! # % & ( &) &) % + % # % ( &) &) % +!, (./ # % ##0 & ( &) % +, /77 2,
|
|
- Anissa Warner
- 5 years ago
- Views:
Transcription
1 MBE Advance Access published November 12, 2008! # % & ( &) &) % + % # % ( &) &) % +!, (./ # % ##0 & ( &) % +, /77 2, : ; <,! ( ; = ; ; The Author Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please journals.permissions@oxfordjournals.org
2 ! # >? ; = = 8 6 6? ? 9 2(!!! ( (! ( =! = # =? = = (! % = % ( ( = Α! (! = =! ( = = > = 9 ( 8 % ( 9? =!!! #?!!!! = ( >!!! (! ( = ( = < ;
3 # %& ( = 8; 9 Β + < 6! = (! = ; 8!( < 33 9!!! ;? 8? 9 6 = (! = 8 ( 33Χ9 >= =? 8%! ! 3 9 #? < = 6 = ( (! + ; % 8 6 < 2 / Χ < +! 6!! α 6 9 ; 8?? α 6 < 9 8 Ε 33/9 # ;! 6 = 8 6 6? = 9 = + α 6 6β 6 < ε 6 > + 6 +? + 6 < & < # = ( 6 6 <! 8> Φ 2 9 ;6 (! 8! 9 6 <! 8# Φ 2 9 (! ;6 8
4 = < 6 6 <! 8 Φ 2 / <! <! 6 < (! 6 < 6Γ6 + 8 Η; 2. 9! 6 < = ( 6 < 6 /6 <! 8Ε 2 Χ 9 α 6 6β 6 < ε 6 = +? 8 ( 33 9! (! (! + = +? 8 ( 7 Ι Ε 7Χ Ι > 7Χ.9 + ( 8&! 753Ι % = 75Χ9 # 6= % =! ( = = = + = Ε = ( ( = =!!? + 8 ( 33 9! =! ( (? = < (!?! = (? = = = = ( ( ( = =! =! % /
5 ( )%! &? = 8! % % ;! 9! Χ33! 8 = ; %# < & ( 8Α! >#Α = = +! 2ΑΑ = ( % 2; + 8&! 33/9 Α ( 8&! 33.9 &22 & 8Φ( Α! + ( (? = 8!?! =! ϑ &3 ΚΙ ( = 6( Λ 3 63! /3Μ9 = = (! < 8 ( = Φ Φ( 33 9 Α % (! &3!! + (?? Φ 3 ( &!? =!! &> 3! =!! =! (!! = <? 8Α2;2 Φ! ; =! =! Φ> #&>! ΕΗ # Χ.! Α / 3 8> 33.9 = Ν>> 8Ν Ο
6 > Ο> 9! 6 8/! 9 6 6! =!!! 6Β! 8;Ν9! 8;2#ΑΕ%Φ 6ΝΦ#;#;Α! 9 %! 8 9 = = &2Π%ΦΦ>! < 8 9 = = <. 3 / 8& 33Χ9 = Ν>> (! 6! 8/! 9 Φ 6 = < ( = 6! 6 > = ( +! 2Α / 3 > 22 #2 8! 77Χ9! = 8! ( = 9 (!&! +!#&!!+% # ( = ( = 8!! # % & 9 (! ( = 2! Ε = ( =! (?? 6 6? ( ( = ; (!!! = Χ33! (! 3 Χ
7 !!! Β!! = 8 9 Ε = ( =!!! (! # <! %! =! =!, % 9 % 8 ( % 6 8% 9 Α 6 8 9!! 8! 3 9 (! (! 6 ( > = = = 8! = 33.9 #!! < 6 > # ;! =! < Ε = ( % < (! 6! =! > Φ Η; + 8! ( 9 = ( 6 > Φ = ( + Η; 8! Θ! 33 Ι ( 33 Ι = 33.9 #! 6 6? =.
8 = 6! (! =?! ; ( (! = 8 9 = 8!! 9 >! 8 9!! = =! > %, = ( ( %! 6 6? = 8> 3 9 #! ( ) Α =!! #!!?! 8! &3 9,!! ( Ο Ο =!!! >!! >!! (! =! ( ( 8 =9 ( = (!!!! 8 33Ι
9 =!!!! ( > =!! 8 (! (,!!!! 8! &3 =? (! 9 >!!!! (! 8 = 9 #! = 6! =! 6 + 8! % 9 8 ( 33 9! ( Ι 339 > =!! + = > 3! = % 8 %!! 6!! 9 Φ (! = 8 ( 33 9 Ε = ( 8> 3 9! ( ( 6! 8! &3 9 > + =! =!! 7
10 > ( = ( ( < # (!!! =! = 8! 3 &3 9 >! ( =!! ( #!! = 2! (?!!!!!! 6 6 8! 3 9 8! 3 9 8! &3 9! = %!!! 8! +! Ι ( = ( 6& 33 9 = ( = 8 9! =!!! Φ Ε = (!! ( 2 >! =! 8! 3 %9 Ε = (! ( = 2 = 8!! & & 9 >!! %! ( ;Ν 3
11 !! 8 = 9 ( = 2 8! = = 9 = Α ( 8 9Ι! #!! = 2 (!!? ( 8> 9! > = 6!! =!? = 8! 9 %! = = <! Φ? = = ( >? =! ( Ρ > < = = =!!!! = Α = = ( (! 6! Ε = ( ( < = ( >! 8 9 %! =!? =!! >! ( 2!! ( =!
