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https://www.readbyqxmd.com/read/28238724/proximity-biotinylation-as-a-method-for-mapping-proteins-associated-with-mtdna-in-living-cells
#1
Shuo Han, Namrata D Udeshi, Thomas J Deerinck, Tanya Svinkina, Mark H Ellisman, Steven A Carr, Alice Y Ting
A recurring challenge in cell biology is to define the molecular components of macromolecular complexes of interest. The predominant method, immunoprecipitation, recovers only strong interaction partners that survive cell lysis and repeated detergent washes. We explored peroxidase-catalyzed proximity biotinylation, APEX, as an alternative, focusing on the mitochondrial nucleoid, the dynamic macromolecular complex that houses the mitochondrial genome. Via 1-min live-cell biotinylation followed by quantitative, ratiometric mass spectrometry, we enriched 37 nucleoid proteins, seven of which had never previously been associated with the nucleoid...
February 20, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28237840/comparison-between-in-vitro-properties-of-washed-platelet-concentrates-suspended-in-m-sol-and-those-in-brs-a-both-of-which-were-prepared-with-an-automated-cell-processor
#2
Akira Iwama, Junichi Hirayama, Masayuki Nogawa, Masayuki Shiba, Masahiro Satake, Shigeru Takamoto, Kenji Tadokoro
BACKGROUND: Washed platelet concentrate (WPC) is prepared manually in general, but automated preparation is desirable to minimize variation in the WPC quality and enhance WPC production. Recently, the software was improved for an automated cell processor (ACP) to control all processes of WPC preparation. M-sol and BRS-A, which are mixtures of medical solutions, are widely used for WPC preparation with a manual method in Japan. In this study, we prepared WPC suspended in M-sol (WPC-M) or BRS-A (WPC-B) with the ACP, and compared their in vitro properties during 7-day storage...
February 9, 2017: Transfusion and Apheresis Science
https://www.readbyqxmd.com/read/28236656/recovery-from-desensitization-of-ige-dependent-responses-in-human-lung-mast-cells
#3
Amy Lewis, Donald W MacGlashan, S Kim Suvarna, Peter T Peachell
BACKGROUND: Clinical desensitization and oral food immunotherapy are therapeutic interventions that allow individuals who react adversely to an allergen (drug or food) to be made tolerant to the allergen. However, tolerance is brief and allergen hypersensitivity can recur within days following allergen withdrawal. OBJECTIVE: We hypothesize that the reason these treatments are temporary reflects rapid recovery of mast cells from a desensitized state. We sought to test this...
February 25, 2017: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28230980/chitosan-modified-filter-paper-for-nucleic-acid-extraction-and-in-situ-pcr-on-a-thermoplastic-microchip
#4
Wupeng Gan, Yin Gu, Junping Han, Caixia Li, Jing Sun, Peng Liu
Plastic microfluidic devices with embedded chitosan-modified Fusion 5 filter paper (unmodified one purchased from GE Healthcare) have been successfully developed for DNA extraction and concentration, utilizing two different mechanisms for DNA capture: the physical entanglement of long-chain DNA molecules with the fiber matrix of the filter paper and the electrostatic adsorption of DNA to the chitosan-modified filter fibers. This new method not only provided a high DNA extraction efficiency at a pH of 5 by synergistically combining these two capture mechanisms together, but also resisted the elution of DNA from filters at a pH >8 due to the entanglement of DNA with fibers...
February 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28228166/methylene-blue-assay-for-estimation-of-regenerative-re-epithelialization-in-vivo
#5
Maresha Milyavsky, Renee Dickie
The rapidity with which epithelial cells cover a wound surface helps determine whether scarring or scar-less healing results. As methylene blue is a vital dye that is absorbed by damaged tissue but not undamaged epidermis, it can be used to assess wound closure. We sought to develop a quantitative methylene blue exclusion assay to estimate the timeframe for re-epithelialization in regenerating appendages in zebrafish and axolotls, two classic model systems of regeneration. Following application of methylene blue to the amputation plane and extensive washing, the regenerating tail was imaged in vivo until staining was no longer visible...
