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https://www.readbyqxmd.com/read/29151218/structures-of-dynamic-protein-complexes-hybrid-techniques-to-study-map-kinase-complexes-and-the-escrt-system
#1
Wolfgang Peti, Rebecca Page, Evzen Boura, Bartosz Różycki
The integration of complementary molecular methods (including X-ray crystallography, NMR spectroscopy, small angle X-ray/neutron scattering, and computational techniques) is frequently required to obtain a comprehensive understanding of dynamic macromolecular complexes. In particular, these techniques are critical for studying intrinsically disordered protein regions (IDRs) or intrinsically disordered proteins (IDPs) that are part of large protein:protein complexes. Here, we explain how to prepare IDP samples suitable for study using NMR spectroscopy, and describe a novel SAXS modeling method (ensemble refinement of SAXS; EROS) that integrates the results from complementary methods, including crystal structures and NMR chemical shift perturbations, among others, to accurately model SAXS data and describe ensemble structures of dynamic macromolecular complexes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29151208/strategies-for-efficient-sample-preparation-for-dynamic-nuclear-polarization-solid-state-nmr-of-biological-macromolecules
#2
Boris Itin, Ivan V Sergeyev
Solid-state NMR (SSNMR) is a powerful tool for the elucidation of structure and dynamics in biological macromolecules. Over the years, SSNMR spectroscopists have developed an array of techniques enabling the measurement of internuclear correlations, distances, and torsional angles; these have been applied to the study of a number of biological systems that are difficult to study by X-ray crystallography and solution NMR, including key biological targets such as membrane proteins and amyloid fibrils. Applications of SSNMR to other topic areas, including materials science, pharmaceuticals, and small molecules, have also flourished in recent years...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29151207/rapid-prediction-of-multi-dimensional-nmr-data-sets-using-fandas
#3
Siddarth Narasimhan, Deni Mance, Cecilia Pinto, Markus Weingarth, Alexandre M J J Bonvin, Marc Baldus
Solid-state NMR (ssNMR) can provide structural information at the most detailed level and, at the same time, is applicable in highly heterogeneous and complex molecular environments. In the last few years, ssNMR has made significant progress in uncovering structure and dynamics of proteins in their native cellular environments [1-4]. Additionally, ssNMR has proven to be useful in studying large biomolecular complexes as well as membrane proteins at the atomic level [5]. In such studies, innovative labeling schemes have become a powerful approach to tackle spectral crowding...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29151139/integration-of-bacterial-expansin-on-agarolytic-complexes-to-enhance-the-degrading-activity-of-red-algae-by-control-of-gelling-properties
#4
Da Woon Jeong, Jeong Eun Hyeon, Young-Chul Joo, Sang Kyu Shin, Sung Ok Han
Expansin act by loosening hydrogen bonds in densely packed polysaccharides. This work characterizes the biological functions of expansin in the gelling and degradation of algal polysaccharides. In this study, the bacterial expansin BpEX from Bacillus pumilus was fused with the dockerin module of a cellulosome system for assembly with agarolytic complexes. The assembly of chimeric expansin caused an indicative enhancement in agarase activity. The enzymatic activities on agar substrate and natural biomass were 3...
November 18, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/29151020/complications-of-regional-citrate-anticoagulation-accumulation-or-overload
#5
Antoine G Schneider, Didier Journois, Thomas Rimmelé
Regional citrate anticoagulation (RCA) is now recommended over systemic heparin for continuous renal replacement therapy in patients without contraindications. Its use is likely to increase throughout the world. However, in the absence of citrate blood level monitoring, the diagnosis of citrate accumulation, the most feared complication of RCA, remains relatively complex. It is therefore commonly mistaken with other conditions. This review aims at providing clarifications on RCA-associated acid-base disturbances and their management at the bedside...
November 19, 2017: Critical Care: the Official Journal of the Critical Care Forum
https://www.readbyqxmd.com/read/29150984/how-the-environment-shapes-animal-signals-a-test-of-the-acoustic-adaptation-hypothesis-in-frogs
#6
Sandra Goutte, Alain Dubois, Samuel D Howard, Rafael Márquez, Jodi J L Rowley, J Maximilian Dehling, Philippe Grandcolas, Rongchuan Xiong, Frédéric Legendre
Long distance acoustic signals are widely used in animal communication systems and, in many cases, essential for reproduction. The Acoustic Adaptation Hypothesis (AAH) implies that acoustic signals should be selected for further transmission and better content integrity under the acoustic constraints of the habitat in which they are produced. In the present study, we test predictions derived from the AAH in frogs. Specifically, we focus on the difference between torrent frogs and frogs calling in less noisy habitats...
November 18, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29150951/inflammasome-its-role-in-traumatic-brain-and-spinal-cord-injury
#7
REVIEW
Keywan Mortezaee, Neda Khanlarkhani, Cordian Beyer, Adib Zendedel
Traumatic brain injury (TBI) and spinal cord injury (SCI) are pathological events that lead to neuropathological conditions which have in consequence the initiation of pro-inflammatory cytokine production. Neuroinflammation plays a key role in the secondary phase of both TBI and SCI after initial cell death. Activation of cytoplasmic inflammasome complexes is regarded as the essential step of neuroinflammation and a key trigger for neuronal death called pyroptosis. Inflammasome complexes are involved in activation of caspase-1 which catalyzes the cleavage of pro-interleukins into their active forms (including interleukin-18 (IL-18) and IL-1β)...
