DNA Microarray and PCR Quiz

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Questions and Answers

What is the preferred sampling method for COVID-19 detection using PCR?

Saliva sample
Blood sample
Nasal and throat swab (correct)
Urine sample

What does a lower Ct value in RT-PCR indicate?

Positive COVID-19 case (correct)
Higher viral loads
Contamination in the sample
Negative COVID-19 case

What is the purpose of the TaqMan probe in RT-PCR?

To convert RNA to cDNA
To detect the virus genome in the patient sample (correct)
To isolate the RNA
To amplify the virus genome

What does a Ct value of 20 indicate in RT-PCR testing for COVID-19?

Positive result with higher viral loads (B)

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What is a challenge for the TaqMan probe used in RT-PCR for COVID-19 detection?

Virus mutations affecting the probe's effectiveness (A)

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What does RT-PCR measure to monitor the severity of infection in COVID-19 patients?

Amount of fluorescence in the sample after each cycle (A)

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What happens if a signal comes after Ct 36 or 37, 38 in RT-PCR testing for COVID-19?

The patient is negative for COVID-19 (B)

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What does RT-PCR measure to monitor virus severity?

Number of cycles it takes in the test (A)

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What does a Ct value higher than 35 indicate in RT-PCR testing for COVID-19?

Positive result with lower viral loads (A)

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What is one limitation mentioned for RT-PCR testing for COVID-19?

Quality of kits used and different standards (C)

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What are DNA microarrays also known as?

DNA chips (C)

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What is the typical size of DNA microarray supports?

The size of a microscope slide (A)

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How are DNA samples attached to DNA microarray supports?

Spotted, printed, or synthesized directly on to the support phase (D)

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What is photolithography in the context of DNA microarrays?

A chemical synthesis of oligonucleotides using light source (B)

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What technology underlies the development of DNA microarrays?

Genomics, PCR, and nucleic acid hybridization (C)

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What is the main function of DNA microarrays?

To allow rapid and simultaneous screening of many thousands of genes. (A)

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Which materials can be used to make DNA microarray supports?

Glass, plastic, or nylon (C)

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What are the two main types of DNA samples that can be attached to DNA microarray supports?

Gene-specific synthetic oligonucleotides (Photolithography) or cDNAs (RT-PCR) (D)

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What is the purpose of PCR in COVID-19 detection?

To amplify viral RNA for detection (A)

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What is the significance of DNA microarrays as a diagnostic tool?

They enable comprehensive gene screening for disease detection. (D)

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What is the process used in genomic research?

PCR (D)

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What is used to create DNA chips for gene amplification?

cDNAs and photolithography (D)

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What is the interaction between oligonucleotides, such as probes used in gene cloning?

Nucleic acid hybridization (A)

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What type of microarray measures gene expression (mRNA) and is used to compare healthy and cancer cells?

Expression microarray (A)

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What dyes are used to label mRNA for hybridization to the microarray?

(CY 3 and CY5) cyanin dyes (B)

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What is used to detect the SARS-CoV-2 genomic sequence from a sample taken from a suspected individual for COVID-19 detection?

(RT-PCR) Reverse Transcription Polymerase Chain Reaction (B)

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What can be used to detect damage or overexpression of genes associated with various conditions, including cancer?

Microarray (A)

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What competes with ssDNA in the microchip for hybridization during the microarray process?

Denatured cDNA (D)

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What is initially not designed for diagnostic purposes but has been extensively used for COVID-19 detection since 2020?

PCR (Polymerase Chain Reaction) (C)

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What is isolated from samples taken for COVID-19 detection before being treated with chemicals to extract the viral genetic material RNA?

Viral RNA (A)

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What is the main function of Neostigmine and pyridostigmine?

Inhibit acetylcholinesterase (D)

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What is the primary adverse effect associated with nondepolarizing blockers?

Bronchospasm (C)

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Which neuromuscular blocking drug has a rapid onset of 1 minute and a duration of action of 55 minutes?

Rocuronium (C)

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What is the mode of action of Baclofen, a centrally acting spasmolytic drug?

GABAB agonist causing membrane hyper-polarization (B)

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What is the primary mode of action of Diazepam, a centrally acting spasmolytic drug?

