Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: Insights into structure and function

The availability of the genome sequence of Mycobacterium tuberculosis H37Rv has encouraged determination of large numbers of protein structures and detailed definition of the biological information encoded therein; yet, the functions of many proteins in M. tuberculosis remain unknown. The emergence of multidrug resistant strains makes it a priority to exploit recent advances in homology recognition and structure prediction to re-analyse its gene products. Here we report the structural and functional characterization of gene products encoded in the M. tuberculosis genome, with the help of sensitive profile-based remote homology search and fold recognition algorithms resulting in an enhanced annotation of the proteome where 95% of the M. tuberculosis proteins were identified wholly or partly with information on structure or function. New information includes association of 244 proteins with 205 domain families and a separate set of new association of folds to 64 proteins. Extending structural information across uncharacterized protein families represented in the M. tuberculosis proteome, by determining superfamily relationships between families of known and unknown structures, has contributed to an enhancement in the knowledge of structural content. In retrospect, such superfamily relationships have facilitated recognition of probable structure and/or function for several uncharacterized protein families, eventually aiding recognition of probable functions for homologous proteins corresponding to such families. Gene products unique to mycobacteria for which no functions could be identified are 183. Of these 18 were determined to be M. tuberculosis specific. Such pathogen-specific proteins are speculated to harbour virulence factors required for pathogenesis. A re-annotated proteome of M. tuberculosis, with greater completeness of annotated proteins and domain assigned regions, provides a valuable basis for experimental endeavours designed to obtain a better understanding of pathogenesis and to accelerate the process of drug target discovery. (C) 2014 Elsevier Ltd. All rights reserved.

Estimates of site response based on spectral ratio between horizontal and vertical components of ambient vibrations in the source zone of 2001 Bhuj earthquake

We investigated the site response characteristics of Kachchh rift basin over the meizoseismal area of the 2001, Mw 7.6, Bhuj (NW India) earthquake using the spectral ratio of the horizontal and vertical components of ambient vibrations. Using the available knowledge on the regional geology of Kachchh and well documented ground responses from the earthquake, we evaluated the H/V curves pattern across sediment filled valleys and uplifted areas generally characterized by weathered sandstones. Although our HIV curves showed a largely fuzzy nature, we found that the hierarchical clustering method was useful for comparing large numbers of response curves and identifying the areas with similar responses. Broad and plateau shaped peaks of a cluster of curves within the valley region suggests the possibility of basin effects within valley. Fundamental resonance frequencies (f(0)) are found in the narrow range of 0.1-2.3 Hz and their spatial distribution demarcated the uplifted regions from the valleys. In contrary, low HIV peak amplitudes (A(0) = 2-4) were observed on the uplifted areas and varying values (2-9) were found within valleys. Compared to the amplification factors, the liquefaction indices (kg) were able to effectively indicate the areas which experienced severe liquefaction. The amplification ranges obtained in the current study were found to be comparable to those obtained from earthquake data for a limited number of seismic stations located on uplifted areas; however the values on the valley region may not reflect their true amplification potential due to basin effects. Our study highlights the practical usefulness as well as limitations of the HIV method to study complex geological settings as Kachchh. (C) 2014 Elsevier Ltd. All rights reserved.

Crystal Structure and Prediction

The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

Differential proteomic and genomic profiling of mouse striatal cell model of Huntington's disease and control; probable implications to the disease biology

