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:
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