149 research outputs found
Hyperon-Produktion und -Polarisation in der Reaktion p (3,5 GeV) + Nb mit HADES
Zur Erforschung des Verhaltens der Kernmaterie wurde mit dem Dielektronen-Spektrometer HADES am GSI Helmholtzzentrum für Schwerionenforschung in Darmstadt unter anderem die Reaktion p + Nb bei 3,5 GeV kinetischer Strahlenergie untersucht.
Obwohl HADES primär für den Nachweis seltener leptonischer Zerfälle der Vektormesonen ρ, ω und φ konzipiert wurde, eignet sich das Spektrometer aufgrund seiner präzisen Spurrekonstruktion auch für die Untersuchung von hadronischen Kanälen. Zum Studium der Strangeness-Signaturen in der Reaktion p + Nb wird in dieser Arbeit der im Jahr 2008 aufgezeichnete Datensatz von ca. 4,2 Milliarden Kollisionen hinsichtlich der Produktion und der dabei auftretenden Polarisation von Λ-Hyperonen untersucht.
Die polarisierte Produktion von Hyperonen in Kernreaktionen mit unpolarisierten Ausgangsteilchen wurde entgegen den theoretischen Erwartungen erstmals 1976 beobachtet und fand bis heute keine allgemein akzeptierte und alle beobachteten Abhängigkeiten umfassende Erklärung auf Grundlage der starken Wechselwirkung. Es werden zunächst die theoretischen Modelle der Hyperonpolarisation diskutiert und der experimentelle Zugang erklärt. Dieser gelingt über den schwachen Zerfall des Λ-Hyperons, der als natürliches Polarimeter wirkt und somit insbesondere in Reaktionen mit unpolarisierten Nukleonen ein ideales Instrument zur Untersuchung der Polarisation darstellt.
Aufgrund der großen Raumwinkelabdeckung ermöglicht HADES, Λ-Hyperonen in einem weiten Phasenraumbereich zu rekonstruieren, sodass deren Produktionsrate und Polarisation in Abhängigkeit der Observablen Transversalimpuls pt und Rapidität y analysiert werden. Aus insgesamt 1,1 Millionen rekonstruierten Λ-Hyperonen werden nach der Korrektur bezüglich der Detektorakzeptanz und -effizienz transversale Massenspektren extrahiert. Deren inverser Steigungsparameter TB (y) nimmt ein Maximum von rund 90 MeV bei y = 1, d.h. unterhalb der Schwerpunktsrapidität im Nukleon-Nukleon-Stoß (ycm = 1,12), an und fällt zu kleinen Rapiditäten deutlich schneller ab als für Teilchen im thermischen Gleichgewicht.
Die Λ-Rapiditätsdichte zeigt eine asymmetrische Verteilung, die aufgrund von Mehrfachstreuung der Λ-Hyperonen hauptsächlich mit Kern-Nukleonen deutlich zur Targetrapidität verschoben ist und mit steigender Rapidität > 0,3 stark abnimmt. Auf den vollständigen Phasenraum extrapoliert, erfüllt die Produktionsrate von 0,018 ± 0,004 Λ-0 Hyperons je Ereignis, verbunden mit der Multiplizität von Ks -Mesonen und den mittels Transportmodell abgeleiteten Produktionsverhältnissen zu den übrigen Kaonen und Hyperonen, die Strangeness-Erhaltung im Mittel der gemessenen Kollisionen.
Darüber hinaus zeigt das Λ-Hyperon eine signifikant negative Polarisation relativ zur Normalen seiner Produktionsebene, die über den verfügbaren Phasenraum gemittelt Px = (−10,6 ± 1,3) % beträgt und deren Betrag mit steigendem Transversalimpuls entsprechend Px (pt ) = (−0,19 ± 0,02) (GeV/c)−1 pt linear zunimmt.
Die Ergebnisse bezüglich der Λ-Polarisation und Phasenraumverteilung werden mit denen anderer Experimente ähnlicher Stoßsysteme verglichen und im Rahmen von systematischen Untersuchungen mit Transportmodellen interpretiert, um Details zur Dynamik der Hyperon-Produktion in Proton-Kern-Reaktionen abzuleiten. Derzeit verfügbare Versionen der GiBUU- und UrQMD-Modelle können die experimentellen Verteilungen im Phasenraum jedoch nicht hinreichend reproduzieren.
