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Structural biology

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https://www.readbyqxmd.com/read/28212489/direct-single-enzyme-biomineralization-of-catalytically-active-ceria-and-ceria-zirconia-nanocrystals
#1
Christopher D Curran, Li Lu, Yue Jia, Christopher J Kiely, Bryan W Berger, Steven McIntosh
Biomineralization is an intriguing approach to the synthesis of functional inorganic materials for energy applications whereby biological systems are engineered to mineralize inorganic materials and control their structure over multiple length scales under mild reaction conditions. Herein we demonstrate a single enzyme mediated biomineralization route to synthesize crystalline, catalytically active, quantum confined ceria (CeO2-x) and ceria-zirconia (Ce1-yZryO2-x) nanocrystals for application as environmental catalysts...
February 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/28212460/do-low-oxygen-environments-facilitate-marine-invasions-relative-tolerance-of-native-and-invasive-species-to-low-oxygen-conditions
#2
Marcelo E Lagos, Diego R Barneche, Craig R White, Dustin J Marshall
Biological invasions are one of the biggest threats to global biodiversity. Marine artificial structures are proliferating worldwide and provide a haven for marine invasive species. Such structures disrupt local hydrodynamics, which can lead to the formation of oxygen-depleted microsites. The extent to which native fauna can cope with such low oxygen conditions, and whether invasive species, long associated with artificial structures in flow-restricted habitats, have adapted to these conditions remains unclear...
February 17, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28212382/de-novo-assembly-of-the-sea-trout-salmo-trutta-m-trutta-skin-transcriptome-to-identify-putative-genes-involved-in-the-immune-response-and-epidermal-mucus-secretion
#3
Magdalena Malachowicz, Roman Wenne, Artur Burzynski
In fish, the skin is a multifunctional organ and the first barrier against pathogens. Salmonids differ in their susceptibility to microorganisms due to varied skin morphology and gene expression patterns. The brown trout is a salmonid species with important commercial and ecological value in Europe. However, there is a lack of knowledge regarding the genes involved in the immune response and mucus secretion in the skin of this fish. Thus, we characterized the skin transcriptome of anadromous brown trout using next-generation sequencing (NGS)...
2017: PloS One
https://www.readbyqxmd.com/read/28212306/metabolic-effects-of-berries-with-structurally-diverse-anthocyanins
#4
John Overall, Sierra A Bonney, Mickey Wilson, Arnold Beermann, Mary H Grace, Debora Esposito, Mary Ann Lila, Slavko Komarnytsky
Overconsumption of energy dense foods and sedentary lifestyle are considered as major causes of obesity-associated insulin resistance and abnormal glucose metabolism. Results from both cohort studies and randomized trials suggested that anthocyanins from berries may lower metabolic risks, however these reports are equivocal. The present study was designed to examine effects of six berries with structurally diverse anthocyanin profiles (normalized to 400 µg/g total anthocyanin content) on development of metabolic risk factors in the C57BL/6 mouse model of polygenic obesity...
February 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28212112/cancer-as-robust-intrinsic-state-shaped-by-evolution-a-key-issues-review
#5
Ruoshi Yuan, Xiaomei Zhu, Gaowei Wang, Site Li, Ping Ao
Cancer is a complex disease: its pathology cannot be properly understood in terms of independent players-genes, proteins, molecular pathways, or their simple combinations. This is similar to many-body physics of a condensed phase that many important properties are not determined by a single atom or molecule. The rapidly accumulating large 'omics' data also require a new mechanistic and global underpinning to organize for rationalizing cancer complexity. A unifying and quantitative theory was proposed by some of the present authors that cancer is a robust state formed by the endogenous molecular-cellular network, which is evolutionarily built for the developmental processes and physiological functions...
February 17, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28212091/multistability-and-bifurcation-analysis-of-inhibitory-coupled-cyclic-genetic-regulatory-networks-with-delays
#6
Guang Ling, Zhi-Hong Guan, Bin Hu, Qiang Lai, Yonghong Wu
Many biological systems have the conspicuous property to present more than one stable state and diverse rhythmic behaviors. A closed relationship between these complex dynamic behaviors and cyclic genetic structures has been witnessed by pioneering works. In this paper, a typical structure of inhibitory coupled cyclic genetic networks is introduced to further enlighten this mechanism of stability and biological rhythms of living cells. The coupled networks consist two identical cyclic genetic subnetworks, which inhibit each other directly...
February 14, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28212034/observation-of-the-global-dynamic-collectivity-of-a-hydration-shell-around-apomyoglobin
#7
Yangzhong Qin, Luyuan Zhang, Lijuan Wang, Dongping Zhong
Protein surface hydration is critical to its structural properties and biological activities. However, it is still unknown whether the hydration shell is intrinsically connected and how its fluctuations dynamically interact with protein motions. Here, by selecting five site-specific locations with distinctly different environments around apomyoglobin surface, we used a tryptophan scan with femtosecond fluorescence spectroscopy and simultaneously detected hydration-water dynamics and tryptophan sidechain relaxations with temperature dependence...
