上芒岗金矿床成矿作用过程研究

上芒岗金矿床位于三江褶皱系怒江大断裂西南段，龙陵～瑞丽大断裂(F_1)南东盘，上芒岗次级断裂(F_4)之中。赋矿地层为下二叠统沙子坡组(P_(1s))和中侏罗统勐嘎组(J_(2m))。矿石主要有两种类型，硅质矿石和粘土质矿石；前者主要由石英和少量黄铁矿所组成，金品位平均为2 * 10~(-6)；后者主要由伊利石、高岭石和黄铁矿所组成，金品位一般为2 * 10~(-6) ～ 4 * 10~(-6)。矿石中金星次显微状态，主要元素组合为Au、Ag、As、Sb、Hg、Ba。矿床以强烈的黄铁粘土岩化为特征，热液蚀变作用过程即是金矿化作用过程。根据热液蚀变的矿物共生组合及其生成序次，将金矿化作用过程分为五个阶段：黄铁矿-石英阶段(I)；镁贝得-白云石阶段(II)；辉锑矿-石英阶段(IlI)：黄铁矿-高岭石-伊利石阶段(IV)；网脉状石英阶段(V)。其中黄铁矿-高岭石-伊利石阶段(IV)是金矿化的主成矿阶段。该矿床属于卡林型金矿床。由石英流体包裹体获得不同成矿阶段的温度为，成矿阶段I：210～170 ℃、成矿阶段III：190～160 ℃、成矿阶段V：173～144 ℃。伊利石-水氢同位素温度计测得成矿阶段IV的温度为165 ℃。石英流体包裹体液相成分以K~+、Na~+和Cl~- (F~-)为主，其次为Ca~(2+)、Mg~(2+)和HC0_3~-，由早到晚K~+、Na~+和Cl~-降低，而Ca~(2+)、Mg~(2+)和HC0_3~-升高；气相组分以C0_2为主。石英流体包裹体成分富F，其含量高达8.03 * 10~(-3) mol／kg，正是由于成矿热液富含F，Al才可以与F形成络合物进入热液迁移，即Al成为活动组份，从而形成该矿床所独特的强烈粘土岩化蚀变。稀土元素特征方面，矿石和赋矿地层下二叠统沙子坡以及中侏罗统勐嘎组岩石的稀土配分曲线十分相似，均为右倾型，但是两者的稀土元素总量不同，前者的相对较高。矿石和蚀变岩具有相似的稀土元素配分曲线，但是矿石的稀土元素总量相对较高。与勐嘎组泥岩相比，粘土质蚀变岩和矿石更加富集轻稀土元素，并且更富Eu。这些特征表明，粘土质蚀变岩和矿石是由热液作用形成的，而不是风化作用的产物；矿石与赋矿地层在物质来源上有亲缘关系。不同矿段、不同阶段和不同类型矿石和蚀变岩的Au、Ag、As以及Sb的含量同步变化，这表明在整个成矿作用过程中，成矿流体来源统一，且在成矿体系起主导作用。不同类型的矿石及蚀变岩中Au与Al_20_3，和TFe的含量呈正相关，表明黄铁粘土岩化与成矿关系最为密切。矿石铅同位素~(208)Pb／~(204)Pb、~(207)Pb／~(204)Pb和~(206)Pb/~(204)Pb比值分别为39.12～39.54、15.85～15.95、19.75～20.33；沙子坡组(P_(1s))岩石铅同位素比值分别为:38.407～37.868、15.921～15.589、22.685～22.367;孟嘎组(J_(2m))岩石铅同位素比值分别为：39.499～39.222，15.821～15.772、19.207～18.709。在铅同位素组成相关图中矿石与地层铅的投影点分别集中成群分布。矿石铅与地层铅呈线性分布，而且矿石铅的集中区位于沙子坡组铅集中区和勐嘎组铅集中区之间。这些特征表明矿石铅系由沙子坡组铅和勐嘎组铅混合而成。成矿热液的δ~(18)O由早到晚逐渐升高，I、III、IV、V阶段流体的δ~(18)O值分别为-4.2‰，+0.59‰；+0.76‰，+1.98‰，表现出明显的漂移特征；而δD则表现出高度的一致性，变化范围为-82.5 ～ 79.48‰。由此认为成矿热液系大气降水起源。成矿热液氢、氧同位素组成的这种规律性变化还说明，成矿热液的演化具有继承性和连续性。应用CHILLERR软件包，对上芒岗金矿床的成矿作用过程进行化学反应途径数字模拟。所展示的成矿作用过程为：大气降水沿断裂带下渗，加热循环，获取成矿物质(但不排除有深源成矿物质加入的可能性)；形成起始成矿热液：T = 200℃ P = 228.8bar；pH = 4.4；fs_2 = 10~(-9.89); fo_2 = 10~(-41.28)；aAu(HS)_2~- = 10~(-9.64)，aAuCl_2~- = 10~(-17.86);富含F、Al和Au，贫As、Hg、Zn、Cu和Pb。成矿热液在构造作用的驱动下，上升进入上芒岗断裂上部含水构造破碎带，并与下渗雨水混合而淬冷，形成沿上芒岗断裂呈线状分布的早期硅化石英岩(成矿阶段I)，成矿热液与下渗雨水之比为16:l(成矿阶段I)；继而热液扩散进入下盘破碎带，与白云岩反应，形成矿体下盘的白云石化，水:岩比为193:l(成矿阶段II)。此后成矿热液上升充填裂隙空间，由于热传导而缓慢冷却，成矿体系的温度由189 ℃降为165 ℃，形成含辉锑矿的梳状石英脉(成矿阶段1II)。成矿热液继续上升进入上盘碎屑岩破碎带，停积于构造揉皱的泥质岩，并与之反应，形成上芒岗矿床金矿化的主体—粘占土质矿石，水:岩比为29:1(成矿阶段IV)。最后成矿残液逐渐冷却, 同时伴随C0_2的起泡，形成晚期石英网脉(成矿阶段V)，至此热液金矿化过程结束。由上述可见上芒岗金矿床的成矿作用过程经历了：(初始)成矿热液与下渗大气降水混合(I) → 成矿热液与沙子坡组白云岩反应(II) → 成矿热液缓慢冷却(III) → 成矿热液与勐嘎组泥质岩石反应(IV) → 成矿热液冷却沸腾(V)等5个演化阶段。模拟结果进一步证实了上芒岗金矿床的热液成因。上芒岗金矿床成作用过程化学反应途径数字模拟与地质事实高度吻合，与地球化学研究结果相互印证，再现了上芒岗金矿床的成矿作用过程。由矿床的地质地球化学特征及成矿作用过程化学反应途径模拟结果，归纳出上芒岗金矿床成矿作用过程模型。

