Upscaling diffusion through first-order volumetric sinks: a homogenization of bacterial nutrient uptake

In mathematical models that include nutrient delivery to bacteria, it is prohibitively expensive to include a pointwise nutrient uptake within small bacterial regions over bioreactor length-scales, and so such models often impose an effective uptake instead. In this paper, we systematically investigate how the effective uptake should scale with bacterial size and other microscale properties under first-order uptake kinetics. We homogenize the unsteady problem of nutrient diffusing through a locally periodic array of spherical bacteria, within which it is absorbed. We introduce a general model that could also be applied to other single-cell microorganisms, such as cyanobacteria, microalgae, protozoa, and yeast and we consider generalizations to arbitrary bacterial shapes, including some analytic results for ellipsoidal bacteria. We explore in detail the three distinguished limits of the system on the timescale of diffusion over the macroscale. When the bacterial size is of the same order as the distance between them, the effective uptake has two limiting behaviours, scaling with the bacterial volume for weak uptake and with the bacterial surface area for strong uptake. We derive the function that smoothly transitions between these two behaviours as the system parameters vary. Additionally, we explore the distinguished limit in which bacteria are much smaller than the distance between them and have a very strong uptake. In this limit, we find that the effective uptake is bounded above as the uptake rate grows without bound; we are able to quantify this and characterise the transition to the other limits we consider

Applying asymptotic methods to synthetic biology: modelling the reaction kinetics of the mevalonate pathway

The mevalonate pathway is normally found in eukaryotes, and allows for the production of isoprenoids, a useful class of organic compounds. This pathway has been successfully introduced to Escherichia coli, enabling a biosynthetic production route for many isoprenoids. In this paper, we develop and solve a mathematical model for the concentration of metabolites in the mevalonate pathway over time, accounting for the loss of acetyl-CoA to other metabolic pathways. Additionally, we successfully test our theoretical predictions experimentally by introducing part of the pathway into Cupriavidus necator. In our model, we exploit the natural separation of time scales as well as of metabolite concentrations to make significant asymptotic progress in understanding the system. We confirm that our asymptotic results agree well with numerical simulations, the former enabling us to predict the most important reactions to increase isopentenyl diphosphate production whilst minimizing the levels of HMG-CoA, which inhibits cell growth. Thus, our mathematical model allows us to recommend the upregulation of certain combinations of enzymes to improve production through the mevalonate pathway

Applying asymptotic methods to synthetic biology: modelling the reaction kinetics of the mevalonate pathway

The mevalonate pathway is normally found in eukaryotes, and allows for the production of isoprenoids, a useful class of organic compounds. This pathway has been successfully introduced to Escherichia coli, enabling a biosynthetic production route for many isoprenoids. In this paper, we develop and solve a mathematical model for the concentration of metabolites in the mevalonate pathway over time, accounting for the loss of acetyl-CoA to other metabolic pathways. Additionally, we successfully test our theoretical predictions experimentally by introducing part of the pathway into Cupriavidus necator. In our model, we exploit the natural separation of time scales as well as of metabolite concentrations to make significant asymptotic progress in understanding the system. We confirm that our asymptotic results agree well with numerical simulations, the former enabling us to predict the most important reactions to increase isopentenyl diphosphate production whilst minimizing the levels of HMG-CoA, which inhibits cell growth. Thus, our mathematical model allows us to recommend the upregulation of certain combinations of enzymes to improve production through the mevalonate pathway

Brief Note Elemental Analysis of Biological Material in the Fresh-Frozen State

Author Institution: Department of Zoology and Department of Surgery, The Ohio State Universit

Using singular perturbation theory to determine kinetic parameters in a non-standard coupled enzyme assay

