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Pulse and chase

Jared T Hammill, Daniel C Scott, Jaeki Min, Michele C Connelly, Gloria Holbrook, Fangyi Zhu, Amy Matheny, Lei Yang, Bhuvanesh Singh, Brenda A Schulman, R Kiplin Guy
We previously discovered and validated a class of piperidinyl ureas that regulate defective in cullin neddylation 1 (DCN1)-dependent neddylation of cullins. Here, we report preliminary structure-activity relationship studies aimed at advancing our high-throughput screen hit into a tractable tool compound for dissecting the effects of acute DCN1-UBE2M inhibition on the NEDD8/cullin pathway. Structure-enabled optimization led to a 100-fold increase in biochemical potency and modestly increased solubility and permeability as compared to our initial hit...
March 16, 2018: Journal of Medicinal Chemistry
Alden Curtis, Chase Calvi, James Tinsley, Reed Hollinger, Vural Kaymak, Alexander Pukhov, Shoujun Wang, Alex Rockwood, Yong Wang, Vyacheslav N Shlyaptsev, Jorge J Rocca
Nuclear fusion is regularly created in spherical plasma compressions driven by multi-kilojoule pulses from the world's largest lasers. Here we demonstrate a dense fusion environment created by irradiating arrays of deuterated nanostructures with joule-level pulses from a compact ultrafast laser. The irradiation of ordered deuterated polyethylene nanowires arrays with femtosecond pulses of relativistic intensity creates ultra-high energy density plasmas in which deuterons (D) are accelerated up to MeV energies, efficiently driving D-D fusion reactions and ultrafast neutron bursts...
March 14, 2018: Nature Communications
Cheryl Q E Lee, Margherita Turco, Lucy Gardner, Benjamin Simons, Myriam Hemberger, Ashley Moffett
During pregnancy the trophoblast cells of the placenta are the only fetal cells in direct contact with maternal blood and decidua. Their functions include transport of nutrients and oxygen, secretion of pregnancy hormones, remodelling the uterine arteries, and communicating with maternal cells. Despite the importance of trophoblast cells in placental development and successful pregnancy, little is known about the identity, location and differentiation of human trophoblast progenitors. We identify a proliferative trophoblast niche at the base of the cytotrophoblast cell columns in first trimester placentas that is characterised by integrin α2 (ITGA2) expression...
March 14, 2018: Development
Anwar S Shatil, Md Nasir Uddin, Kant M Matsuda, Chase R Figley
Purpose: Postmortem MRI can be used to reveal important pathologies and establish radiology-pathology correlations. However, quantitative MRI values are altered by tissue fixation. Therefore, the purpose of this study was to investigate time-dependent effects of formalin fixation on MRI relaxometry (T1 and T2 ), diffusion tensor imaging (fractional anisotropy, FA; and mean diffusivity, MD), and myelin water fraction (MWF) measurements throughout intact human brain specimens. Methods: Two whole, neurologically-healthy human brains were immersed in 10% formalin solution and scanned at 13 time points between 0 and 1,032 h...
2018: Frontiers in Medicine
Deepak B Thimiri Govinda Raj, Niamat Ali Khan
In this article, we elaborate the application of thermal decomposition based synthesis of Fe3 O4 superparamagnetic nanoparticle (SPMNP) in subcellular fractionation context. Here, we performed surface functionalization of SPMNP with phospholipids and dimercaptosuccinic acid. Surprisingly, we observed surface functionalization dependent SPMNP localization in subcellular compartments such as plasma membrane, endosomes and lysosomes. By using SPMNP based subcellular localization with pulse-chase methodology, we could use SPMNP for high pure-high yield organelle (plasma membrane, endosomes and lysosome) fractionation...
2018: Nano Convergence
Yu Liu, Kun Miao, Yinghao Li, Matthew Fares, Shuyuan Chen, Xin Zhang
Protein homeostasis, or proteostasis, is essential for cellular fitness and viability. Many environmental factors compromise proteostasis, induce global proteome stress, and cause diseases. Proteome stress sensor is a powerful tool to dissect the mechanism of cellular stress and find therapeutics that ameliorate these diseases. In this work, we present a multi-color HaloTag-based sensor (named AgHalo) to visualize and quantify proteome stresses in live cells. The current AgHalo sensor is equipped with three fluorogenic probes that turn on fluorescence when the sensor forms either soluble oligomers or insoluble aggregates upon exposure to stress conditions, both in vitro and in cellulo...
February 23, 2018: Biochemistry
Mohammad Chegeni, Mahdi Amiri, Buford L Nichols, Hassan Y Naim, Bruce R Hamaker
Dietary starch is finally converted to glucose for absorption by the small intestine mucosal α-glucosidases (sucrase-isomaltase [SI] and maltase-glucoamylase), and control of this process has health implications. Here, the molecular mechanisms were analyzed associated with starch-triggered maturation and transport of SI. Biosynthetic pulse-chase in Caco-2 cells revealed that the high MW SI species (265 kDa) induced by maltose (an α-amylase starch digestion product) had a higher rate of early trafficking and maturation compared with a glucose-induced SI (245 kDa)...
