A comparative Docking Analysis of Non-carcinogenic DNA staining Dyes to propose the best Alternative to Ethidium Bromide
Fluorescent dyes that stain a cell’s DNA are used in live cell imaging as they allow for tracking of cell division, for the visualization and sizing of dsDNA restriction fragments, and for the examination of properties of the isolated DNA molecules. Conventionally, Ethidium bromide (EtBr) is the cationic dye used to visualize DNA after separating the fragments on Agarose Gel Electrophoresis. It is widely used due to the striking fluorescence enhancement it displays upon intercalation into the dsDNA at the minor groove. Although a highly sensitive stain, it is notoriously unsafe, not only is it a very strong mutagen, it may also be a carcinogen or teratogenic. Histopathological changes of Ethidium Bromide treated rats showed little degenerative changes characterized by glomerular and tubulointerstitial injury, nephrosis, synechia, necrotic changes, cirrhosis, and ischemia. Ethidium bromide revealed pronounced degenerative changes in ovarian histoarchitecture. The sequence of atretic changes involved nuclear degeneration, characterized by Chromatolysis, rupture, and dissolution of the nuclear membrane. Granulosa cells associated with degenerating follicle types (bilaminar, Multilaminar and graffian follicle) showed desquamation, cytolysis, and nuclear dissolution.Extensive vacuolation also occurred in these follicles. Only a few follicles reached the maturity. In most of the females, Graffian follicle failed to rupture, which led to failure in ovulation. This resulted in Sterility of the females.Hence need has arisen for now –carcinogenic and not- hazardous nucleic acid staining dyes.Our Present study has thus been aimed at finding out the non-carcinogenic DNA staining dyes and to compare their binding efficiency with DNA and find out which is the best DNA staining Dye which has least binding energy score and is non-carcinogenic as well. Hence now-a- days safer alternatives to EtBr are being sought after. A comparative docking study of six of such The interaction of EtBr and the six other alternative dyes (Crystal violet, GelRed, Hoechst 33258, Methylene blue, SYBR Green and GelGreen) with the ds-B-DNA were studied, their chemical structures were drawn using ChemSketch and the potential ligands were optimized using ArgusLab. Further, the docking studies of these DNA stains on a dsDNA molecule (1D49) was performed using AutoDock tools and their interaction with the DNA was visualized using Discovery Studio. The binding energies of Hoechst 33258 with the DNA was found to be better (-11.96 Kcal/mol) as compared to the other strains, thus suggesting its use as both a non-carcinogenic and highly sensitive alternative to EtBr.
Published by: Manisha Mathur, Parakh Sharma, Priyanka Yadav, Christy Joseph
Author: Manisha Mathur
Paper ID: V3I2-1226
Paper Status: published
Published: March 14, 2017
ANXA5 Gene: An Insilco approach for SNP analysis associated with RPL
Miscarriage is the most familiar pregnancy obstacle affecting up to 15% of all clinically recognized pregnancies. Annexin A5 gene is a well-recognized predisposition factor for recurrent spontaneous abortion. Annexin A5 is both Ca2+ and phospholipids binding protein that is localized at the surface of the placental syncytiotrophoblast layer and performs a vital role in anticoagulant function in the maternal blood at the inter villous space. It has been recently shown that polymorphisms in the promoter region of the annexin A5 gene (ANXA5) are significantly associated with RPL. The present study focuses on the comprehensive analysis of the functional and structural impact of all known SNPs of ANXA5 gene by using computational approaches. Comprehensive analysis was performed to filter the most probable mutation that might be associated with RSA. It resulted in identification of SNPs which are most deleterious and disease associated. The study reveals that these two rs111418524, rs41278081 SNPs have more significant effect on structure and function of the protein.