Mit der Rekonstruktion von Ξ− -Hyperonen und φ-Mesonen wird ein Ausblick auf weiterführende Studien zur Strangeness-Produktion in Nukleon-Kern-Stößen gegeben.:1 Einleitung 11
1.1 Struktur der Materie 11
1.2 Schwellennahe Erzeugung von Hadronen mit Strangeness 13
1.3 Modellbeschreibungen der Strangeness-Produktion 15
1.4 Untersuchung von Kernmaterie in Nukleon-Kern-Reaktionen 19
1.5 Zielsetzung und Gliederung der Arbeit 20
2 Hyperonpolarisation 23
2.1 Experimentelle Beobachtungen 23
2.2 Modellbeschreibungen 25
2.2.1 SU(6)-Modell 25
2.2.2 s-Quark-Streumodell 27
2.2.3 Lund-Modell (Farb-Flussröhre) 28
2.2.4 Rekombinationsmodell (Thomas-Präzession) 28
2.2.5 Quantenmechanische Modelle 29
2.3 Der selbstanalysierende Λ-Zerfall als Spin-Polarimeter 30
3 Experimentiersystem HADES und Analysewerkzeuge 33
3.1 Komponenten zur Teilchenidentifikation 35
3.2 Magnetspektrometer 37
3.3 Datenerfassung und -verarbeitung 43
3.4 Analyse- und Simulationssoftware 45
3.5 Transportmodelle 46
4 Datenanalyse zur Reaktion p + Nb 51
4.1 Charakteristika des Experiments 51
4.2 Teilchenidentifikation 55
4.2.1 Flugzeitmethode 56
4.2.2 Energieverlustmethode 58
4.3 Rekonstruktion des Λ-Hyperons 60
4.3.1 Teilchenselektion bezüglich des Energieverlustes 61
4.3.2 Invariantes Massenspektrum 62
4.3.3 Zerfallsgeometrie 65
4.3.4 Vertexrekonstruktion 66
4.3.5 Determination des kombinatorischen Untergrundes 69
4.3.6 Differentielle Analyse bezüglich des Phasenraums 73
4.4 Rekonstruktion des Ξ -Hyperons 77
4.5 Effizienz- und Akzeptanzbestimmung mittels Detektorsimulation 82
4.5.1 Selbstkonsistenz der Simulation 86
4.5.2 Überprüfung der Vertexrekonstruktion 89
4.5.3 Rekonstruktion der Zerfallslänge 91
4.5.4 Normierung der Produktionsrate 93
4.5.5 Differentielle Produktionsrate der Λ-Hyperonen 95
4.6 Messung der Λ-Polarisation 97
4.6.1 Referenzkoordinatensystem 97
4.6.2 Akzeptanzkorrektur 99
4.6.3 Bestimmung der mittleren Polarisation 101
4.6.4 Differentielle Untersuchung der Polarisation 104
5 Diskussion der Ergebnisse
5.1 Λ-Phasenraumverteilung 109
5.1.1 Transversalimpulsverteilungen 110
5.1.2 Extrapolation der transversalen Impulsspektren 113
5.1.3 Systematische Unsicherheiten 114
5.1.4 Vergleich mit Vorhersagen von Transportmodellen 117
5.1.5 Λ-Produktionsmechanismen im BUU-Modell 121
5.1.6 Vergleich mit Ergebnissen anderer Experimente 124
5.2 Strangeness-Erhaltung 131
5.3 Λ-Polarisation 134
5.3.1 Phasenraumabhängigkeit der Polarisation 135
5.3.2 Einordnung der Ergebnisse in den vorhanden Weltdatensatz 139
6 Zusammenfassung und Ausblick 143
A Anhang
A.1 Definition teilchenphysikalischer Variablen 149
A.2 Effizienzkorrektur für Λ-Hyperonen 153
A.3 Simulationen mit Transportmodellen 154
A.3.1 Ultrarelativistic Quantum Molecular Dynamics (UrQMD) 154
A.3.2 Giessen Boltzmann-Uehling-Uhlenbeck (GiBUU) 157
A.3.2.1 Eingangsparameter 157
A.3.2.2 Systematische Untersuchung der Λ-Produktion 159
A.3.3 Implementierung elementarer Wirkungsquerschnitte 167
Abbildungsverzeichnis 169
Tabellenverzeichnis 172
Literaturverzeichnis 173With the dielectron spectrometer HADES, located at the GSI Helmholtzzentrum für Schwerionenforschung in Darmstadt, p + Nb reactions at a kinetic beam energy of 3.5 GeV were measured to study the behavior of nuclear matter. Although primarily designed for the detection of rare leptonic decays of the light vector mesons ρ, ω and φ, the spectrometer renders itself very well suited for the investigation of hadrons, due to its excellent tracking capability. This thesis presents results of the production and polarization of strange Λ hyperons in about 4.2 billion reactions of p + Nb recorded in 2008.
