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https://www.readbyqxmd.com/read/28934663/using-a-fluorescence-quenching-method-to-detect-dna-adsorption-onto-single-walled-carbon-nanotube-surfaces
#1
Kazuo Umemura, Shizuma Sato, Gilbert Bustamante, Jing Yong Ye
Surface modification of single-walled carbon nanotubes (SWNTs) with DNA molecules has attracted much attention in recent years to increase SWNT solubility and make various SWNT-based nanobiodevices. Therefore, there is a critical need to quantify the interaction between DNA molecules and SWNT surfaces, particularly the intermediate structures during DNA adsorption. In this study, we demonstrate the ability to detect the adsorption of DNA oligomers on SWNT surfaces by fluorescence spectroscopy. Fluorescein-labelled, 30mer, thymine oligonucleotides (F-T30) were employed as a fluorescent probe to study the interaction of DNA with SWNTs...
September 12, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28933917/grape-and-wine-polymeric-polyphenols-their-importance-in-enology
#2
Lingxi Li, Baoshan Sun
Phenolic compounds are important constituents of red wine, contributing to its sensory properties and antioxidant activity. Owing to the diversity and structural complexity, study of these compounds was mainly limited, during the last three decades, on their low-molecular-mass compounds or simple phenolic compounds. Only in recent years, much attention has been paid to highly polymerized polyphenols in grape and red wines. The reason for this is largely due to the development of analytical techniques, especially those of HPLC-ESI-MS, permitting the structural characterization of highly polymerized polyphenols...
September 21, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28933436/stereodivergent-synthesis-with-a-programmable-molecular-machine
#3
Salma Kassem, Alan T L Lee, David A Leigh, Vanesa Marcos, Leoni I Palmer, Simone Pisano
It has been convincingly argued that molecular machines that manipulate individual atoms, or highly reactive clusters of atoms, with Ångström precision are unlikely to be realized. However, biological molecular machines routinely position rather less reactive substrates in order to direct chemical reaction sequences, from sequence-specific synthesis by the ribosome to polyketide synthases, where tethered molecules are passed from active site to active site in multi-enzyme complexes. Artificial molecular machines have been developed for tasks that include sequence-specific oligomer synthesis and the switching of product chirality, a photo-responsive host molecule has been described that is able to mechanically twist a bound molecular guest, and molecular fragments have been selectively transported in either direction between sites on a molecular platform through a ratchet mechanism...
September 20, 2017: Nature
https://www.readbyqxmd.com/read/28931902/red-light-phenotype-in-a-marine-diatom-involves-a-specialized-oligomeric-red-shifted-antenna-and-altered-cell-morphology
#4
Miroslava Herbstová, David Bína, Radek Kaňa, František Vácha, Radek Litvín
Diatoms greatly contribute to carbon fixation and thus strongly influence the global biogeochemical balance. Capable of chromatic acclimation (CA) to unfavourable light conditions, diatoms often dominate benthic ecosystems in addition to their planktonic lifestyle. Although CA has been studied at the molecular level, our understanding of this phenomenon remains incomplete. Here we provide new data to better explain the acclimation-associated changes under red-enhanced ambient light (RL) in diatom Phaeodactylum tricornutum, known to express a red-shifted antenna complex (F710)...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931425/neutralizing-immune-responses-induced-by-oligomeric-h5n1-hemagglutinins-from-plants
#5
Hoang Trong Phan, Thuong Thi Ho, Ha Hoang Chu, Trang Huyen Vu, Ulrike Gresch, Udo Conrad
Plant-based transient expression is an alternative platform to produce hemagglutinin-based subunit vaccines. This production system provides not only fast and effective response in the context of a pandemic but also enables the supply of big volume vaccines at low cost. Crude plant extracts containing influenza hemagglutinin are considered to use as vaccine sources because of avoidance of related purification steps resulting in low cost production allowing veterinary applications. Highly immunogenic influenza hemagglutinins are urgently required to meet these pre-conditions...
