Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis

Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP) dependent enzyme that catalyses degradation of D-Ser to pyruvate and ammonia. The first crystal structure of D-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase beta subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild-type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the cofactor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modelling suggests that Thr166 may be involved in abstraction of proton from the C alpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses a, b elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.

Understanding the building-up process of three dimensional open-framework metal phosphates: Acid degradation of the 3D structures to lower dimensional structures

Acid degradation of 3D zinc phosphates primarily yields a one-dimensional ladder compound, an observation that is significant considering that the latter forms 3D structures on heating in water.

Geographic Resources Decision Support System – an Open Source GIS

Fully structured and matured open source spatial and temporal analysis technology seems to be the official carrier of the future for planning of the natural resources especially in the developing nations. This technology has gained enormous momentum because of technical superiority, affordability and ability to join expertise from all sections of the society. Sustainable development of a region depends on the integrated planning approaches adopted in decision making which requires timely and accurate spatial data. With the increased developmental programmes, the need for appropriate decision support system has increased in order to analyse and visualise the decisions associated with spatial and temporal aspects of natural resources. In this regard Geographic Information System (GIS) along with remote sensing data support the applications that involve spatial and temporal analysis on digital thematic maps and the remotely sensed images. Open source GIS would help in wide scale applications involving decisions at various hierarchical levels (for example from village panchayat to planning commission) on economic viability, social acceptance apart from technical feasibility. GRASS (Geographic Resources Analysis Support System, http://wgbis.ces.iisc.ernet.in/grass) is an open source GIS that works on Linux platform (freeware), but most of the applications are in command line argument, necessitating a user friendly and cost effective graphical user interface (GUI). Keeping these aspects in mind, Geographic Resources Decision Support System (GRDSS) has been developed with functionality such as raster, topological vector, image processing, statistical analysis, geographical analysis, graphics production, etc. This operates through a GUI developed in Tcltk (Tool command language / Tool kit) under Linux as well as with a shell in X-Windows. GRDSS include options such as Import /Export of different data formats, Display, Digital Image processing, Map editing, Raster Analysis, Vector Analysis, Point Analysis, Spatial Query, which are required for regional planning such as watershed Analysis, Landscape Analysis etc. This is customised to Indian context with an option to extract individual band from the IRS (Indian Remote Sensing Satellites) data, which is in BIL (Band Interleaved by Lines) format. The integration of PostgreSQL (a freeware) in GRDSS aids as an efficient database management system.

Open source drug discovery- A new paradigm of collaborative research in tuberculosis drug development

It is being realized that the traditional closed-door and market driven approaches for drug discovery may not be the best suited model for the diseases of the developing world such as tuberculosis and malaria, because most patients suffering from these diseases have poor paying capacity. To ensure that new drugs are created for patients suffering from these diseases, it is necessary to formulate an alternate paradigm of drug discovery process. The current model constrained by limitations for collaboration and for sharing of resources with confidentiality hampers the opportunities for bringing expertise from diverse fields. These limitations hinder the possibilities of lowering the cost of drug discovery. The Open Source Drug Discovery project initiated by Council of Scientific and Industrial Research, India has adopted an open source model to power wide participation across geographical borders. Open Source Drug Discovery emphasizes integrative science through collaboration, open-sharing, taking up multi-faceted approaches and accruing benefits from advances on different fronts of new drug discovery. Because the open source model is based on community participation, it has the potential to self-sustain continuous development by generating a storehouse of alternatives towards continued pursuit for new drug discovery. Since the inventions are community generated, the new chemical entities developed by Open Source Drug Discovery will be taken up for clinical trial in a non-exclusive manner by participation of multiple companies with majority funding from Open Source Drug Discovery. This will ensure availability of drugs through a lower cost community driven drug discovery process for diseases afflicting people with poor paying capacity. Hopefully what LINUX the World Wide Web have done for the information technology, Open Source Drug Discovery will do for drug discovery. (C) 2011 Elsevier Ltd. All rights reserved.

Fast Direct Torque Control of an Open-End Induction Motor Drive Using 12-Sided Polygonal Voltage Space Vectors

A torque control scheme, based on a direct torque control (DTC) algorithm using a 12-sided polygonal voltage space vector, is proposed for a variable speed control of an open-end induction motor drive. The conventional DTC scheme uses a stator flux vector for the sector identification and then the switching vector to control stator flux and torque. However, the proposed DTC scheme selects switching vectors based on the sector information of the estimated fundamental stator voltage vector and its relative position with respect to the stator flux vector. The fundamental stator voltage estimation is based on the steady-state model of IM and the synchronous frequency of operation is derived from the computed stator flux using a low-pass filter technique. The proposed DTC scheme utilizes the exact positions of the fundamental stator voltage vector and stator flux vector to select the optimal switching vector for fast control of torque with small variation of stator flux within the hysteresis band. The present DTC scheme allows full load torque control with fast transient response to very low speeds of operation, with reduced switching frequency variation. Extensive experimental results are presented to show the fast torque control for speed of operation from zero to rated.

