Enlarging the synthetic biology toolbox for Pichia pastoris: Golden Gate cloning and CRISPR/Cas9

State-of-the-art strain engineering techniques for the protein producing yeast host Pichia pastoris include overexpression of homologous and heterologous genes, and deletion of host genes. For this purpose overexpression vectors and gene deletion methods such as the split marker technique have been established. For metabolic and cell engineering purposes, the simultaneous overexpression of more than one gene is often needed. Previous approaches employing subsequent steps of overexpression and marker recycling were time- and labor-consuming. Therefore, efficient systems allowing multiple gene overexpression are required, that can be stably integrated into the P. pastoris genome. To this end, we developed a synthetic biology toolbox based on Golden Gate cloning to enable efficient construction of complex and versatile over-expression vectors. Up to five different expression cassettes, employing a library of promoters and terminators can be combined into one vector, and successfully integrated into the genomic DNA of P. pastoris at targeted loci in one step. Recent trends in synthetic biology, however, go into the direction of building up large and complex reaction networks. To allow for clean and unscarred genetic engineering, a CRISPR/Cas9 based method for gene insertions, deletions and replacements was developed, which paves the way for precise genomic rearrangements in P. pastoris. By using this technique precise genomic integrations were performed efficiently without integrative selection markers. The repertoire of genetic techniques developed so far, will provide a wide variety of possibilities to engineer P. pastoris. Applications for these synthetic biology tools in cell engineering of recombinant P. pastoris will be presented

Photoassociation and coherent transient dynamics in the interaction of ultracold rubidium atoms with shaped femtosecond pulses - I. Experiment

We experimentally investigate various processes present in the photoassociative interaction of an ultracold atomic sample with shaped femtosecond laser pulses. We demonstrate the photoassociation of pairs of rubidium atoms into electronically excited, bound molecular states using spectrally cut femtosecond laser pulses tuned below the rubidium D1 or D2 asymptote. Time-resolved pump-probe spectra reveal coherent oscillations of the molecular formation rate, which are due to coherent transient dynamics in the electronic excitation. The oscillation frequency corresponds to the detun-ing of the spectral cut position to the asymptotic transition frequency of the rubidium D1 or D2 lines, respectively. Measurements of the molecular photoassociation signal as a function of the pulse energy reveal a non-linear dependence and indicate a non-perturbative excitation process. Chirping the association laser pulse allowed us to change the phase of the coherent transients. Furthermore, a signature for molecules in the electronic ground state is found, which is attributed to molecule formation by femtosecond photoassociation followed by spontaneous decay. In a subsequent article [A. Merli et al., submitted] quantum mechanical calculations are presented, which compare well with the experimental data and reveal further details about the observed coherent transient dynamics

Recent Progress in Direct DME Synthesis and Potential of Bifunctional Catalysts

PtX technologies are one major building block of the future energy system based on renewables sources. Dimethyl ether (DME) is an important PtX product that can be used as intermediate the production of CO$_{2}$-neutral base chemicals. New applications lead to an increase of the global production and the optimization of the process efficiency, especially when considering decentralized synthesis. This review article puts some spotlights on recent developments in methanol and the direct DME synthesis with a special focus on the modeling and bifunctional catalyst. This study is expected to provide a foundation for future works in the field of catalysis research based on catalysts design and kinetic modeling

Coherent control with shaped femtosecond laser pulses applied to ultracold molecules

We report on coherent control of excitation processes of translationally ultracold rubidium dimers in a magneto-optical trap by using shaped femtosecond laser pulses. Evolution strategies are applied in a feedback loop in order to optimize the photoexcitation of the Rb2 molecules, which subsequently undergo ionization or fragmentation. A superior performance of the resulting pulses compared to unshaped pulses of the same pulse energy is obtained by distributing the energy among specific spectral components. The demonstration of coherent control to ultracold ensembles opens a path to actively influence fundamental photo-induced processes in molecular quantum gases