September 20, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28931050/saxs-and-stability-studies-of-iron-induced-oligomers-of-bacterial-frataxin-cyay
#6
Mostafa Fekry, Wessen Alshokry, Przemysław Grela, Marek Tchórzewski, Eva-Christina Ahlgren, Christopher A Söderberg, Oleksandr Gakh, Grazia Isaya, Salam Al-Karadaghi
Frataxin is a highly conserved protein found in both prokaryotes and eukaryotes. It is involved in several central functions in cells, which include iron delivery to biochemical processes, such as heme synthesis, assembly of iron-sulfur clusters (ISC), storage of surplus iron in conditions of iron overload, and repair of ISC in aconitase. Frataxin from different organisms has been shown to undergo iron-dependent oligomerization. At least two different classes of oligomers, with different modes of oligomer packing and stabilization, have been identified...
2017: PloS One
https://www.readbyqxmd.com/read/28930470/structure-related-roles-for-the-conservation-of-the-hiv-1-fusion-peptide-sequence-revealed-by-nmr
#7
Soraya Serrano, Nerea Huarte, Edurne Rujas, David Andreu, Jose L Nieva, M Angeles Jimenez
Despite extensive characterization of the human immunodeficiency virus type-1 (HIV-1) hydrophobic fusion peptide (FP), the structure-function relationships underlying its extraordinary degree of conservation remain poorly understood. Specifically, the fact that the tandem repeat of the tripeptide FLGFLG is absolutely conserved suggests that high hydrophobicity may not suffice to unleash FP function. Here, we have compared the NMR structures adopted in nonpolar media by two FP surrogates, wtFP-tag and scrFP-tag, which had equal hydrophobicity but contained wild-type and scrambled core sequences LFLGFLG and FGLLGFL, respectively...
September 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28929138/cryoem-structure-of-mxb-reveals-a-novel-oligomerization-interface-critical-for-hiv-restriction
#8
Frances J D Alvarez, Shaoda He, Juan R Perilla, Sooin Jang, Klaus Schulten, Alan N Engelman, Sjors H W Scheres, Peijun Zhang
Human dynamin-like, interferon-induced myxovirus resistance 2 (Mx2 or MxB) is a potent HIV-1 inhibitor. Antiviral activity requires both the amino-terminal region of MxB and protein oligomerization, each of which has eluded structural determination due to difficulties in protein preparation. We report that maltose binding protein-fused, full-length wild-type MxB purifies as oligomers and further self-assembles into helical arrays in physiological salt. Guanosine triphosphate (GTP), but not guanosine diphosphate, binding results in array disassembly, whereas subsequent GTP hydrolysis allows its reformation...
September 2017: Science Advances
https://www.readbyqxmd.com/read/28928905/fucoxanthin-a-marine-carotenoid-attenuates-%C3%AE-amyloid-oligomer-induced-neurotoxicity-possibly-via-regulating-the-pi3k-akt-and-the-erk-pathways-in-sh-sy5y-cells
#9
Jiajia Lin, Jie Yu, Jiaying Zhao, Ke Zhang, Jiachen Zheng, Jialing Wang, Chunhui Huang, Jingrong Zhang, Xiaojun Yan, William H Gerwick, Qinwen Wang, Wei Cui, Shan He
Alzheimer's disease (AD), the most common neurodegenerative disorder, is characterized by neurofibrillary tangles, synaptic impairments, and loss of neurons. Oligomers of β-amyloid (Aβ) are widely accepted as the main neurotoxins to induce oxidative stress and neuronal loss in AD. In this study, we discovered that fucoxanthin, a marine carotenoid with antioxidative stress properties, concentration dependently prevented Aβ oligomer-induced increase of neuronal apoptosis and intracellular reactive oxygen species in SH-SY5Y cells...
2017: Oxidative Medicine and Cellular Longevity
https://www.readbyqxmd.com/read/28928403/dimerization-regulates-both-deaminase-dependent-and-deaminase-independent-hiv-1-restriction-by-apobec3g
#10
Michael Morse, Ran Huo, Yuqing Feng, Ioulia Rouzina, Linda Chelico, Mark C Williams
APOBEC3G (A3G) is a human enzyme that inhibits human immunodeficiency virus type 1 (HIV-1) infectivity, in the absence of the viral infectivity factor Vif, through deoxycytidine deamination and a deamination-independent mechanism. A3G converts from a fast to a slow binding state through oligomerization, which suggests that large A3G oligomers could block HIV-1 reverse transcriptase-mediated DNA synthesis, thereby inhibiting HIV-1 replication. However, it is unclear how the small number of A3G molecules found in the virus could form large oligomers...
