Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs

The HIV Reverse Transcriptase and Protease Sequence Database is an on-line relational database that catalogs evolutionary and drug-related sequence variation in the human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease enzymes, the molecular targets of anti-HIV therapy (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protease sequences, including submissions from International Collaboration databases and sequences published in journal articles. Sequences are linked to data about the source of the sequence sample and the antiretroviral drug treatment history of the individual from whom the isolate was obtained. During the past year 3500 sequences have been added and the data model has been expanded to include drug susceptibility data on sequenced isolates. Database content has also been integrated with didactic text and the output of two sequence analysis programs.

How amoeboids self-organize into a fruiting body: Multicellular coordination in Dictyostelium discoideum

When individual amoebae of the cellular slime mold Dictyostelium discoideum are starving, they aggregate to form a multicellular migrating slug, which moves toward a region suitable for culmination. The culmination of the morphogenesis involves complex cell movements that transform a mound of cells into a globule of spores on a slender stalk. The movement has been likened to a “reverse fountain,” whereby prestalk cells in the upper part form a stalk that moves downwards and anchors to the substratum, while prespore cells in the lower part move upwards to form the spore head. So far, however, no satisfactory explanation has been produced for this process. Using a computer simulation that we developed, we now demonstrate that the processes that are essential during the earlier stages of the morphogenesis are in fact sufficient to produce the dynamics of the culmination stage. These processes are cAMP signaling, differential adhesion, cell differentiation, and production of extracellular matrix. Our model clarifies the processes that generate the observed cell movements. More specifically, we show that periodic upward movements, caused by chemotactic motion, are essential for successful culmination, because the pressure waves they induce squeeze the stalk downwards through the cell mass. The mechanisms revealed by our model have a number of self-organizing and self-correcting properties and can account for many previously unconnected and unexplained experimental observations.

Flower color variation: A model for the experimental study of evolution

We review the study of flower color polymorphisms in the morning glory as a model for the analysis of adaptation. The pathway involved in the determination of flower color phenotype is traced from the molecular and genetic levels to the phenotypic level. Many of the genes that determine the enzymatic components of flavonoid biosynthesis are redundant, but, despite this complexity, it is possible to associate discrete floral phenotypes with individual genes. An important finding is that almost all of the mutations that determine phenotypic differences are the result of transposon insertions. Thus, the flower color diversity seized on by early human domesticators of this plant is a consequence of the rich variety of mobile elements that reside in the morning glory genome. We then consider a long history of research aimed at uncovering the ecological fate of these various flower phenotypes in the southeastern U.S. A large body of work has shown that insect pollinators discriminate against white phenotypes when white flowers are rare in populations. Because the plant is self-compatible, pollinator bias causes an increase in self-fertilization in white maternal plants, which should lead to an increase in the frequency of white genes, according to modifier gene theory. Studies of geographical distributions indicate other, as yet undiscovered, disadvantages associated with the white phenotype. The ultimate goal of connecting ecology to molecular genetics through the medium of phenotype is yet to be attained, but this approach may represent a model for analyzing the translation between these two levels of biological organization.

Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis.

Phylogenetic analyses are increasingly used in attempts to clarify transmission patterns of human immunodeficiency virus type 1 (HIV-1), but there is a continuing discussion about their validity because convergent evolution and transmission of minor HIV variants may obscure epidemiological patterns. Here we have studied a unique HIV-1 transmission cluster consisting of nine infected individuals, for whom the time and direction of each virus transmission was exactly known. Most of the transmissions occurred between 1981 and 1983, and a total of 13 blood samples were obtained approximately 2-12 years later. The p17 gag and env V3 regions of the HIV-1 genome were directly sequenced from uncultured lymphocytes. A true phylogenetic tree was constructed based on the knowledge about when the transmissions had occurred and when the samples were obtained. This complex, known HIV-1 transmission history was compared with reconstructed molecular trees, which were calculated from the DNA sequences by several commonly used phylogenetic inference methods [Fitch-Margoliash, neighbor-joining, minimum-evolution, maximum-likelihood, maximum-parsimony, unweighted pair group method using arithmetic averages (UPGMA), and a Fitch-Margoliash method assuming a molecular clock (KITSCH)]. A majority of the reconstructed trees were good estimates of the true phylogeny; 12 of 13 taxa were correctly positioned in the most accurate trees. The choice of gene fragment was found to be more important than the choice of phylogenetic method and substitution model. However, methods that are sensitive to unequal rates of change performed more poorly (such as UPGMA and KITSCH, which assume a constant molecular clock). The rapidly evolving V3 fragment gave better reconstructions than p17, but a combined data set of both p17 and V3 performed best. The accuracy of the phylogenetic methods justifies their use in HIV-1 research and argues against convergent evolution and selective transmission of certain virus variants.

