A Newly Discovered Bordetella Species Carries a Transcriptionally Active CRISPR-Cas with a Small Cas9 Endonuclease

Background Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) are widely distributed among bacteria. These systems provide adaptive immunity against mobile genetic elements specified by the spacer sequences stored within the CRISPR. Methods The CRISPR-Cas system has been identified using Basic Local Alignment Search Tool (BLAST) against other sequenced and annotated genomes and confirmed via CRISPRfinder program. Using Polymerase Chain Reactions (PCR) and Sanger DNA sequencing, we discovered CRISPRs in additional bacterial isolates of the same species of Bordetella. Transcriptional activity and processing of the CRISPR have been assessed via RT-PCR. Results Here we describe a novel Type II-C CRISPR and its associated genes—cas1, cas2, and cas9—in several isolates of a newly discovered Bordetella species. The CRISPR-cas locus, which is absent in all other Bordetella species, has a significantly lower GC-content than the genome-wide average, suggesting acquisition of this locus via horizontal gene transfer from a currently unknown source. The CRISPR array is transcribed and processed into mature CRISPR RNAs (crRNA), some of which have homology to prophages found in closely related species B. hinzii. Conclusions Expression of the CRISPR-Cas system and processing of crRNAs with perfect homology to prophages present in closely related species, but absent in that containing this CRISPR-Cas system, suggest it provides protection against phage predation. The 3,117-bp cas9 endonuclease gene from this novel CRISPR-Cas system is 990 bp smaller than that of Streptococcus pyogenes, the 4,017-bp allele currently used for genome editing, and which may make it a useful tool in various CRISPR-Cas technologies

Localization of the gamma-radiation sources using the gamma-visor

The search of the main gamma-radiation sources at the site of the temporary storage of solid radioactive wastes was carried out. The relative absorbed dose rates were measured for some of the gamma-sources before and after the rehabilitation procedures. The effectiveness of the rehabilitation procedures in the years 2006-2007 was evaluated qualitatively and quantitatively. The decrease of radiation background at the site of the temporary storage of the solid radioactive wastes after the rehabilitation procedures allowed localizing the new gamma-source

The study of spectral changes in THz range in normal and pathological skin in vivo depending on the dehydration methods used

The terahertz (THz) attenuated total reflectance (ATR) imaging of normal and pathological skin under the action of various dehydration agents was carried out in vivo. Studies were conducted on animal models (the mouse), patients with diabetes, and healthy volunteers. For measurements, each animal was leaned against the ATR prism of the skin surface, and several locations in the skin of each animal were analyzed. Places on the skin for analysis were chosen so that the intensity spectra of the THz signal were practically the same for selected points. THz spectra measurements were carried out every 10 minutes within 45 minutes interval under the action of a dehydration agent. 40% glucose was shown to provide the most effective improving tissue optical clearing effect in the THz range

An X-ray photoelectron spectroscopy study of the products of the interaction of gaseous IrF6 with fine UO2F2

Nuclear fuel reprocessing by fluorination, a dry method of regeneration of spent nuclear fuel, uses UO2F2 for the separation of plutonium from gaseous mixtures. Since plutonium requires special treatment, IrF6 was used as a thermodynamic model of PuF6. The model reaction of the interaction of gaseous IrF6 with fine UO2F2 in the sorption column revealed a change of color of the sorption column contents from pale-yellow to gray and black, indicating the formation of products of such an interaction. The X-ray photoelectron spectroscopy study showed that the interaction of gaseous IrF6 with fine UO2F2 at 125 °C results in the formation of stable iridium compounds where the iridium oxidation state is close to Ir3+. The dependence of the elemental compositions of the layers in the sorption column on the penetration depth of IrF6 was established

Asymptomatic cholelithiasis in bariatric practice

Background: The need for simultaneous cholecystectomy for asymptomatic cholelithiasis in patients undergoing bariatric intervention has not been proven. The experience of managing patients with obesity and concomitant disease cholelithiasis is presented. Aim: to determine the indications for simultaneous cholecystectomy and bariatric surgery in the combination of morbid obesity and a asymptomatic cholelithiasis. Methods: The results of observation of 37 patients with initially asymptomatic cholelithiasis were analyzed: 27 patients underwent bariatric surgery and simultaneous cholecystectomy, and 10 patients underwent only bariatric surgery. The immediate and long-term results of the treatment, the quality of life of patients and the cost of the treatment were assessed. Results: During 12 months of the follow-up, none of the patients who underwent simultaneous cholecystectomy developed any complications. Of the 10 patients in the observation group, 3 were operated on. Two patients underwent laparoscopic cholecystectomy for acute cholecystitis and one patient was operated on for choledocholithiasis with obstructive jaundice. The greatest improvement in the quality of life was observed in the gastric bypass group with simultaneous cholecystectomy. The treatment cost per patient was lower in that group, too. Conclusion: In the presence of asymptomatic cholelithiasis in a patient with morbid obesity, bariatric intervention and simultaneous cholecystectomy prevents the development of complications of cholelithiasis and thereby potentially improves the quality of life and reduces the cost of medical care

The electronic structure and the nature of the chemical bond in CeO2.

