Molecular coevolution within a Drosophila clock gene

The period (per) gene in Drosophila melanogaster provides an integral component of biological rhythmicity and encodes a protein that includes a repetitive threonine-glycine (Thr-Gly) tract. Similar repeats are found in the frq and wc2 clock genes of Neurospora crassa and in the mammalian per homologues, but their circadian functions are unknown. In Drosophilids, the length of the Thr-Gly repeat varies widely between species, and sequence comparisons have suggested that the repeat length coevolves with the immediately flanking amino acids. A functional test of the coevolution hypothesis was performed by generating several hybrid per transgenes between Drosophila pseudoobscura and D. melanogaster, whose repetitive regions differ in length by about 150 amino acids. The positions of the chimeric junctions were slightly altered in each transgene. Transformants carrying per constructs in which the repeat of one species was juxtaposed next to the flanking region of the other were almost arrhythmic or showed a striking temperature sensitivity of the circadian period. In contrast, transgenes in which the repeat and flanking regions were conspecific gave wild-type levels of circadian rescue. These results support the coevolutionary interpretation of the interspecific sequence changes in this region of the PER molecule and reveal a functional dimension to this process related to the clock’s temperature compensation.

Natural genetic exchange between Haemophilus and Neisseria: Intergeneric transfer of chromosomal genes between major human pathogens

Members of the bacterial families Haemophilus and Neisseria, important human pathogens that commonly colonize the nasopharynx, are naturally competent for DNA uptake from their environment. In each genus this process is discriminant in favor of its own and against foreign DNA through sequence specificity of DNA receptors. The Haemophilus DNA uptake apparatus binds a 29-bp oligonucleotide domain containing a highly conserved 9-bp core sequence, whereas the neisserial apparatus binds a 10-bp motif. Each motif (“uptake sequence”, US) is highly over-represented in the chromosome of the corresponding genus, particularly concentrated with core sequences in inverted pairs forming gene terminators. Two Haemophilus core USs were unexpectedly found forming the terminator of sodC in Neisseria meningitidis (meningococcus), and sequence analysis strongly suggests that this virulence gene, located next to IS1106, arose through horizontal transfer from Haemophilus. By using USs as search strings in a computer-based analysis of genome sequence, it was established that while USs of the “wrong” genus do not occur commonly in Neisseria or Haemophilus, where they do they are highly likely to flag domains of chromosomal DNA that have been transferred from Haemophilus. Three independent domains of Haemophilus-like DNA were found in the meningococcal chromosome, associated respectively with the virulence gene sodC, the bio gene cluster, and an unidentified orf. This report identifies intergenerically transferred DNA and its source in bacteria, and further identifies transformation with heterologous chromosomal DNA as a way of establishing potentially important chromosomal mosaicism in these pathogenic bacteria.

Nuclear Domains Enriched in RNA 3′-processing Factors Associate with Coiled Bodies and Histone Genes in a Cell Cycle–dependent Manner

Nuclear domains, called cleavage bodies, are enriched in the RNA 3′-processing factors CstF 64 kDa and and CPSF 100 kDa. Cleavage bodies have been found either overlapping with or adjacent to coiled bodies. To determine whether the spatial relationship between cleavage bodies and coiled bodies was influenced by the cell cycle, we performed cell synchronization studies. We found that in G1 phase cleavage bodies and coiled bodies were predominantly coincident, whereas in S phase they were mostly adjacent to each other. In G2 cleavage bodies were often less defined or absent, suggesting that they disassemble at this point in the cell cycle. A small number of genetic loci have been reported to be juxtaposed to coiled bodies, including the genes for U1 and U2 small nuclear RNA as well as the two major histone gene clusters. Here we show that cleavage bodies do not overlap with small nuclear RNA genes but do colocalize with the histone genes next to coiled bodies. These findings demonstrate that the association of cleavage bodies and coiled bodies is both dynamic and tightly regulated and suggest that the interaction between these nuclear neighbors is related to the cell cycle–dependent expression of histone genes.

