10,040 research outputs found
Role of the central cations in the mechanical unfolding of DNA and RNA G-quadruplexes.
Cations are known to mediate diverse interactions in nucleic acids duplexes but they are critical in the arrangement of four-stranded structures. Here, we use all-atom molecular dynamics simulations with explicit solvent to analyse the mechanical unfolding of representative intramolecular G-quadruplex structures: a parallel, a hybrid and an antiparallel DNA and a parallel RNA, in the presence of stabilising cations. We confirm the stability of these conformations in the presence of [Formula: see text] central ions and observe distortions from the tetrad topology in their absence. Force-induced unfolding dynamics is then investigated. We show that the unfolding events in the force-extension curves are concomitant to the loss of coordination between the central ions and the guanines of the G-quadruplex. We found lower ruptures forces for the parallel configuration with respect to the antiparallel one, while the behaviour of the force pattern of the parallel RNA appears similar to the parallel DNA. We anticipate that our results will be essential to interpret the fine structure rupture profiles in stretching assays at high resolution and will shed light on the mechanochemical activity of G-quadruplex-binding machinery
Development of a species-specific coproantigen ELISA for human taenia solium taeniasis
Taenia solium causes human neurocysticercosis and is endemic in underdeveloped countries where backyard pig keeping is common. Microscopic fecal diagnostic methods for human T. solium taeniasis are not very sensitive, and Taenia saginata and Taenia solium eggs are indistinguishable under the light microscope. Coproantigen (CoAg) ELISA methods are very sensitive, but currently only genus (Taenia) specific. This paper describes the development of a highly species-specific coproantigen ELISA test to detect T. solium intestinal taeniasis. Sensitivity was maintained using a capture antibody of rabbit IgG against T. solium adult whole worm somatic extract, whereas species specificity was achieved by utilization of an enzyme-conjugated rabbit IgG against T. solium adult excretory-secretory (ES) antigen. A known panel of positive and negative human fecal samples was tested with this hybrid sandwich ELISA. The ELISA test gave 100% specificity and 96.4% sensitivity for T. solium tapeworm carriers (N = 28), with a J index of 0.96. This simple ELISA incorporating anti-adult somatic and anti-adult ES antibodies provides the first potentially species-specific coproantigen test for human T. solium taeniasis
Critical Kauffman networks under deterministic asynchronous update
We investigate the influence of a deterministic but non-synchronous update on
Random Boolean Networks, with a focus on critical networks. Knowing that
``relevant components'' determine the number and length of attractors, we focus
on such relevant components and calculate how the length and number of
attractors on these components are modified by delays at one or more nodes. The
main findings are that attractors decrease in number when there are more
delays, and that periods may become very long when delays are not integer
multiples of the basic update step.Comment: 8 pages, 3 figures, submitted to a journa
Testing matter effects in propagation of atmospheric and long-baseline neutrinos
We quantify our current knowledge of the size and flavor structure of the
matter effects in the evolution of atmospheric and long-baseline neutrinos
based solely on the analysis of the corresponding neutrino data. To this aim we
generalize the matter potential of the Standard Model by rescaling its
strength, rotating it away from the e-e sector, and rephasing it with respect
to the vacuum term. This phenomenological parametrization can be easily
translated in terms of non-standard neutrino interactions in matter. We show
that in the most general case, the strength of the potential cannot be
determined solely by atmospheric and long-baseline data. However its flavor
composition is very much constrained and the present determination of the
neutrino masses and mixing is robust under its presence. We also present an
update of the constraints arising from this analysis in the particular case in
which no potential is present in the e-mu and e-tau sectors. Finally we
quantify to what degree in this scenario it is possible to alleviate the
tension between the oscillation results for neutrinos and antineutrinos in the
MINOS experiment and show the relevance of the high energy part of the spectrum
measured at MINOS.Comment: PDFLaTeX file using JHEP3 class, 25 pages, 7 figures included.
