1,129 research outputs found
Monodisperse self-assembly in a model with protein-like interactions
We study the self-assembly behaviour of patchy particles with `protein-like'
interactions that can be considered as a minimal model for the assembly of
viral capsids and other shell-like protein complexes. We thoroughly explore the
thermodynamics and dynamics of self assembly as a function of the parameters of
the model and find robust assembly of all target structures considered. Optimal
assembly occurs in the region of parameter space where a free energy barrier
regulates the rate of nucleation, thus preventing the premature exhaustion of
the supply of monomers that can lead to the formation of incomplete shells. The
interactions also need to be specific enough to prevent the assembly of
malformed shells, but whilst maintaining kinetic accessibility. Free-energy
landscapes computed for our model have a funnel-like topography guiding the
system to form the target structure, and show that the torsional component of
the interparticle interactions prevents the formation of disordered aggregates
that would otherwise act as kinetic traps.Comment: 11 pages; 10 figure
The Function of Communities in Protein Interaction Networks at Multiple Scales
Background: If biology is modular then clusters, or communities, of proteins
derived using only protein interaction network structure should define protein
modules with similar biological roles. We investigate the link between
biological modules and network communities in yeast and its relationship to the
scale at which we probe the network.
Results: Our results demonstrate that the functional homogeneity of
communities depends on the scale selected, and that almost all proteins lie in
a functionally homogeneous community at some scale. We judge functional
homogeneity using a novel test and three independent characterizations of
protein function, and find a high degree of overlap between these measures. We
show that a high mean clustering coefficient of a community can be used to
identify those that are functionally homogeneous. By tracing the community
membership of a protein through multiple scales we demonstrate how our approach
could be useful to biologists focusing on a particular protein.
Conclusions: We show that there is no one scale of interest in the community
structure of the yeast protein interaction network, but we can identify the
range of resolution parameters that yield the most functionally coherent
communities, and predict which communities are most likely to be functionally
homogeneous.Comment: 26 pages, 6 figure
The self-assembly and evolution of homomeric protein complexes
We introduce a simple "patchy particle" model to study the thermodynamics and
dynamics of self-assembly of homomeric protein complexes. Our calculations
allow us to rationalize recent results for dihedral complexes. Namely, why
evolution of such complexes naturally takes the system into a region of
interaction space where (i) the evolutionarily newer interactions are weaker,
(ii) subcomplexes involving the stronger interactions are observed to be
thermodynamically stable on destabilization of the protein-protein interactions
and (iii) the self-assembly dynamics are hierarchical with these same
subcomplexes acting as kinetic intermediates.Comment: 4 pages, 4 figure
The Lyman Continuum Escape Fraction of The Cosmic Horseshoe: A Test of Indirect Estimates
High redshift star-forming galaxies are likely responsible for the
reionization of the Universe, yet direct detection of their escaping ionizing
(Lyman continuum) photons has proven to be extremely challenging. In this
study, we search for escaping Lyman continuum of the Cosmic Horseshoe, a
gravitationally lensed, star-forming galaxy at z=2.38 with a large
magnification of . Transmission at wavelengths of low ionization
interstellar absorption lines in the rest-frame ultraviolet suggest a patchy,
partially transparent interstellar medium. This makes it an ideal candidate for
direct detection of the Lyman continuum. We obtained a 10-orbit Hubble near-UV
image using the WFC3/UVIS F275W filter that probes wavelengths just below the
Lyman limit at the redshift of the Horseshoe in an attempt to detect escaping
Lyman continuum radiation. After fully accounting for the uncertainties in the
opacity of the intergalactic medium as well as accounting for the charge
transfer inefficiency in the WFC3 CCDs, we find a upper-limit for
the relative escape fraction of . This value is a factor of
five lower than the value (0.4) predicted by the 40\% transmission in the
low-ion absorption lines. We discuss the possible causes for this discrepancy
and consider the implications for future attempts at both direct Lyman
continuum detection as well as indirect estimates of the escape fraction.Comment: 10 pages, 8 Figures, submitted to the Astrophysical Journa
A New Collisional Ring Galaxy at z = 0.111: Auriga's Wheel
We report the serendipitous discovery of a collision ring galaxy, identified
as 2MASX J06470249+4554022, which we have dubbed 'Auriga's Wheel', found in a
SUPRIME-CAM frame as part of a larger Milky Way survey. This peculiar class of
galaxies is the result of a near head-on collision between typically, a late
type and an early type galaxy. Subsequent GMOS-N long-slit spectroscopy has
confirmed both the relative proximity of the components of this interacting
pair and shown it to have a redshift of 0.111. Analysis of the spectroscopy
reveals that the late type galaxy is a LINER class Active Galactic Nuclei while
the early type galaxy is also potentially an AGN candidate, this is very
uncommon amongst known collision ring galaxies. Preliminary modeling of the
ring finds an expansion velocity of ~200 kms^-1 consistent with our
observations, making the collision about 50 Myr old. The ring currently has a
radius of about 10 kpc and a bridge of stars and gas is also visible connecting
the two galaxies.Comment: 9 pages, 5 figures and 4 tables. Accepted for publication in Ap
Centerscope
Centerscope, formerly Scope, was published by the Boston University Medical Center "to communicate the concern of the Medical Center for the development and maintenance of improved health care in contemporary society.
