Using the space-borne NASA scatterometer (NSCAT) to determine the frozen and thawed seasons

We hypothesize that the strong sensitivity of radar backscatter to surface dielectric properties, and hence to the phase (solid or liquid) of any water near the surface should make space-borne radar observations a powerful tool for large-scale spatial monitoring of the freeze/thaw state of the land surface, and thus ecosystem growing season length. We analyzed the NASA scatterometer (NSCAT) backscatter from September 1996 to June 1997, along with temperature and snow depth observations and ecosystem modeling, for three BOREAS sites in central Canada. Because of its short wavelength (2.14 cm), NSCAT was sensitive to canopy and surface water. NSCAT had 25 km spatial resolution and approximately twice-daily temporal coverage at the BOREAS latitude. At the northern site the NSCAT signal showed strong seasonality, with backscatter around −8 dB in winter and −12 dB in early summer and fall. The NSCAT signal for the southern sites had less seasonality. At all three sites there was a strong decrease in backscatter during spring thaw (4–6 dB). At the southern deciduous site, NSCAT backscatter rose from −11 to −9.2 dB during spring leaf-out. All sites showed 1–2 dB backscatter shifts corresponding to changes in landscape water state coincident with brief midwinter thaws, snowfall, and extreme cold (Tmax\u3c−25°C). Freeze/thaw detection algorithms developed for other radar instruments gave reasonable results for the northern site but were not successful at the two southern sites. We developed a change detection algorithm based on first differences of 5-day smoothed NSCAT backscatter measurements. This algorithm had some success in identifying the arrival of freezing conditions in the autumn and the beginning of thaw in the spring. Changes in surface freeze/thaw state generally coincided with the arrival and departure of the seasonal snow cover and with simulated shifts in the directions of net carbon exchange at each of the study sites

Influence of soil properties on archaeal diversity and distribution in the McMurdo Dry Valleys, Antarctica

Archaea are the least understood members of the microbial community in Antarctic mineral soils. Although their occurrence in Antarctic coastal soils has been previously documented, little is known about their distribution in soils across the McMurdo Dry Valleys, Victoria Land. In this study, terminal-restriction fragment length polymorphism (t-RFLP) analysis and 454 pyrosequencing were coupled with a detailed analysis of soil physicochemical properties to characterize archaeal diversity and identify environmental factors that might shape and maintain archaeal communities in soils of the three southern most McMurdo Dry Valleys (Garwood, Marshall, and Miers Valley). Archaea were successfully detected in all inland and coastal mineral soils tested, revealing a low overall richness (mean of six operational taxonomic units [OTUs] per sample site). However, OTU richness was higher in some soils and this higher richness was positively correlated with soil water content, indicating water as a main driver of archaeal community richness. In total, 18 archaeal OTUs were detected, predominately Thaumarchaeota affiliated with Marine Group 1.1b (> 80% of all archaeal sequences recovered). Less abundant OTUs (2% of all archaeal sequences) were loosely related to members of the phylum Euryarchaeota. This is the first comprehensive study showing a widespread presence and distribution of Archaea in inland Antarctic soils

Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast

A combined multidimensional chromatography-mass spectrometry approach known as "MudPIT" enables rapid identification of proteins that interact with a tagged bait while bypassing some of the problems associated with analysis of polypeptides excised from SDS-polyacrylamide gels. However, the reproducibility, success rate, and applicability of MudPIT to the rapid characterization of dozens of proteins have not been reported. We show here that MudPIT reproducibly identified bona fide partners for budding yeast Gcn5p. Additionally, we successfully applied MudPIT to rapidly screen through a collection of tagged polypeptides to identify new protein interactions. Twenty-five proteins involved in transcription and progression through mitosis were modified with a new tandem affinity purification (TAP) tag. TAP-MudPIT analysis of 22 yeast strains that expressed these tagged proteins uncovered known or likely interacting partners for 21 of the baits, a figure that compares favorably with traditional approaches. The proteins identified here comprised 102 previously known and 279 potential physical interactions. Even for the intensively studied Swi2p/Snf2p, the catalytic subunit of the Swi/Snf chromatin remodeling complex, our analysis uncovered a new interacting protein, Rtt102p. Reciprocal tagging and TAP-MudPIT analysis of Rtt102p revealed subunits of both the Swi/Snf and RSC complexes, identifying Rtt102p as a common interactor with, and possible integral component of, these chromatin remodeling machines. Our experience indicates it is feasible for an investigator working with a single ion trap instrument in a conventional molecular/cellular biology laboratory to carry out proteomic characterization of a pathway, organelle, or process (i.e. "pathway proteomics") by systematic application of TAP-MudPIT

Impacts of large-scale oscillations on pan-Arctic terrestrial net primary production

Analyses of regional climate oscillations and satellite remote sensing derived net primary production (NPP) and growing season dynamics for the pan-Arctic region indicate that the oscillations influence NPP by regulating seasonal patterns of low temperature and moisture constraints to photosynthesis. Early-spring (Feb–Apr) patterns of the Arctic Oscillation (AO) are proportional to growing season onset (r = −0.653; P = 0.001), while growing season patterns of the Pacific Decadal Oscillation (PDO) are proportional to plant-available moisture constraints to NPP (Im) (r = −0.471; P = 0.023). Relatively strong, negative PDO phases from 1988–1991 and 1998–2002 coincided with prolonged regional droughts indicated by a standardized moisture stress index. These severe droughts resulted in widespread reductions in NPP, especially for relatively drought prone boreal forest and grassland/cropland ecosystems. The influence of AO and PDO patterns on northern vegetation productivity appears to be decreasing and increasing, respectively, as low temperature constraints to plant growth relax and NPP becomes increasingly limited by available water supply under a warming climate

The manifest association structure of the single-factor model: insights from partial correlations

The association structure between manifest variables arising from the single-factor model is investigated using partial correlations. The additional insights to the practitioner provided by partial correlations for detecting a single-factor model are discussed. The parameter space for the partial correlations is presented, as are the patterns of signs in a matrix containing the partial correlations that are not compatible with a single-factor model

Cosmological evolution of scalar fields and gravitino dark matter in gauge mediation at low reheating temperatures

We consider the dynamics of the supersymmetry-breaking scalar field and the production of dark matter gravitinos via its decay in a gauge-mediated supersymmetry breaking model with metastable vacuum. We find that the scalar field amplitude and gravitino density are extremely sensitive to the parameters of the hidden sector. For the case of an O'Raifeartaigh sector, we show that the observed dark matter density can be explained by gravitinos even for low reheating temperatures T_{R} < 10 GeV. Such low reheating temperatures may be implied by detection of the NLSP at the LHC if its thermal freeze-out density is in conflict with BBN.Comment: 11 pages RevTex. Extended discussion and minor corrections, conclusions unaltered. Version to be published in JCA

Charting the protein complexome in yeast by mass spectrometry

It has become evident over the past few years that many complex cellular processes, including control of the cell cycle and ubiquitin-dependent proteolysis, are carried out by sophisticated multisubunit protein machines that are dynamic in abundance, post-translational modification state, and composition. To understand better the nature of the macromolecular assemblages that carry out the cell cycle and ubiquitin-dependent proteolysis, we have used mass spectrometry extensively over the past few years to characterize both the composition of various protein complexes and the modification states of their subunits. In this article we review some of our recent efforts, and describe a promising new approach for using mass spectrometry to dissect protein interaction networks

Proposal for a low cost close air support aircraft for the year 2000: The Raptor

The Raptor is a proposed low cost Close Air Support (CAS) aircraft for the U.S. Military. The Raptor incorporates a 'cranked arrow' wing planform, and uses canards instead of a traditional horizontal tail. The Raptor is designed to be capable of responsive delivery of effective ordnance in close proximity to friendly ground forces during the day, night, and 'under the weather' conditions. Details are presented of the Raptor's mission, configuration, performance, stability and control, ground support, manufacturing, and overall cost to permit engineering evaluation of the proposed design. A description of the design process and analysis methods used is also provided

Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences

BACKGROUND: LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. RESULTS: To explore the evolutionary history of long terminal repeat (LTR) retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTR-retrotransposons per Mb were detected in Chromosome 10. CONCLUSIONS: Gypsy-like elements were found to be >4 × more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (< 680,000 years). LTR-retrotransposons present in the rice genome range in age from those just recently inserted up to nearly 10 million years old. Approximately 20% of LTR retrotransposon sequences lie within putative genes. The distribution of elements across chromosome 10 is non-random with the highest density (48 elements per Mb) being present in the pericentric region