200 million humans infected (83 million with s. mansoni) annual mortality 280,000 (130,000 due to s....
TRANSCRIPT
200 million humans infected (83 million with S. mansoni)Annual mortality 280,000 (130,000 due to S. mansoni)
Morbidity 120 million humans600 million more humans at risk
Impact of schistosomiasis second only to malaria (WHO)
SCHISTOSOMIASIS
TRANSMISSION?• Only 1-6% of snails shed cercaria
(transmit schistosomes)• Up to 50% of snails may be infected
with schistosomes (Hamburger et al, 2004)
• Experimental exposure of field-collected snails with low parasite doses does not always result in infection. High parasite doses yield ~100% infection
Why does Biomphalaria not always host S. mansoni? • Genetic determinants (Newton 1950; Richards and Shade, 1987)
• Differential expression/activity of defenses (Bender et al, 2007)
• Matching or mismatching phenotypes of recognition/ antigens of individual snails and parasites (Theron and Coustau, 2005).
Need more insight into snail internal defenses, compatibility
FLUKES AND SNAILS
parasites are excellent cell biologistsspecific manipulation of host cell function
Trichobilharzia ocellata
Schistosoma mansoni
Echinostomaparaensei
Adema et al., 1994a,bLoker & Adema, 1995 Adema et al., 1997a
SNAIL ANTI-PARASITE RESPONSE INCLUDES FREPs
FREP = FIBRINOGEN-RELATED PROTEIN
80-120
180-200
65
kDa
UNIQUE COMBINATION
IgSFS/ICRFBGC CN C
IMMUNOGLOBULIN SUPERFAMILY
(IgSF)-LIKE DOMAIN
FIBRINOGEN /b g (FBG)-LIKE DOMAIN
N C C C C C
CELL ADHERENCEMULTIMERIZATION
LECTIN FUNCTION NON-SELF RECOGNITION
FREP POLYMORPHISME H
Bg
MULTIPLE FBG- HYBRIDIZING SEQUENCES IN THE GENOME OF BIOMPHALARIA GLABRATA (Bg)
E= ECO RI, H= HAE III
BgMF2BgMF3
HtrF1
Balf4
BgSF1
BgMF4
BgMF1Balf1
Balf2Balf3
HtrF2
HtrF3
HtrF6
HtrF7 BtrF1
Balf5
BgBF1 BgRF1
Sea CucumberMouse
Human
LfllAb
LflAc
LflAa
OTHER PLANORBIDS ALSO HAVE FREP GENES.INTERSPERSED SEQUENCES FROM DIFFERENTSPECIES UNDERLINE POLYMORPHISMS
Biomphalaria glabrataBiomphalaria alexandrina
Bulinus truncatusHelisoma trivolvis
NJ TREE (AA)FREP FBG
DEUTEROSTOME FBG
SLUG FBG
QUESTIONS RE: FREPs • How are FREPs diversified, but not other genes?
• Do biological data agree with the in silico model?
• Genomic architecture of FREP loci?
• Regulation of FREP expression?
LOOK AWAY FROM THE LAMP POST
What don’t we know?