岩浆－热液过渡阶段体系中不相容元素地球化学行为及其机制－以新疆阿尔泰3号伟晶岩脉研究为例

伟晶岩形成和演化中岩浆-热液过渡阶段物理化学性质、过铝质富挥发分岩浆体系岩浆液相不混溶、流体相出溶事件的相对时间尺度以及在岩浆-热液过渡阶段体系中稀土和其它微量元素地球化学行为(稀土“四重效应”机制和微量元素分异及控制因素等)是目前过铝质岩浆体系研究的焦点问题。对上述问题的研究和探讨，将有助于了解伟晶岩形成和演化的全过程，有助于了解挥发分(H_20、F、B、P)对过铝质岩浆体系物理性质以及对REE和其它微量元素地球化学行为影响，这对于理解过铝质岩浆体系成岩、成矿作用过程具有重大的理论和实际意义。本论文选择著名的新疆阿尔泰3号伟晶岩脉为研究对象，由于它具有完美的分带特征，使我们有可能通过各结构带矿物学、地球化学的研究揭示伟晶岩成因和演化过程以及讨论岩浆-热液过渡阶段体系中的稀土和微量元素地球化学行为。由于LCT型伟晶岩具有明显的分带性、矿物颗粒大小不均匀性等特点，因此利用全岩样品研究伟晶岩往往因取样没有代表性而被大多数岩石学家和地球化学家所否定。考虑到这点，本文系统采集阿尔泰3号伟晶岩脉各结构带磷灰石、电气石、碱性长石、石英矿物，部分结构带的石榴石、绿柱石、锂辉石矿物以及伟晶岩冷凝边和蚀变围岩的全岩样品，通过各结构带磷灰石矿物化学组成和~(87)Sr／~(86)Sr比值测定，电气石矿物的化学组成和硼同位素组成分析，碱性长石中磷含量的电子探针分析和碱性长石-石英矿物对的氧同位素体系研究以及蚀变围岩和冷凝边的化学组成分析，本文较为详尽系统地探讨以上所有的问题。通过本次多年的研究，我们获得了以下几点新的认识：f1) 富挥发分过铝质岩浆体系的样品存在稀土“四重效应”和Y-Ho、Zr-Hf、Nb-Ta、Sr-Eu元素对的显著分异，表明在过铝质岩浆演化过程中含氟流体相起着重要的作用；目前，稀土“四重效应”机制被认为是含水流体相与过铝质岩浆熔体相互作用的结果(Irber 1999；Bau 1997)，而不是独居石、磷钇矿、石榴石矿物等矿物的早期结晶引起的残余熔体稀土含量的异常变化。由于阿尔泰3号伟晶岩脉各带磷灰石以及与其共生的石榴石、绿柱石、碱性长石、锂辉石矿物均存存明显的稀土“四重效应”以及相同电价、相似离子半径的不相容元素间存在显著的分异，并结合最近赵振华等(1999)和Sba and Chappell(1999)报道S型花岗岩全岩和单矿物(磷灰石、独居石、长石、黄玉等)均存在稀土“四重效应”这一现象，本文研究提出，稀土“四重效应”是富挥发分过铝质岩浆体系的一个基本特征，其机制既不可能由含稀土的副矿物早期结晶引起残余熔体相中REE含量变化的结果，也不能定性地归因于流体相与熔体相相互作用过程中稀土元素在流体／熔体之间分异的结果，而很可能与伟晶岩岩浆形成之前某些过程密切相关，S型花岗岩岩浆在液相线以上存在硅酸盐熔体与高盐熔体(或卤水相)的不混溶液相分离有可能是过铝质岩浆体系产生稀土“四重效应”的主要原因。