Haplotype block structure is conserved across mammals

Genetic variation in genomes is organized in haplotype blocks, and species-specific block structure is defined by differential contribution of population history effects in combination with mutation and recombination events. Haplotype maps characterize the common patterns of linkage disequilibrium in populations and have important applications in the design and interpretation of genetic experiments. Although evolutionary processes are known to drive the selection of individual polymorphisms, their effect on haplotype block structure dynamics has not been shown. Here, we present a high-resolution haplotype map for a 5-megabase genomic region in the rat and compare it with the orthologous human and mouse segments. Although the size and fine structure of haplotype blocks are species dependent, there is a significant interspecies overlap in structure and a tendency for blocks to encompass complete genes. Extending these findings to the complete human genome using haplotype map phase I data reveals that linkage disequilibrium values are significantly higher for equally spaced positions in genic regions, including promoters, as compared to intergenic regions, indicating that a selective mechanism exists to maintain combinations of alleles within potentially interacting coding and regulatory regions. Although this characteristic may complicate the identification of causal polymorphisms underlying phenotypic traits, conservation of haplotype structure may be employed for the identification and characterization of functionally important genomic regions

Identification of genes encoding squalestatin S1 biosynthesis and in vitro production of new squalestatin analogues

A gene cluster responsible for the biosynthesis of squalestatin S1 (SQS1, 1) was identified by full genome sequencing of two SQS1-producing ascomycetes: Phoma sp. C2932 and unidentified fungus MF5453. A transformation protocol was established and a subsequent knockout of one PKS gene from the cluster led to loss of SQS1 production and enhanced concentration of an SQS1 precursor. An acyltransferase gene from the cluster was expressed in E. coli and the expressed protein MfM4 shown to be responsible for loading acyl groups from CoA onto the squalestatin core as the final step of biosynthesis. MfM4 appears to have a broad substrate selectivity for its acyl CoA substrate, allowing the in vitro synthesis of novel squalestatins

Further spectral and chromatographic studies of ambergris.

Jetsam ambergris, found washed ashore on beaches, is an environmentally modified form of a natural product of Sperm whales which sometimes develops a pleasant odour. Odorous samples have proved valuable in perfumery. Identification of jetsam ambergris by analysis of organic-soluble extracts by Fourier transform infra-red spectroscopy (FTIR) and of derivatised samples by gas chromatography-mass spectrometry (GC-MS) has already been shown. Here, we describe a different method, in which characteristic alkenic protons and carbon atoms of the major constituent ambrein, were identified in whole extracts using nuclear magnetic resonance spectroscopy (NMR). The advantages of employing NMR spectroscopy included rapidity, reduced losses of volatiles compared to GC-MS and detection of non-GC amenable constituents. However, the identities and quantities of co-occurring individual components (e.g. steroids) could not easily be assigned in the unfractionated extracts by NMR spectroscopy, whereas they were by GC-MS, so an approach combining FTIR, GC-MS and NMR spectroscopic methods is advocated

Precise microwave characterization of MgO substrates for HTS circuits with superconducting post dielectric resonator

Accurate data of complex permittivity of dielectric substrates are needed for efficient design of HTS microwave planar circuits. We have tested MgO substrates from three different manufacturing batches using a dielectric resonator with superconducting parts recently developed for precise microwave characterization of laminar dielectrics at cryogenic temperatures. The measurement fixture has been fabricated using a SrLaAlO3 post dielectric resonator with DyBa2Cu3O7 end plates and silver-plated copper sidewalls to achieve the resolution of loss tangent measurements of 2 {\times} 10-6. The tested MgO substrates exhibited the average relative permittivity of 9.63 and tan {\delta} from 3.7 {\times} 10-7 to 2 {\times} 10-5 at frequency of 10.5 GHz in the temperature range from 14 to 80 K.Comment: 6 pages, 8 figures, 3 table

Faddeev Calculations of Proton-Deuteron Radiative Capture with Exchange Currents

pd capture processes at various energies have been analyzed based on solutions of 3N-Faddeev equations and using modern NN forces. The application of the Siegert theorem is compared to the explicit use of $\pi$- and $\rho$-like exchange currents connected to the AV18 NN interaction. Overall good agreement with cross sections and spin observables has been obtained but leaving room for improvement in some cases. Feasibility studies for 3NF's consistently included in the 3N continuum and the 3N bound state have been performed as well.Comment: Minor changes in notation, ps files for figure

Monitoring photo-oxidative and salinity-induced bacterial stress in the Canadian Arctic using specific lipid tracers

Publisher policy: author can archive post-print on open access repository after an embargo period of 18 months.Publisher's version/PDF cannot be used. Must link to publisher version with DOI. Author's post-print must be released with a Creative Commons Attribution Non-Commercial No Derivatives License

Sea ice dynamics across the Mid-Pleistocene transition in the Bering Sea.

Sea ice and associated feedback mechanisms play an important role for both long- and short-term climate change. Our ability to predict future sea ice extent, however, hinges on a greater understanding of past sea ice dynamics. Here we investigate sea ice changes in the eastern Bering Sea prior to, across, and after the Mid-Pleistocene transition (MPT). The sea ice record, based on the Arctic sea ice biomarker IP25 and related open water proxies from the International Ocean Discovery Program Site U1343, shows a substantial increase in sea ice extent across the MPT. The occurrence of late-glacial/deglacial sea ice maxima are consistent with sea ice/land ice hysteresis and land-glacier retreat via the temperature-precipitation feedback. We also identify interactions of sea ice with phytoplankton growth and ocean circulation patterns, which have important implications for glacial North Pacific Intermediate Water formation and potentially North Pacific abyssal carbon storage

Temporal evolution of IP₂₅ and other highly branched isoprenoid lipids in sea ice and the underlying water column during an Arctic melting season

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