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Liquid crystal ordering of nucleic acids
No full textSeveral analytical calculations and computer simulations propose that cylindrical monodispersive rods having an aspect ratio (ratio of length to diameter) greater than 4 can exhibit liquid crystal (LC) ordering. But, recent experiments demonstrated the signature of LC ordering in systems of 4- to 20-base pair (bp) long nucleic acids (NAs) that do not satisfy the shape anisotropy criterion. Mechanisms of end-to-end adhesion and stacking have been proposed to explain this phenomenon. In this study, using all-atom molecular dynamics (MD) simulation, we explicitly verify the end-to-end stacking of double-stranded RNA (dsRNA) and demonstrate the LC ordering at the microscopic level. Using umbrella sampling (US) calculation, we quantify the potential of mean force (PMF) between two dsRNAs for various reaction coordinates (RCs) and compare our results with previously reported PMFs for double-stranded DNA (dsDNA). The PMF profiles demonstrate the anisotropic nature of inter-NA interaction. We find that, like dsDNA, dsRNA also prefers to stack on top of each other while repelling sideways, leading to the formation of supra-molecular-columns that undergo LC ordering at high NA volume fraction (�). We also demonstrate and quantify the nematic ordering of the RNAs using several hundred nanosecond-long MD simulations that remain almost invariant for different initial configurations and under different external physiological conditions
Reply to Friedrich et al.: Both genetic and environmental factors may contribute to laterality in mesencephalic connectivity and bias
No full textElectrowetting based local sensing of liquid properties using relaxation dynamics of stretched liquid interface
No full textHypothesis: Monitoring progression of biochemical processes is required for medical and industrial applications. Spatiotemporal changes in fluid properties can be measured to determine progress of biochemical processes like blood coagulation. Localised electrowetting-on-dielectric (EWOD) actuates a part of droplet contact line, allowing local measurement of fluid properties without inducing bulk fluid motion, which is unlike full droplet oscillation-based techniques. Experiments: In this work, narrow electrodes (50�450 μm) were used to actuate a portion of drop interface. Dynamics of interface actuation and relaxation was used to estimate the local visco-elastic properties of the droplet. Findings: For local interface motion, theory predicts a generic dispersion relation �=cqn. In agreement with theory, decay time was found to be proportional to viscosity and inversely proportional to surface tension. Interface displacement remained almost constant for different viscosities, but it decreased with increase in surface tension. Capability to measure spatiotemporal dynamics of chemical process was demonstrated for sugar dissolution in a droplet of water. For full droplet oscillation-based techniques, the induced bulk flows adversely affect the monitored process. Localised EWOD reduces bulk flows in the sample. So, this technique was applied to study blood coagulation dynamics, enlightening the future prospect of developing biomedical sensors
Optical frequency comb based on nonlinear spectral broadening of a phase modulated comb source driven by dual offset locked carriers
No full textWe demonstrate a versatile technique to generate a broadband optical frequency comb source in the C-band. This is accomplished by nonlinear spectral broadening of a phase modulated comb source driven by dual frequency offset locked carriers. The locking is achieved by setting up a heterodyne optical frequency locked loop to lock two phase modulated electro-optic 25 GHz frequency combs sourced from individual seed carriers offset by 100 GHz, to within 6.7 MHz of each other. We realize spectral broadening in highly nonlinear fiber after suitable amplification to obtain an equalized, nonlinearly broadened frequency comb. We obtain � 86 lines in a 20 dB band spanning over 2 THz
Region specific seismic hazard analysis of Krishna Raja Sagara Dam, India
No full textRegion-specific seismic hazard analysis was carried out for Krishna Raja Sagara Dam site in Karnataka, India. Seismic event data and seismic source data within a 500 km radius were collected. Deterministic seismic hazard analysis was conducted for different methods of earthquake magnitude and location estimation. It was observed that the ground motion estimates vary widely with different methods of Mmax estimation and that the rupture based method, which calculates Mmax based on fault dimensions, can give a reliable estimate of the possible maximum magnitude in regions of low to moderate seismicity. Based on this study, the greatest median ground motion at the dam site is estimated as 0.43 g and the ground motion required to be tolerated without catastrophic failure is considered as 0.11 g. In Stable Continental Regions across the world, where earthquake data is scarce, the methodology followed here can be adopted to conduct region-specific seismic hazard analysis
Efficient Representation of Ducts and Cluttered Spaces for Realistic Motion Planning of Hyper-Redundant Robots through Confined Paths
No full textApplication of highly articulated hyper-redundant robots to manoeuvre in narrow and confined spaces is gaining popularity due to their obvious advantages. In this paper, we describe an optimization based approach for motion planning of hyper-redundant robots, which results in a natural motion of the links through ducts and confined spaces. It is shown that for a desired motion of the end-effector or the head of the hyper-redundant robot, the motion of the subsequent links attenuate and all the links avoid collision with the walls of the ducts and any other obstacles in the confined spaces. We discuss several ways to represent ducts in 2D and 3D space and also how the proposed algorithm is applied in these representations. It is shown that the complexity of the algorithm, with m constraints is at most O(m(3.5)) and in case where the ducts can be modeled with polyhedra, the complexity can be as low as O(m(1.5)). The proposed approach is also used to determine the largest link length in the hyper-redundant robot which can traverse the confined path. The concepts developed in this paper are demonstrated using simulations conducted on three practical scenarios: 1) hyper-redundant manipulators inspecting an industrial pipeline, 2) motion of an endoscopic robot through gastro-intestinal (Gl) tract and 3) motion of hyper-redundant manipulators in search and rescue operations. Analysis on the computational complexity and the simulations shows that the method is feasible for practical implementation. (C) 2019 Elsevier Ltd. All rights reserved
