The PE and PPE proteins of Mycobacterium tuberculosis

India already has earned the dubious distinction of being one of the countries with the highest incidence of tuberculosis (TB). The conventional control measures have had little impact on the relentless march of the TB epidemic. Potential solutions to this problem include the development of new drugs and an effective TB vaccine. In this perspective, identification of the mycobacterial components that have important role(s) in the establishment of the infection assumes crucial importance. Mycobacterium tuberculosis is an intracellular pathogen and it resides inside the macrophage, which is considered to be the most important component of the immune system. M. tuberculosis possesses two highly polymorphic sets of genes called the PE and PPE families. These unique families of proteins account for about 10% of the mycobacterial genome and have drawn considerable interest from different schools of M. tuberculosis researchers across the globe. In this review, we discuss the importance of these proteins in the regulation of dendritic cell and macrophage immune-effector functions, as well as the relevance of these proteins in the clinical manifestation of TB. This information may be helpful to better understand the immunological importance of PE/PPE proteins and their roles in mycobacterial virulence. (C) 2011 Elsevier Ltd. All rights reserved.

Structural biology of Mycobacterium tuberculosis proteins: The Indian efforts

Among the many different objectives of large scale structural genomics projects are expanding the protein fold space, enhancing understanding of a model or disease-related organism, and providing foundations for structure-based drug discovery. Systematic analysis of protein structures of Mycobacterium tuberculosis has been ongoing towards meeting some of these objectives. Indian participation in these efforts has been enthusiastic and substantial. The proteins of M. tuberculosis chosen for structural analysis by the Indian groups span almost all the functional categories. The structures determined by the Indian groups have led to significant improvement in the biochemical knowledge on these proteins and consequently have started providing useful insights into the biology of M. tuberculosis. Moreover, these structures form starting points for inhibitor design studies, early results of which are encouraging. The progress made by Indian structural biologists in determining structures of M. tuberculosis proteins is highlighted in this review. (C) 2011 Elsevier Ltd. All rights reserved.

Optimal Exact-Regenerating Codes for Distributed Storage at the MSR and MBR Points via a Product-Matrix Construction

Regenerating codes are a class of distributed storage codes that allow for efficient repair of failed nodes, as compared to traditional erasure codes. An [n, k, d] regenerating code permits the data to be recovered by connecting to any k of the n nodes in the network, while requiring that a failed node be repaired by connecting to any d nodes. The amount of data downloaded for repair is typically much smaller than the size of the source data. Previous constructions of exact-regenerating codes have been confined to the case n = d + 1. In this paper, we present optimal, explicit constructions of (a) Minimum Bandwidth Regenerating (MBR) codes for all values of [n, k, d] and (b) Minimum Storage Regenerating (MSR) codes for all [n, k, d >= 2k - 2], using a new product-matrix framework. The product-matrix framework is also shown to significantly simplify system operation. To the best of our knowledge, these are the first constructions of exact-regenerating codes that allow the number n of nodes in the network, to be chosen independent of the other parameters. The paper also contains a simpler description, in the product-matrix framework, of a previously constructed MSR code with [n = d + 1, k, d >= 2k - 1].

Stability of domain structures in multi-domain proteins

Multi-domain proteins have many advantages with respect to stability and folding inside cells. Here we attempt to understand the intricate relationship between the domain-domain interactions and the stability of domains in isolation. We provide quantitative treatment and proof for prevailing intuitive ideas on the strategies employed by nature to stabilize otherwise unstable domains. We find that domains incapable of independent stability are stabilized by favourable interactions with tethered domains in the multi-domain context. Stability of such folds to exist independently is optimized by evolution. Specific residue mutations in the sites equivalent to inter-domain interface enhance the overall solvation, thereby stabilizing these domain folds independently. A few naturally occurring variants at these sites alter communication between domains and affect stability leading to disease manifestation. Our analysis provides safe guidelines for mutagenesis which have attractive applications in obtaining stable fragments and domain constructs essential for structural studies by crystallography and NMR.

Long term stability studies of particle storage rings using polynomial Maps

Long-term stability studies of particle storage rings can not be carried out using conventional numerical integration algorithms. We require symplectic integration algorithms which are both fast and accurate. In this paper, we study a symplectic integration method wherein the sym-plectic map representing the Hamiltonian system is refactorized using polynomial symplectic maps. This method is used to perform long term integration on a particle storage ring.

