Generation, Mutagenesis, and Removal of Mini-F Sequences

Maintenance and manipulation of large DNA and RNA virus genomes had presented an obstacle for virological research. BAC vectors provided a solution to both problems as they can harbor large DNA sequences and can efficiently be modified using well-established mutagenesis techniques in Escherichia coli. Numerous DNA virus genomes of herpesvirus and pox virus were cloned into mini-F vectors. In addition, several reverse genetic systems for RNA viruses such as members of Coronaviridae and Flaviviridae could be established based on BAC constructs. Transfection into susceptible eukaryotic cells of virus DNA cloned as a BAC allows reconstitution of recombinant viruses. In this paper, we provide an overview on the strategies that can be used for the generation of virus BAC vectors and also on systems that are currently available for various virus species. Furthermore, we address common mutagenesis techniques that allow modification of BACs from single-nucleotide substitutions to deletion of viral genes or insertion of foreign sequences. Finally, we review the reconstitution of viruses from BAC vectors and the removal of the bacterial sequences from the virus genome during this process

Viral Bacterial Artificial Chromosomes: Generation, Mutagenesis, and Removal of Mini-F Sequences

Maintenance and manipulation of large DNA and RNA virus genomes had presented an obstacle for virological research. BAC vectors provided a solution to both problems as they can harbor large DNA sequences and can efficiently be modified using well-established mutagenesis techniques in Escherichia coli. Numerous DNA virus genomes of herpesvirus and pox virus were cloned into mini-F vectors. In addition, several reverse genetic systems for RNA viruses such as members of Coronaviridae and Flaviviridae could be established based on BAC constructs. Transfection into susceptible eukaryotic cells of virus DNA cloned as a BAC allows reconstitution of recombinant viruses. In this paper, we provide an overview on the strategies that can be used for the generation of virus BAC vectors and also on systems that are currently available for various virus species. Furthermore, we address common mutagenesis techniques that allow modification of BACs from single-nucleotide substitutions to deletion of viral genes or insertion of foreign sequences. Finally, we review the reconstitution of viruses from BAC vectors and the removal of the bacterial sequences from the virus genome during this process

Red-Mediated Transposition and Final Release of the Mini-F Vector of a Cloned Infectious Herpesvirus Genome

Bacterial artificial chromosomes (BACs) are well-established cloning vehicles for functional genomics and for constructing targeting vectors and infectious viral DNA clones. Red-recombination-based mutagenesis techniques have enabled the manipulation of BACs in Escherichia coli without any remaining operational sequences. Here, we describe that the F-factor-derived vector sequences can be inserted into a novel position and seamlessly removed from the present location of the BAC-cloned DNA via synchronous Red-recombination in E. coli in an en passant mutagenesis-based procedure. Using this technique, the mini-F elements of a cloned infectious varicella zoster virus (VZV) genome were specifically transposed into novel positions distributed over the viral DNA to generate six different BAC variants. In comparison to the other constructs, a BAC variant with mini-F sequences directly inserted into the junction of the genomic termini resulted in highly efficient viral DNA replication-mediated spontaneous vector excision upon virus reconstitution in transfected VZV-permissive eukaryotic cells. Moreover, the derived vector-free recombinant progeny exhibited virtually indistinguishable genome properties and replication kinetics to the wild-type virus. Thus, a sequence-independent, efficient, and easy-to-apply mini-F vector transposition procedure eliminates the last hurdle to perform virtually any kind of imaginable targeted BAC modifications in E. coli. The herpesviral terminal genomic junction was identified as an optimal mini-F vector integration site for the construction of an infectious BAC, which allows the rapid generation of mutant virus without any unwanted secondary genome alterations. The novel mini-F transposition technique can be a valuable tool to optimize, repair or restructure other established BACs as well and may facilitate the development of gene therapy or vaccine vectors

Engineering Development of Slurry Bubble Column Reactor (SBCR) Technology. Quarterly Report, January 1--March 31, 1996

The major technical objectives of this program are threefold: (1) to develop the design tools and a fundamental understanding of the fluid dynamics of a slurry bubble column reactor to maximize reactor productivity; (2) to develop the mathematical reactor design models and gain an understanding of the hydrodynamic fundamentals under industrially relevant process conditions; and (3) to develop an understanding of the hydrodynamics and their interaction with the chemistries occurring in the bubble column reactor. Successful completion of these objectives will permit more efficient usage of the reactor column and tighter design criteria, increase overall reactor efficiency, and ensure a design that leads to stable reactor behavior when scaling up to large diameter reactors. The main part of this report describes tracer studies of slurry bubble column hydrodynamics during methanol synthesis

Einfluss von Biogasgärrückständen auf Abundanz und Biomasse von Lumbriciden

Die Novellierung des Erneuerbaren-Energien-Gesetzes im Jahr 2004 hat zu einem starken Anstieg der Zahl an Biogasanlagen beigetragen. Die entstehenden Fermentationsrückstände werden als Dünger in der Landwirtschaft eingesetzt. Die Ausbringung von Biogasgärrückständen und Rohgülle wirkt sich an den Standorten Cunnersdorf und Pfahlheim insgesamt positiv auf die Abundanz und Bio-asse der Lumbriciden aus. Die Artenzu-sammensetzung wird maßgeblich durch die Applikation von Biogasgärrückständen beeinfluss

