WOMEN SCIENTISTS FELLOWSHIP SCHEME (WOS-A) - 2013 DEPARTMENT OF SCIENCE AND TECHNOLOGY,

Section A SECTION A GENERAL INFORMATION

1. Name (in Block Letters) : 2. Husbands name : 3. Postal address for correspondence : 4. E-mail (mandatory) : 5. Permanent address : 6. Date of Birth : 7. Whether belong to SC/ST/OBC/PH : (Attach copy of the relevant certificate) 8. Married/Unmarried : 9. Academic record (from matriculation onwards): S.No. 01 Class/Degree 10th (High School) Board/ University ICSE Subjects English, Hindi, History Civics & Geography, Mathematics, SciencePhy,Che,Bio, Computer Science. English, Physics, Chemistry, Biology, Computer Science. Period of Percent study/Year age 1998 85.6% Ms. SHAZIYA UMAIR Dr. S.M.Umair 4/677-A,Firdaus Complex, Hamdard NagarA, Anoop Shahr Road, Aligarh, U. P., India shaziya_javed@yahoo.com 4/677-A,Firdaus Complex, Hamdard NagarA, Anoop Shahr Road, Aligarh, U. P., India 06-08-1982 No Married

02 03

12th (Intermediate) BCA (Bachellor of Computer Applications) M.Sc. Bioinformatics

ISC

2000 2004

84.4% 66.25%

04

Indira Gandhi All computer subjects National Open University, C.S.J.M. All computer and Bioinformatics University, subjects Kanpur

2007

85.2%

10. Scholarships, Medals, Fellowships, Awards, 1

Throughout distinction holder from

Distinctions or Honors received during your University/academic career:

primary school to post graduation.

11. Whether passed examinations conducted by None NET/GATE/UGC/ICAR, etc. If yes, indicate the name of the examination, year and grade 12. Professional/employment record (if any, in chronological order) : None

13. Provide details of demonstrable research experience (e.g. publications, dissertations, patents, etc.): Two-month project in Central Drug Research Institute(CDRI) on Homology Based modeling of Phosphoribosyl-AMP cyclohydrolase enzyme of Mycobacterium tuberculosis , under the supervision of Dr. M.I. Siddiqi, Scientist, Department of Molecular and Structural Biology, CDRI, Lucknow from May 2006- to Jul 2006. Research papers generated: Presented a paper entitled Diet Therapy of Migraine-A Pilot Study in a National Seminar on Naturopathy jointly conducted by Department of AYUSH & Aligarh Muslim University(AMU). Presented a paper entitled Pre-operative contraindications of herbs-A Therapeutic Evaluation in a National Conference of Surgery JCON -2009(Jarahat Conference) conducted by Department of AYUSH & Aligarh Muslim University(AMU) jointly.

14. Title of Ph.D. thesis and name of Supervisor: M.Sc. Thesis details are as under : Title of thesis :- Microarray Data Analysis of Vibrio cholerae bacterium Supervisor:- Mr. B. Gautam, Assistant Professor, Department of Bioinformatics, UIET, CSJM University, Kanpur. 15. Details of break in career after highest qualification, if any (gap period in years with reasons for break) : Six years ( from 2007- till date) (Marriage and raising the family)

16. Name three (3) institutions and scientists in the country who are working in the proposed area of research: 1) Narayanaswamy Srinivasan Molecular Biophysics Unit Indian Institute of Science Bangalore 560 012 U.P.,India 2

Email:ns@mbu.iisc.ernet.in 2) Prof. Jayaram B. Supercomputing Facility for Bioinformatics and Computational Biology, School of Biological Sciences, Indian Institute of Technology, New Delhi-110016 U.P.,India. Email: bjayaram@scfbio-iitd.res.in 3) Dr. M.I.Siddiqui Scientist -E-I Computational Biology & Bioinformatics Group Molecular and Structural Biology Division Central Drug Research Institute Lucknow- 226001 U.P., India Email: mi_siddiqi@cdri.res.in 17. Are you getting or availed fellowship/scholarship through any other scheme. If yes, please provide details. 18. Any other relevant information: Proficient in following Bioinformatics Softwares/Tools : BLAST, ClustalW, Genesis, Chimera, SwissPDBViewer, Rasmol, ChemDraw, Geno3D. Certificate in Computing (CIC) from Indira Gandhi National Open University (IGNOU) with 74.3% marks in the year 2001.

