Chapman J

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Full name : Chapman Joab

First name : Joab

Mail : Dept. of Biochemistry, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978

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Country : Israel

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References (30)

Title : Design and Synthesis of Ranitidine Analogs as Multi-Target Directed Ligands for the Treatment of Alzheimer's Disease - Gao_2021_Int.J.Mol.Sci_22_
Author(s) : Gao J , Suo C , Tseng JH , Moss MA , Terry AV, Jr. , Chapman J
Ref : Int J Mol Sci , 22 : , 2021
Abstract : The aggregation of amyloid beta (Abeta) peptides and deposition of amyloid plaques are implicated in the pathogenesis of Alzheimer's disease (AD). Therefore, blocking Abeta aggregation with small molecules has been proposed as one therapeutic approach for AD. In the present study, a series of ranitidine analogs containing cyclic imide isosteres were synthesized and their inhibitory activities toward Abeta aggregation were evaluated using in vitro thioflavin T assays. The structure-activity relationship revealed that the 1,8-naphthalimide moiety provided profound inhibition of Abeta aggregation and structural modifications on the other parts of the parent molecule (compound 6) maintained similar efficacy. Some of these ranitidine analogs also possessed potent inhibitory activities of acetylcholinesterase (AChE), which is another therapeutic target in AD. These ranitidine analogs, by addressing both Abeta aggregation and AChE, offer insight into the key chemical features of a new type of multi-target directed ligands for the pharmaceutical treatment of AD.
ESTHER : Gao_2021_Int.J.Mol.Sci_22_
PubMedSearch : Gao_2021_Int.J.Mol.Sci_22_
PubMedID: 33803769

Title : The Capsella rubella genome and the genomic consequences of rapid mating system evolution - Slotte_2013_Nat.Genet_45_831
Author(s) : Slotte T , Hazzouri KM , Agren JA , Koenig D , Maumus F , Guo YL , Steige K , Platts AE , Escobar JS , Newman LK , Wang W , Mandakova T , Vello E , Smith LM , Henz SR , Steffen J , Takuno S , Brandvain Y , Coop G , Andolfatto P , Hu TT , Blanchette M , Clark RM , Quesneville H , Nordborg M , Gaut BS , Lysak MA , Jenkins J , Grimwood J , Chapman J , Prochnik S , Shu S , Rokhsar D , Schmutz J , Weigel D , Wright SI
Ref : Nat Genet , 45 :831 , 2013
Abstract : The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.
ESTHER : Slotte_2013_Nat.Genet_45_831
PubMedSearch : Slotte_2013_Nat.Genet_45_831
PubMedID: 23749190
Gene_locus related to this paper: arath-CGEP , 9bras-r0h1k6 , 9bras-r0gvg3 , 9bras-r0gv62 , 9bras-r0g5k5 , 9bras-r0f1u1 , 9bras-r0guy4 , 9bras-r0ien7 , 9bras-r0i2r7 , 9bras-r0fbh7 , 9bras-r0fnq1 , 9bras-r0hae6 , 9bras-r0gwt8 , 9bras-r0ewe4 , 9bras-r0gsz7 , 9bras-r0ij26 , 9bras-r0h783 , 9bras-r0i5w1 , 9bras-r0fgs3 , 9bras-r0h1e1 , 9bras-r0fme4 , 9bras-r0ieh8 , 9bras-r0f5l9 , 9bras-r0ffy6

Title : Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri - Prochnik_2010_Science_329_223
Author(s) : Prochnik SE , Umen J , Nedelcu AM , Hallmann A , Miller SM , Nishii I , Ferris P , Kuo A , Mitros T , Fritz-Laylin LK , Hellsten U , Chapman J , Simakov O , Rensing SA , Terry A , Pangilinan J , Kapitonov V , Jurka J , Salamov A , Shapiro H , Schmutz J , Grimwood J , Lindquist E , Lucas S , Grigoriev IV , Schmitt R , Kirk D , Rokhsar DS
Ref : Science , 329 :223 , 2010
Abstract : The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are well suited for the investigation of the evolution of multicellularity and development. We sequenced the 138-mega-base pair genome of V. carteri and compared its approximately 14,500 predicted proteins to those of its unicellular relative Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials and few species-specific protein-coding gene predictions. Volvox is enriched in volvocine-algal-specific proteins, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity.
ESTHER : Prochnik_2010_Science_329_223
PubMedSearch : Prochnik_2010_Science_329_223
PubMedID: 20616280
Gene_locus related to this paper: volca-d8tmz1 , volca-d8tne9 , volca-d8tnn6 , volca-d8tns6 , volca-d8tr92 , volca-d8u2d3 , volca-d8u5r0 , volca-d8u7s7 , volca-d8u7s8 , volca-d8u9w4 , volca-d8u460 , volca-d8uab7 , volca-d8uai0 , volca-d8uev0 , volca-d8uhi9 , volca-d8uiw9 , volca-d8ujv0 , volca-d8uf23 , volca-d8tmz9 , volca-d8u6e0

Title : The genome of Naegleria gruberi illuminates early eukaryotic versatility - Fritz-Laylin_2010_Cell_140_631
Author(s) : Fritz-Laylin LK , Prochnik SE , Ginger ML , Dacks JB , Carpenter ML , Field MC , Kuo A , Paredez A , Chapman J , Pham J , Shu S , Neupane R , Cipriano M , Mancuso J , Tu H , Salamov A , Lindquist E , Shapiro H , Lucas S , Grigoriev IV , Cande WZ , Fulton C , Rokhsar DS , Dawson SC
Ref : Cell , 140 :631 , 2010
Abstract : Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.
ESTHER : Fritz-Laylin_2010_Cell_140_631
PubMedSearch : Fritz-Laylin_2010_Cell_140_631
PubMedID: 20211133
Gene_locus related to this paper: naegr-d2ux86 , naegr-d2uyl7 , naegr-d2uyn1 , naegr-d2uzk6 , naegr-d2uzp4 , naegr-d2v1m1 , naegr-d2v3p5 , naegr-d2v5p1 , naegr-d2v6f6 , naegr-d2v6y9 , naegr-d2v8x8 , naegr-d2v186 , naegr-d2v339 , naegr-d2v556 , naegr-d2vbq7 , naegr-d2vdq6 , naegr-d2ve51 , naegr-d2vga2 , naegr-d2vgm9 , naegr-d2vh14 , naegr-d2vha2 , naegr-d2vj80 , naegr-d2vjj7 , naegr-d2vl41 , naegr-d2vmj5 , naegr-d2vms7 , naegr-d2vqi5 , naegr-d2vr44 , naegr-d2vrq2 , naegr-d2vs01 , naegr-d2vs58 , naegr-d2vts5 , naegr-d2vu69 , naegr-d2vvg8 , naegr-d2vxp2 , naegr-d2vyl1 , naegr-d2vzy5 , naegr-d2w0l5 , naegr-d2w0v9 , naegr-d2w3g8 , naegr-d2w3v7 , naegr-d2w3v8 , naegr-d2vct1

