Sequence diversity and functional conformity

At least four phylogenetically distinct groups of bacteria encode repeat proteins with the common ability to bind specific DNA sequences with a unique but conserved code. Each repeat binds a single DNA base, and specificity is determined by the amino acid residue at position 13 of each repeat. Repeats are typically 33-35 amino acids long. Comparing repeat sequences across all groups reveals that only three positions are hyper-conserved. Repeats are in most cases functionally compatible such that they can be assembled together into a single chimeric array. This functional conformity and inter-compatibility is a result of structural conservation. Repeat arrays of these proteins have been demonstrated or predicted to form almost identical tertiary structures: a right-handed super helix that wraps around the DNA double strand with the base specifying residue of each repeat positioned in the major groove next to its cognate target base. The mechanism of DNA binding is conserved. The first discovered group, providing the name for the rest, are the Transcription Activator Like Effectors (TALEs) of plant-pathogenic Xanthomonas bacteria. The eukaryotic transactivation domain, which lends this group their name, allows them to activate specifically targeted host genes for the benefit of the bacterial invader. The other groups, discovered after the TALEs, are the RipTALs of Ralstonia solanacearum, the Bats of Burkholderia rhizoxinica, and MOrTL1 and MOrTL2 of unknown marine bacteria. Together they are designated TALE-likes. Each designation contains some allusion to the TALEs. The term RipTAL stands for Ralstonia injected proteins TALE-like, the Bats are Burkholderia TALE likes, and the MOrTLs Marine Organism TALE-likes. This unity of terminology belies disunity in the lifestyles of these different bacteria, and the biological roles fulfilled by these proteins. The TALEs have already been researched extensively. The code that describes the relationship between the base specifying residues and their cognate bases is often referred to as the TALE code. This code was deciphered by two groups independently and published in 2009, a year before I began my doctoral work. Since then research into TALEs has not slowed and a great deal has been learnt both about the native biology and biotechnological uses of TALEs. My work has been focused on the other TALE-like groups, none of which had been previously characterized in terms of DNA recognition properties, before I began my work. RipTALs are effector proteins delivered during bacterial wilt disease caused by R. solanacearum strains. This devastating disease affects numerous crop species worldwide. Characterizing the molecular properties of the RipTALs provides a first step towards uncovering their role in the disease. The Bats and MOrTLs are primarily of interest as comparison groups to the TALEs and RipTALs and as sources of sequence diversity for future efforts into TALE repeat engineering. In the introduction of this dissertation, which explores TALE biology, a particular focus will be placed on the DNA binding properties of TALEs and how this can be put to use in TALE technology. After this the RipTALs, Bats and MOrTLs are each introduced, explaining what is known about their provenance and sequence features. The aims of my doctoral work are then listed and expounded in turn. The proximal goal of my doctoral work was to carry out a comparative molecular characterization of each group of non-TALE TALE-likes. In doing so we hoped to gain insights into the principles of TALE-like DNA-binding properties, evolutionary history of the different groups and their potential uses in biotechnology. In the case of the RipTALs this work should begin to unravel the role these proteins play in bacterial wilt disease, as a means to fight this devastating pathogen. The articles I have worked on covering the molecular characterizations of RipTALs, Bats and MOrTLs are then presented in turn. Working together with others I was able to show that repeats from each group of TALE-likes mediate sequence specific DNA binding, revealing a conserved code in each case. This code links position 13 of any TALE-like repeat to a specific DNA base preference in a reliable fashion. I will argue that the TALE-likes represent a fascinating case of conserved structure and function in a diverse sequence space. In addition the TALEs and RipTALs may simply represent one face of the TALE-likes, a protein family mediating as yet unknown biological roles as bacterial DNA binding