64 research outputs found
Brownian Motion of Black Holes in Dense Nuclei
We evaluate the Brownian motion of a massive particle ("black hole") at the
center of a galaxy using N-body simulations. Our galaxy models have power-law
central density cusps like those observed at the centers of elliptical
galaxies. The simulations show that the black hole achieves a steady-state
kinetic energy that is substantially different than would be predicted based on
the properties of the galaxy model in the absence of the black hole. The reason
appears to be that the black hole responds to stars whose velocities have
themselves been raised by the presence of the black hole. Over a wide range of
density slopes and black hole masses, the black hole's mean kinetic energy is
equal to what would be predicted under the assumption that it is in energy
equipartition with stars lying within a distance ~r_h/2 from it, where r_h is
the black hole's influence radius. The dependence of the Brownian velocity on
black hole mass is approximately ~ 1/M^{1/(3-gamma)} with gamma the
power-law index of the stellar density profile, rho~1/r^gamma. This is less
steep than the 1/M dependence predicted in a model where the effect of the
black hole on the stellar velocities is ignored. The influence of a stellar
mass spectrum on the black hole's Brownian motion is also evaluated and found
to be consistent with predictions from Chandrasekhar's theory. We use these
results to derive a probability function for the mass of the Milky Way black
hole based on a measurement of its proper motion velocity. Interesting
constraints on M will require a velocity resolution exceeding 0.5 km/s.Comment: 11 pages, uses emulateapj.st
The Geometry of the Catalytic Active Site in [FeFe]-hydrogenases is Determined by Hydrogen Bonding and Proton Transfer
[FeFe]-hydrogenases are efficient metalloenzymes that catalyze the oxidation and evolution of molecular hydrogen, H2. They serve as a blueprint for the design of synthetic H2-forming catalysts. [FeFe]-hydrogenases harbor a six-iron cofactor that comprises a [4Fe-4S] cluster and a unique diiron site with cyanide, carbonyl, and hydride ligands. To address the ligand dynamics in catalytic turnover and upon carbon monoxide (CO) inhibition, we replaced the native aminodithiolate group of the diiron site by synthetic dithiolates, inserted into wild-type and amino acid variants of the [FeFe]-hydrogenase HYDA1 from Chlamydomonas reinhardtii. The reactivity with H2 and CO was characterized using in situ and transient infrared spectroscopy, protein crystallography, quantum chemical calculations, and kinetic simulations. All cofactor variants adopted characteristic populations of reduced species in the presence of H2 and showed significant changes in CO inhibition and reactivation kinetics. Differences were attributed to varying interactions between polar ligands and the dithiolate head group and/or the environment of the cofactor (i.e., amino acid residues and water molecules). The presented results show how catalytically relevant intermediates are stabilized by inner-sphere hydrogen bonding suggesting that the role of the aminodithiolate group must not be restricted to proton transfer. These concepts may inspire the design of improved enzymes and biomimetic H2-forming catalysts
Revealing Hidden Potentials of the q-Space Signal in Breast Cancer
Mammography screening for early detection of breast lesions currently suffers
from high amounts of false positive findings, which result in unnecessary
invasive biopsies. Diffusion-weighted MR images (DWI) can help to reduce many
of these false-positive findings prior to biopsy. Current approaches estimate
tissue properties by means of quantitative parameters taken from generative,
biophysical models fit to the q-space encoded signal under certain assumptions
regarding noise and spatial homogeneity. This process is prone to fitting
instability and partial information loss due to model simplicity. We reveal
unexplored potentials of the signal by integrating all data processing
components into a convolutional neural network (CNN) architecture that is
designed to propagate clinical target information down to the raw input images.