Title : The Sorghum bicolor genome and the diversification of grasses - Paterson_2009_Nature_457_551
Author(s) : Paterson AH , Bowers JE , Bruggmann R , Dubchak I , Grimwood J , Gundlach H , Haberer G , Hellsten U , Mitros T , Poliakov A , Schmutz J , Spannagl M , Tang H , Wang X , Wicker T , Bharti AK , Chapman J , Feltus FA , Gowik U , Grigoriev IV , Lyons E , Maher CA , Martis M , Narechania A , Otillar RP , Penning BW , Salamov AA , Wang Y , Zhang L , Carpita NC , Freeling M , Gingle AR , Hash CT , Keller B , Klein P , Kresovich S , McCann MC , Ming R , Peterson DG , Mehboob ur R , Ware D , Westhoff P , Mayer KF , Messing J , Rokhsar DS
Ref : Nature , 457 :551 , 2009
Abstract : Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.
ESTHER : Paterson_2009_Nature_457_551
PubMedSearch : Paterson_2009_Nature_457_551
PubMedID: 19189423
Gene_locus related to this paper: sorbi-b3vtb2 , sorbi-c5wp75 , sorbi-c5wts6 , sorbi-c5wu07 , sorbi-c5wvl7 , sorbi-c5ww85 , sorbi-c5ww86 , sorbi-c5wxa4 , sorbi-c5x1f6 , sorbi-c5x2x9 , sorbi-c5x5z9 , sorbi-c5x6q0 , sorbi-c5x230 , sorbi-c5x290 , sorbi-c5x345 , sorbi-c5x399 , sorbi-c5x610 , sorbi-c5xbm4 , sorbi-c5xct0 , sorbi-c5xdv0 , sorbi-c5xe87 , sorbi-c5xf40 , sorbi-c5xfu9 , sorbi-c5xh40 , sorbi-c5xh41 , sorbi-c5xh42 , sorbi-c5xh43 , sorbi-c5xh44 , sorbi-c5xh46 , sorbi-c5xhr2 , sorbi-c5xiw7 , sorbi-c5xjf0 , sorbi-c5xky2 , sorbi-c5xm54 , sorbi-c5xmb9 , sorbi-c5xmz5 , sorbi-c5xp10 , sorbi-c5xpm6 , sorbi-c5xr91 , sorbi-c5xr92 , sorbi-c5xs33 , sorbi-c5xtz0 , sorbi-c5xwd3 , sorbi-c5y0d2 , sorbi-c5y0h4 , sorbi-c5y3i5 , sorbi-c5y7x0 , sorbi-c5y517 , sorbi-c5y545 , sorbi-c5ydr3 , sorbi-c5yec0 , sorbi-c5yf71 , sorbi-c5yi32 , sorbi-c5yih2 , sorbi-c5ylw6 , sorbi-c5yn66 , sorbi-c5ynp8 , sorbi-c5yt11 , sorbi-c5yur5 , sorbi-c5ywz3 , sorbi-c5ywz4 , sorbi-c5yx73 , sorbi-c5yyn0 , sorbi-c5z2m6 , sorbi-c5z6a9 , sorbi-c5z6j1 , sorbi-c5z6s5 , sorbi-c5z177 , sorbi-Q9XE80 , sorbi-c5xyg4 , sorbi-c5z4q0 , sorbi-c5xly4 , sorbi-c5z4u8 , sorbi-c5xxg5 , sorbi-c5z9b9 , sorbi-a0a1z5r970 , sorbi-c5xhf9 , sorbi-c5yxt7 , sorbi-c5yxt6 , sorbi-c5y1m2 , sorbi-c5xdy6 , sorbi-a0a194ysf6 , sorbi-a0a1b6pnr2 , sorbi-a0a1b6qcb9 , sorbi-c5xx30 , sorbi-a0a1b6psg4 , sorbi-a0a1z5rj80 , sorbi-a0a1b6qfm2 , sorbi-a0a1b6qmu5 , sorbi-c6jru0

Title : The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans - King_2008_Nature_451_783
Author(s) : King N , Westbrook MJ , Young SL , Kuo A , Abedin M , Chapman J , Fairclough S , Hellsten U , Isogai Y , Letunic I , Marr M , Pincus D , Putnam N , Rokas A , Wright KJ , Zuzow R , Dirks W , Good M , Goodstein D , Lemons D , Li W , Lyons JB , Morris A , Nichols S , Richter DJ , Salamov A , Sequencing JG , Bork P , Lim WA , Manning G , Miller WT , McGinnis W , Shapiro H , Tjian R , Grigoriev IV , Rokhsar D
Ref : Nature , 451 :783 , 2008
Abstract : Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans.
ESTHER : King_2008_Nature_451_783
PubMedSearch : King_2008_Nature_451_783
PubMedID: 18273011
Gene_locus related to this paper: monbe-a9up87 , monbe-a9uq69 , monbe-a9uq70 , monbe-a9uqa7 , monbe-a9urz6 , monbe-a9usu1 , monbe-a9usy8 , monbe-a9uta2 , monbe-a9uu09 , monbe-a9uxl2 , monbe-a9uy23 , monbe-a9uy95 , monbe-a9uym3 , monbe-a9uyw1 , monbe-a9uzc1 , monbe-a9v0e1 , monbe-a9v2b0 , monbe-a9v3a5 , monbe-a9v3t2 , monbe-a9v4h5 , monbe-a9v6i1 , monbe-a9v7b2 , monbe-a9v7c1 , monbe-a9v8k9 , monbe-a9v8u8 , monbe-a9v9i9 , monbe-a9v9k6 , monbe-a9v028 , monbe-a9v108 , monbe-a9v315 , monbe-a9v345 , monbe-a9v368 , monbe-a9v719 , monbe-a9v871 , monbe-a9vac5 , monbe-a9vah5 , monbe-a9van7 , monbe-a9vbp2 , monbe-a9vcn6 , monbe-a9vd99 , monbe-a9vdj5 , monbe-a9vag0

Title : Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) - Martinez_2008_Nat.Biotechnol_26_553
Author(s) : Martinez D , Berka RM , Henrissat B , Saloheimo M , Arvas M , Baker SE , Chapman J , Chertkov O , Coutinho PM , Cullen D , Danchin EG , Grigoriev IV , Harris P , Jackson M , Kubicek CP , Han CS , Ho I , Larrondo LF , de Leon AL , Magnuson JK , Merino S , Misra M , Nelson B , Putnam N , Robbertse B , Salamov AA , Schmoll M , Terry A , Thayer N , Westerholm-Parvinen A , Schoch CL , Yao J , Barabote R , Nelson MA , Detter C , Bruce D , Kuske CR , Xie G , Richardson P , Rokhsar DS , Lucas SM , Rubin EM , Dunn-Coleman N , Ward M , Brettin TS
Ref : Nat Biotechnol , 26 :553 , 2008
Abstract : Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.
ESTHER : Martinez_2008_Nat.Biotechnol_26_553
PubMedSearch : Martinez_2008_Nat.Biotechnol_26_553
PubMedID: 18454138
Gene_locus related to this paper: hypjq-g0rh85 , hypjq-cip2 , hypjq-g0r9d1 , hypjq-g0r810 , hypjq-g0rbm4 , hypjq-g0rez4 , hypjq-g0rfr3 , hypjq-g0rg60 , hypjq-g0rij9 , hypjq-g0riu1 , hypjq-g0rl87 , hypjq-g0rlh4 , hypjq-g0rme5 , hypjq-g0rwy5 , hypje-axylest , hypje-q7z9m3 , hypjq-g0r6x2 , hypje-a0a024s1b8 , hypjr-a0a024s1s9 , hypjq-g0rxi5