September 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28928359/hydrodeoxygenation-of-water-insoluble-bio-oil-to-alkanes-using-a-highly-dispersed-pd-mo-catalyst
#11
Haohong Duan, Juncai Dong, Xianrui Gu, Yung-Kang Peng, Wenxing Chen, Titipong Issariyakul, William K Myers, Meng-Jung Li, Ni Yi, Alexander F R Kilpatrick, Yu Wang, Xusheng Zheng, Shufang Ji, Qian Wang, Junting Feng, Dongliang Chen, Yadong Li, Jean-Charles Buffet, Haichao Liu, Shik Chi Edman Tsang, Dermot O'Hare
Bio-oil, produced by the destructive distillation of cheap and renewable lignocellulosic biomass, contains high energy density oligomers in the water-insoluble fraction that can be utilized for diesel and valuable fine chemicals productions. Here, we show an efficient hydrodeoxygenation catalyst that combines highly dispersed palladium and ultrafine molybdenum phosphate nanoparticles on silica. Using phenol as a model substrate this catalyst is 100% effective and 97.5% selective for hydrodeoxygenation to cyclohexane under mild conditions in a batch reaction; this catalyst also demonstrates regeneration ability in long-term continuous flow tests...
September 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28928293/comparison-of-a-lyophilized-drug-product-to-other-solid-and-liquid-media-for-the-extraction-of-elastomeric-oligomers-from-a-butyl-rubber-stopper
#12
Steven A Zdravkovic
Lyophilization is commonly used to extend the shelf life of pharmaceutical products which are otherwise unstable when stored as a liquid formulation. However, the ability of a lyophilized drug, or other solid medium, to leach or extract substances from a pharmaceutical packaging material is not well characterized. To provide insight into this area of uncertainty, the extraction properties of a lyophilized drug product, the lyophilized drug product reconstituted in water, and several other solid and liquid media of varying polarity were determined using a glass vial with a butyl rubber stopper as a representative pharmaceutical packaging system...
September 19, 2017: PDA Journal of Pharmaceutical Science and Technology
https://www.readbyqxmd.com/read/28928145/structure-insight-of-gsdmd-reveals-the-basis-of-gsdmd-autoinhibition-in-cell-pyroptosis
#13
Siyun Kuang, Jun Zheng, Hui Yang, Suhua Li, Shuyan Duan, Yanfang Shen, Chaoneng Ji, Jianhua Gan, Xue-Wei Xu, Jixi Li
Recent findings have revealed that the protein gasdermin D (GSDMD) plays key roles in cell pyroptosis. GSDMD binds lipids and forms pore structures to induce pyroptosis upon microbial infection and associated danger signals. However, detailed structural information for GSDMD remains unknown. Here, we report the crystal structure of the C-terminal domain of human GSDMD (GSDMD-C) at 2.64-Å resolution. The first loop on GSDMD-C inserts into the N-terminal domain (GSDMD-N), which helps stabilize the conformation of the full-length GSDMD...
September 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28927930/biodegradable-and-adjustable-sol-gel-glass-based-hybrid-scaffolds-from-multi-armed-oligomeric-building-blocks
#14
Christian Kascholke, Stephan Hendrikx, Tobias Flath, Dzmitry Kuzmenka, Hans-Martin Dörfler, Dirk Schumann, Mathias Gressenbuch, F Peter Schulze, Michaela Schulz-Siegmund, Michael C Hacker
Biodegradability is a crucial characteristic to improve the clinical potential of sol-gel-derived glass materials. To this end, a set of degradable organic/inorganic class II hybrids from a tetraethoxysilane(TEOS)-derived silica sol and oligovalent cross-linker oligomers containing oligo(D,L-lactide) domains was developed and characterized. A series of 18 oligomers (Mn: 1100-3200 Da) with different degrees of ethoxylation and varying length of oligoester units was established and chemical composition was determined...
September 16, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28927263/molecular-and-cellular-basis-of-neurodegeneration-in-alzheimer-s-disease
#15
Sangyun Jeong
The most common form of senile dementia is Alzheimer's disease (AD), which is characterized by the extracellular deposition of amyloid beta-peptide (Abeta) plaques and the intracellular formation of neurofibrillary tangles (NFTs) in the cerebral cortex. Tau abnormalities are commonly observed in many neurodegenerative diseases including AD, Parkinson's disease, and Pick's disease. Interestingly, tau-mediated formation of NFTs in AD brains shows better correlation with cognitive impairment than Abeta plaque accumulation; pathological tau alone is sufficient to elicit frontotemporal dementia, but it does not cause AD...
