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https://www.readbyqxmd.com/read/29228314/demodifying-rna-for-transcriptomic-analyses-of-archival-formalin-fixed-paraffin-embedded-samples
#1
Leah C Wehmas, Charles E Wood, Remi Gagne, Andrew Williams, Carole Yauk, Mark M Gosink, Deidre Dalmas, Ruixin Hao, Raegan O'Lone, Susan Hester
Archival formalin-fixed paraffin-embedded (FFPE) tissue samples offer a vast but largely untapped resource for genomic research. The primary technical issues limiting use of FFPE samples are RNA yield and quality. In this study, we evaluated methods to demodify RNA highly fragmented and crosslinked by formalin fixation. Primary endpoints were RNA recovery, RNA-sequencing quality metrics, and transcriptional responses to a reference chemical (phenobarbital, PB). Frozen mouse liver samples from control and PB groups (n = 6/group) were divided and preserved for 3 months as follows: frozen (FR); 70% ethanol (OH); 10% buffered formalin for 18 hours followed by ethanol (18F); or 10% buffered formalin (3F)...
December 7, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29228303/identifying-possible-pheromones-of-cerambycid-beetles-by-field-testing-known-pheromone-components-in-four-widely-separated-regions-of-the-united-states
#2
Jocelyn G Millar, Robert F Mitchell, Judith A Mongold-Diers, Yunfan Zou, Carlos E Bográn, Melissa K Fierke, Matthew D Ginzel, Crawford W Johnson, James R Meeker, Therese M Poland, Iral Ragenovich, Lawrence M Hanks
The pheromone components of many cerambycid beetles appear to be broadly shared among related species, including species native to different regions of the world. This apparent conservation of pheromone structures within the family suggests that field trials of common pheromone components could be used as a means of attracting multiple species, which then could be targeted for full identification of their pheromones. Here, we describe the results of such field trials that were conducted in nine states in the northeastern, midwestern, southern, and western United States...
December 8, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/29228269/electroactive-haloalkaliphiles-exhibit-exceptional-tolerance-to-free-ammonia
#3
Pablo Ledezma, Yang Lu, Stefano Freguia
Electrochemical activity in bacteria has been observed in numerous environments and conditions. However, enrichments in circumneutral freshwater media where acetate is the main electron donor seem to invariably lead to the dominance of Geobacter spp. Here we report on an electroactive bacterial consortium which was enriched on acetate as electron donor, but in a medium which reproduces hydrolysed urine (high pH, high salinity and high free ammonia). The consortium was found to be free of Geobacter species, whereas a previously undescribed community dominated by species closely related to Pseudomonas and Desulfuromonas was established...
December 4, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29228224/relationship-between-escherichia-coli-growth-rate-and-bacterial-susceptibility-to-ciprofloxacin
#4
Galina V Smirnova, Oleg N Oktyabrsky
The effect of Escherichia coli growth rate on its susceptibility to ciprofloxacin was investigated using bacteria grown on different carbon sources and harboring mutations in genes encoding tricarboxylic acid cycle enzymes. A 1-h treatment of the wild type (wt) grown on glucose, succinate, malate, α-ketoglutarate or acetate with 0.3 μg ml-1 ciprofloxacin decreased the number of surviving cells (CFU ml-1), 560, 110, 74, 62 and 5 times, respectively. Among the mutants tested, sucB strain, which grew 1.75 times slower than wt, was 7...
December 6, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29227976/progesterone-receptor-isoforms-nuclear-corepressor-1-and-steroid-receptor-coactivator-1-and-b-cell-lymphoma-2-and-akt-and-akt-phosphorylation-status-in-uterine-myomas-after-ulipristal-acetate-treatment-a-systematic-immunohistochemical-evaluation
#5
Guillaume E Courtoy, Jacques Donnez, Etienne Marbaix, Matilde Barreira, Mathieu Luyckx, Marie-Madeleine Dolmans
OBJECTIVE: To investigate whether ulipristal acetate (UPA) treatment modifies the expression of progesterone receptor (PR), its nuclear cofactors steroid receptor coactivator-1 (SRC1) and nuclear corepressor-1 (NCoR1), prosurvival factor B-cell lymphoma 2 (Bcl-2), and Akt in uterine myomas. PATIENTS: Prospective study of 59 women with symptomatic myomas undergoing myomectomy. Forty-two patients were treated preoperatively with UPA; the remaining 17 were not and they served as controls...
