Elicitin genes in Phytophthora infestans are clustered and interspersed with various transposon-like elements

Sequencing and annotation of a contiguous stretch of genomic DNA (112.3 kb) from the oomycete plant pathogen Phytophthora infestans revealed the order, spacing and genomic context of four members of the elicitin (inf) gene family. Analysis of the GC content at the third codon position (GC3) of six genes encoded in the region, and a set of randomly selected coding regions as well as random genomic regions, showed that a high GC3 value is a general feature of Phytophthora genes that can be exploited to optimize gene prediction programs for Phytophthora species. At least one-third of the annotated 112.3-kb P. infestans sequence consisted of transposons or transposon-like elements. The most prominent were four Tc3/gypsy and Tc1/copia type retrotransposons and three DNA transposons that belong to the Tc1/mariner, Pogo and PiggyBac groups, respectively. Comparative analysis of other available genomic sequences suggests that transposable elements are highly heterogeneous and ubiquitous in the P. infestans genome

Microwave determination of the quasiparticle scattering time in YBa2Cu3O6.95

We report microwave surface resistance (Rs) measurements on two very-high-quality YBa2Cu3O6.95 crystals which exhibit extremely low residual loss at 1.2 K (2-6 μΩ at 2 GHz), a broad, reproducible peak at around 38 K, and a rapid increase in loss, by 4 orders of magnitude, between 80 and 93 K. These data provide one ingredient in the determination of the temperature dependence of the real part of the microwave conductivity, σ1(T), and of the quasiparticle scattering time. The other necessary ingredient is an accurate knowledge of the magnitude and temperature dependence of the London penetration depth, λ(T). This is derived from published data, from microwave data of Anlage, Langley, and co-workers and from, high-quality μSR data. We infer, from a careful analysis of all available data, that λ2(0)/λ2(T) is well approximated by the simple function 1-t2, where t=T/Tc, and that the low-temperature data are incompatible with the existence of an s-wave, BCS-like gap. Combining the Rs and λ(T) data, we find that σ1(T), has a broad peak around 32 K with a value about 20 times that at Tc. Using a generalized two-fluid model, we extract the temperature dependence of the quasiparticle scattering rate which follows an exponential law, exp(T/T0), where T0≊12 K, for T between 15 and 84 K. Such a temperature dependence has previously been observed in measurements of the nuclear spin-lattice relaxation rate. Both the uncertainties in our analysis and the implications for the mechanism of high-temperature superconductivity are discussed

The On-orbit Calibrations for the Fermi Large Area Telescope

The Large Area Telescope (LAT) on--board the Fermi Gamma ray Space Telescope began its on--orbit operations on June 23, 2008. Calibrations, defined in a generic sense, correspond to synchronization of trigger signals, optimization of delays for latching data, determination of detector thresholds, gains and responses, evaluation of the perimeter of the South Atlantic Anomaly (SAA), measurements of live time, of absolute time, and internal and spacecraft boresight alignments. Here we describe on orbit calibration results obtained using known astrophysical sources, galactic cosmic rays, and charge injection into the front-end electronics of each detector. Instrument response functions will be described in a separate publication. This paper demonstrates the stability of calibrations and describes minor changes observed since launch. These results have been used to calibrate the LAT datasets to be publicly released in August 2009.Comment: 60 pages, 34 figures, submitted to Astroparticle Physic

Elicitin genes in Phytophthora infestans are clustered and interspersed with various transposon-like elements

Sequencing and annotation of a contiguous stretch of genomic DNA (112.3 kb) from the oomycete plant pathogen Phytophthora infestans revealed the order, spacing and genomic context of four members of the elicitin (inf) gene family. Analysis of the GC content at the third codon position (GC3) of six genes encoded in the region, and a set of randomly selected coding regions as well as random genomic regions, showed that a high GC3 value is a general feature of Phytophthora genes that can be exploited to optimize gene prediction programs for Phytophthora species. At least one-third of the annotated 112.3-kb P. infestans sequence consisted of transposons or transposon-like elements. The most prominent were four Tc3/gypsy and Tc1/copia type retrotransposons and three DNA transposons that belong to the Tc1/mariner, Pogo and PiggyBac groups, respectively. Comparative analysis of other available genomic sequences suggests that transposable elements are highly heterogeneous and ubiquitous in the P. infestans genome

Remodeling of tissue-engineered bone structures in vivo

Implant design for bone regeneration is expected to be optimized when implant structures resemble the anatomical situation of the defect site. We tested the validity of this hypothesis by exploring the feasibil- ity of generating different in vitro engineered bone-like structures originating from porous silk fibroin scaffolds decorated with RGD sequences (SF-RGD), seeded with human mesenchymal stem cells (hMSC). Scaffolds with small (106–212 lm), medium (212–300 lm), and large pore diameter ranges (300– 425 lm) were seeded with hMSC and subsequently differentiated in vitro into bone-like tissue resem- bling initial scaffold geometries and featuring bone-like structures. Eight weeks after implantation into calvarial defects in mice, the in vitro engineered bone-like tissues had remodeled into bone featuring dif- ferent proportions of woven/lamellar bone bridging the defects. Regardless of pore diameter, all implants integrated well, vascularization was advanced, and bone marrow ingrowth had started. Ultimately, in this defect model, the geometry of the in vitro generated tissue-engineered bone structure, trabecular- or plate-like, had no significant impact on the healing of the defect, owing to an efficient remodeling of its structure after implantation

Molecular characterization of vegetative incompatibility genes that restrict hypovirus transmission in the chestnut blight fungus Cryphonectria parasitica

Genetic nonself recognition systems such as vegetative incompatibility operate in many filamentous fungi to regulate hyphal fusion between genetically dissimilar individuals and to restrict the spread of virulence-attenuating mycoviruses that have potential for biological control of pathogenic fungi. We report here the use of a comparative genomics approach to identify seven candidate polymorphic genes associated with four vegetative incompatibility (vic) loci of the chestnut blight fungus Cryphonectria parasitica. Disruption of candidate alleles in one of two strains that were heteroallelic at vic2, vic6, or vic7 resulted in enhanced virus transmission, but did not prevent barrage formation associated with mycelial incompatibility. Detailed characterization of the vic6 locus revealed the involvement of nonallelic interactions between two tightly linked genes in barrage formation, heterokaryon formation, and asymmetric, gene-specific influences on virus transmission. The combined results establish molecular identities of genes associated with four C. parasitica vic loci and provide insights into how these recognition fa