Facilitates GABAergic transmission in the central nervous system (B)

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What is the mode of action of Tizanidine, a centrally acting spasmolytic drug?

α2-Adrenoceptor agonist in the spinal cord (C)

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What is the mode of action of Dantrolene, a directly-acting spasmolytic drug?

Blocks RyR1 Ca2+ release channels in the sarcoplasmic reticulum of skeletal muscle (B)

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What is the primary mode of action of Cyclobenzaprine, a drug for acute muscle spasm?

Acts in the brain stem, possibly by interfering with polysynaptic reflexes that maintain skeletal muscle tone (B)

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What is the primary use of Baclofen, a centrally acting spasmolytic drug?

Severe spasticity - cerebral palsy, multiple sclerosis, stroke (B)

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Which drug is primarily used for acute spasm due to muscle injury and inflammation?

Cyclobenzaprine (D)

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Which type of skeletal muscle relaxant interferes with the transmission at the neuromuscular end plate?

Neuromuscular blockers (A)

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Which drug is a prototype of nondepolarizing neuromuscular blocking drugs?

D-tubocurarine (D)

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Which event characterizes Phase 1 of the depolarization block caused by succinylcholine?

Na channel inactivation (C)

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Which class of neuromuscular blockers releases histamine from mast cells?

Depolarizing blockers (D)

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Which type of skeletal muscle relaxants is traditionally called 'centrally acting' muscle relaxants?

Directly-Acting Spasmolytic Drugs (A)

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Which drug is used for short-term procedures and is associated with adverse drug reactions like hyperkalemia and malignant hyperthermia?

Mivacurium (D)

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Which compound can reverse the block caused by non-depolarizing neuromuscular blockers?

Acetylcholine esterase inhibitors (D)

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Which type of blockade at the end plate is due to desensitization of Ach Receptors?

Depolarizing blocker_3 phase 2 (desensitization block) (A)

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Which drugs reduce spasticity in a variety of painful conditions and are used for chronic back pain and painful fibromyalgias?

Centrally Acting Directly-Acting Spasmolytic Drugs (C)

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Which drugs interfere with transmission at the neuromuscular end plate and are used for ICU and general anesthesia?

Neuromuscular blockers (A), Neuromuscular blockers (B), Neuromuscular blockers (C), Neuromuscular blockers (D)

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Flashcards

Nasal and throat swab

A type of swab that is used to collect samples from the nose and throat to detect COVID-19.

Lower Ct value in RT-PCR

A lower Ct value indicates a higher viral load, suggesting a more active infection.

TaqMan probe in RT-PCR

It binds to a specific sequence of the virus's genetic material and emits fluorescence when it binds, indicating the presence of the virus.

Ct value of 20 in RT-PCR

A Ct value of 20 indicates a high viral load, suggesting a strong positive result for COVID-19.

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Challenge with TaqMan probes

Mutations in the virus's genome can affect the TaqMan probe's ability to bind to the target sequence, making detection less effective.

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Monitoring infection severity in RT-PCR

It measures the amount of fluorescence emitted during each cycle of PCR, which correlates to the amount of viral genetic material present.

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Signal after Ct 36 or 37 in RT-PCR

A signal after Ct 36 or 37 indicates that there is not enough viral RNA to be detected, suggesting a negative result for COVID-19.

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RT-PCR and virus severity

It measures the number of cycles it takes for the PCR reaction to reach a detectable level of fluorescence, which is indicative of the viral load.

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Ct value higher than 35 in RT-PCR

Indicates a lower viral load, suggesting a milder infection or a later stage of infection.

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Limitation of RT-PCR for COVID-19

Factors like the quality of kits used and varying standards can influence the accuracy of results.

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DNA microarrays

DNA microarrays are also known as DNA chips.

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Size of DNA microarray supports

DNA microarrays are typically the size of a microscope slide.

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DNA sample attachment on microarrays

DNA samples can be spotted, printed, or synthesized directly on the support phase of a DNA microarray.

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Photolithography in DNA microarrays

A chemical synthesis of oligonucleotides using light source, which is used in the production of DNA microarrays.

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Technology behind DNA microarrays

Genomics, PCR, and nucleic acid hybridization are the key technologies that led to the development of DNA microarrays.

