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https://www.readbyqxmd.com/read/27912002/a-novel-application-of-multi-event-modeling-to-estimate-class-segregation-in-a-highly-migratory-oceanic-vertebrate
#1
T K Chapple, T Chambert, P E Kanive, S J Jorgensen, J J Rotella, S D Anderson, A B Carlisle, B A Block
Spatial segregation of animals by class (i.e., maturity or sex) within a population due to differential rates of temporary emigration (TE) from study sites can be an important life history feature to consider in population assessment and management. However, such rates are poorly known; new quantitative approaches to address these knowledge gaps are needed. We present a novel application of multi-event models that takes advantage of two sources of detections to differentiate temporary emigration from apparent absence to quantify class segregation within a study population of double-marked (photo-identified and tagged with coded acoustic transmitters) white sharks (Carcharodon carcharias) in central California...
December 2016: Ecology
https://www.readbyqxmd.com/read/27908071/measurements-of-humpback-whale-song-sound-levels-received-by-a-calf-in-association-with-a-singer
#2
Jessica Chen, Adam A Pack, Whitlow W L Au, Alison K Stimpert
Male humpback whales produce loud "songs" on the wintering grounds and some sing while escorting mother-calf pairs, exposing them to near-continuous sounds at close proximity. An Acousonde acoustic and movement recording tag deployed on a calf off Maui, Hawaii captured sounds produced by a singing male escort. Root-mean-square received levels ranged from 126 to 158 dB re 1 μPa. These levels represent rare direct measurements of sound to which a newly born humpback calf may be naturally exposed by a conspecific, and may provide a basis for informed decisions regarding anthropogenic sound levels projected near calves...
November 2016: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/27883075/direct-electrical-control-of-igg-conformation-and-functional-activity-at-surfaces
#3
Paola Ghisellini, Marialuisa Caiazzo, Andrea Alessandrini, Roberto Eggenhöffner, Massimo Vassalli, Paolo Facci
We have devised a supramolecular edifice involving His-tagged protein A and antibodies to yield surface immobilized, uniformly oriented, IgG-type, antibody layers with Fab fragments exposed off an electrode surface. We demonstrate here that we can affect the conformation of IgGs, likely pushing/pulling electrostatically Fab fragments towards/from the electrode surface. A potential difference between electrode and solution acts on IgGs' charged aminoacids modulating the accessibility of the specific recognition regions of Fab fragments by antigens in solution...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27881095/a-regional-consensus-recommendation-on-brain-atrophy-as-an-outcome-measure-in-multiple-sclerosis
#4
Raed Alroughani, Dirk Deleu, Khalid El Salem, Jasem Al-Hashel, K John Alexander, Mohamed Assem Abdelrazek, Adel Aljishi, Jaber Alkhaboori, Faisal Al Azri, Nahida Al Zadjali, Majed Hbahbih, Tag Eldin Sokrab, Mohamed Said, Àlex Rovira
BACKGROUND: Multiple sclerosis (MS) is a chronic autoimmune disease characterized by inflammatory and neurodegenerative processes leading to irreversible neurological impairment. Brain atrophy occurs early in the course of the disease at a rate greater than the general population. Brain volume loss (BVL) is associated with disability progression and cognitive impairment in patients with MS; hence its value as a potential target in monitoring and treating MS is discussed. METHODS: A group of MS neurologists and neuro-radiologists reviewed the current literature on brain atrophy and discussed the challenges in assessing and implementing brain atrophy measurements in clinical practice...
November 24, 2016: BMC Neurology
https://www.readbyqxmd.com/read/27880036/protein-phosphotyrosine-proteome-profiling-by-superbinder-sh2-domain-affinity-purification-mass-spectrometry-ssh2-ap-ms
#5
Jiefei Tong, Biyin Cao, Gregory D Martyn, Jonathan R Krieger, Paul Taylor, Bradley Yates, Sachdev S Sidhu, Shawn S C Li, Xinliang Mao, Michael F Moran
Recently, "superbinder" SH2 domain variants with three amino acid substitutions (sSH2) were reported to have 100-fold or greater affinity for protein-phosphotyrosine (pY) than natural SH2 domains. Here we report a protocol in which His-tagged Src sSH2 efficiently captures pY-peptides from protease-digested HeLa cell total protein extracts. Affinity purification of pY-peptides by this method shows little bias for pY-proximal amino acid sequences, comparable to that achieved by using antibodies to pY, but with equal or higher yield...
