Morphology and electrostatics play active role in neuronal differentiation processes on flexible conducting substrates

This commentary discusses and summarizes the key highlights of our recently reported work entitled ``Neuronal Differentiation of Embryonic Stem Cell Derived Neuronal Progenitors Can Be Regulated by Stretchable Conducting Polymers.'' The prospect of controlling the mechanical-rigidity and the surface conductance properties offers a unique combination for tailoring the growth and differentiation of neuronal cells. We emphasize the utility of transparent elastomeric substrates with coatings of electrically conducting polymer to realize the desired substrate-characteristics for cellular development processes. Our study showed that neuronal differentiation from ES cells is highly influenced by the specific substrates on which they are growing. Thus, our results provide a better strategy for regulated neuronal differentiation by using such functional conducting surfaces.

Recent Seismicity in India and Adjoining Regions

In the present work, historical and instrumental seismicity data of India and its adjoining areas (within 300km from Indian political boundary) are compiled to form the earthquake catalog for the country covering the period from 1505 to 2009. The initial catalogue consisted of about 139563 earthquake events and after declustering,the total number of events obtained was 61315. Region specific earthquake magnitude scaling relations correlating different magnitude scales were achieved and a homogenous earthquake catalogue in moment magnitude (MW) scale was developed for the region. This paper also presents the results of the use of Geographic Information Systems (GIS) to prepare a digitized seismic source map of India. The latest earthquake data were superimposed on the digitized source map to get a final Seismotectonic map of India. The study area has been divided into 1225 grid points (approximately 110km×110km) and the seismicity analysis has been done to get the spatial variation of seismicity parameters ‘a’ and ‘b’ across the country. The homogenized earthquake catalogue with the event details is listed in the website http://civil.iisc.ernet.in/~sreevals/resource.htm

Variability of cloud liquid water and ice over South Asia from TMI estimates

In this study, the Tropical Rainfall Measurement Mission based Microwave Imager estimates (2A12) have been used to compare and contrast the characteristics of cloud liquid water and ice over the Indian land region and the ocean surrounding it, during the premonsoon (May) and monsoon (June-September) seasons. Based on the spatial homogeneity of rainfall, we have selected five regions for our study (three over ocean, two over land). Comparison across three ocean regions suggests that the cloud liquid water (CLW) over the orographically influenced Arabian Sea (close to the Indian west coast) behaves differently from the CLW over a trapped ocean (Bay of Bengal) or an open ocean (equatorial Indian Ocean). Specifically, the Arabian Sea region shows higher liquid water for a lower range of rainfall, whereas the Bay of Bengal and the equatorial Indian Ocean show higher liquid water for a higher range of rainfall. Apart from geographic differences, we also documented seasonal differences by comparing CLW profiles between monsoon and premonsoon periods, as well as between early and peak phases of the monsoon. We find that the CLW during the lean periods of rainfall (May or June) is higher than during the peak and late monsoon season (July-September) for raining clouds. As active and break phases are important signatures of the monsoon progression, we also analysed the differences in CLW during various phases of the monsoon, namely, active, break, active-to-break and break-to-active transition phases. We find that the cloud liquid water content during the break-to-active transition phase is significantly higher than during the active-to-break transition phase over central India. We speculate that this could be attributed to higher amount of aerosol loading over this region during the break phase. We lend credence to this aerosol-CLW/rain association by comparing the central Indian CLW with that over southeast Asia (where the aerosol loading is significantly smaller) and find that in the latter region, there are no significant differences in CLW during the different phases of the monsoon. While our hypothesis needs to be further investigated with numerical models, the results presented in this study can potentially serve as a good benchmark in evaluating the performance of cloud resolving models over the Indian region.

