H-1, C-13, N-15 assignment and secondary structure determination of glutamine amido transferase subunit of gaunosine monophosphate synthetase from Methanocaldococcus jannaschii

Sequence specific resonance assignments have been obtained for H-1, C-13 and N-15 nuclei of the 21 kDa (188 residues long) glutamine amido transferase subunit of guanosine monophosphate synthetase from Methanocaldococcus jannaschii. From an analysis of H-1 and C-13(alpha), C-13(beta) secondary chemical shifts, (3) JH(N)H(alpha) scalar coupling constants and sequential, short and medium range H-1-H-1 NOEs, it was deduced that the glutamine amido transferase subunit has eleven strands and five helices as the major secondary structural elements in its tertiary structure.

Experimental study of phase equilibria in the system Cu-Al-Sn

Phase equilibria in the Cu-rich corner of the ternary system Cu-Al-Sn have been re-investigated. Final equilibrium microstructures of 20 ternary alloy compositions near Cu3Al were used to refine the ternary phase diagram. The microstructures were characterized using optical microscopy (OM), x-ray diffraction (XRD), electron probe microanalysis and transmission electron microscopy. Isothermal sections at 853, 845, 833, 818, 808, 803 and 773 K have been composed. Vertical sections have been drawn at 2 and 3 at% Sn, showing beta(1) as a stable phase. Three-phase fields (alpha + beta + beta(1)) and (beta + beta(1) + gamma(1)) result from beta -> alpha + beta(1) eutectoid and beta + gamma(1) -> beta(1) peritectoid reactions forming metastable beta(1) in the binary Cu-Al. With the lowering of temperature from 853 to 818 K, these three-phase fields are shifted to lower Sn concentrations, with simultaneous shrinkage and shifting of (beta + beta(1)) two-phase field. The three-phase field (alpha + beta + gamma(1)) resulting from the binary reaction beta -> alpha + gamma(1) shifts to higher Sn contents, with associated shrinkage of the beta field, with decreasing temperature. With further reduction of temperature, a new ternary invariant reaction beta + beta(1) -> alpha + gamma(1) is observed at similar to 813 K. The beta disappears completely at 803 K, giving rise to the three-phase field (alpha + beta(1) + gamma(1)). Some general guidelines on the role of ternary additions (M) on the stability of the ordered beta(1) phase are obtained by comparing the results of this study with data in the literature on other systems in the systems group Cu-Al-M.

Locating the attacker of wormhole attack by using the honeypot

Mobile Ad hoc Networks (MANETs) having strikingly superior features also come with notable disadvantage and troubles and the most exigent amongst all being security related issues. Such an ringent network dexterously pave approach for the malicious nodes. Hence providing security is a tedious task. For such a dynamic environment, a security system which dynamically observes the attacker's plans and protect the highly sophisticated resources is in high demand. In this paper we present a method of providing security against wormhole attacks to a MANET by learning about the environment dynamically and adapting itself to avoid malicious nodes. We accomplish this with the assistance of Honeypot. Our method predicts the wormhole attack that may take place and protect the resources well-in advance. Also it cleverly deal with the attacker by using previous history and different type of messages to locate the attacker. Several experiments suggest that the system is accurate in handling wormhole attack.

Delineating Ecological Boundaries of Hanuman Langur Species Complex in Peninsular India Using MaxEnt Modeling Approach

Hanuman langur is one of the widely distributed and extensively studied non-human diurnal primates in India. Until recently it was believed to be a single species - Semnopithecus entellus. Recent molecular and morphological studies suggest that the Hanuman langurs consists of at least three species S. entellus, S. hypoleucos and S. priam. Furthermore, morphological studies suggested that both S. hypoleucos and S. priam have at least three subspecies in each. We explored the use of ecological niche modeling (ENM) to confirm the validity of these seven taxa and an additional taxon S. johnii belonging to the same genus. MaxEnt modeling tool was used with 19 bioclimatic, 12 vegetation and 6 hydrological environmental layers. We reduced total environmental variables to 14 layers after testing for collinearity and an independent test for model prediction was done using ENMTools. A total of 196 non-overlapping data points from primary and secondary sources were used as inputs for ENM. Results showed eight distinct ecological boundaries, corroborating the eight taxa mentioned above thereby confirming validity of these eight taxa. The study, for the first time provided ecological variables that determined the ecological requirements and distribution of members of the Hanuman langur species complex in the Indian peninsula.

