2,167 research outputs found
Constraints on Fluid Dynamics from Equilibrium Partition Functions
We study the thermal partition function of quantum field theories on
arbitrary stationary background spacetime, and with arbitrary stationary
background gauge fields, in the long wavelength expansion. We demonstrate that
the equations of relativistic hydrodynamics are significantly constrained by
the requirement of consistency with any partition function. In examples at low
orders in the derivative expansion we demonstrate that these constraints
coincide precisely with the equalities between hydrodynamical transport
coefficients that follow from the local form of the second law of
thermodynamics. In particular we recover the results of Son and Surowka on the
chiral magnetic and chiral vorticity flows, starting from a local partition
function that manifestly reproduces the field theory anomaly, without making
any reference to an entropy current. We conjecture that the relations between
transport coefficients that follow from the second law of thermodynamics agree
to all orders in the derivative expansion with the constraints described in
this paper.Comment: Typos corrected, References adde
The Methylococcus capsulatus (Bath) Secreted Protein, MopE*, Binds Both Reduced and Oxidized Copper
Under copper limiting growth conditions the methanotrophic bacterium Methylococcus capsulatus (Bath) secrets essentially only one protein, MopE*, to the medium. MopE* is a copper-binding protein whose structure has been determined by X-ray crystallography. The structure of MopE* revealed a unique high affinity copper binding site consisting of two histidine imidazoles and one kynurenine, the latter an oxidation product of Trp130. In this study, we demonstrate that the copper ion coordinated by this strong binding site is in the Cu(I) state when MopE* is isolated from the growth medium of M. capsulatus. The conclusion is based on X-ray Near Edge Absorption spectroscopy (XANES), and Electron Paramagnetic Resonance (EPR) studies. EPR analyses demonstrated that MopE*, in addition to the strong copper-binding site, also binds Cu(II) at two weaker binding sites. Both Cu(II) binding sites have properties typical of non-blue type II Cu (II) centres, and the strongest of the two Cu(II) sites is characterised by a relative high hyperfine coupling of copper (
Investigating the Links between Lower Iron Status in Pregnancy and Respiratory Disease in Offspring Using Murine Models.
Maternal iron deficiency occurs in 40-50% of all pregnancies and is associated with an increased risk of respiratory disease and asthma in children. We used murine models to examine the effects of lower iron status during pregnancy on lung function, inflammation and structure, as well as its contribution to increased severity of asthma in the offspring. A low iron diet during pregnancy impairs lung function, increases airway inflammation, and alters lung structure in the absence and presence of experimental asthma. A low iron diet during pregnancy further increases these major disease features in offspring with experimental asthma. Importantly, a low iron diet increases neutrophilic inflammation, which is indicative of more severe disease, in asthma. Together, our data demonstrate that lower dietary iron and systemic deficiency during pregnancy can lead to physiological, immunological and anatomical changes in the lungs and airways of offspring that predispose to greater susceptibility to respiratory disease. These findings suggest that correcting iron deficiency in pregnancy using iron supplements may play an important role in preventing or reducing the severity of respiratory disease in offspring. They also highlight the utility of experimental models for understanding how iron status in pregnancy affects disease outcomes in offspring and provide a means for testing the efficacy of different iron supplements for preventing disease
Random walk with barriers: Diffusion restricted by permeable membranes
Restrictions to molecular motion by barriers (membranes) are ubiquitous in
biological tissues, porous media and composite materials. A major challenge is
to characterize the microstructure of a material or an organism
nondestructively using a bulk transport measurement. Here we demonstrate how
the long-range structural correlations introduced by permeable membranes give
rise to distinct features of transport. We consider Brownian motion restricted
by randomly placed and oriented permeable membranes and focus on the
disorder-averaged diffusion propagator using a scattering approach. The
renormalization group solution reveals a scaling behavior of the diffusion
coefficient for large times, with a characteristically slow inverse square root
time dependence. The predicted time dependence of the diffusion coefficient
agrees well with Monte Carlo simulations in two dimensions. Our results can be
used to identify permeable membranes as restrictions to transport in disordered
materials and in biological tissues, and to quantify their permeability and
surface area.Comment: 8 pages, 3 figures; origin of dispersion clarified, refs adde
Holographic Thermalization with Chemical Potential
We study the thermalization of a strongly coupled quantum field theory in the
presence of a chemical potential. More precisely, using the holographic
prescription, we calculate non- local operators such as two point function,