In contrast to theoretical expectations, the polarized production of hyperons was observed in 1976 for the first time in nuclear reactions with unpolarized beams. Based on the fundamental properties of strong interaction, to date no single explanation exists describing all dependencies of the observed hyperon polarization. Therefore, common theoretical models of hyperon polarization are introduced. Acting as a natural polarimeter, the Λ hyperon represents an excellent tool to study the phenomenon of hyperon polarization especially in reactions with unpolarized beams and targets. Hence, the experimental technique for extracting the polarization using the weak decay of the Λ hyperon is explained.
Due to a large solid angle coverage, HADES allows for the reconstruction of hadrons within a wide phase space range. Consequently, a double-differential analysis of the polarization and production probability as a function of transverse momentum pt and rapidity y is performed.
In total, 1.1 million Λ hyperons are reconstructed and corrected for detector acceptance and efficiency. The inverse slope parameter TB is extracted from transverse mass spectra. Its rapidity dependence TB (y) shows a maximum of 90 MeV at y = 1, i.e. below the center-of-mass rapidity of the nucleon-nucleon collision ycm = 1.12, and a stronger decrease to lower rapidities than particles in thermal equilibrium. The Λ rapidity density shows an asymmetric distribution, shifted towards target rapidity, which is probably caused by multiple scattering on target nucleons. Extrapolated to the full phase space, the total multiplicity of 0.018 ± 0.004 Λ hyperons per event satisfies strangeness conservati- 0 on on average. For that purpose, the Ks production rate from another analysis and ratios to the other, unmeasured, strange hadrons, derived from transport simulations, are taken into account.
Furthermore, the Λ hyperon shows a significant negative polarization perpendicular to its production plane, which amounts to Px = (−10.6 ± 1.3) % averaged over the phase space accessible to HADES. The measured Λ polarization increases almost linearly with increasing transverse momentum pt , according to Px (pt ) = (−0.19 ± 0.02) (GeV/c)−1 pt .
In order to spot details on the dynamics of hyperon production in proton-nucleus reactions, the results on Λ polarization and phase space distribution are compared to those of similar reactions. Additionally, a systematic investigation with transport model simulations is performed. The experimental distributions can not be reproduced sufficiently well by the presently available GiBUU and URQMD models.
Moreover, an outlook on further studies of strangeness production in nucleon-nucleus collisions by reconstruction of Ξ− hyperons and φ mesons is given.:1 Einleitung 11
1.1 Struktur der Materie 11
1.2 Schwellennahe Erzeugung von Hadronen mit Strangeness 13
1.3 Modellbeschreibungen der Strangeness-Produktion 15
1.4 Untersuchung von Kernmaterie in Nukleon-Kern-Reaktionen 19
1.5 Zielsetzung und Gliederung der Arbeit 20
2 Hyperonpolarisation 23
2.1 Experimentelle Beobachtungen 23
2.2 Modellbeschreibungen 25
2.2.1 SU(6)-Modell 25
2.2.2 s-Quark-Streumodell 27
2.2.3 Lund-Modell (Farb-Flussröhre) 28
2.2.4 Rekombinationsmodell (Thomas-Präzession) 28
2.2.5 Quantenmechanische Modelle 29
2.3 Der selbstanalysierende Λ-Zerfall als Spin-Polarimeter 30
3 Experimentiersystem HADES und Analysewerkzeuge 33
3.1 Komponenten zur Teilchenidentifikation 35
3.2 Magnetspektrometer 37
3.3 Datenerfassung und -verarbeitung 43
3.4 Analyse- und Simulationssoftware 45
3.5 Transportmodelle 46
4 Datenanalyse zur Reaktion p + Nb 51
4.1 Charakteristika des Experiments 51
4.2 Teilchenidentifikation 55
4.2.1 Flugzeitmethode 56
4.2.2 Energieverlustmethode 58
4.3 Rekonstruktion des Λ-Hyperons 60
4.3.1 Teilchenselektion bezüglich des Energieverlustes 61
4.3.2 Invariantes Massenspektrum 62
4.3.3 Zerfallsgeometrie 65
4.3.4 Vertexrekonstruktion 66
4.3.5 Determination des kombinatorischen Untergrundes 69
4.3.6 Differentielle Analyse bezüglich des Phasenraums 73
4.4 Rekonstruktion des Ξ -Hyperons 77
4.5 Effizienz- und Akzeptanzbestimmung mittels Detektorsimulation 82
4.5.1 Selbstkonsistenz der Simulation 86
4.5.2 Überprüfung der Vertexrekonstruktion 89
4.5.3 Rekonstruktion der Zerfallslänge 91
4.5.4 Normierung der Produktionsrate 93
4.5.5 Differentielle Produktionsrate der Λ-Hyperonen 95
4.6 Messung der Λ-Polarisation 97
4.6.1 Referenzkoordinatensystem 97
4.6.2 Akzeptanzkorrektur 99
4.6.3 Bestimmung der mittleren Polarisation 101
4.6.4 Differentielle Untersuchung der Polarisation 104
5 Diskussion der Ergebnisse
5.1 Λ-Phasenraumverteilung 109
5.1.1 Transversalimpulsverteilungen 110
5.1.2 Extrapolation der transversalen Impulsspektren 113
5.1.3 Systematische Unsicherheiten 114
5.1.4 Vergleich mit Vorhersagen von Transportmodellen 117
5.1.5 Λ-Produktionsmechanismen im BUU-Modell 121