Acquired resistance
AMPsROIs
Hemolin (MDM)
NO productionFREPs
Toll
RNAi
DSCAM
A GAP IN MOLECULAR DATA
El-Sayed, Bartholomeu,Ivens, Johnston,LoVerde
Fist draft stage of 270Mb genome
COMPLETE 3.2 Gb
http://www.genome.gov/Images/dir_image.jpg
Snail Sympathizers &Molluscan Partisans
Informal group meeting
All are welcomeMonday, 2 July, from 1-2pm, in room C
ASP 2001
DEFENSE FACTORS• Non self recognition: beta-1,3-glucan binding protein,
selectin, galectin, hemolectin, C-type lectins, ficolin, FREPs, lipopolysacaharide protein-binding protein, peptidoglycan recognition protein
• Signal transduction/regulatory pathways: TNF-R, IFN-R SF, NILT-1, NFKB inhibitor, NFKB-like, Toll-like receptor, death-associated protein kinase, apoptosis inhibitor, arginine kinase, kinase-like protein, rabconnectin 3 b, transducin, proteases, serine protease inhibitors, transcription factors
• AMP: DRAGP, LBP-BPI, achacin, aplysianin, cystatins, theromacin
• Cytoskeleton/Cell adhesion: Actin, calponin, Myosin, amiloride binding protein, apical early endosomal glycoprotein, intermediate filament protein A, paramyosin, tropomyosin, tubulin, twitchin, supervillin, collagen, peroxinectin, Cadherin, hepatocyte growth factor, integrin
• Cell-mediated cytotoxicity/Lysosomal enzymes: carboxypeptidase A, cathepsin F, cellulase, disintegrin-like and metalloprotease, endo-1,4-mannanase, endo-1,4 glucanase, endochitinase, enolase, hydrolase, perforin aminopeptidase 2, Peptidase, macrophage expressed protein, vacuolar proton-translocating ATPase, peroxidase, peroxidases, amoebocyte agglutination factor
• RNAi: Helicase, PIWI/argonaute-like• Stress response proteins: several HSPs, SOD, GST
THE MITOCHONDRIAL GENOME OF Biomphalaria glabrata
DeJong, Emery, Adema, 2004 Journal of Parasitology 90:991-997
Biomphalaria glabrata snails were collected by Dr Omar dos Santos Carvalho in the metropolitan region of Belo Horizonte, district of Barreiro, Brazil (19oS59min/44oW02min). Susceptible to Schistosoma mansoni
GENOME SEQUENCE TARGETBB02 STRAIN Biomphalaria glabrata
BAC-ACCESS TO GENOME
pAGIBAC1
61,824 BAC clones, average insert 136 Kb, 9.05x coverage of genome (931 Mb),
161 (384 well) plates
x pAGIBAC
GENOME “BAC-DOOR” ACCESS61,824 BAC clones161 (384 well) platesaverage insert 136 Kb 9.1x genome coverage
Target recoveredActin 45hsp70 13Myoglobin 22FREP4 4FREP13 7L32 15Ferritin 2Lectin 3Ubiquitin 3MnSOD 10
Clone Bg-BB 117G16 BAC end sequenceheat shock protein 70 [Biomphalaria glabrata] Length=636 Score = 229 bits (583), Expect = 3e-59 Identities = 110/123 (89%), Positives = 117/123 (95%), Gaps = 0/123 (0%) Frame = +3Query 12 MPGRNKAPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLVGDAAKN 191 M GRNKAPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLVGDAAKN Sbjct 1 MSGRNKAPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLVGDAAKN 60
Query 192 QAAMNPSNTIFDAKRLIGRKFNDKTVQSXXKHWPFKVVEVDGKPKIKAEYRGEQKLFAPX 371 QAAMNPSNT++DAKRLIGRKF+DKTVQ+ KHWPFKVVEVDG+PKI+AEYRGE KLFAP Sbjct 61 QAAMNPSNTVYDAKRLIGRKFDDKTVQNDMKHWPFKVVEVDGRPKIQAEYRGENKLFAPE 120
Snail Genome Meeting November 6, 2007
Biomphalaria glabrata(Photo Courtesy of Matty Knight)
• Initial sequencing plan
• Revised sequencing plan
• Project direct costs
• Accessing data
• Project contacts
• High repeat content
• High heterozygosity levels
• High GC or AT content
• Large genome size
What are the properties of a difficult genome ?
Newbler Assembly 4.1 Input Data
Biomphalaria glabrata Final Improved Assembly Statistics Version 4.3
Sin
gle
IG
FR
EP
Du
al I
G F
RE
P
Biomphalariaglabrata
Aplysiacalifornica