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https://www.readbyqxmd.com/read/29150508/community-composition-and-ultrastructure-of-a-nitrate-dependent-anaerobic-methane-oxidizing-enrichment-culture
#1
Lavinia Gambelli, Simon Guerrero-Cruz, Rob J Mesman, Geert Cremers, Mike S M Jetten, Huub J M Op den Camp, Boran Kartal, Claudia Lueke, Laura van Niftrik
Methane is a very potent greenhouse gas and can be oxidized aerobically or anaerobically through microbial-mediated processes, thus decreasing methane emissions to the atmosphere. Using a complementary array of methods including phylogenetic analysis, physiological experiments, and light and electron microscopy techniques (including electron tomography), we investigated the community composition and ultrastructure of a continuous bioreactor enrichment culture, in which anaerobic methane oxidation (AOM) was coupled to nitrate reduction...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150077/unique-arginine-array-improves-cytosolic-localization-of-hydrocarbon-stapled-peptides
#2
Kim Quach, Jonathan LaRochelle, Xiao-Han Li, Elizabeth Rhoades, Alanna Schepartz
We have previously reported that miniature proteins containing a distinct array of 5 arginine residues on a folded α-helix - a penta-arg motif - traffic with high efficiency from endosomes into the cytosol and nucleus of mammalian cells. Here we evaluate whether a penta-arg motif can improve the intracellular trafficking of an otherwise impermeant hydrocarbon-stapled peptide, SAH-p53-4(Rho). We prepared a panel of SAH-p53-4(Rho) variants containing penta-arg sequences with different spacings and axial arrangement and evaluated their overall uptake (as judged by flow cytometry) and their intracellular access (as determined by fluorescence correlation spectroscopy, FCS)...
November 7, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29149812/architectures-and-mechanical-properties-of-drugs-and-complexes-of-surface-active-compounds-at-air-water-and-oil-water-interfaces
#3
Dipak K Sarker
BACKGROUND: Drugs can represents a multitude of compounds from proteins and peptides, such as growth hormones and insulin and on to simple organic molecules such as flurbiprofen, ibuprofen and lidocaine. Given the chemical nature of these compounds two features are always present. A portion or portions of the molecule that has little affinity for apolar surfaces and media and the opposite a series of part or one large part that has considerable affinity for hydrophilic, polar or charged media and surfaces...
November 17, 2017: Current Drug Discovery Technologies
https://www.readbyqxmd.com/read/29149347/signal-recognition-particle-binds-to-translating-ribosomes-before-emergence-of-a-signal-anchor-sequence
#4
Evan Mercier, Wolf Holtkamp, Marina V Rodnina, Wolfgang Wintermeyer
The bacterial signal recognition particle (SRP) is part of the machinery that targets ribosomes synthesizing membrane proteins to membrane-embedded translocons co-translationally. Recognition of nascent membrane proteins occurs by virtue of a hydrophobic signal-anchor sequence (SAS) contained in the nascent chain, usually at the N terminus. Here we use fluorescence-based stopped-flow to monitor SRP-ribosome interactions with actively translating ribosomes while an SRP substrate is synthesized and emerges from the peptide exit tunnel...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29148897/oxidative-stress-response-in-sh-sy5y-cells-exposed-to-short-term-1800%C3%A2-mhz-radiofrequency-radiation
#5
Ana Marija Marjanovic Cermak, Ivan Pavicic, Ivancica Trosic
The exact mechanism that could explain the effects of radiofrequency (RF) radiation exposure at non-thermal level is still unknown. Increasing evidence suggests a possible involvement of reactive oxygen species (ROS) and development of oxidative stress. To test the proposed hypothesis, human neuroblastoma cells (SH-SY5Y) were exposed to 1800 MHz short-term RF exposure for 10, 30 and 60 minutes. Electric field strength within Gigahertz Transverse Electromagnetic cell (GTEM) was 30 V m(-1) and specific absorption rate (SAR) was calculated to be 1...
