Rationalization and prediction of drug resistant mutations in targets for clinical anti-tubercular drugs

Resistance to therapy limits the effectiveness of drug treatment in many diseases. Drug resistance can be considered as a successful outcome of the bacterial struggle to survive in the hostile environment of a drug-exposed cell. An important mechanism by which bacteria acquire drug resistance is through mutations in the drug target. Drug resistant strains (multi-drug resistant and extensively drug resistant) of Mycobacterium tuberculosis are being identified at alarming rates, increasing the global burden of tuberculosis. An understanding of the nature of mutations in different drug targets and how they achieve resistance is therefore important. An objective of this study is to first decipher sequence as well as structural bases for the observed resistance in known drug resistant mutants and then to predict positions in each target that are more prone to acquiring drug resistant mutations. A curated database containing hundreds of mutations in the 38 drug targets of nine major clinical drugs, associated with resistance is studied here. Mutations have been classified into those that occur in the binding site itself, those that occur in residues interacting with the binding site and those that occur in outer zones. Structural models of the wild type and mutant forms of the target proteins have been analysed to seek explanations for reduction in drug binding. Stability analysis of an entire array of 19 mutations at each of the residues for each target has been computed using structural models. Conservation indices of individual residues, binding sites and whole proteins are computed based on sequence conservation analysis of the target proteins. The analyses lead to insights about which positions in the polypeptide chain have a higher propensity to acquire drug resistant mutations. Thus critical insights can be obtained about the effect of mutations on drug binding, in terms of which amino acid positions and therefore which interactions should not be heavily relied upon, which in turn can be translated into guidelines for modifying the existing drugs as well as for designing new drugs. The methodology can serve as a general framework to study drug resistant mutants in other micro-organisms as well.

Automatic Tonic Identification in Indian Art Music: Approaches and Evaluation

The tonic is a fundamental concept in Indian art music. It is the base pitch, which an artist chooses in order to construct the melodies during a rg(a) rendition, and all accompanying instruments are tuned using the tonic pitch. Consequently, tonic identification is a fundamental task for most computational analyses of Indian art music, such as intonation analysis, melodic motif analysis and rg recognition. In this paper we review existing approaches for tonic identification in Indian art music and evaluate them on six diverse datasets for a thorough comparison and analysis. We study the performance of each method in different contexts such as the presence/absence of additional metadata, the quality of audio data, the duration of audio data, music tradition (Hindustani/Carnatic) and the gender of the singer (male/female). We show that the approaches that combine multi-pitch analysis with machine learning provide the best performance in most cases (90% identification accuracy on average), and are robust across the aforementioned contexts compared to the approaches based on expert knowledge. In addition, we also show that the performance of the latter can be improved when additional metadata is available to further constrain the problem. Finally, we present a detailed error analysis of each method, providing further insights into the advantages and limitations of the methods.

Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue96 in the Plasmodial Enzyme

Despite extensive research into triosephosphate isomerases (TIMs), there exists a gap in understanding of the remarkable conjunction between catalytic loop-6 (residues 166-176) movement and the conformational flip of Glu165 (catalytic base) upon substrate binding that primes the active site for efficient catalysis. The overwhelming occurrence of serine at position96 (98% of the 6277 unique TIM sequences), spatially proximal to E165 and the loop-6 residues, raises questions about its role in catalysis. Notably, Plasmodium falciparum TIM has an extremely rare residuephenylalanineat this position whereas, curiously, the mutant F96S was catalytically defective. We have obtained insights into the influence of residue96 on the loop-6 conformational flip and E165 positioning by combining kinetic and structural studies on the PfTIM F96 mutants F96Y, F96A, F96S/S73A, and F96S/L167V with sequence conservation analysis and comparative analysis of the available apo and holo structures of the enzyme from diverse organisms.

