Top-quark rare decay $tto c h$ in R-parity-violating SUSY

[6—10] [5]
and CLEOc
[23]
collabo-
rations using either double-tag or single-tag method. The simple average of the values in the two tables gives σ obs (ψ ) 7.75nb and σ (DD) 6.27nb, respectively, with the difference of about 1.5nb (about 19% of the total cross section of the ψ production), which implies the non-DD decays of the ψ are important. However, the existence of substantial non-DD decays is not unambiguous due to the poor statistics of the
experiment/ accelerator LGW/SPEAR
[13] [14] [15]
Mψ / (MeV/c2 ) 3772 ± 6 3770 ± 6 3764 ± 5 3768 ± 2 3773 ± 1 3772
Γψ / (MeV/c2 ) 28 ± 5 24 ± 5 24 ± 5 34 ± 8 26 ± 4 23.2
第 31 卷 第 2 期 2007 年 2 月
高 能 物 理 与 核 物 理
HIGH ENERGY PHYSICS AND NUCLEAR PHYSICS
Vol. 31, No. 2 Feb., 2007
Experimental Searches for the Non-DD Decays of ψ(3770) in e+ e− Collider *

the CDF and D experiments using data collected at s = 1:8 TeV during the 19941995 data taking run. CDF nds a preliminary mass of MW = 80:43 0:16 GeV and D measures a mass of MW = 80:44 0:12 GeV.
I INTRODUCTION
During the 1994-1995 collider run of the Fermilab Tevatron, the CDF and D experiments collected data corresponding to integrated luminosities of 90 pb?1 and 82 pb?1 respectively. From this data, CDF extracted 21,000 W ! events while D obtained 28,000 W ! e events. These W events were used to make measurements2 of the mass of the W boson 1].
C Event Selection
The signature for W events is a high momentum muon or electron (pT > 25 GeV)4, and large missing energy from the undetected neutrino (Et > 25 GeV). = This missing energy is the transverse momentum needed to balance the visible transverse momentum in the event. The visible momentum is the sum of the muon or electron momentum and a vector sum of the energy in the calorimeter towers of the detector (not including the energy from the lepton of course; see Sec. III A). The lepton must be central (j j < 1) and satisfy various quality cuts. For D , these cuts require the electron to be isolated, to have a calorimeter shower shape consistent with Monte Carlo expectations, and to have a track pointing at the calorimeter

Conjugation vs hyperconjugation in molecular structure of acroleinSvitlana V.Shishkina a ,⇑,Anzhelika I.Slabko b ,Oleg V.Shishkin a ,caDivision of Functional Materials Chemistry,SSI ‘Institute for Single Crystals’,National Academy of Science of Ukraine,60Lenina Ave.,Kharkiv 61001,Ukraine bDepartment of Technology of Plastic Masses,National Technical University ‘Kharkiv Polythechnic Institute’,21Frunze Str.,Kharkiv 61002,Ukraine cDepartment of Inorganic Chemistry,V.N.Karazin Kharkiv National University,4Svobody Sq.,Kharkiv 61077,Ukrainea r t i c l e i n f o Article history:Received 4August 2012In final form 16November 2012Available online 29November 2012a b s t r a c tAnalysis of geometric parameters of butadiene and acrolein reveals the contradiction between the Csp 2–Csp 2bond length in acrolein and classical concept of conjugation degree in the polarized molecules.In this Letter the reasons of this contradiction have been investigated.It is concluded that the Csp 2–Csp 2bond length in acrolein is determined by influence of the bonding for it p –p conjugation and antibonding n ?r ⁄hyperconjugation between the oxygen lone pair and the antibonding orbital of the single bond.It was shown also this bond length depends on the difference in energy of conjugative and hyperconjuga-tive interactions.Ó2012Elsevier B.V.All rights reserved.1.IntroductionButadiene and acrolein belong to the most fundamental mole-cules in the organic chemistry.They are canonical objects for the investigation of phenomena of p –p conjugation between double bonds and polarization of p -system by heteroatom [1].According to many experimental [2–16]as well as theoretical studies [13,17–23]the molecular structure of butadiene is determined by conjugation between p -orbitals of two double bonds and may be described as superposition of two resonance structures (Scheme 1).The presence of zwitterionic structure causes the shortening of the central single Csp 2–Csp 2bond as compare with similar unconjugated bond [24].Acrolein differs from butadiene by presence of the oxygen atom instead terminal methylene group.According to classical concepts of organic chemistry such replacement should causes polarization of p -system due to presence of highly polar C @O bond [25].This leads to significant increase of the contribution of the zwitterionic resonance structure (Scheme 1)reflecting strengthening of conju-gation between p -systems of double bonds.Therefore the central Csp 2–Csp 2bond must be shorter in acrolein as compared with one in butadiene.However numerous investigations of acrolein by experimental [26–28]and theoretical methods [26,27,29–36]demonstrate an opposite situation:the Csp 2–Csp 2bond length varies within the range 1.469Ä1.481Åin acrolein as compared with 1.454Ä1.467in butadiene.Based on these data one can conclude that conjugation between double bonds in acrolein is weaker than in butadiene.At that time the rotation barrier obtained from quan-tum-chemical calculations is higher in acrolein [26,27],confirming stronger conjugation between double bonds.Thus,results of experimental and theoretical investigations demonstrate the con-tradiction between the strengthening of the conjugation in acrolein as compare with butadiene and the values of the Csp 2–Csp 2bond length in these molecules.Recently such illogical situation was observed also in derivatives of cyclohexene containing conjugated endocyclic and exocyclic double bonds [37].It was assumed that elongation of the Csp 2–Csp 2bond in cycloxen-2-enone as compare with one in 3-methylene-cyclohexene is caused by the influence of n ?r ⁄hyperconjugation.In this Letter we demonstrate the results of the investigation of intramolecular interactions in butadiene and acrolein which ex-plain the experimentally observed contradiction between the length of the Csp 2–Csp 2bond and degree of conjugation in acrolein.2.Method of calculationsThe structures of all investigated molecules were optimized using second-order Møller-Plesset perturbation theory [38].The standard aug-cc-pvtz basis set [39]was applied.The character of stationary points on the potential energy surface was verified by calculations of vibrational frequencies within the harmonic approximation using analytical second