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https://www.readbyqxmd.com/read/28337070/genomic-methods-and-microbiological-technologies-for-profiling-novel-and-extreme-environments-for-the-extreme-microbiome-project-xmp
#1
Scott Tighe, Ebrahim Afshinnekoo, Tara M Rock, Ken McGrath, Noah Alexander, Alexa McIntyre, Sofia Ahsanuddin, Daniela Bezdan, Stefan J Green, Samantha Joye, Sarah Stewart Johnson, Don A Baldwin, Nathan Bivens, Nadim Ajami, Joseph R Carmical, Ian Charold Herriott, Rita Colwell, Mohamed Donia, Jonathan Foox, Nick Greenfield, Tim Hunter, Jessica Hoffman, Joshua Hyman, Ellen Jorgensen, Diana Krawczyk, Jodie Lee, Shawn Levy, Natàlia Garcia-Reyero, Matthew Settles, Kelley Thomas, Felipe Gómez, Lynn Schriml, Nikos Kyrpides, Elena Zaikova, Jon Penterman, Christopher E Mason
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines...
March 10, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28332232/paper-based-colorimetric-sensor-system-for-high-throughput-screening-of-c-h-borylation
#2
Han-Sung Kim, Min Sik Eom, Min Su Han, Sunwoo Lee
A paper-based colorimetric sensor system (PBCSS) was developed to detect the amount of bis(pinacolato)diboron (B2Pin2) and applied as a high-throughput screening protocol in Ir-catalyzed C-H borylation. First, 96 ligands were screened for the borylation of benzene, and then 12 of them were selected and tested for five substrates. These reaction mixtures were spotted in the PBCSS, showing a blue-violet color. The value of the gray scale of each reaction was obtained from these colored spots and converted to the extent of conversion of B2Pin2...
March 22, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28323589/preventing-high-altitude-cerebral-edema-in-rats-with-repurposed-anti-angiogenesis-pharmacotherapy
#3
Samantha Tarshis, Joanne Maltzahn, Zoe Loomis, David C Irwin
BACKGROUND: High altitude cerebral edema (HACE) is a fulminant, deadly, and yet still unpredictable brain disease. A new prophylactic treatment for HACE and its predecessor, acute mountain sickness (AMS), needs to be developed without the contraindications or adverse effect profiles of acetazolamide and dexamethasone. Since neovascularization signals are likely key contributors to HACE/AMS, our approach was to examine already existing anti-angiogenic drugs to inhibit potential initiating HACE pathway(s)...
December 1, 2016: Aerospace Medicine and Human Performance
https://www.readbyqxmd.com/read/28301624/photodynamic-therapy-effectively-treats-actinic-keratoses-without-pre-illumination-incubation-time
#4
Jessica Gandy, Brian Labadie, Dina Bierman, Christopher Zachary
<p>BACKGROUND: Actinic keratoses (AKs) are dysplastic lesions of the epidermis that have the potential to progress to non-melanoma skin cancers (NMSC). Traditional photodynamic therapy (PDT) requires a pre-illumination incubation time, which adds to overall in-office time and has been linked to pain. Our group has found a novel protocol to effectively treat AKs with PDT that eliminates the pre-illumination incubation period and uses 2 back-to-back cycles of 16 minute 40 seconds.</p> <p>METHODS: The patient was prepped with soapy water and isopropyl alcohol, and thick AKs were descaled with a curette...
March 1, 2017: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/28298984/an-in-vitro-analysis-model-for-investigating-the-staining-effect-of-various-chlorhexidine-based-mouthwashes
#5
Alain-Ayepa Kouadio, Xavier Struillou, Céline Bories, Jean-Michel Bouler, Zahi Badran, Assem Soueidan
BACKGROUND: There are different mouthwashes containing chlorhexidine in different concentrations, as well as various excipients. Chlorhexidine induce stains or discoloration in teeth and mucous membranes. The aim of this work was to design a model to reproduce in vitro staining associated with the use of different mouthwashes containing chlorhexidine. MATERIAL AND METHODS: We used as substrates of natural teeth and elephant ivory slices. Different incubation baths were conducted over 21 days in culture dishes at 37°C...