Ab-initio study of model guanine assemblies: The role of pi-pi coupling and band transport
Several assemblies of guanine molecules are investigated by means of
first-principle calculations. Such structures include stacked and
hydrogen-bonded dimers, as well as vertical columns and planar ribbons,
respectively, obtained by periodically replicating the dimers. Our results are
in good agreement with experimental data for isolated molecules, isolated
dimers, and periodic ribbons. For stacked dimers and columns, the stability is
affected by the relative charge distribution of the pi orbitals in adjacent
guanine molecules. pi-pi coupling in some stacked columns induces dispersive
energy bands, while no dispersion is identified in the planar ribbons along the
connections of hydrogen bonds. The implications for different materials
comprised of guanine aggregates are discussed. The bandstructure of dispersive
configurations may justify a contribution of band transport (Bloch type) in the
conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations
band transport should be negligible.Comment: 21 pages, 6 figures, 3 tables, to be published in Phys. Rev.
Ancestry: How researchers use it and what they mean by it
Background: Ancestry is often viewed as a more objective and less objectionable population descriptor than race or ethnicity. Perhaps reflecting this, usage of the term âancestryâ is rapidly growing in genetics research, with ancestry groups referenced in many situations. The appropriate usage of population descriptors in genetics research is an ongoing source of debate. Sound normative guidance should rest on an empirical understanding of current usage; in the case of ancestry, questions about how researchers use the concept, and what they mean by it, remain unanswered.Methods: Systematic literature analysis of 205 articles at least tangentially related to human health from diverse disciplines that use the concept of ancestry, and semi-structured interviews with 44 lead authors of some of those articles.Results: Ancestry is relied on to structure research questions and key methodological approaches. Yet researchers struggle to define it, and/or offer diverse definitions. For some ancestry is a genetic concept, but for manyâincluding geneticistsâancestry is only tangentially related to genetics. For some interviewees, ancestry is explicitly equated to ethnicity; for others it is explicitly distanced from it. Ancestry is operationalized using multiple data types (including genetic variation and self-reported identities), though for a large fraction of articles (26%) it is impossible to tell which data types were used. Across the literature and interviews there is no consistent understanding of how ancestry relates to genetic concepts (including genetic ancestry and population structure), nor how these genetic concepts relate to each other. Beyond this conceptual confusion, practices related to summarizing patterns of genetic variation often rest on uninterrogated conventions. Continental labels are by far the most common type of label applied to ancestry groups. We observed many instances of slippage between reference to ancestry groups and racial groups.Conclusion: Ancestry is in practice a highly ambiguous concept, and far from an objective counterpart to race or ethnicity. It is not uniquely a âbiologicalâ construct, and it does not represent a âsafe havenâ for researchers seeking to avoid evoking race or ethnicity in their work. Distinguishing genetic ancestry from ancestry more broadly will be a necessary part of providing conceptual clarity
Constraining Primordial Non-Gaussianity with High-Redshift Probes
We present an analysis of the constraints on the amplitude of primordial
non-Gaussianity of local type described by the dimensionless parameter . These constraints are set by the auto-correlation functions (ACFs) of two
large scale structure probes, the radio sources from NRAO VLA Sky Survey (NVSS)
and the quasar catalogue of Sloan Digital Sky Survey Release Six (SDSS DR6
QSOs), as well as by their cross-correlation functions (CCFs) with the cosmic
microwave background (CMB) temperature map (Integrated Sachs-Wolfe effect).
Several systematic effects that may affect the observational estimates of the
ACFs and of the CCFs are investigated and conservatively accounted for. Our
approach exploits the large-scale scale-dependence of the non-Gaussian halo
bias. The derived constraints on {} coming from the NVSS CCF and
from the QSO ACF and CCF are weaker than those previously obtained from the
NVSS ACF, but still consistent with them. Finally, we obtain the constraints on
() and () from
NVSS data and SDSS DR6 QSO data, respectively.Comment: 16 pages, 8 figures, 1 table, Accepted for publication on JCA
Formalin Fixation at Low Temperature Better Preserves Nucleic Acid Integrity
Fixation with formalin, a widely adopted procedure to preserve tissue samples, leads to extensive degradation of nucleic acids and thereby compromises procedures like microarray-based gene expression profiling. We hypothesized that RNA fragmentation is caused by activation of RNAses during the interval between formalin penetration and tissue fixation. To prevent RNAse activation, a series of tissue samples were kept under-vacuum at 4°C until fixation and then fixed at 4°C, for 24 hours, in formalin followed by 4 hours in ethanol 95%. This cold-fixation (CF) procedure preserved DNA and RNA, so that RNA segments up to 660 bp were efficiently amplified. Histological and immunohistochemical features were fully comparable with those of standard fixation. Microarray-based gene expression profiles were comparable with those obtained on matched frozen samples for probes hybridizing within 700 bases from the reverse transcription start site. In conclusion, CF preserves tissues and nucleic acids, enabling reliable gene expression profiling of fixed tissues
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