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https://www.readbyqxmd.com/read/28938685/a-case-control-study-of-the-association-between-the-egfr-gene-and-glioma-risk-in-a-chinese-han-population
#1
Mengdan Yan, Jingjie Li, Na He, Xugang Shi, Shuli Du, Bin Li, Tianbo Jin
The Epidermal Growth Factor Receptor gene has been reported to be involved in the progression of gliomas which is one of the deadliest primary brain tumors in humans. To determine potential association between EGFR and glioma risk, we performed a case-control study with 394 glioma patients and 298 cancer-free controls in which captured a total of 8 tag single nucleotide polymorphisms of EGFR gene from Xi'an, China. SPSS 19.0 statistical packages, χ(2) test, genetic model analysis and SHEsis software platform were analyzed s the variants in EGFR gene associations with glioma risk...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28929229/a-novel-method-for-concentration-of-porcine-reproductive-and-respiratory-syndrome-virus-from-the-environmental-samples-using-self-aggregating-peptide-tagged-cd151-binding-capture
#2
Yang Zong, Xiaoyin Zong, Wenlong Xia, Zhi Wu, Guangya Li, Yangyang Li, Xinyu Zhang, Xiaoli Xia, Huaichang Sun
Environmental surveillance of porcine reproductive and respiratory syndrome virus (PRRSV) represents a key issue in control of the disease. CD151 has recently been recognized as one of several receptors for PRRSV. We describe here a novel method for concentration of PRRSV from the environmental samples by CD151-binding capture. After fusion to self-aggregating peptide ELK16, the large extracellular loop (LEL) of porcine CD151 and its two segments (namely N63 and C63) were expressed in E. coli as protein aggregates...
September 19, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28915027/structure-and-dynamics-of-membrane-proteins-and-membrane-associated-proteins-with-native-bicelles-from-eukaryotic-tissues
#3
Sean T Smrt, Adrian W Draney, Indira Singaram, Justin L Lorieau
In vitro studies of protein structure, function and dynamics typically preclude the complex range of molecular interactions found in living tissues. In vivo studies elucidate these complex relationships, yet they are typically incompatible with the extensive and controlled biophysical experiments available in vitro. We present an alternative approach by extracting membranes from eukaryotic tissues to produce native bicelles to capture the rich and complex molecular environment of in vivo studies while retaining the advantages of in vitro experiments...
September 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28915003/the-evolution-of-dna-templated-synthesis-as-a-tool-for-materials-discovery
#4
Rachel K O'Reilly, Andrew J Turberfield, Thomas R Wilks
Precise control over reactivity and molecular structure is a fundamental goal of the chemical sciences. Billions of years of evolution by natural selection have resulted in chemical systems capable of information storage, self-replication, catalysis, capture and production of light, and even cognition. In all these cases, control over molecular structure is required to achieve a particular function: without structural control, function may be impaired, unpredictable, or impossible. The search for molecules with a desired function is often achieved by synthesizing a combinatorial library, which contains many or all possible combinations of a set of chemical building blocks (BBs), and then screening this library to identify "successful" structures...
September 15, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28906437/developing-fine-grained-actigraphies-for-rheumatoid-arthritis-patients-from-a-single-accelerometer-using-machine-learning
#5
Javier Andreu-Perez, Luis Garcia-Gancedo, Jonathan McKinnell, Anniek Van der Drift, Adam Powell, Valentin Hamy, Thomas Keller, Guang-Zhong Yang
In addition to routine clinical examination, unobtrusive and physical monitoring of Rheumatoid Arthritis (RA) patients provides an important source of information to enable understanding the impact of the disease on quality of life. Besides an increase in sedentary behaviour, pain in RA can negatively impact simple physical activities such as getting out of bed and standing up from a chair. The objective of this work is to develop a method that can generate fine-grained actigraphies to capture the impact of the disease on the daily activities of patients...
