Podcast
Questions and Answers
What is the primary purpose of using transgenic animal models in infection research?
What is the primary purpose of using transgenic animal models in infection research?
- To eliminate the need for studying infections in humans.
- To reveal how specific genes influence infection processes. (correct)
- To understand how immune system genes respond during infection.
- To observe real-time bacterial growth inside living organisms.
Knock-in mice are used to study the effect of a gene's absence on infection.
Knock-in mice are used to study the effect of a gene's absence on infection.
False (B)
What is the purpose of using humanized mice in infection research?
What is the purpose of using humanized mice in infection research?
To make the infection process more similar to human infections
In the context of infection research, SCID mice are useful because they lack certain ______ components.
In the context of infection research, SCID mice are useful because they lack certain ______ components.
What is the main advantage of using bacteria that glow in infection studies?
What is the main advantage of using bacteria that glow in infection studies?
Genome-wide association studies (GWAS) are used to compare genetic similarities between individuals.
Genome-wide association studies (GWAS) are used to compare genetic similarities between individuals.
What type of plot is commonly used to visualize the results of genome-wide association studies (GWAS)?
What type of plot is commonly used to visualize the results of genome-wide association studies (GWAS)?
Scientists use transgenic animals to observe how ______ genes respond during an infection.
Scientists use transgenic animals to observe how ______ genes respond during an infection.
What is the role of Toll-like receptors (TLRs) in the context of infection?
What is the role of Toll-like receptors (TLRs) in the context of infection?
Gene silencing changes the DNA sequence of an organism.
Gene silencing changes the DNA sequence of an organism.
What molecule does RNA interference (RNAi) break down to reduce or stop protein production?
What molecule does RNA interference (RNAi) break down to reduce or stop protein production?
The protein complex called ______ destroys mRNA, stopping protein production.
The protein complex called ______ destroys mRNA, stopping protein production.
What is a key challenge when using RNAi libraries in infection research?
What is a key challenge when using RNAi libraries in infection research?
CRISPR-Cas9, unlike RNAi, only temporarily edits genes.
CRISPR-Cas9, unlike RNAi, only temporarily edits genes.
What is the function of guide RNA (sgRNA) in the CRISPR-Cas9 system?
What is the function of guide RNA (sgRNA) in the CRISPR-Cas9 system?
In CRISPR-Cas9, ______-directed repair fixes DNA breaks using a DNA template.
In CRISPR-Cas9, ______-directed repair fixes DNA breaks using a DNA template.
What is the primary mechanism of action of the Type 3 Secretion System (T3SS) used by V. parahaemolyticus?
What is the primary mechanism of action of the Type 3 Secretion System (T3SS) used by V. parahaemolyticus?
Transcriptomics studies protein expression.
Transcriptomics studies protein expression.
What is the function of microarrays in studying gene expression during infection?
What is the function of microarrays in studying gene expression during infection?
[Blank] technology is now the preferred method for studying gene expression.
[Blank] technology is now the preferred method for studying gene expression.
What is the main advantage of dual RNA-Seq in infection research?
What is the main advantage of dual RNA-Seq in infection research?
Laser-capture microdissection (LCM) is used to study infections at a broad, tissue-wide level.
Laser-capture microdissection (LCM) is used to study infections at a broad, tissue-wide level.
What tool is used in laser-capture microdissection (LCM) to cut out small sections of infected cells?
What tool is used in laser-capture microdissection (LCM) to cut out small sections of infected cells?
Combining LCM with ______ provides more precise insights into infection research.
Combining LCM with ______ provides more precise insights into infection research.
What is the purpose of proteomic profiling?
What is the purpose of proteomic profiling?
In 2D gel electrophoresis, proteins are first separated by size, then by charge.
In 2D gel electrophoresis, proteins are first separated by size, then by charge.
What is the first step in 2D gel electrophoresis, which separates proteins based on their charge?
What is the first step in 2D gel electrophoresis, which separates proteins based on their charge?
SDS-PAGE separates proteins based on ______ in a denatured state.
SDS-PAGE separates proteins based on ______ in a denatured state.
What can proteins in amniotic fluid indicate?
What can proteins in amniotic fluid indicate?
Proteomics can only identify proteins that are directly involved in the infection process.
Proteomics can only identify proteins that are directly involved in the infection process.
The release of what type of proteins is measured to assess inflammation during infection?
The release of what type of proteins is measured to assess inflammation during infection?
Subcellular ______ can reduce the complexity of proteomic analysis by separating proteins from different parts of the cell.
Subcellular ______ can reduce the complexity of proteomic analysis by separating proteins from different parts of the cell.
What is the primary goal of metabolomics?
What is the primary goal of metabolomics?
Untargeted metabolomics measures only a specific set of metabolites.
Untargeted metabolomics measures only a specific set of metabolites.
Studying fluctuations in metabolite levels can help scientists detect what three things?
Studying fluctuations in metabolite levels can help scientists detect what three things?
Metagenomics involves the study of microbial ______.
Metagenomics involves the study of microbial ______.
Match the following omics technologies with their primary focus:
Match the following omics technologies with their primary focus:
Which of the following is a major challenge in metabolomics?
Which of the following is a major challenge in metabolomics?
Date complexity is not a problem for interpreting metabolomics data.
Date complexity is not a problem for interpreting metabolomics data.
What type of tools are required for interpreting the huge amounts of data produced by metabolomics?
What type of tools are required for interpreting the huge amounts of data produced by metabolomics?
Genome-wide metabolic reconstructions use ______ date to predict metabolic pathways and how they interact.
Genome-wide metabolic reconstructions use ______ date to predict metabolic pathways and how they interact.
In the context of studying infections, what does SDS-PAGE primarily achieve?
In the context of studying infections, what does SDS-PAGE primarily achieve?
