Overdensity of i'-Dropout Galaxies in the Subaru Deep Field A Candidate Protocluster at z ~

物理学咬文嚼字
物理学咬文嚼字之四十四
（ 下） Ｕ ｎ ｃ ｅ ｒ ｔ ａ ｉ ｎ ｔ ｆ ｔ ｈ ｅ Ｕ ｎ ｃ ｅ ｒ ｔ ａ ｉ ｎ ｔ ｒ ｉ ｎ ｃ ｉ ｌ ｅ ｙｏ ｙＰ ｐ
曹则贤
（ ） 中国科学院物理研究所 北京 １ ０ ０ １ ９ ０
经典不确定性 所谓的 “ 不能够无限精确地确定一个物理量 ” 给 欧洲的物理学家们 带 来 了 惶 恐 ， 但是经典世界里存 在ｅ ｏ ｓ ｉ ｔ ｉ ｏ ｎ ｉ ｎ ｘ ａ ｃ ｔ ｐ ｇ的 说 法 似 乎 也 是 毫 无 根 据 的． 确定公路上一辆汽 车 的 位 置 ， 精确到毫米量级都是 没必要的 、 原则 上 不 可 能 的 （ 用汽车的哪个部位标 ） ， 定它 的 位 置 呢 ， 部 位 又 如 何 定 位 呢？ 遑论无限精 确． 观察过程中光子 对 车 子 的 位 置 当 然 也 是 有 扰 动 ） 但这丝毫 不 影 响 确 定 车 子 （ 这 的， ｌ ｏ ｃ ａ ｔ ｉ ｎ ｔ ｈ ｅ ｃ ａ ｒ ｇ 个物理事件 ． 一个有必要问的问题是 ， 远小于物体尺 度的位置精度有 意 义 吗 ？ 笔 者 以 为 ， 科学定律可能 比如描述种群数量演 本身就有可容忍的 不 确 定 性 ， 化的ｌ 本身就是处理大数目的群体演 ｏ ｉ ｓ ｔ ｉ ｃ方 程 ， ｇ 而无限精确地 描 述 物 理 世 界 的 想 法 只 是 理 想 化的 ． 化的愿望 ， 数学的理 想 不 可 以 用 来 取 代 或 否 定 现 实 — — 一只足球对运动员来说等价于数学家的 的世界 —
１ ７） 确定 、 一定以及肯定 ” 的吗 ？Ｋ 是“ ａ ｒ ｌ Ｐ ｏ ｅ ｒ继续 ｐ ｐ ２ ０］ ， 对经典决定性加以批判 ［ 他引入了 同 样 属 于 经 典
物理的相对论来佐 证 ． 他认为狭义相对论就堵死了 如 图 ８ 所 示， 在Ｓ 通往决定论的路 ． １ 点能够测到的 物理事件在 Ｓ 而能影响到Ｓ １ 点的 未 来 光 锥 内 ； ２ 点 上事件的物理事件在 它 的 过 去 光 锥 靠 Ｓ １ 未来一侧 的部分 ， 显然前者 大 于 后 者 ． 也 就 是 说， 在此时空点 上我们不可能接近 影 响 未 来 某 时 空 点 的 全 部 事 件 ， 当然也就不可能测量之以作为初始条件 ．

圈 量 子 引 力 的 回 顾
龙 芸
（ 北第二 师 范 学院 物 理与 电子 工程 系，武汉 湖 ４００ ３ ２ ５）
摘要： 圈量子 引力在物理学 中占据非常重要的地位 。０ 纪 ９ ２世 ０年代后 ， 圈量子 引力得到 了很 大的发展 ， 建立 了数学上定义严 格 的运动学框架， 引入 自 结网圈作 为量子 引力态， 出了很 多有意 义的物理 结论 ， 几何 算符 的量子化 ， 旋 给 如 并且它还 在黑洞物 理和宇宙学等方向上展现 了强有 力的发展势 头 它是一个非常活跃 的量子 引力理论 ， 越来越广泛地应用到普 朗克尺度 物理 被 中去 ， 这也加 强了理论学家们 的信 心。 本文试 着对 圈量子 引力的这些主要 结果做 个回顾 。
图 ２ 三 阶顶 角
三阶展 开表 示的一个例子
ｆ ６＋ 叶 ｃ＝ｅ ｅｎ ｖ
正 则 量 子 广 义 相 对 论 希 望 能 从 数 学 上 广 义 地 定 义 出 一 个 非
微 扰 的 、 背景 度 规 无 关 的量 子 引 力 理 论 。 与 大约 ２ ０年 前 ． ｓ ｔ ａ Ａ ｈｅ ｒ ｋ 率 先 提 出 ， 重 建 的 广 义相 对 论 相 空 间 由广 义 坐标 与 广 义 动 量 形 他 成 ， 杨 密 Ｓ ２ 规 范 理论 相 同 ， 义 坐 标 变 成 一 个 三 维 规 范 矩 与 Ｕ（ ） 广 阵 向量 场 ， 应 的 广 义 动量 和 三 维 度 规 的关 系 为 ： 对
维普资讯
２ｏ ｏ ８年 ２月
湖北第二师范学院学报
Ｊｕ ａ ｆＨｕ ｅ ｎｖ ｒｉ ｕ ａ ｏ ｏ ｒ ｌｏ ｂ ｉＵ ｉｅｓｔ ｏ Ｅｄ ｃ ｔ ｎ ｎ ｙｆ ｉ
Ｆ ｂ２ ｏ ｅ ．ｏ ８ Ｖｏ ．５ Ｎｏ２ １２ ．

a r X i v :a s t r o -p h /9906247v 1 15 J u n 1999A&A manuscript no.(will be inserted by hand later)ASTRONOMYANDASTROPHY SICS1.IntroductionGlobular star clusters (GCs)are among the oldest stellar systems in the Universe and provide a powerful tracer of2S.Holland et al.:Globular clusters in NGC5128Sharples1988).Recently G.Harris et al.(1998)used HST WFPC2images to construct a color–magnitude diagram for C44,a GC in the halo of NGC5128.They found that this GC was an old,intermediate-metallicity object simi-lar to the GCs in the Milky Way.G.Harris et al.(1992, hereafter referred to as HG92)used Washington CMT1T2 photometry to derive metallicities for62of confirmed GCs in NGC5128and found a mean iron abundance of [Fe/H]=−0.8±0.2,which suggest that the NGC5128 GC system is∼3times more metal rich than the Milky Way GC system.They found no evidence for any GCs having metallicities significantly greater than those found in the Milky Way GCs.Such metal-rich GCs might be ex-pected if some of the NGC5128GCs had formed recently in a gas-rich merger event.HG92do,however,suggest that several blue GCs in NGC5128may be analogues of the intermediate-age GCs found in the Magellanic Clouds. On the other hand,Zepf&Ashman(1993)suggest that the metallicity distribution of the NGC5128GCs is bi-modal,with the high-metallicity peak at[Fe/H]=+0.25 due to GCs formed in a merger.Hui et al.(1995)analyzed the kinematics of the NGC5128GC system and found that the metal-rich GCs are part of a dynamically sepa-rate system from the metal-poor GCs.Numerical simula-tions suggest that the merger event occurred between160 (Quillen et al.1993)and500(D/5Mpc)Myr ago,where D is the distance to NGC5128in Mpc(Tubbs1980). This suggests that any GCs that formed in this particular merger should be quite young and,therefore,rather blue (∼0.4<V−I<0.6;see Sect.5).Minniti et al.