Bounds on Codes Derived by Counting Components in Varshamov Graphs

We are interested in improving the Varshamov bound for finite values of length n and minimum distance d. We employ a counting lemma to this end which we find particularly useful in relation to Varshamov graphs. Since a Varshamov graph consists of components corresponding to low weight vectors in the cosets of a code it is a useful tool when trying to improve the estimates involved in the Varshamov bound. We consider how the graph can be iteratively constructed and using our observations are able to achieve a reduction in the over-counting which occurs. This tightens the lower bound for any choice of parameters n, k, d or q and is not dependent on information such as the weight distribution of a code. This work is taken from the author’s thesis [10]     

WEIGLE-REACTIVATION IN A CYANOBACTERIUM (Synechococcus PCC7934) IS INDUCED BY UV BUT NOT BY MITOMYCIN-C OR NALIDIXIC ACID

Abstract— The cyanobacterium Synechococcus PCC7943 (Anacystis nidulans 602) exhibited UV induced Weigle-reactivation of irradiated cyanophaseAs–1. Weigle-reactivation had a half-life of approximately 34 min. It was not induced by treatments with the SOS inducing agents mitomycin-C or nalidixic acid.     

Monotone Chemical Reaction Networks

We analyze certain chemical reaction networks and show that every solution converges to some steady state. The reaction kinetics are assumed to be monotone but otherwise arbitrary. When diffusion effects are taken into account, the conclusions remain unchanged. The main tools used in our analysis come from the theory of monotone dynamical systems. We review some of the features of this theory and provide a self-contained proof of a particular attractivity result which is used in proving our main result.     

Purification and characterization of lamb pregastric lipase

Lamb pregastric lipase was purified from a commercial source using delipidation, solubilization with KSCN, acid-precipitation, pepsin-digestion, affinity chromatography with agarose-Cibacron Blue F3GA, gel filtration, and elution from a native 10% (w/v) polyacrylamide gel. The enzyme had a single subunit of 68,000 Da with maximum esterase activity when measured at pH 6.0 and 30 degrees C. The enzyme preferentially hydrolyzed short- and medium-chain (C4, C6, and C8) synthetic esters and short-chain (C4 and C6) monoacid triglycerides. The NH2-terminal sequence demonstrated high homology with gastric and lingual lipases.     

Bismuth compounds in organic synthesis. A one-pot synthesis of homoallyl ethers and homoallyl acetates from aldehydes catalyzed by bismuth triflate

[reaction: see text] Three one-pot methods for the conversion of aldehydes to homoallyl ethers catalyzed by Bi(OTf)(3).xH(2)O (1 < x < 4) have been developed. The one-pot synthesis of homoallyl ethers can be achieved either by in situ generation of the acetal followed by its reaction with allyltrialkylsilane or by a three-component synthesis in which the aldehyde, trimethylorthoformate or an alkoxytrimethylsilane and allyltrimethylsilane are mixed together in the presence of bismuth triflate (0.1-1.0 mol %). In addition, a three-component synthesis of homoallyl acetates, which is achieved by reacting the aldehyde, acetic anhydride, and allyltrimethylsilane in the presence of bismuth triflate (3.0-5.0 mol %), has been developed. The use of a relatively nontoxic, easy to handle, and inexpensive catalyst adds to the versatility of these methods.     