November 17, 2017: Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering
https://www.readbyqxmd.com/read/29148818/dissociation-constants-of-cytochrome-p450-2c9-cytochrome-p450-reductase-complexes-in-a-lipid-bilayer-membrane-depend-on-nadph-a-single-protein-tracking-study
#6
Carlo Barnaba, Evan Taylor, James A Brozik
Cytochrome P450-Reductase (CPR) is a versatile NADPH-dependent electron donor located in the cytoplasmic side of the endoplasmic reticulum. It is an electron transferase that is able to deliver electrons to a variety of membrane-bound oxidative partners, including the drug-metabolizing enzymes of the cytochrome P450s (P450). CPR is also stoichiometrically limited compared to its oxidative counterparts and hypotheses have arisen about possible models that can overcome the stochiometric imbalance, including quaternary organization of P450 and diffusion-limited models...
November 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29148811/continuous-pore-spanning-lipid-bilayers-on-silicon-oxide-coated-porous-substrates
#7
Nelli Teske, Jeremias Sibold, Johannes Schumacher, Nikolas K Teiwes, Martin Gleisner, Ingo P Mey, Claudia Steinem
A number of techniques has been developed and analyzed in recent years to generate pore-spanning membranes (PSMs). While quite a number of methods rely on nanoporous substrates, only a few use micrometer-sized pores to be able to individually resolve suspending membranes by means of fluorescence microscopy. To be able to produce PSMs on pores that are micrometer in size, an orthogonal functionalization strategy resulting in a hydrophilic surface is highly desirable. Here, we report on a method to prepare PSMs based on the evaporation of a thin layer of silicon monoxide on top of the porous substrate...
November 17, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29148737/site-specific-one-to-one-click-coupling-of-single-proteins-to-individual-carbon-nanotubes-a-single-molecule-approach
#8
Mark Freeley, Harley Worthy, Rochelle Ahmed, Ben Bowen, Daniel Watkins, John Emyr Macdonald, Ming Zheng, Darran Dafydd Jones, Matteo Palma
We report the site-specific coupling of single proteins to individual carbon nanotubes (CNTs) in solution and with single-molecule control. Using an orthogonal Click reaction, Green Fluorescent Protein (GFP) was engineered to contain a genetically encoded azide group and then bound to CNT ends in different configurations: in close proximity or at longer distances from the GFP's functional centre. Atomic force microscopy and fluorescence analysis in solution and on surfaces at the single-protein level confirmed the importance of bioengineering optimal protein attachment sites to achieve direct protein-nanotube communication and bridging...
November 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29148725/chromophore-isomer-stabilization-is-critical-to-efficient-fluorescence-in-cyan-fluorescent-proteins
#9
Guillaume Gotthard, David von Stetten, Damien Clavel, Marjolaine Noirclerc-Savoye, Antoine Royant
ECFP, the first usable Cyan Fluorescent Protein, was obtained by adapting the tyrosine-based chromophore environment in Green Fluorescent Protein to that of a tryptophan-based one. This 1(st)-generation CFP was superseded by the popular Cerulean, CyPet and SCFP3A that were engineered by rational and random mutagenesis. Yet, the latter CFPs still exhibit suboptimal properties of pH sensitivity and reversible photobleaching behavior. These flaws were serendipitously corrected in the 3(rd)-generation CFP mTurquoise and its successors without obvi-ous rationale...
November 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/29148271/high-refractive-index-of-acrylate-embedding-resin-clarifies-mouse-brain-tissue
#10
Hongfu Zhou, Yumiao Xiong, Yu Wang, Xiaojun Wang, Pei Li, Yadong Gang, Xiuli Liu, Shaoqun Zeng
Biological tissue transparency combined with light-sheet fluorescence microscopy is a useful method for studying the neural structure of biological tissues. The development of light-sheet fluorescence microscopy also promotes progress in biological tissue clearing methods. The current clarifying methods mostly use liquid reagent to denature protein or remove lipids first, to eliminate or reduce the scattering index or refractive index of the biological tissue. However, denaturing protein and removing lipids require complex procedures or an extended time period...
November 2017: Journal of Biomedical Optics
https://www.readbyqxmd.com/read/29148254/connecting-color-with-assembly-in-the-fluorescent-b-phycoerythrin-protein-complex
#11
Aneika C Leney, Aline Tschanz, Albert J R Heck
Phycoerythrin is the major light-harvesting pigment protein in red algae and is nowadays widely used as a fluorescent probe in biotechnological applications such as flow cytometry and immunofluorescence microscopy. In addition, it has had substantial economic impact due to its potential as a natural food colorant. However, knowledge on the precise molecular composition of phycoerythrin is limited. Here, we use a combination of high resolution native mass spectrometry (MS) and fluorescence spectroscopy to characterize the assembly properties of the B-phycoerythrin protein complex from Porphyridium cruentum...