Federated Search Service for OAI-compliant, Open-Access Repositories in India

Many of the research institutions and universities across the world are facilitating open-access (OA) to their intellectual outputs through their respective OA institutional repositories (IRs) or through the centralized subject-based repositories. The registry of open access repositories (ROAR) lists more than 2850 such repositories across the world. The awareness about the benefits of OA to scholarly literature and OA publishing is picking up in India, too. As per the ROAR statistics, to date, there are more than 90 OA repositories in the country. India is doing particularly well in publishing open-access journals (OAJ). As per the directory of open-access journals (DOAJ), to date, India with 390 OAJs, is ranked 5th in the world in terms of numbers of OAJs being published. Much of the research done in India is reported in the journals published from India. These journals have limited readership and many of them are not being indexed by Web of Science, Scopus or other leading international abstracting and indexing databases. Consequently, research done in the country gets hidden not only from the fellow countrymen, but also from the international community. This situation can be easily overcome if all the researchers facilitate OA to their publications. One of the easiest ways to facilitate OA to scientific literature is through the institutional repositories. If every research institution and university in India set up an open-access IR and ensure that copies of the final accepted versions of all the research publications are uploaded in the IRs, then the research done in India will get far better visibility. The federation of metadata from all the distributed, interoperable OA repositories in the country will serve as a window to the research done across the country. Federation of metadata from the distributed OAI-compliant repositories can be easily achieved by setting up harvesting software like the PKP Harvester. In this paper, we share our experience in setting up a prototype metadata harvesting service using the PKP harvesting software for the OAI-compliant repositories in India.

Tar characterisation in new generation agro-residue gasifiers - Cyclone and downdraft open top twin air entry systems

This paper deals with the characterisation of tar from two configurations of bioresidue thermochemical conversion reactors designed for producer gas based power generation systems. The pulverised fuel reactor is a cyclone system (R1) and the solid bioresidue reactor (denoted R2) is an open top twin air entry system both at 75-90 kg/h capacity (to generate electricity similar to 100 kVA). The reactor, R2, has undergone rigorous test in a major Indo-Swiss programme for the tar quantity at various conditions. The former is a recent technology development. Tars collected from these systems by a standard tar collection apparatus at the laboratory at Indian Institute of Science have been analysed at the Royal Institute of Technology (KTH), Sweden. The results of these analyses show that these thermochemical conversion reactors behave differently from the earlier reactors reported in literature in so far as tar generation is concerned. The extent of tar in hot gas is about 700-800 ppm for R1 and 70-100 ppm for R2. The amounts of the major compounds - naphthalene and phenol-are much lower that what is generally understood to happen in the gasifiers in Europe. It is suggested that the longer residence times at high temperatures allowed for in these reactors is responsible for this behavior. It is concluded the new generation reactor concepts extensively tried out at lower power levels hold promise for high power atmospheric gasification systems for woody as well as pulverisable bioresidues.

Five-level inverter voltage-space phasor generation for an open-end winding induction motor drive

A topology for voltage-space phasor generation equivalent to a five-level inverter for an open-end winding induction motor is presented. The open-end winding induction motor is fed from both ends by two three-level inverters. The three-level inverters are realised by cascading two two-level inverters. This inverter scheme does not experience neutral-point fluctuations. Of the two three-level inverters only one will be switching at any instant in the lower speed ranges. In the multilevel carrier-based SPWM used for the proposed drive, a progressive discrete DC bias depending on the speed range is given to the reference wave to reduce the inverter switchings. The drive is implemented and tested with a 1 HP open-end winding induction motor and experimental results are presented.

Self Repair in Circuits-Automating Open Fault Repair in Integrated Circuits Using Field-Induced Aggregation of Carbon Nanotubes

This paper presents studies on the use of carbon nanotubes dispersed in an insulating fluid to serve as an automaton for healing open-circuit interconnect faults in integrated circuits. The physics behind the repair mechanism is the electric-field-induced diffusion limited aggregation. On the occurrence of an open fault, the repair is automatically triggered due to the presence of an electric field across the gap. We perform studies on the repair time as a function of the electric field and dispersion concentrations with the above application in mind.

Novel tetranuclear distorted open-cubane copper complex containing oximate bridges: Synthesis, crystal structure, DNA binding and cleavage activity

The synthesis, molecular structure, DNA binding and nuclease activity of Cu4O4 open-cubane tetranuclear copper(II) complex with 3-2-(ethyl amino)ethyl]imino]-2-butanoneoxime (HL) are reported for the first time. The neutral tetranuclear Cu4L4(ClO4)(4)] complex crystallizes in tetragonal space group P (4) over bar2(1)c with the unit cell parameters; a = 13.798(4) angstrom, b = 13.798(4) angstrom, c = 14.119(6) angstrom, V = 2688(16) angstrom(3), Z = 8, R = 0.0636. Symmetrically equivalent copper atoms exhibit a CuN3O3 elongated distorted octahedral coordination environment, with three nitrogen atoms of the L ligand and one oxime-oxygen atom of second L ligand at equatorial positions, one oxime-oxygen atom of the third L ligand and perchlorate oxygen at axial positions. The complex shows quasireversible cyclic voltammetric response at 0.805 V (Delta E-p = 277 mV) at 100 mV s (1) in DMF for the Cu(II)/Cu(I) redox couple. The binding study of the complex with calf-thymus DNA has been investigated using absorption spectrophotometry. The complex shows strong nuclease activity on stranded pBR 322 plasmid DNA in the presence of hydrogen peroxide and marginal nuclease activity in the presence of reducing agent (dithiothreitol). (C) 2012 Elsevier B. V. All rights reserved.

Self-Assembled Pd6 Open Cage with Triimidazole Walls and the Use of Its Confined Nanospace for Catalytic Knoevenagel- and Diels-Alder Reactions in Aqueous Medium

The two-component self-assembly of a 90 degrees PdII acceptor and a triimidazole donor led to the formation of a water-soluble semi-cylindrical cage with a hydrophobic cavity, which was separately crystallized with hydrophilic- and hydrophobic guests. The parent cage was found to catalyze the Knoevenagel condensation reaction of a series of aromatic mono-aldehydes with active methylene compounds, such as Meldrum's acid or 1,3-dimethylbarbituric acid. The confined hydrophobic nanospace within this cage was also used in the catalytic DielsAlder reactions of 9-hydroxymethylanthracene with N-phenylmaleimide or N-cyclohexylmaleimide.