三叶木通花发育相关基因的结构、功能和进化研究

花是被子植物最关键的创新（innovation）性状。在被子植物的不同类群中，其形态多种多样，尤其以基部真双子叶植物的花形态最为丰富。大量的系统发育分析表明，在核心真双子叶植物起源之前，几个与花发育相关的MADS-box基因亚家族均发生了大尺度的基因重复事件。因此，在被子植物的不同物种中，花发育相关基因的组成并不相同，并且它们经历了不同的进化历史，这意味着这些基因可能以不同的方式调控花的发育。基部真双子叶植物，作为基部被子植物和核心真双子叶植物之间的过渡类群，对于我们理解被子植物花的进化，揭示核心真双子叶植物花的起源以及基部真双子叶植物花多样性分化的分子机制非常重要。本文以基部真双子叶植物三叶木通为研究材料，着重进行了以下研究工作： 1. 花器官发生过程的观察。三叶木通的花为雌雄同序的单性花。而且，根据成熟花的形态，三叶木通的雌花和雄花都只有一轮花被器官，即三个花瓣状的萼片。扫描电镜的观察结果表明：1）在花器官的发生和发育过程中，在萼片和雄蕊原基之间，确实没有花瓣原基或另一轮萼片原基发生。2）雌花和雄花都是以两性花的方式发生发育的。3）单性花是由于在花发育的最后阶段，雌花中雄蕊或者雄花中心皮的退化而产生的。 2. 花发育相关基因的克隆。应用5’/3’ RACE的方法，我们从三叶木通不同发育阶段的混合花芽中共分离到九个与花发育相关的MADS-box基因： AktFL1、AktFL2、AktAP3_1、AktAP3_2、AktAP3_3、AktPI、AktAG1、AktAG2和AktSEP3。 3. A类MADS-box基因的进化。由于A类基因在进化过程中序列结构的改变，再加上取样的限制，使得A类基因间的进化历史一直不能被很好的理解。因此，本文对A类基因的研究从构建该基因亚家族的系统发育树开始。主要结果如下：1）通过扩大在基部真双子叶植物和被子植物其它重要类群的取样，我们的系统发育树基本上反映了现存被子植物的系统发育关系。2）核心真双子叶植物的A类基因由三个分支组成：euFUL、euAP1和AGL79，它们是通过发生在核心真双子叶植物起源之前的两次几乎同时的基因重复事件产生的。3）在基部真双子叶植物中，山龙眼目、毛茛目和黄杨科的A类基因各形成一支。而且，在这些类群内，发生了多次小尺度的独立的基因重复事件。4）来自单子叶植物的FUL-like基因明显地构成一个单系，并且包括三个分支：OsAMDS14、OsMADS15和OsMADS18。它们是由于两次不连续的基因重复事件产生的。5）不同类型的A类基因产物在C末端拥有不同的保守基元。6）从基因组结构上看，所有的A类基因都拥有八个外显子和七个内含子。7）通过对三叶木通中两个FUL-like型基因（AktFL1和AktFL2）表达式样的观察，我们发现它们在叶原基和发育早期的花原基以及发育着的花器官中都有表达。此外，A类基因表达式样的进化分析结果表明被子植物中该类基因的祖先可能具有广泛的功能，既在营养器官中表达又在生殖器官中表达 。 4. B类基因表达式样的保守性和多样性。通过对B类基因的系统发育和表达式样分析，得到以下结果：1）三叶木通中的三个paleoAP3基因是通过两次基因重复事件产生的。2）在木通科或木通属内，PI型基因并没有发生基因重复事件。3）RT-PCR结果表明，AktAP3_1在雌花中的表达量比雄花中高，而AktAP3_2则在雄花中的表达量比雌花中高。AktAP3_3和AktPI在雌花和雄花中的表达水平相似。4）原位杂交分析显示这些基因在发育着的雄蕊和心皮中表达。此外，AktAP3_3和AktPI还在萼片中表达，可能参与花瓣状萼片的发育。 5. 三叶木通C/D和E类基因的序列结构和表达分析。通过序列结构分析，我们发现，与其它被子植物AG同源基因编码的MADS-domain蛋白一样，AktAG1和AktAG2在MADS结构域的N末端都拥有一段氨基酸序列的延伸，AktAG1为20个氨基酸;AktAG2为7个氨基酸。原位杂交分析表明AktAG1和AktAG2主要在发育着的雄蕊和心皮中表达，说明它们具有决定生殖器官发育这一保守的功能。 AktSEP3属于AGL9型的E类基因。该基因在所有花器官中都有表达，说明和其它被子植物的E类基因一样，AktSEP3在三叶木通中对于所有花器官的发育都是必需的。 6. 各类MADS-domain蛋白间的相互作用。在前面工作的基础上，我们首次对三叶木通中上述MADS-domain蛋白间的作用方式进行了研究。酵母双杂交结果表明：1）AktSEP3的C末端具有转录激活功能。2）三个AktAP3蛋白与AktPI蛋白都能够形成异源二聚体，但是它们之间的作用能力并不相同。3）AktSEP3蛋白可以与AktFL1、AktPI、AktAG1和AktAG2形成异源二聚体，充分体现了E类基因产物作用式样的保守性。4）AktFL1与AktPI、AktSEP3和AktAG2也能形成异源二聚体，这与核心真双子叶植物的euFUL型蛋白在作用式样上是非常相似的。 综合以上结果，我们探讨了三叶木通花发育的分子机制。在三叶木通的三轮花器官中，与拟南芥等模式植物相似的是：E类（AktSEP3）基因在每一轮花器官中都起作用;此外，A类（AktFL1）和B类（AktAP3_3和AktPI）基因在花瓣状的萼片中有不同程度的表达，类似于拟南芥的第二轮;B类（AktAP3_1、AktAP3_2、AktAP3_3和AktPI）和C/D类（AktAG1和AktAG2）基因在雄蕊的发育过程中起作用;C/D类（AktAG1和AktAG2）基因对心皮的发育起作用。与拟 南芥等模式植物不同的是：1）虽然原位杂交分析表明，AktFL1、AktAP3_3、AktPI和AktSEP3都在花瓣状的萼片中有 不同程度的表达，但是它们的蛋白质产物AktFL1与AktSEP3和AktAP3_3与AktPI都只能形成较弱的异源二聚体。而 且，根据我们的研究结果，在三叶木通中没有找到euAP1型的A类基因，只有两个FUL-like型的A类基因。它们的功能 与核心真双子叶植物中的euFUL型基因相似。因此，AktFL1很可能与其它调控因子共同作用负责花分生组织的形成;AktFL1/AktAG2则可能在花发育的后期起作用。那么，三叶木通花瓣状萼片的发育是否需要AktFL1/AktSEP3和 AktAP3_3/AktPI的参与，还是另有其它转录因子的参与，仍然需要更深入的研究。2）虽然在三叶木通中，雄蕊的发 育同样需要B、C/D和E类基因的参与，但是由于小尺度的基因重复事件，在该物种中只拥有三个paleoAP3型基因，而没有euAP3型基因。而且，由于复制拷贝间的亚功能化，AktAP3_1/AktPI主要参与雌花的发育过程;而AktAP3_2/AktPI主要参与雄花的发育过程。

