Beruflich Dokumente
Kultur Dokumente
Essen(alness
of
Water
Blood
in
our
veins
approximates
composi3on
of
sea
water
Concept
of
hydrophilic
and
hydrophobic
nature
of
biological
molecules
These
molecules
determine
shape
of
biological
molecules
and
thus
decide
the
specicity
of
all
living
processes
Essen(al
for
All
living
organisms
97%
of
the
water
is
in
the
oceans
Water
covers
70%
of
the
world
We are a burgeoning human popula(on unable to move away from its waste
asparagus irriga(on
Saturated salt solu3ons Below freezing to >110C Waters full of toxic substance , i.e. copper, cyanide, lead, silver, gasoline, oil, benzene, and many others
Terminology
Potable
-
(clean)
water
free
of
all
objec(onable
material,
including
pathogens,
tastes,
odors,
colors,
toxins,
radioac3ve
material,
organisms,
oils,
gases,
etc.
Fresh
non-salt
or
sea
water
Pollu(on
anything
that
makes
it
Non-Potable
Sewage
the
community
waste
or
garbage
that
mother
nature
and
we
dump
onto
sewers
or
land
Recrea3onal
water
200
fecal
coliforms
/100
ml
Shellsh
14
fecal
coliforms/100
ml
Disease/ infection
Enteritis Campilobacteriose
Symptoms
Very thin, blood- and mucus-containing diarrhea Flue, diarrhea, head- and stomachaches, fever, cramps and nausea Watery diarrhea, headaches, fever, homiletic uremia, kidney damage Nausea, stomachaches and watery diarrhea, sometimes fevers, headaches and vomiting Fevers Sickness, intestinal cramps, vomiting, diarrhea and sometimes light fevers Stomach aches, diarrhea and fevers, sometimes vomiting Heavy diarrhea
Escherichia coli
Plesiomonas shigelloides
Typhus Salmonella
Streptococcus
Viruses (Hepa33s A, Norwalk) Parasites/Protozoa- (Giardia, Entamoeba, Toxoplasma, Sarccys7s, Isopora, Cryptosporidium, Eimeria, Cyclospora)
Giardiasis Giardia lambia 4 159 Cryptoporidiosis Cryptosporidium parvum 2 1432 Gastroenteri3s E. Coli 0157:H7 3 164 Acute Unknown 5 163 gastrointes3nal illness
Shigella
Vibrio
cholerae
Prevalent
in
U.
S.
in
1800s
Currently
common
in
Asia,
Africa,
La3n
America
Over
100,000
deaths
and
2345
deaths
in
2004
Transmihed
through
water,
fresh
vegetables
and
shellsh
Amoeba
Amoebic dysentery
Severe diarrhea, headache, abdominal pain, chills, fever; if not treated can cause liver abscess, bowel perforation and death
Cryptosporidium parvum
Cryptosporidiosis
Giardia
Giardiasis
Diarrhea, abdominal cramps, flatulence, belching, fatigue Flu, swelling of lymph glands With pregnant women subtle abortion and brain infections
Toxoplasm gondii
Toxoplasmosis
Agricultural
Water
Iden(fy
source
and
distribu3on
of
water
used
Be
aware
of
current
and
historical
use
of
land
Review
exis3ng
prac3ces
and
condi3ons
to
iden3fy
poten(al
sources
of
contamina(on.
Maintain
wells
in
good
working
condi(on
Minimize
contact
of
edible
por(on
of
fresh
produce
with
contaminated
irriga(on
water.
Munciple water source Capped well, Annual test date Uncapped well, canal, reservoir, etc. Quarterly test date Municipal water source Quality report date
Y N
Y N
Y N
Y N
Fecal coliform/fecal streptococci ra(os for humans and other animals Human Duck Sheep Chicken Pig Cow Turkey 4.4 0.6 0.4 0.4 0.4 0.2 0.1
Indicator
Organisms
General
coliforms
indicate
water
in
contact
with
plant
or
animal
life
(universally
present)
Enterobacter areogenes
False Nega3ves
Salmonella typhi
Molecular
tests
Require
tes3ng
for
each
pathogen
Expensive
Require
exper3se
Virus
Detec3on
Very
dicult
and
costly
Electron
microscopy
Immunoassays
Cell
cultures
Reverse
transcrip3on-polymerase
chain
reac3on
(RT- PCR)
Chlorina3on of Water
Methods
of
Treatment
Shock
Chlorina3on
(50-100
ppm,
contact
of
at
least
6
hours)
Chlorine
Terms
Chlorine
Dosage
total
added
Chlorine
Demand
-
inorganic
Combined
Residual
Chlorine
-
organic
Free
Residual
Chlorine
Chlorine Dosage
Chlorine Dosage
Chlorine Demand
Residual Chlorine
Chlorine Dosage
Inorganic
Chlorine Demand
Kill
Bohom
Line
Test
your
water
as
required
and
any3me
you
suspect
a
problem
Work
with
your
County
Environmental
Health
Department
Seek
advise
on
interpre3ng
the
results
what
do
they
mean?
If
you
ques3on
the
results,
resample
and
retest
NEW
Human reservoir
Animal reservoirs
Wastewater
Groundwater
Surface water
Land surface
Aerosols
Domestic use
Crops
Aerosol
Shellfish
Recreation
Domestic use
Three main routes must be considered to prevent the spread of waterborne (& foodborne) diseases. The particular pathogen, its reservoir and its mode of transmission. The figuree shows the potential route(s) of transmission and the reservoirs. For examples, cows are sources for crypotosporodiosis and poultry are sources for campylosis.
