Modern approaches to artificial gene synthesis: aspects of oligonucleotide synthesis, enzymatic assembly, sequence verification and error correction

Synthetic biology is a rapidly developing field aimed at engineering of biological systems with predictable properties. Synthetic biology accumulates the achievements of modern biological sciences, programming and computational model­ing as well as engineering technologies for creation of biologi­cal objects with user-defined properties. Evolution of synthetic biology has been marked by a number of technological developments in each of the mentioned fields. Thus, significant reduction in cost of DNA sequencing has provided an easy access to large amounts of data on the genetic sequences of various organisms, and decreased the price of the DNA sequence synthesis, which, analogous to Moore’s law, resulted in an opportunity to create a lot of potential genes without the time – consuming and labor – intensive traditional methods of molecular biology. Development of system biology has allowed forming a deeper understanding of the functions and relationship of natural biological models, as well as of the computational models describing processes at the cell and system levels. Combination of these factors has created an op­portunity for conscious changes of natural biological systems. In this review the modern approaches to oligonucleotide gene assembly synthesis are discussed, including such aspects as protocols for gene assembly, sequence verification, error cor­rection and further applications of synthesized genes

Radioluminescence properties of nanocomposite scintillators with BaF 2 fillers

In this paper, studies of the luminescence properties of nanocrystalline BaF 2 samples synthesized by laser ablation and pulse electron beam evaporation method are presented. The measurements of X-ray excited luminescence (XEL) showed the dependence between luminescence intensity and the shape of the spectrum on the morphology and particle size. Also, studies of X-ray excited luminescence, decay curves and optical transmittance for nanocomposite materials containing BaF 2 nanopowder are presented. Barium fluoride nanopowder, obtained by pulsed electron beam evaporation method is characterized by a lower intensity than the initial microcrystalline powder, but at the same time, XEL spectrum of the nanocomposite material with this nanocrystalline filler is more intense, then that for nanocomposite material with initial powder. © Published under licence by IOP Publishing Ltd

New Debris Disks Around Nearby Main Sequence Stars: Impact on The Direct Detection of Planets

Using the MIPS instrument on the Spitzer telescope, we have searched for infrared excesses around a sample of 82 stars, mostly F, G, and K main-sequence field stars, along with a small number of nearby M stars. These stars were selected for their suitability for future observations by a variety of planet-finding techniques. These observations provide information on the asteroidal and cometary material orbiting these stars - data that can be correlated with any planets that may eventually be found. We have found significant excess 70um emission toward 12 stars. Combined with an earlier study, we find an overall 70um excess detection rate of $13 \pm 3$% for mature cool stars. Unlike the trend for planets to be found preferentially toward stars with high metallicity, the incidence of debris disks is uncorrelated with metallicity. By newly identifying 4 of these stars as having weak 24um excesses (fluxes $\sim$10% above the stellar photosphere), we confirm a trend found in earlier studies wherein a weak 24um excess is associated with a strong 70um excess. Interestingly, we find no evidence for debris disks around 23 stars cooler than K1, a result that is bolstered by a lack of excess around any of the 38 K1-M6 stars in 2 companion surveys. One motivation for this study is the fact that strong zodiacal emission can make it hard or impossible to detect planets directly with future observatories like the {\it Terrestrial Planet Finder (TPF)}. The observations reported here exclude a few stars with very high levels of emission, $>$1,000 times the emission of our zodiacal cloud, from direct planet searches. For the remainder of the sample, we set relatively high limits on dust emission from asteroid belt counterparts

Formation of Galactic Systems in Light of the Magnesium Abundance in Field Stars: The Thin Disk

We analyze the relations between the relative magnesium abundances in stars and their metallicities, Galactic orbital elements, and ages. The relative magnesium abundances in metal-poor ([Fe/H] < -0.4) thin-disk stars have been found to systematically decrease with increasing stellar orbital radii in such a way that magnesium over abundances ([Mg/Fe]>0.2 dex) are essentially observed only in the stars whose orbits lie almost entirely within the solar circle. At the same time, the range of metallicities in magnesium-poor stars is displaced from (-0.5<[Fe/H]<+0.3 dex) to (-0.7<[Fe/H]<+0.2 dex) as their orbital radii increase. This behavior suggests that, first, the star formation rate decreases with increasing Galactocentric distance and, second, there was no star formation for some time outside the solar circle while this process was continuous within the solar circle. The decrease in the star formation rate with increasing Galactocentric distance is responsible for the existence of a negative radial metallicity gradient (grad_{R}[Fe/H]=(-0.05 \pm 0.01) kpc^{-1}) in the disk, which shows a tendency to increase with decreasing age. At the same time the relative magnesium abundance exhibits no radial gradient. We have confirmed the existence of a steep negative vertical metallicity gradient (grad_Z [Fe/H]=(-0.29 \pm 0.06) kpc^{-1}) and detected a significant positive vertical gradient in relative magnesium abundance (grad_Z [Mg/Fe]=(0.13 \pm 0.02) kpc^{-1}); both gradients increase appreciably in absolute value with decreasing age. We have found that there is not only an age-metallicity relation, but also an age-magnesium abundance relation in the thin disk.Comment: accepted 2006, Astronomy Letters, Vol. 32 No. 6, P.376-392, 14 pages, 10 figure

