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Bacterial Pathogenesis > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

What is empiricism?

A

Theory that knowledge is derived from sensory evidence

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2
Q

What is determinism?

A

Notion that events are determined by existing laws and causes

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3
Q

What is skepticism?

A

Notion that any proposition is open to question and critique?

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4
Q

What is the first step of PCR and what temperature does it take place at?

A

Denaturation; 95 degrees

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5
Q

What is the second step of PCR and approximately what temperature does it occur at?

A

Annealing (attachment of primers to the template strands); about 50 degrees

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6
Q

What is the third step of PCR and what temperature does it occur at?

A

Extension; 72 degrees

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7
Q

What antibiotics bind to the 50S ribosomal subunit, prevent peptide bond formation, and stop protein synthesis?

A

Chloramphenicol, macrolides, and lincosamides

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8
Q

What class of antibacterials bind to the 30S ribosomal subunit, impair proofreading and result in production of faulty proteins?

A

Aminoglycosides

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9
Q

What class of antibacterials bind to the 30S ribosomal subunit, block the binding of tRNAs and inhibit protein synthesis?

A

Tetracyclines

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10
Q

Which microbiota resident is a huge player in breaking down polysaccharides?

A

Bacteroides thetaiotaamicron (B. theta)

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11
Q

What are the two dominant phyla of the human gut microbiota?

A

Bacteroides and Firmicutes

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12
Q

What well known microbiota resident is a member of the Firmicutes phyla?

A

Clostridium spp.

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13
Q

What are two lower prevalence microbes of the human gut microbiota?

A

E. coli and Methanobrevibacter smithii (a symbiotic archaea species)

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14
Q

What does E. coli do for us?

A

Helps produce vitamin K

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15
Q

What does M. smithii do for us?

A

Helps remove excess hydrogen

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16
Q

What are three examples of microbiota immune function?

A
  1. Resident microbes inhibit colonization of pathogens, 2. Inducing cross-protective immunity, 3. Guides immune system development
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17
Q

What microbiota immune function is this an example of?

“Intestinal load of Salmonella is highest in mice with reduced or no microbiota.”

A

Colonization resistance

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18
Q

What microbiota immune function is this an example of?

“Microbiota can stimulate immune cells to produce cytokines that protect against pathogens.”

A

Cross-protective immunity

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19
Q

What cytokines produced by cross-protective immunity are known as for protection against Toxoplasma gondii?

A

IL-12 and IFN-gamma

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20
Q

What is an example of microbes guiding immune cell development?

A

Filamentous bacteria guide a naive T cell to develop into a TH17 lymphocyte, which secretes IL-17 and promotes inflammation.

Clostridium spp. guides naive T cell to become a Treg cell, which secretes cytokines that suppress inflammation.

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21
Q

What is regIII?

A

A lectin that separates microbiota from small intestine epithelial surface; expression is induced by microbiota but produced by epithelium

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22
Q

What type of bacteria does RegIII target?

A

Gram positive peptidoglycan

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23
Q

What is essential for maintaining osmotic pressure of bacteria?

A

Peptidoglycan cell walls

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24
Q

What histological technique was used to visualize the neutral zone between the intestinal epithelium and the microbiota?

A

Fluorescent In Situ Hybridization (FISH)

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25
Q

What protein has been shown to be responsible for the neutral zone?

A

MyD88

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26
Q

What does MyD88 induce?

A

The secretion of antimicrobial peptides

27
Q

What activates MyD88 to trigger the secretion of AMP?

A

The binding of a pathogen-associated molecular pattern (PAMP) to a toll-like receptor on the surface of an epithelial cell.

28
Q

What does MyD88 activate in all cases?

A

NF-kB, a transcription factor that directs the expression of AMP genes (including RegIIIy)

29
Q

What is the purpose of antimicrobial peptides released from intestinal epithelial cells?

A

To limit microbiota interaction with intestinal epithelia to prevent invasion and infection

30
Q

What is the difference between horizontal gene transfer and vertical gene transfer?

A

Vertical gene transfer involves the passing along of genes to offspring, such as to daughter bacterial cells during binary fission. Horizontal gene transfer is faster because it happens when DNA is taken up by a bacteria and integrated into their genome or kept as a plasmid. This can happen via transformation, transduction, or conjugation.

31
Q

Why doesn’t horizontal gene transfer happen often in eukaryotes?

A

Chromosomes are in the membrane-bound nucleus and genetic info is transferred primarily by sexual reproduction. Our cells have great defenses for preventing foreign DNA from entering. The DNA must get into the nucleus and incorporate, then must survive RNA splicing. The protein must be useful to be selected. Codon bias.

32
Q

What is an example of horizontal gene transfer in eukaryotes?

A

Our mitochondria are the result of an endosymbiosis of a bacterium that occurred over 2 million years ago. Most mitochondrial genes transferred to the nuclear genome, leaving about 40 genes in the mitochondria. To this day, the mitochondrial genome is circular like a bacterium’s. All of its genes code for energy production.

33
Q

What is the most common way for HGT to occur?

A

Via transformation

34
Q

What are a few characteristics of HGT that happens via transformation?

A

The donor and recipient do not need to be there at the same time. It can occur across different species. The efficiency depends on the competency of the recipient, though electricity and chemicals can be used to promote uptake in the lab.