Which method is used in infection research to study responses that vary across different tissue areas, allowing for focused analysis at the exact interaction site between bacteria and immune cells?
Which method is used in infection research to study responses that vary across different tissue areas, allowing for focused analysis at the exact interaction site between bacteria and immune cells?
What is a primary advantage of using genome-wide screening approaches in infection research?
What is a primary advantage of using genome-wide screening approaches in infection research?
In RNA interference (RNAi), what type of RNA molecule is introduced into mammalian cells to initiate gene silencing?
In RNA interference (RNAi), what type of RNA molecule is introduced into mammalian cells to initiate gene silencing?
What is the main mechanism by which siRNA induces gene silencing in mammalian cells?
What is the main mechanism by which siRNA induces gene silencing in mammalian cells?
Why are viral-based vectors used in RNAi library screening?
Why are viral-based vectors used in RNAi library screening?
In the Listeria monocytogenes RNAi screen described, what phenotype indicated a knockdown of a host factor needed for bacterial escape from the entry vacuole but not replication?
In the Listeria monocytogenes RNAi screen described, what phenotype indicated a knockdown of a host factor needed for bacterial escape from the entry vacuole but not replication?
What is a key advantage of RNAi technology in the context of identifying host targets for therapy against bacterial infections?
What is a key advantage of RNAi technology in the context of identifying host targets for therapy against bacterial infections?
Compared to ZFN and TALEN genome editing systems, what is a significant advantage of the CRISPR-Cas9 system?
Compared to ZFN and TALEN genome editing systems, what is a significant advantage of the CRISPR-Cas9 system?
What is the role of the single guide RNA (sgRNA) in the CRISPR-Cas9 system?
What is the role of the single guide RNA (sgRNA) in the CRISPR-Cas9 system?
What is the function of the PAM sequence in CRISPR-Cas9 genome editing?
What is the function of the PAM sequence in CRISPR-Cas9 genome editing?
In the CRISPR-Cas9 screen for host factors mediating α-hemolysin toxicity, what type of cells were used?
In the CRISPR-Cas9 screen for host factors mediating α-hemolysin toxicity, what type of cells were used?
What method was used to monitor cytotoxicity in the CRISPR-Cas9 screen for α-hemolysin host factors?
What method was used to monitor cytotoxicity in the CRISPR-Cas9 screen for α-hemolysin host factors?
In the CRISPR-Cas9 screen studying Vibrio parahaemolyticus T3SS-mediated cytotoxicity, resistance to bacterial killing was defined by:
In the CRISPR-Cas9 screen studying Vibrio parahaemolyticus T3SS-mediated cytotoxicity, resistance to bacterial killing was defined by:
What cellular process was found to be associated with T3SS1-mediated cytotoxicity in the Vibrio parahaemolyticus CRISPR-Cas9 screen?
What cellular process was found to be associated with T3SS1-mediated cytotoxicity in the Vibrio parahaemolyticus CRISPR-Cas9 screen?
What cellular component was found to be associated with T3SS2-mediated cytotoxicity in the Vibrio parahaemolyticus CRISPR-Cas9 screen?
What cellular component was found to be associated with T3SS2-mediated cytotoxicity in the Vibrio parahaemolyticus CRISPR-Cas9 screen?
What is a major advantage of using genome-wide CRISPR-Cas9 screening over traditional single-gene knockout studies in infection research?
What is a major advantage of using genome-wide CRISPR-Cas9 screening over traditional single-gene knockout studies in infection research?
Which of the following is a potential drawback of RNAi-based screening approaches?
Which of the following is a potential drawback of RNAi-based screening approaches?
To improve the statistical power and reliability of RNAi screening, what strategy is commonly employed?
To improve the statistical power and reliability of RNAi screening, what strategy is commonly employed?
What is the primary purpose of gene silencing and gene editing technologies in the context of genome-wide screening for host factors in infection?
What is the primary purpose of gene silencing and gene editing technologies in the context of genome-wide screening for host factors in infection?
Which of the following organisms was initially used to demonstrate the gene-silencing effect of double-stranded RNA?
Which of the following organisms was initially used to demonstrate the gene-silencing effect of double-stranded RNA?
What is the length of siRNA molecules typically used in RNAi screening?
What is the length of siRNA molecules typically used in RNAi screening?
In the context of CRISPR-Cas9, what is the function of the Cas9 protein?
In the context of CRISPR-Cas9, what is the function of the Cas9 protein?
Which domain of the Cas9 protein nicks the DNA strand that has the PAM motif?
Which domain of the Cas9 protein nicks the DNA strand that has the PAM motif?
What is the typical PAM sequence recognized by Streptococcus pyogenes Cas9?
What is the typical PAM sequence recognized by Streptococcus pyogenes Cas9?
In the Listeria monocytogenes RNAi screen, what dye was used to stain the host nuclei?
In the Listeria monocytogenes RNAi screen, what dye was used to stain the host nuclei?
What is the primary goal of comparative genomics in the context of host susceptibility to bacterial infections?
What is the primary goal of comparative genomics in the context of host susceptibility to bacterial infections?
What is the term for the synthetic chimeric RNA in CRISPR-Cas9 that is derived from the fusion of crRNA and tracrRNA?
What is the term for the synthetic chimeric RNA in CRISPR-Cas9 that is derived from the fusion of crRNA and tracrRNA?
Which of the following is NOT a cellular function category of host proteins identified in the Listeria monocytogenes RNAi screen?
Which of the following is NOT a cellular function category of host proteins identified in the Listeria monocytogenes RNAi screen?
What does 'off-target effect' refer to in the context of RNAi and CRISPR-Cas9 screening?
What does 'off-target effect' refer to in the context of RNAi and CRISPR-Cas9 screening?
What is the advantage of using fluorescence microscopy in the Listeria monocytogenes RNAi screen?