Huntington's disease (HD) is an autosomal dominant disorder of central nervous system caused by expansion of CAG repeats in exon1 of the huntingtin gene (Htt). Among various dysfunctions originated from the mutation in Htt gene, transcriptional deregulation has been considered to be one of the most important abnormalities. Large numbers of investigations identified altered expressions of genes in brains of HD patients and many models of HD. In this study we employed 2D SDS-PAGE/MALDI-MS coupled with 2D-DIGE and real-time PCR experiments of an array of genes focused to HD pathway to determine altered protein and gene expressions in STHdh(Q111)/Hdh(Q111) cells, a cell model of HD and compared with STHdh(Q7)/Hdh(Q7) cells, its wild type counterpart. We annotated 76 proteins from these cells and observed differential expressions of 31 proteins (by 2D-DIGE) involved in processes like unfolded protein binding, negative regulation of neuron apoptosis, response to superoxides etc. Our PCR array experiments identified altered expressions of 47 genes. Altogether significant alteration of 77 genes/proteins could be identified in this HD cell line with potential relevance to HD biology. Biological significance: In this study we intended to find out differential proteomic and genomic profiles in HD condition. We used the STHdh cells, a cellular model for HD and control. These are mouse striatal neuronal cell lines harboring 7 and 111 knock -in CAG repeats in their two alleles. The 111Q containing cell line (STHdh(Q111)/Hdh(Q111)) mimics diseased condition, whereas the 7Q containing ones (STHdh(Q7)/Hdh(Q7)), serves as the proper control cell line. Proteomic experiments were performed earlier to obtain differential expressions of proteins in R6/2 mice models, Hdh(Q) knock -in mice and in plasma and CSF from HD patients. However, no earlier report on proteomic alterations in these two HD cell lines and control was available in literature. It was, therefore, an important objective to find out differential expressions of proteins in these two cell lines. In this study, we annotated 76 proteins from STHdh(Q7)/Hdh(Q7) and STHdh(Q111)/Hdh(Q111) cells using 2D-gel/mass spectrometry. Next, by performing 2D-DIGE, we observed differential expressions of 31 proteins (16 upregulated and 15 downregulated) between these two cell lines. We also performed customized qRT-PCR array focused to HD pathway and found differential expressions of 47 genes (8 gene exptessions increased and 39 genes were decreased significantly). A total of 77 genes/proteins (Htt downregulated in both the studies) were found to be significantly altered from both the experimental paradigms. We validated the differential expressions of Vim, Hypk, Ran, Dstn, Hspa5 and Sod2 either by qRT-PCR or Western blot analysis or both. Out of these 77, similar trends in alteration of 19 out of 31 and 38 out of 47 proteins/genes were reported in earlier studies. Thus our study confirmed earlier observations on differential gene/protein expressions in HD and are really useful. Additionally, we observed differential expression of some novel genes/proteins. One of this was Hypk, a Htt-interacting chaperone protein with the ability to solubilize mHtt aggregated structures in cell lines. We propose that downregulation of Hypk in STHdh-Qm (Q111)/Hdh(Q111) has a causal effect towards HD pathogenesis. Thus the novel findings from our study need further research and might be helpful to understand the molecular mechanism behind HD pathogenesis. (C) 2015 Elsevier B.V. All rights reserved.

Framework for morphometric classification of cells in imaging flow cytometry

Imaging flow cytometry is an emerging technology that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy. It allows high-throughput imaging of cells with good spatial resolution, while they are in flow. This paper proposes a general framework for the processing/classification of cells imaged using imaging flow cytometer. Each cell is localized by finding an accurate cell contour. Then, features reflecting cell size, circularity and complexity are extracted for the classification using SVM. Unlike the conventional iterative, semi-automatic segmentation algorithms such as active contour, we propose a noniterative, fully automatic graph-based cell localization. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using custom fabricated cost-effective microfluidics-based imaging flow cytometer. The proposed system is a significant development in the direction of building a cost-effective cell analysis platform that would facilitate affordable mass screening camps looking cellular morphology for disease diagnosis. Lay description In this article, we propose a novel framework for processing the raw data generated using microfluidics based imaging flow cytometers. Microfluidics microscopy or microfluidics based imaging flow cytometry (mIFC) is a recent microscopy paradigm, that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy, which allows us imaging cells while they are in flow. In comparison to the conventional slide-based imaging systems, mIFC is a nascent technology enabling high throughput imaging of cells and is yet to take the form of a clinical diagnostic tool. The proposed framework process the raw data generated by the mIFC systems. The framework incorporates several steps: beginning from pre-processing of the raw video frames to enhance the contents of the cell, localising the cell by a novel, fully automatic, non-iterative graph based algorithm, extraction of different quantitative morphological parameters and subsequent classification of cells. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using cost-effective microfluidics based imaging flow cytometer. The cell lines of HL60, K562 and MOLT were obtained from ATCC (American Type Culture Collection) and are separately cultured in the lab. Thus, each culture contains cells from its own category alone and thereby provides the ground truth. Each cell is localised by finding a closed cell contour by defining a directed, weighted graph from the Canny edge images of the cell such that the closed contour lies along the shortest weighted path surrounding the centroid of the cell from a starting point on a good curve segment to an immediate endpoint. Once the cell is localised, morphological features reflecting size, shape and complexity of the cells are extracted and used to develop a support vector machine based classification system. We could classify the cell-lines with good accuracy and the results were quite consistent across different cross validation experiments. We hope that imaging flow cytometers equipped with the proposed framework for image processing would enable cost-effective, automated and reliable disease screening in over-loaded facilities, which cannot afford to hire skilled personnel in large numbers. Such platforms would potentially facilitate screening camps in low income group countries; thereby transforming the current health care paradigms by enabling rapid, automated diagnosis for diseases like cancer.

