Wednesday, October 10, 2012

Winter School on Advance Molecular Techniques in Gene Regulation and Functional Genomics



Winter School on  Advance Molecular Techniques in Gene Regulation and Functional Genomics
At
Animal Biochemistry Division
National Dairy Research Institute
(Deemed University)
Karnal - 132001 Haryana

December 3-23, 2012


Deadline of application October 31, 2012


Animal Biochemistry Division of National Dairy Research Institute (Deemed University) is proud to announce a winter school on “Advance Molecular Techniques in Gene Regulation and Functional Genomics”. The objectives of the winter school is to refresh young, mid-career and senior level scientific professionals with cutting edge advance molecular biology techniques of functional genomics.

Course Summary The proposed intensive laboratory and computer-based training course will introduce participants to a wide range of advance molecular techniques in gene regulation and functional genomics. Techniques includes hands-on experience in performing molecular techniques (i.e. restriction digestion, ligation, DNA gel electrophoresis, and gel extraction, transformation and plasmid purification, cloning and sub-cloning, amplification of DNA fragments by polymerase chain reaction (PCR), expression profiling using the latest platforms (Real-Time Quantitative PCR), Recombinant Protein Expression & Purification and Characterization), Gene regulation studies (chromatin immunoprecipitation (ChIP) assay, Electrophoretic mobility shift assay (EMSA)], Enzyme-linked immunosorbent assay (ELISA), Suppression subtractive hybridization (SSH) technique, Structural single nucleotide polymorphisms (SNP) modelling, High-Throughput Proteomic Analysis (2-D, MALDI) and RNAi experiments in mammalian cells. Laboratory work will be complemented by training in state-ofthe- art approaches to data analysis and interpretation through the use of a wide range of bioinformatics resources related to gene regulation and functional genomics such as promoter analysis pipeline etc. Particular emphasis will be placed upon the integration of complementary approaches to ask specific biological questions. The course will include seminars by distinguished divisional, institute faculties and invited guest speakers who will share cutting-edge research in functional genomics and systems biology. The proposed winter school course will cover following topics: Functional genomics: A field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects (such as genome sequencing projects) to describe gene (and protein) functions and interactions. Unlike genomics and proteomics, functional genomics focuses on the dynamic aspects such as gene transcription, translation, and protein–protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures. Functional genomics attempts to answer questions about the function of DNA at the levels of genes, RNA transcripts, and protein products.
A key characteristic of functional genomics studies is their genome-wide approach to these questions, generally involving high-throughput methods.
Structural single nucleotide polymorphisms (SNP) modelling: Owing to the application of high-throughput SNP detection techniques, the number of identified SNPs is growing rapidly, enabling detailed statistical studies. These include studies of SNPs that affect the amino acid sequence of a gene product (non-synonymous SNPs). To understand the relationship between genetic and phenotypic variation, it is essential to assess the structural consequences of the respective non-synonymous mutations in proteins. To quantify how often a disease phenotype can be explained by a destructive effect on protein structures or functions, we have to map known disease mutations onto known three-dimensional structures of proteins.
Mapping the 5' and 3' ends of mRNA/5' and 3’- RLM-RACE: Rapid amplification of cDNA ends (RACE) is a polymerase chain reaction-based technique which facilitates the cloning of full-length cDNA sequences when only a partial cDNA sequence is available. The techniques can also identify transcriptional start site (TSS) and identification of promoter as well.
Epigenetics, Chromatin remodelling and DNA methylation: Silent genes are assembled in a particular chromatin conformation that restricts the access to the transcriptional machinery. This closed chromatin is usually characterized by covalent modifications of both DNA (cytosine methylation within the CpG dinucleotide) and chromatin proteins (i.e, methylation of key histone residues). Through a complex network of feedback loops, these modifications participate to the stability of the epigenetic memory of gene activity. The activation of silent genes during development and in the adult requires several chromatin opening events triggered by regulatory factors recruiting various chromatin remodelling machineries (enzymes inducing covalent modifications of histone tails or controlling DNA interaction with the nucleosome).
Chromatin Immunoprecipitation (ChIP) Assay: Chromatin Immunoprecipitation (ChIP) assay is used to evaluate the association of proteins with specific DNA regions. The technique involves cross linking of proteins with DNA, fragmentation and preparation of soluble chromatin followed by immunoprecipitation with an antibody recognizing the protein of interest. The segment of the genome associated with the protein is then identified by PCR amplification/QRT-PCR of the DNA in the immunoprecipitates.
Electrophoretic mobility shift assay (EMSA): Also referred as mobility shift electrophoresis or gel shift assay, gel mobility shift assay, band shift assay, or gel retardation assay, is a common affinity electrophoresis technique used to study protein–DNA or protein–RNA interactions. This procedure can determine if a protein or mixture of proteins is capable of binding to a given DNA or RNA sequence, and can sometimes indicate if more than one protein molecule is involved in the binding complex.
RNA interference (RNAi): RNAi has recently emerged as one of the most powerful tools for examining gene function. RNAi refers to the introduction of homologous double stranded RNA (dsRNA) to specifically target a gene's product, resulting in null or hypomorphic phenotypes. The presence of dsRNA, formed from the annealing of sense and antisense strands present in the in vitro RNA preps, which is responsible for producing the interfering activity. Introduction of dsRNA into the cells results in the loss of the targeted endogenous mRNA. This phenomenon has been effectively used to study gene function. The most interesting aspects of RNAi are the following: (i) dsRNA, rather than single-stranded antisense RNA, is the interfering agent, (ii) it is highly specific, (iii) it is remarkably potent (only a few dsRNA molecules per cell are required for effective interference), (iv) the interfering activity (and presumably the dsRNA) can cause interference in cells and tissues far removed from the site of introduction.
Recombinant Protein Expression, Purification and Characterization: Biologically active recombinant proteins are the livelihood of the biotechnology industry and functional genomics. Once a gene has been cloned and its protein product expressed, it must be purified from the cell expression system.
Further, the purified recombinant protein must characterized with regard to it physical and molecular properties.
Eligibility qualification/How to apply: Applications are invited from interested faculty, researchers, teachers, scientists of Animal Biochemistry, Animal Biotechnology, Dairy Microbiology, Dairy Chemistry, Food Sciences and any relevant discipline of animal and veterinary and Dairy sciences/Fisheries/Natural Resources and allied sciences and having interest in Molecular biology and working under NARS (National Agricultural Research System) not below the rank of Scientist/Assistant Professor. Application must reach to course Director positively on or before October 31, 2012. Intending participants, who anticipate delay in sending their application through proper channel, may send advance copy of their application. However, it would be responsibility of the participants to bring duly forwarded copy of application or a no objection certificate before the joining the course. Format of application may be copied as attached with the brochure or it can be downloaded from the institute website (www.ndri.res.in). The application may also be sent though mail to Course Director (drdheer.singh@gmail.com; dheer@ndri.res.in).

