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https://www.readbyqxmd.com/read/29236250/measuring-mrna-decay-in-budding-yeast-using-single-molecule-fish
#1
Tatjana Trcek, Samir Rahman, Daniel Zenklusen
Cellular mRNA levels are determined by the rates of mRNA synthesis and mRNA decay. Typically, mRNA degradation kinetics are measured on a population of cells that are either chemically treated or genetically engineered to inhibit transcription. However, these manipulations can affect the mRNA decay process itself by inhibiting regulatory mechanisms that govern mRNA degradation, especially if they occur on short time-scales. Recently, single molecule fluorescent in situ hybridization (smFISH) approaches have been implemented to quantify mRNA decay rates in single, unperturbed cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236213/structural-probing-screening-and-structure-based-drug-repositioning-insights-into-the-identification-of-potential-cox-2-inhibitors-from-selective-coxibs
#2
Uma Devi Bommu, Kranthi Kumar Konidala, Rishika Pamanji, Suneetha Yeguvapalli
The rate-limiting enzyme cyclooxygenase-2 (COX-2) is considered as an insightful prognostic target for non-small cell lung cancer (NSCLC) therapy. Now, administration and prolonged utilization of selective COX-2 inhibitors (COXIBs) towards moderating the NSCLC has been associated with different side effects. In the present study, we focused on the structure-based drug repositioning approaches for predicting therapeutic potential de novo candidates for human COX-2. Due to discrepancies in the eminence of x-ray diffraction structures, creates a big barrier in drug discovery approach...
December 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29236113/visual-detection-of-a-nerve-agent-simulant-using-chemically-modified-paper-strips-and-dye-assembled-inorganic-nanocomposite
#3
Nilanjan Dey, Satadru Jha, Santanu Bhattacharya
Chromogenic probe with oxidized bis-indolyl scaffold has been synthesized for the detection of a nerve gas mimicking agent, DCNP (diethyl cyanophosphonate) at pH 8.0 in water. The mechanism of interaction was proposed as the release of cyanide ion through the indole group mediating the hydrolysis of phosphorous-hetero atom bond and, thereafter, the Michael addition of the liberated CN- ion to the electron deficient C[double bond, length as m-dash]C bond of the bis-indolyl moiety. The reaction featured a remarkable change in color from red to colorless at ambient condition...
December 13, 2017: Analyst
https://www.readbyqxmd.com/read/29236076/nucleobase-guanidiniocarbonyl-pyrrole-conjugates-as-novel-fluorimetric-sensors-for-single-stranded-rna
#4
Željka Ban, Biserka Žinić, Robert Vianello, Carsten Schmuck, Ivo Piantanida
We demonstrate here for the first time that a guanidiniocarbonyl-pyrrole (GCP) unit can be applied for the fine recognition of single stranded RNA sequences-an intuitively unexpected result since so far binding of the GCP unit to ds-DNA or ds-RNA relied strongly on minor or major groove interactions, as shown in previous work. Two novel nucleobase-GCP isosteric conjugates differing in the flexibility of GCP unit revealed a fluorimetric recognition of various single stranded RNA, which could be additionally regulated by pH...
December 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29235850/a-digital-protocol-for-chemical-analysis-at-ultra-low-concentrations-by-surface-enhanced-raman-scattering
#5
Carlos Diego L de Albuquerque, Regivaldo Gomes Sobral Filho, Ronei Jesus Poppi, Alexandre G Brolo
Single molecule surface-enhanced Raman Spectroscopy (SM-SERS) has the potential to revolutionize quantitative analysis at ultra-low concentrations (less than 1 nM). However, there are no established protocols to generalize the application of this technique in analytical chemistry. Here, a protocol for quantification at ultra-low concentrations using SM-SERS is proposed. The approach aims to take advantage of the stochastic nature of the single-molecule regime to achieved lower limits of detection (LOD) and quantification (LOQ)...