derivatives at the same level of theory.All stationary points possess zero (minima)or one (saddle points)imaginary frequencies.The verification of the calculation method was performed using optimization of butadi-ene and acrolein by MP2/aug-cc-pvqz,CCSD(T)/cc-pvtz and CCSD(T)/6-311G(d,p)methods [40].The geometry of saddle points for the rotation process was lo-cated using standard optimization technique [41].The barrier of the rotation in all molecules was calculated as the difference be-tween the Gibbs free energies at 298K of the most stable s-trans0009-2614/$-see front matter Ó2012Elsevier B.V.All rights reserved./10.1016/j.cplett.2012.11.032Corresponding author.Fax:+3805723409339.E-mail address:sveta@ (S.V.Shishkina).conformer and saddle-point conformation.All calculations were performed using the G AUSSIAN 03program [42].The intramolecular interactions were investigated within the Natural Bonding Orbitals theory [43]with N BO 5.0program [44].Calculations were performed using B3LYP/aug-cc-pvtz wave func-tion obtained from single point calculations by G AUSSIAN 03program.The conjugation and hyperconjugation interactions are referred to as ‘delocalization’corrections to the zeroth-order natural Lewis structure.For each donor N BO (i )and acceptor N BO (j ),the stabiliza-tion energy E (2)associated with delocalization (‘2e-stabilization’)i ?j is estimated asE ð2Þ¼D E ij ¼q iF ði ;j Þ22j À2i;where q i is the donor orbital occupancy,e j and e i are the diagonal elements (orbital energies),and F (i,j )is the off-diagonal N BO Fock matrix element.3.Results and discussionThe equilibrium geometry of s-trans and s-cis conformers of butadiene and acrolein calculated by MP/aug-cc-pvtz method (Ta-ble 2)agrees very well with obtained earlier results [2–23,25–34]and data of higher and more computationally expensive methods (Table 1).It can be noted that the C–C bond length in acrolein(Tables 1and 2)is longer as compared with butadiene in all sta-tionary points on the potential energy surface.Such relation does not agree with the conception of the resonance theory [45–47].Analysis of intramolecular interactions in both molecules using N BO theory indicates that acrolein differs from butadiene by pres-ence of intramolecular interaction between lone pair of the oxygen atom and antibonding orbital of the C–C bond (Figure 1)as well as the polarization of one double bond containing more electronega-tive ually the interactions between lone pair and antibonding orbital of single bond are stronger than the interac-tions between the C–H bond and antibonding orbital [48]and they can influence geometrical characteristics.Such type of interactions is named by anomeric effect and it is studied very well for the case when the central bond between interacted orbitals is single [48,49].It is investigated in details [49]an influence of classical anomeric effect on conformation of the substituents about central single bond as well as on values of bond lengths.In the case of hyperconjugation interactions along double bond in acrolein orien-tation of substituents around it is determined by its double charac-ter.Therefore,n ?r ⁄hyperconjugative interaction can influence on the bond lengths of interacted ones only.It can assume the dou-ble character of the central bond must also promote some strengthening of this influence due to shorter distance between the lone pair of the oxygen atom and antibonding orbital of the C–C bond.Results of N BO analysis of intramolecular interactions in butadi-ene and acrolein demonstrate that the energy of n ?r ⁄interaction between lone pair of the oxygen atom and antibonding orbital of the C–C bond in acrolein is twice as high of the energy of r ?r ⁄interaction between the C–H bond and antibonding orbital of the C–C bond in butadiene (Table 2).At that time the energy of n ?r ⁄interaction is close enough to the energy of p –pTable 2The equilibrium geometries (bond lengths,Åand C @C–C @X (X =CH 2,O)torsion angle,deg.),transition state of the rotation process,bond length alternation (BLA)parameter,related energy (D E rel ,kcal/mol),related stability (D G 298,kcal/mol)and energy of strongest intramolecular interactions (E (2),kcal/mol)for butadiene and acrolein optimized by MP2/aug-cc-pvtz method.The wave function calculated by b3lyp/aug-cc-pvtz method was used for N BO analysis.ConformerBond lengths (Å)C @C–C @X torsion angle deg.BLA (Å)D E rel(kcal/mol)D G 298(kcal/mol)E (2)(kcal/mol)C @CC–C C @X p –pn ?r ⁄(C–C)r ?r ⁄(C–C)Butadiene s-trans 1.341 1.453 1.340180.0+0.1120030.74–8.67gauche 1.340 1.465 1.34036.8+0.125 2.83 2.8921.04–8.94TS 1.3361.4801.336101.8+0.1446.446.102.32–10.66Acrolein s-trans 1.339 1.469 1.219180.0+0.1300027.7518.06–s-cis 1.338 1.481 1.2190.0+0.143 2.26 2.2224.6319.05–TS1.334 1.492 1.21692.5+0.1588.017.46–18.78–Acrolein +BH 3s-trans 1.341 1.449 1.235180.0+0.1080033.12 2.4511.43s-cis 1.340 1.460 1.2340.0+0.120 2.45 2.3829.61 2.6011.43TS1.334 1.476 1.23193.7+0.1429.258.61–2.3911.55Table 1The Csp 2–Csp 2bond length in butadiene and acrolein optimized by different quantum-chemical methods.Method of calculationCsp 2–Csp 2bond length (Å)D (Csp 2–Csp 2)(Å)ButadieneAcrolein MP2/aug-cc-pvtz 1.453 1.4690.016MP2/aug-cc-pvqz 1.451 1.4670.016CCSD(T)/cc-pvtz1.461 1.4780.017CCSD(T)/6–311G(d,p)1.4681.4870.019S.V.Shishkina et al./Chemical Physics Letters 556(2013)18–2219conjugation between two double bonds.Therefore it can assume that the influence of p–p conjugation and n?r⁄hyperconjuga-tion on the C–C bond length should be comparable.However two strongest intramolecular interactions in the acrolein differ from each other:p–p conjugation between double bonds causes the shortening of the C–C bond in contrary to n?r⁄hyperconjugation which leads to the elongation of the C–C bond owing to the popu-lation of its antibonding orbital.Taking into account this situation it is possible to conclude that length of the Csp2–Csp2single bond in acrolein is determined by balance of two opposite factors namely p–p conjugation and n?r⁄hyperconjugation which may be considered as bonding and antibonding interactions for this bond(Figure1).In this case the length of the Csp2–Csp2bond in acrolein depends on the con-tribution of each of these factors.The changing of the delocaliza-tion of the structures due to influence of intramolecular interactions can be analyzed easier by mean of the bond length alternation(BLA)parameter(Table2).The