February 17, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28212005/stimuli-responsive-polymersomes-for-biomedical-applications
#8
Xiuli Hu, Yuqi Zhang, Zhigang Xie, Xiabin Jing, Adriano Bellotti, Zhen Gu
Polymersomes, the structural analogues of liposomes, are hollow structures enclosed by a bilayer membrane made from amphiphilic copolymers. Polymersomes have been proposed to mimic the structure and properties of cellular membranes and viral capsids. Excellent robustness and stability, chemical versatility for tunable membrane properties and surface functionalization make polymersomes attractive candidates for drug delivery, diagnostic imaging, nanoreactor vessels, and artificial organelles. In further biomimetic strategies, stimuli-responsive polymersomes that can recognize various external physical or internal biological environmental stimuli and conduct "on demand" release in dose-, spatial-, and temporal-controlled fashions have been widely developed...
February 17, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28211907/identification-of-extracellular-segments-by-mass-spectrometry-improves-topology-prediction-of-transmembrane-proteins
#9
Tamás Langó, Gergely Róna, Éva Hunyadi-Gulyás, Lilla Turiák, Julia Varga, László Dobson, György Várady, László Drahos, Beáta G Vértessy, Katalin F Medzihradszky, Gergely Szakács, Gábor E Tusnády
Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211640/complexation-of-oxethazaine-with-2-hydroxypropyl-%C3%AE-cyclodextrin-increased-drug-solubility-decreased-cytotoxicity-and-analgesia-at-inflamed-tissues
#10
Andressa R Prado, Fabiano Yokaichiya, Margareth Kazuyo Kobayashi Dias Franco, Camila Morais Gonçalves da Silva, Laura Oliveira-Nascimento, Michelle Franz-Montan, Maria C Volpato, Luís F Cabeça, Eneida de Paula
OBJECTIVES: Oxethazaine (OXZ) is one of the few local anaesthetics that provides analgesia at low pH, but presents poor solubility, cytotoxicity and no parenteral formulations. To address these issues, we aimed to prepare OXZ host-guest inclusion complex with hydroxypropyl-beta-cyclodextrin (HP-β-CD). METHODS: The inclusion complex was formed by co-solubilization, followed by a job plot analysis to determine stoichiometry of complexation and dialysis equilibrium analysis (based on UV/VIS absorption and fluorescence profiles of OXZ)...
February 17, 2017: Journal of Pharmacy and Pharmacology
https://www.readbyqxmd.com/read/28211526/stable-optical-trapping-and-sensitive-characterization-of-nanostructures-using-standing-wave-raman-tweezers
#11
Mu-Ying Wu, Dong-Xiong Ling, Lin Ling, William Li, Yong-Qing Li
Optical manipulation and label-free characterization of nanoscale structures open up new possibilities for assembly and control of nanodevices and biomolecules. Optical tweezers integrated with Raman spectroscopy allows analyzing a single trapped particle, but is generally less effective for individual nanoparticles. The main challenge is the weak gradient force on nanoparticles that is insufficient to overcome the destabilizing effect of scattering force and Brownian motion. Here, we present standing-wave Raman tweezers for stable trapping and sensitive characterization of single isolated nanostructures with a low laser power by combining a standing-wave optical trap with confocal Raman spectroscopy...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211480/visualisation-of-abscisic-acid-and-12-oxo-phytodienoic-acid-in-immature-phaseolus-vulgaris-l-seeds-using-desorption-electrospray-ionisation-imaging-mass-spectrometry
#12
Hirofumi Enomoto, Takuya Sensu, Kei Sato, Futoshi Sato, Thanai Paxton, Emi Yumoto, Koji Miyamoto, Masashi Asahina, Takao Yokota, Hisakazu Yamane
The plant hormone abscisic acid (ABA) and the jasmonic acid related-compound 12-oxo-phytodienoic acid (OPDA) play crucial roles in seed development, dormancy, and germination. However, a lack of suitable techniques for visualising plant hormones has restricted the investigation of their biological mechanisms. In the present study, desorption electrospray ionisation-imaging mass spectrometry (DESI-IMS), a powerful tool for visualising metabolites in biological tissues, was used to visualise ABA and OPDA in immature Phaseolus vulgaris L...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211362/marrow-isolated-adult-multilineage-inducible-cells-embedded-within-a-biologically-inspired-construct-promote-recovery-in-a-mouse-model-of-peripheral-vascular-disease
#13
Cristina Grau-Monge, Gaëtan J-R Delcroix, Andrea Bonnin-Marquez, Mike Valdes, Ead Lewis Mazen Awadallah, Daniel F Quevedo, Maxime R Armour, Ramon B Montero, Paul C Schiller, Fotios M Andreopoulos, Gianluca D'Ippolito
Peripheral vascular disease is one of the major vascular complications in individuals suffering from diabetes and in the elderly that is associated with significant burden in terms of morbidity and mortality. Stem cell therapy is being tested as an attractive alternative to traditional surgery to prevent and treat this disorder. The goal of this study was to enhance the protective and reparative potential of marrow-isolated adult multilineage inducible (MIAMI) cells by incorporating them within a bio-inspired construct (BIC) made of two layers of gelatin B electrospun nanofibers...