Title : The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome - Sela_2008_Proc.Natl.Acad.Sci.U.S.A_105_18964
Author(s) : Sela DA , Chapman J , Adeuya A , Kim JH , Chen F , Whitehead TR , Lapidus A , Rokhsar DS , Lebrilla CB , German JB , Price NP , Richardson PM , Mills DA
Ref : Proc Natl Acad Sci U S A , 105 :18964 , 2008
Abstract : Following birth, the breast-fed infant gastrointestinal tract is rapidly colonized by a microbial consortium often dominated by bifidobacteria. Accordingly, the complete genome sequence of Bifidobacterium longum subsp. infantis ATCC15697 reflects a competitive nutrient-utilization strategy targeting milk-borne molecules which lack a nutritive value to the neonate. Several chromosomal loci reflect potential adaptation to the infant host including a 43 kbp cluster encoding catabolic genes, extracellular solute binding proteins and permeases predicted to be active on milk oligosaccharides. An examination of in vivo metabolism has detected the hallmarks of milk oligosaccharide utilization via the central fermentative pathway using metabolomic and proteomic approaches. Finally, conservation of gene clusters in multiple isolates corroborates the genomic mechanism underlying milk utilization for this infant-associated phylotype.
ESTHER : Sela_2008_Proc.Natl.Acad.Sci.U.S.A_105_18964
PubMedSearch : Sela_2008_Proc.Natl.Acad.Sci.U.S.A_105_18964
PubMedID: 19033196
Gene_locus related to this paper: bifli-c2gxu7 , biflo-BL0073 , biflo-BL0336 , biflo-BL0581 , biflo-BL0582 , biflo-BL0787 , biflo-BL0807 , biflo-BL1514 , biflo-PTRB , bifln-c2gtr2

Title : The Trichoplax genome and the nature of placozoans - Srivastava_2008_Nature_454_955
Author(s) : Srivastava M , Begovic E , Chapman J , Putnam NH , Hellsten U , Kawashima T , Kuo A , Mitros T , Salamov A , Carpenter ML , Signorovitch AY , Moreno MA , Kamm K , Grimwood J , Schmutz J , Shapiro H , Grigoriev IV , Buss LW , Schierwater B , Dellaporta SL , Rokhsar DS
Ref : Nature , 454 :955 , 2008
Abstract : As arguably the simplest free-living animals, placozoans may represent a primitive metazoan form, yet their biology is poorly understood. Here we report the sequencing and analysis of the approximately 98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole-genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome shows conserved gene content, gene structure and synteny in relation to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signalling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages.
ESTHER : Srivastava_2008_Nature_454_955
PubMedSearch : Srivastava_2008_Nature_454_955
PubMedID: 18719581
Gene_locus related to this paper: triad-b3rka6 , triad-b3rkc3 , triad-b3rkc4 , triad-b3rkc5 , triad-b3rkr2 , triad-b3rks9 , triad-b3rkt0 , triad-b3rl14 , triad-b3rls2 , triad-b3rnj7 , triad-b3rnw5 , triad-b3rrr2 , triad-b3rsh1 , triad-b3rsh3 , triad-b3rty7 , triad-b3ru11 , triad-b3rur2 , triad-b3rut0 , triad-b3rvc1 , triad-b3rw12 , triad-b3rwp0 , triad-b3rwr4 , triad-b3rxn2 , triad-b3ry59 , triad-b3s1y9 , triad-b3s3d8 , triad-b3s3e9 , triad-b3s8a0 , triad-b3s9x4 , triad-b3s445 , triad-b3s449 , triad-b3s478 , triad-b3s705 , triad-b3s706 , triad-b3s898 , triad-b3s899 , triad-b3s949 , triad-b3s950 , triad-b3sa20 , triad-b3sa22 , triad-b3sa23 , triad-b3sa24 , triad-b3sa25 , triad-b3sa26 , triad-b3sa27 , triad-b3sa28 , triad-b3sa29 , triad-b3sa31 , triad-b3sa33 , triad-b3sa34 , triad-b3sa36 , triad-b3sb39 , triad-b3scd3 , triad-b3scg3 , triad-b3scg4 , triad-b3scr3 , triad-b3seb0 , triad-b3seb1 , triad-b3seu9 , triad-b3sf12 , triad-b3rt61 , triad-b3rt62 , triad-b3rj15 , triad-b3sdi1

Title : Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization - Putnam_2007_Science_317_86
Author(s) : Putnam NH , Srivastava M , Hellsten U , Dirks B , Chapman J , Salamov A , Terry A , Shapiro H , Lindquist E , Kapitonov VV , Jurka J , Genikhovich G , Grigoriev IV , Lucas SM , Steele RE , Finnerty JR , Technau U , Martindale MQ , Rokhsar DS
Ref : Science , 317 :86 , 2007
Abstract : Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.
ESTHER : Putnam_2007_Science_317_86
PubMedSearch : Putnam_2007_Science_317_86
PubMedID: 17615350
Gene_locus related to this paper: nemve-a7rfc6 , nemve-a7rhs0 , nemve-a7rhw2 , nemve-a7ric9 , nemve-a7riu9 , nemve-a7rk54 , nemve-a7rlg8 , nemve-a7rlv4 , nemve-a7rn07 , nemve-a7rn08 , nemve-a7rn68 , nemve-a7rnv3 , nemve-a7rpb3 , nemve-a7rpq4 , nemve-a7rqa8 , nemve-a7rqw3 , nemve-a7rwv1 , nemve-a7rxl6 , nemve-a7s1d5 , nemve-a7s3l3 , nemve-a7s3q1 , nemve-a7s5u3 , nemve-a7s6g4 , nemve-a7s6s7 , nemve-a7sa46 , nemve-a7sbd9 , nemve-a7sbe0 , nemve-a7sbm6 , nemve-a7scy7 , nemve-a7sex0 , nemve-a7sfa0 , nemve-a7sff3 , nemve-a7sgb1 , nemve-a7shf2 , nemve-a7siv4 , nemve-a7sj77 , nemve-a7sjw1 , nemve-a7skr3 , nemve-a7slm1 , nemve-a7slm2 , nemve-a7sp35 , nemve-a7sq47 , nemve-a7sq73 , nemve-a7sqk0 , nemve-a7su21 , nemve-a7su25 , nemve-a7svn0 , nemve-a7svu2 , nemve-a7sx21 , nemve-a7syk4 , nemve-a7t3e6 , nemve-a7suy2 , nemve-a7s803 , nemve-a7t3m9 , nemve-a0a1t4jh34 , nemve-a7rvd5 , nemve-a7rhu9 , nemve-a7si15