12 % 8! 9!! ( > Α>!! = = (?! >! 2 =! = ; (! <! = (! (!!! # <!! = % ( #!! = 8!)!#!+9 = (!! % ( <!! =! < Ε = ( = (!! > = %!!!!! >! ( = < <! = #? = (! (!! ( <!! # 8! 9!! ( 6 < = = = =
13 #! (!!! (! < ( ( = (! 8Ε 757Ι 6 33Ι 339 & %! 8 33 Ι 33.9 > 0! ( ( = = Ε = (!! < =! =? <! 8 + > Φ Φ Ε 9 = <!? = %!! =!! 6! (!! 8% 33 9 #! > = ( #! ( ; ; % = ( ( <? ( = > =! ( (! ( + Φ = 6 = 6! 8 9 > =! (! <! (
14 #% # &!+%! =!!!! 0 =! 8! 9 >! ( (? 8; 33/Ι 33Ι 33ΧΙ Ε 33.9! ( ( 8% 33 Ι Φ 33 9 > = ( ( ( = ( (? ;! =?! ( ( = # = (!! ( = = =! (!! (! /
15 !&,, ( ( ( + &? 8 &3 9! Γ Α % 8 &3 9! =! 8! &3 9! =! (! 8! &3 9!! 8! &3 9 >? 8 9 Φ > 3 # %. ( ( (! > = = 2& 8&) & % + 9 ;? 8% Σ % + 9 = ( = (!
16 ( ( ( #(! %! > Φ 33 > Ε Χ, % & =! & + Α ?! (! ( (!! Α, Χ6 Χ % Η Ν > % 2 ; Ν 33!!! ( Α., % = >! 7.3! + ( ( ( Ν % 3,/Χ6/Χ % = Ε Ν Χ + ( & ( Ν,/Χ6/. ( 6& > 33 >!!! + # Ν & 2(, 7.6 / ( ΕΝ & 33 > = 6 ; = Ν 2(,. 6.. Θ! % 2 33!!!!! Ν % 5/,Χ/5 6Χ/57 ( Ε = 7 > 6 Ν % 57,/ 6/7 = Ν >= =?! Ν % 57, / 6 / Ν 33 ΕΗ # 8! #! 9 ( Χ Α & (! & & #! Η! > 2! Η & Ε & 33 # < ;! < 6 6 < 8 & = Τ? Τ Ν %.., Χ 6 Χ. Α! 2 Α Ε! #( # % 33 2< &, > ( 6 =! ;,.5/6.55 Ε & ; Η Α Β > ; = 33. Α +! =! (! 5! 6 % 2( /,5365 Ε %! ( =!., Α & ΑΑ!! ( ; Χ, /536/5/ Ε > 33/! % 7,..6 5Χ ( Φ Α Α & & Φ %! > 33 ;,? = % 3, 76 3/ Χ
17 ( Φ Ν % %! > Φ 33! =, ( 2 &., 76. % Α % = ; ( 3 %, 7/.6 7/5 335!! Ν 2( ΧΧ, ΧΧ6.? & 335!! 2 & 5,5.67. & 33 ; 6! 6!! Φ # & 7, Χ36. ( 33Χ ; ; & %,Χ 6Χ/ 33Χ (! +! Ν 2( Χ, 6 / 6 % Φ ( Υ ( 2 & 33 Θ Φ # & 7, /Χ6 7 & +! & ( & Ν 33 (! Φ # & 7,/ 6.Χ ; Η # > Ε Α Β > 33/ %! +!! ; Α Χ,.Χ36.ΧΧ ; % ; Ε%Ν # 77. Α, + Α 2 %;2 ;2 & /, / Φ ( & Η#! + #% ( +!! Α % /, Φ Φ( 33!! =, (! Φ %., 56 Φ( %! > % >! Β 333! ;,Χ7 6.3 Ν2 33,!6 % % 7Χ, 3 6 Ν2 33! < 2< //, 76//! 77Χ > =,! %,.6 5 % Ν 33 ( ( = +! ; Α.,. 6. Ν > Ε 2 Φ 33 > ( ; 7, 6 > ( >! 33 ; %# &? 8 &?9, 6?! ;, 3 63/!( < Α Φ 33! ; %,Χ5 6Χ73 & Φ! 753 Ν Α,/Χ6/..
18 &! #! 2! Α Ε Ε Α &! 33/ % 2; +, Β = ( ;, / 6/ &! Ν Ε Ε ( > Α Α= 6Α! ; Φ 33. >#Α Α,!!! ;, Χ36 Χ/ & 33Χ < 6 #6Ε, < 6! = < < %, Χ556 Χ73 > Ν ; & 33. 2Α /, 2( Α 8 2Α 9 = ( / 3 % 2( /, 7Χ6 77 > Α Α Ν < 2 7Χ. # 6! ! 6 Ν % 7, Χ56.Χ Ν & 2 > ΕΑ 7.5 & + 2 Ν %, 36 / Α Ε 7Χ > 6 Ν % 5, 6 7 Ν %Β Ε Ν! &! Ε Ε Α Ν# 33! ( = 6% & 77, 3./6 3.Χ Ν = ( & % Ε # & %, Χ 5
19 (! /0, Α? %! % 1 % % ( & ( 3Χ 3//5 7 Χ33 Χ3 Χ3 6 6 ( > 7 ( 533/ ( 56 3 ς 3/ 3 3//Χ Χ5 Χ5 Χ /.5 73 Χ/ Χ/ Χ/ 6 6 ( 3 ΦΦ /3.. 7 / 7 / 5 / / 6 6 ( 3 5 ΦΦ 53 Χ/ 3Χ & >ς. 3 6 / & / Χ 6 Χ Χ / > Χ7 35Χ5 Ε> 7 2,! 2 / 2 ) % 5 ) %%. 2 ) Ε>.3 2 7ς 2 /ς %% 5ς %%.ς %.3ς 3 Χ / /57 3./ Χ.Χ /5 7 Χ 3 // 3 Χ/ 3..Χ 7 Χ 3 /5 3 3 / ΧΧ Χ 3 // 375 Χ 3/77 3 / Χ 3Χ ) 3 Β ς 3../ 3/7 33Χ /3 /3Χ ) Ν# 3 05Χ ) 2. 2 # >353! 6 2 & > ς Α Φς # ς.33.ς %! Ε> 3 2 % 3 ς Χ5 3/5 3 / /5 3 /5/ Χ5 Χ / / /. 3 3 / 3. 3 /. 3 / Χ % ς / ! ; > 7 / % /. 33 #6/5 %> Χ/ 5/!! 5 Α Χ Ω Φ! (!!?! Β 2 Φ! =!?!! 9 # = 8 9 = = = (!, 8 3/ ς3//χ9 = 8 3 ς 3 9! Ι
20 + & ( ( (! /0! 3 & ( 6 Ξ Ψ = 6 Ξ Ψ Φ ( > + 2 = < 6 < /5 6 & (! = 8 9! Β! 2< =! =, 7!, + 8 < 9Ι, 8 6> 9Ι / % Ε 8 9Ι ( (! & 8 6 9Ι! Φ Ι 6 >>Φ 8Α 6 9Ι 7! Φ, %. 8 9Ι & 8 6 9Ι 0 8Α 6 9 /8 9 : 7 : 7 %! ;! 8 ( = ( ;Ν Φ ( Ζ Χ3Μ = 9 3
21 De novo eukaryotic pathway De novo prokaryotic pathway Anthranilate branch kynureninase (KYN) EC encoded by kynu gene Anthranilate L-tryptophan tryptophan 2,3-dioxygenase (TDO) EC encoded by kyna gene N-formyl-L-kynurenine kynurenine formamidase (KFA) EC encoded by kynb gene L-Kynurenine kynurenine 3-monooxygenase (KMO) EC encoded by kmo gene 3-hydroxy-L-kynurenine kynureninase (KYN) EC encoded by kynu gene Dihydroxyacetone phosphate L-aspartate L-aspartate oxidase (NadB) EC encoded by nadb gene Iminoaspartate quinolinate synthetase (NadA) encoded by nada gene 3-hydroxyanthranilate 3-hydroxyanthranilate 3,-dioxygenase (HAD) EC encoded by haao gene 2-amino-3-carboxymuconate semialdehyde (non enzymatic) quinolinic acid (quinolinate) (pyridine-2,3-dicarboxylate) FIGURE 01 NAD (Nicotinamide adenine dinucleotide)
22 FIGURE 02