Subunit interactions in coordination of Ni2+ in cyclic nucleotide-gated channels.

Cyclic nucleotide-gated (CNG) channels present a unique model for studying the molecular mechanisms of channel gating. We have studied the mechanism of potentiation of expressed rod CNG channels by Ni2+ as a first step toward understanding the channel gating process. Here we report that coordination of Ni2+ between histidine residues (H420) on adjacent channel subunits occurs when the channels are open. Mutation of H420 to lysine completely eliminated the potentiation by Ni2+ but did not markedly alter the apparent cGMP affinity of the channel, indicating that the introduction of positive charge at the Ni(2+)-binding site was not sufficient to produce potentiation. Deletion or mutation of most of the other histidines present in the channel did not diminish potentiation by Ni2+. We studied the role of subunit interactions in Ni2+ potentiation by generating heteromultimeric channels using tandem dimers of the rod CNG channel sequence. Injection of single heterodimers in which one subunit contained H420 and the other did not (wt/H420Q or H420Q/wt) resulted in channels that were not potentiated by Ni2+. However, coinjection of both heterodimers into Xenopus oocytes resulted in channels that exhibited potentiation. The H420 residues probably occurred predominantly in nonadjacent subunits when each heterodimer was injected individually, but, when the two heterodimers were coinjected, the H420 residues could occur in adjacent subunits as well. These results suggest that the mechanism of Ni2+ potentiation involves intersubunit coordination of Ni2+ by H420. Based on the preferential binding of Ni2+ to open channels, we suggest that alignment of H420 residues of neighboring subunits into the Ni(2+)-coordinating position may be associated with channel opening.

Radiometal labeling of recombinant proteins by a genetically engineered minimal chelation site: technetium-99m coordination by single-chain Fv antibody fusion proteins through a C-terminal cysteinyl peptide.

We describe a method to facilitate radioimaging with technetium-99m (99mTc) by genetic incorporation of a 99mTc chelation site in recombinant single-chain Fv (sFv) antibody proteins. This method relies on fusion of the sFv C terminus with a Gly4Cys peptide that specifically coordinates 99mTc. By using analogues of the 26-10 anti-digoxin sFv as our primary model, we find that addition of the chelate peptide, to form 26-10-1 sFv', does not alter the antigen-binding affinity of sFv. We have demonstrated nearly quantitative chelation of 0.5-50 mCi of 99mTc per mg of 26-10-1 sFv' (1 Ci = 37 GBq). These 99mTc-labeled sFv' complexes are highly stable to challenge with saline buffers, plasma, or diethylenetriaminepentaacetic acid. We find that the 99mTc-labeled 741F8-1 sFv', specific for the c-erbB-2 tumor-associated antigen, is effective in imaging human ovarian carcinoma in a scid mouse tumor xenograft model. This fusion chelate methodology should be applicable to diagnostic imaging with 99mTc and radioimmunotherapy with 186Re or 188Re, and its use could extend beyond the sFv' to other engineered antibodies, recombinant proteins, and synthetic peptides.

