An-Najah Staff

Course Objectives:

The course will focus on biotechnological concepts and applications in industry, medicine and applied bioinformatics. The technology of enzyme production and its industrial applications will be discussed as well as gene therapy, the technology of production of antibiotics, vaccines. monoclonal antibodies, and biopharmaceuticals. An extensive overview of applied bioinformatics related to microbial and eukaryotic genome analysis, biological databases, DNA and protein sequence comparisons, sequence retrieval, alignment of sequences (local and multiple alignments)and phylogenetic relationships will be covered. PCR primer design using bioinformatics software packages will also be discussed.

Course contents-Theoretical lectures (Two one- hour lectures/week):

Week (1)                Chapter 1: Introduction to biotechnology

• Biotechnology- Definitions
• Biotechnology- An interdisciplinary pursuit
• Biotechnology- A three component central core
• Areas of application of biotechnology

Weeks (2 & 3)        Chapter 2: Biotechnology and medicine

                                                    -    Antibiotics: Classification, mode of action, and industrial            

                                         production of antibiotics.

•   Vaccines and monoclonal antibodies
•   Biopharmaceuticals
•   Gene Therapy

Week (4)               Chapter 3: Enzyme technology

•  The technology of enzyme production
•  Immobilized enzymes and their industrial applications

Week (5)               Chapter 4: Microbial and eukaryotic genomics

• Vectors for genomic cloning and sequencing
• Sequencing and annotating the genome
• Genomes: Sizes, bioinformatic analysis and ORF contents
• The human genome project
• Genomes of organelles

Week (6)               Chapter 5: The functional analysis of genomes

•    The identification of cellular functions of gene products
•    Transcriptomics
•    DNA microarrays
•    Proteomics

Week (7)                Chapter 6: Biological foundations of bioinformatics

•    Structure of nucleic acids DNA and RNA
•    The storage of genetic information
•    The structure of proteins

Week (8)               Chapter 7: Applied bioinformatics

•    Defining bioinformatics
•    Understanding the links between molecular biology, genomics and bioinformatics
• DNA and protein sequence analysis
•    Working with protein 3-D structure

Week (9)              Chapter 8: Getting started in applied bioinformatics

• Using PubMed
• Retrieving protein and DNA sequences

Week (10)            Chapter 9: Biological databases

• Storage of biological data in global databases
• Primary databases
  • Nucleotide sequence databases (GenBank, EMBL, DDBJ)
  • Protein sequence databases (SWISS PROT, NCBI protein database)

                                 - Secondary databases

Weeks (11 &12)Chapter 10: Sequence comparisons and sequence-based database searches

• Pairwise and multiple sequence comparisons
• Database searches with nucleotide and protein sequences BLAST
• Important algorithms for database searching
• Importance of database searches for similar sequences

Week (13)          Chapter 11: Microbial systematics

• Methods for determining evolutionary relationships
• Microbial phylogeny derived from ribosomal RNA sequences

Week (14)          Chapter 12: Building phylogenetic trees

• Preparation of multiple sequence alignments
• Building a neighbour-joining tree
• Evaluation of the quality of a tree by bootstrapping

Week (15)          Chapter 13: The polymerase chain reaction (DNA amplification)

                                                    -     PCR primer design using bioinformatic software packages

Practical Part (One lab. session/ week):

Part of the lab. sessions will include studying the antimicrobial activity of plant extracts compared to naturally produced antibiotics. The other part will focus mainly on bioinformatics analysis tools.

Reports and selected topics presented by each student in the lab. are requested.

Grading System

First Hour Exam                   20%                                      

Second Hour Exam               20%

Laboratory Work                  25%

Final Exam                             35%

References

1. Biotechnology by Smith, J. (2004).Cambridge Press

 2.  Applied Bioinformatics: An Introduction by Selzer, P.M., Marhِfer, R.J. and.

            Rohwer, A, (2008). Springer.

3. Introduction to Biotechnology by Thieman, W. and Palladino, M., (2004).

      Pearson