Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data

Background: The genome of the fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genomic era of this increasingly popular model organism. We have built fission yeast microarrays, optimised protocols to improve array performance, and carried out experiments to assess various characteristics of microarrays.|Results: We designed PCR primers to amplify specific probes (180-500 bp) for all known and predicted fission yeast genes, which are printed in duplicate onto separate regions of glass slides together with control elements (similar to13,000 spots/slide). Fluorescence signal intensities depended on the size and intragenic position of the array elements, whereas the signal ratios were largely independent of element properties. Only the coding strand is covalently linked to the slides, and our array elements can discriminate transcriptional direction. The microarrays can distinguish sequences with up to 70% identity, above which cross-hybridisation contributes to the signal intensity. We tested the accuracy of signal ratios and measured the reproducibility of array data caused by biological and technical factors. Because the technical variability is lower, it is best to use samples prepared from independent biological experiments to obtain repeated measurements with swapping of fluorochromes to prevent dye bias. We also developed a script that discards unreliable data and performs a normalization to correct spatial artefacts.|Conclusions: This paper provides data for several microarray properties that are rarely measured. The results define critical parameters for microarray design and experiments and provide a framework to optimise and interpret array data. Our arrays give reproducible and accurate expression ratios with high sensitivity. The scripts for primer design and initial data processing as well as primer sequences and detailed protocols are available from our website

Seasonal dependence of peroxy radical concentrations at a northern hemisphere marine boundary layer site during summer and winter: evidence for photochemical activity in winter

International audiencePeroxy radicals (HO2+?RO2) were measured at the Weybourne Atmospheric Observatory (52° N, 1° E), Norfolk using a PEroxy Radical Chemical Amplifier (PERCA) during the winter and summer of 2002. The peroxy radical diurnal cycles showed a marked difference between the winter and summer campaigns with maximum concentrations of 12 pptv at midday in the summer and maximum concentrations as high as 30 pptv (10 min averages) in winter at night. The corresponding nighttime peroxy radical concentrations were not as high in summer (3 pptv). The peroxy radical concentration shows a distinct anti-correlation with increasing NOx during the daylight hours. At night, peroxy radicals increase with increasing NOx indicative of the role of NO3 chemistry. The average diurnal cycles for net ozone production, N(O3) show a large variability in ozone production, P(O3), and a large ozone loss, L(O3) in summer relative to winter. For a daylight average, net ozone production in summer than winter (1.51±0.5 ppbv h?1 and 1.11±0.47 ppbv h?1 respectively) but summer shows more variability of (meteorological) conditions than winter. The variability in NO concentration has a much larger effect on N(O3) than the peroxy radical concentrations. Photostationary state (PSS) calculations show an NO2 lifetime of 5 min in summer and 21 min in the winter, implying that steady-state NO-NO2 ratios are not always attained during the winter months. The results show an active peroxy radical chemistry at night and the ability of winter to make oxidant. The net effect of this with respect to production of ozone in winter is unclear owing to the breakdown in the photostationary state

Seasonal dependence of peroxy radical concentrations at a Northern hemisphere marine boundary layer site during summer and winter: evidence for radical activity in winter

Peroxy radicals (HO2+Σ RO2) were measured at the Weybourne Atmospheric Observatory (52° N, 1° E), Norfolk using a PEroxy Radical Chemical Amplifier (PERCA) during the winter and summer of 2002. The peroxy radical diurnal cycles showed a marked difference between the winter and summer campaigns with maximum concentrations of 12 pptv at midday in the summer and maximum concentrations as high as 30 pptv (10 min averages) in winter at night. The corresponding nighttime peroxy radical concentrations were not as high in summer (3 pptv). The peroxy radical concentration shows a distinct anti-correlation with increasing NOx during the daylight hours. At night, peroxy radicals increase with increasing NOx indicative of the role of NO3 chemistry. The average diurnal cycles for net ozone production, N(O3) show a large variability in ozone production, P(O3), and a large ozone loss, L(O3) in summer relative to winter. For a daylight average, net ozone production in summer was higher than winter (1.51±0.5 ppbv h−1 and 1.11±0.47 ppbv h−1, respectively). The variability in NO concentration has a much larger effect on N(O3) than the peroxy radical concentrations. Photostationary state (PSS) calculations show an NO2 lifetime of 5 min in summer and 21 minutes in the winter, implying that steady-state NO-NO2 ratios are not always attained during the winter months. The results show an active peroxy radical chemistry at night and that significant oxidant levels are sustained in winter. The net effect of this with respect to production of ozone in winter is unclear owing to the breakdown in the photostationary state