Integrando o conhecimento de usuários: um estudo sobre a capacidade de absorção de conhecimento de lead users

Os custos elevados de aquisição de conhecimento, a intensificação da concorrência e a necessidade de aproximação do consumidor vêm estimulando empresas a buscar formas alternativas de aumentar seu potencial de inovação pela integração de usuários. No entanto, a literatura e o senso comum convergem ao afirmar que nem todo usuário está habilitado a trazer conhecimentos que sustentem a vantagem competitiva das inovações. Nesse contexto, emerge a figura do lead user que, por definição, é capaz de sentir necessidades de produtos e serviços ainda não expressos por usuários regulares. Esses conhecimentos, quando adequadamente absorvidos, trazem benefícios expressivos às empresas que os incorporam ao DNP. Sabendo que as formas de incorporação de usuários apresentam variações, este estudo se destina a entender como empresas de diferentes setores absorvem conhecimentos de lead users por diferentes práticas de integração. Para tanto, foi escolhido o método de estudo de casos múltiplos incorporados, observados em três multinacionais de grande porte: Natura, Whirlpool e Microsoft (Bing). Ao todo foram avalidados cinco modos de integração distintos, escolhidos a partir de duas formações: individual (conhecimentos isolados de usuários distintos) e coletivo (conhecimentos articulados em discussões em grupo), analisados pelos métodos de indução analítica com síntese cruzada de dados. Os resultados mostraram que as categorias teóricas utilizadas para observação inicial do fenômenol: parâmetro de identificação e técnica de seleção (aquisição); mecanismo de interação (assimilação); mecanismos de socialização (transformação) e sistema de formalização (exploração) apoiaram parcialmente o entendimento das atividades do processo e, por esta razão, precisaram se complementadas pelas categorias emergentes: criação de contexto, motivação (aquisição); estímulos, parâmetro de observação, interpretação (assimilação); definição de papéis, coordenação de processos, combinação de conhecimento (transformação) e gestão do conhecimento (exploração), coletadas na fase empírica Essa complementação aumentou a robustez do modelo inicial e mostrou como a absorção de conhecimentos pode ser avaliada pelas dimensões absortivas. No entanto, as análises intra e intercasos que se seguiram, mostraram que esse entendimento era insuficiente para explicar a capacidade de absorção por diferentes práticas, uma vez que o fenômeno é influenciado por fatores contextuais associados tanto à prática de integração quanto ao modo como cada empresa se organiza para inovar (tipo de acesso ao colaborador). As reflexões teóricas realizadas a partir desses resultados permitiram contribuir com a teoria existente de duas formas: I) pelo entendimento estendido das atividades de absorção necessárias para incorporação de conhecimentos de lead users e III) pela proposição de um modelo conceitual amplo que abarcou diferentes práticas de integração considerando também os antecedentes de inovação, as atividades absortivas e os fatores adjuntos, inerentes a cada prática. Esta pesquisa objetiva contribuir para o conhecimento teórico sobre inovação e motivar reflexões que possam ser úteis para gerentes e executivos interessados em aprimorar suas práticas e processos de captação de conhecimentos de lead users.

Model of an Arizona gold mine.

no.1(1922)

Essays on Firm Heterogeneity with Empirical Applications in Economic History and Agricultural Economics

This thesis uses models of firm-heterogeneity to complete empirical analyses in economic history and agricultural economics. In Chapter 2, a theoretical model of firm heterogeneity is used to derive a statistic that summarizes the welfare gains from the introduction of a new technology. The empirical application considers the use of mechanical steam power in the Canadian manufacturing sector during the late nineteenth century. I exploit exogenous variation in geography to estimate several parameters of the model. My results indicate that the use of steam power resulted in a 15.1 percent increase in firm-level productivity and a 3.0-5.2 percent increase in aggregate welfare. Chapter 3 considers various policy alternatives to price ceiling legislation in the market for production quotas in the dairy farming sector in Quebec. I develop a dynamic model of the demand for quotas with farmers that are heterogeneous in their marginal cost of milk production. The econometric analysis uses farm-level data and estimates a parameter of the theoretical model that is required for the counterfactual experiments. The results indicate that the price of quotas could be reduced to the ceiling price through a 4.16 percent expansion of the aggregate supply of quotas, or through moderate trade liberalization of Canadian dairy products. In Chapter 4, I study the relationship between farm-level productivity and participation in the Commercial Export Milk (CEM) program. I use a difference-in-difference research design with inverse propensity weights to test for causality between participation in the CEM program and total factor productivity (TFP). I find a positive correlation between participation in the CEM program and TFP, however I find no statistically significant evidence that the CEM program affected TFP.

