Detection of functional RNAs in genome sequences

Unter Verwendung bewährter Werkzeuge wird eine Pipeline zur fRNA-Vorhersage in kompletten Genomsequenzen entwickelt. Das Programm ermöglicht sowohl die Vorhersage neuer, bisher unbekannter fRNAs, als auch die Vorhersage der Mitglieder bereits bekannter Familien. Hierbei ist kein Expertenwissen zu den einzelnen verwendeten Werkzeugen erforderlich.Die fRNA-Vorhersage basiert auf zwei Säulen. Die erste Säule ist ein komparativer Ansatz, welcher zuerst Sequenzähnlichkeiten zwischen verwandten Genomen aufspürt und aligniert. Die Alignments werden dann auf das Vorkommen stabiler und konservierter Strukturen untersucht. Dieser Ansatz eignet sich vor allem zur Vorhersage neuer fRNAs, da keine Informationen über bekannte fRNAs benötigt werden. Die zweite Säule basiert auf aktuellem Wissen über fRNA-Familien. Dieses Wissen wird genutzt, um gezielt nach Ähnlichkeiten zu bekannten fRNA-Familien zu suchen. Die vorhergesagte Familienzugehörigkeit eines fRNA-Kandidaten gibt gleichzeitig einen Hinweis auf seine Funktion.Die im Rahmen dieser Arbeit entwickelte Pipeline wurde auf mehrere Bakterien- und Archaeengenome angewandt, mit dem Ziel das Vorkommen von fRNA-kodierenden Genen und regulatorischen Elementen vorherzusagen. Die Pipeline ist nicht nur in der Lage komplette Genome zu untersuchen, sondern kann ebenfalls eine Auswahl einzelner Sequenzen behandeln. Sie wurde daher für die Suche nach möglichen regulatorischen Strukturelementen in der mRNA ausgewählter Gene in Saccharomyces cerevisiae und verwandten Spezies genutzt

5′TRU: Identification and Analysis of Translationally Regulative 5′Untranslated Regions in Amino Acid Starved Yeast Cells*

We describe a method to identify and analyze translationally regulative 5′UTRs (5′TRU) in Saccharomyces cerevisiae. Two-dimensional analyses of 35S-methionine metabolically labeled cells revealed 13 genes and proteins, whose protein biosynthesis is post-transcriptionally up-regulated on amino acid starvation. The 5′UTRs of the respective mRNAs were further investigated. A plasmid-based reporter-testing system was developed to analyze their capability to influence translation dependent on amino acid availability. Most of the 13 candidate 5′UTRs are able to enhance translation independently of amino acids. Two 5′UTRs generally repressed translation, and the 5′UTRs of ENO1, FBA1, and TPI1 specifically up-regulated translation when cells were starved for amino acids. The TPI1-5′UTR exhibited the strongest effect in the testing system, which is consistent with elevated Tpi1p-levels in amino acid starved cells. Bioinformatical analyses support that an unstructured A-rich 5′ leader is beneficial for efficient translation when amino acids are scarce. Accordingly, the TPI1-5′UTR was shown to contain an A-rich tract in proximity to the mRNA-initiation codon, required for its amino acid dependent regulatory function

Rhizobium sp. Strain NGR234 Possesses a Remarkable Number of Secretion Systems▿ †

Rhizobium sp. strain NGR234 is a unique alphaproteobacterium (order Rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. We report here that the 3.93-Mbp chromosome (cNGR234) encodes most functions required for cellular growth. Few essential functions are encoded on the 2.43-Mbp megaplasmid (pNGR234b), and none are present on the second 0.54-Mbp symbiotic plasmid (pNGR234a). Among many striking features, the 6.9-Mbp genome encodes more different secretion systems than any other known rhizobia and probably most known bacteria. Altogether, 132 genes and proteins are linked to secretory processes. Secretion systems identified include general and export pathways, a twin arginine translocase secretion system, six type I transporter genes, one functional and one putative type III system, three type IV attachment systems, and two putative type IV conjugation pili. Type V and VI transporters were not identified, however. NGR234 also carries genes and regulatory networks linked to the metabolism of a wide range of aromatic and nonaromatic compounds. In this way, NGR234 can quickly adapt to changing environmental stimuli in soils, rhizospheres, and plants. Finally, NGR234 carries at least six loci linked to the quenching of quorum-sensing signals, as well as one gene (ngrI) that possibly encodes a novel type of autoinducer I molecule

