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https://www.readbyqxmd.com/read/28927140/itraq-coupled-2d-lc-ms-ms-analysis-of-cxcr7-transfected-papillary-thyroid-carcinoma-cells-a-new-insight-into-cxcr7-regulation-of-papillary-thyroid-carcinoma-progression-and-identification-of-potential-biomarkers
#1
Hengwei Zhang, Lei Yang, Zhangyi Liu, Chenxi Liu, Xuyong Teng, Lei Zhang, Bo Yin, Zhen Liu
Previous studies have demonstrated that C-X-C chemokine receptor type 7 (CXCR7) regulates papillary thyroid carcinoma (PTC) growth and metastasis; however, the molecular mechanisms underlying this regulation remain unclear. In the present study, the protein expression profiles of the PTC cell line GLAG-66 and GLAG-66 cells stably transfected with CXCR7 cDNA were analyzed and compared using isobaric tag for relative and absolute quantification-coupled two-dimensional liquid chromatography-tandem mass spectrometry...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28926974/block-v-rtx-domain-of-adenylate-cyclase-from-bordetella-pertussis-a-conformationally-dynamic-scaffold-for-protein-engineering-applications
#2
REVIEW
Beyza Bulutoglu, Scott Banta
The isolated Block V repeats-in-toxin (RTX) peptide domain of adenylate cyclase (CyaA) from Bordetella pertussis reversibly folds into a β-roll secondary structure upon calcium binding. In this review, we discuss how the conformationally dynamic nature of the peptide is being engineered and employed as a switching mechanism to mediate different protein functions and protein-protein interactions. The peptide has been used as a scaffold for diverse applications including: a precipitation tag for bioseparations, a cross-linking domain for protein hydrogel formation and as an alternative scaffold for biomolecular recognition applications...
September 17, 2017: Toxins
https://www.readbyqxmd.com/read/28926941/why-ubiquitin-has-not-evolved
#3
Douglas C Allan, James C Phillips
Ubiquitin, discovered less than 50 years ago, tags thousands of diseased proteins for destruction. It is small (only 76 amino acids), and is found unchanged in mammals, birds, fish, and even worms, indicating that ubiquitin is perfect. Key features of its functionality are identified here using critical point thermodynamic scaling theory. These include synchronized pivots and hinges, a stabilizing central pivot, and Fano interference between first- and second-order elements of correlated long-range (allosteric) globular surface shape transitions...
September 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28926241/supramolecular-chemistry-targeting-proteins
#4
Sam van Dun, Christian Ottmann, Lech-Gustav Milroy, Luc Brunsveld
The specific recognition of protein surface elements is a fundamental challenge in the life sciences. New developments in this field will form the basis of new therapeutic approaches and will lead to applications such as sensors, affinity-tags, immobilization techniques and protein-based materials. Synthetic supramolecular molecules and materials are creating new opportunities for protein recognition, which are orthogonal to classical small molecule and protein-based approaches. As outlined here, their unique molecular features enable the recognition of amino acids, peptides and even whole protein surfaces, which can be applied to the modulation and assembly of proteins...
September 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28925997/precision-annotation-of-digital-samples-in-ncbi-s-gene-expression-omnibus
#5
Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D Azad, Mohamad O Hadied, Shuaib Raza, Benjamin Abhishek Rayikanti, Bin Chen, Hyojung Paik, Dvir Aran, Jordan Spatz, Daniel Himmelstein, Maryam Panahiazar, Sanchita Bhattacharya, Marina Sirota, Mark A Musen, Atul J Butte
The Gene Expression Omnibus (GEO) contains more than two million digital samples from functional genomics experiments amassed over almost two decades. However, individual sample meta-data remains poorly described by unstructured free text attributes preventing its largescale reanalysis. We introduce the Search Tag Analyze Resource for GEO as a web application (http://STARGEO.org) to curate better annotations of sample phenotypes uniformly across different studies, and to use these sample annotations to define robust genomic signatures of disease pathology by meta-analysis...