Using intra-flock association patterns to understand why birds participate in mixed-species foraging flocks in terrestrial habitats

Bird species are hypothesized to join mixed-species flocks (flocks hereon) either for direct foraging or anti-predation-related benefits. In this study, conducted in a tropical evergreen forest in the Western Ghats of India, we used intra-flock association patterns to generate a community-wide assessment of flocking benefits for different species. We assumed that individuals needed to be physically proximate to particular heterospecific individuals within flocks to obtain any direct foraging benefit (flushed prey, kleptoparasitism, copying foraging locations). Alternatively, for anti-predation benefits, physical proximity to particular heterospecifics is not required, i.e. just being in the flock vicinity can suffice. Therefore, we used choice of locations within flocks to infer whether individual species are obtaining direct foraging or anti-predation benefits. A small subset of the bird community (5/29 species), composed of all members of the sallying guild, showed non-random physical proximity to heterospecifics within flocks. All preferred associates were from non-sallying guilds, suggesting that the sallying species were likely obtaining direct foraging benefits either in the form of flushed or kleptoparasitized prey. The majority of the species (24/29) chose locations randomly with respect to heterospecifics within flocks and, thus, were likely obtaining antipredation benefits. In summary, our study indicates that direct foraging benefits are important for only a small proportion of species in flocks and that predation is likely to be the main driver of flocking for most participants. Our findings apart, our study provides methodological advances that might be useful in understanding asymmetric interactions in social groups of single and multiple species.

Delineating Ecological Boundaries of Hanuman Langur Species Complex in Peninsular India Using MaxEnt Modeling Approach

Hanuman langur is one of the widely distributed and extensively studied non-human diurnal primates in India. Until recently it was believed to be a single species - Semnopithecus entellus. Recent molecular and morphological studies suggest that the Hanuman langurs consists of at least three species S. entellus, S. hypoleucos and S. priam. Furthermore, morphological studies suggested that both S. hypoleucos and S. priam have at least three subspecies in each. We explored the use of ecological niche modeling (ENM) to confirm the validity of these seven taxa and an additional taxon S. johnii belonging to the same genus. MaxEnt modeling tool was used with 19 bioclimatic, 12 vegetation and 6 hydrological environmental layers. We reduced total environmental variables to 14 layers after testing for collinearity and an independent test for model prediction was done using ENMTools. A total of 196 non-overlapping data points from primary and secondary sources were used as inputs for ENM. Results showed eight distinct ecological boundaries, corroborating the eight taxa mentioned above thereby confirming validity of these eight taxa. The study, for the first time provided ecological variables that determined the ecological requirements and distribution of members of the Hanuman langur species complex in the Indian peninsula.

Response of vertically loaded pile in clay: a probabilistic study

This study presents the response of a vertically loaded pile in undrained clay considering spatially distributed undrained shear strength. The probabilistic study is performed considering undrained shear strength as random variable and the analysis is conducted using random field theory. The inherent soil variability is considered as source of variability and the field is modeled as two dimensional non-Gaussian homogeneous random field. Random field is simulated using Cholesky decomposition technique within the finite difference program and Monte Carlo simulation approach is considered for the probabilistic analysis. The influence of variance and spatial correlation of undrained shear strength on the ultimate capacity as summation of ultimate skin friction and end bearing resistance of pile are examined. It is observed that the coefficient of variation and spatial correlation distance are the most important parameters that affect the pile ultimate capacity.