(2) 由于Sr~(2+)与Eu~(2+)具有相同的电价、相似的离子半径，根据经典的地球化学原理，它们具有相似的地球化学行为，在各种地质过程中其它们具有紧密的一致性。阿尔泰3号伟晶岩磷灰石中Sr／Eu比值具有二歧变化现象，其中I、Il、III和IV带磷灰石具有低的Sr／Eu比值(16:0～111.2)，而V、VI、VII带、核部带和IV带中的一个磷灰石则显示较大的Sr／Eu比值(主要在246．6～514:9范围，其中IV带的一个磷灰石该比值在10000以上)。对世界范围内的过铝质花岗岩统计表明，过铝质岩浆岩的全岩样品中的Sr／Eu也呈现二歧变化，由此本文提出Sr／Eu比值是指示过铝质岩浆体系中岩浆流体相出溶的有效地球化学参数，大于300的Sr／Eu比值是Eu~(2+)强烈分配进入流体相的地球化学标志。(3) 阿尔泰3号伟晶岩I、II、III带电气石矿物的硼同位素组成(δ~(11)B)分布在-41.11‰～-30.90‰之间，V、VI、VII带电气石矿物硼同位素组成(δ~(11)B)在-15.23‰～-9.20‰范围，IV带电气石硼同位素分布于-39.19～13.10‰范围，如此大的硼同位素分馏无法根据实验研究获得的熔体／流体相间的分馏系数进行合理解释。我们的研究表明岩浆成因电气石的B同位素组成与电气石化学组成具相关性，随电气石Y位上AI、Li阳离子数的增大，δ~(11)B值显示明显增大的趋势。阿尔泰3号伟晶岩最初形成的结构带中电气石的B同位素组成是目前所发现的最低值之一(-41.1l～39.01‰)，指示形成伟晶岩脉的初始岩浆可能由含非海相蒸发岩的泥质岩经变质深熔作用形成，或是伟晶岩岩浆在上侵定位过程中同化了含非海相蒸发岩地层的结果。本次研究利用电气石-白云母和电气石-四硼酸盐矿物间的同位索分馏以及熔体相-流体相间的同位索分馏，合理解释了阿尔泰3号伟晶岩脉电气石B同位素分馏过程，并首次获得伟晶岩形成、演化过程中B同位素组成演化的全程图谱。(4)伟晶岩岩浆形成和演化过程是否存在由过磷引起的液相不混溶现象未见确凿的岩石学和实验地球化学证据。阿尔泰3号伟晶岩脉糖粒状钠长石带(II带)明显由两种不同组构的岩性组成，而且该带是3号脉主要的Be矿化带，也是P、REE最重要的沉淀场所。阿尔泰3号伟晶岩脉梳状结构带和I带的碱性长石具较高P含量(平均值分别为0.42 wt％和0.22 wt％)，随着岩浆的演化进行，从III带到核部带，碱性长石中P含量逐渐增大(平均值由0.21 wt％增至0.50 wt％)，而II带碱性长石中异常低的P含量(平均值为0.08、wt％)是该带大量磷灰石矿物饱和结晶，导致残余熔体相中P极度亏损所造成的，而不是晚期出溶的岩浆热液交代形成的。根据Watson (1978)、Ryerson and Hess(1980)在液相线以上温度下实验研究获得的微量元素在不混溶的基性和酸性液相中分配特征，以及Webster et a1．(1997）对德国Ehrenfriedersdorf矿区伟晶岩石英中熔体包裹体的研究成果，我们推断在富磷岩浆体系中，在其演化的早期将出现由磷引起的液相不混溶作用，它对伟晶岩成岩和Be的成矿具有重大的影响。

