Read by QxMD icon Read

inversion probes

Tomasz Krzywkowski, Malte Kühnemund, Di Wu, Mats Nilsson
Phi29 (Φ29) DNA polymerase is an enzyme commonly used in DNA amplification methods such as rolling circle amplification (RCA) and multiple strand displacement amplification (MDA), as well as in DNA sequencing methods such as single molecule real time (SMRT) sequencing. Here, we report the ability of phi29 DNA polymerase to amplify RNA-containing circular substrates during RCA. We found that circular substrates with single RNA substitutions are amplified at a similar amplification rate as non-chimeric DNA substrates, and that consecutive RNA pyrimidines were generally preferred over purines...
March 15, 2018: Nucleic Acids Research
Racha El-Hajj Ghaoui, Luke St Heaps, Dorothy Hung, Sumanth Nagabushan, Catherine Harris, Oksana Mirochnik, Praveen Sharma, Stewart J Kellie, Dale C Wright
Acute promyelocytic leukaemia with PML-RARA fusion is usually associated with the t(15;17)(q24.1;q21.1) translocation but may also arise from complex or cryptic rearrangements. The fusion usually resides on chromosome 15 but occasionally on others. We describe a cryptic PML-RARA fusion within a novel chromosome 17 rearrangement. We performed interphase fluorescence in situ hybridisation (FISH) using a dual-fusion PML-RARA probe, followed by reverse transcriptase-polymerase chain reaction (RT-PCR) for PML-RARA, karyotyping, and metaphase FISH using RARA break-apart, locus-specific, and subtelomere probes for chromosome 17...
March 17, 2018: Cytogenetic and Genome Research
David Wu, Adam Waalkes, Kelsi Penewit, Stephen J Salipante
BACKGROUND: Genomic chimerism, the co-occurrence of cells from different genetic origins, provides important diagnostic information in diverse clinical contexts, including graft injury detection and longitudinal surveillance of hematopoietic stem cell transplantation patients, but existing assays are limiting. Here we applied single-molecule molecular inversion probes (smMIPs), a high-throughput sequencing technology combining multiplexed target capture with read quantification mediated by unique molecular identifiers, to detect chimerism based on the presence or absence of polymorphic genomic loci...
March 16, 2018: Clinical Chemistry
Eva Vargas, Eloy Povedano, Víctor Ruiz-Valdepeñas Montiel, Rebeca M Torrente-Rodríguez, Mohamed Zouari, Juan José Montoya, Noureddine Raouafi, Susana Campuzano, José M Pingarrón
This work reports an amperometric biosensor for the determination of miRNA-21, a relevant oncogene. The methodology involves a competitive DNA-target miRNA hybridization assay performed on the surface of magnetic microbeads (MBs) and amperometric transduction at screen-printed carbon electrodes (SPCEs). The target miRNA competes with a synthetic fluorescein isothiocyanate (FITC)-modified miRNA with an identical sequence for hybridization with a biotinylated and complementary DNA probe (b-Cp) immobilized on the surface of streptavidin-modified MBs (b-Cp-MBs)...
March 15, 2018: Sensors
Kenta Kuroda, M Ochi, H S Suzuki, M Hirayama, M Nakayama, R Noguchi, C Bareille, S Akebi, S Kunisada, T Muro, M D Watson, H Kitazawa, Y Haga, T K Kim, M Hoesch, S Shin, R Arita, Takeshi Kondo
Experimental determinations of bulk band topology in the solid states have been so far restricted to only indirect investigation through the probing of surface states predicted by electronic structure calculations. We here present an alternative approach to determine the band topology by means of bulk-sensitive soft x-ray angle-resolved photoemission spectroscopy. We investigate the bulk electronic structures of the series materials, Ce monopnictides (CeP, CeAs, CeSb, and CeBi). By performing a paradigmatic study of the band structures as a function of their spin-orbit coupling, we draw the topological phase diagram and unambiguously reveal the topological phase transition from a trivial to a nontrivial regime in going from CeP to CeBi induced by the band inversion...
February 23, 2018: Physical Review Letters
Bin Deng, Mats Lundqvist, Qianqian Fang, Stefan A Carp
Near-infrared diffuse optical tomography (NIR-DOT) is an emerging technology that offers hemoglobin based, functional imaging tumor biomarkers for breast cancer management. The most promising clinical translation opportunities are in the differential diagnosis of malignant vs. benign lesions, and in early response assessment and guidance for neoadjuvant chemotherapy. Accurate quantification of the tissue oxy- and deoxy-hemoglobin concentration across the field of view, as well as repeatability during longitudinal imaging in the context of therapy guidance, are essential for the successful translation of NIR-DOT to clinical practice...