金粟兰花发育相关基因的结构、功能和进化研究

花是被子植物区别于其它植物大类群的最重要的特征，其形态多种多样。花的发育取决于一个复杂的涉及到多个基因和过程的调控体系，因此花的起源和多样化过程实际上可以理解为这个调控体系的进化过程。在被子植物的不同物种中，花发育相关基因的组成并不相同，且经历了不同的进化历史，这意味着这些基因可能以不同的方式调控花的发育。相对于核心真双子叶植物相对稳定的花形态结构而言，基部被子植物的花具有丰富的多样性。因此，对基部被子植物花发育相关基因的研究对于我们理解被子植物花的进化非常重要。 金粟兰科（Chloranthaceae）是基部被子植物的代表类群之一。与研究得比较深入的模式植物相比，花被、雄蕊或雌蕊的缺失，使得该科植物的花比较简单。因此对该科植物中花发育基因的研究不仅有助于揭示花的起源以及花多样性分化的分子机制，还将为认识花部构造简单化的机制提供资料。本文以金粟兰（Chloranthus spicatus）为实验材料，取得了以下研究结果： 1.花发育相关基因的克隆 应用5’/3’RACE的方法，我们从金粟兰不同发育阶段的混合花芽中克隆到了与花发育相关的MADS-box基因：CsPI、CsAG1和CsAG2。 2. 两个A类MADS-box基因表达式样的对比分析 在营养分生组织向生殖分生组织的转变中，花原基的形成，以及随后雄蕊、心皮、花粉、胚珠和胚囊的发育中，CsAP1-1和 CsAP1-2基因均表达。唯一不同之处在于，在花发育成熟期，CsAP1-1在外珠被也有表达，而CsAP1-2在外珠被处没有表达，而只在内珠被处表达。这一结果反映了基因重复事件发生后，两个基因在功能上也有了一些分化。 3. B类基因功能的保守性和多样性 通过转基因实验和蛋白质相互作用研究对B类基因的功能和作用方式进行了研究，得到以下结果：1）金粟兰CsAP3基因的C末端的点突变所造成的paleoAP3基元的部分缺失对该基因的功能没有决定性的影响;2）金粟兰paleoAP3型基因CsAP3所编码蛋白的C末端以及paleoAP3基元，与拟南芥euAP3型基因AtAP3所编码蛋白的C末端以及euAP3基元没有功能上的不同;3）金粟兰paleoAP3型基因CsAP3与拟南芥euAP3型基因AtAP3 的主要功能存在一定差异，前者主要参与雄蕊形成，而后者既参与雄蕊的形成也参与花瓣的形成; 4）CsPI基因所编码的蛋白可以与AP3类蛋白相互作用进而影响花瓣的形成，因此该基因在功能上是保守的。 4. 金粟兰CsAG1基因的序列结构和功能分析 通过序列结构分析发现，CsAG1属于C类基因，具有保守的AG I基元和AG II基元。过量表达实验分析表明CsAG1的功能与A类基因的功能是相拮抗的。 5. 各类MADS-domain蛋白间的相互作用 在前面工作的基础上，我们首次对金粟兰中各类MADS-domain蛋白间的作用方式进行了研究。酵母双杂交结果表明：1）C末端的完整性对于MADS-domain蛋白二聚体的形成没有影响; 2）去掉M区的CsAP3蛋白与CsPI蛋白都能够形成异源二聚体，同时它们又可以各自形成同源二聚体; 3）E类蛋白既可以和A类或C类基因产物相互作用，也可以同AP3和PI型蛋白相互作用，充分体现了E类基因产物作用式样的保守性; 4）金粟兰中，FUL-like型基因所编码的蛋白CsAP1-1与CsSEP3和CsAG1也能形成异源二聚体，这与核心真双子叶植物的euFUL型蛋白在作用式样上是非常相似的。然而，金粟兰CsAP1-1蛋白不能形成同源二聚体。 综合以上结果发现，在无花被的金粟兰中，仍然存在着A、B、C/D、E类花发育相关的基因。这些基因的功能与核心真双子叶植物中同类基因的相比，有些是保守的，比如CsPI基因可以参与花被的形成;但也有一些是不同的，比如CsAP3基因主要参与雄蕊形成而非花被形成过程。由此可以看出被子植物花器官的发育是一个非常复杂的调控过程，不同植物中的调控机理及进化历程可能是不同的。

