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Structural sensing Flashcards

1
Q

What do we mean by structural sensing?

A

detection of a threat by use of the structural elements of the threat, usually from binding to part of these elements with something that is easy to detect

eg an agglutination test

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2
Q

What are the five bio-analysis methods?

A

Culture
Microscopy
Immunoassay
PCR
Chemical Assays

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3
Q

Describe Method of Bioanalysis Culture

A

grow agents in conditions that specifically relate certain types of bacteria/fungi etc ie rose Bengal agar is a growing media that inhibits bacteria and allows the identification of the presence of yeast and moulds

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4
Q

Describe Method of Bioanalysis Microscopy

A

Morphological identification of particles

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5
Q

Describe Method of Bioanalysis Immunoassay

A

particles with specific epitopes matching the assay antibodies

particles with parts of the allergen that are identified by the body (epitodes) that in this case match the antibodies present in the assay test.

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6
Q

Describe Method of Bioanalysis PCR

A

DNA matching test

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7
Q

Describe Method of Bioanalysis chemical assays

A

identify the biomass of specific chemicals eg ATP

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8
Q

Limitations of bioanalysis method culture

A

underestimates concentration of all organisms
nonculturable organisms are invisible
non culturable are classed as noninfective

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9
Q

Limitations of bioanalysis method microscopy

A

limited to groups of organisms, not specific strains

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10
Q

Limitations of bioanalysis method immunoassay

A

limited to organisms that the assay is designed for, therefore only binary results
Cross reactivity is common

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11
Q

Limitations of bioanalysis method PCR

A

limited to organisms that the assay is designed for, therefore only binary results
highly specific
highly sensitive

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12
Q

Limitations of bioanalysis method Chemical analysis

A

only an indicator for large quantities of organisms

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13
Q

what is meant by direct binding event?

A

direct binding of the target to a specific molecular recognition element

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14
Q

how does direct binding event works?

A

a reversable ‘lock and key’ event like and antibody with a viral protein

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15
Q

9 molecular recognition elements for biosensing

A

single strand DNA
Antibody
Peptide
Enzyme
Lectine
Receptor
Aptamer
Small molecule
imprinted molecule

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16
Q

What is an antibody?

A

also known as an immunoglobulin Ig is a large, Y shaped protein produced mainly by plasma cells that is used by the immune system to neutralize pathogens such as pathogenic bacteria and viruses.

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17
Q

How do immunoassay ticket systems work?

A

liquid sample added to test strip and other reagents added if required

target molecules wick through the ticket, bind to immobilized agents and detection molecules in a ‘sandwich’ format

wick usually travels through a testing area before reaching a control line, if no line shows up on control after allotted time, then the test needs repeating.

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18
Q

Define SELEX?

A

Systematic Evolution of Ligands by EXponential Enrichment

a method of increasing the number of DNA/RNA strands required for testing and use them to sequence and characterise DNA found in the environment

The starting single stranded DNA or RNA library
(10 14 ~10 16 random oligonucleotides) is composed of sequences 20~100 nucleotides in length with a random region in the middle flanked by fixed primer sequences.

After incubation with the target of interest, the bound
oligonucleotides are partitioned from unbound
sequences and amplified by PCR . repeated 2-15 times before used as biomarker identification tools.

The resulting enriched DNA pool is used for the next round of selection.

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19
Q

What is SELEX short for?

A

Systematic Evolution of Ligands by EXponential Enrichment

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20
Q

Dog’s nose; how does this compare with current detection systems

A
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21
Q

6 high level approaches for structural sensing

A

Magnetic
optical
electrochemical
mass
acoustic/piezoelectric
MEMS

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22
Q

Types of optical

A

Fluorescence
Absorbance
SPR/RM
Luminescence
RAMAN

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23
Q

Types of magnetic

A

magneto-elastic
giant magneto-resistance (GMR)

