4: Diagnosis of Infectious Diseases Flashcards
1
Q
These are conditions or
associated with pathogens
A
Infectious diseases
2
Q
These are conditions or
associated with pathogens
A
Infectious diseases
3
Q
These are microorganisms or microbes
which has the capability to cause diseases
A
Pathogens
4
Q
Pathogens present in the environment that cause certain diseases which may also cause certain infections are?
A
- Bacteria
- Fungi
- Virus
- Parasites
5
Q
Molecular techniques are also referred to as?
A
GENOTYPE ASSAYS or GENOTYPE TESTING or GENOTYPING
6
Q
HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT
Identify whose role:
Diagnosis?
A
Physician
7
Q
HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT
Identify whose role:
Isolates the pathogen
from different clinical specimens?
A
MT
8
Q
HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT
Identify whose role:
Isolates the pathogen
from different clinical specimens?
A
MT
9
Q
HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT
Summary of the process of identifying diseases?
A
ISOLATE the PATHOGEN (clinical specimens) → MICROBIOLOGY section → IDENTIFY (Genus and Species) ‘name’ → BASIS of TREATMENT
10
Q
HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT
The actual name of microbe/pathogen?
A
Genus and the species
11
Q
HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT
T or F
Identifying isolated genus and species is important since it will be the basis of treatment
A
T
12
Q
HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT
T or F
treatment associated to your pathogen is universal to other genus and speciest
A
F (treatment associated to your pathogen is SPECIFIC for its genus and species)
13
Q
HOW TO ISOLATE THE PATHOGEN?
What classical,traditional,usual or routine method is used to identify microorganism?
A
phenotyping analysis (microscopic analysis)
14
Q
HOW TO ISOLATE THE PATHOGEN?
Focuses more on the physiological or physiologic properties of microorganism
A
Phenotype
15
Q
HOW TO ISOLATE THE PATHOGEN?
2 Common methods of phenotype analysis?
A
- See through naked eye
- Microscope
16
Q
HOW TO ISOLATE THE PATHOGEN?
A Common way of identifying presence of microorganisms in phenotype analysis?
A
staining procedures
17
Q
HOW TO ISOLATE THE PATHOGEN?
T or F
Staining procedures identifies both the presence/absence of microorganism as well as the name (genus and species)
A
F (PRESENCE OR ABSENCE OF MICROORGANISM ONLY)
18
Q
HOW TO ISOLATE THE PATHOGEN?
Before identifying specific name of microogranism in phenotype analysis, this should be done
A
Culture the specimen
19
Q
HOW TO ISOLATE THE PATHOGEN?
Before identifying specific name of microogranism in phenotype analysis, this should be done
A
Culture the specimen
20
Q
HOW TO ISOLATE THE PATHOGEN?
grow the microorganism outside the body using artificial environment
A
Culture
21
Q
HOW TO ISOLATE THE PATHOGEN?
majority of the microorganisms will grow during the span of these hours
A
24-48 hours
22
Q
HOW TO ISOLATE THE PATHOGEN?
Denote the presence or growth of bacteria or pathogen, specifically if the one we isolated is clinically significant.
A
colonies
23
Q
HOW TO ISOLATE THE PATHOGEN?
After presence of colonies, to specifically know the genus and species what dhould be done as a follow up?
A
Follow-up testing through biochemical testing
24
Q
HOW TO ISOLATE THE PATHOGEN?
T or F
One biochemical test is enough to know genus and species of microogranism
A
F (series of biochem test)
25
What are the 2 ways of detection of pathogen/diagnosis?
1. Diagnosis using NAATS
2. Diagnosis using SEQUENCING
26
# WAYS OF DETECTION OF PATHOGENS
→Most common method of diagnosis
→Amplify small amount of nucleic acid
Diagnosis using NAATS
27
# WAYS OF DETECTION OF PATHOGENS: NAATS
→Among all the Amplification assays, this is the most common (very popular method)
PCR based amplification techniques
28
# WAYS OF DETECTION OF PATHOGENS: NAATS
what are the PCR based amplification techniques?
qPCR, RT-PCR, real time PCR, multiplex, duplex PCR, enzyme-based PCR,
29
# WAYS OF DETECTION OF PATHOGENS: NAATS
T or F
when we perform or do a nucleic acid amplification technique, it is important to know the specific target sequence or location or position of the gene
T
30
# WAYS OF DETECTION OF PATHOGENS: NAATS
Common target sequence of genes for bacteria?
