Structure and function of \u3ci\u3ePseudomonas aeruginosa\u3ci\u3e protein PA1324 (21–170)

Pseudomonas aeruginosa is the prototypical biofilm-forming gram-negative opportunistic human pathogen. P. aeruginosa is causatively associated with nosocomial infections and with cystic fibrosis. Antibiotic resistance in some strains adds to the inherent difficulties that result from biofilm formation when treating P. aeruginosa infections. Transcriptional profiling studies suggest widespread changes in the proteome during quorum sensing and biofilm development. Many of the proteins found to be upregulated during these processes are poorly characterized from a functional standpoint. Here, we report the solution NMR structure of PA1324, a protein of unknown function identified in these studies, and provide a putative biological functional assignment based on the observed prealbumin-like fold and FAST-NMR ligand screening studies. PA1324 is postulated to be involved in the binding and transport of sugars or polysaccharides associated with the peptidoglycan matrix during biofilm formation

Statistics for the Evaluation and Comparison of Models

Copyright 1985 by the American Geophysical Union.Procedures that may be used to evaluate the operational performance of a wide spectrum of geophysical models are introduced. Primarily using a complementary set of difference measures, both model accuracy and precision can be meaningfully estimated, regardless of whether the model predictions are manifesteda s scalars,d irections,o r vectors.I t is additionally suggestedth at the reliability of the accuracy and precision measures can be determined from bootstrap estimates of confidence and significance. Recommendedp roceduresa re illustrated with a comparativee valuation of two models that estimate wind velocity over the South Atlantic Bight

Genetic dissection reveals diabetes loci proximal to the gimap5 lymphopenia gene

rats are protected from type 1 diabetes (T1D) by 34 Mb of F344 DNA introgressed proximal to the gimap5 lymphopenia gene. To dissect the genetic factor(s) that confer protection from T1D in the DRF. f/f rat line, DRF. f/f rats were crossed to inbred BBDR or DR. lyp/lyp rats to generate congenic sublines that were genotyped and monitored for T1D, and positional candidate genes were sequenced. All (100%) DR. f/f congenic sublines further refined the RNO4 region 1 interval to ϳ670 kb and region 2 to the 340 kb proximal to gimap5. All congenic DRF. f/f sublines were prone to low-grade pancreatic mononuclear cell infiltration around ducts and vessels, but Ͻ20% of islets in nondiabetic rats showed islet infiltration. Coding sequence analysis revealed TCR V␤ 8E, 12, and 13 as candidate genes in region 1 and znf467 and atp6v0e2 as candidate genes in region 2. Our results show that spontaneous T1D is controlled by at least two genetic loci 7 Mb apart on rat chromosome 4. type 1 diabetes; BB rat; T cell receptor; autoimmune CHARACTERISTICS OF TYPE 1 DIABETES (T1D) in both human and the BioBreeding spontaneously diabetes-prone (BBDP) rat include polyuria, hyperglycemia, ketoacidosis, insulitis, and insulin dependency for life. As in human T1D, islets are infiltrated by mononuclear cells at the time of onset with rapid hyperglycemia due to a complete loss of islet ␤-cells (32). The genetic etiology of human T1D remains complex and although the major histocompatibility complex (MHC) (HLA DQ) on chromosome 6 accounts for ϳ40% of T1D risk, the number of non-HLA genetic factors is increasing steadily (2, 7). The BB rat offers a powerful model to dissect both genetic contributions and mechanisms by which immunemediated beta cell killing induces T1D (3, 4, 15, 17-21, 27, 28, 46). As in humans, the major genetic determinant of susceptibility in the BB rat is the MHC (Iddm1) on rat chromosome (RNO) 20. The class II MHC locus RT1B/D. u/u ), an ortholog of human HLA DQ (9), is necessary but not sufficient for T1D in the BBDP rat and other RT1. u/u -related rat strains with spontaneous (24, 47) or induced T1D (8, 43). In BBDP, a null mutation in the gimap5 gene (lyp; Iddm2) on RNO4 (14, 27) causes lymphopenia and is tightly linked to spontaneous T1D development. The DR. lyp/lyp rat with 2 Mb of BBDP DNA encompassing gimap5 introgressed into the genome of related BBDR rats (BioBreeding resistant to spontaneous T1D) are also 100% lymphopenic and 100% spontaneously diabetic (11). With complete T1D penetrance and tight regulation of onset, the congenic DR. lyp/lyp rat line offers distinct advantages in identification of genes responsible for disease progression. It is possible to induce T1D in BBDR rats (32) and related RT1 u/u rats (8) by administration of polyinosinic: polycytidylic acid (poly I:C, an activator of innate immunity), the T reg depleting cytotoxic DS4.23 anti-ART2.1 (formerly RT6) monoclonal antibody or by viral infection (34). This indicates that the BBDR has an underlying genetic susceptibility to T1D. In crosses between WF and either BBDP or BBDR rats, a quantitative trait locus (QTL) important for induced T1D (Iddm14, previously designated Iddm4) was mapped to RNO4 (6, Interestingly, F344 DNA introgressed between D4Rat253 and D4Rhw6 into the congenic DR. lyp/lyp genetic background resulted in a lymphopenic but nondiabetic rat (designated DRF. f/f ) (11). Protection from T1D in the DRF. f/f congenic rat line led us to conclude that spontaneous T1D in the BB rat is controlled, in part, by a diabetogenic factor(s) independent of the gimap5 mutation (76.84 Mb) on RNO4. This congenic interval is encompassed within Iddm14, raising the possibility that the Iddm14 locus could be required for both spontaneous and induced T1D in the BB rat. The aim of this study was to cross the DRF. f/f rat to BBDR and DR. lyp/lyp rats and produce recombinant sublines that could be assessed for both lymphopenia and diabetes and to estimate the number of independent genes on RNO4 that control spontaneous T1D