September 14, 2017: Sensors
https://www.readbyqxmd.com/read/28906111/synthesis-and-deployment-of-an-elusive-fluorovinyl-cation-equivalent-access-to-quaternary-%C3%AE-1-fluoro-vinyl-amino-acids-as-potential-plp-enzyme-inactivators
#6
Christopher D McCune, Matthew L Beio, Jill M Sturdivant, Roberto de la Salud-Bea, Brendan M Darnell, David B Berkowitz
Developing specific chemical functionalities to deploy in biological environments for targeted enzyme inactivation lies at the heart of mechanism-based inhibitor (MBI) development, but also is central to other protein-tagging methods in modern chemical biology including activity-based protein profiling (ABPP) and proteolysis-targeting chimeras (PROTACS). We describe here a previously unknown class of potential PLP enzyme inactivators; namely, a family of quaternary, α-(1'fluoro)vinyl amino acids, bearing the side chains of the cognate amino acids...
September 14, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28903049/a-mass-spectrometry-based-approach-for-mapping-protein-subcellular-localization-reveals-the-spatial-proteome-of-mouse-primary-neurons
#7
Daniel N Itzhak, Colin Davies, Stefka Tyanova, Archana Mishra, James Williamson, Robin Antrobus, Jürgen Cox, Michael P Weekes, Georg H H Borner
We previously developed a mass spectrometry-based method, dynamic organellar maps, for the determination of protein subcellular localization and identification of translocation events in comparative experiments. The use of metabolic labeling for quantification (stable isotope labeling by amino acids in cell culture [SILAC]) renders the method best suited to cells grown in culture. Here, we have adapted the workflow to both label-free quantification (LFQ) and chemical labeling/multiplexing strategies (tandem mass tagging [TMT])...
September 12, 2017: Cell Reports
https://www.readbyqxmd.com/read/28873399/systematic-analysis-of-transcription-start-sites-in-avian-development
#8
Marina Lizio, Ruslan Deviatiiarov, Hiroki Nagai, Laura Galan, Erik Arner, Masayoshi Itoh, Timo Lassmann, Takeya Kasukawa, Akira Hasegawa, Marian A Ros, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, Hideya Kawaji, Oleg Gusev, Guojun Sheng
Cap Analysis of Gene Expression (CAGE) in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs) and genome-wide capture of promoter activities in differentiated and steady state cell populations. Much less is known about whether TSS profiling can characterize diverse and non-steady state cell populations, such as the approximately 400 transitory and heterogeneous cell types that arise during ontogeny of vertebrate animals. To gain such insight, we used the chick model and performed CAGE-based TSS analysis on embryonic samples covering the full 3-week developmental period...
September 2017: PLoS Biology
https://www.readbyqxmd.com/read/28871789/production-and-purification-of-the-native-saccharomyces-cerevisiae-hsp12-in-escherichia-coli
#9
Antoine Léger, Agnès Hocquellet, Wilfrid Dieryck, Virginie Moine, Axel Marchal, Philippe Marullo, Annabelle Josseaume, Charlotte Cabanne
Hsp12 is a small heat shock protein produced in many organisms, including the yeast Saccharomyces cerevisiae. It has been described as an indicator of yeast stress rate and has also been linked to the sweetness sensation of wine. To obtain a sufficient amount of protein, we produced and purified Hsp12 without tag in Escherichia coli. A simple fast two-step process was developed using a microplate approach and a design of experiments. A capture step on an anion-exchange salt-tolerant resin was followed by size exclusion chromatography for polishing, leading to a purity of 97%...
September 11, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28870833/multivalent-interactions-between-streptavidin-based-pretargeting-fusion-proteins-and-cell-receptors-impede-efficient-internalization-of-biotinylated-nanoparticles
#10
Christina L Parker, Qi Yang, Bing Yang, Justin D McCallen, Steven I Park, Samuel K Lai
Pretargeting represents a promising strategy to enhance delivery of nanoparticles. The strategy involves first introducing bispecific antibodies or fusion proteins (BFP) that can bind specific epitopes on target cells, which in turn can capture subsequently administered effector molecules, such as radionuclides or drug-loaded nanoparticles. Nevertheless, it remains unclear whether BFP that bind slowly- or non-internalizing epitopes on target cells can facilitate efficient intracellular delivery. Here, we investigated the cellular uptake of biotin-functionalized nanoparticles with streptavidin-scFv against TAG-72, a membrane protein on Jurkat T-cell leukemia cell...