太行花TrMADS3基因的结构、功能和进化研究

休眠是温带多年生植物的特性之一。为了适应温带地区寒冷的冬季，多年生植物的分生组织通常在秋末冬初进入休眠状态，这样有利于它们在低温下的存活。因此，温带多年生植物的生长和开花具有季节性。植物的生长发育需要与季节的交替变化同步，才能适应环境，保证繁殖成功。多年生植物通过“生长－休眠－生长”的循环过程适应温带地区寒冷的冬季。休眠既有利于植物存活又可调节开花时间。因此，探索温带多年生植物休眠过程的分子调控机理具有重要的应用价值。 太行花（Taihangia rupestris）是蔷薇科仙女木族的一种多年生草本。它生长在海拔1000到1200米的温带山区。太行花需要两个生长季节才能开花，这一点与模式植物拟南芥、水稻不同。在第一个生长季节花芽诱导，花序发育到秋末冬初时进入休眠状态;过冬花序包裹在叶柄基部，接近土壤表面;到了第二个生长季节，花进一步发育完全，开花结果。休眠过程对太行花花序的存活以及来年的开花时间控制非常关键，对这个过程的调控基因的研究不仅有助于理解太行花休眠的分子机制，还将为其它经济植物在这个方面的研究提供资料。 本研究以太行花为研究材料，从它的过冬花序中分离得到了一个MADS-box基因，分析了它的序列结构、系统发育关系、表达式样和功能，探讨了FLC亚家族基因在太行花这种多年生植物和一年生、两年生植物之间发生的表达功能分化。主要研究结果包括： 1. 从太行花的过冬花序中分离出了TrMADS3基因。氨基酸序列分析结果表明它是MIKCc型MADS-box基因，系统发育分析结果表明TrMADS3与FLC类基因聚在一起。 2. 实时定量PCR和RT-PCR实验显示TrMADS3在冬季休眠期太行花的花序、根、叶中广泛表达。从十月底到一月底的冬季低温期户外太行花植株中TrMADS3表达量比同期温室植株的表达量高，也比夏季户外植株的表达量高。对温室植株进行低温处理能明显上调TrMADS3的表达量，而短光照、干旱、高盐和脱落酸（ABA）处理对TrMADS3的表达影响不明显。 3. 用原位杂交的方法分析了TrMADS3的表达式样。营养器官中，TrMADS3在营养顶端分生组织、叶原基、幼叶边缘细胞中表达量高;生殖器官中，TrMADS3在侧生分生组织、花序原基、花原基、幼苞片、萼片原基、花瓣原基、雄蕊原基、心皮原基、发育中的雄蕊、心皮中表达量高。TrMADS3的表达模式反映了TrMADS3调控营养生长和不同阶段的花序、花发育过程。 4. TrMADS3在拟南芥中异位表达不影响拟南芥开花时间。在高盐和干旱胁迫条件下，TrMADS3异位表达能够明显提高转基因拟南芥后熟种子的萌发率。 5. 建立了太行花的组培体系。 综上所述，TrMADS3属于FLC进化支，这一亚家族基因还未在多年生植物中报道。TrMADS3在太行花休眠期表达量很高。在实验控制条件下，一至两周低温能够明显促进TrMADS3表达量的上调。低温处理后回到生长温度的太行花在一月内依然保持较高的TrMADS3的表达。原位杂交实验显示TrMADS3在营养和生殖分生组织中表达量高。TrMADS3在拟南芥中异位表达促进后熟种子在高盐和干旱胁迫下萌发。因此，我们推测TrMADS3具有响应低温调节太行花休眠期营养和生殖分生组织活性的功能。在一、二年生植物中分离的FLC-like基因响应春化作用，具有抑制花芽诱导的保守功能，这些基因在营养器官中表达，受春化作用调节，对应一、二年生植物的成花诱导受春化作用促进的过程，但TrMADS3在太行花营养和生殖器官中均表达，对应太行花花芽诱导后营养和生殖器官均进入休眠状态的生理特性，因此，我们推测FLC-like基因有可能在太行花这种温带多年生植物和一、二年生植物之间发生功能分化。

