Lecture 231. Describe the role of microbes on early earth in the rise of oxygen in the atmospherea. Anoxygenic photosynthetic bacteria used H2S or S˚ (element sulfur) as sources ofelectronsb. Organisms evolved the ability to use H2O as a source of electronsi. The resulting O2 accumulated in the atmosphereii. Iron banding in rock formations as evidence of oxygenation event. 2. Know what microbial mats are and what evidence we have that they formedon the ancient earth a. Microbial mats- layered communites of micro organisms, in a lot of aquaticenvironmentsb. Evidencei. Stromatolites- fossilized microbial mats3. Describe what molecule is most commonly used for sequence comparisons for phylogenetic comparisons a. Ribosomes b. Small subunit 16S ribosomal RNA sequence comparisons are our current method for phylogenyc. Application of 16S rRNA sequence comparisons reveal 3 domainsof life.4. Explain what PCR is and how it is used to obtain sequence information a. Locate the 16S rRNA geneb. DNA is isolated from pure cultures of microbes, or from entire microbial communitiesc. 16S rRNA genes are amplified by PCR using primers designed for this purposed. PCR reaction products are checked by gel electrophoresise. We detect organisms by finding their genesf. Sequences of the 16S rRNA gene are complied into a computer alignment programi. Software is designed to find overlaps in sequencesii. Differences between sequences are then calculated 1. Sequence differences are proportional to evolutionary distance between organisms5. Understand how comparison of DNA sequences is used to build a distance matrix and phylogenetic trees a. Sequences in the dataset are aligned and comparedb. Differences are calculated to make a distance matrixc. A tree is constructedi. Branchesii. Nodesiii. The length of the branches (through nodes) implies evolutionary distance 1. This distance is proportional to the sequence differences from the alignment6. Describe the role of mutations and recombination in evolution a. Mutationsi. Random changes in DNA sequence- can accumulate over time b. Recombinationi. Needed for horizontal gene transferii. Can also result in rearrangements of large segments of a genome7. Explain how the increase of antibiotic resistant pathogens resulted from evolutiona. Overuse of antibiotics over time creates selection for resistant organisms and against non-resistant organisms 8. Summarize how genetic drift can result in evolution of organisms and populationsa. Genetic drift is where some members of a population reproduce slightly faster than others i. Thus, individual sub-populations can change and evolve in differentways9. Describe the core genome and the pan genome when comparing two or more organisms a. The study of comparative genomics shows that closely related microbes can have significant differences in genetic makeup.b. Core genomei. What all the genes have in commonc. Pan genomei. All the genes that are different10. Explain how following a single organism through thousands of generationscan yield information about evolution a. You can see where mutations happen and genes change and organisms either gain or lose a trait in the generation. b. You can also see how that mutation changed the fitness of the organism11. Be able to briefly describe multi-locus sequence typing, ribotyping, whole genome analysis, and FAME a. Multi-locus sequence typingi. Analyzing DNA sequences of several essential genesb. Ribotypingi. 16S rRNA classification by analyzing restriction enzyme fragmentsrather than DNA sequencec. Whole genome analysisi. Because of decreased cost of genome sequencing, this approach is now becoming more commond. FAMEi. Chemically derivatizes bacterial fatty acids and then examines profiles of the resulting fatty acid methyl esters by gas chromatography1. Is only useful for pure cultures- will not work for mixtures of microorganisms or microbial communities2. Can be performed as a diagnostic
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