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https://www.readbyqxmd.com/read/28103588/quantifying-kinetics-from-time-series-of-single-molecule-fret-efficiency-histograms
#1
Stephan Benke, Daniel Nettels, Hagen Hofmann, Benjamin Schuler
Single-molecule fluorescence spectroscopy is a powerful approach for probing biomolecular structure and dynamics, including protein folding. For the investigation of nonequilibrium kinetics, F��rster resonance energy transfer (FRET) in combination with confocal multiparameter detection has proven particularly versatile, owing to the large number of observables and the broad range of accessible timescales, especially in combination with rapid microfluidic mixing. However, a comprehensive kinetic analysis of the resulting time series of transfer efficiency histograms and complementary observables can be challenging owing to the complexity of the data...
January 19, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28103487/a-turn-on-thiol-functionalized-fluorescent-carbon-quantum-dot-based-chemosensory-system-for-arsenite-detection
#2
Pooja D, Sonia Saini, Anupma Thakur, Baban Kumar, Sachin Tyagi, Manoj K Nayak
Carbon quantum dots (CQDs) have emerged out as promising fluorescent probes for hazardous heavy metals detection in recent past. In this study, water soluble CQDs were synthesized by facile microwave pyrolysis of citric acid & cysteamine, and functionalized with ditheritheritol to impart thiol functionalities at surface for selective detection of toxic arsenite in water. Microscopic analysis reveals that the synthesized CQDs are of uniform size (diameter ∼5nm) and confirmed to have surface SH groups by FT-IR...
January 12, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28103321/derivative-of-extremophilic-50s-ribosomal-protein-l35ae-as-an-alternative-protein-scaffold
#3
Anna V Lomonosova, Andrei B Ulitin, Alexei S Kazakov, Tajib A Mirzabekov, Eugene A Permyakov, Sergei E Permyakov
Small antibody mimetics, or alternative binding proteins (ABPs), extend and complement antibody functionality with numerous applications in research, diagnostics and therapeutics. Given the superiority of ABPs, the last two decades have witnessed development of dozens of alternative protein scaffolds (APSs) for the design of ABPs. Proteins from extremophiles with their high structural stability are especially favorable for APS design. Here, a 10X mutant of the 50S ribosomal protein L35Ae from hyperthermophilic archaea Pyrococcus horikoshii has been probed as an APS...
2017: PloS One
https://www.readbyqxmd.com/read/28103286/mirnas-do-not-regulate-circadian-protein-synthesis-in-the-dinoflagellate-lingulodinium-polyedrum
#4
Steve Dagenais-Bellefeuille, Mathieu Beauchemin, David Morse
Dinoflagellates have been shown to express miRNA by bioinformatics and RNA blot (Northern) analyses. However, it is not yet known if miRNAs are able to alter gene expression in this class of organisms. We have assessed the possibility that miRNA may mediate circadian regulation of gene expression in the dinoflagellate Lingulodinium polyedrum using the Luciferin Binding Protein (LBP) as a specific example. LBP is a good candidate for regulation by miRNA since mRNA levels are constant over the daily cycle while protein synthesis is restricted by the circadian clock to a period of several hours at the start of the night phase...
2017: PloS One
https://www.readbyqxmd.com/read/28103285/radioiodinated-exendin-4-is-superior-to-the-radiometal-labelled-glucagon-like-peptide-1-receptor-probes-overcoming-their-high-kidney-uptake
#5
Tilman Läppchen, Roswitha Tönnesmann, Jos Eersels, Philipp T Meyer, Helmut R Maecke, Svetlana N Rylova
GLP-1 receptors are ideal targets for preoperative imaging of benign insulinoma and for quantifying the beta cell mass. The existing clinical tracers targeting GLP-1R are all agonists with low specific activity and very high kidney uptake. In order to solve those issues we evaluated GLP-1R agonist Ex-4 and antagonist Ex(9-39) radioiodinated at Tyr40 side by side with [Nle14,Lys40(Ahx-DOTA-68Ga)NH2]Ex-4 (68Ga-Ex-4) used in the clinic. The Kd, Bmax, internalization and binding kinetics of [Nle14,125I-Tyr40-NH2]Ex-4 and [Nle14,125I-Tyr40-NH2]Ex(9-39) were studied in vitro using Ins-1E cells...