A topological algorithm for identification of structural domains of proteins

Background: Identification of the structural domains of proteins is important for our understanding of the organizational principles and mechanisms of protein folding, and for insights into protein function and evolution. Algorithmic methods of dissecting protein of known structure into domains developed so far are based on an examination of multiple geometrical, physical and topological features. Successful as many of these approaches are, they employ a lot of heuristics, and it is not clear whether they illuminate any deep underlying principles of protein domain organization. Other well-performing domain dissection methods rely on comparative sequence analysis. These methods are applicable to sequences with known and unknown structure alike, and their success highlights a fundamental principle of protein modularity, but this does not directly improve our understanding of protein spatial structure.

Causes and consequences of variation in nestling immune function

Defence against pathogens is a vital need of all living organisms that has led to the evolution of complex immune mechanisms. However, although immunocompetence the ability to resist pathogens and control infection has in recent decades become a focus for research in evolutionary ecology, the variation in immune function observed in natural populations is relatively little understood. This thesis examines sources of this variation (environmental, genetic and maternal effects) during the nestling stage and its fitness consequences in wild populations of passerines: the blue tit (Cyanistes caeruleus) and the collared flycatcher (Ficedula albicollis). A developing organism may face a dilemma as to whether to allocate limited resources to growth or to immune defences. The optimal level of investment in immunity is shaped inherently by specific requirements of the environment. If the probability of contracting infection is low, maintaining high growth rates even at the expense of immune function may be advantageous for nestlings, as body mass is usually a good predictor of post-fledging survival. In experiments with blue tits and haematophagous hen fleas (Ceratophyllus gallinae) using two methods, methionine supplementation (to manipulate nestlings resource allocation to cellular immune function) and food supplementation (to increase resource availability), I confirmed that there is a trade-off between growth and immunity and that the abundance of ectoparasites is an environmental factor affecting allocation of resources to immune function. A cross-fostering experiment also revealed that environmental heterogeneity in terms of abundance of ectoparasites may contribute to maintaining additive genetic variation in immunity and other traits. Animal model analysis of extensive data collected from the population of collared flycatchers on Gotland (Sweden) allowed examination of the narrow-sense heritability of PHA-response the most commonly used index of cellular immunocompetence in avian studies. PHA-response is not heritable in this population, but is subject to a non-heritable origin (presumably maternal) effect. However, experimental manipulation of yolk androgen levels indicates that the mechanism of the maternal effect in PHA-response is not in ovo deposition of androgens. The relationship between PHA-response and recruitment was studied for over 1300 collared flycatcher nestlings. Multivariate selection analysis shows that it is body mass, not PHA-response, that is under direct selection. PHA-response appears to be related to recruitment because of its positive relationship with body mass. These results imply that either PHA-response fails to capture the immune mechanisms that are relevant for defence against pathogens encountered by fledglings or that the selection pressure from parasites is not as strong as commonly assumed.