Tid1/Rdh54 promotes colocalization of Rad51 and Dmc1 during meiotic recombination

Two RecA homologs, Rad51 and Dmc1, assemble as cytologically visible complexes (foci) at the same sites on meiotic chromosomes. Time course analysis confirms that co-foci appear and disappear as the single predominant form. A large fraction of co-foci are eliminated in a red1 mutant, which is expected as a characteristic of the interhomolog-specific recombination pathway. Previous studies suggested that normal Dmc1 loading depends on Rad51. We show here that a mutation in TID1/RDH54, encoding a RAD54 homolog, reduces Rad51-Dmc1 colocalization relative to WT. A rad54 mutation, in contrast, has relatively little effect on RecA homolog foci except when strains also contain a tid1/rdh54 mutation. The role of Tid1/Rdh54 in coordinating RecA homolog assembly may be very direct, because Tid1/Rdh54 is known to physically bind both Dmc1 and Rad51. Also, Dmc1 foci appear early in a tid1/rdh54 mutant. Thus, Tid1 may normally act with Rad51 to promote ordered RecA homolog assembly by blocking Dmc1 until Rad51 is present. Finally, whereas double-staining foci predominate in WT nuclei, a subset of nuclei with expanded chromatin exhibit individual Rad51 and Dmc1 foci side-by-side, suggesting that a Rad51 homo-oligomer and a Dmc1 homo-oligomer assemble next to one another at the site of a single double-strand break (DSB) recombination intermediate.

In vitro roles of invariant helix–turn–helix motif residue R383 in σ54 (σN)

In vitro DNA-binding and transcription properties of σ54 proteins with the invariant Arg383 in the putative helix–turn–helix motif of the DNA-binding domain substituted by lysine or alanine are described. We show that R383 contributes to maintaining stable holoenzyme–promoter complexes in which limited DNA opening downstream of the –12 GC element has occurred. Unlike wild-type σ54, holoenzymes assembled with the R383A or R383K mutants could not form activator-independent, heparin-stable complexes on heteroduplex Sinorhizobium meliloti nifH DNA mismatched next to the GC. Using longer sequences of heteroduplex DNA, heparin-stable complexes formed with the R383K and, to a lesser extent, R383A mutant holoenzymes, but only when the activator and a hydrolysable nucleotide was added and the DNA was opened to include the –1 site. Although R383 appears inessential for polymerase isomerisation, it makes a significant contribution to maintaining the holoenzyme in a stable complex when melting is initiating next to the GC element. Strikingly, Cys383-tethered FeBABE footprinting of promoter DNA strongly suggests that R383 is not proximal to promoter DNA in the closed complex. This indicates that R383 is not part of the regulatory centre in the σ54 holoenzyme, which includes the –12 promoter region elements. R383 contributes to several properties, including core RNA polymerase binding and to the in vivo stability of σ54.

A Family of Small Coiled-Coil–forming Proteins Functioning at the Late Endosome in Yeast

The multispanning membrane protein Ste6, a member of the ABC-transporter family, is transported to the yeast vacuole for degradation. To identify functions involved in the intracellular trafficking of polytopic membrane proteins, we looked for functions that block Ste6 transport to the vacuole upon overproduction. In our screen, we identified several known vacuolar protein sorting (VPS) genes (SNF7/VPS32, VPS4, and VPS35) and a previously uncharacterized open reading frame, which we named MOS10 (more of Ste6). Sequence analysis showed that Mos10 is a member of a small family of coiled-coil–forming proteins, which includes Snf7 and Vps20. Deletion mutants of all three genes stabilize Ste6 and show a “class E vps phenotype.” Maturation of the vacuolar hydrolase carboxypeptidase Y was affected in the mutants and the endocytic tracer FM4-64 and Ste6 accumulated in a dot or ring-like structure next to the vacuole. Differential centrifugation experiments demonstrated that about half of the hydrophilic proteins Mos10 and Vps20 was membrane associated. The intracellular distribution was further analyzed for Mos10. On sucrose gradients, membrane-associated Mos10 cofractionated with the endosomal t-SNARE Pep12, pointing to an endosomal localization of Mos10. The growth phenotypes of the mutants suggest that the “Snf7-family” members are involved in a cargo-specific event.