December 11, 2017: Gynecologic and Obstetric Investigation
https://www.readbyqxmd.com/read/29227917/design-synthesis-molecular-docking-of-new-lipophilic-acetamide-derivatives-affording-potential-anticancer-and-antimicrobial-agents
#6
Hany E A Ahmed, Saleh K Ihmaid, Abdelsattar M Omar, Ahmed M Shehata, Heba S Rateb, Mohammed F Zayed, Sahar Ahmed, Mahmoud M Elaasser
Fifteen new substituted N-2-(2-oxo-3-phenylquinoxalin-1(2H)-yl) acetamides 5a-f, 6a-f, and 8a-c were synthesized by reacting ethyl 2-(2-oxo-3-phenylquinoxalin-1(2H)-yl)acetate with various primary amines including benzylamines, sulfonamides, and amino acids. The in vitro antimicrobial screening of the target compounds was screened to assess their antibacterial and antifungal activity. As a result, seven compounds namely; 5a, 5c, 5d, 6a, 6c, 8b and 8c showed a promising broad spectrum antibacterial activity against both Gram-positive and Gram-negative strains...
December 2, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/29227833/vitamin-a-deficiency-in-mice-alters-host-and-gut-microbial-metabolism-leading-to-altered-energy-homeostasis
#7
Yuan Tian, Robert G Nichols, Jingwei Cai, Andrew D Patterson, Margherita T Cantorna
Vitamin A deficiency (A-) is a worldwide public health problem. To better understand how vitamin A status influences gut microbiota and host metabolism, we systematically analyzed urine, cecum, serum and liver samples from vitamin A sufficient (A+) and deficient (A-) mice using 1H NMR-based metabolomics, quantitative (q)PCR and 16S rRNA gene sequencing coupled with multivariate data analysis. The microbiota in the cecum of A- mice showed compositional as well as functional shifts compared to the microbiota from A+ mice...
November 5, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/29227679/thermally-tunable-pickering-emulsions-stabilized-by-carbon-dots-incorporated-core-shell-nanospheres-with-fluorescence-on-off-behavior
#8
Jianqiang Chen, Chenyang Zhu, Zhen Yang, Yiying Yue, Ping Wang, Takuya Kitaoka
Lack of deep understanding of nanoparticles (NPs) actions in oil/water interface set an obstacle to practical applications of Pickering emulsions. Fluorescence labels by incorporation of carbon dots (CDs) into poly(N-isopropylacrylamide) (PNIPAM) matrix can not only mark the action of PNIPAM-based NPs in the interface, but also reflect the colloidal morphologies of PNIPAM. In this work, we employed coaxial electrospraying for fabricating core-shell nanospheres of cellulose acetate encapsulated by PNIPAM and facile incorporation of CDs in PNIPAM shell was achieved simultaneously...
December 11, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29227665/rare-sulfur-containing-compounds-kujounins-a1-and-a2-and-allium-sulfoxide-a1-from-allium-fistulosum-kujou
#9
Masashi Fukaya, Seikou Nakamura, Ryota Nakagawa, Souichi Nakashima, Masayuki Yamashita, Hisashi Matsuda
Three sulfur-containing compounds, kujounins A1 (1) and A2 (2) and allium sulfoxide A1 (3), were isolated from the acetone extract of Allium fistulosum 'Kujou'. Their chemical structures were elucidated on the basis of physicochemical evidence, including X-ray crystallographic data. Compounds 1 and 2 possess three rings and an acetal structure and were obtained as complex compounds having disulfide and monosaccharide moieties. On the other hand, compound 3 has a thiolane skeleton derived from allicin. Naturally occurring compounds 1-3 have rare molecular skeletons...
December 11, 2017: Organic Letters
https://www.readbyqxmd.com/read/29227209/simultaneous-determination-of-organochlorine-and-pyrethriod-pesticide-residues-in-the-chinese-patent-medicines-by-gas-chromatography-tandem-mass-spectrometry
#10
Xue J Mao, Yao Zhong, Ai P Yan, Bin Wang, Yuan X Wang, Yi Q Wan
A simple, sensitive, reliable method was developed for the simultaneous determination of organochlorine and pyrethriod pesticide residues in Chinese patent medicines Six ingredient rehmannia pills and Xiaoyao pills. These pesticides were extracted by ethyl acetate. The extraction time and volume of ethyl acetate were optimized. Cleanup of extracts was performed with dispersive-solid phase extraction using graphitized carbon black as the sorbent. The determination of pesticides in the final extracts was carried out by gas chromatography-tandem mass spectrometry in multiple reaction monitoring mode (GC-MS/MS, MRM)...