November 18, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29150791/16-channel-flexible-system-to-measure-electrophysiological-properties-of-bioengineered-hearts
#8
Betsy H Salazar, Kristopher A Hoffman, Anilkumar K Reddy, Sridhar Madala, Ravi K Birla
As tissue engineering continues to mature, it is necessary to develop new technologies that bring insight into current paradigms and guide improvements for future experiments. To this end, we have developed a system to characterize our bioartificial heart model and compare them to functional native structures. In the present study, the hearts of adult Sprague-Dawley were decellularized resulting in a natural three-dimensional cardiac scaffold. Neonatal rat primary cardiac cells were then cultured within a complex 3D fibrin gel, forming a 3-dimensional cardiac construct, which was sutured to the acellular scaffold and suspended in media for 24-48 h...
November 17, 2017: Cardiovascular Engineering and Technology
https://www.readbyqxmd.com/read/29150770/population-in-vitro-in-vivo-pharmacokinetic-model-of-first-pass-metabolism-itraconazole-and-hydroxy-itraconazole
#9
Ahmad Y Abuhelwa, Stuart Mudge, Richard N Upton, David J R Foster
The aim of this study was to develop a population in vitro-in vivo pharmacokinetic model that simultaneously describe the absorption and accumulation kinetics of itraconazole (ICZ) and hydroxy-itraconazole (HICZ) in healthy subjects. The model integrated meta-models of gastrointestinal pH and gastrointestinal transit time and in vitro dissolution models of ICZ with the absorption and disposition kinetics of ICZ and HICZ. Mean concentration intravenous data, and single- and multi-dose oral data were used for model development...
November 17, 2017: Journal of Pharmacokinetics and Pharmacodynamics
https://www.readbyqxmd.com/read/29150709/simultaneous-detection-of-nadph-consumption-and-h2o2-production-using-the-ampliflu%C3%A2-red-assay-for-screening-of-p450-activities-and-uncoupling
#10
Lisa K Morlock, Dominique Böttcher, Uwe T Bornscheuer
Cytochrome P450s belong to a large and diverse group of heme-containing enzymes. These monooxygenases catalyze the incorporation of a single atom of molecular oxygen into their substrate. In contrast to most other enzymes, the activity of P450 enzymes is not only dependent on substrate and cofactor availability and reaction conditions, but also depends on the coupling efficiency of the catalytic cycle itself. Through the electron transfer from NAD(P)H to the heme-center of the P450, the enzyme becomes activated and binds oxygen...
November 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29150664/histological-evidence-for-a-dynamic-dental-battery-in-hadrosaurid-dinosaurs
#11
Katherine Bramble, Aaron R H LeBlanc, Denis O Lamoureux, Mateusz Wosik, Philip J Currie
The first histological study of an entire hadrosaurid dental battery provides a comprehensive look at tooth movement within this complex structure. Previous studies have focused on isolated teeth, or in-situ batteries, but this is the first study to examine an entire dental battery of any dinosaur. The absence of direct tooth-to-tooth contact across the entire battery and a unique arrangement of the dental tissues in hadrosaurids led us to compare their teeth with the ever-growing incisors of mammals. The similarity in the distributions of tissues along the incisor, coupled with continuous eruption, make for helpful comparisons to hadrosaurid teeth...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150653/a-theoretical-quest-for-high-temperature-superconductivity-on-the-example-of-low-dimensional-carbon-structures
#12
C H Wong, R Lortz, E A Buntov, R E Kasimova, A F Zatsepin
High temperature superconductivity does not necessarily require correlated electron systems with complex competing or coexisting orders. Instead, it may be achieved in a phonon-mediated classical superconductor having a high Debye temperature and large electronic density of states at the Fermi level in a material with light atoms and strong covalent bonds. Quasi-1D conductors seem promising due to the Van Hove singularities in their electronic density of states. In this sense, quasi-1D carbon structures are good candidates...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150651/comprehensive-functional-enrichment-analysis-of-male-infertility
#13
Seyed Morteza Razavi, Marjan Sabbaghian, Mahdi Jalili, Adeleh Divsalar, Olaf Wolkenhauer, Ali Salehzadeh-Yazdi
Spermatogenesis is a multifactorial process that forms differentiated sperm cells in a complex microenvironment. This process involves the genome, epigenome, transcriptome, and proteome to ensure the stability of the spermatogonia and supporting cells. The identification of signaling pathways linked to infertility has been hampered by the inherent complexity and multifactorial aspects of spermatogenesis. Systems biology is a promising approach to unveil underlying signaling pathways and genes and identify putative biomarkers...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150635/one-pot-synthesis-of-trifunctional-chitosan-edta-%C3%AE-cyclodextrin-polymer-for-simultaneous-removal-of-metals-and-organic-micropollutants
#14
Feiping Zhao, Eveliina Repo, Dulin Yin, Li Chen, Simo Kalliola, Juntao Tang, Evgenia Iakovleva, Kam Chiu Tam, Mika Sillanpää
