L17 - Whole Genome Sequencing (WGS) and Bacterial Diagnostics Flashcards

1
Q

What are first-generation vaccines?

A

Whole pathogen vaccines, including inactivated (killed) and live-attenuated vaccines.

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2
Q

Give an example of an inactivated vaccine.

A

The polio vaccine.

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3
Q

What are second-generation vaccines?

A

Subunit vaccines that use isolated proteins or viral vectors to deliver genes of interest.

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4
Q

Give an example of a live-attenuated vaccine.

A

The MMR (measles, mumps, and rubella) vaccine.

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5
Q

What are third-generation vaccines?

A

Nucleic acid vaccines that use RNA or DNA, often encapsulated in nanoparticles.

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6
Q

What are the two main types of viral vector vaccines?

A

Replicating and non-replicating.

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7
Q

Which viral vector vaccine was used for COVID-19?

A

The Oxford-AstraZeneca vaccine, which uses a non-replicating adenovirus vector.

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8
Q

What are virus-like particle (VLP) vaccines?

A

Vaccines that mimic viruses but lack genetic material, such as HPV and Hepatitis B vaccines.

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9
Q

What is an advantage of mRNA vaccines?

A

Rapid development and adaptability to emerging viral variants.

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10
Q

Why do mRNA vaccines require lipid nanoparticles?

A

To facilitate cell entry and protect the mRNA from degradation.

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11
Q

What is self-amplifying RNA?

A

A form of mRNA that produces more antigenic material to enhance immune response.

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12
Q

How do high-throughput analyses aid vaccine development?

A

They track viral mutations and help adapt vaccines accordingly.

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13
Q

What is structural vaccinology?

A

The study of antigen structures to design more effective vaccines.

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14
Q

How can stabilizing mutations improve vaccines?

A

By ensuring antigens retain their proper structure, enhancing immunogenicity.

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15
Q

What is epitope mapping?

A

Identifying specific antigen regions that trigger immune responses.

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16
Q

What is germ-line targeting?

A

A strategy to guide immune responses toward broadly neutralizing antibodies.

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17
Q

Why is germ-line targeting useful for HIV vaccines?

A

Because HIV rapidly mutates, making broadly neutralizing antibodies essential.

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18
Q

What is systems immunology?

A

A holistic approach to understanding immune responses using multidimensional data.

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19
Q

How does systems immunology improve vaccine safety?

A

By identifying biomarkers linked to vaccine efficacy and adverse reactions.

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20
Q

Why is demographic data important in vaccine design?

A

Age, sex, and genetics influence immune responses and vaccine effectiveness.

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21
Q

How can vaccines be rapidly adapted to new viral strains?

A

By utilizing genomic surveillance and mRNA vaccine platforms.

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22
Q

What was a key finding from COVID-19 vaccine studies?

A

mRNA vaccines can be updated quickly in response to emerging variants.

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23
Q

Why is antigen stability important in vaccine development?

A

Unstable antigens may lead to weak or short-lived immune responses.

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24
Q

What is the role of adjuvants in vaccines?

A

They enhance immune response and prolong immunity.

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25
Q

Why do live-attenuated vaccines pose risks for immunocompromised individuals?

A

Because they contain weakened but still replicating viruses.

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26
Q

How did genome sequencing help during an E. coli outbreak?

A

It traced the epidemic strain and identified resistance genes.

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27
Q

What is the role of structural biology in vaccine development?

A

It helps design stable, highly immunogenic proteins.

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28
Q

Why are RNA vaccines considered the future of immunization?

A

They are adaptable, scalable, and can target emerging diseases quickly.

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29
Q

How does high-throughput sequencing aid disease surveillance?

A

By monitoring genetic changes in pathogens in real time.

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30
Q

What are some advantages of subunit vaccines?

A

They avoid live pathogens, reducing safety concerns.

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31
Q

Why are virus-like particle (VLP) vaccines effective?

A

They mimic real viruses, stimulating strong immune responses.

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32
Q

What are neutralizing antibodies?

A

Antibodies that prevent viruses from infecting cells.

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33
Q

How can epitope optimization improve vaccines?

A

By ensuring vaccines target the most effective immune responses.

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34
Q

What is a major limitation of inactivated vaccines?

A

They often require booster doses to maintain immunity.

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35
Q

How do mRNA vaccines differ from protein subunit vaccines?

A

mRNA vaccines instruct cells to produce antigens, while subunit vaccines deliver antigens directly.

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36
Q

What is the benefit of using nanoparticle delivery for vaccines?

