Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution

DNA shuffling is widely used for optimizing complex properties contained within DNA and proteins. Demonstrated here is the amplification of a gene library by PCR using uridine triphosphate (dUTP) as a fragmentation defining exchange nucleotide with thymidine, together with the three other nucleotides. The incorporated uracil bases were excised using uracil-DNA-glycosylase and the DNA backbone subsequently cleaved with piperidine. These end-point reactions required no adjustments. Polyacrylamide urea gels demonstrated adjustable fragmentation size over a wide range. The oligonucleotide pool was reassembled by internal primer extension to full length with a proofreading polymerase to improve yield over Taq. We present a computer program that accurately predicts the fragmentation pattern and yields all possible fragment sequences with their respective likelihood of occurrence, taking the guesswork out of the fragmentation. The technique has been demonstrated by shuffling chloramphenicol acetyltransferase gene libraries. A 33% dUTP PCR resulted in shuffled clones with an average parental fragment size of 86 bases even without employment of a fragment size separation, and revealed a low mutation rate (0.1%). NExT DNA fragmentation is rational, easily executed and reproducible, making it superior to other techniques. Additionally, NExT could feasibly be applied to several other nucleotide analogs

Stability with respect to domain of the low Mach number limit of compressible viscous fluids

We study the asymptotic limit of solutions to the barotropic Navier-Stokes system, when the Mach number is proportional to a small parameter \ep \to 0 and the fluid is confined to an exterior spatial domain \Omega_\ep that may vary with \ep. As $\epsilon \rightarrow 0$, it is shown that the fluid density becomes constant while the velocity converges to a solenoidal vector field satisfying the incompressible Navier-Stokes equations on a limit domain. The velocities approach the limit strongly (a.a.) on any compact set, uniformly with respect to a certain class of domains. The proof is based on spectral analysis of the associated wave propagator (Neumann Laplacian) governing the motion of acoustic waves.Comment: 32 page

Gadolinium tissue deposition in the periodontal ligament of mice with reduced renal function exposed to Gd-based contrast agents

Gadolinium deposition in tissue is linked to nephrogenic systemic fibrosis (NSF): a rare disorder occurring in patients with severe chronic kidney disease and associated with administration of Gd-based contrast agents (GBCAs) for Magnetic Resonance Imaging (MRI). It is suggested that the GBCAs prolonged permanence in blood in these patients may result in a Gd precipitation in peripheral or central organs, where it initiates a fibrotic process. In this study we investigated new sites of retention/precipitation of Gd in a mouse model of renal disease (5/6 nephrectomy) receiving two doses (closely after each other) of a linear GBCA. Two commercial GBCAs (Omniscan\uae and Magnevist\uae) were administered at doses slightly higher than those used in clinical practice (0.7 mmol/kg body weight, each). The animals were sacrificed one month after the last administration and the explanted organs (kidney, liver, femur, dorsal skin, teeth) were analysed by X-ray fluorescence (XRF) at two synchrotron facilities. The XRF analysis with a millimetre-sized beam at the SYRMEP beamline (Elettra, Italy) produced no detectable levels of Gd in the examined tissues, with the notable exception of the incisors of the nephrectomised mice. The XRF analyses at sub-micron resolution performed at ID21 (ESRF, France) allowed to clearly localize Gd in the periodontal ligaments of teeth both from Omniscan\uae and Magnevist\uae treated nephrectomised mice. The latter results were further confirmed by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The study prompts that prolonged permanence of GBCAs in blood may result in Gd retention in this particular muscular tissue, opening possibilities for diagnostic applications at this level when investigating Gd-related toxicities

Experimental study of a R290 variable geometry ejector

Ejectors are classified as fluid-dynamics controlled devices where the "component-scale"performances are imposed by the local-scale fluid dynamic phenomena. For this reason, ejector performances (measured by the pressure-entrainment ratio coordinate of the critical point) are determined by the connection of operation conditions, working fluid and geometrical parameters. Given such a connection, variable geometry ejector represents a promising solution to increase the flexibility of ejector-based systems. The present study aims to extend knowledge on variable geometry systems, evaluating the local and global performances of the R290 ejector equipped with a spindle. The prototype ejector was installed at the R290 vapour compression test rig adapted and modified for the required experimental campaign. The test campaign considered global parameter measurements, such as the pressure and the temperature at inlets and outlet ports together with the mass flow rates at both inlet nozzles, and the local pressure drop measurements inside the ejector. In addition, the experimental data were gathered for different spindle positions starting from fully open position the spindle position limited by the mass flow rate inside the test rig with the step of 1.0 mm