2017: PloS One
https://www.readbyqxmd.com/read/28103284/gene-expression-profiling-of-bronchoalveolar-lavage-cells-preceding-a-clinical-diagnosis-of-chronic-lung-allograft-dysfunction
#6
S Samuel Weigt, Xiaoyan Wang, Vyacheslav Palchevskiy, Aric L Gregson, Naman Patel, Ariss DerHovanessian, Michael Y Shino, David M Sayah, Shirin Birjandi, Joseph P Lynch, Rajan Saggar, Abbas Ardehali, David J Ross, Scott M Palmer, David Elashoff, John A Belperio
BACKGROUND: Chronic Lung Allograft Dysfunction (CLAD) is the main limitation to long-term survival after lung transplantation. Although CLAD is usually not responsive to treatment, earlier identification may improve treatment prospects. METHODS: In a nested case control study, 1-year post transplant surveillance bronchoalveolar lavage (BAL) fluid samples were obtained from incipient CLAD (n = 9) and CLAD free (n = 8) lung transplant recipients. Incipient CLAD cases were diagnosed with CLAD within 2 years, while controls were free from CLAD for at least 4 years following bronchoscopy...
2017: PloS One
https://www.readbyqxmd.com/read/28103242/genome-wide-binding-of-posterior-hoxa-d-transcription-factors-reveals-subgrouping-and-association-with-ctcf
#7
Ivana Jerković, Daniel M Ibrahim, Guillaume Andrey, Stefan Haas, Peter Hansen, Catrin Janetzki, Irene González Navarrete, Peter N Robinson, Jochen Hecht, Stefan Mundlos
Homeotic genes code for key transcription factors (HOX-TFs) that pattern the animal body plan. During embryonic development, Hox genes are expressed in overlapping patterns and function in a partially redundant manner. In vitro biochemical screens probing the HOX-TF sequence specificity revealed largely overlapping sequence preferences, indicating that co-factors might modulate the biological function of HOX-TFs. However, due to their overlapping expression pattern, high protein homology, and insufficiently specific antibodies, little is known about their genome-wide binding preferences...
January 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28103219/the-pharmacological-regulation-of-cellular-mitophagy
#8
Nikolaos D Georgakopoulos, Geoff Wells, Michelangelo Campanella
Small molecules are pharmacological tools of considerable value for dissecting complex biological processes and identifying potential therapeutic interventions. Recently, the cellular quality-control process of mitophagy has attracted considerable research interest; however, the limited availability of suitable chemical probes has restricted our understanding of the molecular mechanisms involved. Current approaches to initiate mitophagy include acute dissipation of the mitochondrial membrane potential (ΔΨm) by mitochondrial uncouplers (for example, FCCP/CCCP) and the use of antimycin A and oligomycin to impair respiration...
January 19, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28103053/mercury-amalgam-diffusion-in-human-teeth-probed-using-femtosecond-libs
#9
Liciane Toledo Bello, Patricia Aparecida da Ana, Dário Santos, Francisco José Krug, Denise Maria Zezell, Nilson Dias Vieira, Ricardo Elgul Samad
In this work the diffusion of mercury and other elements from amalgam tooth restorations through the surrounding dental tissue (dentin) was evaluated using femtosecond laser-induced breakdown spectroscopy (fs-LIBS). To achieve this, seven deciduous and eight permanent extracted human molar teeth with occlusal amalgam restorations were half-sectioned and analyzed using pulses from a femtosecond laser. The measurements were performed from the amalgam restoration along the amalgam/dentin interface to the apical direction...
January 1, 2017: Applied Spectroscopy
https://www.readbyqxmd.com/read/28103050/silane-induced-n-polarity-in-wires-probed-by-a-synchrotron-nanobeam
#10
Damien Salomon, Agnès Messanvi, Joel Eymery, Gema Martínez-Criado
Noncentrosymmetric one dimensional structures are key driving forces behind advanced nanodevices. Owing to the critical role of silane injection in creating nanosized architectures, it has become a challenge to investigate the induced local lattice polarity in single GaN wires. Thus, if axial and radial structures are well-grown by a silane-mediated approach, an ideal model to study their polar orientations is formed. By combining synchrotron X-ray fluorescence and X-ray excited optical luminescence, we show here experimental evidence of the role of silane to promote the N-polarity, light emission and elemental incorporation within single wires...