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Main function DNA microarrays

DNA microarrays allow rapid and simultaneous screening of many thousands of genes, enabling comprehensive gene analysis.

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Materials for DNA microarray supports

Glass, plastic, or nylon can be used as materials for the support phase of DNA microarrays.

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DNA samples on microarray supports

Gene-specific synthetic oligonucleotides (Photolithography) or cDNAs (RT-PCR) are the two main types of DNA samples that can be attached to DNA microarray supports.

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Purpose of PCR in COVID-19 detection

It amplifies viral RNA to a detectable level, allowing for the identification of COVID-19.

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DNA microarrays as diagnostic tools

DNA microarrays are a powerful tool for disease detection, enabling comprehensive gene screening to identify specific patterns of gene expression associated with different diseases.

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PCR in genomic research

PCR is a fundamental technique used in genomic research to amplify specific DNA segments for analysis.

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Creating DNA chips

cDNAs and photolithography are used to create DNA chips for gene amplification and analysis in DNA microarrays.

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Nucleic acid hybridization

Nucleic acid hybridization refers to the process where complementary strands of DNA or RNA bind to each other, forming a double helix.

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Expression microarray

An expression microarray measures the levels of mRNA in different samples, revealing changes in gene expression that can be used to compare healthy and diseased cells, such as cancer.

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Dyes used for mRNA labeling

Cyanin dyes, specifically CY3 and CY5, are used to label mRNA for hybridization to the microarray, allowing for the detection of gene expression.

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RT-PCR for COVID-19 detection

Reverse Transcription Polymerase Chain Reaction (RT-PCR) is a technique used to detect the SARS-CoV-2 genomic sequence in a sample taken from a suspected individual for COVID-19 detection.

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Microarray and disease detection

Microarrays can be used to detect damage or overexpression of genes associated with various conditions, including cancer, providing insights into disease mechanisms and potential treatment targets.

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Competition in the microarray

Denatured cDNA competes with ssDNA for hybridization to the probes on the microchip during the microarray process.

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PCR for COVID-19 detection

PCR, although initially not designed for diagnostic purposes, has been widely used for COVID-19 detection since 2020, highlighting its versatility and adaptability.

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Viral RNA in COVID-19 detection

Viral RNA is isolated from samples taken for COVID-19 detection before being treated with chemicals to extract the virus's genetic material RNA.

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Study Notes

Genomics involves the study of DNA structure, properties, replication, and more.
PCR (polymerase chain reaction) is a process used in genomic research.
cDNAs and photolithography are used to create DNA chips, which are used in gene amplification.
Nucleic acid hybridization is the interaction between oligonucleotides, such as probes used in gene cloning.
DNA chips are single-stranded sequence and come in a kit containing a microchip with a barcode and a manual.
Microarray, also known as Affymetrix, comes in different types for gene expression, comparative genomic, and mutation detection.
Expression microarray measures gene expression (mRNA) and is used to compare healthy and cancer cells.
To perform microarray, collect tissue, isolate RNA, isolate mRNA, make labeled DNA copy, and apply DNA to the microarray.
Cyanin dyes (CY 3 and CY5) are used to label mRNA for hybridization to the microarray.
In the case of COVID-19 detection, RT-PCR is used to detect the SARS-CoV-2 genomic sequence from a sample taken from a suspected individual.
PCR was initially not designed for diagnostic purposes but has been used extensively for COVID-19 detection since 2020.
Samples for COVID-19 detection can be taken from the nose (nasopharyngeal swabs) or throat (oropharyngeal swabs) and are treated with chemicals to extract the viral genetic material RNA.
Microarray can be used to detect damage or overexpression of genes associated with various conditions, including cancer.
During the microarray process, denatured cDNA competes with ssDNA in the microchip for hybridization.
After the microarray is scanned, the data is analyzed to determine the presence or absence of gene expression in both the healthy and suspected samples.

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DNA Microarray and PCR Quiz

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Podcast

Questions and Answers

What is the preferred sampling method for COVID-19 detection using PCR?

What does a lower Ct value in RT-PCR indicate?

What is the purpose of the TaqMan probe in RT-PCR?

What does a Ct value of 20 indicate in RT-PCR testing for COVID-19?

