Transcriptome of the deep-sea black scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae) : tissue-specific expression patterns and candidate genes associated to depth adaptation

Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues of A. carbo. Assemblage and annotations were performed by Newbler and InterPro/Pfam analyses, respectively. The assembly of 544,491 high quality reads provided 8,319 contigs, 55.6% of which retrieved blast hits against the NCBI nonredundant database or were annotated with ESTscan. Comparison of functional genes at both the protein sequences and protein stability levels, associated with adaptations to depth, revealed similarities between A. carbo and other bathypelagic fishes. A selection of putative genes was standardized to evaluate the correlation between number of contigs and their normalized expression, as determined by qPCR amplification. The screening of the libraries contributed to the identification of new EST simple-sequence repeats (SSRs) and to the design of primer pairs suitable for population genetic studies as well as for tagging and mapping of genes. The characterization of the deep-sea fish A. carbo first transcriptome is expected to provide abundant resources for genetic, evolutionary, and ecological studies of this species and the basis for further investigation of depth-related adaptation processes in fishes.Publisher PDFPeer reviewe

Computational approaches to shed light on molecular mechanisms in biological processes

Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines. © Springer-Verlag 2007

Investigation of Gasoline Partially Premixed Combustion with External Exhaust Gas Recirculation

The stringent emission regulations for Internal Combustion Engines (ICEs) spawned a great amount of research in the field of innovative combustion approaches characterized by high efficiency and low emissions. Previous research demonstrate that such promising techniques, named Low-Temperature Combustion (LTC), combine the benefits of Compression Ignition (CI) engines, such as high compression ratio and unthrottled lean mixture, with low engine-out emissions using a properly premixed air-fuel mixture. Due to longer ignition delay and high volatility compared to diesel, gasoline-like fuels show good potential for the generation of a highly premixed charge, which is needed to reach LTC characteristics. In this scenario, gasoline Partially Premixed Combustion (PPC), characterized by the high-pressure direct injection of gasoline, showed good potential for the simultaneous reduction of pollutants and emissions in CI engines. However, previous research on gasoline CI highlight that a key factor for the optimization of both efficiency and pollutants is the proper management of Exhaust Gas Recirculation (EGR). This work presents the experimental investigation performed running a light-duty CI engine, operated with gasoline PPC, and varying the mass of recirculated gases trapped in the combustion chamber. To guarantee the stability of gasoline autoignition in all the tested conditions, a specific experimental layout has been developed to accurately quantify the amount of trapped residual gases due to the internal and external EGR. The obtained results clearly highlight the impact of EGR on the combustion process and emissions, demonstrating that optimization of charge dilution with EGR is fundamental to guarantee the optimal compromise between efficiency and emissions over the whole operating range

Adiabatic orientation of rotating dipole molecules in an external field

The induced polarization of a beam of polar clusters or molecules passing through an electric or magnetic field region differs from the textbook Langevin-Debye susceptibility. This distinction, which is important for the interpretation of deflection and focusing experiments, arises because instead of acquiring thermal equilibrium in the field region, the beam ensemble typically enters the field adiabatically, i.e., with a previously fixed distribution of rotational states. We discuss the orientation of rigid symmetric-top systems with a body-fixed electric or magnetic dipole moment. The analytical expression for their "adiabatic-entry" orientation is elucidated and compared with exact numerical results for a range of parameters. The differences between the polarization of thermodynamic and "adiabatic-entry" ensembles, of prolate and oblate tops, and of symmetric-top and linear rotators are illustrated and identified.Comment: 18 pages, 4 figure

Avaliação de diferentes métodos para extração de RNA total de folhas e raízes de braquiária.

A extração de RNA a partir de tecidos específicos consiste no primeiro passo para estudos de expressão gênica e caracterização de transcritos. Plantas, em geral, contêm grande quantidade de compostos fenólicos e/ou polissacarídeos em seus tecidos, o que pode comprometer a extração e purificação de moléculas de RNA. O objetivo principal deste trabalho foi testar diferentes protocolos para extrair RNA total de folhas e raízes de braquiária. Sementes de Brachiaria decumbens cv. Basilisk foram germinadas e plântulas com12 dias foram utilizadas. As extrações de RNA foram feitas em duplicatas de 200 mg de amostras de folhas ou raízes pulverizadas com nitrogênio líquido. Para as extrações de RNA de folhas foram testados os reagentes Trizol® e Brazol® e para as extrações de RNA de raízes foram testados estes reagentes mais dois kits comerciais: SV Wizard Isolation RNA system (Promega®) e Invisorb Spin Plant RNA Mini Kit (Invitek®). ANOVA e teste Tukey (1% de significância) foram utilizados para comparar as médias das concentrações e de qualidade das amostras de RNA extraídas. Os resultados mostraram diferenças não-significativas entre as concentrações e a qualidade do RNA extraído de folhas pelos reagentes Trizol® e Brazol®. Entretanto, para as amostras de raízes as concentrações e qualidade do RNA isolado foram significativamente diferentes, sendo o reagente Trizol® mais eficiente. Os dois kits isolaram menores concentrações de RNA com qualidade inferir a obtida com os dois reagentes testados. Para síntese de DNA complementar (cDNA) foram testadas duas enzimas: SuperScript RTII (Invitrogen®) e M-MLV-RT (Sigma®), sendo esta última mais eficiente, pois foi possível obter maior quantidade e qualidade de cDNA, com relação a presença de contaminantes. Esses resultados podem ser considerados como ponto de partida para a execução de trabalhos sobre expressão gênica em espécies de Brachiaria.bitstream/item/56268/1/BP29.pd

Deposição de material orgânico e nutrientes em plantios de Eucalyptus grandis em diferentes regimes de adubação.