16S rRNA or 23S rRNA (have varying degrees)
31
# WAYS OF DETECTION OF PATHOGENS: NAATS
Common target sequence of genes for fungi?
18S rRNA (have varying degrees)
32
# WAYS OF DETECTION OF PATHOGENS: NAATS
T or F
Identifiers and sequences (like the 16s rrNA) does not matter
F (it does since these will be used as a basis for **designing primers**)
33
# WAYS OF DETECTION OF PATHOGENS
→sequencing in detecting pathogens.
DIAGNOSIS WITH SEQUENCING
34
# WAYS OF DETECTION OF PATHOGENS: DIAGNOSIS WITH SEQUENCING
Most common sequencing tests for sequencing?
NGS or next generation sequencing technique.
35
# WAYS OF DETECTION OF PATHOGENS: DIAGNOSIS WITH SEQUENCING
Under NGS, one of the most important things to know is the part of the gene/commonly sequenced is the?
16S rRNA
36
# WAYS OF DETECTION OF PATHOGENS: DIAGNOSIS WITH SEQUENCING
Under NGS, one of the most important things to know is the part of the gene/commonly sequenced is the?
16S rRNA
37
# WAYS OF DETECTION OF PATHOGENS: DIAGNOSIS WITH SEQUENCING
Why is 16s rRNA the most common target to use for nGS?
it contains alternating sequence with conserved regions which contains the signature sequence and makes the organism unique, making it
also highly specific.
38
# IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA
→ belongs to the Fastidious microorganisms or Fastidious bacterium
→Arthropod borne
→ Serology is most common method of diagnosis
→ Screening assay is qPCR/real time PCR
→ Confirmatory assays are enzyme-based PCR, microarray techniques, ISH, Blotting techniques
BARTONELLAE SPECIES
39
# IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA
is fastidious meaning it very selective in such a way that it requires a special environment or special requirement or special procedures before you can grow it.
BARTONELLAE SPECIES
40
# IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA
T or F
Molecular techniques is performed for BARTONELLAE since it is difficult to grow in the lab as it requires a lot of special requirements.
T
41
# IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA
T or F
Isolation using classical bacteriological methods is easy to do since it requires minimum requirements
F (Isolation using classical bacteriological methods is **laborious** and **requires specific conditions** and **prolonged incubation periods**)
42
# MOLECULAR DETECTION OF BACTERIA
Most commonly used method of diagnosis for bacteria that looks for antibody production when infected with species
SEROLOGY
43
# MOLECULAR DETECTION OF BACTERIAL BARTONELLA SPECIES
T or F
Serological assay is diffucult for bartonellae since it contain lots of species – more than 30 which cannot be differentiated
T
44
# MOLECULAR DETECTION OF BACTERIA: BARTONELLAE SPECIES
To screen presence of Bartonellae in an infection or condition, the most commonly used assay is?
real-
time PCR techniques (qpcr)
45
# MOLECULAR DETECTION OF BACTERIA: BARTONELLAE SPECIES
After screening through qPCR, waht should be followed?
molecular confirmatory assays targeting several loci
46
# MOLECULAR DETECTION OF BACTERIA: BARTONELLAE SPECIES
Familiarize the confirmatory assays under bartonellae
enzyme-based PCR, microarray techniques, ISH, Blotting techniques
47
# IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA
→ arthropod borne
→ genus is under the group of Spirochetes
→ One of its most common arthropod or insect associated with it are ticks
BORELLA SPECIES
48
# MOLECULAR DETECTION OF BACTERIA: BORELLA
→ refer to bacteria that have spiral shape, a feature for BORELLA
Spirochetes
49
# IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA
Common insects associated with BORELLA
Ticks
50
# MOLECULAR DETECTION OF BACTERIA: BORELLA
Characteristic symptoms for BORELLA?