This approach enables simultaneous and target-specific optimization of image
normalization, signal exploitation, global representation learning and
classification. Using a multicentric data set of 222 patients, we demonstrate
that our approach significantly improves clinical decision making with respect
to the current state of the art.Comment: Accepted conference paper at MICCAI 201
Yeast mother cell-specific ageing, genetic (in)stability, and the somatic mutation theory of ageing
Yeast mother cell-specific ageing is characterized by a limited capacity to produce daughter cells. The replicative lifespan is determined by the number of cell cycles a mother cell has undergone, not by calendar time, and in a population of cells its distribution follows the Gompertz law. Daughter cells reset their clock to zero and enjoy the full lifespan characteristic for the strain. This kind of replicative ageing of a cell population based on asymmetric cell divisions is investigated as a model for the ageing of a stem cell population in higher organisms. The simple fact that the daughter cells can reset their clock to zero precludes the accumulation of chromosomal mutations as the cause of ageing, because semiconservative replication would lead to the same mutations in the daughters. However, nature is more complicated than that because, (i) the very last daughters of old mothers do not reset the clock; and (ii) mutations in mitochondrial DNA could play a role in ageing due to the large copy number in the cell and a possible asymmetric distribution of damaged mitochondrial DNA between mother and daughter cell. Investigation of the loss of heterozygosity in diploid cells at the end of their mother cell-specific lifespan has shown that genomic rearrangements do occur in old mother cells. However, it is not clear if this kind of genomic instability is causative for the ageing process. Damaged material other than DNA, for instance misfolded, oxidized or otherwise damaged proteins, seem to play a major role in ageing, depending on the balance between production and removal through various repair processes, for instance several kinds of proteolysis and autophagy. We are reviewing here the evidence for genetic change and its causality in the mother cell-specific ageing process of yeast
Spectroscopical Investigations on the Redox Chemistry of [FeFe]-Hydrogenases in the Presence of Carbon Monoxide
[FeFe]-hydrogenases efficiently catalyzes hydrogen conversion at a unique [4Fe–4S]-[FeFe] cofactor, the so-called H-cluster. The catalytic reaction occurs at the diiron site, while the [4Fe–4S] cluster functions as a redox shuttle. In the oxidized resting state (Hox), the iron ions of the diiron site bind one cyanide (CN−) and carbon monoxide (CO) ligand each and a third carbonyl can be found in the Fe–Fe bridging position (µCO). In the presence of exogenous CO, A fourth CO ligand binds at the diiron site to form the oxidized, CO-inhibited H-cluster (Hox-CO). We investigated the reduced, CO-inhibited H-cluster (Hred´-CO) in this work. The stretching vibrations of the diatomic ligands were monitored by attenuated total reflection Fourier-transform infrared spectroscopy (ATR FTIR). Density functional theory (DFT) at the TPSSh/TZVP level was employed to analyze the cofactor geometry, as well as the redox and protonation state of the H-cluster. Selective 13CO isotope editing, spectro-electrochemistry, and correlation analysis of IR data identified a one-electron reduced, protonated [4Fe–4S] cluster and an apical CN− ligand at the diiron site in Hred´-CO. The reduced, CO-inhibited H-cluster forms independently of the sequence of CO binding and cofactor reduction, which implies that the ligand rearrangement at the diiron site upon CO inhibition is independent of the redox and protonation state of the [4Fe–4S] cluster. The relation of coordination dynamics to cofactor redox and protonation changes in hydrogen conversion catalysis and inhibition is discussed
Protonengekoppelte Reduktion des katalytischen [4Fe-4S]-Zentrums in [FeFe]-Hydrogenasen
In der Natur katalysieren [FeFe]-Hydrogenasen die Abgabe und Aufnahme von
molekularem Wasserstoff (H2) an einem einzigartigen Eisen-Schwefel-Kofaktor.
Das geringe elektrochemische Überpotential in der Wasserstoffabgabe-Reaktion
macht die [FeFe]-Hydrogenasen zu einem hervorragenden Beispiel für effiziente
Biokatalyse. Gegenwärtig sind die molekularen Details des Wasserstoffumsatzes
jedoch noch nicht vollständig verstanden. Daher adressieren wir in dieser
Untersuchung die initiale Reduktion des katalytischen Zentrums der
[FeFe]-Hydrogenasen mittels Infrarotspektroskopie und Elektrochemie und
zeigen, dass der reduzierte Zustand Hred′ durch protonengekoppelten
Elektronentransport gebildet wird. Ladungskompensation bindet das
überschüssige Elektron am [4Fe-4S]-Zentrum und führt zu einer Stabilisierung
der konservativen Konfiguration des [FeFe]-Kofaktors. Die Rolle von Hred′ beim
Wasserstoffumsatz und mögliche Auswirkungen auf den katalytischen Mechanismus
werden diskutiert. Es liegt nahe, dass die Regulation elektronischer
Eigenschaften in der Umgebung von metallischen Kofaktoren die Grundlage für
Multielektronenprozesse bildet
