Training Courses and Workshops at College of Agriculture and Natural Resources

Workshop Title

Code

Agenda

Course duration

 (day)

Fee per person

 (USD)

Bioinformatics: Basic and Advanced Insights

2012-01

DNA and Protein Databases (NCBI, EMBL, DBJ…), Pairwise and multiple alignment of sequences (BLAST, …), Computer Softwares for Multiple Alignment, Primer design (gene specific and degenerate primers), Genome projects, Gene finder, ORF finder, Codon bias, EST and UniGene databases, EST profiling, Protein motif and domain analysis, Finding promoters, In Silico expression and cloning, Contig assembly, Sequencing data analysis and troubleshooting, Modelling and prediction of protein structure, Training softwares (Vector NTI, DNA Star, GeneDoc, Mega5, CLC Bio, Primer3 Plus,…)

4

1000

Gene Cloning and Transformation into Prokaryotes and Eukaryotes

2012-02

Regulatory sequences and Regulatory engineering, Primer design strategies, Primer design softwares, Homology search in databases, Find genes and promoters, Design gene cloning strategy, RACE PCR, Nested PCR, Digestion, Gel recovery, Ligation (T4, TOPO and GateWay Cloning), Sequencing, Transformation into competent cells (Heat shock/ electroporation), Selection of transformed and recombinant colonies, Colony PCR, Plasmid DNA extraction, Expression and Binary vectors, DNA/RNA and protein extraction, Agrobacterium gene transformation, GUS assay, GFP/YFP assay, Gene Gun transformation, Floral dip methodology, selection techniques for transgenic lines (PCR using gene specific primers/Promoter-terminator primers, Sothern blot, Western blot, RT-PCR), Biosafety of GMO,s and related protocols

5

1500

Gene Silencing Applications: Antisense, RNAi and VIGS

2012-03

Cloning technologies, In Silico Cloning and modelling, Antisense, RNAi and VIGS, Primer design and gene silencing constructs, RNAi constructs, VIGS vectors and constructs (TRV1/TRV2), Phenotypic markers to detect silencing in different tissues, pds and Chalcone synthase gene structure, Agro infiltration

4

1000

Molecular Markers: Basic and Advanced Applications

2012-04

Theory and applied courses about different molecular markers, i.e. RAPDs, ISSRs, SSRs, AFLPs, RFLPs, SNPs and statically analysis of morphological and Molecular traits, as well as Map-based cloning of genes and QTLs, BSA and Marker Assisted Selection (MAS)

5

1500

Basic Principles of RT-PCR and Real-Time PCR

2012-05

Primer and Probe design, DNA/RNA extraction, cDNA synthesis, One Step and Two Step RT-PCR, Housekeeping gene selection, Basic principles of Real-Time PCR, Detection formats (SYBR Green, TaqMan probes, HybProbe Probes), Absolute and relative quantification, Gene expression analysis, Melt curve analysis, Bioinformatics and data analysis (Pfaffl, E-method, ∆∆Ct)

4

1000

Advanced Principles of Real-Time PCR

2012-06

Bioinformatics and primer and probe design, DNA/RNA extraction and cDNA synthesis, Advanced principles of Real-Time PCR, Real-Time PCR detection formats (SYBR Green, TaqMan probes, HybProbe Probes, ResoLight for HRM, Scorpion, …), Standard curve analysis for absolute and relative quantification, Gene expression analysis by Ct method, DNA methylation analysis, SNPs detection and haplotyping, Qualitative detection (Absence/Presence), GMO,s detection, De novo mutation detection by HRM analysis, Training softwares (Oligo Calculator, Beacon designer, Primer Express)

5

1500

Applied Techniques in Molecular Labs

2012-07

Bioinformatics and primer design, DNA/RNA extraction, PCR and RT-PCR, Electrophoresis, DNA gel recovery, PCR product and digestion product purification, Ligation (T4, TOPO and GateWay Cloning), Competent cells (Bacteria and Yeast), Transformation (Heat shock and electroporation), Selection media, Select transformed and recombinant cells, Digestion and Colony PCR, Plasmid DNA extraction, Principles of Sequencing, In vitro gene expression, Cloning and Binary vectors, Protein extraction, Purification of recombinant proteins from E. coli, Agrobacterium gene transformation, Gene Gun transformation, Floral dip transformation, selection techniques for transgenic lines

6

2000

Effectormics: Tools for Breeding Resistance to Pathogens

2012-08

Pathogens Genome Browser, Plant-Pathogen interactions, Gene-for-Gene theory, Different types of effectors, Agro infiltration, Agro infection, Agro co-infiltration, PVX tooth pick, VIGS, High throughput phenotyping using Chlorophyll Fluorescence Imaging

4

1000

Recombinant Proteins

2012-09

Recombinant protein technology, international trades, Cloning strategies, Gene cloning and expression, Expression vectors i.e. pET, Bacterial cell induction, Isolation and Purification of recombinant proteins, protein production in plants, Agro infiltration

5

1500

Genetic Engineering of Plants

2012-10

Principles of growing model plants (Arabidopsis thaliana, Nicotinia benthamiana), Tissue culture and embryogenesis, Agrobacterium gene transformation protocols, Transformation by Gene Gun, Floral dip transformation, Hairy roots production using Agrobacterium rhizogenesis, Making cloning, expression and binary constructs, DNA/RNA extraction,

High throughput DNA extraction of putative transgenic plants, DNA gel recovery and PCR product purification, Ligation protocols, Competent cells, Transformation (Heat shock and electroporation), Selection media, Select transformed and recombinant cells, Digestion and Colony PCR, Plasmid DNA extraction, Direct sequencing and plasmid sequencing, In vitro gene expression, Protein extraction, Selection techniques for transgenic lines (PCR, RT-PCR, Southern blot. Western blot, Real-Time gene expression), GUS assay

5

1500

High Resolution Melting Curve Analysis (HRM): De novo Genotyping and Allelic Discrimination

2012-11

HRM Technology, SYBR Green vs. Resolight dye, HRM informatics, SNPs genotyping, Allelic discrimination, Gene Haplotyping, De Novo mutation detection, HRM data analysis

3

1000

Diversity, Evolution and Molecular Phylogeny

2012-12

Genetic diversity using molecular markers, Genetic data scoring, Inter- and Intra-specific relationships, Chloroplast genome and cpDNA diversity and Phylogeny, Mitochondria genome, Phylogenetic tree, IRAP, IGS and ITS markers, PCR-RFLP, Phylogenetic softwares (PAUP, Darwin, etc.)

3

1000

Electrophoresis and Blotting Techniques

2012-13

Agarose and Acrilamide gel electrophoresis,  PFGE for large segment separation, SDS-PAGE, Southern Blot, Northern Blot, Western Blot

5

1500

Plant tissue culture

2012-14

History and principles of plant tissue culture, Chemical, composition and preparation of culture media, transfer and sub-culturing of explants into multiplication and rooting media

3

1000

Phytochemical analysis

2012-15

Metabolic and essential oil extractions, Metabolic analysis by HPLC, TLC, Gas chromatography (GC), Metabolic engineering

3

1000

Seed Quality Testing and Evaluation

2013-15

Seed sampling, Vigour test methods, Pure seed definition, Seedling evaluation, Tetrazolium testing, Seed health testing, variety testing, Quality Assurance System

4

1000