23 98 Xanthomonas campestris pv. vesicatoria Xanthomonas oryzae pv. oryzae 97 Xanthomonas campestris pv. campestris A) Stenotrophomonas maltophilia 81 Pseudomonas fluorescens 85 Salinispora arenicola Monosiga brevicollis Gemmata sp. Acidobacteria bacterium Myxococcus xanthus Stigmatella aurantiaca Flavobacteriales bacterium Polaribacter filamentus Tenacibaculum sp. Flavobacterium johnsoniae Robiginitalea biformata Flavobacteria bacterium Sus scrofa Homo sapiens Polaribacter irgensii Leeuwenhoekiella blandensis Psychroflexus torquis Cellulophaga sp. Salinispora tropica Croceibacter atlanticus Dictyostelium discoideum Tetraodon nigroviridis Brachydanio rerio Xenopus tropicalis Rattus norvegicus Mus musculus 98 Anopheles stephensi 95 Anopheles gambiae Aedes aegypti Bombyx mori Drosophila melanogaster Tribolium castaneum Caenorhabditis elegans Caenorhabditis briggsae 97 Xanthomonas axonopodis pv. citri Legionella pneumophila Neurospora crassa Aspergillus oryzae Emericella nidulans Cryptococcus neoformans Candida albicans Debaryomyces hansenii Ashbya gossypii Saccharomyces cerevisiae Xanthomonadales Flavobacteriales Flavobacteriales Eukaryota B) Cellulophaga sp. Leeuwenhoekiella blandensis Croceibacter atlanticus Psychroflexus torquis Flavobacteriales bacterium Tenacibaculum sp. Polaribacter filamentus Polaribacter irgensii Myxococcus xanthus Stigmatella aurantiaca Stenotrophomonas maltophilia Xanthomonas campestris pv. campestris 95 Xanthomonas oryzae pv. oryzae Xanthomonas campestris pv. vesicatoria Xanthomonas axonopodis pv. citri Flavobacteria bacterium Robiginitalea biformata Flavobacterium johnsoniae Acidobacteria bacterium Salinispora tropica Salinispora arenicola Schistosoma japonicum Mus musculus Rattus norvegicus Homo sapiens Caenorhabditis briggsae Caenorhabditis elegans Candida albicans 9 Ashbya gossypii 98 Saccharomyces cerevisiae 93 Yarrowia lipolytica Monosiga brevicollis Leishmania major Trypanosoma cruzi Dictyostelium discoideum Neurospora crassa 98 Chaetomium globosum 77 Gibberella zeae 98 Aspergillus oryzae Aspergillus fumigatus Aspergillus nidulans Cytophaga hutchinsonii Bacillus thuringiensis Bacillus anthracis Bacillus cereus Bacillus clausii Oceanobacillus iheyensis Exiguobacterium sibiricum Kineococcus radiotolerans Idiomarina loihiensis Roseobacter denitrificans Silicibacter pomeroyi Jannaschia sp. 95 Rhodobacter sphaeroides 98 Bradyrhizobium japonicum Rhizobium loti Paracoccus denitrificans Thermobifida fusca Streptomyces coelicolor Streptomyces avermitilis Marinomonas sp. Erythrobacter litoralis Maricaulis maris Sphingopyxis laskensis Nitrococcus mobilis Roseiflexus sp. Acidovorax avenae Polaromonas sp. Bordetella pertussis Bordetella bronchiseptica 90 8 Burkholderia cepacia Burkholderia vietnamiensis Burkholderia mallei Ralstonia eutropha Ralstonia metallidurans Ralstonia solanacearum Pseudomonas aeruginosa Pseudomonas fluorescens Flavobacteriales Xanthomonadales Eukaryota Firmicutes Proteobacteria
NAD Biosynthesis Evolution in Bacteria: Lateral Gene Transfer of Kynurenine Pathway in Xanthomonadales and Flavobacteriales
NAD Biosynthesis Evolution in Bacteria: Lateral Gene Transfer of Kynurenine Pathway in Xanthomonadales and Flavobacteriales Wanessa C. Lima,* Alessandro M. Varani, and Carlos F.M. Menck* *Department of
More informationSolution structure of Cox11: a novel type of immunoglobulin-like. cytochrome c oxidase
SUPPLEMENTARY MATERIAL Solution structure of Cox11: a novel type of immunoglobulin-like fold involved in Cu B site formation of cytochrome c oxidase Lucia Banci *, Ivano Bertini *, Francesca Cantini *,
More informationSUPPLEMENTARY INFORMATION
doi:1.138/nature1213 Supplementary Table 1. The Taxonomy of the Organisms Used in this Study Organism (acronym) Taxonomy Yeasts Zygosacharomyces rouxii (Zrou) Verterbrates Xenopus tropicalis (Xtro) Gallus
More informationSheet1. Page 1. protein
build 1 version 1 Ab initio model Ab initio GPIPE/6085/1.1/gnomon_prot build 1 version 1 Build GPIPE/6085/1.1/ Acyrthosiphon pisum build 2 version 1 Build GPIPE/7029/2.1/ Acyrthosiphon pisum build 2.1
More informationComparing Genomes! Homologies and Families! Sequence Alignments!