Supporting data and methods for the characterization of iron oxide nanoparticles conjugated with pH-(low)-insertion peptide, testing their cytotoxicity and analyses of biodistribution in SCID mice bearing MDA-MB231 tumor

The method of Fe3O4 magnetic nanoparticle synthesis by co-precipitation, modification by 3-aminopropylsilane and conjugation with pH-(low)-insertion peptide (pHLIP) is reported. The characterization of nanoparticles by scanning electron microscopy, transmission electron microscopy, Fourier-transform infrared spectroscopy, elemental and thermogravimetric analyses as well as dynamic light scattering and z-potential measurements is provided. The effect of nanoparticles on the viability of mouse and human peripheral blood mononuclear cells is tested by flow cytometry. The experimental details of nanoparticle administration to tumor-bearing mice, magnetic resonance imaging scanning as well as subsequent tumor sample collection and their processing for transmission electron microscopy, inductively coupled plasma atomic emission spectroscopy, histological and immunohistochemical analyses are described. Biodistribution of the nanoparticles in mice and blood serum analysis data for experimental animals are given. The data are useful for an experiment workflow design and for the development of theranostic systems based on magnetic nanoparticles. © 2020 The AuthorsRussian Foundation for Basic Research, RFBR: 18-015-00319_aMinistry of Education and Science of the Russian Federation, Minobrnauka: RFMEFI62117X0015This work was supported by the Russian Foundation for Basic Research [grant number 18-015-00319_a ]. The ICP-AES measurements were carried out using the core facilities of TPU's “Physical and chemical methods of analysis” (project VIU-RSCBS-142/2019). The research involving PBMC experiments was carried out within the framework of the state assignment theme (No. AAAA-A18-118031490008-7) of the Siberian State Medical University. The research into nanoparticle characterization by IR spectroscopy, elemental analysis (CHN) and TGA was carried out within the framework of the state assignment theme (No. АААА-А19-119011790130-3) in the Joint-Use Center for Spectroscopy and Analysis of Organic Compounds, Postovsky Institute of Organic Synthesis UB RAS. Dynamic light scattering (DLS) and zeta potential (z P ) characterization were carried out within the framework of the state assignment theme No. АААА-А18-118020290129-5 in the Miheev Institute of Metal Physics UB RAS. The experiments with animals and MRI were carried out at the Center for Genetic Resources of Laboratory Animals at the Institute of Cytology and Genetics SB RAS, supported by the Ministry of Education and Science of Russia (Unique identifier of the project RFMEFI62117X0015 ). TEM analysis was carried out at the Multiple-access Center for Microscopy of Biological Subjects, Institute of Cytology and Genetics SB RAS

The Age-Metallicity Relation in the Thin Disk of the Galaxy

HST trigonometric distances, photometric metallicities, isochronic ages from the second revised version of the Geneva--Copenhagen survey, and uniform spectroscopic Fe and Mg abundances from our master catalog are used to construct and analyze the age--metallicity and age-relative Mg abundance relations for stars of the thin disk. The influences of selection effects are discussed in detail. It is demonstrated that the radial migration of stars does not lead to appreciable distortions in the age dependence of the metallicity. During the first several billion years of the formation of the thin disk, the interstellar material in this disk was, on average, fairly rich in heavy elements ( ~-0.2) and poorly mixed. However, the metallicity dispersion continuously decreased with age, from \sigma_{[Fe/H]}~0.22 to ~0.13. All this time, the mean relative abundance of Mg was somewhat higher than the solar value (~0.1). Roughly four to five billion years ago, the mean metallicity began to systematically increase, while retaining the same dispersion; the mean relative Mg abundance began to decrease immediately following this. The number of stars in this subsystem increased sharply at the same time. These properties suggest that the star-formation rate was low in the initial stage of formation of the thin disk, but abruptly increased about four to five billion years ago.Comment: 16 page, 7 figures, accepted 2011, Astron. Rep., v.55, No.8, p.667-68

Acetylation Regulates WRN Catalytic Activities and Affects Base Excision DNA Repair