氟、氯对热液钨、铜成矿的制约-以江西德兴铜矿、大吉山钨矿为例

矿化剂在热液矿床成矿过程中的重要作用一直为人们所关注，矿化剂地球化学行为直接影响成矿元素的富集成矿，不同的矿化剂元素可能对金属成矿具有一定的专属性。本文以著名的江西德兴铜厂超大型斑岩铜矿床和大吉山钨矿床作为研究对象，研究F、Cl与W、Cu成矿的关系。主要的认识如下：（1）F在花岗质岩浆中，可以降低岩浆的粘度、密度、固液相线温度、改变熔体结构，而Cl对熔体结构没有多大的影响。F在流体一花岗质熔体相间，绝大多数配分系数小于1.0，趋向于熔体相中配分，DF随体系中F浓度的升高而增加。Cl在流体一花岗质熔体相间的配分系数均大于1.0，且Dc1 随体系中Cl浓度的升高而增大·Cl强烈地趋向富集于流体相中。（2）Cu在流体一花岗质熔体作用过程中，铜总趋向于流体相中分布（DCu都大于1）。特别是在富Cl流体中Cu浓度较高，说明在富含Cl的热液流体能够从共存的熔体中活化迁移出大量的 Cu，S的加入DCu有降低的趋势。钨趋向于熔体相中富集，其配分系数大多小于1.0。（3）德兴铜厂花岗闪长斑岩属钙碱性系列岩石属I型花岗岩类，具有埃达克岩的特征。岩浆来源于深部，在结晶演化过程中发生了围岩物质的混染，这种高铜含量围岩的混染使成矿物质在岩浆中得到富集，有利于铜的活化、迁移。在铜厂岩体不同的蚀变带中，SiO2、K2O、Cu、Mo等从新鲜斑岩甚至弱蚀变带中带出，而在强蚀变带强烈富集，Cl同样有在强蚀变岩石中富集的趋势；而Na2O、Fe从斑岩体中带出，进入流体相中，流体中大量Fe的存在，有利于铜的沉淀、富集成矿。（4）德兴铜厂斑岩体微量元素和稀土元素地球化学特征表明，该岩体发生了流体一熔体作用，分异出来的流体是一种相对富氯的流体，同时成矿流体的流向是从岩体中心向接触带方向流动。（5）大吉山花岗岩具有高SiO2、A/CNK值，显示过铝质特点。黑云母花岗岩是壳源花岗岩但又受到慢源岩浆或慢源流体的影响。随着花岗岩的演化（从I→II→III）SiO2、K2O＋Na2O逐渐增加，ΣFe、Al2O3、CaO、F含量降低，为成矿提供了大量的矿化剂（F）和沉淀剂（Fe、Ca）。Eu负异常从I至III阶段花岗岩逐渐加强，表明该岩浆经历了高度的分异演化。（6）大吉山花岗岩类稀土元素具有“四重效应”配分的特点以及微量元素对玲Rb、Y/Ho、Zr/Hf以及Nb／Ta发生明显分异，暗示在花岗岩岩浆的演化过程中，经历了充分的流体一熔体作用，同时分异出大量富含F、W等矿化剂元素和成矿元素的热液流体，致使钨矿的形成。大吉山石英脉型钨矿的成矿年龄大约在155 Ma。（7）通过对成矿流体和花岗质岩石黑云母、白云母中卤素相对逸度的研究（log(H2O/fHCl）fluid、log（fHF/fHCl）fluid）发现，铜厂斑岩型铜矿床的成矿体系是相对富氯体系，而大吉山石英脉型钨矿床成矿体系相对富氟，同时氟可能主要迁移W、Sn、Nb、Ta等金属元素。（8）结合斑岩型铜矿床成矿流体特征，铜主要以C1的络合物形式存在和迁移，迁移形式主要是CuCl0、CuCl2等。石英脉型钨矿床中，钨主要以钨酸、钨酸盐及其离解形式存在和迁移，如WO42-、HWO4-、NaHWO4、Naw伍．等；在高度富氟的成矿流体中，钨的氟氧络合物（如WO3F-，WO2F42-等）对钨迁移也具有重要的作用。因此，不同矿化剂类型具有一定的成矿专属性，热液铜矿床主要与Cl、S有 关，而热液钨矿床大多与F有关。

