788 research outputs found
The rapid formation a large rotating disk galaxy three billion years after the Big Bang
[Abridged] Over the past two decades observations and theoretical simulations
have established a global frame-work of galaxy formation and evolution in the
young Universe. Galaxies formed as baryonic gas cooled at the centres of
collapsing dark matter halos. Mergers of halos led to the build up of galaxy
mass. A major step forward in understanding these issues requires well resolved
physical information on individual galaxies at high redshift. Here we report
adaptive optics, spectroscopic observations of a representative luminous star
forming galaxy when the Universe was only twenty percent of its age. The
superior angular resolution of these data reveals the physical and dynamical
properties of a high redshift galaxy in unprecedented detail. A large and
massive rotating proto-disk is channelling gas towards a growing central
stellar bulge hosting an accreting massive black hole.Comment: Narure, accepted (Released Aug 17th
Gas accretion as the origin of chemical abundance gradients in distant galaxies
It has recently been suggested that galaxies in the early Universe can grow
through the accretion of cold gas, and that this may have been the main driver
of star formation and stellar mass growth. Because the cold gas is essentially
primordial, it has a very low abundance of elements heavier than helium
(metallicity). As it is funneled to the centre of a galaxy, it will lead the
central gas having an overall lower metallicity than gas further from the
centre, because the gas further out has been enriched by supernovae and stellar
winds, and not diluted by the primordial gas. Here we report chemical
abundances across three rotationally-supported star-forming galaxies at z~3,
only 2 Gyr after the Big Bang. We find an 'inverse' gradient, with the central,
star forming regions having a lower metallicity than less active ones, opposite
to what is seen in local galaxies. We conclude that the central gas has been
diluted by the accretion of primordial gas, as predicted by 'cold flow' models.Comment: To Appear in Nature Oct 14, 2010; Supplementary Information included
her
High star formation rates as the origin of turbulence in early and modern disk galaxies
High spatial and spectral resolution observations of star formation and
kinematics in early galaxies have shown that two-thirds are massive rotating
disk galaxies with the remainder being less massive non-rotating objects. The
line of sight averaged velocity dispersions are typically five times higher
than in today's disk galaxies. This has suggested that
gravitationally-unstable, gas-rich disks in the early Universe are fuelled by
cold, dense accreting gas flowing along cosmic filaments and penetrating hot
galactic gas halos. However these accreting flows have not been observed, and
cosmic accretion cannot power the observed level of turbulence. Here we report
on a new sample of rare high-velocity-dispersion disk galaxies we have
discovered in the nearby Universe where cold accretion is unlikely to drive
their high star-formation rates. We find that the velocity dispersion is most
fundamentally correlated with their star-formation rates, and not their mass
nor gas fraction, which leads to a new picture where star formation itself is
the energetic driver of galaxy disk turbulence at all cosmic epochs.Comment: 9 pages, 2 figures, Supplimentary Info available at:
http://pulsar.swin.edu.au/~agreen/nature/sigma_mean_arXiv.pdf. Accepted for
publication in Natur
Causes of discontinuity of blood donation among donors in Shiraz, Iran: cross-sectional study
Invasion speeds for structured populations in fluctuating environments
We live in a time where climate models predict future increases in
environmental variability and biological invasions are becoming increasingly
frequent. A key to developing effective responses to biological invasions in
increasingly variable environments will be estimates of their rates of spatial
spread and the associated uncertainty of these estimates. Using stochastic,
stage-structured, integro-difference equation models, we show analytically that
invasion speeds are asymptotically normally distributed with a variance that
decreases in time. We apply our methods to a simple juvenile-adult model with
stochastic variation in reproduction and an illustrative example with published
data for the perennial herb, \emph{Calathea ovandensis}. These examples
buttressed by additional analysis reveal that increased variability in vital
rates simultaneously slow down invasions yet generate greater uncertainty about
rates of spatial spread. Moreover, while temporal autocorrelations in vital
rates inflate variability in invasion speeds, the effect of these
autocorrelations on the average invasion speed can be positive or negative
depending on life history traits and how well vital rates ``remember'' the
past
Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-depleted Murine Embryonic Stem Cells
Embryonic stem cells (ESC) have the potential to self-renew indefinitely and
to differentiate into any of the three germ layers. The molecular mechanisms
for self-renewal, maintenance of pluripotency and lineage specification are
poorly understood, but recent results point to a key role for epigenetic
mechanisms. In this study, we focus on quantifying the impact of histone 3
acetylation (H3K9,14ac) on gene expression in murine embryonic stem cells. We
analyze genome-wide histone acetylation patterns and gene expression profiles
measured over the first five days of cell differentiation triggered by
silencing Nanog, a key transcription factor in ESC regulation. We explore the