What is the advantage of using fluorescence microscopy in the Listeria monocytogenes RNAi screen?
What is the role of tracrRNA in the CRISPR-Cas9 system?
What is the role of tracrRNA in the CRISPR-Cas9 system?
What is the main reason ZFN and TALEN genome editing approaches have not advanced as rapidly as CRISPR-Cas9?
What is the main reason ZFN and TALEN genome editing approaches have not advanced as rapidly as CRISPR-Cas9?
In the CRISPR-Cas9 screen for α-hemolysin toxicity, what was identified as the known cell surface receptor for α-hemolysin?
In the CRISPR-Cas9 screen for α-hemolysin toxicity, what was identified as the known cell surface receptor for α-hemolysin?
Which of the following proteins identified in the α-hemolysin CRISPR-Cas9 screen is involved in Golgi trafficking?
Which of the following proteins identified in the α-hemolysin CRISPR-Cas9 screen is involved in Golgi trafficking?
What is the function of the SWI/SNF chromatin remodeling complex, which was implicated in T3SS1 resistance in the Vibrio parahaemolyticus screen?
What is the function of the SWI/SNF chromatin remodeling complex, which was implicated in T3SS1 resistance in the Vibrio parahaemolyticus screen?
What is the role of protein Ser/Thr kinases, which were linked to T3SS2 resistance in the Vibrio parahaemolyticus screen?
What is the role of protein Ser/Thr kinases, which were linked to T3SS2 resistance in the Vibrio parahaemolyticus screen?
What is the significance of identifying host factors like ADAM10, SGMS1, SYS1, and ARF1 in the α-hemolysin CRISPR-Cas9 screen?
What is the significance of identifying host factors like ADAM10, SGMS1, SYS1, and ARF1 in the α-hemolysin CRISPR-Cas9 screen?
Which of the following transgenic animal models is best suited for studying the function of a particular gene during infection by replacing it with a human version?
Which of the following transgenic animal models is best suited for studying the function of a particular gene during infection by replacing it with a human version?
In infection research, how do cytokine receptor knockout mice contribute to understanding the development of live vaccines?
In infection research, how do cytokine receptor knockout mice contribute to understanding the development of live vaccines?
What is the primary advantage of using genetic ablation in transgenic animals for infection studies?
What is the primary advantage of using genetic ablation in transgenic animals for infection studies?
How do "humanized" transgenic mice, particularly SCID mice with human tissue xenografts, enhance infection research?
How do "humanized" transgenic mice, particularly SCID mice with human tissue xenografts, enhance infection research?
In the context of studying Listeria monocytogenes infection, how did transgenic mice expressing the human E-cadherin receptor contribute to understanding bacterial invasion?
In the context of studying Listeria monocytogenes infection, how did transgenic mice expressing the human E-cadherin receptor contribute to understanding bacterial invasion?
What is the utility of creating transgenic animals with inducible reporter gene fusions, such as the NFκB-responsive lacZ reporter, in infection studies?
What is the utility of creating transgenic animals with inducible reporter gene fusions, such as the NFκB-responsive lacZ reporter, in infection studies?
How does whole-body biophotonic imaging enhance the study of bacterial infections in vivo?
How does whole-body biophotonic imaging enhance the study of bacterial infections in vivo?
Why is red fluorescent protein (RFP) often preferred over green fluorescent protein (GFP) for biophotonic imaging in animals?
Why is red fluorescent protein (RFP) often preferred over green fluorescent protein (GFP) for biophotonic imaging in animals?
In biophotonic imaging, what is the purpose of fusing host genes to luciferase or fluorescent proteins?
In biophotonic imaging, what is the purpose of fusing host genes to luciferase or fluorescent proteins?
How is the use of tagged molecules, such as antibodies or lectins with synthetic fluorescent dye labels, useful in biophotonic imaging when studying bacterial infections?
How is the use of tagged molecules, such as antibodies or lectins with synthetic fluorescent dye labels, useful in biophotonic imaging when studying bacterial infections?
What is the modern definition of systems genetics in the context of host-microbe interactions?
What is the modern definition of systems genetics in the context of host-microbe interactions?
How do single nucleotide polymorphisms (SNPs) contribute to variations in host response to pathogens?
How do single nucleotide polymorphisms (SNPs) contribute to variations in host response to pathogens?
What is the purpose of using genetic reference populations of mice, such as the Collaborative Cross (CC) and Diversity Outbred (DO) collections, in systems genetics?
What is the purpose of using genetic reference populations of mice, such as the Collaborative Cross (CC) and Diversity Outbred (DO) collections, in systems genetics?
In genome-wide association studies (GWAS), what is the primary goal of comparing DNA sequence variations within a population?
In genome-wide association studies (GWAS), what is the primary goal of comparing DNA sequence variations within a population?
How does the concept of linkage in GWAS affect the interpretation of results when identifying SNPs associated with a disease trait?
How does the concept of linkage in GWAS affect the interpretation of results when identifying SNPs associated with a disease trait?
What is the purpose of a Manhattan plot in genome-wide association studies (GWAS)?
What is the purpose of a Manhattan plot in genome-wide association studies (GWAS)?
How does multilocus trait analysis (MLTA) enhance the insights gained from GWAS?
How does multilocus trait analysis (MLTA) enhance the insights gained from GWAS?
What is the significance of identifying a 'loss-of-function' SNP in TLR1 that is associated with decreased incidence of leprosy?
What is the significance of identifying a 'loss-of-function' SNP in TLR1 that is associated with decreased incidence of leprosy?
In the context of infection research, what is an advantage of using immunodeficient transgenic animal models?
In the context of infection research, what is an advantage of using immunodeficient transgenic animal models?
How does the use of Nramp1 mutant mice contribute to understanding the host defense against intracellular pathogens?
