110 research outputs found
Gating-induced large aqueous volumetric remodeling and aspartate tolerance in the voltage sensor domain of Shaker K+ channels
IndexaciĂłn: Scopus.ACKNOWLEDGMENTS. We thank Chris Lingle and Yu Zhou (Washington University) for critical reading of the manuscript and Victoria Prado for Xenopus care and oocyte preparation. We also thank Millennium Scientific Initiative P029-022-F. This work was supported by Fondecyt Postdoctoral Grants 3170599 (to I.D.-F.) and 3160321 (to H.M.).Neurons encode electrical signals with critically tuned voltage-gated ion channels and enzymes. Dedicated voltage sensor domains (VSDs) in these membrane proteins activate coordinately with an unresolved structural change. Such change conveys the transmembrane translocation of four positively charged arginine side chains, the voltage-sensing residues (VSRs; R1âR4). Countercharges and lipid phosphohead groups likely stabilize these VSRs within the low-dielectric core of the protein. However, the role of hydration, a sign-independent charge stabilizer, remains unclear. We replaced all VSRs and their neighboring residues with negatively charged aspartates in a voltage-gated potassium channel. The ensuing mild functional effects indicate that hydration is also important in VSR stabilization. The voltage dependency of the VSR aspartate variants approached the expected arithmetic summation of charges at VSR positions, as if negative and positive side chains faced similar pathways. In contrast, aspartates introduced between R2 and R3 did not affect voltage dependence as if the side chains moved outside the electric field or together with it, undergoing a large displacement and volumetric remodeling. Accordingly, VSR performed osmotic work at both internal and external aqueous interfaces. Individual VSR contributions to volumetric works approached arithmetical additivity but were largely dissimilar. While R1 and R4 displaced small volumes, R2 and R3 volumetric works were massive and vectorially opposed, favoring large aqueous remodeling during VSD activation. These diverse volumetric works are, at least for R2 and R3, not compatible with VSR translocation across a unique stationary charge transfer center. Instead, VSRs may follow separated pathways across a fluctuating low-dielectric septum. © National Academy of Sciences. All rights reserved.https://www.pnas.org/content/115/32/820
A Computational Complexity Theory in Membrane Computing
In this paper, a computational complexity theory within the framework
of Membrane Computing is introduced. Polynomial complexity classes associated with
di erent models of cell-like and tissue-like membrane systems are de ned and the most
relevant results obtained so far are presented. Many attractive characterizations of P 6=
NP conjecture within the framework of a bio-inspired and non-conventional computing
model are deduced.Ministerio de EducaciĂłn y Ciencia TIN2006-13425Junta de AndalucĂa P08âTIC-0420
Azimuthal asymmetry in the risetime of the surface detector signals of the Pierre Auger Observatory
The azimuthal asymmetry in the risetime of signals in Auger surface detector
stations is a source of information on shower development. The azimuthal
asymmetry is due to a combination of the longitudinal evolution of the shower
and geometrical effects related to the angles of incidence of the particles
into the detectors. The magnitude of the effect depends upon the zenith angle
and state of development of the shower and thus provides a novel observable,
, sensitive to the mass composition of cosmic rays
above eV. By comparing measurements with predictions from
shower simulations, we find for both of our adopted models of hadronic physics
(QGSJETII-04 and EPOS-LHC) an indication that the mean cosmic-ray mass
increases slowly with energy, as has been inferred from other studies. However,
the mass estimates are dependent on the shower model and on the range of
distance from the shower core selected. Thus the method has uncovered further
deficiencies in our understanding of shower modelling that must be resolved
before the mass composition can be inferred from .Comment: Replaced with published version. Added journal reference and DO
MAPPING COMMUNITY INTEREST HABITATS IN THE COLUMBRETES ARCHIPELAGO, AN EXTRAORDINARY HOT SPOT OF BIODIVERSITY
The Columbretes Archipelago and their submerged surroundings are part of an unusual,
Pleistocene volcanic field located in the Western Mediterranean designated as a Site of
Community Importance (SCI) of the Natura 2000 Network. In the present study, 4 benthic
habitats of community interest (1110, 1170, 1180 and 8330) have been identified by analyzing
several sources of information. Generalized additive models (GAMs) have been used to model
the potential distribution of reefs (1170) and maërl beds (1110). Our results highlight the
diversity and extent of these habitats and allow comparisons to other marine SCIs of Spain. This
can be attributed to the variability of the environment of this site. The Columbretes Islands
combine a relatively shallow environment with volcanic structures, hydrothermalism with active
degassing, current-driven sedimentary lobes and the influence of inland flows. Understanding
high biodiversity spots is crucial as they offer natural laboratories to describe how ecosystems
respond to the effects of global change. The knowledge obtained will be of paramount
importance for the conservation of species and habitats. Furthermore, it will establish a
baseline for future monitoring and assist in the development of effective management plans
Calibration of the Logarithmic-Periodic Dipole Antenna (LPDA) Radio Stations at the Pierre Auger Observatory using an Octocopter
An in-situ calibration of a logarithmic periodic dipole antenna with a
frequency coverage of 30 MHz to 80 MHz is performed. Such antennas are part of
a radio station system used for detection of cosmic ray induced air showers at
the Engineering Radio Array of the Pierre Auger Observatory, the so-called
Auger Engineering Radio Array (AERA). The directional and frequency
characteristics of the broadband antenna are investigated using a remotely
piloted aircraft (RPA) carrying a small transmitting antenna. The antenna
sensitivity is described by the vector effective length relating the measured
voltage with the electric-field components perpendicular to the incoming signal
direction. The horizontal and meridional components are determined with an
overall uncertainty of 7.4^{+0.9}_{-0.3} % and 10.3^{+2.8}_{-1.7} %
respectively. The measurement is used to correct a simulated response of the
frequency and directional response of the antenna. In addition, the influence
of the ground conductivity and permittivity on the antenna response is
simulated. Both have a negligible influence given the ground conditions
measured at the detector site. The overall uncertainties of the vector
effective length components result in an uncertainty of 8.8^{+2.1}_{-1.3} % in
the square root of the energy fluence for incoming signal directions with
zenith angles smaller than 60{\deg}.Comment: Published version. Updated online abstract only. Manuscript is
unchanged with respect to v2. 39 pages, 15 figures, 2 table
Multi-resolution anisotropy studies of ultrahigh-energy cosmic rays detected at the Pierre Auger Observatory
We report a multi-resolution search for anisotropies in the arrival
directions of cosmic rays detected at the Pierre Auger Observatory with local
zenith angles up to and energies in excess of 4 EeV ( eV). This search is conducted by measuring the angular power spectrum
and performing a needlet wavelet analysis in two independent energy ranges.