January 19, 2017: Nano Letters
https://www.readbyqxmd.com/read/28103019/highly-water-stable-novel-lanthanide-wheel-cluster-organic-frameworks-featuring-coexistence-of-hydrophilic-cage-like-chambers-and-hydrophobic-nanosized-channels
#11
Yuan-Yuan Zhou, Yang Shi, Bing Geng, Qi-Bing Bo
In attempts to investigate the potential luminescent sensing materials for sensitive detection of environmental pollutants, a new family of lanthanide wheel cluster organic frameworks (Ln-WCOFs) UJN-Ln4 has been constructed by employing one of the cycloalkane dicarboxylic acid derivatives. Adopting different conformations, the ligand links Ln4 second building units (SBUs) and Ln24 tertiary building unit (TBUs) to form a unique wheel cluster layer-pillared 3D framework featuring the coexistence of hydrophobic nanosized channels and trigonal anti-prism arrays with hydrophilic cage-like chambers...
January 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28103010/a-fluorescent-hsp90-probe-demonstrates-the-unique-association-between-extracellular-hsp90-and-malignancy-in-vivo
#12
Lauren B Crowe, Philip F Hughes, David A Alcorta, Takuya Osada, Aaron P Smith, Juliane Totzke, David R Loiselle, Isaac D Lutz, Madhusudhana Gargesha, Debasish Roy, Jose Roques, David Darr, H Kim Lyerly, Neil L Spector, Timothy Aj Haystead
Extracellular expression of heat shock protein 90 (eHsp90) by tumor cells is correlated with malignancy. Development of small molecule probes that can detect eHsp90 in vivo may therefore have utility in the early detection of malignancy. We synthesized a cell impermeable far-red fluorophore-tagged Hsp90 inhibitor to target eHsp90 in vivo. High resolution confocal and lattice light sheet microscopy show that probe-bound eHsp90 accumulates in punctate structures on the plasma membrane of breast tumor cells and is actively internalized...
January 19, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28102965/isotope-probing-of-the-udp-apiose-udp-xylose-synthase-reaction-evidence-of-a-mechanism-via-a-coupled-oxidation-and-aldol-cleavage
#13
Thomas Eixelsberger, Doroteja Horvat, Alexander Gutmann, Hansjörg Weber, Bernd Nidetzky
The C-branched sugar d-apiose (Api) is essential for plant cell-wall development. An enzyme-catalyzed decarboxylation/pyranoside ring-contraction reaction leads from UDP-α-d-glucuronic acid (UDP-GlcA) to the Api precursor UDP-α-d-apiose (UDP-Api). We examined the mechanism of UDP-Api/UDP-α-d-xylose synthase (UAXS) with site-selectively (2) H-labeled and deoxygenated substrates. The analogue UDP-2-deoxy-GlcA, which prevents C-2/C-3 aldol cleavage as the plausible initiating step of pyranoside-to-furanoside conversion, did not give the corresponding Api product...
January 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28102825/versatile-modular-three-dimensional-microelectrode-arrays-for-neuronal-ensemble-recordings-from-design-to-fabrication-assembly-and-functional-validation-in-non-human-primates
#14
Falk Barz, Alessandro Livi, Marco Lanzilotto, Monica Maranesi, Luca Bonini, Oliver Paul, Patrick Ruther
<i>Objective. </i>Application-specific designs of electrode arrays offer an improved effectiveness for providing access to targeted brain regions in neuroscientific research and brain machine interfaces. The simultaneous and stable recording of neuronal ensembles is the main goal in the design of advanced neural interfaces. Here, we describe the development and assembly of highly customizable three-dimensional microelectrode arrays and demonstrate their recording performance in chronic applications in non-human primates...
January 19, 2017: Journal of Neural Engineering
https://www.readbyqxmd.com/read/28102732/exacerbating-effects-of-pm2-5-in-ova-sensitized-and-challenged-mice-and-the-expression-of-trpa1-and-trpv1-protein-in-lung
#15
Hong Liu, Xinsheng Fan, Naiqian Wang, Yuyan Zhang, Jinghua Yu
OBJECTIVE: To investigate the effects of PM2.5 on asthma-related phenotypes and on the expression of TRPA1, V1 protein in lung in a mouse model of asthma. METHODS: Female Balb/c mice were utilized to establish 28 and 42 day asthma models. Mice were sensitized with OVA and challenged with OVA, OVA plus normal saline (NS), or OVA plus PM2.5 at two doses, 1.6 mg·kg(-1) or 8.0 mg·kg(-1). PM2.5 was administrated by intratracheal instillationwithout anesthesia. 24 hours after the final OVA challenge changes in airway resistance (RI) and lung compliance (Cdyn) in response to acetylcholine chloride (ACH) were evaluated, and blood, bronchoalveolar lavage fluid (BALF) and lung tissue samples were taken...