None

Diploma in Office Management with grade A from LOGIN Computers goverened by Login Educational Society (Regd. by U.P. Govt.) in the year 2002. Certificate of proficiency in C & Data Structures with grade A from NICE Computer Institute, (Regd No. 451) Lucknow in the year 2002. Certificate of proficiency in Visual Basic with grade A from NICE Computer Institute (Regd No. 451), Lucknow in the year 2003.

SECTION B DETAILS OF THE R&D PROJECT

1. Title of the Project : Homology based Modeling of new strain of H1N1 Influenza Virus (Swine Flu) proteins. Life Sciences Bioinformatics 15,00,000/- (Fifteen lacs I.N.R.)

2. Broad subject area (as given in Subject Code) : 3. Area of specialization : 4. Total cost of the project :

5. Summary of the proposal (not exceeding 500 words) : The 2012-13 flu pandemic is a global outbreak of a new strain of H1N1 influenza virus, often referred to as swine flu, and because laboratory testing showed that many of the genes in this new virus was very similar to influenza viruses that normally occur in pigs in North America. But further study has shown that this new virus is very different from what normally circulates in North American pigs. It has two genes from flu viruses that normally circulate in pigs in Europe and Asia and avian genes and human genes. Scientists call this a quadruple reassortant virus. This swine H1N1 virus has put the world on pandemic alert mainly because of two reasons. Firstly, the disease is highly infectious and contagious and can be deadly in humans. Secondly, the details of what makes swine influenza virus so infectious in humans are largely unknown. There are many constitutive proteins of this virus whose structures are unknown.With the development of techniques in molecular biology that allow rapid identification, isolation, and sequencing of genes, we are now able to infer the sequences of many proteins. However, it is still a time-consuming task to obtain the three-dimensional structures of these proteins. A major goal of structural biology is to predict the three-dimensional structure from the sequence. Thus, alternative strategies are being applied to develop models of protein structure when the constraints from X-ray diffraction or NMR are not yet available. One method that can be applied to generate reasonable models of protein structures is homology modeling. This procedure, also termed comparative modeling or knowledge-based modeling, develops a three-dimensional model from a protein sequence based on the structures of homologous proteins. Homology has a precise definition: having a common evolutionary origin. 4

Homology modeling involves taking a known sequence with an unknown structure and mapping it against a known structure of one or several similar (homologous) proteins. It would be expected that two proteins of similar origin and function would have reasonable structural similarity. Therefore it is possible to use the known structure as a template for modeling the structure of the unknown structure. Thus the revelation of the three-dimensional structures may lead to new targets for the drugs, thereby promoting a better cure for it. 6. Objectives : I. Predicting the unknown structures of new strains of swine flu virus proteins using homology based modeling technique. II. Creation of database of the predicted structures of swine flu virus proteins. 7. National and international status : a. Review of literature in the proposed area of research: Deadly new flu virus in US and Mexico may go pandemic". New Scientist. 2009-04-26. http://www.newscientist.com/article/dn17025-deadly-new-flu-virus-in-us-and-mexico-maygo-pandemic.html. Retrieved 2009-04-26. Susan Watts (2009-04-25). "Experts concerned about potential flu pandemic". BBC. http://www.bbc.co.uk/blogs/newsnight/susanwatts/2009/04/experts_concerned_about_potent. html. Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites Sebastian Maurer-Stroh, Jianmin Ma, Raphael Tze Chuen Lee, Fernanda L Sirota and Frank Eisenhaber Biology Direct 2009, 4:18doi:10.1186/17456150-4-18 Whats Different (and Dangerous) About Swine Flu? Kara Rogers - April 29th, 2009 http://www.britannica.com/blogs/2009/04/whats-different-and-dangerous-about-swineflu/ H1N1 update review Saudi Med J. 2010 Mar; 31(3):235-46. Alenzi FQ. Associate Professor of Immunology, Department of Clinical Laboratory Sciences, College of Applied Medial Sciences, Al-Kharj University. The organic chemistry of drug design and drug action by Silverman,R.(Ed.) 5