December 11, 2017: Journal of Environmental Science and Health. Part. B, Pesticides, Food Contaminants, and Agricultural Wastes
https://www.readbyqxmd.com/read/29227099/activity-of-icacinol-from-icacina-trichantha-on-seedling-growth-of-oryza-sativa-and-arabidopsis-thaliana
#11
Ming Zhao, Brian Guo, Michael M Onakpa, Tiffany Wong, Kyo Wakasa, Chun-Tao Che, Katherine Warpeha
Broadleaf weeds are very costly for crop growers. Additional herbicidal compounds need to be obtained, especially from natural sources. Extracts of Icacina trichantha were evaluated for responses in germinating seeds and seedlings of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana). An ethyl acetate fraction of I. trichantha tuber and a diterpenoid constituent, icacinol (1), were found to have impacts on germination and growth of seedlings. The seed germination inhibitory activity on rice was minimal, but significant on Arabidopsis...
December 11, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/29227091/a-vuv-excited-and-ch2cl2-h2o-amplified-ionization-coupled-mass-spectrometry-for-oxygenated-organics-analysis
#12
Bo Yang, Haixu Zhang, Jinian Shu, Pengkun Ma, Peng Zhang, Jingyun Huang, Zhen Li, Ce Xu
The mass spectrometry analysis of oxygenated volatile organic compounds (OVOCs) remains challenging due to their limited ionization efficiencies. In this study, we surprisingly found that, under VUV excitation, a gaseous mixture of CH2Cl2/H2O/analyte (OVOCs) in N2 buffer generated large amounts of H3O+ and protonated analyte even when the photon energy was lower than the ionization energy of the neutral species involved. In contrast to those obtained with VUV photoionization alone, the signal intensities of oxygenated organics can be amplified by more than three orders of magnitude...
December 11, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29227025/light-driven-c-h-oxygenation-of-methane-into-methanol-and-formic-acid-by-molecular-oxygen-using-perfluorinated-solvent
#13
Kei Ohkubo, Kensaku Hirose
Chlorine dioxide radical (ClO2*) was found to act as an efficient oxidizing agent in the aerobic oxygenation of methane to methanol and formic acid under photoirradiation. Photochemical oxygenation of methane occurred in a two-phase system comprising perfluorohexane and water under ambient conditions (298 K, 1 atm). The yields of methanol and formic acid were 14% and 85%, respectively, with a methane conversion of 99% without formation of the further oxygenated products such as CO2 and CO. Ethane was also photochemically converted into ethanol (19%) and acetic acid (78%)...
December 11, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29226978/simultaneous-determination-of-residues-of-metalaxyl-cyazofamid-and-a-cyazofamid-metabolite-in-tobacco-leaves-and-soil-by-liquid-chromatography-with-tandem-mass-spectrometry
#14
Sizhuo Wu, Weiwei Yu, Caiyuan Sun, Kunming Zheng, Haizhen Zhang, Min Huang, Deyu Hu, Kankan Zhang
A simple method was developed and validated for the simultaneous determination of metalaxyl, cyazofamid, and the cyazofamid metabolite 4-chloro-5-p-tolylimidazole-2-carbonitrile (CCIM) by liquid chromatography with tandem mass spectrometry. The three target compounds were extracted from tobacco and soil with acetonitrile containing 0.1% acetic acid, and the extracts were purified using octadecylsilane. The proposed method showed satisfactory linearity (R2 ≥ 0.9985) for the target compounds. The limits of detection for metalaxyl, cyazofamid, and CCIM were 0...
December 11, 2017: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/29226938/pd-catalyzed-c-h-aziridination-of-3-3-5-5-tetrasubstituted-piperazin-2-ones
#15
Thomas A Alanine, Stephen Stokes, Craig A Roberts, James S Scott
A palladium mediated C-H aziridination reaction of 3,3,5,5-substituted-piperazin-2-ones has been developed using phenyliodonium diacetate (PIDA) and succinic acid to give synthetically useful bicyclic aziridines, in moderate to good yields. Succinic acid was found to be key for selectively promoting C-N bond formation (aziridination) and suppressing competitive acetoxylation. Analysis of the reaction kinetics revealed the role of succinic acid in promoting an equilibrium between monomeric and dimeric palladium species in the rate determining step of the reaction...