Asymmetric cell division in Mycobacterium tuberculosis and its unique features

Recently, several reports showed that about 80 % of mid-log phase Mycobacterium smegmatis, Mycobacterium marinum, and Mycobacterium bovis BCG cells divide symmetrically with 5-10 % deviation in the septum position from the median. However, the mode of cell division of the pathogenic mycobacterial species, Mycobacterium tuberculosis, remained unclear. Therefore, in the present study, using electron microscopy, fluorescence microscopy of septum- and nucleoid-stained live and fixed cells, and live cell time-lapse imaging, we show the occurrence of asymmetric cell division with unusually deviated septum/constriction in 20 % of the 15 % septating M. tuberculosis cells in the mid-log phase population. The remaining 80 % of the 15 % septating cells divided symmetrically but with 2-5 % deviation in the septum/constriction position, as reported for M. smegmatis, M. marinum, and M. bovis BCG cells. Both the long and the short portions of the asymmetrically dividing M. tuberculosis cells with unusually deviated septum contained nucleoids, thereby generating viable short and long cells from each asymmetric division. M. tuberculosis short cells were acid fast positive and, like the long cells, further readily underwent growth and division to generate micro-colony, thereby showing that they were neither mini cells, spores nor dormant forms of mycobacteria. The freshly diagnosed pulmonary tuberculosis patients' sputum samples, which are known for the prevalence of oxidative stress conditions, also contained short cells at the same proportion as that in the mid-log phase population. The probable physiological significance of the generation of the short cells through unusually deviated asymmetric cell division is discussed.

Characterising weather patterns associated with fire in a seasonally dry tropical forest in southern India

Anthropogenic fires in seasonally dry tropical forests are a regular occurrence during the dry season. Forest managers in India, who presently follow a fire suppression policy in such forests, would benefit from a system of assessing the potential risk to fire on a particular day. We examined the relationship between weather variables (seasonal rainfall, relative humidity, temperature) and days of fire during the dry seasons of 2004-2010, based on MODIS fire incident data in the seasonally dry tropical forests of Mudumalai in the Western Ghats, southern India. Logistic regression analysis showed that high probabilities of a fire day, indicating successful ignition of litter and grass fuel on the forest floor, were associated with low levels of early dry season rainfall, low daily average relative humidity and high daily average temperatures. These weather conditions are representative of low moisture levels of fine fuels, suggesting that the occurrence of fire is moderated by environmental conditions that reduce the flammability of fine fuels in the dry tropics. We propose a quantitative framework for assessing risk of a fire day to assist forest managers in anticipating fire occurrences in this seasonally dry tropical forest, and possibly for those across South Asia.

How Many Initiator tRNA Genes Does Escherichia coli Need?

Multiple copies of a gene require enhanced investment on the part of the cell and, as such, call for an explanation. The observation that Escherichia coli has four copies of initiator tRNA (tRNA(i)) genes, encoding a special tRNA (tRNA(fMet)) required to start protein synthesis, is puzzling particularly because the cell appears to be unaffected by the removal of one copy. However, the fitness of an organism has both absolute and relative connotations. Thus, we carried out growth competition experiments between E. coli strains that differ in the number of tRNA(i) genes they contain. This has enabled us to uncover an unexpected link between the number of tRNA(i) genes and protein synthesis, nutritional status, and fitness. Wild-type strains with the canonical four tRNA(i) genes are favored in nutrient-rich environments, and those carrying fewer are favored in nutrient-poor environments. Auxotrophs behave as if they have a nutritionally poor internal environment. A heuristic model that links tRNA(i) gene copy number, genetic stress, and growth rate accounts for the findings. Our observations provide strong evidence that natural selection can work through seemingly minor quantitative variations in gene copy number and thereby impact organismal fitness.

HupB, a Nucleoid-Associated Protein of Mycobacterium tuberculosis, Is Modified by Serine/Threonine Protein Kinases In Vivo

HU, a widely conserved bacterial histone-like protein, regulates many genes, including those involved in stress response and virulence. Whereas ample data are available on HU-DNA communication, the knowledge on how HU perceives a signal and transmit it to DNA remains limited. In this study, we identify HupB, the HU homolog of the human pathogen Mycobacterium tuberculosis, as a component of serine/threonine protein kinase (STPK) signaling. HupB is extracted in its native state from the exponentially growing cells of M. tuberculosis H37Ra and is shown to be phosphorylated on both serine and threonine residues. The STPKs capable of modifying HupB are determined in vitro and the residues modified by the STPKs are identified for both in vivo and the in vitro proteins through mass spectrometry. Of the identified phosphosites, Thr(65) and Thr(74) in the DNA-embracing beta-strand of the N-terminal domain of HupB (N-HupB) are shown to be crucial for its interaction with DNA. In addition, Arg(55) is also identified as an important residue for N-HupB-DNA interaction. N-HupB is shown to have a diminished interaction with DNA after phosphorylation. Furthermore, hupB is shown to be maximally expressed during the stationary phase in M. tuberculosis H37Ra, while HupB kinases were found to be constitutively expressed (PknE and PknF) or most abundant during the exponential phase (PknB). In conclusion, HupB, a DNA-binding protein, with an ability to modulate chromatin structure is proposed to work in a growth-phase-dependent manner through its phosphorylation carried out by the mycobacterial STPKs.

