Addressing a source of trouble outside of the repair space

A body of research in conversation analysis has identified a range of structurally-provided positions in which sources of trouble in talk-in-interaction can be addressed using repair. These practices are contained within what Schegloff (1992) calls the repair space. In this paper, I examine a rare instance in which a source of trouble is not resolved within the repair space and comes to be addressed outside of it. The practice by which this occurs is a post-completion account; that is, an account that is produced after the possible completion of the sequence containing a source of trouble. Unlike fourth position repair, the final repair position available within the repair space, this account is not made in preparation for a revised response to the trouble-source turn. Its more restrictive aim, rather, is to circumvent an ongoing difference between the parties involved. I argue that because the trouble is addressed in this manner, and in this particular position, the repair space can be considered as being limited to the sequence in which a source of trouble originates.

A population-specific HTR2B stop codon predisposes to severe impulsivity

Impulsivity, describing action without foresight, is an important feature of several psychiatric diseases, suicidality and violent behaviour. The complex origins of impulsivity hinder identification of the genes influencing it and the diseases with which it is associated. Here we perform exon-focused sequencing of impulsive individuals in a founder population, targeting fourteen genes belonging to the serotonin and dopamine domain. A stop codon in HTR2B was identified that is common (minor allele frequency > 1%) but exclusive to Finnish people. Expression of the gene in the human brain was assessed, as well as the molecular functionality of the stop codon, which was associated with psychiatric diseases marked by impulsivity in both population and family-based analyses. Knockout of Htr2b increased impulsive behaviours in mice, indicative of predictive validity. Our study shows the potential for identifying and tracing effects of rare alleles in complex behavioural phenotypes using founder populations, and indicates a role for HTR2B in impulsivity.

Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer

Improved sequencing technologies offer unprecedented opportunities for investigating the role of rare genetic variation in common disease. However, there are considerable challenges with respect to study design, data analysis and replication. Using pooled next-generation sequencing of 507 genes implicated in the repair of DNA in 1,150 samples, an analytical strategy focused on protein-truncating variants (PTVs) and a large-scale sequencing case-control replication experiment in 13,642 individuals, here we show that rare PTVs in the p53-inducible protein phosphatase PPM1D are associated with predisposition to breast cancer and ovarian cancer. PPM1D PTV mutations were present in 25 out of 7,781 cases versus 1 out of 5,861 controls (P = 1.12 × 10-5), including 18 mutations in 6,912 individuals with breast cancer (P = 2.42 × 10-4) and 12 mutations in 1,121 individuals with ovarian cancer (P = 3.10 × 10-9). Notably, all of the identified PPM1D PTVs were mosaic in lymphocyte DNA and clustered within a 370-base-pair region in the final exon of the gene, carboxy-terminal to the phosphatase catalytic domain. Functional studies demonstrate that the mutations result in enhanced suppression of p53 in response to ionizing radiation exposure, suggesting that the mutant alleles encode hyperactive PPM1D isoforms. Thus, although the mutations cause premature protein truncation, they do not result in the simple loss-of-function effect typically associated with this class of variant, but instead probably have a gain-of-function effect. Our results have implications for the detection and management of breast and ovarian cancer risk. More generally, these data provide new insights into the role of rare and of mosaic genetic variants in common conditions, and the use of sequencing in their identification.

Studies of the genetic epidemiology of cardiovascular disease: focus on inflammatory candidate genes

