Characterization of Fine Particulate Matter (PM) and Secondary PM Precursor Gases in Mexico City

This project was one of three collaborating grants designed to understand the atmospheric chemistry and aerosol particle microphysics impacting air quality in the Mexico City Metropolitan Area (MCMA) and its urban plume. The overall effort, titled MCMA- 2006, focused on: 1) the primary emissions of fine particles and precursor gases leading to photochemical production of atmospheric oxidants and secondary aerosol particles and 2) the measurement and analysis of secondary oxidants and secondary fine particular matter (PM) production, with particular emphasis on secondary organic aerosol (SOA). MCAM-2006 pursued it goals through three main activities: 1) performance and publication of detailed analyses of extensive MCMA trace gas and fine PM measurements made by the collaborating groups and others during earlier MCMA field campaigns in 2002 and 2003; 2) deployment and utilization of extensive real-time trace gas and fine PM instrumentation at urban and downwind MCMA sites in support of the MAX-Mex/MILAGRO field measurements in March, 2006; and, 3) analyses of the 2006 MCMA data sets leading to further publications that are based on new data as well as insights from analysis and publication of the 2002/2003 field data. Thirteen archival publications were coauthored with other MCMA-2003 participants. Documented findings included a significantly improved speciated emissions inventory from on-road vehicles, a greatly enhanced understanding of the sources and atmospheric loadings of volatile organic compounds, a unique analysis of the high fraction of ambient formaldehyde from primary emission sources, a much more extensive knowledge of the composition, size distributions and atmospheric mass loadings of both primary and secondary fine PM, including the fact that the rate of MCMA SOA production greatly exceeded that predicted by current atmospheric models, and evaluations of significant errors that can arise from standard air quality monitors for ozone and nitrogen dioxide. Deployment of the Aerodyne mobile laboratory, equipped with instruments from five collaborating laboratories, at the T0 urban supersite, four downwind sites and the Tula industrial area yielded unique trace gas and fine PM data sets during the March 2006 MAXMex/MILAGRO campaign. In addition, on-road measurements as the mobile laboratory moved between sites provided extensive data on 2006 MCMA fleet averaged vehicle emissions. Analyses of 2006 data sets have yielded the identification of a close correlation between the rate of production of SOA and “Odd Oxygen” (O3 + NO2) and primary organic PM with CO in the MCMA urban plume, a more sophisticated understanding of the interplay between nitrogen oxide speciation and ozone production, the identification of significant vehicular emission sources of HCN and CH3CN (usually associated with biomass burning), characterization of the aging of primary carbonaceous PM, and updated 2006 MCMA fleet on-road trace gas and fine PM emissions. Results from analyses of 2002/2003 and 2006 emissions and ambient measurements have conveyed to Mexican air quality managers who are using these data to devise and assess air quality management strategies. All data sets and published analyses are available to DOE/ASP researchers evaluating the impact of urban emissions on regional climate

The Escherichia coli effector EspJ blocks Src kinase activity via amidation and ADP ribosylation

J.C.Y. was funded by an MRC PhD studentship. D.J.B. is supported by a London Research Institute, Cancer Research UK Postdoctoral Fellowship award and M.W. is supported by Cancer Research UK. K.A. was supported by the Deutsche Forschungsgemeinschaft (AK 6/22-1 and AK 6/22-2) and the Center for Biological Signaling Studies in Freiburg (Germany). This work was supported by grants from the Wellcome Trust to G.F. and S.J.M

Identifying Critical Non-Catalytic Residues that Modulate Protein Kinase A Activity

Distal interactions between discrete elements of an enzyme are critical for communication and ultimately for regulation. However, identifying the components of such interactions has remained elusive due to the delicate nature of these contacts. Protein kinases are a prime example of an enzyme with multiple regulatory sites that are spatially separate, yet communicate extensively for tight regulation of activity. Kinase misregulation has been directly linked to a variety of cancers, underscoring the necessity for understanding intramolecular kinase regulation.A genetic screen was developed to identify suppressor mutations that restored catalytic activity in vivo from two kinase-dead Protein Kinase A mutants in S. cerevisiae. The residues defined by the suppressors provide new insights into kinase regulation. Many of the acquired mutations were distal to the nucleotide binding pocket, highlighting the relationship of spatially dispersed residues in regulation.The suppressor residues provide new insights into kinase regulation, including allosteric effects on catalytic elements and altered protein-protein interactions. The suppressor mutations identified in this study also share overlap with mutations identified from an identical screen in the yeast PKA homolog Tpk2, demonstrating functional conservation for some residues. Some mutations were independently isolated several times at the same sites. These sites are in agreement with sites previously identified from multiple cancer data sets as areas where acquired somatic mutations led to cancer progression and drug resistance. This method provides a valuable tool for identifying residues involved in kinase activity and for studying kinase misregulation in disease states

Analyzing the Impacts of Off-Road Vehicle (ORV) Trails on Watershed Processes in Wrangell-St. Elias National Park and Preserve, Alaska

Trails created by off-road vehicles (ORV) in boreal lowlands are known to cause local impacts, such as denuded vegetation, soil erosion, and permafrost thaw, but impacts on stream and watershed processes are less certain. In Wrangell-St. Elias National Park and Preserve (WRST), Alaska, ORV trails have caused local resource damage in intermountain lowlands with permafrost soils and abundant wetlands and there is a need to know whether these impacts are more extensive. Comparison of aerial photography from 1957, 1981, and 2004 coupled with ground surveys in 2009 reveal an increase in trail length and number and show an upslope expansion of a trail system around points of stream channel initiation. We hypothesized that these impacts could also cause premature initiation and headward expansion of channels because of lowered soil resistance and greater runoff accumulation as trails migrate upslope. Soil monitoring showed earlier and deeper thaw of the active layer in and adjacent to trails compared to reference sites. Several rainfall-runoff events during the summer of 2009 showed increased and sustained flow accumulation below trail crossings and channel shear forces sufficient to cause headward erosion of silt and peat soils. These observations of trail evolution relative to stream and wetland crossings together with process studies suggest that ORV trails are altering watershed processes. These changes in watershed processes appear to result in increasing drainage density and may also alter downstream flow regimes, water quality, and aquatic habitat. Addressing local land-use disturbances in boreal and arctic parklands with permafrost soils, such as WRST, where responses to climate change may be causing concurrent shifts in watershed processes, represents an important challenge facing resource managers

Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping

Protein kinases are key signaling enzymes that catalyze the transfer of γ-phosphate from an ATP molecule to a phospho-accepting residue in the substrate. Unraveling the molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor is important for understanding kinase specificities toward their substrates and for designing substrate-like peptidic inhibitors. We applied ANCHORSmap, a new fragment-based computational approach for mapping amino acid side chains on protein surfaces, to predict and characterize the preference of kinases toward Arginine binding. We focus on positions P−2 and P−5, commonly occupied by Arginine (Arg) in substrates of basophilic Ser/Thr kinases. The method accurately identified all the P−2/P−5 Arg binding sites previously determined by X-ray crystallography and produced Arg preferences that corresponded to those experimentally found by peptide arrays. The predicted Arg-binding positions and their associated pockets were analyzed in terms of shape, physicochemical properties, amino acid composition, and in-silico mutagenesis, providing structural rationalization for previously unexplained trends in kinase preferences toward Arg moieties. This methodology sheds light on several kinases that were described in the literature as having non-trivial preferences for Arg, and provides some surprising departures from the prevailing views regarding residues that determine kinase specificity toward Arg. In particular, we found that the preference for a P−5 Arg is not necessarily governed by the 170/230 acidic pair, as was previously assumed, but by several different pairs of acidic residues, selected from positions 133, 169, and 230 (PKA numbering). The acidic residue at position 230 serves as a pivotal element in recognizing Arg from both the P−2 and P−5 positions

Classification of river morphology and hydrology to support management and restoration

The work leading to this paper has received funding from the European Union’s FP7 programme under Grant Agreement No. 282656 (REFORM

Identifying and Characterizing a Novel Protein Kinase STK35L1 and Deciphering Its Orthologs and Close-Homologs in Vertebrates

The human kinome containing 478 eukaryotic protein kinases has over 100 uncharacterized kinases with unknown substrates and biological functions. The Ser/Thr kinase 35 (STK35, Clik1) is a member of the NKF 4 (New Kinase Family 4) in the kinome with unknown substrates and biological functions. Various high throughput studies indicate that STK35 could be involved in various human diseases such as colorectal cancer and malaria. In this study, we found that the previously published coding sequence of the STK35 gene is incomplete. The newly identified sequence of the STK35 gene codes for a protein of 534 amino acids with a N-terminal elongation of 133 amino acids. It has been designated as STK35L (STK35 long). Since it is the first of further homologous kinases we termed it as STK35L1. The STK35L1 protein (58 kDa on SDS-PAGE), but not STK35 (44 kDa), was found to be expressed in all human cells studied (endothelial cells, HeLa, and HEK cells) and was down-regulated after silencing with specific siRNA. EGFP-STK35L1 was localized in the nucleus and the nucleolus. By combining syntenic and gene structure pattern data and homology searches, two further STK35L1 homologs, STK35L2 (previously known as PDIK1L) and STK35L3, were found. All these protein kinase homologs were conserved throughout the vertebrates. The STK35L3 gene was specifically lost during placental mammalian evolution. Using comparative genomics, we have identified orthologous sets of these three protein kinases genes and their possible ancestor gene in two sea squirt genomes. We found the full-length coding sequence of the STK35 gene and termed it as STK35L1. We identified a new third STK35-like gene, STK35L3, in vertebrates and a possible ancestor gene in sea squirt genome. This study will provide a comprehensive platform to explore the role of STK35L kinases in cell functions and human diseases

Plasma fibrin D-dimer levels correlate with tumour volume, progression rate and survival in patients with metastatic breast cancer

Plasma levels of D-dimer are elevated in cancer patients. Activation of the extrinsic coagulation system and the fibrinolytic cascade within a tumour is thought to be related with growth, invasion and metastasis. We have investigated the relationship between these markers of fibrin metabolism, standard clinicopathological variables and serum levels of angiogenic cytokines in three cohorts: group A (n=30) consisted of 30 healthy female volunteers, group B (n=23) of consecutive patients with operable breast cancer and group C (n=84) of patients with untreated or progressive metastatic breast cancer. Plasma D-dimers, fibrinogen, IL-6, vascular endothelial growth factor and calculated vascular endothelial growth factor load in platelets are clearly increased in patients with breast cancer. D-dimers were increased in nearly 89% of patients with progressive metastatic disease. The level of D-dimers was positively correlated with tumour load (P<0.0001), number of metastatic sites (P=0.002), progression kinetics (P<0.0001) and the cytokines related to angiogenesis: serum vascular endothelial growth factor (P=0.0016, Spearman correlation=0.285), calculated vascular endothelial growth factor load in platelets (P<0.0001, Spearman correlation=0.37) and serum interleukin-6 (P<0.0001, Spearman correlation=0.59). Similarly increased D-dimer levels were positively correlated with increased fibrinogen levels (P<0.0001, Spearman correlation=0.38). The association between markers of fibrin degradation in patients with progressive breast cancer suggests that the D-dimer level is a clinically important marker for progression and points towards a relation between haemostasis and tumour progression. A role of interleukin-6, by influencing both angiogenesis and haemostasis, is suggested by these observations