November 17, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29148176/differential-proteomic-analysis-reveals-protein-networks-and-pathways-that-may-contribute-to-helicobacter-pylori-fkbp-type-ppiase-associated-gastric-diseases
#12
Yanmei Zhu, Yuehua Gong, Aodi Li, Moye Chen, Dan Kang, Jun Liu, Yuan Yuan
PURPOSE: Though Helicobacter pylori (H. pylori) has been classified as class I carcinogen, key virulence factor generated by H. pylori that causes gastric cancer remains to be fully determined. Recently, we identified a gastric cancer-associated H. pylori gene, peptidylprolyl isomerase-FK506 binding protein (PPIase-FKBP), and showed that PPIase-FKBP was capable of inducing oncogenic transformation of gastric epithelial cells. But its mechanism was unclear. EXPERIMENTAL DESIGN: We carried out a comparative proteomic analysis of human gastric epithelial cells that either express PPIase-FKBP or green fluorescent protein (GFP) using two-dimensional (2-D) gel electrophoresis and then matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS/MS)...
November 16, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29148062/flagellar-incorporation-of-proteins-follows-at-least-two-different-routes-in-trypanosomes
#13
Laetitia Vincensini, Thierry Blisnick, Eloïse Bertiaux, Sebastian Hutchinson, Christina Georgikou, Cher-Pheng Ooi, Philippe Bastin
BACKGROUND INFORMATION: Eukaryotic cilia and flagella are sophisticated organelles composed of several hundreds of proteins that need to be incorporated at the right time and the right place during assembly. RESULTS: Two methods were used to investigate this process in the model protist Trypanosoma brucei: inducible expression of epitope-tagged labelled proteins and fluorescence recovery after photobleaching (FRAP) of fluorescent fusion proteins. This revealed that skeletal components of the radial spokes (RSP3), the central pair (PF16) and the outer dynein arms (DNAI1) are incorporated at the distal end of the growing flagellum...
November 16, 2017: Biology of the Cell
https://www.readbyqxmd.com/read/29147940/interaction-of-proteins-with-ionic-liquid-alcohol-and-dmso-and-in-situ-generation-of-gold-nano-clusters-in-a-cell
#14
REVIEW
Somen Nandi, Sridip Parui, Ritaban Halder, Biman Jana, Kankan Bhattacharyya
In this review, we give a brief overview on how the interaction of proteins with ionic liquids, alcohols and dimethyl sulfoxide (DMSO) influences the stability, conformational dynamics and function of proteins/enzymes. We present experimental results obtained from fluorescence correlation spectroscopy on the effect of ionic liquid or alcohol or DMSO on the size (more precisely, the diffusion constant) and conformational dynamics of lysozyme, cytochrome c and human serum albumin in aqueous solution. The interaction of ionic liquid with biomolecules (e...
November 16, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29147836/effects-of-saffron%C3%A2-and-its-constituents-%C3%A2-crocin-1-crocin-2-and-crocetin-on-%C3%AE-synuclein-fibrils
#15
Eiji Inoue, Yasuharu Shimizu, Ryo Masui, Tomomi Hayakawa, Tomoe Tsubonoya, Satoko Hori, Keiichi Sudoh
Saffron, the stigma of Crocus sativus Linné (Iridaceae family), has been known to inhibit aggregation of β-amyloid, a nerve tissue protein. α-Synuclein (αS) is a 140-amino acid protein found abundantly in various regions of the brain. Its abnormal aggregation and accumulation in nerve tissue are said to cause neurodegenerative diseases such as Parkinson's disease, Lewy body dementia, and multiple-system atrophy. This study (part of this study was presented at the 137th Annual Meeting of the Pharmaceutical Society of Japan) examined the effects of saffron, its constituents (crocin-1, crocin-2, crocetin, and safranal), and crocetin structural analogs (hexadecanedioic acid, norbixin, and trans, trans-muconic acid) on αS aggregation, and αS fibril dissociation...