February 20, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Jean-Marie Volland, Arno Schintlmeister, Helena Zambalos, Siegfried Reipert, Patricija Mozetič, Salvador Espada-Hinojosa, Valentina Turk, Michael Wagner, Monika Bright
The giant colonial ciliate Zoothamnium niveum harbors a monolayer of the gammaproteobacteria Cand. Thiobios zoothamnicoli on its outer surface. Cultivation experiments revealed maximal growth and survival under steady flow of high oxygen and low sulfide concentrations. We aimed at directly demonstrating the sulfur-oxidizing, chemoautotrophic nature of the symbionts and at investigating putative carbon transfer from the symbiont to the ciliate host. We performed pulse-chase incubations with 14C- and 13C-labeled bicarbonate under varying environmental conditions...
February 9, 2018: ISME Journal
Fang Cheng, Lars-Åke Fransson, Katrin Mani
Import of the polyamine spermine from the extracellular environment depends on the presence of cell surface heparan sulfate proteoglycans, such as glypican-1. This proteoglycan is internalized by endocytosis, releases its heparan sulfate chains in endosomes by a nitric oxide-, copper- and amyloid precursor protein-dependent mechanism, then penetrates the membrane and is transported to the nucleus and then to autophagosomes. This process is spontaneous or induced by ascorbate depending on the growth-state of the cell...
February 2, 2018: Experimental Cell Research
Eri Kitamura, Tomonori Kotajima, Ken Sawada, Iwane Suzuki, Yoshihiro Shiraiwa
The cosmopolitan marine haptophyte alga Emiliania huxleyi accumulates very long-chain (C37-C40) alkyl ketones with two to four trans-type carbon-carbon double bonds (alkenones). These compounds are used as biomarkers of haptophytes and as palaeothermometers for estimating sea-surface temperatures in biogeochemistry. However, the biosynthetic pathway of alkenones in algal cells remains enigmatic, although it is well known that the C37 tri-unsaturated alkenone (K37:3) becomes dominant at low temperatures, either by desaturation of K37:2 or by a separate pathway involving the elongation of tri-unsaturated alkenone precursors...
February 2, 2018: Scientific Reports
Lu Zhou, Minoas Evangelinos, Valentin Wernet, Antonia F Eckert, Yuji Ishitsuka, Reinhard Fischer, G Ulrich Nienhaus, Norio Takeshita
Polarized growth of filamentous fungi requires continuous transport of biomolecules to the hyphal tip. To this end, construction materials are packaged in vesicles and transported by motor proteins along microtubules and actin filaments. We have studied these processes with quantitative superresolution localization microscopy of live Aspergillus nidulans cells expressing the photoconvertible protein mEosFPthermo fused to the chitin synthase ChsB. ChsB is mainly located at the Spitzenkörper near the hyphal tip and produces chitin, a key component of the cell wall...
January 2018: Science Advances
Paul C Guest
Pulse-chase radiolabeling of cells with radioactive amino acids is a common method for studying the biosynthesis of proteins. The labeled proteins can then be immunoprecipitated and analyzed by electrophoresis and gel imaging techniques. This chapter presents a protocol for the biosynthetic labeling and immunoprecipitation of pancreatic islet proteins which are known to be affected in disorders such as diabetes, obesity, and metabolic syndrome.
2018: Methods in Molecular Biology
Chris H Wilson, Michael S Strickland, Jack A Hutchings, Thomas S Bianchi, S Luke Flory
Despite the large contribution of rangeland and pasture to global soil organic carbon (SOC) stocks, there is considerable uncertainty about the impact of large herbivore grazing on SOC, especially for understudied subtropical grazing lands. It is well known that root system inputs are the source of most grassland SOC, but the impact of grazing on partitioning of carbon allocation to root tissue production compared to fine root exudation is unclear. Given that different forms of root C have differing implications for SOC synthesis and decomposition, this represents a significant gap in knowledge...
January 27, 2018: Global Change Biology
A H Reid, X Shen, P Maldonado, T Chase, E Jal, P W Granitzka, K Carva, R K Li, J Li, L Wu, T Vecchione, T Liu, Z Chen, D J Higley, N Hartmann, R Coffee, J Wu, G L Dakovski, W F Schlotter, H Ohldag, Y K Takahashi, V Mehta, O Hellwig, A Fry, Y Zhu, J Cao, E E Fullerton, J Stöhr, P M Oppeneer, X J Wang, H A Dürr
Magnetostriction, the strain induced by a change in magnetization, is a universal effect in magnetic materials. Owing to the difficulty in unraveling its microscopic origin, it has been largely treated phenomenologically. Here, we show how the source of magnetostriction-the underlying magnetoelastic stress-can be separated in the time domain, opening the door for an atomistic understanding. X-ray and electron diffraction are used to separate the sub-picosecond spin and lattice responses of FePt nanoparticles...