How does the use of Nramp1 mutant mice contribute to understanding the host defense against intracellular pathogens?
What can be inferred from studies in which immunodeficient mice infected with wild-type Bordetella experience lethal infection while those infected with a ΔcyaA mutant do not?
What can be inferred from studies in which immunodeficient mice infected with wild-type Bordetella experience lethal infection while those infected with a ΔcyaA mutant do not?
What is a key advantage of combining tagged bacteria with transgenic animals harboring reporter genes in biophotonic imaging studies?
What is a key advantage of combining tagged bacteria with transgenic animals harboring reporter genes in biophotonic imaging studies?
How have studies using cytokine receptor knockout mice impacted the methods for vaccine development?
How have studies using cytokine receptor knockout mice impacted the methods for vaccine development?
How does understanding the minor allele frequency of a SNP contribute to infection biology research?
How does understanding the minor allele frequency of a SNP contribute to infection biology research?
What is the significance of selecting quantitative traits as measures for disease risk when conducting GWAS?
What is the significance of selecting quantitative traits as measures for disease risk when conducting GWAS?
How do researchers use genetically modified animals to understand the role of host genes in infection and disease?
How do researchers use genetically modified animals to understand the role of host genes in infection and disease?
What is the main application of transgenic animal technology in studying infections?
What is the main application of transgenic animal technology in studying infections?
When scientists are using immunodeficient animals in infection research, what is often the goal of comparing responses to wild-type versus mutant bacterial strains?
When scientists are using immunodeficient animals in infection research, what is often the goal of comparing responses to wild-type versus mutant bacterial strains?
When researchers are studying how bacteria infect their host in real-time, why might they choose to focus on a living animal rather than just cells in a lab?
When researchers are studying how bacteria infect their host in real-time, why might they choose to focus on a living animal rather than just cells in a lab?
In studies examining the genetic variations that make individuals more or less susceptible to infections, what kind of variations are scientists typically looking for?
In studies examining the genetic variations that make individuals more or less susceptible to infections, what kind of variations are scientists typically looking for?
How does the approach of altering the genome or environment impact the study of host-microbe interactions?
How does the approach of altering the genome or environment impact the study of host-microbe interactions?
What happens when a SNP introduces a stop codon into the gene for Toll-like receptor 5 (TLR5)?
What happens when a SNP introduces a stop codon into the gene for Toll-like receptor 5 (TLR5)?
If scientists discover that a particular SNP is common among individuals with resistance to a certain infection, what might they conclude?
If scientists discover that a particular SNP is common among individuals with resistance to a certain infection, what might they conclude?
What is the purpose of using live animals with bacterial infections to conduct drug efficacy studies?
What is the purpose of using live animals with bacterial infections to conduct drug efficacy studies?
Why is it important to consider both direct and indirect associations when interpreting the results of genome-wide association studies (GWAS)?
Why is it important to consider both direct and indirect associations when interpreting the results of genome-wide association studies (GWAS)?
How does combining systems genetics with microbiome profiling enhance the understanding of host-microbe interactions?
How does combining systems genetics with microbiome profiling enhance the understanding of host-microbe interactions?
If an infection study reveals that TLR4 and TLR5 SNPs independently contribute to disease susceptibility, what does their combined effect suggest?
If an infection study reveals that TLR4 and TLR5 SNPs independently contribute to disease susceptibility, what does their combined effect suggest?
How does the use of gene replacement mice contribute to a deeper understanding of host-pathogen interactions?
How does the use of gene replacement mice contribute to a deeper understanding of host-pathogen interactions?
What is the benefit of comparing the host immune response in immunodeficient transgenic animals infected with wild-type bacteria versus those infected with mutant bacterial strains?
What is the benefit of comparing the host immune response in immunodeficient transgenic animals infected with wild-type bacteria versus those infected with mutant bacterial strains?
How did studies involving Nramp1 mutant mice enhance the understanding of host defense mechanisms against intracellular pathogens?
How did studies involving Nramp1 mutant mice enhance the understanding of host defense mechanisms against intracellular pathogens?
What conclusion was supported by studies using cytokine receptor knockout mice in the context of live vaccine development?
What conclusion was supported by studies using cytokine receptor knockout mice in the context of live vaccine development?
In the Bordetella adenylyl cyclase toxin (CyaA) infection model using immunodeficient mice, what key insight was gained about the role of adaptive immunity?
In the Bordetella adenylyl cyclase toxin (CyaA) infection model using immunodeficient mice, what key insight was gained about the role of adaptive immunity?
How does the genetic ablation technique, utilizing diphtheria toxin (DT), enable researchers to study specific gene functions in transgenic animals?
How does the genetic ablation technique, utilizing diphtheria toxin (DT), enable researchers to study specific gene functions in transgenic animals?
What is the primary advantage of using 'humanized' transgenic mice with human tissue xenografts in infection studies?
What is the primary advantage of using 'humanized' transgenic mice with human tissue xenografts in infection studies?
How did the 'humanized' transgenic mouse model expressing human E-cadherin contribute to understanding Listeria monocytogenes infection?
How did the 'humanized' transgenic mouse model expressing human E-cadherin contribute to understanding Listeria monocytogenes infection?
What is the utility of transgenic animals harboring inducible reporter gene fusions, such as the NFκB-responsive lacZ reporter, in infection studies?
What is the utility of transgenic animals harboring inducible reporter gene fusions, such as the NFκB-responsive lacZ reporter, in infection studies?
In the context of whole-body biophotonic imaging, why is red fluorescent protein (RFP) often favored over green fluorescent protein (GFP) when studying bacterial infections in animals?
In the context of whole-body biophotonic imaging, why is red fluorescent protein (RFP) often favored over green fluorescent protein (GFP) when studying bacterial infections in animals?