Certificate: A certificate will be awarded to the participants on successful completion of the training.
Financial assistance/Course fee: The winter school is sponsored by Education Division (ICAR) with the objective to train the scientists of NARS in the frontier area of Research and therefore no major course fee. However, a registration fee of Rs. 50 per participants will be charged and the same will be collected from the participants at the time of their registration for joining the Summer school/Winter school/Short courses. The participants will be paid TA for to and fro journey by rail/bus/public transport by the shortest route as per the entitlement class but restricted to A.C. II train fare (on producing ticket/ fare document). They should also certify or to submit the certificate from the parent institute/organization to the effect that that they are not being paid TA/DA for this course.

Boarding and Lodging: Accommodation will be arranged for the participants free of cost in the institute scientist home/Govt. accommodation for the period of their stay during the course. Wholesome food will be provided to all the outside participants. Local participants will be provided with minimum hospitality with lunch, tea, coffee etc. as per the ICAR norms. Due to restricted availability of accommodation, please do not bring the family members with you.

How to apply:
Format of application may be copied as attached with the brochure at http://www.ndri.res.in/ndri/Design/documents/Brochure_17may12.pdf  or it can be downloaded from the website www.ndri.res.in.  The application may also be sent though mail to Course Director (drdheer.singh@gmail.com ; dheer@ndri.res.in ).

Application must reach to course Director positively on or before October 31, 2012. Intending participants, who anticipate delay in sending their application through proper channel, may send advance copy of their application.

For further details, visit the link:


All Correspondence should be address to
Dr. Dheer Singh
Senior Scientist & Course Director
Animal Biochemistry Division
National Dairy Research Institute
(Deemed University)
Karnal- 132001 (Haryana) India
Email: drdheer.singh@gmail.com; dheer@ndri,res.in
Phone: 0184-2259135 (work), 09416411258 (Cell); Fax: 0184- 2250042

1 comment:

Unknown said...

Thanks for your grateful informations, this blogs will be really help for Students admissions.