Identifying and interpreting stratification in sedimentary rocks on Mars : insight from Rover and orbital observations and terrestrial field analogs

Sedimentary rocks on Mars provide insight into past aqueous and atmospheric processes, climate regimes, and potential habitability. The stratigraphic architecture of sedimentary rocks on Mars is similar to that of Earth, indicating that the processes that govern deposition and erosion on Mars can be reasonably inferred through reference to analogous terrestrial systems. This dissertation aims to understand Martian surface processes through the use of (1) ground-based observations from the Mars Exploration Rovers, (2) orbital data from the High Resolution Imaging Science Experiment onboard the Mars Reconnaissance Orbiter, and (3) the use of terrestrial field analogs to understand bedforms and sediment transport on Mars. Chapters 1 and 2 trace the history of aqueous activity at Meridiani Planum, through the reconstruction of eolian bedforms at Victoria crater, and the identification of a potential mudstone facies at Santa Maria crater. Chapter 3 uses Terrestrial Laser Scanning to study cross-bedding in pyroclastic surge deposits on Earth in order to understand sediment transport in these events and to establish criteria for their identification on Mars. The final chapter analyzes stratal geometries in the Martian North Polar Layered Deposits using tools for sequence stratigraphic analysis, to better constrain past surface processes and past climate conditions on Mars.

绣球族的系统学研究

绣球科绣球族包含9属：草绣球属、叉叶蓝属、Broussaisia、常山属、绣球属、蛛网萼属、赤壁木属、冠盖藤属和钻地风属。到目前为止，绣球族内的属间关系还不清楚，族内的系统发育关系还有争论。本研究的目的是在前人研究的基础上，进一步发现新的系统学性状，为绣球族乃至绣球科补充新的证据;并综合多学科的研究结果进行分析，探讨绣球族的系统学关系。 本文研究了绣球族的外部形态学、花发育形态学、解剖学、分子系统学和分支系统学。 主要内容包括： 1. 形态学 通过标本室研究和野外观察，对绣球族植物的形态分化进行了分析。发现习性、地上茎的生存期限、花冠卷叠式、花瓣联合与否、花柱的联合程度、雄蕊的数目及排列具有系统学价值;放射花和果实是很好的分类性状，但并非可靠的系统学性状。 2. 