Published by: Nasreen Sultana, Jeevan Amos. S, Kasturi. K
Author: Nasreen Sultana
Paper ID: V3I2-1221
Paper Status: published
Published: March 13, 2017
Insilico studies on Taste Receptor Gene (Tas2r38) and Tas2r38 Protein interaction with Ligands PTC and PROP using Docking Approach
The G protein-coupled receptor(gpcr)Tas2r38 is a bitter taste receptor that can respond to bitter compounds such as phenylthiocarbamide(PTC) and 6-n-PROPylthiouracil(PROP).This receptor was chosen because of its haplotypes (based on three residue site polymorphism) htas2r38pav, htas2r38avi are known to have a dramatically different response to ligands PTC and PROP. A docking study is performed to propose the best affinity between ligands PTC & PROP against the various active site of tas2r38 protein. The 3D structure of tas2r38 bitter taste receptor was predicted using GPCR-I-TASSER. The interaction of tas2r38 protein with ligands PTC & PROP were studied, their chemical structures were drawn using Marvin sketch and the potential ligands were optimized using pyrx. Meta pocket tool was used to predict the binding sites for htas2r38pav, htas2r38avi bound to Ptc & PROP respectively. Further, the docking studies of tas2r38 protein with Ptc & PROP was performed using pyrx tools and their interaction with the tas2r38 protein was visualized using discovery studio. The ligand PTC & PROP was docked on the protein PAV at the active sites 108,112,199 & 266 which showed a docking efficiencies of -4.6,-4.5,-4.7 &-5.3 respectively. Also, these ligands were docked on another haplotype AVI at the active sites 198,262,266 which showed a docking efficiencies of -4.7,-5.1, respectively. On the basis of their binding scores, it was predicted that the ligand PTC has a higher binding affinity to the haplotypes PAV and AVI as compared to the ligand PROP.
Published by: Manisha Mathur, Parakh Sharma, Faiza S. Khan, Mrunmai Pednekar
Author: Manisha Mathur
Paper ID: V3I2-1216
Paper Status: published
Published: March 11, 2017
A Review on Distribution Feeder Reconfiguration Methods
Distribution Feeder Reconfiguration (DFR) is a critical analysis to optimize and control the distribution system and an important function of distribution automation system. Distribution feeders are configured radially. Their configurations may be varied with manual or automatic switching operations so that all of the loads are supplied with acceptable voltage levels, reduce power loss and enhance power quality. DFR also relieves the overloading of the network components. The change in network configuration is performed by opening sectionalizing (normally closed) and closing tie (normally open) switches of the network. These switchings are performed in such a way that the radiality of the network is maintained and all of the loads are energized. This paper presents a review of Distribution Feeder Reconfiguration (DFR) methods which includes heuristic and genetic algorithm approach.
Published by: K. K. S. V. V Prakasa Rao, V. C Veera Reddy
Author: K. K. S. V. V Prakasa Rao
Paper ID: V3I2-1215
Paper Status: published
Published: March 11, 2017
Optimize workflow scheduling Using Hybrid Ant Colony Optimization (ACO) & Particle Swarm Optimization (PSO) Algorithm in Cloud Environment
AbstractThose days are gone when storing and accessing of data were done on computer’s hard drive. Now with innovation in technology and with the great success of Internet Computing resources have become more economical, more powerful and more ubiquitously available than ever before. This technological trend of the 21st century has given birth to the realization of a new computing model called Cloud Computing. This Computing is not only about the hard drives were storing and accessing can be done but it is latest computing paradigm and it offers tremendous opportunities to solve the large-scale scientific problem. To fully exploit the applications of cloud, various challenges need to be addressed where scheduling is one among them. Although catholic research has been done on Workflow Scheduling, there are very few edges tailored for Cloud environments. For some basic principles of Cloud such as elasticity and heterogeneity existing work fails to meet optimal solution. Therefore our work focuses on the scheduling strategies for scientific workflow on IaaS cloud. We present an algorithm based on the meta- heuristic optimization technique where the best of two algorithms Ant colony Optimization (ACO) and Particle Swarm Optimization (PSO) are merged to optimize locally and globally which minimizes the overall workflow time (makespan) and reduces the cost. Our heuristic is evaluated using CloudSim and several well-known scientific workflows of different sizes. The results show that our approach performs better when compared to PSO algorithm.
Published by: Misha Goyal, Mehak Aggarwal
Author: Misha Goyal
Paper ID: V3I2-1213
Paper Status: published
Published: March 11, 2017
A Survey on How Main Method Working in C Programming
Abstract: By the completion of this paper study we have the better idea about the main method. Generally, many people have the doubt about the main method is the predefined or user defined method? If it is user defined where is the prototype of that method? or If it is predefined in which header file its prototype is present? By the end of this paper study, we have the clarity of Is main method is a user-defined or predefined method. And also this paper give the clarity about user-defined and predefined methods in C Programming.
Published by: G. Anupama, M. Phani Anusha, Y. Vasanthi
Author: G. Anupama
Paper ID: V3I2-1212
Paper Status: published
Published: March 11, 2017