Differences in cortical contractile properties between healthy epithelial and cancerous mesenchymal breast cells

Cell contractility is mainly imagined as a force dipole-like interaction based on actin stress fibers that pull on cellular adhesion sites. Here, we present a different type of contractility based on isotropic contractions within the actomyosin cortex. Measuring mechanosensitive cortical contractility of suspended cells among various cell lines allowed us to exclude effects caused by stress fibers. We found that epithelial cells display a higher cortical tension than mesenchymal cells, directly contrasting to stress fiber-mediated contractility. These two types of contractility can even be used to distinguish epithelial from mesenchymal cells. These findings from a single cell level correlate to the rearrangement effects of actomyosin cortices within cells assembled in multicellular aggregates. Epithelial cells form a collective contractile actin cortex surrounding multicellular aggregates and further generate a high surface tension reminiscent of tissue boundaries. Hence, we suggest this intercellular structure as to be crucial for epithelial tissue integrity. In contrast, mesenchymal cells do not form collective actomyosin cortices reducing multicellular cohesion and enabling cell escape from the aggregates

Golden Pi CS : a golden gate-derived modular cloning system for applied synthetic biology in the yeast Pichia pastoris

This work has been supported by the Federal Ministry of Science, Research and Economy (BMWFW), the Federal Ministry of Traffic, Innovation and Technology (bmvit), the Styrian Business Promotion Agency SFG, the Standortagentur Tirol, the Government of Lower Austria and ZIT - Technology Agency of the City of Vienna through the COMET-Funding Program managed by the Austrian Research Promotion Agency FFG.State-of-the-art strain engineering techniques for the host Pichia pastoris (syn. Komagataella spp.) include overexpression of homologous and heterologous genes, and deletion of host genes. For metabolic and cell engineering purposes the simultaneous overexpression of more than one gene would often be required. Very recently, Golden Gate based libraries were adapted to optimize single expression cassettes for recombinant proteins in P. pastoris. However, an efficient toolbox allowing the overexpression of multiple genes at once was not available for P. pastoris. With the Golden Pi CS system, we provide a flexible modular system for advanced strain engineering in P. pastoris based on Golden Gate cloning. For this purpose, we established a wide variety of standardized genetic parts (20 promoters of different strength, 10 transcription terminators, 4 genome integration loci, 4 resistance marker cassettes). All genetic parts were characterized based on their expression strength measured by eGFP as reporter in up to four production-relevant conditions. The promoters, which are either constitutive or regulatable, cover a broad range of expression strengths in their active conditions (2-192% of the glyceraldehyde-3-phosphate dehydrogenase promoter P ), while all transcription terminators and genome integration loci led to equally high expression strength. These modular genetic parts can be readily combined in versatile order, as exemplified for the simultaneous expression of Cas9 and one or more guide-RNA expression units. Importantly, for constructing multigene constructs (vectors with more than two expression units) it is not only essential to balance the expression of the individual genes, but also to avoid repetitive homologous sequences which were otherwise shown to trigger "loop-out" of vector DNA from the P. pastoris genome. Golden Pi CS, a modular Golden Gate-derived P. pastoris cloning system, is very flexible and efficient and can be used for strain engineering of P. pastoris to accomplish pathway expression, protein production or other applications where the integration of various DNA products is required. It allows for the assembly of up to eight expression units on one plasmid with the ability to use different characterized promoters and terminators for each expression unit. Golden Pi CS vectors are available at Addgene. The online version of this article (10.1186/s12918-017-0492-3) contains supplementary material, which is available to authorized users

Rapid and High-Throughput Detection of Highly Pathogenic Bacteria by Ibis PLEX-ID Technology