The global contamination of water resources with inorganic and organic micropollutants, such as metals and pharmaceuticals, poses a critical threat to the environment and human health. Herein, we report on a bio-derived chitosan-EDTA-β-cyclodextrin (CS-ED-CD) trifunctional adsorbent fabricated via a facile and green one-pot synthesis method using EDTA as a cross-linker, for the adsorption of toxic metals and organic micropollutants from wastewater. In this system, chitosan chain is considered as the backbone, and the immobilized cyclodextrin cavities capture the organic compounds via host-guest inclusion complexation, while EDTA-groups complex metals...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150615/balancing-a-genetic-toggle-switch-by-real-time-feedback-control-and-periodic-forcing
#15
Jean-Baptiste Lugagne, Sebastián Sosa Carrillo, Melanie Kirch, Agnes Köhler, Gregory Batt, Pascal Hersen
Cybergenetics is a novel field of research aiming at remotely pilot cellular processes in real-time with to leverage the biotechnological potential of synthetic biology. Yet, the control of only a small number of genetic circuits has been tested so far. Here we investigate the control of multistable gene regulatory networks, which are ubiquitously found in nature and play critical roles in cell differentiation and decision-making. Using an in silico feedback control loop, we demonstrate that a bistable genetic toggle switch can be dynamically maintained near its unstable equilibrium position for extended periods of time...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29150508/community-composition-and-ultrastructure-of-a-nitrate-dependent-anaerobic-methane-oxidizing-enrichment-culture
#16
Lavinia Gambelli, Simon Guerrero-Cruz, Rob J Mesman, Geert Cremers, Mike S M Jetten, Huub J M Op den Camp, Boran Kartal, Claudia Lueke, Laura van Niftrik
Methane is a very potent greenhouse gas and can be oxidized aerobically or anaerobically through microbial-mediated processes, thus decreasing methane emissions to the atmosphere. Using a complementary array of methods including phylogenetic analysis, physiological experiments, and light and electron microscopy techniques (including electron tomography), we investigated the community composition and ultrastructure of a continuous bioreactor enrichment culture, in which anaerobic methane oxidation (AOM) was coupled to nitrate reduction...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150402/network-science-of-biological-systems-at-different-scales-a-review
#17
REVIEW
Marko Gosak, Rene Markovič, Jurij Dolenšek, Marjan Slak Rupnik, Marko Marhl, Andraž Stožer, Matjaž Perc
Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present research highlights ranging from determination of the molecular interaction network within a cell to studies of architectural and functional properties of brain networks and biological transportation networks...
November 3, 2017: Physics of Life Reviews
https://www.readbyqxmd.com/read/29150313/safety-practices-perceptions-and-behaviors-in-radiation-oncology-a-national-survey-of-radiation-therapists
#18
Kristina Demas Woodhouse, David Hashemi, Kathryn Betcher, Abigail Doucette, Allison Weaver, Brian Monzon, Seth A Rosenthal, Neha Vapiwala
PURPOSE: Radiation therapy is complex and demands high vigilance and precise coordination. Radiation therapists (RTTs) directly deliver radiation and are often the first to discover an error. Yet, few studies have examined the practices of RTTs regarding patient safety. We conducted a national survey to explore the perspectives of RTTs related to quality and safety. METHODS AND MATERIALS: In 2016, an electronic survey was sent to a random sample of 1500 RTTs in the United States...
June 15, 2017: Practical Radiation Oncology
https://www.readbyqxmd.com/read/29150015/the-flotation-and-adsorption-of-mixed-collectors-on-oxide-and-silicate-minerals
#19
REVIEW
Longhua Xu, Jia Tian, Houqin Wu, Zhongyuan Lu, Wei Sun, Yuehua Hu
The analysis of flotation and adsorption of mixed collectors on oxide and silicate minerals is of great importance for both industrial applications and theoretical research. Over the past years, significant progress has been achieved in understanding the adsorption of single collectors in micelles as well as at interfaces. By contrast, the self-assembly of mixed collectors at liquid/air and solid/liquid interfaces remains a developing area as a result of the complexity of the mixed systems involved and the limited availability of suitable analytical techniques...
November 11, 2017: Advances in Colloid and Interface Science
https://www.readbyqxmd.com/read/29150007/crispr-in-animals-and-animal-models
#20
Ellen Shrock, Marc Güell
CRISPR-Cas9 has revolutionized the generation of transgenic animals. This system has demonstrated an unprecedented efficiency, multiplexability, and ease of use, thereby reducing the time and cost required for genome editing and enabling the production of animals with more extensive genetic modifications. It has also been shown to be applicable to a wide variety of animals, from early-branching metazoans to primates. Genome-wide screens in model organisms have been performed, accurate models of human diseases have been constructed, and potential therapies have been tested and validated in animal models...
2017: Progress in Molecular Biology and Translational Science
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