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https://www.readbyqxmd.com/read/28288157/modelling-t-cell-proliferation-dynamics-heterogeneity-depending-on-cell-differentiation-age-and-genetic-background
#1
Julien Vibert, Véronique Thomas-Vaslin
Cell proliferation is the common characteristic of all biological systems. The immune system insures the maintenance of body integrity on the basis of a continuous production of diversified T lymphocytes in the thymus. This involves processes of proliferation, differentiation, selection, death and migration of lymphocytes to peripheral tissues, where proliferation also occurs upon antigen recognition. Quantification of cell proliferation dynamics requires specific experimental methods and mathematical modelling...
March 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28272897/magnetic-switching-in-granular-fept-layers-promoted-by-near-field-laser-enhancement
#2
Patrick W Granitzka, Emmanuelle Jal, Loïc Le Guyader, Matteo Savoini, Daniel J Higley, Tianmin Liu, Zhao Chen, Tyler Chase, Hendrik Ohldag, Georgi L Dakovski, William F Schlotter, Sebastian Carron, Matthias C Hoffman, Alexander X Gray, Padraic Shafer, Elke Arenholz, Olav Hellwig, Virat Mehta, Yukiko K Takahashi, Jian Wang, Eric E Fullerton, Joachim Stöhr, Alexander H Reid, Hermann A Dürr
Light-matter interaction at the nanoscale in magnetic materials is a topic of intense research in view of potential applications in next-generation high-density magnetic recording. Laser-assisted switching provides a pathway for overcoming the material constraints of high-anisotropy and high-packing density media, though much about the dynamics of the switching process remains unexplored. We use ultrafast small-angle X-ray scattering at an X-ray free-electron laser to probe the magnetic switching dynamics of FePt nanoparticles embedded in a carbon matrix following excitation by an optical femtosecond laser pulse...
March 17, 2017: Nano Letters
https://www.readbyqxmd.com/read/28250203/microprocessor-dynamics-shows-co-and-post-transcriptional-processing-of-pri-mirnas
#3
Annita Louloupi, Evgenia Ntini, Julia Liz, Ulf Andersson Ørom
miRNAs are small regulatory RNAs involved in the regulation of translation of target transcripts. miRNA biogenesis is a multi-step process starting with the cleavage of the primary miRNA transcript in the nucleus by the Microprocessor complex. Endogenous processing of pri-miRNAs is challenging to study and the in vivo kinetics of this process is not known. Here, we present a method for determining the processing kinetics of pri-miRNAs within intact cells over time using a pulse-chase approach to label transcribed RNA during 15 minutes and follow the processing within a 1-hour window after labeling with bromouridine...
March 1, 2017: RNA
https://www.readbyqxmd.com/read/28219720/lipidomics-in-research-on-yeast-membrane-lipid-homeostasis
#4
Anton I P M de Kroon
Mass spectrometry is increasingly used in research on membrane lipid homeostasis, both in analyses of the steady state lipidome at the level of molecular lipid species, and in pulse-chase approaches employing stable isotope-labeled lipid precursors addressing the dynamics of lipid metabolism. Here my experience with, and view on mass spectrometry-based lipid analysis is presented, with emphasis on aspects of quantification of membrane lipid composition of the yeast Saccharomyces cerevisiae. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein...
February 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28205173/measurement-of-mitochondrial-cholesterol-import-using-a-mitochondria-targeted-cyp11a1-fusion-construct
#5
Barry E Kennedy, Mark Charman, Barbara Karten
All animal membranes require cholesterol as an essential regulator of biophysical properties and function, but the levels of cholesterol vary widely among different subcellular compartments. Mitochondria, and in particular the inner mitochondrial membrane, have the lowest levels of cholesterol in the cell. Nevertheless, mitochondria need cholesterol for membrane maintenance and biogenesis, as well as oxysterol, steroid, and hepatic bile acid production. Alterations in mitochondrial cholesterol have been associated with a range of pathological conditions, including cancer, hepatosteatosis, cardiac ischemia, Alzheimer's, and Niemann-Pick Type C Disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28193451/prolonged-pharmacological-inhibition-of-cathepsin-c-results-in-elimination-of-neutrophil-serine-proteases
#6
Carla Guarino, Yveline Hamon, Cécile Croix, Anne-Sophie Lamort, Sandrine Dallet-Choisy, Sylvain Marchand-Adam, Adam Lesner, Thomas Baranek, Marie-Claude Viaud-Massuard, Conni Lauritzen, John Pedersen, Nathalie Heuzé-Vourc'h, Mustapha Si-Tahar, Erhan Fıratlı, Dieter E Jenne, Francis Gauthier, Marshall S Horwitz, Niels Borregaard, Brice Korkmaz
Cathepsin C (CatC) is a tetrameric cysteine dipeptidyl aminopeptidase that plays a key role in activation of pro-inflammatory serine protease zymogens by removal of a N-terminal pro-dipeptide sequence. Loss of function mutations in the CatC gene is associated with lack of immune cell serine protease activities and cause Papillon-Lefèvre syndrome (PLS). Also, only very low levels of elastase-like protease zymogens are detected by proteome analysis of neutrophils from PLS patients. Thus, CatC inhibitors represent new alternatives for the treatment of neutrophil protease-driven inflammatory or autoimmune diseases...
