Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides

Cyclohexenyl nucleic acid (CeNA) is a nucleic acid mimic, where the (deoxy)ribose sugar has been replaced by cyclohexenyl moieties. In order to study the conformation of cyclohexenyl nucleosides by NMR, the HexRot program was developed to calculate conformations from scalar coupling constants of cyclohexenyl compounds, analogous to the methods applied for (deoxy)ribose nucleosides. The conformational equilibria and the values of the thermodynamic parameters are very similar between a cyclohexenyl nucleoside [energy difference between (2)H(3) (N-type) and (2)H(3) (S-type) is 1.8 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 10.9 kJ/mol] and a natural ribose nucleoside (energy difference between N-type and S-type is 2 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 4–20 kJ/mol). The flexibility of the cyclohexenyl nucleoside was demonstrated by the fast equilibrium between two conformational states that was observed in a CeNA-U monomer, combined with the (2)H(3) conformation of the cyclohexene moiety when incorporated into a Dickerson dodecamer and the (2)H(3) conformation when incorporated in a d(5′-GCGT*GCG-3′)/d(5′-CGCACGC-3′) duplex, as determined by the NMR spectroscopy. This represents the first example of a synthetic nucleoside that adopts different conformations when incorporated in different double-stranded DNA sequences

Constraining the nuclear equation of state at subsaturation densities

Only one third of the nucleons in $^{208}$Pb occupy the saturation density area. Consequently nuclear observables related to average properties of nuclei, such as masses or radii, constrain the equation of state (EOS) not at saturation density but rather around the so-called crossing density, localised close to the mean value of the density of nuclei: $\rho\simeq$0.11 fm$^{-3}$. This provides an explanation for the empirical fact that several EOS quantities calculated with various functionals cross at a density significantly lower than the saturation one. The third derivative M of the energy at the crossing density is constrained by the giant monopole resonance (GMR) measurements in an isotopic chain rather than the incompressibility at saturation density. The GMR measurements provide M=1110 $\pm$ 70 MeV (6% uncertainty), whose extrapolation gives K$_\infty$=230 $\pm$ 40 MeV (17% uncertainty).Comment: 4 pages, 4 figure

Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources

<p>Abstract</p> <p>Background</p> <p>Gene expression profiling studies of mastitis in ruminants have provided key but fragmented knowledge for the understanding of the disease. A systematic combination of different expression profiling studies via meta-analysis techniques has the potential to test the extensibility of conclusions based on single studies. Using the program Pointillist, we performed meta-analysis of transcription-profiling data from six independent studies of infections with mammary gland pathogens, including samples from cattle challenged <it>in vivo </it>with <it>S. aureus</it>, <it>E. coli</it>, and <it>S. uberis</it>, samples from goats challenged <it>in vivo </it>with <it>S. aureus</it>, as well as cattle macrophages and ovine dendritic cells infected <it>in vitro </it>with <it>S. aureus</it>. We combined different time points from those studies, testing different responses to mastitis infection: overall (common signature), early stage, late stage, and cattle-specific.</p> <p>Results</p> <p>Ingenuity Pathway Analysis of affected genes showed that the four meta-analysis combinations share biological functions and pathways (e.g. protein ubiquitination and polyamine regulation) which are intrinsic to the general disease response. In the overall response, pathways related to immune response and inflammation, as well as biological functions related to lipid metabolism were altered. This latter observation is consistent with the milk fat content depression commonly observed during mastitis infection. Complementarities between early and late stage responses were found, with a prominence of metabolic and stress signals in the early stage and of the immune response related to the lipid metabolism in the late stage; both mechanisms apparently modulated by few genes, including <it>XBP1 </it>and <it>SREBF1</it>.</p> <p>The cattle-specific response was characterized by alteration of the immune response and by modification of lipid metabolism. Comparison of <it>E. coli </it>and <it>S. aureus </it>infections in cattle <it>in vivo </it>revealed that affected genes showing opposite regulation had the same altered biological functions and provided evidence that <it>E. coli </it>caused a stronger host response.</p> <p>Conclusions</p> <p>This meta-analysis approach reinforces previous findings but also reveals several novel themes, including the involvement of genes, biological functions, and pathways that were not identified in individual studies. As such, it provides an interesting proof of principle for future studies combining information from diverse heterogeneous sources.</p

