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https://www.readbyqxmd.com/read/28927262/autophagy-is-pro-senescence-when-seen-in-close-up-but-anti-senescence-in-long-shot
#1
Yoojin Kwon, Ji Wook Kim, Jo Ae Jeoung, Mi-Sung Kim, Chanhee Kang
When mammalian cells and animals face a variety of internal or external stresses, they need to make homeostatic changes so as to cope with various stresses. To this end, mammalian cells are equipped with two critical stress responses, autophagy and cellular senescence. Autophagy and cellular senescence share a number of stimuli including telomere shortening, DNA damage, oncogenic stress and oxidative stress, suggesting their intimate relationship. Autophagy is originally thought to suppress cellular senescence by removing damaged macromolecules or organelles, yet recent studies also indicated that autophagy promotes cellular senescence by facilitating the synthesis of senescence-associated secretory proteins...
September 20, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28924669/measuring-nanometer-distances-between-fluorescent-labels-step-by-step
#2
Susanna Maria Früh, Ingmar Schoen
Super-resolution fluorescence microscopy methods are increasingly applied to study the structure of biological molecules within their natural context or at biomaterial interfaces. We here provide a protocol for Single-molecule High-Resolution Imaging with Photobleaching (SHRImP) that can be used to obtain information about the conformation of large proteins or other macromolecules at the single-molecule level. This procedure requires site-specific protein labeling with fluorescent dyes, immobilization and sample preparation, optimization of imaging buffer composition and microscope settings, and acquisition of short time-lapse movies that capture the stepwise bleaching behavior of individual molecules...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28924037/intrinsically-disordered-sequences-enable-modulation-of-protein-phase-separation-through-distributed-tyrosine-motifs
#3
Yuan Lin, Simon L Currie, Michael Keith Rosen
Liquid-liquid phase separation (LLPS) is thought to contribute to establishment of many biomolecular condensates, eukaryotic cell structures that concentrate diverse macromolecules but lack a bounding membrane. RNA granules control RNA metabolism and comprise a large class of condensates that are enriched in RNA-binding proteins and RNA molecules. Many RNA granule proteins are composed of both modular domains and intrinsically disordered regions (IDRs) having low amino acid sequence complexity. Phase separation of these molecules likely plays an important role in the generation and stability of RNA granules...
September 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28923564/multi-step-synthesis-spectroscopic-studies-of-biological-active-steroidal-thiosemicarbazones-and-their-palladium-ii-complex-as-macromolecules
#4
Salman A Khan, Abdullah M Asiri
Steroidal Pd (II) metal complexes were synthesized by the reaction of steroidal thiosemicarbazones with [Pd (DMSO)2 Cl2]. The steroidal thiosemicarbazones coordinate to palladium through the azomethine nitrogen and thionic sulfur. The thiosemicarbazone derivatives were obtained by the reaction of thiosemicarbazide with steroidal ketones. The identity of steroidal thiosemicarbazones and their Pd(II) metal complexes were elucidated by IR, (1)H, (13)C NMR, FAB mass spectroscopic methods, elemental analysis and TGA analysis...
September 15, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28923365/mitochondrial-dynamics-at-the-interface-of-immune-cell-metabolism-and-function
#5
REVIEW
Angelika S Rambold, Erika L Pearce
Immune cell differentiation and function are crucially dependent on specific metabolic programs dictated by mitochondria, including the generation of ATP from the oxidation of nutrients and supplying precursors for the synthesis of macromolecules and post-translational modifications. The many processes that occur in mitochondria are intimately linked to their morphology that is shaped by opposing fusion and fission events. Exciting evidence is now emerging that demonstrates reciprocal crosstalk between mitochondrial dynamics and metabolism...
September 8, 2017: Trends in Immunology
https://www.readbyqxmd.com/read/28922528/mass-production-and-pore-size-control-of-holey-carbon-microcages
#6
Lei Zhang, Xiaoxiao Liu, Yuhai Dou, Binwei Zhang, Huiling Yang, Shixue Dou, Huakun Liu, Yunhui Huang, Xianluo Hu
Architectural control of porous solids, such as porous carbon cages, has received considerable attention for versatile applications because of their attractive ability to interact with liquids and gases not only at the surface, but throughout the bulk. Here we report a scalable, facile spray-pyrolysis route to synthesize holey carbon microcages with mosquito-net-like shells. Using the surfaces of water droplets as the growth templates, styrene-butadiene rubber macromolecules are controllably cross-linked, and size-tunable holes on the carbon shells are generated...
September 18, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28921961/three-dimensional-reconstruction-of-nuclear-envelope-architecture-using-dual-color-metal-induced-energy-transfer-imaging
#7
Anna M Chizhik, Daja Ruhlandt, Janine Pfaff, Narain Karedla, Alexey I Chizhik, Ingo Gregor, Ralph Heinz Kehlenbach, Joerg Enderlein
The nuclear envelope, comprising the inner and the outer nuclear membrane, separates the nucleus from the cytoplasm and plays a key role in cellular functions. Nuclear pore complexes (NPCs), which are embedded in the nuclear envelope, control transport of macromolecules between the two compartments. Here, using dual-color Metal-Induced Energy Transfer (MIET), we determine the axial distance between Lap2β and Nup358 as markers for the inner nuclear membrane and the cytoplasmic side of the NPC, respectively...