February 11, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28160404/evaluating-flow-cytometer-performance-with-weighted-quadratic-least-squares-analysis-of-led-and-multi-level-bead-data
#7
David R Parks, Faysal El Khettabi, Eric Chase, Robert A Hoffman, Stephen P Perfetto, Josef Spidlen, James C S Wood, Wayne A Moore, Ryan R Brinkman
We developed a fully automated procedure for analyzing data from LED pulses and multilevel bead sets to evaluate backgrounds and photoelectron scales of cytometer fluorescence channels. The method improves on previous formulations by fitting a full quadratic model with appropriate weighting and by providing standard errors and peak residuals as well as the fitted parameters themselves. Here we describe the details of the methods and procedures involved and present a set of illustrations and test cases that demonstrate the consistency and reliability of the results...
February 3, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28152100/genetic-and-isotope-ratio-mass-spectrometric-evidence-for-the-occurrence-of-starch-degradation-and-cycling-in-illuminated-arabidopsis-leaves
#8
Marouane Baslam, Edurne Baroja-Fernández, Adriana Ricarte-Bermejo, Ángela María Sánchez-López, Iker Aranjuelo, Abdellatif Bahaji, Francisco José Muñoz, Goizeder Almagro, Pablo Pujol, Regina Galarza, Pilar Teixidor, Javier Pozueta-Romero
Although there is a great wealth of data supporting the occurrence of simultaneous synthesis and breakdown of storage carbohydrate in many organisms, previous 13CO2 pulse-chase based studies indicated that starch degradation does not operate in illuminated Arabidopsis leaves. Here we show that leaves of gwd, sex4, bam4, bam1/bam3 and amy3/isa3/lda starch breakdown mutants accumulate higher levels of starch than wild type (WT) leaves when cultured under continuous light (CL) conditions. We also show that leaves of CL grown dpe1 plants impaired in the plastidic disproportionating enzyme accumulate higher levels of maltotriose than WT leaves, the overall data providing evidence for the occurrence of extensive starch degradation in illuminated leaves...
2017: PloS One
https://www.readbyqxmd.com/read/28133646/moxdendra2-an-inert-photoswitchable-protein-for-oxidizing-environments
#9
Andrii A Kaberniuk, Nicholas C Morano, Vladislav V Verkhusha, Erik Lee Snapp
Fluorescent proteins (FPs) that can be optically highlighted enable PALM super-resolution microscopy and pulse-chase experiments of cellular molecules. Most FPs evolved in cytoplasmic environments either in the original source organism or in the cytoplasm of bacteria during the course of optimization for research applications. Consequently, many FPs may fold incorrectly in the chemically distinct environments in subcellular organelles. Here, we describe the first monomeric photoswitchable (from green to bright red) FP adapted for oxidizing environments...
February 9, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28111744/passive-acoustic-monitoring-development-of-disturbance-calls-and-differentiation-of-disturbance-and-advertisement-calls-in-the-argentine-croaker-umbrina-canosai-sciaenidae
#10
J S Tellechea, M L Fine, W Norbis
Disturbance and advertisement calls of the Argentine croaker Umbrina canosai were recorded from coastal Uruguayan waters. Dissections indicate typical sciaenid extrinsic swimbladder muscles present exclusively in males. Disturbance calls were produced when captive U. canosai were startled, chased with a net or grabbed by the tail. Calls were unusual for sciaenids because each pulse consisted of multiple cycles. The number of cycles per pulse and dominant frequency did not change with U. canosai size, but pulse duration and interpulse interval increased...
