| Week One | Activities | Learning Outcomes |
| DNA Technology in Laboratory Medicine | Diagnostic Relevance and future prospects. Interesting and Relevant Applications of DNA Technology Areas Most striking and need further review in my career | – modernized to detect pathogens from the clinical samples in the diagnostic hospitals. Preferred method of identifying organisms based on genomic make up. Detection of major infectious diseases, genetic disorders, forensic cases (both civil and criminal cases), vaccine development and further research are based on this Technology. In the near future I see all the countries in the world having a bank of DNA for its entire citizens now that terrorism is on high alert. -Saudi Arabia too, has scaled up its involvement in medical research. There are many genetics research centre such as KFSHRC (King Faisal Specialist Hospital & Research Centre, Riyadh) where the Genetics department does basic and translational research on molecular pathogenesis of various diseases prevalent in Saudi Arabia. They also study simple or single gene disorders, multi-genic disorders like type II diabetes and cardiovascular diseases. -Production of millions of identical copies of a fragment of DNA material through amplification of a target gene with both forward and reverse primers is just amazing. Relevant in the world of science research now that diseases keeps adapting and changing their genomic. It’s therefore important to identify a certain pathogen at genomic level. This would save more lifes and resources and at the same time speed up diagnosis of major life threatening diseases that cannot be diagnosed using gold standard methods. -Its amazing how an organism’s genomic material can be extracted and sequenced after producing millions of copies. Am interested on how such important information could be used to make a target vaccine against it, with the effort of developing DNA vaccines. |
| Week two | Activities | Learning Outcomes |
| Eukaryotic Gene Structure Accessed Griffith et. al., Modern Genetics analysis 2ndEd. (2002) Accessed Accessed Accessed | Structure of DNA and RNA . -DNA molecule = form of a double helix spiral strand made up of four bases (thymine, adenine, guanine and cytosine bases), sugar moiety and phosphate molecule as the backbone. -A nucleotide= composed of nitrogenous base, a five carbon sugar which can either be ribose or deoxyribose and a phosphate group, while a nucleoside lacks the phosphate group, it only has the nucleobase and a carbon sugar. – bases make bonding between complementary strands of DNA; can either be purines or pyrimidines. Purines are Adenine and Guanine, while pyrimidines are Cytosine, Uracil and Thymine. Uracil is only found in RNA and is substituted by Thymine in DNA. Purines will always pair with pyrimidines and never will they pair amongst themselves. -each base is joined to a complimentary strand by a non-covalent bonding= hydrogen bond. Adenine (A) pairs with Thymine (T) using two bonds, while Guanine (G) pairs with Cytosine (C) on three bonds. The replication of DNA DNA polymerase is aligned in the same direction with the enzyme involved, on 5’ to 3’ direction hence the enzyme is able to synthesize the strand in a continuous manner unlike in the lagging strand whose terminus are aligned in the opposite direction of 3’ to 5’, this is synthesized in bits, discontinuous to produce what are called Okazaki fragments (short single stranded DNA) but are later on joined together by DNA ligase enzyme. Transcription of DNA to RNA Translation of RNA to proteins | Genomic differences between prokaryotes and eukaryotes Prokaryotes very small (>~5Mb), eukaryotes are extremely larger (10 Mb- 100,000Mb) Prokaryotes contains one large circular DNA ‘chromosomes’, eukaryotic DNA is held in linear chromosome and a small circular mitochondrial chromosome. Prokaryotes have plasmids, their genes with related functions found closely in operons. Eukaryotes have introns with many genomic repeats, prokaryotes lacks introns and have very few repeated sequence. Prokaryotes have few non coding regions with insertion elements/transposons, can share genes within the environment. Eukaryotes have many non-coding sequence Eukaryotes- the number of genes between strains of specie is the same, in prokaryotes genes vary between different strains of the same specie. Processing mRNA |
| Week Three | Activities | Learning Outcomes |