What is a challenge for the TaqMan probe used in RT-PCR for COVID-19 detection?

What does RT-PCR measure to monitor the severity of infection in COVID-19 patients?

What happens if a signal comes after Ct 36 or 37, 38 in RT-PCR testing for COVID-19?

What does RT-PCR measure to monitor virus severity?

What does a Ct value higher than 35 indicate in RT-PCR testing for COVID-19?

What is one limitation mentioned for RT-PCR testing for COVID-19?

What are DNA microarrays also known as?

What is the typical size of DNA microarray supports?

How are DNA samples attached to DNA microarray supports?

What is photolithography in the context of DNA microarrays?

What technology underlies the development of DNA microarrays?

What is the main function of DNA microarrays?

Which materials can be used to make DNA microarray supports?

What are the two main types of DNA samples that can be attached to DNA microarray supports?

What is the purpose of PCR in COVID-19 detection?

What is the significance of DNA microarrays as a diagnostic tool?

What is the process used in genomic research?

What is used to create DNA chips for gene amplification?

What is the interaction between oligonucleotides, such as probes used in gene cloning?

What type of microarray measures gene expression (mRNA) and is used to compare healthy and cancer cells?

What dyes are used to label mRNA for hybridization to the microarray?

What is used to detect the SARS-CoV-2 genomic sequence from a sample taken from a suspected individual for COVID-19 detection?

What can be used to detect damage or overexpression of genes associated with various conditions, including cancer?

What competes with ssDNA in the microchip for hybridization during the microarray process?

What is initially not designed for diagnostic purposes but has been extensively used for COVID-19 detection since 2020?

What is isolated from samples taken for COVID-19 detection before being treated with chemicals to extract the viral genetic material RNA?

What is the main function of Neostigmine and pyridostigmine?

What is the primary adverse effect associated with nondepolarizing blockers?

Which neuromuscular blocking drug has a rapid onset of 1 minute and a duration of action of 55 minutes?

What is the mode of action of Baclofen, a centrally acting spasmolytic drug?

What is the primary mode of action of Diazepam, a centrally acting spasmolytic drug?

What is the mode of action of Tizanidine, a centrally acting spasmolytic drug?

What is the mode of action of Dantrolene, a directly-acting spasmolytic drug?

What is the primary mode of action of Cyclobenzaprine, a drug for acute muscle spasm?

What is the primary use of Baclofen, a centrally acting spasmolytic drug?

Which drug is primarily used for acute spasm due to muscle injury and inflammation?

Which type of skeletal muscle relaxant interferes with the transmission at the neuromuscular end plate?

Which drug is a prototype of nondepolarizing neuromuscular blocking drugs?

Which event characterizes Phase 1 of the depolarization block caused by succinylcholine?

Which class of neuromuscular blockers releases histamine from mast cells?

Which type of skeletal muscle relaxants is traditionally called 'centrally acting' muscle relaxants?

Which drug is used for short-term procedures and is associated with adverse drug reactions like hyperkalemia and malignant hyperthermia?

Which compound can reverse the block caused by non-depolarizing neuromuscular blockers?

Which type of blockade at the end plate is due to desensitization of Ach Receptors?

Which drugs reduce spasticity in a variety of painful conditions and are used for chronic back pain and painful fibromyalgias?

Which drugs interfere with transmission at the neuromuscular end plate and are used for ICU and general anesthesia?

Flashcards

Nasal and throat swab

Lower Ct value in RT-PCR

TaqMan probe in RT-PCR

Ct value of 20 in RT-PCR

Challenge with TaqMan probes

Monitoring infection severity in RT-PCR

Signal after Ct 36 or 37 in RT-PCR

RT-PCR and virus severity

Ct value higher than 35 in RT-PCR

Limitation of RT-PCR for COVID-19

DNA microarrays

Size of DNA microarray supports

DNA sample attachment on microarrays

Photolithography in DNA microarrays

Technology behind DNA microarrays

Main function DNA microarrays

Materials for DNA microarray supports

DNA samples on microarray supports

Purpose of PCR in COVID-19 detection

DNA microarrays as diagnostic tools

PCR in genomic research

Creating DNA chips

Nucleic acid hybridization

Expression microarray

Dyes used for mRNA labeling