NON-GLYCINE RESIDUES IN THE DISALLOWED REGIONS OF THE RAMACHANDRAN MAP AND THEIR NEIGHBORHOOD PREFERENCES

The allowed and the ``disallowed'' regions in the celebrated Ramachandran map (phi-psi] map) was elegantly deduced by Ramachandran, Ramakrishnan and Sasisekharan even before the protein crystal structures became available. This powerful map was derived based on rigid geometry of the peptide group and later several investigations on protein crystal structures reported the occurrence of a small fraction of the phi-psi] torsion angles in the disallowed region. The question is what factors make these residues adopt disallowed conformations? Is it driven by the necessity to maintain the overall topology or is it associated with function or is it just that the disallowed conformations are extreme limits of the allowed conformations? Today, with the availability of a large number of high resolution crystal structures, we have revisited this problem. Apart from validating some of the earlier findings such as residue propensities, preferred location in the secondary structure, we have explored their spatial neighborhood preferences using the protein structure network PSN] approach developed in our lab. Finally, the structural and functional implications of the disallowed conformations are examined.

PROPENSITIES OF AMINO ACID RESIDUES IN PROTEINS FOR DIFFERENT REGIONS OF THE RAMACHANDRAN MAP

Using a dataset of 1164 crystal structures of largely non-homologous proteins defined at a resolution of 1.5 angstrom or better, we have investigated the (phi,psi) preferences of 20 residue types by considering the residues which occur in loops. Propensities of residue types to occur in the loops with (phi,psi) values in the aa region of the Ramachandran map has a poor correlation coefficient of 0.48 to the Chou-Fasman propensities of the residue types to occur in the a-helical segments. However the correlation coefficient between propensities of residues in loops to adopt beta conformations and those in beta-sheet is much higher (0.95). These observations suggest that a-helix formation is well influenced by the local amino acid sequence while intrinsic preference of residue types for beta-sheet plays a major role in the formation of beta-sheet. The main chain polar groups of residues in loops, that can affect the (phi,psi) values, can be involved in intra-molecular hydrogen bonding. Therefore we investigated further by considering subset of residues in loops with low (0 to 2) number of intra-molecular hydrogen bonds per residue involving main chain polar atoms. For this subset, the correlation coefficients between propensities for alpha-helix and alpha(R) region and between beta-sheet and beta-region are 0.26 and 0.64 respectively. This reiterates higher intrinsic tendency of beta-region favouring residues to adopt beta-sheet than alpha(R) region favouring residues to adopt alpha-helical structure.

Shape Memory Alloy based Active Chiral Composite Cells

Wing morphing is one of the emerging methodology towards improving aerodynamic efficiency of flight vehicle structures. In this paper a morphing structural element is designed and studied which has its origin in the well known chiral structures. The new aspect of design and functionality explored in this paper is that the chiral cell is actuated using thermal Shape Memory Alloy (SMA) actuator wires to provide directional motion. Such structure utilizes the potential of different actuations concepts based on actuator embedded in the chiral structure skin. This paper describes a new class of chiral cell structure with integrated SMA wire for actuation. Chiral topological constructs are obtained by considering passive and active load path decoupling and sub-optimal shape changes. Single cell of chiral honeycomb with actuators are analyzed using finite element simulation results and experiments. To this end, a multi-cell plan-form is characterized showing interesting possibilities in structural morphing applications. The applicability of the developed chiral cell to flexible wing skin, variable stiffness based design and controlling longitudinal-to-transverse stiffness ratio are discussed.

Online Estimation of Evolving Human Visual Interest

Regions in video streams attracting human interest contribute significantly to human understanding of the video. Being able to predict salient and informative Regions of Interest (ROIs) through a sequence of eye movements is a challenging problem. Applications such as content-aware retargeting of videos to different aspect ratios while preserving informative regions and smart insertion of dialog (closed-caption text) into the video stream can significantly be improved using the predicted ROIs. We propose an interactive human-in-the-loop framework to model eye movements and predict visual saliency into yet-unseen frames. Eye tracking and video content are used to model visual attention in a manner that accounts for important eye-gaze characteristics such as temporal discontinuities due to sudden eye movements, noise, and behavioral artifacts. A novel statistical-and algorithm-based method gaze buffering is proposed for eye-gaze analysis and its fusion with content-based features. Our robust saliency prediction is instantiated for two challenging and exciting applications. The first application alters video aspect ratios on-the-fly using content-aware video retargeting, thus making them suitable for a variety of display sizes. The second application dynamically localizes active speakers and places dialog captions on-the-fly in the video stream. Our method ensures that dialogs are faithful to active speaker locations and do not interfere with salient content in the video stream. Our framework naturally accommodates personalisation of the application to suit biases and preferences of individual users.