proteins.Gene die ähnlichen repeat-enthaltende Proteine kodieren finden sich in den Genomen von mindestens vier phylogenetischen Gruppen von Bakterien. Alle diese verschiedene Proteine nutzen den gleichen, einzigartigen Code um bestimmte DNS Basen zu binden. Repeats bestehen in der Regel aus 33-35 Aminosäuren und jeder Repeat bindet eine einzige Base, wobei die Spezifität durch die Aminosäure an Position 13 im Repeat bestimmt wird. Ein Vergleich der Repeatsequenzen aus den verschiedenen Proteinen zeigt nur drei hyperkonservierte Aminosäuren, aber chimäre Repeat-domänen sind meistens dennoch Funktionsfähig. Funktionseinigkeit und Kompatibilität sind Folge struktureller Konservation. Es wurde schon gezeigt oder vorhergesagt dass die Repeat-Domäne dieser Proteine fast identische Strukturen bilden: Eine rechtsgängige Superhelix die sich um die DNS wickelt, wobei die basenbestimmenden Aminosäuren in der großen Furche neben der verwandte Base positioniert werden. Dieser Bindungsmechanismus ist innerhalb dieser Gruppe von Proteinen konserviert. Die erste beschriebene Gruppe sind die Transcription Activator Like Effectors (TALEs) aus pflanzenkrankheitserregenden Xanthomonas Bakterien, und ist namensgebend für diese Klasse von Proteinen. Der Name stammt von der eukaryotischen Aktivierungsdomäne durch die ermöglicht wird, dass die TALEs spezifische Wirtsgene aktivieren zum Vorteil der Bakterien. Die anderen Gruppen sind RipTALs aus Ralstonia solanacearum, Bats aus Burkholderia rhizoxinica, und MOrTL1 und MOrTL2 aus bis jetzt unbekannten Meeresbakterien. Kollektivbegriff dafür ist TALE-likes. Der Name jeder Gruppe deutet darauf hin, dass diese Proteine TALEs ähnlich sind. RipTAL bedeutet Ralstonia injected proteins TALE-like; Bats sind Burkholderia TALE likes; und die MOrTLs Marine Organism TALE-likes. Diese Namenseinigkeit verbirgt die unterschiedliche Lebensweisen dieser Bakterien und die verschiedenen natürliche Rollen dass die TALE-likes annehmen könnten. TALEs werden schon seit langem erforscht. Der TALE-Code beschreibt die Beziehung zwischen bestimmten Resten und passenden Basen. Er wurde in 2009 entschlüsselt und von zwei unabhängigen Forschungsgruppen veröffentlicht. Das war ein Jahr bevor ich mit meiner Doktorarbeit anfing. Seitdem hat die TALE-Forschung stark weiterentwickelt und vieles wurde über die natürliche Biologie und biotechnische Applikation dieser Proteine gelernt. Meine Arbeit fokussiert sich auf die anderen TALE-likes, von denen zuvor kein einziges charakterisiert war. RipTALs sind Effektor-Proteine, die von R. solanacearum im Laufe der Entwicklung der bakterieller Schleimkrankheit sekretiert werden. Diese Krankheit betrifft weltweit viele wichtige Nutz- und Kulturpflanzen. Eine Charakterisierung der molekularen Eigenschaften der RipTALs ist der erste Schritt um die Rolle dieser Proteine in der Pathogenese zu verstehen. Die Bats und MOrTls sind als Vergleichsgruppe zu den TALEs und RipTALs relevant. Ausserdem könnten die Polymorphismen die einen leichten Einfluss auf DNS-Bindung als eine Ressource genutzt werden um TALE-Technologie zu verstärke. Die Einleitung dieser Dissertation erklärt das Wesentliche über TALE Biologie mit Schwerpunkt auf DNA-Bindung und wie diese zur TALE-Technologie entwickelt wurde. Anschließend werden die RipTALs, Bats und MOrTLs der Reihe nach vorgestellt, und das Wissen über Herkunft und Sequenzmerkmale präsentiert. Die Ziele meiner Doktorarbeit werden dann ausgeführt. Das Hauptziel meiner Arbeit war ein Vergleich der molekularen Eigenschaften der einzelnen TALE-like Gruppen anzustellen. Davon erhofften wir neue Einblicke in die Interaktion zwischen TALE-likes und DNS, die Evolution der TALE-likes sowie eventuelle Biotechnologische Anwendungen zu gewinnen. Im Falle der RipTALs ist dieses Wissen direkt einsetzbar um die bakterielle Schleimkrankheit zu bekämpfen. Artikel zur Charakterisierung von RipTALs, Bats und MOrTls sind Resultate meiner Doktorarbeit und kommen als Ergebnisteil der Dissertation vor. Zusammen mit Kollegen konnte ich zeigen dass die Repeats aus jeder TALE-like Gruppe Basen-spezifisch DNS-Binden. Der TALE Code, aus dem hervorgeht welche Aminosäurereste an Position 13 Bindung an welche Base vermitteln, ist in allen Gruppen konserviert. Ich beschreibe auch wie ich die TALE-likes als faszinierender Fall von struktureller Konservation in einem vielfaltigem Sequenzraum verstehe. Überdies könnte es sein dass die TALE-likes, trotz dem akzeptierten Bild als eukaryotische Transkriptionsfaktoren, eine viel diversere Gruppe sind mit Exemplaren die bis jetzt unerklärte Rollen erfüllen