analysis of BLA shows the presence of n?r⁄hyperconjugative interaction in acrolein what results in the increasing of alternation of double bonds as compare with butadiene.Clear estimation of influence of both interactions on geometri-cal parameters of molecule may be performed by comparison of properties of single C–C bond and BLA parameter in equilibrium s-trans conformation and in situations where one or both intramo-lecular interactions are absent.It is well known that p–p conjugation between double bonds decreases appreciably up to disappearing(in acrolein)in the tran-sition state for the rotation around single bond process(Figure2). The data of N BO analysis for butadiene and acrolein in the transition state confirm this evidence(Table2).As expected the absence of p–p conjugation results in the elongation of the Csp2–Csp2bond and increasing of BLA as compare with equilibrium geometry.At that time single C–C bond remains longer in the transition state for acrolein as compare with one for butadiene’s transition state.1.4921.4691.4491.476π−π is present n σ* is presentπ−π is absentn σ* is absent without π−πwithout n σ∗Figure2.Influence of p–p⁄conjugation and n?r⁄hyperconjugation on the C–Cbond length in acrolein.Table3The energy(E(2),kcal/mol)of the conjugative(bonding)and hyperconjugative(antibonding)intramolecular interactions influencing the Csp2–Csp2bond length in butadiene, acrolein and its complex with BH3.Molecule Bonding interactions E(2)(kcal/mol)Antibonding interactions E(2)(kcal/mol)Butadienes-trans BD(2)C1-C2–BD(2)C3-C430.74BD(1)C1-H5–BD(1)C2-C38.67 BD(1)C2-H7–BD(1)C3-H87.68BD(1)C4-H9–BD(1)C2-C38.67 gauche BD(2)C1-C2–BD(2)C3-C421.04BD(1)C1-H5–BD(1)C2-C38.94 BD(1)C2-H7–BD(1)C3-C4 5.36BD(1)C4-H9–BD(1)C2-C39.01BD(1)C3-H8–BD(1)C1-C2 5.36TS BD(1)C1-C2–BD(1)C3-C4 3.5BD(1)C1-H5–BD(1)C2-C310.66 BD(1)C1-C2–BD(2)C3-C4 3.46BD(1)C4-H9–BD(1)C2-C310.66BD(1)C3-C4–BD(2)C1-C2 3.46BD(2)C1-C2–BD(2)C3-C4 2.32BD(1)C3-H8–BD(2)C1-C29.57BD(1)C2-H7–BD(2)C3-C49.57Acroleins-trans BD(1)C1-C2–BD(1)C3-O4 2.73BD(1)C1-H5–BD(1)C2-C38.25 BD(2)C1-C2–BD(2)C3-O427.75LP(2)O4–BD(1)C2-C318.06BD(1)C2-H7–BD(1)C3-H8 5.95s-cis BD(2)C1-C2–BD(2)C3-O424.63BD(1)C1-H5–BD(1)C2-C38.76 BD(1)C2-H7–BD(1)C3-O4 4.05LP(2)O4–BD(1)C2-C319.05BD(1)C3-H8–BD(1)C1-C2 5.01TS BD(1)C1-C2–BD(2)C3-O4 2.98BD(1)C1-H5–BD(1)C2-C39.07 BD(1)C3-O4–BD(2)C1-C2 4.48LP(2)O4–BD(1)C2-C318.78BD(1)C3-H8–BD(2)C1-C2 5.85BD(1)C2-H7–BD(2)C3-O4 6.16Acrolein+BH3s-trans BD(1)C1-C2–BD(1)C3-O4 3.07BD(1)C1-H6–BD(1)C2-C38.09 BD(2)C1-C2–BD(2)C3-O433.12BD(1)C2-C3–BD(1)O4-B511.43BD(1)C2-H8–BD(1)C3-H9 5.97LP(1)O4–BD(1)C2-C3 2.45 s-cis BD(1)C1-C2–BD(1)C3-H9 4.98BD(1)C1-H6–BD(1)C2-C38.51 BD(2)C1-C2–BD(2)C3-O429.61BD(1)C2-C3–BD(1)O4-B511.43BD(1)C2-H8–BD(1)C3-O4 4.41LP(1)O4–BD(1)C2-C3 2.60 TS BD(1)C1-C2–BD(1)C3-O40.55BD(1)C1-H6–BD(1)C2-C39.05 BD(1)C1-C2–BD(2)C3-O4 3.01BD(1)C2-C3–BD(1)O4-B511.55BD(2)C1-C2–BD(1)C3-O4 4.90LP(1)O4–BD(1)C2-C3 2.39BD(1)C3-H9–BD(2)C1-C2 6.13BD(1)C2-H8–BD(2)C3-O4 6.8820S.V.Shishkina et al./Chemical Physics Letters556(2013)18–22It is additional argument about the influence of n?r⁄hypercon-jugation on the C–C bond length through the C@O double bond.In contrary to p–p conjugation n?r⁄hyperconjugation is present in all stationary points on the potential energy surface for acrolein(Table2).But this interaction can be shielded by for-mation of dative bond involving lone pair of the oxygen atom and unoccupied orbital of Lewis acid,for example,BH3.The formed O–B bond has r-character and the energy of its interaction with antibonding orbital of the central C–C bond is very close to the en-ergy of similar C–H?r⁄(C–C)interaction in butadiene(Table2). The absence of n?r⁄hyperconjugation results significant short-ening of the Csp2–Csp2bond and decreasing of BLA in all stationary points for acrolein.It is more interesting that the C–C bond in acro-lein becomes shorter and p–p conjugation becomes stronger as compare with ones in butadiene in the case of absence of n?r⁄hyperconjugative interaction(Table2)what agrees well with the resonance theory.This evidence is confirmed also by values of BLA parameter.It is very interesting the situation when both strong intramolec-ular interactions are absent namely acrolein with shielded by BH3 lone pair in the transition state for the rotation process.In absence of p–p conjugative and n?r⁄hyperconjugative interactions the C–C bond length is almost equal to mean value for length of this bond for s-trans and s-cis conformers of acrolein with both interac-tions(Table2).This fact confirms that the C–C bond length in acro-lein in the equilibrium state is determined by balance of p–p conjugation and n?r⁄hyperconjugation.Taking into account the opposite influence of two types of intra-molecular interactions on the C–C bond one may assume that its length depends on the difference in energy of bonding and antibonding interactions for this bond.In such case all bonding for C–C bond and antibonding for it interactions(Table3)must be taken into account.Specially,this is important for transition states where p–p conjugative interaction is minimal and r(c-H)–p interaction appears instead it.This interaction has bond-ing for Csp2–Csp2bond character and it is weaker as compare with p–p interaction.Analysis of relation between C–C bond length and total energy of intramolecular interaction influencing on it demon-strates good correlation between them(Figure3)with correlation coefficient aboutÀ0.93.The barrier of the rotation around ordinary C–C bond is also sensitive to intramolecular interactions.The absence of n?r⁄hyperconjugation in acrolein results the increase of conjugation in molecule what leads to the increase of the rotation barrier (Table2).4.ConclusionsResults of quantum-chemical calculations demonstrate the structure of acrolein does not correspond to conventional views about influence of the polarization of p-system by the oxygen atom.According to classic viewpoint this effect should lead to in-crease of conjugation between double bonds and shortening of central single C–C bond as compared to butadiene.However,anal-ysis of intramolecular interactions shows that the geometry of acrolein is determined by counteraction of p–p conjugation and n?r⁄hyperconjugation.The energies of these interactions are very close but ones influence on the C–C bond lengths in opposite directions.Conjugation promotes the shortening of the central sin-gle bond