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Emerging Diagnostics - A Sneak Peak at How Tomorrow’s Technologies are Being Used at the University of Wisconsin Today. Sharon C. Long. Today’s Objective. To get you thinking about new tools and approaches to diagnosing the biology in your processes Activated sludge Biosolids Source water

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slide1

Emerging Diagnostics - A Sneak Peak at How Tomorrow’s Technologies are Being Used at the University of Wisconsin Today

Sharon C. Long

today s objective
Today’s Objective

To get you thinking about new tools and approaches to diagnosing the biology in your processes

  • Activated sludge
  • Biosolids
  • Source water
  • Distribution systems
  • Etc.
omics
“Omics”
  • Metabolomics – aims to compare differences between biological samples based on their metabolic profiles
  • Genomics – using sequences of DNA and RNA to develop useful biological knowledge
  • Proteomics –used to relate microbial activities to the identity of organisms in multispecies communities
today s examples
Today’s Examples
  • Using ATP profiles to evaluate overall microbial community changes
  • Recognition of short sequences of DNA to evaluate presence of certain target microorganism - FISH
  • Measuring the presence of short sequences of DNA to evaluate presence of certain target microorganism - PCR
  • Sequencing the DNA of environmental samples to assess community structure
slide5
ATP
  • Transports chemical energy within cells for metabolism
  • Present in all living cells
  • Amount in a sample is roughly proportional to the number of cells present
  • Measure the amount of light produced using firefly enzymes
study of microbial occurrence in wells
Study of Microbial Occurrence in Wells

370

ME/ml

45,300

ME/ml

12,600

ME/ml

860

ME/ml

460

ME/ml

1,912,000

ME/ml

801,000

ME/ml

241,000

ME/ml

8,620

ME/ml

5,200

ME/ml

From: Andrew Jacque, PhD, PE, Water Quality Investigations LLC and Town & Country Engineering

well study
370

ME/ml

Well Study

45,300

ME/ml

12,600

ME/ml

860

ME/ml

From: Andrew Jacque, PhD, PE, Water Quality Investigations LLC and Town & Country Engineering

fluorescent in situ hybridization fish
Fluorescent in situ Hybridization (FISH)
  • Use short sequences of single stranded DNA complimentary to a sequence unique or general to the target organism(s)
  • Attach a fluorescent dye
  • Prepare a sample
    • Permeation
    • Hybridization
  • Quantify using microscopy
applications of fish
Applications of FISH
  • Diagnosis of foaming in biosolids anaerobic digesters

Klare Keadle, Zachary Carroll, Daniel R. Noguera, and Sharon C. Long

foaming and fish results
Foaming and FISH Results
  • Provided qualitative confirmation of the presence and relative density of target filaments
  • M. parvicella was confirmed to be numerous
  • Other known filamentous Archeae also present in digesters
applications of fish 2
Applications of FISH 2
  • Characterize microorganisms in aerated anoxic Enhanced Biological Phosphorus Removal

Ramesh K. Goel, Patricia Sanhueza and Daniel R. Noguera

ebpr fish results
120

Run II ( 0.3 % O

)

2

100

80

60

120

%

Run III ( 0.6 % O

)

2

40

100

% P removal

20

% Rhodocyclus related

80

120

Run IV ( 1.2 % O

)

2

0

0

10

20

30

40

50

60

100

60

Time (days)

%

80

40

% P removal

60

20

%

% Rhodocyclus related

40

0

% P removal

0

5

10

15

20

25

30

20

% Rhodocyclus related

Time (days)

0

0

10

20

30

40

Time (days)

EBPR FISH Results

More than 90 % Population was Rhodocyclus related

polymerase chain reaction pcr
Polymerase Chain Reaction (PCR)
  • Use of Taq polymerase
  • Target short (~100 to 400 bp), unique sequences of DNA or RNA for species identification
  • Target broadly occurring sequences of DNA for organism family identification
  • Products may also be sequenced to yield further information

Exponential Replication

1 2 3 4 5

measure presence of stec in wastewater
Measure Presence of STEC in Wastewater

(A) E. coli O157:H7

(B) Non-STEC E. coli or Shigella

(C) E. coli absent

(D) Toxigenic organism, not STEC, not Shigella

(E) Non-O157:H7 STEC or Shigella

India Mansour, Mark Walter, and Sharon C. Long

dna sequencing
DNA Sequencing

Trevor Ghylin

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