Design and Modeling of an Active Five-Axis Compliant Micromanipulator

This paper presents the design and modeling of an active five-axis compliant micromanipulator whose tip orientation can be independently controlled by large angles about two axes and the tip-position can be controlled in three dimensions. These features enable precise control of the contact point of the tip and the tip-sample interaction forces with three-dimensional nanoscale objects, including those features that are conventionally inaccessible. Control of the tip-motion is realized by means of electromagnetic actuation combined with a novel kinematic and structural design of the micromanipulator, which, in addition, also ensures compatibility with existing high-resolution motion-measurement systems. The design and analysis of the manipulator structure and those of the actuation system are first presented. Quasi-static and dynamic lumped-parameter (LP) models are then derived for the five-axis compliant micromanipulator. Finite element (FE) analysis is employed to validate these models, which are subsequently used to study the effects of tip orientation on the mechanical characteristics of the five-axis micromanipulator. Finally, a prototype of the designed five-axis manipulator is fabricated by means of focused ion-beam milling (FIB).

Flocking at a distance in active granular matter

The self-organized motion of vast numbers of creatures in a single direction is a spectacular example of emergent order. Here, we recreate this phenomenon using actuated nonliving components. We report here that millimetre-sized tapered rods, rendered motile by contact with an underlying vibrated surface and interacting through a medium of spherical beads, undergo a phase transition to a state of spontaneous alignment of velocities and orientations above a threshold bead area fraction. Guided by a detailed simulation model, we construct an analytical theory of this flocking transition, with two ingredients: a moving rod drags beads; neighbouring rods reorient in the resulting flow like a weathercock in the wind. Theory and experiment agree on the structure of our phase diagram in the plane of rod and bead concentrations and power-law spatial correlations near the phase boundary. Our discovery suggests possible new mechanisms for the collective transport of particulate or cellular matter.

Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA

In this study, we combine available high resolution structural information on eukaryotic ribosomes with low resolution cryo-EM data on the Hepatitis C Viral RNA (IRES) human ribosome complex. Aided further by the prediction of RNA-protein interactions and restrained docking studies, we gain insights on their interaction at the residue level. We identified the components involved at the major and minor contact regions, and propose that there are energetically favorable local interactions between 40S ribosomal proteins and IRES domains. Domain II of the IRES interacts with ribosomal proteins S5 and S25 while the pseudoknot and the downstream domain IV region bind to ribosomal proteins S26, S28 and S5. We also provide support using UV cross-linking studies to validate our proposition of interaction between the S5 and IRES domains II and IV. We found that domain IIIe makes contact with the ribosomal protein S3a (S1e). Our model also suggests that the ribosomal protein S27 interacts with domain IIIc while S7 has a weak contact with a single base RNA bulge between junction IIIabc and IIId. The interacting residues are highly conserved among mammalian homologs while IRES RNA bases involved in contact do not show strict conservation. IRES RNA binding sites for S25 and S3a show the best conservation among related viral IRESs. The new contacts identified between ribosomal proteins and RNA are consistent with previous independent studies on RNA-binding properties of ribosomal proteins reported in literature, though information at the residue level is not available in previous studies.

Active guests in the MoS2/MoSe2 host lattice: efficient hydrogen evolution using few-layer alloys of MoS2(1-x)Se2x

Few-layer transition metal dichalcogenide alloys based on molybdenum sulphoselenides MoS2(1-x)Se2x] possess higher hydrogen evolution (HER) activity compared to pristine few-layer MoS2 and MoSe2. Variation of the sulphur or selenium content in the parent dichalcogenides reveals a systematic structure-activity relationship for different compositions of alloys, and it is found that the composition MoS1.0Se1.0 shows the highest HER activity amongst the catalysts studied. The tunable electronic structure of MoS2/MoSe2 upon Se/S incorporation probably assists in the realization of high HER activity.