A

It improves stability and enhances immune uptake.

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37
Q

Why are lipid nanoparticles used in mRNA vaccines?

A

They protect mRNA and facilitate cell delivery.

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38
Q

What was a key advantage of the COVID-19 mRNA vaccines?

A

Their rapid adaptability to new variants.

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39
Q

What is the significance of T-cell immunity in vaccines?

A

It provides long-lasting protection beyond antibody responses.

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40
Q

How does computational modeling aid vaccine development?

A

By predicting immune responses and optimizing antigen design.

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41
Q

What are some challenges of RNA vaccines?

A

Storage at low temperatures and potential need for boosters.

42
Q

Why is early-stage immune profiling important in vaccine trials?

A

It helps predict vaccine efficacy and safety.

43
Q

What is the primary role of Fc receptors in immunity?

A

They help immune cells recognize and clear pathogens.

44
Q

How does the immune system recognize mRNA vaccines?

A

Through innate sensors that trigger immune activation.

45
Q

What role do dendritic cells play in vaccination?

A

They process and present antigens to T cells.

46
Q

How does TLR activation improve vaccine responses?

A

It stimulates innate immunity, enhancing adaptive responses.

47
Q

What is the goal of universal vaccines?

A

To protect against multiple strains or variants of a virus.

48
Q

How does vaccine durability affect immunization strategies?

A

Longer-lasting immunity reduces the need for frequent boosters.

49
Q

What is a major advantage of using computational immunology in vaccine research?

A

It allows for faster vaccine design and testing.

50
Q

What is the future direction of vaccine development?

A

Personalized vaccines tailored to genetic and immunological differences.

51
Q

What is metagenomics and how does it relate to WGS?

A

Metagenomics involves sequencing genetic material from environmental samples, allowing WGS to identify microbial communities without culture.

52
Q

How does WGS assist in differentiating bacterial strains?

A

WGS can identify single nucleotide polymorphisms (SNPs) that distinguish closely related bacterial strains. What is a core genome vs. a pan-genome?

53
Q

What is a core genome vs. a pan-genome?

A

The core genome includes genes shared by all strains of a species while the pan-genome consists of all possible genes

54
Q

How does WGS improve infection control in hospitals?

A

It rapidly identifies outbreak sources allowing targeted infection prevention measures.

55
Q

What is the significance of phylogenetic analysis in WGS?

A

It helps determine evolutionary relationships and track bacterial transmission patterns.

56
Q

Why is WGS preferred for detecting horizontal gene transfer events?

A

It can identify genetic material exchanged between bacteria which may confer antibiotic resistance.

57
Q

What is a core genome vs. a pan-genome?

A

The core genome includes genes shared by all

58
Q

How can WGS identify emerging bacterial pathogens?

A

By detecting novel genetic mutations and virulence factors associated with increased pathogenicity.

59
Q

What is genome-wide association study (GWAS) in bacterial genomics?

A

GWAS links genetic variations to specific bacterial traits, such as antibiotic resistance or virulence.

60
Q

How does WGS help in understanding bacterial evolution?

A

It tracks mutations over time, revealing how bacteria adapt to antibiotics and host environments.

61
Q

What are single nucleotide polymorphisms (SNPs), and why are they important in WGS?

A

SNPs are single base-pair changes in the genome that help differentiate bacterial strains.

62
Q

What is the role of plasmids in antimicrobial resistance?

A

Plasmids carry resistance genes that can be transferred between bacteria, spreading AMR.

63
Q

How does WGS help predict bacterial pathogenicity?

A

By identifying genes associated with toxin production, adhesion, and immune evasion.

64
Q

Why is WGS useful for foodborne outbreak investigations?

A

It can quickly identify the bacterial strain responsible and track contamination sources.

65
Q

How does WGS contribute to vaccine development?

A

By identifying conserved bacterial genes that can serve as vaccine targets.

66
Q

What is the role of CRISPR in bacterial genomes, and how does WGS help study it?

A

CRISPR provides bacterial immunity against viruses, and WGS helps analyze its diversity and function.

67
Q

How can WGS predict antibiotic susceptibility?

A

By detecting known resistance genes and mutations affecting drug efficacy.

68
Q

What is shotgun sequencing, and how is it used in WGS?

A

It randomly fragments DNA for sequencing, allowing assembly of complete bacterial genomes.

69
Q

How does WGS assist in detecting bacterial biofilm formation?

A

It identifies genes involved in biofilm production, which contributes to antibiotic resistance.

