Diagnosis of Viral Infections 3 - L14 (Exam II) Flashcards
The study of virus evolution using genome sequence data is known as _______
A. Metagenomics
B. Phylogenetics
C. PCR
D. Microarray
B. Phylogenetics
Which of the following is false about the Polymerase chain reaction (PCR) ?
A. It is a laboratory technique used to make multiple copies of a segment of DNA.
B. Can be used to amplify, or copy, a specific DNA target from a mixture of DNA molecules because it is so precise
C. Sometimes called “molecular photocopying”
D. Fast and inexpensive technique
E. Amplified DNA can be visualized by ethidium bromide staining
F. Since it involves chain-terminating dideoxynucleotides, it is the most widely used method of DNA sequencing
F. Since it involves chain-terminating dideoxynucleotides, it is the most widely used method of DNA sequencing
Note: The most widely used method of DNA sequencing is the modification of the Sanger dideoxy method….All the other are true of PCR.
The PCR involves three steps; what are they?
- Denaturation: (DNA strands separate by heating it)
- Annealing: (Primers binds to ends of both strands of DNA)
- Elongation: (Each strand of DNA is copied by Taq Polymerase using free nucleotides added to primer. As a result, two new DNA molecules are obtained from original one. Each new DNA molecule have one old strand and one new strand)
Note: The cycle of denaturing and synthesizing new DNA is repeated as many as 30 or 40 times, leading to more than one billion exact copies of the original DNA segment.
Real-Time PCR or Quantitative PCR is an advanced form of PCR which allows monitoring and quantification of increasing accumulation of PCR products/nucleic acid load as the reaction progresses. Useful to study virus load in patient.
True or False ?
True
Note: Using the QPCR you can study the virus load in a patient.
In real-time PCR assays: A specific probe is targeted/labelled with a fluorescent dye or intercalating dyes.
True or False ?
True
Note: Same process as PCR but a florescent dye is added
DNA sequencing refers to the process by which the sequence of bases in a DNA molecule is elucidated/can be obtained and read.
True or False ?
True
The most widely used method of DNA sequencing is the modification of the Sanger dideoxy method, which involves using chain-terminating dideoxynucleotides.
True or False ?
True
Next Generation Sequencing (NGS) platforms, such as Illumina (Solexa) sequencing, are significantly cheaper, quicker, needs significantly less DNA, has high throughput, and is more accurate and reliable than Sanger sequencing.
True or False ?
True
Which viral diagnostic technique can you get tons of data using it ? and can even determine the sequences of viruses for which no information is previously known about the virus?
A. PCR
B. Genome Sequencing
C. Next Generation Sequencing
D. Viral Assays
C. Next Generation Sequencing
Note: Currently, surveillance studies are more relying on Next Generation Sequencing (NGS) technologies that are gradually replacing the conventional sequencing methods.
What is the branch of science which tries to find out what pathogens are present in a sample ?
A. Metagenomics
B. Phylogenetics
C. PCR
D. Microarray
A. Metagenomics
Note: Metagenomics is defined as the study of the collective set of microbial populations in a sample by analyzing the sample’s entire nucleotide sequence content, and is a powerful method for random detection of existing and new pathogens.
Metagenomics is achieved by amplification and sequencing of whole genome (DNA and/or RNA) content of a given sample followed by filtering and analysis of obtained data by comparing with genome databases and using different softwares.
True or False ?
True
Note: NGS are being used for these types of studies
Genome sequencing is of importance because it allows all of the following EXCEPT:
A. Pathogen detection
B. Cure of diseases
C. Studies on genetic variation, such as genotyping, evolution and interspecies transmission of pathogens
D. Identification of genes associated with drug resistance
E. Development of therapeutics
B. Cure of diseases
___________ Is the use of Virus genome sequence data to study evolution of viruses and genetic relationships among viruses.
A. Phylogenetic Analysis
B. PCR
C. Phylogeny
D. NGS
A. Phylogenetic Analysis
In microarray, several thousands of known DNAs (probes), amplified by PCRs/RT-PCRs, are spotted onto a glass or a silicon chip. The target/sample DNA are fluorescently labeled and then hybridized/added to the chip containing DNA probes.
True or False ?
True
Note: The intensity of fluorescence can be measured using a fluorescent scanner, and the data analyzed by a variety of methods.
In microarrays negative reactions between probe-DNA and Sample DNA (hybridization) generate a fluorescent signal from the spot where probe DNA is spotted in the chip.
True or False ?
False
Note: Positive reactions generate a fluorescent signal