花发育形态学 在扫描电子显微镜下，研究了绣球族常山属、绣球属、冠盖藤属、蛛网萼属共4种植物花器官发生和发育的全过程。发现它们的花萼均为螺旋式相继发生，花瓣的发生近乎同时。冠盖藤、马桑绣球及常山具两轮雄蕊，第一轮雄蕊发生于花瓣内轮正对萼片中部的位置，随后第二轮雄蕊发生于正对花瓣中部的位置。在第一轮雄蕊略靠内的位置形成第二轮雄蕊的时候，多数情况下，相邻的对萼雄蕊之间只形成1个对瓣雄蕊，但有时却形成2个对瓣雄蕊，使雄蕊群的数目略多于花被的数目。对萼雄蕊与对瓣雄蕊的分化方式基本一致，但它们在花芽中空间取向不同。 蛛网萼雄蕊数目极多，雄蕊群的发生式样较为独特，并不始于对萼三联体。最早的雄蕊于杯状体近基部发生，之后雄蕊的发生大致沿杯状体壁向上，具离心趋势。在雄蕊发生过程中杯状体继续伸长，为众多雄蕊的发生提供了空间。蛛网萼雌蕊的发生明显早于雄蕊，其它3种植物雌蕊的发生晚于雄蕊。4种植物的雌蕊在发生上较为相似，发育却不同。在常山、马桑绣球和蛛网萼中，花柱从开始到发育成熟始终分离，柱头在每个花柱的顶端形成;而冠盖藤属的花柱裂片从开始就是联合的，最终形成单一的花柱，柱头从合生花柱顶端远轴面分化形成。 3. 解剖学 在光学显微镜和扫描电子显微镜下，观察了绣球族9属42种1变种及近缘8属11种共53种1变种的叶表皮特征。发现气孔的分布、气孔器的类型、表皮细胞的形状及其垂周壁式样、毛被等具有一定的系统学意义和分类价值。绣球族各属的气孔仅散生于下表皮;而在绣球族的几个近缘属中，上下表皮均有气孔分布。气孔器在多数类群中为无规则型，仅常山属和绣球属离瓣组的成员为平列型。气孔多为椭圆形，稀近圆形;外拱盖表面通常光滑，仅在钻地风属中具条状纹饰;外拱盖内缘具环状加厚，近全缘、不规则波状或浅波状。表皮细胞在多数种中为不规则形，垂周壁波状、浅波状或深波状;在有些种中为（近）多边形，垂周壁平直或弓形。叶表皮细胞形状、垂周壁式样在绣球族寡种属属级水平比较稳定，但在绣球属中变化较大。表皮角质膜纹饰形态多样，有网纹、粗网纹、浅波状条纹、波状条纹、条纹、粗条纹及丝状条纹;在钻地风属及绣球属的少数种中，角质膜条纹有时汇集呈球形或玫瑰型。表皮毛状附属物有单细胞2分枝毛（黄山梅属）、多细胞星状毛（星毛冠盖藤）、单细胞星状毛（溲疏属）和单细胞不分枝毛四种。对钻地风属所有种的观察结果表明，仅在椭圆钻地风的下表皮细胞中央观察到乳突状结构，而在白背钻地风和圆叶钻地风中并未观察到前人描述的附属物。 4. 叶绿体DNA trnL-F序列的分析 首次对绣球族9属23种及近缘类群3属3种的trnL-F序列进行了测定。序列长度在860 bp~970 bp范围内变化。在以山梅花属、溲疏属和黄山梅属为外类群，基于trnL-F序列构建的系统树上，绣球族作为一个单系群得到很高的支持率。绣球属的种出现在不同的分支上，表明该属不是一个单系群。绣球族被分为两大支：第一支由绣球属离瓣组的中国绣球、绣球、以及常山和Broussaisia arguta组成;第二支由绣球属另外的9个种与草绣球属、叉叶蓝属、蛛网萼属、赤壁木属、冠盖藤属以及钻地风属组成。在第二支中，下列类群的近缘关系得到支持：① 草绣球与叉叶蓝属;② 绣球属挂苦子组的东陵绣球、圆锥绣球和挂苦绣球。③ 钻地风属、赤壁木属和冠盖藤属;④ 蜡莲绣球、莼兰绣球、马桑绣球、粗枝绣球。 5. 分支分析 以山梅花属为外类群，基于形态、解剖、花发育、孢粉等32个性状（或性状状态）对绣球族9属的系统发育关系进行了分支分析。结果表明：草绣球属和叉叶蓝属为基出类群，这两个属有多个共同特征;绣球族其余的成员聚成一支，该支又有5个分支。其中蛛网萼属和绣球属冠盖组各为单独的分支，它们有多个自衍征，可能有各自独立的演化线;绣球属离瓣组与常山属聚成一分支，二者的密切关系得到解剖学证据的支持;绣球属绣球组和星毛组聚成一分支，这两个组包含了绣球属的多数种类;钻地风属、赤壁木属、冠盖藤属、Broussaisia和绣球属挂苦子组聚成一分支。其中钻地风属、赤壁木属与冠盖藤属具多个近裔衍征，表明它们是绣球族的晚出类群。 通过对绣球族植物外部形态、花器官发生、叶表皮微形态特征、叶绿体DNA trnL-F区的研究以及基于形态性状的分支分析，并综合已有的研究结果，我们认为： 1. 绣球族是一个单系群;绣球属不是一个单系群。 2. 在绣球族中，草绣球属和叉叶蓝属关系密切，它们可能是绣球族其余成员的姐妹群。 3. 绣球组和星毛组可能是绣球属的核心成员;离瓣组和常山属关系密切;冠盖组有单独的演化线。 4. 赤壁木属、冠盖藤属和钻地风属为单系群，它们在绣球族处于较高的演化位置。 5. 绣球属需重新界定。