A new dominant peroxiredoxin allele identified by whole-genome re-sequencing of random mutagenized yeast causes oxidant-resistance and premature aging
The
combination of functional genomics with next generation sequencing
facilitates new experimental strategies for addressing complex biological
phenomena. Here, we report the identification of a gain-of-function allele
of peroxiredoxin (thioredoxin peroxidase, Tsa1p) via whole-genome
re-sequencing of a dominantSaccharomyces cerevisiae mutant obtained
by chemical mutagenesis. Yeast strain K6001, a screening system for
lifespan phenotypes, was treated with ethyl methanesulfonate (EMS). We
isolated an oxidative stress-resistant mutant (B7) which transmitted this
phenotype in a background-independent, monogenic and dominant way. By
massive parallel pyrosequencing, we generated an 38.8 fold whole-genome
coverage of the strains, which differed in 12,482 positions from the
reference (S288c) genome. Via a subtraction strategy, we could narrow this
number to 13 total and 4 missense nucleotide variations that were specific for
the mutant. Via expression in wild type backgrounds, we show that one of
these mutations, exchanging a residue in the peroxiredoxin Tsa1p, was
responsible for the mutant phenotype causing background-independent
dominant oxidative stress-resistance. These effects were not provoked by
altered Tsa1p levels, nor could they be simulated by deletion,
haploinsufficiency or over-expression of the wild-type allele. Furthermore,
via both a mother-enrichment technique and a micromanipulation assay, we
found a robust premature aging phenotype of this oxidant-resistant strain.
Thus, TSA1-B7 encodes for a novel dominant form of peroxiredoxin,
and establishes a new connection between oxidative stress and aging. In
addition, this study shows that the re-sequencing of entire genomes is
becoming a promising alternative for the identification of functional
alleles in approaches of classic molecular genetics
Protonation/reduction dynamics at the [4Fe–4S] cluster of the hydrogen-forming cofactor in [FeFe]-hydrogenases
The [FeFe]-hydrogenases of bacteria and algae are the most efficient hydrogen
conversion catalysts in nature. Their active-site cofactor (H-cluster)
comprises a [4Fe–4S] cluster linked to a unique diiron site that binds three
carbon monoxide (CO) and two cyanide (CN−) ligands. Understanding microbial
hydrogen conversion requires elucidation of the interplay of proton and
electron transfer events at the H-cluster. We performed real-time spectroscopy
on [FeFe]-hydrogenase protein films under controlled variation of atmospheric
gas composition, sample pH, and reductant concentration. Attenuated total
reflection Fourier-transform infrared spectroscopy was used to monitor shifts
of the CO/CN− vibrational bands in response to redox and protonation changes.
Three different [FeFe]-hydrogenases and several protein and cofactor variants
were compared, including element and isotopic exchange studies. A protonated
equivalent (HoxH) of the oxidized state (Hox) was found, which preferentially
accumulated at acidic pH and under reducing conditions. We show that the one-
electron reduced state Hred′ represents an intrinsically protonated species.
Interestingly, the formation of HoxH and Hred′ was independent of the
established proton pathway to the diiron site. Quantum chemical calculations
of the respective CO/CN− infrared band patterns favored a cysteine ligand of
the [4Fe–4S] cluster as the protonation site in HoxH and Hred′. We propose
that proton-coupled electron transfer facilitates reduction of the [4Fe–4S]
cluster and prevents premature formation of a hydride at the catalytic diiron
site. Our findings imply that protonation events both at the [4Fe–4S] cluster
and at the diiron site of the H-cluster are important in the hydrogen
conversion reaction of [FeFe]-hydrogenases
The control of translational accuracy is a determinant of healthy ageing in yeast
Life requires the maintenance of molecular function in the face of stochastic processes that tend to adversely affect macromolecular integrity. This is particularly relevant during ageing, as many cellular functions decline with age, including growth, mitochondrial function and energy metabolism. Protein synthesis must deliver functional proteins at all times, implying that the effects of protein synthesis errors like amino acid misincorporation and stop-codon read-through must be minimized during ageing. Here we show that loss of translational accuracy accelerates the loss of viability in stationary phase yeast. Since reduced translational accuracy also reduces the folding competence of at least some proteins, we hypothesize that negative interactions between translational errors and age-related protein damage together overwhelm the cellular chaperone network. We further show that multiple cellular signalling networks control basal error rates in yeast cells, including a ROS signal controlled by mitochondrial activity, and the Ras pathway. Together, our findings indicate that signalling pathways regulating growth, protein homeostasis and energy metabolism may jointly safeguard accurate protein synthesis during healthy ageing
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