November 23, 2016: Proteomics
https://www.readbyqxmd.com/read/27867058/application-of-strep-tactin-xt-for-affinity-purification-of-twin-strep-tagged-cb2-a-g-protein-coupled-cannabinoid-receptor
#6
Alexei Yeliseev, Lioudmila Zoubak, Thomas G M Schmidt
Human cannabinoid receptor CB2 belongs to the class A of G protein-coupled receptor (GPCR). High resolution structural studies of CB2 require milligram quantities of purified, structurally intact protein. Here we describe an efficient protocol for purification of this protein using the Twin-Strep-tag/Strep-Tactin XT system. To improve the affinity of interaction of the recombinant CB2 with the resin, the double repeat of the Strep-tag was attached either to the N- or C-terminus of CB2 via a short linker. The CB2 was isolated at high purity from dilute solutions containing high concentrations of detergents, glycerol and salts, by capturing onto the Strep-Tactin XT resin, and was eluted from the resin under mild conditions upon addition of biotin...
November 17, 2016: Protein Expression and Purification
https://www.readbyqxmd.com/read/27861577/identifying-causal-genes-at-the-multiple-sclerosis-associated-region-6q23-using-capture-hi-c
#7
Paul Martin, Amanda McGovern, Jonathan Massey, Stefan Schoenfelder, Kate Duffus, Annie Yarwood, Anne Barton, Jane Worthington, Peter Fraser, Stephen Eyre, Gisela Orozco
BACKGROUND: The chromosomal region 6q23 has been found to be associated with multiple sclerosis (MS) predisposition through genome wide association studies (GWAS). There are four independent single nucleotide polymorphisms (SNPs) associated with MS in this region, which spans around 2.5 Mb. Most GWAS variants associated with complex traits, including these four MS associated SNPs, are non-coding and their function is currently unknown. However, GWAS variants have been found to be enriched in enhancers and there is evidence that they may be involved in transcriptional regulation of their distant target genes through long range chromatin looping...
2016: PloS One
https://www.readbyqxmd.com/read/27846446/studies-in-using-a-universal-exchange-and-inference-language-for-evidence-based-medicine-semi-automated-learning-and-reasoning-for-pico-methodology-systematic-review-and-environmental-epidemiology
#8
Barry Robson
The Q-UEL language of XML-like tags and the associated software applications are providing a valuable toolkit for Evidence Based Medicine (EBM). In this paper the already existing applications, data bases, and tags are brought together with new ones. The particular Q-UEL embodiment used here is the BioIngine. The main challenge is one of bringing together the methods of symbolic reasoning and calculative probabilistic inference that underlie EBM and medical decision making. Some space is taken to review this background...
October 17, 2016: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/27825887/electrochemical-immunosensor-for-n6-methyladenosine-detection-in-human-cell-lines-based-on-biotin-streptavidin-system-and-silver-sio2-signal-amplification
#9
Huanshun Yin, Haiyan Wang, Wenjing Jiang, Yunlei Zhou, Shiyun Ai
N6-methyladenosine (m6A), a kind of RNA methylation form and important epigenetic event, plays crucial roles in many biological progresses. Thus it is essential to quantitatively detect m6A in complicated biological samples. Herein, a simple and sensitive electrochemical method was developed for m6A detection using N6-methyladenosine-5'-triphosphate (m6ATP) as detection target molecule. In this detection strategy, anti-m6A antibody was selected as m6A recognition and capture reagent, silver nanoparticles and amine-PEG3-biotin functionalized SiO2 nanospheres (Ag@SiO2) was prepared and used as signal amplification label, and phos-tag-biotin played a vital role of "bridge" to link m6ATP and Ag@SiO2 through the two forms of specific interaction between phosphate group of m6ATP and phos-tag, biotin and streptavidin, respectively...
October 27, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27825522/practical-and-regenerable-electrochemical-aptasensor-based-on-nanoporous-gold-and-thymine-hg-2-thymine-base-pairs-for-hg-2-detection
#10
Guangming Zeng, Chen Zhang, Danlian Huang, Cui Lai, Lin Tang, Yaoyu Zhou, Piao Xu, Hou Wang, Lei Qin, Min Cheng
A simple, practical and reusable electrochemical aptasensor, based on thymine-Hg(2+)-thymine (T-Hg(2+)-T) coordination chemistry and nanoporous gold (NPG) for signal amplification, was designed for sensitive and selective detection of mercury ions (Hg(2+)). The thiol modified T-rich hairpin capture probe was self-assembled onto the surface of the NPG modified electrode for hybridizing with ferrocene-labeled T-rich probe in the presence of Hg(2+) via T-Hg(2+)-T coordination chemistry. As a result, the hairpin capture probe was opened, and the ferrocene tags were close to the NPG modified electrode...
