Gapless provides combined scaffolding, gap filling, and assembly correction with long reads

Continuity, correctness, and completeness of genome assemblies are important for many biological projects. Long reads represent a major driver towards delivering high-quality genomes, but not everybody can achieve the necessary coverage for good long read-only assemblies. Therefore, improving existing assemblies with low-coverage long reads is a promising alternative. The improvements include correction, scaffolding, and gap filling. However, most tools perform only one of these tasks and the useful information of reads that supported the scaffolding is lost when running separate programs successively. Therefore, we propose a new tool for combined execution of all three tasks using PacBio or Oxford Nanopore reads. gapless is available at: https://github.com/schmeing/gapless

Integrated Gallium Phosphide Photonics

The integration of new materials mediating light-matter interaction in nanoscale devices is a persistent goal in nanophotonics. One of these materials is Gallium phosphide, which offers an attractive combination of a high refractive index (n=3.05 at a wavelength of 1550 nm) and a large bandgap (Eg =2.26 eV), enabling photonic devices with strongly confined light fields, not suffering from heating due to two-photon absorption at telecommunication wavelengths. Furthermore, due to its non-centrosymmetric crystal structure, it has a non-vanishing second-order susceptibility and is piezoelectric. Related to its large refractive index is a high third-order susceptibility. Prior to this work the use of GaP for photonic devices was limited to individual non-integrated components, as GaP was not available on a substrate with substantially lower refractive index equivalent to SOI-wafers for silicon. In this work a process was developed that allows the integration of GaP devices onto SiO2. It exploits direct wafer bonding of a GaP/AlxGa1-xP/GaP heterostructure onto a SiO2-on-Si wafer. After substrate removal, photonic devices are patterned by dry-etching in the top GaP device layer. The GaP devices investigated here are used to explore nonlinear optics and optomechanics. In the area of nonlinear optics, second- and third-harmonic generation are observed. The Kerr coefficient is experimentally estimated as n2[1550nm] = 1.2(5)x10^17m^2/W, for the first time in a precision measurement at telecommunication wavelengths. Four-wave mixing is used for broadband frequency comb generation, where a power threshold as low as 3 mW is obtained. The combination of four-wave mixing and second-harmonic generation leads to frequency-doubled combs. The optomechanical properties of GaP one-dimensional photonic crystal cavities are optimized by simulations and fabricated devices are characterized. Optical quality factors of Qo>10^5 and optomechanical coupling strengths of g0/2pi=400 kHz are measured. Dynamical backaction in the form of the spring effect and the parametric amplification are observed, as well as optomechanically induced transparency and absorption. A device design for a microwave-to-optical transducer is developed, relying on the piezoelectricity of GaP. It combines electromechanical and optomechanical transduction. The predicted electromechanical coupling strength is in the MHz range. Furthermore, photonic crystal cavity designs containing a slot at the center of the cavity are studied. According to simulations for slot widths below 30 nm, optomechanical coupling strengths g0/2pi>1 MHz could be achieved. Fabricated silicon photonic crystal cavities show high quality factors of Qo=8x10^4 while hosting a mechanical eigenmode with a frequency of 2.7 GHz. Because of process technology limitations, only slot widths as narrow as 40 nm can be fabricated, the achieved g0/2pi is limited to 300 kHz. The new GaP-on-insulator material platform opens the door to integrated GaP devices. Frequency combs are of interest for soliton comb formation, mid-IR frequency combs, and ultra-broadband supercontinuum generation. Microwave-to-optical transducers are on the one hand desired for quantum information processing, on the other hand they are applicable as efficient modulators or detectors for classical signals

How mutations in tRNA distant from the anticodon affect the fidelity of decoding

The ribosome converts genetic information into protein by selecting aminoacyl tRNAs whose anticodons base-pair to an mRNA codon. Mutations in the tRNA body can perturb this process and affect fidelity. The Hirsh suppressor is a well-studied tRNA^(Trp) harboring a G24A mutation that allows readthrough of UGA stop codons. Here we present crystal structures of the 70S ribosome complexed with EF-Tu and aminoacyl tRNA (native tRNA^(Trp), G24A tRNA^(Trp) or the miscoding A9C tRNA^(Trp)) bound to cognate UGG or near-cognate UGA codons, determined at 3.2-Å resolution. The A9C and G24A mutations lead to miscoding by facilitating the distortion of tRNA required for decoding. A9C accomplishes this by increasing tRNA flexibility, whereas G24A allows the formation of an additional hydrogen bond that stabilizes the distortion. Our results also suggest that each native tRNA will adopt a unique conformation when delivered to the ribosome that allows accurate decoding

