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https://www.readbyqxmd.com/read/27915380/proteins-interacting-with-crea-and-creb-in-the-carbon-catabolite-repression-network-in-aspergillus-nidulans
#1
Md Ashiqul Alam, Joan M Kelly
In Aspergillus nidulans, carbon catabolite repression (CCR) is mediated by the global repressor protein CreA. The deubiquitinating enzyme CreB is a component of the CCR network. Genetic interaction was confirmed using a strain containing complete loss-of-function alleles of both creA and creB. No direct physical interaction was identified between tagged versions of CreA and CreB. To identify any possible protein(s) that may form a bridge between CreA and CreB, we purified both proteins from mycelia grown in media that result in repression or derepression...
December 3, 2016: Current Genetics
https://www.readbyqxmd.com/read/27914894/scope-manual-curation-and-artifact-removal-in-the-structural-classification-of-proteins-extended-database
#2
John-Marc Chandonia, Naomi K Fox, Steven E Brenner
SCOPe (Structural Classification of Proteins - extended, http://scop.berkeley.edu) is a database of relationships between protein structures that extends the Structural Classification of Proteins (SCOP) database. SCOP is an expert-curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. SCOPe classifies the majority of protein structures released since SCOP development concluded in 2009, using a combination of manual curation and highly precise automated tools, aiming to have the same accuracy as fully hand-curated SCOP releases...
November 30, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27914064/computational-tools-for-aiding-rational-antibody-design
#3
Konrad Krawczyk, James Dunbar, Charlotte M Deane
Antibodies are a group of proteins responsible for mediating immune reactions in vertebrates. They are able to bind a variety of structural motifs on noxious molecules tagging them for elimination from the organism. As a result of their versatile binding properties, antibodies are currently one of the most important classes of biopharmaceuticals. In this chapter, we discuss how knowledge-based computational methods can aid experimentalists in the development of potent antibodies. When using common experimental methods for antibody development, we often know the sequence of an antibody that binds to our molecule, antigen, of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914046/production-of-computationally-designed-small-soluble-and-membrane-proteins-cloning-expression-and-purification
#4
Barsa Tripathy, Rudresh Acharya
This book chapter focuses on expression and purification of computationally designed small soluble proteins and membrane proteins that are ordinarily difficult to express in good amounts for experiments. Over-expression of such proteins can be achieved by using the solubility tag such as maltose binding protein (MBP), Thioredoxin (Trx), and Gultathione-S-transferase (GST) fused to the protein of interest. Here, we describe and provide the protocols for cloning, expression and purification of such proteins using the solubility tag...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914033/l-carnitine-simvastatin-reduces-lipoprotein-a-levels-compared-with-simvastatin-monotherapy-a-randomized-double-blind-placebo-controlled-study
#5
M Florentin, M S Elisaf, C V Rizos, V Nikolaou, E Bilianou, C Pitsavos, E N Liberopoulos
Lipoprotein (a) [Lp(a)] is an independent risk factor for cardiovascular disease. There are currently limited therapeutic options to lower Lp(a) levels. L-Carnitine has been reported to reduce Lp(a) levels. The aim of this study was to compare the effect of L-carnitine/simvastatin co-administration with that of simvastatin monotherapy on Lp(a) levels in subjects with mixed hyperlipidemia and elevated Lp(a) concentration. Subjects with levels of low-density lipoprotein cholesterol (LDL-C) >160 mg/dL, triacylglycerol (TAG) >150 mg/dL and Lp(a) >20 mg/dL were included in this study...
December 2, 2016: Lipids
https://www.readbyqxmd.com/read/27913332/a-method-for-accurate-modeling-of-baw-filters-at-high-power-levels
#6
Andreas Tag, Vikrant Chauhan, Christian Huck, Bernhard Bader, Dominik Karolewski, F Maximilian Pitschi, Robert Weigel, Amelie Hagelauer
A novel approach for multiphysics modeling of bulk acoustic wave (BAW) filters is presented allowing accurate and at the same time efficient modeling of BAW filters at high power levels. The approach takes the different types of losses and their spatial distribution into account in order to provide the required input for thermal simulation. The temperature distribution determined by thermal simulation is used to modify the geometry and the layer stack of each single resonator of the filter. In this way, the required input for modeling of electromagnetic (EM) and acoustic behavior at high power level is generated...
December 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/27913309/sequence-determinants-of-the-caenhorhabditis-elegansdopamine-transporter-dictating-in-vivoaxonal-export-and-synaptic-localization
#7
Sarah B Robinson, J Andrew Hardaway, Shannon L Hardie, Jane Wright, Ryan M Glynn, Daniel P Bermingham, Qiao Han, Sarah M Sturgeon, Phyllis Freeman, Randy D Blakely
The monoamine neurotransmitter dopamine (DA) acts across phylogeny to modulate both simple and complex behaviors. The presynaptic DA transporter (DAT) is a major determinant of DA signaling capacity in ensuring efficient extracellular DA clearance. In humans, DAT is also a major target for prescribed and abused psychostimulants. Multiple structural determinants of DAT function and regulation have been defined, though largely these findings have arisen from heterologous expression or ex vivo cell culture studies...
