Abstract

Motivation: Various types of functional RNAs-tRNA, Ribosomes, Introns, Aptamers, Ribozymes Diverse and Dynamic molecules Recent availability of RNA crystal structures has facilitated study and analysis

Abstract

Schistosoma mansoni, a trematode parasite causes schistosomiasis, a tropical disease affecting more than 200 million people. It lives in an aerobic environment and therefore has effective redox mechanisms for its survival as well as to evade reactive oxygen species from its host. Although, the host performs these activities by two different systems: thioredoxin and glutaredoxin separately, the parasite has only one unique multifunctional enzyme, thioredoxin glutathione reductase (TGR) for both the activities which is its main bottleneck. Therefore this emerges as a promising target for schistosomiasis. TGR is a homodimer of 65kDa sub units. each consisting 598 amino acids with a selenocysteine residue in the C-terminus. It shows an unprecedented fusion of two proteins: glutaredoxin (Grx) and thioredoxin reductase (TR). Although many biochemical studies have been reported for TGR, the three dimensional structural information is still missing. Herein, we present some of our efforts towards development of a homology model for S. mansoni TGR (SmTGR) using Modeller9.1. A BLAST search with SmTGR sequence revealed about 60% homology with different mammalian TRs and the initial 100 residues showed close similarity with Grx. Therefore, homology modeling was carried out using both TR and Grx templates. The developed models were dimerized and validated by Procheck analysis. The validated structure was then minimized by MD simulations using heated simulated annealing method.

Abstract

The need for computational characterization of DNA structure in the context of DNA bending/binding, B ->A transitions in protein-DNA complexes and also in the context of strand orientation especially in DNA triplexes and quadruplexes have given rise to several fine grained parameters, such as backbone conformations, sugar pucker and chi angle, local strand orientation, base pair and base pair step parameters backbone base inclination etc. With their unpaired bases, extensive non helical regions, non-canonical base pairs and tertiary interactions, RNA molecules host a large variety of recurrent structural and functional motifs and parameters such as Zp, defined in the context of double helical DNA base pairs and base pair steps and effectively used for A and B DNA differentiations, can not be used for computationally driven automated mining of complex RNA motifs. Though several algorithms have been proposed based on backbone conformational parameters and though algorithms for computational detection of base pairs and analysis of base pair parameters, are available, there are no reports of motif mining studies involving parameters which, as with Zp, simultaneously involve backbone conformation as well as base pairing geometry. In this work, we propose a novel set of parameters, Omega Pseudo-Torsions and Omega Distances, which capture backbone geometries at base(i) - base(j) interaction points and which can be used to computationally characterize structural features both in RNA and DNA. Pseudo torsion angles: Omega eta: P(i)-C4'(j)-P(j); Omega theta: P(i+1)-C4'(j)-P(j+1) Omega 1: P(i)-C4'(i)-C4'(j)-P(j+1); Omega 2: P(i+1)-C4'(i)-C4'(j)-P(j) Pseudo bond distance: Omega distance: C4'(i)-C4'(j) Where 'i' and 'j' are bases interacting through hydrogen bonds. We report the results of our benchmarking studies of Omega parameters with standard DNA structure classification parameters and of our preliminary studies on their effectiveness in classifying local geometries of RNA strands in different base pairing (canonical and non-canonical) contexts.

Abstract

DNA structures and their variations are important in several contexts such as chromatin remodeling and transcriptional initiation and regulation etc. Theneed for computational characterization of DNA structures associated with DNA bending/binding, B ? A transitions in protein-DNA complexes, molecular dynamics trajectory analysis and also in the context of strand orientation, especially in DNA triplexes and quadruplexes, have given rise to several fine grained parameters, such as backbone conformations, sugar pucker and ? angle, local strand orientation, base pair and base pair step parameters, backbone base inclination etc. With their unpaired bases, extensive non helical regions, non-canonical base pairs and tertiary interactions, RNA molecules host a large variety of recurrent structural and functional motifs and parameters such as zp, defined in the context of double helical DNA base pairs and base pair steps and effectively used for A and B DNA differentiations, can not be used for computationally driven automated mining of complex RNA motifs. Thus for RNA structures, though several motif mining algorithms based on backbone conformational parameters and involving computational detection and analysis of base pairs and their parameters are available, there are no reports of studies involving parameters which simultaneously involve backbone conformation as well as base pairing geometry. In this work, we propose a novel set of parameters, Omega Torsions and Omega Distances, which captures backbone geometries at base(i) ? base(j) interaction points and which can be used to computationally characterize structural features both in RNA and DNA. Pseudo torsion angles: Omega ?: P(i)-C4'(i)-C4'(j)-P(j); Omega ?: P(i+1)-C4'(i)-C4'(j)-P(j+1) Omega 1: P(i)-C4'(i)-C4'(j)-P(j+1); Omega 2: P(i+1)-C4'(i)-C4'(j)-P(j) Pseudo bond distance: Omega distance: C4'(i)-C4'(j) Where 'i' and 'j' are bases interacting through hydrogen bonds. We report the results of our benchmarking studies of Omega parameters, as applied to protein DNA complexes including e.g. TATA box-TBP complexes and nucleosomal DNA, with standard DNA structure classification parameters, such as zp, and of our preliminary studies on their effectiveness in classifying local geometries of RNA strands in different base pairing contexts. We conclude that omega parameters can potentially lead to the development of a single set of parameters which can be used to characterize both DNA as well as RNA structures.

