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.
2
Q
Give an example of an inactivated vaccine.
A
The polio vaccine.
3
Q
What are second-generation vaccines?
A
Subunit vaccines that use isolated proteins or viral vectors to deliver genes of interest.
4
Q
Give an example of a live-attenuated vaccine.
A
The MMR (measles, mumps, and rubella) vaccine.
5
Q
What are third-generation vaccines?
A
Nucleic acid vaccines that use RNA or DNA, often encapsulated in nanoparticles.
6
Q
What are the two main types of viral vector vaccines?
A
Replicating and non-replicating.
7
Q
Which viral vector vaccine was used for COVID-19?
A
The Oxford-AstraZeneca vaccine, which uses a non-replicating adenovirus vector.
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.
9
Q
What is an advantage of mRNA vaccines?
A
Rapid development and adaptability to emerging viral variants.
10
Q
Why do mRNA vaccines require lipid nanoparticles?
A
To facilitate cell entry and protect the mRNA from degradation.
11
Q
What is self-amplifying RNA?
A
A form of mRNA that produces more antigenic material to enhance immune response.
12
Q
How do high-throughput analyses aid vaccine development?
A
They track viral mutations and help adapt vaccines accordingly.
13
Q
What is structural vaccinology?
A
The study of antigen structures to design more effective vaccines.
14
Q
How can stabilizing mutations improve vaccines?
A
By ensuring antigens retain their proper structure, enhancing immunogenicity.
15
Q
What is epitope mapping?
A
Identifying specific antigen regions that trigger immune responses.
16
Q
What is germ-line targeting?
A
A strategy to guide immune responses toward broadly neutralizing antibodies.
17
Q
Why is germ-line targeting useful for HIV vaccines?
A
Because HIV rapidly mutates, making broadly neutralizing antibodies essential.
18
Q
What is systems immunology?
A
A holistic approach to understanding immune responses using multidimensional data.
19
Q
How does systems immunology improve vaccine safety?
A
By identifying biomarkers linked to vaccine efficacy and adverse reactions.
20
Q
Why is demographic data important in vaccine design?
A
Age, sex, and genetics influence immune responses and vaccine effectiveness.
21
Q
How can vaccines be rapidly adapted to new viral strains?
A
By utilizing genomic surveillance and mRNA vaccine platforms.
22
Q
What was a key finding from COVID-19 vaccine studies?
A
mRNA vaccines can be updated quickly in response to emerging variants.
23
Q
Why is antigen stability important in vaccine development?
A
Unstable antigens may lead to weak or short-lived immune responses.
24
Q
What is the role of adjuvants in vaccines?
A
They enhance immune response and prolong immunity.
25
Why do live-attenuated vaccines pose risks for immunocompromised individuals?
Because they contain weakened but still replicating viruses.
26
How did genome sequencing help during an E. coli outbreak?
It traced the epidemic strain and identified resistance genes.
27
What is the role of structural biology in vaccine development?
It helps design stable, highly immunogenic proteins.
28
Why are RNA vaccines considered the future of immunization?
They are adaptable, scalable, and can target emerging diseases quickly.
29
How does high-throughput sequencing aid disease surveillance?
By monitoring genetic changes in pathogens in real time.
30
What are some advantages of subunit vaccines?
They avoid live pathogens, reducing safety concerns.
31
Why are virus-like particle (VLP) vaccines effective?
They mimic real viruses, stimulating strong immune responses.
32
What are neutralizing antibodies?
Antibodies that prevent viruses from infecting cells.
33
How can epitope optimization improve vaccines?
By ensuring vaccines target the most effective immune responses.
34
What is a major limitation of inactivated vaccines?
They often require booster doses to maintain immunity.
35
How do mRNA vaccines differ from protein subunit vaccines?
mRNA vaccines instruct cells to produce antigens, while subunit vaccines deliver antigens directly.
36
What is the benefit of using nanoparticle delivery for vaccines?
It improves stability and enhances immune uptake.
37
Why are lipid nanoparticles used in mRNA vaccines?
They protect mRNA and facilitate cell delivery.
38
What was a key advantage of the COVID-19 mRNA vaccines?
Their rapid adaptability to new variants.
39
What is the significance of T-cell immunity in vaccines?
It provides long-lasting protection beyond antibody responses.
40
How does computational modeling aid vaccine development?
By predicting immune responses and optimizing antigen design.
41
What are some challenges of RNA vaccines?
Storage at low temperatures and potential need for boosters.
42
Why is early-stage immune profiling important in vaccine trials?
