Analytical methods for bacterial kinetics studies

Methods utilize mathematical equations and models and specialized computer techniques. Techniques apply to food production, complex chemicals production, and polluted water purification

Tradeoff between short-term and long-term adaptation in a changing environment

We investigate the competition dynamics of two microbial or viral strains that live in an environment that switches periodically between two states. One of the strains is adapted to the long-term environment, but pays a short-term cost, while the other is adapted to the short-term environment and pays a cost in the long term. We explore the tradeoff between these alternative strategies in extensive numerical simulations, and present a simple analytic model that can predict the outcome of these competitions as a function of the mutation rate and the time scale of the environmental changes. Our model is relevant for arboviruses, which alternate between different host species on a regular basis.Comment: 9 pages, 3 figures, PRE in pres

High-efficiency, high-power difference-frequency generation of 0.9–1.5 μm light in BBO

An efficient method for generation of high energy pulsed ir light between 0.9 and 1.5 μm is described. The technique uses difference frequency mixing of pulsed, visible dye and Nd:YAG laser light in a 10 mm long BBO crystal. Quantum efficiencies of up to 23% and ir pulse energies up to 4.5 mJ are demonstrated. The low shot-to-shot fluctuations of difference frequency generation in BBO make this technique an attractive alternative to the conventional optical parametric oscillator or Raman shifting methods that are currently used to access this spectral region

The Error and Repair Catastrophes: A Two-Dimensional Phase Diagram in the Quasispecies Model

This paper develops a two gene, single fitness peak model for determining the equilibrium distribution of genotypes in a unicellular population which is capable of genetic damage repair. The first gene, denoted by $\sigma_{via}$, yields a viable organism with first order growth rate constant $k > 1$ if it is equal to some target ``master'' sequence $\sigma_{via, 0}$. The second gene, denoted by $\sigma_{rep}$, yields an organism capable of genetic repair if it is equal to some target ``master'' sequence $\sigma_{rep, 0}$. This model is analytically solvable in the limit of infinite sequence length, and gives an equilibrium distribution which depends on \mu \equiv L\eps , the product of sequence length and per base pair replication error probability, and \eps_r , the probability of repair failure per base pair. The equilibrium distribution is shown to exist in one of three possible ``phases.'' In the first phase, the population is localized about the viability and repairing master sequences. As \eps_r exceeds the fraction of deleterious mutations, the population undergoes a ``repair'' catastrophe, in which the equilibrium distribution is still localized about the viability master sequence, but is spread ergodically over the sequence subspace defined by the repair gene. Below the repair catastrophe, the distribution undergoes the error catastrophe when $\mu$ exceeds \ln k/\eps_r , while above the repair catastrophe, the distribution undergoes the error catastrophe when $\mu$ exceeds $\ln k/f_{del}$, where $f_{del}$ denotes the fraction of deleterious mutations.Comment: 14 pages, 3 figures. Submitted to Physical Review

SB37-08/09: LGBTIQ Bills in the Montana Legislature

SB37-08/09: LGBTIQ Bills in the Montana Legislature. This resolution passed 18Y-1N on a roll call vote during the February 4, 2009 meeting of the Associated Students of the University of Montana (ASUM)

Ergosterol Effect on the Desaturation of 14C-Cis-Vaccenate in Tetrahymena

Supplement of ergosterol to the growth medium of the ciliated protozoan Tetrahymena pyriformis W leads to incorporation of the foreign sterol within cell membranes and suppression of synthesis of the native sterol-like compound tetrahymanol, as well as to changes in the fatty acid compositions of several major classes of membrane lipid. Alteration of fatty acid composition is thought to represent a regulatory mechanism whereby optimum membrane fluidity is maintained when the slightly dissimilar foreign sterol is added into the phospholipid bilayer of the membranes. The present study, using several different conditions of growth temperature, substrate concentrations and incubation time, and ergosterol concentrations and exposure time, is an attempt to provide evidence supporting a hypothetical regulatory mechanism. This mechanism proposes that there is a feedback regulation by membrane-bound sterol on an enzyme or enzymes involved in synthesis of the long chain fatty acids contained in membrane phospholipid. Such a mechanism could account for the balance between sterol and fatty acid content of membrane. The data presented here show that a statistically significant increase in desaturation of 14C-cis-vaccenate can be demonstrated in Tetrahymena cell cultures whose membranes contain the foreign sterol, when growth temperature is maintained at 20° or 29.5°. Tetrahymena desaturated 14C-cis-vaccenate substrate in both ergosterol supplemented and normal cultures. The 14C labeled product, 6,11-18:2 was recovered and separated by silver nitrate-Unisil column chromatography