Morphological and Chemical Investigation of Ovarian Structures in a Bovine Model by Contrast-Enhanced X-ray Imaging and Microscopy

An improved understanding of an ovary’s structures is highly desirable to support advances in folliculogenesis knowledge and reproductive medicine, with particular attention to fertility preservation options for prepubertal girls with malignant tumors. Although currently the golden standard for structural analysis is provided by combining histological sections, staining, and visible 2D microscopic inspection, synchrotron radiation phase-contrast microtomography is becoming a new challenge for three-dimensional studies at micrometric resolution. To this aim, the proper use of contrast agents can improve the visualization of internal structures in ovary tissues, which normally present a low radiopacity. In this study, we report a comparison of four staining protocols, based on iodine or tungsten containing agents, applied to bovine ovarian tissues fixed in Bouin’s solution. The microtomography (microCT) analyses at two synchrotron facilities under different set-ups were performed at different energies in order to maximize the image contrast. While tungsten-based agents allow large structures to be well identified, Iodine ones better highlight smaller features, especially when acquired above the K-edge energy of the specific metal. Further scans performed at lower energy where the setup was optimized for overall quality and sensitivity from phase-contrast still provided highly resolved visualization of follicular and intrafollicular structures at different maturation stages, independent of the staining protocol. The analyses were complemented by X-ray Fluorescence mapping on 2D sections, showing that the tungsten-based agent has a higher penetration in this type of tissues

Regional Aerosol Optical Properties and Radiative Impact of the Extreme Smoke Event in the European Arctic in Spring 2006

In spring 2006 a special meteorological situation occurred in the European Arctic region giving record high levels of air pollution. The synoptic situation resulted in extensive transport of pollution predominantly from agricultural fires in Eastern Europe into the Arctic region and record high air-pollution levels were measured at the Zeppelin observatory at Ni-Alesun(78deg 54'N, 11deg 53'E) in the period from 25 April to 12 May. In the present study we investigate the optical properties of the aerosols from this extreme event and we estimate the radiative forcing of this episode. We examine the aerosol optical properties from the source region and into the European Arctic and explore the evolution of the episode and the changes in the optical properties. A number of sites in Eastern Europe, Northern Scandinavia and Svalbard are included in the study. In addition to AOD measurements, we explored lidar measurements from Minsk, ALOMAR (Arctic Lidar Observatory for Middle Atmosphere Research at Andenes) and Ny-Alesund. For the AERONET sites included (Minsk, Toravere, Hornsund) we have further studied the evolution of the aerosol size. Importantly, at Svalbard it is consistency between the AERONET measurements and calculations of single scattering albedo based on aerosol chemical composition. We have found strong agreement between the satellite dally MODIS AOD and the ground-based AOD observations. This agreement is crucial for the radiative forcing calculations. We calculate a strong negative radiative forcing for the most polluted days employing the analysed ground based data, MODIS AOD and a multi-stream model for radiative transfer of solar radiation

Four-dimensional distribution of the 2010 Eyjafjallajökull volcanic cloud over Europe observed by EARLINET

