Molecular Diagnostics including Microbial Community Ecology
November 3Notes regarding brached DNA technology - via Dave @ NOAA
Basically like Western
Two types
Single Plex - probe on plate
Multi Plex - probes for different genes - each gene has a different size bead
For single all you need is plate reader, multi- flow cytometer
Pros
No extraction
RNA can be very small (degraded?)
Cons
Cost- (approx $1000 for 9 target plate)
Validating (multi)
Do not know exact info on probes
Papers to Discuss:
A novel epiphytic cyanobacterium associated with reservoirs affected by avian vacuolar myelinopathy
Harmful Algae 6 (2007) 343–353 Sarah K. Williams *, Jason Kempton , Susan B. Wilde , Alan Lewitus
Williams et al PCR probe for Stigo.pdf
Burreson 2008.pdf
Misuse of PCR assay for diagnosis of mollusc protistan infections
DISEASES OF AQUATIC ORGANISMS Vol. 80: 81–83 (2008) Eugene M. Burreson (Lets discuss this one)-
HEY! This was my paper! -
@ John -- the papers you placed here should be for week7, I moved them -
Berry and Sarre 2007.pdf
Gel-free species identification using melt-curve analysis
Molecular Ecology Notes (2007) 7, 1-4
Microbial Ecology Papers:
And a good review paper of Molecular Techniques for Microbe stuff:
Molecular Tech. in Microbial Ecol. - Review
Genotypic Microbial Community Profiling: A Critical
Technical Review (Microbial Ecology, Nocker, Burr, and Camper, (2007))
Cool Aquatic Animal Disease Links:
OIE (World Organization for Animal Health) Manual of Diagnostics Tests for Aquatic Animals -
DNA-based Molecular Diagnostic Techniques: Research Needs for Standardization and Validation of the Detection of Aquatic Animal Pathogens and Diseases -
Additional Papers on the topic:
Comparison of different quantitative gene expression platforms
Canales et al.pdf
Evaluation of DNA microarray results with quantitative gene expression platforms
Nature Biotechnology Vol. 24, No. 9, September 2006
Molecular diagnostics of infectious diseases
Clinical Chemistry 43:11 2021–2038 (1997) Yi-Wei Tang, Gary W. Procop, and David H. Persing
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This one looks really interesting too (on microbial ecology):
Human Microbiome.pdf
Evolution of Mammals and Their Gut Microbes (Science, 320:1627 (2008))
Here is the supplemental for the Science paper:
This is long, don't print it all out! Materials and Methods end on page 8 ...
Supplemental for Science paper.pdf
Density Gradient Gel Electrophoresis:
http://www.sfam.org.uk/pdf/features/dgge.pdf
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Good intro for those of us new to aquatic microbiology
Aquatic microbiology intro slides
~ABruner - embed, embed, it is not that difficult :) -
Images and Foods for Thought
Tree of Life (Bacteria, blue, Archaea, green, Eukayra, pink)
TreeofLife.pdf
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