A two step approach for semi-automated particle selection from low contrast cryo-electron micrographs

Over recent years advances in cryo-electron microscopy for the study of macromolecular structure have resulted in resolutions in the range 10-15 A becoming routine. With this drive for increased resolution comes the need to collect larger datasets, commonly >10,000 particle images. Manual selection of particles from micrographs is often difficult and with such large numbers of particles now involved it is also laborious and a common bottleneck. Automated methods do exist but are normally restricted to specific samples or data, i.e., spherical particles, no aggregation, high contrast, and low noise. A two step approach has been developed that remains general and can be applied to low contrast, high noise micrographs of small molecules. Specifically, application of the approach is presented using micrographs of Escherichia coli RNA polymerase, which due to low contrast and the relatively small size of the molecule prove difficult to pick manually. To test the automated approach, independent reconstructions of RNA polymerase were carried out using manual and automatically picked data. The two reconstructions are shown to be comparable and the reconstruction from the automatically picked dataset is at a higher resolution, due to an increase in the number of particles picked.     

A new method for three-dimensional otolith analysis

The three-dimensional (3-D) shape and density distribution of a cod otolith was determined using a newly developed micro X-ray tomograph. The technique requires no special treatment of the otolith and could yield the entire 3-D growth history in a single analysis. 999 The Fisheries Society of the British Isles     

Animal models of spinal cord contusion injuries.

BACKGROUND AND PURPOSE: Traumatic spinal cord injury causes initial mechanical disruption of tissue, leading to a complex secondary sequence of pathophysiologic changes and neurologic impairment. These sequelae depend on the impact force delivered to the spinal cord at the time of injury. Successful clinical evaluation of the efficacy of any therapeutic regimen depends on the reliability and reproducibility of an experimental animal model. We describe a trauma device and the biomechanical parameters required to induce severe or moderate spinal cord contusion injury in cats and rats. METHODS: Recovery after injury was determined by behavioral, electrophysiologic, and histologic evaluations. RESULTS: Behavioral and electrophysiologic tests after injury clearly identified the experimental groups. A stable severe paraplegic state (defined as 6 months for cats and 8 weeks for rats), without evidence of behavioral or electrophysiologic recovery, was induced by a 65-Newton (N) load for cats and a 35-N load for rats. Moderate spinal cord contusion injury, from which cats and rats partially recovered after approximately 3 months and 4 weeks, respectively, was induced by a 45- and 25-N load, respectively. CONCLUSION: Use of these injury conditions provides reliable animal models for studies designed to evaluate potential therapeutic regimens for spinal cord injury.     

Purification and properties of polyphenoloxidase of mango peel (Mangifera indica)

Polyphenoloxidase from mango(Mangifera indica) peel was purified to homogeneity by ammonium sulphate fractionation, chromatography on DEAE-Sephadex and gel filtration of Sephadex G-200. The enzyme had an apparent molecular weight of 136,000. Its pH and temperature optimum were 5.4 and 50‡C, respectively. The enzyme possessed catecholase activity and was specific too-dihydroxy phenols. The enzyme also exhibited peroxidase activity. Some non-oxidizable phenolic compounds inhibited the enzyme competitively. High inhibitory effects were also shown by some metal chelators and reducing agents, Mango peel polyphenol oxidase when immobilized onto DEAE Sephadex showed slightly higher Km for catechol and lower pH and temperature optima.     

Natural products drug discovery: accelerating the clinical candidate development using reverse pharmacology approaches

The pharmaceutical industry is facing serious challenges as the drug discovery process is becoming extremely expensive, riskier and critically inefficient. A significant shift from single to multi targeted drugs especially for polygenic syndromes is being witnessed. Strategic options based on natural product drug discovery, ethnopharmacology and traditional medicines are re-emerging to offer good base as an attractive discovery engine. Approaches based on reverse pharmacology may offer efficient development platforms for herbal formulations. Relevant case studies from India and other countries where such approaches have expedited the drug discovery and development process by reducing time and economizing investments with better safety are discussed.     

Reaction of adenosylcobalamin-dependent glutamate mutase with 2-thiolglutarate

We have investigated the reaction of glutamate mutase with the glutamate analogue, 2-thiolglutarate. In the standard assay, 2-thiolglutarate behaves as a competitive inhibitor with a Ki of 0.05 mM. However, rather than simply binding inertly at the active site, 2-thiolglutarate elicits cobalt-carbon bond homolysis and the formation of 5'-deoxyadenosine. The enzyme exhibits a complicated EPR spectrum in the presence of 2-thiolglutarate that is markedly different from any previously observed with the enzyme. The spectrum was simulated well by assuming that it arises from electron-electron spin coupling between a thioglycolyl radical and low-spin Co2+ in cob(II)alamin. Analysis of the zero-field splitting parameters obtained from the simulations places the organic radical approximately 10 A from the cobalt and at a tilt angle of approximately 70 degrees to the normal of the corrin ring. This orientation is in good agreement with that expected from the crystal structure of glutamate mutase complexed with the substrate. 2-Thiolglutarate appears to react in a manner analogous to that of glutamate by first forming a thiolglutaryl radical at C-4 that then undergoes fragmentation to produce acrylate and the sulfur-stabilized thioglycolyl radical. The thioglycolyl radical accumulates on the enzyme, suggesting it is too stable to undergo further steps in the mechanism at a detectable rate.     

Fed-batch cultivation of Wautersia eutropha

Batch kinetics of polyhydroxybutyrate (PHB) synthesis in a bioreactor under controlled conditions of pH and dissolved oxygen gave a biomass of 14 g l(-1) with a PHB concentration of 6.1 g l(-1) in 60 h. The data of the batch kinetics was used to develop a mathematical model, which was then extrapolated to fed-batch by incorporating the dilution due to substrate feeding. Offline computer simulation of the fed-batch model was done to develop the nutrient feeding strategies in the fed-batch cultivation. Fed-batch strategies with constant feeding of only nitrogen and constant feeding of both nitrogen and fructose were tried. Constant feeding strategy for nitrogen and fructose gave a better PHB production rate of 0.56 g h(-1) over the value obtained in batch cultivation (PHB production rate - 0.4 g h(-1)).     

Factors affecting the development of the perithecial stage of powdery mildew of Helianthus annuus l. in India

Summary This is the first record of the perithecial state ofSphaerotheca fuliginea onHelianthus annuus L. from India. The perithecial state is collected in the dry cool weather but is absent in wet monsoon season due to the mildew being parasitizing by the hyperparasite,Ampelomyces sp., which thus, appears to influence the development of the perfect state in this mildew.     

Maximizing productivity of a continuous fermenter using nonlinear adaptive optimizing control

The control of a continuously operated fermenter at its maximum productivity level gives rise to a difficult control problem as the location of the optimum operating point changes due to the disturbances. In addition, the fermenter exhibits a change in the sign of the steady state gain near the optimum operating point. This study is aimed at developing an on-line optimizing control scheme that can track the changing location of the steady state optimum so as to maximize the fermenter productivity. A nonlinear Laguerre model, whose parameters are estimated on-line, is used for tracking the optimum operating point. The control at the optimum point is achieved using an adaptive nonlinear MPC strategy that uses the nonlinear Laguerre model for prediction. The efficiency of the proposed algorithm is demonstrated by simulating the control of a continuous fermenter that exhibits shift in the location of the optimum operating point in response to the changes in the maximum specific growth rate. The proposed on-line optimizing control strategy is shown to result in a considerable improvement in the closed loop performance even in the presence of measurement noise.