How can biophotonic imaging be used to study the dynamics of host gene expression in response to bacterial infections in vivo?
How can biophotonic imaging be used to study the dynamics of host gene expression in response to bacterial infections in vivo?
In Pasteur's recognition of host factors and Nicolle's observations of asymptomatic infections, how did the discovery of the sickle-cell anemia trait influence the understanding of host-pathogen interactions?
In Pasteur's recognition of host factors and Nicolle's observations of asymptomatic infections, how did the discovery of the sickle-cell anemia trait influence the understanding of host-pathogen interactions?
How do systems genetics approaches enhance our understanding of host-microbe interactions, beyond traditional genetic studies?
How do systems genetics approaches enhance our understanding of host-microbe interactions, beyond traditional genetic studies?
What is a primary aim of genome-wide association studies (GWAS) in the context of host response to bacterial infection?
What is a primary aim of genome-wide association studies (GWAS) in the context of host response to bacterial infection?
How does the concept of linkage influence the interpretation of results in genome-wide association studies (GWAS)?
How does the concept of linkage influence the interpretation of results in genome-wide association studies (GWAS)?
What information is typically represented in a Manhattan plot used in genome-wide association studies (GWAS)?
What information is typically represented in a Manhattan plot used in genome-wide association studies (GWAS)?
How does multilocus trait analysis (MLTA) improve upon single QTL analysis in GWAS?
How does multilocus trait analysis (MLTA) improve upon single QTL analysis in GWAS?
What can be concluded from the identification of a 'loss-of-function' SNP in TLR1 that is associated with decreased incidence of leprosy?
What can be concluded from the identification of a 'loss-of-function' SNP in TLR1 that is associated with decreased incidence of leprosy?
What can be inferred from studies where immunodeficient mice infected with wild-type Bordetella experience lethal infection, while those infected with a ΔcyaA mutant do not?
What can be inferred from studies where immunodeficient mice infected with wild-type Bordetella experience lethal infection, while those infected with a ΔcyaA mutant do not?
How do studies using cytokine receptor knockout mice influence vaccine development?
How do studies using cytokine receptor knockout mice influence vaccine development?
Beyond identifying individual genes, proteins, and metabolites, what is a broader application of host response profiling in infection research?
Beyond identifying individual genes, proteins, and metabolites, what is a broader application of host response profiling in infection research?
How might understanding the host transcriptome's response to complex microbial communities explain discrepancies in infection outcomes?
How might understanding the host transcriptome's response to complex microbial communities explain discrepancies in infection outcomes?
How can comparing host gene expression profiles after bacterial adherence help characterize bacterial virulence?
How can comparing host gene expression profiles after bacterial adherence help characterize bacterial virulence?
Why is qPCR recommended to verify microarray results when studying host gene expression during infection?
Why is qPCR recommended to verify microarray results when studying host gene expression during infection?
What is the primary advantage of using poly-A tail selection in RNA-Seq for eukaryotic transcriptomic analysis?
What is the primary advantage of using poly-A tail selection in RNA-Seq for eukaryotic transcriptomic analysis?
In the RNA-Seq study of lung cells infected with Streptococcus pneumoniae, what key finding suggested a mechanism for immune modulation by the bacteria?
In the RNA-Seq study of lung cells infected with Streptococcus pneumoniae, what key finding suggested a mechanism for immune modulation by the bacteria?
How does LCM enhance the study of host responses to infection within specific tissue regions?
How does LCM enhance the study of host responses to infection within specific tissue regions?
In the Y. pestis study using LCM, what conclusion was supported by comparing neutrophil transcriptional responses at different locations within lung lesions?
In the Y. pestis study using LCM, what conclusion was supported by comparing neutrophil transcriptional responses at different locations within lung lesions?
What is the initial step in 2D gel electrophoresis for proteomic analysis?
What is the initial step in 2D gel electrophoresis for proteomic analysis?
How can proteomic profiling of amniotic fluid be used during pregnancy?
How can proteomic profiling of amniotic fluid be used during pregnancy?
What is the primary use of multiplex cytokine profiling in infection studies?
What is the primary use of multiplex cytokine profiling in infection studies?
How do researchers reduce complexity in gel electrophoresis-based proteomic profiling when studying complex host cell signaling patterns?
How do researchers reduce complexity in gel electrophoresis-based proteomic profiling when studying complex host cell signaling patterns?
How have current differential 2D-gel approaches addressed limitations in comparing protein spots from different gels?
How have current differential 2D-gel approaches addressed limitations in comparing protein spots from different gels?
What is a major disadvantage of protein microarrays compared to gel-based proteomics?
What is a major disadvantage of protein microarrays compared to gel-based proteomics?
Why are isobaric tags (iTRAQ or TMT) used in gel-less proteomics?
Why are isobaric tags (iTRAQ or TMT) used in gel-less proteomics?
How can comparative immunoproteomics be used to study Helicobacter pylori infection?
How can comparative immunoproteomics be used to study Helicobacter pylori infection?
What is the primary goal of metabolic profiling (metabolomics)?
What is the primary goal of metabolic profiling (metabolomics)?
How can metabolomics be used to assess the degree of disease susceptibility of the host?
How can metabolomics be used to assess the degree of disease susceptibility of the host?
What is the benefit of combining metabolomics with transcriptomics and proteomics in infection research?
What is the benefit of combining metabolomics with transcriptomics and proteomics in infection research?
What is a major limitation of global genome-wide profiling in identifying virulence factors?
What is a major limitation of global genome-wide profiling in identifying virulence factors?
What is necessary to translate the massive amounts of data obtained through multi-omics approaches into coherent models of disease and virulence mechanisms?
What is necessary to translate the massive amounts of data obtained through multi-omics approaches into coherent models of disease and virulence mechanisms?