September 1, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28862836/generation-of-clickable-pittsburgh-compound-b-for-the-detection-and-capture-of-%C3%AE-amyloid-in-alzheimer-s-disease-brain
#11
Ian Diner, Jeromy Dooyema, Marla Gearing, Lary C Walker, Nicholas T Seyfried
The benzothiazole-aniline derivative Pittsburgh Compound B (PiB) is the prototypical amyloid affinity probe developed for the in vivo positron emission tomography (PET) detection of amyloid beta (Aβ) deposits in Alzheimer's disease (AD). Specific high-affinity binding sites for PiB have been found to vary among AD cases with comparable Aβ load, and they are virtually absent on human-sequence Aβ deposits in animal models, none of which develop the full phenotype of AD. PiB thus could be an informative probe for studying the pathobiology of Aβ, but little is known about the localization of PiB binding at the molecular or structural level...
September 22, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28857397/correct-modeling-of-cisplatin-a-paradigmatic-case
#12
Nicola Tasinato, Cristina Puzzarini, Vincenzo Barone
Quantum chemistry is a useful tool in modern approaches to drug and material design, but only when the adopted model reflects a correct physical picture. Paradigmatic is the case of cis-diaminodichloroplatinum(II), cis-[Pt(NH3 )2 Cl2 ], for which the correct simulation of the structural and vibrational properties measured experimentally still remains an open question. By using this molecule as a proof of concept, it is shown that state-of-the-art quantum chemical calculations and a simple model, capturing the basic physical flavors, a cis-[Pt(NH3 )2 Cl2 ] dimer, can provide the accuracy required for interpretative purposes...
August 30, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28843001/cell-free-production-of-a-therapeutic-protein-expression-purification-and-characterization-of-recombinant-streptokinase-using-a-cho-lysate
#13
Kevin Tran, Chandrasekhar Gurramkonda, Merideth A Cooper, Manohar Pilli, Joseph Tarris, Nick Selock, Tzu-Chiang Han, Michael Tolosa, Adil Zuber, Chariz Peñalber-Johnstone, Christina Dinkins, Niloufar Pezeshk, Yordan Kostov, Douglas D Frey, Leah Tolosa, David Wood, Govind Rao
The use of cell-free systems to produce recombinant proteins has grown rapidly over the past decade. In particular, cell-free protein synthesis (CFPS) systems based on mammalian cells provide alternative methods for the production of many proteins, including those that contain disulfide bonds, glycosylation and complex structures such as monoclonal antibodies. In the present study, we show robust production of turbo green fluorescent protein (tGFPi and streptokinase in a cell-free system using instrumented mini-bioreactors for highly reproducible protein production...
August 26, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28832842/estimation-of-peacock-bass-cichla-spp-mortality-rate-during-catch-release-fishing-employing-different-post-capture-procedures
#14
L S A Barroco, C E C Freitas, Á C Lima
The effect of catch-and-release fishing on the survival of peacock bass (Cichla spp.) was evaluated by comparing two types of artificial bait (jig and shallow-diver plugs) and two types of post-catch confinement. Two experiments were conducted during the periods January-February and October-November 2012 in the Unini River, a right-bank tributary of the Negro River. In total, 191 peacock bass were captured. Both groups of fish were subjected to experimental confinement (collective and individual) for three days...
August 17, 2017: Brazilian Journal of Biology, Revista Brasleira de Biologia
https://www.readbyqxmd.com/read/28827572/seal-whiskers-vibrate-over-broad-frequencies-during-hydrodynamic-tracking
#15
Christin T Murphy, Colleen Reichmuth, William C Eberhardt, Benton H Calhoun, David A Mann
Although it is known that seals can use their whiskers (vibrissae) to extract relevant information from complex underwater flow fields, the underlying functioning of the system and the signals received by the sensors are poorly understood. Here we show that the vibrations of seal whiskers may provide information about hydrodynamic events and enable the sophisticated wake-tracking abilities of these animals. We developed a miniature accelerometer tag to study seal whisker movement in situ. We tested the ability of the tag to measure vibration in excised whiskers in a flume in response to laminar flow and disturbed flow...