Jesvsen amore-nequeei dagozten, cembait otoitz gai

Error tipográfico en el pie de imprenta del t. I: --Castilpa-ren-- en lugar de --Castilla-ren--

Perda de dimensão vertical de oclusão e estruturas dentárias remanescentes

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Medicina Dentária

De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex.

The de novo design of membrane proteins remains difficult despite recent advances in understanding the factors that drive membrane protein folding and association. We have designed a membrane protein PRIME (PoRphyrins In MEmbrane) that positions two non-natural iron diphenylporphyrins (Fe(III)DPP's) sufficiently close to provide a multicentered pathway for transmembrane electron transfer. Computational methods previously used for the design of multiporphyrin water-soluble helical proteins were extended to this membrane target. Four helices were arranged in a D(2)-symmetrical bundle to bind two Fe(II/III) diphenylporphyrins in a bis-His geometry further stabilized by second-shell hydrogen bonds. UV-vis absorbance, CD spectroscopy, analytical ultracentrifugation, redox potentiometry, and EPR demonstrate that PRIME binds the cofactor with high affinity and specificity in the expected geometry.

Daily intake of antioxidants in relation to survival among adult patients diagnosed with malignant glioma.

BACKGROUND: Malignant glioma is a rare cancer with poor survival. The influence of diet and antioxidant intake on glioma survival is not well understood. The current study examines the association between antioxidant intake and survival after glioma diagnosis. METHODS: Adult patients diagnosed with malignant glioma during 1991-1994 and 1997-2001 were enrolled in a population-based study. Diagnosis was confirmed by review of pathology specimens. A modified food-frequency questionnaire interview was completed by each glioma patient or a designated proxy. Intake of each food item was converted to grams consumed/day. From this nutrient database, 16 antioxidants, calcium, a total antioxidant index and 3 macronutrients were available for survival analysis. Cox regression estimated mortality hazard ratios associated with each nutrient and the antioxidant index adjusting for potential confounders. Nutrient values were categorized into tertiles. Models were stratified by histology (Grades II, III, and IV) and conducted for all (including proxy) subjects and for a subset of self-reported subjects. RESULTS: Geometric mean values for 11 fat-soluble and 6 water-soluble individual antioxidants, antioxidant index and 3 macronutrients were virtually the same when comparing all cases (n=748) to self-reported cases only (n=450). For patients diagnosed with Grade II and Grade III histology, moderate (915.8-2118.3 mcg) intake of fat-soluble lycopene was associated with poorer survival when compared to low intake (0.0-914.8 mcg), for self-reported cases only. High intake of vitamin E and moderate/high intake of secoisolariciresinol among Grade III patients indicated greater survival for all cases. In Grade IV patients, moderate/high intake of cryptoxanthin and high intake of secoisolariciresinol were associated with poorer survival among all cases. Among Grade II patients, moderate intake of water-soluble folate was associated with greater survival for all cases; high intake of vitamin C and genistein and the highest level of the antioxidant index were associated with poorer survival for all cases. CONCLUSIONS: The associations observed in our study suggest that the influence of some antioxidants on survival following a diagnosis of malignant glioma are inconsistent and vary by histology group. Further research in a large sample of glioma patients is needed to confirm/refute our results.