We investigate how to characterize the kinetic parameters of an aminotransaminase using a non-standard coupled (or auxiliary) enzyme assay, where the peculiarity arises for two reasons. First, one of the products of the auxiliary enzyme is a substrate for the primary enzyme and, second, we explicitly account for the reversibility of the auxiliary enzyme reaction. Using singular perturbation theory, we characterize the two distinguished asymptotic limits in terms of the strength of the reverse reaction, which allows us to determine how to deduce the kinetic parameters of the primary enzyme for a characterized auxiliary enzyme. This establishes a parameter-estimation algorithm that is applicable more generally to similar reaction networks. We demonstrate the applicability of our theory by performing enzyme assays to characterize a novel putative aminotransaminase enzyme, CnAptA (UniProtKB Q0KEZ8) from Cupriavidus necator H16, for two different omega-amino acid substrates

A genetic assay for gene essentiality in Clostridium

Essential genes of pathogens are potential therapeutic targets, but are difficult to verify. Here, gene essentiality was determined by targeted knockout following engineered gene duplication. Null mutants of candidate essential genes of Clostridium difficile were viable only in the presence of a stable second copy of the gene

Astrophysical and Astrobiological Implications of Gamma-Ray Burst Properties

Combining results for the local cosmic rate and mean peak luminosity of GRBs with the cosmic history of the star formation rate, we provide estimates for the local GRB rate per unit blue luminosity in galaxies. We find a typical GRB rate per unit B luminosity of 2.4x10^-17 h_{70}^2/Lsun/yr. The corresponding mean rate in the Milky Way is 5.5x10^-7 h_{70}^2/yr. We conclude: 1) the ratio of supernova rate to isotropic equivalent GRB rate is large: more than 6000 SNIbc per GRB or 30,000 SNII per GRB. GRBs could arise in a large fraction of black hole-forming events only with collimation in the range 0.01 - 0.001 and a steep enough slope of the IMF; 2) GRBs cannot account for the majority of large HI holes observed in galaxies; 3) the probability that the solar system was exposed to a fluence large enough to melt the chondrules during the first 10^7 yr of solar system history is negligibly small; 4) Even for very opaque atmospheres, a significant fraction of the GRB energy is transmitted as UV lines due to excitation by secondary electrons. For eukaryotic-like organisms in thin atmospheres (e.g. contemporary Mars), or for UV line exposure in thick atmospheres (e.g. Earth), biologically significant events occur at a rate of about 100--500 /Gyr. The direct contribution of these "jolts" to mutational evolution may, however, be negligible because of the short duration of the GRBs. Evolutionary effects due to partial sterilizations and to longer-lived disruptions of atmospheric chemistry should be more important. (Abridged)Comment: 36 pages, no figures Accepted by Astrophysical Journal Oct. 2001. First submitted December,1999. Substantially rewritten discussion of burst source count distributions and of biological implication

The indirect action of ions upon amino acid transport system L in the S37 cell

The uptake into S37 ascites cells of an L-system specific analog, 2-amino-bicyclo-(3,2,1)-octanecarboxylic acid (ABOCA), wasinconsistently inhibited by deletion of sodium ion from the incubation medium. We note that there have been conflicting reports from various other laboratories as to the effect of sodium ion on the transport of L-system specific analogs. The uptake of labeled exo-2-aminobicyclo-(2.2,1)-heptane-2-carboxylic acid (BCH) wasalso diminished by the removal of sodium from the medium. The Km values for these substrates were increased and [nu]max values decreased as the sodium ion concentration was decreased or abolished. Transport behavior was also found to be affected by varying the medium potassium ion concentration with valinomycin present. The sodium effect was abolished by preincubation with cyanide and deoxyglucose. The results suggest an indirect effect of sodium ion upon transport system L: system L is energetically supported by a membrane potential.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24714/1/0000136.pd

Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824

BackgroundClostridium acetobutylicum represents a paradigm chassis for the industrial production of the biofuel biobutanol and a focus for metabolic engineering. We have previously developed procedures for the creation of in-frame, marker-less deletion mutants in the pathogen Clostridium difficile based on the use of pyrE and codA genes as counter selection markers. In the current study we sought to test their suitability for use in C. acetobutylicum.ResultsBoth systems readily allowed the isolation of in-frame deletions of the C. acetobutylicum ATCC 824 spo0A and the cac824I genes, leading to a sporulation minus phenotype and improved transformation, respectively. The pyrE-based system was additionally used to inactivate a putative glycogen synthase (CA_C2239, glgA) and the pSOL1 amylase gene (CA_P0168, amyP), leading to lack of production of granulose and amylase, respectively. Their isolation provided the opportunity to make use of one of the key pyrE system advantages, the ability to rapidly complement mutations at appropriate gene dosages in the genome. In both cases, their phenotypes were restored in terms of production of granulose (glgA) and amylase (amyP). Genome re-sequencing of the ATCC 824 COSMIC consortium laboratory strain used revealed the presence of 177 SNVs and 49 Indels, including a 4916-bp deletion in the pSOL1 megaplasmid. A total of 175 SNVs and 48 Indels were subsequently shown to be present in an 824 strain re-acquired (Nov 2011) from the ATCC and are, therefore, most likely errors in the published genome sequence, NC_003030 (chromosome) and NC_001988 (pSOL1).ConclusionsThe codA or pyrE counter selection markers appear equally effective in isolating deletion mutants, but there is considerable merit in using a pyrE mutant as the host as, through the use of ACE (Allele-Coupled Exchange) vectors, mutants created (by whatever means) can be rapidly complemented concomitant with restoration of the pyrE allele. This avoids the phenotypic effects frequently observed with high copy number plasmids and dispenses with the need to add antibiotic to ensure plasmid retention. Our study also revealed a surprising number of errors in the ATCC 824 genome sequence, while at the same time emphasising the need to re-sequence commonly used laboratory strains

Why do UK banks securitize?

Working paper seriesThe eight years from 2000 to 2008 saw a rapid growth in the use of securitization by UK banks. We aim to identify the reasons that contributed to this rapid growth. The time period (2000 to 2010) covered by our study is noteworthy as it covers the pre- nancial crisis credit- boom, the peak of the nancial crisis and its aftermath. In the wake of the nancial crisis, many governments, regulators and political commentators have pointed an accusing nger at the securitization market - even in the absence of a detailed statistical and economic analysis. We contribute to the extant literature by performing such an analysis on UK banks, fo- cussing principally on whether it is the need for liquidity (i.e. the funding of their balance sheets), or the desire to engage in regulatory capital arbitrage or the need for credit risk trans- fer that has led to UK banks securitizing their assets. We show that securitization has been signi cantly driven by liquidity reasons. In addition, we observe a positive link between securitization and banks credit risk. We interpret these latter ndings as evidence that UK banks which engaged in securitization did so, in part, to transfer credit risk and that, in comparison to UK banks which did not use securitization, they had more credit risk to transfer in the sense that they originated lower quality loans and held lower quality assets. We show that banks which issued more asset-backed securities before the nancial crisis su¤ered more defaults after the nancial crisis.The eight years from 2000 to 2008 saw a rapid growth in the use of securitization by UK banks. We aim to identify the reasons that contributed to this rapid growth. The time period (2000 to 2010) covered by our study is noteworthy as it covers the pre-financial crisis credit- boom, the peak of the financial crisis and its aftermath. In the wake of the financial crisis, many governments, regulators and political commentators have pointed an accusing finger at the securitization market - even in the absence of a detailed statistical and economic analysis. We contribute to the extant literature by performing such an analysis on UK banks, fo- cussing principally on whether it is the need for liquidity (i.e. the funding of their balance sheets), or the desire to engage in regulatory capital arbitrage or the need for credit risk trans- fer that has led to UK banks securitizing their assets. We show that securitization has been significantly driven by liquidity reasons. In addition, we observe a positive link between securitization and banks credit risk. We interpret these latter findings as evidence that UK banks which engaged in securitization did so, in part, to transfer credit risk and that, in comparison to UK banks which did not use securitization, they had more credit risk to transfer in the sense that they originated lower quality loans and held lower quality assets. We show that banks which issued more asset-backed securities before the financial crisis suffered more defaults after the financial crisis