March 2017: Journal of Clinical and Experimental Dentistry
https://www.readbyqxmd.com/read/28293892/light-regulated-protein-kinases-based-on-the-cry2-cib1-system
#6
Wignand W D Mühlhäuser, Maximilian Hörner, Wilfried Weber, Gerald Radziwill
Optogenetic approaches enable the control of biological processes in a time- and space-resolved manner. These light-based methods are noninvasive and by using light as sole activator minimize side effects in contrast to chemical inducers. Here, we provide a protocol for the targeted control of the activity of protein kinases in mammalian cells based on the photoreceptor cryptochrome 2 (CRY2) of Arabidopsis thaliana and its interaction partner CIB1. Blue light (450 nm)-induced binding of CRY2 to CIB1 allows the recruitment of a chimeric cytosolic protein kinase AKT1 to the plasma membrane accompanied with stimulation of its kinase activity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28288928/in%C3%A2-vitro-cytotoxicity-evaluation-of-resveratrol-loaded-nanoparticles-focus-on-the-challenges-of-in%C3%A2-vitro-methodologies
#7
V Rocha, C Marques, J L Figueiredo, A R Gaio, P C Costa, J M Sousa Lobo, I F Almeida
Assessment of toxic effects is mandatory before market placement of pharmaceutical and cosmetic products. Nanotoxicology is an emerging regulatory concern and still a challenging field. Topical application of resveratrol (RSV) has been extensively studied owing to its multi-mechanistic skin anti-aging effects. Nanoencapsulation has been suggested as a promising solution to overcome RSV stability issues. In this work RSV-loaded solid lipid nanoparticles (SLN) and nanostructured lipid carriers (NLC) were prepared using a homogenization/sonication technique...
March 10, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28283890/estimation-of-photosynthesis-in-cyanobacteria-by-pulse-amplitude-modulation-chlorophyll-fluorescence-problems-and-solutions
#8
REVIEW
Takako Ogawa, Masahiro Misumi, Kintake Sonoike
Cyanobacteria are photosynthetic prokaryotes and widely used for photosynthetic research as model organisms. Partly due to their prokaryotic nature, however, estimation of photosynthesis by chlorophyll fluorescence measurements is sometimes problematic in cyanobacteria. For example, plastoquinone pool is reduced in the dark-acclimated samples in many cyanobacterial species so that conventional protocol developed for land plants cannot be directly applied for cyanobacteria. Even for the estimation of the simplest chlorophyll fluorescence parameter, F v/F m, some additional protocol such as addition of DCMU or illumination of weak blue light is necessary...
March 10, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28281564/standardized-and-flexible-eight-colour-flow-cytometry-panels-harmonized-between-different-laboratories-to-study-human-nk-cell-phenotype-and-function
#9
John P Veluchamy, María Delso-Vallejo, Nina Kok, Fenna Bohme, Ruth Seggewiss-Bernhardt, Hans J van der Vliet, Tanja D de Gruijl, Volker Huppert, Jan Spanholtz
Advancements in multi-colour fluorescence activated cell sorting (FACS) panel warrant harmonized procedures to obtain comparable data between various laboratories. The intensifying clinical exploration of Natural Killer (NK) cell-based immunotherapy demands standardized and harmonized NK cell FACS panels and acquisition protocols. Eight colour FACS panels were designed to study human NK cell phenotype and function within peripheral blood mononuclear cells (PBMC). The panels were designed around fixed backbone markers and channels, covering antigens for non-NK lineage exclusion (CD3, TCRγδ, CD19, CD14, SYTOX(®) Blue) and NK cell selection (CD45, CD56, CD16), complemented with variable drop-in markers/channels to study NK cell phenotype (NKG2A, NKG2C, NKG2D and KIR2D) or NK cell function and activation (CD25, NKp44 and CD107a)...
March 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28260668/can-the-sensitivity-of-the-histopathological-diagnosis-of-coeliac-disease-be-increased-and-can-treatment-progression-be-monitored-using-mathematical-modelling-of-histological-sections-a-pilot-study
#10
Richard P G Charlesworth, Nicholas M Andronicos, David R Scott, James R McFarlane, Linda L Agnew
PURPOSE: The aim of this pilot study was to attempt to define a set of equations from histological observations of tissue affected with coeliac disease (CD) to predict Marsh score. MATERIAL/METHODS: Tissue from 15 patients with untreated CD, 6 patients with treated CD and 9 healthy control patients were stained using the standard H&E, Giemsa's staining for tissue sections and Alcian Blue protocols. A number of histological measures were then taken from each section and the data was used to ultimately design a set of linear predictive algorithms to calculate Marsh score...