Highly sensitive, scalable reduced graphene oxide with palladium nano-composite as strain sensor
No full textWe report a novel strain sensor based on reduced graphene oxide (rGO) with palladium (Pd) nano-composite. The sensor was fabricated on the SS304 stainless-steel substrate using a screen-printing method. Graphene oxide was synthesized using a modified Hummer's method and reduced using a chemical route. Field emission-scanning electron microscope, x-ray diffraction and Raman spectroscopy were used to characterize the as-synthesized nano-composite. The as-fabricated strain sensor was tested for tensile strain using Micro-universal Test Machine and the change in resistance for different strains was recorded. The sensor response was observed to be stable and linear within the applied strain range of 0-3000 microstrains, and an average gauge factor of 42.69 was obtained in this range
Looking beyond protected areas: Identifying conservation compatible landscapes in agro-forest mosaics in north-eastern India
No full textSmall-sized protected areas face increasing pressures from developmental activities and are often rendered inadequate and isolated to conserve wide-ranging species. However, in situations where wildlife persists outside protected areas, conservation goals may be met by aligning the ecological needs of wildlife with the socio-economic needs of local communities and offsetting losses arising due to shared spaces. We explore the potential of a tea-plantation dominated landscape of multiple land-use in north-eastern India to conserve the Asian elephant and the Indian leopard. We assess conservation potential by identifying predictors of species use of particular habitats using species distribution models and identify challenges by reviewing the available literature. Elephants used ~680 km2 of this 1200 km2 non-forested landscape; within this area, habitats with a higher proportion of deciduous forest patches were favored. Leopards were found to be ubiquitous in tea-plantation and used ~950 km2 of the study area, with the proportion of tea cover being the single best predictor of leopard habitat-use. With more than 30 human deaths and 100 injuries per year caused by these two species in the study area alone, the high frequency of human casualties and economic losses remain the prime hurdles to long-term conservation efforts. We discuss specific mitigation measures to reduce human casualties and call for the inclusion of important stakeholders in the mitigation process. The study provides a template for identifying conservation-compatible landscapes outside protected areas and a framework for identifying challenges and potential to mitigate current or future conservation conflicts
Deciphering the essentiality and function of SxSx motif in Mycobacterium tuberculosis UvrB
No full textThe UvrB subunit is a central component of the UvrABC incision complex and plays a pivotal role in damage recognition, strand excision and repair synthesis. A conserved structural motif (the SxSx motif) present in UvrB is analogous to a similar motif (TxGx) in the helicases of superfamily 2, whose function is not fully understood. To elucidate the significance of the SxSx (Ser143-Val144-Ser145-Cys146) motif in Mycobacterium tuberculosis UvrB (MtUvrB), different variants of MtUvrB subunit were constructed and characterized. The SxSx motif indeed was found to be essential for MtUvrB function: while Ser143 and Cys146 residues within this motif were crucial for MtUvrB function, Ser145 plays an important but less essential role. The SxSx motif-deleted mutant was drastically attenuated and three single (S143A, S145A and C146A) mutants and a double (S143A/S145A) mutant exhibited various degrees of severity in their DNA-binding, DNA helicase and ATPase activities. Taken together, these results highlight a hitherto unrecognized role for SxSx motif in the catalytic activities of UvrB. © 2020 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM
Sirtuin 6 deficiency transcriptionally up-regulates TGF-β signaling and induces fibrosis in mice
No full textCaloric restriction has been associated with increased life span and reduced aging-related disorders and reduces fibrosis in several diseases. Fibrosis is characterized by deposition of excess fibrous material in tissues and organs and is caused by aging, chronic stress, injury, or disease. Myofibroblasts are fibroblast-like cells that secrete high levels of extracellular matrix proteins, resulting in fibrosis. Histological studies have identified many-fold increases of myofibroblasts in aged organs where myofibroblasts are constantly generated from resident tissue fibroblasts and other cell types. However, it remains unclear how aging increases the generation of myofibroblasts. Here, using mouse models and biochemical assays, we show that sirtuin 6 (SIRT6) deficiency plays a major role in aging-associated transformation of fibroblasts to myofibroblasts, resulting in tissue fibrosis. Our findings suggest that SIRT6-deficient fibroblasts transform spontaneously to myofibroblasts through hyperactivation of transforming growth factor β (TGF-β) signaling in a cell-autonomous manner. Importantly, we noted that SIRT6 haploinsufficiency is sufficient for enhancing myofibroblast generation, leading to multiorgan fibrosis and cardiac dysfunction in mice during aging. Mechanistically, SIRT6 bound to and repressed the expression of key TGF-β signaling genes by deacetylating SMAD family member 3 (SMAD3) and Lys-9 and Lys-56 in histone 3. SIRT6 binding to the promoters of genes in the TGF-β signaling pathway decreased significantly with age and was accompanied by increased binding of SMAD3 to these promoters. Our findings reveal that SIRT6 may be a potential candidate for modulating TGF-β signaling to reduce multiorgan fibrosis during aging and fibrosis-associated diseases