(1996)and Alonso&Minniti(1997, hereafter referred to as AM97)used HST Wide-Field/Planetary-Camera1(WF/PC-1)images,taken be-fore the corrective optics package was installed in1993, to search for GCs in the inner regions of NGC5128. They identified125GC candidates,young associations, and open cluster candidates in the inner three kpc of NGC5128.They also used ground-based RK photometry to estimate metallicities for47GC candidates.Schreier et al.(1996)found74compact sources along the northern edge of the NGC5128dust lane using HST WF/PC-1im-ages.They estimate that most of these sources are young stars(spectral class A or earlier)but note that some are resolved and may be GCs.Identifying GC candidates in the inner regions of NGC 5128is difficult since there is nonuniform extinction,con-tamination from foreground stars and background galax-ies,and confusion with open clusters and blue,star-forming knots in NGC5128.GC candidates can not be identified based solely on their colors since the large amount of uneven reddening makes it very difficult to determine the dereddened color of an object.A better approach is a scheme to identify GC candidates based solely on their structural parameters.All known GCs in the Local Group can be reasonably wellfit by Michie–King models(Michie1963;King1966),although∼20%Table1.Log of the observations.Fieldα(J2000)δ(J2000)Filter ExposureS.Holland et al.:Globular clusters in NGC51283cleus of NGC5128.Adjacentfields overlap by∼0.′5givinga total effective area of∼25⊓⊔′for the survey.2.2.Data ReductionsWe combined the exposures for eachfield by taking the average of the three images in eachfilter(four images for the F555W exposures of Field2).No re-registration of the images was performed since the shifts between the images were typically less than0.1pixel(0.′′01on the WFC and 0.′′005on the PC).We estimate that combining the images in this way may result in the sizes of the GC candidates be-ing systematically overestimated by no more than∼0.′′02. We prefer to introduce this simple systematic offset than deal with the poorly-understood systematic uncertainties that arise from interpolatingflux across fractional-pixel shifts.2.2.1.Identifying Globular Cluster CandidatesAt the distance of NGC5128(d=3.6±0.2Mpc),the mean King core-and tidal-radii of the Milky Way GCs would appear to be r t=2.′′59±0.′′20,respec-tively.Therefore,any GCs in NGC5128will appear to be semi-stellar and be strongly affected by the point spread function(PSF)of the WFPC2.After some experimenta-tion,we adopted the following procedure for identifying GC candidates.We wish to stress that this procedure is quite strict and will probably result in the rejection of some legitimate GC candidates.However,we prefer to re-ject real GCs rather than have our sample contaminated with stars or background galaxies.In order to increase the signal-to-noise ratio(S/N)of the GC candidates–a particularly important point for the faint(V<20)GC candidates–we combined the F555W and F814W images for eachfield to getfinding images. The dust lane introduces variations in the background on spatial scales of∼1′′,comparable to the expected sizes of the GC candidates in NGC5128.To reduce the effects of the uneven background light,large-scale spatial varia-tions in the background were removed by running a ring medianfilter(Secker1995)over thefinding image,sub-tracting the resulting smoothed background,and adding back the mean background value.The medianfilter radius was set to1′′,which is∼3.5times the expected full-width at half maximum(FWHM)of a typical GC candidate. This choice offilter radius ensures that the cores of the GC candidates will