Bull’s eye rash
51
# MOLECULAR DETECTION OF BACTERIA: BORELLA
Classical microbiology method or traditional method for diagnosing bacterial isolate, Borella species ?
Blood Smear preparation
52
# MOLECULAR DETECTION OF BACTERIA: BORELLA
T or F
Blood smear detection analysis is ideal since it gives early diagnostics
F (blood smear can only detect bacteria if it is high enough; meraning the patient is already highly infectious, therefore NOT IDEAL)
53
# MOLECULAR DETECTION OF BACTERIA: BORELLA
Instead of blood smear, what molecular techniques can be used to give early diagnosis?
1. PCR
2. NGS
3. Proteomic Approaches
54
# MOLECULAR DETECTION OF BACTERIA: BORELLA
→ gives the highest viable diagnostic approach specifically during the early stages/acute phases
→ valuable diagnostic approach in acutely ill
patients
| early diagnosis thorugh molecular technqiues
PCR
55
# MOLECULAR DETECTION OF BACTERIA: BORELLA
most recently applied techniques for detecting Borella species
| early diagnosis thorugh molecular technqiues
NGS and PROTEOMIC APPROACHES
56
This bacterium is an important cause of Sexually Transmitted Diseases (STD) specifically in the United States (US)
CHLAMYDIA TRACHOMATIS
57
# Chlamydia Trachomatis - T or F
when an individual presents with an infection associated with it, the said infected individual presents as symptomatic
F - Asymptomatic (Majority of cases)
| have signs of
symptoms but are very mild
58
what should be done for patients that are suspected with Chalmydia Trachomatis?
Early diagnosis or
Early screening test
59
What is the most concernincg factor of Chlamydia Trachomatis?
When missed out, it can easily spread
60
What ate the three main target genes in chlamydia trachomatis?
* Cryptic plasmid
* Genomic sequences
* rRNA (16S rRNA and 23S rRNA)
61
in chlamydia what was considered the best target gene specifically for the AMPLIFICATION TECHNIQUES?
| also commonly used
cryptic plasmid
62
# CHLAMYDIA TRACHOMATIS
What does the cryptic plasmid contains
introns or the intracellular sequences which can be amplified via a multicopy.
63
Reasons and applications of typing Chlamydia
trachomatis?
detecting the transmission pattern or
pattern of spread
64
Reasons and applications of typing Chlamydia
trachomatis? - FORENSIC PRUPOSES
typing for
cases associated with sexual assault
65
In typing the chlamydia trachomatis, it is based
mainly on the discrimination of?
** 15 different serovars** encoded by the ompA (omp1) gene
66
# CHLAMYDIA TRACHOMATIS
What encodes the 15 different serovars?
ompA (omp1) gene
| main focus of its sequencing
67
# CHLAMYDIA TRACHOMATIS
Main advantage when we do typing:
differentiate, which can identify diff serovars (Strains)
68
A microorganism that is difficult to grow using the classical method because an anaerobe.
CLOSTRIDIUM DIFFICILEA
69
For an anaerobic microorganism to grow? what is the pre-requisite
NO OXYGEN in the environment
70
an important cause of nosocomial type
of diarrhea
Clostridium Difficilea
| clue: DIFFI = DIFFICATE (natae rawr)
71
# CLOSTRIDIUM DIFFICILEA
what does nosocomial Diarrhea means
hospital-acquired or antibiotic-associated diarrhea
72
# CLOSTRIDIUM DIFFICILEA
Main responsible for hospitalacquired diarrhea.
Nosocomial Diarrhea
73
is Clostrodium Difficilea are photogenic? TOF
F (Pathogenic)
74
What is the relative activity of Clostrodium Difficilea when it can be considered pathogenic?
Once it release toxic
75
Best method for detect Clostrodium Difficilea and why?
TISSUE CULTURE CYTOTOXIN ASSAY -- bcos its pathogenic and in this assay we culture the toxic release
76
In Clostrodium Difficilea what is the target toxin genes of real time PCR?