December 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29235697/remote-sampling-mass-spectrometry-for-dry-samples-sheath-flow-probe-electrospray-ionization-pesi-using-a-gel-loading-tip-inserted-with-an-acupuncture-needle
#6
Dilshadbek T Usmanov, Khatam B Ashurov, Satoshi Ninomiya, Kenzo Hiraoka, Hiroshi Wada, Hiroshi Nakano, Masaya Matsumura, Sachiyo Sanada-Morimura, Hiroshi Nonami
RATIONALE: Probe electrospray ionization (PESI) is only applicable to liquid or wet samples. In this study, a sheath-flow PESI method for remote sampling mass spectrometry that can be applied to dry samples was developed. METHODS: An acupuncture needle (0.12 mm outer diameter, 700 nm tip diameter) was inserted into a gel-loading tip with a 0.1 mm protrusion out of the tip. Analytes were extracted by filling the latter tip with solvent and softly touching the sample surface for a short time (<1 s)...
December 13, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/29235482/ratiometric-fluorescence-imaging-of-cell-surface-ph-by-poly-ethylene-glycol-phospholipid-conjugated-with-fluorescein-isothiocyanate
#7
Ryuichi Ohgaki, Yuji Teramura, Daichi Hayashi, Lili Quan, Suguru Okuda, Shushi Nagamori, Madoka Takai, Yoshikatsu Kanai
Various physiological and pathological processes are accompanied with the alteration of pH at extracellular juxtamembrane region. Accordingly, the methods to analyze the cell surface pH have been demanded in biological and medical sciences. In this study, we have established a novel methodology for cell surface pH imaging using poly(ethylene glycol)-phospholipid (PEG-lipid) as a core structure of ratiometric fluorescent probes. PEG-lipid is a synthetic amphiphilic polymer originally developed for the cell surface modification in transplantation therapy...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235479/dynamic-cortical-representations-of-perceptual-filling-in-for-missing-acoustic-rhythm
#8
Francisco Cervantes Constantino, Jonathan Z Simon
In the phenomenon of perceptual filling-in, missing sensory information can be reconstructed via interpolation or extrapolation from adjacent contextual cues by what is necessarily an endogenous, not yet well understood, neural process. In this investigation, sound stimuli were chosen to allow observation of fixed cortical oscillations driven by contextual (but missing) sensory input, thus entirely reflecting endogenous neural activity. The stimulus employed was a 5 Hz frequency-modulated tone, with brief masker probes (noise bursts) occasionally added...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235467/in-situ-functional-dissection-of-rna-cis-regulatory-elements-by-multiplex-crispr-cas9-genome-engineering
#9
Qianxin Wu, Quentin R V Ferry, Toni A Baeumler, Yale S Michaels, Dimitrios M Vitsios, Omer Habib, Roland Arnold, Xiaowei Jiang, Stefano Maio, Bruno R Steinkraus, Marta Tapia, Paolo Piazza, Ni Xu, Georg A Holländer, Thomas A Milne, Jin-Soo Kim, Anton J Enright, Andrew R Bassett, Tudor A Fulga
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29235353/sensing-ppm-level-ammonia-and-ppb-level-acetic-acid-in-the-gas-phase-by-common-black-film-with-a-fluorescent-ph-probe
#10
Jingni Fu, Luning Zhang
Relying on the nanometer-thick water core and large surface area-to-volume ratio (~2×108 m-1) of common black film (CBF), we are able to use a pH-sensitive dye (carboxy-seminaphthorhodafluor-1, SNARF-1) to detect ammonia and acetic acid gas adsorption into the CBF, with the limit of detection reaching 0.8 ppm for NH3 gas and 3 ppb for CH3COOH gas in the air. Data analysis reveals that fluorescence signal change is linearly proportional to the gas concentration up to 15 ppm and 65 ppb for NH3 and CH3COOH, respectively...
December 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29235352/systems-approaches-to-understanding-and-designing-allosteric-proteins
#11
Srivatsan Raman
The study of allostery has a central place in biology due to the myriad roles of allosteric proteins in cellular function. As technologies to probe spatiotemporal resolution of biomolecules have become increasingly sophisticated, so has our understanding of the diverse structural and molecular mechanisms of allosteric proteins. Studies have shown that allosteric signal is transmitted a through a network of residue-residue interactions connecting distal sites on a protein. Linking structural and dynamical changes to the functional role of individual residues will give a more complete molecular view of allostery...
