high eigenfactor and impact factor. 
I have seen published yeast genomes and am amazed that there is only 20% of gene function still to be worked out.
I got the definition of auxotrophic wrong - I saw this  "An organism, such as a strain of bacteria, that has lost the ability to synthesize certain substances required for its growth and metabolism  etc." and didn't realize that by definition all animal and yeasts that need vitamins and fatty acids are auxotrophs. My bad. 
I think the last point is a definition problem over vital. vital (adj.) late 14c., "of or manifesting life," from Latin vitalis "of or belonging to life," from vita "life," related to vivere "to live," from PIE root *gweie- (1) "to live" (see bio-). The sense of "necessary or important" is from 1610s, via the notion of "essential to life" (late 15c.). 
 Are iodine, selenium or vitamin E vital because people can live for decades without them but cannot reproduce if they are absent? 

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Re: Off topic discussions and journal club for LG11's thread

Post by LG11 » Sun Dec 07, 2014 4:20 am

The 20% figure isnt exactly correct, the problem you face with yeast and its genome is the following, it can respire under many many different conditions and use many different sources for fuel. When as a scientist you try and work on a gene pathway with yeast you have almost unlimited variations to follow, some genes are used one way under say aerobic conditions and used another way or not at all under anaerobic condition's.
Its not a plant or a animal it fits in as a type of fungi but then again it dosnt, no idea if you know this but under the right conditions it can grow spontaneously into a filamentous type strain resembling mycelium. In our lab we treat yeast as a separate organism (against convention), many of us here think there is a good case for yeast to sit in a group of its own rather than be lumped in with fungi. Off the top of my head I cant think of a single other organism that can act in so many different ways as S.cerevisiae. I have seen it act as symbiote, and as a parasite, It needs nitrogen but cannot use nitrate directly.
A good scientist views all science as valid, I have a slightly odd background however. My first degree was a masters in electronic engineering, I didnt like the smell of solder much and had biology as a hobby, so a year after my degree I went back to university and studied microbiology. I ended up doing a masters in Micro biology then kind of wondered into doing a phD bacteriology. Then came and worked here at my present job, I started off in the soap department!! eventually found myself working in the R&D blue sky labs on fermentation. I still do electronics as I always get nominated as the one to make the odd control system we cant buy in.
I work under 2 highly regarded Professors, I have no ambition however to follow the academic path. I publish as and when I feel I have something of use to publish or when I get told too! My current personal project is to get yeast to make high quality Isoamyl Alcohol and various other products. I am also working on a new class of antibiotics made via fermentation of micro organisms.

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