Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Part Two Identification of bacteria by DNA sequencing Sequencing Reaction: One Primer, labeled dNTPs, other PCR reagents Beckman CEQ 8000 Capillary Head Sequencer Sequences emailed from facility. FinchTVTM: A free Chromatograph Viewing Program Each sample: Analyze overall quality of sequence Example Chromatogram: Identify Unknown Bacteria at NCBI: Basic Local Alignment Search Tool NCBI: A Worldwide Resource Origination of some “HITS” to our sequences RESULTS: Monday Lab 2005 Student Bacteria Source Primers NCBI NCBI % match Monday BH Control Set One Bacillus subtilis 98 Monday PM Control Set One Pseudomonas aeroginosa 98 Monday PS Control Set One Citrobacter freundii 99 Monday KY Control Set One Citrobacter freundii 95 Monday MW Control Set One Enterococcus faecalis 99 Monday MT Control Set One Enterococcus faecalis 98 Monday ZZ Soda Can Set One Psuedomonas geroginosa 99 Monday SN Soda Can Set One Neisserra cinerea 98 Monday DR Soda Can Set One Brevundimonas vesicularis 99 Monday JC Soda Can Set One Serratia marcescens 99 Monday AE Soda Can Set One Klebsiella sp 94 RESULTS: Tuesday Lab 2005 Student Bacteria Source Primers NCBI NCBI % match Tuesday TMM Control Set Two Pseudomonas aeruginosa 96 Tuesday JM Control Set Two Pseudomonas aeruginosa 96 Tuesday ES Control Set Two Enterococcus faecalis 99 Tuesday AM Soda Can Set Two Brevundimonas vesicularis 99 Tuesday MO Soda Can Set Two Neisseria subflava 99 Tuesday DA Soda Can Set Two Klebsiella planticola 98 Tuesday BB Soda Can Set Two Klebsiella sp. 98 Tuesday BK Soda Can Set Two Neisseria sp. 95 Tuesday AP Soda Can Set Two Neisseria sp. 99 Tuesday JS Soda Can Set Two Klebsiella sp. 98 Tuesday IF Soda Can Set Two Nesseria sp. 97 Tuesday JW Soda Can Set Two Neisseria sp. 99 RESULTS: Alignment All Samples Monday Lab Conserved and Variable Regions Generated using ClustalW (free Alignment maker) RESULTS: Relatedness Alignments are the Basis of Phylogenic Trees 16SrRNA DNA amplified using Primer Set #1 Unrooted tree (generated by Phylip's Drawtree: another online program) RESULTS: Generating a longer fragment The first primer set amplifies the middle of the 16s DNA, and the second primer set amplifies an end. The sequences overlap so in the future these primers could be used to get a longer sequence. Example Next Slide: Pseudomonas aeruginosa Primer Set #1 Pseudomonas aeruginosa isolate: 82% identity match with E. coli Region of Alignment PCR sample Full length E. coli 16S rRNA gene ~425 bases of alignable DNA sequence generated Primer Set #2 Pseudomonas aeruginosa isolate: 83% identity match with E. coli Region of Alignment of PCR Full length E. coli 16S rRNA gene ~280 bases of alignable DNA sequence generated Class Results on Spreadsheet Communicating Science: The Real World It is just as important to be able to communicate your results to others as it is to gather and interpret data. 1) Peer Reviewed Journal Articles 2) Conferences: a) Short Presentations b) Poster Sessions 3) Informal Networking, Retreats etc. Real Deal 2) Talks in General: Title: Often good to come up with your own Background: Attention grabber What was the question they were trying to answer? Methods Compare to those we know Results: Figures are often the best way to show results Conclusions….. Critiques…. What you would do differently POSITIVE Future directions………….Applications 2a) Sample Science Talk: One variant of an Intro to Our Project Attention grabber Methods Some Key Results….not all Discussion + Critique Put in Posters Are the Bacteria Dangerous? Does this change your view? 2a) Science Talks 2b) Poster sessions: Adult versions of the Science Fair Poster session in the parking structure! Sections for the Poster TITLE (Name; Organization) INTRODUCTION METHODS RESULTS Figures and Tables are good…. Use some we made and Make some of your own Gels, Chromatographs, Alignments etc… Goal: to show a story start to finish in a visual way CONCLUSIONS / Future Research Making a Poster STANDARD WAY: A Giant Power Point Slide Power Point: under File Menu Choose “Page Set Up” Select Dimensions for Poster Standard Poster Sizes: Width 48 inches Height 36 inches Slides: “landscape” Or Use a Template (steal from a friend) Google “poster template” science; or use link on webpage Often Easiest to: Put together text in Word or Regular Power Point size slides Cut and paste into the giant slide. Groups for Posters….. End of semester poster setup and presentations Check talk beforehand Please practice with your group so everyone knows their part Want to Post Your Sequence? http://www.ncbi.nih.gov/Genbank/index.html END