October 7, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27795422/native-folding-of-a-recombinant-gpe1-gpe2-heterodimer-vaccine-antigen-from-a-precursor-protein-fused-with-fc-igg
#11
Michael Logan, John Law, Jason Alexander Ji-Xhin Wong, Darren Hockman, Amir Landi, Chao Chen, Kevin Crawford, Juthika Kundu, Lesley Baldwin, Janelle Johnson, Anita Dahiya, Gerald LaChance, Joseph Marcotrigiano, Mansun Law, Steven Foung, Lorne Tyrrell, Michael Houghton
: A recombinant HCV-1 (1a) gpE1/gpE2 (E1E2) vaccine candidate was previously shown by our group to protect chimpanzees and generate broad cross-neutralizing antibodies in animals and humans. In addition, recent independent studies have highlighted the importance of conserved neutralizing epitopes in HCV vaccine development that map to antigenic clusters in E2 or the E1E2 heterodimer. E1E2 can be purified using Galanthis nivalis lectin agarose (GNA), but this technique is suboptimal for global production...
October 19, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27791142/capture-of-micrococcin-biosynthetic-intermediates-reveals-c-terminal-processing-as-an-obligatory-step-for-in-vivo-maturation
#12
Kathryn D Bewley, Philip R Bennallack, Mark A Burlingame, Richard A Robison, Joel S Griffitts, Susan M Miller
Thiopeptides, including micrococcins, are a growing family of bioactive natural products that are ribosomally synthesized and heavily modified. Here we use a refactored, modular in vivo system containing the micrococcin P1 (MP1) biosynthetic genes (TclIJKLMNPS) from Macrococcus caseolyticus str 115 in a genetically tractable Bacillus subtilis strain to parse the processing steps of this pathway. By fusing the micrococcin precursor peptide to an affinity tag and coupling it with catalytically defective enzymes, biosynthetic intermediates were easily captured for analysis...
November 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27782203/super-resolution-imaging-of-fluorescently-labeled-endogenous-rna-polymerase-ii-in-living-cells-with-crispr-cas9-mediated-gene-editing
#13
Won-Ki Cho, Namrata Jayanth, Susan Mullen, Tzer Han Tan, Yoon J Jung, Ibrahim I Cissé
Live cell imaging of mammalian RNA polymerase II (Pol II) has previously relied on random insertions of exogenous, mutant Pol II coupled with the degradation of endogenous Pol II using a toxin, α-amanitin. Therefore, it has been unclear whether over-expression of labeled Pol II under an exogenous promoter may have played a role in reported Pol II dynamics in vivo. Here we label the endogenous Pol II in mouse embryonic fibroblast (MEF) cells using the CRISPR/Cas9 gene editing system. Using single-molecule based super-resolution imaging in the living cells, we captured endogenous Pol II clusters...
October 26, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27780212/effects-of-an-offshore-wind-farm-owf-on-the-common-shore-crab-carcinus-maenas-tagging-pilot-experiments-in-the-lillgrund-offshore-wind-farm-sweden
#14
Olivia Langhamer, Håkon Holand, Gunilla Rosenqvist
Worldwide growth of offshore renewable energy production will provide marine organisms with new hard substrate for colonization in terms of artificial reefs. The artificial reef effect is important when planning offshore installations since it can create habitat enhancement. Wind power is the most advanced technology within offshore renewable energy sources and there is an urgent need to study its impacts on the marine environment. To test the hypothesis that offshore wind power increases the abundance of reef species relative to a reference area, we conduct an experiment on the model species common shore crab (Carcinus maenas)...