MODEL COUNTRIES IN POLITICAL ANALYSIS. Is Turkey a Model for State-Building in the Arab World? Jean Monnet Occasional Paper No. 10/2014

This study analyzes the Turkish case as a model country for the state-building processes in the Arab world in the aftermath of the Arab revolts that took place in Tunisia, Egypt and Libya. To this end, it deals with the Turkish case in three phases: the founding of the Turkish Republic, political developments until 2002, and the post-2002 Justice and Development Party period. The study focuses on state-society relations manifested in the form of a secular-religious cleavage intertwined with problematic civil-military relations. Each phase of Turkey’s history is compared to cleavages and civil-military relations in Egypt, Tunisia and Libya. After analyzing the constitution-making processes in the latter three countries following the Arab revolts, the study concludes by discussing the viability of the Turkish model in the light of Turkey’s search for a new constitution.

The Danish Flexicurity Model - a Lesson for the US? ACES Working Paper No. 2, May 2007

Within recent years, increasing international competition has caused an increase in job transitions worldwide. Many countries find it difficult to manage these transitions in a way that ensures a match between labour and demand. One of the countries that seem to manage the transitions in a successful way is Denmark, where unemployment has been dropping dramatically over the last decade without a drop in job quality. This success is ascribed the so-called Danish flexicurity model, where an easy access to hiring and firing employees (flexibility) is combined with extensive active and passive labour market policies (security). The Danish results have gained interest not only among other European countries, where unemployment rates remain high, but also in the US, where job loss is often related to lower job quality. It has, however, been subject to much debate both in Europe and in the US, whether or not countries with distinctively different political-economic settings can learn from one another. Some have argued that cultural differences impose barriers to successful policy transfer, whereas others see it as a perfectly rational calculus to introduce 'best practices' from elsewhere. This paper presents a third strategy. Recent literature on policy transfer suggests that successful cross national policy transfer is possible, even across the Atlantic, but that one must be cautious in choosing the form, content and level of the learning process. By analysing and comparing the labour market policies and their settings in Denmark and the US in detail, this paper addresses the question, what and how the US can learn from the Danish model. Where the US and Denmark share a high degree of flexibility, they differ significantly on the level of security. This also means that the Danish budget for active and passive labour market policies is significantly higher than the American, and it seems unlikely that political support for the introduction of Danish levels of security in the US can be established. However, the paper concludes that there is a learning potential between the US and Demnark in the different local level efficiency of the money already spent. A major reason for the Danish success has been the introduction of tailor made initiatives to the single displaced worker and a stronger coordination between local level actors. Both of which are issues, where a lack of efficiency in the implementation of American active labour market policies has been reported.

Evolutionary history of the recruitment of conserved developmental genes in association to the formation and diversification of a novel trait

The origin and modification of novel traits are important aspects of biological diversification. Studies combining concepts and approaches of developmental genetics and evolutionary biology have uncovered many examples of the recruitment, or co-option, of genes conserved across lineages for the formation of novel, lineage-restricted traits. However, little is known about the evolutionary history of the recruitment of those genes, and of the relationship between them -for example, whether the co-option involves whole or parts of existing networks, or whether it occurs by redeployment of individual genes with de novo rewiring. We use a model novel trait, color pattern elements on butterfly wings called eyespots, to explore these questions. Eyespots have greatly diversified under natural and sexual selection, and their formation involves genetic circuitries shared across insects.