February 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28225151/cytopathologic-differential-diagnosis-of-low-grade-urothelial-carcinoma-and-reactive-urothelial-proliferation-in-bladder-washings-a-logistic-regression-analysis
#6
Ebru Cakir, Ulku Kucuk, Emel Ebru Pala, Ozlem Sezer, Rahmi Gokhan Ekin, Ozgur Cakmak
Conventional cytomorphologic assessment is the first step to establish an accurate diagnosis in urinary cytology. In cytologic preparations, the separation of low-grade urothelial carcinoma (LGUC) from reactive urothelial proliferation (RUP) can be exceedingly difficult. The bladder washing cytologies of 32 LGUC and 29 RUP were reviewed. The cytologic slides were examined for the presence or absence of the 28 cytologic features. The cytologic criteria showing statistical significance in LGUC were increased numbers of monotonous single (non-umbrella) cells, three-dimensional cellular papillary clusters without fibrovascular cores, irregular bordered clusters, atypical single cells, irregular nuclear overlap, cytoplasmic homogeneity, increased N/C ratio, pleomorphism, nuclear border irregularity, nuclear eccentricity, elongated nuclei, and hyperchromasia (p ˂ 0...
February 22, 2017: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
https://www.readbyqxmd.com/read/28223388/in-vitro-and-in-vivo-antifungal-profile-of-a-novel-and-long-acting-inhaled-azole-pc945-on-aspergillus-fumigatus-infection
#7
Thomas Colley, Alexandre Alanio, Steven L Kelly, Gurpreet Sehra, Yasuo Kizawa, Andrew G S Warrilow, Josie E Parker, Diane E Kelly, Genki Kimura, Lauren Anderson-Dring, Takahiro Nakaoki, Mihiro Sunose, Stuart Onions, Damien Crepin, Franz Lagasse, Matthew Crittall, Jonathan Shannon, Michael Cooke, Stéphane Bretagne, John King-Underwood, John Murray, Kazuhiro Ito, Pete Strong, Garth Rapeport
The profile of PC945, a novel triazole antifungal, designed for administration via inhalation, has been assessed in a range of in vitro and in vivo studies. PC945 was characterized as a potent, tight-binding inhibitor of Aspergillus fumigatus sterol 14α-demethylase (CYP51A and CYP51B) activity (IC50, 0.23 μM and 0.22 μM, respectively), with characteristic type II azole binding spectra. Against 96 clinically isolated A. fumigatus strains, the MIC values of PC945 ranged from 0.032∼>8 μg/ml, whilst those of voriconazole ranged from 0...
February 21, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28221782/the-cation-%C3%AF-interaction-enables-a-halo-tag-fluorogenic-probe-for-fast-no-wash-live-cell-imaging-and-gel-free-protein-quantification
#8
Yu Liu, Kun Miao, Noah P Dunham, Hongbin Liu, Matthew Fares, Amie K Boal, Xiaosong Li, Xin Zhang
Design of fluorogenic probes for Halo-tag is highly desirable but challenging. Previous work achieved this goal by controlling the chemical switch of spirolactones upon the covalent conju-gation between Halo-tag and probes or by incorporating a 'channel dye' into the substrate bind-ing tunnel of Halo-tag. In this work, we have developed a novel class of Halo-tag fluorogenic probes that are derived from solvatochromic fluorophores. The optimal probe, harboring a ben-zothiadiazole scaffold, exhibits a 1000-fold fluorescence enhancement upon reaction with Halo-tag...
February 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28220432/genome-wide-analysis-of-chromatin-accessibility-in-arabidopsis-infected-with-pseudomonas-syringae
#9
Yogendra Bordiya, Hong-Gu Kang
Changes in chromatin accessibility are an important aspect of the molecular changes that occur in eukaryotic cells responding to stress, and they appear to play a critical role in stress-induced transcriptional activation/reprogramming and epigenetic changes. In plants, pathogen infection has been shown to induce rapid and drastic transcriptional reprogramming; growing evidence suggests that chromatin remodeling plays an essential role in this phenomenon. The recent development of genomic tools to assess chromatin accessibility presents a significant opportunity to investigate the relationship between chromatin dynamicity and gene expression...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28217943/fine-needle-cytology-pre-surgical-differentiation-of-parathyroid-neoplasms-is-it-reliable
#10
A Caleo, M Vitale, L Valvano, M Siano, B Angrisani, M Forlenza, A Massari, A Puzziello, F Salzano, P Zeppa
BACKGROUND: Fine needle cytology (FNC) of a parathyroid neoplasia (PN) is reliable, but needs to be confirmed by Parathormone (PTH) and Thyroglobulin (TG) immunoassay on needle washing or by immunocytochemistry (ICC) evaluation. The differentiation between parathyroid adenoma (PA), atypical adenoma (PAA) and carcinoma (PC) is difficult on histology or even impossible on FNC. The aim of this study was to evaluate possible cytological criteria to classify FNC-PN further. METHODS: Twenty-three FNC samples of PN and parathyroid cysts were rather then have been reviewed...
