10:11:48 From Mikhail Tikhonov to Everyone : In the chemical composition column, what does "4-10% ash" mean? 10:12:28 From Srividya Iyer-Biswas to Everyone : Is it significant that the pathways on both ends (top + bottom) of the bow tie in the last slide are “linear”? 10:12:32 From Marco Cosentino Lagomarsino to Everyone : How much does the /chemical/ composition vary with growth conditions and environments? 10:12:41 From Alfred Spormann to Everyone : It might be K, potassium, that’s where the ‘ash’ comes from. 10:13:34 From Mikhail Tikhonov to Everyone : thanks! 10:14:33 From Terry Hwa to Everyone : @Marco: chemical composition can vary as reflected e.g. by protein (N) and RNA (P) ratio. There are other factors such as carbon storage. 10:14:46 From Marco Cosentino Lagomarsino to Everyone : Thanks! 10:15:47 From Avi Flamholz to Everyone : also various storage molecules like polyphosphate, polyhydroxybutyrate, glycogen, etc can cause the composition to vary 10:16:54 From Daniel Fisher to Everyone : does the intermediate list also needs amino acids or just ammonia? 10:17:12 From Mikhail Tikhonov to Everyone : Is there a simple way of seeing why there should be such a separation between NADH and NADPH (for biosynthsis vs not)? 10:17:28 From Terry Hwa to Everyone : @daniel: the intermediates listed are all carbon intermediates. 10:17:31 From Srividya Iyer-Biswas to Everyone : Terry/Uwe, I would love to hear why Uwe thinks it’s significant that those pathways are linear (re my question @1:12 ET). 10:18:31 From Alfred Spormann to Everyone : These are two competing metabolic reactions, and ta growing cell needs to balance the electron flow through both major pathway sets. If not, the kinetically most electrons will flow through energy metabolism. 10:18:49 From Avi Flamholz to Everyone : @mikhail - the concentration ratios NAD/NADH and NADP/NADPH are typically inverted from each other 10:19:07 From Avi Flamholz to Everyone : you can think of them as different “effective” compartments 10:19:18 From Avi Flamholz to Everyone : one driving oxidative and the other driving reductive reactions 10:19:48 From Mikhail Tikhonov to Everyone : cool, thanks! 10:19:56 From Avi Flamholz to Everyone : @marco - I find this table on the growth rate dependent composition of E. coli very useful to look at to see how much the composition can change. https://bionumbers.hms.harvard.edu/bionumber.aspx?id=103890&ver=11&trm=composition+coli++growth+rate&org= 10:21:04 From Avi Flamholz to Everyone : @mikhail NAD/NADH and NADP/NADPH bionumbers show that the ratios differ by ~tenfold 10:21:11 From Avi Flamholz to Everyone : https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105022&ver=8&trm=coli+nad+nadh&org= 10:21:16 From Avi Flamholz to Everyone : https://bionumbers.hms.harvard.edu/bionumber.aspx?s=n&v=6&id=105023 10:21:58 From Avi Flamholz to Everyone : @Daniel Fisher — the answer depends on the organism. E. coli is a “prototroph” for amino acids - it can make all of them from ammonia and glucose 10:22:23 From Alfred Spormann to Everyone : The difference in ration of NAD+/NADH vs NADP+/NADPH is important for the in vivo redox potentials. 10:22:31 From Avi Flamholz to Everyone : but many other bugs are not prototrophs, even some related strains of E. coli are not (i.e. other than the typical lab strains) 10:29:48 From Srividya Iyer-Biswas to Everyone : Great, thanks Uwe, Wenying, Arvind 10:33:29 From Roderich Römhild to Everyone : What is the missing 11th biosynthetic precursor metabolite in the large schematic? I only see 10 in the list. Or does Triose-3P count twice? 10:42:46 From Akorede Seriki to Everyone : Is central metabolism needed for all other pathways, regardless of the organism? 10:43:25 From Ashish B. George to Everyone : Naively, an enzyme good for the forward reaction should be good at doing the reverse reaction as well (if it just changed the activation energy)Are the new enzymes required in gluconeogenesis because those reactions are coupled to ATP? 10:45:47 From Ashish B. George to Everyone : very interesting! Thank you! 10:48:18 From Terry Hwa to Everyone : this review and another are already posted on the reference page. 10:51:19 From Ramis Rafay to Everyone : Could you please explain in more detail what is meant by 'scope of possible fluxes' rather than 'fine-tuned for metabolic fluxes'? 10:51:22 From Daniel Fisher to Everyone : Does active destruction of the enzymes that go in the opposite direction play an important role? 10:52:11 From Alfred Spormann to Everyone : Daniel, yes, as it prevents futile cycles. 10:52:26 From Terry Hwa to Everyone : @daniel: not in the cases that we looked at (next hour) where the enzyme in the opposite direction actually caused a lot of problems. 10:53:28 From Terry Hwa to Everyone : for e. coli (perhaps due to its fast growth), protein degradation is generally sparingly employed, at least in the exponential growth phase. 10:55:05 From Srividya Iyer-Biswas to Everyone : @Terry: Was that finding also true for E. coli in minimal media growth conditions? 10:55:55 From Terry Hwa to Everyone : yes, by fast growth, I mean exponential growth in the batch 10:56:37 From Astrid Stubbusch to Everyone : Re the ‘small repertoire’ of some specialised bacteria or body cells: Did you mean genetic reduction, or less repertoire of changing metabolic fluxes (so less regulation). How would we study the latter? Thanks! 