Role of the C2A domain of synaptotagmin in transmitter release as determined by specific antibody injection into the squid giant synapse preterminal.

Squid synaptotagmin (Syt) cDNA, including its open reading frame, was cloned and polyclonal antibodies were obtained in rabbits immunized with glutathione S-transferase (GST)-Syt-C2A. Binding assays indicated that the antibody, anti-Syt-C2A, recognized squid Syt and inhibited the Ca(2+)-dependent phospholipid binding to the C2A domain. This antibody, when injected into the preterminal at the squid giant synapse, blocked transmitter release in a manner similar to that previously reported for the presynaptic injection of members of the inositol high-polyphosphate series. The block was not accompanied by any change in the presynaptic action potential or the amplitude or voltage dependence of the presynaptic Ca2+ current. The postsynaptic potential was rather insensitive to repetitive presynaptic stimulation, indicating a direct effect of the antibody on the transmitter release system. Following block of transmitter release, confocal microscopical analysis of the preterminal junction injected with rhodamine-conjugated anti-Syt-C2A demonstrated fluorescent spots at the inner surface of the presynaptic plasmalemma next to the active zones. Structural analysis of the same preparations demonstrated an accumulation of synaptic vesicles corresponding in size and distribution to the fluorescent spots demonstrated confocally. Together with the finding that such antibody prevents Ca2+ binding to a specific receptor in the C2A domain, these results indicate that Ca2+ triggers transmitter release by activating the C2A domain of Syt. We conclude that the C2A domain is directly related to the fusion of synaptic vesicles that results in transmitter release.

The anchorage function of CipA (CelL), a scaffolding protein of the Clostridium thermocellum cellulosome.

Enzymatic cellulose degradation is a heterogeneous reaction requiring binding of soluble cellulase molecules to the solid substrate. Based on our studies of the cellulase complex of Clostridium thermocellum (the cellulosome), we have previously proposed that such binding can be brought about by a special "anchorage subunit." In this "anchor-enzyme" model, CipA (a major subunit of the cellulosome) enhances the activity of CelS (the most abundant catalytic subunit of the cellulosome) by anchoring it to the cellulose surface. We have subsequently reported that CelS contains a conserved duplicated sequence at its C terminus and that CipA contains nine repeated sequences with a cellulose binding domain (CBD) in between the second and third repeats. In this work, we reexamined the anchor-enzyme mechanism by using recombinant CelS (rCelS) and various CipA domains, CBD, R3 (the repeat next to CBD), and CBD/R3, expressed in Escherichia coli. As analyzed by non-denaturing gel electrophoresis, rCelS, through its conserved duplicated sequence, formed a stable complex with R3 or CBD/R3 but not with CBD. Although R3 or CBD alone did not affect the binding of rCelS to cellulose, such binding was dependent on CBD/R3, indicating the anchorage role of CBD/R3. Such anchorage apparently increased the rCelS activity toward crystalline cellulose. These results substantiate the proposed anchor-enzyme model and the expected roles of individual CipA domains and the conserved duplicated sequence of CelS.

Lymphocytes selected in allogeneic thymic epithelium mediate dominant tolerance toward tissue grafts of the thymic epithelium haplotype.

Athymic mice grafted at birth with allogeneic thymic epithelium (TE) from day 10 embryos before hematopoietic cell colonization reconstitute normal numbers of T cells and exhibit full life-long tolerance to skin grafts of the TE haplotype. Intravenous transfers of splenic cells, from these animals to adult syngeneic athymic recipients, reconstitute T-cell compartments and the ability to reject third-party skin grafts. The transfer of specific tolerance to skin grafts of the TE donor strain, however, is not observed in all reconstituted recipients, and the fraction of nontolerant recipients increases with decreasing numbers of cells transferred. Furthermore, transfers of high numbers of total or CD4+ T cells from TE chimeras to T-cell receptor-anti-H-Y antigen transgenic immunocompetent syngeneic hosts specifically hinder the rejection of skin grafts of the TE haplotype that normally occurs in such recipients. These observations demonstrate (i) that mice tolerized by allogeneic TE and bearing healthy skin grafts harbor peripheral immunocompetent T cells capable of rejecting this very same graft; and (ii) that TE selects for regulatory T cells that can inhibit effector activities of graft-reactive cells.