V(2)O(5)-Anchored Carbon Nanotubes for Enhanced Electrochemical Energy Storage

Functionalized multiwalled carbon nanotubes (CNTs) are coated with a 4-5 nm thin layer of V(2)O(5) by controlled hydrolysis of vanadium alkoxide. The resulting V(2)O(5)/CNT composite has been investigated for electrochemical activity with lithium ion, and the capacity value shows both faradaic and capacitive (nonfaradaic) contributions. At high rate (1 C), the capacitive behavior dominates the intercalation as 2/3 of the overall capacity value out of 2700 C/g is capacitive, while the remaining is due to Li-ion intercalation. These numbers are in agreement with the Trasatti plots and are corroborated by X-ray photoelectron spectroscopy (XPS) studies on the V(2)O(5)/CNTs electrode, which show 85% of vanadium in the +4 oxidation state after the discharge at 1 C rate. The cumulative high-capacity value is attributed to the unique property of the nano V(2)O(5)/CNTs composite, which provides a short diffusion path for Lit-ions and an easy access to vanadium redox centers besides the high conductivity of CNTs. The composite architecture exhibits both high power density and high energy density, stressing the benefits of using carbon substrates to design high performance supercapacitor electrodes.

Scalable processes for fabricating non-volatile memory devices using self-assembled 2D arrays of gold nanoparticles as charge storage nodes

We propose robust and scalable processes for the fabrication of floating gate devices using ordered arrays of 7 nm size gold nanoparticles as charge storage nodes. The proposed strategy can be readily adapted for fabricating next generation (sub-20 nm node) non-volatile memory devices.

Investigating Diproline Segments in Proteins: Occurrences, Conformation and Classification

The covalent linkage between the side-chain and the backbone nitrogen atom of proline leads to the formation of the five-membered pyrrolidine ring and hence restriction of the backbone torsional angle phi to values of -60 degrees +/- 30 degrees for the L-proline. Diproline segments constitute a chain fragment with considerably reduced conformational choices. In the current study, the conformational states for the diproline segment ((L)Pro-(L)Pro) found in proteins has been investigated with an emphasis on the cis and trans states for the Pro-Pro peptide bond. The occurrence of diproline segments in turns and other secondary structures has been studied and compared to that of Xaa-Pro-Yaa segments in proteins which gives us a better understanding on the restriction imposed on other residues by the diproline segment and the single proline residue. The study indicates that P(II)-P(II) and P(II)-alpha are the most favorable conformational states for the diproline segment. The analysis on Xaa-Pro-Yaa sequences reveals that the XaaPro peptide bond exists preferably as the trans conformer rather than the cis conformer. The present study may lead to a better understanding of the behavior of proline occurring in diproline segments which can facilitate various designed diproline-based synthetic templates for biological and structural studies. (C) 2011 Wiley Periodicals, Inc. Biopolymers 97: 54-64, 2012.

Filling Characteristics for an Activated Carbon Based Adsorbed Natural Gas Storage System

The storage capacity of an activated carbon bed is studied using a 2D transport model with constant inlet flow conditions. The predicted filling times and variation in bed pressure and temperature are in good agreement with experimental observations obtained using a 1.82 L prototype ANG storage cylinder. Storage efficiencies based on the maximum achievable V/V (volume of gas/volume of container) and filling times are used to quantify the performance of the charging process. For the high permeability beds used in the experiments, storage efficiencies are controlled by the rate of heat removal. Filling times, defined as the time at which the bed pressure reaches 3.5 MPa, range from 120 to 3.4 min for inlet flow rates of 1.0 L min(-1) and 30.0 L min(-1), respectively. The corresponding storage efficiencies, eta(s), vary from 90% to 76%, respectively. Simulations with L/D ratios ranging from 0.35 to 7.8 indicate that the storage efficiencies can be improved with an increase in the LID ratios and/or with water cooled convection. Thus for an inlet flow rate of 30.0 L min(-1), an eta(s) value of 90% can be obtained with water cooling for an L/D ratio of 7.8 and a filling time of a few minutes. In the absence of water cooling the eta(s) value reduces to 83% at the same L/D ratio. Our study suggests that with an appropriate choice of cylinder dimensions, solutions based on convective cooling during adsorptive storage are possible with some compromise in the storage capacity.

Enhancement of charge and energy storage in sol-gel derived pure and La-modified PbZrO3 thin films

Antiferroelectric lanthanum-modified PbZrO3 thin films with La contents between 0 and 6 at. % have been deposited on Pt(111)/Ti/SiO2/Si substrate by sol-gel route. On the extent of La-modification, maximum polarization (Pmax) and recoverable energy density (W) have been enhanced followed by their subsequent reduction. A maximum Pmax ( ∼ 0.54 C/m2 at ∼ 60 MV/m) as well as a maximum W ( ∼ 14.9 J/cc at ∼ 60 MV/m) have been achieved on 5% La modification. Both Pmax and W have been found to be strongly dependent on La-induced crystallographic orientations.