February 17, 2017: Biomedical Materials
https://www.readbyqxmd.com/read/28211331/sulfamethoxazole-and-cod-increase-abundance-of-sulfonamide-resistance-genes-and-change-bacterial-community-structures-within-sequencing-batch-reactors
#14
Xueping Guo, Weihai Pang, Chunling Dou, Daqiang Yin
The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove...
February 1, 2017: Chemosphere
https://www.readbyqxmd.com/read/28211277/antineoplastic-agents-603-quinstatins-exceptional-cancer-cell-growth-inhibitors
#15
George R Pettit, Noeleen Melody, Jean-Charles Chapuis
Discovery of the exceptionally powerful anticancer drug dolastatin 10 (1), contained in the sea hare Dolabella auricularia, opened a new frontier needed for improving human cancer treatment. Subsequently, major advances have been achieved based on results of structurally modifying this unusual natural peptide while maintaining the remarkable anticancer activity necessary for preparation of successful monoclonal antibody drug conjugates (ADC). Among the first several hundred SAR products based on dolastatin 10 our group synthesized and termed auristatins was auristatin E (2a)...
February 17, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28211170/endothelial-glycocalyx-as-a-critical-signalling-platform-integrating-the-extracellular-haemodynamic-forces-and-chemical-signalling
#16
REVIEW
Ye Zeng
The glycocalyx covers the human mammalian cells and plays important roles in stroke, inflammation and atherosclerosis. It has also been shown to be involved in endothelial mechanotransduction of shear stress. Shear stress induces the remodelling of the major component of the glycocalyx including glypican-1, a cell membrane heparan sulphate proteoglycan. Other factors, such as sphingosine-1-phosphate (S1P), protect the glycocalyx against syndecan-1 ectodomain shedding and induce the synthesis of heparan sulphate...
February 17, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28211013/electrostatic-forces-as-dominant-interactions-between-proteins-and-polyanions-an-esi-ms-study-of-fibroblast-growth-factor-binding-to-heparin-oligomers
#17
Burcu Baykal Minsky, Paul L Dubin, Igor A Kaltashov
The interactions between fibroblast growth factors (FGFs) and their receptors (FGFRs) are facilitated by heparan sulfate (HS) and heparin (Hp), highly sulfated biological polyelectrolytes. The molecular basis of FGF interactions with these polyelectrolytes is highly complex due to the structural heterogeneity of HS/Hp, and many details still remain elusive, especially the significance of charge density and minimal chain length of HS/Hp in growth factor recognition and multimerization. In this work, we use electrospray ionization mass spectrometry (ESI MS) to investigate the association of relatively homogeneous oligoheparins (octamer, dp8, and decamer, dp10) with acidic fibroblast growth factor (FGF-1)...
February 16, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28210797/mathematical-modelling-of-clostridial-acetone-butanol-ethanol-fermentation
#18
REVIEW
Thomas Millat, Klaus Winzer
Clostridial acetone-butanol-ethanol (ABE) fermentation features a remarkable shift in the cellular metabolic activity from acid formation, acidogenesis, to the production of industrial-relevant solvents, solventogensis. In recent decades, mathematical models have been employed to elucidate the complex interlinked regulation and conditions that determine these two distinct metabolic states and govern the transition between them. In this review, we discuss these models with a focus on the mechanisms controlling intra- and extracellular changes between acidogenesis and solventogenesis...
February 16, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28210337/extraction-of-knowledge-from-the-topographic-attentive-mapping-network-and-its-application-in-skill-analysis-of-table-tennis
#19
Isao Hayashi, Masanori Fujii, Toshiyuki Maeda, Jasmin Leveille, Tokio Tasaka
The Topographic Attentive Mapping (TAM) network is a biologically-inspired classifier that bears similarities to the human visual system. In case of wrong classification during training, an attentional top-down signal modulates synaptic weights in intermediate layers to reduce the difference between the desired output and the classifier's output. When used in a TAM network, the proposed pruning algorithm improves classification accuracy and allows extracting knowledge as represented by the network structure...
January 1, 2017: Journal of Human Kinetics
https://www.readbyqxmd.com/read/28209616/octn1-is-a-high-affinity-carrier-of-nucleoside-analogs
#20
Christina Drenberg, Alice A Gibson, Stanley Pounds, Lei Shi, Dena Rhinehart, Lie Li, Shuiying Hu, Guoqing Du, Anne T Nies, Matthias Schwab, Navjotsingh Pabla, William Blum, Tanja A Gruber, Sharyn D Baker, Alex Sparreboom
Resistance to xenobiotic nucleosides used to treat acute myeloid leukemia (AML) and other cancers remains a major obstacle to clinical management. One process suggested to participate in resistance is reduced uptake into tumor cells via nucleoside transporters, although precise mechanisms are not understood. Through transcriptomic profiling, we determined that low expression of the ergothioneine transporter OCTN1 (SLC22A4; ETT) strongly predicts poor event-free survival and overall survival in multiple cohorts of AML patients receiving treatment with the cytidine nucleoside analog cytarabine...
February 16, 2017: Cancer Research
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