Evolution and functional relevance of Ataxin-3 paralogues

O gene ataxin-3 (ATXN3; 14q32.1) codifica uma proteína expressa ubiquamente, envolvida na via ubiquitina-proteassoma e na repressão da transcrição. Grande relevância tem sido dada ao gene ATXN3 após a identificação de uma expansão (CAG)n na sua região codificante, responsável pela ataxia mais comum em todo o mundo, SCA3 ou doença de Machado-Joseph (DMJ). A DMJ é uma doença neurodegenerativa, autossómica dominante, de início tardio. O tamanho do alelo expandido explica apenas uma parte do pleomorfismo da doença, evidenciando a importância do estudo de outros modificadores. Em doenças de poliglutaminas (poliQ), a toxicidade é causada por um ganho de função da proteína expandida; no entanto, a proteína normal parece ser, também, um dos agentes modificadores da patogénese. O gene ATXN3 possui dois parálogos humanos gerados por retrotransposição: ataxin-3 like (ATXN3L) no cromossoma X, e LOC100132280, ainda não caracterizado, no cromossoma 8. Estudos in vitro evidenciaram a capacidade da ATXN3L para clivar cadeias de ubiquitina, sendo o seu domínio proteolítico mais eficiente do que o domínio da ATXN3 parental. O objetivo deste estudo foi explorar a origem e a evolução das retrocópias ATXN3L e LOC100132280 (aqui denominadas ATXN3L1 e ATXN3L2), assim como testar a relevância funcional de ambas através de abordagens evolutivas e funcionais. Deste modo, para estudar a divergência evolutiva dos páralogos do gene ATXN3: 1) analisaram-se as suas filogenias e estimou-se a data de origem dos eventos de retrotransposição; 2) avaliaram-se as pressões seletivas a que têm sido sujeitos os três parálogos, ao longo da evolução dos primatas; e 3) explorou-se a evolução das repetições CAG, localizadas em três contextos genómicos diferentes, provavelmente sujeitos a diferentes pressões seletivas. Finalmente, para o retrogene que conserva uma open reading frame (ORF) intacta, ATXN3L1, analisou-se, in silico, a conservação dos locais e domínios proteicos da putativa proteína. Ademais, para este retrogene, foi estudado o padrão de expressão de mRNA, através da realização de PCR de Transcriptase Reversa, em 16 tecidos humanos. Os resultados obtidos sugerem que dois eventos independentes de retrotransposição estiveram na origem dos retrogenes ATXN3L1 e ATXN3L2, tendo o primeiro ocorrido há cerca de 63 milhões de anos (Ma) e o segundo após a divisão Platirrínios-Catarrínios, há cerca de 35 Ma. Adicionalmente, outras retrocópias foram encontradas em primatas e outros mamíferos, correspondendo, no entanto, a eventos mais recentes e independentes de retrotransposição. A abordagem evolutiva mostrou a existência de algumas constrições selectivas associadas à evolução do gene ATXN3L1, à semelhança do que acontece com ATXN3. Por outro lado, ATXN3L2 adquiriu codões stop prematuros que, muito provavelmente, o tornaram num pseudogene processado. Os resultados da análise de expressão mostraram que o gene ATXN3L1 é transcrito, pelo menos, em testículo humano; no entanto, a optimização final da amplificação específica dos transcriptos ATXN3L1 permitirá confirmar se a expressão se estende a outros tecidos. Relativamente ao mecanismo de mutação inerente à repetição CAG, os dois parálogos mostraram diferentes padrões de evolução: a retrocópia ATXN3L1 é altamente interrompida e pouco polimórfica, enquanto a ATXN3L2 apresenta tratos puros de (CAG)n em algumas espécies e tratos hexanucleotídicos de CGGCAG no homem e no chimpanzé. A recente aquisição da repetição CGGCAG pode ter resultado de uma mutação inicial de CAG para CGG, seguida de instabilidade que proporcionou a expansão dos hexanucleótidos.Estudos futuros poderão ser realizados no sentido de confirmar o padrão de expressão do gene ATXN3L1 e de detetar proteína endógena in vivo. Adicionalmente, a caracterização da proteina ataxina-3 like 1 e dos seus interatores moleculares poderá povidenciar informação acerca da sua relevância no estado normal e patológico.

