149 research outputs found
RIM-Binding Protein 2 organizes Ca2+channel topography and regulates release probability and vesicle replenishment at a fast central synapse
RIM-Binding Protein 2 (RIM-BP2) is a multi-domain protein of the presynaptic active zone (AZ). By binding to Rab-interacting protein (RIM), bassoon and voltage-gated Ca²⁺channels (CaV), it is considered to be a central organizer of the topography of CaVand release sites of synaptic vesicles (SVs) at the AZ. Here, we investigated the role of RIM-BP2 at the endbulb of Held synapse of auditory nerve fibers with bushy cells of the cochlear nucleus, a fast relay of the auditory pathway with high release probability. Disruption of RIM-BP2 lowered release probability altering short-term plasticity and reduced evoked excitatory postsynaptic currents (EPSCs). Analysis of SV pool dynamics during high frequency train stimulation indicated a reduction of SVs with high release probability but an overall normal size of the readily releasable SV pool (RRP). The Ca2+-dependent fast component of SV replenishment after RRP depletion was slowed. Ultrastructural analysis by super-resolution light and electron microscopy revealed an impaired topography of presynaptic CaVand a reduction of docked and membrane-proximal SVs at the AZ. We conclude that RIM-BP2 organizes the topography of CaV, and promotes SV tethering and docking. This way RIM-BP2 is critical for establishing a high initial release probability as required to reliably signal sound onset information that we found to be degraded in bushy cells of RIM-BP2-deficient mice in vivo
Are there Local Minima in the Magnetic Monopole Potential in Compact QED?
We investigate the influence of the granularity of the lattice on the
potential between monopoles. Using the flux definition of monopoles we
introduce their centers of mass and are able to realize continuous shifts of
the monopole positions. We find periodic deviations from the -behavior of
the monopole-antimonopole potential leading to local extrema. We suppose that
these meta-stabilities may influence the order of the phase transition in
compact QED.Comment: 11 pages, 5 figure
Confinement effects on glass forming liquids probed by DMA
Many molecular glass forming liquids show a shift of the glass transition T-g
to lower temperatures when the liquid is confined into mesoporous host
matrices. Two contrary explanations for this effect are given in literature:
First, confinement induced acceleration of the dynamics of the molecules leads
to an effective downshift of T-g increasing with decreasing pore size. Second,
due to thermal mismatch between the liquid and the surrounding host matrix,
negative pressure develops inside the pores with decreasing temperature, which
also shifts T-g to lower temperatures. Here we present dynamic mechanical
analysis measurements of the glass forming liquid salol in Vycor and Gelsil
with pore sizes of d=2.6, 5.0 and 7.5 nm. The dynamic complex elastic
susceptibility data can be consistently described with the assumption of two
relaxation processes inside the pores: A surface induced slowed down relaxation
due to interaction with rough pore interfaces and a second relaxation within
the core of the pores. This core relaxation time is reduced with decreasing
pore size d, leading to a downshift of T-g proportional to 1/d in perfect
agreement with recent differential scanning calorimetry (DSC) measurements.
Thermal expansion measurements of empty and salol filled mesoporous samples
revealed that the contribution of negative pressure to the downshift of T-g is
small (<30%) and the main effect is due to the suppression of dynamically
correlated regions of size xi when the pore size xi approaches
Finite strain Landau theory of high pressure phase transformations
The properties of materials near structural phase transitions are often
successfully described in the framework of Landau theory. While the focus is
usually on phase transitions, which are induced by temperature changes
approaching a critical temperature T-c, here we will discuss structural phase
transformations driven by high hydrostatic pressure, as they are of major
importance for understanding processes in the interior of the earth. Since at
very high pressures the deformations of a material are generally very large,
one needs to apply a fully nonlinear description taking physical as well as
geometrical nonlinearities (finite strains) into account. In particular it is
necessary to retune conventional Landau theory to describe such phase
transitions. In Troster et al (2002 Phys. Rev. Lett. 88 55503) we constructed a
Landau-type free energy based on an order parameter part, an order
parameter-(finite) strain coupling and a nonlinear elastic term. This model
provides an excellent and efficient framework for the systematic study of phase
transformations for a wide range of materials up to ultrahigh pressures
Understanding public speakers’ performance: first contributions to support a computational approach