In studying host-microbe interactions, which factor is crucial for understanding disease progression and resolution of infection?
In studying host-microbe interactions, which factor is crucial for understanding disease progression and resolution of infection?
What is the primary purpose of upregulating the expression of colonic epithelial cell genes associated with growth and innate immune responses in germ-free mice reconstituted with commensal bacteria?
What is the primary purpose of upregulating the expression of colonic epithelial cell genes associated with growth and innate immune responses in germ-free mice reconstituted with commensal bacteria?
How do individual or combined effects of host gene expression influence the study of P. aeruginosa strains producing toxic effector proteins?
How do individual or combined effects of host gene expression influence the study of P. aeruginosa strains producing toxic effector proteins?
How were mutants of Y. enterocolitica with deletions in genes (YopP and YopM) used to determine protein functions?
How were mutants of Y. enterocolitica with deletions in genes (YopP and YopM) used to determine protein functions?
What is the advantage of using RNA-Seq technology in infection transcriptomics from a host-microbe perspective?
What is the advantage of using RNA-Seq technology in infection transcriptomics from a host-microbe perspective?
How do bioinformatics analysis and chimeric genome sequences benefit the RNA sequencing process?
How do bioinformatics analysis and chimeric genome sequences benefit the RNA sequencing process?
What is a practical application of understanding the reduction of host epithelial genes associated with innate immune responses?
What is a practical application of understanding the reduction of host epithelial genes associated with innate immune responses?
What is a key benefit of qPCR analysis following laser-capture microdissection (LCM) and cDNA conversion?
What is a key benefit of qPCR analysis following laser-capture microdissection (LCM) and cDNA conversion?
What does the finding that expression profiles of neutrophils at the center of highly inflammatory microenvironments resembled those of unstimulated bone marrow neutrophils suggest?
What does the finding that expression profiles of neutrophils at the center of highly inflammatory microenvironments resembled those of unstimulated bone marrow neutrophils suggest?
What is the significance of analyzing the protein patterns in amniotic fluid?
What is the significance of analyzing the protein patterns in amniotic fluid?
How has multiplex cytokine profiling advanced our ability to determine the molecular basis of the host’s inflammatory response?
How has multiplex cytokine profiling advanced our ability to determine the molecular basis of the host’s inflammatory response?
What is an innovative approach some researchers have taken to overcome the complexity of spot patterns in gel electrophoresis for proteomic profiling?
What is an innovative approach some researchers have taken to overcome the complexity of spot patterns in gel electrophoresis for proteomic profiling?
The translated genome sequence can be used to predict the tryptic peptide profiles of all the proteins encoded by the study organism; how can this process be useful?
The translated genome sequence can be used to predict the tryptic peptide profiles of all the proteins encoded by the study organism; how can this process be useful?
Why is it useful to assess the host’s immune response in order to identify bacterial origins of disease?
Why is it useful to assess the host’s immune response in order to identify bacterial origins of disease?
What can be suggested from identifying commonalities and distinctions between host responses associated with different gastric diseases?
What can be suggested from identifying commonalities and distinctions between host responses associated with different gastric diseases?
In the context of metabolic profiling, what do the metabolites and their relative composition reflect?
In the context of metabolic profiling, what do the metabolites and their relative composition reflect?
What are common problems researchers run into that should be considered when evaluating global genome-wide profiling?
What are common problems researchers run into that should be considered when evaluating global genome-wide profiling?
What is the primary advantage of using RNA-Seq over microarray technology for transcriptomic analysis?
What is the primary advantage of using RNA-Seq over microarray technology for transcriptomic analysis?
How does laser-capture microdissection (LCM) enhance the study of host responses to infection?
How does laser-capture microdissection (LCM) enhance the study of host responses to infection?
In proteomic profiling, what is the purpose of separating proteins using two-dimensional (2D) gel electrophoresis?
In proteomic profiling, what is the purpose of separating proteins using two-dimensional (2D) gel electrophoresis?
How can metabolic profiling (metabolomics) be used to assess the degree of disease susceptibility in a host?
How can metabolic profiling (metabolomics) be used to assess the degree of disease susceptibility in a host?
Which of the following describes how transcriptomics reveals insights into host-microbe interactions?
Which of the following describes how transcriptomics reveals insights into host-microbe interactions?
How does comparing host gene expression profiles after bacterial adherence contribute to characterizing bacterial virulence?
How does comparing host gene expression profiles after bacterial adherence contribute to characterizing bacterial virulence?
What is the purpose of performing poly-A tail selection in RNA-Seq analysis of eukaryotic transcriptomes?
What is the purpose of performing poly-A tail selection in RNA-Seq analysis of eukaryotic transcriptomes?
What does the downregulation of genes involved in leukocyte migration and apoptotic pathways in the center of lung lesions infected with Y. pestis suggest?
What does the downregulation of genes involved in leukocyte migration and apoptotic pathways in the center of lung lesions infected with Y. pestis suggest?
How can proteomic profiling of amniotic fluid be used in clinical diagnostics?
How can proteomic profiling of amniotic fluid be used in clinical diagnostics?
Why were isobaric tags (iTRAQ or TMT) developed for proteomics?
Why were isobaric tags (iTRAQ or TMT) developed for proteomics?
What is the role of computational integration of 'omics' data in studying host-pathogen interactions?
What is the role of computational integration of 'omics' data in studying host-pathogen interactions?
Based on the text, what factor is crucial for understanding disease progression and the resolution of infection?
Based on the text, what factor is crucial for understanding disease progression and the resolution of infection?
What findings can be used to assess to bacterial origins of disease?
What findings can be used to assess to bacterial origins of disease?
What occurs so there is an up regulation in the expression of colonic epithelial cell genes associated with growth and innate immune responses in germ-free mice reconstituted with commensal bacteria?