11:00:17 From Avi Flamholz to Everyone : @daniel in the specific case that Uwe is talking about, the mechanism is allosteric regulation by sentinel metabolites whose accumulation signals the change in pathway direction 11:00:28 From Avi Flamholz to Everyone : which is much faster than degredation and new production 11:00:45 From Avi Flamholz to Everyone : seconds vs minutes to hours 11:03:04 From Avi Flamholz to Everyone : @akorede - the specific set of reactions in central metabolism changes a bit from organism to organism (e.g. there are a couple of variants on glycolysis) but the over all concept of the bowtie is (so far as I know) applies in all cases that we know of 11:19:08 From Matteo Mori to Everyone : question for Uwe and all C13 people: to apply C13 MFA one needs to assume an underlying metabolic network (with mass-balanced fluxes). I imagine that using a network too large compared to the available data does not allow to determine all flux ratios. What about the opposite case? Are there signatures that allow to determine whether some important reaction is missing from the model? 11:20:10 From Akorede Seriki to Everyone : Thank you, @Avi 11:20:36 From Daniel Fisher to Everyone : in primary pathways how much is lost to spurious reactions? 11:21:02 From Avi Flamholz to Everyone : @daniel I don’t think this is known 11:21:50 From Avi Flamholz to Everyone : also depends on the definition of spurious 11:22:34 From Daniel Fisher to Everyone : @Avi presumably has to be small fractions to not mess up FBA? 11:22:51 From Avi Flamholz to Everyone : hmm, interesting point 11:23:13 From Avi Flamholz to Everyone : most cases where people run FBA they are not comparing the intracellular fluxes to measurements/inferences that Uwe is describing 11:23:47 From Avi Flamholz to Everyone : rather (in the best case) they measure the inputs and outputs and use those to constrain the model and infer bounds for the intracellular fluxes 11:24:27 From Avi Flamholz to Everyone : so the actual comparisons between FBA and measurements are rare 11:34:54 From Ralf Steuer to Everyone : @Avi: the FBA field is huge … I have seen quite a few papers that compare flux predictions to measured fluxes using scatter plots/correlations. And this indeed is a bit misleading since both are subject to the same constraint (the steady state), so you'll get a "correlation" no matter what. 11:35:43 From Avi Flamholz to Everyone : hmm I suppose I have to think on this point more 11:36:34 From Avi Flamholz to Everyone : but it seems like we arrive at an agreement on the answer to daniel’s question about the magnitude of non-specific catalysis, which is “not well understood, but probably small in central metabolism” - do you agree @ralf? 11:47:32 From Ralf Steuer to Everyone : yes, non-specific pathways should be small otherwise you would see a mismatch (as Uwe says) … but did not read much about it. 12:08:56 From Avi Flamholz to Everyone : qn for uwe: would you then expect to find allostery with TCA enzymes in organisms (e.g. cyanobacteria) that operate the TCA as a fork? 12:33:16 From Michael Rust to Everyone : question: are the many hour lags partially a result of rapidly switching from glucose to acetate? if you switched gradually over 30 min would the lag be much milder? 12:33:44 From Srividya Iyer-Biswas to Everyone : + 1 Mike’s question 12:34:14 From Terry Hwa to Everyone : it all depends on how do you switch slowly over 30min? 12:34:43 From Terry Hwa to Everyone : you can always pre-make the enzyme in shortage to remove the lag. 12:34:44 From Michael Rust to Everyone : e.g. in a microfluidic where you could vary glucose and acetate concentration continuously 12:35:59 From Terry Hwa to Everyone : we haven’t done that experiment, but I would guess the lag will be short in this case. But at appreciable cell density, glucose runs out very abruptly, in a few minutes. 12:40:49 From Shreyansh Umale to Everyone : Instead of gradually switching what would happen if the cells were starved for varying periods? 12:41:38 From Avi Flamholz to Everyone : Uwe - could you select for fast switching between glucose and acetate somehow and see what happens to protein expression and activity? 12:42:14 From Terry Hwa to Everyone : pls ask your question directly 12:42:25 From Avi Flamholz to Everyone : sure 12:49:15 From Jeffrey Barrick to Everyone : @Avi Some evolution experiments by Mike Travisano, Michael Doebeli, and others have isolated mutant E. coli that change how they switch from acetate to glucose utilization. They called them fast-switchers. If I recall correctly, they reduce/eliminate the diauxic shift when E. coli is grown on large concentrations of glucose then changes over to using the acetate that is produced as a byproduct of fast growth on glucose. I don't know what happened to lag phase or recall the genetic basis. 12:49:39 From Avi Flamholz to Everyone : Thanks Jeff! 13:01:03 From Ralf Steuer to Everyone : thanks! 13:01:37 From Hector Hernandez Gonzalez to Everyone : Thank you very much 13:01:41 From Ralf Steuer to Everyone : [btw, glycogen storage would also be a trade-off between faster growth and being on the side]