Cardiovascular disease (CVD) is a complex disease with multifactorial aetiology. Both genetic and environmental factors contribute to the disease risk. The lifetime risk for CVD differs markedly between men and women, men being at increased risk. Inflammatory reaction contributes to the development of the disease by promoting atherosclerosis in artery walls. In the first part of this thesis, we identified several inflammatory related CVD risk factors associating with the amount of DNA from whole blood samples, indicating a potential source of bias if a genetic study selects the participants based on the available amount of DNA. In the following studies, this observation was taken into account by applying whole genome amplification to samples otherwise subjected to exclusion due to very low DNA yield. We continued by investigating the contribution of inflammatory genes to the risk for CVD separately in men and women, and looked for sex-genotype interaction. In the second part, we explored a new candidate gene and its role in the risk for CVD. Selenoprotein S (SEPS1) is a membrane protein residing in the endoplasmic reticulum where it participates in retro-translocation of unfolded proteins to cytosolic protein degradation. Previous studies have indicated that SEPS1 protects cells from oxidative stress and that variations in the gene are associated with circulating levels of inflammatory cytokines. In our study, we identified two variants in the SEPS1 gene, which associated with coronary heart disease and ischemic stroke in women. This is, to our knowledge, the first study suggesting a role of SEPS1 in the risk for CVD after extensively examining the variation within the gene region. In the third part of this thesis, we focused on a set of seven genes (angiotensin converting enzyme, angiotensin II receptor type I, C-reactive protein (CRP), and fibrinogen alpha-, beta-, and gamma-chains (FGA, FGB, FGG)) related to inflammatory cytokine interleukin 6 (IL6) and their association with the risk for CVD. We identified one variant in the IL6 gene conferring risk for CVD in men and a variant pair from IL6 and FGA genes associated with decreased risk. Moreover, we identified and confirmed an association between a rare variant in the CRP gene and lower CRP levels, and found two variants in the FGA and FGG genes associating with fibrinogen. The results from this third study suggest a role for the interleukin 6 pathway genes in the pathogenesis of CVD and warrant further studies in other populations. In addition to the IL6 -related genes, we describe in this thesis several sex-specific associations in other genes included in this study. The majority of the findings were evident only in women encouraging other studies of cardiovascular disease to include and analyse women separately from men.

Novel 1122 thallium cuprates showing high Tc superconductivity: TlCa1-xY,Ba2Cu2Oy,T,1-xPbxCaSr2Cu2Oy and TlCa0.5Ln0.5Sr2Cu2Oy

Substitution of Ca by Y in TlCaBa2Cu2Oy does not favour superconductivity, but substitution of Tl by Pb or of Ca by Ln (Ln = Y or rare earth) in TlCaSr2Cu2Oy results in high Tc superconductivity (Tc π 60-90 K). TlCa1-xLnxSr2Cu2Oy is a new series of high Tc superconductors, but the x = 0.0 composition does not exhibit bulk superconductivity.

Low-temperature internal friction of glass ceramics

Low-temperature internal-friction measurements have been used to study the universal low-energy excitations in glasses before and after crystallization in two glass ceramics, one based on MgO-Al2O3-SiO2 (Corning Code 9606) and one based on Li2O-Al2O3-SiO2 (Corning Code 9623). In the Code 9606 sample, the number density of excitations is greatly reduced, while in the Code 9623 sample, their number density remains practically unaltered in the crystallized state. These measurements confirm the conclusions reached by Cahill et al. (preceding paper), which were based on thermal measurements up to room temperature. These measurements also demonstrate the usefulness of internal friction as a tool for the study of these low-energy excitations, since internal friction is less sensitive to defects common to glass ceramics, like magnetic impurities and grain boundaries, which tend to dominate low-temperature specific heat and thermal conductivity, respectively.

Familial Diarrhea Syndrome Caused by an Activating GUCY2C Mutation

BACKGROUND Familial diarrhea disorders are, in most cases, severe and caused by recessive mutations. We describe the cause of a novel dominant disease in 32 members of a Norwegian family. The affected members have chronic diarrhea that is of early onset, is relatively mild, and is associated with increased susceptibility to inflammatory bowel disease, small-bowel obstruction, and esophagitis. METHODS We used linkage analysis, based on arrays with single-nucleotide polymorphisms, to identify a candidate region on chromosome 12 and then sequenced GUCY2C, encoding guanylate cyclase C (GC-C), an intestinal receptor for bacterial heat-stable enterotoxins. We performed exome sequencing of the entire candidate region from three affected family members, to exclude the possibility that mutations in genes other than GUCY2C could cause or contribute to susceptibility to the disease. We carried out functional studies of mutant GC-C using HEK293T cells. RESULTS We identified a heterozygous missense mutation (c.2519G -> T) in GUCY2C in all affected family members and observed no other rare variants in the exons of genes in the candidate region. Exposure of the mutant receptor to its ligands resulted in markedly increased production of cyclic guanosine monophosphate (cGMP). This may cause hyperactivation of the cystic fibrosis transmembrane regulator (CFTR), leading to increased chloride and water secretion from the enterocytes, and may thus explain the chronic diarrhea in the affected family members. CONCLUSIONS Increased GC-C signaling disturbs normal bowel function and appears to have a proinflammatory effect, either through increased chloride secretion or additional effects of elevated cellular cGMP. Further investigation of the relevance of genetic variants affecting the GC-C-CFTR pathway to conditions such as Crohn's disease is warranted. (Funded by Helse Vest Western Norway Regional Health Authority] and the Department of Science and Technology, Government of India.)