10. Drinking water Filtration plant 11. Constructed wetland 12. Urban run-offs 13. Wastewater treatment 14. Industrial use 15. Industrial Re-use 16. Bore 17. Water table 18. River sediment 19. Mangrooves 20. Estuary 21. Recreational use
Recreation
Farming ac3vi3es
Forestry ac3vi3es
pump
stratification
Distribu3on system
INTERACTIVITY & INTERDEPENDENCY Ecology, Environmental & Public Health Microbiology Groups Regulatory Group Transparency Group
Primary assessment: Correct operation of water supply system Verification: Proof that water is safe after supply. This includes monitoring for compliance. Risk assessment: Maximum Acceptable Concentration (MAC). Should be zero but rarely technically & economically feasible. Compliance parameters Compliance & risk assessment may be different for countries, states and applications. Improved awarness: Flexible, transparent, achievable & realistic outcomes
" "
Table
Bacteriological
drinking
water
&
recrea3onal
freshwater
standards
or
guidelines
Maximum no of indicated organisms permitted / 100 ml of water type Total coliformsa Source of standard WHO Canada European Economic Community United States
a
Recreational
1 (monthly)
< 1 out of the <40 monthly samples analysed or < 5% of the > 40 samples analysed monthly should be positive for coliforms b Nephlometric Turbidity Units C > 90% are E.coli d Compulsory limits, bathing is restricted if >20% samples over 14 day period are positive e If 5 samples taken over 30 days are positive
Klebsiella, Enterobacter, Citrobacter Yersinia, Serratia, Hafnia, Pantoea, Kluyvera Cedecea Edwingella Moellerella Leclercia Rahnella Yokenella Coliforms that can be present in the environment & in human faeces (bold ) and coliforms that are only environmental (bold & underlined)
Enterococci
Coliforms
assay for
Lactose
If
growth
at
at
Enzyme
named
35
oC
Elevated
temperature
of
uses
-glucoronidase
detected
with
Enzyme
44.5
oC
designate
as
named
MUG
designate
as
-galactosidase
E.
coli
detected
with
designate as
Total coliforms
" Faecal coliform absence indicates enetric pathogens most likely absent but does not guarantee absence of viruses & protozoal cysts (survive longer in water & more resistant to disinfection) " Enterococci, sulfite-reducing clostridia, Bacteroides fragilis, Bifidobacteria, bacteriophages & non-microbiological indicators (faecal sterols) have been proposed as alternatives to fecal coliforms " Entercocci is the most preferred (also as alternative to E. coli) ommon commensals in warm blooded guts C 9 species (faecium, faecalis, durans, hirae dominate) 1 urvive longer & do not grow in the environment S n order of magnitude less than coliforms A ommercial test available C
" are classified as members of domains Bacteria, Eucarya or virus. " they differ in: orphologies m rowth g hysiology & metabolism p ine genetic details f Both classification & Identification is now increasingly based on their molecular events & molecular details (see next figure). The pathogens listed in the following tables have been detected in water and / or in outbreaks. An attempt has been made to provide their classification on the newly introduced molecular trend. The biology of a number of the pathogens will be described and the possible targets sites for their identification highlighted.
Crenarchaeota
Dinoflagellates Ciliates Green algae Plants Red algae
Animals
Methanopyru
Korarchaeota
Evolution of Universal Ancestor (3.5 billion yrs) The Tree of Life - 16th November 2000
Thermococcus
Aquifex
Bacterial pathogen
Sphingomonas Burkeholdaria E. E. E. E. coli coli coli coli 0157:H7 (hemorrhagic) (enteroinvasive) (enterpathogenic) (enteroitoxigenic)
P r o t e o b a c t e r i a
Phylum
Feces
H A
Urine
H A Potential
Disease
Enterobacterales + + + + + + + ? + + + + ? + + ? + ? -
Salmonellae species Salmonella enterica (serovar typhi) Shigella (S.flexneri, S. sonnei, S. dysenteriae, S. boydii) Plesiomonas shigelloides Vibrio cholera 01 Vibrio cholera non-01 Legionella Pseudomonas Aermomonas hydrophila Desulfovibrio species Campylobacteria Arcobacter
Enterobacterales
Watery, bloody diarrhea Typhoid, enteric fever, abdominal pain Shigellosis (bacillary dysentery) Fish & crustaceans Cholera (Asiatic flu, Indian, El Tor) Legionellosis Potential
+ + + +
+ + + + +
+ -
Helicobacteria Duration of disease is between 1 to 42 days Leptospira Spirochaetes Mycobacteria aviumintracelllare Actinobacteria
Information modified
" Some 50 to 60 genera; some produce oligopeptide toxins& are of increasing concern (dermal, cytotoxin, mutantion causing and carcinogens). Lifelong exposure vs short term acute exposure " Toxins are produced by (a) nonribosomal peptide synthetase (NRPS) which have iterative catalytic domains. Overproduction of one or several sets up a catalytic reaction leading to production of the toxins. (b) Peptide kinase synthetase (PKS). " ALDI-TOF MS shows a large spectrum of oligopeptides & other poorly undertood M metabolities from cyanobacteria. " icrocystis exist as toxigenic organism in reservoirs & form blooms (summer to late M autumn) but reports of non-toxicogenic strains have been reported. " Some 60 toxins (collectively called Microcystin) are produced; these are thought to react with chlorine to produce other toxin bye-products " They have been traditionally classified on the basis of morphology & physiology which has created confusion. Based on 16S rRNA and DNA homology studies, the 23 species have now been identified as belonging to M. aeruginosa " Toxin production in strains vary based on growth conditions (in vivo and in situ) causing more confusion.