Specific Heat Discontinuity, deltaC, at Tc in BaFe2(As0.7P0.3)2 - Consistent with Unconventional Superconductivity

We report the specific heat discontinuity, deltaC/Tc, at Tc = 28.2 K of a collage of single crystals of BaFe2(As0.7P0.3)2 and compare the measured value of 38.5 mJ/molK**2 with other iron pnictide and iron chalcogenide (FePn/Ch) superconductors. This value agrees well with the trend established by Bud'ko, Ni and Canfield who found that deltaC/Tc ~ a*Tc**2 for 14 examples of doped Ba1-xKxFe2As2 and BaFe2-xTMxAs2, where the transition metal TM=Co and Ni. We extend their analysis to include all the FePn/Ch superconductors for which deltaC/Tc is currently known and find deltaC/Tc ~ a*Tc**1.9 and a=0.083 mJ/molK**4. A comparison with the elemental superconductors with Tc>1 K and with A-15 superconductors shows that, contrary to the FePn/Ch superconductors, electron-phonon-coupled conventional superconductors exhibit a significantly different dependence of deltaC on Tc, namely deltaC/Tc ~ Tc**0.9. However deltaC/gamma*Tc appears to be comparable in all three classes (FePn/Ch, elemental and A-15) of superconductors with, e. g., deltaC/gamma*Tc=2.4 for BaFe2(As0.7P0.3)2. A discussion of the possible implications of these phenomenological comparisons for the unconventional superconductivity believed to exist in the FePn/Ch is given.Comment: some disagreement in reference and footnote numbering with the published versio

Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA

Background: Abnormal CpG methylation in cancer is ubiquitous and generally detected in tumour specimens using a variety of techniques at a resolution encompassing single CpG loci to genome wide coverage. Analysis of samples with very low DNA inputs, such as formalin fixed (FFPE) biopsy specimens from clinical trials or circulating tumour DNA is challenging at the genome-wide level because of lack of available input. We present the results of low input experiments into the Illumina Infinium HD methylation assay on FFPE specimens and ctDNA samples. Methods: For all experiments, the Infinium HD assay for methylation was used. In total, forty-eight FFPE specimens were used at varying concentrations (lowest input 50 ng); eighteen blood derived specimens (lowest input 10 ng) and six matched ctDNA input (lowest input 10 ng)/fresh tumour specimens (lowest input 250 ng) were processed. Downstream analysis was performed in R/Bioconductor for quality control metrics and differential methylation analysis as well as copy number calls. Results: Correlation coefficients for CpG methylation were high at the probe level averaged R2 = 0.99 for blood derived samples and R2 > 0.96 for the FFPE samples. When matched ctDNA/fresh tumour samples were compared, R2 > 0.91 between the two. Results of differential methylation analysis did not vary significantly by DNA input in either the blood or FFPE groups. There were differences seen in the ctDNA group as compared to their paired tumour sample, possibly because of enrichment for tumour material without contaminating normal. Copy number variants observed in the tumour were generally also seen in the paired ctDNA sample with good concordance via DQ plot. Conclusions: The Illumina Infinium HD methylation assay can robustly detect methylation across a range of sample types, including ctDNA, down to an input of 10 ng. It can also reliably detect oncogenic methylation changes and copy number variants in ctDNA. These findings demonstrate that these samples can now be accessed by methylation array technology, allowing analysis of these important sample types

Strange particle production in proton-proton collisions at s=0.9\sqrt{s}=0.9 TeV with ALICE at the LHC