March 1, 2018: Biomedical Optics Express
Thomas Liehr, Isolde Schreyer, Alma Kuechler, Emmanouil Manolakos, Sylke Singer, Andreas Dufke, Kathleen Wilhelm, Tereza Jančušková, Radek Čmejla, Moneeb A K Othman, Ahmed H Al-Rikabi, Kristin Mrasek, Monika Ziegler, Stefanie Kankel, Katharina Kreskowski, Anja Weise
Background: Copy number variants (CNVs) are the genetic bases for microdeletion/ microduplication syndromes (MMSs). Couples with an affected child and desire to have further children are routinely tested for a potential parental origin of a specific CNV either by molecular karyotyping or by two color fluorescence in situ hybridization (FISH), yet. In the latter case a critical region probe (CRP) is combined with a control probe for identification of the chromosome in question. However, CNVs can arise also due to other reasons, like a recombination-event based on a submicroscopic, cryptic inversion in one of the parents...
2018: Molecular Cytogenetics
Mohammad Noor-A-Alam, Hamid Ullah, Young-Han Shin
Graphene, despite its many unique properties, is neither intrinsically polar due to inversion symmetry nor magnetic. However, based on density functional theory, we find that Mn, one of transition metals, embedded in single or double vacancy (Mn@SV and Mn@DV) in a graphene monolayer induces a dipole moment perpendicular to the sheet, which can be switched from up to down by Mn penetration through the graphene. Such switching could be realized by an external stimuli introduced through the tip of a scanning probe microscope, as already utilized in the studies of molecular switches...
March 14, 2018: Scientific Reports
Christian Filss, Alexander Heinzel, Berthold Miiller, Andreas T J Vogg, Karl-Josef Langen, Felix M Mottaghy
AIM: In metastatic prostate cancer patients PSMA targeting radioligands have gained significant impact as theranostic probes. In this study a correlation between total tumor volume (TTV) and measured kidney dose as well as salivary glands (SG) uptake in177 Lu-PSMA-617 therapy was evaluated. METHODS: Eleven consecutive prostate cancer patients receiving a first cylcle of177 Lu-PSMA-617 (administered activity of approximately 6GBq) were included. The68 Ga-PSMA-11 PET/CT scan previous to therapy was used to determine TTV and SG uptake (glandulae submandibularis) employing PMOD version 3...
February 2018: Nuklearmedizin. Nuclear Medicine
Neha Saxena, Pankaj Mogha, Silalipi Dash, Abhijit Majumder, Sameer Jadhav, Shamik Sen
Efficient homing of human mesenchymal stem cells (hMSCs) is likely to be dictated by the combination of physical and chemical factors present in the microenvironment. However, the crosstalk between the physical and chemical cues remains incompletely understood. Here, we address this question by probing the efficiency of epidermal growth factor (EGF)-induced hMSC chemotaxis on substrates of varying stiffness (3, 30 and 600 kPa, respectively) inside a PDMS microfluidic device. Chemotactic speed was found to be the sum of a stiffness-dependent component and a chemotactic component...
March 13, 2018: Journal of Cell Science
Oliver Mattausch, Orcun Goksel
Numerical simulation of ultrasound images can facilitate the training of sonographers. An efficient and realistic model for the simulation of ultrasonic speckle is the convolution of the ultrasound point-spread function with a distribution of point scatterers. Nevertheless, for a given arbitrary tissue type, a scatterer map that would generate a realistic appearance of that tissue is not known a priori. In this paper, we introduce a principled approach to estimate (reconstruct) such a scatterer map from images, by solving the inverse-problem of ultrasound speckle formation, such that images from arbitrary view angles and transducer settings can be generated from those scatterer maps later in simulations...
March 2018: IEEE Transactions on Medical Imaging
Josep Saurí, Wolfgang Bermel, Teodor Parella, R Thomas Williamson, Gary E Martin
1,n-ADEQUATE is a powerful NMR technique for elucidating the structure of proton-deficient small molecules that can help to establish the carbon skeleton of a given molecule by providing long-range three-bond13 C-13 C correlations. Care must be taken when using the experiment to identify the simultaneous presence of one-bond13 C-13 C correlations that are not filtered out, unlike the HMBC experiment that has a low-pass J-filter to filter1 JCH responses out. Dual-optimized, inverted1 JCC 1,n-ADEQUATE is an improved variant of the experiment that affords broadband inversion of direct responses, obviating the need to take additional steps to identify these correlations...
March 13, 2018: Magnetic Resonance in Chemistry: MRC
Thomas Rossor, Ingran Lingam, Abdel Douiri, Ravindra Bhat, Anne Greenough
AIM: To determine whether a pH probe or multichannel intraluminal impedance (MII) more frequently detected gastro-oesophageal reflux and test the hypothesis that acid reflux was associated with lower baseline impedance. METHODS: A prospective study of infants in whom reflux was suspected and evaluated using combined pH and multichannel impedance. Studies were considered abnormal if the acid index was >10% or there were > 79MII reflux events in 24 hours. The acid index was the percentage of total study time with a pH<four and the acid clearance time (ACT) the time from the pH falling below four to rising above four...