Experimental signatures of a nonequilibrium phase transition governing the yielding of a soft glass

We present direct experimental signatures of a nonequilibrium phase transition associated with the yield point of a prototypical soft solid-a binary colloidal glass. By simultaneously quantifying single-particle dynamics and bulk mechanical response, we identified the threshold for the onset of irreversibility with the yield strain. We extracted the relaxation time from the transient behavior of the loss modulus and found that it diverges in the vicinity of the yield strain. This critical slowing down is accompanied by a growing correlation length associated with the size of regions of high Debye-Waller factor, which are precursors to yield events in glasses. Our results affirm that the paradigm of nonequilibrium critical phenomena is instrumental in achieving a holistic understanding of yielding in soft solids.

Din, don, don: Mestre Paraná e o Grupo Folclórico de Capoeira São Bento Pequeno (1950-1960)

Este trabalho questiona a construção da memória e da história da capoeira no Rio de Janeiro na segunda metade do século XX. A capoeira como manifestação cultural é tema de um crescente número de trabalhos artísticos, desde peças de teatro, filmes para o cinema, bem como de ações do governo, com destaque para seu tombamento como "patrimônio imaterial da cultura brasileira". É praticada em mais de 150 países, onde se apresenta como mais uma das identidades dos brasileiros no exterior. No Rio de Janeiro, deixou marcas profundas na memória do século XIX, representada em documentos variados do Estado e nas letras dos intelectuais da época. História que tem sido pesquisada por autores que já assistem suas obras sendo consagradas pelo crescente número de interessados no tema. Em contrapartida, a história recente desta prática ainda é assunto raro na historiografia, bem como nas demais disciplinas das ciências humanas. Assim, através da pesquisa etnográfica com o Grupo Folclórico de Capoeira São Bento Pequeno, escola de capoeira de Mestre Paraná, questionamos esta lacuna no conhecimento acadêmico, bem como seu reflexo na formação das "tradições" da capoeira no Rio de Janeiro. O Grupo São Bento Pequeno esteve em atividade nas décadas de 1950 e 1960, período de retomada do crescimento da capoeira no Rio de Janeiro.

Infrared-to-visible upconversion fluorescence of Er3+-doped novel lithium-barium-lead-bismuth glass

Er3+-doped lithium-barium-lead-bismuth glass for developing upconversion lasers has been fabricated and characterized. The Judd-Ofelt intensity parameters Omega(t) (t = 2, 4, 6), calculated based on the experimental absorption spectrum and Judd-Ofelt theory, were found to be Omega(2) = 3.05 x 10(-20) cm(2), Omega(4) = 0.95 x 10(-20) cm(2), and Omega(6) = 0.39 x 10(-20) cm(2). Under 975 nm excitation, intense green and red emissions centered at 525, 546, and 657 nm, corresponding to the transitions H-2(11/2) -> I-4(15/2), S-4(3/2) -> I-4(15/2), and F-4(9/2) -> I-4(15/2), respectively, were observed at room temperature. The upconversion mechanisms are discussed based on the energy matching and quadratic dependence on excitation power, and the dominant mechanisms are excited state absorption and energy transfer upconversion for the green and red emissions. The long-lived I-4(11/2) level is supposed to serve as the intermediate state responsible for the intense upconversion processes. The intense upconversion luminescence of Er3+-doped lithium-barium-lead-bismuth glass may be a potentially useful material for developing upconversion optical devices. (c) 2004 Elsevier B.V. All rights reserved.