"Calothrix desertica" PCC 7102. Cylindrospermopsis raciborskii str. AWT205. "Anabaena variabilis" IAM M-3. Nostoc muscorum PCC 7120. Planktothrix rubescens str. BC-Pla 9303. "Oscillatoria agardhii" str. CYA 18. "Oscillatoria corallinae" str. CJ1 SAG8.92. Trichodesmium species
Nostoc punctiforme PCC 73102. "Anabaena cylindrica" str. NIES19 PCC 7122. Pseudoanabaena biceps PCC 7367. Lyngbya confervoides PCC 7419. 10%
Spirulina subsalsa str. M-223. Prochloron didemni. Cyanobacterium stanieri PCC 7202. "Oscillatoria rosea" str. M-220. Merismopedia glauca str. B1448-1. Gloeothece membranacea. Microcystis wesenbergii. Microcystis novacekii str. TAC20. Microcystis viridis. Microcystis ichthyoblabe str. TAC48. Microcystis aeruginosa. Chamaesiphon subglobosus PCC 7430. Octopus Spring microbial mat DNA Yellow Leptolyngbya boryanum PCC 73110. "Plectonema boryanum" UTEX 485. Leptolyngbya foveolarum str. Komarek 1964/112. Gloeochaete wittrockiana str. SAG B 46.84 Glaucocystis nostochinearum str. SAG 45 Cyanophora paradoxa (colorless flagellate alga) -- cyanelle. "Oscillatoria limnetica" str. MR1 Phormidium mucicola str. M-221. Phormidium ambiguum str. M-71. Microcystis holsatica. Microcystis elabens. Prochlorococcus marinus PCC 9511. Synechococcus elongatus. Prochlorothrix hollandica. "Oscillatoria neglecta" str. M-82 Phormidium "ectocarpi" str. N182. Phormidium minutum str. D5.
The identification of cyanobacteria, the causative agents for a number of toxinproducing illnesses, is in a state of flux. The previous identification by morphology & / or toxin production does not reflect the rRNA based molecular phylogeny.
Protozoa
Disease
Entamoeba histolytica Giardia lamblia Cryptosporidium parvum Microsporidia: Enterocytozoon Septata Cyclospora cayatenensis Toxoplasma gondii Acanthamoeba Blantidium coli
Amebiasis (dysentry, enetritis, colitis) Giardiasis (hikers disease) Cryptosporodiosis (cramp, vomit, fever, diarrhea) Cramp, vomit, fever, diarrhea
? Yes No Yes
Virus Cytopathogenic human orphan (ECHO), polio, coxsackies Hepatitis A Virus (HAV) Hepatitis E Virus (HEV) Rotavirus A Rotavirus B Nowalk virus Snow mountain Astrovirus 100s of others (Developing new method to work with them?) Small small round structured virus (SSRV)
Group Entero
Disease Aseptic meningitis, infantile diarrhea, polio Infectious Hepatitis Acute gastroenteritis Acute gastroenteritis Acute gastroenteritis Uncertain
Viruses: " Role of some human enteric & respiratory viruses (& some animal viruses) as waterborne pathogens has been well established " Most are nonenveloped (except corona & picobirnaviruses) more ressistant to physical & chemical agents then the lipid containing enveloped viruses " Potential transmission route directly or indirectly from animal human & this is of concern
Detection:
Source water quality Watershed management Treatment process configuration (driven by source water quality) Distribution concerns Treatment chain Distribution system Ingestion Dermal Inhalation
Microbial adaptation:
Pathways:
The Need for Molecular methods for the identification & detection of pathogens
Current US$380 million market & a 20% annual increase is expected Emerging sophisticated gene technologies (indicators & pathogens) Skilled (bioinformatics, genomics, phenomics) staff required. Multicomprehension (ecology, environmental etc) required Method rapid flexible, reproducible & can be ariticulated to particular needs of different countries Initial research & development outlay is expensive (research costs)
Next?
Finding molecular biology information libraries Understanding the principles of molecular biology Finding & using tools for molecular methods
SECTION IV. The Biology, Methods for Detection, Identification & Quantitation of Waterborne Pathogens
CONTENT
1. The Biomolecules & Molecular Biology of Cells 2. Biomolecule Based Technics 3. The Biology & Detection Methods of Some Pathogens 4. Modern Techologies a. Polymerase Chain Reaction (PCR) b. Real Time PCR c. Pulse Field Gel Electrophoresis d. New High Throughput Methods
DNA
TOTAL
DNA:
ol%G+C
M estric3on
Paherns
(RFLP,
PFGE)
R enome
size
G NA
homology
D DNA
SEGMENTS:
PCR
based
ngerprin3ng
(ribotyping,
ARDDRA,
RAPD,
AFLP,
AP-PCR,
rep-PCR)
NA
probes
D NA
sequencing
D
RNA
rRNA
sequencing
MW
RNA
proles
L
Plasmid DNA
DNA lectrophore3c paherns of total cellular or E cell envelope proteins (1D or 2D) ul3enzyme paherns (mul3locus enzyme M electrophoresis)
PROTEINS
mRNA
CHEMOTAXONOMIC MARKERS ellular fahy acids (FAME) C ycolic acids M olar lipids P uinones Q olyamines P ell wall compounds C xopolysaccharides E
EXPRESSED FEATURES orphology M hysiology (Biolog, API, ) P nzymololgy (APIzyme) E erology (monoclonal, polyclonal) S
New
1. Cell surface: a. proteins (receptors, porins, siderophores): 200,000 / cell b. Polysaccharides (LPS): 2 million in Gram ve cells 2. Cytoplasmic: a. Ribosomes (rproteins & rRNA): 20,000 in dividing cells. b. Non-ribosomal RNA: 100 1,000 / cell (depending on rate of transcription or rate of degradation) c. Non-iobosomal proteins (RNA polymerase): 3,000 / cell The target concentrations in a 1 ml sample will be 0.03 attomolar(3,000 molecules / cell) to 20 attomolar (2 million / cell)
Technique
Restric3on
Fragment
Length
Polymorphism
(RFLP)
Low
frequency
restric3on
fragment
analysis
(PFGE)
Phage
and
bacteriocin
typing
Serological
techniques
Ribotyping
DNA
amplica3on
(AFLP,
AP-PCR,
RAPD)
Zymograms
(mul3locus
enzymes)
Total
cellular
protein
electrophore3c
paherns
DNA
homology
Mol%
G+C
DNA
amplica3on
(ARDRA)
tDNA-PCR
Chemotaxonomic
markers
Cellular
fahy
acid
ngerprin3ng
(FAME)
rDNA
/
rRNA
sequencing
DNA
probes
DNA
sequencing
Highthrougput
assays
(Microarrays,
Can3lever
arrays)
Vibrio cholera: Cholera txin resides on plasmids which are transferred by phage
Protozoal Parasites: Detection in water supplies is a challenge Biology remains unstudied, biomarkers unavailable Methods have limitation & cannot differentiate:
uman species form animal species h nfectious forms from noninfectious forms i
Techniques such as Microscopy, PCR & RFLP of limited use for diagnostics Characteristics: Entamoeba histolytica: a long history as a waterborne pathogen (no US major
outbreaks reported for decades, no major nonhuman reservoir) Cryptosporidium parvum: Major problem. unknown.