not be altered by the medianfilter and that any background structure larger than a typical GC candidate will be removed.Since the most extended Milky Way GCs have tidal radii that are significantly greater than2.5times their FWHM,and extended halos have been detected around several Galactic and extra-Galactic GCs(Grillmair et al.1995;1996;Holland et al.1997), this approach will alter the distribution of light in the outer regions of most of the GC candidates.However,this is not important since thefinding images are used only to construct a preliminary list of GC candidates.A more rigorous set of criteria,based on the structures of the GC candidates as determined from the original images,will be applied to the preliminary list to obtain afinal list of GC candidates in the central regions of NGC5128.Thefirst step in our identification procedure was to run the daophot ii(Stetson1987;1994)find routine on the background-subtracted images to identify GC can-didates.Thefinding thresholds were set to6σsky for the PC images and10σsky for the WFC images.Tests with artificial GCs suggested that any detections below these thresholds would be rejected at some point in our identifi-cation process.Daophot ii find has an algorithm for re-jecting non-stellar objects based on two parameters called “sharpness”and“round”.This algorithm was turned offsince images of GCs can have different shapes and concen-trations from images of stars.Next,the daophot ii photometry routine was used to obtain aperture photometry for each of these detec-tions.The photometry was performed separately on each of the combined F555W and F814W frames,not on the combinedfinding frame.An aperture radius of0.′′2was used since most Galactic GCs,if moved to the distance of NGC5128,would appear to have core radii smaller than this.Therefore,the signal within the aperture will be dominated by the light from the object and not from the background.Candidate objects with S/N<5within the photometry aperture were discarded since the signal was not strong enough to determine reliable shape parameters. The sky brightness was determined in an annulus with an inner radius of∼0.′′9and an outer radius of∼1.′′1.This annulus was chosen to be far enough from the center of the GC candidate that the light in the annulus will be dominated by the background,yet near enough to the GC candidate that the light in the annulus will be a reasonable approximation of the mean background at the location of the object.For large GC candidates this annulus will be inside the tidal radius of the object so our estimate of the background will be contaminated.However,the values determined at this stage are only preliminary estimates, which will be improved upon later in the identification process when Michie–King models arefit to the GC can-didates.The lists of GC candidates in each of the F555W and F814W images were matched using the daomatch and daomaster software.Only objects that appeared in both the F555W and F814W images,and whose centers matched to within0.′′05(∼1.1pixel on the PC images and∼0.5pix on the WFC images),were considered to be real GC candidates.Distinguishing bonafide GCs from stars and back-ground galaxies is challenging.The colors of the objects can not be used since we are interested in studying the color distribution of GCs in NGC5128and do not wish to bias our sample.To make matters worse,the presence of dust in NGC5128will add a significant amount of scatter4S.Holland et al.:Globular clusters in NGC5128to the intrinsic color distribution,and may cause legit-imate GCs to be rejected if a color-based identificationscheme is used.The solution is to identify GC candidatesby their structural parameters,although the best choiceof structural parameters is not obvious.At the distanceof NGC5128a typical Galactic GC would appear to havean intrinsic FWHM of∼0.