The production of mesons containing strange quarks (K$^0_s$, $\phi$) and both singly and doubly strange baryons ($\Lambda$, Anti-$\Lambda$, and $\Xi$+Anti-$\Xi$) are measured at central rapidity in pp collisions at $\sqrt{s}$ = 0.9 TeV with the ALICE experiment at the LHC. The results are obtained from the analysis of about 250 k minimum bias events recorded in 2009. Measurements of yields (dN/dy) and transverse momentum spectra at central rapidities for inelastic pp collisions are presented. For mesons, we report yields () of 0.184 $\pm$ 0.002 stat. $\pm$ 0.006 syst. for K$^0_s$ and 0.021 $\pm$ 0.004 stat. $\pm$ 0.003 syst. for $\phi$. For baryons, we find = 0.048 $\pm$ 0.001 stat. $\pm$ 0.004 syst. for $\Lambda$, 0.047 $\pm$ 0.002 stat. $\pm$ 0.005 syst. for Anti-$\Lambda$ and 0.0101 $\pm$ 0.0020 stat. $\pm$ 0.0009 syst. for $\Xi$+Anti-$\Xi$. The results are also compared with predictions for identified particle spectra from QCD-inspired models and provide a baseline for comparisons with both future pp measurements at higher energies and heavy-ion collisions.Comment: 33 pages, 21 captioned figures, 10 tables, authors from page 28, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/387

Mergers and Acquisitions in Latin America: Industrial Productivity and Corporate Governance

This paper examines the impact of industrial productivity on transnationals M&As from OECD countries towards Latin American countries in the period 1996 to 2010. It also analyzes the relationship between external mechanism of corporate governance and transnational M&As. For this purpose we use a gravitational model at the industry level. We find that industry productivity and higher standards of corporate governance in the country of origin promote transnational M&As activity. However, it is also found that higher levels of capital and technological productivity decreases transnational M&As activity

Suppression of charged particle production at large transverse momentum in central Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm NN}} = 2.76 TeV

Inclusive transverse momentum spectra of primary charged particles in Pb-Pb collisions at $\sqrt{s_{_{\rm NN}}}$ = 2.76 TeV have been measured by the ALICE Collaboration at the LHC. The data are presented for central and peripheral collisions, corresponding to 0-5% and 70-80% of the hadronic Pb-Pb cross section. The measured charged particle spectra in $|\eta|<0.8$ and $0.3 < p_T < 20$ GeV/$c$ are compared to the expectation in pp collisions at the same $\sqrt{s_{\rm NN}}$, scaled by the number of underlying nucleon-nucleon collisions. The comparison is expressed in terms of the nuclear modification factor $R_{\rm AA}$. The result indicates only weak medium effects ($R_{\rm AA} \approx$ 0.7) in peripheral collisions. In central collisions, $R_{\rm AA}$ reaches a minimum of about 0.14 at $p_{\rm T}=6$-7GeV/$c$ and increases significantly at larger $p_{\rm T}$. The measured suppression of high-$p_{\rm T}$ particles is stronger than that observed at lower collision energies, indicating that a very dense medium is formed in central Pb-Pb collisions at the LHC.Comment: 15 pages, 5 captioned figures, 3 tables, authors from page 10, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/98

Two-pion Bose-Einstein correlations in central Pb-Pb collisions at sNN\sqrt{s_{\rm NN}} = 2.76 TeV

The first measurement of two-pion Bose-Einstein correlations in central Pb-Pb collisions at $\sqrt{s_{\rm NN}} = 2.76$ TeV at the Large Hadron Collider is presented. We observe a growing trend with energy now not only for the longitudinal and the outward but also for the sideward pion source radius. The pion homogeneity volume and the decoupling time are significantly larger than those measured at RHIC.Comment: 17 pages, 5 captioned figures, 1 table, authors from page 12, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/388

Particle-yield modification in jet-like azimuthal di-hadron correlations in Pb-Pb collisions at sNN\sqrt{s_{\rm NN}} = 2.76 TeV

The yield of charged particles associated with high-$p_{\rm T}$ trigger particles ($8 < p_{\rm T} < 15$ GeV/$c$) is measured with the ALICE detector in Pb-Pb collisions at $\sqrt{s_{\rm NN}}$ = 2.76 TeV relative to proton-proton collisions at the same energy. The conditional per-trigger yields are extracted from the narrow jet-like correlation peaks in azimuthal di-hadron correlations. In the 5% most central collisions, we observe that the yield of associated charged particles with transverse momenta $p_{\rm T}> 3$ GeV/$c$ on the away-side drops to about 60% of that observed in pp collisions, while on the near-side a moderate enhancement of 20-30% is found.Comment: 15 pages, 2 captioned figures, 1 table, authors from page 10, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/350