Diagnostic Methods
1. Recovery and Concentration: To increase pathogen concentration by physical, chemical or enrichments. 2. Purification & Separation: Methods use knowledge of pathogen size, shape, density etc surface properties (hydrophilicity, reactivity, receptors), growth stages (spores, capsules, ooocytes) for this. 3. Assay & Characterisation: Differentiate pathogens from all others: Qualitative / quantitative, viable / nonviable. Cultural, immunological and NA based [ NA amplification (PCR), NA identification & characterisation methods (hybridisation by gene probes, RFLP & nucleotide sequencing)]. NA based methods are specific & sensitive but incapable of differentiating live but inactivated cells from dead / noninfectious ones.
4. Modern Techologies
Figure 1B
Figure 1A
Figure 1C
DNA Fundamentals
2. What is PCR? DNA replication in a tube (in vitro). Xeroxing (copying) of DNA. 3. The Components of PCR The basic components of a PCR reaction are - one or more molecules of target DNA -two oligonucleotide primers - thermostable DNA polymerase - dNTPs 4. The Process of PCR Each PCR cycle requires three temperature steps to complete a round of DNA synthesis:
Cycle 1: The original DNA template will continue to be copied by the DNA polymerase until it stops or the process is interrupted by the start of the next cycle. Cycle 2: Amplicons of intermediate lengths produced Cycle 3: Amplicons of defined lengths will be produced. Cycle 4 onwards: Target sequence will be amplified exponentially The final number of copies of the target sequences is expressed as: (2n-2n)x where n = no of cycles, 2n = 1st product obtained after cycle 1 & 2nd products obtained after cycle 2 with undefined length and x= no. of copies of the original template
PCR target molecules accumulate as a function of cycle number with the exponential phase lasting for about 30 cycles under standard reactions conditions. The plateau phase results from limiting amounts of enzyme and reduced enzyme activity. The production of 1 billion copies of the specific targeted DNA from 1 template during the 30 cycles is theoretically possible but never practically achieved because of lack of 100% PCR efficiency. The products formed during the process could be mixtures of specific and non-specific products and these factors reduce PCR efficiency from the theoretical 100%.
5. The Factors Affecting PCR I. Generalities: pipette water first, followed by the other ingredients. work on ice in order to minimise primers binding to the DNA template and to prevent functioning of the polymerase (even theoretically) prior to the first denaturing step. avoid aerosols while pipetting (or use aerosol-ressistant pipette tips) & work under laminar flow hoods. Be very accurate when dealing with small volumes. (Multiplex PCR of two different genomic DNA samples can be very susceptible to errors in pipetting). II Thermocyclers and PCR vials: The same PCR program will work slightly different on different thermocyclers (temperature and time profiles may differ) and therefore the PCR results using the same primer pair may vary. New PCR machine designs accommodate thin-walled 0.2 ml PCR vials (and/or 96 wells microtiter dishes). Contact between the metal and plastic is very good and aided by the downward pressure from the heated lid. Older machines accommodated 0.5 or 1.5 ml vials and the contact between the vials and the metal block is not always perfect because of slight differences in shape and wall thickness amongst manufacturers, often resulting in reduced or no amplification
50mM NaCl decreases the melting (denaturing) temperatures of 91-97oC (not 100 oC) 1 aq polymerase has a half-life of 30 min at 95oC. Denaturation temp as short as possible T 2-5 minutes initial denaturing step prior to the start of cycling is not necessary 1 min at 94oC (usually between 15 sec to 30 secs) avoids loss of Taq enzyme activity 7-28 bases. Longer primers 30-35 bp for multiplexing 1 both primers have a close melting temperature or Tm of within 5 oC. G+C content of 40-60% (Tms between 55-80oC are preferred). primer sequence with 1-2 GC pairs at the start and end improves priming efficiency three or more Cs or Gs at the 3'-ends of primers may promote mispriming Check for primer-primer interactions: 3'-ends of primers not complimentary Check for primer self-complementarity (ability to form 2o structures such as hairpins) primer sequences checked against DNA database (using BLAST programs) for uniqueness Useful ON-LINE programs for primer design can be found at the following URLs Primer0.5: http://trishul.sci.gu.edu.au/JaMBW/5/2/index.html WebPrimer:http://genome-www2.stanford.edu/cgi-bin/SGD/web-primer Primer3: http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi alculate Tm of primer using rule of thumb 4(G + C) + 2(A + T)oC. C Temperature of annealing (Ta) should be about < 5oC below the lowest Tm of the pair of primers aq polymerase incorporates about 2000 nucleotides/minute at optimal temperature 72-78o C T Rule of thumb 1 min for a 1 kb product, 2 min for a two kb
V. Extension or Polymerisation:
thin walled, 0.2 ml plastic vials for 96 well thermocyclers have heated lids (no oil). Reaction volumes (5, 25 or 100 ul) okay PCR product yield is higher in 5 L compared to 100 L volumes (product can be visualised) 100-500 nM each primer Purchased as 10-25 mM; 0.5-1ml primer is sufficient for 25-100 ml PCR reactions
ithin limits, increasing primer and template concentration may improve the outcome of the W PCR reaction, and should be considered as a way to optimize PCR reactions Stock of 25 mM each stored as small aliquots (2-5 l) at -20o C. Centrifuge long term stored solutions as water condenses on the walls changing conc Dilute stocks in buffered water (10mM Tris pH 7.7-8.0) as acid pH hydrolysis dNTP to dNDP and dNMP
00M dNTP each and 1.5mM MgCl2 is recommended with Taq polymerase, (Perkin Elmer 2 Cetus). Theoretically 6-6.5 g of DNA is synthesised from 25 l reaction. Besides magnesium bound by the dNTP and the DNA, Taq polymerase requires free magnesium. This is probably the reason why small increases in the dNTP concentrations can rapidly inhibit the PCR reaction (Mg gets "trapped") whereas increases in magnesium concentration often have positive effects.
