Laser Control of Electronic Exchange Interaction within a Molecule.

Electronic interactions play a fundamental role in atoms, molecular structure and reactivity. We introduce a general concept to control the effective electronic exchange interaction with intense laser fields via coupling to excited states. As an experimental proof of principle, we study the SF_{6} molecule using a combination of soft x-ray and infrared (IR) laser pulses. Increasing the IR intensity increases the effective exchange energy of the core hole with the excited electron by 50%, as observed by a characteristic spin-orbit branching ratio change. This work demonstrates altering electronic interactions by targeting many-particle quantum properties.

Transmating: conjugative transfer of a new broad host range expression vector to various Bacillus species using a single protocol.

BACKGROUND: The genus Bacillus includes a great variety of species with potential applications in biotechnology. While species such as B. subtilis or B. licheniformis are well-known and used to provide various products at industrial scale, other Bacillus species are less characterized and are not yet used in commercial processes. One reason for this is the fact that genetic manipulation of new isolates is usually complicated with conventional techniques which have to be adapted to each new strain. Even in well-established strains, the available transformation protocols often suffer from low efficiencies. RESULTS: In this paper, we provide a new broad host range E. coli/Bacillus shuttle vector, named pBACOV (Bacillus conjugation vector), that can be efficiently transferred to various Bacillus species using a single protocol. A variant of pBACOV carrying the sfGFP gene was successfully transferred to eight different species from the genus Bacillus and to one Paenibacillus species using triparental conjugation ("transmating"). This was achieved using a single protocol and worked for nine out of eleven tested acceptor species. The transmating procedure was used to test expression of the heterologous reporter gene sfGFP under control of the PaprE-promoter from B. subtilis in several Bacillus species in parallel. Expression of sfGFP was found in eight out of nine transmates. For several of the tested species, this is the first report of a method for genetic modification and heterologous gene expression. The expression level, analyzed by measuring the relative sfGFP-fluorescence normalized to the cell density of the cultures, was highest in B. mojavensis. CONCLUSIONS: The new shuttle vector pBACOV can be transferred to many different Bacillus and Paenibacillus species using a simple and efficient transmating protocol. It is a versatile tool facilitating the application of recombinant DNA technology in new as well as established strains, or selection of an ideal host for heterologous gene expression from a multitude of strains. This paves the way for the genetic modification and biotechnological exploitation of the broad diversity of species of Bacillus and related genera as well as different strains from these species.

Treatment planning for spinal radiosurgery : A competitive multiplatform benchmark challenge.

PURPOSE: To investigate the quality of treatment plans of spinal radiosurgery derived from different planning and delivery systems. The comparisons include robotic delivery and intensity modulated arc therapy (IMAT) approaches. Multiple centers with equal systems were used to reduce a bias based on individual's planning abilities. The study used a series of three complex spine lesions to maximize the difference in plan quality among the various approaches. METHODS: Internationally recognized experts in the field of treatment planning and spinal radiosurgery from 12 centers with various treatment planning systems participated. For a complex spinal lesion, the results were compared against a previously published benchmark plan derived for CyberKnife radiosurgery (CKRS) using circular cones only. For two additional cases, one with multiple small lesions infiltrating three vertebrae and a single vertebra lesion treated with integrated boost, the results were compared against a benchmark plan generated using a best practice guideline for CKRS. All plans were rated based on a previously established ranking system. RESULTS: All 12 centers could reach equality (n = 4) or outperform (n = 8) the benchmark plan. For the multiple lesions and the single vertebra lesion plan only 5 and 3 of the 12 centers, respectively, reached equality or outperformed the best practice benchmark plan. However, the absolute differences in target and critical structure dosimetry were small and strongly planner-dependent rather than system-dependent. Overall, gantry-based IMAT with simple planning techniques (two coplanar arcs) produced faster treatments and significantly outperformed static gantry intensity modulated radiation therapy (IMRT) and multileaf collimator (MLC) or non-MLC CKRS treatment plan quality regardless of the system (mean rank out of 4 was 1.2 vs. 3.1, p = 0.002). CONCLUSIONS: High plan quality for complex spinal radiosurgery was achieved among all systems and all participating centers in this planning challenge. This study concludes that simple IMAT techniques can generate significantly better plan quality compared to previous established CKRS benchmarks.