Academic Press, 2004 [Amazon] Bioinformatics : From Genomes to Drugs by Lengauer, T. (Ed.) VCH Verlagsgessellscchaft mbH, 2001 [Amazon] Protein Ligand interactions : From Molecular Recognition to Drug design by Bohm, HJ,;Schneider, G. (Eds.) ; John Wiley & Sons, 2003 [Amazon] Drug Discovery and Evaluation , Pharmacological Assays; H. Gerhard Vogel (Ed.);CoEditors: Wolfgang H.Vogel,Bernward A. Schlkens,Jrgen Sandow,Gnter Muller, Wolfgang F. Vogel; Second Edition Structural Bioinformatics ; Editors: Phil Bourne and Helge Weissig

8. Methodology : Study design: 1. Find the sequences of the proteins with unknown 3D structure, the "target sequence". 2. Then 3D templates are chosen by virtue of having the highest sequence identity with the target sequence. The 3D structure of the template must be determined by reliable empirical methods such as crystallography or NMR, and is typically a published atomic coordinate "PDB" file from the Protein Data Bank. 3. Align the sequences 4. Identify structurally conserved and structurally variable regions structure from those of the known structure(s) 6. Generate conformations for the loops (structurally variable) in the unknown structure 7. Build the side-chain conformations 8. Refine and evaluate the unknown structure 9. Create a database and save the predicted 3D structures in it. Sample size and Selection of Subject/Plants Our aim is to find the 3D structures of proteins of H1N1 swine flu virus that caused pandemic in the year 2009. There are more than 4000 entries of this strain in the UniProt -SwissProt database. In this project atleast 500 such proteins will be considered whose structures are unknown and which are functionally important. However the sample size may increase or decrease depending on the time elapsed in modeling of single protein. 5. Generate coordinates for core (structurally conserved) residues of the unknown

Survey tools There are several tools that may be required in this project. These are: 1) Protein databases like UniProt/ Swiss Prot and Protein DataBank(PDB) 2) Sequence similarity searching tools like FASTA and BLAST. 3) Protein structure modeling tools like Geno3D , MODELLER 9v7 4) Structure visualization tools like UCSF Chimera, Ras Mol and Swiss PDB viewer 5) Model evaluation tools like PROCHECK provided by the SAVS SERVER, ProSA and Verify3D. 6) Database Creation and management tools like MySQL and Microsoft-Access. 9. Work plan : Methods of estimations proposed Retrieval of target sequences The query sequence or the target sequences of proteins of H1N1 virus are retrieved from UniProtKB /Swiss-Prot database. It is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Search for homologous sequence The query sequence or the target sequence is used as the query in the similarity search programs like BLAST ( Basic Local Alignment Search Tool) and FASTA. BLAST is an algorithm for comparing primary biological sequence information that enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. The similar sequences are called template sequences. FASTA is also a DNA and protein sequence alignment software package. Modeling of the protein 3D structure Protein structure modeling tools like Geno3D, MODELLER 9v7 are used for this. Geno3D is an automatic web server for protein molecular modeling. Starting with a query protein sequence, the server performs the homology modeling in six successive steps: (i) identify homologous proteins with known 3D structures by using PSI-BLAST; (ii) provide the user all 7

potential templates through a very convenient user interface for target selection; (iii) perform the alignment of both query and subject sequences; (iv) extract geometrical restraints (dihedral angles and distances) for corresponding atoms between the query and the template; (v) perform the 3D construction of the protein by using a distance geometry approach and (vi) finally send the results by e-mail to the user. MODELLER is a computer program that models three-dimensional structures of proteins and their assemblies by satisfaction of spatial restraints. It is most frequently used for homology or comparative protein structure modeling: The user provides an alignment of a sequence to be modeled with known related structures and it will automatically calculate a model with all nonhydrogen atoms. More generally, the inputs to the program are restraints on the spatial structure of the amino acid sequence(s) and Ligands to be modeled. The output is a 3D structure that satisfies these restraints as well as possible. Restraints can in principle be derived from a number of different sources. These include related protein structures (comparative modeling), NMR experiments (NMR refinement), rules of secondary structure packing (combinatorial modeling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue-residue and atom-atom potentials of mean force, etc. The restraints can operate on distances, angles, dihedral angles, pairs of dihedral angles and some other spatial features defined by atoms or pseudo atoms. Presently, MODELLER automatically derives the restraints only from the known related structures and their alignment with the target sequence. A 3D model is obtained by optimization of a molecular probability density function (pdf). The molecular pdf for comparative modeling is optimized with the variable target function procedure in Cartesian space that employs methods of conjugate gradients and molecular dynamics with simulated annealing. Model visualisation We visualize the model obtained from GENO3D and MODELLER through following softwares UCSF Chimera, RasMol and Swiss-PDB Viewer. UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and movies can be created.

RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, Hbonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Model evaluation The aim of model evaluation is to determine whether the model is acceptable or not. If it is not acceptable, that is if current model violates some restrictions, these evaluations should help to re-align the target sequence and template for the next cycle of modeling. Some tools used for this are PROCHECK, ProSA and Verify3D. PROCHECK provided by the SAVS SERVER. PROCHECK checks the stereo chemical quality of a protein structure, producing a number of postscript plots analyzing its overall and residue-by- residue geometry. This program is useful for accessing the quality not only of the protein structures in the process of being solved, but also of the existing structures and those being modeled on the known structures. The aim of PROCHECK is to access how normal, or conversely how unusual, the geometry of the residues in a given protein structures, as compared with the stereo chemical parameters derived from well-refined, high-resolution structures. Unusual regions highlighted by PROCHECK are not necessarily errors as such, but may be unusual features for which there is a reasonable explanation Verify3D Structure Evaluation Server is a tool designed to help in the refinement of crystallographic structures. It will provide you with a visual analysis of the quality of a putative crystal structure for a protein. Verify3D expects this crystal structure to be submitted in PDB format. Database creation After the structures are modelled and validated, they will be assembled in a database.A database is a collection of data for one or more multiple uses. A Database Management System (DBMS) is a set of computer programs that controls the creation, maintenance, and the use of the database 9

with computer as a platform or of an organization and its end users. Various DBMS softwares are there for this purpose like MySQL and Microsoft-Access. 10. Expected deliverables/outcome : There is worldwide concern on the spreading pandemic wave of the new swine influenza virus. The WHO has placed the pandemic threat alert to level 6. World leaders and scientists importantly stress that regulations and pandemic preparedness may lower the morbidity and mortality. With the development of techniques like homology modeling the 3D structure of a target protein for which only the sequence is available can be approximated, that in turn may be helpful in determining their role in metabolic pathways. Since Swine flu is such a deadly disease, identifying the structure and functions of its various proteins may lead to better drug targets which may further lead to the design of a better drug in near future moreover understanding the proteins of this particular strain of virus will automatically help to contain its other strains since all have remarkable similarities. Henceforth this work will directly or indirectly going to benefit the masses in many ways. The expected deliverables are: 1. Better understanding of 3D structure of previously unknown proteins of this new strain of H1N1 Influenza Virus. 2. Designing of novel drugs to fight the virus by incorporating the knowledge gained by 3D Homology of Proteins that is identification of better drug targets. 3. Better understanding of prevention stragedies using the gene mapping resources. 11. Significance of the expected outcome with respect to the state-of-the-art in the field : The main utility of the successful completion of research project will be in the field of drug designing against new deadly threats to mankind in the form of nowel pathogens and microbes. The protein identification and modeling once done will be verified using wet lab studies. Thus a database having the 3d homology modeled structures of its potential proteins will pave a way towards better understanding of this hybrid strain of virus that creates a havoc globally not seen before. 12. Name, address of the institution and bio-data of the scientist-mentor (including last 5 years publications in cited journals) with whom the proposed R&D study will be executed. 13. Facilities in terms of laboratory, equipment, etc. likely to be made available to the 10

candidate by the host institution for pursuing the above studies : 14. Details of financial requirements (with justification) for the duration of the project (3 years) and year-wise phasing : S.No. Head 1st Year 2nd Year 3rd Year Total : Proposed Budget for two years (Fellowship,Consumables,Travels,Equipments,Overhead charges with detailed justification for each item) S.No. 1. 2. 3. 4. 5. HEAD Research Fellowship Consumables (includes day to day expenses ) Travel (within India) Contingencies ( include licensed system softwares) Minor equipments (IBM fully loaded system with LCD monitor, 4 GB DDR-3 RAM, INTEL CORE I-3 Processor; Paid homology modeling Softwares etc.) Overhead charges Grand Total 1st YEAR 1,20,000/50,000/15,000/1,50,000/2nd YEAR 1,20,000/50,000/15,000/1,50,000/TOTAL 2,40,000/1,00,000/30,000/3,00,000/-

2,00,000/-

1,50,000/-

3,50,000/-

6.