Fluid Mechanics of Aquatic Locomotion at Large Reynolds Numbers

Abstract | There exist a huge range of fish species besides other aquatic organisms like squids and salps that locomote in water at large Reynolds numbers, a regime of flow where inertial forces dominate viscous forces. In the present review, we discuss the fluid mechanics governing the locomotion of such organisms. Most fishes propel themselves by periodic undulatory motions of the body and tail, and the typical classification of their swimming modes is based on the fraction of their body that undergoes such undulatory motions. In the angulliform mode, or the eel type, the entire body undergoes undulatory motions in the form of a travelling wave that goes from head to tail, while in the other extreme case, the thunniform mode, only the rear tail (caudal fin) undergoes lateral oscillations. The thunniform mode of swimming is essentially based on the lift force generated by the airfoil like crosssection of the fish tail as it moves laterally through the water, while the anguilliform mode may be understood using the “reactive theory” of Lighthill. In pulsed jet propulsion, adopted by squids and salps, there are two components to the thrust; the first due to the familiar ejection of momentum and the other due to an over-pressure at the exit plane caused by the unsteadiness of the jet. The flow immediately downstream of the body in all three modes consists of vortex rings; the differentiating point being the vastly different orientations of the vortex rings. However, since all the bodies are self-propelling, the thrust force must be equal to the drag force (at steady speed), implying no net force on the body, and hence the wake or flow downstream must be momentumless. For such bodies, where there is no net force, it is difficult to directly define a propulsion efficiency, although it is possible to use some other very different measures like “cost of transportation” to broadly judge performance.

The shear dynamo problem for small magnetic Reynolds numbers

We study large-scale kinematic dynamo action due to turbulence in the presence of a linear shear flow in the low-conductivity limit. Our treatment is non-perturbative in the shear strength and makes systematic use of both the shearing coordinate transformation and the Galilean invariance of the linear shear flow. The velocity fluctuations are assumed to have low magnetic Reynolds number (Re-m), but could have arbitrary fluid Reynolds number. The equation for the magnetic fluctuations is expanded perturbatively in the small quantity, Re-m. Our principal results are as follows: (i) the magnetic fluctuations are determined to the lowest order in Rem by explicit calculation of the resistive Green's function for the linear shear flow; (ii) the mean electromotive force is then calculated and an integro-differential equation is derived for the time evolution of the mean magnetic field. In this equation, velocity fluctuations contribute to two different kinds of terms, the 'C' and 'D' terms, respectively, in which first and second spatial derivatives of the mean magnetic field, respectively, appear inside the space-time integrals; (iii) the contribution of the D term is such that its contribution to the time evolution of the cross-shear components of the mean field does not depend on any other components except itself. Therefore, to the lowest order in Re-m, but to all orders in the shear strength, the D term cannot give rise to a shear-current-assisted dynamo effect; (iv) casting the integro-differential equation in Fourier space, we show that the normal modes of the theory are a set of shearing waves, labelled by their sheared wavevectors; (v) the integral kernels are expressed in terms of the velocity-spectrum tensor, which is the fundamental dynamical quantity that needs to be specified to complete the integro-differential equation description of the time evolution of the mean magnetic field; (vi) the C term couples different components of the mean magnetic field, so they can, in principle, give rise to a shear-current-type effect. We discuss the application to a slowly varying magnetic field, where it can be shown that forced non-helical velocity dynamics at low fluid Reynolds number does not result in a shear-current-assisted dynamo effect.

Large eddy simulation of a premixed flame with approximate deconvolution modeling

Approximate deconvolution modeling is a very recent approach to large eddy simulation of turbulent flows. It has been applied to compressible flows with success. Here, a premixed flame which forms in the wake of a flameholder has been selected to examine the subgrid-scale modeling of reaction rate by this new method because a previous plane two-dimensional simulation of this wake flame, using a wrinkling function and artificial flame thickening, had revealed discrepancies when compared with experiment. The present simulation is of the temporal evolution of a round wakelike flow at two Reynolds numbers, Re = 2000 and 10,000, based on wake defect velocity and wake diameter. A Fourier-spectral code has been used. The reaction is single-step and irreversible, and the rate follows an Arrhenius law. The reference simulation at the lower Reynolds number is fully resolved. At Re = 10,000, subgrid-scale contributions are significant. It was found that subgrid-scale modeling in the present simulation agrees more closely with unresolved subgrid-scale effects observed in experiment. Specifically, the highest contributions appeared in thin folded regions created by vortex convection. The wrinkling function approach had not selected subgrid-scale effects in these regions.