temporal and spatial dynamics of histone acetylation data and its correlation
with gene expression using supervised and unsupervised statistical models. On a
genome-wide scale, changes in acetylation are significantly correlated to
changes in mRNA expression and, surprisingly, this coherence increases over
time. We quantify the predictive power of histone acetylation for gene
expression changes in a balanced cross-validation procedure. In an in-depth
study we focus on genes central to the regulatory network of Mouse ESC,
including those identified in a recent genome-wide RNAi screen and in the
PluriNet, a computationally derived stem cell signature. We find that compared
to the rest of the genome, ESC-specific genes show significantly more
acetylation signal and a much stronger decrease in acetylation over time, which
is often not reflected in an concordant expression change. These results shed
light on the complexity of the relationship between histone acetylation and
gene expression and are a step forward to dissect the multilayer regulatory
mechanisms that determine stem cell fate.Comment: accepted at PLoS Computational Biolog
ACL graft re-rupture after double-bundle reconstruction: factors that influence the intra-articular pattern of injury
To determine the most common rupture patterns of previously reconstructed DB-ACL cases, seen at the time of revision surgery, and to determine the influence of age, gender, time between the initial ACL reconstruction and re-injury, tunnel angle and etiology of failure. Forty patients who presented for revision surgery after previous double-bundle ACL reconstruction were enrolled. Three orthopedic surgeons independently reviewed the arthroscopic videos and determined the rupture pattern of both the anteromedial and posterolateral grafts. The graft rupture pattern was then correlated with the previously mentioned factors. The most common injury pattern seen at the time of revision ACL surgery was mid-substance AM and PL bundle rupture. Factors that influenced the rupture pattern (proximal vs. mid-substance and distal rupture vs. elongated, but in continuity) were months between ACL reconstruction and re-injury (P = 0.002), the etiology of failure (traumatic vs. atraumatic) (P = 0.025) and the measured graft tunnel angle (P = 0.048). The most common pattern of graft re-rupture was mid-substance AM and mid-substance PL. As the length of time from the initial DB-ACL reconstruction to revision surgery increased, the pattern of injury more closely resembled that of the native ACL. Evaluation of patients who have undergone double-bundle ACL reconstruction, with a particular focus on graft maturity, mechanism of injury and femoral tunnel angles, and graft rupture pattern assists in preoperative planning for revision surger
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
Background: Phylogenetic studies using expressed sequence tags (EST) are becoming a standard approach to answer evolutionary questions. Such studies are usually based on large sets of newly generated, unannotated, and error-prone EST sequences from different species. A first crucial step in EST-based phylogeny reconstruction is to identify groups of orthologous sequences. From these data sets, appropriate target genes are selected, and redundant sequences are eliminated to obtain suitable sequence sets as input data for tree-reconstruction software. Generating such data sets manually can be very time consuming. Thus, software tools are needed that carry out these steps automatically. Results: We developed a flexible and user-friendly software pipeline, running on desktop machines or computer clusters, that constructs data sets for phylogenomic analyses. It automatically searches assembled EST sequences against databases of orthologous groups (OG), assigns ESTs to these predefined OGs, translates the sequences into proteins, eliminates redundant sequences assigned to the same OG, creates multiple sequence alignments of identified orthologous sequences and offers the possibility to further process this alignment in a last step by excluding potentially homoplastic sites and selecting sufficiently conserved parts. Our software pipeline can be used as it is, but it can also be adapted by integrating additional external programs. This makes the pipeline useful for non-bioinformaticians as well as to bioinformatic experts. The software pipeline is especially designed for ESTs, but it can also handle protein sequences.
Conclusion: OrthoSelect is a tool that produces orthologous gene alignments from assembled ESTs. Our tests show that OrthoSelect detects orthologs in EST libraries with high accuracy. In the absence of a gold standard for orthology prediction, we compared predictions by OrthoSelect to a manually created and published phylogenomic data set. Our tool was not only able to rebuild the data set with a specificity of 98%, but it detected four percent more orthologous sequences. Furthermore, the results OrthoSelect produces are in absolut agreement with the results of other programs, but our tool offers a significant speedup and additional functionality, e.g. handling of ESTs, computing sequence alignments, and refining them. To our knowledge, there is currently no fully automated and freely available tool for this purpose. Thus, OrthoSelect is a valuable tool for researchers in the field of phylogenomics who deal with large quantities of EST sequences. OrthoSelect is written
in Perl and runs on Linux/Mac OS X
The value of testicular ultrasound in the prediction of the type and size of testicular tumors
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