15 research outputs found
Band shifting for ocean color multi-spectral reflectance data
No full textAn 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
Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides
Get PDFCyclohexenyl nucleic acid (CeNA) is a nucleic acid mimic, where the (deoxy)ribose sugar has been replaced by cyclohexenyl moieties.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 cal-culate conformations from scalar coupling const-ants of cyclohexenyl compounds, analogous to the methods applied for (deoxy)ribose nucleosides. The conformational equilibria and the values of the ther-modynamic parameters are very similar between a cyclohexenyl nucleoside [energy difference between 2H 3 (N-type) and 2H3 (S-type) is 1.8 kJ/mol and equi-librium occurs via the eastern hemisphere with a barrier of 10.9 kJ/mol] and a natural ribose nucleo-side (energy difference between N-type and S-type is 2 kJ/mol and equilibrium occurs via the eastern hemi-sphere 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, com-bined with the 2H 3 conformation of the cyclohexene moiety when incorporated into a Dickerson dode-camer and the 2H3 conformation when incorporated in a d(50-GCGT*GCG-30)/d(50-CGCACGC-30) duplex, as determined by the NMR spectroscopy. This repres-ents the first example of a synthetic nucleoside that adopts different conformations when incorporated in different double-stranded DNA sequences
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′)
No full text<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
Potential energy plots of a cyclohexenyl nucleoside, a 2′-ribo-OH cyclohexenyl nucleoside and a 2′-ara-OH cyclohexenyl nucleoside
No full text<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
Uncertainty estimates of remote sensing reflectance derived from comparison of ocean color satellite data sets
No full textAssigning 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
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes
Get PDFBackground: The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and
flexibility to regularly update the GST collection according to evolving knowledge about the gene
repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference.
Results: GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts,
TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To
complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA.Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 proteinencoding
nuclear gene models in the TAIR6 and EuGène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family
Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition.
Conclusion: To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale
cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA
repertoire is available through the CATMA database http://www.catma.org
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes-0
No full text<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>types of information: the exon coordinates of the TIGR5 annotated protein-coding nuclear genes, the exon coordinates of Eugène 040917, an in-house generated and curated annotation, and the BLAST hit coordinates of the CATMAv2 GSTs, blasted against the Arabidopsis genome. For each annotation source, regions of overlapping genes were marked and gene models that ended with the ORF stop codon were extended with an 'artificial 3' UTR of 150 bp. Information on the prior CATMAv2 GST amplification success or failure was also added to the database. In a second step, both GSTs and genes were classified into five different categories. The classification routine is depicted in Additional File and the categories themselves are described in detail in Table 2. Only successfully amplified GSTs were taken into consideration for the gene classification. When a gene was classified as GE5, it was considered as having a 'unique' tag. When a GST was classified as GST5, it was considered as 'tagging uniquely'. The GST classification was added to the CATMA database, flagging the non-tagging GSTs without actually removing them from the repository. The gene classification was used as a basis for the third and final step, the design of new GSTs for all genes not classified as GE5. To this end, we used the SPADS 1.1.5 software on virtual gene models from which all overlapping exon regions and all exon regions not common to all of the gene's alternative splice forms were removed When no GST can be designed in the most divergent exon regions, SPADS increasingly incorporates less divergent exon regions in its search space (producing GSTs with progressively lower specificity (high, medium or low) and at one point also allows the design of intron-spanning GSTs. At each design level, SPADS scans the gene model from the 3' end to the 5' end. Newly designed GSTs were added to the CATMA database
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes-3
No full text<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-2
No full text<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> hybridizations) in which a given probe had a statistically significant foreground signal. One bar corresponded to one GST feature that was ordered from left to right according to that number. The size (n) of each class is indicated in the top left corner of the five top graphs. The microarray design used for all experiments was registered as A-MEXP-58 in the ArrayExpress repository [17,18]. The graph in the bottom panel presents the curve overlay after scaling the X axis to 100% of the probes in each class. This graph also shows a cumulative distribution of the Cy3 channel signal of the Lucidea [21] background control spikes present on the microarray
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes-1
No full text<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
