Capping Strategies for Covalent Template-Directed Synthesis of Linear Oligomers Using CuAAC.

Covalent templating provides an attractive solution to the controlled synthesis of linear oligomers because a template oligomer can be used to define the precise length and sequence of the product. If the monomer units are attached to the template using kinetically inert covalent bonds it should be possible to operate at high dilution to favor intramolecular over intermolecular reaction. However, for oligomerization reactions using copper-catalyzed azide alkyne cycloaddition (CuAAC) this is not the case. The rate-limiting step is formation of an activated copper complex, so any alkyne that is activated by copper reacts rapidly with the nearest available azide. As a result, every time a chain end alkyne is activated, rapid intermolecular reaction takes place with a different oligomer leading to the formation of higher order products. It proved possible to block these intermolecular reactions by adding an excess of an azide capping agent that intercepts the chain end of the growing oligomer on the template. By adjusting the concentration of the capping agent to compete effectively with the unwanted intermolecular reactions without interfering with the desired intramolecular reactions, it was possible to obtain quantitative yields of copy strands from covalent template-directed oligomerization reactions. Remarkably, the capping agent could also be used to control the stereochemistry of the duplex formed in the templated oligomerization reaction to give exclusively the antiparallel product.ERC-2012-AdG 320539-duplex, Herchel Smith Fun

An Alternative Tool for Intra-Row Weed Control in a High-Density Olive Orchard

none6openAssirelli, Alberto; Ciaccia, Corrado; Giorgi, Veronica; Zucchini, Matteo; Neri, Davide; Lodolini, Enrico MariaAssirelli, Alberto; Ciaccia, Corrado; Giorgi, Veronica; Zucchini, Matteo; Neri, Davide; Lodolini, Enrico Mari

Controlled membrane translocation provides a mechanism for signal transduction and amplification.

Transmission and amplification of chemical signals across lipid bilayer membranes is of profound significance in many biological processes, from the development of multicellular organisms to information processing in the nervous system. In biology, membrane-spanning proteins are responsible for the transmission of chemical signals across membranes, and signal transduction is often associated with an amplified signalling cascade. The ability to reproduce such processes in artificial systems has potential applications in sensing, controlled drug delivery and communication between compartments in tissue-like constructs of synthetic vesicles. Here we describe a mechanism for transmitting a chemical signal across a membrane based on the controlled translocation of a synthetic molecular transducer from one side of a lipid bilayer membrane to the other. The controlled molecular motion has been coupled to the activation of a catalyst on the inside of a vesicle, which leads to a signal-amplification process analogous to the biological counterpart.We thank the University of Cambridge Oppenheimer Fund for an Early Career Research Fellowship (M.J.L); the Wiener-Anspach Foundation (FWA) for postdoctoral fellowship (FK) ; and Franziska Kundel and David Klenerman for TIRFM imaging experiments

Epidemiological, serological and molecular aspects of hepatitis A, B and C in children and teenagers enrolled at municipal daycare facilities, pre-schools and elementary schools in the city of Santos