December 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/29235348/carbon-dots-with-red-emission-for-sensing-of-pt2-au3-and-pd2-and-their-bio-applications-in-vitro-and-in-vivo
#12
Wenli Gao, Haohan Song, Xiao Wang, Xiaoqiang Liu, Xiaobin Pang, Yanmei Zhou, Bin Gao, Xiaojun Peng
Red emissive carbon dots (CDs) have drawn more and more attention due to their good organ penetration depth and slight biological tissues photodamage. Herein, the fluorescent CDs with red emission were synthesized by facile one-pot hydrothermal treatment of citric acid and neutral red, and they show red fluorescence both in aqueous solution and solid state. The solution of CDs exhibits the quantum yield (QY) of 12.1%, good stability against photobleaching, and low cytotoxicity. As-prepared CDs can be used as fluorescent probe for peculiar detection of Pt2+, Au3+ and Pd2+...
December 13, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29235296/-effect-of-astragaloside-%C3%A2-combined-with-panax-notoginseng-saponins-on-cerebral-ischemia-reperfusion-injury-and-study-of-pharmacokinetics-in-rats
#13
Jing-Xian Li, Xiao-Qian Yang, Biao Tang, Xiao-Dan Liu, Ying-Hong Tang, Chang-Qing Deng, Xiao-Ping Huang
The aim is to study the effect of astragaloside Ⅳ (AST Ⅳ) combined with Panax notoginseng saponins (PNS) on cerebral ischemia-reperfusion injury, and to probe the synergistic mechanism through the pharmacokinetics of the four major components such as AST Ⅳ, ginsenoside Rg₁ (Rg₁), ginsenoside Rb₁ (Rb₁), notoginsenoside R₁ (R₁) in cerebral ischemia-reperfusion rats. Following the establishment of cerebral ischemia/reperfusion model in rats by modified suture method, neurological function score, cerebral infarction area and pathomorphology were used to evaluate the pharmacological effect that the combination of AST Ⅳ and PNS antagonized cerebral ischemia-reperfusion injury; the contents of AST Ⅳ, Rg₁, Rb₁, R₁ in rat plasma of different time points were determined with ultra performance liquid chromatography tandem massspectrometry (UPLC-MS/MS), pharmacokinetic parameters were calculated and pharmacokinetics changes of the main effective components were analyzed...
October 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29235250/discovery-and-mechanistic-elucidation-of-a-class-of-pdi-inhibitors-for-the-treatment-of-glioblastoma
#14
Anahita Kyani, Shuzo Tamura, Suhui Yang, Andrea Shergalis, Soma Somanta, Yuting Kuang, Mats Ljungman, Nouri Neamati
Protein disulfide isomerase (PDI) is overexpressed in glioblastoma, the most aggressive form of brain cancer, and folds nascent proteins responsible for the progression and spread of the disease. Herein, we describe a novel, nanomolar PDI inhibitor, pyrimidotriazinedione 35G8, that is toxic in a panel of human glioblastoma cell lines. We performed a medium throughput 20,000-compound screen of a diverse subset of 1,000,000 compounds to identify cytotoxic small molecules. Cytotoxic compounds were screened for PDI inhibition, and, from the screen, 35G8 emerged as the most cytotoxic inhibitor of PDI...
December 12, 2017: ChemMedChem
https://www.readbyqxmd.com/read/29235233/sodium-4-mercaptophenolate-capped-cdse-zns-quantum-dots-as-a-fluorescent-probe-for-ph-detection-in-acidic-aqueous-media
#15
Hu Xu, Dong Li, Yun Zhao, Xiaomei Wang, Dan Li, Yuhong Wang
Development of the fluorescent pH detection method is promising due to the sensitivity, easy operation, and low-cost, etc. However, traditional organic fluorophores have still some disadvantages such as the tedious preparation and purification as well as low photostability and water solubility, which limits the rapid detection application. Semiconductor quantum dots (QDs) have recently risen to prominence as an alternative for organic fluorophores in fluorescence analysis by virtue of their convenient synthesis and superior optical properties...
