Proteomic approaches for the detection of unusual post-translational modifications in simple and complex bacterial protein mixtures

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal

Herschel SPIRE-FTS Observations of Excited CO and [CI] in the Antennae (NGC 4038/39): Warm and Cold Molecular Gas

We present Herschel SPIRE-FTS observations of the Antennae (NGC 4038/39), a well studied, nearby ($22$ Mpc) ongoing merger between two gas rich spiral galaxies. We detect 5 CO transitions ($J=4-3$ to $J=8-7$), both [CI] transitions and the [NII]$205\mu m$ transition across the entire system, which we supplement with ground based observations of the CO $J=1-0$, $J=2-1$ and $J=3-2$ transitions, and Herschel PACS observations of [CII] and [OI]$63\mu m$. Using the CO and [CI] transitions, we perform both a LTE analysis of [CI], and a non-LTE radiative transfer analysis of CO and [CI] using the radiative transfer code RADEX along with a Bayesian likelihood analysis. We find that there are two components to the molecular gas: a cold ($T_{kin}\sim 10-30$ K) and a warm ($T_{kin} \gtrsim 100$ K) component. By comparing the warm gas mass to previously observed values, we determine a CO abundance in the warm gas of $x_{CO} \sim 5\times 10^{-5}$. If the CO abundance is the same in the warm and cold gas phases, this abundance corresponds to a CO $J=1-0$ luminosity-to-mass conversion factor of $\alpha_{CO} \sim 7 \ M_{\odot}{pc^{-2} \ (K \ km \ s^{-1})^{-1}}$in the cold component, similar to the value for normal spiral galaxies. We estimate the cooling from H$_2$, [CII], CO and [OI]$63\mu m$to be$\sim 0.01 L_{\odot}/M_{\odot}$. We compare PDR models to the ratio of the flux of various CO transitions, along with the ratio of the CO flux to the far-infrared flux in NGC 4038, NGC 4039 and the overlap region. We find that the densities recovered from our non-LTE analysis are consistent with a background far-ultraviolet field of strength$G_0\sim 1000$. Finally, we find that a combination of turbulent heating, due to the ongoing merger, and supernova and stellar winds are sufficient to heat the molecular gas.Comment: 50 pages, 15 figures, 8 tables, Accepted for publication in The Astrophysical Journa

Host Protein Biomarkers Identify Active Tuberculosis in HIV Uninfected and Co-infected Individuals

AbstractBiomarkers for active tuberculosis (TB) are urgently needed to improve rapid TB diagnosis. The objective of this study was to identify serum protein expression changes associated with TB but not latent Mycobacterium tuberculosis infection (LTBI), uninfected states, or respiratory diseases other than TB (ORD). Serum samples from 209 HIV uninfected (HIV−) and co-infected (HIV+) individuals were studied. In the discovery phase samples were analyzed via liquid chromatography and mass spectrometry, and in the verification phase biologically independent samples were analyzed via a multiplex multiple reaction monitoring mass spectrometry (MRM-MS) assay. Compared to LTBI and ORD, host proteins were significantly differentially expressed in TB, and involved in the immune response, tissue repair, and lipid metabolism. Biomarker panels whose composition differed according to HIV status, and consisted of 8 host proteins in HIV− individuals (CD14, SEPP1, SELL, TNXB, LUM, PEPD, QSOX1, COMP, APOC1), or 10 host proteins in HIV+ individuals (CD14, SEPP1, PGLYRP2, PFN1, VASN, CPN2, TAGLN2, IGFBP6), respectively, distinguished TB from ORD with excellent accuracy (AUC=0.96 for HIV− TB, 0.95 for HIV+ TB). These results warrant validation in larger studies but provide promise that host protein biomarkers could be the basis for a rapid, blood-based test for TB