(1) tcdA
(2) tcdB
(3) tcdC117
77
# C. Difficile
What method besides tissue culture cytotoxin assay and Real time pcr can be used?
Multiplex PCR - one-step, rapid, and specific screening method for C. difficile toxin genes
78
bacterium which is commonly missed out because it is not quick to be identified since it is the only bacteria that has no cell wall---therefore does not retain any dye
MYCOPLASMA PNEUMONIAE
79
Almost all the bacteria are observable under the microscope as long as we stain it, except
mycoplasma pneumoniae
80
Why is Mycoplasma pneumoniae not microscopically observable?
does not retain
any dye or stain
| bcos it lacks CELL WALL
81
one of the most common
causes of community-acquired type of
pneumonia
Mycoplasma pneumoniae
82
# TOF
M. pneumoniae is easily
transmitted from one individual
to another via vehicle
droplets.
F - Respiratory
83
What are the molecular techiniques can be used in mycoplasma pneuomoniae
PCR
84
Gene targets of mycoplasma pneumoniae
(1) 16S rRNA
(2) P1
(3) Tuf
(4) parE
(5) dnak
(6) pdhA
(7) ATPase operon
(8) CARDS toxin gene (mpn372)
(9) repMp1
85
what is the target gene that is commonly used for mcyoplasma pneomoniae
P1 gene, there is the
unique signature sequence of
mycoplasma pneumoniae
86
What are the two types of Rickettsia Species?
arthropod-borne insects or Bacteria
87
What is its difference of rickettsia specied from other
arthropod-borne infections?
Early treatment should be provided when the physician suspected the patient with Rickettsia species
## Footnote
infection associated with Rickettsia is considered lifethreatening
88
How the physician suspects that the patient’s condition is associated with Rickettsia?
| Clue: 3 unique manifestation
(1) Fever
(2) Rash
(3) Presence of Eschar
89
How do we diagnose Rickettsia through
Molecular Techniques
Mainly through PCR-BASED ASSAY
90
if u see this card
study the table specimen used in rickettsia detection
91
Among all the specimens, the best to use for rickketseria are?
* skin or eschar biopsy
* autopsy organ tissue.
| there is high amount of bacterium present,
92
# Rickettsia
Molecular detection is based mainly on recognition of sequences from different targets
| what specific genes are these
(1) 16S rRNA
(2) Protein-coding genes
93
most common isolates
in the laboratory
STAPHYLOCOCCUS AUREUS
94
TOF
Staphylococcus auerus causes a wide variation of disease?
T
| It does not only infect the skin but also the other organs.
95
An invasive, life-threatening infection
associated with Staphylococcus aureus
Methicillin Resistant Staphylococcus Aureus (MRSA)
96
this is the strain of S. aureus due to MUTATION OF MecA and MecB gene
Methicillin Resistant Staphylococcus Aureus (MRSA)
97
# TOF
MRSA is life-threatening
because S. aureus is almost
resistant to all beta lactum
drugs/antibiotics
F (Lactam)
| it aint milk tf
98
best molecular diagnostic tool for MRSA
detection
PCR
99
Among the latest development in the direct
MRSA detection and identification,
REAL-TIME PCR
100
# S. Aureus
Method that could be used to predict resistance, assess virulence, and type isolates at the highest possible resolution
Whole Genome Sequencing (WGS)
101
What are the molecular techniques of S. Aureus?
- PCR
- Real-time PCR
- Whole Genome Sequencing
102
Causative agent of pneumonia
Streptococcus pneumoniae
103
when under microscope this genus is identified with an arrangement like a LINE
Streptococcus pneumoniae
104
What prier can be used with Streptococcus pneuminae?
specific to repetitive regions
105
# Streptococcus Pneumoniae
Primers used in PCR testing are specific to REPETITIVE REGIONS and genes encoding:
* rRNA
* Pneumococcal surface adhesion A molecule (psaA)
* Pneumolysin (ply)
* Penicillin binding protein
* Autolysin (lytA)
106
# TOF Streptococcus Pnuemininadifaw
the best na ginagamit ng majority ng laboratory targets Autolysin (lytA) gene (the focus of majority of different techniques).