Evolution of the extracellular matrix in deuterostomes and the influence of calcitropic hormones

Tese de dout., Biologia (Biologia Molecular), Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2010

Evolution, gene regulation and functional analysis of BMP2 in fish

Bone morphogenetic proteins (BMPs) are multifunctional growth factors belonging to the transforming growth factor β (TGFβ) superfamily with a central role in bone formation and mineralization. BMP2, a founding member of this family, has demonstrated remarkable osteogenic properties and is clinically used to promote bone repair and fracture healing. Lack of basic data on factors regulating BMP2 expression and activity have hampered a better understanding of its role in bone formation and bone-related diseases. The objective of this work was to collect new functional data and determine spatiotemporal expression patterns in a fish system aiming towards a better understanding of BMP2 function and regulation. Transcriptional and post-transcriptional regulation of gilthead seabream BMP2 gene was inferred from luciferase reporter systems. Several bone- and cartilage-related transcription factors (e.g. RUNX3, MEF2c, SOX9 and ETS1) were found to regulate BMP2 transcription, while microRNA 20a was shown to affect stability of the BMP2 transcript and thus the mineralogenic capacity of fish bone-derived host cells. The regulation of BMP2 activity through an interaction with the matrix Gla protein (MGP) was investigated in vitro using BMP responsive elements (BRE) coupled to luciferase reporter gene. Although we demonstrated the functionality of the experimental system in a fish cell line and the activation of BMP signaling pathway by seabream BMP2, no conclusive evidence could be collected on a possible interaction beween MGP and BMP2. The evolutionary relationship among the members of BMP2/4/16 subfamily was inferred from taxonomic and phylogenetic analyses. BMP16 diverged prior to BMP2 and BMP4 and should be the result of an ancient genome duplication that occurred early in vertebrate evolution. Structural and functional data suggested that all three proteins are effectors of the BMP signaling pathway, but expression data revealed different spatiotemporal patterns in teleost fish suggesting distinct mechanisms of regulation. In this work, through the collection of novel data, we provide additional insight into the regulation, the structure and the phylogenetic relationship of BMP2 and its closely related family members.

Adaptive evolution of four microcephaly genes and the evolution of brain size in anthropoid primates

The anatomical basis and adaptive function of the expansion in primate brain size have long been studied; however, we are only beginning to understand the genetic basis of these evolutionary changes. Genes linked to human primary microcephaly have received much attention as they have accelerated evolutionary rates along lineages leading to humans. However, these studies focus narrowly on apes, and the link between microcephaly gene evolution and brain evolution is disputed. We analyzed the molecular evolution of four genes associated with microcephaly (ASPM, CDK5RAP2, CENPJ, MCPH1) across 21 species representing all major clades of anthropoid primates. Contrary to prevailing assumptions, positive selection was not limited to or intensified along the lineage leading to humans. In fact we show that all four loci were subject to positive selection across the anthropoid primate phylogeny. We developed clearly defined hypotheses to explicitly test if selection on these loci was associated with the evolution of brain size. We found positive relationships between both CDK5RAP2 and ASPM and neonatal brain mass and somewhat weaker relationships between these genes and adult brain size. In contrast, there is no evidence linking CENPJ and MCPH1 to brain size evolution. The stronger association of ASPM and CDK5RAP2 evolution with neonatal brain size than with adult brain size is consistent with these loci having a direct effect on prenatal neuronal proliferation. These results suggest that primate brain size may have at least a partially conserved genetic basis. Our results contradict a previous study that linked adaptive evolution of ASPM to changes in relative cortex size; however, our analysis indicates that this conclusion is not robust. Our finding that the coding regions of two widely expressed loci has experienced pervasive positive selection in relation to a complex, quantitative developmental phenotype provides a notable counterexample to the commonly asserted hypothesis that cisregulatory regions play a dominant role in phenotypic evolution. Key words: ASPM, MCPH1, CDK5RAP2, CENPJ, brain, neurogenesis, primates.

Respiratory chemoreceptor function in vertebrates - Comparative and evolutionary aspects

