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https://www.readbyqxmd.com/read/28735876/methods-for-automatic-detection-of-artifacts-in-microelectrode-recordings
#1
Eduard Bakštein, Tomáš Sieger, Jiří Wild, Daniel Nova'k, Jakub Schneider, Pavel Vostatek, Dušan Urgošík, Robert Jech
BACKGROUND: Extracellular microelectrode recording (MER) is a prominent technique for studies of extracellular single-unit neuronal activity. In order to achieve robust results in more complex analysis pipelines, it is necessary to have high quality input data with a low amount of artifacts. We show that noise (mainly electromagnetic interference and motion artifacts) may affect more than 25% of the recording length in a clinical MER database. NEW METHOD: We present several methods for automatic detection of noise in MER signals, based on i) unsupervised detection of stationary segments, ii) large peaks in the power spectral density, and iii) a classifier based on multiple time- and frequency-domain features...
July 20, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28732502/chronic-glucocorticoid-exposure-activates-bk-nlrp1-signal-involving-in-hippocampal-neuron-damage
#2
Biqiong Zhang, Yaodong Zhang, Wenning Wu, Tanzhen Xu, Yanyan Yin, Junyan Zhang, Dake Huang, Weizu Li
BACKGROUND: Neuroinflammation mediated by NLRP1 (nucleotide-binding oligomerization domain (NOD)-like receptor protein 1) inflammasome plays an important role in many neurological diseases such as Parkinson's disease (PD) and Alzheimer's disease (AD). Our previous studies showed that chronic glucocorticoid (GC) exposure increased brain inflammation via NLRP1 inflammasome and induce neurodegeneration. However, little is known about the mechanism of chronic GC exposure on NLRP1 inflammasome activation in hippocampal neurons...
July 21, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28731220/mechanically-tunable-bioink-for-3d-bioprinting-of-human-cells
#3
Aurelien Forget, Andreas Blaeser, Florian Miessmer, Marius Köpf, Daniela F Duarte Campos, Nicolas H Voelcker, Anton Blencowe, Horst Fischer, V Prasad Shastri
This study introduces a thermogelling bioink based on carboxylated agarose (CA) for bioprinting of mechanically defined microenvironments mimicking natural tissues. In CA system, by adjusting the degree of carboxylation, the elastic modulus of printed gels can be tuned over several orders of magnitudes (5-230 Pa) while ensuring almost no change to the shear viscosity (10-17 mPa) of the bioink solution; thus enabling the fabrication of 3D structures made of different mechanical domains under identical printing parameters and low nozzle shear stress...
July 21, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28722599/assessment-of-fecal-exposure-pathways-in-low-income-urban-neighborhoods-in-accra-ghana-rationale-design-methods-and-key-findings-of-the-sanipath-study
#4
Katharine Robb, Clair Null, Peter Teunis, Habib Yakubu, George Armah, Christine L Moe
Rapid urbanization has contributed to an urban sanitation crisis in low-income countries. Residents in low-income, urban neighborhoods often have poor sanitation infrastructure and services and may experience frequent exposure to fecal contamination through a range of pathways. There are little data to prioritize strategies to decrease exposure to fecal contamination in these complex and highly contaminated environments, and public health priorities are rarely considered when planning urban sanitation investments...
July 17, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28719134/development-and-implementation-of-a-clinical-pathway-for-cardiac-surgery-in-the-intensive-care-unit-effects-on-protocol-adherence
#5
Marion van der Kolk, Mark van den Boogaard, Corine Ter Brugge-Speelman, Jeroen Hol, Luc Noyez, Kees van Laarhoven, Hans van der Hoeven, Peter Pickkers
RATIONALE, AIMS AND OBJECTIVES: Cardiac surgery (CS) is facilitated by multiple perioperative guidelines and protocols. Use of a clinical pathway (CP) may facilitate the care of these patients. METHODS: This is a pre-post design study in the ICU of a tertiary referral centre. A CP for CS patients in the ICU was developed by ICU-nurses and enabled them to execute proactively predefined actions in accordance with and within the preset boundaries which were part of a variance report...
