System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

Yeast remains an important model for systems biology and for evaluating proteomics strategies. In-depth shotgun proteomics studies have reached nearly comprehensive coverage, and rapid, targeted approaches have been developed for this organism. Recently, we demonstrated that single LC-MS/MS analysis using long columns and gradients coupled to a linear ion trap Orbitrap instrument had an unexpectedly large dynamic range of protein identification (Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J., and Mann, M. (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell Proteomics 10, 10.1074/mcp.M110.003699). Here we couple an ultra high pressure liquid chromatography system to a novel bench top Orbitrap mass spectrometer (Q Exactive) with the goal of nearly complete, rapid, and robust analysis of the yeast proteome. Single runs of filter-aided sample preparation (FASP)-prepared and LysC-digested yeast cell lysates identified an average of 3923 proteins. Combined analysis of six single runs improved these values to more than 4000 identified proteins/run, close to the total number of proteins expressed under standard conditions, with median sequence coverage of 23%. Because of the absence of fractionation steps, only minuscule amounts of sample are required. Thus the yeast model proteome can now largely be covered within a few hours of measurement time and at high sensitivity. Median coverage of proteins in Kyoto Encyclopedia of Genes and Genomes pathways with at least 10 members was 88%, and pathways not covered were not expected to be active under the conditions used. To study perturbations of the yeast proteome, we developed an external, heavy lysine-labeled SILAC yeast standard representing different proteome states. This spike-in standard was employed to measure the heat shock response of the yeast proteome. Bioinformatic analysis of the heat shock response revealed that translation-related functions were down-regulated prominently, including nucleolar processes. Conversely, stress-related pathways were up-regulated. The proteomic technology described here is straightforward, rapid, and robust, potentially enabling widespread use in the yeast and other biological research communities

Dipyrrinato‐Iridium(III) Complexes for Application in Photodynamic Therapy and Antimicrobial Photodynamic Inactivation

The generation of bio-targetable photosensitizers is of utmost importance to the emerging field of photodynamic therapy and antimicrobial (photo-)therapy. A synthetic strategy is presented in which chelating dipyrrin moieties are used to enhance the known photoactivity of iridium(III) metal complexes. Formed complexes can thus be functionalized in a facile manner with a range of targeting groups at their chemically active reaction sites. Dipyrrins with N- and O-substituents afforded (dipy)iridium(III) complexes via complexation with the respective Cp*-iridium(III) and ppy-iridium(III) precursors (dipy=dipyrrinato, Cp*=pentamethyl-eta(5)-cyclopentadienyl, ppy=2-phenylpyridyl). Similarly, electron-deficient [Ir-III(dipy)(ppy)(2)] complexes could be used for post-functionalization, forming alkenyl, alkynyl and glyco-appended iridium(III) complexes. The phototoxic activity of these complexes has been assessed in cellular and bacterial assays with and without light; the [Ir-III(Cl)(Cp*)(dipy)] complexes and the glyco-substituted iridium(III) complexes showing particular promise as photomedicine candidates. Representative crystal structures of the complexes are also presented

Strain-relief by single dislocation loops in calcite crystals grown on self-assembled monolayers

Most of our knowledge of dislocation-mediated stress relaxation during epitaxial crystal growth comes from the study of inorganic heterostructures. Here we use Bragg coherent diffraction imaging to investigate a contrasting system, the epitaxial growth of calcite (CaCO3) crystals on organic self-assembled monolayers, where these are widely used as a model for biomineralization processes. The calcite crystals are imaged to simultaneously visualize the crystal morphology and internal strain fields. Our data reveal that each crystal possesses a single dislocation loop that occupies a common position in every crystal. The loops exhibit entirely different geometries to misfit dislocations generated in conventional epitaxial thin films and are suggested to form in response to the stress field, arising from interfacial defects and the nanoscale roughness of the substrate. This work provides unique insight into how self-assembled monolayers control the growth of inorganic crystals and demonstrates important differences as compared with inorganic substrates

Solution of spin-boson systems in one and two-dimensional geometry via the asymptotic iteration method

We consider solutions of the $2\times 2$ matrix Hamiltonian of physical systems within the context of the asymptotic iteration method. Our technique is based on transformation of the associated Hamiltonian in the form of the first order coupled differential equations. We construct a general matrix Hamiltonian which includes a wide class of physical models. The systematic study presented here reproduces a number of earlier results in a natural way as well as leading to new findings. Possible generalizations of the method are also suggested.Comment: 13 pages, 5 figures. Please check "http://www1.gantep.edu.tr/~ozer/" for other studies of Nuclear Physics Group at University of Gaziante