OLIMPO: A few arcmin resolution survey of the sky at mm and sub-mm wavelengths

Abstract. OLIMPO is a 2.6 meter on-axis millimeter-wave Cassegrain telescope, mounted on an attitude controlled stratospheric balloon payload. This telescope is designed to be flown with a > 10 days Long Duration CircumPolar flight. The system contains 4 arrays of bolometers in the wavelength bands centered at 150, 220, 350, 600 GHz. The instrument will be diffraction limited at 150 GHz (3.5 arcminutes FWHM). It is currently planned to have a test flight from Trapani in 2003/4

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Search for R-parity-violating supersymmetry in events with four or more leptons in sqrt(s) =7 TeV pp collisions with the ATLAS detector

A search for new phenomena in final states with four or more leptons (electrons or muons) is presented. The analysis is based on 4.7 fb−1 of $\sqrt{s}=7\;\mathrm{TeV}$ proton-proton collisions delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in two signal regions: one that requires moderate values of missing transverse momentum and another that requires large effective mass. The results are interpreted in a simplified model of R-parity-violating supersymmetry in which a 95% CL exclusion region is set for charged wino masses up to 540 GeV. In an R-parity-violating MSUGRA/CMSSM model, values of m 1/2 up to 820 GeV are excluded for 10 < tan β < 40

Search for high-mass resonances decaying to dilepton final states in pp collisions at s√=7 TeV with the ATLAS detector

The ATLAS detector at the Large Hadron Collider is used to search for high-mass resonances decaying to an electron-positron pair or a muon-antimuon pair. The search is sensitive to heavy neutral Z′ gauge bosons, Randall-Sundrum gravitons, Z * bosons, techni-mesons, Kaluza-Klein Z/γ bosons, and bosons predicted by Torsion models. Results are presented based on an analysis of pp collisions at a center-of-mass energy of 7 TeV corresponding to an integrated luminosity of 4.9 fb−1 in the e + e − channel and 5.0 fb−1 in the μ + μ −channel. A Z ′ boson with Standard Model-like couplings is excluded at 95 % confidence level for masses below 2.22 TeV. A Randall-Sundrum graviton with coupling k/MPl=0.1 is excluded at 95 % confidence level for masses below 2.16 TeV. Limits on the other models are also presented, including Technicolor and Minimal Z′ Models

Measurement of the cross-section of high transverse momentum vector bosons reconstructed as single jets and studies of jet substructure in pp collisions at √s = 7 TeV with the ATLAS detector

This paper presents a measurement of the cross-section for high transverse momentum W and Z bosons produced in pp collisions and decaying to all-hadronic final states. The data used in the analysis were recorded by the ATLAS detector at the CERN Large Hadron Collider at a centre-of-mass energy of √s = 7 TeV;{\rm Te}{\rm V}$and correspond to an integrated luminosity of$4.6\;{\rm f}{{{\rm b}}^{-1}}$. The measurement is performed by reconstructing the boosted W or Z bosons in single jets. The reconstructed jet mass is used to identify the W and Z bosons, and a jet substructure method based on energy cluster information in the jet centre-of-mass frame is used to suppress the large multi-jet background. The cross-section for events with a hadronically decaying W or Z boson, with transverse momentum${{p}_{{\rm T}}}\gt 320\;{\rm Ge}{\rm V}$and pseudorapidity$|\eta |\lt 1.9$, is measured to be${{\sigma }_{W+Z}}=8.5\pm 1.7$ pb and is compared to next-to-leading-order calculations. The selected events are further used to study jet grooming techniques

Measurement of the production of a W boson in association with a charm quark in pp collisions at √s = 7 TeV with the ATLAS detector

The production of a W boson in association with a single charm quark is studied using 4.6 fb−1 of pp collision data at s√ = 7 TeV collected with the ATLAS detector at the Large Hadron Collider. In events in which a W boson decays to an electron or muon, the charm quark is tagged either by its semileptonic decay to a muon or by the presence of a charmed meson. The integrated and differential cross sections as a function of the pseudorapidity of the lepton from the W-boson decay are measured. Results are compared to the predictions of next-to-leading-order QCD calculations obtained from various parton distribution function parameterisations. The ratio of the strange-to-down sea-quark distributions is determined to be 0.96+0.26−0.30 at Q 2 = 1.9 GeV2, which supports the hypothesis of an SU(3)-symmetric composition of the light-quark sea. Additionally, the cross-section ratio σ(W + +c¯¯)/σ(W − + c) is compared to the predictions obtained using parton distribution function parameterisations with different assumptions about the s−s¯¯¯ quark asymmetry

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured