Genomic organization of the mouse T-cell receptor β-chain gene family

We have combined three different methods, deletion mapping of T-cell lines, field-inversion gel electrophoresis, and the restriction mapping of a cosmid clone, to construct a physical map of the murine T-cell receptor β-chain gene family. We have mapped 19 variable (Vβ) gene segments and the two clusters of diversity (Dβ) and joining (Jβ) gene segments and constant (Cβ) genes. These members of the β-chain gene family span ~450 kilobases of DNA, excluding one potential gap in the DNA fragment alignments

"The Hero as Man of Letters": Intellectual Politics and the Construction of the Romantic Epic

Although the thirty years from 1794 to 1824 saw the production of more epic poetry than any other period in British literary history, the epic's function within the culture of Romanticism remains largely misunderstood and neglected. The problem in theorizing the Romantic epic stems from the uncommon diversity of epic performances during this period and from the epic's sudden reappearance after a long period of apparent dormancy in the eighteenth century. When the Romantic epic is defined, however, not as poetic form but as a repeated political act, the epic's eighteenth-century history now appears as a continuous process of generic transformation and its formal diversity no longer threatens its generic categorization. In place of understanding the epic as literary genre, I define the Romantic epic as a recurring and highly stylized rhetorical intervention by the intellectual community beginning in the mid-eighteenth century with the primary function of expanding the power of the intellectual "class." Investigating the epic's eighteenth-century transformation, I examine the relationship between classical epics and William Collins and Thomas Gray's Pindaric odes, James Macpherson's Ossian "translations," and James Beattie's Minstrel. I argue that these so-called pre-Romantic poems reveal both a Romantic rejection of the Augustan epic and a Romantic desire to repurpose the epic's structures toward the emerging interests of the intellectual community. The conscious task was to develop a new epic mode, one that would make a hero of the man of letters, to write the kind of epic performance found in Robert Southey's Joan of Arc. Focusing on the Romantic epic's function, I demonstrate that the Romantic epic provided a pattern through which intellectuals began to see themselves and the world. In order to change society Romantic intellectuals were modifying the genre which, in turn, was reshaping intellectual consciousness. Thus, acting reciprocally, I show that the epic was at the center of the larger Romantic project: an intellectual effort to deliver humanity from commercial society

MHD Mode Conversion around a 2D Magnetic Null Point

Mode conversion occurs when a wave passes through a region where the sound and Alfven speeds are equal. At this point there is a resonance, which allows some of the incident wave to be converted into a different mode. We study this phenomenon in the vicinity of a two-dimensional, coronal null point. As a wave approaches the null it passes from low- to high-beta plasma, allowing conversion to take place. We simulate this numerically by sending in a slow magnetoacoustic wave from the upper boundary; as this passes through the conversion layer a fast wave can clearly be seen propagating ahead. Numerical simulations combined with an analytical WKB investigation allow us to determine and track both the incident and converted waves throughout the domain.Comment: 4 pages, 2 figure

Juvenile salmon density on marsh surfaces versus within tidal channels

Use of tidal marsh surfaces by juvenile salmon in Pacific Northwest estuaries has generally been ignored by ecologists, engineers and planners involved in salmon habitat restoration. In contrast, fish use of marsh plains has been documented in many other parts of the world. Are Pacific Northwest marshes an exception to the pattern of fish use that is so common elsewhere? For three consecutive years, fish were sampled bi-monthly in tidal channels and on tidal marsh plains of the Skagit Delta to answer this question. Juvenile Chinook and chum salmon, as well as sticklebacks were the most consistently caught and abundant fish in channels and on the marsh surface, but eight other fish species were also found on the marsh surface. While fish densities were much higher in tidal channels than on marsh surfaces, marsh surface area was much greater than channel area, so sticklebacks and juvenile chum were potentially 50% more numerous on the marsh surface than in channels. However, due to their high channel densities, juvenile Chinook were nevertheless more abundant in tidal channels than on the marsh surface; those on the marsh surface amounted to 40% of those in tidal channels. The ratio of marsh surface to channel fish density peaks late in the season for all three fish species, which may be a response to increased prey production over the marsh plain. The substantial use of the marsh surface by juvenile salmon that we observed suggests estuarine habitat restoration for salmon recovery should not neglect the direct value of vegetated marsh plains to juvenile salmon. Tidal marsh habitat for juvenile salmon is more than just tidal channels. Partial habitat restoration that only restores tidal flow to channels and not to adjacent marshes, e.g., using self-regulating tide gates (SRTs), has a direct impact on juvenile salmon habitat use

AMPR/SSMI data comparisons

The AMPR was flown during CAPE and STORMFEST, during which some good data were gathered. Significant instrument noise problems were encountered in both deployments which appear to be temperature related. These are being fixed before the TOGA COARE deployment. New calibration loads have also been manufactured for the TOGA COARE configuration. Eric Smith at FSU had been analyzing the AMPR data and has written a journal article to be submitted early this summer. The emphasis of his work is on the interpretation of low resolution microwave data from space, based upon what we have learned from the high-resolution AMPR signatures

EST analysis of gene expression in early cleavage-stage sea urchin embryos

A set of 956 expressed sequence tags derived from 7-hour (mid-cleavage) sea urchin embryos was analyzed to assess biosynthetic functions and to illuminate the structure of the message population at this stage. About a quarter of the expressed sequence tags represented repetitive sequence transcripts typical of early embryos, or ribosomal and mitochondrial RNAs, while a majority of the remainder contained significant open reading frames. A total of 232 sequences, including 153 different proteins, produced significant matches when compared against GenBank. The majority of these identified sequences represented ‘housekeeping’ proteins, i.e., cytoskeletal proteins, metabolic enzymes, transporters and proteins involved in cell division. The most interesting finds were components of signaling systems and transcription factors not previously reported in early sea urchin embryos, including components of Notch and TGF signal transduction pathways. As expected from earlier kinetic analyses of the embryo mRNA populations, no very prevalent protein-coding species were encountered; the most highly represented such sequences were cDNAs encoding cyclins A and B. The frequency of occurrence of all sequences within the database was used to construct a sequence prevalence distribution. The result, confirming earlier mRNA population analyses, indicated that the poly(A) RNA of the early embryo consists mainly of a very complex set of low-copy-number transcripts

ENV-644: USE OF NEW MODELS TO SUPPORT VAPOUR INTRUSION MITIGATION DESIGN

Soil vapour intrusion of subsurface volatile organic compounds (VOCs) into indoor air of buildings is a significant potential concern at existing sites where chemical releases occur, or at new buildings at Brownfield sites with residual chemical impacts. While soil vapour intrusion mitigation systems are increasingly being implemented, there are limited published data on mitigation performance for VOCs particularly for industrial or commercial buildings or high density residential buildings with below ground parking garages. Data gaps include the effectiveness of passive and active venting systems and reduction in vapour intrusion that can be achieved relative to unmitigated buildings. Because of lack of knowledge and standardization, design practices and post-mitigation monitoring requirements vary widely and are, in some cases, over-conservative. To address these gaps, a comprehensive empirical review of data on the performance of active and passive venting systems and a study using the Modified Johnson and Ettinger Model was completed. The empirical data indicate performance of passive venting systems are variable in terms of venting air flow rates and pressures. The results of modelling for passive venting indicate a wide range of predicted reduction factors, defined as the vapour attenuation factor for a baseline unmitigated building divided by the attenuation factor for the mitigated case. Because of the potential for depressurized buildings and/or reverse vent stack effect, for passive venting systems a continuous leak free barrier that reduces the potential for soil gas diffusion and advection is essential. The performance of active venting systems can be more readily controlled and quantified based on design principles as supported by the results of modelling, which indicated higher reduction factors than for passive venting systems. For both passive and active venting systems, improved efficiency in venting can be achieved through aerated subfloors. A monitoring framework that is robust but efficient and sustainable is presented that incorporates the concept of a concentration exceedance factor and the type of mitigation system

Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1

BACKGROUND: Large fractions of all fully sequenced genomes code for proteins of unknown function. Annotating these proteins of unknown function remains a critical bottleneck for systems biology and is crucial to understanding the biological relevance of genome-wide changes in mRNA and protein expression, protein-protein and protein-DNA interactions. The work reported here demonstrates that de novo structure prediction is now a viable option for providing general function information for many proteins of unknown function. RESULTS: We have used Rosetta de novo structure prediction to predict three-dimensional structures for 1,185 proteins and protein domains (<150 residues in length) found in Halobacterium NRC-1, a widely studied halophilic archaeon. Predicted structures were searched against the Protein Data Bank to identify fold similarities and extrapolate putative functions. They were analyzed in the context of a predicted association network composed of several sources of functional associations such as: predicted protein interactions, predicted operons, phylogenetic profile similarity and domain fusion. To illustrate this approach, we highlight three cases where our combined procedure has provided novel insights into our understanding of chemotaxis, possible prophage remnants in Halobacterium NRC-1 and archaeal transcriptional regulators. CONCLUSIONS: Simultaneous analysis of the association network, coordinated mRNA level changes in microarray experiments and genome-wide structure prediction has allowed us to glean significant biological insights into the roles of several Halobacterium NRC-1 proteins of previously unknown function, and significantly reduce the number of proteins encoded in the genome of this haloarchaeon for which no annotation is available

Assessing tidal marsh vulnerability to sea-level rise in the Skagit Delta

Historical aerial photos, from 1937 to the present, show Skagit Delta tidal marshes prograding into Skagit Bay throughout most of the record, but the progradation rates have been steadily declining and become negative in recent decades, i.e., the marshes have begun to erode. If past trends continue, the marshes will continue eroding despite the large suspended sediment load provided by the river. Within the bay-fringe region between the North and South Fork Skagit River distributaries, an area isolated from direct riverine sediment supply by anthropogenic blockage of historical distributaries, 0.5-m tall marsh cliffs along with concave marsh profiles indicate wave erosion is contributing to marsh retreat. This is further supported by a “natural experiment” provided by rocky outcrops that shelter high marsh in their lee, while being bounded by 0.5-m lower eroded marsh to windward and on either side. GIS analysis of the bay-fringe marsh indicates that relative to modern LIDAR data the seaward edge of the 1972 marsh (its maximal extent) was 15 cm lower in elevation than the 2012 marsh edge; this comparison assumes no change in marsh slope during the last 40 years. Tide gauge data show sea level rose 7.9 ± 4.6 cm during this time, suggesting sea level rise accounts for a substantial portion of the elevation difference, while erosion may have contributed to the rest. Coastal wetlands with high sediment supply are considered resilient to sea level rise, but the Skagit Delta shows this is not necessarily true. A combination of sea level rise and wave-generated erosion may overwhelm sediment supply. Additionally, constructed levees intensify river jet momentum thereby delivering most suspended sediment far offshore where it is unavailable for marsh accretion. Adaptive response to the threat of sea level rise should consider the efficacy of restoring historical distributaries and managed retreat of constrictive river levees to maximize sediment delivery to delta marshes

The Hurricane Imaging Radiometer (HIRAD): Instrument Status and Performance Predictions

The Hurricane Imaging Radiometer (HIRAD) is an innovative radiometer which offers new and unique remotely sensed observations of both extreme oceanic wind events and strong precipitation. It is based on the airborne Stepped Frequency Microwave Radiometer (SFMR) [Uhlhorn and Black, 2004]. The HIRAD instrument advances beyond the current nadir viewing SFMR to an equivalent wide-swath SFMR imager using passive microwave synthetic thinned aperture radiometer (STAR) technology [Ruf et al., 1988]. This sensor operates over 4-7 GHz, where the required tropical cyclone remote sensing physics has been validated by both SFMR and WindSat radiometer [Bettenhausen et al., 2006; Brown et al., 2006]. HIRAD incorporates a new and unique array antenna design along with several technologies successfully demonstrated by the Lightweight Rain Radiometer instrument [Ruf et al., 2002; Ruf and Principe, 2003]. HIRAD will be a compact, lightweight, low-power instrument with no moving parts that will produce wide-swath imagery of ocean winds and rain in hurricane conditions. Accurate observations of surface ocean vector winds (OVW) with high spatial and temporal resolution are required for understanding and predicting tropical cyclones. The Hurricane Imaging Radiometer (HIRAD) is an innovative architecture which offers new and unique remotely sensed observations of both extreme oceanic wind events and strong precipitation. It is based on the airborne Stepped Frequency Microwave Radiometer (SFMR), which is a proven remote sensing technique for observing tropical cyclone (TC) ocean surface wind speeds and rain rates. The proposed HIRAD instrument advances beyond the current nadir viewing SFMR to an equivalent wide-swath SFMR imager using passive microwave synthetic thinned aperture radiometer (STAR) technology combined with a a unique array antenna design. The overarching design concept of HIRAD is to combine the multi-frequency C-band observing strategy of the SFMR with STAR technology to produce a wide-swath imager. Single frequency STAR technology The Hurricane Imaging Radiometer (HIRAD) is an innovative radiometer which offers new and unique remotely sensed observations of both extreme oceanic wind events and strong precipitation. It is based on the airborne Stepped Frequency Microwave Radiometer (SFMR) [Uhlhorn and Black, 2004]. The HIRAD instrument advances beyond the current nadir viewing SFMR to an equivalent wide-swath SFMR imager using passive microwave synthetic thinned aperture radiometer (STAR) technology [Ruf et al., 1988]. This sensor operates over 4-7 GHz, where the required tropical cyclone remote sensing physics has been validated by both SFMR and WindSat radiometer [Bettenhausen et al., 2006; Brown et al., 2006]. HIRAD incorporates a new and unique array antenna design along with several technologies successfully demonstrated by the Lightweight Rain Radiometer instrument [Ruf et al., 2002; Ruf and Principe, 2003]. HIRAD will be a compact, lightweight, low-power instrument with no moving parts that will produce wide-swath imagery of ocean winds and rain in hurricane conditions. Accurate observations of surface ocean vector winds (OVW) with high spatial and temporal resolution are required for understanding and predicting tropical cyclones. The Hurricane Imaging Radiometer (HIRAD) is an innovative architecture which offers new and unique remotely sensed observations of both extreme oceanic wind events and strong precipitation. It is based on the airborne Stepped Frequency Microwave Radiometer (SFMR), which is a proven remote sensing technique for observing tropical cyclone (TC) ocean surface wind speeds and rain rates. The proposed HIRAD instrument advances beyond the current nadir viewing SFMR to an equivalent wide-swath SFMR imager using passive microwave synthetic thinned aperture radiometer (STAR) technology combined with a a unique array antenna design. The overarching design concept of HIRAD is to combine the multi-frequency C-banbserving strategy of the SFMR with STAR technology to produce a wide-swath imager. Single frequency STAR technolog