| Genetic Disease Accessed Accessed Accessed Accessed | Organisation of DNA into chromosomes Mitosis and meiosis Genetic disorders | -each chromosome has one linear DNA molecule and multiple origins of replication. These winds around octameric histone core forming nucleosome. Size of nucleosome=10nm. Characteristics of human chromosomes -varies in length (large, medium and small). Varying percentage of the total combined length of a haploid set of 22 autosomes. Chromosome visualisation Painting distinguishes each homologous pair by color Homozygous- non mutant alleles Karyotype- number and size of chromosome/cells varies between and within species Alleles- different forms of a gene at a locus Locus- physical position of a gene on a chromosome Heterozygous- mutant alleles (either compound where both at one locus or double where one mutant allele at two loci) Phenotypes- physical expression by allele products, characteristic determined by genotype and environmental interaction Autosomal dominant inheritance |
| Week Four | Activities | Learning Outcomes |
| DNA Technology Accessed Accessed Accessed Accessed | DNA Techniques | Autosomal recessive inheritance -Requires 2 copies of mutant genes where the affected individuals are homozygous for the same mutation, or compound heterozygotes. For example cystic fibrosis leads to lung disorder when there is faulty in Cl- transport. High accumulation of iron in the liver leads to genetic Haemochromatosis. Autosomal dominant inheritance ½ the offspring of affected parent will be affected, mutation can be traced through generation. the parent may appear normal when the disease is an isolated case (no family history) but new mutations during meiosis may lead to conditions like dwarfism and achondroplasia X-Linked inheritance A recessive inheritance where mother is the carrier. Boys have 50% chances of being affected, girls remains carriers. Happens through X-inactivation or lyonisatopm which occurs during early embryonic life when either paternal or maternal X is inactivated. This will carry mutation. Leads to a condition called Duchenne muscular dystrophy when X was inactivated in progenitor muscle cellsDNA digestion restriction enzymes Those producing blunt ends cuts both strands while those producing sticky ends make staggered cuts -e.g EcoRI, does not cleave methylated DNA. HphI and Hgal cleavage sites occur several nucleotides away from recognition sequence Hybridisation I-dentifies a DNA fragment with a known sequence of interest -Uses radio labeled DNA/RNA probes Process= melting double stranded DNA to ssDNA, then bound to a filter which is incubated with labeled DNA, wash unbound and perform autoradiography. Ligase reaction -enzyme helps to join the sticky ends Restriction fragments with complementary sticky ends are ligated more easily Gel electrophoresis Uses either agarose or poly-acrylamide as the stationary phase, Allows separation of DNA restriction fragments according to their chain length DNA moves a long a charged field. Enables visualization of restricted fragments once separated. Samples are run with molecular markers of known weight. Pulse field gel electrophoresis separates large DNA molecules >900kb. Real time PCR Amplification of target nucleic acid. These are detected every cycle using fluorescence monitoring. Process=short, 30minutes. Done on a Roche Light cycler. Both quantitative and qualitative, no electrophoresis needed. Detection systems (labeling systems of the oligonucleotide primers) = Sybr Green, FRET, Taq Man, Molecular Beacons, scorpion probes. DNA Sequencing -Done manually or automatically. -manual is labour intensive, radiolabelling, and can only run 200 – 300 bases at a time -automated uses chain terminators (the dideoxy procedure) with fluorescence labeled dyes. Relies on capillary electrophoresis to enable separation of various chain terminatesd strands instead of agarose gel electrophoresis. Process=reagent dispensing, amplification, plate piercing, loading PCR products, takes 2 hours before storage. Southern blotting |
| Week Five | Activities | Learning Outcomes |
| Molecular basis of Cancer -Lodish et. al., Molecular Cell Biology (2000) Presentation on Cancer oncogenes I and II | Aspect of molecular basis of cancer -identification of the causes of cancer at molecular level is a milestone achievement; equally the discovery of tumour viruses provides insight into the molecular basis of cancer. However, understanding malignant transformation and its pathogenesis will unravel treatment options. Cancer can only be fought successfully through knowing how it begins. Other non molecular aspects of carcinogens are diet/lifestyle and environmental stressors whose regulation can really help in cutting down incidences. | Proto- oncogenes and oncogenes Proto- oncogenes are small cellular genes which encodes signaling pathway protein while oncogenes are mutated form of proto-oncogenes/abnormal cellular gene, they encode a protein