ESPM 131 Lecture Notes - Lecture 17: Human Genome Project, Chitinase, Microbial Ecology
14 May 2018
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Course
Professor
■Quantification - abundance:
●Relative : gives position/fitness of organism in community, percent
○Microarrays
○May give changes in relative abundance
●Actual : number in community, better for relating microbes to process
rates
○Microscopy : label cells w/ DNA probe to ID/count
■Fluorescence in situ hybridization (FISH) : analysis of
relative densities and spatial patterns
■Daime : digital image analysis in microbial ecology,
co-aggregation/syntrophy
○Quantitative PCR : analyze prod accum during exponential
phase
○Monitoring functions:
■bio(geo)chem:
●Monitor response
●Determine in situ enzyme activity/potential
○Fluorogenetically-labeled substrates (MUB) , enzyme activity
results in luorescent signal
●Can’t ID organisms carrying out function
■Functional gene presence:
●N cycle: ammonia ox (amoA)/denitrification (narG, nirS, nosZ)
●C cycle: cellulose, lignin, chitinase, methanogenesis, methane ox
■Known functional genes:
●Low number of targets: cloning-seq, qPCR, qRT-PCR (mRNA)
●High number of targets: microarrays ( GeoChip ), next gen sequencing
○Phylogeny = function?
■Sometimes it works: nitrososome sp. are ammonia ox
■nitrate/Fe reduction: capability found in many phyla, can use other e- acceptors
○Systems biology: metagenomics → metatranscriptomics → metaproteomics →
metabolomics
○Undiscovered genes:
■DNA from entire community:
●Metagenomics : application of modern techniques to study communities
and bypass need for isolation
○Metagenome assemblers : short read w/ supercomputer, predict
genes and annotate functions
○Reads → contigs → scafolds → genome associations
●Enabled by the Human Genome Project - focused on microbes ater
humans
■Shotgun genomics: put back together
■Shotgun metagenomics : put library/assembly back together, store data
●Approaches with soil: genome vs gene-centric approach
Document Summary
Relative : (cid:322)i(cid:475)es position/ tness o(cid:321) o(cid:418)(cid:322)anism in (cid:283)ommunit(cid:482), pe(cid:418)(cid:283)ent. A(cid:283)tual : num(cid:282)e(cid:418) in (cid:283)ommunit(cid:482), (cid:282)ette(cid:418) (cid:321)o(cid:418) (cid:418)elatin(cid:322) mi(cid:283)(cid:418)o(cid:282)es to p(cid:418)o(cid:283)ess (cid:418)ates. Mi(cid:283)(cid:418)os(cid:283)op(cid:482) : la(cid:282)el (cid:283)ells (cid:476)/ dna p(cid:418)o(cid:282)e to id/(cid:283)ount. Fluo(cid:418)es(cid:283)en(cid:283)e in situ h(cid:482)(cid:282)(cid:418)idization (cid:1827)fish(cid:1828) : anal(cid:482)sis o(cid:321) (cid:418)elati(cid:475)e densities and spatial patte(cid:418)ns. Daime : di(cid:322)ital ima(cid:322)e anal(cid:482)sis in mi(cid:283)(cid:418)o(cid:282)ial e(cid:283)olo(cid:322)(cid:482), (cid:283)o-a(cid:322)(cid:322)(cid:418)e(cid:322)ation/s(cid:482)nt(cid:418)oph(cid:482) Quantitative pcr : anal(cid:482)ze p(cid:418)od a(cid:283)(cid:283)um du(cid:418)in(cid:322) e(cid:481)ponential phase. Fluo(cid:418)o(cid:322)eneti(cid:283)all(cid:482)-la(cid:282)eled su(cid:282)st(cid:418)ates (cid:1827)mub(cid:1828) , enz(cid:482)me a(cid:283)ti(cid:475)it(cid:482) (cid:418)esults in (cid:500)luo(cid:418)es(cid:283)ent si(cid:322)nal. N (cid:283)(cid:482)(cid:283)le: ammonia o(cid:481) (cid:1827)amoa(cid:1828)/denit(cid:418)i (cid:283)ation (cid:1827)na(cid:418)g, ni(cid:418)s, nosz(cid:1828) C (cid:283)(cid:482)(cid:283)le: (cid:283)ellulose, li(cid:322)nin, (cid:283)hitinase, methano(cid:322)enesis, methane o(cid:481) Lo(cid:476) num(cid:282)e(cid:418) o(cid:321) ta(cid:418)(cid:322)ets: (cid:283)lonin(cid:322)-se(cid:417), (cid:417)pcr, (cid:417)rt-pcr (cid:1827)mrna(cid:1828) Hi(cid:322)h num(cid:282)e(cid:418) o(cid:321) ta(cid:418)(cid:322)ets: mi(cid:283)(cid:418)oa(cid:418)(cid:418)a(cid:482)s (cid:1827) geochip (cid:1828), ne(cid:481)t (cid:322)en se(cid:417)uen(cid:283)in(cid:322) Sometimes it (cid:476)o(cid:418)ks: nit(cid:418)ososome sp. a(cid:418)e ammonia o(cid:481) Nit(cid:418)ate/fe (cid:418)edu(cid:283)tion: (cid:283)apa(cid:282)ilit(cid:482) (cid:321)ound in man(cid:482) ph(cid:482)la, (cid:283)an use othe(cid:418) e- a(cid:283)(cid:283)epto(cid:418)s. S(cid:482)stems (cid:282)iolo(cid:322)(cid:482): meta(cid:322)enomi(cid:283)s metat(cid:418)ans(cid:283)(cid:418)iptomi(cid:283)s metap(cid:418)oteomi(cid:283)s meta(cid:282)olomi(cid:283)s. Meta(cid:322)enomi(cid:283)s : appli(cid:283)ation o(cid:321) mode(cid:418)n te(cid:283)hni(cid:417)ues to stud(cid:482) (cid:283)ommunities and (cid:282)(cid:482)pass need (cid:321)o(cid:418) isolation. Meta(cid:322)enome assem(cid:282)le(cid:418)s : sho(cid:418)t (cid:418)ead (cid:476)/ supe(cid:418)(cid:283)ompute(cid:418), p(cid:418)edi(cid:283)t (cid:322)enes and annotate (cid:321)un(cid:283)tions.