January 23, 2017: Journal of Fish Biology
https://www.readbyqxmd.com/read/28095497/replication-coupled-recruitment-of-viral-and-cellular-factors-to-herpes-simplex-virus-type-1-replication-forks-for-the-maintenance-and-expression-of-viral-genomes
#11
Jill A Dembowski, Sarah E Dremel, Neal A DeLuca
Herpes simplex virus type 1 (HSV-1) infects over half the human population. Much of the infectious cycle occurs in the nucleus of cells where the virus has evolved mechanisms to manipulate host processes for the production of virus. The genome of HSV-1 is coordinately expressed, maintained, and replicated such that progeny virions are produced within 4-6 hours post infection. In this study, we selectively purify HSV-1 replication forks and associated proteins from virus-infected cells and identify select viral and cellular replication, repair, and transcription factors that associate with viral replication forks...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28088608/gene-analysis-of-six-cases-of-congenital-protein-s-deficiency-and-functional-analysis-of-protein-s-mutations-a139v-c449f-r451q-c475f-a525v-and-d599tfster13
#12
Fumina Taniguchi, Eriko Morishita, Akiko Sekiya, Haruka Nomoto, Shiori Katsu, Shounosuke Kaneko, Hidesaku Asakura, Shigeki Ohtake
Congenital deficiency of protein S (PS), an anticoagulant factor, leads to venous thrombosis, with onset predominantly beginning in adolescence. In the present study, gene analysis of six unrelated Japanese families diagnosed with congenital PS deficiency identified five missense mutations in the PROS1 gene - c.757C>T (Ala139Val; A139V), c.1346 G>T (Cys449Phe; C449F), c.1352G>A (Arg451Gln; R451Q), c.1424G>T (Cys475Phe; C475F) and c.1574C>T (Ala525Val; A525V) - and one frameshift mutation, c.2135delA (Asp599ThrfsTer13; D599TfsTer13)...
December 24, 2016: Thrombosis Research
https://www.readbyqxmd.com/read/28079880/nonradioactive-quantification-of-autophagic-protein-degradation-with-l-azidohomoalanine-labeling
#13
Jigang Wang, Jianbin Zhang, Yew Mun Lee, Shukie Ng, Yin Shi, Zi-Chun Hua, Qingsong Lin, Han-Ming Shen
At present, several assays that use radioisotope labeling to quantify the degradation of long-lived proteins have been developed to measure autophagic flux. Here, we describe a nonradioactive pulse-chase protocol using L-azidohomoalanine (AHA) labeling to quantify long-lived protein degradation during autophagy. AHA is used as a surrogate for L-methionine, and, when added to cultured cells grown in methionine-free medium, AHA is incorporated into proteins during de novo protein synthesis. After a chase period to remove short-lived proteins, autophagy is induced by starvation or other stimuli...
December 2017: Nature Protocols
https://www.readbyqxmd.com/read/28076784/coupled-proliferation-and-apoptosis-maintain-the-rapid-turnover-of-microglia-in-the-adult-brain
#14
Katharine Askew, Kaizhen Li, Adrian Olmos-Alonso, Fernando Garcia-Moreno, Yajie Liang, Philippa Richardson, Tom Tipton, Mark A Chapman, Kristoffer Riecken, Sol Beccari, Amanda Sierra, Zoltán Molnár, Mark S Cragg, Olga Garaschuk, V Hugh Perry, Diego Gomez-Nicola
Microglia play key roles in brain development, homeostasis, and function, and it is widely assumed that the adult population is long lived and maintained by self-renewal. However, the precise temporal and spatial dynamics of the microglial population are unknown. We show in mice and humans that the turnover of microglia is remarkably fast, allowing the whole population to be renewed several times during a lifetime. The number of microglial cells remains steady from late postnatal stages until aging and is maintained by the spatial and temporal coupling of proliferation and apoptosis, as shown by pulse-chase studies, chronic in vivo imaging of microglia, and the use of mouse models of dysregulated apoptosis...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28069747/a-targeted-rnai-screen-identifies-factors-affecting-diverse-stages-of-receptor-mediated-transcytosis
#15
Bradlee Nelms, Natasha Furtado Dalomba, Wayne Lencer
Endosome transport by transcytosis is the primary mechanism by which proteins and other large cargo traverse epithelial barriers in normal tissue. Transcytosis is also essential for establishing and maintaining membrane polarity in epithelia and other polarized cells. To identify novel components of this pathway, we conducted a high-throughput RNA interference screen for factors necessary for the bidirectional transcytosis of IgG by the Fcγ receptor FcRn. This screen identified 23 genes whose suppression resulted in a reproducible decrease in FcRn-mediated transcytosis...