Communication is part of our everyday life and our ability to communicate can have a significant role in a variety of contexts in our personal, academic, and professional lives. For long, the characterization of what is a good communicator has been subject to research and debate by several areas, particularly in Education, with a focus on improving the performance of teachers. In this context, the literature suggests that the ability to communicate is not only defined by the verbal component, but also by a plethora of non-verbal contributions providing redundant or complementary information, and, sometimes, being the message itself. However, even though we can recognize a good or bad communicator, objectively, little is known about what aspects – and to what extent—define the quality of a presentation. The goal of this work is to create the grounds to support the study of the defining characteristics of a good communicator in a more systematic and objective form. To this end, we conceptualize and provide a first prototype for a computational approach to characterize the different elements that are involved in communication, from audiovisual data, illustrating the outcomes and applicability of the proposed methods on a video database of public speakers.publishe
Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized
Understanding protein structure is of crucial importance in science, medicine
and biotechnology. For about two decades, knowledge based potentials based on
pairwise distances -- so-called "potentials of mean force" (PMFs) -- have been
center stage in the prediction and design of protein structure and the
simulation of protein folding. However, the validity, scope and limitations of
these potentials are still vigorously debated and disputed, and the optimal
choice of the reference state -- a necessary component of these potentials --
is an unsolved problem. PMFs are loosely justified by analogy to the reversible
work theorem in statistical physics, or by a statistical argument based on a
likelihood function. Both justifications are insightful but leave many
questions unanswered. Here, we show for the first time that PMFs can be seen as
approximations to quantities that do have a rigorous probabilistic
justification: they naturally arise when probability distributions over
different features of proteins need to be combined. We call these quantities
reference ratio distributions deriving from the application of the reference
ratio method. This new view is not only of theoretical relevance, but leads to
many insights that are of direct practical use: the reference state is uniquely
defined and does not require external physical insights; the approach can be
generalized beyond pairwise distances to arbitrary features of protein
structure; and it becomes clear for which purposes the use of these quantities
is justified. We illustrate these insights with two applications, involving the
radius of gyration and hydrogen bonding. In the latter case, we also show how
the reference ratio method can be iteratively applied to sculpt an energy
funnel. Our results considerably increase the understanding and scope of energy
functions derived from known biomolecular structures
Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients: a pilot study
Co-infections with bacterial or fungal pathogens could be associated with severity and outcome of disease in COVID-19 patients. We, therefore, used a 16S and ITS-based sequencing approach to assess the biomass and composition of the bacterial and fungal communities in endotracheal aspirates of intubated COVID-19 patients. Our method combines information on bacterial and fungal biomass with community profiling, anticipating the likelihood of a co-infection is higher with (1) a high bacterial and/or fungal biomass combined with (2) predominance of potentially pathogenic microorganisms. We tested our methods on 42 samples from 30 patients. We observed a clear association between microbial outgrowth (high biomass) and predominance of individual microbial species. Outgrowth of pathogens was in line with the selective pressure of antibiotics received by the patient. We conclude that our approach may help to monitor the presence and predominance of pathogens and therefore the likelihood of co-infections in ventilated patients, which ultimately, may help to guide treatment
The Intracellular Virus-Containing Compartments in Primary Human Macrophages Are Largely Inaccessible to Antibodies and Small Molecules
HIV-1 assembly and release occurs at the plasma membrane of human T lymphocytes and model epithelial cell lines, whereas in macrophages intracellular sites of virus assembly or accumulation predominate. The origin of the intracellular virus-containing compartment (VCC) has been controversial. This compartment is enriched in markers of the multivesicular body, and has been described as a modified endosomal compartment. Several studies of this compartment have revealed the presence of small channels connecting to the plasma membrane, suggesting that instead of an endosomal origin the compartment is a modified plasma membrane compartment. If the compartment is accessible to the external environment, this would have important implications for antiviral immune responses and antiviral therapy. We performed a series of experiments designed to determine if the VCC in macrophages was open to the external environment and accessible to antibodies and small molecules. The majority of VCCs were found to be inaccessible to exogenously-applied antibodies to tetraspanins in the absence of membrane permeabilization, while tetraspanin staining was readily observed following membrane permeabilization. Cationized ferritin was utilized to stain the plasma membrane, and revealed that the majority of virus-containing compartments were inaccessible to ferritin. Low molecular weight dextrans could access only a very small percentage of VCCs, and these tended to be more peripheral compartments. We conclude that the VCCs in monocyte-derived human macrophages are heterogeneous, but the majority of VCCs are closed to the external environment
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