It helps predict vaccine efficacy and safety.
43
What is the primary role of Fc receptors in immunity?
They help immune cells recognize and clear pathogens.
44
How does the immune system recognize mRNA vaccines?
Through innate sensors that trigger immune activation.
45
What role do dendritic cells play in vaccination?
They process and present antigens to T cells.
46
How does TLR activation improve vaccine responses?
It stimulates innate immunity, enhancing adaptive responses.
47
What is the goal of universal vaccines?
To protect against multiple strains or variants of a virus.
48
How does vaccine durability affect immunization strategies?
Longer-lasting immunity reduces the need for frequent boosters.
49
What is a major advantage of using computational immunology in vaccine research?
It allows for faster vaccine design and testing.
50
What is the future direction of vaccine development?
Personalized vaccines tailored to genetic and immunological differences.
51
What is metagenomics and how does it relate to WGS?
Metagenomics involves sequencing genetic material from environmental samples, allowing WGS to identify microbial communities without culture.
52
How does WGS assist in differentiating bacterial strains?
WGS can identify single nucleotide polymorphisms (SNPs) that distinguish closely related bacterial strains. What is a core genome vs. a pan-genome?
53
What is a core genome vs. a pan-genome?
The core genome includes genes shared by all strains of a species while the pan-genome consists of all possible genes
54
How does WGS improve infection control in hospitals?
It rapidly identifies outbreak sources allowing targeted infection prevention measures.
55
What is the significance of phylogenetic analysis in WGS?
It helps determine evolutionary relationships and track bacterial transmission patterns.
56
Why is WGS preferred for detecting horizontal gene transfer events?
It can identify genetic material exchanged between bacteria which may confer antibiotic resistance.
57
What is a core genome vs. a pan-genome?
The core genome includes genes shared by all
58
How can WGS identify emerging bacterial pathogens?
By detecting novel genetic mutations and virulence factors associated with increased pathogenicity.
59
What is genome-wide association study (GWAS) in bacterial genomics?
GWAS links genetic variations to specific bacterial traits, such as antibiotic resistance or virulence.
60
How does WGS help in understanding bacterial evolution?
It tracks mutations over time, revealing how bacteria adapt to antibiotics and host environments.
61
What are single nucleotide polymorphisms (SNPs), and why are they important in WGS?
SNPs are single base-pair changes in the genome that help differentiate bacterial strains.
62
What is the role of plasmids in antimicrobial resistance?
Plasmids carry resistance genes that can be transferred between bacteria, spreading AMR.
63
How does WGS help predict bacterial pathogenicity?
By identifying genes associated with toxin production, adhesion, and immune evasion.
64
Why is WGS useful for foodborne outbreak investigations?
It can quickly identify the bacterial strain responsible and track contamination sources.
65
How does WGS contribute to vaccine development?
By identifying conserved bacterial genes that can serve as vaccine targets.
66
What is the role of CRISPR in bacterial genomes, and how does WGS help study it?
CRISPR provides bacterial immunity against viruses, and WGS helps analyze its diversity and function.
67
How can WGS predict antibiotic susceptibility?
By detecting known resistance genes and mutations affecting drug efficacy.
68
What is shotgun sequencing, and how is it used in WGS?
It randomly fragments DNA for sequencing, allowing assembly of complete bacterial genomes.
69
How does WGS assist in detecting bacterial biofilm formation?
It identifies genes involved in biofilm production, which contributes to antibiotic resistance.
70
What is comparative genomics, and why is it important?
It compares bacterial genomes to identify genetic variations linked to pathogenicity and resistance.
71
How does WGS help in tracking zoonotic bacterial diseases?
It identifies genetic links between human and animal bacterial strains.
72
What is the role of WGS in detecting mobile genetic elements?
It helps track transposons, integrons, and phages that spread antibiotic resistance.
73
How does WGS improve tuberculosis control strategies?
By identifying drug-resistant TB strains early, guiding treatment choices.
74
What is the significance of GC content in bacterial genome analysis?
GC content varies between species and helps in identifying foreign DNA in bacterial genomes.
75
How does WGS contribute to forensic microbiology?
It helps link bacterial strains to crime scenes or bioterrorism events.
76
What is the role of WGS in monitoring antibiotic resistance globally?
It enables real-time tracking of resistance genes across different regions.
77
Why is functional annotation of bacterial genomes important in WGS?
It assigns functions to genes, helping understand bacterial physiology and resistance mechanisms.
78
How does WGS support drug discovery?