March 13, 2018: Acta Paediatrica
Qingwen Wan, Najeah Okashah, Asuka Inoue, Rony Nehmé, Byron Carpenter, Christopher G Tate, Nevin A Lambert
G protein-coupled receptors (GPCRs) are key signaling proteins that regulate nearly every aspect of cell function. Studies of GPCRs have benefitted greatly from the development of molecular tools to monitor receptor activation and downstream signaling. Here we show that mini G proteins are robust probes that can be used in a variety of assay formats to report GPCR activity in living cells. Mini G (mG) proteins are engineered GTPase domains of Gα subunits that were developed for structural studies of active state GPCRs...
March 9, 2018: Journal of Biological Chemistry
K Tabeta, M Hosojima, M Nakajima, S Miyauchi, H Miyazawa, N Takahashi, Y Matsuda, N Sugita, Y Komatsu, K Sato, T Ishikawa, K Akiishi, K Yamazaki, K Kato, A Saito, H Yoshie
BACKGROUND AND OBJECTIVES: Previous reports suggest that several serum biomarkers play roles in the pathogenesis, inflammatory response, and oxidative stress in periodontitis caused by bacterial infections, linking chronic periodontitis to atherosclerotic vascular disease (ASVD). The aim of this preliminary study was to investigate, in a Japanese cross-sectional community survey, potential serum biomarkers of periodontitis that are associated with ASVD and chronic periodontitis. MATERIAL AND METHODS: The study cohort included a total of 108 male subjects who underwent annual health examinations...
March 8, 2018: Journal of Periodontal Research
Meysam Hashemi, Axel Hutt, Laure Buhry, Jamie Sleigh
Mathematical modeling is a powerful tool that enables researchers to describe the experimentally observed dynamics of complex systems. Starting with a robust model including model parameters, it is necessary to choose an appropriate set of model parameters to reproduce experimental data. However, estimating an optimal solution of the inverse problem, i.e., finding a set of model parameters that yields the best possible fit to the experimental data, is a very challenging problem. In the present work, we use different optimization algorithms based on a frequentist approach, as well as Monte Carlo Markov Chain methods based on Bayesian inference techniques to solve the considered inverse problems...
March 7, 2018: Neuroinformatics
Benjamin D G Chandran
In this paper, weak turbulence theory is used to investigate the nonlinear evolution of the parametric instability in 3D low- β plasmas at wavelengths much greater than the ion inertial length under the assumption that slow magnetosonic waves are strongly damped. It is shown analytically that the parametric instability leads to an inverse cascade of Alfvén wave quanta, and several exact solutions to the wave kinetic equations are presented. The main results of the paper concern the parametric decay of Alfvén waves that initially satisfy e + ≫ e - , where e + and e - are the frequency ( f ) spectra of Alfvén waves propagating in opposite directions along the magnetic field lines...
February 2018: Journal of Plasma Physics
Guangchuan Wang, Ryan D Chow, Lupeng Ye, Christopher D Guzman, Xiaoyun Dai, Matthew B Dong, Feng Zhang, Phillip A Sharp, Randall J Platt, Sidi Chen
Cancer genomics consortia have charted the landscapes of numerous human cancers. Whereas some mutations were found in classical oncogenes and tumor suppressors, others have not yet been functionally studied in vivo. To date, a comprehensive assessment of how these genes influence oncogenesis is lacking. We performed direct high-throughput in vivo mapping of functional variants in an autochthonous mouse model of cancer. Using adeno-associated viruses (AAVs) carrying a single-guide RNA (sgRNA) library targeting putative tumor suppressor genes significantly mutated in human cancers, we directly pool-mutagenized the livers of Cre-inducible CRISPR (clustered regularly interspaced short palindromic repeats)-associated protein 9 (Cas9) mice...
February 2018: Science Advances
Xiaorong Zhang, Bincheng Li
An accurate theoretical model based on thermoelasticity theory and Fresnel diffraction integral is developed to describe the photothermal deflection (PTD) signal with a continuous-wave modulated Gaussian beam excitation. A PTD experiment is performed to investigate the dependence of PTD amplitude on the experimental parameters, such as the radius, waist position, and wavelength of the probe beam, and the detection distance. Good agreement between the experimental and theoretical results is obtained. The results reveal that the optimal detection distance highly depends on the probe beam waist position and wavelength, and the PTD amplitude can be enhanced by optimizing the probe beam radius and waist position as well as the detection distance...
February 2018: Review of Scientific Instruments
P F Jarschel, L S Magalhaes, I Aldaya, O Florez, P Dainese
We propose a fast and non-destructive method to characterize the absolute diameter and uniformity of micrometer-scale fiber tapers using a pump and probe forward Brillouin scattering setup. The fundamental torsional-radial acoustic mode supported by the wire is excited using a pulsed pump laser and oscillates at a frequency that is inversely proportional to the taper waist diameter. This standing time-varying torsional-radial wave induces polarization modulation on a probe signal, whose spectrum structure reveals the sample diameter and its non-uniformity...
March 1, 2018: Optics Letters
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"