Herschel/SPIRE Sub-millimeter Spectra of Local Active Galaxies

We present the sub-millimeter spectra from 450 GHz to 1550 GHz of eleven nearby active galaxies observed with the SPIRE Fourier Transform Spectrometer (SPIRE/FTS) onboard Herschel. We detect CO transitions from J_up = 4 to 12, as well as the two [CI] fine structure lines at 492 and 809 GHz and the [NII] 461 GHz line. We used radiative transfer models to analyze the observed CO spectral line energy distributions (SLEDs). The FTS CO data were complemented with ground-based observations of the low-J CO lines. We found that the warm molecular gas traced by the mid-J CO transitions has similar physical conditions (n_H2 ~ 10^3.2 - 10^3.9 cm^-3 and T_kin ~ 300 - 800 K) in most of our galaxies. Furthermore, we found that this warm gas is likely producing the mid-IR rotational H2 emission. We could not determine the specific heating mechanism of the warm gas, however it is possibly related to the star-formation activity in these galaxies. Our modeling of the [CI] emission suggests that it is produced in cold (T_kin 10^3 cm^-3) molecular gas. Transitions of other molecules are often detected in our SPIRE/FTS spectra. The HF J=1-0 transition at 1232 GHz is detected in absorption in UGC05101 and in emission in NGC7130. In the latter, near-infrared pumping, chemical pumping, or collisional excitation with electrons are plausible excitation mechanisms likely related to the AGN of this galaxy. In some galaxies few H2O emission lines are present. Additionally, three OH+ lines at 909, 971, and 1033 GHz are identified in NGC7130.Comment: Accepted for publication in ApJ; 20 pages, 9 figure

Integration of the End Cap TEC+ of the CMS Silicon Strip Tracker

The silicon strip tracker of the CMS experiment has been completed and inserted into the CMS detector in late 2007. The largest sub-system of the tracker is its end cap system, comprising two large end caps (TEC) each containing 3200 silicon strip modules. To ease construction, the end caps feature a modular design: groups of about 20 silicon modules are placed on sub-assemblies called petals and these self-contained elements are then mounted into the TEC support structures. Each end cap consists of 144 petals, and the insertion of these petals into the end cap structure is referred to as TEC integration. The two end caps were integrated independently in Aachen (TEC+) and at CERN (TEC--). This note deals with the integration of TEC+, describing procedures for end cap integration and for quality control during testing of integrated sections of the end cap and presenting results from the testing

Reception Test of Petals for the End Cap TEC+ of the CMS Silicon Strip Tracker

The silicon strip tracker of the CMS experiment has been completed and was inserted into the CMS detector in late 2007. The largest sub system of the tracker are its end caps, comprising two large end caps (TEC) each containing 3200 silicon strip modules. To ease construction, the end caps feature a modular design: groups of about 20 silicon modules are placed on sub-assemblies called petals and these self-contained elements are then mounted onto the TEC support structures. Each end cap consists of 144 such petals, which were built and fully qualified by several institutes across Europe. Fro

Glycosylation of b-Type Flagellin of Pseudomonas aeruginosa: Structural and Genetic Basis

The flagellin of Pseudomonas aeruginosa can be classified into two major types—a-type or b-type—which can be distinguished on the basis of molecular weight and reactivity with type-specific antisera. Flagellin from the a-type strain PAK was shown to be glycosylated with a heterogeneous O-linked glycan attached to Thr189 and Ser260. Here we show that b-type flagellin from strain PAO1 is also posttranslationally modified with an excess mass of up to 700 Da, which cannot be explained through phosphorylation. Two serine residues at positions 191 and 195 were found to be modified. Each site had a deoxyhexose to which is linked a unique modification of 209 Da containing a phosphate moiety. In comparison to strain PAK, which has an extensive flagellar glycosylation island of 14 genes in its genome, the equivalent locus in PAO1 comprises of only four genes. PCR analysis and sequence information suggested that there are few or no polymorphisms among the islands of the b-type strains. Mutations were made in each of the genes, PA1088 to PA1091, and the flagellin from these isogenic mutants was examined by mass spectrometry to determine whether they were involved in posttranslational modification of the type-b flagellin. While mutation of PA1088, PA1089, and PA1090 genes altered the composition of the flagellin glycan, only unmodified flagellin was produced by the PA1091 mutant strain. There were no changes in motility or lipopolysaccharide banding in the mutants, implying a role that is limited to glycosylation