The X-ray photoelectron spectral structure of CeO2 valence electrons in the binding energy range of 0 to ∼50 eV was analyzed. The core-electron spectral structure parameters and the results of relativistic discrete-variational calculations of CeO8 and Ce63O216 clusters were taken into account. Comparison of the valence and the core-electron spectral structures showed that the formation of the inner (IVMO) and the outer (OVMO) valence molecular orbitals contributes to the spectral structure more than the many-body processes. The Ce 4f electrons were established to participate directly in chemical bond formation in CeO2 losing partially their f character. They were found to be localized mostly within the outer valence band. The Ce 5p atomic orbitals were shown to participate in the formation of both the inner and the outer valence molecular orbitals (MOs). A large part in the IVMO formation is taken by the filled Ce 5p1/2, 5p3/2 and O 2s atomic shells, while the Ce 5s electrons participate weakly in the chemical bond formation. The composition and the sequent order of the molecular orbitals in the binding energy range of 0 to ∼50 eV were established. A quantitative scheme for the molecular orbitals of CeO2 was built. This scheme is fundamental for understanding the nature of chemical bonding and also for the interpretation of other X-ray spectra of CeO2. Evaluations revealed that the IVMO electrons weaken the chemical bond formed by the OVMO electrons by 37%.The work was supported by the RFBR grant № 17-03-00277a. M.V. Ryzhkov acknowledges financial support of FASO of Russia ISSC of the Ural Branch of RAS № AAAA-A16-116122810214-9. A.J. Popel acknowledges funding from the UK EPSRC (grant EP/I036400/1) and Radioactive Waste Management Ltd (formerly the Radioactive Waste Management Directorate of the UK Nuclear Decommissioning Authority, contract NPO004411A-EPS02), a maintenance grant from the Russian Foundation for Basic Research (projects 13-03-90916) and CSAR bursary

XPS Study of Ion Irradiated and Unirradiated UO2 Thin Films.

XPS determination of the oxygen coefficient kO = 2 + x and ionic (U(4+), U(5+), and U(6+)) composition of oxides UO2+x formed on the surfaces of differently oriented (hkl) planes of thin UO2 films on LSAT (Al10La3O51Sr14Ta7) and YSZ (yttria-stabilized zirconia) substrates was performed. The U 4f and O 1s core-electron peak intensities as well as the U 5f relative intensity before and after the (129)Xe(23+) and (238)U(31+) irradiations were employed. It was found that the presence of uranium dioxide film in air results in formation of oxide UO2+x on the surface with mean oxygen coefficients kO in the range 2.07-2.11 on LSAT and 2.17-2.23 on YSZ substrates. These oxygen coefficients depend on the substrate and weakly on the crystallographic orientation. On the basis of the spectral parameters it was established that uranium dioxide films AP2,3 on the LSAT substrates have the smallest kO values, and from the XRD and EBSD results it follows that these samples have a regular monocrystalline structure. The XRD and EBSD results indicate that samples AP5-7 on the YSZ substrates have monocrystalline structure; however, they have the highest kO values. The observed difference in the kO values was probably caused by the different nature of the substrates: the YSZ substrates provide 6.4% compressive strain, whereas (001) LSAT substrates result only in 0.03% tensile strain in the UO2 films. (129)Xe(23+) irradiation (92 MeV, 4.8 × 10(15) ions/cm(2)) of uranium dioxide films on the LSAT substrates was shown to destroy both long-range ordering and uranium close environment, which results in an increase of uranium oxidation state and regrouping of oxygen ions in uranium close environment. (238)U(31+) (110 MeV, 5 × 10(10), 5 × 10(11), 5 × 10(12) ions/cm(2)) irradiations of uranium dioxide films on the YSZ substrates were shown to form the lattice damage only with partial destruction of the long-range ordering.The irradiation experiment was performed at the Grand Accelé rateur National d ́ ’Ions Lourds (GANIL) Caen, France, and supported by the French Network EMIR. The support in planning and execution of the experiment by the CIMAPCIRIL and the GANIL staff, especially I. Monnet, C. Grygiel, T. Madi, and F. Durantel, is much appreciated. The work was supported by RFBR grant no. 16-03-00914-a and partially supported by M.V. Lomonosov Moscow State University Program of Development. A.J.P. acknowledges funding from the UK EPSRC (grant EP/I036400/1) and Radioactive Waste Management Ltd. (formerly the Radioactive Waste Management Directorate of the UK Nuclear Decommissioning Authority, contract NPO004411A-EPS02), a maintenance grant from the Russian Foundation for Basic Research (projects 13-03-90916) and CSAR bursary. Thanks are given to A.M. Adamska, G.I. Lampronti, V.A. Lebedev, P.G. Martin, L. Payne, and A.A. Shiryaev for their help in characterization of the samples

Erratum to: "Double volume reflection of a proton beam by a sequence of two bent crystals" [Phys. Lett. B 658 (2008) 109]

n/