5.1.6 Vergleich mit Ergebnissen anderer Experimente 124
5.2 Strangeness-Erhaltung 131
5.3 Λ-Polarisation 134
5.3.1 Phasenraumabhängigkeit der Polarisation 135
5.3.2 Einordnung der Ergebnisse in den vorhanden Weltdatensatz 139
6 Zusammenfassung und Ausblick 143
A Anhang
A.1 Definition teilchenphysikalischer Variablen 149
A.2 Effizienzkorrektur für Λ-Hyperonen 153
A.3 Simulationen mit Transportmodellen 154
A.3.1 Ultrarelativistic Quantum Molecular Dynamics (UrQMD) 154
A.3.2 Giessen Boltzmann-Uehling-Uhlenbeck (GiBUU) 157
A.3.2.1 Eingangsparameter 157
A.3.2.2 Systematische Untersuchung der Λ-Produktion 159
A.3.3 Implementierung elementarer Wirkungsquerschnitte 167
Abbildungsverzeichnis 169
Tabellenverzeichnis 172
Literaturverzeichnis 17
Complete genome sequence of Paenibacillus riograndensis SBR5T, a Gram-positive diazotrophic rhizobacterium
AbstractPaenibacillus riograndensis is a Gram-positive rhizobacterium which exhibits plant growth promoting activities. It was isolated from the rhizosphere of wheat grown in the state of Rio Grande do Sul, Brazil. Here we announce the complete genome sequence of P. riograndensis strain SBR5T. The genome of P. riograndensis SBR5T consists of a circular chromosome of 7,893,056bps. The genome was finished and fully annotated, containing 6705 protein coding genes, 87 tRNAs and 27 rRNAs. The knowledge of the complete genome helped to explain why P. riograndensis SBR5T can grow with the carbon sources arabinose and mannitol, but not myo-inositol, and to explain physiological features such as biotin auxotrophy and antibiotic resistances. The genome sequence will be valuable for functional genomics and ecological studies as well as for application of P. riograndensis SBR5T as plant growth-promoting rhizobacterium
A new airborne broadband radiometer system and an efficient method to correct thermal offsets
The instrumentation of the High Altitude and Long Range (HALO) research aircraft is extended by the new Broadband AirCrAft RaDiometer Instrumentation (BACARDI) to quantify the radiative energy budget. Two sets of pyranometers and pyrgeometers are mounted to measure upward and downward solar (0.3–3 μm) and thermal-infrared (3–100 μm) irradiances. The radiometers are installed in a passively ventilated fairing to reduce the effects of the dynamic environment, e.g., fast changes of altitude and temperature. The remaining thermal effects range up to 20 W m-2 for the pyranometers and 10 W m-2 for the pyrgeometers; they are corrected using an new efficient method that is introduced in this paper. Using data collected by BACARDI during a night flight, the thermal offsets are parameterized by the rate of change of the radiometer sensor temperatures. Applying the sensor temperatures instead of ambient air temperature for the parameterization provides a linear correction function (200–600 W m-2 K-1 s), that depends on the mounting position of the radiometer on HALO. Furthermore, BACARDI measurements from the EUREC4A (Elucidating the role of clouds-circulation coupling in climate) field campaign are analyzed to characterize the performance of the radiometers and to evaluate all corrections applied in the data processing. Vertical profiles of irradiance measurements up to 10 km altitude show that the thermal offset correction limits the bias due to temperature changes to values below 10 W m-2. Measurements with BACARDI during horizontal, circular flight patterns in cloud-free conditions demonstrate that the common geometric attitude correction of the solar downward irradiance provides reliable measurements in this typical flight sections of EUREC4A, even without active stabilization of the radiometer.</p
Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape
Irla M, Neshat A, Brautaset T, Rückert C, Kalinowski J, Wendisch VF. Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape. BMC Genomics. 2015;16(1): 73.Background
Bacillus methanolicus MGA3 is a thermophilic, facultative ribulose monophosphate (RuMP) cycle methylotroph. Together with its ability to produce high yields of amino acids, the relevance of this microorganism as a promising candidate for biotechnological applications is evident. The B. methanolicus MGA3 genome consists of a 3,337,035 nucleotides (nt) circular chromosome, the 19,174 nt plasmid pBM19 and the 68,999 nt plasmid pBM69. 3,218 protein-coding regions were annotated on the chromosome, 22 on pBM19 and 82 on pBM69. In the present study, the RNA-seq approach was used to comprehensively investigate the transcriptome of B. methanolicus MGA3 in order to improve the genome annotation, identify novel transcripts, analyze conserved sequence motifs involved in gene expression and reveal operon structures. For this aim, two different cDNA library preparation methods were applied: one which allows characterization of the whole transcriptome and another which includes enrichment of primary transcript 5′-ends.