True
107
Other name: Group A Streptococcus (GAS)
Streptococcus pyogenes
108
Molecular test for Strptococcus pyogenes
GASDirect test
109
# Streptococcus pyogenes
Identifies specific rRNA sequences of
Streptococcus pyogenes in pharyngeal
specimens by a single-stranded
chemiluminescent nucleic acid probe f
GASDirect test
110
what are the specimen used in Streptococcus pyogenes?
pharyngeal
specimens
111
what are the probe for identification used in Streptococcus pyogenes
single-stranded
chemiluminescent nucleic acid probe
112
Main application/advantages of GASDirect test for Streptococcus pyogene
- Applied for primary testing
- Use as a backup test to negative
antigen/serology tests
Batch screening test of throat cultures
113
Other name: Group B Streptococcus (GBS)
Streptococcus agalactiae
114
Clinically significant to neonates/newborn because
it is a very important cause of a highly life-threatening
condition termed as neonatal meningitis.
Streptococcus agalactiae
115
# Group B Streptococcus (GBS)
Clinically significant to neonates/newborn because
it is a very important cause of a highly life-threatening
condition termed as
neonatal meningitis.
116
What is the detection for Streptococcus agalactiae
Screen the pregnant mother
during the 35th
-37th week of gestation - can be seen in VAGINA or RECTUM
117
Where does the colonization of GBS SEEN
vaginal area or it can be in rectal area too
118
How is the GBS passed to new born?
during normal delivery, bacterium is transferred to baby
119
# Streptococcus agalactiae
Using the classical method in microbiology, it can be
identified/screened via
culture method
120
only bacterium that produces a
pattern of growth -- arrow head zone of hemolysis:
Group B Streptococcus (GBS)
| Streptococcus agalactiae
121
arrow head zone of hemolysis is caused
by GBS releasing the so-called?
CAMP factor
(due to one gene).
122
Main disadvantage of this culture technique for GBS?
matagal siyang gawin (at least
2 days or 24-48 hours)
123
what is the solution for slow TAT culture for GBS?
conventional or real-time PCR assays (mol bio)
may be used
124
# Streptococcus agalactiae
Target genes for PCR or Conventional
* sip
* cfb - common
* scpB
* ptsl genes
125
# Streptococcus agalactiae
s one of most common targets
because it is responsible for the release
of CAMP factor
cfb gene
126
what are the other method for detection of GBS besides culture, and pcr methods?
LAMP Method
| Maximum time of detection is within 90 minutes
127
Most common method in detecting Fungi
PCR or amplification techniques
128
Why is it important to have unique probes and formats in the molecular formats of Fungi detection?
bc it will help in the **identification**
129
# MOLECULAR DETECTION OF FUNGI
Enumerate DNA targets
* rDNA,
* cytochrome b,
* β-tubulin,
* calmodulin,
* enolase,
* chitin synthase, and
* heat shock protein
130
# MOLECULAR DETECTION OF FUNGI
DNA target to be used depends on what?
Genus of the Fungi
131
# MOLECULAR DETECTION OF FUNGI
Identify the Target Fungi: Actin
Aspergillus
132
# MOLECULAR DETECTION OF FUNGI
Identify the Target Fungi: beta - Tubulin
Phaeacremonium
Aspergillus
Pseudallescheria
133
# MOLECULAR DETECTION OF FUNGI
Identify the Target Fungi: Calmodulin
Aspergillus
Pseudallescheria info
134
# MOLECULAR DETECTION OF FUNGI
Identify the Target Fungi: Chitin synthase 2
Lacazai loboi
135
# MOLECULAR DETECTION OF FUNGI
Identify the Target Fungi: Cytochrome b
Aspergillus,
Trichosporon, and
Rhodotorula
135
# MOLECULAR DETECTION OF FUNGI
Identify the Target Fungi: D1-D2
Most Fungi
136
# MOLECULAR DETECTION OF FUNGI
Identify the Target Fungi: Elongation factor 1a
Fusarium species
137
# MOLECULAR DETECTION OF FUNGI
Identify the Target Fungi: ITS
| its what?