Genetic Studies Identify Critical Biomarkers and Refine the Classification of Malignant Gliomas

Gliomagenesis is driven by a complex network of genetic alterations and while the glioma genome has been a focus of investigation for many years; critical gaps in our knowledge of this disease remain. The identification of novel molecular biomarkers remains a focus of the greater cancer community as a method to improve the consistency and accuracy of pathological diagnosis. In addition, novel molecular biomarkers are drastically needed for the identification of targets that may ultimately result in novel therapeutics aimed at improving glioma treatment. Through the identification of new biomarkers, laboratories will focus future studies on the molecular mechanisms that underlie glioma development. Here, we report a series of genomic analyses identifying novel molecular biomarkers in multiple histopathological subtypes of glioma and refine the classification of malignant gliomas. We have completed a large scale analysis of the WHO grade II-III astrocytoma exome and report frequent mutations in the chromatin modifier, alpha thalassemia mental retardation x-linked (ATRX), isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2), and mutations in tumor protein 53 (TP53) as the most frequent genetic mutations in low grade astrocytomas. Furthermore, by analyzing the status of recurrently mutated genes in 363 brain tumors, we establish that highly recurrent gene mutational signatures are an effective tool in stratifying homogeneous patient populations into distinct groups with varying outcomes, thereby capable of predicting prognosis. Next, we have established mutations in the promoter of telomerase reverse transcriptase (TERT) as a frequent genetic event in gliomas and in tissues with low rates of self renewal. We identify TERT promoter mutations as the most frequently mutated gene in primary glioblastoma. Additionally, we show that TERT promoter mutations in combination with IDH1 and IDH2 mutations are able to delineate distinct clinical tumor cohorts and are capable of predicting median overall survival more effectively than standard histopathological diagnosis alone. Taken together, these data advance our understanding of the genetic alterations that underlie the transformation of glial cells into neoplasms and we provide novel genetic biomarkers and multi – gene mutational signatures that can be utilized to refine the classification of malignant gliomas and provide opportunity for improved diagnosis.

Time for treating bone fracture using rhBMP-2: a randomised placebo controlled mouse fracture trial.

Although the mechanisms of osteoinduction by bone morphogenic proteins (BMPs) are increasingly understood, the most appropriate time to administer BMPs exogenously is yet to be clarified.The purpose of this study was to investigate when BMP may be administered to a fracture arena to maximise the enhancement of healing.Forty mice with externally fixed left femoral fractures were randomised into four groups: Group I, the control group was given a placebo of 30 ll saline at day 0; Groups II, III and IV were given 30 ll saline plus 2.5 lg rhBMP-2, at post-operative days 0, 4 or 8, respectively.Sequential radiographs were taken at days 0, 8, 16.On day 22 the mice were sacrificed and both femora were harvested for biomechanical assessment in 3-point bending and histological evaluation.Radiographic analysis indicated that healing of fractures in Groups II and III was significantly greater (p <0.05) than those in Groups I and IV, at both 16 and 22 days post-fracture. The highest median bone mineral content at the fracture site was evidenced in Group III and II.Furthermore, Group III also had the highest relative ultimate load values, followed by Groups II, IV and I.Greater percentage peak loads were observed between Group I and both Groups II and III (p <0.05). Histological examination confirmed that at 22 days post-fracture, only fractures in Groups II and III had united with woven bone, and Groups I and IV still had considerable amounts of fibrous tissue and cartilage at the fracture gap.Data presented herein indicates that there is a time after fracture when rhBMP administration is most effective, and this may be at the time of surgery as well as in the early fracture healing phases.

A randomized controlled trial of tea tree oil (5%) body wash versus standard body wash to prevent colonization with methicillin-resistant Staphylococcus aureus (MRSA) in critically ill adults: research protocol

Background
Over the past ten years MRSA has become endemic in hospitals and is associated with increased healthcare costs. Critically ill patients are most at risk, in part because of the number of invasive therapies that they require in the intensive care unit (ICU). Washing with 5% tea tree oil (TTO) has been shown to be effective in removing MRSA on the skin. However, to date, no trials have evaluated the potential of TTO body wash to prevent MRSA colonization or infection. In addition, detecting MRSA by usual culture methods is slow. A faster method using a PCR assay has been developed in the laboratory, but requires evaluation in a large number of patients.