Title : The genome of black cottonwood, Populus trichocarpa (Torr. &\; Gray) - Tuskan_2006_Science_313_1596
Author(s) : Tuskan GA , Difazio S , Jansson S , Bohlmann J , Grigoriev I , Hellsten U , Putnam N , Ralph S , Rombauts S , Salamov A , Schein J , Sterck L , Aerts A , Bhalerao RR , Bhalerao RP , Blaudez D , Boerjan W , Brun A , Brunner A , Busov V , Campbell M , Carlson J , Chalot M , Chapman J , Chen GL , Cooper D , Coutinho PM , Couturier J , Covert S , Cronk Q , Cunningham R , Davis J , Degroeve S , Dejardin A , dePamphilis C , Detter J , Dirks B , Dubchak I , Duplessis S , Ehlting J , Ellis B , Gendler K , Goodstein D , Gribskov M , Grimwood J , Groover A , Gunter L , Hamberger B , Heinze B , Helariutta Y , Henrissat B , Holligan D , Holt R , Huang W , Islam-Faridi N , Jones S , Jones-Rhoades M , Jorgensen R , Joshi C , Kangasjarvi J , Karlsson J , Kelleher C , Kirkpatrick R , Kirst M , Kohler A , Kalluri U , Larimer F , Leebens-Mack J , Leple JC , Locascio P , Lou Y , Lucas S , Martin F , Montanini B , Napoli C , Nelson DR , Nelson C , Nieminen K , Nilsson O , Pereda V , Peter G , Philippe R , Pilate G , Poliakov A , Razumovskaya J , Richardson P , Rinaldi C , Ritland K , Rouze P , Ryaboy D , Schmutz J , Schrader J , Segerman B , Shin H , Siddiqui A , Sterky F , Terry A , Tsai CJ , Uberbacher E , Unneberg P , Vahala J , Wall K , Wessler S , Yang G , Yin T , Douglas C , Marra M , Sandberg G , Van de Peer Y , Rokhsar D
Ref : Science , 313 :1596 , 2006
Abstract : We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
ESTHER : Tuskan_2006_Science_313_1596
PubMedSearch : Tuskan_2006_Science_313_1596
PubMedID: 16973872
Gene_locus related to this paper: burvg-a4jw31 , delas-a9c1v9 , poptr-a9pfp5 , poptr-a9ph43 , poptr-a9ph71 , poptr-a9pha7 , poptr-b9giq0 , poptr-b9gjs0 , poptr-b9gl72 , poptr-b9gmx8 , poptr-b9gnp9 , poptr-b9gny4 , poptr-b9grg2 , poptr-b9gsc2 , poptr-b9gvp3 , poptr-b9gvs3 , poptr-b9gwn9 , poptr-b9gy32 , poptr-b9gyq1 , poptr-b9gys8 , poptr-b9h0h0 , poptr-b9h4j2 , poptr-b9h6c2 , poptr-b9h6c5 , poptr-b9h6l8 , poptr-b9h8c9 , poptr-b9h301 , poptr-b9h579 , poptr-b9hbl2 , poptr-b9hbw5 , poptr-b9hcn9 , poptr-b9hee0 , poptr-b9hee2 , poptr-b9hee5 , poptr-b9hee6 , poptr-b9hef3 , poptr-b9hfa7 , poptr-b9hfd3 , poptr-b9hfi6 , poptr-b9hft8 , poptr-b9hg83 , poptr-b9hif5 , poptr-b9hll5 , poptr-b9hmd0 , poptr-b9hnv3 , poptr-b9hqr6 , poptr-b9hqr7 , poptr-b9hrv7 , poptr-b9hs66 , poptr-b9huf0 , poptr-b9hur3 , poptr-b9hux1 , poptr-b9hwp2 , poptr-b9hxr7 , poptr-b9hyk8 , poptr-b9hyx2 , poptr-b9i2q8 , poptr-b9i5b8 , poptr-b9i5j8 , poptr-b9i5j9 , poptr-b9i5k0 , poptr-b9i6b6 , poptr-b9i7b7 , poptr-b9i9p8 , poptr-b9i484 , poptr-b9i994 , poptr-b9ial3 , poptr-b9ial4 , poptr-b9ib28 , poptr-b9ibr8 , poptr-b9id97 , poptr-b9idr4 , poptr-b9iid9 , poptr-b9iip0 , poptr-b9ik80 , poptr-b9ik90 , poptr-b9il63 , poptr-b9ink7 , poptr-b9iqa0 , poptr-b9iqd5 , poptr-b9mwf1 , poptr-b9mwi8 , poptr-b9n0c6 , poptr-b9n0n1 , poptr-b9n0n4 , poptr-b9n0z5 , poptr-b9n1t8 , poptr-b9n1z3 , poptr-b9n3m7 , poptr-b9n233 , poptr-b9n236 , poptr-b9n395 , poptr-b9nd33 , poptr-b9nd34 , poptr-b9ndi6 , poptr-b9ndj5 , poptr-b9p9i8 , poptr-a9pfa7 , poptr-b9hdp2 , poptr-b9inj0 , poptr-b9n5g7 , poptr-b9i8q4 , poptr-u5g0r4 , poptr-u5gf59 , poptr-u7e1l9 , poptr-b9hj61 , poptr-b9hwd0 , poptr-u5fz17 , poptr-a0a2k2brq1 , poptr-a0a2k2b9i6 , poptr-a0a2k1x9y8 , poptr-a9pch4 , poptr-a0a2k1wwt1 , poptr-a0a2k1wv10 , poptr-a0a2k2a850 , poptr-a0a2k2asj6 , poptr-a0a2k1x6k1 , poptr-u5fv96 , poptr-a0a2k2blg2 , poptr-a0a2k1xpi3 , poptr-a0a2k1xpj0 , poptr-a0a2k2b331 , poptr-a0a2k2byl7 , poptr-b9iek5 , poptr-a9pfg4 , poptr-a0a2k1xzs5 , poptr-b9gga9 , poptr-b9guw6 , poptr-b9hff2

Title : Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis - Tyler_2006_Science_313_1261
Author(s) : Tyler BM , Tripathy S , Zhang X , Dehal P , Jiang RH , Aerts A , Arredondo FD , Baxter L , Bensasson D , Beynon JL , Chapman J , Damasceno CM , Dorrance AE , Dou D , Dickerman AW , Dubchak IL , Garbelotto M , Gijzen M , Gordon SG , Govers F , Grunwald NJ , Huang W , Ivors KL , Jones RW , Kamoun S , Krampis K , Lamour KH , Lee MK , McDonald WH , Medina M , Meijer HJ , Nordberg EK , Maclean DJ , Ospina-Giraldo MD , Morris PF , Phuntumart V , Putnam NH , Rash S , Rose JK , Sakihama Y , Salamov AA , Savidor A , Scheuring CF , Smith BM , Sobral BW , Terry A , Torto-Alalibo TA , Win J , Xu Z , Zhang H , Grigoriev IV , Rokhsar DS , Boore JL
Ref : Science , 313 :1261 , 2006
Abstract : Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes.
ESTHER : Tyler_2006_Science_313_1261
PubMedSearch : Tyler_2006_Science_313_1261
PubMedID: 16946064
Gene_locus related to this paper: phyrm-h3ga89 , phyrm-h3gbl6.1 , phyrm-h3gbl6.2 , phyrm-h3gbl7 , phyrm-h3gdd4 , phyrm-h3gl36 , phyrm-h3gq42 , phyrm-h3gx86 , phyrm-h3gyi2 , phyrm-h3gyi3 , phyrm-h3gyi4 , phyrm-h3h292 , phyrm-h3h293 , phyrm-h3h967 , phyrm-h3hcf9 , physp-g4ynp3 , physp-g4yut6 , physp-g4yut8 , physp-g4yw23 , physp-g4zis3 , physp-g4zqe3 , physp-g4zqe4 , physp-g4zqf0 , physp-g4zqn9 , physp-g4zwy9 , physp-g5a582 , physp-g5a583 , physp-g5aav9 , phyrm-h3g9e7 , physp-g4zwu9 , phyrm-h3ggp1 , physp-g4ztq5 , physp-g4zwu8 , physp-g4zwv7 , physp-g4zwv6 , physp-g4zwv0 , physp-g4zwv8 , phyrm-h3gp95 , phyrm-h3g6r5 , physp-g4zwv9 , physp-g5a510 , phyrm-h3glu3 , physp-g5aci1 , phyrm-h3h2d0 , physp-g4ztb2 , physp-g4yg47 , phyrm-h3h2c9 , physp-g4ztb3 , phyrm-h3gvj3 , phyrm-h3gy62 , physp-g4yg46 , physp-g4zdt9 , phyrm-h3gdh5 , physp-g4zm41 , physp-g5abj7 , phyrm-h3gz76 , physp-g5a425 , phyrm-h3h080 , physp-g4ytv0 , phyrm-h3gcw7