Use of binding energy by an RNA enzyme for catalysis by positioning and substrate destabilization.

A fundamental catalytic principle for protein enzymes in the use of binding interactions away from the site of chemical transformation for catalysis. We have compared the binding and reactivity of a series of oligonucleotide substrates and products of the Tetrahymena ribozyme, which catalyzes a site-specific phosphodiester cleavage reaction: CCCUCUpA+G<-->CCCUCU-OH+GpA. The results suggest that this RNA enzyme, like protein enzymes, can utilize binding interactions to achieve substantial catalysis via entropic fixation and substrate destabilization. The stronger binding of the all-ribose oligonucleotide product compared to an analog with a terminal 3' deoxyribose residue gives an effective concentration of 2200 M for the 3' hydroxyl group, a value approaching those obtained with protein enzymes and suggesting the presence of a structurally well defined active site capable of precise positioning. The stabilization from tertiary binding interactions is 40-fold less for the oligonucleotide substrate than the oligonucleotide product, despite the presence of the reactive phosphoryl group in the substrate. This destabilization is accounted for by a model in which tertiary interactions away from the site of bond cleavage position the electron-deficient 3' bridging phosphoryl oxygen of the oligonucleotide substrate next to an electropositive Mg ion. As the phosphodiester bond breaks and this 3' oxygen atom develops a negative charge in the transition state, the weak interaction of the substrate with Mg2+ becomes strong. These strategies of "substrate destabilization" and "transition state stabilization" provide estimated rate enhancements of approximately 280- and approximately 60-fold, respectively. Analogous substrate destabilization by a metal ion or hydrogen bond donor may be used more generally by RNA and protein enzymes catalyzing reactions of phosphate esters.

Polpa de guavira (Campomanesia cambessedeana Berg) desidratada em spray dryer: efeitos das condições de processo e composição da alimentação nas propriedades físico químicas e atividade antioxidante

O objetivo desse trabalho foi obter polpa de guavira desidratada por atomização, utilizando maltodextrina ou goma arábica como agentes carreadores. Inicialmente, avaliou-se a influência das condições de processo, temperatura do ar de secagem (130, 155 e 180) °C e vazão volumétrica da mistura (20 e 40) mL/min, o tipo e concentração de agente carreador (10 e 20) % nas características físicas, físico-químicas e atividade antioxidante do produto obtido. As propriedades analisadas foram umidade, atividade de água, higroscopicidade, solubilidade, cor, distribuição e tamanho médio de partículas, morfologia, compostos fenólicos totais e atividade antioxidante. A temperatura do ar de secagem e a vazão volumétrica de alimentação influenciaram significativamente todas as propriedades da guavira em pó. A umidade e atividade de água apresentaram os menores valores na temperatura intermediária, independentemente do tipo e concentração do carreador usado. A solubilidade das amostras adicionadas de maltodextrina foram superiores às amostras com goma arábica. O aumento da concentração de agente carreador, em geral, proporcionou um aumento no parâmetro L* e diminuição dos parâmetros a* e b*, tornando as amostras mais claras e reduzindo as tonalidades vermelha e amarela. A guavira em pó apresentou coloração próxima do amarelo e marrom, com grande variação nos parâmetros de cor C* e H* em função das diferentes condições de secagem. A distribuição do tamanho de partículas não teve um padrão definido e o tamanho médio das amostras com maltodextrina foram maiores do que as com goma arábica para a temperatura do ar a 130 °C. No entanto, para as outras temperaturas (155 e 180) °C não houve um comportamento específico do tamanho das partículas em função da vazão de alimentação, tipo e ou concentração de agente carreador. A análise de microscopia eletrônica de varredura permitiu observar que as partículas obtidas tanto com maltodextrina como goma arábica apresentaram formato esférico, superfície rugosa e com adesão de partículas menores nas de maior tamanho, sendo que a superfície das partículas com goma arábica também apresentaram concavidades. A atividade antioxidante foi superior quando utilizada a temperatura de secagem intermediária. A partir das condições selecionadas na primeira etapa (temperatura do ar de 155 °C, vazão volumétrica da mistura de 40 mL/min e 10% de maltodextrina ou goma arábica) a polpa de guavira em pó foi caracterizada quanto a temperatura de transição vítrea, as isotermas de adsorção e a estabilidade à estocagem do ácido ascórbico, compostos fenólicos totais e da atividade antioxidante da polpa de guavira em pó produzida por spray drying ao longo de 120 dias. As temperaturas de transição vítrea foram de (25,2 ± 2,7 °C e 31,4 ± 0,4) °C para os pós produzidos com goma arábica e maltodextrina, respectivamente. O modelo de BET apresentou ajuste muito bom (R2>0,99) para descrever o comportamento de sorção de água das amostras nas temperaturas de (20, 30 e 40) °C. A polpa de guavira em pó produzida com goma arábica apresentou maior adsorção de água do que as amostras obtidas com maltodextrina. No estudo da estabilidade, as amostras foram acondicionadas em embalagem de polietileno laminado e armazenadas a 25 °C e umidade relativa de 75%. A embalagem de polietileno laminado foi eficiente na manutenção do teor de ácido ascórbico e atividade antioxidante da guavira em pó por um período de 120 dias, independente do carreador adicionado. O teor de compostos fenólicos para a guavira em pó com goma arábica apresentou uma redução nos primeiros 22 dias, contudo a amostra com maltodextrina manteve-se estável durante 120 dias de armazenamento.

