Multiple DNA and protein sequence alignment based on segment-to-segment comparison.

In this paper, a new way to think about, and to construct, pairwise as well as multiple alignments of DNA and protein sequences is proposed. Rather than forcing alignments to either align single residues or to introduce gaps by defining an alignment as a path running right from the source up to the sink in the associated dot-matrix diagram, we propose to consider alignments as consistent equivalence relations defined on the set of all positions occurring in all sequences under consideration. We also propose constructing alignments from whole segments exhibiting highly significant overall similarity rather than by aligning individual residues. Consequently, we present an alignment algorithm that (i) is based on segment-to-segment comparison instead of the commonly used residue-to-residue comparison and which (ii) avoids the well-known difficulties concerning the choice of appropriate gap penalties: gaps are not treated explicity, but remain as those parts of the sequences that do not belong to any of the aligned segments. Finally, we discuss the application of our algorithm to two test examples and compare it with commonly used alignment methods. As a first example, we aligned a set of 11 DNA sequences coding for functional helix-loop-helix proteins. Though the sequences show only low overall similarity, our program correctly aligned all of the 11 functional sites, which was a unique result among the methods tested. As a by-product, the reading frames of the sequences were identified. Next, we aligned a set of ribonuclease H proteins and compared our results with alignments produced by other programs as reported by McClure et al. [McClure, M. A., Vasi, T. K. & Fitch, W. M. (1994) Mol. Biol. Evol. 11, 571-592]. Our program was one of the best scoring programs. However, in contrast to other methods, our protein alignments are independent of user-defined parameters.

Integration of multiple repeats of geminiviral DNA into the nuclear genome of tobacco during evolution.

Integration of viral DNA into the host nuclear genome, although not unusual in bacterial and animal systems, has surprisingly not been reported for plants. We have discovered geminvirus-related DNA (GRD) sequences, in the form of distinct sets of multiple direct repeats comprising three related repeat classes, situated in a unique locus in the Nicotiana tabacum (tobacco) nuclear genome. The organization of these sequences is similar or identical in eight different tobacco cultivars we have examined. DNA sequence analysis reveals that each repeat has sequences most resembling those of the New World geminiviral DNA replication origin plus the adjacent AL1 gene, encoding the viral replication protein. We believe these GRD sequences originated quite recently in Nicotiana evolution through integration of geminiviral DNA by some combination of the processes of illegitimate recombination, amplification, deletions, and rearrangements. These events must have occurred in plant tissue that was subsequently able to contribute to meristematic tissue yielding gametes. GRD may have been retained in tobacco by selection or by random fixation in a small evolving population. Although we cannot detect transcription of these sequences, this does not exclude the possibility that they may originally have been expressed.

Dual transcriptional control by Ear3/COUP: negative regulation through the DR1 direct repeat and positive regulation through a sequence downstream of the transcriptional start site of the mouse mammary tumor virus promoter.

Ear3/COUP is an orphan member of the steroid/thyroid hormone receptor superfamily of transcription factors and binds most tightly to a direct repeat of AGGTCA with 1 nucleotide in between (DR1). Ear3/COUP also binds with a similar affinity to the palindromic thyroid hormone response element (TRE). This binding preference of Ear3/COUP is same as that of the retinoid X receptor (RXR), which is another member of the superfamily. In the present study, we identified a sequence responsible for Ear3/COUP-mediated transactivation in the region downstream of the transcription start site of the mouse mammary tumor virus promoter. This cis-acting sequence was unresponsive to RXR. When the DR1 or TRE sequence was added upstream of the promoter, transactivation by Ear3/COUP was completely abolished, whereas RXR enhanced transcription from the promoter. The mode of action of Ear3/COUP could be utilized to control complex gene expressions in morphogenesis, homeostasis, and development.

Projeto e desenvolvimento de uma arquitetura de baixo consumo de potência para microprocessadores.

O trabalho trata do projeto e do desenvolvimento de um processador de baixo consumo de potência, de forma simplificada, explorando técnicas de microarquitetura, para atingir menor consumo de potência. É apresentada uma sequência lógica de desenvolvimento, a partir de conceitos e estruturas básicas, até chegar a estruturas mais complexas e, por fim, mostrar a microarquitetura completa do processador. Esse novo modelo de processador é comparado com estudos prévios de três processadores, sendo o primeiro modelo síncrono, o segundo assíncrono e o terceiro uma versão melhorada do primeiro modelo, que inclui minimizações de registradores e circuitos. Uma nova metodologia de criação de padring de microcontroladores, baseada em reuso de informações de projetos anteriores, é apresentada. Essa nova metodologia foi criada para a rápida prototipagem e para diminuir possíveis erros na geração do código do padring. Comparações de resultados de consumo de potência e área são apresentadas para o processador desenvolvido e resultados obtidos com a nova metodologia de geração de padring também são apresentados. Para o processador, um modelo, no qual se utilizam múltiplos barramentos para minimizar o número de ciclos de máquina por instrução, é apresentado. Também foram ressaltadas estruturas que podem ser otimizadas e circuitos que podem ser reaproveitados para diminuir a quantidade de circuito necessário na implementação. Por fim, a nova implementação é comparada com os três modelos anteriores; os ganhos obtidos de desempenho com a implementação dessas estruturas foram de 18% que, convertidos em consumo de potência, representam economia de 13% em relação ao melhor caso dos processadores comparados. A tecnologia utilizada no desenvolvimento dos processadores foi CMOS 250nm da TSMC.