In this manuscript, we describe the identification of highly pathogenic bacteria using an assay coupling biothreat group-specific PCR with electrospray ionization mass spectrometry (PCR/ESI-MS) run on an Ibis PLEX-ID high-throughput platform. The biothreat cluster assay identifies most of the potential bioterrorism-relevant microorganisms including Bacillus anthracis, Francisella tularensis, Yersinia pestis, Burkholderia mallei and pseudomallei, Brucella species, and Coxiella burnetii. DNA from 45 different reference materials with different formulations and different concentrations were chosen and sent to a service screening laboratory that uses the PCR/ESI-MS platform to provide a microbial identification service. The standard reference materials were produced out of a repository built up in the framework of the EU funded project “Establishment of Quality Assurances for Detection of Highly Pathogenic Bacteria of Potential Bioterrorism Risk” (EQADeBa). All samples were correctly identified at least to the genus level

Departure from the vogel behaviour in the glass transition region-thermally stimulated recovery, creep and dynamic mechanical analysis studies

In this work the study of the dynamics of the segmental motions close to Tg of a poly(methyl methacrylate), PMMA, network was analysed by distinct mechanical spectroscopy techniques. Three techniques were employed: dynamic mechanical analysis (DMA), creep and thermally stimulated recovery (TSR). The time–temperature superposition principle was applied to the DMA and creep results, and master curves were successfully constructed. A change from a Vogel to an Arrhenius behaviour was observed in these results. Above Tg it was found a distinct temperature dependence for the retardation times calculated from creep and the relaxation times calculated from DMA. This unexpected behaviour was attributed to the merging of the a and the b relaxations that occurs in PMMA systems. The apparent activation energies ðEaÞ were also calculated from DMA, creep and TSR experiments. Above Tg the Ea values obtained agreed very well for all the techniques. In addition, the fragility exhibited by this material was investigated by the mechanical spectroscopy techniques referred above and by differential scanning calorimetry (DSC). The obtained values of the fragility index m indicated that the PMMA network is a kinetically fragile system. The thermodynamic manifestation of the fragility was also analysed

Organic Reference Materials for Hydrogen, Carbon, and Nitrogen Stable Isotope-Ratio Measurements: Caffeines, n-Alkanes, Fatty Acid Methyl Esters, Glycines, L-Valines, Polyethylenes, and Oils

An international project developed, quality-tested, and determined isotope−δ values of 19 new organic reference materials (RMs) for hydrogen, carbon, and nitrogen stable isotope-ratio measurements, in addition to analyzing pre-existing RMs NBS 22 (oil), IAEA-CH-7 (polyethylene foil), and IAEA-600 (caffeine). These new RMs enable users to normalize measurements of samples to isotope−δ scales. The RMs span a range of δ^2H_(VSMOW-SLAP) values from −210.8 to +397.0 mUr or ‰, for δ^(13)C_(VPDB-LSVEC) from −40.81 to +0.49 mUr and for δ^(15)N_(Air) from −5.21 to +61.53 mUr. Many of the new RMs are amenable to gas and liquid chromatography. The RMs include triads of isotopically contrasting caffeines, C_(16) n-alkanes, n-C_(20)-fatty acid methyl esters (FAMEs), glycines, and L-valines, together with polyethylene powder and string, one n-C_(17)-FAME, a vacuum oil (NBS 22a) to replace NBS 22 oil, and a ^2H-enriched vacuum oil. A total of 11 laboratories from 7 countries used multiple analytical approaches and instrumentation for 2-point isotopic normalization against international primary measurement standards. The use of reference waters in silver tubes allowed direct normalization of δ2H values of organic materials against isotopic reference waters following the principle of identical treatment. Bayesian statistical analysis yielded the mean values reported here. New RMs are numbered from USGS61 through USGS78, in addition to NBS 22a. Because of exchangeable hydrogen, amino acid RMs currently are recommended only for carbon- and nitrogen-isotope measurements. Some amino acids contain ^(13)C and carbon-bound organic ^2H-enrichments at different molecular sites to provide RMs for potential site-specific isotopic analysis in future studies