910 resultados para m-sequences


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Although mangroves represent ecosystems of global importance, the genetic diversity and abundance of functional genes that are key to their functioning scarcely have been explored. Here, we present a survey based on the nifH gene across transects of sediments of two mangrove systems located along the coast line of Sao Paulo state (Brazil) which differed by degree of disturbance, i.e., an oil-spill-affected and an unaffected mangrove. The diazotrophic communities were assessed by denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR), and clone libraries. The nifH gene abundance was similar across the two mangrove sediment systems, as evidenced by qPCR. However, the nifH-based PCR-DGGE profiles revealed clear differences between the mangroves. Moreover, shifts in the nifH gene diversities were noted along the land-sea transect within the previously oiled mangrove. The nifH gene diversity depicted the presence of nitrogen-fixing bacteria affiliated with a wide range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and also a group of anaerobic sulfate-reducing bacteria. We also detected a unique mangrove-specific cluster of sequences denoted Mgv-nifH. Our results indicate that nitrogen-fixing bacterial guilds can be partially endemic to mangroves, and these communities are modulated by oil contamination, which has important implications for conservation strategies.

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We study the spectral functions, and in particular the zeta function, associated to a class of sequences of complex numbers, called of spectral type. We investigate the decomposability of the zeta function associated to a double sequence with respect to some simple sequence, and we provide a technique for obtaining the first terms in the Laurent expansion at zero of the zeta function associated to a double sequence.

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Background: Hepatitis B virus (HBV) infection is one of the most prevalent viral infections in humans and represents a serious public health problem. In Colombia, our group reported recently the presence of subgenotypes F3, A2 and genotype G in Bogota. The aim of this study was to characterize the HBV genotypes circulating in Quibdo, the largest Afro-descendant community in Colombia. Sixty HBsAg-positive samples were studied. A fragment of 1306 bp (S/POL) was amplified by nested PCR. Positive samples to S/POL fragment were submitted to PCR amplification of the HBV complete genome. Findings: The distribution of HBV genotypes was: A1 (52.17%), E (39.13%), D3 (4.3%) and F3/A1 (4.3%). An HBV recombinant strain subgenotype F3/A1 was found for the first time. Conclusions: This study is the first analysis of complete HBV genome sequences from Afro-Colombian population. It was found an important presence of HBV/A1 and HBV/E genotypes. A new recombinant strain of HBV genotype F3/A1 was reported in this population. This fact may be correlated with the introduction of these genotypes in the times of slavery.

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Abstract Background Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C. Results We have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein. Conclusion We have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.

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Abstract Background The metabolic capacity for nitrogen fixation is known to be present in several prokaryotic species scattered across taxonomic groups. Experimental detection of nitrogen fixation in microbes requires species-specific conditions, making it difficult to obtain a comprehensive census of this trait. The recent and rapid increase in the availability of microbial genome sequences affords novel opportunities to re-examine the occurrence and distribution of nitrogen fixation genes. The current practice for computational prediction of nitrogen fixation is to use the presence of the nifH and/or nifD genes. Results Based on a careful comparison of the repertoire of nitrogen fixation genes in known diazotroph species we propose a new criterion for computational prediction of nitrogen fixation: the presence of a minimum set of six genes coding for structural and biosynthetic components, namely NifHDK and NifENB. Using this criterion, we conducted a comprehensive search in fully sequenced genomes and identified 149 diazotrophic species, including 82 known diazotrophs and 67 species not known to fix nitrogen. The taxonomic distribution of nitrogen fixation in Archaea was limited to the Euryarchaeota phylum; within the Bacteria domain we predict that nitrogen fixation occurs in 13 different phyla. Of these, seven phyla had not hitherto been known to contain species capable of nitrogen fixation. Our analyses also identified protein sequences that are similar to nitrogenase in organisms that do not meet the minimum-gene-set criteria. The existence of nitrogenase-like proteins lacking conserved co-factor ligands in both diazotrophs and non-diazotrophs suggests their potential for performing other, as yet unidentified, metabolic functions. Conclusions Our predictions expand the known phylogenetic diversity of nitrogen fixation, and suggest that this trait may be much more common in nature than it is currently thought. The diverse phylogenetic distribution of nitrogenase-like proteins indicates potential new roles for anciently duplicated and divergent members of this group of enzymes.