Both analyses are complementary since the angular power spectrum achieves a
better performance in identifying large-scale patterns while the needlet
wavelet analysis, considering the parameters used in this work, presents a
higher efficiency in detecting smaller-scale anisotropies, potentially
providing directional information on any observed anisotropies. No deviation
from isotropy is observed on any angular scale in the energy range between 4
and 8 EeV. Above 8 EeV, an indication for a dipole moment is captured; while no
other deviation from isotropy is observed for moments beyond the dipole one.
The corresponding -values obtained after accounting for searches blindly
performed at several angular scales, are in the case of
the angular power spectrum, and in the case of the needlet
analysis. While these results are consistent with previous reports making use
of the same data set, they provide extensions of the previous works through the
thorough scans of the angular scales.Comment: Published version. Added journal reference and DOI. Added Report
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Ultrahigh-energy neutrino follow-up of Gravitational Wave events GW150914 and GW151226 with the Pierre Auger Observatory
On September 14, 2015 the Advanced LIGO detectors observed their first
gravitational-wave (GW) transient GW150914. This was followed by a second GW
event observed on December 26, 2015. Both events were inferred to have arisen
from the merger of black holes in binary systems. Such a system may emit
neutrinos if there are magnetic fields and disk debris remaining from the
formation of the two black holes. With the surface detector array of the Pierre
Auger Observatory we can search for neutrinos with energy above 100 PeV from
point-like sources across the sky with equatorial declination from about -65
deg. to +60 deg., and in particular from a fraction of the 90% confidence-level
(CL) inferred positions in the sky of GW150914 and GW151226. A targeted search
for highly-inclined extensive air showers, produced either by interactions of
downward-going neutrinos of all flavors in the atmosphere or by the decays of
tau leptons originating from tau-neutrino interactions in the Earth's crust
(Earth-skimming neutrinos), yielded no candidates in the Auger data collected
within s around or 1 day after the coordinated universal time (UTC)
of GW150914 and GW151226, as well as in the same search periods relative to the
UTC time of the GW candidate event LVT151012. From the non-observation we
constrain the amount of energy radiated in ultrahigh-energy neutrinos from such
remarkable events.Comment: Published version. Added journal reference and DOI. Added Report
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Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish
Zebrafish, a popular model for embryonic development and for modelling human diseases, has so far lacked a systematic functional annotation programme akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created the first central repository to store and process zebrafish developmental functional genomic data. Our Data Coordination Center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and reanalysed published genomics data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements in development, including novel classes with distinct features dependent on their activity in time and space. We delineated the distinction between regulatory elements active during zygotic genome activation and those active during organogenesis, identifying new aspects of how they relate to each other. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predict functional relationships between them beyond sequence similarity, extending the utility of zebrafish developmental genomics to mammals
Evidence for a mixed mass composition at the `ankle' in the cosmic-ray spectrum
We report a first measurement for ultra-high energy cosmic rays of the
correlation between the depth of shower maximum and the signal in the water
Cherenkov stations of air-showers registered simultaneously by the fluorescence
and the surface detectors of the Pierre Auger Observatory. Such a correlation
measurement is a unique feature of a hybrid air-shower observatory with
sensitivity to both the electromagnetic and muonic components. It allows an
accurate determination of the spread of primary masses in the cosmic-ray flux.
Up till now, constraints on the spread of primary masses have been dominated by
systematic uncertainties. The present correlation measurement is not affected
by systematics in the measurement of the depth of shower maximum or the signal
in the water Cherenkov stations. The analysis relies on general characteristics
of air showers and is thus robust also with respect to uncertainties in
hadronic event generators. The observed correlation in the energy range around
the `ankle' at differs significantly from
expectations for pure primary cosmic-ray compositions. A light composition made
up of proton and helium only is equally inconsistent with observations. The
data are explained well by a mixed composition including nuclei with mass . Scenarios such as the proton dip model, with almost pure compositions, are
thus disfavoured as the sole explanation of the ultrahigh-energy cosmic-ray
flux at Earth.Comment: Published version. Added journal reference and DOI. Added Report
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