Quantum simulation of a topological Mott insulator with Rydberg atoms in a Lieb lattice

We propose a realistic scheme to quantum simulate the so-far experimentally unobserved topological Mott insulator phase-an interaction-driven topological insulator-using cold atoms in an optical Lieb lattice. To this end, we study a system of spinless fermions in a Lieb lattice, exhibiting repulsive nearest-and next-to-nearest-neighbor interactions and derive the associated zero-temperature phase diagram within mean-field approximation. In particular, we analyze how the interactions can dynamically generate a charge density wave ordered, a nematic, and a topologically nontrivial quantum anomalous Hall phase. We characterize the topology of the different phases by the Chern number and discuss the possibility of phase coexistence. Based on the identified phases, we propose a realistic implementation of this model using cold Rydberg-dressed atoms in an optical lattice. The scheme, which allows one to access, in particular, the topological Mott insulator phase, robustly and independently of its exact position in parameter space, merely requires global, always-on off-resonant laser coupling to Rydberg states and is feasible with state-of-the-art experimental techniques that have already been demonstrated in the laboratory.

Influência das áreas verdes urbanas na temperatura e na umidade do ar em São Carlos-SP

A remoção da vegetação para dar lugar a edificações e superfícies pavimentadas implica na anulação de diversos serviços ambientais. Entre eles está o sombreamento, que impede a aquecimento do ar derivado da re-emissão da radiação solar pelas superfícies. O ar quente e seco contribui para o aumento da sensação de desconforto e favorece a incidência de doenças respiratórias. O objetivo deste trabalho foi analisar valores de temperatura e umidade do ar, comparando-se dados coletados por estações meteorológicas automáticas instaladas em regiões arborizadas e áridas da cidade, durante a ocorrência de episódios representativos do clima da região. Os procedimentos metodológicos, baseados na Climatologia Dinâmica, consistiram em relacionar a sucessão de tipos de tempo meteorológico de escala regional às diferenças observadas entre os pontos de estudo, provocadas por fenômenos provenientes das atividades humanas. Isto permitiu a clara identificação de variações climáticas críticas para o conforto e a saúde humanos, tais como grandes amplitudes térmicas e baixos valores de umidade do ar. Os resultados mostraram amplitudes térmicas menores nas áreas arborizadas (em média 3ºC) e, em alguns casos, umidade do ar mais elevada em comparação aos valores observados nas partes áridas estudadas. Estas verificações reforçam a afirmação da necessidade de ampliação das áreas verdes de São Carlos, que contribuem na atenuação as condições climáticas de desconforto e insalubridade. Em conseqüência, aumentam a qualidade de vida da população e as condições de sustentabilidade do ambiente urbano. Tal afirmação vem ao encontro da legislação ambiental brasileira e dos anseios da população são-carlense. Espera-se que as constatações deste trabalho sejam um elemento adicional na adoção de políticas públicas mais comprometidas com a saúde humana e ambiental.