Between 5-10% DMSO or glycerol promotes increase in PCR yield 0.8g/l BSA promotes better yield than DMSO or glycerol
6-10% PAA gels used for PCR products differing in only a few bp in length % PAA/7M urea sequencing gel is used to separate radiolabeled multiplex PCR products 6
o gels required. Recent method. Relies on the ability of a dye, SYBR Green, to N intercalate with double stranded amplicons produced during PCR, to produce fluorescence which is detected in a flurometer. (Dealt with in a subsequent section)
New
b. RealTime-PCR
3. Instruments
A. LightCycler (Idaho Technologies ! Roche) B. Rotor-Gene (Corbett Research) C. iCycler (BioRad) D. Mx4000 Multiplex Quantitative PCR System (Stratagene) E. ABI Prism 7700 (Perkin-Elmer-Applied-Biosystem) F. SmartCycler (Cephid)
A. DNA binding dyes B. Oligonucleotide Hybridisation Probes I. Hydrolysis Probes (TaqMan) II. Strand Displacement Probes A. Roche Dual probe B. Hair Pin Probes Molecular Beacon Sunrise UniPrimer Scorpion
Stem & Loop Duplex FRET Duplex
5. Applications
1. Introduction
New
When a population of fluorochrome molecules is excited by light of an appropriate wavelength, fluorescent light is emitted. The light intensity can be measured using a flurometer or by measuring a pixel-by-pixel digital image of the sample. In the later case, image analysis software, makes it possible to view, measure, render, and quantitate the resulting image. Excitation and Emission: Fluorodyes absorb light at one level (wavelength) & thereby boosts an electron to a higher energy shell (an unstable, excited state). The excited electron falls back to the ground state and the flurophore reemits light but at a second lower , longer wavelength. This shift makes it possible to separate excitation light from emission light with the use of optical filters. The wavelength (nm) where photon energy is most efficiently captured is defined as the Absorbancemax & the wavelength (nm) where light is most efficiently released is defined as the Emissionmax. The difference in absorbed & emitted wavelength = Stokes shift (). can be a large or small number depending on the loss of energy during fluorescence process.
New
The wavelegth range for which flurodyes absorb light is small (~ < 50nm) and light outside this range will not cause the molecule to fluoresce. 2. Linearity: Theintensity of the emitted fluorescent light is a linear function of the amount of fluorochrome present when the illuminating light has a constant wavelength and intensity (for example, using a controlled laser light source). The signal becomes nonlinear at very high fluorochrome concentrations. 3. Brightness: Fluorochromes differ in how much intensity they are capable of producing. This is important because a dull fluorochrome is a less sensitive probe than a bright fluorochrome. The brightness depends on two properties of the fluorochrome ts ability to absorb light (extinction coefficient). I he efficiency with which it converts absorbed light into emitted T fluorescent light (quantum efficiency). 4. Environmental factors: Environmental conditions can affect the brightness or the wavelength of the absorption or emission peaks. Such fluorochromes are useful for analyzing changes in H+, Mg2+, or Ca2+ concentration & detecting lipids or double-stranded DNA. Photodestruction (photobleaching) of photosensitive dyes (eg fluorescein) is caused by intense light. Use antifade agents or lower the laser power
Fluorescent dyes have become the preferred method of detection for nucleic acids in Molecular Biology. " hey are used as single conjugated dyes to oligonucleotides for: T Automated fluorescent DNA sequencing, Fluorescent genotyping & Terminal Fragment Restriction Length Polymorphism (TFRLF) AND " As double or multiple conjugated dyes to oligonucleotides for simultaneous detection, identification and quantitative techniques in Real Time PCR (Molecular Beacons) based on the principle of Fluorescence Resonance Energy Transfer (FRET) or quenching.
Modified
2B. What is Fluorescence Resonance Energy Transfer (FRET)? FRET is a distance dependent interaction interaction between the excited states of 2 dye molecules in which excitation is transferred from a donor molecule to an acceptor molecule without emission of a photon
Hybridization probes
(c) No hv
hv
hv
R R Q Q
(e) No Physical proximity + hv (Quenching released)
494 / 518 nm
TET CY 3
650 / 690 nm
HEX
TEXAS RED
LC-RED
" he filtered light then strikes a photodetector or photomultiplier which T allows the instrument to give a relative measurement of the intensity of the emitted light. " luorescent molecules can be detected at concentrations below a level F visible to the subjective human eye & as fluorescence intensity vs. concentration is a linear relationship, dye concentrations can be determined with a good degree of accuracy
A number of ways are available to improve detection and measurement of the emitted fluorescent signal. a. Elimination of the excited light from the collection pathway by several methods: Orienting the excitation light path so that the light does not shine into the collection pathway. Inserting optical filters into the collection pathway to reject the excitation wavelength. Delaying collection until after a pulse of excitation light has disappeared. b. The fluorescent signal can also be enhanced by increasing the dwell time or by scanning the sample multiple times and mathematically processing the signals to reduce random noise. Such methods are useful and practical for increasing the sensitivity at the low end. c. A band-pass optical filter can be used to reject broad-spectrum background emissions. This type of filter rejects wavelengths shorter and longer than the selected band, while allowing wavelengths in the selected wavelength range (centered around the fluorescent emissions of the sample) to pass through to the collection pathway.