September 19, 2017: Scientific Data
https://www.readbyqxmd.com/read/28924696/guidelines-for-quality-control-of-pet-ct-scans-in-a-multicenter-clinical-study
#6
Ivalina Hristova, Ronald Boellaard, Paul Galette, Lalitha K Shankar, Yan Liu, Sigrid Stroobants, Otto S Hoekstra, Wim J G Oyen
To date, there is no published detailed checklist with parameters referencing the DICOM tag information with respect to the quality control (QC) of PET/CT scans. The aims of these guidelines are to provide the know-how for effectively controlling the quality of PET/CT scans in multicenter studies, to standardize the QC, to give sponsors and regulatory agencies a basis for justification of the data quality when using standardized uptake values as an imaging biomarker, to document the compliance with the imaging guidelines, to verify the per protocol population versus intent to treat population, and to safeguard the validity of multicenter study conclusions employing standardized uptake value (SUV) as an imaging biomarker which is paramount to the scientific community...
September 18, 2017: EJNMMI Physics
https://www.readbyqxmd.com/read/28924668/synthesis-of-janelia-fluor-halotag-and-snap-tag-ligands-and-their-use-in-cellular-imaging-experiments
#7
Jonathan B Grimm, Timothy A Brown, Brian P English, Timothée Lionnet, Luke D Lavis
The development of genetically encoded self-labeling protein tags such as the HaloTag and SNAP-tag has expanded the utility of chemical dyes in microscopy. Intracellular labeling using these systems requires small, cell-permeable dyes with high brightness and photostability. We recently discovered a general method to improve the properties of classic fluorophores by replacing N,N-dimethylamino groups with four-membered azetidine rings to create the "Janelia Fluor" dyes. Here, we describe the synthesis of the HaloTag and SNAP-tag ligands of Janelia Fluor 549 and Janelia Fluor 646 as well as standard labeling protocols for use in ensemble and single-molecule cellular imaging...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28924664/two-color-single-molecule-tracking-in-live-cells
#8
Siegfried Hänselmann, Dirk-Peter Herten
Measuring the kinetics of protein-protein interactions between molecules in the plasma membrane of live cells provides valuable information for understanding dynamic processes, like cellular signaling, on a molecular scale. Two-color single-molecule tracking is a fluorescence microscopy-based method to detect and quantify specific protein-protein interactions on a single-event level, providing sensitivity to heterogeneities and rare events. Fundamentally, it allows following the movement of single molecules of two different protein species in live cells with a localization precision beyond the diffraction limit of light in real time...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28924659/sted-imaging-of-golgi-dynamics-with-cer-sir-a-two-component-photostable-high-density-lipid-probe-for-live-cells
#9
Roman S Erdmann, Derek Toomre, Alanna Schepartz
Long time-lapse super-resolution imaging in live cells requires a labeling strategy that combines a bright, photostable fluorophore with a high-density localization probe. Lipids are ideal high-density localization probes, as they are >100 times more abundant than most membrane-bound proteins and simultaneously demark the boundaries of cellular organelles. Here, we describe Cer-SiR, a two-component, high-density lipid probe that is exceptionally photostable. Cer-SiR is generated in cells via a bioorthogonal reaction of two components: a ceramide lipid tagged with trans-cyclooctene (Cer-TCO) and a reactive, photostable Si-rhodamine dye (SiR-Tz)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28924654/super-resolution-microscopy-techniques-and-their-potential-for-applications-in-radiation-biophysics
#10
Jan Philipp Eberle, Alexander Rapp, Matthias Krufczik, Marion Eryilmaz, Manuel Gunkel, Holger Erfle, Michael Hausmann
Fluorescence microscopy is an essential tool for imaging tagged biological structures. Due to the wave nature of light, the resolution of a conventional fluorescence microscope is limited laterally to about 200 nm and axially to about 600 nm, which is often referred to as the Abbe limit. This hampers the observation of important biological structures and dynamics in the nano-scaled range ~10 nm to ~100 nm. Consequentially, various methods have been developed circumventing this limit of resolution. Super-resolution microscopy comprises several of those methods employing physical and/or chemical properties, such as optical/instrumental modifications and specific labeling of samples...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28924458/control-of-nuclear-cytoplasmic-shuttling-of-ankrd54-by-pkc%C3%AE
#11
Amy L Samuels, Alison Louw, Reza Zareie, Evan Ingley
AIM: To identify and characterize the effect of phosphorylation on the subcellular localization of Ankrd54. METHODS: HEK293T cells were treated with calyculin A, staurosporin or phorbol 12-myristate 13-acetate (PMA). Cells were transfected with eGFP-tagged Ankrd54 with or without Lyn tyrosine kinase (wild-type, Y397F mutant, or Y508F mutant). The subcellular localization was assessed by immunofluorescence imaging of cells, immunoblotting of subcellular fractionations...