As hepatites virais continuam sendo uma preocupação em nível de saúde pública no Brasil e no Mundo, tanto pelo número de indivíduos atingidos, como pela possibilidade de complicação das formas agudas e crônicas. Segundo a Organização Mundial de Saúde (OMS), 170 milhões de pessoas são portadoras crônicas de hepatite C e 350 milhões portadoras crônicas de hepatite B. No Brasil, a estimativa de portadores de hepatite B crônica é de aproximadamente 600 mil pessoas e de hepatite C crônica, 1,5 milhão. Quanto à hepatite aguda A foram confirmados no país, em 2010, 5943 casos. O objetivo deste estudo foi conhecer a prevalência de marcadores sorológicos dos vírus das hepatites A, B e C em crianças e adolescentes matriculados em creches e escolas de ensino infantil e fundamental da rede municipal na cidade de Santos; conhecer os aspectos moleculares dos vírus das hepatites B e C, identificando o genótipo dos dois agentes e estudar modo de aquisição nos casos com sorologias positivas. Tratou-se de um estudo transversal realizado no período de 28 de Junho a 14 de Dezembro de 2007 onde foram coletadas 4680 amostras de sangue colhidas através de punção capilar e ao mesmo tempo aplicado um questionário nos familiares das crianças e adolescentes. Os exames sorológicos foram realizados utilizando a técnica de ELISA. O estudo molecular foi realizado pela técnica de reação em cadeia de polimerase \"in House\". A idade da população estudada variou de 7 meses a 18 anos e 1 m. A prevalência geral do anti-HVA IgG reagente foi de 9,7% e desses 74,6% foi anti-HVA IgM reagente. A prevalência de anti-HVA IgG foi maior entre as crianças mais velhas, meninas, aquelas que brincavam em córregos, sem esgoto em sua moradia, de pais com baixa instrução, de baixa renda familiar e aquelas que não eram moradoras da Orla. A prevalência de anti-HVA IgM, não foi diferente entre as diferentes categorias, exceção feita à faixa etária (pico no primeiros anos e posterior queda) e morro e Zona Noroeste foi mais baixa. A prevalência geral do anti-HBc reagente foi de 0,1%, do AgHBs de 0,02% e do anti-HVC foi de 0,02%. Conclui-se que a prevalência geral em crianças dos marcadores sorológicos para hepatites A, B e C na cidade de Santos foi baixa, quando comparada com os dados de literatura. Apesar dos nossos dados confirmarem uma mudança no perfil epidemiológico da hepatite A, as medidas preventivas atuais quanto ao saneamento, grau de instrução, habitação, ainda permanece com uma deficiência em Santos, cidade balneária com o maior porto do Brasil. A vacinação para hepatite B foi altamente eficaz com a baixa prevalência encontrada dos marcadores sorológicos. A utilização do papel de filtro em estudos epidemiológicos para hepatite A foi eficaz. Entretanto para o vírus da hepatite C ainda necessita de estudos comparativos utilizando sangue venoso, uma vez que a prevalência de crianças infectadas com hepatite C foi muito baixa na cidade de Santos.Viral hepatitis are still a concern in the public health level in Brazil and around the Word, due both to the number of affected subjects and the possibility of complication in the acute and chronic forms. According to the World Health organization (WHO), 170 million people are chronic carriers of hepatitis C and 350 million chronic carriers of hepatitis B. In Brasil, the estimate of people with chronic hepatitis B is approximately 600 thousand people and chronic hepatitis C, 1,5 million. It has been confirmed in the country, in 2010, 5943 cases of acute hepatitis A. The The aim of this study was to learn the prevalence of serological markers of hepatitis A, B and C virus in children and teenagers enrolled at the municipal education network in the city of Santos, to learn molecular aspects of hepatitis B and C, identifying the genotype of the two agents and to study the acquisition mode in cases with positive serology. Cross-sectional study carried out over the period from June 28 to December 14, 2007, in which 4680 fingerprick blood samples were collected; at the same time, a survey questionnaire was applied to the family members of the children and teenagers. The serological tests were performed using the ELISA technique. The molecular analysis was performed using the technique of polymerase chain reaction \"in House\". Age of the population studied ranged from 7 months to 18 years and 1 month. . The general prevalence of serological markers anti-HAV IgG reagent was 9.7% and between them 74,7% was anti-HAV IgM reagent. There was higher prevalence among older children, females, those who used to play in streams near their home, the absence of a sewage system in home, parents with low education, low household income and among those who did not live in the seashore. The prevalence of anti-HAV IgM was not different between the categories, except for the age (peak in the early years and subsequent fall) and lower on the Hills and Northweast Zone. The general prevalence of anti-HBc reagent was 0,1%, AgHBs was 0,02% and anti-HCV was 0,02%. It is concluded that, in children, the general prevalence of serological markers for hepatitis A, B and C in the city of Santos was low when compared with literature data. Although our data confirm a change in the epidemiological profile of hepatitis A, the current preventive measures regarding sanitation, education level and housing still remain with a deficiency in Santos, the coastal city with the largest harbor in Brazil. Vaccination for hepatitis B was highly effective because it found a low prevalence of serological markers. The use of filter paper in epidemiological studies for hepatitis A was effective. However for the vírus of hepatitis C still requires comparative studies using venous blood because the prevalence of infected children was very low in the city of Santos

Mechanisms of imine exchange reactions in organic solvents

The state of the art in the mechanisms operating in imine chemistry in organic solvents is critically discussed in the present review. In particular, the reaction pathways involved in imine formation, transimination and imine metathesis in organic media are taken into account, with the aim of organizing the poor, and sometimes scattered, information available in the literature. It is shown that 4-membered cyclic transition states, either polar or apolar, can be considered a leitmotif for the chemistry of imines in organic solvents. However, it is pointed out that further investigations will be necessary to reach an adequate degree of knowledge of the mechanisms involved in such important reversible processes

Cap control: cyclic versus linear oligomerisation in covalent template-directed synthesis.

Covalent template-directed synthesis was used to oligomerise monomer building blocks in a controlled manner to give exclusively the linear trimer. Competing reaction pathways were blocked by addition of a large excess of a monomeric capping agent. At a concentration of 1 mM, the cap selectively prevented further reaction of the product chain ends to give polymeric and macrocyclic products, but did not interfere with the templating process.Engineering and Physical Sciences Research Council (EP/P027067/1), Herchel Smith Fund

Elucidating the editome: bioinformatics approaches for RNA editing detection

RNA editing is a widespread co/posttranscriptional mechanism affecting primary RNAs by specific nucleotide modifications, which plays relevant roles in molecular processes including regulation of gene expression and/or the processing of noncoding RNAs. In recent years, the detection of editing sites has been improved through the availability of high-throughput RNA sequencing (RNA-Seq) technologies. Accurate bioinformatics pipelines are essential for the analysis of next-generation sequencing (NGS) data to ensure the correct identification of edited sites. Several pipelines, using various read mappers and variant callers with a wide range of adjustable parameters, are available for the detection of RNA editing events. In this review, we discuss some of the most recent and popular tools and provide guidelines for RNA-Seq data generation and analysis for the detection of RNA editing in massive transcriptome data. Using simulated and real data sets, we provide an overview of their behavior, emphasizing the fact that the RNA editing detection in NGS data sets remains a challenging task