Title : Hidden function of neuronal nicotinic acetylcholine receptor beta2 subunits in ganglionic transmission: comparison to alpha5 and beta4 subunits - Wang_2005_J.Neurol.Sci_228_167
Author(s) : Wang N , Orr-Urtreger A , Chapman J , Ergun Y , Rabinowitz R , Korczyn AD
Ref : Journal of Neurology Sci , 228 :167 , 2005
Abstract : Neuronal nicotinic acetylcholine receptors (nAChR), which modulate fast excitatory postsynaptic potentials (f-EPSP), are located on both pre- and postganglionic sites in the autonomic nervous system (ANS). The receptor subunits alpha3, alpha5, alpha7, beta2 and beta4 are present in autonomic ganglia in various combinations and modulate acetylcholine (ACh) transmission. In the present study, autonomic functions were systemically examined in mice lacking beta2 subunits (beta2-/-) to further understand the functional role of beta2 subunits in modulating ganglionic transmission. The results show normal autonomic functions, both under physiological conditions and in perturbed conditions, on thermoregulation, pupillary size, heart rate responses and ileal contractile reactions. This suggests that the function of beta2-containing receptors in ganglionic transmission is hidden by the predominant beta4 containing receptors and confirms previous studies which suggest that alpha3alpha5beta4 nAChRs are sufficient for autonomic transmission. On the other hand, beta2-containing receptors have only a minor function on postsynaptic responses to ACh, but may modulate ACh release presynaptically, although there is no evidence for this.
ESTHER : Wang_2005_J.Neurol.Sci_228_167
PubMedSearch : Wang_2005_J.Neurol.Sci_228_167
PubMedID: 15694199

Title : Nicotinic acetylcholine receptor alpha5 subunits modulate oxotremorine-induced salivation and tremor - Wang_2004_J.Neurol.Sci_222_87
Author(s) : Wang N , Orr-Urtreger A , Chapman J , Rabinowitz R , Korczyn AD
Ref : Journal of Neurology Sci , 222 :87 , 2004
Abstract : Neuronal nicotinic acetylcholine receptors (nAChRs) are composed of 12 subunits (alpha2-alpha10 and beta2-beta4). alpha5 Subunits, expressed throughout the central nervous system (CNS) and the autonomic nervous system (ANS), possess unique pharmacological properties. The effects of oxotremorine (OXO) on autonomic functions and tremor were examined in mice lacking alpha5 nAChR subunits (alpha5-/-) and compared with those in wild-type (WT) control mice. The alpha5-/- mice showed significantly increased salivation and tremor responses to OXO. The hypothermia, bradycardia and defecation induced by OXO were of similar magnitudes in the two mouse strains. The enhanced OXO effects in alpha5-/- mice indicate inhibitory effects of alpha5 subunits in autonomic ganglia, and support the participation of these subunits in cholinergic transmission in autonomic ganglia.
ESTHER : Wang_2004_J.Neurol.Sci_222_87
PubMedSearch : Wang_2004_J.Neurol.Sci_222_87
PubMedID: 15240201

Title : Community structure and metabolism through reconstruction of microbial genomes from the environment - Tyson_2004_Nature_428_37
Author(s) : Tyson GW , Chapman J , Hugenholtz P , Allen EE , Ram RJ , Richardson PM , Solovyev VV , Rubin EM , Rokhsar DS , Banfield JF
Ref : Nature , 428 :37 , 2004
Abstract : Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.
ESTHER : Tyson_2004_Nature_428_37
PubMedSearch : Tyson_2004_Nature_428_37
PubMedID: 14961025

Title : Deficiency of nicotinic acetylcholine receptor beta 4 subunit causes autonomic cardiac and intestinal dysfunction - Wang_2003_Mol.Pharmacol_63_574
Author(s) : Wang N , Orr-Urtreger A , Chapman J , Rabinowitz R , Korczyn AD
Ref : Molecular Pharmacology , 63 :574 , 2003
Abstract : Neuronal nicotinic acetylcholine receptors (nAChR) are composed of 12 subunits (alpha 2-alpha 10 and beta 2-beta 4), which play the central role in autonomic transmission. beta 4 subunits are abundantly expressed in autonomic ganglia, forming acetylcholine binding sites and ion channels with alpha 3 or alpha 3 and alpha 5 subunits as pentameric receptors. To investigate the physiological and pharmacological properties of beta 4 subunits in autonomic ganglia, we measured autonomic functions in knockout mice lacking nAChR subunit beta 4 (beta 4(-/-)) and wild-type mice. beta 4(-/-) mice had an attenuated bradycardiac response to high frequency (60 pulse/s) vagal stimulation, as well as an increased sensitivity to hexamethonium blockade at low dose (3 mg/kg) and a reduced ileal contractile response to the nicotinic agonists cytisine, dimethylphenylpiperazinium iodide, nicotine (10 mg/kg each), and epibatidine (0.1 mg/kg). The results suggest that beta 4 subunits are important components of nAChRs in autonomic ganglia. Deficiency of beta 4 subunits altered ion channel properties, conductance, and sensitivity and affinity of receptors to agonists and antagonists, affecting ganglionic transmission.
ESTHER : Wang_2003_Mol.Pharmacol_63_574
PubMedSearch : Wang_2003_Mol.Pharmacol_63_574
PubMedID: 12606764