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[EN] We present in this paper a variational approach to accurately estimate simultaneously the velocity field and its derivatives directly from PIV image sequences. Our method differs from other techniques that have been presented in the literature in the fact that the energy minimization used to estimate the particles motion depends on a second order Taylor development of the flow. In this way, we are not only able to compute the motion vector field, but we also obtain an accurate estimation of their derivatives. Hence, we avoid the use of numerical schemes to compute the derivatives from the estimated flow that usually yield to numerical amplification of the inherent uncertainty on the estimated flow. The performance of our approach is illustrated with the estimation of the motion vector field and the vorticity on both synthetic and real PIV datasets.

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Facial expression recognition is one of the most challenging research areas in the image recognition ¯eld and has been actively studied since the 70's. For instance, smile recognition has been studied due to the fact that it is considered an important facial expression in human communication, it is therefore likely useful for human–machine interaction. Moreover, if a smile can be detected and also its intensity estimated, it will raise the possibility of new applications in the future

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Forecasting the time, location, nature, and scale of volcanic eruptions is one of the most urgent aspects of modern applied volcanology. The reliability of probabilistic forecasting procedures is strongly related to the reliability of the input information provided, implying objective criteria for interpreting the historical and monitoring data. For this reason both, detailed analysis of past data and more basic research into the processes of volcanism, are fundamental tasks of a continuous information-gain process; in this way the precursor events of eruptions can be better interpreted in terms of their physical meanings with correlated uncertainties. This should lead to better predictions of the nature of eruptive events. In this work we have studied different problems associated with the long- and short-term eruption forecasting assessment. First, we discuss different approaches for the analysis of the eruptive history of a volcano, most of them generally applied for long-term eruption forecasting purposes; furthermore, we present a model based on the characteristics of a Brownian passage-time process to describe recurrent eruptive activity, and apply it for long-term, time-dependent, eruption forecasting (Chapter 1). Conversely, in an effort to define further monitoring parameters as input data for short-term eruption forecasting in probabilistic models (as for example, the Bayesian Event Tree for eruption forecasting -BET_EF-), we analyze some characteristics of typical seismic activity recorded in active volcanoes; in particular, we use some methodologies that may be applied to analyze long-period (LP) events (Chapter 2) and volcano-tectonic (VT) seismic swarms (Chapter 3); our analysis in general are oriented toward the tracking of phenomena that can provide information about magmatic processes. Finally, we discuss some possible ways to integrate the results presented in Chapters 1 (for long-term EF), 2 and 3 (for short-term EF) in the BET_EF model (Chapter 4).

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It is usual to hear a strange short sentence: «Random is better than...». Why is randomness a good solution to a certain engineering problem? There are many possible answers, and all of them are related to the considered topic. In this thesis I will discuss about two crucial topics that take advantage by randomizing some waveforms involved in signals manipulations. In particular, advantages are guaranteed by shaping the second order statistic of antipodal sequences involved in an intermediate signal processing stages. The first topic is in the area of analog-to-digital conversion, and it is named Compressive Sensing (CS). CS is a novel paradigm in signal processing that tries to merge signal acquisition and compression at the same time. Consequently it allows to direct acquire a signal in a compressed form. In this thesis, after an ample description of the CS methodology and its related architectures, I will present a new approach that tries to achieve high compression by design the second order statistics of a set of additional waveforms involved in the signal acquisition/compression stage. The second topic addressed in this thesis is in the area of communication system, in particular I focused the attention on ultra-wideband (UWB) systems. An option to produce and decode UWB signals is direct-sequence spreading with multiple access based on code division (DS-CDMA). Focusing on this methodology, I will address the coexistence of a DS-CDMA system with a narrowband interferer. To do so, I minimize the joint effect of both multiple access (MAI) and narrowband (NBI) interference on a simple matched filter receiver. I will show that, when spreading sequence statistical properties are suitably designed, performance improvements are possible with respect to a system exploiting chaos-based sequences minimizing MAI only.