The sensing of blood gas tensions and/or pH is an evolutionarily conserved, homeostatic mechanism, observable in almost all species studied from invertebrates to man. In vertebrates, a shift from the peripheral O2-oriented sensing in fish, to the central CO2/pH sensing in most tetrapods reflects the specific behavioral requirements of these two groups whereby, in teleost fish, a highly O2-oriented control of breathing matches the ever-changing and low oxygen levels in water, whilst the transition to air-breathing increased the importance of acid-base regulation and O2-related drive, although retained, became relatively less important. The South American lungfish and tetrapods are probably sister groups, a conclusion backed up by many similar features of respiratory control. For example, the relative roles of peripheral and central chemoreceptors are present both in the lungfish and in land vertebrates. In both groups, the central CO2/pH receptors dominate the ventilatory response to hypercarbia (60-80), while the peripheral CO2/pH receptors account for 20-30. Some basic components of respiratory control have changed little during evolution. This review presents studies that reflect the current trends in the field of chemoreceptor function, and several laboratories are involved. An exhaustive review on the previous literature, however, is beyond the intended scope of the article. Rather, we present examples of current trends in respiratory function in vertebrates, ranging from fish to humans, and focus on both O2 sensing and CO2 sensing. As well, we consider the impact of chronic levels of hypoxia - a physiological condition in fish and in land vertebrates resident at high elevations or suffering from one of the many cardiorespiratory disease states that predispose an animal to impaired ventilation or cardiac output. This provides a basis for a comparative physiology that is informative about the evolution of respiratory functions in vertebrates and about human disease. Currently, most detail is known for mammals, for which molecular biology and respiratory physiology have combined in the discovery of the mechanisms underlying the responses of respiratory chemoreceptors. Our review includes new data on nonmammalian vertebrates, which stresses that some chemoreceptor sites are of ancient origin.

Effects of the administration of pentoxifylline and prednisolone on the evolution of portal fibrogenesis secondary to biliary obstruction in growing animals: immunohistochemical analysis of the expression of TGF-BETA; and VEGF

OBJECTIVE: During the neonatal and infancy periods, some chronic liver diseases may lead to progressive hepatic fibrosis, which is a condition that can ultimately result in the loss of organ function and severe portal hypertension necessitating hepatic transplantation. In a previous report, pharmacological interventions were demonstrated to modulate hepatic fibrosis induced by bile duct ligation in young rats. The administration of pentoxifylline or prednisolone, or the combination of both, resulted in reduced fibrogenesis in portal spaces. The objectives of the present study were to evaluate the expression of transforming growth factor beta and vascular endothelial growth factor after bile duct ligation in young rats and to assess the effect of those same drugs on cytokine expression. METHODS: In this experimental study, 80 young rats (21 or 22 days old) were submitted either to laparotomy and common bile duct ligation or to sham surgery. The animals were allocated into four groups according to surgical procedure, and the following treatments were administered: (1) common bile duct ligation + distilled water, (2) sham surgery + distilled water, (3) common bile duct ligation + pentoxifylline, or (4) common bile duct ligation + prednisolone. After 30 days, a hepatic fragment was collected from each animal for immunohistochemical analysis using monoclonal antibodies against transforming growth factor beta and vascular endothelial growth factor. Digital morphometric and statistical analyses were performed. RESULTS: The administration of pentoxifylline reduced the transforming growth factor beta-marked area and the amount of transforming growth factor beta expressed in liver tissue. This effect was not observed after the administration of prednisolone. There was a significant reduction in vascular endothelial growth factor expression after the administration of either drug compared with the non-treatment group. CONCLUSIONS: The administration of pentoxifylline to cholestatic young rats resulted in the diminished expression of transforming growth factor beta and vascular endothelial growth factor in liver tissue. The administration of steroids resulted in the diminished expression of vascular endothelial growth factor only. These pathways may be involved in hepatic fibrogenesis in young rats submitted to bile duct ligation and exposed to pentoxifylline or prednisolone.

Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction

In protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them. (C) 2012 Elsevier Ltd. All rights reserved.

Effects of the administration of pentoxifylline and prednisolone on the evolution of portal fibrogenesis secondary to biliary obstruction in growing animals: immunohistochemical analysis of the expression of TGF-β and VEGF

OBJECTIVE: During the neonatal and infancy periods, some chronic liver diseases may lead to progressive hepatic fibrosis, which is a condition that can ultimately result in the loss of organ function and severe portal hypertension necessitating hepatic transplantation. In a previous report, pharmacological interventions were demonstrated to modulate hepatic fibrosis induced by bile duct ligation in young rats. The administration of pentoxifylline or prednisolone, or the combination of both, resulted in reduced fibrogenesis in portal spaces. The objectives of the present study were to evaluate the expression of transforming growth factor β and vascular endothelial growth factor after bile duct ligation in young rats and to assess the effect of those same drugs on cytokine expression. METHODS: In this experimental study, 80 young rats (21 or 22 days old) were submitted either to laparotomy and common bile duct ligation or to sham surgery. The animals were allocated into four groups according to surgical procedure, and the following treatments were administered: (1) common bile duct ligation + distilled water, (2) sham surgery + distilled water, (3) common bile duct ligation + pentoxifylline, or (4) common bile duct ligation + prednisolone. After 30 days, a hepatic fragment was collected from each animal for immunohistochemical analysis using monoclonal antibodies against transforming growth factor β and vascular endothelial growth factor. Digital morphometric and statistical analyses were performed. RESULTS: The administration of pentoxifylline reduced the transforming growth factor β-marked area and the amount of transforming growth factor β expressed in liver tissue. This effect was not observed after the administration of prednisolone. There was a significant reduction in vascular endothelial growth factor expression after the administration of either drug compared with the non-treatment group. CONCLUSIONS: The administration of pentoxifylline to cholestatic young rats resulted in the diminished expression of transforming growth factor β and vascular endothelial growth factor in liver tissue. The administration of steroids resulted in the diminished expression of vascular endothelial growth factor only. These pathways may be involved in hepatic fibrogenesis in young rats submitted to bile duct ligation and exposed to pentoxifylline or prednisolone.

