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Optimal gridding and degridding in radio interferometry imaging
In radio interferometry imaging, the gridding procedure of convolving
visibilities with a chosen gridding function is necessary to transform
visibility values into uniformly sampled grid points. We propose here a
parameterised family of "least-misfit gridding functions" which minimise an
upper bound on the difference between the DFT and FFT dirty images for a given
gridding support width and image cropping ratio. When compared with the widely
used spheroidal function with similar parameters, these provide more than 100
times better alias suppression and RMS misfit reduction over the usable dirty
map. We discuss how appropriate parameter selection and tabulation of these
functions allow for a balance between accuracy, computational cost and storage
size. Although it is possible to reduce the errors introduced in the gridding
or degridding process to the level of machine precision, accuracy comparable to
that achieved by CASA requires only a lookup table with 300 entries and a
support width of 3, allowing for a greatly reduced computation cost for a given
performance
Dipolar collisions of polar molecules in the quantum regime
Ultracold polar molecules offer the possibility of exploring quantum gases
with interparticle interactions that are strong, long-range, and spatially
anisotropic. This is in stark contrast to the dilute gases of ultracold atoms,
which have isotropic and extremely short-range, or "contact", interactions. The
large electric dipole moment of polar molecules can be tuned with an external
electric field; this provides unique opportunities such as control of ultracold
chemical reactions, quantum information processing, and the realization of
novel quantum many-body systems. In spite of intense experimental efforts aimed
at observing the influence of dipoles on ultracold molecules, only recently
have sufficiently high densities been achieved. Here, we report the observation
of dipolar collisions in an ultracold molecular gas prepared close to quantum
degeneracy. For modest values of an applied electric field, we observe a
dramatic increase in the loss rate of fermionic KRb molecules due to ultrcold
chemical reactions. We find that the loss rate has a steep power-law dependence
on the induced electric dipole moment, and we show that this dependence can be
understood with a relatively simple model based on quantum threshold laws for
scattering of fermionic polar molecules. We directly observe the spatial
anisotropy of the dipolar interaction as manifested in measurements of the
thermodynamics of the dipolar gas. These results demonstrate how the long-range
dipolar interaction can be used for electric-field control of chemical reaction
rates in an ultracold polar molecule gas. The large loss rates in an applied
electric field suggest that creating a long-lived ensemble of ultracold polar
molecules may require confinement in a two-dimensional trap geometry to
suppress the influence of the attractive dipolar interactions
Ultraviolet electroluminescence from two-dimensional ZnO nanomesh/GaN heterojunction light emitting diodes
2010-2011 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe
Molecular cloning and transcriptional activity of a new Petunia calreticulin gene involved in pistil transmitting tract maturation, progamic phase, and double fertilization
Calreticulin (CRT) is a highly conserved and ubiquitously expressed Ca2+-binding protein in multicellular eukaryotes. As an endoplasmic reticulum-resident protein, CRT plays a key role in many cellular processes including Ca2+ storage and release, protein synthesis, and molecular chaperoning in both animals and plants. CRT has long been suggested to play a role in plant sexual reproduction. To begin to address this possibility, we cloned and characterized the full-length cDNA of a new CRT gene (PhCRT) from Petunia. The deduced amino acid sequence of PhCRT shares homology with other known plant CRTs, and phylogenetic analysis indicates that the PhCRT cDNA clone belongs to the CRT1/CRT2 subclass. Northern blot analysis and fluorescent in situ hybridization were used to assess PhCRT gene expression in different parts of the pistil before pollination, during subsequent stages of the progamic phase, and at fertilization. The highest level of PhCRT mRNA was detected in the stigma–style part of the unpollinated pistil 1 day before anthesis and during the early stage of the progamic phase, when pollen is germinated and tubes outgrow on the stigma. In the ovary, PhCRT mRNA was most abundant after pollination and reached maximum at the late stage of the progamic phase, when pollen tubes grow into the ovules and fertilization occurs. PhCRT mRNA transcripts were seen to accumulate predominantly in transmitting tract cells of maturing and receptive stigma, in germinated pollen/growing tubes, and at the micropylar region of the ovule, where the female gametophyte is located. From these results, we suggest that PhCRT gene expression is up-regulated during secretory activity of the pistil transmitting tract cells, pollen germination and outgrowth of the tubes, and then during gamete fusion and early embryogenesis
FLORA: a novel method to predict protein function from structure in diverse superfamilies
Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure embellishments to a common structural core. The majority of prediction algorithms employ local templates built on known or predicted functional residues. Here, we present a novel method (FLORA) that automatically generates structural motifs associated with different functional sub-families (FSGs) within functionally diverse domain superfamilies. Templates are created purely on the basis of their specificity for a given FSG, and the method makes no prior prediction of functional sites, nor assumes specific physico-chemical properties of residues. FLORA is able to accurately discriminate between homologous domains with different functions and substantially outperforms (a 2–3 fold increase in coverage at low error rates) popular structure comparison methods and a leading function prediction method. We benchmark FLORA on a large data set of enzyme superfamilies from all three major protein classes (α, β, αβ) and demonstrate the functional relevance of the motifs it identifies. We also provide novel predictions of enzymatic activity for a large number of structures solved by the Protein Structure Initiative. Overall, we show that FLORA is able to effectively detect functionally similar protein domain structures by purely using patterns of structural conservation of all residues
Lepton Acceleration in Pulsar Wind Nebulae
Pulsar Wind Nebulae (PWNe) act as calorimeters for the relativistic pair
winds emanating from within the pulsar light cylinder. Their radiative
dissipation in various wavebands is significantly different from that of their
pulsar central engines: the broadband spectra of PWNe possess characteristics
distinct from those of pulsars, thereby demanding a site of lepton acceleration
remote from the pulsar magnetosphere. A principal candidate for this locale is
the pulsar wind termination shock, a putatively highly-oblique,
ultra-relativistic MHD discontinuity. This paper summarizes key characteristics
of relativistic shock acceleration germane to PWNe, using predominantly Monte
Carlo simulation techniques that compare well with semi-analytic solutions of
the diffusion-convection equation. The array of potential spectral indices for
the pair distribution function is explored, defining how these depend
critically on the parameters of the turbulent plasma in the shock environs.