July 18, 2017: Journal of Evaluation in Clinical Practice
https://www.readbyqxmd.com/read/28717195/stability-of-the-phf10-subunit-of-pbaf-signature-module-is-regulated-by-phosphorylation-role-of-%C3%AE-trcp
#6
Victor V Tatarskiy, Yuriy P Simonov, Dmitrii S Shcherbinin, Alexander V Brechalov, Sofia G Georgieva, Nataliya V Soshnikova
The PBAF chromatin-remodeling complexes are multi-protein machines, regulating expression of genes involved in proliferation and differentiation. PHF10 is a subunit of the PBAF essential for its association with chromatin. Mammalian PHF10 is expressed as four ubiquitous isoforms, which are alternatively incorporated in the complex and differ by their influence on transcription of target genes. PHF10 have different domain structure and two of them (PHF10-S isoforms) lack C-terminal PHD domains, which enables their phosphorylation by CK-1...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717148/human-ribosomal-p1-p2-heterodimer-represents-an-optimal-docking-site-for-ricin-a-chain-with-a-prominent-role-for-p1-c-terminus
#7
Przemysław Grela, Xiao-Ping Li, Patrycja Horbowicz, Monika Dźwierzyńska, Marek Tchórzewski, Nilgun E Tumer
The eukaryotic P-stalk contains two P1-P2 protein dimers with a conserved C- terminal domain (CTD) critical for the interaction with external factors. To understand the role of the individual CTD of human P1/P2 proteins, we examined the interaction of reconstituted human P-protein complexes and C-terminally truncated forms with ricin A chain (RTA), which binds to the stalk to depurinate the sarcin/ricin loop (SRL). The interaction between P-protein complexes and RTA was examined by surface plasmon resonance, isothermal titration calorimetry, microscale thermophoresis and bio-layer interferometry...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28715328/recovery-of-damped-exponentials-using-structured-low-rank-matrix-completion
#8
Arvind Balachandrasekaran, Vincent Magnotta, Mathews Jacob
We introduce a structured low rank matrix completion algorithm to recover a series of images from their undersampled measurements, where the signal along the parameter dimension at every pixel is described by a linear combination of exponentials. We exploit the exponential behavior of the signal at every pixel, along with the spatial smoothness of the exponential parameters to derive an annihilation relation in the Fourier domain. This relation translates to a low-rank property on a structured matrix constructed from the Fourier samples...
July 14, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28714556/non-canonical-activation-of-histidine-kinase-kdpd-by-phosphotransferase-protein-ptsn-through-interaction-with-the-transmitter-domain
#9
Markus Mörk-Mörkenstein, Ralf Heermann, Yvonne Göpel, Kirsten Jung, Boris Görke
The two-component system KdpD/KdpE governs K(+) homeostasis by controlling synthesis of the high affinity K(+) transporter KdpFABC. When sensing low environmental K(+) concentrations, the dimeric kinase KdpD autophosphorylates in trans and transfers the phosphoryl-group to the response regulator KdpE, which subsequently activates kdpFABC transcription. In Escherichia coli, KdpD can also be activated by interaction with the non-phosphorylated form of the accessory protein PtsN. PtsN stimulates KdpD kinase activity thereby increasing phospho-KdpE levels...
July 17, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28712573/ve-cadherin-phosphorylation-regulates-endothelial-fluid-shear-stress-responses-through-the-polarity-protein-lgn
#10
Daniel E Conway, Brian G Coon, Madhusuthan Budatha, Paul T Arsenovic, Fabrizio Orsenigo, Florian Wessel, Jiasheng Zhang, Zhenwu Zhuang, Elisabetta Dejana, Dietmar Vestweber, Martin A Schwartz
Fluid shear stress due to blood flow on the vascular endothelium regulates blood vessel development, remodeling, physiology, and pathology [1, 2]. A complex consisting of PECAM-1, VE-cadherin, and vascular endothelial growth factor receptors (VEGFRs) that resides at endothelial cell-cell junctions transduces signals important for flow-dependent vasodilation, blood vessel remodeling, and atherosclerosis. PECAM-1 transduces forces to activate src family kinases (SFKs), which phosphorylate and transactivate VEGFRs [3-5]...