35
Q

What are some characteristics of HGT that happens via transduction?

A

DNA size is limited by capsid. The recipient must be able to uptake the phage (have the correct receptors).

36
Q

What are some characteristics of HGT that happens via conjugation?

A

Cells must be in the same space and have the ability to conjugate. DNA is transferred via plasmid.

37
Q

What is an example of plasmid-acquired antibiotic resistance?

A

Metallo-beta-lactamase gene in Klebsiella pneumoniae, first seen in New Delhi in 2009 and found in the UK and US by 2010 (all patients had received treatment in India)

38
Q

What are some examples of how transferred DNA is replicated and passed on?

A

Episomal replication (plasmids), integration along with phage genomes or transposable elements, homologous and non-homologous recombination

39
Q

List examples of obstacles to HGT.

A

DNA instability in new host, restriction enzymes, codon usage incompatibility, lack of appropriate interacting genes or pathways

40
Q

What are restriction enzymes?

A

Endonucleases that cleave foreign DNA into fragments at specific sequences

41
Q

What is a structural difference that has been found between integrated DNA and the rest of the chromosomal DNA?

A

Differing G-C content.

42
Q

An area of lower G-C content that contains integrated DNA that contributes to increased virulence in the host is called a:

A

Pathogenicity island

43
Q

What is an example of a pathogenicity island?

A

The locus of enterocyte effacement (LEE) found in EHEC and EPEC (enteropathogenic and enterohemorrhagic E. coli)

44
Q

Why does the LEE make EHEC and EPEC so much more pathogenic than regular E. coli?

A

Genes of intimin adhesins are included in the pathogenicity island, which allows the bacteria to bind tightly to intimin receptors on epithelial cells of the intestine. This causes attaching and effacing lesions. They secrete Esp proteins into the cytosol of the affected cell, which also contribute to A&E lesions.

45
Q

What is a host-derived mechanism that increases the virulence of LEE genomic island?

A

The LEE genomic island is unregulated by the presence of our own stress hormones. Epinephrine and norepinephrine induce the A&E lesions, making the disease process worse.

46
Q

What are characteristics of HGT sequences that assist researchers in identifying them?

A

Often have unusual sequence characteristics, signatures of other genomes can be present. They are often flanked by repeat elements (phages and transposons) or tRNAs (where integration is common). Gene tree is very different from species tree. Detection of variable gene sequences in isolates of the same species.

47
Q

What do we call DNA molecules made by bringing genetic material from multiple (foreign) sources, creating a sequence that would not otherwise by found in the genome?

A

Recombinant DNA

48
Q

What are some ways in which we use PCR?

A

Genetic counseling (checking to see if you have the gene connected with an illness), pathogen identification, identifying an active infection (COVID), forensic analysis

49
Q

What are the ingredients of PCR?

A

Template DNA, dNTPs, primers, DNA polymerase from Thermus aquaticus (high heat tolerance).

50
Q

What does :: denote?

Example: mecA::Kn^R

A

An insertion into the gene

51
Q

How are genes denoted using genetic nomenclature? How are the protein products of those genes denoted?

A

Genetic pathways are denoted by three lowercase letters that indicate their pathway or process (rpo), followed by a capital letter signifying the actual gene (A). Protein products and phenotypes are capitalized and not italicized (RpoA).

52
Q

What does a delta sign or a “-“ indicate?

A

A mutation in which the entire coding region has been removed from the chromosome.

53
Q

What does a superscript R denote?

A

Resistant

54
Q

What does a single : or a “-“ between genes indicate?

Example: mecA:Kan^R or mecA-Kan^R

A

A gene fusion - both genes are still active

55
Q

How is a protein fusion denoted?

A

RpoA:Cam^R or RpoA-Cam^R

56
Q

What are selectable markers?

A

Genes introduced in a cell that confer a trait suitable for artificial selection.

57
Q

What is a positive selection?

A

An advantageous genetic determinant - looking for what survives. For example, acquiring an antibiotic resistant gene that promotes survival.

58
Q

What is a negative selection?

A

Removal of deleterious alleles - looking for what dies. For example, looking for mutations that lead directly to death

59
Q

What are the benefits of whole genome sequencing? What technique is used for sequencing?

A

It can determine if a bacterium is pathogenic or has antibiotic resistance, find mutations, genetic anomalies, perform comparative genomics, phylogenetic analysis, transmission mapping, etc. Total DNA is fragmented and sequenced with Illumina.

60
Q

What sequencing technique offers insight into relative changes in gene expression of bacteria?

A

RNA sequencing

61
Q

What are the steps involved in RNA sequencing?

A

Isolate total RNA, deplete rRNA, use reverse transcriptase to synthesize cDNA, add adaptors and amplify, align sequences to reference genome.

62
Q

What is Tn-Seq?

A

Transposon sequencing: a pool of bacteria is randomly mutagenized with transposons (1 transposons per chromosome) and allowed to grow under various conditions. Regions of Tn insertion are isolated using PCR-ligate adapters and sequenced. Sequences are aligned to an annotated genome.

63
Q

What is Tn-Seq useful for?

A

Provides fitness data or genes that are important for survival in a particular environment, such as virulence factor. Can also determine positive or negative selection events based on which genes were knocked out due to the transposon insertions.

Bacterial Pathogenesis (1 decks)

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