Wide variety: Fluorochromes with a wide variety of characteristics are available, including fluorochromes that espond to pH or ion concentrations. R ocalize based on hydrophobic and hydrophilic interactions. L an be cross-linked to proteins, NA, lipids, or polysaccharides. C Commercial available: Fluorochromes are available crosslinked to many other molecules (eg fluorescently labeled monoclonal and polyclonal antibodies with a choice of fluorochrome, fluorescently labeled enzyme substrates, such as fluorescent chloramphenicol for chloramphenicol acetyl transferase (CAT) assays and fluorescein digalactoside for b-galactosidase assays (lacZ gene). Multiple-label possibility: A significant advantage of fluorescent labeling over other methods is the possibility of recording the fluorescence of two or more fluorochromes separately using optical filters and a fluorochrome separation algorithm. Thus, components can be labeled specifically and identified separately in the same sample or lane (EG Real Time PCR applications)
(New)
Stability: The long shelf life compared to radiolabeled molecules. Fluoromonoclonal antibodies, oligonucleotide hybridization probes, and PCR primers can be stored for six months or more but antibodies labeled with 125I and 32P-labeled nucleotides and oligonucleotides become unusable in a month and a week respectively. Reagent batches can be standardized and used for extended periods in antigen localization, ELISAs, enzyme assays (such as CAT and kinase), PCR-based genetic typing assays (such as STR analyses), DNA sizing and quantitation, DNA sequencing, protein sizing and quantitation. Low hazard: Most fluorochromes are easy to handle, however, proper care should be observed (eg gloves) with DNA and RNA stains (mutagenic as they bind to these molecules). In contrast, lead or acrylic shields are required for handling radioactive materials and require special disposal protocols (eg shielded storage, long-term decay, or regulated land-fill disposal) Lower cost: The long shelf life and cheaper transportation and disposal costs for fluorochromes make fluorescent labeling, in many cases, less expensive than radiolabeling.
(New)
General Description of Instruments 1. PCR cycler: 1. 96 well format, 8 tube format, capillary (glass) 2. Air or block heater 3. Temeperature ramp, temperature gradient 2. Fluorescence emission & detection : 1. Fluorometer 2. CCD camera 3. Excitation source: xenon, halogen, laser 3. Fluorescent Dye Labeling of: 1. Oligonucleotides 2. Peptide Nucleic acids (PNA) 4. Near Infra Red Dyes: 1. Available but no commercial labeling service available
Xenon Arc lamp (250-1000 continuous) Glass capillaries + Air (not metal block) = rapid
Idaho LightCycler
The Lightcycler performs PCR in small-volume glass capillary tubes, contained within a rotor-like carousel, that are heated and cooled in an airstream. The carousel is rotated past a blue light-emitting diode, and fluorescence is read by three photodetection diodes with different wavelength filters that allow the use of spectrally distinct fluorescent probes. Assays based on DNA-binding dyes, hydrolysis probes, molecular beacons and dual hybridisation probes are possible. Up to 32 reactions are typically carried out in 520 l volumes and PCR is completed in less than 20 min. The fluorescence readings taken at every cycle of the PCR reaction are displayed immediately after each measurement, allowing amplification runs to be terminated or extended, as appropriate, during individual runs.
Dual Light source Excitation: 470 & 530 32 x 0.2 ml plastic tubes Air heated, centrifugal mixing
1a. Excitation filters 1b. Emission filters Tungsten halogen light source Microplate format Cycler
(350 - 1000nm continuous)
Biorad Instruments have recently launched an optical module that fits their standard thermal cycler and transforms it into a real-time RT-PCR system. This instrument is capable of generating and detecting a wider range of excitation frequencies than either the ABI 7700 or the Lightcycler. At present, it can monitor up to four different fluorescent reporters at any one time and can be used for any one of of the alternative fluorescent RT-PCR strategies. Furthermore, unlike the ABI 7700 which scans its 96 samples sequentially, this instrument can scan up to 96 samples simultaneously, with a sampling frequency that can be defined by the user.
Quartz tungsten halogen lamp (excitation range of 350 to 750nm) 96 well plates Fast cycling (90 min) CCD camera for capturing fluorescence
The ABI Prism 7700 (Perkin-ElmerApplied Biosystems) contains a built-in thermal cycler with 96-well positions, and is able to detect fluorescence between 500 nm and 660 nm. Fluorescence is induced during the PCR by distributing laser light to all 96 samples contained in thin-walled reaction tubes via a multiplexed array of optical fibres. The resulting fluorescent emission returns via the fibres and is directed to a spectrograph with a charge-coupled device (CCD) camera. Because each well is irradiated sequentially, the dimensions of the CCD array can be used for spectral resolution of the fluorescent light. This instrument can be used for assays based on DNA-binding dyes, molecular beacons and hydrolysis probes.
TaqMan Probe
Forward Primer
Probe
Reverse Primer
R
Forward Primer
Forward Primer
Q
Probe
The TaqMan probe binds to ssDNA at a combined annealing and elongation step. It is degraded by the polymerase which releases the reporter dye (R) from the quencher (Q).
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TaqMan Probe Design: Keep the G-C content in the 3080% range. Avoid runs of an identical nucleotide especially Guanine Do not put Gs on the 5' end. Select the strand that gives the probe more Cs than Gs. For single-probe assays, Tm should be 6870 C Primer Design: Choose the primers after designing the probe. Design the primers as close as possible to the probe without overlapping the probe. Keep the G-C content in the 3080% range. Avoid runs of an identical nucleotide especially Guanine The Tm should be 5860 C. The five nucleotides at the 3' end should have no more than two G and/or C bases.