Alkyl nitrates in outflow from North America over the North Atlantic during Intercontinental Transport of Ozone and Precursors 2004

This paper is based on alkyl nitrate measurements made over the North Atlantic as part of the International Consortium for Research on Atmospheric Transport and Transformation (ICARTT). The focus is on the analysis of air samples collected on the UK BAe-146 aircraft during the Intercontinental Transport of Ozone and Precursors (ITOP) project, but air samples collected on board the NASA DC-8 and NOAA WP-3D aircraft as part of a Lagrangian experiment are also used. The ratios between the alkyl nitrates and their parent hydrocarbons are compared with those expected from chemical theory. Further, a box model is run to investigate the temporal evolution of the alkyl nitrates in three Lagrangian case studies and compared to observations. The air samples collected during ITOP do not appear to be strongly influenced by oceanic sources, but rather are influenced by emissions from the N.E. United States and from Alaskan fires. There also appears to be a widespread common source of ethyl nitrate and 1-propyl nitrate other than from their parent hydrocarbons. The general agreement between the alkyl nitrate data and photochemical theory suggests that during the first few days of transport from the source region, photochemical production of alkyl nitrates, and thus ozone, had taken place. The observations in the more photochemically processed air masses are consistent with the alkyl nitrate production reactions no longer dominating the peroxy radical self/cross reactions. Further, the results also suggest that the rates of photochemical processing in the Alaskan smoke plumes were small

Intercomparison of aircraft instruments on board the <i>C-130</i> and <i>Falcon 20</i> over southern Germany during EXPORT 2000

International audienceIn the summer 2000 Export aircraft campaign (European eXport of Precursors and Ozone by long-Range Transport), two comprehensively instrumented research aircraft measuring a variety of chemical species flew wing tip to wing tip for a period of one and a quarter hours. During this interval a comparison was undertaken of the measurements of nitrogen oxide (NO), odd nitrogen species (NOy), carbon monoxide (CO) and ozone (O3). The comparison was performed at two different flight levels, which provided a 10-fold variation in the concentrations of both NO (10 to 1000 parts per trillion by volume (pptv)) and NOy (200 to over 2500 pptv). Large peaks of NO and NOy observed from the Falcon 20, which were at first thought to be from the exhaust of the C-130, were also detected on the 4 channel NOx,y instrument aboard the C-130. These peaks were a good indication that both aircraft were in the same air mass and that the Falcon 20 was not in the exhaust plume of the C-130. Correlations and statistical analysis are presented between the instruments used on the two separate aircraft platforms. These were found to be in good agreement giving a high degree of correlation for the ambient air studied. Any deviations from the correlations are accounted for in the estimated inaccuracies of the instruments. These results help to establish that the instruments aboard the separate aircraft are reliably able to measure the corresponding chemical species in the range of conditions sampled and that data collected by both aircraft can be co-ordinated for purposes of interpretation

Mutational and phenotypic characterisation of hereditary hemorrhagic telangiectasia

Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant vascular dysplasia. Care delivery for HHT patients is impeded by the need for laborious, repeated phenotyping and gaps in knowledge regarding the relationships between causal DNA variants in ENG, ACVRL1, SMAD4 and GDF2, and clinical manifestations. To address this, we analyzed DNA samples from 183 previously uncharacterized, unrelated HHT and suspected HHT cases using the ThromboGenomics high-throughput sequencing platform. We identified 127 rare variants across 168 heterozygous genotypes. Applying modified American College of Medical Genetics and Genomics Guidelines, 106 variants were classified as pathogenic/likely pathogenic and 21 as nonpathogenic (variant of uncertain significance/benign). Unlike the protein products of ACVRL1 and SMAD4, the extracellular ENG amino acids are not strongly conserved. Our inferences of the functional consequences of causal variants in ENG were therefore informed by the crystal structure of endoglin. We then compared the accuracy of predictions of the causal gene blinded to the genetic data using 2 approaches: subjective clinical predictions and statistical predictions based on 8 Human Phenotype Ontology terms. Both approaches had some predictive power, but they were insufficiently accurate to be used clinically, without genetic testing. The distributions of red cell indices differed by causal gene but not sufficiently for clinical use in isolation from genetic data. We conclude that parallel sequencing of the 4 known HHT genes, multidisciplinary team review of variant calls in the context of detailed clinical information, and statistical and structural modeling improve the prognostication and treatment of HHT

