Оценка коллатеральной активности CRISPR/Cas13a-рибонуклеазы на биоанализаторе Agilent 2100

The paper describes an original technique for detecting the collateral activity of CRISPR/Cas 13a ribonuclease based on the assessment of ribosomal RNA degradation. The Agilent 2100 bioanalyzer is used as an analyzing device. This approach is an alternative to existing detection methods and has a number of advantages over them in the case when a quantitative assessment of activity is not required. On the example of the test sample, the optimal concentrations and ratios of the components of the reaction mixture, which are necessary to obtain the most indicative result, were determined. The proposed technique can be used for qualitative assessment of the activity of recombinant ribonuclease Cas13a preparations obtained under different conditions of heterologous protein expression and purification, as well as for testing guide RNAs.В работе описывается оригинальная методика детекции коллатеральной активности CRISPR/Cas13a-рибонуклеазы, основанная на оценке деградации рибосомальной РНК. В качестве анализирующего прибора используется биоанализатор Agilent 2100. Данный подход является альтернативой существующим методам детекции и имеет ряд преимуществ по сравнению с ними в том случае, когда не требуется количественная оценка активности. На примере тестового образца определены оптимальные концентрации и соотношения компонентов реакционной смеси, необходимые для получения наиболее показательного результата. Предлагаемая методика может быть использована для качественной оценки активности препаратов рекомбинантной рибонуклеазы Cas13а, полученных при разных условиях гетерологической экспрессии белка и его очистки, а также для тестирования направляющих РНК

ММП-9, ММП-2, VEGF и VEGFR2 как факторы инвазии и ангиогенеза при плоскоклеточной карциноме шейки матки

Tissue destruction and angiogenesis play an important role in malignant tumor progression. They are responsible for the tumor growth and progress and its ability to invade and metastasize. The key role in the destructive processes belongs to matrix metalloproteinases (MMPs), which are able to cleave almost all components of the extracellular matrix (ECM). Gelatinases MMP-2 and MMP-9 hydrolyze type IV collagen, the main component of basement membranes, thereby releasing various biologically active molecules from ECM, including vascular endothelial growth factor (VEGF). VEGF is a key regulator of angiogenesis. The main mediator of the biological action of VEGF is its receptor VEGFR2. This study was aimed at assessing the relationship between the expression of the main factors of tissue destruction and angiogenesis - MMP-2, MMP-9, VEGF and VEGFR2 in the early and later stages of cervical squamous cell carcinoma (CSCC). The work was performed using samples of tumor and surrounding morphologically normal tissue, obtained from patients with or without metastases to regional lymph nodes. We have shown that MMP- 9 is significantly expressed in tumors in CSCC already at the early stages of tumor progression. At later stages of the disease (when metastases to regional lymph nodes are detected in patients), the expression of MMP-2, VEGF and VEGFR2 increases markedly both in the tumor and in the morphologically normal tissue surrounding the tumor and makes an additional contribution to the processes of destruction, angiogenesis and metastasis. We assume that MMP-2, VEGF and VEGFR2 can be considered as negative markers of the course of CSCC.Деструкция ткани и ангиогенез играют важную роль в прогрессии злокачественных опухолей. Они отвечают за рост и развитие опухоли, ее способность к инвазии и метастазированию. Ключевая роль в деструктивных процессах отводится матриксным металлопротеиназам (ММП), которые способны расщеплять практически все компоненты соединительнотканного матрикса (СТМ). Желатиназы ММП-2 и ММП-9 гидролизуют коллаген IV типа – основу базальных мембран, – освобождая тем самым из СТМ различные биологически активные молекулы, включая эндотелиальный фактор роста сосудов (VEGF) – ключевой регулятор ангиогенеза. Его действие реализуется рецепторами VEGF-VEGFR. В данной работе исследовали экспрессию ММП-2, ММП-9, VEGF и VEGFR2 на ранних и более поздних стадиях плоскоклеточной карциномы шейки матки (ПКШМ). Работа проведена на клиническом материале (образцы опухолевой и морфологически нормальной ткани, окружающей опухоль), полученном от пациентов с наличием или отсутствием метастазов в регионарные лимфоузлы. Мы показали, что при ПКШМ существенная экспрессия ММП-9 наблюдается в опухолях уже на ранних стадиях опухолевой прогрессии. На более поздних стадиях заболевания (при обнаружении у пациентов метастазов в регионарные лимфоузлы) заметно повышается экспрессия ММП-2, VEGF и VEGFR2 как в опухоли, так и в морфологически нормальной ткани, окружающей опухоль, что вносит дополнительный вклад в процессы деструкции, ангиогенеза и метастазирования. Мы предполагаем, что ММП-2, VEGF и VEGFR2 могут рассматриваться в качестве маркеров неблагоприятного течения ПКШМ

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Measurement of the View the tt production cross-section using eμ events with b-tagged jets in pp collisions at √s = 13 TeV with the ATLAS detector