NOTE: Applied Biosystems provide Primer Express for design of primers and probes in real time with Real Time Quantitative PCR systems (7700, 5700)
Adjacent probes
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(i) Identify useful Primer / probe regions (use any of the Primer software) (ii) Check primer / probe specificity using Fasta against Genbank database (iii) Check Tm using http://alces.med.umn.edu/rawtm.html (iv) Check propenisity of probe to self anneal using Oligo Selection Program (v) Probe Tms should be near equal and 5-10C greater than primer Tms (vi) The 3 end of the upstream probe should be labeled by fluorescein, which serves as the donor in the FRET and blocks extension from the probe (vii) the 5 end of the downstream probe should be labeled by Cy5, which serves as the acceptor in the FRET, and the 3 end of the probe should be phosphorylated to block extension the probes should be separated by one base (viii) the probes should be placed on one strand near a primer on the opposite strand.
Designing rRNA gene directed fluorroprobes for detection & identification of Campylobacter & Arcobacter by Real Time PCR
Forward PCR primer
FITC probe
Cy5 probe
2 1
Figure 1: Continuous monitoring of fluorescence during PCR in which DNA templates from A. butzleri ATCC (--), C. jejuni ATCC (-+-) and A. skirrowii ATCC (--) show a significant increase in fluorescence emission whereas templates from E. coli (--), C. upsaliensis (--) and C. hyointestinalis (-o-) show only a marginal increase when compared to no DNA template control (--) which shows no increase. Template DNA was prepared using the rapid boiling method Figure 2. Derivative melting curves (-dF/dT) determined by the dissociation of fluorogenic adjacent hybridisation probes from the target amplicons enables discrimination of A. butzleri ATCC (Tm 68 oC), A. skirrowii (Tm 64 oC), C. jejuni ATCC and C. coli (Tm \ 66 oC) from each other. E. coli, C. upsaliensis, and C. hyointestinalis and template DNA produce no Tm.
Designing virulence gene directed fluorroprobes for detection, identification & differentiation of Campylobacter coli & Campylobacter jejuni from other species by Real Time PCR
Cy5 probe
Figure-1- Real time detection Real time detection of hippuricase gene for Campylobacter jejuni (--), Campylobacter coli (--), Campyloacter hyointestinalis (-),Campylobacter upsaliansis(--),E. coli (--) and Negative control (-+-) (No template Figure 2: Melting temperature of hippuricase gene for Campylobacter species
MOLECULAR BEACONS Molecular Beacons are hairpin structures composed of a nucleotide base paired stem and a target specific nucleotide loop. The loop consists of target specific nucleotide (probe) sequences The stem is formed by annealing of complementary nucleotide bases of the probe sequence. A fluorescent moiety (reporter)is attached to one end of the arm and a non-fluorescent quenching moiety is attached to the other arm. The stem keeps both the moieties in close proximity so that fluorescence is quenched
(Loop)
Stem
5 3
3 5
5 5 3
Q
5
Denaturation
3 5
5 3
3 5
Extension
5 3
Operation of Molecular Beacon (MB): MB is non-fluorescent due to close proximity of the non-fluorescent quencer (Q) and the fluorescent Reporter. However when the probe denatures and the loop anneals to the target sequence of the amplicon, a conformational reorganization occurs separating the quencher from the fluorophore and thereby producing fluorescence which is proportional to the amplicons produced during PCR
AAAAAAAAAAAAAAA
Q
PolyA Tail
Sunrise Probe with polyA tail binds to the primer polyT tail at annealing.
Q
hv
Q
AAAAAAAAAAAAAA
The Sunrise probe changes conformation during denaturation & quenching by DABCYL is removed allowing FITC to fluoresce
The template & probe denature The primer is part of the Scorpion probe
Primer, stopper to prevent read PCR through, probe sequence, fluorophore & quencher (detection system).
Similar to the Ste-loop Scorpion except the probe sequence is part of the stem. There is no loop in this case.
In general, design complexty: Dual adjacent > Taqman > Stem Loop Ideally, MBs should hybridise at their annealing temps (fluorescent) & free MBs should be closed (nonfluorescent) Use Oligo4.0 or percent GC rule to calculate that the loop sequence length (usually 15-30 nucleotides) is such that it dissociates from its target at temperatures 7-10 oC higher then the annealing temp of the PCR. Add two complimentary arms on either side of the loop probe sequence. (usually 5-7 nucleotides; 5 GC rich stems melt between 55 & 60, 6 between 60 & 65 and 7 between 65 & 70). In order that it remains closed in the absence of the target, the length & GC content should be 7-10 oC higher then the annealing temp of the PCR. The melting temperature of the stem cannot be predicted by the GC rule as the stems forms by an intramolecular hybridisation event There should be no in between conformational changes, ie should always be the intended hairpin structure an d nothing in between. Commercial program available for making MB probes. ..\..\My Documents\My Pictures\BD100Tour.exe
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Probe Detection of the different fluorescent probes during Real Time PCR
, Dual probe
Application: Bacterial Pathogen detection isteria monocytogenes L ampylobacter jejuni group C rcobacter group A eptospira group L Application: Bacterial Non-Pathogen detection hermoanaerobacter species T aloramator species C ervidobacterium species F
Advantages of Adjacent Probe Technique with Real Time PCR (Idaho -> Roche):
1. Rapid requiring < 30 mins in a Light Cycler 2. rRNA and / or rRNA genes can be used = flexible 3. Simultaneous detection, identification & quantitation 4. PCR primer design + probe design = extremely specific assays possible 5. Different flurodyes available. Multiplexing possible 6. Population dynamics in an ecosystem can be followed 7. Forms a powerful tool when used in conjunction with rRNA sequencing & FISH
agarose gel electrophoresis is a fundamental technique in molecular biology but is generally unable to resolve fragments greater than 20 kilobases in size (whole microbial genomes are usually greater than 1000 kilobases in size) PFGE (pulsed field gel electrophoresis) is a adaptation of conventional agarose gel electrophoresis that allows extremely large DNA fragments to be resolved (up to megabase size fragments) essential technique for estimating the sizes of whole genomes/chromosomes prior to sequencing and is necessary for preparing large DNA fragments for large insert DNA cloning and analysis of subsequent clones also a commonly used and extremely powerful tool for genotyping and epidemiology studies for pathogenic microorganisms