X-ray photoelectron spectroscopy and differential capacitance study of thiol-functional polysiloxane films on gold supports

Polymeric molecules containing multiple thiol groups (polythiols) provide tenacious attachment to metal surfaces such as gold. Polythiol films are also well suited for subsequent derivatization with biomacromolecules through remnant free thiol groups of the film. In this study, 1-3 nm thick layers of a commercial polythiol, poly((mercaptopropyl)methylsiloxane) (PMPMS), are investigated with X-ray photoelectron spectroscopy (XPS) and electrochemical impedance spectroscopy. XPS is used to reveal the surface coverage of thiolate-Au bonds between the polythiol and the metal support, which is found to be approximately 30% lower than that in alkanethiol self-assembled monolayers. The surface density of thiolate-Au bonds did not depend on film thickness provided sufficient PMPMS material was present. Differential capacitance measurements show that the effective dielectric barrier presented by PMPMS films under aqueous environments corresponds closely to their physical thickness, with even approximately 1 nm films remaining impermeable to electrolyte species. Modification of the films with an oligoethylene glycol compound was also examined, in anticipation of future applications in label-free, impedance-based biomolecular diagnostics.     

Action of photoreactivating light on pyrimidine heteroadduct in bacteria

Abstract— In stationary-phase Escherichia coli B/r, photoreactivation (PR) at 313 nm of ultraviolet (u.v.) killing is inefficient compared with PR at 405 nm, and can be explained solely by photoenzymatic reversal of pyrimidine dimers. In Staphylococcus epidermidis, PR shows a maximum at 313 nm, suggesting that this organism shows the Type III PR proposed by Jagger et al.[5] for Streptomyces strains. Reversal of pyrimidine dimers is not sufficient to explain this PR. The mechanism of Type III PR remains unknown. With both S. epidermidis and E. coli B/r, the amount of uracil–thymine heteroadduct in DNA hydrolysates decreases if the cells are given a post-u.v. treatment at 313 nm, but no decrease is observed if the post-u.v. treatment is at 405 nm. The biological significance of this adduct and of its removal is not clear. It may play a role in Type III PR.     

THE EFFECTS OF HOST-CELL REACTIVATION ON ASSAY OF U.V.-IRRADIATED HAEMOPHILUS INFLUENZAE TRANSFORMING DNA

Abstract— The host cell reactivation (HCR) mechanism in Haemophilus influenzae cells is inhibited by sub-microgram concentrations of acriflavine (as is already known to be true for Escherichia coli ). Exposure of these cells to similar concentrations of the drug during bacterial transformation increases the apparent ultraviolet light (u.v.) sensitivity of previously irradiated transforming DNA, indicating a repair of this DNA after uptake by the cells under normal conditions. Repair is inhibited by applying acriflavine at any time up to one hour after competent cells contact the irradiated transforming DNA. The fraction of the u.v. damage repaired by HCR is very different for different genetic markers. Those markers which are most u.v. sensitive when assayed in the absence of acriflavine are most poorly repaired, suggesting that this is the reason for their higher sensitivity. For all markers the fraction of the damage repairable by in vitro photoreactivation is approximately constant, and strongly overlaps the damage repairable by HCR. The degree of HCR achieved can be altered by experimental treatment of the H. influenzae DNA prior to transformation. Thus treatment of irradiated DNA with an enzyme from Micrococcus lysodeikticus –known to attack u.v. damaged, but not undamaged DNA–prevents subsequent intracellular repair of the same u.v. lesions whose repair is inhibited by acriflavine. Similarly, partial replacement of the thymine in transforming DNA by 5-bromouracil (BU) strongly inhibits repair of subsequent u.v. damage. As in bacteriophage, the BU effect is relieved if the u.v. exposure occurs in the presence of cysteamine. It is clear that intracellular repair must be considered in interpreting experiments with u.v.-irradiated transforming DNA.     

Transient response of a Brownian particle with general damping

We study the transient response of a Brownian particle with general damping in a system of metastable potential well. The escape rate is evaluated as a function of time after an infinite wall is removed from the potential barrier. It takes a relaxation time for the rate to reach its limit value and this rate relaxation time differs from the relaxation time of the majority of the probability around the bottom of the potential well. The rate relaxation time is found to depend on the temperature as well as the damping constant. It involves the diffusion time and the instanton time, in general agreement with recent studies of the overdamped case by Bier et al. [Phys. Rev. E 59, 6422 (1999)].