MICR 4280 Lecture Notes - Lecture 9: Primer Walking, Phylotype, Metagenomics

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Monday january 28 t h lecture 9. Phylotype vs species: a band is not necessarily one specific species (co migration of bands) being amplified: advantages: Can use specific pcr primers to ask specific questions: what experimental steps are required before doing statistical analyses of a dge gel. Single band analyses vs whole profile analyses: whole profile is more related to diversity. Spatial vs temporal shifts in structure: winter vs. summer, correlation of community structure with environmental factors. Known environmental factors that are being examined, change in ph, temperature, salinity, etc, Level of expression: control on gene expression, reverse transcription and cloning of the mrna, purify the mrna from the environment no rt-pcr + sequencing required, transcriptome studies by microarrays. Examination of physical arrangement of different species in consortia and/or biofilms: consortia: growing organisms in partnership. Labeled pcr amplicon of hypervariable ssu region =probe: one of the primers will target hypervariable region of the gene, is labelled with a fluorescent die.

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