Medically significant yeasts
& fungi
138
# MOLECULAR DETECTION OF FUNGI
Identify the Target Fungi: 26S
Medically relevant Fusarium and Scedosporium
139
# Molecular Detection of Fungi
Among all medically important fungi, what is the most common target gene
Internally transcribed spacer (ITS)
| Note: it le universal target gene
140
# Molecular Detection of Fungi
Among all the medically important fungi, majority focuses on what genus?
Aspergillus
141
# Molecular Detection of Fungi:
List molecular techniques employed in detecting Aspergillus
* Nucleic Acid Amplification Test (NAAT)
* In situ hybridization (ISH) techniques
141
# Molecular Detection of Fungi
Identify the molecular technique used in identifying Aspergillus:
Provides rapid and accurate diagnosis
NAAT
142
# Molecular Detection of Fungi
Identify the molecular technique used in identifying Aspergillus:
used in fresh and formalin-fixed, paraffin-embedded (FFPE) tissues without requiring nucleic acid extraction or amplification
In situ hybridization (ISH) techniques
142
# Molecular Detection of Virus
Human Immunodeficiency Virus (HIV),,, Identify:
* Family
* Genus
* Types
Fam: Retroviridae
Genus: Lentivirus
Types: HIV 1 and 2
143
# Molecular Detection of Virus
globally; majority causative agent of HIV infections; most virulent
HIV 1
144
# Molecular Detection of Virus
Commonly isolated in the **West and Central part of Africa**
HIV 2
145
# Molecular Detection of Virus
In performing molecular detections, what are the 3 main targets in detecting HIV?
* gag
* polymerase (pol)
* envelope (env)
146
# Molecular Detection of Virus
Identify the Viral Gene Products of the gene: GAG
p24, p18, and p15
147
# Molecular Detection of Virus
Identify the Function of the Gene: gag
Codes for **core structural CHON**
| arrangement/shape seen under the microscope
148
# Molecular Detection of Virus
Identify the viral gene products of the gene: pol
- Reverse Transcriptase
- RNAse
- Protease
- Integrase
149
# Molecular Detection of Virus
Identify the function of the gene: pol
- **Transcribes** RNA into DNA
- **Degrades** RNA
- **Makes HIV particles** into complete and functional HIV virus
- **Inserts viral DNA** into host DNA
150
# Molecular Detection of Virus
Identify the viral gene product of the gene: env
gp120
151
# Molecular Detection of Virus
Identify the function of the gene: env
binds CD4 receptor
152
# Molecular Detection of Virus
Identify the function of the viral gene product: gp41
Viral fusion of the cell
153
# Molecular Detection of Virus
Among the 3 genes identified in HIV, what gene is the main focus in detection?
gag
| specifically the viral gene product: **p24**
154
# Molecular Detection of Virus
Target of drugs or treatment for HIV
| anong gene/s?
pol and env genes
155
# Molecular Detection of Virus
Among all techniques in molbio, what technique/s do they use for HIV?
| clue: HIV is an RNA type of Virus
RT PCR
| reverse transcription
156
# Molecular Detection of VIrus
The methods of its identification can be detected in HIV through?
antigen, antibody, and
DNA/RNA of the virus.
157
# Molecular Detection of VIrus
Most of the time, the ____ is commonly detected
HIV Antibody
157
If u see this card, review mo table ng HIV diagnostics table
yes
158
# Molecular Detection of Virus
One of the most commonly used technique for HIV Diagnostics
| confirmatory test
Western blot
159
# Molecular Detection of Virus
it is method that focuses on detecting the protein of the extracted sample from the assay.
Western blot
159
# Molecular Detection of Virus
This group of virus contains lots of strains which
causes different wide varying types of infection.
Human Papillomavirus
160
# Molecular Detection of Virus
most clinically significant strain which causes cancer in humans
Human Papillomavirus
| ewan q kung nagkamali k p dyan
161
# Molecular Detection of Virus
the most popular HPV that causes cancer. The causative agents of cervical CA.
