Understand the basic strategies for sequencing the genome of organisms clone by clone vs shotgun You should know the basic steps associated with each their similarities and differences only 100 1000 we can only do short reads of DNA must be broken into readable pieces DNA is broken up into fragments cutting it with enzymes or sheering DNA making random breaks shotgun repeats make issues it is the unique sequences which allow us to order the fragments clone by clone top down approach 1 fragment genome into workable sizes 2 clone fragments 3 order fragments so they represent overlapping bits of chromosome difficult and slow done by restriction mapping and other methods 4 sequence fragments that allow you to find out the linear sequence of chromosomes lot of time figuring out the order of the clones not necessary in shotgun method order first sequence second assemble easy because we know order shotgun sequencing 1 fragment genome into workable sizes 2 clone fragments 3 sequence all clones a lot of redundancy in the collection of clones lots of sequencing and sequenced data 4 look at each fragment and try to link it to other fragments use sequence similarity to join overlapping fragments lots of fragments to assemble sequence first order assembly second most genome sequencing is done using shotgun because computers can do it was used to first sequence human genome too much repeat DNA make this process difficult You should know and understand the basic steps in sequencing a genome sequence assemble annotate 1 genome sequencing clone by clone or shotgun 2 assemble genome 3 annotate genome Know how genome assembly an annotation is done to the extent discussed in lecture annotation seeing that the functional sequences are start by looking for known consensus sequences TATA boxes splice sites open reading frames etc Ab initio methods predictions based on known spelling and grammar functional annotation sequence mRNA and compare it to the genome to figure out expressed genes comparative approach use genes from other organisms to find genes in your species Understand and appreciate the power and uses of DNA hybridization Understand how it is used as the basis for asking question about the genome This includes the concept of a microarray DNA hybridization complementary sequences find each other have DNA of known sequence can see if it binds to another unknown sequence to figure out the sequence of the unknown DNA microarray orderly arrangement of genome DNA fragments Understand that microarrays can be constructed to contain any number of features of a genome and then used to ask questions using those features WHAT GENES ARE EXPRESSED 1 place DNA fragments in an ordered array 2 collect all mRNA and convert it to cDNA tag the cDNA fluorescent 3 apply tagged cDNA to microarray complementary fragments will anneal 4 genes that annealed to cDNA are expressed used to compare genes under two different conditions ex health disease time 1 time 2 treatment 1 treatment 2 Expression studies with gene or open reading frame arrays polymorphism studies using SNP arrays etc Know how DNA hybridization is used in each case Know what Single Nucleotide Polymorphisms are and how they can be used essentially just genetic markers single nucleotide differences in sequences compared with reference genome our genome differs by 1 base in 1000 SNP chips to genotype people microarray for detecting SNPs use SNPs to find genes associated with phenotype or disease Know what a Genome Wide Association Study is how it is basically done and what the data actually tell you compare SNPs between 2 groups disease vs healthy look at the differences to see what SNPs are related to the disease ex Rheumatoid Arthritis Understand and appreciate how genomic data are being used in the variety of applications discussed in class metagenomics sequencing DNA from environmental samples determine what the genes are determine what the genes do human microbiome manipulating microbe communities can be beneficial to out health Know what cancer is and how it can arise a disease of the cell cycle failure of normal growth controls tumors all cancer results from somatic mutations caused by virus or environment Know and understand the concepts of internal and external growth control signals and how these relate to cancer internal signals cyclin CDK external signals hormones and growth factors membrane bound receptors can bind external factors inner side of membrane receptors interact with kinases etc Know what cyclins and CDKs are and their general role in the cell cycle cyclins intracellular proteins that vary in amount depending on cycle phase function as internal timers and triggers cyclins associated with cyclin dependent kinases c CDK phosphorylate specific proteins to regulate gene expression Understand the regulation of G1 S transition as discussed in class role of Rb etc RB retinoblastoma protein RB interacts with E2F transcription factor for genes involved in proliferation CDKs 4 6 2 phosphorylate RB in presence of D and E phosphorylated RB dissociated from E2F cell proliferation Understand the concept of external growth control signals and signaling cascades RAS was an example of such a system Understand that there are numerous such systems that depend on membrane receptors to detect particular growth signals These form a network of signals that impinge on the nucleus RAS signal transduction pathway involved in cell survival and death RAS is one of a family of proteins GTPases can be activated by membrane receptors that respond to specific ligands it then activates other proteins leading to cell growth Appreciate that the network aspect of growth control relates to the multi hit theory of cancer mutagenesis complex network of signaling pathways means that a defect will probably not be a major problem because there are other control pathways Understand the basic evidence for cancer being viewed as a genetic disease mutagens carcinogens implies that genetic damage is involved in cancer chromosomal abnormalities correlated with cancer there are some hereditary predispositions to cancers although this is rare Know and appreciate the multi hit theory of cancer Know the concepts of driver and passenger mutations driver contribute to the development of cancer cancer phenotype passenger mutations that are neutral with respect to cancer development but happen to be in cells that undergo clonal expansion during development of cancers not contributing