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

status: publishe

Band shifting for ocean color multi-spectral reflectance data

An approach to perform band shifting applied to multi-spectral ocean remote sensing reflectance RRS values in the visible spectral range is presented. The band-shifting scheme aims at expressing RRS at a wavelength not originally part of the spectrum from data at neighboring bands. The scheme relies on the determination of inherent optical properties (IOPs) by a bio-optical model, the calculation of the IOPs at the target wavelength using the spectral shapes assumed for each IOP, and the operation of the bio-optical model in forward mode to express RRS at the target wavelength. The performance of the band-shifting scheme applied to bands typical of satellite missions is assessed with hyper-spectral data sets obtained from radiative transfer simulations or from field measurements. The relative error epsilon on the conversion factors from 488 to 490 nm is mostly within 1%. Analogous results are obtained for conversions in the red spectral domain (665, 667 and 670 nm) only for synthetic data sets. The range of epsilon for conversions between green bands (547, 555 and 560 nm) is within 2% to 5% depending on the data set considered. Similar results are obtained when RRS values are computed at 510 nm from data at 488 and 531 nm. In the case of the assessment with simulated data, all band-shifting operations are characterized by an epsilon range within 2% for all conversions when the concentration of chlorophyll-a is lower than 1 mg m-3. Applied to satellite data, the band-shifting scheme noticeably improves the agreement between RRS data from different missions.JRC.H.1-Water Resource

Uncertainty estimates of remote sensing reflectance derived from comparison of ocean color satellite data sets

Assigning uncertainty to ocean-color satellite products is a requirement to allow informed use of these data. Here, uncertainty estimates are derived using the comparison on a 12th-degree grid of coincident daily records of the remote-sensing reflectance RRS obtained with the same processing chain from three satellite missions, MERIS, MODIS and SeaWiFS. The approach is spatially resolved and produces σ, the part of the RRS uncertainty budget associated with random effects. The global average of σ decreases with wavelength from approximately 0.7-0.9 10-3 sr-1 at 412 nm to 0.05-0.1 10-3 sr-1 at the red band, with uncertainties on σ evaluated as 20-30% between 412 and 555 nm, and 30-40% at 670 nm. The distribution of σ shows a restricted spatial variability and small variations with season, which makes the multi-annual global distribution of σ an estimate applicable to all retrievals of the considered missions. The comparison of σ with other uncertainty estimates derived from field data or with the support of algorithms provides a consistent picture. When translated in relative terms, and assuming a relatively low bias, the distribution of σ suggests that the objective of a 5% uncertainty is fulfilled between 412 and 490 nm for oligotrophic waters (chlorophyll-a concentration below 0.1 mg m-3). This study also provides comparison statistics. Spectrally, the mean absolute relative difference between RRS from different missions shows a characteristic U-shape with both ends at blue and red wavelengths inversely related to the amplitude of RRS. On average and for the considered data sets, SeaWiFS RRS tend to be slightly higher than MODIS RRS, which in turn appear higher than MERIS RRS. Biases between mission-specific RRS may exhibit a seasonal dependence, particularly in the subtropical belt.JRC.H.1-Water Resource

Potential energy plots of a cyclohexenyl nucleoside, a 2′-ribo-OH cyclohexenyl nucleoside and a 2′-ara-OH cyclohexenyl nucleoside

<p><b>Copyright information:</b></p><p>Taken from "Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides"</p><p>Nucleic Acids Research 2005;33(8):2452-2463.</p><p>Published online 29 Apr 2005</p><p>PMCID:PMC1087899.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p

Important NOE contacts observed in the thymine cyclohexenyl residue (T*) in a DNA duplex consisting of d(5′-GCGT*GCG-3′) hybridized with d(5′-CGCACGC-3′)

<p><b>Copyright information:</b></p><p>Taken from "Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides"</p><p>Nucleic Acids Research 2005;33(8):2452-2463.</p><p>Published online 29 Apr 2005</p><p>PMCID:PMC1087899.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p

CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes-3

<p><b>Copyright information:</b></p><p>Taken from "CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes"</p><p>http://www.biomedcentral.com/1471-2105/8/400</p><p>BMC Bioinformatics 2007;8():400-400.</p><p>Published online 18 Oct 2007</p><p>PMCID:PMC2147040.</p><p></p>orresponds to the number of probes in the length bins. Upper and lower panels represent the length distribution of the GFTs and GSTs, respectively

CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes-1

<p><b>Copyright information:</b></p><p>Taken from "CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes"</p><p>http://www.biomedcentral.com/1471-2105/8/400</p><p>BMC Bioinformatics 2007;8():400-400.</p><p>Published online 18 Oct 2007</p><p>PMCID:PMC2147040.</p><p></p>bottom panels show the distribution of the probes with regard to their mapping location on the cognate gene and the cumulative distribution of the probe specificity, measured as the percentage sequence identity of the best non-trivial BLAST hit when comparing the probe against the TIGR5 genome, respectively