February 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28062662/disease-causing-mutations-affecting-surface-residues-of-mitochondrial-glutaryl-coa-dehydrogenase-impair-stability-heteromeric-complex-formation-and-mitochondria-architecture
#16
Jessica Schmiesing, Benjamin Lohmöller, Michaela Schweizer, Henning Tidow, Søren W Gersting, Ania C Muntau, Thomas Braulke, Chris Mühlhausen
The neurometabolic disorder glutaric aciduria type 1 (GA1) is caused by mutations in the GCDH gene encoding the mitochondrial matrix protein glutaryl-CoA dehydrogenase (GCDH), which forms homo- and heteromeric complexes. Twenty percent of all pathogenic mutations affect single amino acid residues on the surface of GCDH resulting in a severe clinical phenotype. We report here on heterologous expression studies of 18 missense mutations identified in GA1 patients affecting surface amino acids. Western blot and pulse chase experiments revealed that the stability of half of the GCDH mutants was significantly reduced...
January 5, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28002502/ehnpc1-and-ehnpc2-proteins-participate-in-trafficking-of-exogenous-cholesterol-in-entamoeba-histolytica-trophozoites-relevance-for-phagocytosis
#17
Jeni Bolaños, Abigail Betanzos, Rosario Javier-Reyna, Guillermina García-Rivera, Miriam Huerta, Jonnatan Pais-Morales, Arturo González-Robles, Mario A Rodríguez, Michael Schnoor, Esther Orozco
Entamoeba histolytica, the highly phagocytic protozoan causative of human amoebiasis lacks the machinery to synthesize cholesterol. Here, we investigated the presence of NPC1 and NPC2 proteins in this parasite, which are involved in cholesterol trafficking in mammals. Bioinformatics analysis revealed one Ehnpc1 and two Ehnpc2 genes. EhNPC1 appeared as a transmembrane protein and both EhNPC2 as peripheral membrane proteins. Molecular docking predicted that EhNPC1 and EhNPC2 bind cholesterol and interact with each other...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27974639/visualizing-the-dynamic-coupling-of-claudin-strands-to-the-actin-cytoskeleton-through-zo-1
#18
Christina M Van Itallie, Amber Jean Tietgens, James M Anderson
The organization and integrity of epithelial tight junctions depend on interactions between claudins, ZO scaffolding proteins, and the cytoskeleton. However, although binding between claudins and ZO-1/2/3 and between ZO-1/2/3 and numerous cytoskeletal proteins has been demonstrated in vitro, fluorescence recovery after photobleaching analysis suggests interactions in vivo are likely highly dynamic. Here we use superresolution live-cell imaging in a model fibroblast system to examine relationships between claudins, ZO-1, occludin, and actin...
February 15, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27932476/high-fat-diet-induced-lysosomal-dysfunction-and-impaired-autophagic-flux-contribute-to-lipotoxicity-in-the-kidney
#19
Takeshi Yamamoto, Yoshitsugu Takabatake, Atsushi Takahashi, Tomonori Kimura, Tomoko Namba, Jun Matsuda, Satoshi Minami, Jun-Ya Kaimori, Isao Matsui, Taiji Matsusaka, Fumio Niimura, Motoko Yanagita, Yoshitaka Isaka
Excessive fat intake contributes to the progression of metabolic diseases via cellular injury and inflammation, a process termed lipotoxicity. Here, we investigated the role of lysosomal dysfunction and impaired autophagic flux in the pathogenesis of lipotoxicity in the kidney. In mice, a high-fat diet (HFD) resulted in an accumulation of phospholipids in enlarged lysosomes within kidney proximal tubular cells (PTCs). In isolated PTCs treated with palmitic acid, autophagic degradation activity progressively stagnated in association with impaired lysosomal acidification and excessive lipid accumulation...
December 8, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/27929926/comparing-lamin-proteins-post-translational-relative-stability-using-a-2a-peptide-based-system-reveals-elevated-resistance-of-progerin-to-cellular-degradation
#20
Di Wu, Phillip A Yates, Haoyue Zhang, Kan Cao
Nuclear lamins are the major components of the nuclear lamina at the periphery of the nucleus, supporting the nuclear envelope and participating in many nuclear processes, including DNA replication, transcription and chromatin organization. A group of diseases, the laminopathies, is associated with mutations in lamin genes. One of the most striking cases is Hutchinson-Gilford progeria syndrome (HGPS) which is the consequence of a lamin A dominant negative mutant named progerin. Due to the abnormal presence of a permanent C-terminal farnesyl tail, progerin gradually accumulates on the nuclear membrane, perturbing a diversity of signalings and transcriptional events...
November 2016: Nucleus
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