Structure of Cdc4p, a Contractile Ring Protein Essential for Cytokinesis in Schizosaccharomyces pombe

The Schizosaccharomyces pombe Cdc4 protein is required for the formation and function of the contractile ring, presumably acting as a myosin light chain. By using NMR spectroscopy, we demonstrate that purified Cdc4p is a monomeric protein with two structurally independent domains, each exhibiting a fold reminiscent of the EF-hand class of calcium-binding proteins. Although Cdc4p has one potentially functional calcium-binding site, it does not bind calcium in vitro. Three variants of Cdc4p containing single point mutations responsible for temperature-sensitive arrest of the cell cycle at cytokinesis (Gly-19 to Glu, Gly-82 to Asp, and Gly-107 to Ser) were also characterized by NMR and circular dichroism spectroscopy. In each case, the amino acid substitution only leads to small perturbations in the conformation of the protein. Furthermore, thermal unfolding studies indicate that, like wild-type Cdc4p, the three mutant forms are all extremely stable, remaining completely folded at temperatures significantly above those causing failure of cytokinesis in intact cells. Therefore, the altered phenotype must arise directly from a disruption of the function of Cdc4p rather than indirectly through a disruption of its overall structure. Several mutant alleles of Cdc4p also show interallelic complementation in diploid cells. This phenomenon can be explained if Cdcp4 has more than one essential function or, alternatively, if two mutant proteins assemble to form a functional complex. Based on the structure of Cdc4p, possible models for interallelic complementation including interactions with partner proteins and the formation of a myosin complex with Cdc4p fulfilling the role of both an essential and regulatory light chain are proposed

Establishing Lagrangian connections between observations within air masses crossing the Atlantic during the International Consortium for Atmospheric Research on Transport and Transformation experiment

The ITCT-Lagrangian-2K4 (Intercontinental Transport and Chemical Transformation) experiment was conceived with an aim to quantify the effects of photochemistry and mixing on the transformation of air masses in the free troposphere away from emissions. To this end, attempts were made to intercept and sample air masses several times during their journey across the North Atlantic using four aircraft based in New Hampshire (USA), Faial (Azores) and Creil (France). This article begins by describing forecasts from two Lagrangian models that were used to direct the aircraft into target air masses. A novel technique then identifies Lagrangian matches between flight segments. Two independent searches are conducted: for Lagrangian model matches and for pairs of whole air samples with matching hydrocarbon fingerprints. The information is filtered further by searching for matching hydrocarbon samples that are linked by matching trajectories. The quality of these "coincident matches'' is assessed using temperature, humidity and tracer observations. The technique pulls out five clear Lagrangian cases covering a variety of situations and these are examined in detail. The matching trajectories and hydrocarbon fingerprints are shown, and the downwind minus upwind differences in tracers are discussed

The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress

BACKGROUND: Yeast responding to stress activate a large gene expression program called the Environmental Stress Response that consists of approximately 600 repressed genes and approximately 300 induced genes. Numerous factors are implicated in regulating subsets of Environmental Stress Response genes; however, a complete picture of Environmental Stress Response regulation remains unclear. We investigated the role of the histone deacetylase Rpd3p, previously linked to the upstream regions of many Environmental Stress Response genes, in producing Environmental Stress Response gene expression changes in response to stress. RESULTS: We found that the Rpd3-Large complex is required for proper expression of both induced and repressed Environmental Stress Response genes under multiple stress conditions. Cells lacking RPD3 or the Rpd3-Large subunit PHO23 had a major defect in Environmental Stress Response initiation, particularly during the transient phase of expression immediately after stress exposure. Chromatin-immunoprecipitation showed a direct role for Rpd3-Large at representative genes; however, there were different effects on nucleosome occupancy and histone deacetylation at different promoters. Computational analysis implicated regulators that may act with Rpd3p at Environmental Stress Response genes. We provide genetic and biochemical evidence that Rpd3p is required for binding and action of the stress-activated transcription factor Msn2p, although the contribution of these factors differs for different genes. CONCLUSIONS: Our results implicate Rpd3p as an important co-factor in the Environmental Stress Response regulatory network, and suggest the importance of histone modification in producing transient changes in gene expression triggered by stress

