On the response output from non-linear switching elements with different types of finite dead times

In investigating the response of systems to random input events, dead times in registering these events are met with, as in the case of neuronal behaviour. These situations are studied in terms of product densities making use of the renewal nature of the problem. Different types of cumulative responses of systems are investigated. Some interesting features of a system, which breaks down at a critical value of the cumulative response are analysed.     

Deactivation of catalase by hydrogen peroxide

When a mechanism is used to determine possible deactivation kinetics, a certain consistency with the kinetics of the main reaction is found. This result is examined in the light of experimental evidence obtained with bovine liver and Aspergillus catalases.     

Studies on the deactivation of immobilized urease

The results of experiments in a fixed-bed reactor and a CSTR containing urease immobilized on a nonporous support and conducted in the absence of diffusional limitations are reported. Kinetic parameters were established by separate batch experiments. The key observation was that the product ammonia attacked the free form of the enzyme and thereby illustrates the importance of mechanism in determining deactivation kinetics.     

Preferred conformations and flexibility of aminoacyl side chain of penicillins

Possible conformations of penicillin G; d and l isomers of ampicillin; α-amino-α-methyl-benzyl penicillins and 3- pyridyl methyl penicillin have been studied by an energy minimization procedure using empirical potential functions. The preferred conformations of these antibiotics have been correlated with their biological activity. The conformational requirement of the antibiotic to be active against Gram-positive and Gram-negative (β-lactamase-negative) bacterial strains seems to be the same. The reduced activity of penicillin G against Gram-negative bacteria has been attributed to its lower ability to permeate the outer membrane. The flexibility of the sidechains of these antibiotics is also shown to be important for the desired biological activity.     

Microbial diversity in hypersaline wastewater: the example of tanneries

In contrast to conventional wastewater treatment plants and saline environments, little is known regarding the microbial diversity of hypersaline wastewater. In this study, the microbial communities of a hypersaline tannery effluent, and those of three treatment systems operating with the tannery effluent, were investigated using 16S rDNA phylogenetic markers. The comparative analysis of 377 bacterial sequences revealed the high diversity of this type of hypersaline environment, clustering within 193 phylotypes (≥ 97% similarity) and covering 14 of the 52 divisions of the bacterial domain, i.e. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chlorobi, Planctomycetes, Spirochaetes, Synergistes, Chloroflexi, Thermotogae, Verrucomicrobia, OP3, OP11 and TM7. Most of the phylotypes were related to halophilic and pollutant-degrading bacteria. Using statistical analysis, the diversity of this type of environment was compared to that of other environmental samples selected on the basis of their salinity, oxygen content and organic load.     

Heterocyclic ketones as inhibitors of histone deacetylase

Several heterocyclic ketones were investigated as potential inhibitors of histone deacetylase. Nanomolar inhibitors such as 22 and 25 were obtained, the anti-proliferative activity of which were shown to be mediated by HDAC inhibition.     

A stochastic model for eye movements during fixation on a stationary target

A stochastic model describing small eye movements occurring during steady fixation on a stationary target is presented. Based on eye movement data for steady gaze, the model has a hierarchical structure; the principal level represents the random motion of the image point within a local area of fixation while the higher level mimics the jump processes involved in transitions from one local area to another. Target image motion within a local area is described by a Langevinlike stochastic differential equation taking into consideration, the microsaccadic jumps pictured as being due to point processes and the high frequency muscle tremor, represented as a white noise. The transform of the probability density function for local area motion is obtained, leading to explicit expressions for their means and moments. Evaluation of these moments based on the model are comparable with experimental results. A physiologically based criterion for the occurrence of local area changes is assumed and the renewal density of these transitions is obtained. These transitions are brought about by the occurrence of large saccades. Hence, our analysis leads us to derive expressions for the mean and moments of the occurrence of large saccades in a given time T. These predictions may be checked against experimental results.This investigation was supported by National Institutes of Health under Grants Numbers GM 16197-03, GM 16437, and RR-0712-04, by the National Science Foundation under Grant Number GK-1834X, and by the National Aeronautics and Space Administration under Grant Number NGL-05-018-022.R.Vasudevan and J.D. Smith are with the Department of Electrical Engineering, University of Southern California, Los Angeles, California. —R.Vasudevan is on leave of absence from the Institute of Mathematical Sciences, Madras, India.A.V. Phatak is now with Systems Control, Inc. in Palo Alto, California.     