August 26, 2017: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28924207/novel-ecto-tagged-integrins-reveal-their-trafficking-in-live-cells
#12
Clotilde Huet-Calderwood, Felix Rivera-Molina, Daniel V Iwamoto, Emil B Kromann, Derek Toomre, David A Calderwood
Integrins are abundant heterodimeric cell-surface adhesion receptors essential in multicellular organisms. Integrin function is dynamically modulated by endo-exocytic trafficking, however, major mysteries remain about where, when, and how this occurs in living cells. To address this, here we report the generation of functional recombinant β1 integrins with traceable tags inserted in an extracellular loop. We demonstrate that these 'ecto-tagged' integrins are cell-surface expressed, localize to adhesions, exhibit normal integrin activation, and restore adhesion in β1 integrin knockout fibroblasts...
September 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28924142/the-role-of-social-status-and-testosterone-in-human-conspicuous-consumption
#13
Yin Wu, Christoph Eisenegger, Niro Sivanathan, Molly J Crockett, Luke Clark
Conspicuous consumption refers to the phenomenon where individuals purchase goods for signalling social status, rather than for its inherent functional value. This study (n = 166 male participants) investigated how the outcome of a social competition influenced conspicuous consumption, and its association with competition-induced testosterone reactivity. Winning a competition increased both explicit and implicit preferences for higher-status vs. lower-status products, using both natural stimuli (prestigious cars) and laboratory-tagged stimuli of matched value (university T-shirts)...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28924045/interaction-between-repressor-opi1p-and-er-membrane-protein-scs2p-facilitates-transit-of-phosphatidic-acid-from-the-er-to-mitochondria-and-is-essential-for-ino1-gene-expression-in-the-presence-of-choline
#14
Maria L Gaspar, Yu-Fang Chang, Stephen A Jesch, Manuel Aregullin, Susan A Henry
In the yeast Saccharomyces cerevisiae, the Opi1p repressor controls the expression of INO1 via the Opi1p/Ino2p-Ino4p regulatory circuit. Inositol depletion favors Opi1p interaction with both Scs2p and phosphatidic acid at the ER membrane. Inositol supplementation, however, favors the translocation of Opi1p from the ER into the nucleus where it interacts with the Ino2p-Ino4p complex, attenuating transcription of INO1. A strain devoid of Scs2p (scs2) and a mutant, OPI1FFAT, lacking the ability to interact with Scs2p were utilized to examine the specific role(s) of the Opi1p-Scs2p interaction in the regulation of INO1 expression and overall lipid metabolism...
September 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28924015/no-mediates-nitrite-sensing-and-adaptation-and-triggers-a-remodeling-of-lipids
#15
Lina J Dolch, Josselin Lupette, Guillaume Tourcier, Mariette Bedhomme, Séverine Collin, Leonardo Magneschi, Melissa Conte, Khawla Seddiki, Christelle Richard, Erwan Corre, Laurent Fourage, Frédéric Laeuffer, Robert Richards, Michael Reith, Fabrice Rébeillé, Juliette Jouhet, Patrick McGinn, Eric Marechal
Nitric oxide (NO) is an intermediate of the nitrogen cycle, an industrial pollutant and a marker of climate change. NO also acts as a gaseous transmitter in a variety of biological processes. The impact of environmental NO needs to be addressed. In diatoms, a dominant phylum in phytoplankton, NO was reported to mediate programmed cell death (PCD) in response to diatom derived polyunsaturated aldehydes. Here, using the Phaeodactylum Pt1 strain, 2E,4E-decadienal supplied in the micromolar concentration range led to a non-specific cell toxicity...
September 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28923894/h-ipse-is-a-pathogen-secreted-host-nucleus-infiltrating-protein-infiltrin-expressed-exclusively-by-the-schistosoma-haematobium-egg-stage
#16
Luke F Pennington, Abdulaziz Alouffi, Evaristus C Mbanefo, Debalina Ray, David M Heery, Theodore S Jardetzky, Michael H Hsieh, Franco H Falcone
Urogenital schistosomiasis, caused by the parasitic trematode Schistosoma haematobium, affects over 112 million people worldwide. As with S. mansoni infections, the pathology in urogenital schistosomiasis is mainly related to the egg stage, which induces granulomatous inflammation of affected tissues. Schistosoma eggs and their secretions have been studied extensively for the related S. mansoni organism which is more amenable to laboratory studies. Indeed, we have shown that IPSE/alpha-1 (M-IPSE herein), a major protein secreted from S ...