Recovery of infectious virus from full-length cowpox virus (CPXV) DNA cloned as a bacterial artificial chromosome (BAC)

Transmission from pet rats and cats to humans as well as severe infection in felids and other animal species have recently drawn increasing attention to cowpox virus (CPXV). We report the cloning of the entire genome of cowpox virus strain Brighton Red (BR) as a bacterial artificial chromosome (BAC) in Escherichia coli and the recovery of infectious virus from cloned DNA. Generation of a full-length CPXV DNA clone was achieved by first introducing a mini-F vector, which allows maintenance of large circular DNA in E. coli, into the thymidine kinase locus of CPXV by homologous recombination. Circular replication intermediates were then electroporated into E. coli DH10B cells. Upon successful establishment of the infectious BR clone, we modified the full-length clone such that recombination-mediated excision of bacterial sequences can occur upon transfection in eukaryotic cells. This self-excision of the bacterial replicon is made possible by a sequence duplication within mini-F sequences and allows recovery of recombinant virus progeny without remaining marker or vector sequences. The in vitro growth properties of viruses derived from both BAC clones were determined and found to be virtually indistinguishable from those of parental, wild-type BR. Finally, the complete genomic sequence of the infectious clone was determined and the cloned viral genome was shown to be identical to that of the parental virus. In summary, the generated infectious clone will greatly facilitate studies on individual genes and pathogenesis of CPXV. Moreover, the vector potential of CPXV can now be more systematically explored using this newly generated tool

Automating the Optimization of Catalytic Reaction Mechanism Parameters Using Basin-Hopping: A Proof of Concept

Parameter estimation is a crucial step for successful microkinetic modeling in catalysis. However, the large number of parameters to be optimized in order to match the experimental data is a bottleneck. In this regard, the global optimization algorithm Basin-Hopping is utilized to automate the typically time-extensive and error-prone task of manual fitting of kinetic parameters for a heterogeneous catalytic system. The stochastic approach of the Basin-Hopping algorithm to explore the kinetic parameter solution space coupled with local search methods makes it possible to screen the high-dimensional space for an optimal set of kinetic parameters giving the least residual between the simulated and the experimentally measured catalytic performance data. Our approach also ensures that only thermodynamically consistent solution candidates are explored at each optimization step. We utilize two example case studies in heterogeneous catalysis, namely, methane oxidation over a palladium catalyst and carbon monoxide methanation over a nickel catalyst, with corresponding detailed kinetic models to illustrate the applicability of the algorithm to efficiently fine-tune detailed kinetic models

Oxalobacter formigenes: a potential tool for the treatment of primary hyperoxaluria type 1

Primary hyperoxaluria is characterized by severe urolithiasis, nephrocalcinosis, and early renal failure. As treatment options are scarce, we aimed for a new therapeutic tool using colonic degradation of endogenous oxalate by Oxalobactor formigenes. Oxalobacter was orally administered for 4 weeks as frozen paste (IxOC-2) or as enteric-coated capsules (IxOC-3). Nine patients (five with normal renal function, one after liver–kidney transplantation, and three with renal failure) completed the IxOC-2 study. Seven patients (six with normal renal function and one after liver–kidney transplantation) completed the IxOC-3 study. Urinary oxalate or plasma oxalate in renal failure was determined at baseline, weekly during treatment and for a 2-week follow-up. The patients who showed >20% reduction both at the end of weeks 3 and 4 were considered as responders. Under IxOC-2, three out of five patients with normal renal function showed a 22–48% reduction of urinary oxalate. In addition, two renal failure patients experienced a significant reduction in plasma oxalate and amelioration of clinical symptoms. Under IxOC-3 treatment, four out of six patients with normal renal function responded with a reduction of urinary oxalate ranging from 38.5 to 92%. Although all subjects under IxOC-2 and 4 patients under IxOC-3 showed detectable levels of O. formigenes in stool during treatment, fecal recovery dropped directly at follow up, indicating only transient gastrointestinal-tract colonization. The preliminary data indicate that O. formigenes is safe, leads to a significant reduction of either urinary or plasma oxalate, and is a potential new treatment option for primary hyperoxaluria

Hydrogen Production and Carbon Capture by Gas‐Phase Methane Pyrolysis: A Feasibility Study

Using natural gas and sustainable biogas as feed, high-temperature pyrolysis represents a potential technology for large-scale hydrogen production and simultaneous carbon capture. Further utilization of solid carbon accruing during the process (i. e., in battery industry or for metallurgy) increases the process\u27s economic chances. This study demonstrated the feasibility of gas-phase methane pyrolysis for hydrogen production and carbon capture in an electrically heated high-temperature reactor operated between 1200 and 1600 °C under industrially relevant conditions. While hydrogen addition controlled methane conversion and suppressed the formation of undesired byproducts, an increasing residence time decreased the amount of byproducts and benefited high hydrogen yields. A temperature of 1400 °C ensured almost full methane conversion, moderate byproduct formation, and high hydrogen yield. A reaction flow analysis of the gas-phase kinetics revealed acetylene, ethylene, and benzene as the main intermediate products and precursors of carbon formation