What occurs so there is an up regulation in the expression of colonic epithelial cell genes associated with growth and innate immune responses in germ-free mice reconstituted with commensal bacteria?
What is an advantage of the proteins on a protein microarray chip?
What is an advantage of the proteins on a protein microarray chip?
What tool is used for assessing the immune status of a patient and discerning the molecular basis of the host inflammatory response?
What tool is used for assessing the immune status of a patient and discerning the molecular basis of the host inflammatory response?
How can scientists determine protein functions using mutants of Y. enterocolitica with deletions in specific genes?
How can scientists determine protein functions using mutants of Y. enterocolitica with deletions in specific genes?
What is facilitated by the the incorporation of mass tags into mass spectrometry?
What is facilitated by the the incorporation of mass tags into mass spectrometry?
Flashcards
Transgenic animal models
Transgenic animal models
Genetically modified animals used to study infection; altered to reveal gene roles.
Knockout mice
Knockout mice
Mice with a specific gene inactivated to observe the effects of its absence.
Knockin mice
Knockin mice
Mice with a new gene introduced to study its role.
Humanized mice
Humanized mice
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Understanding infection w/ transgenic models
Understanding infection w/ transgenic models
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InIA protein
InIA protein
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Immunodeficient animal models
Immunodeficient animal models
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SCID Mice
SCID Mice
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Tracking infection in animals
Tracking infection in animals
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GWAS
GWAS
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Manhattan plots (GWAS)
Manhattan plots (GWAS)
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Understanding host immune responses
Understanding host immune responses
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Systems genetics and comparative genomics
Systems genetics and comparative genomics
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Gene silencing
Gene silencing
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Gene editing
Gene editing
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RNA interference (RNAi)
RNA interference (RNAi)
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RISC
RISC
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RNAi libraries
RNAi libraries
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Off-target effects
Off-target effects
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CRISPR-Cas9
CRISPR-Cas9
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Homology-directed repair (HDR)
Homology-directed repair (HDR)
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Non-homologous end joining (NHEJ)
Non-homologous end joining (NHEJ)
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CRISPR-Cas9 in infection research
CRISPR-Cas9 in infection research
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V. parahaemolyticus
V. parahaemolyticus
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Studying host responses to infection
Studying host responses to infection
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Transcriptomics
Transcriptomics
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Microarray technology
Microarray technology
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RNA-Seq technology
RNA-Seq technology
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RNA-Seq advantages
RNA-Seq advantages
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Dual RNA-Seq
Dual RNA-Seq
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Laser-capture microdissection (LCM)
Laser-capture microdissection (LCM)
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Metabolomics
Metabolomics
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Targeted metabolomics
Targeted metabolomics
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Untargeted metabolomics
Untargeted metabolomics
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Metabolomics applications
Metabolomics applications
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Transcriptomics in Multi-omics
Transcriptomics in Multi-omics
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Proteomics in Multi-omics
Proteomics in Multi-omics
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Metagenomics in Multi-omics
Metagenomics in Multi-omics
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Glycomics in Multi-omics
Glycomics in Multi-omics
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Future goal of Metabolomics
Future goal of Metabolomics
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Genome-wide screening
Genome-wide screening
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Short interfering RNA (siRNA)
Short interfering RNA (siRNA)
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RNAi off-target effects
RNAi off-target effects
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α-hemolysin
α-hemolysin
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ADAM10
ADAM10
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ADAM10 regulator
ADAM10 regulator
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Sphingomyelin synthase 1 (SGMS1)
Sphingomyelin synthase 1 (SGMS1)
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SYS1
SYS1
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ADP-ribosylation factor 1 (ARF1)
ADP-ribosylation factor 1 (ARF1)
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Type 3 secretion system (T3SS)
Type 3 secretion system (T3SS)
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Protospacer-adjacent motif (PAM)
Protospacer-adjacent motif (PAM)
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Single guide RNA (sgRNA)
Single guide RNA (sgRNA)
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Loss-of-function screen
Loss-of-function screen
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Gene knockout
Gene knockout
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Gene knockin
Gene knockin
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Gene-edited mice
Gene-edited mice
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Nramp1
Nramp1
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Cytokine receptor knockout mice
Cytokine receptor knockout mice
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Bordetella adenylyl cyclase toxin (CyaA)
Bordetella adenylyl cyclase toxin (CyaA)
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Genetic ablation
Genetic ablation
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NFκB-responsive reporter mice
NFκB-responsive reporter mice
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Whole-body biophotonic imaging
Whole-body biophotonic imaging
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Systems genetics
Systems genetics
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Single Nucleotide Polymorphism (SNP)
Single Nucleotide Polymorphism (SNP)
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Minor allele frequency
Minor allele frequency
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Collaborative Cross (CC) and Diversity Outbred (DO) mice
Collaborative Cross (CC) and Diversity Outbred (DO) mice
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Manhattan plot
Manhattan plot
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Toll-like receptor 5 (TLR5)
Toll-like receptor 5 (TLR5)
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Toll-like receptor 4 (TLR4)
Toll-like receptor 4 (TLR4)
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Proteomics
Proteomics
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Multiplex Cytokine Profiling
Multiplex Cytokine Profiling
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Multi-omics approach
Multi-omics approach
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Immunoproteomics
Immunoproteomics
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Two-dimensional (2D) gel electrophoresis
Two-dimensional (2D) gel electrophoresis
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biomarkers
biomarkers
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Differential 2D-gel approaches
Differential 2D-gel approaches
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Isobaric tags for relative and absolute quantitation (iTRAQ or TMT)
Isobaric tags for relative and absolute quantitation (iTRAQ or TMT)
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Study Notes
Host Response Profiling
- Host transcriptional, proteomic, and metabolomic responses to infection are used to identify host factors involved in pathogenicity.
