Class Notes (839,559)
Canada (511,394)
Immunology (194)
IMM250H1 (167)
all (42)
Lecture

06 - February 12, 2013.docx

5 Pages
120 Views

Department
Immunology
Course Code
IMM250H1
Professor
all

This preview shows pages 1 and half of page 2. Sign up to view the full 5 pages of the document.
Description
February 12, 2013 – The microbiome in immune system development, function and disease Diversity of genes of microbiome >>>>> human genome Large scale projects to map human microbiomes – Metagenomics – without prior culture – these organisms discussed today are difficult to culture, does not like to live as single organisms Probiotic – do not colonize humans; come largely from cows and non-humans; cultured in labs; not part of humans, go through us Prebiotics – foodstuffs – promote growth of beneficial bacteria – Commensal bacteria – bacteria that are part of us; million genes – display mutually beneficial interactions with us – critical for nutrition, metabolism, etc – bacteria in intestines that without whom, we cannot digest food; they make vitamins – critical!! High through put sequencing – method of choice when confronted with the diversity 16S ribosomal gene – all bacteria have this gene Moutains and valleys of diversity – make sets of oligonucleotide primers based on conserved regions of gene, PCR amplify, make libraries of amplicons; these amplicons include more variable regions where the sequences used to distinguish – DNA Isolate DNA Barcodes and adaptors – isolate DNA from fifty samples, second round of PCR to add barcodes to distinguish hem from each other, and have them sequenced all together – this increases efficiency – use computorial approach to individualize the fifty samples Quantitative – can determine frequency of given group of bacteira in A and B? Map of diversity in human microbiome – sequence microbiota from different sources from internal and external body Take 16S data from large samples and try to organize by making sense of bacteria – taxonomic group of bacteria contained in samples Phylogenetic map of microbial diversity – many different parts of body evaluated – height of bars displays relative abundance of groups of bacteria Include opportunistic pathogens – ex. Surveying lungs of cystic fibrosis patients vs controls – Survey health and disease states of bacteria Microbiome diversity – other sets of algorithms to try to affiliate variable parts of sequences with KNOWN bacteria, which we have good sequences (this does not include majority of bacteria in gut) OTU- operational taxonomic unit – unknown whether strain or species – operational definition, no external meaning Sequences are related to each other in phylogenetic tree – representation of any of OTU grouping is collated in table – more biological replicates, the better the statistical analysis – generate massive OTU tables What is the diversity of the flora? New approach – shotgun metagenome sequencing – take all the genomic DNA From the sample of gut or fecal matter – blast apart into tiny fragments, put tags on ends, and high throhgput sequence them – when reassemble the sequences – try to relate them to all bacteria genes in databases – for sample 1 through 4, what are the frequency of – get back hundreds of millions of sequences – computational – compare samples to each other regarding frequency of different genes in them – No reference genome – What factors?? – how do they correlate with overall composition of bacteria – Principle component analysis – statistical method – take complex data set and find structure inside of it EX. Enterotype – change in microbial diversity in gut as function of age on left Red – young; blue – old Signatures can be found that distinguish the groups On the right – Malawi and Central America – more similarity than USA Order out of seeming chaos Left side – regular sequencing using 16S – diversity in OUT, taxonomy Right side – using shotgun sequencing – similarity Many different combinations ofbacteria that can confer optimal function in given environment – shown in this comparison – do not get hung up on Diversity – how and when people acquire gut microbiota – Correlating changes in intestinal microbiome with milestones in life – lots of variation of proportion of major phyla over time – but later in life, Environmental factors affecting human microbiota – Seniors have far less stability in gut flora – more likely subject to infection by enteric pathogens Gut epithelial barrier In inner lumen of colon – 10^12 g bacteria One cell thick layer of epitheial that separtes that density to essentially zero Need to avoid innate immune sensing of bacteria – compromise the one-cell thick barrier and deliver into systemic immune system bacteria that will disturb metabolic Immune system on the zero side of bacteria barrier/epithelium Stratification – luminal side to cellular side – in lumen of small intestine and large intestine Small intestine –w here vast majority of nutrients absorbed, need access to metabolic products and nutrients produced by commensal bacteria – Large intestine – density of bacteira very high – outer mucus layer that is essential to keeping bacteria- rich regions segregated from inner layer, which is more bacteria-poor Mucus – mixture of differnet molecules – produced by goblet cells – secrete mucin-rich proteins, important for repairing tears in gut – these cells turnover at RAPID rate – Goblet cells also receiving input from bacteria products – production of mucins regulated by bacteria products there – a number of bacteria groups called peptidoglycan – stimulate secretion of mucus – short chain fatty acids and low molecular fatty acids (butarate) that cause increase in release of mucins – two way interaction to produce stratification – feedback loop Mouse expts – one mucin-producing enzyme, Muc2 – knockout – increased translocation of commensal bacterial into systemic circulation, reduced integrity of lining of epithelium – The mucus layer also – segmented filamentous bacteria line epithelial interfaces – biofilims help exclude pathogens – ecology problem, competing for space – high fitness of commensal bacteria helps exclude pathogenic bacteria competing the niches – Stratification II – epitheial cells that line the gut make series of specialized antimicrobial peptides – paneth cells – make antimicrobial peptides called alpha defensins – related to defensins that amphibians have on skin – Inner mucus layer is kill zone – concentration of a number of differnet host secreted factors – closer to the wall, heavier the armament becomes Antimicrobial lectin – Generation of secreted IgA – IgA is commensal cell specific – ferried across epitheial surface on specialized immunoglobulin receptor – Microbe-specific IgA – present in high concentration in barriers – contribute to limiting bacterial penetration Some bacteria do get throug
More Less
Unlock Document

Only pages 1 and half of page 2 are available for preview. Some parts have been intentionally blurred.

Unlock Document
You're Reading a Preview

Unlock to view full version

Unlock Document

Log In


OR

Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


OR

By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.


Submit