Principle of PFGE
two factors influence DNA migration rates through conventional gels - charge differences between DNA fragments - molecular sieve effect of DNA pores DNA fragments normally travel through agarose pores as spherical coils, fragments greater than 20 kb in size form extended coils and therefore are not subjected to the molecular sieve effect the charge effect is countered by the proportionally increased friction applied to the molecules and therefore fragments greater than 20 kb do not resolve PFGE works by periodically altering the electric field orientation the large extended coil DNA fragments are forced to change orientation and size dependent separation is reestablished because the time taken for the DNA to reorient is size dependent
Principle of PFGE
Principle of PFGE
the most important factor in PFGE resolution is switching time, longer switching times generally lead to increased size of DNA fragments which can be resolved switching times are optimised for the expected size of the DNA being run on the PFGE gel switch time ramping increases the region of the gel in which DNA separation is linear with respect to size a number of different apparatus have been developed in order to generate this switching in electric fields however most commonly used in modern laboratories are FIGE (Field Inversion Gel Electrophoresis) and CHEF (ContourClamped Homogenous Electrophoresis)
a. DNA MicroArrays
DNA Microarray
a completely annotated microbial genome sequence, whilst a powerful scientific tool, still doesnt provide all of the information needed to understand the complete biology of an organism as it essentially a static picture of the genome for truly complete characterisation, the dynamic nature of gene expression within a microbial cell needs to be determined microarray technology allows whole organism gene expression to be investigated PCR products of every gene from a complete genome sequence are bound in a high density array on a glass slide these arrays are probed with fluorescently labelled cDNA prepared from whole RNA under specific environmental conditions the level of cDNA for each ORF is then quantified using high resolution image scanners
DNA MICROARRAYS TECHNIQUES: The development based on bioinformatics knowledge genes & genomes; High throughput & can analysise complex gene expression profiles There are different formats for DNA high density microarrays:
DNA arrays (Stanford University development 1999): 0.5 5kb c ligonucleotide synthesised (Genechip) arrays (Affymetrix, 1998): O 20-25 base ligomers / PNA, in situ or spotted O An example of how a microarray is made by in situ synthesis approach is shown as a movie. ..\..\My Documents\GeneChip.mov
STEPS IN THE DNA ARRAY TECHNIQUE: 1. Probe Selection - cDNA / oligo with known identify: Small oligos, cDNA, chromosome 2. Chip Fabrication Putting probes on the chip: photolithography, pipette, drop-touch, piezoelectric (inkjet), electric 3. Target fluroscently labeled sample: RNA (mRNA) to cDNA 4. Assay: Hybridisation, ligase, base addition, electric, electrophoresis, fluocytometry, PCRDIRECT, TaqMan 5. Readout: Flurorescence 6. Informatics: Robotic controls, image processing, DBMA, WWW, bioinformatics EXAMPLES: BioMerieux is developing for a water company a 4 h fecal indicator test using Affymetrix technology 2 has 400k oligonucleotide probes, small volumes of sample required limits the usefulness 1cm TaqMan type: Leptospira for WHO regional reference laboratory, Campylobacter & Arcobacter for QHSS, Brisbane.
Yellow = Red + Green (no change in expression) Green (untreated controls) ie expressed without INH treatment Red = expressed as a result of INH treatment
The effect of Isoniazid (INH) on the gene expression of Mycobacterium tuberculosis using DNA microarray technique
New
INH is very safe, but like any medicine it can sometimes cause side effects. (yellowish skin, dark urine, vomiting, loss of appetite, nausea, changes in eyesight, unexplained fever, unexplained fatigue & stomach cramps). Human DNA arrays can be used to investigate the mechanism of toxicity on human which may not be possible using animal models.
A human DNA array can be used for testing water which has been contaminated by cyanobacterial blooms before and after treatment. This will provide useful information on exposure levels (time & concentration).
This will provide a rapid method for identifying the most susceptible cell lines that can be used to isolate the offending pathogen.
Cantilever arrays
What are cantilever arrays? Cantilever arrays are produced by microfabrication in silicon using dryand wet-ething techniques. The cantilevers are 500 m long, 100 m wide and about 1 m thick. The spring constant is 20 milliNewton per meter, resulting in a resonance frequency of about 4 kHz. The reproducibility of the resonance frequency from cantilever to cantilever within the array is better than 2%. Owing to their high flexibility, such cantilevers are appropriate for measuring tiny changes in surface stress. For such applications as mass determination, we have designed special cantilevers with a thickness of about 8 m, producing a resonance frequency of around 50 kHz.
Cantilevers are used for imaging in scanning force microscopy but is now being tested as a nanotech sensor. A thin flexible beam made of silicon coated with a sensor layer serves as a chemical sensor. Eight cantilevers aligned in a row form a nanomechanical cantilever sensor array, which can detect small amounts of analytes via very specific reactions. The analyte can also be characterized via its diffusion properties through the coating, e.g. a polymer layer.
Nanomechanical cantilever array sensor If analyte molecules dock on the surface of the cantilevers the surface stress at the interface changes, causing the cantilever to bend.The amount of bending is quantitated.
DNA hybridisation cantilever array The binding of two complementary single stranded oligonucleotides can be observed in a setup of two cantilevers, each functionalized with a different synthetic oligonucleotide (red and blue). If the complementary oligonucleotide (green) is injected, it binds preferably to the red oligomer, but not to the blue one. This hybridization process involves bending of the cantilever due to steric and charging effects. If the complementary sequence to the blue strand is injected, the second cantilever bends.