Comparing Genomes! Homologies and Families! Sequence Alignments! Allows us to achieve a greater understanding of vertebrate evolution! Tells us what is common and what is unique between different species
More information. α β γ δ ε ζ η θ ι κ λ μ Aμ ν(x) ξ ο π ρ ς σ τ υ φ χ ψ ω. Α Β Γ Δ Ε Ζ Η Θ Ι Κ Λ Μ Ν Ξ Ο Π Ρ Σ Τ Υ Φ Χ Ψ Ω. Friday April 1 ± ǁ
. α β γ δ ε ζ η θ ι κ λ μ Aμ ν(x) ξ ο π ρ ς σ τ υ φ χ ψ ω. Α Β Γ Δ Ε Ζ Η Θ Ι Κ Λ Μ Ν Ξ Ο Π Ρ Σ Τ Υ Φ Χ Ψ Ω Friday April 1 ± ǁ 1 Chapter 5. Photons: Covariant Theory 5.1. The classical fields 5.2. Covariant
More informationSupporting Information
Supporting Information Systematic analyses reveal uniqueness and origin of the CFEM domain in fungi Zhen-Na Zhang 1,2,, Qin-Yi Wu 1,, Gui-Zhi Zhang 2, Yue-Yan Zhu 1, Robert W. Murphy 3, Zhen Liu 3, * and
More informationA novel laminin β gene BmLanB1-w regulates wing-specific cell adhesion in silkworm, Bombyx mori
Supplementary information A novel laminin β gene BmLanB1-w regulates wing-specific cell adhesion in silkworm, Bombyx mori Xiaoling Tong*, Songzhen He *, Jun Chen, Hai Hu, Zhonghuai Xiang, Cheng Lu and
More informationNucleotide Cycle Metabolism in Microbial Systems
MICROBIOLOGICAL REVIEWS, Ma. 1980, p. 83-105 Vol. 44, No. 1 0146-0749/80/01-0083/23$02.00/0 Nicotinamide Adenine Dinucleotide Biosynthesis and Pyridine Nucleotide Cycle Metabolism in Microbial Systems
More informationLicense: Creative Commons Attribution Non-commercial No Derivatives
Title Type URL Design in the Time of Policy Problems Article Date 2016 Citation Creators http://ualresearchonline.arts.ac.uk/9542/ Kimbell, Lucy (2016) Design in the Time of Policy Problems. Proceedings
More informationPerspective. Abundant Microbial Inorganic Polyphosphate, Poly P Kinase Are Underappreciated
Abundant Microbial Inorganic Polyphosphate, Poly P Kinase Are Underappreciated Although some view poly P as a mere molecular fossil, the author thought that it plays a more prominent role in microorganisms
More informationPhylogenomics of phosphoinositide lipid kinases: perspectives on the evolution of second messenger signaling and drug discovery
RESEARCH ARTICLE Open Access Phylogenomics of phosphoinositide lipid kinases: perspectives on the evolution of second messenger signaling and drug discovery James R Brown 1, Kurt R Auger 2 Abstract Background:
More informationNew Universal Rules of Eukaryotic Translation Initiation Fidelity
New Universal Rules of Eukaryotic Translation Initiation Fidelity Hadas Zur 1, Tamir Tuller 2,3 * 1 The Blavatnik School of Computer Science, Tel Aviv University, Tel-Aviv, Israel, 2 Department of Biomedical
More informationComputational Structural Bioinformatics
Computational Structural Bioinformatics ECS129 Instructor: Patrice Koehl http://koehllab.genomecenter.ucdavis.edu/teaching/ecs129 koehl@cs.ucdavis.edu Learning curve Math / CS Biology/ Chemistry Pre-requisite
More informationFurther Maths A2 (M2FP2D1) Assignment ψ (psi) A Due w/b 19 th March 18
α β γ δ ε ζ η θ ι κ λ µ ν ξ ο π ρ σ τ υ ϕ χ ψ ω The mathematician s patterns, like the painter s or the poet s, must be beautiful: the ideas, like the colours or the words, must fit together in a harmonious
More informationECOL/MCB 320 and 320H Genetics
ECOL/MCB 320 and 320H Genetics Instructors Dr. C. William Birky, Jr. Dept. of Ecology and Evolutionary Biology Lecturing on Molecular genetics Transmission genetics Population and evolutionary genetics
More informationHigh Throughput Scientific Computing in Vaccine Research: Challenges and Opportunities
High Throughput Scientific Computing in Vaccine Research: Challenges and Opportunities Riccardo Beltrami Head, Data Science Unit Novartis Vaccines Univ. di Siena, Dec. 10 th 2014 Rev. 1.2.3 PDC# SIE-14-0923
More informationProduct Catalogue 2015 Clinical and Industrial Microbiology
Acinetobacter baumannii ATCC BAA-747 * 89141 Actinomyces odontolyticus ATCC 17929 * 89114 Aeromonas hydrophila ATCC 7966 * 89119 Aggregatibacter aphrophilus ATCC 7901 * 89091 Aspergillus brasiliensis ATCC
More informationPurpose. Process. Students will locate the species listed below on the infographic and write down the domain to which they belong:
Purpose This activity gives students practice with interpreting infographics and also supports student understanding of the similarities and differences between humans and other species. Process Students
More informationSUPPLEMENTARY INFORMATION
doi:10.1038/nature11541 Supplementary Figure 1. Genome-wide analysis of the phylogenetic relationships Phylogenetic tree of NDH-2s from Prokaryota, Protista, Plantae, Fungi and Metazoa. The WWW.NATURE.COM/NATURE
More information. α β γ δ ε ζ η θ ι κ λ μ Aμ ν(x) ξ ο π ρ ς σ τ υ φ χ ψ ω. Α Β Γ Δ Ε Ζ Η Θ Ι Κ Λ Μ Ν Ξ Ο Π Ρ Σ Τ Υ Φ Χ Ψ Ω. Wednesday March 30 ± ǁ