Methods/Design
This study protocol describes the design of a multicentre, phase II/III prospective open-label randomized controlled clinical trial to evaluate whether a concentration of 5% TTO is effective in preventing MRSA colonization in comparison with a standard body wash (Johnsons Baby Softwash) in the ICU. In addition we will evaluate the cost-effectiveness of TTO body wash and assess the effectiveness of the PCR assay in detecting MRSA in critically ill patients. On admission to intensive care, swabs from the nose and groin will be taken to screen for MRSA as per current practice. Patients will be randomly assigned to be washed with the standard body wash or TTO body wash. On discharge from the unit, swabs will be taken again to identify whether there is a difference in MRSA colonization between the two groups.

Discussion
If TTO body wash is found to be effective, widespread implementation of such a simple colonization prevention tool has the potential to impact on patient outcomes, healthcare resource use and patient confidence both nationally and internationally.

Trial Registration
[ISRCTN65190967]

The Opportunistic Pathogen Propionibacterium acnes: Insights into Typing, Human Disease, Clonal Diversification and CAMP Factor Evolution

We previously described a Multilocus Sequence Typing (MLST) scheme based on eight genes that facilitates population genetic and evolutionary analysis of P. acnes. While MLST is a portable method for unambiguous typing of bacteria, it is expensive and labour intensive. Against this background, we now describe a refined version of this scheme based on two housekeeping (aroE; guaA) and two putative virulence (tly; camp2) genes (MLST) that correctly predicted the phylogroup (IA, IA, IB, IC, II, III), clonal complex (CC) and sequence type (ST) (novel or described) status for 91% isolates (n = 372) via cross-referencing of the four gene allelic profiles to the full eight gene versions available in the MLST database (http://pubmlst.org/pacnes/). Even in the small number of cases where specific STs were not completely resolved, the MLST method still correctly determined phylogroup and CC membership. Examination of nucleotide changes within all the MLST loci provides evidence that point mutations generate new alleles approximately 1.5 times as frequently as recombination; although the latter still plays an important role in the bacterium's evolution. The secreted/cell-associated 'virulence' factors tly and camp2 show no clear evidence of episodic or pervasive positive selection and have diversified at a rate similar to housekeeping loci. The co-evolution of these genes with the core genome might also indicate a role in commensal/normal existence constraining their diversity and preventing their loss from the P. acnes population. The possibility that members of the expanded CAMP factor protein family, including camp2, may have been lost from other propionibacteria, but not P. acnes, would further argue for a possible role in niche/host adaption leading to their retention within the genome. These evolutionary insights may prove important for discussions surrounding camp2 as an immunotherapy target for acne, and the effect such treatments may have on commensal lineages. © 2013 McDowell et al.

Evaluating Many Treatments and Biomarkers in Oncology: A New Design

There is a pressing need for more-efficient trial designs for biomarker-stratified clinical trials. We suggest a new approach to trial design that links novel treatment evaluation with the concurrent evaluation of a biomarker within a confirmatory phase II/III trial setting. We describe a new protocol using this approach in advanced colorectal cancer called FOCUS4. The protocol will ultimately answer three research questions for a number of treatments and biomarkers: (1) After a period of first-line chemotherapy, do targeted novel therapies provide signals of activity in different biomarker-defined populations? (2) If so, do these definitively improve outcomes? (3) Is evidence of activity restricted to the biomarker-defined groups? The protocol randomizes novel agents against placebo concurrently across a number of different biomarker-defined population-enriched cohorts: BRAF mutation; activated AKT pathway: PI3K mutation/absolute PTEN loss tumors; KRAS and NRAS mutations; and wild type at all the mentioned genes. Within each biomarker-defined population, the trial uses a multistaged approach with flexibility to adapt in response to planned interim analyses for lack of activity. FOCUS4 is the first test of a protocol that assigns all patients with metastatic colorectal cancer to one of a number of parallel population-enriched, biomarker-stratified randomized trials. Using this approach allows questions regarding efficacy and safety of multiple novel therapies to be answered in a relatively quick and efficient manner, while also allowing for the assessment of biomarkers to help target treatment.

AXL Is a Key Regulator of Inherent and Chemotherapy-Induced Invasion and Predicts a Poor Clinical Outcome in Early-Stage Colon Cancer

Purpose: Despite the use of 5-fluorouracil (5-FU)–based adjuvant treatments, a large proportion of patients with high-risk stage II/III colorectal cancer will relapse. Thus, novel therapeutic strategies are needed for early-stage colorectal cancer. Residual micrometastatic disease from the primary tumor is a major cause of patient relapse.