Western Pacific atmospheric nutrient deposition fluxes, their impact on surface ocean productivity

The atmospheric deposition of both macronutrients and micronutrients plays an important role in driving primary productivity, particularly in the low-latitude ocean. We report aerosol major ion measurements for five ship-based sampling campaigns in the western Pacific from similar to 25 degrees N to 20 degrees S and compare the results with those from Atlantic meridional transects (similar to 50 degrees N to 50 degrees S) with aerosols collected and analyzed in the same laboratory, allowing full incomparability. We discuss sources of the main nutrient species (nitrogen (N), phosphorus (P), and iron (Fe)) in the aerosols and their stoichiometry. Striking north-south gradients are evident over both basins with the Northern Hemisphere more impacted by terrestrial dust sources and anthropogenic emissions and the North Atlantic apparently more impacted than the North Pacific. We estimate the atmospheric supply rates of these nutrients and the potential impact of the atmospheric deposition on the tropical western Pacific. Our results suggest that the atmospheric deposition is P deficient relative to the needs of the resident phytoplankton. These findings suggest that atmospheric supply of N, Fe, and P increases primary productivity utilizing some of the residual excess phosphorus (P*) in the surface waters to compensate for aerosol P deficiency. Regional primary productivity is further enhanced via the stimulation of nitrogen fixation fuelled by the residual atmospheric iron and P*. Our stoichiometric calculations reveal that a P* of 0.1 mu mol L-1 can offset the P deficiency in atmospheric supply for many months. This study suggests that atmospheric deposition may sustain similar to 10% of primary production in both the western tropical Pacific

Atmospheric sulfur cycling in the southeastern Pacific – longitudinal distribution, vertical profile, and diel variability observed during VOCALS-REx

Dimethylsulfide (DMS) emitted from the ocean is a biogenic precursor gas for sulfur dioxide (SO<sub>2</sub>) and non-sea-salt sulfate aerosols (SO<sub>4</sub><sup>2−</sup>). During the VAMOS-Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx) in 2008, multiple instrumented platforms were deployed in the Southeastern Pacific (SEP) off the coast of Chile and Peru to study the linkage between aerosols and stratocumulus clouds. We present here observations from the NOAA Ship <i>Ronald H. Brown</i> and the NSF/NCAR C-130 aircraft along ~20° S from the coast (70° W) to a remote marine atmosphere (85° W). While SO<sub>4</sub><sup>2−</sup> and SO<sub>2</sub> concentrations were distinctly elevated above background levels in the coastal marine boundary layer (MBL) due to anthropogenic influence (~800 and 80 pptv, respectively), their concentrations rapidly decreased west of 78° W (~100 and 25 pptv). In the remote region, entrainment from the free troposphere (FT) increased MBL SO<sub>2</sub> burden at a rate of 0.05 ± 0.02 μmoles m<sup>−2</sup> day<sup>−1</sup> and diluted MBL SO<sub>4</sub><sup>2</sup> burden at a rate of 0.5 ± 0.3 μmoles m<sup>−2</sup> day<sup>−1</sup>, while the sea-to-air DMS flux (3.8 ± 0.4 μmoles m<sup>−2</sup> day<sup>−1</sup>) remained the predominant source of sulfur mass to the MBL. In-cloud oxidation was found to be the most important mechanism for SO<sub>2</sub> removal and in situ SO<sub>4</sub><sup>2−</sup> production. Surface SO<sub>4</sub><sup>2−</sup> concentration in the remote MBL displayed pronounced diel variability, increasing rapidly in the first few hours after sunset and decaying for the rest of the day. We theorize that the increase in SO<sub>4</sub><sup>2−</sup> was due to nighttime recoupling of the MBL that mixed down cloud-processed air, while decoupling and sporadic precipitation scavenging were responsible for the daytime decline in SO<sub>4</sub><sup>2−</sup>

Multi-Decadal Aerosol Variations from 1980 to 2009: A Perspective from Observations and a Global Model

