# User:Janet B. Matsen/never forget

(Difference between revisions)
 Revision as of 00:14, 21 July 2013 (view source) (→Metrics of yield/success)← Previous diff Revision as of 00:16, 21 July 2013 (view source) (→Maximum Theoretical Yield Calculations)Next diff → Line 32: Line 32: === Maximum Theoretical Yield Calculations === === Maximum Theoretical Yield Calculations === *Options: *Options: - ** Use FBA [http://www.ncbi.nlm.nih.gov/pubmed/16619212 example] + ** Use FBA + *** [http://www.ncbi.nlm.nih.gov/pubmed/16619212 example]: "Metabolic ﬂux analysis is used to determine the relative ﬂux of all the reactions in a cell while satisfying all cellular constraints of mass, energy, and redox. When the uptake rates are experimentally determined, metabolic ﬂux analysis + can be used to determine the maximum production rate, and subsequently yield, of the product of interest." ** Use chemical formula of dry biomass and the desired product ** Use chemical formula of dry biomass and the desired product

## Significant Figures

• If you have a measurement like 12.34, and you are showing the error, would you write
• (a) 12.34 ± 1.56
• (b) or do you include the number of significant figures in your measurement: 12.34 ± 1.567?
• Mary: I would go with (a). That is certainly how all of the journals I publish in handle this.
• If you are using a lac promoter and you add IPTG, arent you also inducing expression of LacZYA?
• I think so. But if you have a high copy plasmid, you are making much much more of your enzyme. :w

## Chemicals

• NH3 = ammonia, NO2 = nitrite, NO3 = nitrate
• "The preferred nitrogen electron acceptors in order of most to least thermodynamically favorable include nitrate (NO3−), nitrite (NO2−), nitric oxide (NO), nitrous oxide (N2O) finally resulting in the production of dinitrogen (N2) completing the nitrogen cycle." Wikipedia
• Nitrifying bacteria: ammonia --> nitrite OR nitrite --> nitrate
• Denitrification = reduction of nitrates back into the largely inert nitrogen gas (N2): NO3− → NO2− → NO + N2O → N2 (g)
• performed by bacterial species such as Pseudomonas and Clostridium in anaerobic conditions: use the nitrate as an electron acceptor in the place of oxygen during respiration.
• Some types eat ammonia; they produce nitrites as waste. Others eat nitrites; they produce nitrates as waste.
• DTT is a reducing agent which will help keep the Cys thiol groups from getting oxidized
• Tris-HCl and Tris are NOT the same! (2012/11/14)

## Biotechnology

### Why are bacteriophages a big problem for bacterial biotech, but viruses in mammalian biotech not?

Ans (from dialogue with Mary Lidstrom 8/2012)

• Phage can be encapsulated in tough capsids. However, viruses infecting multicellular organisms, they evade the immune system by coating themselves with a portion of the cell membrane, but that makes them fragile outside a host.
• That doesn't happen for yeast, but the yeast viruses seem to be transmitted through the yeast mating process and don't infect the host cells from the outside. I don't know why that would be, except perhaps because it is a safe mechanism for transfer and yeast do mate at a high frequency. That means of course that even if an infection occurs, sterilization to get rid of the infected yeast gets rid of the virus also. That's much less problematic than having to scrub all the ventilation systems, walls, etc. to get rid of phage.

### Metrics of yield/success

• Yield (%), titer (g/L), productivity (g/L/hr) - Eli Groban of Intrexon 2/2013
• byproduct proﬁle & strain robustness - "From the ﬁrst drop to the ﬁrst truckload: commercialization of microbial processes for renewable chemicals" by Stephen Van Dien 2013
• Also in Van Dien paper:
• "For production of basic and intermediate chemicals with selling price near \$1.00/lb or lower, the raw material cost of sugar represents a significant fraction of the value of the product even at near theoretical yield. Thus target yields generally need to be at least 80% of theoretical yield even be considered for commercialization. In contrast, with a few notable exceptions cells do not direct a high percentage of carbon flux to these compounds, if any at all. Therefore, the metabolic engineer is faced with the challenge of redirecting a major portion of flux away from biomass production and natural fermentation products, and toward the product of interest."
• "As a rule of thumb, 50 g/L is the minimum acceptable titer for any basic or intermediate chemical, and may be higher in many cases."

### Maximum Theoretical Yield Calculations

• Options:
• Use FBA
• example: "Metabolic ﬂux analysis is used to determine the relative ﬂux of all the reactions in a cell while satisfying all cellular constraints of mass, energy, and redox. When the uptake rates are experimentally determined, metabolic ﬂux analysis

can be used to determine the maximum production rate, and subsequently yield, of the product of interest."

• Use chemical formula of dry biomass and the desired product

### Desireable metabolic products

• branched chain alcohols
• "branched" is key because these compounds' properties include...

### Why are yeast a favorite industrial organism?

• Oxygen transfer is the largest thing to scale in industrial processes, so you want an organism that can grow anaerobically. You don't, however, want an obligate anaerobe because it is so much harder to work with and grow starter cultures of.
• Example: clostridium naturally produces butanol, but the fact that it is an obligate anaerobe motivated scientists to move its butanol production pathway into E. coli.

## Protein Modeling/Fusion Proteins

### Can you use a protein structure from a database to preduct whether you can use that protein as part of a fusion protein?

Ans: from 2012_09_11 summary from e-mail from Justin about visualizing FLS &

• You may have the structure file, but you are going to run into two issues:
• "First, the floppy ends of the proteins are not in the structures. At the N and C terminal, you will often see a discrepancy between the actual sequence and what you see in a crystal. This is because you can only see parts of the protein that are essentially fixed in space and not moving around much. So where exactly to overlay the proteins won't be totally clear.
• Second, as long as the ends are floppy you really won't be able to predict how it looks and the units interact. The only reason to look at a structure for fusions is to know if the ends are highly structured and an integral part of the protein (i.e. in a sheet or helix). If this is the case it is best to avoid fusing those sections. However, if the ends are "floppy" or "unstructured" (as in not a helix or sheet, and not an integral part of the protein... this is for sure the case if you can't see the actual ends in the structure) you can most likely make a functional fusion. Now... there may be empirical differences between how well an N vs C terminal function, but their will really be no sound way to predict that. This is generally speaking, there are special cases, such as a protein that ends in a helix and a fusion made starting at a helix so the two proteins are very specifically oriented relative to each other. But these cases are extremely rare."

## Basic Biology

### How do cells incorporate N from minimal media?

• reduced nitrogen (NH4+) is assimilated into glutamate and glutamine, then into other nitrogen-containing biomolecules.
• assimilation of NH4+ into glutamate requires two reactions:
• glutamine synthetase catalyzes the reaction of glutamate and NH4+ to yield glutamine (in 2 steps)
• Glutamate is the source of amino groups for most other amino acids, through transamination reactions.
• If NO3- (nitrate) is provided, they must expend NADH to reduce it to ammonium before it can be assimilated.
• Some organisms prefer to do this than start with ammonium. See MM1/MM2/MM3/HY

## Mass Spec

### What can internal standard correct for?

• ion supression