Threatened corals provide underexplored microbial habitats

Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these “rare” organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA) sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family) harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7–49.1%) were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under the U.S. Endangered Species Act, our results add an important microbial diversity-based perspective to the significance of conserving coral reefs.

新疆紫草细胞悬浮培养生产紫草宁衍生物的动态测定机理化因子调控

本文在本实验室提供的新疆紫草愈伤组织高产系A1的基础上，采用二步培养法，进行摇瓶悬浮培养，分别在生长及生产培养基中测定了细胞生长，次生产物合成，培养基的C源（蔗糖）消耗，溶氧，电导率和pH值的动态变化曲线，确定了各动态曲线之间的关系，为进一步的放大培养提供了参考依据。同时，还测定了与细胞生长密切相关的过氧化物酶及与产物合成密切相关的苯丙氨酸解氨酶(PAL)的活性的动态变化曲线，进一步将宏观参数的动态变化与微观参数的动态变化联系起来。 本文还对不同理化因子对生产培养基中悬浮培养的细胞的生长及紫草宁衍生物合成的影响进行了研究。结果表明：过高或过低的供氧水平均不利于细胞的生长及产物的合成;C源及N源有较好的协同作用，适当地提高C源及N源的水平能明显提高紫草宁衍生物的产量：接种前往培养基里加入一定量的前体苯丙氨酸( Phe)，能明显提高紫草宁衍生物的产量，而在培养中期添加则有一定的负致应;一定量的拜土及琼脂(agar)的添加，对产物的合成均具有正效应，并且作用大小和细胞的生理状态有关。高密度培养的研究表明，在合适的接种量和培养基浓度下，适当提高溶氧，较大幅度地提高产量是有可能的，这还有待于进一步的研究验证。

稀土元素生物效应的蛋白质组学研究

蛋白质组学是研究细胞内全部蛋白的动态表达及其相互关系的新兴学科，是功能基因组学研究的重要组成部分和战略制高点，广泛应用于生命科学的各个领域，研究对象涵盖微生物、动物和植物等。 　　稀土元素（rare earth elements），亦称镧系元素（lanthanides），是性质相似的15种金属元素。随着稀土元素在工业、农牧业和医疗等领域的应用日益深入，它们对生物体的作用机制亟待研究。生物固氮作用为生命世界提供75%的绿色氮源，根瘤菌是重要的固氮微生物，具有基因组结构简单、培养周期短等特点。酿酒酵母是与人类关系最密切的一种酵母，不仅因为传统上其用于制作食品及酿酒，而且是现代分子生物学和细胞生物学中的真核模式生物。为了全面地了解稀土元素对细胞的作用，我们运用高分辨率的蛋白质双向电泳分离技术和高通量的蛋白质质谱分析手段以及生物信息学等方法，分析了稀土元素钆（Gadolinium，Gd）在原核生物费氏中华根瘤菌（Sinorhizobium fredii）USDA205和真核生物酿酒酵母（Saccharomyces cerevisiae）YM4271的生物效应。 　　结果表明，经1mM Gd(NO3)3处理12小时后，费氏中华根瘤菌USDA205中 22个蛋白质表达有差异。这些蛋白质可根据功能分为8类，包括转运蛋白、胁迫相关蛋白、代谢相关蛋白等。其中13个蛋白质表达量增加，9个蛋白质表达量下降。膜蛋白在差异蛋白中占有很大比重。另外，我们分析了不同浓度的钆处理后蛋白质表达的变化情况，发现蛋白质组的变化是与处理浓度密切相关的。研究中还发现同种浓度的钆与另一种稀土元素铒（Erbium，Er）相比，离子半径较小的铒离子对根瘤菌的抑制作用更加明显。 　　比较不同浓度的钆对酿酒酵母YM4271的影响，发现酵母对稀土元素的反应不及根瘤菌敏感，对数生长初期的酵母经钆处理12小时或24小时后均无显著变化。 　　本研究首次用蛋白质组学的方法研究稀土元素对微生物的作用，鉴定了一些有价值的蛋白质，并得到了它们的表达特点和相关数据，为更好地理解稀土元素的生物效应提供了有力的分子生物学证据。