1,354,224 research outputs found
A lattice polymer study of DNA renaturation dynamics
No full textDNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double-stranded nucleus of several base pairs (the rate limiting step) followed by a much faster zippering. We consider a lattice polymer model undergoing Rouse dynamics and focus on the nucleation of two diffusing strands. We study numerically the dependence of various nucleation rates on the strand lengths and on an additional local nucleation barrier. When the local barrier is sufficiently high, all renaturation rates considered scale with the length as predicted by Kramers' rate theory and are also in agreement with experiments: their scaling behavior is governed by exponents describing equilibrium properties of polymers. When the local barrier is lowered, renaturation occurs in a regime of genuine non-equilibrium behavior and the scaling deviates from the rate theory prediction
Breakdown of thermodynamic equilibrium for DNA hybridization in microarrays
No full textTest experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic model. Experiments confirm the model predictions for the intensity vs free-energy behavior. The existence of slow relaxation phenomena has important consequences for the specificity of microarrays as devices for the detection of a target sequence from a complex mixture of nucleic acids
Characterization of a novel Holospora-like symbiont from Frontonia (Ciliophora, Oligohymenophorea)
No full textThe existence of symbiotic relationships between prokaryotes
and ciliate protozoa is known from over a century. Most studies
concerned obligatory mutualistic symbiosis, whereas there is little
knowledge about facultative non-mutualistic symbiotic relationships,
mainly because these associations can be spatially and temporally
variable in natural populations and are especially difficult
to maintain in lab conditions. Nevertheless, they seem to be more
widespread among ciliates than so far supposed. A research
project was recently started in order to get data about such kind
of association in ciliate populations living in a coastal brackish
environment. During this study, we observed some individuals
from a population of Frontonia sp. (Oligohymenophorea, Peniculia)
showing roundish macronuclei instead of ellipsoidal ones.
Observation at DIC microscope revealed the presence of some
relatively large spindle-shaped objects in all macronuclei. According
to the general shape and morphological features, the identification
of these objects as Holospora infectious forms was
hypothesized. The genus Holospora (Alphaproteobacteria, Rickettsiales)
comprises bacterial endosymbionts, which are resident
in the nuclear apparatus of ciliates belonging to the genus Paramecium
(Oligohymenophorea, Peniculia). Their life cycle presents
two different forms: a large infectious form and a smaller
reproductive form. Experiments of in situ hybridization using a
genus-specific probe confirmed the identification of the observed
endonuclear objects as Holospora infectious forms; it made also
possible to observe even the smaller reproductive forms in macronuclei
that were not clearly visible at DIC observation. To further
characterize this symbiont, bacterial DNA was extracted from a
population of infected Frontonia sp. cells. The 16S rRNA gene
sequence was obtained by touchdown PCR reaction with a-proteobacteria-
specific primers and direct sequencing of reaction
product. The new sequence shows a similarity value of about
95% with that of H. obtusa. Indeed, analysis of phylogenetic relationships
revealed that the two sequences are firmly associated.
Molecular data obtained up to now suggest the belonging of this
organism to a novel species of Holospora
Fractional Brownian motion and the critical dynamics of zipping polymers
No full textWe consider two complementary polymer strands of length L attached by a common-end monomer. The two strands bind through complementary monomers and at low temperatures form a double-stranded conformation (zipping), while at high temperature they dissociate (unzipping). This is a simple model of DNA (or RNA) hairpin formation. Here we investigate the dynamics of the strands at the equilibrium critical temperature T = T-c using Monte Carlo Rouse dynamics. We find that the dynamics is anomalous, with a characteristic time scaling as tau similar to L-2.26(2), exceeding the Rouse time similar to L-2.18. We investigate the probability distribution function, velocity autocorrelation function, survival probability, and boundary behavior of the underlying stochastic process. These quantities scale as expected from a fractional Brownian motion with a Hurst exponent H = 0.44(1). We discuss similarities to and differences from unbiased polymer translocation
Betaproteobacterial symbionts of the ciliate Euplotes: origin and tangled evolutionary path of an obligate microbial association.
No full textThe Polynucleobacter-Euplotes association is an obligatory symbiotic system between a monophyletic group of ciliate species belonging to the genus Euplotes and bacteria of the species Polynucleobacter necessarius (Betaproteobacteria). Both organisms are unable to survive independently. Several studies revealed the existence of free-living populations of Polynucleobacter bacteria which are phylogenetically closely related to the endosymbiotic ones, but never share associations with Euplotes in the natural environment. Hence, following the most parsimonious explanation on the origin of the association, this symbiosis should represent a synapomorphic character for the hosts’ clade. Nevertheless, phylogenetic analyses performed on an increased number of strains here presented suggest that Euplotes species, during their evolution, recruited Polynucleobacter bacteria as symbionts more than once. Moreover, in three cases, we observed different bacteria as obligate symbionts. These symbionts are the first characterized representatives of a phylogenetic lineage branching in a basal position with respect to the genus Polynucleobacter. The hypothesis that the original obligate symbionts belonged to this newly discovered clade, and that, only subsequently, in most cases they have been replaced by Polynucleobacter bacteria recruited from the environment is proposed and discussed. The evolutionary path of this association seems anyway to have been more complex than so far supposed
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
No full text“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
A new obligate bacterial symbiont colonizing the ciliate Euplotes in brackish and freshwater: "Candidatus Protistobacter heckmanni"
No full textA monophyletic group of freshwater and brackish ciliate species belonging to the
genus Euplotes is known to harbor bacterial endosymbionts of the class Betaproteobacteria permanently
in the natural environment. One or other of 2 different species of bacteria have been
shown to be present: the obligate symbiont Polynucleobacter necessarius or a recently described
betaproteobacterium. While the association between P. necessarius and its Euplotes hosts has
been well studied in the past, knowledge about the relationship between the newly discovered
symbiont and its Euplotes hosts is still very poor. Here we present the SSUrRNA gene characterization
of both host and symbiont for an additional brackish-water population of Euplotes hosting
the newly discovered symbiont. We also provide the symbiont genome size determination and
ultrastructural description. Attempts to cultivate the new symbiont outside its host, using many
different methods, failed. This result indicates that, as in the case of the symbiotic P. necessarius,
we are probably dealing with an obligate symbiont, unable to grow outside the cytoplasm of its
natural host. On the basis of the results obtained we propose the new symbiont as a candidate new
species with the name of ‘Candidatus Protistobacter heckmanni’, according to the current rules of
prokaryotic nomenclature
Uma contribuição para a reflexão sobre a didática na história do ensino superior no Brasil
No full textDissertação (mestrado) - Universidade Federal de Santa Catarina, Centro Tecnológico. Programa de Pós-Graduação em Engenharia de ProduçãoDesde os tempos coloniais, até a década de 30 do século passado, o Brasil não coutou com universidades dignas deste nome. Mesmo a partir daí, o modelo que se foi impondo é o das escolas superiores isoladas, profissionais, criadas separadamente, e por injunções políticas imediatas e nem sempre preocupadas com as reais necessidades da sociedade. Tais universidades souberam romper o isolamento medieval ao unir o mundo das idéias com o mundo das doutrinas. A sociedade da Era da Informação e da Informatização vivencia uma nova estruturação social e desafia o Ensino Superior e a didática do Magistério Superior. No âmbito destas questões foi desenvolvido este trabalho de pesquisa apresentando a Evolução do Ensino Superior no Brasil, a Didática na atualização do Ensino Superior e a Didática e o Professor de Ensino Superior, complementado com uma pesquisa de campo que envolveu 50 professores universitários sobre a relevância da didática na formação de professore
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