2,626 research outputs found
SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification
With rapid advances in the development of DNA sequencing technologies, a plethora of high-throughput genome and proteome data from a diverse spectrum of organisms have been generated. The functional annotation and evolutionary history of proteins are usually inferred from domains predicted from the genome sequences. Traditional database-based domain prediction methods cannot identify novel domains, however, and alignment-based methods, which look for recurring segments in the proteome, are computationally demanding. Here, we propose a novel genome-wide domain prediction method, SECOM. Instead of conducting all-against-all sequence alignment, SECOM first indexes all the proteins in the genome by using a hash seed function. Local similarity can thus be detected and encoded into a graph structure, in which each node represents a protein sequence and each edge weight represents the shared hash seeds between the two nodes. SECOM then formulates the domain prediction problem as an overlapping community-finding problem in this graph. A backward graph percolation algorithm that efficiently identifies the domains is proposed. We tested SECOM on five recently sequenced genomes of aquatic animals. Our tests demonstrated that SECOM was able to identify most of the known domains identified by InterProScan. When compared with the alignment-based method, SECOM showed higher sensitivity in detecting putative novel domains, while it was also three orders of magnitude faster. For example, SECOM was able to predict a novel sponge-specific domain in nucleoside-triphosphatase (NTPases). Furthermore, SECOM discovered two novel domains, likely of bacterial origin, that are taxonomically restricted to sea anemone and hydra. SECOM is an open-source program and available at http://sfb.kaust.edu.sa/Pages/Software.aspx
Effects of the Non-Equipartition of Electrons and Ions in the Outskirts of Relaxed Galaxy Clusters
(abridged) We have studied the effects of electron-ion non-equipartition in
the outer regions of relaxed clusters for a wide range of masses in the
\LambdaCDM cosmology using one-dimensional hydrodynamic simulations. The
effects of the non-adiabatic electron heating efficiency, \beta, on the degree
of non-equipartition are also studied. Using the gas fraction f_gas = 0.17
(which is the upper limit for a cluster), we give a conservative lower limit of
the non-equipartition effect on clusters. Beyond the virial radius, the
non-equipartition effect depends rather strongly on \beta, and such a strong
dependence at the shock radius can be used to distinguish shock heating models
or constrain the shock heating efficiency of electrons. We have also studied
systematically the signatures of non-equipartition on X-ray and SZ observables.
We have calculated the effect of non-equipartition on the projected temperature
and X-ray surface brightness profiles using the MEKAL emission model. The
non-equipartition effect can introduce a ~10% bias in the projected temperature
at R_vir for a wide range of \beta. We also found that the effect of
non-equipartition on the projected temperature profiles can be enhanced by
increasing metallicity. We found that for our model in the \LambdaCDM Universe,
the integrated SZ bias, Y_{non-eq}/Y_{eq}, evolves slightly (at a percentage
level) with redshift, which is in contrast to the self-similar model in the
Einstein-de Sitter Universe. This may introduce biases in cosmological studies
using the f_gas technique. We discussed briefly whether the equipartition and
non-equipartition models near the shock region can be distinguished by future
radio observations with, for example, ALMA.Comment: 28 pages, 19 figures, accepted for publication in the Astrophysical
Journal. Typos corrected in version
High-Fidelity Tissue Engineering of Patient-Specific Auricles for Reconstruction of Pediatric Microtia and Other Auricular Deformities
Introduction: Autologous techniques for the reconstruction of pediatric microtia often result in suboptimal aesthetic outcomes and morbidity at the costal cartilage donor site. We therefore sought to combine digital photogrammetry with CAD/CAM techniques to develop collagen type I hydrogel scaffolds and their respective molds that would precisely mimic the normal anatomy of the patient-specific external ear as well as recapitulate the complex biomechanical properties of native auricular elastic cartilage while avoiding the morbidity of traditional autologous reconstructions. Methods: Three-dimensional structures of normal pediatric ears were digitized and converted to virtual solids for mold design. Image-based synthetic reconstructions of these ears were fabricated from collagen type I hydrogels. Half were seeded with bovine auricular chondrocytes. Cellular and acellular constructs were implanted subcutaneously in the dorsa of nude rats and harvested after 1 and 3 months. Results: Gross inspection revealed that acellular implants had significantly decreased in size by 1 month. Cellular constructs retained their contour/projection from the animals' dorsa, even after 3 months. Post-harvest weight of cellular constructs was significantly greater than that of acellular constructs after 1 and 3 months. Safranin O-staining revealed that cellular constructs demonstrated evidence of a self-assembled perichondrial layer and copious neocartilage deposition. Verhoeff staining of 1 month cellular constructs revealed de novo elastic cartilage deposition, which was even more extensive and robust after 3 months. The equilibrium modulus and hydraulic permeability of cellular constructs were not significantly different from native bovine auricular cartilage after 3 months. Conclusions: We have developed high-fidelity, biocompatible, patient-specific tissue-engineered constructs for auricular reconstruction which largely mimic the native auricle both biomechanically and histologically, even after an extended period of implantation. This strategy holds immense potential for durable patient-specific tissue-engineered anatomically proper auricular reconstructions in the future. © 2013 Reiffel et al
Comments on Holographic Entanglement Entropy and RG Flows
Using holographic entanglement entropy for strip geometry, we construct a
candidate for a c-function in arbitrary dimensions. For holographic theories
dual to Einstein gravity, this c-function is shown to decrease monotonically
along RG flows. A sufficient condition required for this monotonic flow is that
the stress tensor of the matter fields driving the holographic RG flow must
satisfy the null energy condition over the holographic surface used to
calculate the entanglement entropy. In the case where the bulk theory is
described by Gauss-Bonnet gravity, the latter condition alone is not sufficient
to establish the monotonic flow of the c-function. We also observe that for
certain holographic RG flows, the entanglement entropy undergoes a 'phase
transition' as the size of the system grows and as a result, evolution of the
c-function may exhibit a discontinuous drop.Comment: References adde
Is Renormalized Entanglement Entropy Stationary at RG Fixed Points?