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Most electronic systems can be described in a very simplified way as an assemblage of analog and digital components put all together in order to perform a certain function. Nowadays, there is an increasing tendency to reduce the analog components, and to replace them by operations performed in the digital domain. This tendency has led to the emergence of new electronic systems that are more flexible, cheaper and robust. However, no matter the amount of digital process implemented, there will be always an analog part to be sorted out and thus, the step of converting digital signals into analog signals and vice versa cannot be avoided. This conversion can be more or less complex depending on the characteristics of the signals. Thus, even if it is desirable to replace functions carried out by analog components by digital processes, it is equally important to do so in a way that simplifies the conversion from digital to analog signals and vice versa. In the present thesis, we have study strategies based on increasing the amount of processing in the digital domain in such a way that the implementation of analog hardware stages can be simplified. To this aim, we have proposed the use of very low quantized signals, i.e. 1-bit, for the acquisition and for the generation of particular classes of signals.

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The present study has been carried out with the following objectives: i) To investigate the attributes of source parameters of local and regional earthquakes; ii) To estimate, as accurately as possible, M0, fc, Δσ and their standard errors to infer their relationship with source size; iii) To quantify high-frequency earthquake ground motion and to study the source scaling. This work is based on observational data of micro, small and moderate -earthquakes for three selected seismic sequences, namely Parkfield (CA, USA), Maule (Chile) and Ferrara (Italy). For the Parkfield seismic sequence (CA), a data set of 757 (42 clusters) repeating micro-earthquakes (0 ≤ MW ≤ 2), collected using borehole High Resolution Seismic Network (HRSN), have been analyzed and interpreted. We used the coda methodology to compute spectral ratios to obtain accurate values of fc , Δσ, and M0 for three target clusters (San Francisco, Los Angeles, and Hawaii) of our data. We also performed a general regression on peak ground velocities to obtain reliable seismic spectra of all earthquakes. For the Maule seismic sequence, a data set of 172 aftershocks of the 2010 MW 8.8 earthquake (3.7 ≤ MW ≤ 6.2), recorded by more than 100 temporary broadband stations, have been analyzed and interpreted to quantify high-frequency earthquake ground motion in this subduction zone. We completely calibrated the excitation and attenuation of the ground motion in Central Chile. For the Ferrara sequence, we calculated moment tensor solutions for 20 events from MW 5.63 (the largest main event occurred on May 20 2012), down to MW 3.2 by a 1-D velocity model for the crust beneath the Pianura Padana, using all the geophysical and geological information available for the area. The PADANIA model allowed a numerical study on the characteristics of the ground motion in the thick sediments of the flood plain.

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Questa tesi si inserisce nell'ambito delle analisi statistiche e dei metodi stocastici applicati all'analisi delle sequenze di DNA. Nello specifico il nostro lavoro è incentrato sullo studio del dinucleotide CG (CpG) all'interno del genoma umano, che si trova raggruppato in zone specifiche denominate CpG islands. Queste sono legate alla metilazione del DNA, un processo che riveste un ruolo fondamentale nella regolazione genica. La prima parte dello studio è dedicata a una caratterizzazione globale del contenuto e della distribuzione dei 16 diversi dinucleotidi all'interno del genoma umano: in particolare viene studiata la distribuzione delle distanze tra occorrenze successive dello stesso dinucleotide lungo la sequenza. I risultati vengono confrontati con diversi modelli nulli: sequenze random generate con catene di Markov di ordine zero (basate sulle frequenze relative dei nucleotidi) e uno (basate sulle probabilità di transizione tra diversi nucleotidi) e la distribuzione geometrica per le distanze. Da questa analisi le proprietà caratteristiche del dinucleotide CpG emergono chiaramente, sia dal confronto con gli altri dinucleotidi che con i modelli random. A seguito di questa prima parte abbiamo scelto di concentrare le successive analisi in zone di interesse biologico, studiando l’abbondanza e la distribuzione di CpG al loro interno (CpG islands, promotori e Lamina Associated Domains). Nei primi due casi si osserva un forte arricchimento nel contenuto di CpG, e la distribuzione delle distanze è spostata verso valori inferiori, indicando che questo dinucleotide è clusterizzato. All’interno delle LADs si trovano mediamente meno CpG e questi presentano distanze maggiori. Infine abbiamo adottato una rappresentazione a random walk del DNA, costruita in base al posizionamento dei dinucleotidi: il walk ottenuto presenta caratteristiche drasticamente diverse all’interno e all’esterno di zone annotate come CpG island. Riteniamo pertanto che metodi basati su questo approccio potrebbero essere sfruttati per migliorare l’individuazione di queste aree di interesse nel genoma umano e di altri organismi.