2016: PloS One
https://www.readbyqxmd.com/read/27778282/activity-based-lipid-esterase-profiling-of-m-bovis-bcg-at-different-metabolic-states-using-tetrahydrolipstatin-thl-as-bait
#15
Madhu Sudhan Ravindran, Markus R Wenk
This chapter provides a step-by-step protocol using activity-based protein profiling (ABPP) as a chemical-proteomic tool to survey the antibiotic properties of a small molecule. Here, we investigate the molecular mechanism behind the bactericidal activity of tetrahydrolipstatin (THL). ABPP relies on small molecule probes that target the active site of specific enzymes in complex proteomes. These probes in turn are equipped with a reporter tag that allows capturing, visualization, enrichment, identification, and quantification of its targets either in vitro or in situ...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27777836/affinity-capturing-and-surface-enrichment-of-a-membrane-protein-embedded-in-a-continuous-supported-lipid-bilayer
#16
Anders Gunnarsson, Lisa Simonsson Nyström, Sabina Burazerovic, Jenny Gunnarsson, Arjan Snijder, Stefan Geschwindner, Fredrik Höök
Investigations of ligand-binding kinetics to membrane proteins are hampered by their poor stability and low expression levels, which often translates into sensitivity-related limitations impaired by low signal-to-noise ratios. Inspired by affinity capturing of water-soluble proteins, which utilizes water as the mobile phase, we demonstrate affinity capturing and local enrichment of membrane proteins by using a fluid lipid bilayer as the mobile phase. Specific membrane-protein capturing and enrichment in a microfluidic channel was accomplished by immobilizing a synthesized trivalent nitrilotriacetic acid (tris-NTA)-biotin conjugate...
October 2016: ChemistryOpen
https://www.readbyqxmd.com/read/27773392/tryptophan-tags-and-de-novo-designed-complementary-affinity-ligands-for-the-expression-and-purification-of-recombinant-proteins
#17
Ana Sofia Pina, Sara Carvalho, Ana Margarida G C Dias, Márcia Guilherme, Alice S Pereira, Luciana T Caraça, Ana Sofia Coroadinha, Christopher R Lowe, A Cecília A Roque
A common strategy for the production and purification of recombinant proteins is to fuse a tag to the protein terminal residues and employ a "tag-specific" ligand for fusion protein capture and purification. In this work, we explored the effect of two tryptophan-based tags, NWNWNW and WFWFWF, on the expression and purification of Green Fluorescence Protein (GFP) used as a model fusion protein. The titers obtained with the expression of these fusion proteins in soluble form were 0.11mgml(-1) and 0.48mgml(-1) for WFWFWF and NWNWNW, respectively...
October 19, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/27764671/nascent-proteome-remodeling-following-homeostatic-scaling-at-hippocampal-synapses
#18
Christoph T Schanzenbächer, Sivakumar Sambandan, Julian D Langer, Erin M Schuman
Homeostatic scaling adjusts the strength of synaptic connections up or down in response to large changes in input. To identify the landscape of proteomic changes that contribute to opposing forms of homeostatic plasticity, we examined the plasticity-induced changes in the newly synthesized proteome. Cultured rat hippocampal neurons underwent homeostatic up-scaling or down-scaling. We used BONCAT (bio-orthogonal non-canonical amino acid tagging) to metabolically label, capture, and identify newly synthesized proteins, detecting and analyzing 5,940 newly synthesized proteins using mass spectrometry and label-free quantitation...
October 19, 2016: Neuron
https://www.readbyqxmd.com/read/27764130/first-results-in-the-use-of-bovine-ear-notch-tag-for-bovine-viral-diarrhoea-virus-detection-and-genetic-analysis
#19
Christian Quinet, Guy Czaplicki, Elise Dion, Fabiana Dal Pozzo, Anke Kurz, Claude Saegerman
BACKGROUND: Infection due to bovine viral diarrhoea virus (BVDV) is endemic in most cattle-producing countries throughout the world. The key elements of a BVDV control programme are biosecurity, elimination of persistently infected animals and surveillance. Bovine viral diarrhoea (BVD) is a notifiable disease in Belgium and an official eradication programme started from January 2015, based on testing ear notches sampled during the official identification and registration of calves at birth...
2016: PloS One
https://www.readbyqxmd.com/read/27763643/mitochondrial-angiotensin-receptors-in-dopaminergic-neurons-role-in-cell-protection-and-aging-related-vulnerability-to-neurodegeneration
#20
Rita Valenzuela, Maria A Costa-Besada, Javier Iglesias-Gonzalez, Emma Perez-Costas, Begoña Villar-Cheda, Pablo Garrido-Gil, Miguel Melendez-Ferro, Ramon Soto-Otero, Jose L Lanciego, Daniel Henrion, Rafael Franco, Jose L Labandeira-Garcia
The renin-angiotensin system (RAS) was initially considered as a circulating humoral system controlling blood pressure, being kidney the key control organ. In addition to the 'classical' humoral RAS, a second level in RAS, local or tissular RAS, has been identified in a variety of tissues, in which local RAS play a key role in degenerative and aging-related diseases. The local brain RAS plays a major role in brain function and neurodegeneration. It is normally assumed that the effects are mediated by the cell-surface-specific G-protein-coupled angiotensin type 1 and 2 receptors (AT1 and AT2)...
October 20, 2016: Cell Death & Disease
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