Injection efficiencies into the acceleration process are also addressed.
Informative constraints on the frequency of particle scattering and the level
of field turbulence are identified using the multiwavelength observations of
selected PWNe. These suggest that the termination shock can be comfortably
invoked as a principal injector of energetic leptons into PWNe without
resorting to unrealistic properties for the shock layer turbulence or MHD
structure.Comment: 19 pages, 5 figures, invited review to appear in Proc. of the
inaugural ICREA Workshop on "The High-Energy Emission from Pulsars and their
Systems" (2010), eds. N. Rea and D. Torres, (Springer Astrophysics and Space
Science series
Extensive Copy-Number Variation of Young Genes across Stickleback Populations
MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
Increased S-nitrosylation and proteasomal degradation of caspase-3 during infection contribute to the persistence of adherent invasive escherichia coli (AIEC) in immune cells
Adherent invasive Escherichia coli (AIEC) have been implicated as a causative agent of Crohn's disease (CD) due to their isolation from the intestines of CD sufferers and their ability to persist in macrophages inducing granulomas. The rapid intracellular multiplication of AIEC sets it apart from other enteric pathogens such as Salmonella Typhimurium which after limited replication induce programmed cell death (PCD). Understanding the response of infected cells to the increased AIEC bacterial load and associated metabolic stress may offer insights into AIEC pathogenesis and its association with CD. Here we show that AIEC persistence within macrophages and dendritic cells is facilitated by increased proteasomal degradation of caspase-3. In addition S-nitrosylation of pro- and active forms of caspase-3, which can inhibit the enzymes activity, is increased in AIEC infected macrophages. This S-nitrosylated caspase-3 was seen to accumulate upon inhibition of the proteasome indicating an additional role for S-nitrosylation in inducing caspase-3 degradation in a manner independent of ubiquitination. In addition to the autophagic genetic defects that are linked to CD, this delay in apoptosis mediated in AIEC infected cells through increased degradation of caspase-3, may be an essential factor in its prolonged persistence in CD patients
Molecular cloning and expression profiling of a chalcone synthase gene from hairy root cultures of Scutellaria viscidula Bunge
A cDNA encoding chalcone synthase (CHS), the key enzyme in flavonoid biosynthesis, was isolated from hairy root cultures of Scutellaria viscidula Bunge by rapid amplification of cDNA ends (RACE). The full-length cDNA of S. viscidula CHS, designated as Svchs (GenBank accession no. EU386767), was 1649 bp with a 1170 bp open reading frame (ORF) that corresponded to a deduced protein of 390 amino acid residues, a calculated molecular mass of 42.56 kDa and a theoretical isoelectric point (pI) of 5.79. Multiple sequence alignments showed that SvCHS shared high homology with CHS from other plants. Functional analysis in silico indicated that SvCHS was a hydrophilic protein most likely associated with intermediate metabolism. The active sites of the malonyl-CoA binding motif, coumaroyl pocket and cyclization pocket in CHS of Medicago sativa were also found in SvCHS. Molecular modeling indicated that the secondary structure of SvCHS contained mainly α-helixes and random coils. Phylogenetic analysis showed that SvCHS was most closely related to CHS from Scutellaria baicalensis. In agreement with its function as an elicitor-responsive gene, the expression of Svchs was induced and coordinated by methyl jasmonate. To our knowledge, this is the first report to describe the isolation and expression of a gene from S. viscidula
Preservation of Genes Involved in Sterol Metabolism in Cholesterol Auxotrophs: Facts and Hypotheses
Background: It is known that primary sequences of enzymes involved in sterol biosynthesis are well conserved in organisms that produce sterols de novo. However, we provide evidence for a preservation of the corresponding genes in two animals unable to synthesize cholesterol (auxotrophs): Drosophila melanogaster and Caenorhabditis elegans. Principal Findings: We have been able to detect bona fide orthologs of several ERG genes in both organisms using a series of complementary approaches. We have detected strong sequence divergence between the orthologs of the nematode and of the fruitfly; they are also very divergent with respect to the orthologs in organisms able to synthesize sterols de novo (prototrophs). Interestingly, the orthologs in both the nematode and the fruitfly are still under selective pressure. It is possible that these genes, which are not involved in cholesterol synthesis anymore, have been recruited to perform different new functions. We propose a more parsimonious way to explain their accelerated evolution and subsequent stabilization. The products of ERG genes in prototrophs might be involved in several biological roles, in addition to sterol synthesis. In the case of the nematode and the fruitfly, the relevant genes would have lost their ancestral function in cholesterogenesis but would have retained the other function(s), which keep them under pressure. Conclusions: By exploiting microarray data we have noticed a strong expressional correlation between the orthologs of ERG24 and ERG25 in D. melanogaster and genes encoding factors involved in intracellular protein trafficking and folding an
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