′′25,or approximately twicethe FWHM of the WFPC2PSFs.Therefore,the observedFWHM,concentration,and ellipticity of a GC candidatecan be heavily influenced by the PSF.Since the PSF variesstrongly with position on the WFPC2CCDs,the poten-tial for confusion between stellar images and concentratedGC candidates is great if the PSF is not removed,in someway,from the data.Therefore,the observed shape of anobject can not be directly used to classify it as a star,GCcandidate,or galaxy.After some experimentation with adding and recover-ing artificial GCs and artificial stars,we found that thefollowing procedure was reasonably reliable for identify-ing GC candidates.For each GC candidate we took allthe pixel values within1′′of the center of the object andsubtracted an estimate of the local background(the centerand background were determined by the daophot ii pho-tometry algorithm).A one-dimensional Moffatian(Mof-fat1969),M(r eff)=M(0) 1+ r eff1Image Reduction and Analysis Facility(IRAF),a softwaresystem distributed by the National Optical Astronomy Obser-vatories(NOAO).S.Holland et al.:Globular clusters in NGC51285Fig.2.Thisfigure shows the best-fitting Moffatianαand βparameters for each object(small circles)on the F555W images.Simulated data(see Fig.1)suggest that objects that lie inside the wedge formed by the solid lines are ex-tended objects.Therefore we consider any objects that lie inside the wedge to to be GC candidates.The solid squares show the locations of the GC candidates from Table2. 2.2.2.Fitting Michie–King ModelsWefit a two-dimensional,PSF-convolved,single-mass Michie–King model to each of the403GC candidate us-ing software developed by Holland(1997).This software assumes that the surface brightness profile along the ef-fective radius axis of a GC candidate with an ellipticity ofǫand a position angle ofθ0has a King profile with a concentration of c and a core radius of r c.It then builds a two-dimensional model based on this surface brightness profile,ǫ,andθ0.The two-dimensional model is convolved with the appropriate PSF for the location on the CCD and a chi-square minimization is performed between the PSF-convolved model and the original data image.The soft-ware uses CERN’s minuit function minimization package tofit simultaneously the concentration,core radius,to-talflux in the object,ellipticity,position angle,and mean background.Objects located within32pixels of the edge of a CCD(=3.′′2for the WFC and1.′′6for the PC)were notfit to avoid the edges of the CCD biasing thefits.Once a bestfit had been determined,the King tidal radius,r t, and the half-mass radius,r h,of the model were computed.Separatefits were made to the F555W images and the F814W images and an object was considered to be GC Fig.3.Thisfigure shows the best-fitting Moffatianαand βparameters for each object(small circles)on the F814W images.Simulated data(see Fig.1)suggest that objects that lie inside the wedge formed by the solid lines are ex-tended objects.Therefore we consider any objects that lie inside the wedge to to be GC candidates.The solid squares show the locations of the GC candidates from Table2. candidate only if a Michie–King model could befit in both colors.We were able tofit Michie–King models to98of the 403potential GC candidates.Mean structural parameters were calculated for these object by taking the mean of the values found in eachfilter.Four objects(#8,#113, #128,and#129)(see Tables2,3,and4)were identified on multiplefields.In these cases