Rocaglates as dual-targeting agents for experimental cerebral malaria

Cerebral malaria (CM) is a severe and rapidly progressing complication of infection by Plasmodium parasites that is associated with high rates of mortality and morbidity. Treatment options are currently few, and intervention with artemisinin (Art) has limited efficacy, a problem that is compounded by the emergence of resistance to Art in Plasmodium parasites. Rocaglates are a class of natural products derived from plants of the Aglaia genus that have been shown to interfere with eukaryotic initiation factor 4A (eIF4A), ultimately blocking initiation of protein synthesis. Here, we show that the rocaglate CR-1-31B perturbs association of Plasmodium falciparum eIF4A (PfeIF4A) with RNA. CR-1-31B shows potent prophylactic and therapeutic antiplasmodial activity in vivo in mouse models of infection with Plasmodium berghei (CM) and Plasmodium chabaudi (blood-stage malaria), and can also block replication of different clinical isolates of P. falciparum in human erythrocytes infected ex vivo, including drug-resistant P. falciparum isolates. In vivo, a single dosing of CR-1-31B in P. berghei-infected animals is sufficient to provide protection against lethality. CR-1-31B is shown to dampen expression of the early proinflammatory response in myeloid cells in vitro and dampens the inflammatory response in vivo in P. berghei-infected mice. The dual activity of CR-1-31B as an antiplasmodial and as an inhibitor of the inflammatory response in myeloid cells should prove extremely valuable for therapeutic intervention in human cases of CM.We thank Susan Gauthier, Genevieve Perreault, and Patrick Senechal for technical assistance. This work was supported by a research grant (to P.G.) from the Canadian Institutes of Health Research (CIHR) (Foundation Grant). J.P. and P.G. are supported by a James McGill Professorship salary award. D.L. is supported by fellowships from the Fonds de recherche sante Quebec, the CIHR Neuroinflammation training program. J.P. is supported by CIHR Research Grant FDN-148366. M.S. is supported by a CIHR Foundation grant. J.A.P. is supported by NIH Grant R35 GM118173. Work at the Boston University Center for Molecular Discovery is supported by Grant R24 GM111625. K.C.K. was supported by a CIHR Foundation Grant and the Canada Research Chair program. (Canadian Institutes of Health Research (CIHR); James McGill Professorship salary award; Fonds de recherche sante Quebec; CIHR Neuroinflammation training program; FDN-148366 - CIHR Research Grant; CIHR Foundation grant; R35 GM118173 - NIH; Canada Research Chair program; R24 GM111625

The isolation of novel "Erwinia" phages and their use in the study of bacterial phytopathogenicity

A number of bacteriophages were isolated on the "soft rot" phytopathogens Erwinia carotovora subsp. atroseptica SCRI1043 and Erwinia carotovora subsp. carotovora SCRI193. Several of these phages were used to obtain phage resistant mutants of SCRI1043, in order to investigate the role of the bacterial cell surface in virulence. While a number of phenotypic properties relating to pathogenicity and virulence of this strain have already been uncovered, little is known about the role of the cell surface in virulence. It was hoped that the use of phages would allow selection of mutants altered in both cell surface and virulence. Two phage resistant mutants, A5/22 and A5/8, exhibited reduced virulence when inoculated into potato plants, and were investigated further. Both mutants showed pleiotropic phenotypes. As well as reduced virulence and phage resistance, these mutants showed a number of other phenotypic alterations including, a reduction in the production of plant cell wall degrading enzymes, increased sensitivity to surface active agents, alterations in lipopolysaccharide and outer membrane protein profiles and reduced motility. A5/22 also exhibited bacteriostasis in the presence of galactose. Mutant A5/22 was more severely affected in its virulence than A5/8, which reflected in its greater deviation from the wild type phenotype. While no one phenotypic alteration could be directly associated with the reduced virulence of either mutant, a combination of several phenotypes may have been responsible. The phages isolated in this study were the first reported for these strains of Erwinia, and were therefore characterised under a number of criteria. All phages were grouped on the basis of structural morphology, restriction endonuclease digestion and host range. This is the first detailed characterisation of phages for Erwinia carotovora subsp. atroseptica. All isolated phages were tested for generalised transduction, a method of molecular genetic analysis so far unavailable to Erwinia carotovora subsp. atroseptica SCRI1043 and Erwinia carotovora subsp. carotovora SCRI193. Two phages, ØKP and ØMl, were capable of generalised transduction in SCRI193 and SCRI1043 respectively. Both these phages were characterised and transducing frequencies improved. ØMl is the first transducing phage reported for Erwinia carotovora subsp. atroseptica and ØKP is only the second for Erwinia carotovora subsp. carotovora. Both phages are now being used extensively in the laboratory