. α β γ δ ε ζ η θ ι κ λ μ Aμ ν(x) ξ ο π ρ ς σ τ υ φ χ ψ ω. Α Β Γ Δ Ε Ζ Η Θ Ι Κ Λ Μ Ν Ξ Ο Π Ρ Σ Τ Υ Φ Χ Ψ Ω Wednesday March 30 ± ǁ 1 Chapter 5. Photons: Covariant Theory 5.1. The classical fields 5.2. Covariant
More information11/24/13. Science, then, and now. Computational Structural Bioinformatics. Learning curve. ECS129 Instructor: Patrice Koehl
Computational Structural Bioinformatics ECS129 Instructor: Patrice Koehl http://www.cs.ucdavis.edu/~koehl/teaching/ecs129/index.html koehl@cs.ucdavis.edu Learning curve Math / CS Biology/ Chemistry Pre-requisite
More informationQuantitative Measurement of Genome-wide Protein Domain Co-occurrence of Transcription Factors
Quantitative Measurement of Genome-wide Protein Domain Co-occurrence of Transcription Factors Arli Parikesit, Peter F. Stadler, Sonja J. Prohaska Bioinformatics Group Institute of Computer Science University
More information4sec 2xtan 2x 1ii C3 Differentiation trig
A Assignment beta Cover Sheet Name: Question Done Backpack Topic Comment Drill Consolidation i C3 Differentiation trig 4sec xtan x ii C3 Differentiation trig 6cot 3xcosec 3x iii C3 Differentiation trig
More informationUreaplasma Urease Genes have Undergone a Unique Evolutionary Process
The Open Systems Biology Journal, 2009, 2, 1-7 1 Open Access Ureaplasma Urease Genes have Undergone a Unique Evolutionary Process Hiromi Nishida * Agricultural Bioinformatics Research Unit, Graduate School
More informationAdditional file 1 for Structural correlations in bacterial metabolic networks by S. Bernhardsson, P. Gerlee & L. Lizana
Additional file 1 for Structural correlations in bacterial metabolic networks by S. Bernhardsson, P. Gerlee & L. Lizana Table S1 The species marked with belong to the Proteobacteria subset and those marked
More informationBioinformatics Bioinf and E ormatics volu and E tionar volu y Genomics Genom 5/2/2011 1
Bioinformatics and Evolutionary Genomics 5/2/2011 1 Fritz-Laylin et al. cell 2010 Gene Trees, Gene Duplications, and Orthology How to make trees Bootstrap Interpreting trees duplications vs speciations
More informationThe natural history of the WRKY GCM1 zinc fingers and the relationship between transcription factors and transposons
Nucleic Acids Research, 2006, Vol. 00, No. 00 1 16 doi:10.1093/nar/gkl888 The natural history of the WRKY GCM1 zinc fingers and the relationship between transcription factors and transposons M. Madan Babu
More informationand in each case give the range of values of x for which the expansion is valid.
α β γ δ ε ζ η θ ι κ λ µ ν ξ ο π ρ σ τ υ ϕ χ ψ ω Mathematics is indeed dangerous in that it absorbs students to such a degree that it dulls their senses to everything else P Kraft Further Maths A (MFPD)
More informationExpanded View Figures
Eukaryotic kinetochore evolution Jolien JE van Hooff et al Expanded View Figures Opisthokonta moebozoa Excavata Stramenopila-lveolata-hizaria rchaeplastida present absent Homo sapiens Mus musculus enopus
More informationIn silico analysis of the adenylation domains of the freestanding enzymes belonging to the eucaryotic nonribosomal peptide synthetase-like family
In silico analysis of the adenylation domains of the freestanding enzymes belonging to the eucaryotic nonribosomal peptide synthetase-like family Leonardo Di Vincenzo 1, Ingeborg Grgurina 1 and Stefano
More information6.096 Algorithms for Computational Biology. Prof. Manolis Kellis
6.096 Algorithms for Computational Biology Prof. Manolis Kellis Today s Goals Introduction Class introduction Challenges in Computational Biology Gene Regulation: Regulatory Motif Discovery Exhaustive
More informationGene mention normalization in full texts using GNAT and LINNAEUS
Gene mention normalization in full texts using GNAT and LINNAEUS Illés Solt 1,2, Martin Gerner 3, Philippe Thomas 2, Goran Nenadic 4, Casey M. Bergman 3, Ulf Leser 2, Jörg Hakenberg 5 1 Department of Telecommunications
More informationComparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi
Resource Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi Michael J. Cornell, 1,2 Intikhab Alam, 1 Darren M. Soanes, 3 Han Min Wong,
More informationBiased amino acid composition in warm-blooded animals
Biased amino acid composition in warm-blooded animals Guang-Zhong Wang and Martin J. Lercher Bioinformatics group, Heinrich-Heine-University, Düsseldorf, Germany Among eubacteria and archeabacteria, amino
More informationY1 Double Maths Assignment λ (lambda) Exam Paper to do Core 1 Solomon C on the VLE. Drill
α β γ δ ε ζ η θ ι κ λ µ ν ξ ο π ρ σ τ υ ϕ χ ψ ω Nature is an infinite sphere of which the centre is everywhere and the circumference nowhere Blaise Pascal Y Double Maths Assignment λ (lambda) Tracking
More informationOrigin of the Bacterial SET Domain Genes: Vertical or Horizontal?