we computed the mean of the structural parameters measured in eachfield.We elected to separate GC candidates from back-ground galaxies based on theirfitted ellipticities and half-mass radii(see Fig.4).Half-mass radii are preferred to tidal radii or core radii because Fokker–Planck models of spherical stellar systems show that half-mass radii re-main reasonably constant over periods of several Gyr (e.g.Cohn1979;Takahashi1997),making it a unique length scale for GCs.The mass interior to the half-mass radius tends to undergo a gravo-thermal collapse and become concentrated at the center of the GC over time(i.e.core-collapse),which results in the core radius shrinking.Meanwhile,the mass exterior to the half-mass radius tends to expand outwards,causing the tidal ra-dius to grow.Since we are interested infinding young, intermediate-age,and old GCs in NGC5128,it is useful to have a selection criterion that does not depend on the age6S.Holland et al.:Globular clusters in NGC5128Fig.4.The ellipticity vs.half-mass radius of the best-fitting single-mass Michie–King model for each object where a Michie–King model was successfully fit.Objects with r h >10′′(∼175pc)have not been plotted.The solid box in the lower left of the plot shows the region occupied by Galactic GCs.Based on this plot we have assumed that any object with r h <2′′(∼35pc)and ǫ<0.4(the dashed box)is a GC candidate in the NGC 5128system.of the GC candidate.Galactic GCs have half-mass radii of approximately 1.3<r h <31.9pc (W.Harris 1996),which corresponds to 0.′′07<r h <1.′′83at the distance of NGC 5128.There is no evidence that the radius of a Galactic GC depends on its mass (van den Bergh et al.1991).There-fore,we have assumed that only objects with r h ≤2′′(∼35pc at the distance of NGC 5128)were GC candi-dates.It is possible that some of the objects in Fig.4that have high ellipticities and low half-mass radii are double clusters.However,Innanen et al.1983have shown that a binary GC could not survive a single Galactic orbit in the Milky Way so it is unlikely that there are any old,or intermediate-age double GCs in NGC 5128.It is possi-ble that very young multiple GCs that formed within the last ∼100−200Gyr could have survived to the present day,but we are unable to differentiate between them and background galaxies.The most elliptical Galactic GC is M19with ǫ=0.27(White &Shawl 1987)and the most elliptical GC known is NGC 2193in the Large Magellanic Cloud (LMC)which has ǫ=0.33(Geisler &Hodge 1980).Geisler &Hodge (1980)modelled the distribution of observed el-lipticities for 25GCs in the LMC and found that it was unlikely that the largest true ellipticity exceeded ǫ=0.4.The LMC contains both dynamically young and dynami-Fig.5.A finding chart for Field 1.The GC candidates are circled with their identification numbers (see Table 2)printed near each object.Fig.6.A finding chart for Field 2.Fig.7.A finding chart for Field 3.Fig.8.A finding chart for Field 4.cally old GCs,so the largest ellipticity seen in the LMC is a reasonable estimate of the largest ellipticity that we can expect to see in NGC 5128.Therefore,only objects with ǫ≤0.4were considered to be GC candidates.The final step was to examine visually the WFPC2images of each GC candidate to ensure that the Michie–King model fits looked realistic.We found that ∼20%of the objects were either located on diffraction spikes from saturated stars,or exhibited unusually large resid-uals when the best-fitting Michie–King models were sub-tracted.These spurious identifications were discarded.Fig.4shows the measured half-mass radii and ellip-ticities for the surviving objects in NGC 5128and Ta-ble 2shows the final