July 10, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28708999/splicing-activation-by-rbfox-requires-self-aggregation-through-its-tyrosine-rich-domain
#11
Yi Ying, Xiao-Jun Wang, Celine K Vuong, Chia-Ho Lin, Andrey Damianov, Douglas L Black
Proteins of the Rbfox family act with a complex of proteins called the Large Assembly of Splicing Regulators (LASR). We find that Rbfox interacts with LASR via its C-terminal domain (CTD), and this domain is essential for its splicing activity. In addition to LASR recruitment, a low-complexity (LC) sequence within the CTD contains repeated tyrosines that mediate higher-order assembly of Rbfox/LASR and are required for splicing activation by Rbfox. This sequence spontaneously aggregates in solution to form fibrous structures and hydrogels, suggesting an assembly similar to the insoluble cellular inclusions formed by FUS and other proteins in neurologic disease...
July 13, 2017: Cell
https://www.readbyqxmd.com/read/28701714/structural-and-biochemical-characterization-of-apicomplexan-inorganic-pyrophosphatases
#12
Abhishek Jamwal, Manickam Yogavel, Malik Z Abdin, Swatantra K Jain, Amit Sharma
Inorganic pyrophosphatases (PPase) participate in energy cycling and they are essential for growth and survival of organisms. Here we report extensive structural and functional characterization of soluble PPases from the human parasites Plasmodium falciparum (PfPPase) and Toxoplasma gondii (TgPPase). Our results show that PfPPase is a cytosolic enzyme whose gene expression is upregulated during parasite asexual stages. Cambialistic PfPPase actively hydrolyzes linear short chain polyphosphates like PPi, polyP3 and ATP in the presence of Zn(2+)...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28695738/proton-shuttling-and-reaction-paths-in-dissociative-electron-attachment-to-o-and-p-tetrafluorohydroquinone-an-experimental-and-theoretical-study
#13
Benedikt Ómarsson, Ragnar Bjornsson, Oddur Ingólfsson
Here we present a combined experimental and theoretical study on the fragmentation of o- and p-tetrafluorohydroquinone upon low energy electron attachment. Despite an identical ring-skeleton and identical functional groups in these constitutional isomers, they show distinctly different fragmentation patterns, a phenomenon that cannot be explained by distinct resonances or different thermochemistry. Using high-level quantum chemical calculations with the computationally affordable domain localized pair natural orbital approach, DLPNO-CCSD(T), we are able to provide a complete and accurate description of the respective reaction dynamics, revealing proton shuttling and transition states for competing channels as the explanation for the different behavior of these isomers...
July 21, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28695448/mitochondrial-atp-mg-phosphate-carriers-transport-divalent-inorganic-cations-in-complex-with-atp
#14
Magnus Monné, Lucia Daddabbo, Lorena Carla Giannossa, Maria Cristina Nicolardi, Luigi Palmieri, Daniela Valeria Miniero, Annarosa Mangone, Ferdinando Palmieri
The ATP-Mg/phosphate carriers (APCs) modulate the intramitochondrial adenine nucleotide pool size. In this study the concentration-dependent effects of Mg(2+) and other divalent cations (Me(2+)) on the transport of [(3)H]ATP in liposomes reconstituted with purified human and Arabidopsis APCs (hAPCs and AtAPCs, respectively, including some lacking their N-terminal domains) have been investigated. The transport of Me(2+) mediated by these proteins was also measured. In the presence of a low external concentration of [(3)H]ATP (12 μM) and increasing concentrations of Me(2+), Mg(2+) stimulated the activity (measured as initial transport rate of [(3)H]ATP) of hAPCs and decreased that of AtAPCs; Fe(2+) and Zn(2+) stimulated markedly hAPCs and moderately AtAPCs; Ca(2+) and Mn(2+) markedly AtAPCs and moderately hAPCs; and Cu(2+) decreased the activity of both hAPCs and AtAPCs...
July 10, 2017: Journal of Bioenergetics and Biomembranes
https://www.readbyqxmd.com/read/28694351/phosphorylation-of-ampk-by-upstream-kinases-is-required-for-activity-in-mammalian-cells
#15
Robin Willows, Matthew J Sanders, Bing Xiao, Bhakti R Patel, Stephen R Martin, Jon Read, Jon R Wilson, Julia Hubbard, Steven J Gamblin, David Carling
AMP-activated protein kinase (AMPK) plays a major role in regulating metabolism and has attracted significant attention as a therapeutic target for treating metabolic disorders. AMPK activity is stimulated more than one hundred fold by phosphorylation of threonine 172 (Thr(172)). Binding of AMP to the γ subunit allosterically activates the kinase. Additionally, a number of small molecules e.g. 991, have been identified that bind between the kinase domain and the carbohydrate binding module of the β subunit, stabilising their interaction and leading to activation...