Background: The Werner protein (WRN), defective in the premature aging disorder Werner syndrome, participates in a number of DNA metabolic processes, and we have been interested in the possible regulation of its function in DNA repair by post-translational modifications. Acetylation mediated by histone acetyltransferases is of key interest because of its potential importance in aging, DNA repair and transcription. Methodology/Principal Findings: Here, we have investigated the p300 acetylation mediated changes on the function of WRN in base excision DNA repair (BER). We show that acetylation of WRN increases in cells treated with methyl methanesulfonate (MMS), suggesting that acetylation of WRN may play a role in response to DNA damage. This hypothesis is consistent with our findings that acetylation of WRN stimulates its catalytic activities in vitro and in vivo, and that acetylated WRN enhances pol b-mediated strand displacement DNA synthesis more than unacetylated WRN. Furthermore, we show that cellular exposure to the histone deacetylase inhibitor sodium butyrate stimulates long patch BER in wild type cells but not in WRN depleted cells, suggesting that acetylated WRN participates significantly in this process. Conclusion/Significance: Collectively, these results provide the first evidence for a specific role of p300 mediated WRN acetylation in regulating its function during BER

The Pixel Luminosity Telescope: a detector for luminosity measurement at CMS using silicon pixel sensors

The Pixel Luminosity Telescope is a silicon pixel detector dedicated to luminosity measurement at the CMS experiment at the LHC. It is located approximately 1.75 m from the interaction point and arranged into 16 “telescopes”, with eight telescopes installed around the beam pipe at either end of the detector and each telescope composed of three individual silicon sensor planes. The per-bunch instantaneous luminosity is measured by counting events where all three planes in the telescope register a hit, using a special readout at the full LHC bunch-crossing rate of 40 MHz. The full pixel information is read out at a lower rate and can be used to determine calibrations, corrections, and systematic uncertainties for the online and offline measurements. This paper details the commissioning, operational history, and performance of the detector during Run 2 (2015–18) of the LHC, as well as preparations for Run 3, which will begin in 2022

Modelling of the effect of ELMs on fuel retention at the bulk W divertor of JET

Effect of ELMs on fuel retention at the bulk W target of JET ITER-Like Wall was studied with multi-scale calculations. Plasma input parameters were taken from ELMy H-mode plasma experiment. The energetic intra-ELM fuel particles get implanted and create near-surface defects up to depths of few tens of nm, which act as the main fuel trapping sites during ELMs. Clustering of implantation-induced vacancies were found to take place. The incoming flux of inter-ELM plasma particles increases the different filling levels of trapped fuel in defects. The temperature increase of the W target during the pulse increases the fuel detrapping rate. The inter-ELM fuel particle flux refills the partially emptied trapping sites and fills new sites. This leads to a competing effect on the retention and release rates of the implanted particles. At high temperatures the main retention appeared in larger vacancy clusters due to increased clustering rate

Progress from ASDEX Upgrade experiments in preparing the physics basis of ITER operation and DEMO scenario development

An overview of recent results obtained at the tokamak ASDEX Upgrade (AUG) is given. A work flow for predictive profile modelling of AUG discharges was established which is able to reproduce experimental H-mode plasma profiles based on engineering parameters only. In the plasma center, theoretical predictions on plasma current redistribution by a dynamo effect were confirmed experimentally. For core transport, the stabilizing effect of fast ion distributions on turbulent transport is shown to be important to explain the core isotope effect and improves the description of hollow low-Z impurity profiles. The L-H power threshold of hydrogen plasmas is not affected by small helium admixtures and it increases continuously from the deuterium to the hydrogen level when the hydrogen concentration is raised from 0 to 100%. One focus of recent campaigns was the search for a fusion relevant integrated plasma scenario without large edge localised modes (ELMs). Results from six different ELM-free confinement regimes are compared with respect to reactor relevance: ELM suppression by magnetic perturbation coils could be attributed to toroidally asymmetric turbulent fluctuations in the vicinity of the separatrix. Stable improved confinement mode plasma phases with a detached inner divertor were obtained using a feedback control of the plasma β. The enhanced D α H-mode regime was extended to higher heating power by feedback controlled radiative cooling with argon. The quasi-coherent exhaust regime was developed into an integrated scenario at high heating power and energy confinement, with a detached divertor and without large ELMs. Small ELMs close to the separatrix lead to peeling-ballooning stability and quasi continuous power exhaust. Helium beam density fluctuation measurements confirm that transport close to the separatrix is important to achieve the different ELM-free regimes. Based on separatrix plasma parameters and interchange-drift-Alfvén turbulence, an analytic model was derived that reproduces the experimentally found important operational boundaries of the density limit and between L- and H-mode confinement. Feedback control for the X-point radiator (XPR) position was established as an important element for divertor detachment control. Stable and detached ELM-free phases with H-mode confinement quality were obtained when the XPR was moved 10 cm above the X-point. Investigations of the plasma in the future flexible snow-flake divertor of AUG by means of first SOLPS-ITER simulations with drifts activated predict beneficial detachment properties and the activation of an additional strike point by the drifts