Evaluation of promoter sequences for the secretory production of a Clostridium thermocellum cellulase in Paenibacillus polymyxa.

Due to their high secretion capacity, Gram-positive bacteria from the genus Bacillus are important expression hosts for the high-yield production of enzymes in industrial biotechnology; however, to date, strains from only few Bacillus species are used for enzyme production at industrial scale. Herein, we introduce Paenibacillus polymyxa DSM 292, a member of a different genus, as a novel host for secretory protein production. The model gene cel8A from Clostridium thermocellum was chosen as an easily detectable reporter gene with industrial relevance to demonstrate heterologous expression and secretion in P. polymyxa. The yield of the secreted cellulase Cel8A protein was increased by optimizing the expression medium and testing several promoter sequences in the expression plasmid pBACOV. Quantitative mass spectrometry was used to analyze the secretome in order to identify promising new promoter sequences from the P. polymyxa genome itself. The most abundantly secreted host proteins were identified, and the promoters regulating the expression of their corresponding genes were selected. Eleven promoter sequences were cloned and tested, including well-characterized promoters from Bacillus subtilis and Bacillus megaterium. The best result was achieved with the promoter for the hypothetical protein PPOLYM_03468 from P. polymyxa. In combination with the optimized expression medium, this promoter enabled the production of 5475 U/l of Cel8A, which represents a 6.2-fold increase compared to the reference promoter PaprE. The set of promoters described in this work covers a broad range of promoter strengths useful for heterologous expression in the new host P. polymyxa.

Design and implementation of a "cheese" phantom-based Tomotherapy TLD dose intercomparison.

BACKGROUND: The unique beam-delivery technique of Tomotherapy machines (Accuray Inc., Sunnyvale, Calif.) necessitates tailored quality assurance. This requirement also applies to external dose intercomparisons. Therefore, the aim of the 2014 SSRMP (Swiss Society of Radiobiology and Medical Physics) dosimetry intercomparison was to compare two set-ups with different phantoms. MATERIALS AND METHODS: A small cylindrical Perspex phantom, which is similar to the IROC phantom (Imaging and Radiation Oncology Core, Houston, Tex.), and the "cheese" phantom, which is provided by the Tomotherapy manufacturer to all institutions, were used. The standard calibration plans for the TomoHelical and TomoDirect irradiation techniques were applied. These plans are routinely used for dose output calibration in Tomotherapy institutions. We tested 20 Tomotherapy machines in Germany and Switzerland. The ratio of the measured (Dm) to the calculated (Dc) dose was assessed for both phantoms and irradiation techniques. The Dm/Dc distributions were determined to compare the suitability of the measurement set-ups investigated. RESULTS: The standard deviations of the TLD-measured (thermoluminescent dosimetry) Dm/Dc ratios for the "cheese" phantom were 1.9 % for the TomoHelical (19 measurements) and 1.2 % (11 measurements) for the TomoDirect irradiation techniques. The corresponding ratios for the Perspex phantom were 2.8 % (18 measurements) and 1.8 % (11 measurements). CONCLUSION: Compared with the Perspex phantom-based set-up, the "cheese" phantom-based set-up without individual planning was demonstrated to be more suitable for Tomotherapy dose checks. Future SSRMP dosimetry intercomparisons for Tomotherapy machines will therefore be based on the "cheese" phantom set-up.

Intermixing-Driven Surface and Bulk Ferromagnetism in the Quantum Anomalous Hall Candidate MnBi6 Te10.