Molecular cloning and functional expression of a novelNeurospora crassa xylose reductase inSaccharomyces cerevisiae in the development of a xylose fermenting strain

The development of a xylose-fermentingSaccharomyces cerevisiae yeast would be of great benefit to the bioethanol industry. The conversion of xylose to ethanol involves a cascade of enzymatic reactions and processes. Xylose (aldose) reductases catalyse the conversion of xylose to xylitol. The aim of this study was to clone, characterise and express a cDNA copy of a novel aldose reductase (NCAR-X) from the filamentous fungusNeurospora crassa inS. cerevisiae. NCAR-X harbours an open reading frame (ORF) of 900 nucleotides. This ORF encodes a protein (NCAR-X, assigned NCBI protein accession ID: XP_956921) consisting of 300 amino acids, with a predicted molecular weight of 34 kDa. TheNCAR-X-encoded aldose reductase showed significant homology to the xylose reductases ofCandida tenuis andPichia stipitis. WhenNCAR-X was expressed under the control of phosphoglycerate kinase I gene (PGK1) regulatory sequences inS. cerevisiae, its expression resulted in the production of biologically active xylose reductase. Small-scale oxygen-limited xylose fermentation with theNCAR-X containingS. cerevisiae strains resulted in the production of less xylitol and at least 15% more ethanol than the strains transformed with theP. stipitis xylose reductase gene (PsXYL1). TheNCAR-X-encoded enzyme produced byS. cerevisiae was NADPH-dependent and no activity was observed in the presence of NADH. The co-expression of theNCAR-X andPsXYL1 gene constructs inS. cerevisiae constituted an important part of an extensive research program aimed at the development of xylolytic yeast strains capable of producing ethanol from plant biomass.     

Molecular dynamics simulations of alpha2 --> 8-linked disialoside: conformational analysis and implications for binding to proteins.

Computational methods have played a key role in elucidating the various three-dimensional structures of oligosaccharides. Such structural information, together with other experimental data, leads to a better understanding of the role of oligosaccharide in various biological processes. The disialoside Neu5Ac-alpha2-->8-Neu5Ac appears as the terminal glycan in glycoproteins and glycolipids, and is known to play an important role in various events of cellular communication. Neurotoxins such as botulinum and tetanus require Neu5Ac-alpha2 --> 8-Neu5Ac for infecting the host. Glycoconjugates containing this disialoside and the enzymes catalyzing their biosynthesis are also regulated during cell growth, development, and differentiation. Unlike other biologically relevant disaccharides that have only two linkage bonds, the alpha2-->8-linked disialoside has four: C2-O, O-C8', C8'-C7', and C7'-C6'. The present report describes the results from nine 1 ns MD simulations of alpha2-->8-linked disialoside (Neu5Ac-alpha2-->8-Neu5Ac); simulations were run using GROMOS96 by explicitly considering the solvent molecules. Conformations around the O-C8' bond are restricted to the +sc/+ap regions due to stereochemical reasons. In contrast, conformations around the C2-O and C8'-C7' bonds were found to be largely unrestricted and all the three staggered regions are accessible. The conformations around the C7'-C6' bond were found to be in either the -sc or the anti region. These results are in excellent agreement with the available NMR and potential energy calculation studies. Overall, the disaccharide is flexible and adopts mainly two ensembles of conformations differing in the conformation around the C7'-C6' bond. The flexibility associated with this disaccharide allows for better optimization of intermolecular contacts while binding to proteins and this may partially compensate for the loss of conformational entropy that may be incurred due to disaccharide's flexibility.     

Biochemical characterization of an E. coli cell division factor FtsE shows ATPase cycles similar to the NBDs of ABC-transporters

The peptidoglycan (PG) layer is an intricate and dynamic component of the bacterial cell wall, which requires a constant balance between its synthesis and hydrolysis. FtsEX complex present on the inner membrane is shown to transduce signals to induce PG hydrolysis. FtsE has sequence similarity with the nucleotide-binding domains (NBDs) of ABC transporters. The NBDs in most of the ABC transporters couple ATP hydrolysis to transport molecules inside or outside the cell. Also, this reaction cycle is driven by the dimerization of NBDs. Though extensive studies have been carried out on the Escherchia coli FtsEX complex, it remains elusive regarding how FtsEX complex helps in signal transduction or transportation of molecules. Also, very little is known about the biochemical properties and ATPase activities of FtsE. Because of its strong interaction with the membrane-bound protein FtsX, FtsE stays insoluble upon overexpression in E. coli, and thus, most studies on E. coli FtsE (FtsE_Ec) in the past have used refolded FtsE. Here in the present paper, for the first time, we report the soluble expression, purification, and biochemical characterization of FtsE from E. coli. The purified soluble FtsE exhibits high thermal stability, exhibits ATPase activity and has more than one ATP-binding site. We have also demonstrated a direct interaction between FtsE and the cytoplasmic loop of FtsX. Together, our findings suggest that during bacterial division, the ATPase cycle of FtsE and its interaction with the FtsX cytoplasmic loop may help to regulate the PG hydrolysis at the mid cell.