Análise do impacto do novo plano diretor estratégico da cidade de São Paulo no planejamento de produtos residenciais.

Diferentemente de muitas cidades europeias, a urbanização da cidade de São Paulo ocorreu na medida de seu crescimento econômico e populacional, formando um desenho urbano heterogêneo, sem padrões. A falta de um planejamento eficaz somada à priorização do transporte individual geraram problemas urbanos tais como congestionamentos, degradação ambiental, transporte público incipiente, etc. O novo plano diretor estratégico de São Paulo surge com uma proposta para reorganização da cidade, adensando regiões providas de maior infraestrutura e limitando a densidade populacional das outras regiões. Responsável pelo desenvolvimento imobiliário, o setor de real estate é afetado diretamente pelas novas diretrizes do plano diretor. Neste trabalho, são discutidos os impactos do novo plano diretor no planejamento de produtos residenciais, identificando os efeitos na formação de preços e das tipologias que passarão a ser ofertadas de acordo com as novas diretrizes de uso do solo, bem como as possíveis respostas do mercado, ou seja, empreendedores e a população. A metodologia de pesquisa contou com estudos bibliográficos, coleta de dados em uma incorporadora tradicional da cidade de São Paulo, e estudos de qualidade de investimento. Uma base de dados de terrenos foi submetida ao modelo de modo a comparar os resultados de empreender considerando a legislação anterior e a atual imposta pelo plano. Como resultado, verificou-se que a consequência indireta do plano será o aumento de preço de venda de apartamentos. Para minimizar esse efeito, será necessário: reduzir as taxas de retorno do empreendedor, reduzir as áreas privativas, custos de obra e os custos de terreno. Para os empreendedores, o planejamento de produtos se tornará ainda mais importante, diante das novas limitações e da provável redução de seus resultados financeiros. Ainda, a tendência é que terrenos localizados próximos dos eixos de transporte tenham seus preços de comercialização elevados, e a oferta de apartamentos nessas regiões será de produtos de até 80 metros quadrados. Já os terrenos localizados em regiões de baixo aproveitamento poderão ter a atividade de incorporação inviabilizada, a não ser que haja reduções consideráveis dos custos de terreno.

Otimização acústica e análise numérica do escoamento ao redor de um conjunto cilindro-placa separadora.

RESUMO Simulações de aeroacústica computacional demandam uma quantidade considerável de tempo, o que torna complicada a realização de estudos paramétricos. O presente trabalho propõe uma metodologia viável para otimização aeroacústica. Através da análise numérica utilizando dinâmica dos fluidos computacional, foi estudada a aplicação de uma placa separadora desacoplada como método de controle passivo da esteira turbulenta de um cilindro e avaliou-se a irradiação de ruído causado pela interação do escoamento com ambos os corpos, empregando ferramentas de aeroacústica computacional baseadas no método de Ffowcs-Williams e Hawkings. Algumas abordagens distintas de metodologias de otimização de projeto foram aplicadas neste problema, com o objetivo de chegar a uma configuração otimizada que permita a redução do nível sonoro ao longe. Assim, utilizando uma ferramenta de otimização multidisciplinar, pode-se avaliar a capacidade de modelos heurísticos e a grande vantagem do emprego de algoritmos baseados em método de superfície de resposta quando aplicados em um problema não linear, pois requerem a avaliação de um menor número de alternativas para se obter um ponto ótimo. Além disso, foi possível identificar e agrupar os resultados em 5 clusters baseados em seus parâmetros geométricos, nível de pressão sonora global e o valor quadrático médio do coeficiente de arrasto, confirmando a eficiência da aplicação de placas separadoras longas desacopladas posicionadas próximas ao cilindro na estabilização da esteira turbulenta, enquanto que o posicionamento de placas acima de um espaçamento crítico aumentou o nível de pressão acústica irradiado devido à formação de vórtices no espaço entre o cilindro e a placa separadora.