The renormalized entanglement entropy (REE) across a circle of radius R has
been proposed as a c-function in Poincar\'e invariant (2+1)-dimensional field
theory. A proof has been presented of its monotonic behavior as a function of
R, based on the strong subadditivity of entanglement entropy. However, this
proof does not directly establish stationarity of REE at conformal fixed points
of the renormalization group. In this note we study the REE for the free
massive scalar field theory near the UV fixed point described by a massless
scalar. Our numerical calculation indicates that the REE is not stationary at
the UV fixed point.Comment: 15 pages, 4 figure
Holographic c-theorems in arbitrary dimensions
We re-examine holographic versions of the c-theorem and entanglement entropy
in the context of higher curvature gravity and the AdS/CFT correspondence. We
select the gravity theories by tuning the gravitational couplings to eliminate
non-unitary operators in the boundary theory and demonstrate that all of these
theories obey a holographic c-theorem. In cases where the dual CFT is
even-dimensional, we show that the quantity that flows is the central charge
associated with the A-type trace anomaly. Here, unlike in conventional
holographic constructions with Einstein gravity, we are able to distinguish
this quantity from other central charges or the leading coefficient in the
entropy density of a thermal bath. In general, we are also able to identify
this quantity with the coefficient of a universal contribution to the
entanglement entropy in a particular construction. Our results suggest that
these coefficients appearing in entanglement entropy play the role of central
charges in odd-dimensional CFT's. We conjecture a new c-theorem on the space of
odd-dimensional field theories, which extends Cardy's proposal for even
dimensions. Beyond holography, we were able to show that for any
even-dimensional CFT, the universal coefficient appearing the entanglement
entropy which we calculate is precisely the A-type central charge.Comment: 62 pages, 4 figures, few typo's correcte
Expression and Subcellular Localization of Mammalian Formin Fhod3 in the Embryonic and Adult Heart
The formin family proteins play pivotal roles in actin filament assembly via the FH2 domain. The mammalian formin Fhod3 is highly expressed in the heart, and its mRNA in the adult heart contains exons 11, 12, and 25, which are absent from non-muscle Fhod3 isoforms. In cultured neonatal cardiomyocytes, Fhod3 localizes to the middle of the sarcomere and appears to function in its organization, although it is suggested that Fhod3 localizes differently in the adult heart. Here we show, using immunohistochemical analysis with three different antibodies, each recognizing distinct regions of Fhod3, that Fhod3 localizes as two closely spaced bands in middle of the sarcomere in both embryonic and adult hearts. The bands are adjacent to the M-line that crosslinks thick myosin filaments at the center of a sarcomere but distant from the Z-line that forms the boundary of the sarcomere, which localization is the same as that observed in cultured cardiomyocytes. Detailed immunohistochemical and immuno-electron microscopic analyses reveal that Fhod3 localizes not at the pointed ends of thin actin filaments but to a more peripheral zone, where thin filaments overlap with thick myosin filaments. We also demonstrate that the embryonic heart of mice specifically expresses the Fhod3 mRNA isoform harboring the three alternative exons, and that the characteristic localization of Fhod3 in the sarcomere does not require a region encoded by exon 25, in contrast to an essential role of exons 11 and 12. Furthermore, the exon 25-encoded region appears to be dispensable for actin-organizing activities both in vivo and in vitro, albeit it is inserted in the catalytic FH2 domain
Novel functions and regulation of cryptic cellobiose operons in Escherichia coli
Presence of cellobiose as a sole carbon source induces mutations in the chb and asc operons of Escherichia coli and allows it to grow on cellobiose. We previously engineered these two operons with synthetic constitutive promoters and achieved efficient cellobiose metabolism through adaptive evolution. In this study, we characterized two mutations observed in the efficient cellobiose metabolizing strain: duplication of RBS of ascB gene, (beta-glucosidase of asc operon) and nonsense mutation in yebK, (an uncharacterized transcription factor). Mutations in yebK play a dominant role by modulating the length of lag phase, relative to the growth rate of the strain when transferred from a rich medium to minimal cellobiose medium. Mutations in ascB, on the other hand, are specific for cellobiose and help in enhancing the specific growth rate. Taken together, our results show that ascB of the asc operon is controlled by an internal putative promoter in addition to the native cryptic promoter, and the transcription factor yebK helps to remodel the host physiology for cellobiose metabolism. While previous studies characterized the stress-induced mutations that allowed growth on cellobiose, here, we characterize the adaptation-induced mutations that help in enhancing cellobiose metabolic ability. This study will shed new light on the regulatory changes and factors that are needed for the functional coupling of the host physiology to the activated cryptic cellobiose metabolismopen1
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