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24
Q

types of MEMS

A

MEOMS
cantilevers
microfluids
microcalorimetry

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25
types of acoustic/piezo-electric
surface wave acoustic quartz microbalance
26
types of mass
time of flight ion trap ion mobility (MS/MS)
27
types of electrochemical
amperometry potentiometric conductimetric molecular electronics
28
What is a molecular recognition element?
Molecular recognition event is typically a specific interaction that is reversible, analogous to the interaction between a lock and a key, although in many cases the binding would more accurately be described as induced fit, during which the recognition element changes shape upon binding.
29
What does a direct binding event rely on?
Affinity of the target for the molecular recognition elements Non-specific binding of extraneous material at the binding site Sensitivity of detection If attomolar (10 18 ) detection levels are required then high affinity molecular recognition elements with minimal non specific binding required
30
considerations for structure based sensing?
Sample collection, Sample concentration, Binding of the target to the molecular recognition element, Possible addition and removal of "reporter" groups, Detection of target molecular recognition element complex, Analysis of the output signal, Renewal of the sensor surface for repeated monitoring.
31
target inhibitor for single strand DNA?
complementary sequence of DNA
32
target inhibitor for Antibody
proteins, carbohydrates, small organic molecules etc
33
target inhibitor for Peptide
proteins, carbohydrates, small organic molecules etc
34
target inhibitor for enzyme
substrate such as biochemicals like glucose, acetic acid
35
target inhibitor for lectin
carbohydrate
36
target inhibitor for receptor
proteins, carbohydrates, small organic molecules
37
target inhibitor for aptamer
proteins, carbohydrates, small organic molecules etc
38
target inhibitor for small molecules
proteins, cells etc
39
target inhibitor for imprinted moelcules
proteins, small organics molecules, whole cells etc
40
target inhibitor for
41
8 SELEX methods
IP-SELEX Capture-SELEX Cell-SELEX CE-SELEX M-SELEX AFM-SELEX AEGIS-SELEX Animal-SELEX
42
Key aspects of IP-SELEX
includes immunoprecipitation
43
Key aspects of Capture-SELEX
oligonucleotide library is immobilized on a support instead of the targets to identify aptamers against small soluble molecules
44
Key aspects of Call-SELEX
utilizes whole live cells as targets for selection of aptamers
45
Key aspects of CE-SELEX
involes separation of ions based on electrophoretic mobility
46
Key aspects of M-SELEX
combines SELEX with a microfluid system
47
Key aspects of AFM-SELEX
employs AFM to create a 3D image of the sample surface
48
Key aspects of AEGIS-SELEX
utilizes libraries with the artificially expanded genetic code
49
Key aspects of animal-SELEX
aptamers are selected directly within live animal models
50
advantages of IP-SELEX
selects aptamers against proteins under normal physiological conditions increased affinity and specificity
51
advantages of Capture-SELEX
suitable for the selection of aptamers against small molecules immobilization of the target not required used for discovery of structure switching aptamers
52
advantages of Cell-SELEX
Prior knowledge of the target not required Aptamers are selected against molecules in their native state Many potential targets available on the cell surface Protein purification not required
53
advantages of CE-SELEX
Fast only 1-4 rounds of selection required reduced non specific binding target immobilization not required
54
advantages of M-SELEX
Rapid Very effective (small amounts of reagents required) Applicable to small molecules Automatable
55
advantages of AFM-SELEX
able to isolate high affinity aptamers Fast 3-4 rounds
56
advantages of AEGIS-SELEX
high specificity of the selected aptamers
57
advantages of animal-SELEX
selected aptamers bind the targets in their natural environment Prior knowledge of target not required Minimal optimization needed
58
advantages of -SELEX
59
disadvantages of IP-SELEX
more time consuming than standard SELEX
60
disadvantages of Capture-SELEX
some oligonucleotides from the library might not be released/selected
61
disadvantages of Cell-SELEX
suitable for cell surface targets Requires high level of technical expertise Costly Time consuming Post SELEX identification of target required
62
disadvantages of CE-SELEX
not suitable for small targets expensive equipment
63
disadvantages of M-SELEX
Not suitable low purity/recovery of aptamers target immobilization required
64
disadvantages of AFM-SELEX
expensive equipment required Immobilization of target aptamers required
65
disadvantages of AEGIS-SELEX
Poor recognition of the unnatural bases by natural DNA polymerases
66
disadvantages of Animal-SELEX
time consuming (man rounds required)
67
Dog’s nose; how does this compare with current detection systems?
test kits in the range of 1g-1ug (visible to particles) Field instruments in the range of 1ug-1pg (particles/vapour) Dogs in the range of 1fg-1ag (vapour)
68
Dog density of olfactory epithelium?
170cm^2 (humans have 10cm^2)
69
How does the dog receptors mean it has a better sense of smell?
It is the interactions of odour molecules with specific receptor proteins that give specificity. Each olfactory odour receptor neuron has only one functional odour receptor; if the odour molecule interacts with the receptor then the nerve cell will respond.

Sensors (17 decks)

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