The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics

Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major principles used in proteomics. Although based on simple fundamentals, it has over the last decades greatly evolved in terms of achievable resolution, mass accuracy, and dynamic range. The Bruker impact platform of QTOF instruments takes advantage of these developments and here we develop and evaluate the impact II for shotgun proteomics applications. Adaption of our heated liquid chromatography system achieved very narrow peptide elution peaks. The impact II is equipped with a new collision cell with both axial and radial ion ejection, more than doubling ion extraction at high tandem MS frequencies. The new reflectron and detector improve resolving power compared with the previous model up to 80%, i.e. to 40,000 at m/z 1222. We analyzed the ion current from the inlet capillary and found very high transmission (>80%) up to the collision cell. Simulation and measurement indicated 60% transfer into the flight tube. We adapted MaxQuant for QTOF data, improving absolute average mass deviations to better than 1.45 ppm. More than 4800 proteins can be identified in a single run of HeLa digest in a 90 min gradient. The workflow achieved high technical reproducibility (R2 > 0.99) and accurate fold change determination in spike-in experiments in complex mixtures. Using label-free quantification we rapidly quantified haploid against diploid yeast and characterized overall proteome differences in mouse cell lines originating from different tissues. Finally, after high pH reversed-phase fractionation we identified 9515 proteins in a triplicate measurement of HeLa peptide mixture and 11,257 proteins in single measurements of cerebellum-the highest proteome coverage reported with a QTOF instrument so far

Гангрена фурньє – сучасний погляд на діагностику та лікування в умовах сьогодення

The article adduces the etiology and pathogenesis of this nosology. For example, in treated 43 patients, special attention is paid to ways of improving the diagnosis and treatment of Fournier gangrene which in itself includes how adequate surgical treatment of purulent necrotic foci and maximalism treatment in intensive care. The percentage mortality was 20.6 %.У статті розкрито етіологію та патогенез даної нозології. На прикладі пролікованих 43 хворих особливу увагу приділено шляхам поліпшення діагностики та лікування гангрени Фурньє, що в собі включає як адекватну хірургічну обробку гнійно-некротичного вогнища, так і максималізм лікування в умовах відділення інтенсивної терапії. Відсоток летальності становив 20,6 %

Influence of wide band gap oxide substrates on the photoelectrochemical properties and structural disorder of CdS nanoparticles grown by the successive ionic layer adsorption and reaction (SILAR) method

The photoelectrochemical properties of nanoheterostructures based on the wide band gap oxide substrates (ZnO, TiO2, In2O3) and CdS nanoparticles deposited by the successive ionic layer adsorption and reaction (SILAR) method have been studied as a function of the CdS deposition cycle number (N). The incident photon-to-current conversion efficiency (IPCE) passes through a maximum with the increase of N, which is ascribed to the competition between the increase in optical absorption and photocarrier recombination. The maximal IPCE values for the In2O3/CdS and ZnO/CdS heterostructures are attained at N ≈ 20, whereas for TiO2/CdS, the appropriate N value is an order of magnitude higher. The photocurrent and Raman spectroscopy studies of CdS nanoparticles revealed the occurrence of the quantum confinement effect, demonstrating the most rapid weakening with the increase of N in ZnO/CdS heterostructures. The structural disorder of CdS nanoparticles was characterized by the Urbach energy (EU), spectral width of the CdS longitudinal optical (LO) phonon band and the relative intensity of the surface optical (SO) phonon band in the Raman spectra. Maximal values of EU (100–120 meV) correspond to СdS nanoparticles on a In2O3 surface, correlating with the fact that the CdS LO band spectral width and intensity ratio for the CdS SO and LO bands are maximal for In2O3/CdS films. A notable variation in the degree of disorder of CdS nanoparticles is observed only in the initial stages of CdS growth (several tens of deposition cycles), indicating the preservation of the nanocrystalline state of CdS over a wide range of SILAR cycles

Технологічні засади організації метапошукових систем доступу до документальних інформаційних ресурсів

Кулак О. І. Технологічні засади організації метапошукових систем доступу до документальних інформаційних ресурсів / О. І. Кулак, П. С. Клімушин // Застосування інформаційних технологій у діяльності правоохоронних органів : зб. матеріалів кругл. столу (м. Харків, 9 груд. 2020 р.) / МВС України, Харків. нац. ун-т внутр. справ. – Харків : ХНУВС, 2020. – С. 60-63.Зазначено, що для підтримки інформаційно-аналітичної діяльності правоохоронних органів, необхідно знати технологічні засади організації метапошукових систем доступу до документальних інформаційних ресурсів, щоб реалізувати обґрунтовані технології, що охоплюють всі ланцюжки роботи з інформацією, включаючи моніторинг, агрегування та узагальнення потоків інформації. Отмечено, что для поддержания информационно-аналитической деятельности правоохранительных органов необходимо знать технологические основы организации метапоисковых систем доступа к документальным информационным ресурсам, чтобы реализовать обоснованные технологии, охватывающие все цепочки работы с информацией, включая мониторинг, агрегирование и обобщение потоков информации. It is noted that in order to support the information and analytical activities of law enforcement agencies, it is necessary to know the technological foundations for organizing metasearch systems for accessing documentary information resources in order to implement reasonable technologies covering all chains of working with information, including monitoring, aggregation and generalization of information flows