5,639 research outputs found
Using competition assays to quantitatively model cooperative binding by transcription factors and other ligands.
BACKGROUND: The affinities of DNA binding proteins for target sites can be used to model the regulation of gene expression. These proteins can bind to DNA cooperatively, strongly impacting their affinity and specificity. However, current methods for measuring cooperativity do not provide the means to accurately predict binding behavior over a wide range of concentrations.
METHODS: We use standard computational and mathematical methods, and develop novel methods as described in Results.
RESULTS: We explore some complexities of cooperative binding, and develop an improved method for relating in vitro measurements to in vivo function, based on ternary complex formation. We derive expressions for the equilibria among the various complexes, and explore the limitations of binding experiments that model the system using a single parameter. We describe how to use single-ligand binding and ternary complex formation in tandem to determine parameters that have thermodynamic relevance. We develop an improved method for finding both single-ligand dissociation constants and concentrations simultaneously. We show how the cooperativity factor can be found when only one of the single-ligand dissociation constants can be measured.
CONCLUSIONS: The methods that we develop constitute an optimized approach to accurately model cooperative binding.
GENERAL SIGNIFICANCE: The expressions and methods we develop for modeling and analyzing DNA binding and cooperativity are applicable to most cases where multiple ligands bind to distinct sites on a common substrate. The parameters determined using these methods can be fed into models of higher-order cooperativity to increase their predictive power
Signatures of multiple stellar populations in unresolved extragalactic globular/ young massive star clusters
We present an investigation of potential signatures of the formation of
multiple stellar populations in recently formed extragalactic star clusters.
All of the Galactic globular clusters for which good samples of individual
stellar abundances are available show evidence for multiple populations. This
appears to require that multiple episodes of star formation and light element
enrichment are the norm in the history of a globular cluster. We show that
there are detectable observational signatures of multiple formation events in
the unresolved spectra of massive, young extragalactic star clusters. We
present the results of a pilot program to search for one of the cleanest
signatures that we identify - the combined presence of emission lines from a
very recently formed population and absorption lines from a somewhat older
population. A possible example of such a system is identified in the Antennae
galaxies. This source's spectrum shows evidence of two stellar populations with
ages of 8 Myr and 80 Myr. Further investigation shows that these populations
are in fact physically separated, but only by a projected distance of 59 pc. We
show that the clusters are consistent with being bound and discuss the
possibility that their coalescence could result in a single globular cluster
hosting multiple stellar populations. While not the prototypical system
proposed by most theories of the formation of multiple populations in clusters,
the detection of this system in a small sample is both encouraging and
interesting. Our investigation suggests that expanded surveys of massive young
star clusters should detect more clusters with such signatures.Comment: 11 pages, 7 figures: accepted for publication in Ap
Continuing the education of autistic pupils while focusing on family wellbeing during the Coronavirus Pandemic
This advice is given in the form of numbered points in no
particular order. Some will be very relevant and useful to
some autistic children and young people and their families
and others will not. It is for the reader to select those that make most sense and seem worth trying. As this document was developed at the start of the pandemic lockdown, transition back in to school /college was not then at
the top of the priority list. Supporting learners going back
into schools and colleges which may look very different
from their pre pandemic presentation is clearly an important consideration now. The first bullet point raises this
concern which is unpacked further later in the document
Radio Galaxy Clustering at z~0.3
Radio galaxies are uniquely useful as probes of large-scale structure as
their uniform identification with giant elliptical galaxies out to high
redshift means that the evolution of their bias factor can be predicted. As the
initial stage in a project to study large-scale structure with radio galaxies
we have performed a small redshift survey, selecting 29 radio galaxies in the
range 0.19<z<0.45 from a contiguous 40 square degree area of sky. We detect
significant clustering within this sample. The amplitude of the two-point
correlation function we measure is consistent with no evolution from the local
(z<0.1) value. This is as expected in a model in which radio galaxy hosts form
at high redshift and thereafter obey a continuity equation, although the
signal:noise of the detection is too low to rule out other models. Larger
surveys out to z~1 should reveal the structures of superclusters at
intermediate redshifts and strongly constrain models for the evolution of
large-scale structure.Comment: 7 pages, 3 figures, accepted by ApJ Letter
Limits on [OIII] 5007 emission from NGC4472's globular clusters: constraints on planetary nebulae and ultraluminous black hole X-ray binaries in globular clusters
We have searched for [OIII] 5007 emission in high resolution spectroscopic
data from Flames/Giraffe VLT observations of 174 massive globular clusters
(GCs) in NGC4472. No planetary nebulae (PNe) are observed in these clusters,
constraining the number of PNe per bolometric luminosity,
\alpha<0.8*10^{-7}PN/L_{\odot}. This is significantly lower than the rate
predicted from stellar evolution, if all stars produce PNe. Comparing our
results to populations of PNe in galaxies, we find most galaxies have a higher
\alpha than these GCs (more PNe per bolometric luminosity - though some massive
early-type galaxies do have similarly low \alpha). The low \alpha required in
these GCs suggests that the number of PNe per bolometric luminosity does not
increase strongly with decreasing mass or metallicity of the stellar
population. We find no evidence for correlations between the presence of known
GC PNe and either the presence of low mass X-ray binaries (LMXBs) or the
stellar interaction rates in the GCs. This, and the low \alpha observed,
suggests that the formation of PNe may not be enhanced in tight binary systems.