due to the overlapping of the p-orbitals of two double bonds.In the contrary the n?r⁄hyperconjugation causes the elongation of the C–C bond due to the population of its antibonding orbital.The absence of conjugation in the 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DOI: 10.1126/science.1094786, 441 (2004);304Science et al.Mitchell S. Abrahamsen,Cryptosporidium parvum Complete Genome Sequence of the Apicomplexan, (this information is current as of October 7, 2009 ):The following resources related to this article are available online at/cgi/content/full/304/5669/441version of this article at:including high-resolution figures, can be found in the online Updated information and services,/cgi/content/full/1094786/DC1 can be found at:Supporting Online Material/cgi/content/full/304/5669/441#otherarticles , 9 of which can be accessed for free: cites 25 articles This article 239 article(s) on the ISI Web of Science. cited by This article has been /cgi/content/full/304/5669/441#otherarticles 53 articles hosted by HighWire Press; see: cited by This article has been/cgi/collection/genetics Genetics: subject collections This article appears in the following/about/permissions.dtl in whole or in part can be found at: this article permission to reproduce of this article or about obtaining reprints Information about obtaining registered trademark of AAAS.is a Science 2004 by the American Association for the Advancement of Science; all rights reserved. The title Copyright American Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by the Science o n O c t o b e r 7, 2009w w w .s c i e n c e m a g .o r g D o w n l o a d e d f r o m3.R.Jackendoff,Foundations of Language:Brain,Gram-mar,Evolution(Oxford Univ.Press,Oxford,2003).4.Although for Frege(1),reference was established rela-tive to objects in the world,here we follow Jackendoff’s suggestion(3)that this is done relative to objects and the state of affairs as mentally represented.5.S.Zola-Morgan,L.R.Squire,in The Development andNeural Bases of Higher Cognitive Functions(New York Academy of Sciences,New York,1990),pp.434–456.6.N.Chomsky,Reflections on Language(Pantheon,New York,1975).7.J.Katz,Semantic Theory(Harper&Row,New York,1972).8.D.Sperber,D.Wilson,Relevance(Harvard Univ.Press,Cambridge,MA,1986).9.K.I.Forster,in Sentence Processing,W.E.Cooper,C.T.Walker,Eds.(Erlbaum,Hillsdale,NJ,1989),pp.27–85.10.H.H.Clark,Using Language(Cambridge Univ.Press,Cambridge,1996).11.Often word meanings can only be fully determined byinvokingworld knowledg e.For instance,the meaningof “flat”in a“flat road”implies the absence of holes.However,in the expression“aflat tire,”it indicates the presence of a hole.The meaningof“finish”in the phrase “Billfinished the book”implies that Bill completed readingthe book.However,the phrase“the g oatfin-ished the book”can only be interpreted as the goat eatingor destroyingthe book.The examples illustrate that word meaningis often underdetermined and nec-essarily intertwined with general world knowledge.In such cases,it is hard to see how the integration of lexical meaning and general world knowledge could be strictly separated(3,31).12.W.Marslen-Wilson,C.M.Brown,L.K.Tyler,Lang.Cognit.Process.3,1(1988).13.ERPs for30subjects were averaged time-locked to theonset of the critical words,with40items per condition.Sentences were presented word by word on the centerof a computer screen,with a stimulus onset asynchronyof600ms.While subjects were readingthe sentences,their EEG was recorded and amplified with a high-cut-off frequency of70Hz,a time constant of8s,and asamplingfrequency of200Hz.14.Materials and methods are available as supportingmaterial on Science Online.15.M.Kutas,S.A.Hillyard,Science207,203(1980).16.C.Brown,P.Hagoort,J.Cognit.Neurosci.5,34(1993).17.C.M.Brown,P.Hagoort,in Architectures and Mech-anisms for Language Processing,M.W.Crocker,M.Pickering,C.Clifton Jr.,Eds.(Cambridge Univ.Press,Cambridge,1999),pp.213–237.18.F.Varela et al.,Nature Rev.Neurosci.2,229(2001).19.We obtained TFRs of the single-trial EEG data by con-volvingcomplex Morlet wavelets with the EEG data andcomputingthe squared norm for the result of theconvolution.We used wavelets with a7-cycle width,with frequencies ranging from1to70Hz,in1-Hz steps.Power values thus obtained were expressed as a per-centage change relative to the power in a baselineinterval,which was taken from150to0ms before theonset of the critical word.This was done in order tonormalize for individual differences in EEG power anddifferences in baseline power between different fre-quency bands.Two relevant time-frequency compo-nents were identified:(i)a theta component,rangingfrom4to7Hz and from300to800ms after wordonset,and(ii)a gamma component,ranging from35to45Hz and from400to600ms after word onset.20.C.Tallon-Baudry,O.Bertrand,Trends Cognit.Sci.3,151(1999).tner et al.,Nature397,434(1999).22.M.Bastiaansen,P.Hagoort,Cortex39(2003).23.O.Jensen,C.D.Tesche,Eur.J.Neurosci.15,1395(2002).24.Whole brain T2*-weighted echo planar imaging bloodoxygen level–dependent(EPI-BOLD)fMRI data wereacquired with a Siemens Sonata1.5-T magnetic reso-nance scanner with interleaved slice ordering,a volumerepetition time of2.48s,an echo time of40ms,a90°flip angle,31horizontal slices,a64ϫ64slice matrix,and isotropic voxel size of3.5ϫ3.5ϫ3.5mm.For thestructural magnetic resonance image,we used a high-resolution(isotropic voxels of1mm3)T1-weightedmagnetization-prepared rapid gradient-echo pulse se-quence.The fMRI data were preprocessed and analyzedby statistical parametric mappingwith SPM99software(http://www.fi/spm99).25.S.E.Petersen et al.,Nature331,585(1988).26.B.T.Gold,R.L.Buckner,Neuron35,803(2002).27.E.Halgren et al.,J.Psychophysiol.88,1(1994).28.E.Halgren et al.,Neuroimage17,1101(2002).29.M.K.Tanenhaus et al.,Science268,1632(1995).30.J.J.A.van Berkum et al.,J.Cognit.Neurosci.11,657(1999).31.P.A.M.Seuren,Discourse Semantics(Basil Blackwell,Oxford,1985).32.We thank P.Indefrey,P.Fries,P.A.M.Seuren,and M.van Turennout for helpful discussions.Supported bythe Netherlands Organization for Scientific Research,grant no.400-56-384(P.H.).Supporting Online Material/cgi/content/full/1095455/DC1Materials and MethodsFig.S1References and Notes8January2004;accepted9March2004Published online18March2004;10.1126/science.1095455Include this information when citingthis paper.Complete Genome Sequence ofthe Apicomplexan,Cryptosporidium parvumMitchell