September 20, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28926714/janus-and-strawberry-like-particles-from-azo-molecular-glass-and-polydimethylsiloxane-oligomer
#16
Chungen Hsu, Yi Du, Xiaogong Wang
This study investigated Janus and strawberry-like particles composed of azo molecular glass and polydimethylsiloxane (PDMS) oligomer, focusing on controllable fabrication and formation mechanism of these unique structures and morphologies. Two materials, the azo molecular glass (IA-Chol) and PDMS oligomer (H2pdca-PDMS), were prepared for this purpose. The Janus and strawberry-like particles were obtained from the droplets of a dichloromethane (DCM) solution containing both IA-Chol and H2pdca-PDMS, dispersed in water and stabilized by poly(vinyl alcohol)...
September 19, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28926691/cobalt-porphyrin-thiazyl-radical-coordination-polymers-towards-metal-organic-electronics
#17
Delia A Haynes, Laura J van Laeren, Orde Q Munro
Herein we delineate an unusual one-dimensional coordination polymer (CP), 3, prepared from S = ½ Co(TPP), 1, (TPP = 5,10,15,20-tetraphenylporphyrin dianion) and S = ½ 4-(4'-pyridyl)-1,2,3,5-dithiadiazolyl (py-DTDA) radical, 2. The atypically long S-S distance for CP 3 (2.12 Å) reflects fractional electron transfer from the formally Co(II) ion into the antibonding π-SOMO of the metal-bound py-DTDA bridging ligand. The bonding in solid CP 3 involves non-integer redox states in a resonance hybrid repeat unit best formulated as [Co(TPP)](0...
September 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28924170/the-tyrosine-phosphatase-ptpn13-fap-1-links-calpain-2-tbi-and-tau-tyrosine-phosphorylation
#18
Yubin Wang, Randy A Hall, Moses Lee, Andysheh Kamgar-Parsi, Xiaoning Bi, Michel Baudry
Traumatic brain injury (TBI) increases the risk of Alzheimer's disease (AD). Calpain activation and tau hyperphosphorylation have been implicated in both TBI and AD. However, the link between calpain and tau phosphorylation has not been fully identified. We recently discovered that the two major calpain isoforms in the brain, calpain-1 and calpain-2, play opposite functions in synaptic plasticity and neuronal survival/death, which may be related to their different C-terminal PDZ binding motifs. Here, we identify the tyrosine phosphatase PTPN13 as a key PDZ binding partner of calpain-2...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28924167/a-toxic-conformer-of-a%C3%AE-42-with-a-turn-at-22-23-is-a-novel-therapeutic-target-for-alzheimer-s-disease
#19
Naotaka Izuo, Chihiro Kasahara, Kazuma Murakami, Toshiaki Kume, Masahiro Maeda, Kazuhiro Irie, Koutaro Yokote, Takahiko Shimizu
Immunotherapy targeting Aβ42 is drawing attention as a possible therapeutic approach for Alzheimer's disease (AD). Considering the significance of reported oligomerized Aβ42 species, selective targeting of the oligomer will increase the therapeutic efficacy. However, what kinds of oligomers are suitable targets for immunotherapy remains unclear. We previously identified a toxic conformer of Aβ42, which has a turn structure at 22-23 ("toxic turn"), among Aβ42 conformations. This toxic conformer of Aβ42 has been reported to show rapid oligomerization and to exhibit strong neurotoxicity and synaptotoxicity...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28924148/investigation-of-the-inhibition-effect-and-mechanism-of-myricetin-to-suilysin-by-molecular-modeling
#20
Xiaodi Niu, Lin Sun, Guizhen Wang, Yawen Gao, Yanan Yang, Xiyan Wang, Hongsu Wang
In the present study, the inhibitory effect and mechanism of myricetin, a natural flavonoid compound, in relation to Suilysin (SLY) were investigated through molecular dynamics simulations, mutational analysis and fluorescence-quenching assays. Myricetin is a potential inhibitor that does not exhibit antimicrobial activity but has been shown to inhibit SLY cytotoxicity. Molecular dynamics simulations and mutational analysis revealed that myricetin binds directly to SLY in the gap between domains 2 and 3, an important region for oligomerization and pore formation...
September 18, 2017: Scientific Reports
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