November 29, 2016: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/27912144/elucidation-of-%C3%AE-s-dynamics-of-domain-iii-of-human-serum-albumin-during-the-chemical-and-thermal-unfolding-a-fluorescence-correlation-spectroscopic-investigation
#8
Bhaswati Sengupta, Nilimesh Das, Pratik Sen
The local structural dynamics and denaturation profile of domain-III of HSA against guanidine hydrochloride (GnHCl) and temperature has been studied using a coumarin based solvatochromic fluorescent probe p-nitrophenyl coumarin ester (NPCE), covalently tagged to Tyr-411 residue. By the steady state, time-resolved and single molecular level fluorescence studies it has been established that the domain-III of HSA is very sensitive to GnHCl but somewhat resistant to temperature and the domain specific unfolding proceeds in an altered way as compared to the overall unfolding of HSA...
November 18, 2016: Biophysical Chemistry
https://www.readbyqxmd.com/read/27912002/a-novel-application-of-multi-event-modeling-to-estimate-class-segregation-in-a-highly-migratory-oceanic-vertebrate
#9
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/27911605/gnrh-neuron-activity-and-pituitary-response-in-estradiol-induced-vs-proestrous-luteinizing-hormone-surges-in-female-mice
#10
Marina Silveira, Laura L Burger, R Anthony DeFazio, Elizabeth R Wagenmaker, Suzanne M Moenter
During the female reproductive cycle, estradiol exerts negative and positive feedback at both the central level to alter GnRH release and at the pituitary to affect response to GnRH. Many studies of the neurobiological mechanisms underlying estradiol feedback have been done on ovariectomized, estradiol-replaced (OVX+E) mice. In this model, GnRH neuron activity depends on estradiol and time of day, increasing in estradiol-treated mice in the late afternoon coincident with a daily LH surge. Amplitude of this surge appears lower than in proestrous mice, perhaps because other ovarian factors are not replaced...
December 2, 2016: Endocrinology
https://www.readbyqxmd.com/read/27911484/platinum-complex-assemblies-as-luminescent-probes-and-tags-for-drugs-and-toxins-in-water
#11
Stephan Sinn, Frank Biedermann, Luisa De Cola
A reactive phosphorescent probe for aza-heterocyclic drugs and toxins was developed, affording a supramolecular emission-switch-on chemosensor in water. Complex formation of the heterocycles with a platinum(II) precursor proceeds readily at ambient conditions, allowing for facile analyte screening. 52 structurally diverse compounds were tested, out of which 23 pyridines, imidazole, and triazoles formed strongly emissive complex aggregates. Importantly, they all can be clearly distinguished from each other through a principal component analysis, but often already by simple visual inspection, e...
December 1, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27911413/fabricating-a-uv-vis-and-raman-spectroscopy-immunoassay-platform
#12
Cynthia Hanson, Nathan D Israelsen, Michael Sieverts, Elizabeth Vargis
Immunoassays are used to detect proteins based on the presence of associated antibodies. Because of their extensive use in research and clinical settings, a large infrastructure of immunoassay instruments and materials can be found. For example, 96- and 384-well polystyrene plates are available commercially and have a standard design to accommodate ultraviolet-visible (UV-Vis) spectroscopy machines from various manufacturers. In addition, a wide variety of immunoglobulins, detection tags, and blocking agents for customized immunoassay designs such as enzyme-linked immunosorbent assays (ELISA) are available...
November 10, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911411/preparation-and-in-vivo-use-of-an-activity-based-probe-for-n-acylethanolamine-acid-amidase
#13
Elisa Romeo, Silvia Pontis, Stefano Ponzano, Fabiola Bonezzi, Marco Migliore, Simona Di Martino, Maria Summa, Daniele Piomelli
Activity-based protein profiling (ABPP) is a method for the identification of an enzyme of interest in a complex proteome through the use of a chemical probe that targets the enzyme's active sites. A reporter tag introduced into the probe allows for the detection of the labeled enzyme by in-gel fluorescence scanning, protein blot, fluorescence microscopy, or liquid chromatography-mass spectrometry. Here, we describe the preparation and use of the compound ARN14686, a click chemistry activity-based probe (CC-ABP) that selectively recognizes the enzyme N-acylethanolamine acid amidase (NAAA)...
November 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911380/method-for-identifying-small-molecule-inhibitors-of-the-protein-protein-interaction-between-hcn1-and-trip8b
#14
Ye Han, Kyle A Lyman, Matt Clutter, Gary E Schiltz, Quratul-Ain Ismail, Xiangying Cheng, Chi-Hao Luan, Dane M Chetkovich
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are expressed ubiquitously throughout the brain, where they function to regulate the excitability of neurons. The subcellular distribution of these channels in pyramidal neurons of hippocampal area CA1 is regulated by tetratricopeptide repeat-containing Rab8b interacting protein (TRIP8b), an auxiliary subunit. Genetic knockout of HCN pore forming subunits or TRIP8b, both lead to an increase in antidepressant-like behavior, suggesting that limiting the function of HCN channels may be useful as a treatment for Major Depressive Disorder (MDD)...