Wilson loop and entanglement entropy in a time- dependent background that
interpolates between AdSd+1 and AdSd+1 -Reissner-Nordstr\"om for d = 3, 4. We
find that it is the entanglement entropy that thermalizes the latest and thus
sets a time-scale for equilibration in the field theory. We study the
dependence of the thermalization time on the probe length and the chemical
potential. We find an interesting non-monotonic behavior. For a fixed small
value of T l and small values of \mu/T the thermalization time decreases as we
increase \mu/T, thus the plasma thermalizes faster. For large values of \mu/T
the dependence changes and the thermalization time increases with increasing
\mu/T . On the other hand, if we increase the value of T l this non-monotonic
behavior becomes less pronounced and eventually disappears indicating two
different regimes for the physics of thermalization: non-monotonic dependence
of the thermalization time on the chemical potential for T l << 1 and monotonic
for T l >> 1.Comment: 49 pages, v2 references added, typo correcte
Full-length Ebola glycoprotein accumulates in the endoplasmic reticulum
The Filoviridae family comprises of Ebola and Marburg viruses, which are known to cause lethal hemorrhagic fever. However, there is no effective anti-viral therapy or licensed vaccines currently available for these human pathogens. The envelope glycoprotein (GP) of Ebola virus, which mediates entry into target cells, is cytotoxic and this effect maps to a highly glycosylated mucin-like region in the surface subunit of GP (GP1). However, the mechanism underlying this cytotoxic property of GP is unknown. To gain insight into the basis of this GP-induced cytotoxicity, HEK293T cells were transiently transfected with full-length and mucin-deleted (Δmucin) Ebola GP plasmids and GP localization was examined relative to the nucleus, endoplasmic reticulum (ER), Golgi, early and late endosomes using deconvolution fluorescent microscopy. Full-length Ebola GP was observed to accumulate in the ER. In contrast, GPΔmucin was uniformly expressed throughout the cell and did not localize in the ER. The Ebola major matrix protein VP40 was also co-expressed with GP to investigate its influence on GP localization. GP and VP40 co-expression did not alter GP localization to the ER. Also, when VP40 was co-expressed with the nucleoprotein (NP), it localized to the plasma membrane while NP accumulated in distinct cytoplasmic structures lined with vimentin. These latter structures are consistent with aggresomes and may serve as assembly sites for filoviral nucleocapsids. Collectively, these data suggest that full-length GP, but not GPΔmucin, accumulates in the ER in close proximity to the nuclear membrane, which may underscore its cytotoxic property
Structural and biochemical characterization of the exopolysaccharide deacetylase Agd3 required for Aspergillus fumigatus biofilm formation
The exopolysaccharide galactosaminogalactan (GAG) is an important virulence factor of the fungal pathogen Aspergillus fumigatus. Deletion of a gene encoding a putative deacetylase, Agd3, leads to defects in GAG deacetylation, biofilm formation, and virulence. Here, we show that Agd3 deacetylates GAG in a metal-dependent manner, and is the founding member of carbohydrate esterase family CE18. The active site is formed by four catalytic motifs that are essential for activity. The structure of Agd3 includes an elongated substrate-binding cleft formed by a carbohydrate binding module (CBM) that is the founding member of CBM family 87. Agd3 homologues are encoded in previously unidentified putative bacterial exopolysaccharide biosynthetic operons and in other fungal genomes. The exopolysaccharide galactosaminogalactan (GAG) is an important virulence factor of the fungal pathogen Aspergillus fumigatus. Here, the authors study an A. fumigatus enzyme that deacetylates GAG in a metal-dependent manner and constitutes a founding member of a new carbohydrate esterase family.Bio-organic Synthesi
Towards the reconstruction of integrated genome-scale models of metabolism and gene expression
The reconstruction of integrated genome-scale models of metabolism and gene expression has been a challenge for a while now. In fact, various methods that allow integrating reconstructions of Transcriptional Regulatory Networks, gene expression data or both into Genome-Scale Metabolic Models have been proposed. Several of these methods are surveyed in this article, which allowed identifying their strengths and weaknesses concerning the reconstruction of integrated models for multiple prokaryotic organisms. Additionally, the main resources of regulatory information were also surveyed, as the existence of novel sources of regulatory information and gene expression data may contribute for the improvement of methodologies referred herein.This study was supported by the Portuguese Foundation for Science andTechnology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unit andBioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European RegionalDevelopment Fund under the scope of Norte2020-Programa Operacional Regional do Norte. Fernando Cruz holds a doctoral fellowship (SFRH/BD/139198/2018) funded by the FCT. The authors thank project SHIKIFACTORY100 - Modular cell factories for the production of 100 compounds from the shikimate pathway (814408) funded by the European Commission.info:eu-repo/semantics/publishedVersio
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