January 26, 2018: Nature Communications
Martin Whitham, Benjamin L Parker, Martin Friedrichsen, Janne R Hingst, Marit Hjorth, William E Hughes, Casey L Egan, Lena Cron, Kevin I Watt, Rhiannon P Kuchel, Navind Jayasooriah, Emma Estevez, Tim Petzold, Catherine M Suter, Paul Gregorevic, Bente Kiens, Erik A Richter, David E James, Jørgen F P Wojtaszewski, Mark A Febbraio
Exercise stimulates the release of molecules into the circulation, supporting the concept that inter-tissue signaling proteins are important mediators of adaptations to exercise. Recognizing that many circulating proteins are packaged in extracellular vesicles (EVs), we employed quantitative proteomic techniques to characterize the exercise-induced secretion of EV-contained proteins. Following a 1-hr bout of cycling exercise in healthy humans, we observed an increase in the circulation of over 300 proteins, with a notable enrichment of several classes of proteins that compose exosomes and small vesicles...
January 9, 2018: Cell Metabolism
Jaume Amengual, Liang Guo, Alanna Strong, Julio Madrigal-Matute, Haizhen Wang, Susmita Kaushik, Jeffrey L Brodsky, Daniel J Rader, Ana Maria Cuervo, Edward A Fisher
RATIONALE: Genome-wide association studies identified single-nucleotide polymorphisms near the SORT1 locus strongly associated with decreased plasma LDL-C (low-density lipoprotein cholesterol) levels and protection from atherosclerotic cardiovascular disease and myocardial infarction. The minor allele of the causal SORT1 single-nucleotide polymorphism locus creates a putative C/EBPα (CCAAT/enhancer-binding protein α)-binding site in the SORT1 promoter, thereby increasing in homozygotes sortilin expression by 12-fold in liver, which is rich in this transcription factor...
February 16, 2018: Circulation Research
Yoshimi Kanie, Mizuki Taniuchi, Osamu Kanie
Pulse chase analysis is often used in investigating dynamics of cellular substances. Fluorescently labeled lactosyl sphingosine molecule is useful in chasing its transformation, however the analysis of such metabolites in attomole level is of extreme difficult due to the presence of large amount of endogenous amphiphilic molecules such as glycosphingolipids, sphingomyerin, and glycerophospholipids. Nano LC suites for analyzing the attomole scale metabolites, therefore removal of endogenous substances prior to nano LC and finding appropriate nano LC conditions are necessary...
December 23, 2017: Journal of Chromatography. A
K Moubri, J Kleuskens, J Van de Crommert, N Scholtes, T Van Kasteren, S Delbecq, B Carcy, E Précigout, A Gorenflot, Th Schetters
Soluble parasite antigens (SPA) in supernatants of in vitro cultures of Babesia canis can be used to vaccinate dogs against virulent B. canis infection. The moment that immunity becomes apparent coincides with the appearance of antibodies against SPA in the serum of the vaccinated animals. This so-called vaccination-challenge serum (VC-serum) was used to precipitate antigens from B. canis culture supernatants in agarose gels. This antigen preparation was then used to analyse the reactivity of sera from vaccinated dogs on western blots...
January 15, 2018: Veterinary Parasitology
Alexander Lubsch, Klaas Timmermans
Dissolved inorganic phosphorus (DIP) is an essential macronutrient for maintaining metabolism and growth in autotrophs. Little is known about DIP-uptake kinetics and internal P-storage capacity in seaweeds, such as Ulva lactuca (Chlorophyta). Ulva lactuca is a promising candidate for biofiltration purposes and mass commercial cultivation. We exposed U. lactuca to a wide range of DIP concentrations (1 - 50 μmol · L-1 ) and a non-limiting concentration of dissolved inorganic nitrogen (DIN; 5000 μmol · L-1 ) under fully controlled laboratory conditions in a 'pulse-and-chase' assay over 10 days...
December 14, 2017: Journal of Phycology
Thomas D Baird, J Robert Hogg
Cellular mRNA levels are determined by the competing forces of transcription and decay. A wide array of cellular mRNA decay pathways carry out RNA turnover either on a constitutive basis or in response to changing cellular conditions. Here, we outline a method to investigate mRNA decay that employs RNAi knockdown of known or putative decay factors in commercially available Tet-off cell systems. Reporter mRNAs of interest are expressed under the control of a tetracycline-regulated promoter, allowing pulse-chase mRNA decay assays to be conducted...
2018: Methods in Molecular Biology
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