which can induce cancer. Classes of oncogenic protein coding genes -growth factors like EGF growth factor. -receptors like Erythropoietin (Epo), once mutated results in permanent activation –signal transduction like Ras -transcription factors like fos, jun and myc which turns on genes involved in growth -tumour suppressor gene like p53,it detects DNA damaged (mutation) and stops multiplication of oncogenes. Involvement of DNA mismatch repair gene in colon cancer If mutation occurs in one or more of the DNA mismatch repair gene it leads to a condition called Hereditary non-polyposis colorectal cancer (HNPCC) These tumuors associated with HNPCC have defects in the DNA mismatch repair system. This occurs if DNA mismatch are not repaired leading to mutation on other genes Examples of inactivated genes leading to this are p53, ras, APC Tumour suppressor Genes mutated in colon cancer are p53, APC and DCC while oncogenes are Ras and Myc |
| Week Six | Activities | Learning Outcomes |
| Human genome project and applications to disease presentation on Human genomic Project Scientific journal article presentation of DNA microarray Presentation on Human Genetic Variation | Project significance and initial finding Has enabled researchers to have vast information on molecular biology. They can now examine biological processes and associated diseases within a global view as opposed to previous ‘blinkered view’ Has also enabled easy study of several genes simultaneously. DNA microarrays Human genetic variation and application of Genomic Project | Application In gene discovery. Identification of all common variants in human gene Simultaneous monitoring of the expression of gene Significance Provision of extensive knowledge/information on genes Allows simultaneous study of many genes Understanding Human genome from simple organism studies It’s easy to study genes on E coliand C elegans since they are made up of smaller genomes. If the entire genes of these animals were known then studying a more complex human gene would be easier. C. elegans- its developmental process is fundamental to modern biology, transparent body and visible on a microscope Differences between public and private Human genomic project -public were a group of government who funded research institute from US and Europe while private company were owned by Perkin Elmer.Initial findings Genome contains ~25,000 genes. 50% of genome is repetitive DNA Unequal distribution of genes, repetitive DNA and other features throughout the genome. That 100% of human genes are due to horizontal transfer from the bacteria Role of Human Genomic project to understand diseases Identification of genes for complex traits Identification of gene responsible for complex disease Helps to identify genetic variation which affect drug treatment/pharmacogenomics Clinical diagnosis |
| Week seven | Activities | Learning Outcomes |
| Human genome project and applications to disease presentation on Human genomic Project Scientific journal article presentation of DNA microarray Presentation on Human Genetic Variation | Project significance and initial finding Aspect of molecular basis of cancer -identification of the causes of cancer at molecular level is a milestone achievement; equally the discovery of tumour viruses provides insight into the molecular basis of cancer. However, understanding malignant transformation and its pathogenesis will unravel treatment options. simultaneously. Human genetic variation and application of Genomic Project | Application In gene discovery. Identification of all common variants in human gene Simultaneous monitoring of the expression of gene Significance Provision of extensive knowledge/information on genes Allows simultaneous study of many genes Differences between public and private Human genomic project -public were a group of government who funded research institute from US and Europe while private company were owned by Perkin Elmer. The public consortium started in 1990 and finished in 2001, while private started human project and finished in 2001. The major contributors for public were Whitehead Institute USA and The Sanger Centre UK. While for private its private Bioinformatics company Initial findings Genome contains ~25,000 genes. 50% of genome is repetitive DNA Unequal distribution of genes, repetitive DNA and other features throughout the genome. That 100% of human genes are due to horizontal transfer from the bacteria Role of Human Genomic project to understand diseases Identification of genes for complex traits Identification of gene responsible for complex disease Helps to identify genetic variation which affect drug treatment/pharmacogenomics Clinical diagnosis |