HPV 16/18
162
# Molecular Detection of Virus
Strains of HPV are based on what
numbers
| review the major clinical association of genital tract and other mucosal
## Footnote
....HPV; I dont make the rules
163
# MOLECULAR DETECTION OF VIRUS
medically important genes detected for HPV 16&18
E6 and E7
164
# Molecular Detection for Virus
Hepatitis virus is caused by allat of viruses. Now, what is the common target of these types?
Liver cells
165
# MD of Virus (pagoda na)
Enumerate the types of Hepatitis virus
HAV, HBV, HCV, HDV, HEV, HGV
166
# MD of Virus (pagoda na)
ONE OF THE MOST WIDELY USED ASSAY FOR HEPA VIRUS
qPCR
167
TOF. targets for qPCR depends on the family of the virus
F (type)
168
# MD of Virus
review the Hepa V regions used as qPCR templates
| TW: next page
## Footnote
review mo nalang din sa table
HAV: 5' UTR
HBV: S-gene & X-gene
HCV: 5' UTR
HDV: Ribozyme -1
HEV: ORF 2 and 3
HGV: 5' UTR
| left Virus; right Conserved Regions
169
# MD of Virus
Among the types of hepa v, which of them most commonly use molecular techniques?
HBV
170
# MD of Virus
Type of Hepa V which causes life threatening complications, such as Liver CA and Liver Cirrhosis
HBV
171
# MD of Virus
what is detected and targeted in detecting HBV using nucleic acid based testing?
cccDNA minichromosome
172
# MD of Virus
- covalently closed circular DNA.
- It is produced during its life cycle.
- Molecular techniques take advantage of
this for detection purposes.
cccDNA
173
An emerging technique in Microbiology used
for identification of genus and species of
microorganisms (e.g. bacteria).
Matrix Assisted Laser Desorption Ionization – Time of Flight Mass Spectroscopy.
| MALDI-TOF MS
174
It is an automated method for the identification
of the genus and species of bacterium.
MALDI-TOF MS
175
# PRINCPIPLE OF MALDI-TOF MS
From ________, put a sample on a test tube where the assay will be mixed.
| 1st step
bacterial culture
176
# PRINCIPLES OF MALDI-TOF MS
The matrix/reagents used in this method is composed of what?
SATURATED LOW IONIC ORGANIC MASS
| in short, BIOMASS
177
# PRINCIPLE OF MALDI-TOFF MS
After mixing reagents with the samples, you transfer it to the
________________________
MALDI-TOF MS PLATE
178
# PRINCIPLE OF MALDI-TOF MS
TOF. After mixing samples and transferring it to the MALDI-TOF MS plate, next step is to analyze it in the microscope
F. automated identification
179
What is the defining feature of MALDI-TOF MS as compared to other molecular techniques?
- extracts purified proteins
- extraction method is already mixed into the matrix (specifically extracts protein of the bacterial sample)
180
# PRINCIPLE OF MALDI-TOF MS
TOF. Bacterial sample/Clinical sample at first has no charge/it is in neutral charge
T
181
# MALDI-TOF MS PRINCIPLE
What provides the charge to the samples?
Matrix (satured low ionic organic mass/ biomass)
| provides **protons**
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# PRINCIPLE OF MALDI-TOF MS
measures the net charge produced during the procedure.
Ionization process
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# PRINCIPLES OF MALDI-TOF MS
MAIN PRINCIPLE OF MALDI-TOF
SOFT IONIZATION
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# MALDI TOF
SOFT IONIZATION IS MEASURED THRU?
MS PROFILE (PATTERNS)
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# MALDI TOF
TOF. MS profiles of each bacterium is identical from one organism to another
f (unik)
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In MALDI-TOF assay, the most important
consideration during the procedure is
sample preparation
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# MALDI-TOF SAMPLE PREP
main consideration in the prep of sample?
isolate a purified protein
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# MALDI-TOF
protein can be purified by mixing what?
specific reagents
| eme **formic acid**
## Footnote
sabi nila depends on bacterium pero formic acid parin naman gamit
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# MALDI-TOUGH
TOF. for better extraction, methanol is added
F (-m)