Results
Analysis of the primary transcriptome data enabled the detection of 2,167 putative transcription start sites (TSSs) which were categorized into 1,642 TSSs located in the upstream region (5′-UTR) of known protein-coding genes and 525 TSSs of novel antisense, intragenic, or intergenic transcripts. Firstly, 14 wrongly annotated translation start sites (TLSs) were corrected based on primary transcriptome data. Further investigation of the identified 5′-UTRs resulted in the detailed characterization of their length distribution and the detection of 75 hitherto unknown cis-regulatory RNA elements. Moreover, the exact TSSs positions were utilized to define conserved sequence motifs for translation start sites, ribosome binding sites and promoters in B. methanolicus MGA3. Based on the whole transcriptome data set, novel transcripts, operon structures and mRNA abundances were determined. The analysis of the operon structures revealed that almost half of the genes are transcribed monocistronically (940), whereas 1,164 genes are organized in 381 operons. Several of the genes related to methylotrophy had highly abundant transcripts.
Conclusion
The extensive insights into the transcriptional landscape of B. methanolicus MGA3, gained in this study, represent a valuable foundation for further comparative quantitative transcriptome analyses and possibly also for the development of molecular biology tools which at present are very limited for this organism
Corynebacterium glutamicum possesses β-N-acetylglucosaminidase
Matano C, Kolkenbrock S, Hamer SN, Sgobba E, Moerschbacher BM, Wendisch VF. Corynebacterium glutamicum possesses β-N-acetylglucosaminidase. BMC Microbiology. 2016;16(1): 177.Background
In Gram-positive Corynebacterium glutamicum and other members of the suborder Corynebacterianeae, which includes mycobacteria, cell elongation and peptidoglycan biosynthesis is mainly due to polar growth. C. glutamicum lacks an uptake system for the peptidoglycan constituent N-acetylglucosamine (GlcNAc), but is able to catabolize GlcNAc-6-phosphate. Due to its importance in white biotechnology and in order to ensure more sustainable processes based on non-food renewables and to reduce feedstock costs, C. glutamicum strains have previously been engineered to produce amino acids from GlcNAc. GlcNAc also is a constituent of chitin, but it is unknown if C. glutamicum possesses chitinolytic enzymes.
Results
Chitin was shown here not to be growth substrate for C. glutamicum. However, its genome encodes a putative N-acetylglucosaminidase. The nagA 2 gene product was active as β-N-acetylglucosaminidase with 0.27 mM 4-nitrophenyl N,N’-diacetyl-β-D-chitobioside as substrate supporting half-maximal activity. NagA2 was secreted into the culture medium when overproduced with TAT and Sec dependent signal peptides, while it remained cytoplasmic when overproduced without signal peptide. Heterologous expression of exochitinase gene chiB from Serratia marcescens resulted in chitinolytic activity and ChiB secretion was enhanced when a signal peptide from C. glutamicum was used. Colloidal chitin did not support growth of a strain secreting exochitinase ChiB and β-N-acetylglucosaminidase NagA2.
Conclusions
C. glutamicum possesses β-N-acetylglucosaminidase. In the wild type, β-N-acetylglucosaminidase activity was too low to be detected. However, overproduction of the enzyme fused to TAT or Sec signal peptides led to secretion of active β-N-acetylglucosaminidase. The finding that concomitant secretion of endogenous NagA2 and exochitinase ChiB from S. marcescens did not entail growth with colloidal chitin as sole or combined carbon source, may indicate the requirement for higher or additional enzyme activities such as processive chitinase or endochitinase activities
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Chassis organism from Corynebacterium glutamicum – a top-down approach to identify and delete irrelevant gene clusters
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