小麦×玉米的小麦DH后代的分子生物学分析

植物远缘杂交是作物育种实践及其相关的基础遗传中应用最广泛的技术之一，几乎涉及到所有与栽培作物有关的科属内相对近缘的植物种类。除核型稳定的种间杂交可得到杂种外，还可以利用核型不稳定的种间杂交过程中父本染色体全部被消除的现象，通过胚培养和加倍处理获得大量的双单倍体（DH）杂交后代。然而，这种从小麦与玉米杂交获得的小麦DH后代与其理论上应完全同质的遗传表现却不相符，总有2-5%的DH植株发生了形态学变异，虽然没有明显的来自玉米的性状特征，而且一些研究者也认为它们是配子无性系变异，但是，不论是理论上还是一些间接的细胞学和生化证据都表明，有玉米的染色体DNA通过受精过程转移到小麦DH后代的基因组中，然而到目前为止，仍缺乏DNA水平上的直接证据。 本文在对来自小麦 * 玉米的谱通小麦DH系进行生化分析取得初步证据的基础上，构建玉米的随机基因组文库，从中筛选玉米的重复DNA序列作探针分别对普通小麦和波斯小麦的DH群体进行了系统的RFLP分析，并用有关的玉米重复列克隆对一些禾本科种和不同的玉米生物型基因组进行了比较研究，主要结果如下： 1、八种同工酶电泳分析表明，MDH、ADH、GDH、SKDH4种脱氢酶和GOT在后代中没有检测到任何变异，但21株普通小麦的DH后代群体中有7株在PER同工酶的慢区出现了增加一条酶带的变异，这条带在亲本小麦和玉米中均没有，它们与通常报道的无性系变异十分类似。其中有一株（第4号株）在迁移率为0.22的位置上出现了一条小麦所不具有的酶活性较强的EST带，在玉米同迁移率的位置上也有一条带，但活性十分微弱。此外，大部分小麦DH后代的AMY同工酶恬性有十分明显的增强。 2、可溶性蛋白质的SDS-PAGE分析，在小麦的DH后代中，有几株的变异很明显，其中第4、7、19号株（图2）在分子量为43000道尔顿的位置上出现了和玉米同迁移率而小麦不具有的蛋白质带，这强烈地暗示了玉米DNA的确通过受精作用导入小麦。 3、构建了玉米的随机基因组文库，依据菌落原位杂交结果，从中挑出了500个重组克隆。用其中的100个强信号的重复DNA克隆为探针对亲本小麦和玉米进行了RFLP筛选，其中80多个为玉米基因组特异的，9个与小麦有部分同源性，随后用它们探针分别对两个小麦DH群体进行RFLP分析。 4、用上文筛选的玉米特异的重复DNA克隆作探针进行RFLP分析，只有玉米的MR64克隆同时导入到两个小麦群体的各一株后代中，即普通小麦DH系的18号株和波斯小麦DH系的15号株检测到强杂交信号;另外一个克隆MR72只在4株波斯小麦DH后代中有杂交信号，这个结果首次从DNA水平上证明，的确有某些玉米特异的DNA序列通过受精作用以很低的频率转移到小麦DH后代的基因组中。 5、与小麦有部分同源性的玉米克隆MR13和MR50在一些普通小麦DH后代中检测到了缺失变异。特别是用MR13在普通小麦DH系的18号株（即导入了玉米特异的MR64的DNA的那一株小麦DH后代）的基因组中检测到了大幅度的限制性片段长度的变化，即原来的4.3kb的强信号带消失了，取而代之的是增加40kb、15kb、2.5kb和2.0kb四条杂交带，这要么与小麦基因组DNA较大的重俳事件有关，要么是由外源的玉米DNA插入造成的，但从增加的片段长度如此之大以及杂交信号变弱来看，它很可能就是玉米DNA插入到这个较强信号的小麦单拷贝序列中的结果。用小麦的DNA克隆pTa71也检测到了明显的变异。 6、测序分析发现，克隆MP64的插入片段长度为695bp，A+T含量为58%，经在GENEBANK中检索证实它是一个新克隆的DNA序列。序列中分别含有两对正向和反向重 序列及三个回文序列，对多种酶切的玉米基因组的RFLP分析表明它是一个带1-3个主串联重复单位的散布重复序列，在序列中的CCGG的第二个C高度甲基化，拷贝数约为5600左右。染色体原位杂交表明，MR64在玉米的每条染色体上均有分布，但拷贝数不同，这暗示它可能与玉米基因组的演化历程有密切的关系。 7、比较分析发现，MR64是玉米基因组特异的;而MR72在高粱、珍株粟、糜子和狼尾草等四个和玉米较近缘的种的基因组中有部分同源序列，这个比较结果更加肯定了小麦DH系所新增的DNA序列的确是异源的玉米DNA通过受精过程导入的。 8、初步分析发现，玉米的卫星DNA克隆MR4和其它卫星DNA一样也有严谨的重复等级结构，而且在主要禾本科种基因组中有较低的同源性。经在GENEBANK检索，串联重复DNA克隆MR68是一个新克隆的DNA序列，它在不同的玉米生物型基因组中表现出明显的分化特征，可用它作进一步的基因组的比较分析。 9、本文对染色体消除过程度中异源小片段DNA导入的可能机制和散布重复序列在远缘杂交的异源DNA鉴定中的应用进行了讨论，并分析了染色体消除型远缘杂交所获得的DH后代的变异来源。

Molecular characterization of a weak fibrinogen-clotting enzyme from Trimeresurus jerdonii venom

A fibrinogen-clotting enzyme designed as jerdonobin-II was isolated from the venom of Trimeresurus jerdonii. It differed in molecular weight and N-terminal sequence with the previously isolated jerdonobin, a thrombin-like enzyme from the same venom. The enzyme consists of a single polypeptide chain with molecular weights of 30,000 and 32,000 under non-reducing and reducing conditions, respectively. Jerdonobin-II showed weak fibrinogen clotting activity and its activity unit on fibrinogen was calculated to be less than one unit using human thrombin as standard. The precursor protein sequence of jerodonobin-II was deduced from cloned cDNA sequence. The sequence shows high similarity (identity = 89%) to TSV-PA, a specific plasminogen activator from venom of T stejnegeri. Despite of the sequence similarity, jerdonobin-II was found devoid of plasminogen activating effect. Sequence alignment analysis suggested that the replacement of Lys(239) in TSV-PA to Gln(239) in jerdonobin-II might play an important role on their plasminogen activating activity difference. (C) 2005 Elsevier Ltd. All rights reserved.

Metallothionein-2 gene from the mandarin fish Siniperca chuatsi: cDNA cloning, tissue expression, and immunohistochemical localization

The metallothionein-2 (MT-2) gene was isolated from the mandarin fish, one of the most important industrial aquatic animals in China, by using rapid amplification of cDNA ends (RACE). The deduced amino acid sequence of MT-2 comprised 60 amino acids and showed approximately 62.3% identity to human metallothionein. Its promoter region was amplified by thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR). The MT-2 gene consists of 3 exons and 2 introns, extending approximately 900 bp of genomic sequence. Phylogenetic analysis clearly demonstrated that MT-2 formed a clade with fish metallothionein. The promoter region contained 5 putative metal-regulatory elements (MREs) and 1 TATA box. Real-time quantitative RT-PCR analysis revealed that MT-2 transcripts were significantly increased in the brain and gills and were stable in the muscles, liver, and trunk kidney in Cd2+-stimulated fish. Western blotting analysis demonstrated that the protein of the MT-2 gene was expressed mainly in the gills, liver, heart, trunk kidney, muscle, and intestine; it was weakly detected in the brain and head kidney. Moreover, the MT-2 protein was immunohistochemically detected in the cytoplasm in the liver and trunk kidney. All the above results revealed that the mandarin fish MT-2 would be a useful biomarker for metal pollution. (C) 2008 Published by Elsevier Inc.

Intelectin gene from the grass carp Ctenopharyngodon idella: cDNA cloning, tissue expression, and immunohistochemical localization

The cDNA encoding grass carp intelectin was isolated from a head kidney cDNA library, and termed gcIntL. The deduced amino acid sequence of gcIntL consists of 318 amino acids, and about 55% identical and 74% similar to human intelectin, which is a new type of lectin recognizing galactofuranose, and plays a role in the recognition of bacteria-specific components in animal hosts. The gcIntL gene consists of seven exons and six introns, spacing over approximately 3 kb of genomic sequence. Phylogenetic analysis clearly demonstrated that the gcIntL formed a clade with Danio rerio intelectin and 35 kDa serum lectin. By real-time quantitative RT-PCR analysis, gcIntL transcripts were significantly induced in head kidney, trunk kidney, spleen, and intestine from LPS-stimulated fish. RT-PCR and Western blotting analysis demonstrated that the mRNA and protein of gcIntL gene have the same expression pattern, and both were detected in brain, gill, intestine, head kidney, trunk kidney, spleen, and heart. Furthermore, gcIntL protein could be detected in gill, intestine, trunk kidney, head kidney, spleen, heart, and brain including medulla oblongata and optic lobe, as determined by immunohistochemistry. This is the first report of intelectin expression pattern in fish, and of recombinant gcIntL and polyclonal antibody against gcIntL. (c) 2006 Elsevier Ltd. All rights reserved.

Features of Late Cenozoic Deepwater Sedimentation in Southern Qiongdongnan Basin, Northwestern South China Sea

Based on high resolution 2D and 3D seismic data acquired in recent years, using sequence stratigraphy analysis and geophysical methods, we discuss the features of Late Cenozoic deepwater sedimentation in the southern Qiongdongnan (sic) basin. The study area entered a bathyal slope environment in the Miocene. The channel developed in the Sanya (sic) Formation was controlled by a fault break, and its shingled seismic characteristics represent multiple erosion and fill, which may indicate that turbidite current developed in the slope environment. The polygon faults found in mudstone of the Meishan (sic) Formation represent the deepwater hungry sedimentary environment. The large-scale channels developed on the top of Huangliu (sic) Formation could be the result of a big sea level drop and an increase of sediment supply. The fantastic turbidite channel developed in Late Quaternary in the slope environment has "fan-like" body and long frontal tiny avulsion channel. The analysis of these features suggests that the sediment supply of the study area in the post-rifting period was dominant from the Vietnam uplift in the southwest. These deepwater sedimentary features could be potential reservoirs or migration pathways for deepwater petroleum systems.

Expression of muscle-related genes and two MyoD genes during amphioxus notochord development

The notochord is one of the diagnostic features of the phylum Chordata. Despite the similarities in the early morphogenetic patterns of the notochords of various chordates, they are strikingly distinct from one another at the histological level. The amphioxus notochord is one example of an evolutionary novelty because it is made up of muscle cells. Our previous expressed sequence tag analysis, targeting messenger RNAs expressed in the adult amphioxus notochord, demonstrated that many muscle-related genes are expressed there. To characterize amphioxus notochord cells and to gain insights into the myogenic program in the notochord, we determined the spatial and temporal expression patterns of these muscle-related genes during amphioxus development. We found that BbNA1 (notochord actin), Amphi-Trop I (troponin I), Amphi-TPmyosin (tropomyosin), Amphi-MHC2 (myosin heavy chain), Amphi-nMRLC (notochord-specific myosin regulatory light chain), AmphinTitin/MLCK (notochord-specific titin/myosin light chain kinase), Amphi-MLP/CRP3 (muscle LIM protein), and Amphi-nCalponin (notochord-specific calponin) are expressed with characteristic patterns in notochord cells, including the central cells, dorsally located cells, and ventrally located cells, suggesting that each notochord cell has a unique molecular architecture that may reflect its function. In addition, we characterized two MyoD genes (Amphi-MyoD1 and Amphi-MyoD2) to gain insight into the genetic circuitry governing the formation of the notochord muscle. One of the MyoD genes (Amphi-MyoD2) is expressed in the central notochord cells, and the coexistence of Amphi-MyoD2 transcripts along with the Amphi-MLP/CRP3 transcripts implies the participation of Amphi-MyoD2 in the myogenic program in the notochord muscle.

Seismic characteristics of a reef carbonate reservoir and implications for hydrocarbon exploration in deepwater of the Qiongdongnan Basin, northern South China Sea

Our analysis of approximately 40,000 km of multichannel 2-D seismic data, reef oil-field seismic data, and data from several boreholes led to the identification of two areas of reef carbonate reservoirs in deepwater areas (water depth >= 500 in) of the Qiongdongnan Basin (QDNB), northern South China Sea. High-resolution sequence stratigraphic analysis revealed that the transgressive and highstand system tracts of the mid-Miocene Meishan Formation in the Beijiao and Ledong-Lingshui Depressions developed reef carbonates. The seismic features of the reef carbonates in these two areas include chaotic bedding, intermittent internal reflections, chaotic or blank reflections, mounded reflections, and apparent amplitude anomalies, similar to the seismic characteristics of the LH11-1 reef reservoir in the Dongsha Uplift and Island Reef of the Salawati Basin, Indonesia, which house large oil fields. The impedance values of reefs in the Beijiao and Ledong-Lingshui Depressions are 8000-9000 g/cc x m/s. Impedance sections reveal that the impedance of the LH11-1 reef reservoir in the northern South China Sea is 800010000 g/cc x m/s, whereas that of pure limestone in BD23-1-1 is > 10000 g/cc x m/s. The mid-Miocene paleogeography of the Beijiao Depression was dominated by offshore and neritic environments, with only part of the southern Beijiao uplift emergent at that time. The input of terrigenous sediments was relatively minor in this area, meaning that terrigenous source areas were insignificant in terms of the Beijiao Depression: reef carbonates were probably widely distributed throughout the depression, as with the Ledong-Lingshui Depression. The combined geological and geophysical data indicate that shelf margin atolls were well developed in the Beijiao Depression, as in the Ledong-Lingshui Depression where small-scale patch or pinnacle reefs developed. These reef carbonates are promising reservoirs, representing important targets for deepwater hydrocarbon exploration. (C) 2008 Elsevier Ltd. All rights reserved.

Bayesian variable selection in structured high-dimensional covariate spaces with applications in genomics

We consider the problem of variable selection in regression modeling in high-dimensional spaces where there is known structure among the covariates. This is an unconventional variable selection problem for two reasons: (1) The dimension of the covariate space is comparable, and often much larger, than the number of subjects in the study, and (2) the covariate space is highly structured, and in some cases it is desirable to incorporate this structural information in to the model building process. We approach this problem through the Bayesian variable selection framework, where we assume that the covariates lie on an undirected graph and formulate an Ising prior on the model space for incorporating structural information. Certain computational and statistical problems arise that are unique to such high-dimensional, structured settings, the most interesting being the phenomenon of phase transitions. We propose theoretical and computational schemes to mitigate these problems. We illustrate our methods on two different graph structures: the linear chain and the regular graph of degree k. Finally, we use our methods to study a specific application in genomics: the modeling of transcription factor binding sites in DNA sequences. © 2010 American Statistical Association.

PURIFICATION AND PARTIAL CHARACTERIZATION OF AN ENDO-POLYGALACTURONASE FROM ASPERGILLUS NIGER

A pectinase was identified and isolated from a commercial Aspergillus niger pectinase preparation. The crude enzyme preparation, which was prepared by precipitation of the water extract of the culture of A. niger with ammonium sulfate, was further fractionated by three steps of chromatography, i. e., cation exchange, hydrophobic interaction and onion exchange, to obtain an electrophoretically homogeneous pectinase. The molecular weight of the purified enzyme was estimated by SDS-PAGE to be about 40.4 kDa under both nonreducing and reducing conditions, with the optimum pH at 5.0 and the optimum temperature at 36C. The enzyme was stable at temperatures below 35C. The partial N-terminal ammo acid sequence data analysis of the first 19 amina acids of the obtained pectinase revealed 94.7% and 89.5% homology with two reported pectinases from A. niger.

Conserved amino acid residues found in a predicted cytosolic domain of the lipopolysaccharide biosynthetic protein WecA are implicated in the recognition of UDP-N-acetylglucosamine

WecA, an integral membrane protein that belongs to a family of polyisoprenyl phosphate N-acetylhexosamine-1-phosphate transferases, is required for the biosynthesis of O-specific LPS and enterobacterial common antigen in Escherichia coli and other enteric bacteria. WecA functions as an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate GlcNAc-1-phosphate transferase. A conserved short sequence motif (His-Ile-His-His; HIHH) and a conserved arginine were identified in WecA at positions 279-282 and 265, respectively. This region is located within a predicted cytosolic segment common to all bacterial homologues of WecA. Both HIHH279-282 and the Arg265 are reminiscent of the HIGH motif (His-Ile-Gly-His) and a nearby upstream lysine, which contribute to the three-dimensional architecture of the nucleotide-binding site among various enzymes displaying nucleotidyltransferase activity. Thus, it was hypothesized that these residues may play a role in the interaction of WecA with UDP-GlcNAc. Replacement of the entire HIHH motif by site-directed mutagenesis produced a protein that, when expressed in the E. coli wecA mutant MV501, did not complement the synthesis of O7 LPS. Membrane extracts containing the mutated protein failed to transfer UDP-GlcNAc into a lipid-rich fraction and to bind the UDP-GlcNAc analogue tunicamycin. Similar results were obtained by individually replacing the first histidine (H279) of the HIHH motif as well as the Arg265 residue. The functional importance of these residues is underscored by the high level of conservation of H279 and Arg265 among bacterial WecA homologues that utilize several different UDP-N-acetylhexosamine substrates.