Aerosol variations and trends over different land and ocean regions during 1980-2009 are analyzed with the Goddard Chemistry Aerosol Radiation and Transport (GOCART) model and observations from multiple satellite sensors and ground-based networks. Excluding time periods with large volcanic influences, the tendency of aerosol optical depth (AOD) and surface concentration over polluted land regions is consistent with the anthropogenic emission changes.The largest reduction occurs over Europe, and regions in North America and Russia also exhibit reductions. On the other hand, East Asia and South Asia show AOD increases, although relatively large amount of natural aerosols in Asia makes the total changes less directly connected to the pollutant emission trends. Over major dust source regions, model analysis indicates that the dust emissions over the Sahara and Sahel respond mainly to the near-surface wind speed, but over Central Asia they are largely influenced by ground wetness. The decreasing dust trend in the tropical North Atlantic is most closely associated with the decrease of Sahel dust emission and increase of precipitation over the tropical North Atlantic, likely driven by the sea surface temperature increase. Despite significant regional trends, the model-calculated global annual average AOD shows little changes over land and ocean in the past three decades, because opposite trends in different regions cancel each other in the global average. This highlights the need for regional-scale aerosol assessment, as the global average value conceals regional changes, and thus is not sufficient for assessing changes in aerosol loading

Computational analyses of eukaryotic promoters

Computational analysis of eukaryotic promoters is one of the most difficult problems in computational genomics and is essential for understanding gene expression profiles and reverse-engineering gene regulation network circuits. Here I give a basic introduction of the problem and recent update on both experimental and computational approaches. More details may be found in the extended references. This review is based on a summer lecture given at Max Planck Institute at Berlin in 2005

Ozone observations and a model of marine boundary layer photochemistry during SAGA 3

A major purpose of the third joint Soviet‐American Gases and Aerosols (SAGA 3) oceanographic cruise was to examine remote tropical marine O3 and photochemical cycles in detail. On leg 1, which took place between Hilo, Hawaii, and Pago‐Pago, American Samoa, in February and March 1990, shipboard measurements were made of O3, CO, CH4, nonmethane hydrocarbons (NMHC), NO, dimethyl sulfide (DMS), H2S, H2O2, organic peroxides, and total column O3. Postcruise analysis was performed for alkyl nitrates and a second set of nonmethane hydrocarbons. A latitudinal gradient in O3 was observed on SAGA 3, with O3 north of the intertropical convergence zone (ITCZ) at 15–20 parts per billion by volume (ppbv) and less than 12 ppbv south of the ITCZ but never ≤3 ppbv as observed on some previous equatorial Pacific cruises (Piotrowicz et al., 1986; Johnson et al., 1990). Total column O3 (230–250 Dobson units (DU)) measured from the Akademik Korolev was within 8% of the corresponding total ozone mapping spectrometer (TOMS) satellite observations and confirmed the equatorial Pacific as a low O3 region. In terms of number of constituents measured, SAGA 3 may be the most photochemically complete at‐sea experiment to date. A one‐dimensional photochemical model gives a self‐consistent picture of O3‐NO‐CO‐hydrocarbon interactions taking place during SAGA 3. At typical equatorial conditions, mean O3 is 10 ppbv with a 10–15% diurnal variation and maximum near sunrise. Measurements of O3, CO, CH4, NMHC, and H2O constrain model‐calculated OH to 9 × 105 cm−3 for 10 ppbv O3 at the equator. For DMS (300–400 parts per trillion by volume (pptv)) this OH abundance requires a sea‐to‐air flux of 6–8 × 109 cm−2 s−1, which is within the uncertainty range of the flux deduced from SAGA 3 measurements of DMS in seawater (Bates et al., this issue). The concentrations of alkyl nitrates on SAGA 3 (5–15 pptv total alkyl nitrates) were up to 6 times higher than expected from currently accepted kinetics, suggesting a largely continental source for these species. However, maxima in isopropyl nitrate and bromoform near the equator (Atlas et al., this issue) as well as for nitric oxide (Torres and Thompson, this issue) may signify photochemical and biological sources of these species