Origin of the Bacterial SET Domain Genes: Vertical or Horizontal? Raul Alvarez-Venegas,* Monther Sadder,*à Alexander Tikhonov,* and Zoya Avramova* *School of Biological Sciences, University of Nebraska
More informationE1 Enzyme of the Pyruvate Dehydrogenase Complex in Corynebacterium glutamicum: Molecular Analysis of the Gene and Phylogenetic Aspects
JOURNAL OF BACTERIOLOGY, Sept. 2005, p. 6005 6018 Vol. 187, No. 17 0021-9193/05/$08.00 0 doi:10.1128/jb.187.17.6005 6018.2005 Copyright 2005, American Society for Microbiology. All Rights Reserved. E1
More informationApplication of new distance matrix to phylogenetic tree construction
Application of new distance matrix to phylogenetic tree construction P.V.Lakshmi Computer Science & Engg Dept GITAM Institute of Technology GITAM University Andhra Pradesh India Allam Appa Rao Jawaharlal
More informationProduct Catalogue 2016 Clinical and Industrial Microbiology
Acinetobacter baumannii ATCC BAA-747 * 89141 Acinetobacter baumannii ATCC 19606 * 89174 Actinomyces odontolyticus ATCC 17929 * 89114 Aeromonas hydrophila ATCC 7966 * 89119 Aeromonas hydrophila ATCC 35654
More informationCharacterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions
RESEARCH ARTICLE Open Access Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions Minoru Hatayama 1, Jun Aruga 1,2* Abstract Background: The C2H2 zinc finger
More informationMathematics Review Exercises. (answers at end)
Brock University Physics 1P21/1P91 Mathematics Review Exercises (answers at end) Work each exercise without using a calculator. 1. Express each number in scientific notation. (a) 437.1 (b) 563, 000 (c)
More informationList of supplementary data
List of supplementary data Figure S1 Amino acid alignment for GiNT Figure S2Amino acid alignment and phylogenetic analysis for GiGS1 and GiGS2 Figure S3 Amino acid alignment for GiGluS Figure S4 Amino
More informationExploring metazoan evolution through dynamic and holistic changes in protein families and domains
Wang et al. BMC Evolutionary Biology 2012, 12:138 RESEARCH ARTICLE Open Access Exploring metazoan evolution through dynamic and holistic changes in protein families and domains Zhengyuan Wang 1, Dante
More informationPathogenic fungi genomics, evolution and epidemiology! John W. Taylor University of California Berkeley, USA
Pathogenic fungi genomics, evolution and epidemiology! John W. Taylor University of California Berkeley, USA Adaptation! Divergence Divergence Adaptation Darwin 1859 Mendel 1866 1830 1850 1870 1890 1910
More informationASSIGNMENT COVER SHEET omicron
ASSIGNMENT COVER SHEET omicron Name Question Done Backpack Ready for test Drill A differentiation Drill B sketches Drill C Partial fractions Drill D integration Drill E differentiation Section A integration
More informationCAP 5510: Introduction to Bioinformatics CGS 5166: Bioinformatics Tools
CAP 5510: to : Tools ECS 254A / EC 2474; Phone x3748; Email: giri@cis.fiu.edu My Homepage: http://www.cs.fiu.edu/~giri http://www.cs.fiu.edu/~giri/teach/bioinfs15.html Office ECS 254 (and EC 2474); Phone:
More informationA Convolutional Code-Based Sequence Analysis Model and Its Application
Int. J. Mol. Sci. 2013, 14, 8393-8405; doi:10.3390/ijms14048393 Article OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms A Convolutional Code-Based Sequence
More informationSupporting Online Material for
www.sciencemag.org/cgi/content/full/316/5822/288/dc1 Supporting Online Material for Structural Basis for Substrate Delivery by Acyl Carrier Protein in the Yeast Fatty Acid Synthase Marc Leibundgut, Simon
More informationA2 Assignment zeta Cover Sheet. C3 Differentiation all methods. C3 Sketch and find range. C3 Integration by inspection. C3 Rcos(x-a) max and min
A Assignment zeta Cover Sheet Name: Question Done Backpack Ready? Topic Comment Drill Consolidation M1 Prac Ch all Aa Ab Ac Ad Ae Af Ag Ah Ba C3 Modulus function Bb C3 Modulus function Bc C3 Modulus function
More informationStructure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis
Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis Xiuying Liu 1,3, Yan Yin 1,2,3, Jinjun Wu 1 and Zhenfeng Liu 1 1 National Laboratory of Biomacromolecules,
More informationSequence analysis, structure and binding site prediction of Sigma 1 receptor protein by in silico method
www.bioinformation.net Hypothesis Volume 9(19) Sequence analysis, structure and binding site prediction of Sigma 1 receptor protein by in silico method Narayanasamy Lokeswaran Latha 1, Garimella Gyananath
More informationThe origins and early evolution of DNA mismatch repair genes multiple horizontal gene transfers and co-evolution
Published online 26 October 2007 Nucleic Acids Research, 2007, Vol. 35, No. 22 7591 7603 doi:10.1093/nar/gkm921 The origins and early evolution of DNA mismatch repair genes multiple horizontal gene transfers
More informationIncreasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences
Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences Ryan J. Taft 1, 2 * and John S. Mattick 3 1 Rowe Program in Genetics,
More informationMaster Biomedizin ) UCSC & UniProt 2) Homology 3) MSA 4) Phylogeny. Pablo Mier
Master Biomedizin 2018 1) UCSC & UniProt 2) Homology 3) MSA 4) 1 12 a. All of the sequences in file1.fasta (https://cbdm.uni-mainz.de/mb18/) are homologs. How many groups of orthologs would you say there
More informationSupplementary material
Table 1: The number of protein sequences listed for the BacelLo training data set according to each origin and localization. Localization Plants Animal Fungi chloroplast (ch) 204 - - cytoplasm (cy) 58
More informationOur product offering. The ATCC Licensed Derivative Program
Our product offering Currently MECCONTI offers three different product lines of lyophilized micro-organisms: MicroSwabs: A MicroSwab consists of a lyophilized pellet of a single micro-organism strain inside
More informationAdvanced Cell Biology. Lecture 2
Advanced Cell Biology. Lecture 2 Alexey Shipunov Minot State University January 13, 2012 Outline Questions and answers Microscopy Prokaryotic and eukaryotic cells Outline Questions and answers Microscopy
More informationRNA polymerase II clustering through carboxyterminal domain phase separation
SUPPLEMENTARY INFORMATION Articles https://doi.org/10.1038/s41594-018-0112-y In the format provided by the authors and unedited. RNA polymerase II clustering through carboxyterminal domain phase separation
More informationEnsembl focuses on metazoan (animal) genomes. The genomes currently available at the Ensembl site are:
Comparative genomics and proteomics Species available Ensembl focuses on metazoan (animal) genomes. The genomes currently available at the Ensembl site are: Vertebrates: human, chimpanzee, mouse, rat,
More informationC. elegans as an in vivo model to decipher microbial virulence. Centre d Immunologie de Marseille-Luminy
C. elegans as an in vivo model to decipher microbial virulence Centre d Immunologie de Marseille-Luminy C. elegans : a model organism Mechanisms of apoptosis, RNA interference Neuronal function and development
More informationSpeaker: TzeFeng-Tian Advisor: Ruey-Shyang,Hseu, PhD
Diego Martinez, Randy M Berka, Bernard Henrissat, Markku Saloheimo, Mikko Arvas, Scott E Baker, Jarod Chapman, Olga Chertkov, Pedro M Coutinho, Dan Cullen, Etienne G J Danchin, Igor V Grigoriev, Paul Harris,
More informationTable S1. Non-NCBI databases Kingdom Animalia databases D. discoideum, E. histolytica, E. tenella, Leishmania http://www.genedb.org/ species, Plasmodium species, Trypanosome species C. intestinalis, L.