Domino 1,3-Dipolar Cycloadditions of N-Alkyl-α-Amino Esters with Paraformaldehyde: A Direct Access to α-Hydroxymethyl α-Amino Acids

N-Alkyl-α-amino esters undergo a domino reaction, based on the iminium cation generation, with paraformaldehyde, followed by a 1,3-dipolar cycloaddition of the stabilized azometh­ine ylide with another equivalent of formaldehyde. The resulting products are oxazolidines, which can be transformed after hydrolysis into α-hydroxymethyl α-amino acid or its derivatives. The diastereoselective 1,3-dipolar cycloaddition was performed using sarcosine (–)-menthyl or (–)-8-phenylmenthyl esters affording the cyclic product with moderate enantiomeric ratio.

Fluid compositions and mineralogy of precipitates from Mid Atlantic Ridge hydrothermal vents at 4°48'S

The effect of volcanic activity on submarine hydrothermal systems has been well documented along fast- and intermediate-spreading centers but not from slow-spreading ridges. Indeed, volcanic eruptions are expected to be rare on slow-spreading axes. Here we report the presence of hydrothermal venting associated with extremely fresh lava flows at an elevated, apparently magmatically robust segment center on the slow-spreading southern Mid-Atlantic Ridge near 5°S. Three high-temperature vent fields have been recognized so far over a strike length of less than 2 km with two fields venting phase-separated, vapor-type fluids. Exit temperatures at one of the fields reach up to 407°C, at conditions of the critical point of seawater, the highest temperatures ever recorded from the seafloor. Fluid and vent field characteristics show a large variability between the vent fields, a variation that is not expected within such a limited area. We conclude from mineralogical investigations of hydrothermal precipitates that vent-fluid compositions have evolved recently from relatively oxidizing to more reducing conditions, a shift that could also be related to renewed magmatic activity in the area. Current high exit temperatures, reducing conditions, low silica contents, and high hydrogen contents in the fluids of two vent sites are consistent with a shallow magmatic source, probably related to a young volcanic eruption event nearby, in which basaltic magma is actively crystallizing. This is the first reported evidence for direct magmatic-hydrothermal interaction on a slow-spreading mid-ocean ridge.

Chemical and mineral compositions of sediments from ODP Site 127-797

In order to reconstruct past variations in the aeolian dust (Kosa) contribution to the Japan Sea, and to establish a direct link between terrestrial and marine climatic records, we have applied statistical procedures to distinguish and quantify detrital subcomponents within the detrital fraction of the late Quaternary hemipelagic sediments in the Japan Sea. Q-mode factor analysis with varimax and oblique rotation of the factors followed by multiple-regression analysis between mineral composition and factor loadings was conducted using six ''detrital'' elements. Four detrital subcomponents were defined, which are attributed to Kosa derived from ''typical'' loess, Kosa from ''weathered'' loess, and fine and coarse arc-derived detritus, respectively, based on comparisons with the chemical and mineral compositions of probable source materials. Using these detrital subcomponents, the variation in Kosa fraction was reconstructed for the last 200 ky. The results reveal millennial-scale as well as glacial-interglacial scale variations in Kosa contribution. Especially, millennial-scale variability of Kosa contribution suggests the presence of high frequency variation in summer monsoon precipitation in the central to east Asia during the last 200 ky.

Composition of sedimentary rocks from the Shapkina River valley, Bolshezemelskaya Tundra

A facies-genetic and stratigraphic subdivision of the Quaternary sequence in the Shapkina River valley has been accomplished. The riverbank shows outcrops of three glacial complexes with different mineralogical-petrographic compositions and structural characteristics, which can be correlated and stratificated. Datings of intermoraine horizons (alluvial, marine, lacustrine, and lacustrine-boggy sediments) have been based on palynological and paleomicrotheriological data. The Middle Neopleistocene section can be divided into two till horizons corresponding to two autonomous glaciations (Pechora and Vychegda). They are separated by a member of subaqueous Rodionov sediments. The Pechora till formed in the course of glacier motions from the northeast. Glacial horizons are mainly composed of the Vychegda till transported from the Northwest terrigenous provenance. Lithology of the Upper Neopleistocene Polyarnyi till testifies to its formation in the upper course of the river from material transported from the Northeast terrigenous-mineralogical provenance in the upper course of the river and from the Fennoscandian glaciation center in the lower course of the river. The paper presents the first lithological investigation and substantiation of genesis of various facies of Neopleistocene intermoraine marine sediments (sediments of the beach and fore-beach zones and shallow-water shelf).

Multiple imputation of missing blood alcohol concentration (BAC) values in FARS.

National Highway Traffic Safety Administration, Washington, D.C.

Housing codes : the key to housing conservation /

Cover title.

The Tax code of Virginia. With all amendments enacted at the session of the General assembly of 1928.

Mode of access: Internet.

The Tax code of Virginia. With all amendments enacted at the session of the General Assembly of 1928 and 1930.

Mode of access: Internet.

NCI/MARC summer training supplement : Comprehensive Minority Biomedical Program, Division of Extramural Activities, National Cancer Institute in conjunction with Minority Access to Research Careers, National Institute of General Medical Sciences.

Mode of access: Internet.

The Tax code of Virginia. With all amendments enacted at the session of the General Assembly of 1928, 1930 and 1932. Published by the Department of Taxation of the Commonwealth of Virginia

Mode of access: Internet.