Shock tunnel study of spiked aerodynamic bodies flying at hypersonic Mach numbers

A three-component accelerometer balance system is used to study the drag reduction effect of an aerodisc on large angle blunt cones flying at hypersonic Mach numbers. Measurements in a hypersonic shock tunnel at a freestream Mach number of 5.75 indicate more than 50% reduction in the drag coefficient for a 120degrees apex angle blunt cone with a forward facing aerospike having a flat faced aerodisc at moderate angles of attack. Enhancement of drag has been observed for higher angles of attack due to the impingement of the flow separation shock on the windward side of the cone. The flowfields around the large angle blunt cone with aerospike assembly flying at hypersonic Mach numbers are also simulated numerically using a commercial CFD code. The pressure and density levels on the model surface, which is under the aerodynamic shadow of the flat disc tipped spike, are found very low and a drag reduction of 64.34% has been deduced numerically.

Badly approximable numbers and vectors in Cantor-like sets

We show that a large class of Cantor-like sets of R-d, d >= 1, contains uncountably many badly approximable numbers, respectively badly approximable vectors, when d >= 2. An analogous result is also proved for subsets of R-d arising in the study of geodesic flows corresponding to (d+1)-dimensional manifolds of constant negative curvature and finite volume, generalizing the set of badly approximable numbers in R. Furthermore, we describe a condition on sets, which is fulfilled by a large class, ensuring a large intersection with these Cantor-like sets.

Stall flutter of NACA 0012 airfoil at low Reynolds numbers

In the present work, we experimentally study and demarcate the stall flutter boundaries of a NACA 0012 airfoil at low Reynolds numbers (Re similar to 10(4)) by measuring the forces and flow fields around the airfoil when it is forced to oscillate. The airfoil is placed at large mean angle of attack (alpha(m)), and is forced to undergo small amplitude pitch oscillations, the amplitude (Delta alpha) and frequency (f) of which are systematically varied. The unsteady loads on the oscillating airfoil are directly measured, and are used to calculate the energy transfer to the airfoil from the flow. These measurements indicate that for large mean angles of attack of the airfoil (alpha(m)), there is positive energy transfer to the airfoil over a range of reduced frequencies (k=pi fc/U), indicating that there is a possibility of airfoil excitation or stall flutter even at these low Re (c=chord length). Outside this range of reduced frequencies, the energy transfer is negative and under these conditions the oscillations would be damped. Particle Image Velocimetry (PIV) measurements of the flow around the oscillating airfoil show that the shear layer separates from the leading edge and forms a leading edge vortex, although it is not very clear and distinct due to the low oscillation amplitudes. On the other hand, the shear layer formed after separation is found to clearly move periodically away from the airfoil suction surface and towards it with a phase lag to the airfoil oscillations. The phase of the shear layer motion with respect to the airfoil motions shows a clear difference between the exciting and the damping case.

Effect of Rayleigh numbers on the evolution of double-diffusive salt fingers

This is a transient two-dimensional numerical study of double-diffusive salt fingers in a two-layer heat-salt system for a wide range of initial density stability ratio (R-rho 0) and thermal Rayleigh numbers (Ra-T similar to 10(3) - 10(11)). Salt fingers have been studied for several decades now, but several perplexing features of this rich and complex system remain unexplained. The work in question studies this problem and shows the morphological variation in fingers from low to high thermal Rayleigh numbers, which have been missed by the previous investigators. Considerable variations in convective structures and evolution pattern were observed in the range of Ra-T used in the simulation. Evolution of salt fingers was studied by monitoring the finger structures, kinetic energy, vertical profiles, velocity fields, and transient variation of R-rho(t). The results show that large scale convection that limits the finger length was observed only at high Rayleigh numbers. The transition from nonlinear to linear convection occurs at about Ra-T similar to 10(8). Contrary to the popular notion, R-rho(t) first decrease during diffusion before the onset time and then increase when convection begins at the interface. Decrease in R-rho(t) is substantial at low Ra-T and it decreases even below unity resulting in overturning of the system. Interestingly, all the finger system passes through the same state before the onset of convection irrespective of Rayleigh number and density stability ratio of the system. (C) 2014 AIP Publishing LLC.