1,393 research outputs found
Automatically extracting functionally equivalent proteins from SwissProt
In summary, FOSTA provides an automated analysis of annotations in UniProtKB/Swiss-Prot to enable groups of proteins already annotated as functionally equivalent, to be extracted. Our results demonstrate that the vast majority of UniProtKB/Swiss-Prot functional annotations are of high quality, and that FOSTA can interpret annotations successfully. Where FOSTA is not successful, we are able to highlight inconsistencies in UniProtKB/Swiss-Prot annotation. Most of these would have presented equal difficulties for manual interpretation of annotations. We discuss limitations and possible future extensions to FOSTA, and recommend changes to the UniProtKB/Swiss-Prot format, which would facilitate text-mining of UniProtKB/Swiss-Prot
Formation of Supermassive Black Holes
Evidence shows that massive black holes reside in most local galaxies.
Studies have also established a number of relations between the MBH mass and
properties of the host galaxy such as bulge mass and velocity dispersion. These
results suggest that central MBHs, while much less massive than the host (~
0.1%), are linked to the evolution of galactic structure. In hierarchical
cosmologies, a single big galaxy today can be traced back to the stage when it
was split up in hundreds of smaller components. Did MBH seeds form with the
same efficiency in small proto-galaxies, or did their formation had to await
the buildup of substantial galaxies with deeper potential wells? I briefly
review here some of the physical processes that are conducive to the evolution
of the massive black hole population. I will discuss black hole formation
processes for `seed' black holes that are likely to place at early cosmic
epochs, and possible observational tests of these scenarios.Comment: To appear in The Astronomy and Astrophysics Review. The final
publication is available at http://www.springerlink.co
MHD models of Pulsar Wind Nebulae
Pulsar Wind Nebulae (PWNe) are bubbles or relativistic plasma that form when
the pulsar wind is confined by the SNR or the ISM. Recent observations have
shown a richness of emission features that has driven a renewed interest in the
theoretical modeling of these objects. In recent years a MHD paradigm has been
developed, capable of reproducing almost all of the observed properties of
PWNe, shedding new light on many old issues. Given that PWNe are perhaps the
nearest systems where processes related to relativistic dynamics can be
investigated with high accuracy, a reliable model of their behavior is
paramount for a correct understanding of high energy astrophysics in general. I
will review the present status of MHD models: what are the key ingredients,
their successes, and open questions that still need further investigation.Comment: 18 pages, 5 figures, Invited Review, Proceedings of the "ICREA
Workshop on The High-Energy Emission from Pulsars and their Systems", Sant
Cugat, Spain, April 12-16, 201
Gravitational Waves from Gravitational Collapse
Gravitational wave emission from the gravitational collapse of massive stars
has been studied for more than three decades. Current state of the art
numerical investigations of collapse include those that use progenitors with
realistic angular momentum profiles, properly treat microphysics issues,
account for general relativity, and examine non--axisymmetric effects in three
dimensions. Such simulations predict that gravitational waves from various
phenomena associated with gravitational collapse could be detectable with
advanced ground--based and future space--based interferometric observatories.Comment: 68 pages including 13 figures; revised version accepted for
publication in Living Reviews in Relativity (http://www.livingreviews.org
ruvA Mutants that resolve Holliday junctions but do not reverse replication forks
RuvAB and RuvABC complexes catalyze branch migration and resolution of Holliday junctions (HJs) respectively. In addition to their action in the last steps of homologous recombination, they process HJs made by replication fork reversal, a reaction which occurs at inactivated replication forks by the annealing of blocked leading and lagging strand ends. RuvAB was recently proposed to bind replication forks and directly catalyze their conversion into HJs. We report here the isolation and characterization of two separation-of-function ruvA mutants that resolve HJs, based on their capacity to promote conjugational recombination and recombinational repair of UV and mitomycin C lesions, but have lost the capacity to reverse forks. In vivo and in vitro evidence indicate that the ruvA mutations affect DNA binding and the stimulation of RuvB helicase activity. This work shows that RuvA's actions at forks and at HJs can be genetically separated, and that RuvA mutants compromised for fork reversal remain fully capable of homologous recombination
Membranes by the Numbers
Many of the most important processes in cells take place on and across
membranes. With the rise of an impressive array of powerful quantitative
methods for characterizing these membranes, it is an opportune time to reflect
on the structure and function of membranes from the point of view of biological
numeracy. To that end, in this article, I review the quantitative parameters
that characterize the mechanical, electrical and transport properties of
membranes and carry out a number of corresponding order of magnitude estimates
that help us understand the values of those parameters.Comment: 27 pages, 12 figure
The Formation of the First Massive Black Holes
Supermassive black holes (SMBHs) are common in local galactic nuclei, and
SMBHs as massive as several billion solar masses already exist at redshift z=6.