- It allows for monitoring host responses to bacterial colonization and infection on a global scale.
- Numerous innate immune factors are consistently up- or downregulated in host cells infected with pathogenic bacteria.
- Commensal bacteria can upregulate expression of colonic epithelial cell genes associated with growth and innate immune responses, even in germ-free mice.
Transcriptomics
- The host's transcriptional response (transcriptome) can be specific to the microbial challenge.
- Microarray and Illumina RNA-Seq provide expression profiles of thousands of genes, identifying genes turned on or off under different conditions.
- Host transcriptome response to microbial communities may influence phenotypic outcomes differently than individual microbes alone.
Microarray and RNA-Seq Technologies
- Microarrays were first used to identify and monitor genes regulated by immune cytokines like interferons.
- Microarrays have been used to profile the host response to bacterial pathogens like S. enterica, and bacterial factors like LPS.
- Changes in host gene expression profiles are compared following bacterial adherence or infection with wild-type versus mutant bacteria to characterize contributions of virulence factors.
- The host responses to bacterial effector proteins can reveal transcriptome patterns consistent with the functions of these proteins.
- Challenges with microarray technology include normalization difficulties, determining significant gene expression changes, and data interpretation.
- Quantitative real-time PCR (qPCR) is recommended to verify interesting differences found via microarrays.
- Illumina RNA-Seq is a superior method for genome-wide transcriptomic analysis.
- RNA-Seq methods for eukaryotes often use poly-A tail selection to capture mature mRNA transcripts.
- RNA-Seq can analyze transcriptomic changes in both the host and microbe during infection.
- Comparative analysis can reveal host epithelial glutathione-associated genes activated in response to pneumococcal genes producing reactive oxygen species.
- Mutant bacteria lacking capsule may repress host epithelial genes associated with innate immune responses.
Laser-Capture Microdissection (LCM)
- LCM isolates selected single cells or small groups of cells from tissue sections.
- LCM enables the measurement of host responses at the site of infection and can extract RNA, DNA, or proteins, which can be then be analyzed.
- Combining LCM with RNA-Seq allows researchers to interrogate host response to microbes on a genome-wide scale.
- LCM characterized gene expression in host neutrophils in distinct locations within pneumonic plague lung lesions during Y. pestis infection.
- Results showed that the expression profiles of neutrophils at the center of pneumonic lesions resembled that of unstimulated bone marrow neutrophils.
Proteomics
- Proteomic profiling complements transcriptomics, especially when the host response is at the translational or post-translational level.
- Two-dimensional (2D) gel electrophoresis separates proteins in a specimen to form a pattern of protein spots.
- Proteins are separated by isoelectric focusing (IF) based on isoelectric point (pI) and further separated by polyacrylamide gel electrophoresis (PAGE) based on molecular size.
- Proteomic profiling determines protein expression patterns and can be used as a diagnostic tool.
- Changes in amniotic fluid protein patterns can indicate possible infection and risk of preterm delivery or neonatal sepsis.
- Proteomic profiling identifies factors recognized by antibodies generated during infection and distinguishes between different host responses.
- Multiplex cytokine profiling assesses the immune status of a patient and characterizes immunomodulatory effects of bacterial virulence factors.
- Challenges in gel electrophoresis-based proteomic profiling include complex host cell signaling patterns and numerous splice variants.
- Subcellular compartments, such as phagosomes or nuclei, can be separated to overcome complexity.
- Current differential 2D-gel approaches use protein microarrays and automation to overcome previous serious problems through standardization.
- Robotics coupled with instrumentation has made protein identification in 2D gels or protein microarrays routine.
- Proteins on a protein microarray chip can be directly sampled for binding to proteins in extracts.
- Protein microarrays require the production of antibodies to specific proteins and the proteins themselves with good yield, purity, and stability.
- Gel-less or chip-less proteomics are based on high-resolution mass-spectroscopy of protein or tryptic peptide mixtures.
- Isobaric tags (iTRAQ or TMT) must be reacted with tryptic peptide digests, separated by HPLC, and analyzed by tandem mass spectrometry (MS/MS) to determine relative amounts of proteins.
- LCM technology can be used to selectively capture different cell types from tissue samples, which can then be further subjected to separation of content by HPLC and protein identification by mass spectrometry.
- Immunoproteomics uses proteomics to assess the host’s immune response to identify bacterial origins of disease.
- Comparative immunoproteomics can identify bacterial antigens that give common versus distinct host responses associated with different gastric diseases.
Metabolomics
- Comparing metabolic profiles (metabolomics) identifies biomarkers that discriminate healthy from diseased individuals.
- Metabolic profiling identifies and quantifies metabolites associated with a metabolic pathway of interest to genome-wide metabolic reconstructions of entire metabolic networks.
- Monitoring perturbations in the metabolite composition of microbiomes and the host environment can reveal signatures indicative or predictive of infection and/or disease outcome.
- Distinctive associations exist between certain microbes in a community within the host and the metabolites produced.
- Multi-omics, combining metabolomics with transcriptomics and proteomics, links genotype and phenotype.
- This multi-omics approach can reveal connectivity of multiple metabolic or signaling pathways involved in host response to immune challenges.
- Genome-scale metabolic profiling can be implemented.
Caution Regarding Host Response Profiling
- Profiling analysis is limited by the large number of "genes of unknown function" in genome databases, as well as incorrectly annotated genes.
- Global genome-wide profiling, researchers have just begun to explore.
- Multi-omics is used to gain insights about gene functions and annotate with confidence the remaining genes.
- A clear hypothesis and critical biologically oriented thinking are necessary elements to translate data into coherent models of disease and virulence mechanisms.
- Understanding complex interactions between pathogens and their host requires a comprehensive knowledge of the role of bacterial virulence factors in disease progression, host factors, prior exposure history, and interplay during infection.
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