Neste trabalho são apresentados os resultados obtidos para a deposição de serapilheira em plantios de Eucalyptus grandis, que receberam apenas adubos químicos, e plantios adubados e tratados com resíduos e cinza, localizados em áreas de “cerrados” do Estado de São Paulo. As implicações para a nutrição e o manejo e a manutenção da produtividade destes plantios são discutidas. Não foi possível estabelecer-se um padrão de deposição de serapilheira em função das diferentes épocas do ano. Entretanto, as coletas efetuadas em outubro, no quarto ano de idade do experimento apresentaram os valores mais elevados, correspondendo à deposição acumulada em julho, agosto e setembro, ou seja final da estação seca. As folhas predominaram na serapilheira e representam, em peso, 91% do material depositado no terceiro ano e 66% no quarto ano. Os valores observados são próximos dos valores teóricos esperados e de estimativas obtidas em diversas tipologias florestais do sudeste do Brasil. Comparativamente a relatos de deposição de serapilheira em outras formações florestais e para plantações de diversas espécies, os maiores valores de deposição obtidos para os tratamentos com cinza e resíduos, a partir do quarto ano de idade, podem ser considerados elevados. A maior deposição de serapilheira, nos tratamentos com cinza e resíduos, permite concluir que a quantidade de serapilheira depositada depende do estado nutricional dos povoamentos florestais. Os tratamentos com cinza e resíduos depositaram aproximadamente 15% a mais de serapilheira, em peso, que o tratamento que recebeu apenas adubação química. O total de serapilheira depositada, no quarto ano de idade, correspondeu a 24,6% da produção primária liquida de biomassa aérea, produzida em igual período. A maior deposição de nutrientes está relacionada com a maior deposição de serapilheira produzida, entretanto os acréscimos nas quantidades de nutrientes, com exceção do N, foram proporcionalmente mais elevados que o acréscimo observado para a biomassa. A deposição de P, K, Ca e Mg foi 46,5; 45,2; 80,8 e 33,9%, respectivamente mais elevadas que a deposição obtida para o tratamento com adubo químico apenas. Os valores obtidos para deposição anual de biomassa de serapilheira, em peso, sua relação com a produção primária liquida da parte aérea e a contribuição percentual das folhas na composição da serapilheira são bastante próximos das previsões teóricas, e dados estimados relatados na literatura

Pyrazolo-triazolo-pyrimidines as adenosine receptor antagonists: Effect of the N-5 bond type on the affinity and selectivity at the four adenosine receptor subtypes

In the last few years, many efforts have been made to search for potent and selective human A3 adenosine antagonists. In particular, one of the most promising human A3 adenosine receptor antagonists is represented by the pyrazolo-triazolo-pyrimidine family. This class of compounds has been strongly investigated from the point of view of structure-activity relationships. In particular, it has been observed that fundamental requisites for having both potency and selectivity at the human A3 adenosine receptors are the presence of a small substituent at the N8 position and an unsubstitued phenyl carbamoyl moiety at the N5 position. In this study, we report the role of the N5-bond type on the affinity and selectivity at the four adenosine receptor subtypes. The observed structure-activity relationships of this class of antagonists are also exhaustively rationalized using the recently published ligand-based homology modeling approach

A catalogue of observed geo-effective CME/ICME characteristics

One of the goals of Space Weather studies is to achieve a better understanding of impulsive phenomena, such as Coronal Mass Ejections (CMEs), in order to improve our ability to forecast them and mitigate the risk to our technologically driven society. The essential part of achieving this goal is to assess the performance of forecasting models. To this end, the quality and availability of suitable data are of paramount importance. In this work, we have merged already publicly available data of CMEs from both in-situ and remote instrumentation in order to build a database of CME properties. To evaluate the accuracy of such a database and confirm the relationship between in-situ and remote observations, we have employed the drag-based model (DBM) due to its simplicity and inexpensive cost of computational resources. In this study, we have also explored the parameter space for the drag parameter and solar wind speed using a Monte Carlo approach to evaluate how well the DBM determines the propagation of CMEs for the events in the dataset. The dataset of geoeffective CMEs constructed as a result of this work provides validation of the initial hypothesis about DBM, and solar wind speed and also yields further insight into CME features like arrival time, arrival speed, lift-off time, etc. Using a data-driven approach, this procedure allows us to present a homogeneous, reliable, and robust dataset for the investigation of CME propagation. On the other hand, possible CME events are identified where DBM approximation is not valid due to model limitations and higher uncertainties in the input parameters, those events require more thorough investigation