Experimental Design: To model colorectal cancer tumor cell invasion/metastasis, we have generated invasive (KRASMT/KRASWT/+chr3/p53-null) colorectal cancer cell subpopulations. Receptor tyrosine kinase (RTK) screens were used to identify novel proteins that underpin the migratory/invasive phenotype. Migration/invasion was assessed using the XCELLigence system. Tumors from patients with early-stage colorectal cancer (N = 336) were examined for AXL expression.

Results: Invasive colorectal cancer cell subpopulations showed a transition from an epithelial-to-mesenchymal like phenotype with significant increases in migration, invasion, colony-forming ability, and an attenuation of EGF receptor (EGFR)/HER2 autocrine signaling. RTK arrays showed significant increases in AXL levels in all invasive sublines. Importantly, 5-FU treatment resulted in significantly increased migration and invasion, and targeting AXL using pharmacologic inhibition or RNA interference (RNAi) approaches suppressed basal and 5-FU–induced migration and invasion. Significantly, high AXL mRNA and protein expression were found to be associated with poor overall survival in early-stage colorectal cancer tissues.

Conclusions: We have identified AXL as a poor prognostic marker and important mediator of cell migration/invasiveness in colorectal cancer. These findings provide support for the further investigation of AXL as a novel prognostic biomarker and therapeutic target in colorectal cancer, in particular in the adjuvant disease in which EGFR/VEGF–targeted therapies have failed.

Plastin Polymorphisms Predict Gender- and Stage-Specific Colon Cancer Recurrence after Adjuvant Chemotherapy

Tumor recurrence after curative resection remains a major problem in patients with locally advanced colorectal cancer treated with adjuvant chemotherapy. Genetic single-nucleotide polymorphisms (SNP) may serve as useful molecular markers to predict clinical outcomes in these patients and identify targets for future drug development. Recent in vitro and in vivo studies have demonstrated that the plastin genes PLS3 and LCP1 are overexpressed in colon cancer cells and play an important role in tumor cell invasion, adhesion, and migration. Hence, we hypothesized that functional genetic variations of plastin may have direct effects on the progression and prognosis of locally advanced colorectal cancer. We tested whether functional tagging polymorphisms of PLS3 and LCP1 predict time to tumor recurrence (TTR) in 732 patients (training set, 234; validation set, 498) with stage II/III colorectal cancer. The PLS3 rs11342 and LCP1 rs4941543 polymorphisms were associated with a significantly increased risk for recurrence in the training set. PLS3 rs6643869 showed a consistent association with TTR in the training and validation set, when stratified by gender and tumor location. Female patients with the PLS3 rs6643869 AA genotype had the shortest median TTR compared with those with any G allele in the training set [1.7 vs. 9.4 years; HR, 2.84; 95% confidence interval (CI), 1.32-6.1; P = 0.005] and validation set (3.3 vs. 13.7 years; HR, 2.07; 95% CI, 1.09-3.91; P = 0.021). Our findings suggest that several SNPs of the PLS3 and LCP1 genes could serve as gender- and/or stage-specific molecular predictors of tumor recurrence in stage II/III patients with colorectal cancer as well as potential therapeutic targets.

The cyclin D1 (CCND1) rs9344 G>A polymorphism predicts clinical outcome in colon cancer patients treated with adjuvant 5-FU-based chemotherapy

Recent evidence indicates a potential prognostic and predictive value for germline polymorphisms in genes involved in cell cycle control. We investigated the effect of cyclin D1 (CCND1) rs9344 G>A in stage II/III colon cancer patients and validated the findings in an independent study cohort. For evaluation and validation set, a total of 264 and 234 patients were included. Patients treated with 5-fluorouracil-based chemotherapy, carrying the CCND1 rs9344 A/A genotype had significantly decreased time-to-tumor recurrence (TTR) in univariate analysis and multivariate analysis (hazard ratio (HR) 2.47; 95% confidence interval (CI) 1.16-5.29; P=0.019). There was no significant association between CCND1 rs9344 G>A and TTR in patients with curative surgery alone. In the validation set, the A allele of CCND1 rs9344 G>A remained significantly associated with decreased TTR in univariate and multivariate analyses (HR 1.94; 95% CI 1.05-3.58; P=0.035). CCND1 rs9344 G>A may be a predictive and/or prognostic biomarker in stage II/III colon cancer patients, however, prospective trials are warranted to confirm our findings.