Modeling the cosmological co-evolution of supermassive black holes and galaxies

In this Thesis, we investigate the cosmological co-evolution of supermassive black holes (BHs), Active Galactic Nuclei (AGN) and their hosting dark matter (DM) halos and galaxies, within the standard CDM scenario. We analyze both analytic, semi-analytic and hybrid techniques and use the most recent observational data available to constrain the assumptions underlying our models. First, we focus on very simple analytic models where the assembly of BHs is directly related to the merger history of DM haloes. For this purpose, we implement the two original analytic models of Wyithe & Loeb 2002 and Wyithe & Loeb 2003, compare their predictions to the AGN luminosity function and clustering data, and discuss possible modifications to the models that improve the match to the observation. Then we study more sophisticated semi-analytic models in which however the baryonic physics is neglected as well. Finally we improve the hybrid simulation of De Lucia & Blaizot 2007, adding new semi-analytical prescriptions to describe the BH mass accretion rate during each merger event and its conversion into radiation, and compare the derived BH scaling relations, fundamental plane and mass function, and the AGN luminosity function with observations. All our results support the following scenario: • The cosmological co-evolution of BHs, AGN and galaxies can be well described within the CDM model. • At redshifts z & 1, the evolution history of DM halo fully determines the overall properties of the BH and AGN populations. The AGN emission is triggered mainly by DM halo major mergers and, on average, AGN shine at their Eddington luminosity. • At redshifts z . 1, BH growth decouples from halo growth. Galaxy major mergers cannot constitute the only trigger to accretion episodes in this phase. • When a static hot halo has formed around a galaxy, a fraction of the hot gas continuously accretes onto the central BH, causing a low-energy “radio” activity at the galactic centre, which prevents significant gas cooling and thus limiting the mass of the central galaxies and quenching the star formation at late time. • The cold gas fraction accreted by BHs at high redshifts seems to be larger than at low redshifts.

Aggression and its function as a hub mediating host defense against the slavemaking ant Protomognathus americanus

In meiner Dissertation beschäftigte ich mich mit unterschiedlichen Verteidungsstrategien, derenrnEffektivität und Evolution, der Ameisenart Temnothorax longispinosus (“Sklaven”), gegenüberrneinem sozialen Parasiten - der nahverwandten, sklavenhaltenden Art Protomognathusrnamericanus (“Sklavenhalter”). Wir entdeckten eine neue Kategorie der Verteidigungsstrategie,rnwelche es dem Wirten ermöglicht, flexibel auf die nicht vorhersagbaren Angriffe des Parasitenrnzu reagieren. Darüber hinaus erforschten wir, wie die Wirte ihre kollektive Verteidigung an einernVielzahl unterschiedlicher Angreifer anpassen können. Wir konnten feststellen, dass Wirte in derrnLage sind ihre kollektive Verteidigung dem Grad der Bedrohung anzupassen. Dies weist daraufrnhin, dass Selektion die Verteidigung gegen unterschiedliche Typen von Angreifern voneinanderrnunabhängig beeinflussen könnte. In einer dritten Studie belegten wir experimentell, dass diernParasiten die Evolution der Kolonieaggressivität der Wirtsart direkt beeinflussen. Die letztenrnbeiden Publikationen beschäftigten sich mit Sklavenrebellion, einer rätselhaftenrnVerteidigungsstrategie, da noch unklar ist, wie eine Eigenschaft von nicht reproduzierendenrnIndividuen vererbt werden kann. In einer Metaanalyse konnten wir die weite Verbreitung undrnhohe Variabilität dieser Eigenschaft dokumentieren, und fanden Hinweise, dassrnVerwandtenselektion eine mögliche Erklärung für die Evolution dieses Merkmals darstellenrnkönnte.