December 11, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29226932/ligand-induced-decarbonylation-in-diphosphine-ligated-palladium-acetates-ch3co2pd-pr2-2ch2-r-me-and-ph
#16
Michael Lesslie, Yang Yang, Allan J Canty, Elettra Piacentino, Francis Berthias, Philippe Maitre, Victor Ryzhov, Richard A J O'Hair
A new decarbonylation reaction is observed for [(K2-acetate)Pd(K2-diphosphine)]+ complexes. Gas-phase IR experiments identify the product as [CH3Pd(OP(Ph2)CH2PPh2)]+. DFT calculations uncovered a plausible mechanism involving O atom abstraction by the diphosphine ligand within the coordination sphere to yield the acetyl complex, [CH3COPd(OP(Ph2)CH2PPh2)]+, which then undergoes decarbonylation.
December 11, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29226920/coo-microspheres-and-metallic-co-evolved-from-hexagonal-%C3%AE-co-oh-2-plates-in-a-hydrothermal-process-for-lithium-storage-and-magnetic-applications
#17
KeYuan Ma, F Liu, Y F Yuan, X Q Liu, Jun Wang, J Xie, J P Cheng
CoO microspheres and metallic Co could be successfully synthesized by simply reacting cobalt acetate with a mixture solvent of ethylene glycol and deionized water in a hydrothermal process for different times. As the reaction proceeded, α-Co(OH)2, CoO and metallic Co were produced. To understand the phase evolution processes from α-Co(OH)2 to CoO and then metallic Co, a range of time-dependent experiments were carried out, and the intermediate products obtained at different reaction times were investigated in detail...
December 11, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29226678/zinc-and-magnesium-catalysts-for-the-hydrosilylation-of-carbon-dioxide
#18
Michael Rauch, Gerard Parkin
The terminal zinc and magnesium hydride compounds, [κ3-TismPriBenz]ZnH and [TismPriBenz]MgH, which feature the tris[(1-isopropylbenzimidazol-2-yl)dimethylsilyl]methyl ligand, react with B(C6F5)3 to afford the ion pairs, {[TismPriBenz]M}[HB(C6F5)3] (M = Zn, Mg), which are rare examples of these metals in trigonal monopyramidal coordination environments. Significantly, in combination with B(C6F5)3, {[TismPriBenz]M}-[HB(C6F5)3] generates catalytic systems for the hydrosilylation of CO2 by R3SiH to afford sequentially the bis(silyl)acetal, H2C(OSiR3)2, and CH4 (R3SiH = PhSiH3, Et3SiH, and Ph3SiH)...
December 11, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29226610/nuclear-magnetic-resonance-based-metabolomics-identifies-phenylalanine-as-a-novel-predictor-of-incident-heart-failure-hospitalisation-results-from-prosper-and-finrisk-1997
#19
Christian Delles, Naomi J Rankin, Charles Boachie, Alex McConnachie, Ian Ford, Antti Kangas, Pasi Soininen, Stella Trompet, Simon P Mooijaart, J Wouter Jukema, Faiez Zannad, Mika Ala-Korpela, Veikko Salomaa, Aki S Havulinna, Paul Welsh, Peter Würtz, Naveed Sattar
AIMS: We investigated the association between quantified metabolite, lipid and lipoprotein measures and incident heart failure hospitalisation (HFH) in the elderly, and examined whether circulating metabolic measures improve HFH prediction. METHODS AND RESULTS: Overall, 80 metabolic measures from the PROspective Study of Pravastatin in the Elderly at Risk (PROSPER) trial were measured by proton nuclear magnetic resonance spectroscopy (n = 5341; 182 HFH events during 2...
December 11, 2017: European Journal of Heart Failure
https://www.readbyqxmd.com/read/29225728/the-complete-genome-sequence-of-the-rumen-bacterium-butyrivibrio-hungatei-mb2003
#20
Nikola Palevich, William J Kelly, Sinead C Leahy, Eric Altermann, Jasna Rakonjac, Graeme T Attwood
Butyrivibrio hungatei MB2003 was isolated from the plant-adherent fraction of rumen contents from a pasture-grazed New Zealand dairy cow, and was selected for genome sequencing in order to examine its ability to degrade plant polysaccharides. The genome of MB2003 is 3.39 Mb and consists of four replicons; a chromosome, a secondary chromosome or chromid, a megaplasmid and a small plasmid. The genome has an average G + C content of 39.7%, and encodes 2983 putative protein-coding genes. MB2003 is able to use a variety of monosaccharide substrates for growth, with acetate, butyrate and formate as the principal fermentation end-products, and the genes encoding these metabolic pathways have been identified...
2017: Standards in Genomic Sciences
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