Influence of the AgrC-AgrA Complex on the Response Time of Staphylococcus aureus Quorum Sensing

The Staphylococcus aureus agr quorum-sensing system plays a major role in the transition from the persistent to the virulent phenotype. S. aureus agr type I to IV strains are characterized by mutations in the sensor domain of the histidine kinase AgrC and differences in the sequences of the secreted autoinducing peptides (AIP). Here we demonstrate that interactions between the cytosolic domain of AgrC (AgrC(Cyto)) and the response regulator domain of AgrA (AgrA(RR)) dictate the spontaneity of the cellular response to AIP stimuli. The crystal structure of AgrC(Cyto) provided a basis for a mechanistic model of AgrC-AgrA interactions. This model enabled an analysis of the biochemical and biophysical parameters of AgrC-AgrA interactions in the context of the conformational features of the AgrC-AgrA complex. This analysis revealed distinct sequence and conformational features that determine the affinity, specificity, and kinetics of the phosphotransfer reaction. This step, which governs the response time for transcriptional reengineering triggered by an AIP stimulus, is independent of the agr type and similar for agonist and antagonist stimuli. These experimental data could serve as a basis on which to validate simulations of the quorum-sensing response and for strategies that employ the agr quorum-sensing system to combat biofilm formation in S. aureus infections.

Fabrication of back contacts using laser writer and photolithography for inscribing textured solar cells

Semiconductor fabrication process begins with photolithography. Preparing a photo mask is the key process step in photolithography. The photo mask was fabricated by inscribing patterns directly onto a soda lime glass with the help of a laser beam, as it is easily controllable. Laser writer LW405-A was used for preparing the mask in this study. Exposure wavelength of 405 nm was used, with which 1.2 mu m feature size can be written in direct write-mode over the soda lime glass plate. The advantage of using the fabricated mask is that it can be used to design back contacts for thin film Photovoltaic (PV) solar cells. To investigate the process capability of LW405-A, same pattern with different line widths was written on soda lime glass samples at different writing speeds. The pattern was inscribed without proximity effect and stitching errors, which was characterized using optical microscope and field emission scanning electron microscope (FE-SEM). It was proven that writing speed of a mask-writer is decided according to the intended feature size and line width. As the writing speed increases, the edges of the patterns become rougher due to uneven scattering of the laser beam. From the fabricated mask, the solar cell can be developed embedding both the contacts at the bottom layer, to increase the absorption of solar radiation on the top surface effectively by increasing light absorption area.

Structural variations in aromatic 2 pi-electron three-membered rings of the main group elements

Structural variations of different Z pi-aromatic three-membered ring systems of main group elements, especially group 14 and 13 elements as compared to the classical description of cyclopropenyl cation has been reviewed in this article. The structures of heavier analogues as well as group 13 analogues of cyclopropenyl cation showed an emergence of dramatic structural patterns which do not conform, to the general norms of carbon chemistry. Isolobal analogies between the main group fragments have been efficiently used to explain the peculiarities observed in these three-membered ring systems.

Inner Bound on the GDOF of the K-User MIMO Gaussian Symmetric Interference Channel

The K-user multiple input multiple output (MIMO) Gaussian symmetric interference channel where each transmitter has M antennas and each receiver has N antennas is studied from a generalized degrees of freedom (GDOF) perspective. An inner bound on the GDOF is derived using a combination of techniques such as treating interference as noise, zero forcing (ZF) at the receivers, interference alignment (IA), and extending the Han-Kobayashi (HK) scheme to K users, as a function of the number of antennas and the log INR/log SNR level. Several interesting conclusions are drawn from the derived bounds. It is shown that when K > N/M + 1, a combination of the HK and IA schemes performs the best among the schemes considered. When N/M < K <= N/M + 1, the HK-scheme outperforms other schemes and is found to be GDOF optimal in many cases. In addition, when the SNR and INR are at the same level, ZF-receiving and the HK-scheme have the same GDOF performance.