Rollover-Preventive Force Synthesis at Active Suspensions in a Vehicle Performing a Severe Maneuver With Wheels Lifted Off

Among the intelligent safety technologies for road vehicles, active suspensions controlled by embedded computing elements for preventing rollover have received a lot of attention. The existing models for synthesizing and allocating forces in such suspensions are conservatively based on the constraints that are valid until no wheels lift off the ground. However, the fault tolerance of the rollover-preventive systems can be enhanced if the smart/active suspensions can intervene in the more severe situation in which the wheels have just lifted off the ground. The difficulty in computing control in the last situation is that the vehicle dynamics then passes into the regime that yields a model involving disjunctive constraints on the dynamics. Simulation of dynamics with disjunctive constraints in this context becomes necessary to estimate, synthesize, and allocate the intended hardware realizable forces in an active suspension. In this paper, we give an algorithm for the previously mentioned problem by solving it as a disjunctive dynamic optimization problem. Based on this, we synthesize and allocate the roll-stabilizing time-dependent active suspension forces in terms of sensor output data. We show that the forces obtained from disjunctive dynamics are comparable with existing force allocations and, hence, are possibly realizable in the existing hardware framework toward enhancing the safety and fault tolerance.

Characterization of a dual-active enzyme, DcpA, involved in cyclic diguanosine monophosphate turnover in Mycobacterium smegmatis

We have reported previously that the long-term survival of Mycobacterium smegmatis is facilitated by a dual-active enzyme MSDGC-1 (renamed DcpA), which controls the cellular turnover of cyclic diguanosine monophosphate (c-di-GMP). Most mycobacterial species possess at least a single copy of a DcpA orthologue that is highly conserved in terms of sequence similarity and domain architecture. Here, we show that DcpA exists in monomeric and dimeric forms. The dimerization of DcpA is due to non-covalent interactions between two protomers that are arranged in a parallel orientation. The dimer shows both synthesis and hydrolysis activities, whereas the monomer shows only hydrolysis activity. In addition, we have shown that DcpA is associated with the cytoplasmic membrane and exhibits heterogeneous cellular localization with a predominance at the cell poles. Finally, we have also shown that DcpA is involved in the change in cell length and colony morphology of M. smegmatis. Taken together, our study provides additional evidence about the role of the bifunctional protein involved in c-di-GMP signalling in M. smegmatis.

Identifying regions for conservation of sloth bears through occupancy modelling in north-eastern Karnataka, India

In the absence of information on species in decline with contracting ranges, management should emphasize remaining populations and protection of their habitats. Threatened by anthropogenic pressure including habitat degradation and loss, sloth bears (Melursus ursinus) in India have become limited in range, habitat, and population size. We identified ecological and anthropogenic determinants of occurrence within an occupancy framework to evaluate habitat suitability of non-protected regions (with sloth bears) in northeastern Karnataka, India. We employed a systematic sampling methodology to yield presence absence data to examine a priori hypotheses of determinants that affected occupancy. These covariates were broadly classified as habitat or anthropogenic factors. Mean number of termite mounds and trees positively influenced sloth bear occupancy, and grazing pressure expounded by mean number of livestock dung affected it negatively. Also, mean percentage of shrub coverage had no impact on bear inhabitance. The best fitting model further predicted habitats in Bukkasagara, Agoli, and Benakal reserved forests to have 38%, 75%, and 88%, respectively, of their sampled grid cells with high occupancies (>0.70) albeit little or no legal protection. We recommend a conservation strategy that includes protection of vegetation stand-structure, maintenance of soil moisture, and enrichment of habitat for the long-term welfare of this species.

Simultaneously Uncovering the Patterns of Brain Regions Involved in Different Story Reading Subprocesses

Story understanding involves many perceptual and cognitive subprocesses, from perceiving individual words, to parsing sentences, to understanding the relationships among the story characters. We present an integrated computational model of reading that incorporates these and additional subprocesses, simultaneously discovering their fMRI signatures. Our model predicts the fMRI activity associated with reading arbitrary text passages, well enough to distinguish which of two story segments is being read with 74% accuracy. This approach is the first to simultaneously track diverse reading subprocesses during complex story processing and predict the detailed neural representation of diverse story features, ranging from visual word properties to the mention of different story characters and different actions they perform. We construct brain representation maps that replicate many results from a wide range of classical studies that focus each on one aspect of language processing and offer new insights on which type of information is processed by different areas involved in language processing. Additionally, this approach is promising for studying individual differences: it can be used to create single subject maps that may potentially be used to measure reading comprehension and diagnose reading disorders.