Title : The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins - Dehal_2002_Science_298_2157
Author(s) : Dehal P , Satou Y , Campbell RK , Chapman J , Degnan B , De Tomaso A , Davidson B , Di Gregorio A , Gelpke M , Goodstein DM , Harafuji N , Hastings KE , Ho I , Hotta K , Huang W , Kawashima T , Lemaire P , Martinez D , Meinertzhagen IA , Necula S , Nonaka M , Putnam N , Rash S , Saiga H , Satake M , Terry A , Yamada L , Wang HG , Awazu S , Azumi K , Boore J , Branno M , Chin-Bow S , DeSantis R , Doyle S , Francino P , Keys DN , Haga S , Hayashi H , Hino K , Imai KS , Inaba K , Kano S , Kobayashi K , Kobayashi M , Lee BI , Makabe KW , Manohar C , Matassi G , Medina M , Mochizuki Y , Mount S , Morishita T , Miura S , Nakayama A , Nishizaka S , Nomoto H , Ohta F , Oishi K , Rigoutsos I , Sano M , Sasaki A , Sasakura Y , Shoguchi E , Shin-I T , Spagnuolo A , Stainier D , Suzuki MM , Tassy O , Takatori N , Tokuoka M , Yagi K , Yoshizaki F , Wada S , Zhang C , Hyatt PD , Larimer F , Detter C , Doggett N , Glavina T , Hawkins T , Richardson P , Lucas S , Kohara Y , Levine M , Satoh N , Rokhsar DS
Ref : Science , 298 :2157 , 2002
Abstract : The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.
ESTHER : Dehal_2002_Science_298_2157
PubMedSearch : Dehal_2002_Science_298_2157
PubMedID: 12481130
Gene_locus related to this paper: cioin-141645 , cioin-147959 , cioin-150181 , cioin-154370 , cioin-ACHE1 , cioin-ACHE2 , cioin-cxest , cioin-f6qcp0 , cioin-f6r8z1 , cioin-f6u176 , cioin-f6vac9 , cioin-f6x584 , cioin-f6xa69 , cioin-f6y403 , cioin-h2xqb4 , cioin-H2XTI0 , cioin-F6T1M3 , cioin-H2XUP7 , cioin-CIN.7233 , cioin-F6V269 , cioin-Cin16330 , cioin-h2xua2 , cioin-f6vaa5 , cioin-f6v9x6 , cioin-f6swc9 , cioin-f7amz2 , cioin-f6s021 , cioin-h2xxq9 , cioin-h2xne6 , cioin-f6ynr2

Title : Autonomic function in mice lacking alpha5 neuronal nicotinic acetylcholine receptor subunit - Wang_2002_J.Physiol_542_347
Author(s) : Wang N , Orr-Urtreger A , Chapman J , Rabinowitz R , Nachman R , Korczyn AD
Ref : The Journal of Physiology , 542 :347 , 2002
Abstract : Neuronal acetylcholine nicotinic receptors (nAChR) are composed of 12 subunits (alpha2-10, beta2-4), of which alpha3, alpha5, alpha7, beta2 and beta4 subunits are known to exist in the autonomic nervous system (ANS). alpha5 subunits possess unique biophysical and pharmacological properties. The present study was undertaken to examine the functional role and pharmacological properties of the nAChR alpha5 subunits in the ANS using mice lacking alpha5 nAChR subunits (alpha5-/-). These mice grew to normal size showing no obvious physical or neurological deficit. They also showed normality in thermoregulation, pupil size and resting heart rate under physiological conditions. The heart rate and rectal temperature did not differ between alpha5-/- and wild-type mice during exposure to cold stress. An impairment of cardiac parasympathetic ganglionic transmission was observed during high frequency vagal stimulation, which caused cardiac arrest in all wild-type animals while alpha5-/- mice were more resistant. Deficiency of alpha5 subunits strikingly increased the sensitivity to a low concentration of hexamethonium, leading to a nearly complete blockade of bradycardia in response to vagal stimulation. Such a concentration of hexamethonium only slightly depressed the effects of vagal stimulation in control mice. Deficiency of alpha5 subunits significantly increased ileal contractile responses to cytisine and epibatidine. These results suggest that alpha5 subunits may affect the affinity and sensitivity of agonists and antagonists in the native receptors. Previous studies revealed that alpha5 subunits form functional receptors only in combination with other alpha and beta subunits. Thus, the data presented here imply that alpha5 subunits modulate the activity of nAChR in autonomic ganglia in vivo.
ESTHER : Wang_2002_J.Physiol_542_347
PubMedSearch : Wang_2002_J.Physiol_542_347
PubMedID: 12122136

Title : Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes - Aparicio_2002_Science_297_1301
Author(s) : Aparicio S , Chapman J , Stupka E , Putnam N , Chia JM , Dehal P , Christoffels A , Rash S , Hoon S , Smit A , Gelpke MD , Roach J , Oh T , Ho IY , Wong M , Detter C , Verhoef F , Predki P , Tay A , Lucas S , Richardson P , Smith SF , Clark MS , Edwards YJ , Doggett N , Zharkikh A , Tavtigian SV , Pruss D , Barnstead M , Evans C , Baden H , Powell J , Glusman G , Rowen L , Hood L , Tan YH , Elgar G , Hawkins T , Venkatesh B , Rokhsar D , Brenner S
Ref : Science , 297 :1301 , 2002
Abstract : The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.
ESTHER : Aparicio_2002_Science_297_1301
PubMedSearch : Aparicio_2002_Science_297_1301
PubMedID: 12142439
Gene_locus related to this paper: fugru-2balip , fugru-2cxest , fugru-3cxest , fugru-3neur , fugru-4cxest , fugru-4neur , fugru-ACHE , fugru-ACHEE , fugru-balip , fugru-BCHE , fugru-BCHEB , fugru-BCHEC , fugru-cxest , takru-1neur , takru-2bneur , takru-3bneur , takru-h2rsj9 , takru-nlgn2a , takru-nlgn4a

Title : Antineurofilament antibodies in postpolio syndrome - Drory_1998_Neurology_51_1193
Author(s) : Drory VE , Shapira A , Korczyn AD , Shavit S , Kushnir M , Michaelson DM , Chapman J
Ref : Neurology , 51 :1193 , 1998
Abstract : We determined the levels of antineurofilament antibodies in 29 patients with postpolio syndrome (PPS), 26 stable postpolio (PP) patients, 22 patients with ALS, and 20 normal controls (NCs). Patients with PPS had higher antibody levels to cholinergic neurofilaments than did all other groups. PP patients and those with ALS had antibody levels similar to those of NCs. The antibody binding level showed no relation to the age of the patients, duration of disease, or motor score.
ESTHER : Drory_1998_Neurology_51_1193
PubMedSearch : Drory_1998_Neurology_51_1193
PubMedID: 9781558

Title : Antibodies from Down's syndrome patients bind to the same cholinergic neurofilament protein recognized by Alzheimer's disease antibodies - Hassin-Baer_1992_Neurology_42_551
Author(s) : Hassin-Baer S , Wertman E , Raphael M , Stark V , Chapman J , Michaelson DM
Ref : Neurology , 42 :551 , 1992
Abstract : Down's syndrome (DS) patients who survive beyond the third decade develop brain lesions characteristic of Alzheimer's disease (AD). Sera of AD patients contain antibodies that bind specifically to the heavy neurofilament protein (NF-H) of Torpedo cholinergic neurons. In the present report, we examined whether the AD-like pathologic changes in DS are associated with the existence of such antibodies. Our findings show that IgG of older DS patients (greater than 30 years) binds to Torpedo cholinergic NF-H more readily than does that of young DS patients (less than 30 years) and age-matched normal controls. In contrast, the extent of binding of IgG from the young and older DS groups to Torpedo and bovine spinal cords NF-H is similar and equal to that of normal controls. These findings suggest that older DS patients, like AD patients, contain anti-NF-H IgG that binds specifically to epitopes highly enriched in Torpedo cholinergic NF-H.
ESTHER : Hassin-Baer_1992_Neurology_42_551
PubMedSearch : Hassin-Baer_1992_Neurology_42_551
PubMedID: 1532232

