• Molecular Biology Techniques: PCR, RT-PCR
    • Safety principles in molecular laboratories
    • Methods of genomic DNA extraction from blood samples (Manual and Kit)
    • Purification and precipitation of DNA
    • Principles of working with RNA
    • RNA extraction from blood samples using laboratory kits
    • Gel electrophoresis (principles, performing horizontal electrophoresis and analysis of results with UV Box)
    • PCR of target genes (PCR, Optimization)
    • Gel electrophoresis of PCR products
    • Genome library preparation (cDNA)
    • cDNA synthesis
    • Quality analysis of synthetized cDNA with RT-PCR

 

  • Real-Time PCR and its Application in Gene Expression Analysis:
    • Definition of Real-Time PCR and differences with conventional PCR
    • An introduction to different devices
    • Getting to know different probes and their application
    • Various methods of Real-Time PCR including absolute quantification and relative quantification
    • Description of basic concepts and related formulas
    • Various applications of Real-Time PCR

*Laboratory section:

  • Knowing Real-Time PCR, Instruction of using the device and its programs
  • Designing a projects
  • Real-Time PCR samples
  • Analysis and evaluation of results

        Prerequisite:Practical knowledge about DNA and RNA extraction, cDNA synthesis and PCR

 

3-Genetic Engineering and Cloning:

 

  • Principles of medium preparation and bacterial cultivation
  • Gel electrophoresis and observation of amplified region
  • DNA extraction from Agarose gel and purification of target gene for cloning
  • Performing enzymatic digestion
  • Performing ligation
  • Preparing competent cells
  • Vector transformation into bacterial cells
  • Cultivation on selective media and screening of recombinant colonies
  • Enzymatic cleavage of recombinant plasmid
  • Electrophoresis and interpretation of cloning results

In this course only vector cloning in prokaryotic host will be instructed.

 

4- Bioinformatics

  • Search in scientific databases (Google Scholar- PubMed)
  • Primary DNA and protein databases (NCBI- EMBL-DDBJ-PDB)
  • Secondary databases (Swiss Prot- UniProt-PIR- TrEMBL)
  • Data submission in GenBank
  • Double and multiple alignments of biological sequences and methods of constructing phylogenetic trees
  • Practical tools of BioEdit
  • Principles and parameters of primer design (working with Oligo7 and analysis of obtained oligos)
  • Project and correction

5-Metagenomics Analysis of 16S/18S rDNA Using QIIME2

  • A review on Metagenomics basics
  • Principles of DNA sequencing with different Next Generation Sequencing platforms with an emphasis on Illumina
  • Preparation of metagenomic samples from sampling to preparing genome library (Theoretical and Practical)
  • Notes on sequencing 16S/18S Metagenomic samples using Illumina Miseq platforms
  • Methods of managing raw data extracted from metagenome sequencing
  • Installation and application of QIIME2 package in Linux environment and Virtual Box
  • Basics of data analysis with QIIME2 package and quantification of results including:
  • Methods of preparing metadata and manifest
  • Data Multiplexing and summarizing Paired-end data
  • Methods of performing quality control of raw data, denoising and data clustering
  • Obtaining and interpretation of Feature Table
  • Filtering Feature Table and sequences
  • Phylogeny diversity analysis
  •  α and β analysis inside and between samples
  • Classification and taxonomical analysis
  • ANCOM analysis for obtaining difference of frequency between distinct groups in samples
  • Creation of HeatMap, Core microbiome analysis, PICRUSt analysis
  • Supplementary statistical analysis 

 

 

  • Principles of Next-generation Sequencing (Second and Third Generation) and Review on its Applications in Genomics, Metagenomics, Transcriptomics,Metatranscriptomics  and Epigenomics

 

  • A review on history of different generations of DNA sequencing
  • Principles and applications of first generations DNA sequencing (Sanger)
  • Biochemical and technical basics of second generation DNA sequencing (FLX-Illumina-Solid)
  • Applications of second generation sequencing in different Omics studies
  • Biochemical and technical basics of third generation DNA sequencing (PacBio-Ion Torrent)
  • Applications of third generation sequencing in different Omics studies
  • Methods of preparing different samples of genomics, metagenomics, transcriptomics,metatranscriptomics  and epigenomics studies for sequencing with different platforms
  • Comparison of various methods of second and third generations of DNA sequencing based on efficacy and application in different studies
  • Assessment of efficacy and application of prominent platforms of Illumina
  • Essential and key points in developing different NGS-based Omics studies
  • Overview on data analysis methods in different platforms and required computer systems

Prerequisite: The participant should be familiar with Bioinformatics

 

  • Molecular Systematic (Phylogeny) Using Bayesian and Likelihood Approach
  • Preliminary concepts of phylogeny and sampling strategy
  • Basics and concepts of reading electropherograms, trimming sequences and an introduction to databanks
  • Practical concepts of sequence alignments, related software and selecting suitable software
  • Selecting the best evolutionary model
  • Construction of phylogenetic trees using various software including MEGA, MrBayes, BEAST
  • Conclusion and interpretation of resulting phylogenetic trees
  • Methods of uploading different molecular and morphological information

Prerequisite: Bioinformatics

 

8- Workshop on Sequence Analysis and Construction of Phylogenetic Trees Using MEGA Software

  • Analysis of raw sequences and evaluating quality of sequencing
  • Assembling various sequence reads with Chromas Pro or Bioedit software and error detection in sequencing
  • Search and sequence alignment (Blast N,…)
  • Determination of phylogenetic position and tree construction based on Neighbor-Joining, Minimum Evolutionary and Maximum likelihood using MEGA software

Prerequisite: Basic knowledge of molecular biology and computer

  •  Practical Training Workshop ongRNA Synthesis for Editing and Gene Silencing Using CRISPR-Cas9 Platform
  • Basic concepts of CRISPR/Cas9 as a gene editing technology
  • Introduction to transfer methods of CRISPER systems for gene silencing, gene inserting and gene editing in animal cells (vector based and without using vectors)
  • Instructing preparation of applicable vectors for gene silencing in animal cells
  • Instructing bioinformatics and practical methods for identifying Off-Targets before and after insertion of CRISPR system into the cells
  • Introduction of practical strategies for decreasing occurrence of Off-Targets in animal genome editing with CRISPR/Cas9
  • Instructing the most important programmes for identification and selection of best gene positions for genome editing with CRISPR/Cas9
  • Practical instruction of designing gRNA and preparing its coding DNA
  • Practical instruction of making gRNA for target gene and its purification
  • Cleaving target DNA gene in test tube using Cas9 enzyme and gRNA target gene and analysis of results with gel electrophoresis
  • Introduction of valid business resources for preparing genome editing tools with CRISPR/Cas9 system

 

  • R Software
    • R is a statistical software with programing ability. Unlike other software that were designed for calculations like GIS,…; R has been primarily designed for analysis of statistical data. Due to having a robust and flexible programming language, R is regarded as a special and unique software. This programming language is a potent tool for data analysis and performing various statistical analysis especially for graduate students and researchers of different fields. More complicated concepts like drawing professional graphs or data analysis is performed easier with R software comparing with other common software. Being a free and open source software with ability of installation on most operating systems can be mentioned as important advantages of R. R is globally approved and scientific data analysis with this programme has been recommended by many valid journals and because of high accuracy of this programme, papers written by this programme are superiors to other articles and will be more accepted. Moreover, rate of accessing to novel techniques in form of libraries, functions, ability of adding and writing new programmes in R environment are noteworthy capabilities of R software.