The recent realizations of the quantum anomalous Hall effect (QAHE) in MnBi2 Te4 and MnBi4 Te7 benchmark the (MnBi2 Te4 )(Bi2 Te3 )n family as a promising hotbed for further QAHE improvements. The family owes its potential to its ferromagnetically (FM) ordered MnBi2 Te4 septuple layers (SLs). However, the QAHE realization is complicated in MnBi2 Te4 and MnBi4 Te7 due to the substantial antiferromagnetic (AFM) coupling between the SLs. An FM state, advantageous for the QAHE, can be stabilized by interlacing the SLs with an increasing number n of Bi2 Te3 quintuple layers (QLs). However, the mechanisms driving the FM state and the number of necessary QLs are not understood, and the surface magnetism remains obscure. Here, robust FM properties in MnBi6 Te10 (n = 2) with Tc ≈ 12 K are demonstrated and their origin is established in the Mn/Bi intermixing phenomenon by a combined experimental and theoretical study. The measurements reveal a magnetically intact surface with a large magnetic moment, and with FM properties similar to the bulk. This investigation thus consolidates the MnBi6 Te10 system as perspective for the QAHE at elevated temperatures.

Draft Genome Sequence of Paenibacillus polymyxa DSM 292, a Gram-Positive, Spore-Forming Soil Bacterium with High Biotechnological Potential.

Paenibacillus polymyxa DSM 292 was originally isolated from soil in 1947 due to its ability to produce antibiotics. The low proteolytic properties of strain DSM 292 warrant its examination as a host for heterologous protein production. Here, we report the draft genome sequence of DSM 292 as established by Illumina MiSeq paired-end sequencing.

Identification of endoxylanase XynE from Clostridium thermocellum as the first xylanase of glycoside hydrolase family GH141.

Enzymes that cleave polysaccharides in lignocellulose, i. e., cellulases, xylanases, and accessory enzymes, play crucial roles in the natural decomposition of plant-derived biomass and its efficient and sustainable processing into biofuels or other bulk chemicals. The analysis of open reading frame cthe_2195 from the thermophilic, cellulolytic anaerobe Clostridium thermocellum (also known as 'Ruminiclostridium thermocellum') suggested that it encoded a cellulosomal protein comprising a dockerin-I module, a carbohydrate-binding module, and a module of previously unknown function. The biochemical characterisation upon recombinant expression in Escherichia coli revealed that the protein is a thermostable endoxylanase, named Xyn141E with an optimal pH of 6.0-6.5 and a temperature optimum of 67-75 °C. The substrate spectrum of Xyn141E resembles that of GH10 xylanases, because of its side activities on carboxymethyl cellulose, barley ß-glucan, and mannan. Conversely, the product spectrum of Xyn141E acting on arabinoxylan is similar to those of GH11, as established by HPAEC-PAD analysis. Xyn141E is weakly related (20.7% amino acid sequence identity) to the founding member of the recently established GH family 141 and is the first xylanase in this new family of biomass-degrading enzymes.

Functional Screening of Hydrolytic Activities Reveals an Extremely Thermostable Cellulase from a Deep-Sea Archaeon.

Extreme habitats serve as a source of enzymes that are active under extreme conditions and are candidates for industrial applications. In this work, six large-insert mixed genomic libraries were screened for hydrolase activities in a broad temperature range (8-70°C). Among a variety of hydrolytic activities, one fosmid clone, derived from a library of pooled isolates of hyperthermophilic archaea from deep sea vents, displayed hydrolytic activity on carboxymethyl cellulose substrate plates at 70°C but not at lower temperatures. Sequence analysis of the fosmid insert revealed a gene encoding a novel glycoside hydrolase family 12 (GHF12) endo-1,4-ß-glucanase, termed Cel12E. The enzyme shares 45% sequence identity with a protein from the archaeon Thermococcus sp. AM4 and displays a unique multidomain architecture. Biochemical characterization of Cel12E revealed a remarkably thermostable protein, which appears to be of archaeal origin. The enzyme displayed maximum activity at 92°C and was active on a variety of linear 1,4-ß-glucans like carboxymethyl cellulose, ß-glucan, lichenan, and phosphoric acid swollen cellulose. The protein is able to bind to various insoluble ß-glucans. Product pattern analysis indicated that Cel12E is an endo-cleaving ß-glucanase. Cel12E expands the toolbox of hyperthermostable archaeal cellulases with biotechnological potential.