Title : Monoclonal antibodies to the heavy neurofilament subunit (NF-H) of Torpedo cholinergic neurons - Faigon_1991_J.Neurosci.Res_29_490
Author(s) : Faigon M , Hadas E , Alroy G , Chapman J , Auerbach JM , Michaelson DM
Ref : Journal of Neuroscience Research , 29 :490 , 1991
Abstract : Previous studies from our laboratory suggest that Alzheimer's disease sera contain a repertoire of antibodies to the heavy neurofilament subunit (NF-H) and that a subpopulation of these antibodies bind specifically to epitopes highly enriched in NF-H isolated from the purely cholinergic electromotor neurons of Torpedo. In the present study, we prepared and characterized monoclonal antibodies (MAbs) that bind to epitopes specifically enriched in Torpedo cholinergic neurons. This was performed by a differential enzyme-linked immunosorbent assay (ELISA) in which MAbs were selected that bind to epitopes much more abundant in the NF-H protein of Torpedo cholinergic neurons than in NF-H from the chemically heterogeneous Torpedo spinal cord. This yielded four MAbs, three of which (TC4, TC8, and TC21) were found to be specific to NF-H and one (TC15) that reacts with both NF-H and the medium-size neurofilament subunit NF-M. Dephosphorylation abolishes the binding of MAbs TC4 and TC15 to Torpedo cholinergic NF-H, partially reduces that of MAb TC21 and has no effect on the binding of MAb TC8. This suggests that the antigenic sites specific to Torpedo cholinergic NF-H contain phosphorylated as well as non phosphorylated epitopes. All the MAbs cross-react with rat brain NF-H.
ESTHER : Faigon_1991_J.Neurosci.Res_29_490
PubMedSearch : Faigon_1991_J.Neurosci.Res_29_490
PubMedID: 1791640

Title : Anti-neuronal antibodies similar to those found in Alzheimer's disease induce memory dysfunction in rats - Chapman_1991_Neurosci_40_297
Author(s) : Chapman J , Alroy G , Weiss Z , Faigon M , Feldon J , Michaelson DM
Ref : Neuroscience , 40 :297 , 1991
Abstract : Although the etiology and pathogenesis of the cholinergic degeneration in Alzheimer's disease are not known, several reports implicate immunological mechanisms. Recently we have shown that sera of Alzheimer's disease patients contain antibodies which bind specifically to the heavy molecular weight neurofilament protein of Torpedo cholinergic neurons. In the present study we investigated the possibility that such antibodies play a role in neuronal degeneration by examining the behavioral and cellular effects of immunizing rats with the heavy neurofilament protein of Torpedo cholinergic neurons. The immunized rats developed antibodies which were specific to the heavy neurofilament protein of Torpedo cholinergic neurons and which cross-reacted with rat brain neurofilaments. Immunohistochemical studies revealed the accumulation of antibodies in the perikarya and neurites of neurons in the septum and hippocampus of the cholinergic neurofilament immunized rats and in white matter tracts in their forebrains. No such staining was seen in adjuvant immunized control rats. Behavioral tests revealed that rats immunized with the heavy cholinergic neurofilament protein performed significantly worse than controls in a T-maze alternation test and that their performance deteriorated profoundly after the introduction of a 20-s delay in the paradigm, indicating a deficit in short term memory. In contrast, both groups performed similarly in a T-maze discrimination test, indicating that long term reference memory was not affected by immunization with the heavy cholinergic neurofilament protein. Further experiments revealed that the rats immunized with the heavy cholinergic neurofilament protein were also deficient in a reversal of choice paradigm in a position discrimination test.
ESTHER : Chapman_1991_Neurosci_40_297
PubMedSearch : Chapman_1991_Neurosci_40_297
PubMedID: 2027463

Title : Induction of cognitive deficits by immunization with cholinergic cell bodies: the influence of age and integrity of the blood-brain barrier - Alroy_1991_J.Basic.Clin.Physiol.Pharmacol_2_197
Author(s) : Alroy G , Chapman J , Feldon J , Michaelson DM
Ref : J Basic Clin Physiol Pharmacol , 2 :197 , 1991
Abstract : We have recently shown that prolonged immunization of young rats for one year with cholinergic cell bodies (perikarya, PK) purified from Torpedo electric lobe results in the accumulation of IgG in specific brain areas such as the hippocampus and induces behavioral deficits in spatial orientation and short term memory /1, 7/. We presently studied the rate of development of the cognitive deficit in older (12 months old) Sprague Dawley rats which were immunized for periods of up to one year with either Torpedo cholinergic PK or adjuvant (controls). T-maze alternation and Morris swim maze tests revealed a small deficit in the performance of the PK immunized rats after 6 months whereas significant deficits were observed after 12 months of immunization. These results suggest that the duration of immunization is a more significant factor than the age of the animals in the development of the behavioral deficit. In order to examine whether permeability of the blood-brain barrier to IgG influences the rate of development of the cognitive deficit, we disrupted the blood-brain barrier of PK immunized rats by hypercapnia. This treatment repeated weekly for 2 months was found not to accelerate the rate of appearance of deficits in performance of the rats in the T-maze alternation and Morris swim test. These results suggest that penetration of IgG via the blood-brain barrier does not determine the rate of appearance of the cognitive deficits.
ESTHER : Alroy_1991_J.Basic.Clin.Physiol.Pharmacol_2_197
PubMedSearch : Alroy_1991_J.Basic.Clin.Physiol.Pharmacol_2_197
PubMedID: 1797094

Title : Rats immunized with cholinergic synaptosomes: a model for Lambert-Eaton syndrome - Chapman_1990_Muscle.Nerve_13_726
Author(s) : Chapman J , Rabinowitz R , Korczyn AD , Michaelson DM
Ref : Muscle & Nerve , 13 :726 , 1990
Abstract : Lambert-Eaton myasthenic syndrome (LEMS) is an autoimmune disorder characterized by reduced acetylcholine release at the neuromuscular junction. We report a model of the disease developed by active immunization of rats with purely cholinergic nerve terminals (synaptosomes) isolated from the Torpedo electric organ. Electromyographic studies of neuromuscular transmission in these rats showed a weak initial response followed by a pronounced incremental response to paired supramaximal stimuli (8 msec apart). There was no such response in control rats. There was no evidence of a postsynaptic transmission deficit in the synaptosomes immunized rats. We conclude that immunizing rats with Torpedo cholinergic nerve terminals causes a specific presynaptic dysfunction and may serve as a model for the study of LEMS.
ESTHER : Chapman_1990_Muscle.Nerve_13_726
PubMedSearch : Chapman_1990_Muscle.Nerve_13_726
PubMedID: 2385259

Title : Immunization with cholinergic cell bodies induces histopathological changes in rat brains - Michaelson_1990_Mol.Chem.Neuropathol_13_71
Author(s) : Michaelson DM , Kadar T , Weiss Z , Chapman J , Feldon J
Ref : Molecular & Chemical Neuropathology , 13 :71 , 1990
Abstract : We have previously shown that sera from patients with Alzheimer's disease (AD) contain antibodies to the cell bodies (perikarya; PK) of purely cholinergic Torpedo neurons, and that repeated immunization of rats with this neuronal preparation for over a year induces learning and memory impairments. In the present study, we examined the brain morphology of cholinergic PK immunized rats relative to controls. Immunohistochemical studies of the brains of these rats revealed the accumulation of IgG in specific areas, such as, the hippocampus. Parallel histochemical studies demonstrated significant changes in the hippocampus, and in white matter areas. They included large vacuoles and necrotic nuclei in the granular layer of the dentate gyrus, tangle-like appearance in some pyramidal neurons of the hippocampus, and vacuolar degeneration accompanied by oligodendroglia hypertrophy in white matter tracts, such as, the corpus callosum and fimbria. In contrast, immunization with Torpedo cholinergic nerve terminals, that has no cognitive effects on the rat, also did not induce brain morphological changes. These findings suggest that the learning and memory deficits induced by immunizing rats with cholinergic PK are related to the observed brain morphological changes, and support the hypothesis that the antibodies to cholinergic neurons found in the sera of AD patients may play a role in neuronal degeneration in this disease.
ESTHER : Michaelson_1990_Mol.Chem.Neuropathol_13_71
PubMedSearch : Michaelson_1990_Mol.Chem.Neuropathol_13_71
PubMedID: 2095784