August 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28812882/aberrantly-large-single-channel-conductance-of-polyhistidine-arm-containing-protein-nanopores
#16
Avinash Kumar Thakur, Motahareh Ghahari Larimi, Kristin Gooden, Liviu Movileanu
There have been only a few studies reporting on the impact of polyhistidine affinity tags on the structure, function, and dynamics of proteins. Because of the relatively short size of the tags, they are often thought to have little or no effect on the conformation or activity of a protein. Here, using membrane protein design and single-molecule electrophysiology, we determined that the presence of a hexahistidine arm at the N-terminus of a truncated FhuA-based protein nanopore, leaving the C-terminus untagged, produces an unusual increase in the unitary conductance to ∼8 nS in 1 M KCl...
September 12, 2017: Biochemistry
https://www.readbyqxmd.com/read/28810735/accurate-electrochemistry-analysis-of-circulating-methylated-dna-from-clinical-plasma-based-on-paired-end-tagging-and-amplifications
#17
Feng Chen, Xuyao Wang, Xiaowen Cao, Yongxi Zhao
Circulating methylated DNA has been a new kind of cancer biomarker, yet its small fraction of trace total DNA from clinical samples impairs the accurate analysis. Though fluorescence methods based on quantitative methylation specific PCR (qMSP) have been adopted routinely, yet alternative electrochemistry assay of such DNA from clinical samples remains a great challenge. Herein, we report accurate electrochemistry analysis of circulating methylated DNA from clinical plasma samples based on a paired-end tagging and amplifications strategy...
August 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28809819/tamra-tamra-fluorescence-quenching-systems-for-the-activity-assay-of-alkaline-phosphatase
#18
Akio Shiba, Emiko Kinoshita-Kikuta, Eiji Kinoshita, Tohru Koike
We introduce two types of fluorescence-quenching assay for alkaline phosphatases (APs) by using a carboxytetramethyl-rhodamine (TAMRA)-labeled phosphate-binding tag molecule (TAMRA-Phos-tag). In the first assay, TAMRA-labeled O-phosphorylethanolamine (TAMRA-PEA) was used as an artificial AP-substrate. TAMRA-Phos-tag specifically captured TAMRA-PEA to form a 1:1 complex at pH 7.4; the intensity of the fluorescence peak of the complex at 580 nm (λex = 523 nm) was significantly reduced to 32% of the average value for the two individual components as a result of the mutual approach of the TAMRA moieties...
August 15, 2017: Sensors
https://www.readbyqxmd.com/read/28805061/triple-helix-molecular-switch-electrochemical-ratiometric-biosensor-for-ultrasensitive-detection-of-nucleic-acids
#19
Erhu Xiong, Zhenzhen Li, Xiaohua Zhang, Jiawan Zhou, Xiaoxia Yan, Yunqing Liu, Jinhua Chen
Biomolecular receptors such as nucleic acids that switch between two or more conformations upon binding to a specific target can be used to build specific and sensitive biosensors. In this work, based on the electrochemical dual-signaling ratiometric strategy and triple-helix molecular switch, we developed a selective, reusable, and simple electrochemical DNA (E-DNA) biosensor for target DNA (T-DNA) detection. A hairpin DNA capture probe labeled with methylene blue (MB-DNA) self-assembles on the surface of a gold electrode (GE) through Au-S bond, and then a single-strand DNA modified with two ferrocenes (Fc-DNA) on each end to enhance the oxidation signal hybridizes with the MB-DNA to form a triple-helix conformation...
September 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28799505/single-molecular-level-probing-of-structure-and-dynamics-of-papain-under-denaturation
#20
Bhaswati Sengupta, Apala Chaudhury, Nilimesh Das, Pratik Sen
INTRODUCTION: Papain is a cysteine protease enzyme present in papaya and known to help in digesting peptide. Thus the structure and function of the active site of papain is of interest. OBJECTIVE: The objective of present study is to unveil the overall structural transformation and the local structural change around the active site of papain as a function of chemical denaturant. METHODS: Papain has been tagged at Cys-25 with a thiol specific fluorescence probe N-(7-dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA)...
August 11, 2017: Protein and Peptide Letters
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