Essays on coordination problems in economics

No estudo da economia, há diversas situações em que a propensão de um indivíduo a tomar determinada ação é crescente na quantidade de outras pessoas que este indivíduo acredita que tomarão a mesma ação. Esse tipo de complementaridade estratégica geralmente leva à existência de múltiplos equilíbrios. Além disso, o resultado atingido pelas decisões decentralizadas dos agentes pode ser ineficiente, deixando espaço para intervenções de política econômica. Esta tese estuda diferentes ambientes em que a coordenação entre indivíduos é importante. O primeiro capítulo analisa como a manipulação de informação e a divulgação de informação afetam a coordenação entre investidores e o bem-estar em um modelo de corridas bancárias. No modelo, há uma autoridade reguladora que não pode se comprometer a revelar a verdadeira situação do setor bancário. O regulador observa informações idiossincráticas dos bancos (através de um stress test, por exemplo) e escolhe se revela essa informação para o público ou se divulga somente um relatório agregado sobre a saúde do sistema financeiro como um todo. O relatório agregado pode ser distorcido a um custo – um custo mais elevado significa maior credibilidade do regulador. Os investidores estão cientes dos incentivos do regulador a esconder más notícias do mercado, mas a manipulação de informação pode, ainda assim, ser efetiva. Se a credibilidade do regulador não for muito baixa, a política de divulgação de informação é estado-contingente, e existe sempre um conjunto de estados em que há manipulação de informação em equilíbrio. Se a credibilidade for suficientemente baixa, porém, o regulador opta por transparência total dos resultados banco-específicos, caso em que somente os bancos mais sólidos sobrevivem. Uma política de opacidade levaria a uma crise bancária sistêmica, independentemente do estado. O nível de credibilidade que maximiza o bem-estar agregado do ponto de vista ex ante é interior. O segundo e o terceiro capítulos estudam problemas de coordenação dinâmicos. O segundo capítulo analisa o bem-estar em um ambiente em que agentes recebem oportunidades aleatórias para migrar entre duas redes. Os resultados mostram que sempre que a rede de pior qualidade (intrínseca) prevalece, isto é eficiente. Na verdade, um planejador central estaria ainda mais inclinado a escolher a rede de pior qualidade. Em equilíbrio, pode haver mudanças ineficientes que ampliem a rede de qualidade superior. Quando indivíduos escolhem entre dois padrões ou redes com níveis de qualidade diferentes, se todos os indivíduos fizessem escolhas simultâneas, a solução eficiente seria que todos adotassem a rede de melhor qualidade. No entanto, quando há fricções e os agentes tomam decisões escalonadas, a solução eficiente difere ix do senso comum. O terceiro capítulo analisa um problema de coordenação dinâmico com decisões escalonadas em que os agentes são heterogêneos ex ante. No modelo, existe um único equilíbrio, caracterizado por thresholds que determinam as escolhas para cada tipo de agente. Apesar da heterogeneidade nos payoffs, há bastante conformidade nas ações individuais em equilíbrio. Os thresholds de diferentes tipos de agentes coincidem parcialmente contanto que exista um conjunto de crenças arbitrário que justifique esta conformidade. No entanto, as estratégias de equilíbrio de diferentes tipos nunca coincidem totalmente. Além disso, a conformidade não é ineficiente. A solução eficiente apresentaria estratégias ainda mais similares para tipos distintos em comparação com o equilíbrio decentralizado.

Geochemistry and age model of sediment core BDP96-1

Within the framework of the Baikal Drilling Project (BDP), a 192 m long sediment core (BDP-96-1) was recovered from the Academician Ridge, a submerged topographic high between the North and Central Basins of Lake Baikal. Sedimentological, clay mineralogical and geochemical investigations were carried out on the core interval between 90 and 124 m depth, corresponding to ca. 2.4-3.4 Ma. The aim was to reconstruct the climatic and tectonic history of the continental region during the intensification of Northern Hemisphere glaciation in Late Pliocene time. A major climate change occurred in the Lake Baikal area at about 2.65 Ma. Enhanced physical weathering in the catchment, mirrored in the illite to smectite ratio, and temporarily reduced bioproduction in the lake, reflected by the diatom abundance, evidence a change towards a colder and more arid climate, probably associated with an intensification of the Siberian High. In addition, the coincident onset of distinct fluctuations in these parameters and in the Zr/Al ratio suggests the beginning of the Late Cenozoic high amplitude climate cycles at about 2.65 Ma. Fluctuations in the Zr/Al ratio are traced back to changes in the aeolian input, with high values in warmer, more humid phases due to a weaker Siberian High. Assuming that the sand content in the sediment reflects tectonic pulses, the Lake Baikal area was tectonically active during the entire investigated period, but in particular around 2.65 Ma. Tectonic movements have likely led to a gradual catchment change since about 3.15 Ma from the western towards the eastern lake surroundings, as indicated in the geochemistry and clay mineralogy of the sediments. The strong coincidence between tectonic and climatic changes in the Baikal area hints at the Himalayan uplift being one of the triggers for the Northern Hemisphere Glaciation.