These data do identify one [OIII] emission feature, this is the (previously
published) broad [OIII] emission from the cluster RZ 2109. This emission is
thought to originate from the LMXB in this cluster, which is accreting at
super-Eddington rates. The absence of any similar [OIII] emission from the
other clusters favors the hypothesis that this source is a black hole LMXB,
rather than a neutron star LMXB with significant geometric beaming of its X-ray
emission.Comment: 10 pages, 3 figures, accepted for publication in Ap
Large Surveys in Cosmology: The Changing Sociology
Galaxy redshift surveys and Cosmic Microwave Background experiments are
undertaken with larger and larger teams, in a fashion reminiscent of particle
physics experiments and the human genome projects. We discuss the role of young
researchers, the issue of multiple authorship, and ways to communicate
effectively in teams of tens to hundreds of collaborators.Comment: Invited article for "Organizations and Strategies in Astronomy II",
ed. A. Heck, Kluwer Acad. Publ., in press (7 pages, no figures
The finite size effect of galaxies on the cosmic virial theorem and the pairwise peculiar velocity dispersions
We discuss the effect of the finite size of galaxies on estimating
small-scale relative pairwise peculiar velocity dispersions from the cosmic
virial theorem (CVT). Specifically we evaluate the effect by incorporating the
finite core radius in the two-point correlation function of mass, i.e.
and the effective gravitational force
softening on small scales. We analytically obtain the lowest-order
correction term for which is in quantitative agreement with the
full numerical evaluation. With a nonzero and/or the cosmic virial
theorem is no longer limited to the case of . We present accurate
fitting formulae for the CVT predicted pairwise velocity dispersion for the
case of . Compared with the idealistic point-mass approximation
(), the finite size effect can significantly reduce the small-scale
velocity dispersions of galaxies at scales much larger than and .
Even without considering the finite size of galaxies, nonzero values for
are generally expected, for instance, for cold dark matter (CDM) models with a
scale-invariant primordial spectrum. For these CDM models, a reasonable force
softening r_s\le 100 \hikpc would have rather tiny effect. We present the CVT
predictions for the small-scale pairwise velocity dispersion in the CDM models
normalized by the COBE observation. The implication of our results for
confrontation of observations of galaxy pair-wise velocity dispersions and
theoretical predictions of the CVT is also discussed.Comment: 18 pages. LaTeX text and 8 postcript figures. submitted to Ap
Hall Effect and Specific Resistance in Thin Evaporated Film of Fe, Co, Ni, Pd, and Pt
Further investigation of the Hall effect and specific resistance in thin films of iron, cobalt, nickel , palladium, and platinum give the following results: (1) the specific resistances of films deposited on a cool surface range from 4 to 30 times the accepted values for the corresponding bulk metals; (2) the Hall coefficients for the paramagnetic metals palladium and platinum are slightly smaller than bulk values: (3) the Hall coefficients for iron, cobalt, and nickel deposited on a cool surface are respectively 1.8 times, 5 times, and 7 times, the bulk values; (4) heating films of iron, cobalt, and nickel during deposition causes both the Hall coefficients and specific resistances to decrease almost to bulk values; (5) saturation of the Hall effect occurs for iron at a slightly lower magnetic field than for bulk values, for cobalt at 12500 as compared with 13500 for bulk, and for nickel at 2500 as compared with 6000 for bulk; and (6) microscopic investigation of nickel and cobalt shows some evidence of crystal structure
The Hall Effect and Specific Resistance in Evaporated Films of Nickel, Cobalt, Palladium and Platinum
Steinberg has shown that in the case of a thin film of metal formed by evaporation from a heated filament in a high vacuum the specific resistance and Hall coefficient are not the same as for the bulk metal. The metals investigated were silver, copper and iron, and in all of these the specific resistance was found to be about 1000% greater than in the metals in bulk. The Hall coefficients were slightly smaller for silver and copper than for the bulk metals, but for iron this coefficient was about 600% greater than the value generally accepted for iron. Also, the magnetic field necessary to produce saturation in the Hall electromotive force was considerably smaller for evaporated iron than for bulk iron. These differences he explained on the belief that evaporated films consist of granules not in such intimate contact as in the bulk metals which has the effect of increasing the resistance and changing the magnetic properties of the metal. On account of the bearing which this work might have on theories of magnetism and electric conduction, it seemed desirable to extend this investigation to other metals
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