July 10, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28691818/copper-ii-binding-sites-in-n-terminally-acetylated-%C3%AE-synuclein-a-theoretical-rationalization
#16
Rafael Ramis, Joaquín Ortega-Castro, Bartolomé Vilanova, Miquel Adrover, Juan Frau
The interactions between N-terminally acetylated α-synuclein and Cu(II) at several binding sites have been studied with DFT calculations, specifically with the M06 hybrid functional and the ωB97X-D DFT-D functional. In previous experimental studies, Cu(II) was shown to bind several α-synuclein residues, including Met1-Asp2 and His50, forming square planar coordination complexes. Also, it was determined that a low-affinity binding site exists in the C-terminal domain, centered on Asp121. However, in the N-terminally acetylated protein, present in vivo, the Met1 site is blocked...
July 19, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28691114/structure-and-dynamics-of-type-iii-secretion-effector-protein-exou-as-determined-by-sdsl-epr-spectroscopy-in-conjunction-with-de-novo-protein-folding
#17
Axel W Fischer, David M Anderson, Maxx H Tessmer, Dara W Frank, Jimmy B Feix, Jens Meiler
ExoU is a 74 kDa cytotoxin that undergoes substantial conformational changes as part of its function, that is, it has multiple thermodynamically stable conformations that interchange depending on its environment. Such flexible proteins pose unique challenges to structural biology: (1) not only is it often difficult to determine structures by X-ray crystallography for all biologically relevant conformations because of the flat energy landscape (2) but also experimental conditions can easily perturb the biologically relevant conformation...
June 30, 2017: ACS Omega
https://www.readbyqxmd.com/read/28690315/targeting-nucleolin-for-better-survival-in-diffuse-large-b-cell-lymphoma
#18
N Jain, H Zhu, T Khashab, Q Ye, B George, R Mathur, R K Singh, Z Berkova, J F Wise, F K Braun, X Wang, K Patel, Z Y Xu-Monette, J Courty, K H Young, L Sehgal, F Samaniego
Anthracyclines have been a cornerstone in the cure of diffuse large B-cell lymphoma (DLBCL) and other hematological cancers. The ability of anthracyclines to eliminate DLBCL depends on the presence of topoisomerase-II-alpha (TopIIA), a DNA repair enzyme complex. We identified nucleolin as a novel binding partner of TopIIA. Abrogation of nucleolin sensitized DLBCL cells to TopIIA targeting agents (doxorubicin/etoposide). Silencing nucleolin and challenging DLBCL cells with doxorubicin enhanced the phosphorylation of H2AX (γH2AX-marker of DNA damage) and allowed DNA fragmentation...
July 10, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28689418/an-assay-based-on-samdi-mass-spectrometry-for-profiling-protein-interaction-domains
#19
Patrick T O'Kane, Milan Mrksich
This paper describes an assay that can profile the binding of a protein to ligands and can rank the affinities of a library of ligands. The method is based on the enhanced rate of an enzyme-mediated reaction that follows from colocalization of the enzyme and substrate by a protein-ligand interaction. This assay uses a self-assembled monolayer that presents a candidate peptide ligand for a receptor and a peptide substrate for an enzyme. The receptor is prepared as a fusion to the relevant enzyme so that binding of the receptor to the immobilized ligand brings the enzyme to the surface, where it can more rapidly modify its substrate...
July 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28674936/the-fof1-atp-synthase-from-atomistic-three-dimensional-structure-to-the-rotary-chemical-function
#20
REVIEW
Shayantani Mukherjee, Arieh Warshel
Molecular motors are multi-subunit complexes that are indispensable for accomplishing various tasks of the living cells. One such molecular motor is the FOF1 ATP synthase that synthesizes ATP at the expense of the membrane proton gradient. Elucidating the molecular origin of the motor function is challenging despite significant advances in various experimental fields. Currently atomic simulations of whole motor complexes cannot reach to functionally relevant time scales that extend beyond the millisecond regime...
July 3, 2017: Photosynthesis Research
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