© Author(s) 2013. This work is distributed under the Creative Commons Attribution 3.0 License.The eruption of the Icelandic volcano Eyjafjallaj ökull in April-May 2010 represents a "natural experiment" to study the impact of volcanic emissions on a continental scale. For the first time, quantitative data about the presence, altitude, and layering of the volcanic cloud, in conjunction with optical information, are available for most parts of Europe derived from the observations by the European Aerosol Research Lidar NETwork (EARLINET). Based on multi-wavelength Raman lidar systems, EARLINET is the only instrument worldwide that is able to provide dense time series of high-quality optical data to be used for aerosol typing and for the retrieval of particle microphysical properties as a function of altitude. In this work we show the four-dimensional (4-D) distribution of the Eyjafjallajökull volcanic cloud in the troposphere over Europe as observed by EARLINET during the entire volcanic event (15 April-26 May 2010). All optical properties directly measured (backscatter, extinction, and particle linear depolarization ratio) are stored in the EARLINET database available at www.earlinet.org. A specific relational database providing the volcanic mask over Europe, realized ad hoc for this specific event, has been developed and is available on request at www.earlinet.org. During the first days after the eruption, volcanic particles were detected over Central Europe within a wide range of altitudes, from the upper troposphere down to the local planetary boundary layer (PBL). After 19 April 2010, volcanic particles were detected over southern and south-eastern Europe. During the first half of May (5-15 May), material emitted by the Eyjafjallajökull volcano was detected over Spain and Portugal and then over the Mediterranean and the Balkans. The last observations of the event were recorded until 25 May in Central Europe and in the Eastern Mediterranean area. The 4-D distribution of volcanic aerosol layering and optical properties on European scale reported here provides an unprecedented data set for evaluating satellite data and aerosol dispersion models for this kind of volcanic events.Peer reviewe

Photoionization Dynamics of the Tetraoxo Complexes OsO4 and RuO4

The photoionization dynamics of OsO4 and RuO4, chosen as model systems of small-size mononuclear heavy-metal complexes, has been theoretically studied by the time-dependent density functional theory (TDDFT). Accurate experimental measurements of photoionization dynamics as a benchmarking test for the theory are reported for the photoelectron asymmetry parameters of outer valence ionizations of OsO4, measured in the 17-90 eV photon energy range. The theoretical results are in good agreement with the available experimental data. The observed dynamical behavior of partial cross sections and asymmetry parameters has been related to both the coupling to the continuum of discrete excited states, giving strong modulations in the photon energy dependency, and the atomic composition of the initial ionized states, which determines the rate of decay of ionization probability for increasing excitation energies. Overall, an extensive analysis of the photoionization dynamics for valence and core orbitals is presented, showing good agreement with all the available experimental data. This provides confidence for the validity of the TDDFT approach in describing photoionization of heavy transition element compounds, with the perspective of being used for larger systems. Further experimental work is suggested for RuO4 to gather evidence of the sensitivity of the theoretical method to the nature of the metal atom

Arctic smoke ? record high air pollution levels in the European Arctic due to agricultural fires in Eastern Europe

International audienceIn spring 2006, the European Arctic was abnormally warm, setting new historical temperature records. During this warm period, smoke from agricultural fires in Eastern Europe intruded into the European Arctic and caused the most severe air pollution episodes ever recorded there. This paper confirms that biomass burning (BB) was indeed the source of the observed air pollution, studies the transport of the smoke into the Arctic, and presents an overview of the observations taken during the episode. Fire detections from the MODIS instruments aboard the Aqua and Terra satellites were used to estimate the BB emissions. The FLEXPART particle dispersion model was used to show that the smoke was transported to Spitsbergen and Iceland, which was confirmed by MODIS retrievals of the aerosol optical depth (AOD) and AIRS retrievals of carbon monoxide (CO) total columns. Concentrations of halocarbons, carbon dioxide and CO, as well as levoglucosan and potassium, measured at Zeppelin mountain near Ny Ålesund, were used to further corroborate the BB source of the smoke at Spitsbergen. The ozone (O3) and CO concentrations were the highest ever observed at the Zeppelin station, and gaseous elemental mercury was also enhanced. A new O3 record was also set at a station on Iceland. The smoke was strongly absorbing ? black carbon concentrations were the highest ever recorded at Zeppelin ?, and strongly perturbed the radiation transmission in the atmosphere: aerosol optical depths were the highest ever measured at Ny Ålesund. We furthermore discuss the aerosol chemical composition, obtained from filter samples, as well as the aerosol size distribution during the smoke event. Photographs show that the snow at a glacier on Spitsbergen became discolored during the episode and, thus, the snow albedo was reduced. Samples of this polluted snow contained strongly enhanced levels of potassium, sulphate, nitrate and ammonium ions, thus relating the discoloration to the deposition of the smoke aerosols. This paper shows that, to date, BB has been underestimated as a source of aerosol and air pollution for the Arctic, relative to emissions from fossil fuel combustion. Given its significant impact on air quality over large spatial scales and on radiative processes, the practice of agricultural waste burning should be banned in the future