Chemical composition observed over the mid-Atlantic and the detection of pollution signatures far from source regions

The atmospheric composition of the central North Atlantic region has been sampled using the FAAM BAe146 instrumented aircraft during the Intercontinental Transport of Ozone and Precursors (ITOP) campaign, part of the wider International Consortium for Atmospheric Research on Transport and Transformation (ICARTT). This paper presents an overview of the ITOP campaign. Between late July and early August 2004, twelve flights comprising 72 hours of measurement were made in a region from approximately 20 to 40°W and 33 to 47°N centered on Faial Island, Azores, ranging in altitude from 50 to 9000 m. The vertical profiles of O3 and CO are consistent with previous observations made in this region during 1997 and our knowledge of the seasonal cycles within the region. A cluster analysis technique is used to partition the data set into air mass types with distinct chemical signatures. Six clusters provide a suitable balance between cluster generality and specificity. The clusters are labeled as biomass burning, low level outflow, upper level outflow, moist lower troposphere, marine and upper troposphere. During this summer, boreal forest fire emissions from Alaska and northern Canada were found to provide a major perturbation of tropospheric composition in CO, PAN, organic compounds and aerosol. Anthropogenic influenced air from the continental boundary layer of the USA was clearly observed running above the marine boundary layer right across the mid-Atlantic, retaining high pollution levels in VOCs and sulfate aerosol. Upper level outflow events were found to have far lower sulfate aerosol, resulting from washout on ascent, but much higher PAN associated with the colder temperatures. Lagrangian links with flights of other aircraft over the USA and Europe show that such signatures are maintained many days downwind of emission regions. Some other features of the data set are highlighted, including the strong perturbations to many VOCs and OVOCs in this remote region

Germline mutations in the transcription factor IKZF5 cause thrombocytopenia.

To identify novel causes of hereditary thrombocytopenia, we performed a genetic association analysis of whole-genome sequencing data from 13 037 individuals enrolled in the National Institute for Health Research (NIHR) BioResource, including 233 cases with isolated thrombocytopenia. We found an association between rare variants in the transcription factor-encoding gene IKZF5 and thrombocytopenia. We report 5 causal missense variants in or near IKZF5 zinc fingers, of which 2 occurred de novo and 3 co-segregated in 3 pedigrees. A canonical DNA-zinc finger binding model predicts that 3 of the variants alter DNA recognition. Expression studies showed that chromatin binding was disrupted in mutant compared with wild-type IKZF5, and electron microscopy revealed a reduced quantity of α granules in normally sized platelets. Proplatelet formation was reduced in megakaryocytes from 7 cases relative to 6 controls. Comparison of RNA-sequencing data from platelets, monocytes, neutrophils, and CD4+ T cells from 3 cases and 14 healthy controls showed 1194 differentially expressed genes in platelets but only 4 differentially expressed genes in each of the other blood cell types. In conclusion, IKZF5 is a novel transcriptional regulator of megakaryopoiesis and the eighth transcription factor associated with dominant thrombocytopenia in humans

The double [3+2] photocycloaddition reaction

One of a synthetic organic chemists‟ greatest challenges is to create step-efficient routes toward compounds with high molecular complexity. Therefore, reactions such as the meta photocycloaddition of an olefin to a benzene derivative, which provide more than one bond in a single step are of significant importance. It this remarkable reaction three new σ bonds, three new rings and up to six new stereocenters are formed simultaneously. Additional complexity can be added by tethering the two reacting partners together and this form of the reaction has found many uses in natural product synthesis. In this work a remarkable double [3+2] photocycloaddition reaction is reported that results in the formation of a complex cis, cis, cis, trans-[5, 5, 5, 5] fenestrane derivative from a simple flat aromatic acetal with two branching alkenes. During this dramatic transformation four carboncarbon bonds, five new rings and seven new stereocenters are created in a single one-pot process using only UV light. The reaction occurs in a sequential manner from the linear meta photocycloadduct, via a secondary [3+2] addition of the alkene across the cyclopropane of the adduct. In addition, an angular meta photocycloadduct also produced in the initial addition step, undergoes an alternative fragmentation-translocation photoreaction to afford a silphinene-like angular tricyclic compound. In this work the investigation of this newly discovered process is discussed via the synthesis and subsequent irradiation of a series of photosubstrates containing different functional groups in the arene-alkene tether. In addition, attempts toward the synthesis of alternative structures using the same double [3+2] photocycloaddition are reported