September 18, 2017: ACS Nano
https://www.readbyqxmd.com/read/28921693/liquid-cell-electron-microscopy-of-adsorbed-polymers
#8
Kandula Hima Nagamanasa, Huan Wang, Steve Granick
Individual macromolecules of polystyrene sulfonate and poly(ethylene oxide) are visualized with nanometer resolution using transmission electron microscopy (TEM) imaging of aqueous solutions with and without added salt, trapped in liquid pockets between creased graphene sheets. Successful imaging with 0.3 s per frame is enabled by the sluggish mobility of the adsorbed molecules. This study finds, validating others, that an advantage of this graphene liquid-cell approach is apparently to retard sample degradation from incident electrons, in addition to minimizing background scattering because graphene windows are atomically thin...
September 18, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28919443/fv-clasp-an-artificially-designed-small-antibody-fragment-with-improved-production-compatibility-stability-and-crystallizability
#9
Takao Arimori, Yu Kitago, Masataka Umitsu, Yuki Fujii, Ryoko Asaki, Keiko Tamura-Kawakami, Junichi Takagi
Antibody fragments are frequently used as a "crystallization chaperone" to aid structural analysis of complex macromolecules that are otherwise crystallization resistant, but conventional fragment formats have not been designed for this particular application. By fusing an anti-parallel coiled-coil structure derived from the SARAH domain of human Mst1 kinase to the variable region of an antibody, we succeeded in creating a novel chimeric antibody fragment of ∼37 kDa, termed "Fv-clasp," which exhibits excellent crystallization compatibility while maintaining the binding ability of the original IgG molecule...
September 6, 2017: Structure
https://www.readbyqxmd.com/read/28918856/determination-of-molar-masses-of-macromolecules-by-sec-light-scattering-not-requiring-knowledge-of-refractive-index-increments
#10
Simona Lavric, Jasmin Preis, Christine Rosenauer, Wolfgang Radke
A new approach for the calibration of SEC-light scattering (SEC-LS) setups is proposed, which requires solely the molar mass of a reference polymer. Neither the specific refractive index increment of the calibrant nor of the analyte is required. Comparison of the molar masses derived in different solvents for a large number of chemically different polymers shows that the new approach yields the same molar masses as if molar masses were derived using dn/dc to calibrate the light scattering setup. The approach therefore allows easier determination of molar masses by SEC-LS...
September 6, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28917924/synthesis-of-amphoteric-curdlan-derivatives-for-delivery-of-therapeutic-nucleic-acids
#11
Yao Tong, Tsogzolmaa Ganbold, Huricha Baigude
Cationic polymers are powerful carriers for intracellular delivery of therapeutic nucleic acids. However, the positively charged macromolecules have considerable cytotoxicity and often induce irreversible damages to the cells and tissues, which greatly negate the clinical application of such materials as drug delivery system. Herein, we report the synthesis of novel amphoteric polymers based on curdlan, and the evaluation of their cytotoxicity as well as the nucleic acid delivery efficiency. β-(1,3)-polyglucuronic acid, a TEMPO-oxidized derivative of curdlan, was chemically modified by conjugation of tetraethylenepentamine...
November 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28917919/structural-characteristics-of-water-soluble-polysaccharides-from-norway-spruce-picea-abies
#12
Evgeny G Shakhmatov, Vladimir A Belyy, Elena N Makarova
Arabinogalactan proteins and pectic polysaccharides were isolated from greenery of Picea abies by water extraction. Main elements of their structure were determined by ion-exchange chromatography, partial acid and enzymatic hydrolysis, and NMR spectroscopy. It was established that the backbone of pectin macromolecules of greenery of P. abies is represented by segments of partially methyl-esterified and acetylated 1,4-α-d-galactopyranosyluronan, and partially 2-O- and/or 3-O-acetylated RG-I with side chains consisting of highly-branched 1,5-α-l-arabinan segments...
November 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28917856/the-effect-of-ionic-and-non-ionic-surfactants-and-ph-on-the-stability-adsorption-and-electrokinetic-properties-of-the-alginic-acid-alumina-system
#13
E Grządka, J Matusiak
The influence of ionic (CTAB; SDS) and non-ionic (TX-100; TX-165 and TX-405) surfactants as well as pH of the solution on the stability, adsorption and electrokinetic properties of the alginic acid (AA)/alumina (Al2O3) suspensions was studied. The results obtained using the spectrophotometric method show that the addition of ionic surfactants is an effective way to obtain stable AA/Al2O3 suspensions whereas the changes in pH are not sufficient. Surface tension measurements together with the adsorption data show that the macromolecules of alginic acid are able to form complexes with CTAB, however, they compete for the adsorption centers on the metal oxide surface with SDS...