By identifying bacterial metabolic pathways that can be targeted for new antibiotics.
79
What are prophages, and how does WGS help study them?
Prophages are dormant viral DNA in bacterial genomes, and WGS helps analyze their impact on bacterial behavior.
80
How does WGS detect co-infections?
By identifying multiple bacterial species in a single sample.
81
What is MLST, and how does it relate to WGS?
Multi-Locus Sequence Typing (MLST) classifies bacterial strains based on genetic sequences, and WGS provides a more detailed version.
82
How does WGS aid in studying bacterial quorum sensing?
It identifies genes responsible for bacterial communication and coordination of infection strategies.
83
Why is genome assembly important in WGS?
It reconstructs full bacterial genomes, ensuring accurate analysis.
84
What are bacterial pathogenicity islands (PAIs), and how does WGS detect them?
PAIs are clusters of virulence genes, and WGS helps identify their presence and transfer.
85
How does WGS help understand bacterial symbiosis?
It reveals genetic adaptations that allow bacteria to coexist with hosts.
86
What is a reference genome, and why is it important in WGS?
A reference genome is a high-quality representative sequence used for comparing new bacterial genomes.
87
How does WGS improve bacterial species classification?
It provides precise genetic differentiation between closely related species.
88
What is hybrid sequencing, and why is it beneficial?
It combines short- and long-read sequencing technologies for more accurate bacterial genome assembly.
89
How does WGS contribute to personalized infection treatment?
By tailoring antibiotic selection based on a patient’s specific bacterial strain.
90
What role does epigenetics play in bacterial adaptation, and how does WGS help study it?
Epigenetic modifications influence bacterial gene expression, and WGS helps identify these changes.
91
How does WGS aid in studying antibiotic degradation mechanisms?
It identifies bacterial enzymes that break down antibiotics.
92
How does WGS contribute to studying extremophiles?
It reveals genetic adaptations that allow bacteria to survive in extreme environments.
93
What is long-read sequencing, and how does it improve WGS accuracy?
It sequences longer DNA fragments, reducing assembly errors and improving genome completeness.
94
How does WGS support microbiome research?
It helps analyze the composition and function of microbial communities in different environments.
95
How can WGS detect novel bacterial species?
By identifying unique genetic sequences not found in existing databases.
96
What are insertion sequences, and how does WGS detect them?
Insertion sequences are small mobile genetic elements, and WGS tracks their role in genetic variation.
97
How does WGS contribute to bioremediation research?
It helps identify bacteria with genes for breaking down environmental pollutants.
98
How can WGS reveal bacterial adaptation to antibiotics?
By tracking mutations that enhance bacterial survival against drugs.
99
What is gene annotation, and why is it critical in WGS?
Gene annotation assigns functions to DNA sequences, helping interpret genomic data.
100
How does WGS help study bacterial toxin production?
It identifies genes responsible for toxin synthesis and their regulatory mechanisms.
101
How does WGS impact the development of new diagnostic tools?
It provides genetic insights that drive innovation in rapid bacterial detection methods.
102
What are the three main generations of vaccine platforms?
First: whole pathogen vaccines; Second: subunit or viral vector vaccines; Third: nucleic acid-based vaccines.
103
What is the benefit of using proline substitutions in vaccine design?
Proline substitutions stabilize the pre-fusion conformation of viral proteins to enhance immunogenicity.
104
Why might whole pathogen vaccines be less effective against rapidly mutating viruses like SARS-CoV-2?
They may present post-fusion epitopes that do not elicit strong neutralizing antibody responses.
105
What is self-amplifying RNA and how does it improve vaccine response?
It includes a replicase gene that amplifies RNA copies in the cell, increasing antigen production and immune stimulation.
106
How do virus-like particle vaccines work?
They use self-assembling viral proteins that mimic the virus structure without containing genetic material.
107
How does high-throughput sequencing support vaccine design?
It enables rapid tracking of viral mutations, aiding in vaccine updates and development.
108
What is germ-line targeting in vaccine development?
A strategy to activate naive B cells that can mature into cells producing broadly neutralizing antibodies.
109
What is the goal of epitope scaffolding?
To present desired epitopes in optimal conformation on an antigenic scaffold for better immune recognition.
110
Why is structural biology critical in modern vaccine development?
It helps identify and stabilize the most immunogenic conformations of viral proteins for vaccine design.
111
How can systems immunology help improve vaccine safety and efficacy?
By analyzing multi-omics and clinical data to identify immune signatures linked to vaccine response and adverse events.