S.Abrahamsen,1,2*†Thomas J.Templeton,3†Shinichiro Enomoto,1Juan E.Abrahante,1Guan Zhu,4 Cheryl ncto,1Mingqi Deng,1Chang Liu,1‡Giovanni Widmer,5Saul Tzipori,5GregoryA.Buck,6Ping Xu,6 Alan T.Bankier,7Paul H.Dear,7Bernard A.Konfortov,7 Helen F.Spriggs,7Lakshminarayan Iyer,8Vivek Anantharaman,8L.Aravind,8Vivek Kapur2,9The apicomplexan Cryptosporidium parvum is an intestinal parasite that affects healthy humans and animals,and causes an unrelenting infection in immuno-compromised individuals such as AIDS patients.We report the complete ge-nome sequence of C.parvum,type II isolate.Genome analysis identifies ex-tremely streamlined metabolic pathways and a reliance on the host for nu-trients.In contrast to Plasmodium and Toxoplasma,the parasite lacks an api-coplast and its genome,and possesses a degenerate mitochondrion that has lost its genome.Several novel classes of cell-surface and secreted proteins with a potential role in host interactions and pathogenesis were also detected.Elu-cidation of the core metabolism,including enzymes with high similarities to bacterial and plant counterparts,opens new avenues for drug development.Cryptosporidium parvum is a globally impor-tant intracellular pathogen of humans and animals.The duration of infection and patho-genesis of cryptosporidiosis depends on host immune status,ranging from a severe but self-limiting diarrhea in immunocompetent individuals to a life-threatening,prolonged infection in immunocompromised patients.Asubstantial degree of morbidity and mortalityis associated with infections in AIDS pa-tients.Despite intensive efforts over the past20years,there is currently no effective ther-apy for treating or preventing C.parvuminfection in humans.Cryptosporidium belongs to the phylumApicomplexa,whose members share a com-mon apical secretory apparatus mediating lo-comotion and tissue or cellular invasion.Many apicomplexans are of medical or vet-erinary importance,including Plasmodium,Babesia,Toxoplasma,Neosprora,Sarcocys-tis,Cyclospora,and Eimeria.The life cycle ofC.parvum is similar to that of other cyst-forming apicomplexans(e.g.,Eimeria and Tox-oplasma),resulting in the formation of oocysts1Department of Veterinary and Biomedical Science,College of Veterinary Medicine,2Biomedical Genom-ics Center,University of Minnesota,St.Paul,MN55108,USA.3Department of Microbiology and Immu-nology,Weill Medical College and Program in Immu-nology,Weill Graduate School of Medical Sciences ofCornell University,New York,NY10021,USA.4De-partment of Veterinary Pathobiology,College of Vet-erinary Medicine,Texas A&M University,College Sta-tion,TX77843,USA.5Division of Infectious Diseases,Tufts University School of Veterinary Medicine,NorthGrafton,MA01536,USA.6Center for the Study ofBiological Complexity and Department of Microbiol-ogy and Immunology,Virginia Commonwealth Uni-versity,Richmond,VA23198,USA.7MRC Laboratoryof Molecular Biology,Hills Road,Cambridge CB22QH,UK.8National Center for Biotechnology Infor-mation,National Library of Medicine,National Insti-tutes of Health,Bethesda,MD20894,USA.9Depart-ment of Microbiology,University of Minnesota,Min-neapolis,MN55455,USA.*To whom correspondence should be addressed.E-mail:abe@†These authors contributed equally to this work.‡Present address:Bioinformatics Division,Genetic Re-search,GlaxoSmithKline Pharmaceuticals,5MooreDrive,Research Triangle Park,NC27009,USA.R E P O R T S SCIENCE VOL30416APRIL2004441o n O c t o b e r 7 , 2 0 0 9 w w w . s c i e n c e m a g . o r g D o w n l o a d e d f r o mthat are shed in the feces of infected hosts.C.parvum oocysts are highly resistant to environ-mental stresses,including chlorine treatment of community water supplies;hence,the parasite is an important water-and food-borne pathogen (1).The obligate intracellular nature of the par-asite ’s life cycle and the inability to culture the parasite continuously in vitro greatly impair researchers ’ability to obtain purified samples of the different developmental stages.The par-asite cannot be genetically manipulated,and transformation methodologies are currently un-available.To begin to address these limitations,we have obtained the complete C.parvum ge-nome sequence and its predicted protein com-plement.(This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the project accession AAEE00000000.The version described in this paper is the first version,AAEE01000000.)The random shotgun approach was used to obtain the complete DNA sequence (2)of the Iowa “type II ”isolate of C.parvum .This isolate readily transmits disease among numerous mammals,including humans.The resulting ge-nome sequence has roughly 13ϫgenome cov-erage containing five gaps and 9.1Mb of totalDNA sequence within eight chromosomes.The C.parvum genome is thus quite compact rela-tive to the 23-Mb,14-chromosome genome of Plasmodium falciparum (3);this size difference is predominantly the result of shorter intergenic regions,fewer introns,and a smaller number of genes (Table 1).Comparison of the assembled sequence of chromosome VI to that of the recently published sequence of chromosome VI (4)revealed that our assembly contains an ad-ditional 160kb of sequence and a single gap versus two,with the common sequences dis-playing a 99.993%sequence identity (2).The relative paucity of introns greatly simplified gene predictions and facilitated an-notation (2)of predicted open reading frames (ORFs).These analyses provided an estimate of 3807protein-encoding genes for the C.parvum genome,far fewer than the estimated 5300genes predicted for the Plasmodium genome (3).This difference is primarily due to the absence of an apicoplast and mitochondrial genome,as well as the pres-ence of fewer genes encoding metabolic functions and variant surface proteins,such as the P.falciparum var and rifin molecules (Table 2).An analysis of the encoded pro-tein sequences with the program SEG (5)shows that these protein-encoding genes are not enriched in low-complexity se-quences (34%)to the extent observed in the proteins from Plasmodium (70%).Our sequence analysis indicates that Cryptosporidium ,unlike Plasmodium and Toxoplasma ,lacks both mitochondrion and apicoplast genomes.The overall complete-ness of the genome sequence,together with the fact that similar DNA extraction proce-dures used to isolate total genomic DNA from C.parvum efficiently yielded mito-chondrion and apicoplast genomes from Ei-meria sp.and Toxoplasma (6,7),indicates that the absence of organellar genomes was unlikely to have been the result of method-ological error.These conclusions are con-sistent with the absence of nuclear genes for the DNA replication and translation machinery characteristic of mitochondria and apicoplasts,and with the lack of mito-chondrial or apicoplast targeting signals for tRNA synthetases.A number of putative mitochondrial pro-teins were identified,including components of a mitochondrial protein import apparatus,chaperones,uncoupling proteins,and solute translocators (table S1).However,the ge-nome does not encode any Krebs cycle en-zymes,nor the components constituting the mitochondrial complexes I to IV;this finding indicates that the parasite does not rely on complete oxidation and respiratory chains for synthesizing adenosine triphosphate (ATP).Similar to Plasmodium ,no orthologs for the ␥,␦,or εsubunits or the c subunit of the F 0proton channel were detected (whereas all subunits were found for a V-type ATPase).Cryptosporidium ,like Eimeria (8)and Plas-modium ,possesses a pyridine nucleotide tran-shydrogenase integral membrane protein that may couple reduced nicotinamide adenine dinucleotide (NADH)and reduced nico-tinamide adenine dinucleotide phosphate (NADPH)redox to proton translocation across the inner mitochondrial membrane.Unlike Plasmodium ,the parasite has two copies of the pyridine nucleotide transhydrogenase gene.Also present is a likely mitochondrial membrane –associated,cyanide-resistant alter-native oxidase (AOX )that catalyzes the reduction of molecular oxygen by ubiquinol to produce H 2O,but not superoxide or H 2O 2.Several genes were identified as involved in biogenesis of iron-sulfur [Fe-S]complexes with potential mitochondrial targeting signals (e.g.,nifS,nifU,frataxin,and ferredoxin),supporting the presence of a limited electron flux in the mitochondrial remnant (table S2).Our sequence analysis confirms the absence of a plastid genome (7)and,additionally,the loss of plastid-associated metabolic pathways including the type II fatty acid synthases (FASs)and isoprenoid synthetic enzymes thatTable 1.General features of the C.parvum genome and comparison with other single-celled eukaryotes.Values are derived from respective genome project summaries (3,26–28).ND,not determined.FeatureC.parvum P.falciparum S.pombe S.cerevisiae E.cuniculiSize (Mbp)9.122.912.512.5 2.5(G ϩC)content (%)3019.43638.347No.of genes 38075268492957701997Mean gene length (bp)excluding introns 1795228314261424ND Gene density (bp per gene)23824338252820881256Percent coding75.352.657.570.590Genes with introns (%)553.9435ND Intergenic regions (G ϩC)content %23.913.632.435.145Mean length (bp)5661694952515129RNAsNo.of tRNA genes 454317429944No.of 5S rRNA genes 6330100–2003No.of 5.8S ,18S ,and 28S rRNA units 57200–400100–20022Table parison between predicted C.parvum and P.falciparum proteins.FeatureC.parvum P.falciparum *Common †Total predicted proteins380752681883Mitochondrial targeted/encoded 17(0.45%)246(4.7%)15Apicoplast targeted/encoded 0581(11.0%)0var/rif/stevor ‡0236(4.5%)0Annotated as protease §50(1.3%)31(0.59%)27Annotated as transporter ࿣69(1.8%)34(0.65%)34Assigned EC function ¶167(4.4%)389(7.4%)113Hypothetical proteins925(24.3%)3208(60.9%)126*Values indicated for P.falciparum are as reported (3)with the exception of those for proteins annotated as protease or transporter.†TBLASTN hits (e Ͻ–5)between C.parvum and P.falciparum .‡As reported in (3).§Pre-dicted proteins annotated as “protease or peptidase”for C.parvum (CryptoGenome database,)and P.falciparum (PlasmoDB database,).࿣Predicted proteins annotated as “trans-porter,permease of P-type ATPase”for C.parvum (CryptoGenome)and P.falciparum (PlasmoDB).¶Bidirectional BLAST hit (e Ͻ–15)to orthologs with assigned Enzyme Commission (EC)numbers.Does not include EC assignment numbers for protein kinases or protein phosphatases (due to inconsistent annotation across genomes),or DNA polymerases or RNA polymerases,as a result of issues related to subunit inclusion.(For consistency,46proteins were excluded from the reported P.falciparum values.)R E P O R T S16APRIL 2004VOL 304SCIENCE 442 o n O c t o b e r 7, 2009w w w .s c i e n c e m a g .o r g D o w n l o a d e d f r o mare otherwise localized to the plastid in other apicomplexans.C.parvum fatty acid biosynthe-sis appears to be cytoplasmic,conducted by a large(8252amino acids)modular type I FAS (9)and possibly by another large enzyme that is related to the multidomain bacterial polyketide synthase(10).Comprehensive screening of the C.parvum genome sequence also did not detect orthologs of Plasmodium nuclear-encoded genes that contain apicoplast-targeting and transit sequences(11).C.parvum metabolism is greatly stream-lined relative to that of Plasmodium,and in certain ways it is reminiscent of that of another obligate eukaryotic parasite,the microsporidian Encephalitozoon.The degeneration of the mi-tochondrion and associated metabolic capabili-ties suggests that the parasite largely relies on glycolysis for energy production.The parasite is capable of uptake and catabolism of mono-sugars(e.g.,glucose and fructose)as well as synthesis,storage,and catabolism of polysac-charides such as trehalose and amylopectin. Like many anaerobic organisms,it economizes ATP through the use of pyrophosphate-dependent phosphofructokinases.The conver-sion of pyruvate to acetyl–coenzyme A(CoA) is catalyzed by an atypical pyruvate-NADPH oxidoreductase(Cp PNO)that contains an N-terminal pyruvate–ferredoxin oxidoreductase (PFO)domain fused with a C-terminal NADPH–cytochrome P450reductase domain (CPR).Such a PFO-CPR fusion has previously been observed only in the euglenozoan protist Euglena gracilis(12).Acetyl-CoA can be con-verted to malonyl-CoA,an important precursor for fatty acid and polyketide biosynthesis.Gly-colysis leads to several possible organic end products,including lactate,acetate,and ethanol. The production of acetate from acetyl-CoA may be economically beneficial to the parasite via coupling with ATP production.Ethanol is potentially produced via two in-dependent pathways:(i)from the combination of pyruvate decarboxylase and alcohol dehy-drogenase,or(ii)from acetyl-CoA by means of a bifunctional dehydrogenase(adhE)with ac-etaldehyde and alcohol dehydrogenase activi-ties;adhE first converts acetyl-CoA to acetal-dehyde and then reduces the latter to