June 14, 2016: Advances in Medical Sciences
https://www.readbyqxmd.com/read/28245670/optimizing-decellularization-techniques-to-create-a-new-nerve-allograft-an-in-vitro-study-using-rodent-nerve-segments
#11
Caroline A Hundepool, Tim H J Nijhuis, Dimitra Kotsougiani, Patricia F Friedrich, Allen T Bishop, Alexander Y Shin
OBJECTIVE Commercially available processed nerve allografts have been shown to be inferior to autografts in previous animal studies. The authors hypothesized that combining different processing and storage techniques will result in improved nerve ultrastructure preservation, lower immunogenicity, and minimized cellular debris. Different processing protocols were evaluated using chemical detergents, enzymes, and irradiation, with the addition the of enzyme elastase, were used. Additionally, the difference between cold and frozen storage was investigated...
March 2017: Neurosurgical Focus
https://www.readbyqxmd.com/read/28241315/development-of-a-chromatic-pupillography-protocol-for-the-first-gene-therapy-trial-in-patients-with-cnga3-linked-achromatopsia
#12
Jolanta Lisowska, Lukasz Lisowski, Carina Kelbsch, Fumiatsu Maeda, Paul Richter, Susanne Kohl, Ditta Zobor, Torsten Strasser, Krunoslav Stingl, Eberhart Zrenner, Tobias Peters, Helmut Wilhelm, M Dominik Fischer, Barbara Wilhelm
Purpose: To establish a feasible and sensitive pupillographic protocol to assess outer and inner retinal function for the first gene therapy trial in achromatopsia patients (ACHM) with mutations in CNGA3. Methods: Twenty-seven CNGA3-ACHM patients and 22 age-matched control subjects were tested using chromatic pupillography. Three different protocols were established to assess the pupillary light reflex parameters and to create the final protocol. In the individual protocols, various stimulus parameters (i...
February 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28240748/drugs-with-anti-oxidant-properties-can-interfere-with-cell-viability-measurements-by-assays-that-rely-on-the-reducing-property-of-viable-cells
#13
Niraj Shenoy, Mary Stenson, Joshua Lawson, Jithma Abeykoon, Mrinal Patnaik, Xiaosheng Wu, Thomas Witzig
Cell viability assays such as Cell Titer Blue and Alamar Blue rely on the reducing property of viable cells to reduce the reagent dye to a product which gives a fluorescent signal. The current manufacture-recommended protocols do not take into account the possibility of the reagent substrate being reduced directly to the fluorescent product by drugs with an anti-oxidant property. After suspecting spurious results while determining the cytotoxic potential of a drug of interest (DOI) with known anti-oxidant property against a renal cell cancer (RCC) cell line, we aimed to establish that drugs with anti-oxidant property can indeed cause false-negative results with the current protocols of these assays by direct reduction of the reagent substrate...
February 27, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28220426/measuring-callose-deposition-an-indicator-of-cell-wall-reinforcement-during-bacterial-infection-in-arabidopsis
#14
Lin Jin, David M Mackey
The plant cell wall responds dynamically during interaction with various pathogens. Upon recognition of "nonself" components, plant cells deploy a variety of immune responses including cell wall fortification. Callose, a β-(1, 3)-D-glucan polymer, is a component of the material deposited at the site of infection between the plasma membrane and the preexisting cell wall that is hypothesized to serve as a physical barrier and platform for directed antimicrobial compound deposition. The defense-associated function of callose deposition is supported by its induction during pathogen-associated molecular patterns (PAMP)-triggered immunity (PTI) and its inhibition by defense suppressing virulence effectors...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28150881/non-gradient-blue-native-polyacrylamide-gel-electrophoresis
#15
Xiaoting Luo, Jinzi Wu, Zhen Jin, Liang-Jun Yan
Gradient blue native polyacrylamide gel electrophoresis (BN-PAGE) is a well established and widely used technique for activity analysis of high-molecular-weight proteins, protein complexes, and protein-protein interactions. Since its inception in the early 1990s, a variety of minor modifications have been made to this gradient gel analytical method. Here we provide a major modification of the method, which we call non-gradient BN-PAGE. The procedure, similar to that of non-gradient SDS-PAGE, is simple because there is no expensive gradient maker involved...