January 19, 2017: Journal of Asthma: Official Journal of the Association for the Care of Asthma
https://www.readbyqxmd.com/read/28102678/a-self-assembled-cofacial-cobalt-porphyrin-prism-for-oxygen-reduction-catalysis
#16
Amanda N Oldacre, Alan E Friedman, Timothy R Cook
Herein we report the first study of the oxygen reduction reaction (ORR) catalyzed by a cofacial porphyrin scaffold accessed in high yield (overall 53%) using coordination-driven self-assembly with no chromatographic purification steps. The ORR activity was investigated using chemical and electrochemical techniques on monomeric cobalt(II) tetra(meso-4-pyridyl)porphyrinate (CoTPyP) and its cofacial analogue [Ru8(η(6)-iPrC6H4Me)8(dhbq)4(CoTPyP)2][OTf]8 (Co Prism) (dhbq = 2,5-dihydroxy-1,4-benzoquinato, OTf = triflate) as homogeneous oxygen reduction catalysts...
January 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28102671/structural-analysis-of-glycosylated-intact-hiv-1-gp120-b12-antibody-complex-using-hydroxyl-radical-protein-footprinting
#17
Xiaoyan Li, Oliver C Grant, Keigo Ito, Aaron Wallace, Shixia Wang, Peng Zhao, Lance Wells, Shan Lu, Robert J Woods, Joshua S Sharp
Glycoprotein gp120 is a surface antigen and virulence factor of the human immunodeficiency virus-1 (HIV-1). Broadly neutralizing antibodies (bNAbs) that are reactive to gp120 from a variety of HIV isolates offer hope for the development of broadly effective immunogens for vaccination purposes, if the interactions between gp120 and bNAbs can be understood. From a structural perspective, gp120 is a particularly difficult system due to its size, the presence of multiple flexible regions, and the large amount of glycosylation, all of which are important in gp120-bNAb interactions...
January 19, 2017: Biochemistry
https://www.readbyqxmd.com/read/28102570/simultaneous-determination-of-free-and-total-prostate-specific-antigen-by-a-magnetic-particle-based-time-resolved-fluoroimmunoassay
#18
Bin Zhou, Jue Zhang, Zhongwei Lv, Jun Fan, Yi Zhang, Biao Huang
OBJECTIVES: In this paper, a novel, sensitive and rapid method to simultaneously determine the free and total prostate-specific antigen (fPSA and tPSA) in serum by combining a time-resolved fluoroimmunoassay (TRFIA) and immunomagnetic separation was described. METHODS: The new approach uses magnetic particles as an immobilization matrix and means of separation, whereas the luminescent europium (Eu) and samarium (Sm) chelates are used as probes. The proposed method was evaluated via a single-step, sandwich-type TRFIA immunoassay of tPSA and fPSA as model analytes in serum...
January 19, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28102565/development-of-novel-sers-probe-for-selective-screening-of-healthy-prostate-from-malignant-prostate-cancer-cells-using-zn-ii
#19
Paresh Chandra Ray, Avijit Pramanik, Suhash Reddy Chavva, Bhanu Priya Viraka Nellore, Kelli May, Tejus Matthew, Stacy Jones, Aruna Vangara
Even in 21st century, prostate cancer remains the second leading cause of cancer death for men. Since normal prostate gland contains the most Zn(II) and there are huge differences in Zn(II) content between the healthy and malignant prostate cancer cells, mobile zinc can be used as a biomarker for prostate cancer prediction. Current article reports the design of novel and highly efficient surface enhanced Raman spectroscopy (SERS) probe using p-(imidazole)azo) benzenethiol attached gold nanoparticle as a Raman reporter, which has the capability to identify prostate cancer cells based on Zn(II) sensing...
January 19, 2017: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/28102480/dynamic-sentinel-node-biopsy-for-penile-cancer-an-initial-experience-in-an-irish-hospital
#20
P E Lonergan, A Nic An Riogh, F O'Kelly, D J Lundon, D O'Sullivan, M O'Connell, P K Hegarty
BACKGROUND: The presence of nodal metastases is the single most important prognostic factor in penile cancer. However, reliable assessment of nodal status in clinically node-negative (cN0) patients poses a challenge. Approximately 20% of these patients harbour occult nodal metastases. Currently available non-invasive radiological investigations are unreliable in excluding micrometastatic disease. AIM: Dynamic sentinel node biopsy (DSNB) is a minimally invasive procedure for assessing lymph node involvement...
January 19, 2017: Irish Journal of Medical Science
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