BIO 141 LE 1-15-16 PDF

DNA polymerase can then synthesize the complementary strand of the bent DNA strand in a process called Bridge amplification Double stranded is again denatured to form a single stranded DNA DNA polymerase continues cycles of bridge amplification, synthesizing thousands of copies of the DNA fragment a...

DNA polymerase can then synthesize the complementary strand of the bent DNA strand in a process called Bridge amplification Double stranded is again denatured to form a single stranded DNA DNA polymerase continues cycles of bridge amplification, synthesizing thousands of copies of the DNA fragment and resulting to clonal clusters → Cleaving of reverse strand - all reverse complementary strands are then washed off the chip leaving only forward DNA strands immobilized on the chip. → Sequencing Begins with DNA polymerase, adding modified dNTPs with four different fluorescent labels ○ Also contains three prime blocking mostly called reversible terminator ○ Only allows for the addition of one dNTP at a time After each round of dNTp addition to the growing strand, chip is imaged and the emission wavelength from each DNA cluster is used to identify the base The sequence of fluorescent images of the flow cell capture each dNTP addition is used to determine the sequence of DNA fragments Phylogenetic Tree - depict evolutionary relationships among organisms. The relationships take the form of a tree Tips - represent extant or lying taxa Branches - denote evolutionary changes between ancestors and descendants such as change in DNA sequence or evolution of characteristic Sister Taxa - groups that share an immediate common ancestor are their closest relatives Node - most common recent ancestor Basal Node - correspond to most common recent ancestor of all organisms in the tree Group organisms that are descendants of a common ancestor Monophyletic group or clade - when a group contains the most recent common ancestor and all of its descendants. Paraphyletic - includes a common ancestral species and some of its descendants. Polyphyletic - does not share an immediate common ancestor. Relationships can be determined morphological or genetic features. from Maximum parsimony - assumes the least amount of change between organisms. Maximum likelihood - not all changes are equally likely; can be based on the most likely scenario from observed organisms. IV. Multi-locus sequence typing (MLST) unambiguous procedure characterize bacterial isolates into known groups. Identify alleles they possess from established housekeeping genes and designing isolates to sequence types accordingly For each different kind of bacterium you have a specific MLST scheme → Most commonly used for disease epidemiology to track outbreaks, → Does not look at the total sequence similarity bin strains - Rather: each sequence for a given locus is screened for identity with already known sequences of that locus → If that sequence is different, it is considered a new allele and is assigned an allele number → 7 housekeeping genes studied: each strain is characterized by a profile of 7 allele numbers →Study population genetics and reconstruct microevolution of epidemic bacteria and other microorganisms.