December 12, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
https://www.readbyqxmd.com/read/29235227/peptide-based-fluorescent-probes-for-deacetylase-and-decrotonylase-activity-toward-a-general-platform-for-real-time-detection-of-lysine-deacylation
#16
Debra R Rooker, Yuliya Klyubka, Ritika Gautam, Elisa Tomat, Daniela Buccella
Histone deacetylases regulate acetylation levels of numerous proteins and play key roles in physiological processes as well as disease states. In addition to acetyl groups, deacetylases can remove other acyl modifications on lysines whose roles and regulation are far less understood. We report herein a peptide-based fluorescent probe for single-reagent, real time detection of deacetylase activity that can be readily adapted for probing broader lysine deacylation, including decrotonylation. Following cleavage of the lysine modification, the probe undergoes rapid intramolecular imine formation that results in marked optical changes, thus enabling convenient detection of deacylase activity with good statistical Z' factors for both absorption and fluorescence modalities...
December 12, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29235075/plla-phb-fiber-membranes-obtained-by-solvent-free-electrospinning-for-short-time-drug-delivery
#17
K Cao, Y Liu, A A Olkhov, V Siracusa, A L Iordanskii
Fibers of poly(L-lactic acid) (PLLA)/polyhydroxybutyrate (PHB) with different concentrations of the drug dipyridamole (DPD) were prepared using solvent-free melt electrospinning to obtain a polymeric drug delivery system. The electrospun fibers were morphologically, structurally, thermally, and dynamically characterized. Crazes that resemble lotus root crevices were interestingly observed in the 7:3 PLLA/PHB fibers with 1% DPD. The crystallinity of PLLA slightly decreased as PHB was incorporated, and the addition of DPD significantly reduced the melting temperature of the composite...
December 12, 2017: Drug Delivery and Translational Research
https://www.readbyqxmd.com/read/29234759/a-sims-study-of-cation-and-anion-diffusion-in-tantalum-oxide
#18
U N Gries, H Schraknepper, K Skaja, F Gunkel, S Hoffmann-Eifert, R Waser, R A De Souza
Ion transport in ceramics of the low-temperature phase of tantalum pentoxide, L-Ta2O5, was examined by means of diffusion experiments and subsequent analysis of diffusion profiles with time-of-flight secondary ion mass spectrometry (ToF-SIMS). 18O/16O isotope anneals were used to investigate oxygen diffusion, and oxygen tracer diffusion coefficients were obtained for the temperature range of 623 ≤ T/K ≤ 873 at an oxygen partial pressure of pO2 = 0.2 bar and for the oxygen partial pressure range of 10-2 ≤ pO2/bar ≤ 100 at a temperature of T = 723 K...
December 13, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29234750/intraoral-radiography-lacks-accuracy-for-the-assessment-of-peri-implant-bone-level-a-controlled-clinical-study
#19
Véronique Christiaens, Reinhilde Jacobs, Melissa Dierens, Stijn Vervaeke, Hugo De Bruyn, Sebastiaan Koole, Jan Cosyn
PURPOSE: The aim of this study was to compare clinical and radiographic bone level assessments to intra-surgical bone level registration around implants with peri-implantitis and to identify the clinical variables rendering peri-implant bone level assessment accuracy. MATERIALS AND METHODS: The study sample included 50 implants with peri-implantitis in 23 patients. Registration methods included probing of the vertical distance between the implant/abutment interface and the bottom of the pocket (= VPD), intraoral radiography, bone sounding without flap elevation and intra-surgically assessed interproximal bone level...
2017: European Journal of Oral Implantology
https://www.readbyqxmd.com/read/29234749/sinus-lift-grafting-with-anorganic-bovine-bone-vs-50-autologous-bone-mixed-with-50-anorganic-bovine-bone-2-years-after-loading-results-from-a-randomised-controlled-trial
#20
Silvio Mario Meloni, Sascha Alekshander Jovanovic, Milena Pisano, Erta Xhanari, Giacomo De Riu, Antonio Tullio, Marco Tallarico
PURPOSE: To compare the outcome of implants inserted in maxillary sinuses augmented with anorganic bovine bone (ABB) grafts vs mixed 50% ABB and 50% autologous bone graft, using a lateral window approach. MATERIALS AND METHODS: This study was designed as a randomised controlled trial of parallel groups. Patients in need of an implant-supported prosthesis in a maxillary posterior area with a residual alveolar bone height no greater than 4 mm (range 0-4 mm) were recruited for lateral sinus grafting...
2017: European Journal of Oral Implantology
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