Vaccines > Pan genome (lecture 3) Flashcards
What is “in silico”?
and its relevance in vaccinology
Performed by a computer.
Its based on the genome sequence and its prediction of secreted/exposed proteins (putative antigens)
What is the limitation of in silico genomics?
Requires the genome sequence
Not possible for in vivo antigens
Requires high throughput cloning and protein expression experiments to validate predictions
not systematically validated
How many genes do the following organisms have?
Staphlococcus aureus
Mycobacterium tuberculosis
Staphlococcus aureus - 2600
Mycobacterium tuberculosis - 4000
What is a signal peptide?
A signal that is within a secreted protein.
A signal peptide is made of positively charged N-region, Hydrophobic H-region and a polar, neutral C-region.
What is hydrophobicity plot?
signal peptide
A plot that determined number of transmembrane helices
What is the “positive inside rule”? (signal peptide)
Positively charged amino acids are abundant on the citoplasmic side of the membrane
What do on-line tools predict in respect to putative secreted proteins?
It predicts sub-cellular localisation of proteins, specifically it can differentiate proteins as being intracellular, extra-cellular,periplasmic,membrane bound or integral.
E.g P-sort predicts sub-cellular localisation in +ve/-ve bacteria
Predictions needs to be confirmed experimentally
Outline the history of reverse vaccinology
1995 - H.influenza sequenced
2000- Men.B 1 genome, 28novel protective antigens
2003- GBS, 8 genomes, 4 protective pilin antigens
2005- GAS, 5 genomes, 3 pilin antigens
2006-S.pneumoniae, 3 protective pilin antigens
2010-E.coli, 8 pathogens, 1 non pathogenic
2011-structural vaccinology. Chimeric MenB, GBS antigens.
Outline the difference between vaccinology 2000,2012
2000: 1) ORF prediction- of an isolated genome (ZCURVE) 2)cellular localisation - based on the genome (PSORT) 3)Express candidate proteins followed by animal testing, FACS 4)Identifying possible candidates and looking at immunogenicity followed by epidemiology. Look at possible coverage if multiple strains present 5)Combination vaccine
2012:
1) ORF prediction: Initiate by look at epidemiology of hundreds of isolates, sequencing RNA.
2) Cellular localization- Compare the pan-genome of multiple strains and looking at homology of expressed proteins and looking at their cellular localization.
3)In-vivo expression-
Analyses of candidate surface proteins found. Microarrays used to see genes expressed during infection
4)Vaccine candidates found, (expressed during infection). Purification of candidate.
5) Isolating protective candidates
6) Combination vaccine
What are ____?
Core genes
Strain specific genes
Dispensable genes
Core genes - Genes shared between all the known strains
Dispensable genes - Genes shared by some strains
Strain specific genes - Genes only present in 1 strain.
Does the pan genome grow relative to genomes in ____?
Bacillus anthracis
Streptoccus agalactiae
Bacillus anthracis- NO
Streptoccus agalactiae- YES
What is the open pan genome?
A genome that continously grows for each new strain added.
S.agalactiae; 2713 pan genes 1803 core genes 907 dispensable genes 33 genes for new genome sequenced
E.coli:
2865 genes (7genomes)
441 new genes per new genome.
What is the closed pan genome?
When addition of a new genome does not contribute to the pan genome.
Bacillus anthracis
Mycobacterium tuberculosis
Chlamydia trachomatis
What factors influence vaccine efficacy?
Age Gender Ethnic origin Number of doses Route of immunization
What is vaccinomics?
Combination of immunogenetics and immunogenomics