Abstract

Projection of a Markov process with constant rates of transition to a small number of observable aggregated states can result in complex kinetics with memory. Here, we define the entropy production along a single sequence of aggregated states and show that it obeys detailed and integral fluctuation theorems. More importantly, we prove that projection shifts the distribution of entropy production over the ensemble of paths for a nonequilibrium process toward one characteristic of a system at equilibrium. This statement represents an analog of the second law of thermodynamics for path-dependent entropies and thus a new form of constraint of irreversible systems. Numeric examples are presented to illustrate these ideas.

Abstract

Capillary Non-Perfusion (CNP) is a condition in diabetic retinopathy where blood ceases to flow to certain parts of the retina, potentially leading to blindness. This paper presents a solution for automatically detecting and segmenting CNP regions from fundus fluorescein angiograms (FFAs). CNPs are modelled as valleys, and a novel multiresolution technique for trough-based valley detection is presented. The proposed algorithm has been tested on 40 images and validated against expert-marked ground truth. Obtained results are presented as a receiver operating characteristic (ROC) curve. The area under this curve is 0.842 and the distance of ROC from the ideal point (0,1) is 0.31.

Abstract

Extraction of anatomical structures (landmarks), such as optic disk (OD), fovea and blood vessels, from fundus images is useful in automatic diagnosis. Current approaches largely use spatial relationship among the landmarks’ position for detection. In this paper, we present an appearance-based method for detecting fovea and OD from colour images. The strategy used for detection is based on improving the local contrast which is achieved by combining information from two spectral channels of the given image. The proposed method has been successfully tested on different datasets and the results show 96% detection for fovea and 91% detection for OD (a total of 502 and 531 images for fovea and OD are taken respectively).

Abstract

For content level access, very often database needs the query as a sample image. However, the image may contain private information and hence the user does not wish to reveal the image to the database. Private content based image retrieval (PCBIR) deals with retrieving similar images from an image database without revealing the content of the query image - not even to the database server. We propose algorithms for PCBIR, when the database is indexed using hierarchical index structure or hash based indexing scheme. Experiments are conducted on real datasets with popular features and state of the art data structures. It is observed that specialty and subjectivity of image retrieval (unlike SQL queries to a relational database) enables in computationally efficient yet private solutions.

Abstract

(URMT) problem, two non-faulty players, the sender S and the receiver R are part of a synchronous network modeled as a directed graph. S has a message that he wishes to send to R; the challenge is to design a protocol such that after exchanging messages as per the protocol, the receiver R should correctly obtain S’s message with arbitrarily small error probability δ, in spite of the influence of a Byzantine adversary that may actively corrupt up to t nodes in the network (we denote such a URMT protocol as (t,(1− δ))-reliable). While it is known that (2t+ 1) vertex disjoint directed paths from S to R are necessary and sufficient for (t, 1)-reliable URMT (that is with zero error probability), we prove that a strictly weaker condition, which we define and denote as (2t, t)-special-connectivity, together with just (t+ 1) vertex disjoint directed paths from S to R, is necessary and sufficient for (t,(1− δ))-reliable URMT with arbitrarily small (but non-zero) error probability, δ. Thus, we demonstrate the power of randomization in the context of reliable message transmission. In fact, for any positive integer k> 0, we show that there always exists a digraph Gk such that (k, 1)-reliable URMT is impossible over Gk whereas there exists a (2k,(1− δ))-reliable URMT protocol, δ> 0 in Gk. In a digraph G on which (t,(1− δ))-reliable URMT is possible, an edge is called critical if the deletion of that edge renders (t,(1− δ))-reliable URMT impossible. We give an example of a digraph G on n vertices such that G has Ω (n2) critical edges. This is quite baffling since no such graph exists for the case of perfect reliable message transmission (or equivalently (t, 1)-reliable URMT) or when the underlying graph is undirected. Such is the anomalous behavior of URMT protocols (when “randomness meet directedness”) that it makes it extremely hard to design efficient protocols over arbitrary digraphs. However, if URMT is possible between every pair of vertices in the network, then we present efficient protocols for the same.

Abstract

Protocols for Generalized Oblivious Transfer(GOT) were introduced by Ishai and Kushilevitz [10]. They built it by reducing GOT protocols to standard 1-out-of-2 oblivious transfer protocols based on private protocols. In our protocols, we provide alternative reduction by using secret sharing schemes instead of private protocols. We therefore show that there exist a natural correspondence between GOT and general secret sharing schemes and thus the techniques and tools developed for the latter can be applied equally well to the former.