ethanol. AdhE predominantly occurs in bacteria but has recently been identified in several protozoans, including vertebrate gut parasites such as Enta-moeba and Giardia(13,14).Adjacent to the adhE gene resides a second gene encoding only the AdhE C-terminal Fe-dependent alcohol de-hydrogenase domain.This gene product may form a multisubunit complex with AdhE,or it may function as an alternative alcohol dehydro-genase that is specific to certain growth condi-tions.C.parvum has a glycerol3-phosphate dehydrogenase similar to those of plants,fungi, and the kinetoplastid Trypanosoma,but(unlike trypanosomes)the parasite lacks an ortholog of glycerol kinase and thus this pathway does not yield glycerol production.In addition to themodular fatty acid synthase(Cp FAS1)andpolyketide synthase homolog(Cp PKS1), C.parvum possesses several fatty acyl–CoA syn-thases and a fatty acyl elongase that may partici-pate in fatty acid metabolism.Further,enzymesfor the metabolism of complex lipids(e.g.,glyc-erolipid and inositol phosphate)were identified inthe genome.Fatty acids are apparently not anenergy source,because enzymes of the fatty acidoxidative pathway are absent,with the exceptionof a3-hydroxyacyl-CoA dehydrogenase.C.parvum purine metabolism is greatlysimplified,retaining only an adenosine ki-nase and enzymes catalyzing conversionsof adenosine5Ј-monophosphate(AMP)toinosine,xanthosine,and guanosine5Ј-monophosphates(IMP,XMP,and GMP).Among these enzymes,IMP dehydrogenase(IMPDH)is phylogenetically related toε-proteobacterial IMPDH and is strikinglydifferent from its counterparts in both thehost and other apicomplexans(15).In con-trast to other apicomplexans such as Toxo-plasma gondii and P.falciparum,no geneencoding hypoxanthine-xanthineguaninephosphoribosyltransferase(HXGPRT)is de-tected,in contrast to a previous report on theactivity of this enzyme in C.parvum sporo-zoites(16).The absence of HXGPRT sug-gests that the parasite may rely solely on asingle enzyme system including IMPDH toproduce GMP from AMP.In contrast to otherapicomplexans,the parasite appears to relyon adenosine for purine salvage,a modelsupported by the identification of an adeno-sine transporter.Unlike other apicomplexansand many parasitic protists that can synthe-size pyrimidines de novo,C.parvum relies onpyrimidine salvage and retains the ability forinterconversions among uridine and cytidine5Ј-monophosphates(UMP and CMP),theirdeoxy forms(dUMP and dCMP),and dAMP,as well as their corresponding di-and triphos-phonucleotides.The parasite has also largelyshed the ability to synthesize amino acids denovo,although it retains the ability to convertselect amino acids,and instead appears torely on amino acid uptake from the host bymeans of a set of at least11amino acidtransporters(table S2).Most of the Cryptosporidium core pro-cesses involved in DNA replication,repair,transcription,and translation conform to thebasic eukaryotic blueprint(2).The transcrip-tional apparatus resembles Plasmodium interms of basal transcription machinery.How-ever,a striking numerical difference is seenin the complements of two RNA bindingdomains,Sm and RRM,between P.falcipa-rum(17and71domains,respectively)and C.parvum(9and51domains).This reductionresults in part from the loss of conservedproteins belonging to the spliceosomal ma-chinery,including all genes encoding Smdomain proteins belonging to the U6spliceo-somal particle,which suggests that this par-ticle activity is degenerate or entirely lost.This reduction in spliceosomal machinery isconsistent with the reduced number of pre-dicted introns in Cryptosporidium(5%)rela-tive to Plasmodium(Ͼ50%).In addition,keycomponents of the small RNA–mediatedposttranscriptional gene silencing system aremissing,such as the RNA-dependent RNApolymerase,Argonaute,and Dicer orthologs;hence,RNA interference–related technolo-gies are unlikely to be of much value intargeted disruption of genes in C.parvum.Cryptosporidium invasion of columnarbrush border epithelial cells has been de-scribed as“intracellular,but extracytoplas-mic,”as the parasite resides on the surface ofthe intestinal epithelium but lies underneaththe host cell membrane.This niche may al-low the parasite to evade immune surveil-lance but take advantage of solute transportacross the host microvillus membrane or theextensively convoluted parasitophorous vac-uole.Indeed,Cryptosporidium has numerousgenes(table S2)encoding families of putativesugar transporters(up to9genes)and aminoacid transporters(11genes).This is in starkcontrast to Plasmodium,which has fewersugar transporters and only one putative ami-no acid transporter(GenBank identificationnumber23612372).As a first step toward identification ofmulti–drug-resistant pumps,the genome se-quence was analyzed for all occurrences ofgenes encoding multitransmembrane proteins.Notable are a set of four paralogous proteinsthat belong to the sbmA family(table S2)thatare involved in the transport of peptide antibi-otics in bacteria.A putative ortholog of thePlasmodium chloroquine resistance–linkedgene Pf CRT(17)was also identified,althoughthe parasite does not possess a food vacuole likethe one seen in Plasmodium.Unlike Plasmodium,C.parvum does notpossess extensive subtelomeric clusters of anti-genically variant proteins(exemplified by thelarge families of var and rif/stevor genes)thatare involved in immune evasion.In contrast,more than20genes were identified that encodemucin-like proteins(18,19)having hallmarksof extensive Thr or Ser stretches suggestive ofglycosylation and signal peptide sequences sug-gesting secretion(table S2).One notable exam-ple is an11,700–amino acid protein with anuninterrupted stretch of308Thr residues(cgd3_720).Although large families of secretedproteins analogous to the Plasmodium multi-gene families were not found,several smallermultigene clusters were observed that encodepredicted secreted proteins,with no detectablesimilarity to proteins from other organisms(Fig.1,A and B).Within this group,at leastfour distinct families appear to have emergedthrough gene expansions specific to the Cryp-R E P O R T S SCIENCE VOL30416APRIL2004443o n O c t o b e r 7 , 2 0 0 9 w w w . s c i e n c e m a g . o r g D o w n l o a d e d f r o mtosporidium clade.These families —SKSR,MEDLE,WYLE,FGLN,and GGC —were named after well-conserved sequence motifs (table S2).Reverse transcription polymerase chain reaction (RT-PCR)expression analysis (20)of one cluster,a locus of seven adjacent CpLSP genes (Fig.1B),shows coexpression during the course of in vitro development (Fig.1C).An additional eight genes were identified that encode proteins having a periodic cysteine structure similar to the Cryptosporidium oocyst wall protein;these eight genes are similarly expressed during the onset of oocyst formation and likely participate in the formation of the coccidian rigid oocyst wall in both Cryptospo-ridium and Toxoplasma (21).Whereas the extracellular proteins described above are of apparent apicomplexan or lineage-specific in-vention,Cryptosporidium possesses many genesencodingsecretedproteinshavinglineage-specific multidomain architectures composed of animal-and bacterial-like extracellular adhe-sive domains (fig.S1).Lineage-specific expansions were ob-served for several proteases (table S2),in-cluding an aspartyl protease (six genes),a subtilisin-like protease,a cryptopain-like cys-teine protease (five genes),and a Plas-modium falcilysin-like (insulin degrading enzyme –like)protease (19genes).Nine of the Cryptosporidium falcilysin genes lack the Zn-chelating “HXXEH ”active site motif and are likely to be catalytically inactive copies that may have been reused for specific protein-protein interactions on the cell sur-face.In contrast to the Plasmodium falcilysin,the Cryptosporidium genes possess signal peptide sequences and are likely trafficked to a secretory pathway.The expansion of this family suggests either that the proteins have distinct cleavage specificities or that their diversity may be related to evasion of a host immune response.Completion of the C.parvum genome se-quence has highlighted the lack of conven-tional drug targets currently pursued for the control and treatment of other parasitic protists.On the basis of molecular and bio-chemical studies and drug screening of other apicomplexans,several putative Cryptospo-ridium metabolic pathways or enzymes have been erroneously proposed to be potential drug targets (22),including the apicoplast and its associated metabolic pathways,the shikimate pathway,the mannitol cycle,the electron transport chain,and HXGPRT.Nonetheless,complete genome sequence analysis identifies a number of classic and novel molecular candidates for drug explora-tion,including numerous plant-like and bacterial-like enzymes (tables S3and S4).Although the C.parvum genome lacks HXGPRT,a potent drug target in other api-complexans,it has only the single pathway dependent on IMPDH to convert AMP to GMP.The bacterial-type IMPDH may be a promising target because it differs substan-tially from that of eukaryotic enzymes (15).Because of the lack of de novo biosynthetic capacity for purines,pyrimidines,and amino acids,C.parvum relies solely on scavenge from the host via a series of transporters,which may be exploited for chemotherapy.C.parvum possesses a bacterial-type thymidine kinase,and the role of this enzyme in pyrim-idine metabolism and its drug target candida-cy should be pursued.The presence of an alternative oxidase,likely targeted to the remnant mitochondrion,gives promise to the study of salicylhydroxamic acid (SHAM),as-cofuranone,and their analogs as inhibitors of energy metabolism in the parasite (23).Cryptosporidium possesses at least 15“plant-like ”enzymes that are either absent in or highly divergent from those typically found in mammals (table S3).Within the glycolytic pathway,the plant-like PPi-PFK has been shown to be a potential target in other parasites including T.gondii ,and PEPCL and PGI ap-pear to be plant-type enzymes in C.parvum .Another example is a trehalose-6-phosphate synthase/phosphatase catalyzing trehalose bio-synthesis from glucose-6-phosphate and uridine diphosphate –glucose.Trehalose may serve as a sugar storage source or may function as an antidesiccant,antioxidant,or protein stability agent in oocysts,playing a role similar to that of mannitol in Eimeria oocysts (24).Orthologs of putative Eimeria mannitol synthesis enzymes were not found.However,two oxidoreductases (table S2)were identified in C.parvum ,one of which belongs to the same families as the plant mannose dehydrogenases (25)and the other to the plant cinnamyl alcohol dehydrogenases.In principle,these enzymes could synthesize protective polyol compounds,and the former enzyme could use host-derived mannose to syn-thesize mannitol.References and Notes1.D.G.Korich et al .,Appl.Environ.Microbiol.56,1423(1990).2.See supportingdata on Science Online.3.M.J.Gardner et al .,Nature 419,498(2002).4.A.T.Bankier et al .,Genome Res.13,1787(2003).5.J.C.Wootton,Comput.Chem.18,269(1994).Fig.1.(A )Schematic showing the chromosomal locations of clusters of potentially secreted proteins.Numbers of adjacent genes are indicated in paren-theses.Arrows indicate direc-tion of clusters containinguni-directional genes (encoded on the same strand);squares indi-cate clusters containingg enes encoded on both strands.Non-paralogous genes are indicated by solid gray squares or direc-tional triangles;SKSR (green triangles),FGLN (red trian-gles),and MEDLE (blue trian-gles)indicate three C.parvum –specific families of paralogous genes predominantly located at telomeres.Insl (yellow tri-angles)indicates an insulinase/falcilysin-like paralogous gene family.Cp LSP (white square)indicates the location of a clus-ter of adjacent large secreted proteins (table S2)that are cotranscriptionally regulated.Identified anchored telomeric repeat sequences are indicated by circles.(B )Schematic show-inga select locus containinga cluster of coexpressed large secreted proteins (Cp LSP).Genes and intergenic regions (regions between identified genes)are drawn to scale at the nucleotide level.The length of the intergenic re-gions is indicated above or be-low the locus.(C )Relative ex-pression levels of CpLSP (red lines)and,as a control,C.parvum Hedgehog-type HINT domain gene (blue line)duringin vitro development,as determined by semiquantitative RT-PCR usingg ene-specific primers correspondingto the seven adjacent g enes within the CpLSP locus as shown in (B).Expression levels from three independent time-course experiments are represented as the ratio of the expression of each gene to that of C.parvum 18S rRNA present in each of the infected samples (20).R E P O R T S16APRIL 2004VOL 304SCIENCE 444 o n O c t o b e r 7, 2009w w w .s c i e n c e m a g .o r g D o w n l o a d e d f r o m。