November 11, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911324/proteomics-analysis-of-blood-serums-from-alzheimer-s-disease-patients-using-itraq-labeling-technology
#15
Liming Shen, Liping Liao, Cheng Chen, Yi Guo, Dalin Song, Yong Wang, Youjiao Chen, Kaoyuan Zhang, Ming Ying, Shuiming Li, Qiong Liu, Jiazuan Ni
Alzheimer' disease (AD) is the most common form of dementia affecting up to 6% of the population over the age of 65. In order to discover differentially expressed proteins that might serve as potential biomarkers, the serums from AD patients and healthy controls were compared and analyzed using the proteomics approach of isobaric tagging for relative and absolute quantitation (iTRAQ). For the first time, AD biomarkers in serums are investigated in the Han Chinese population using iTRAQ labeled proteomics strategy...
December 1, 2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/27910495/cross-calibration-of-fuji-tr-image-plate-and-rar-2492-x-ray-film-to-determine-the-response-of-a-ditabis-super-micron-image-plate-scanner
#16
G Dunham, E C Harding, G P Loisel, P W Lake, L B Nielsen-Weber
Fuji TR image plate is frequently used as a replacement detector medium for x-ray imaging and spectroscopy diagnostics at NIF, Omega, and Z facilities. However, the familiar Fuji BAS line of image plate scanners is no longer supported by the industry, and so a replacement scanning system is needed. While the General Electric Typhoon line of scanners could replace the Fuji systems, the shift away from photo stimulated luminescence units to 16-bit grayscale Tag Image File Format (TIFF) leaves a discontinuity when comparing data collected from both systems...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910017/fluorescence-in-situ-hybridization-probe-preparation
#17
Doron Tolomeo, Roscoe R Stanyon, Mariano Rocchi
The public human genome sequencing project utilized a hierarchical approach. A large number of BAC/PAC clones, with an insert size approximate from 50 kb to 300 kb, were identified and finely mapped with respect to the Sequence Tagged Site (STS) physical map and with respect to each other. A "golden path" of BACs, covering the entire human genome, was then selected and each clone was fully sequenced. The large number of remaining BACs was not fully sequenced, but the availability of the end sequence (~800-1000 bp) at each end allowed them to be very precisely mapped on the human genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27909709/synthesis-of-a-fluorescent-photoaffinity-probe-of-osw-1-by-site-selective-acylation-of-an-inactive-congener-and-biological-evaluation
#18
K Sakurai, M Hiraizumi, N Isogai, R Komatsu, T Shibata, Y Ohta
A novel fluorescent photoaffinity probe of OSW-1 was prepared in two steps from a naturally occurring inactive congener by a sequential site-selective acylation strategy using Me2SnCl2. It displayed highly potent anticancer activity and a similar intracellular localization property to that of a fluorescently-tagged OSW-1, thereby demonstrating its potential utility in live cell studies.
December 2, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27909430/bacterial-active-community-cycling-in-response-to-solar-radiation-and-their-influence-on-nutrient-changes-in-a-high-altitude-wetland
#19
Verónica Molina, Klaudia Hernández, Cristina Dorador, Yoanna Eissler, Martha Hengst, Vilma Pérez, Chris Harrod
Microbial communities inhabiting high-altitude spring ecosystems are subjected to extreme changes in solar irradiance and temperature throughout the diel cycle. Here, using 16S rRNA gene tag pyrosequencing (cDNA) we determined the composition of actively transcribing bacteria from spring waters experimentally exposed through the day (morning, noon, and afternoon) to variable levels of solar radiation and light quality, and evaluated their influence on nutrient recycling. Solar irradiance, temperature, and changes in nutrient dynamics were associated with changes in the active bacterial community structure, predominantly by Cyanobacteria, Verrucomicrobia, Proteobacteria, and 35 other Phyla, including the recently described Candidate Phyla Radiation (e...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27909276/-closure-of-ascending-aortic-entry-by-debranching-endovascular-management-in-an-elderly-patient-with-acute-stanford-type-a-dissection
#20
Munehiro Saiki, Keiji Yunoki, Naoya Sakoda, Shigeru Hattori, Gaku Uchino, Takuya Kawabata, Yasufumi Fujita, Kunikazu Hisamochi, Hideo Yoshida
An 85-year-old woman was hospitalized by emergency for an acute Stanford type A aortic dissection. Computed tomography showed a primary entry on the ascending aorta and pericardial effusion. Although her hemodynamics was unstable due to cardiac shock, her family wished no open surgery considering her age and frailty. A couple of days later, her condition became stabilized with antihypertensive therapy. Since the dissection was limited within the ascending aorta, closure of the entry with the stentgraft was considered appropriate and much less invasive as compared with an open surgery...
December 2016: Kyobu Geka. the Japanese Journal of Thoracic Surgery
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