Abstract

Land use and land cover (LULC) changes induced by human or natural processes drive biogeochemistryof the Earth influencing the climate at global as well as regional scales. Drastic changes in the land cover with the decline in vegetation and water bodies due to anthropogenic activities enhances the heat emission from land surface and atmospheric temperatures Increased land surface temperature (LST) is mainly due to increase in concentrated human activities, paved land cover or barren lands. Due to complexity of landscapes the sampling was difficult to derive LST and environmental response relationships. Temporal data acquired through space borne remote sensors has bridged the gap of temporal data for the entire earth surface. The current study explores the relation between surface biophysical parameters to sub-pixel thermal variations. The thermal infrared bands of remote sensing data help to retrieve LST, which are supplemented byground based measurements. Analysis of LST with LULC indicates a negative correlation between vegetation indices and LST. The general trend in the ambient temperature of Uttara Kannada over the 31 year period was established. Itclarifies that there was a fundamental drift of temperature rise in recent years, especially during the last decade.

Abstract

: Railway is the largest undertaking in the country. A retrospective study of prevailing conditions is necessary to assimilate the progress of the sector and how far have the changes introduced in previous few years been successful. The paper examines how the proposed changes in the Indian railways have changed the face of it through rigorous spatial analysis in diversified fields. A balanced analysis of shortcomings as well as achievements has been tried to be achieved through this paper for few selected regions of India.Each year there has to be more emphasis on enhancing the services provided. The rail budgets play a vital role and are responsible for taking care of it. The numerous promises made in terms of introduction of trains, electrification of routes, gauge conversion, doubling and increasing frequency of trains are made every year, in order to keep track of fulfillment of those decisions the spatial analysis is conducted rigorously. Railway has also witnessed a number of disasters in past few years; the spatial analysis conducted brings out few major reasons of those. A section of study also covers the topographic conditions in the state of Jammu and Kashmir that have not allowed the progress of railways in these regions.

Abstract

In this work, Spatio-Temporal Data Mining of disease surveillance data is done, to describe the underlying patterns in disease occurrences across populations and to identify possible causes that could explain them; for better disease core prediction, detection and management. MiSTIC algorithm is used to determine spatial spread of disease core regions (scale of disease prevalence), and the frequency & regularity of occurrence of different locations in space as disease cores. The results show good correlation between the etiologic factors of Salmonellosis and the detected core locations, in addition to the significant observation of highly localized nature of disease prevalence.

Abstract

With major aerospace companies showing interest in certifying UAV systems for civilian airspace, their use in commercial remote sensing applications like traffic monitoring, map refinement, agricultural data collection, etc., are on the rise. But ambitious requirements like real-time geo-referencing of data, support for multiple sensor angle-of-views, smaller UAV size and cheaper investment cost have lead to challenges in platform stability, sensor noise reduction and increased onboard processing. Especially in small UAVs the geo-referencing of data collected is only as good as the quality of their localization sensors. This drives a need for developing methods that pickup spatial features from the captured video/image and aid in geo-referencing. This paper presents one such method to identify road segments and intersections based on traffic flow and compares well with the accuracy of manual observation. Two test video datasets, one each from moving and stationary platforms were used. The results obtained show a promising average percentage difference of 7.01% and 2.48% for the road segment extraction process using moving and stationary platform respectively. For the intersection identification process, the moving platform shows an accuracy of 75% where as the stationary platform data reaches an accuracy of 100%.

Abstract

Single stranded RNA molecules are known to fold into complex protein like functional structures, consisting of stems and loops, which are further stabilized through tertiary interactions. While it is remarkable that RNA molecules are able to exhibit such structural complexity and functional specificity, with only an alphabet of four bases, one of the strategies employed for creating variety is through post-transcriptional modifications such as methylation, pseudouridylation, thiolation and isomerization. In fact, modified bases are known to play major role in providing chemical and biological diversity to RNA and contribute to overall fitness of the cell1. Base modifications are also known to help RNA molecules to exhibit alternate conformations2. The objectives of this study are: To understand (1) how these modifications affect the base pairing properties of RNA bases and (2) why nature have adopted mechanism to modified these bases. These objectives are studied through quantum chemical methods. We extracted the coordinates of 32 modified base pairs and 11 base triplets from a total of 208 RNA crystal structures from the PDB database. Of these 208 files, 128 were directly taken from HD-RNAS’s non redundant dataset3 and searched for modified bases using BPFind software4. The remaining 77 PDB files were included in the dataset based on information from HET group information from PDBSum5. We have optimized the initial geometries at B3LYP/6-31G (d,p) level and have evaluated the complete basis set (CBS) extrapolated interaction energies using RIMP2 calculation with aug-cc-pVDZ and aug-cc-pVTZ basis sets. Molecular electrostatic surface potential maps were also generated for modified base pairs. This study provides insights into the characteristics of modified base pairs and triples in complex RNA structure.

Abstract

Schistosomiasis is a disease caused by a trematode parasite, Schistosoma mansoni. The host consists of two different redox systems: Glutaredoxin (Grx) and Thioredoxin (Trx), but the parasite has only one multifunctional enzyme Thioredoxin Glutathione Reductase (TGR), which is responsible for carrying out all the redox activities, necessary for protecting the parasite against oxidative stress inside the host. TGR is a fusion of Thioredoxin Reductase (TR) with Glutaredoxin (Grx) at its N-terminus. The dependence of S. mansoni on a single protein for all its redox functions makes it a potential drug target. We have carried out structural analysis of Glutathione Reductase (GR), Thioredoxin Reductase (TR) and Thioredoxin Glutathione Reductase (TGR) using available crystal structures from PDB to understand the catalytic mechanism in these oxidoreductases. NADPH plays a major role as an electron carrier and transfers the electrons to the oxidized cofactor, FAD, which is non-covalently attached to the enzyme. This initiates further steps of the catalytic process. Here, we investigate how the interplay of conformations of these cofactors and those of the neighbouring residues facilitate the charge transfer process. TR, GR and TGR share similarity in their respective active site regions. Several conserved residues and non covalent interactions, play a major role during the electron transfer process. We hypothesise the function of NADPH during the entire charge transfer process as follows: a Tyr residue moves and facilitates the binding of NADPH to FAD in pi-stacking conformation. Two Arg residues reorient to interact with 2'-phosphate group and adenine ring of NADPH for effective binding. Lys, Glu and His residues near the active site regions form salt bridges and possibly aid the charge transfer mechanism in these redox enzymes.