Analyse von Terminplänen

Das Bachelorprojekt „Analyse von Terminplänen“ beschäftigt sich mit der Analyse der Abhängigkeiten zwischen den unterschiedlichen Vorgängen des Bauablaufs. Die Problematik in der Terminplanerstellung liegt darin, dass ein Terminplan nicht alle Hintergrundinformationen abbildet und es daher zu Projektverzögerungen und Absprachefehlern kommen kann. Dieses Bachelorprojekt macht Gebrauch von bereits aufbereiteten Informationen zur genannten Problematik in Form eines vorangegangen Bachelorprojekts und eines Masterprojekts, sowie einer Umfrage des Instituts für Bauwirtschaft der Universität Kassel. In diesem Projekt werden 50 neue und 100 bereits existierende Terminpläne von diversen Unternehmen aus ganz Deutschland analysiert und ausgewertet. Die Analyse der Terminpläne basiert auf geführten Experteninterviews. Das Interview berücksichtigt Faktoren wie zum Beispiel Darstellungsformen, Detaillierungsgrade, Abhängigkeiten, Vorgangsdauern oder Planungsgrundlagen. Durch die Befragung von möglichst vielen Firmen konnte festgestellt werden, dass jeder Terminplanentwickler eine Vorgehensweise entwickelt, nach welcher er arbeitet. Außerdem ist in den Gesprächen deutlich geworden, dass das Theorie- Praxis-Gefälle sehr groß ist. Das heißt, dass theoretische Modelle aus der Ausbildung an beispielsweise Hochschulen, in der Praxis heutzutage wenig angewandt werden. Nach der Analyse der Terminpläne und Auswertung der Interviews, werden die Daten in eine vom vorangehenden Masterprojekt erstellte Excel-Tabelle eingepflegt. Die vorhandenen Informationen werden dann anhand verschiedenster Diagramme verglichen und ausgewertet

rp-Process weak-interaction mediated rates of waiting-point nuclei

Electron capture and positron decay rates are calculated for neutron-deficient Kr and Sr waiting point nuclei in stellar matter. The calculation is performed within the framework of pn-QRPA model for rp-process conditions. Fine tuning of particle-particle, particle-hole interaction parameters and a proper choice of the deformation parameter resulted in an accurate reproduction of the measured half-lives. The same model parameters were used to calculate stellar rates. Inclusion of measured Gamow-Teller strength distributions finally led to a reliable calculation of weak rates that reproduced the measured half-lives well under limiting conditions. For the rp-process conditions, electron capture and positron decay rates on $^{72}$Kr and $^{76}$Sr are of comparable magnitude whereas electron capture rates on $^{78}$Sr and $^{74}$Kr are 1--2 orders of magnitude bigger than the corresponding positron decay rates. The pn-QRPA calculated electron capture rates on $^{74}$Kr are bigger than previously calculated. The present calculation strongly suggests that, under rp-process conditions, electron capture rates form an integral part of weak-interaction mediated rates and should not be neglected in nuclear reaction network calculations as done previously.Comment: 13 pages, 4 figures, 4 tables; Astrophysics and Space Science (2012