September 18, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28923880/impact-of-liver-fat-on-the-differential-partitioning-of-hepatic-triacylglycerol-into-vldl-subclasses-on-high-and-low-sugar-diets
#17
A Margot Umpleby, Fariba Shojaee-Moradie, Barbara Fielding, Xuefei Li, Andrea Marino, Najlaa Alsini, Cheryl Isherwood, Nicola Jackson, Aryati Ahmad, Michael Stolinski, Julie Anne Lovegrove, Sigurd Johnsen, Jeewaka Mendis, John Wright, Malgorzata E Wilinska, Roman Hovorka, Jimmy Bell, Louise E Thomas, Gary Frost, Bruce Arthur Griffin
Dietary sugars are linked to the development of non-alcoholic fatty liver disease (NAFLD) and dyslipidaemia, but it is unknown if NAFLD itself influences the effects of sugars on plasma lipoproteins. To study this further, men with NAFLD (n=11) and low liver fat 'controls' (n= 14) were fed two iso-energetic diets, high or low in sugars (26% or 6% total energy) for 12 weeks, in a randomised, cross-over design. Fasting plasma lipid and lipoprotein kinetics were measured after each diet by stable isotope trace-labelling...
September 18, 2017: Clinical Science (1979-)
https://www.readbyqxmd.com/read/28923082/characterization-of-a-secreted-cystatin-of-the-parasitic-nematode-haemonchus-contortus-and-its-immune-modulatory-effect-on-goat-monocytes
#18
Yujian Wang, Lingyan Wu, Xinchao Liu, Shuai Wang, Muhammad Ehsan, RuoFeng Yan, XiaoKai Song, LiXin Xu, XiangRui Li
BACKGROUND: Haemonchosis is a disease of the small ruminant caused by a nematode parasite Haemonchus contortus, and it is most important and alarming challenges to the small ruminant's production. The infection of the H. contortus could cause high economic losses worldwide. H. contortus is a blood feeding parasite which penetrates into the abomasal mucosa to feed the blood of the host and causing the anemia and decreased total plasma protein. Modulation and suppression of the immune response of the host by nematode parasites have been reported extensively, and the cysteine protease inhibitor (cystatin) is identified as one of the major immunomodulators...
September 18, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28923010/the-role-of-the-two-component-systems-cpx-and-arc-in-protein-alterations-upon-gentamicin-treatment-in-escherichia-coli
#19
Emina Ćudić, Kristin Surmann, Gianna Panasia, Elke Hammer, Sabine Hunke
BACKGROUND: The aminoglycoside antibiotic gentamicin was supposed to induce a crosstalk between the Cpx- and the Arc-two-component systems (TCS). Here, we investigated the physical interaction of the respective TCS components and compared the results with their respective gene expression and protein abundance. The findings were interpreted in relation to the global proteome profile upon gentamicin treatment. RESULTS: We observed specific interaction between CpxA and ArcA upon treatment with the aminoglycoside gentamicin using Membrane-Strep-tagged protein interaction experiments (mSPINE)...
September 18, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28922409/purification-and-characterisation-of-the-yeast-plasma-membrane-atp-binding-cassette-transporter-pdr11p
#20
Katrine Rude Laub, Magdalena Marek, Lyubomir Dimitrov Stanchev, Sara Abad Herrera, Tamara Kanashova, Adèle Bourmaud, Gunnar Dittmar, Thomas Günther Pomorski
The ATP binding cassette (ABC) transporters Pdr11p and its paralog Aus1p are expressed under anaerobic growth conditions at the plasma membrane of the yeast Saccharomyces cerevisiae and are required for sterol uptake. However, the precise mechanism by which these ABC transporters facilitate sterol movement is unknown. In this study, an overexpression and purification procedure was developed with the aim to characterise the Pdr11p transporter. Engineering of Pdr11p variants fused at the C terminus with green fluorescent protein (Pdr11p-GFP) and containing a FLAG tag at the N terminus facilitated expression analysis and one-step purification, respectively...
2017: PloS One
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