More informationIntragenomic Variation and Evolution of the Internal Transcribed Spacer of the rrna Operon in Bacteria
J Mol Evol (2007) 65:44 67 DOI: 10.1007/s00239-006-0235-3 Intragenomic Variation and Evolution of the Internal Transcribed Spacer of the rrna Operon in Bacteria Frank J. Stewart, Colleen M. Cavanaugh Department
More informationEntities for Symbols and Greek Letters
Entities for Symbols and Greek Letters The following table gives the character entity reference, decimal character reference, and hexadecimal character reference for symbols and Greek letters, as well
More informationAssist. Prof. Martina Šeruga Musić acad. year 2016/17
Assist. Prof. Martina Šeruga Musić acad. year 2016/17 PHYTOPATHOGENIC BACTERIA there are more than 100 species of known phytopathogenic bacteria genera Agrobacterium, Erwinia, Ralstonia, Pseudomonas, Xanthomonas,
More informationA2 Assignment lambda Cover Sheet. Ready. Done BP. Question. Aa C4 Integration 1 1. C4 Integration 3
A Assignment lambda Cover Sheet Name: Question Done BP Ready Topic Comment Drill Mock Exam Aa C4 Integration sin x+ x+ c 4 Ab C4 Integration e x + c Ac C4 Integration ln x 5 + c Ba C Show root change of
More informationCSE 427 Computational Biology Winter Sequence Alignment. Sequence Alignment. Sequence Similarity: What
CSE 427 Computational Biology Winter 2008 Sequence Alignment; DNA Replication Sequence Alignment Part I Motivation, dynamic programming, global alignment 1 3 Sequence Alignment Sequence Similarity: What
More informationSupporting Online Material for
www.sciencemag.org/cgi/content/full/328/5979/624/dc1 Supporting Online Material for Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids Nancy A. Moran* and Tyler Jarvik *To whom
More informationDomain Bacteria. BIO 220 Microbiology Jackson Community College
Domain Bacteria BIO 220 Microbiology Jackson Community College John Ireland, Ph.D. 2006 Scientific Nomenclature Domain - Bacteria Phylum Important for gross characteristics Class Intermediate characteristics
More informationExploring metazoan evolution through dynamic and holistic changes in protein families and domains
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2012 Exploring metazoan evolution through dynamic and holistic changes in protein families and domains Zhengyuan
More informationG4120: Introduction to Computational Biology
ICB Fall 2009 G4120: Introduction to Computational Biology Oliver Jovanovic, Ph.D. Columbia University Department of Microbiology & Immunology Copyright 2008 Oliver Jovanovic, All Rights Reserved. Genome
More informationEZ-COMP EZ-COMP For Training and Proficiency Testing Product Details
EZ-COMP For Training and Proficiency Testing Mixed microorganism populations Identified by codes rather than descriptions Refrigerated storage Traceable to reference culture Product warranty Product Details
More informationSupporting Information
Supporting Information Levy et al. 0.073/pnas.2093209 Schematic view SURFACE INTERIOR cross-section SUPPORT RIM CORE RIM Interacting partner INTERIOR SURFACE SUPPORT RIM CORE rasac < 25% & ΔrASA = 0 rasac
More informationTwo Mathematical Constants
1 Two Mathematical Constants Two of the most important constants in the world of mathematics are π (pi) and e (Euler s number). π = 3.14159265358979323846264338327950288419716939937510... e = 2.71828182845904523536028747135266249775724709369995...
More informationStructural basis for amino acid recognition and transmembrane signaling by tandem-per-arnt-sim (tandem-pas) chemoreceptor sensory domains
Supporting information Volume 71 (2015) Supporting information for article: Structural basis for amino acid recognition and transmembrane signaling by tandem-per-arnt-sim (tandem-pas) chemoreceptor sensory
More informationReassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors
Genes 2011, 2, 449-501; doi:10.3390/genes2030449 Article OPEN ACCESS genes ISSN 2073-4425 www.mdpi.com/journal/genes Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene
More informationCyclin Y Is a Novel Conserved Cyclin Essential for Development in Drosophila
Supporting Information http://www.genetics.org/cgi/content/full/genetics.110.114017/dc1 Cyclin Y Is a Novel Conserved Cyclin Essential for Development in Drosophila Dongmei Liu and Russell L. Finley, Jr.
