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https://www.readbyqxmd.com/read/28335559/the-optimization-and-characterization-of-an-rna-cleaving-fluorogenic-dnazyme-probe-for-mda-mb-231-cell-detection
#1
Pengcheng Xue, Shengnan He, Yu Mao, Long Qu, Feng Liu, Chunyan Tan, Yuyang Jiang, Ying Tan
Breast cancer is one of the most frequently diagnosed cancers in females worldwide and lacks specific biomarkers for early detection. In a previous study, we obtained a selective RNA-cleaving Fluorogenic DNAzyme (RFD) probe against MDA-MB-231 cells, typical breast cancer cells, through the systematic evolution of ligands by exponential process (SELEX). To improve the performance of this probe for actual application, we carried out a series of optimization experiments on the pH value of a reaction buffer, the type and concentration of cofactor ions, and sequence minimization...
March 21, 2017: Sensors
https://www.readbyqxmd.com/read/28335548/study-of-different-variants-of-mo-enzyme-crarc-and-the-interaction-with-its-partners-crcytb5-r-and-crcytb5-1
#2
Alejandro Chamizo-Ampudia, Aurora Galvan, Emilio Fernandez, Angel Llamas
The mARC (mitochondrial Amidoxime Reducing Component) proteins are recently discovered molybdenum (Mo) Cofactor containing enzymes. They are involved in the reduction of several N-hydroxylated compounds (NHC) and nitrite. Some NHC are prodrugs containing an amidoxime structure or mutagens such as 6-hydroxylaminopurine (HAP). We have studied this protein in the green alga Chlamydomonas reinhardtii (crARC). Interestingly, all the ARC proteins need the reducing power supplied by other proteins. It is known that crARC requires a cytochrome b₅ (crCytb5-1) and a cytochrome b₅ reductase (crCytb5-R) that form an electron transport chain from NADH to the substrates...
March 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335416/supplementation-with-phycocyanobilin-citrulline-taurine-and-supranutritional-doses-of-folic-acid-and-biotin-potential-for-preventing-or-slowing-the-progression-of-diabetic-complications
#3
Mark F McCarty
Oxidative stress, the resulting uncoupling of endothelial nitric oxide synthase (eNOS), and loss of nitric oxide (NO) bioactivity, are key mediators of the vascular and microvascular complications of diabetes. Much of this oxidative stress arises from up-regulated nicotinamide adenine dinucleotide phosphate (NADPH) oxidase activity. Phycocyanobilin (PhyCB), the light-harvesting chromophore in edible cyanobacteria such as spirulina, is a biliverdin derivative that shares the ability of free bilirubin to inhibit certain isoforms of NADPH oxidase...
March 14, 2017: Healthcare (Basel, Switzerland)
https://www.readbyqxmd.com/read/28334877/iron-mediates-catalysis-of-nucleic-acid-processing-enzymes-support-for-fe-ii-as-a-cofactor-before-the-great-oxidation-event
#4
C Denise Okafor, Kathryn A Lanier, Anton S Petrov, Shreyas S Athavale, Jessica C Bowman, Nicholas V Hud, Loren Dean Williams
Life originated in an anoxic, Fe2+-rich environment. We hypothesize that on early Earth, Fe2+ was a ubiquitous cofactor for nucleic acids, with roles in RNA folding and catalysis as well as in processing of nucleic acids by protein enzymes. In this model, Mg2+ replaced Fe2+ as the primary cofactor for nucleic acids in parallel with known metal substitutions of metalloproteins, driven by the Great Oxidation Event. To test predictions of this model, we assay the ability of nucleic acid processing enzymes, including a DNA polymerase, an RNA polymerase and a DNA ligase, to use Fe2+ in place of Mg2+ as a cofactor during catalysis...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334792/gwas-identifies-population-specific-new-regulatory-variants-in-fut6-associated-with-plasma-b12-concentrations-in-indians
#5
Suraj S Nongmaithem, Charudatta V Joglekar, Ghattu V Krishnaveni, Sirazul A Sahariah, Meraj Ahmad, Swetha Ramachandran, Meera Gandhi, Harsha Chopra, Anand Pandit, Ramesh D Potdar, Caroline Hd Fall, Chittaranjan S Yajnik, Giriraj R Chandak
Vitamin B12 is an important cofactor in one-carbon metabolism whose dysregulation is associated with various clinical conditions. Indians have a high prevalence of B12 deficiency but little is known about the genetic determinants of circulating B12 concentrations in Indians. We performed a genome-wide association study in 1001 healthy participants in the Pune Maternal Nutrition Study (PMNS), replication studies in 3418 individuals from other Indian cohorts and by meta-analysis identified new variants, rs3760775 (p = 1...
February 27, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334268/an-algorithmic-perspective-of-de-novo-cis-regulatory-motif-finding-based-on-chip-seq-data
#6
Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma
Transcription factors are proteins that bind to specific DNA sequences and play important roles in controlling the expression levels of their target genes. Hence, prediction of transcription factor binding sites (TFBSs) provides a solid foundation for inferring gene regulatory mechanisms and building regulatory networks for a genome. Chromatin immunoprecipitation sequencing (ChIP-seq) technology can generate large-scale experimental data for such protein-DNA interactions, providing an unprecedented opportunity to identify TFBSs (a...