February 20, 2017: Cytopathology: Official Journal of the British Society for Clinical Cytology
https://www.readbyqxmd.com/read/28215401/nickel-salen-supported-paramagnetic-nanoparticles-for-6-his-target-recombinant-protein-affinity-purification
#11
Zahra Rashid, Ramin Ghahremanzadeh, Mohammad-Reza Nejadmoghaddam, Mahboobeh Nazari, Mohammad-Reza Shokri, Hossein Naeimi, Amir-Hassan Zarnani
In this research, a simple, efficient, inexpensive, rapid and high yield method for the purification of 6×histidine-tagged recombinant protein was developed. For this purpose, manganese ferrite magnetic nanoparticles (MNPs) were synthesized through a co-precipitation method and then they were conveniently surface-modified with tetraethyl orthosilicate (TEOS) in order to prevent oxidation and form high density of hydroxyl groups. Next, the salen ligand was prepared from condensation reaction of salicylaldehyde and 3-aminopropyl (trimethoxy) silane (APTMS) in 1:1 molar ratio; followed by complexation with Ni(OAc)2...
February 13, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28211040/anti-cd3-treatment-upregulates-pd-1-expression-on-activated-effector-t-cells-and-severely-impairs-their-inflammatory-capacity
#12
Maja Wallberg, Asha Recino, Jenny Phillips, Duncan Howie, Margaux Vienne, Christopher Paluch, Miyuki Azuma, F Susan Wong, Herman Waldmann, Anne Cooke
T cells play a key role in the pathogenesis of type 1 diabetes, and targeting the CD3 component of the TCR complex provides one therapeutic approach. Anti-CD3 treatment can reverse overt disease in spontaneously diabetic non-obese diabetic mice, an effect proposed to, at least in part, be caused by a selective depletion of pathogenic cells. We have used a transfer model to further investigate the effects of anti-CD3 treatment on green fluorescent protein (GFP)(+) islet-specific effector T cells in vivo. The GFP expression allowed us to isolate the known effectors at different time points during treatment to assess cell presence in various organs as well as gene expression and cytokine production...
February 17, 2017: Immunology
https://www.readbyqxmd.com/read/28208666/the-mechanisms-and-biomedical-applications-of-an-nir-bodipy-based-switchable-fluorescent-probe
#13
Bingbing Cheng, Venugopal Bandi, Shuai Yu, Francis D'Souza, Kytai T Nguyen, Yi Hong, Liping Tang, Baohong Yuan
Highly environment-sensitive fluorophores have been desired for many biomedical applications. Because of the noninvasive operation, high sensitivity, and high specificity to the microenvironment change, they can be used as excellent probes for fluorescence sensing/imaging, cell tracking/imaging, molecular imaging for cancer, and so on (i.e., polarity, viscosity, temperature, or pH measurement). In this work, investigations of the switching mechanism of a recently reported near-infrared environment-sensitive fluorophore, ADP(CA)₂, were conducted...
February 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28208281/enzyme-activated-g-quadruplex-synthesis-for-in-situ-label-free-detection-and-bioimaging-of-cell-apoptosis
#14
Zhuoliang Liu, Xingyu Luo, Zhu Li, Yan Huang, Zhou Nie, Hong-Hui Wang, Shouzhuo Yao
Fluorogenic probes targeting G-quadruplex structures have emerged as the promising toolkit for functional research of G-quadruplex and biosensor development. However, their biosensing applications are still largely limited in in-tube detection. Herein, we proposed a fluorescent bioimaging method based on enzyme-generated G-quadruplexes for detecting apoptotic cells at the cell and tissue level, namely, terminal deoxynucleotidyl transferase (TdT)-activated de novo G-quadruplex synthesis (TAGS) assay. The detection target is genomic DNA fragmentation, a biochemical hallmark of apoptosis...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28195541/assessment-of-egfr-mutation-status-using-cell-free-dna-from-bronchoalveolar-lavage-fluid
#15
Sojung Park, Jae Young Hur, Kye Young Lee, Jae Cheol Lee, Jin Kyung Rho, Sun Hwa Shin, Chang-Min Choi
BACKGROUND: Much attention has been focused on epidermal growth factor receptor (EGFR) mutation testing since the introduction of EGFR-tyrosine kinase inhibitors have improved survival in EGFR-positive lung cancer patients. Liquid biopsy using circulating tumor cells or cell-free DNA (cfDNA) has enabled less invasive testing, but requires a highly sensitive method. To date, liquid biopsy using bronchoalveolar lavage (BAL) fluid has rarely been used. METHODS: From 20 patients with lung adenocarcinoma, we isolated cfDNA from 20 samples of cell-free BAL fluid and 19 cell-free bronchial washing samples...
February 14, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28194258/complete-genome-sequence-of-pseudomonas-stutzeri-strain-rch2-isolated-from-a-hexavalent-chromium-cr-vi-contaminated-site
#16
Romy Chakraborty, Hannah Woo, Paramvir Dehal, Robert Walker, Marcin Zemla, Manfred Auer, Lynne A Goodwin, Alexey Kazakov, Pavel Novichkov, Adam P Arkin, Terry C Hazen
Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28193039/molecularly-imprinted-polymer-based-plasmonic-immunosandwich-assay-for-fast-and-ultrasensitive-determination-of-trace-glycoproteins-in-complex-samples
#17
Xueying Tu, Pir Muhammad, Jia Liu, Yanyan Ma, Shuangshou Wang, Danyang Yin, Zhen Liu
Glycoproteins play significant roles in many biological processes. Assays of glycoproteins have significant biological importance and clinical values, for which immunoassay has been the workhorse tool. However, immunoassay suffers from some disadvantages, such as poor availability of high-specificity antibodies and limited stability of biological reagents. Herein, we present an antibody-free and enzyme-free approach, called molecularly imprinted polymer (MIP)-based plasmonic immunosandwich assay (PISA), for fast and ultrasensitive detection of trace glycoproteins in complex samples...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28191268/automated-electrotransformation-of-escherichia-coli-on-a-digital-microfluidic-platform-using-bioactivated-magnetic-beads
#18
J A Moore, M Nemat-Gorgani, A C Madison, M A Sandahl, S Punnamaraju, A E Eckhardt, M G Pollack, F Vigneault, G M Church, R B Fair, M A Horowitz, P B Griffin
This paper reports on the use of a digital microfluidic platform to perform multiplex automated genetic engineering (MAGE) cycles on droplets containing Escherichia coli cells. Bioactivated magnetic beads were employed for cell binding, washing, and media exchange in the preparation of electrocompetent cells in the electrowetting-on-dieletric (EWoD) platform. On-cartridge electroporation was used to deliver oligonucleotides into the cells. In addition to the optimization of a magnetic bead-based benchtop protocol for generating and transforming electrocompetent E...
January 2017: Biomicrofluidics
https://www.readbyqxmd.com/read/28178957/immunological-aspects-of-the-efficiency-of-protectotype-vaccination-strategy-against-chicken-infectious-bronchitis
#19
Marcin Smialek, Bartlomiej Tykalowski, Daria Dziewulska, Tomasz Stenzel, Andrzej Koncicki
BACKGROUND: One of the most commonly applied protectotype vaccination protocol against infectious bronchitis (IB) in broiler chickens in the EU is simultaneous or alternate use of Ma5 and 4/91 vaccine strains. After IB vaccination and infection, systemic and upper respiratory tract (URT), humoral and cell-mediated immunity (CMI), are stimulated. The level of this stimulation correlates with the level of protection against IB. RESULTS: We've investigated the development of URT and systemic, cell-mediated and humoral immunity in commercial broiler chickens vaccinated with Ma5 and/or 4/91 strains at hatch day...
February 8, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28176876/engineering-a-ph-responsive-pore-forming-protein
#20
Matic Kisovec, Saša Rezelj, Primož Knap, Miša Mojca Cajnko, Simon Caserman, Ajda Flašker, Nada Žnidaršič, Matej Repič, Janez Mavri, Yi Ruan, Simon Scheuring, Marjetka Podobnik, Gregor Anderluh
Listeriolysin O (LLO) is a cytolysin capable of forming pores in cholesterol-rich lipid membranes of host cells. It is conveniently suited for engineering a pH-governed responsiveness, due to a pH sensor identified in its structure that was shown before to affect its stability. Here we introduced a new level of control of its hemolytic activity by making a variant with hemolytic activity that was pH-dependent. Based on detailed structural analysis coupled with molecular dynamics and mutational analysis, we found that the bulky side chain of Tyr406 allosterically affects the pH sensor...
February 8, 2017: Scientific Reports
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