Abstract

BACKGROUND: Thermostable lipases are widely used in the detergent industry and in organic synthesis. B. subtilis lipase (Lip A) is a monomeric protein, which preferentially hydrolyses C8 fatty acid esters. Though the mechanism of thermostability depends on type of lipase, some common factors include additional non-covalent interactions, increase in packing density of the hydrophobic core, stabilization of alpha-helices and shortening of loops between secondary structural elements. RESULTS: We have studied wild type Lip A (WT) and six of its thermostable mutants containing 2, 3, 4, 6, 9 and 12 point mutations respectively, derived from the wild type protein by directed evolution. Experimental observations showed that the most thermostable variant, with twelve mutations, shows remarkable enhancement in melting temperature and temperature optima of activity compared to WT, in vitro. Our MD simulations show decrease in SASA for core regions and slow unfolding rate at several key secondary structural regions due to presence of persistent salt bridges, hydrogen bonds and native contacts for the most thermostable mutant lipase. The principal component (PC) and Free energy landscape (FEL) analyses at 450K suggest that the most thermostable mutant showed least fluctuation and stayed within a single large minimum. The other less thermostable mutants and WT showed higher fluctuation and exhibited two or more minima along the first two PCs. Analysis of representative structures corresponding to each sub-states showed that the most thermostable mutant sampled conformations close to the native state most of the time during the simulation. The other less thermostable mutants and WT lipase sampled non-native conformations more frequently than native conformations. CONCLUSIONS: Our results demonstrate that, the most thermostable lipase maintains its stability and activity at high temperatures by restricting conformational fluctuation through the stabilization of key salt bridges and main-chain H-bonds, which further helped them to maintain the stability of the core regions apart from stabilizing the overall 3D fold.

Abstract

Archaeal chromatin proteins share molecular and functional similarities with both bacterial and eukaryotic chromatin proteins. These proteins play an important role in functionally organizing the genomic DNA into a compact nucleoid. Cren7 and Sul7 are two crenarchaeal nucleoidassociated proteins, which are structurally homologous, but not conserved at the sequence level. Cocrystal structures have shown that these two proteins induce a sharp bend on binding to DNA. In this study, we have investigated the architectural properties of these proteins using atomic force microscopy, molecular dynamics simulations and magnetic tweezers. We demonstrate that Cren7 and Sul7 both compact DNA molecules to a similar extent. Using a theoretical model, we quantify the number of individual proteins bound to the DNA as a function of protein concentration and show that forces up to 3.5 pN do not affect this binding. Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein–DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins.

Abstract

The effect of the linker length (–CH2–) connecting the diene and the dienophile in macrocyclic trienes on their transannular Diels–Alder (TADA) reactivity has been investigated using density functional theory (DFT) calculations. The relationship between the conformational properties of these reactants and their reaction energy barriers was examined and a quantitative relationship has been obtained. The transition state energy barriers were found to increase with an increase in the linker length, which is in contrast to the expected trend. The conformational preferences of the triene reactants were studied using replica exchange molecular dynamics (REMD) simulations. These calculations reveal that longer linkers lead to a decreased probability of the occurrence of conformations with the diene and dienophile parts of the system vicinal to each other, and thus lower reactivity of systems with long linkers. Excellent correlations between the transition state energies and the cumulative probabilities corresponding to a short distance between the reactive sites, along with the ability of the diene to exist in the s-cisoid form, were observed.

Abstract

Locked nucleic acid (LNA) is a chemical modification which introduces a -O-CH2-linkage in the furanose sugar of nucleic acids and blocks its conformation in a particular state. Two types of modifications, namely, 2'-O,4'-C-methylene-β-D-ribofuranose (β-D-LNA) and 2'-O,4'-C-methylene-α-L-ribofuranose (α-L-LNA), have been shown to yield RNA and DNA duplex-like structures, respectively. LNA modifications lead to increased melting temperatures of DNA and RNA duplexes, and have been suggested as potential therapeutic agents in antisense therapy. In this study, molecular dynamics (MD) simulations were performed on fully modified LNA duplexes and pure DNA and RNA duplexes sharing a similar sequence to investigate their structure, stabilities, and solvation properties. Both LNA duplexes undergo unwinding of the helical structure compared to the pure DNA and RNA duplexes. Though the α-LNA substituent has been proposed to mimic deoxyribose sugar in its conformational properties, the fully modified duplex was found to exhibit unique structural and dynamic properties with respect to the other three nucleic acid structures. Free energy calculations accurately capture the enhanced stabilization of the LNA duplex structures compared to DNA and RNA molecules as observed in experiments. π-stacking interaction between bases from complementary strands is shown to be one of the contributors to enhanced stabilization upon LNA substitution. A combination of two factors, namely, nature of the -O-CH2- linkage in the LNAs vs their absence in the pure duplexes and similar conformations of the sugar rings in DNA and α-LNA vs the other two, is suggested to contribute to the stark differences among the four duplexes studied here in terms of their structural, dynamic, and energetic properties