More informationTolerance of E.coli to 6-ACA
Supporting Information 0.9 Tolerance of E.coli to 6-ACA 0.8 0.7 Groth rate (u/h) 0.6 0.5 0.4 0.3 Escherichia coli RV308 6-ACA Escherichia coli RV308 NaCL 0.2 0.1 0 0 g/l 25 g/l 50 g/l 75 g/l 100 g/l 125
More informationQuantitative and qualitative analyses. of in-paralogs
Quantitative and qualitative analyses of in-paralogs Dissertation zur Erlangung des naturwissentschaflichen Doktorgrades der Bayerischen Julius-Maximilians Universität Würzburg vorgelegt von Stanislav
More informationSymbols and dingbats. A 41 Α a 61 α À K cb ➋ à esc. Á g e7 á esc. Â e e5 â. Ã L cc ➌ ã esc ~ Ä esc : ä esc : Å esc * å esc *
Note: Although every effort ws tken to get complete nd ccurte tble, the uhtor cn not be held responsible for ny errors. Vrious sources hd to be consulted nd MIF hd to be exmined to get s much informtion
More informationHonor pledge: I have neither given nor received unauthorized aid on this test. Name :
Midterm exam #2 Take-home questions MB 451 Microbial Diversity The rules: You are free to use any notes, books, or online material while taking this take-home exam. You are NOT allowed to get (or give)
More informationCRISPRseek Workshop Design of target-specific guide RNAs in CRISPR-Cas9 genome-editing systems
April 2008 CRISPRseek Workshop Design of target-specific guide RNAs in CRISPR-Cas9 genome-editing systems Lihua Julie Zhu Sept 10th 2014 Michael Brodsky Jianhong Ou INSTALLATION First install R 3.1.0 Windows:
More informationPROTEINS: Structure, Function and Bioinformatics. In press (Prot R1)
PROTEINS: Structure, Function and Bioinformatics In press (Prot-00261-2006.R1) TITLE: Classification and Functional Annotation of Eukaryotic Protein Kinases RUNNING TITLE: Classification and Annotation
More informationPyrobayes: an improved base caller for SNP discovery in pyrosequences
Pyrobayes: an improved base caller for SNP discovery in pyrosequences Aaron R Quinlan, Donald A Stewart, Michael P Strömberg & Gábor T Marth Supplementary figures and text: Supplementary Figure 1. The
More informationCo-evolution of the branch site and SR proteins in eukaryotes
Supplementary Material Co-evolution of the branch site and SR proteins in eukaryotes Mireya Plass 1, Eneritz Agirre 1, Diana Reyes 2, Francisco Camara 2 and Eduardo Eyras 1,3 1 Computational Genomics Group,
More informationThe Effects of the Carbon Source on Glutamate Dehydrogenase Activities in Aspergillus nidulans
Joiirnal of General Microbiology ( I 974), 81, I 65-1 70 Printed in Gseat Britnin The Effects of the Carbon Source on Glutamate Dehydrogenase Activities in Aspergillus nidulans By M. J. HYNES Department
More informationSUPPLEMENTARY INFORMATION
doi: 1.138/nature6454 SUPPLEMENTARY INFORMATION Supplementary online figures Supplementary Figure 1. Nitrocellulose filter binding of deletion fragments to trna Ala. Binding assays were performed as described
More informationT m / A. Table C2 Submicroscopic Masses [2] Symbol Meaning Best Value Approximate Value
APPENDIX C USEFUL INFORMATION 1247 C USEFUL INFORMATION This appendix is broken into several tables. Table C1, Important Constants Table C2, Submicroscopic Masses Table C3, Solar System Data Table C4,
More informationMicrobiological Testing Summary
BACTERICIDAL ACTIVITY EN 1276 - Chemical disinfectants and antiseptics - Quantitative suspension test for the evaluation of bactericidal activity of chemical disinfectants and antiseptics used in food,
More informationHeuristic Methods. Heuristic methods for alignment Sequence databases Multiple alignment Gene and protein prediction
Heuristic methods for alignment Sequence databases Multiple alignment Gene and protein prediction Armstrong, 2010 Heuristic Methods! FASTA! BLAST! Gapped BLAST! PSI-BLAST Armstrong, 2010 1 Assumptions
More information2 GENE FUNCTIONAL SIMILARITY. 2.1 Semantic values of GO terms
Bioinformatics Advance Access published March 7, 2007 The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
More informationGenome Evolution Greg Lang, Department of Biological Sciences
Genome Evolution Greg Lang, Department of Biological Sciences BioS 010: Bioscience in the 21st Century Mechanisms of genome evolution Gene Duplication Genome Rearrangement Whole Genome Duplication Gene
More informationMCB142/ICB163 Overview. Instructors:
MCB142/ICB163 Overview Instructors: Professor Sharon Amacher Professor Abby Dernburg Professor Monty Slatkin GSIs: Kristin Camfield Nat Hallihan Hana Lee Christine Preston Richard Price Kate Smallenburg
More informationCamello, a novel family of Histone Acetyltransferases that acetylate histone H4 and is essential for zebrafish development
Supplementary Information: Camello, a novel family of Histone Acetyltransferases that acetylate histone H4 and is essential for zebrafish development Krishanpal Karmodiya 1, Krishanpal Anamika 1,2, Vijaykumar
More informationIntroduction to Bioinformatics Integrated Science, 11/9/05
1 Introduction to Bioinformatics Integrated Science, 11/9/05 Morris Levy Biological Sciences Research: Evolutionary Ecology, Plant- Fungal Pathogen Interactions Coordinator: BIOL 495S/CS490B/STAT490B Introduction
More informationProcedure to Create NCBI KOGS
Procedure to Create NCBI KOGS full details in: Tatusov et al (2003) BMC Bioinformatics 4:41. 1. Detect and mask typical repetitive domains Reason: masking prevents spurious lumping of non-orthologs based
More informationPolyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics
/ Journal Homepage / Table of Contents for this issue REVIEW www.rsc.org/npr Natural Product Reports Polyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics
More informationSupporting Information
Supporting Information Burkhardt et al. 10.1073/pnas.1106189108 SI Experimental Procedures Structure Determination and Refinement. Diffraction data were integrated and scaled with XDS (1). The structure
More informationMarine medaka ATP-binding cassette (ABC) superfamily and new insight into teleost Abch nomenclature
Supplementary file for: Marine medaka ATP-binding cassette (ABC) superfamily and new insight into teleost Abch nomenclature Chang-Bum Jeong a,b,#, Bo-Mi Kim a,#, Hye-Min Kang a, Ik-Young Choi c, Jae-Sung
More information