November 17, 2017: Journal of Natural Medicines
https://www.readbyqxmd.com/read/29147545/protein-labeling-for-live-cell-fluorescence-microscopy-with-a-highly-photostable-renewable-signal
#16
Nina G Bozhanova, Mikhail S Baranov, Natalia V Klementieva, Karen S Sarkisyan, Alexey S Gavrikov, Ilia V Yampolsky, Elena V Zagaynova, Sergey A Lukyanov, Konstantin A Lukyanov, Alexander S Mishin
We present protein-PAINT - the implementation of the general principles of PAINT (Point Accumulation for Imaging in Nanoscale Topography) for live-cell protein labeling. Our method employs the specific binding of cell-permeable fluorogenic dyes to genetically encoded protein tags. We engineered three mutants of the bacterial lipocalin Blc that possess different affinities to a fluorogenic dye and exhibit a strong increase in fluorescence intensity upon binding. This allows for rapid labeling and washout of intracellular targets on a time scale from seconds to a few minutes...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29147537/fluorinated-molecular-beacons-as-functional-dna-nanomolecules-for-cellular-imaging
#17
Cheng Jin, Ting Fu, Ruowen Wang, Hui Liu, Jianmei Zou, Zilong Zhao, Mao Ye, Xiaobing Zhang, Weihong Tan
Molecular beacons (MBs) are simple, but practical, fluorescent nanoprobes widely used to detect small molecules, nucleic acids and proteins. However, some challenges still remain when MBs are employed in complex biological environments, such as instability and non-target interference. To meet such challenges, we have designed and synthesized fluorinated molecular beacons (FMBs) as functional DNA nanomolecules for cellular imaging, in which the stem sequence is simply composed of artificial nucleotides with 3,5-bis(trifluoromethyl)benzene (F) as the surrogate base of natural A, T, C and G bases...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29147526/a-ratiometric-fluorescent-probe-for-imaging-and-quantifying-anti-apoptotic-effects-of-gsh-under-temperature-stress
#18
Xiaoyue Han, Xinyu Song, Fabiao Yu, Lingxin Chen
Hypothermia and hyperthermia are cell stressed states resulting from environmental temperature changes, which can abnormally decrease intracellular glutathione (GSH) concentrations and induce apoptosis. As the most abundant intracellular non-protein biothiol, GSH can protect cells from apoptosis. Considering the important roles of GSH in the anti-apoptotic process in cells and in vivo, we strive to develop a powerful chemical tool for the direct detection of GSH concentration changes under temperature stress...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29147508/chiral-nanoprobes-for-targeting-and-long-term-imaging-of-the-golgi-apparatus
#19
Rong Sheng Li, Peng Fei Gao, Hong Zhi Zhang, Lin Ling Zheng, Chun Mei Li, Jian Wang, Yuan Fang Li, Feng Liu, Na Li, Cheng Zhi Huang
The Golgi apparatus is an essential subcellular organelle. Targeting and monitoring the Golgi change at the single-cell level over a long time scale are critical but are challenges that have not yet been tackled. Inspired by the precise Golgi positioning ability of galactosyltransferase and protein kinase D, due to their cysteine residues, we developed a method for long-term Golgi imaging. Fluorescent molecules, carbon quantum dots (CQDs) and silica nanoparticles could target the Golgi when they are modified with l-cysteine...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29147012/piperidylmethyloxychalcone-improves-immune-mediated-acute-liver-failure-via-inhibiting-tak1-activity
#20
Sun Hong Park, Jeong-Ah Kwak, Sang-Hun Jung, Byeongwoo Ahn, Won-Jea Cho, Cheong-Yong Yun, Chang Seon Na, Bang Yeon Hwang, Jin Tae Hong, Sang-Bae Han, Youngsoo Kim
Mice deficient in the toll-like receptor (TLR) or the myeloid differentiation factor 88 (MyD88) are resistant to acute liver failure (ALF) with sudden death of hepatocytes. Chalcone derivatives from medicinal plants protect from hepatic damages including ALF, but their mechanisms remain to be clarified. Here, we focused on molecular basis of piperidylmethyloxychalcone (PMOC) in the treatment of TLR/MyD88-associated ALF. C57BL/6J mice were sensitized with D-galactosamine (GalN) and challenged with Escherichia coli lipopolysaccharide (LPS, TLR4 agonist) or oligodeoxynucleotide containing unmethylated CpG motif (CpG ODN, TLR9 agonist) for induction of ALF...
November 17, 2017: Experimental & Molecular Medicine
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