ILC Reference Design Report Volume 1 - Executive Summary

The International Linear Collider (ILC) is a 200-500 GeV center-of-mass high-luminosity linear electron-positron collider, based on 1.3 GHz superconducting radio-frequency (SCRF) accelerating cavities. The ILC has a total footprint of about 31 km and is designed for a peak luminosity of 2x10^34 cm^-2s^-1. This report is the Executive Summary (Volume I) of the four volume Reference Design Report. It gives an overview of the physics at the ILC, the accelerator design and value estimate, the detector concepts, and the next steps towards project realization.The International Linear Collider (ILC) is a 200-500 GeV center-of-mass high-luminosity linear electron-positron collider, based on 1.3 GHz superconducting radio-frequency (SCRF) accelerating cavities. The ILC has a total footprint of about 31 km and is designed for a peak luminosity of 2x10^34 cm^-2s^-1. This report is the Executive Summary (Volume I) of the four volume Reference Design Report. It gives an overview of the physics at the ILC, the accelerator design and value estimate, the detector concepts, and the next steps towards project realization

ILC Reference Design Report Volume 4 - Detectors

This report, Volume IV of the International Linear Collider Reference Design Report, describes the detectors which will record and measure the charged and neutral particles produced in the ILC's high energy e+e- collisions. The physics of the ILC, and the environment of the machine-detector interface, pose new challenges for detector design. Several conceptual designs for the detector promise the needed performance, and ongoing detector R&D is addressing the outstanding technological issues. Two such detectors, operating in push-pull mode, perfectly instrument the ILC interaction region, and access the full potential of ILC physics.This report, Volume IV of the International Linear Collider Reference Design Report, describes the detectors which will record and measure the charged and neutral particles produced in the ILC's high energy e+e- collisions. The physics of the ILC, and the environment of the machine-detector interface, pose new challenges for detector design. Several conceptual designs for the detector promise the needed performance, and ongoing detector R&D is addressing the outstanding technological issues. Two such detectors, operating in push-pull mode, perfectly instrument the ILC interaction region, and access the full potential of ILC physics

ILC Reference Design Report Volume 3 - Accelerator

The International Linear Collider (ILC) is a 200-500 GeV center-of-mass high-luminosity linear electron-positron collider, based on 1.3 GHz superconducting radio-frequency (SCRF) accelerating cavities. The ILC has a total footprint of about 31 km and is designed for a peak luminosity of 2x10^34 cm^-2 s^-1. The complex includes a polarized electron source, an undulator-based positron source, two 6.7 km circumference damping rings, two-stage bunch compressors, two 11 km long main linacs and a 4.5 km long beam delivery system. This report is Volume III (Accelerator) of the four volume Reference Design Report, which describes the design and cost of the ILC.The International Linear Collider (ILC) is a 200-500 GeV center-of-mass high-luminosity linear electron-positron collider, based on 1.3 GHz superconducting radio-frequency (SCRF) accelerating cavities. The ILC has a total footprint of about 31 km and is designed for a peak luminosity of 2x10^34 cm^-2 s^-1. The complex includes a polarized electron source, an undulator-based positron source, two 6.7 km circumference damping rings, two-stage bunch compressors, two 11 km long main linacs and a 4.5 km long beam delivery system. This report is Volume III (Accelerator) of the four volume Reference Design Report, which describes the design and cost of the ILC