This paper describes a measurement of the inclusive top quark pair production cross-section (σtt¯) with a data sample of 3.2 fb−1 of proton–proton collisions at a centre-of-mass energy of √s = 13 TeV, collected in 2015 by the ATLAS detector at the LHC. This measurement uses events with an opposite-charge electron–muon pair in the final state. Jets containing b-quarks are tagged using an algorithm based on track impact parameters and reconstructed secondary vertices. The numbers of events with exactly one and exactly two b-tagged jets are counted and used to determine simultaneously σtt¯ and the efficiency to reconstruct and b-tag a jet from a top quark decay, thereby minimising the associated systematic uncertainties. The cross-section is measured to be: σtt¯ = 818 ± 8 (stat) ± 27 (syst) ± 19 (lumi) ± 12 (beam) pb, where the four uncertainties arise from data statistics, experimental and theoretical systematic effects, the integrated luminosity and the LHC beam energy, giving a total relative uncertainty of 4.4%. The result is consistent with theoretical QCD calculations at next-to-next-to-leading order. A fiducial measurement corresponding to the experimental acceptance of the leptons is also presented

Search for strong gravity in multijet final states produced in pp collisions at √s=13 TeV using the ATLAS detector at the LHC

A search is conducted for new physics in multijet final states using 3.6 inverse femtobarns of data from proton-proton collisions at √s = 13TeV taken at the CERN Large Hadron Collider with the ATLAS detector. Events are selected containing at least three jets with scalar sum of jet transverse momenta (HT) greater than 1TeV. No excess is seen at large HT and limits are presented on new physics: models which produce final states containing at least three jets and having cross sections larger than 1.6 fb with HT > 5.8 TeV are excluded. Limits are also given in terms of new physics models of strong gravity that hypothesize additional space-time dimensions

Search for TeV-scale gravity signatures in high-mass final states with leptons and jets with the ATLAS detector at sqrt [ s ] = 13TeV

A search for physics beyond the Standard Model, in final states with at least one high transverse momentum charged lepton (electron or muon) and two additional high transverse momentum leptons or jets, is performed using 3.2 fb−1 of proton–proton collision data recorded by the ATLAS detector at the Large Hadron Collider in 2015 at √s = 13 TeV. The upper end of the distribution of the scalar sum of the transverse momenta of leptons and jets is sensitive to the production of high-mass objects. No excess of events beyond Standard Model predictions is observed. Exclusion limits are set for models of microscopic black holes with two to six extra dimensions

Operation and performance of the ATLAS semiconductor tracker

The semiconductor tracker is a silicon microstrip detector forming part of the inner tracking system of the ATLAS experiment at the LHC. The operation and performance of the semiconductor tracker during the first years of LHC running are described. More than 99% of the detector modules were operational during this period, with an average intrinsic hit efficiency of (99.74±0.04)%. The evolution of the noise occupancy is discussed, and measurements of the Lorentz angle, δ-ray production and energy loss presented. The alignment of the detector is found to be stable at the few-micron level over long periods of time. Radiation damage measurements, which include the evolution of detector leakage currents, are found to be consistent with predictions and are used in the verification of radiation background simulations

Measurement of the correlation between flow harmonics of different order in lead-lead collisions at √sNN = 2.76 TeV with the ATLAS detector

Correlations between the elliptic or triangular flow coefficients vm (m=2 or 3) and other flow harmonics vn (n=2 to 5) are measured using √sNN=2.76 TeV Pb+Pb collision data collected in 2010 by the ATLAS experiment at the LHC, corresponding to an integrated luminosity of 7 μb−1. The vm−vn correlations are measured in midrapidity as a function of centrality, and, for events within the same centrality interval, as a function of event ellipticity or triangularity defined in a forward rapidity region. For events within the same centrality interval, v3 is found to be anticorrelated with v2 and this anticorrelation is consistent with similar anticorrelations between the corresponding eccentricities, ε2 and ε3. However, it is observed that v4 increases strongly with v2, and v5 increases strongly with both v2 and v3. The trend and strength of the vm−vn correlations for n=4 and 5 are found to disagree with εm−εn correlations predicted by initial-geometry models. Instead, these correlations are found to be consistent with the combined effects of a linear contribution to vn and a nonlinear term that is a function of v22 or of v2v3, as predicted by hydrodynamic models. A simple two-component fit is used to separate these two contributions. The extracted linear and nonlinear contributions to v4 and v5 are found to be consistent with previously measured event-plane correlations

Search for H→γγ produced in association with top quarks and constraints on the Yukawa coupling between the top quark and the Higgs boson using data taken at 7 TeV and 8 TeV with the ATLAS detector

A search is performed for Higgs bosons produced in association with top quarks using the diphoton decay mode of the Higgs boson. Selection requirements are optimized separately for leptonic and fully hadronic final states from the top quark decays. The dataset used corresponds to an integrated luminosity of 4.5 fb−14.5 fb−1 of proton–proton collisions at a center-of-mass energy of 7 TeV and 20.3 fb−1 at 8 TeV recorded by the ATLAS detector at the CERN Large Hadron Collider. No significant excess over the background prediction is observed and upper limits are set on the tt¯H production cross section. The observed exclusion upper limit at 95% confidence level is 6.7 times the predicted Standard Model cross section value. In addition, limits are set on the strength of the Yukawa coupling between the top quark and the Higgs boson, taking into account the dependence of the tt¯H and tH cross sections as well as the H→γγ branching fraction on the Yukawa coupling. Lower and upper limits at 95% confidence level are set at −1.3 and +8.0 times the Yukawa coupling strength in the Standard Model