These earliest SMBHs may grow by the combination of radiation-pressure-limited
accretion and mergers of stellar-mass seed BHs, left behind by the first
generation of metal-free stars, or may be formed by more rapid direct collapse
of gas in rare special environments where dense gas can accumulate without
first fragmenting into stars. This chapter offers a review of these two
competing scenarios, as well as some more exotic alternative ideas. It also
briefly discusses how the different models may be distinguished in the future
by observations with JWST, (e)LISA and other instruments.Comment: 47 pages with 306 references; this review is a chapter in "The First
Galaxies - Theoretical Predictions and Observational Clues", Springer
Astrophysics and Space Science Library, Eds. T. Wiklind, V. Bromm & B.
Mobasher, in pres
The Formation and Evolution of the First Massive Black Holes
The first massive astrophysical black holes likely formed at high redshifts
(z>10) at the centers of low mass (~10^6 Msun) dark matter concentrations.
These black holes grow by mergers and gas accretion, evolve into the population
of bright quasars observed at lower redshifts, and eventually leave the
supermassive black hole remnants that are ubiquitous at the centers of galaxies
in the nearby universe. The astrophysical processes responsible for the
formation of the earliest seed black holes are poorly understood. The purpose
of this review is threefold: (1) to describe theoretical expectations for the
formation and growth of the earliest black holes within the general paradigm of
hierarchical cold dark matter cosmologies, (2) to summarize several relevant
recent observations that have implications for the formation of the earliest
black holes, and (3) to look into the future and assess the power of
forthcoming observations to probe the physics of the first active galactic
nuclei.Comment: 39 pages, review for "Supermassive Black Holes in the Distant
Universe", Ed. A. J. Barger, Kluwer Academic Publisher
The Kidneys and Aldosterone/Mineralocorticoid Receptor System in Salt-Sensitive Hypertension
Strong evidence supports the ability of the aldosterone/mineralocorticoid receptor (MR) system to dominate long-term blood pressure control. It is also increasingly recognized as an important mediator of cardiovascular and renal diseases, particularly in the presence of excessive salt intake. In a subgroup of individuals with metabolic syndrome, adipocyte-derived aldosterone-releasing factors cause inappropriate secretion of aldosterone in the adrenal glands during salt loading, resulting in the development of salt-induced hypertension and cardiac and renal damage. On the other hand, emerging data reveal that aldosterone is not a sole regulator of MR activity. We have identified the signaling crosstalk between MR and small GTPase Rac1 as a novel pathway to facilitate MR signaling. Such a local control system for MR can also be relevant to the pathogenesis of salt-sensitive hypertension, and future studies will clarify the detailed mechanism for the intricate regulation of the aldosterone/MR cascade
Foundations of Black Hole Accretion Disk Theory
This review covers the main aspects of black hole accretion disk theory. We
begin with the view that one of the main goals of the theory is to better
understand the nature of black holes themselves. In this light we discuss how
accretion disks might reveal some of the unique signatures of strong gravity:
the event horizon, the innermost stable circular orbit, and the ergosphere. We
then review, from a first-principles perspective, the physical processes at
play in accretion disks. This leads us to the four primary accretion disk
models that we review: Polish doughnuts (thick disks), Shakura-Sunyaev (thin)
disks, slim disks, and advection-dominated accretion flows (ADAFs). After
presenting the models we discuss issues of stability, oscillations, and jets.
Following our review of the analytic work, we take a parallel approach in
reviewing numerical studies of black hole accretion disks. We finish with a few
select applications that highlight particular astrophysical applications:
measurements of black hole mass and spin, black hole vs. neutron star accretion
disks, black hole accretion disk spectral states, and quasi-periodic
oscillations (QPOs).Comment: 91 pages, 23 figures, final published version available at
http://www.livingreviews.org/lrr-2013-
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