70
Q

What is comparative genomics, and why is it important?

A

It compares bacterial genomes to identify genetic variations linked to pathogenicity and resistance.

71
Q

How does WGS help in tracking zoonotic bacterial diseases?

A

It identifies genetic links between human and animal bacterial strains.

72
Q

What is the role of WGS in detecting mobile genetic elements?

A

It helps track transposons, integrons, and phages that spread antibiotic resistance.

73
Q

How does WGS improve tuberculosis control strategies?

A

By identifying drug-resistant TB strains early, guiding treatment choices.

74
Q

What is the significance of GC content in bacterial genome analysis?

A

GC content varies between species and helps in identifying foreign DNA in bacterial genomes.

75
Q

How does WGS contribute to forensic microbiology?

A

It helps link bacterial strains to crime scenes or bioterrorism events.

76
Q

What is the role of WGS in monitoring antibiotic resistance globally?

A

It enables real-time tracking of resistance genes across different regions.

77
Q

Why is functional annotation of bacterial genomes important in WGS?

A

It assigns functions to genes, helping understand bacterial physiology and resistance mechanisms.

78
Q

How does WGS support drug discovery?

A

By identifying bacterial metabolic pathways that can be targeted for new antibiotics.

79
Q

What are prophages, and how does WGS help study them?

A

Prophages are dormant viral DNA in bacterial genomes, and WGS helps analyze their impact on bacterial behavior.

80
Q

How does WGS detect co-infections?

A

By identifying multiple bacterial species in a single sample.

81
Q

What is MLST, and how does it relate to WGS?

A

Multi-Locus Sequence Typing (MLST) classifies bacterial strains based on genetic sequences, and WGS provides a more detailed version.

82
Q

How does WGS aid in studying bacterial quorum sensing?

A

It identifies genes responsible for bacterial communication and coordination of infection strategies.

83
Q

Why is genome assembly important in WGS?

A

It reconstructs full bacterial genomes, ensuring accurate analysis.

84
Q

What are bacterial pathogenicity islands (PAIs), and how does WGS detect them?

A

PAIs are clusters of virulence genes, and WGS helps identify their presence and transfer.

85
Q

How does WGS help understand bacterial symbiosis?

A

It reveals genetic adaptations that allow bacteria to coexist with hosts.

86
Q

What is a reference genome, and why is it important in WGS?

A

A reference genome is a high-quality representative sequence used for comparing new bacterial genomes.

87
Q

How does WGS improve bacterial species classification?

A

It provides precise genetic differentiation between closely related species.

88
Q

What is hybrid sequencing, and why is it beneficial?

A

It combines short- and long-read sequencing technologies for more accurate bacterial genome assembly.

89
Q

How does WGS contribute to personalized infection treatment?

A

By tailoring antibiotic selection based on a patient’s specific bacterial strain.

90
Q

What role does epigenetics play in bacterial adaptation, and how does WGS help study it?

A

Epigenetic modifications influence bacterial gene expression, and WGS helps identify these changes.

91
Q

How does WGS aid in studying antibiotic degradation mechanisms?

A

It identifies bacterial enzymes that break down antibiotics.

92
Q

How does WGS contribute to studying extremophiles?

A

It reveals genetic adaptations that allow bacteria to survive in extreme environments.

93
Q

What is long-read sequencing, and how does it improve WGS accuracy?

A

It sequences longer DNA fragments, reducing assembly errors and improving genome completeness.

94
Q

How does WGS support microbiome research?

A

It helps analyze the composition and function of microbial communities in different environments.

95
Q

How can WGS detect novel bacterial species?

A

By identifying unique genetic sequences not found in existing databases.

96
Q

What are insertion sequences, and how does WGS detect them?

A

Insertion sequences are small mobile genetic elements, and WGS tracks their role in genetic variation.

97
Q

How does WGS contribute to bioremediation research?

A

It helps identify bacteria with genes for breaking down environmental pollutants.

98
Q

How can WGS reveal bacterial adaptation to antibiotics?

A

By tracking mutations that enhance bacterial survival against drugs.

99
Q

What is gene annotation, and why is it critical in WGS?

A

Gene annotation assigns functions to DNA sequences, helping interpret genomic data.

100
Q

How does WGS help study bacterial toxin production?

A

It identifies genes responsible for toxin synthesis and their regulatory mechanisms.

101
Q

How does WGS impact the development of new diagnostic tools?

A

It provides genetic insights that drive innovation in rapid bacterial detection methods.