E. coli F1 -ATPase: Site-directed mutagenesis of the β-subunit

AbstractResidues βGlu-181 and βGlu-192 of E. coli F1-ATPase (the DCCD-reactive residues) were mutated to Gln. Purified βGln-181 F1 showed 7-fold impairment of ‘unisite’ Pi formation from ATP and a large decrease in affinity for ATP. Thus the β-181 carboxyl group in normal F1 significantly contributes to catalytic site properties. Also, positive catalytic site cooperativity was attenuated from 5 × 104- to 548-fold in βGln-181 F1. In contrast, purified βGln-192 F1 showed only 6-fold reduction in ‘multisite’ ATPase activity. Residues βGly-149 and βGly-154 were mutated to Ile singly and in combination. These mutations, affecting residues which are strongly conserved in nucleotide-binding proteins, were chosen to hinder conformational motion in a putative ‘flexible loop’ in β-subunit. Impairment of purified F1-ATPase ranged from 5 to 61%, with the double mutant F1 less impaired than either single mutant. F1 preparations containing βIle-154 showed 2-fold activation after release from membranes, suggesting association with F0 restrained turnover on F1 in these mutants

Re-entrant ferroelectricity in liquid crystals

The ferroelectric (Sm C$^*$) -- antiferroelectric (Sm C$^*_A$) -- reentrant ferroelectric (re Sm C$^*$) phase temperature sequence was observed for system with competing synclinic - anticlinic interactions. The basic properties of this system are as follows (1) the Sm C$^*$ phase is metastable in temperature range of the Sm C$^*_A$ stability (2) the double inversions of the helix handedness at Sm C$^*$ -- Sm C$^*_A$ and Sm C$^*_A$% -- re-Sm C$^*$ phase transitions were found (3) the threshold electric field that is necessary to induce synclinic ordering in the Sm C$^*_A$ phase decreases near both Sm C$^*_A$ -- Sm C$^*$ and Sm C$^*_A$ -- re-Sm C$^*$ phase boundaries, and it has maximum in the middle of the Sm C$^*_A$ stability region. All these properties are properly described by simple Landau model that accounts for nearest neighboring layer steric interactions and quadrupolar ordering only.Comment: 10 pages, 5 figures, submitted to PR

Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding

BACKGROUND: The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem natural that random mutations should tend to interact synergistically, such that the rate of mean fitness decline accelerates as the number of random mutations is increased. However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect) has been observed. RESULTS: We studied in silico the net amount and form of epistatic interactions in RNA secondary structure folding by measuring the fraction of neutral mutants as a function of mutational distance d. We found a clear prevalence of antagonistic epistasis in RNA secondary structure folding. By relating the fraction of neutral mutants at distance d to the average neutrality at distance d, we showed that this prevalence derives from the existence of many compensatory mutations at larger mutational distances. CONCLUSIONS: Our findings imply that the average direction of epistasis in simple fitness landscapes is directly related to the density with which fitness peaks are distributed in these landscapes

Nanoscale grains, high irreversibility field, and large critical current density as a function of high energy ball milling time in C-doped magnesium diboride

Magnesium diboride (MgB2) powder was mechanically alloyed by high energy ball milling with C to a composition of Mg(B0.95C0.05)2 and then sintered at 1000 C in a hot isostatic press. Milling times varied from 1 minute to 3000 minutes. Full C incorporation required only 30-60 min of milling. Grain size of sintered samples decreased with increased milling time to less than 30 nm for 20-50 hrs of milling. Milling had a weak detrimental effect on connectivity. Strong irreversibility field (H*) increase (from 13.3 T to 17.2 T at 4.2 K) due to increased milling time was observed and correlated linearly with inverse grain size (1/d). As a result, high field Jc benefited greatly from lengthy powder milling. Jc(8 T, 4.2 K) peaked at > 80,000 A/cm2 with 1200 min of milling compared with only ~ 26,000 A/cm2 for 60 min of milling. This non-compositional performance increase is attributed to grain refinement of the unsintered powder by milling, and to the probable suppression of grain growth by milling-induced MgO nano-dispersions.Comment: 12 pages, 11 figure