list of GC candidates that we find in the central regions of NGC 5128.The second and third columns show the J2000coordinates of the objects as determined using the IRAF/STSDAS (v2.0.1)task sts-das.toolbox.imgtools.xy2rd .Column 4is the ob-served (projected)distance of the GC candidate from the center of NGC 5128in arcminutes.The center of NGC 5128was taken to be αJ2000=13h 25m 27.s 3,δJ2000=−43◦01′09′′(Johnston et al.1995).Columns 5and 6give the field (from Table 1)and CCD that the object was found on.Columns 7and 8give the X and Y coordinates (in pixels)on the CCD.Column 9lists the identification number of the object in Table 1of Minniti et al.(1996).Tables 3and 4lists the coordinates for the 61extended objects with r h >2′and ǫ>0.4.Some of these objects may be GCs in NGC 5128while others may be background galaxies with structures similar to those of Michie–King models.Six of these objects have been previously identi-fied as GCs by Minniti et al.(1996)and Sharples (1988).Figs.5through 10show the locations of the 21GC can-didates on the F814W-band WFPC2images.Only objects that pass all of the criteria described above are marked on these figures.Objects (such as #15)were only marked on the fields that they were identified as GC candidates in.In most of the cases where a GC candidate is present in multiple fields,but only identified in one field,the GC candidate was located very near the edge of one of the CCDs.Spatial variations in the PSF are largest near the edges of the CCDs so the Michie-King model fits are less reliable near the edges of the CCDs.S.Holland et al.:Globular clusters in NGC51287 Table2.The GC candidates in the central regions of NGC5128.IDαJ2000δJ2000D Field CCD X Y Other8S.Holland et al.:Globular clusters in NGC5128Table3.Extended objects with r h>2′′andǫ>0.4in the central regions of NGC5128IDαJ2000δJ2000D Field CCD X Y OtherS.Holland et al.:Globular clusters in NGC51289 Table4.Extended objects with r h>2′′andǫ>0.4in the central regions of NGC5128,continued.IDαJ2000δJ2000D Field CCD X Y Other∆W0)and standard error in the mean ofthesefive values for each GC candidate.This gave us anestimate of the systematic uncertainty in the value of W0that we derived for each GC candidate.Finally,we com-puted the mean,standard error in the mean,and medianof the individual10S.Holland et al.:Globular clusters in NGC5128Table5.The best-fitting structural parameters for the NGC5128GC candidates.The values are the means of the structural parameters derived from the F555W and F814W images.ID W0±σr c±σr h±σr t±σc±σǫ±σθ0±σχ2ν∆r c0.′′0100.′′0030.′′004∆r t0.′′1540.′′0510.′′060∆ǫ0.0240.0040.022n n.(3) The mean core radius for the21NGC5128GC candidates isr c=0.′′11±0.′′01(se).A Kolmogorov–Smirnov(KS)test shows that we can reject the hypothesis that the two samples are drawn from the same distribution at the46%confidence level.Therefore, there is no evidence that the core radii of the GC can-didates in NGC5128are distributed differently from the core radii of the Milky Way GCs.The most noticeable difference between the core radii of the NGC5128GCcandidates and the core radii of the Milky Way GCs in Fig.11is the lack of a tail extend-ing to large core radii in the NGC5128data.This may be an artifact of the small number(21)of NGC5128GC candidates in our sample.The mean of a distribution is sensitive to the presence of tails and outliers,but the me-dian is much more robust against outliers.Therefore we computed the median core radius for each data set.Both the NGC5128GC candidates and the Milky Way GCs have median core radii of[r c]=0.