Accepted for publication in JHE
Phylogenetic And Molecular Variability Studies Reveal A New Genetic Clade Of Citrus Leprosis Virus C
Conselho Nacional de Desenvolvimento CientÃfico e Tecnológico (CNPq)Citrus leprosis virus C (CiLV-C) causes a severe disease affecting citrus orchards in the Western hemisphere. This study reveals the molecular variability of the virus by analyzing four genomic regions (p29, p15, MP and RNA2-intergenic region) distributed over its two RNAs. Nucleotide diversity (pi) values were relatively low but statistically different over the analyzed genes and subpopulations, indicating their distinct evolutionary history. Values of pi(p29) and pi(MP) were higher than those of pi(p15) and pi(RNA2-IR), whereas pi(MP) was increased due to novel discovered isolates phylogenetically clustered in a divergent clade that we called SJP. Isolate BR_SP_SJP_01 RNA1 and RNA2 sequences, clade SJP, showed an identity of 85.6% and 88.4%, respectively, with those corresponding to CiLV-C, the type member of the genus Cilevirus, and its RNA2 5'-proximal region was revealed as a minor donor in a putative inter-clade recombination event. In addition to citrus, BR_SP_SJP_01 naturally infects the weed Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi mites. Our data demonstrated that negative selection was the major force operating in the evaluated viral coding regions and defined amino acids putatively relevant for the biological function of cilevirus proteins. This work provides molecular tools and sets up a framework for further epidemiological studies.8Conselho Nacional de Desenvolvimento Cientifico e Tecnologico [375843/2012-4, 481771/2013-1, 401564/2012-6]Fundacao de Apoio a Pesquisa no Estado de Sao Paulo [2012/18771-0, 2012/20667-7, 2014/08458-9]Conselho Nacional de Desenvolvimento CientÃfico e Tecnológico (CNPq
Patterns of Individual Shopping Behavior
Much of economic theory is built on observations of aggregate, rather than
individual, behavior. Here, we present novel findings on human shopping
patterns at the resolution of a single purchase. Our results suggest that much
of our seemingly elective activity is actually driven by simple routines. While
the interleaving of shopping events creates randomness at the small scale, on
the whole consumer behavior is largely predictable. We also examine
income-dependent differences in how people shop, and find that wealthy
individuals are more likely to bundle shopping trips. These results validate
previous work on mobility from cell phone data, while describing the
unpredictability of behavior at higher resolution.Comment: 4 pages, 5 figure
Effects of intermediate scales on renormalization group running of fermion observables in an SO(10) model
In the context of non-supersymmetric SO(10) models, we analyze the
renormalization group equations for the fermions (including neutrinos) from the
GUT energy scale down to the electroweak energy scale, explicitly taking into
account the effects of an intermediate energy scale induced by a Pati--Salam
gauge group. To determine the renormalization group running, we use a numerical
minimization procedure based on a nested sampling algorithm that randomly
generates the values of 19 model parameters at the GUT scale, evolves them, and
finally constructs the values of the physical observables and compares them to
the existing experimental data at the electroweak scale. We show that the
evolved fermion masses and mixings present sizable deviations from the values
obtained without including the effects of the intermediate scale.Comment: Comments: 20 pages, 3 figures. Final version published in JHE
Direct determination of the solar neutrino fluxes from solar neutrino data
We determine the solar neutrino fluxes from a global analysis of the solar
and terrestrial neutrino data in the framework of three-neutrino mixing. Using
a Bayesian approach we reconstruct the posterior probability distribution
function for the eight normalization parameters of the solar neutrino fluxes
plus the relevant masses and mixing, with and without imposing the luminosity
constraint. This is done by means of a Markov Chain Monte Carlo employing the
Metropolis-Hastings algorithm. We also describe how these results can be
applied to test the predictions of the Standard Solar Models. Our results show
that, at present, both models with low and high metallicity can describe the
data with good statistical agreement.Comment: 24 pages, 1 table, 7 figures. Acknowledgments correcte
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