November 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28917532/effects-of-tumor-microenvironments-on-targeted-delivery-of-glycol-chitosan-nanoparticles
#14
Ji Young Yhee, Sangmin Jeon, Hong Yeol Yoon, Man Kyu Shim, Hyewon Ko, Jiwoong Min, Jin Hee Na, Hyeyoun Chang, Hyounkoo Han, Jong-Ho Kim, Minah Suh, Hyukjin Lee, Jae Hyung Park, Kwangmeyung Kim, Ick Chan Kwon
In cancer theranostics, the main strategy of nanoparticle-based targeted delivery system has been understood by enhanced permeability and retention (EPR) effect of macromolecules. Studies on diverse nanoparticles provide a better understanding of different EPR effects depending on their structure, physicochemical properties, and chemical modifications. Recently the tumor microenvironment has been considered as another important factor for determining tumor-targeted delivery of nanoparticles, but the correlation between EPR effects and tumor microenvironment has not yet been fully elucidated...
September 13, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28917122/structure-determination-based-on-continuous-diffraction-from-macromolecular-crystals
#15
REVIEW
Henry N Chapman, Petra Fromme
Bright and coherent X-ray sources, such free-electron lasers, have spurred large activities in developing new methods to obtain the structures of biological macromolecules. In particular, single-molecule diffraction is highly desired, as it would abolish the need for crystallization. It provides considerably more diffraction intensity information than needed to solve a structure, unlike crystal diffraction, which is usually insufficient for direct phasing. To overcome the challenge of weak scattering signals of single molecules, the direct phasing approaches in coherent diffractive imaging have been combined with crystals in several imaginative ways...
September 13, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28915045/identification-and-validation-of-reaction-coordinates-describing-protein-functional-motion-hierarchical-dynamics-of-t4-lysozyme
#16
Matthias Ernst, Steffen Wolf, Gerhard Stock
While adequately chosen reaction coordinates are expected to reveal the mechanism of a dynamical process, it proves to be notoriously difficult to model the complex structural rearrangement of a macromolecule by a low-dimensional collective coordinate. Adopting the hinge-bending motion of T4 lysozyme (T4L) as a prominent example and performing a 50 microsecond long unbiased molecular dynamics (MD) simulation of T4L, a general strategy to identify reaction coordinates of protein functional dynamics is developed...
September 15, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28913343/exacerbating-and-reversing-lysosomal-storage-diseases-from-yeast-to-humans
#17
REVIEW
Tamayanthi Rajakumar, Andrew B Munkacsi, Stephen L Sturley
Lysosomal storage diseases (LSDs) arise from monogenic deficiencies in lysosomal proteins and pathways and are characterized by a tissue-wide accumulation of a vast variety of macromolecules, normally specific to each genetic lesion. Strategies for treatment of LSDs commonly depend on reduction of the offending metabolite(s) by substrate depletion or enzyme replacement. However, at least 44 of the ~50 LSDs are currently recalcitrant to intervention. Murine models have provided significant insights into our understanding of many LSD mechanisms; however, these systems do not readily permit phenotypic screening of compound libraries, or the establishment of genetic or gene-environment interaction networks...
August 25, 2017: Microbial Cell
https://www.readbyqxmd.com/read/28912550/calcium-mediated-adhesion-of-nanomaterials-in-reservoir-fluids
#18
Shannon L Eichmann, Nancy A Burnham
Globally, a small percentage of oil is recovered from reservoirs using primary and secondary recovery mechanisms, and thus a major focus of the oil industry is toward developing new technologies to increase recovery. Many new technologies utilize surfactants, macromolecules, and even nanoparticles, which are difficult to deploy in harsh reservoir conditions and where failures cause material aggregation and sticking to rock surfaces. To combat these issues, typically material properties are adjusted, but recent studies show that adjusting the dispersing fluid chemistry could have significant impact on material survivability...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911541/food-macromolecule-based-nanodelivery-systems-for-enhancing-the-bioavailability-of-polyphenols
#19
REVIEW
Bing Hu, Xixia Liu, Chunlan Zhang, Xiaoxiong Zeng
Diet polyphenols-primarily categorized into flavonoids (e.g., flavonols, flavones, flavan-3-ols, anthocyanidins, flavanones, and isoflavones) and nonflavonoids (with major subclasses of stilbenes and phenolic acids)-are reported to have health-promoting effects, such as antioxidant, antiinflammatory, anticarcinoma, antimicrobial, antiviral, and cardioprotective properties. However, their applications in functional foods or medicine are limited because of their inefficient systemic delivery and poor oral bioavailability...
January 2017: Journal of Food and Drug Analysis
https://www.readbyqxmd.com/read/28906114/doglycans-tools-for-preparing-carbohydrate-structures-for-atomistic-simulations-of-glycoproteins-glycolipids-and-carbohydrate-polymers-with-gromacs
#20
Reinis Danne, Chetan Poojari, Hector Martinez-Seara, Sami Rissanen, Fabio Lolicato, Tomasz Rog, Ilpo Vattulainen
Carbohydrates constitute a structurally and functionally diverse group of biological and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell-cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models...
September 14, 2017: Journal of Chemical Information and Modeling
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