′′07(=1.22pc,or∼0.7 pixels on the WF CCDs and1.4pixels on the PC CCD). The similarity in the median core radii suggests that theFig.11.Thisfigure compares the distribution of core radii for GC candidates in NGC5128with the distribution of core radii for selected GCs(see Sect.3.1)in the Milky Way.The vertical axis is the fraction of the total number of GCs and the error bars show the Poisson uncertainties in each bin.“typical”core radius of a GC candidate in NGC5128is similar to that of the Milky Way GCs.There may be systematic biases in the core radii that we have derived for the GC candidates in NGC5128.Fit-ting Michie–King models to objects with core radii that are similar to the pixel scales of the images requires that the centers of the objects be accurately known.Small er-rors in determining the center of a candidate GC,and small systematic errors introduced by integrating Michie–King model profiles over the area of a pixel,may be suf-ficient to bias thefitted core radii towards smaller values. In addition to pixelation effects,the similarity between the core radii and the FWHMs of the PSFs may also be biasing ourfits toward smaller core radii.3.2.Tidal RadiiThe tidal radius of a GC is affected by the gravitational potential of its parent galaxy(e.g.,Innanen et al.1983; Heggie&Ramamani1995).In order to compare the tidal radii of GC candidates in NGC5128with those of GCs in the Milky Way it is necessary to correct for the tidal fields of both galaxies.Thefirst step is to normalize the tidal radius of each GC candidate by its mass,M cl,to getr t/M1/3cl .If we assume that the gravitational potentials ofthe Milky Way and NGC5128can be approximated by aspherical logarithmic potential of the formΦ=V2rot ln(R2+R2s)+ln(C),(4)where R is the galactocentric distance,R s is a scale length,and C is a constant,then we can compare the mean valueof the normalized tidal radii of the GC candidates usingr tV rot 2/3GM1/3cl= V rot,MW g(e) 1/3 R2/3pM1/3cl MW,(6)where the subscript MW denotes the value for the MilkyWay.Eq.6assumes that the shape of the galactic potentialis the same in both galaxies,but allows the total mass,as parameterized by V rot,of each galaxy to vary.It alsorequires a knowledge of the distribution of GC orbits ineach galaxy,as parameterized by g(e)and R p.We as-sumed a rotation velocity of V rot,MW=220km s−1for theMilky Way and V rot=245km s−1for NGC5128(Huiet al.1995).The only information available on the distri-bution of orbits for GC candidates in NGC5128is theprojected radial distances of the GC candidates from thecenter of NGC5128,so we have assumed that the NGC5128GC system is dynamically similar to the Milky WayGC system.This involves two assumptions about the na-ture of the GC orbits.First,we assume that the mean ec-centricity of the NGC5128GC orbits is the same as thatfor the Milky Way GCs(Fig.12.Thisfigurecompares the distribution of normal-ized tidal radii(see Sect.3.2)for GC candidates in NGC 5128with the distribution of normalized tidal radii(af-ter correcting for the difference in mass between the two galaxies)for GCs in the Milky Way.The vertical axis is the fraction of the total number of GCs and the error bars show the Poisson uncertainties in each bin.5128GC candidates from the observed distance from the center of NGC5128usingR p=1−e8D.