February 2, 2017: Current Protocols in Protein Science
https://www.readbyqxmd.com/read/28145483/determination-of-blue-light-induced-infrared-absorption-based-on-mode-matching-efficiency-in-an-optical-parametric-oscillator
#16
Yajun Wang, Wenhai Yang, Zhixiu Li, Yaohui Zheng
Non-classical squeezed states of light at a compatible atomic wavelength have a potential application in quantum information protocols for quantum states delaying or storaging. An optical parametric oscillator (OPO) with periodically poled potassium titanyl phosphate (PPKTP) is the most effective method for generating this squeezed state. However, it is a challege for the nonlinear interaction in PPKTP crystal at the D1 line of rubidium atomic, due to a strong blue-light-induced infrared absorption (BLIIRA)...
February 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28139746/a-sensitive-single-enzyme-assay-system-using-the-non-ribosomal-peptide-synthetase-bpsa-for-measurement-of-l-glutamine-in-biological-samples
#17
Alistair S Brown, Katherine J Robins, David F Ackerley
The ability to rapidly, economically and accurately measure L-glutamine concentrations in biological samples is important for many areas of research, medicine or industry, however there is room for improvement on existing methods. We describe here how the enzyme BpsA, a single-module non-ribosomal peptide synthetase able to convert L-glutamine into the blue pigment indigoidine, can be used to accurately measure L-glutamine in biological samples. Although indigoidine has low solubility in aqueous solutions, meaning direct measurements of indigoidine synthesis do not reliably yield linear standard curves, we demonstrate that resolubilisation of the reaction end-products in DMSO overcomes this issue and that spontaneous reduction to colourless leuco-indigoidine occurs too slowly to interfere with assay accuracy...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28139513/transfusion-of-plasma-collected-at-late-phase-after-preconditioning-reduces-myocardial-infarct-size-induced-by-ischemia-reperfusion-in-rats-in-vivo
#18
Yang Zhao, Zhi-Nan Zheng, Chi-Wai Cheung, Zhi-Yi Zuo, San-Qing Jin
BACKGROUND: Plasma transfusion is a common clinical practice. Remote ischemic preconditioning (RIPC) protects organs against ischemia-reperfusion (IR) injury. Whether preconditioned plasma (PP), collected at late phase after RIPC, could protect organs against IR injury in vivo is unknown. This study explored whether transfusion of PP could reduce myocardial infarct size (IS) after IR in rat in vivo. METHODS: Eighty Lewis rats were randomized to eight groups (n = 10 for each group)...
February 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28128400/mir-187-induces-apoptosis-of-siha-cervical-carcinoma-cells-by-downregulating-bcl-2
#19
C Y He, J Yang
Cervical carcinoma is a life-threatening illness posing considerable danger to women's health. microRNAs (miRNAs) have been shown to regulate multiple cellular events, including growth and proliferation, and miR-187 is thought to regulate the growth and apoptosis of certain cell types. Our study focused on the influence of miR-187 on the growth, proliferation, and apoptosis of SiHa cervical carcinoma cells, and explored the mechanism behind its pro-apoptotic effect. miR-187 and control (scrambled) miRNA were synthesized with a standard protocol and lipofected into SiHa cells...
January 23, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28128307/emergent-properties-of-giant-vesicles-formed-by-a-polymerization-induced-self-assembly-pisa-reaction
#20
Anders N Albertsen, Jan K Szymański, Juan Pérez-Mercader
Giant micrometer sized vesicles are of obvious interest to the natural sciences as well as engineering, having potential application in fields ranging from drug delivery to synthetic biology. Their formation often requires elaborate experimental techniques and attempts to obtain giant vesicles from chemical media in a one-pot fashion have so far led to much smaller nanoscale structures. Here we show that a tailored medium undergoing controlled radical polymerization is capable of forming giant polymer vesicles...
January 27, 2017: Scientific Reports
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