Title : Alzheimer's disease antibodies bind specifically to a neurofilament protein in Torpedo cholinergic neurons - Chapman_1989_J.Neurosci_9_2710
Author(s) : Chapman J , Bachar O , Korczyn AD , Wertman E , Michaelson DM
Ref : Journal of Neuroscience , 9 :2710 , 1989
Abstract : Alzheimer's disease (AD) is characterized by neurofibrillary tangles and neuritic plaques and by the degeneration of central cholinergic neurons. Recent studies indicated the presence of antibodies in the sera and cerebrospinal fluid of AD patients which react with neuronal tissue and which recognize cholinergic neurons. In order to identify the cholinergic antigens against which the AD antibodies are directed, we have recently used the purely cholinergic electromotor neurons of the electric fish Torpedo which are chemically homogenous and cross-react antigenically with mammalian cholinergic neurons. This study revealed that immunoglobulins (IgG) from sera of AD patients bind specifically to an antigen in Torpedo electromotor neurons with an apparent molecular weight of 200 kDa. In the present report we attempt to characterize this antigen. The similarity in size of this protein to that of the heavy neurofilament subunit (NF-H) and the association of neurofilaments with plaques and tangles prompted us to examine the possibility that it is a neurofilament protein. Our findings show that IgG from sera of AD patients bind to the NF-H protein of Torpedo cholinergic neurons. Comparison of the binding of AD and control IgG to Torpedo cholinergic NF-H revealed that AD IgG bind to this neurofilament protein more readily than do control IgG. In contrast, AD and control IgG bind similarly to NF-H obtained from the chemically heterogenous Torpedo spinal cord and rat brain. These findings suggest that AD sera contain a repertoire of anti-NF-H IgG and that a subpopulation of these antibodies whose levels are significantly elevated in AD binds to epitopes highly enriched in Torpedo cholinergic NF-H.
ESTHER : Chapman_1989_J.Neurosci_9_2710
PubMedSearch : Chapman_1989_J.Neurosci_9_2710
PubMedID: 2475591

Title : Immunization of rats with cholinergic neurons induces behavioral deficits - Chapman_1989_J.Neural.Transplant_1_63
Author(s) : Chapman J , Feldon J , Alroy G , Michaelson DM
Ref : J Neural Transplant , 1 :63 , 1989
Abstract : We have previously shown that sera from patients with Alzheimer's disease (AD) contain a significantly high level of antibodies to the cell bodies (Perikarya; PK) but not to the nerve terminals (synaptosomes) of purely cholinergic neurons from the electric fish Torpedo. In the present study we examined the effect of repeated immunization of rats with either of these antigens for one year. Immunoblot studies revealed that sera of cholinergic PK immunized rats contained a high level of antibodies to cholinergic PK proteins, in particular to a 200 kilodalton protein, to which there are specifically high levels of antibodies in AD. Sera from rats immunized with cholinergic synaptosomes and from control rats contained very low levels of these antibodies. Behavioral studies performed one year after the initial immunization revealed that the cholinergic PK immunized rats were impaired in spatial learning and memory tasks (Morris swim test and T-maze alternation) when compared to control rats and that the synaptosome-immunized rats showed no such deficit. In contrast, the three groups performed similarly in general activity, active avoidance and conditioned emotional response tests. Further experiments revealed that the cholinergic PK immunized rats displayed a significant deficit in short term memory. The association of antibodies to cholinergic neurons with cognitive deficits in this rat model suggests that such antibodies may be involved in the pathogenesis of AD.
ESTHER : Chapman_1989_J.Neural.Transplant_1_63
PubMedSearch : Chapman_1989_J.Neural.Transplant_1_63
PubMedID: 2519521

Title : Serum antibodies to cholinergic neurons in Alzheimer's disease - Michaelson_1989_Prog.Clin.Biol.Res_317_689
Author(s) : Michaelson DM , Chapman J , Bachar O , Korczyn AD , Wertman E
Ref : Prog Clin Biol Res , 317 :689 , 1989
Abstract : Alzheimer's disease (AD) is associated with degenerative changes in nuclei of the basal forebrain which provide most of the cholinergic innervation of the cortex and hippocampus. Although the etiology and pathogenesis of AD are not known, several reports indicate the involvement of immunological mechanisms. In the present work we examined the existence of antibodies in sera of AD patients which bind specifically to cholinergic neurons. As antigen we employed the purely cholinergic electromotor neurons of the electric fish Torpedo which are chemically homogeneous and cross react antigenically with human and other mammalian cholinergic neurons. Our findings show that immunoglobulins (IgG) from sera of AD patients bind to the heavy neurofilament subunit (NF-H) of these neurons. Comparison of the binding of AD and control IgG to Torpedo cholinergic NF-H revealed that AD IgG bind to this neurofilament protein more than control IgG. In contrast, AD and control IgG bind similarly to NF-H obtained from the chemically heterogeneous Torpedo spinal cord and from rat brain. These findings suggest that AD sera contain a repertoire of anti NF-H IgG and that a subpopulation of these antibodies, whose levels are significantly elevated in AD, binds to epitopes highly enriched in Torpedo cholinergic NF-H. The diagnostic potential of these AD antibodies is discussed.
ESTHER : Michaelson_1989_Prog.Clin.Biol.Res_317_689
PubMedSearch : Michaelson_1989_Prog.Clin.Biol.Res_317_689
PubMedID: 2602432

Title : Antibodies to cholinergic neurons in Alzheimer's disease - Chapman_1988_J.Neurochem_51_479
Author(s) : Chapman J , Bachar O , Korczyn AD , Wertman E , Michaelson DM
Ref : Journal of Neurochemistry , 51 :479 , 1988
Abstract : Alzheimer's disease (AD) is associated with degenerative changes in nuclei of the basal forebrain which provide most of the cholinergic input to the cortex and hippocampus and with a reduction in presynaptic cholinergic parameters in these areas. Although the etiology and pathogenesis of AD are not known, several reports indicate the involvement of immunological mechanisms. In the present work we examined the existence of antibodies in sera of AD patients that bind specifically to cholinergic neurons. As antigens we employed the purely cholinergic electromotor neurons of the electric fish Torpedo which are chemically homogeneous and cross-react antigenically with human and other mammalian cholinergic neurons. Our findings show that immunoglobulins from sera of AD patients bind to a specific antigen (molecular mass 200 kilodaltons) in the cell bodies and axons of Torpedo electromotor neurons and that the levels of such antibodies are significantly higher in AD patients than in controls. The possible role of these antibodies in the cholinergic dysfunction in AD and their diagnostic potential are discussed.
ESTHER : Chapman_1988_J.Neurochem_51_479
PubMedSearch : Chapman_1988_J.Neurochem_51_479
PubMedID: 3292704