(7)Fig.12shows the distribution of the normalized tidal radii for the NGC5128GC candidates and the Milky Way GCs.The cluster masses were computed from their total V-band luminosities assuming a mass-to-light ratio of two.Our sample of GC candidates has r t/M1/3cl=0.36±0.05(se)pc/M1/3⊙(N=21).The mean normalized tidalradius for73selected Milky Way GCs is r t/M1/3clMW=0.69±0.08(se)pc/M1/3⊙.The multiplicative factor in Eq.6is0.703,which yields a corrected r t/M1/3clMW of0.49±0.06(se)pc/M1/3⊙.A KS test says that we can reject the hypothesis that the two samples are drawn from the same distribution at the74%confidence level.Therefore,there is insufficient evidence to state that the distribution of the tidal radii of the NGC5128GC candidates differs from that of the Galactic GCs if the difference in the masses of the two galaxies is taken into account.However,we wish to stress that this calculation assumes that the distribution of GC orbits are statistically similar for both galaxies.Fig.13.Thisfigure compares the distribution of half-mass radii for GC candidates in NGC5128with the distribution of half-mass radii for a subset of GCs in the Milky Way. The vertical axis is the fraction of the total number of GCs and the error bars show the Poisson uncertainties in each bin.3.3.Half-Mass RadiiThe distribution of half-mass radii for the NGC5128GC candidates is shown in Fig.13along with the same dis-tribution for our subsample of73Milky Way GCs.The half-mass radii for the Milky Way GCs were determined by computing a Michie–King model(with concentrations and core radii taken from W.Harris1996)for each Milky Way GC.This allowed us to make a direct comparison between the half-mass radii of the best-fitting single-mass Michie–King models for the NGC5128GC candidates and the half-mass radii of the best-fitting single-mass Michie–King models for the Milky Way GCs.The mean half-mass radius for the21NGC5128GC candidates isr h=0.′′67±0.′′05(se).However, a KS test says that we can reject the hypothesis that the two samples are drawn from the same distribution at only the74%confidence level,so there is no evidence that the distribution of half-mass radii in our sample of NGC5128 GC candidates is different from that of the GCs in the Milky Way.3.4.EllipticitiesThe distribution of ellipticities for the NGC5128GC can-didates is shown in Fig.14.The21NGC5128objects haveFig.14.The upper panel shows the distribution of ellip-ticities for the GC candidates in NGC5128.The lower panel shows the distribution of ellipticities for the Milky Way’s GCs(from White&Shawl1987).ǫ=0.07±0.01(se)for the 73Milky Way GCs.A KS test says that we can reject the hypothesis that the two samples are drawn from the same distribution at the99.7%confidence level.Therefore,we conclude that the NGC5128GC candidates may have a different distribution of ellipticities from the Milky Way GCs.The NGC5128GC candidates appear to be system-atically more elliptical than the Milky Way GCs.There appears to be a lack of objects with low ellipticities and an excess of GC candidates withǫ∼0.3.The lack of GC can-didates withǫ≤0.05is probably due to the elliptical PSF not being fully removed from the data.Another possible source of ellipticity is the stochastic distribution of bright stars near the center of the object.Geisler&Hodge(1980) found that the random placement of stars with respect to the adopted center of a GC can introduce a systematic error in the observed ellipticity of+0.045±0.015for GCs which are intrinsically spherical.This effect acts to make nearly spherical GCs appear to be more elliptical than they actually are.They also found that this systematic error decreases as the intrinsic ellipticity of the GCs in-creases.This would explain the lack of nearly circular GC candidates in NGC5128,relative to the Milky Way.AM97identified125GC candidates in the inner2.′8×2.′8of NGC5128.Table7lists the ellipticities from those GC candidates in common between the two studies.The Table7.A comparison of our ellipticities with those of AM97.ID AM97Ourǫ±σAM97ǫ。

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。