40,000/5,75,000/-

40,000/5,25,000/-

80,000 11,00,000/-

15. Justification for the budgetary requirement item wise based on the scientific needs of the project : Detailed justification of breakup proposed budget for two years: 1. Research Fellowship: The fellowship as suggested by the DST till date is 10,000/- INR per month for the M.Sc. candidates. Thus total budget for two years will come out to be 2, 40,000/- INR.

11

2. Consumables (includes day to day expenses): For the successful running of project there should be no delay in meeting the day to day expenses regarding print material and other small accessories like print cartridge etc. thus this particular amount is always required in hand for quick procurement of desired material related to the project and thereby saving the precious time. 3. Travel (within India): This budget is needed to met out the expenses regarding knowledge exchange programmes with centre of exellences in india like CDRI and to participate in national or international conferences, seminars or workshops relating the subject. This will promote better understanding of the subject. 4. Contingencies (include licensed system softwares): The budget in this head is solely meant for the small but necessary tools that will be used in any system related research work like molecule visualization softwares, antivirus softwares, operating systems, system accessories like external hard disc- 300GB, Scanner, laser printer and system maintenance charges. as the maintenance of these sophisticated electronic systems is of utmost importance. 5. Minor equipments: In this head, a fully loaded computer system is required which will capable of to run highly specific bioinformatics softwares, that is an IBM System with large screen LCD monitor, latest 4 GB DDR-3 RAM, new generation INTEL CORE I-3 Processor; except this some Paid homology modeling Softwares will be needed like MODELLER 9v7, Structure visualization tools like UCSF Chimera, Ras Mol and Swiss PDB viewer, Model evaluation tools like PROCHECK provided by the SAVS SERVER, ProSA and Verify3D, Sequence similarity searching tools like FASTA and BLAST and CLC PROTIEN WORKBENCH KIT(Including secondary protein structure prediction, 3D molecular view, antigenicity analysis, and BLAST on local databases) etc. 6. Overhead charges: Will be needed in this project for Lab maintainance in the host institute. 16. Details of research funding received or applied for (mention reference no., title, duration, cost, funding agency and brief achievements) : None

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Section E Documents to be submitted along with the application: a. Attested copy of the last Degree certificate b. Format for the certificate from the Host institute (on a letter head) regarding extending their commitment for infrastructure and administrative support for the project. c. Certificate from the field agency (on its letter head) indicating the permission and the support for carrying out the field work required in the proposal. d. In case the host is voluntary organization, attested copies of the following document also need to be submitted: 1) 2) 3) 4) Registration certificate of the organization Memorandum of association Annual report of last three years Audited statement of accounts for last three years

Not Applicable

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DECLARATION

I do hereby declare that the statements made in this application are true, complete and correct to the best of my knowledge and belief. In the event of any information being found false or incorrect or ineligibility detected before or after test/interview, my candidature will stand cancelled and my all claims for the scholarship will stand forfeited.

Signature of applicant

Place:

Date:

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Forwarding letter from head of the sponsoring institute on a letter head

To, Director, Science & Society Division DST, New Delhi Dear Sir/Madam, I am forwarding this application under the DST sponsored scheme for Women Scientist for social program WOS-B by Ms. Shaziya Javed. She has formulated this proposal according to the suggestions recommended by selection committee. I hereby certify that Department of Biochemistry, Faculty of Life Sciences of Aligarh Muslim University, Aligarh will host the said project of DST and offer her the necessary infrastructural facilities related to laboratory requirement of work place , administrative support during the entire project period and will receive regularly her fellowship from the date of her joining. The candidate will follow the existing rules and regulations for research student (for M.Sc.) of the institute. She will be working under the guidance of Dr. Mohd. Tabish, Senior Reader of Department of Biochemistry, faculty of life sciences, AMU, Aligarh. Thanking you Yours sincerely

(Name and Sign of Institutional Head)

(Date)

(Place)

(Institutional Stamp)

(Name and Sign of Institutional Guide)

(Date) 15

(Place)

(Institutional Stamp)