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28332661/geometrical-properties-of-the-manganese-iv-iron-iii-cofactor-of-chlamydia-trachomatis-ribonucleotide-reductase-unveiled-by-simulations-of-xas-spectra
#7
Eduardo M Sproviero
Using simulations of Mn/Fe K-edge X-ray absorption spectroscopy (XAS), combined with DFT-optimized structural models and direct comparisons with available experimental data, we determine geometrical and electronic properties of the Mn-Fe active site of Chlamydia trachomatis (Ct) of ribonucleotide reductase (RNR). In the post-edge XAS energy range, we use extended X-ray absorption fine structure (EXAFS) data, to acquire absorber-scatterer geometrical information around each absorber metal center. For this task, we apply a protocol that evaluates Debye-Waller factors in scattering paths instead of scattering shells to fit the experimental EXAFS...
March 23, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28331542/expression-of-a-heat-stable-nadph-dependent-alcohol-dehydrogenase-from-thermoanaerobacter-pseudethanolicus-39e-in-clostridium-thermocellum-1313-results-in-increased-hydroxymethylfurfural-resistance
#8
Sun-Ki Kim, Joseph Groom, Daehwan Chung, James Elkins, Janet Westpheling
BACKGROUND: Resistance to deconstruction is a major limitation to the use of lignocellulosic biomass as a substrate for the production of fuels and chemicals. Consolidated bioprocessing (CBP), the use of microbes for the simultaneous hydrolysis of lignocellulose into soluble sugars and fermentation of the resulting sugars to products of interest, is a potential solution to this obstacle. The pretreatment of plant biomass, however, releases compounds that are inhibitory to the growth of microbes used for CBP...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28331202/immune-evasion-of-borrelia-miyamotoi-cbia-a-novel-outer-surface-protein-exhibiting-complement-binding-and-inactivating-properties
#9
Florian Röttgerding, Alex Wagemakers, Joris Koetsveld, Volker Fingerle, Michael Kirschfink, Joppe W Hovius, Peter F Zipfel, Reinhard Wallich, Peter Kraiczy
Borrelia (B.) miyamotoi, an emerging tick-borne relapsing fever spirochete, resists complement-mediated killing. To decipher the molecular principles of immune evasion, we sought to identify determinants contributing to complement resistance. Employing bioinformatics, we identified a gene encoding for a putative Factor H-binding protein, termed CbiA (complement binding and inhibitory protein A). Functional analyses revealed that CbiA interacted with complement regulator Factor H (FH), C3, C3b, C4b, C5, and C9...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28330993/transition-state-mimics-are-valuable-mechanistic-probes-for-structural-studies-with-the-arginine-methyltransferase-carm1
#10
Matthijs J van Haren, Nils Marechal, Nathalie Troffer-Charlier, Agostino Cianciulli, Gianluca Sbardella, Jean Cavarelli, Nathaniel I Martin
Coactivator associated arginine methyltransferase 1 (CARM1) is a member of the protein arginine methyltransferase (PRMT) family and methylates a range of proteins in eukaryotic cells. Overexpression of CARM1 is implicated in a number of cancers, and it is therefore seen as a potential therapeutic target. Peptide sequences derived from the well-defined CARM1 substrate poly(A)-binding protein 1 (PABP1) were covalently linked to an adenosine moiety as in the AdoMet cofactor to generate transition state mimics...
March 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28330952/effects-of-insulin-and-the-glucagon-like-peptide-1-receptor-agonist-liraglutide-on-the-kidney-proteome-in-db-db-mice
#11
Leena Liljedahl, Jenny Norlin, James N McGuire, Peter James
Diabetes mellitus (DM) is a worldwide disease that affects 9% of the adult world population and type 2 DM accounts for 90% of those. A common consequence of DM is kidney complications, which could lead to kidney failure. We studied the potential effects of treatment with insulin and the glucagon-like peptide 1 receptor (GLP-1R) agonist liraglutide on the diabetic kidney proteome through the use of the db/db mouse model system and mass spectrometry (MS). Multivariate analyses revealed distinct effects of insulin and liraglutide on the db/db kidney proteome, which was seen on the protein levels of, for example, pterin-4 α-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor-1α (PCBD1), neural precursor cell expressed developmentally down-regulated-8 (NEDD8), transcription elongation factor-B polypeptide-1 (ELOC) and hepcidin (HEPC)...
March 2017: Physiological Reports
https://www.readbyqxmd.com/read/28330374/recent-developments-in-the-use-of-tyrosinase-and-laccase-in-environmental-applications
#12
Sidy Ba, Vaidyanathan Vinoth Kumar
Our current global environmental challenges include the reduction of harmful chemicals and their derivatives. Bioremediation has been a key strategy to control the massive presence of chemicals in the environment. Enzymes including the phenoloxidases, laccases and tyrosinases, are increasingly being investigated as "green products" in the removal of many chemical contaminants in waters and soils. Both phenoloxidases are widespread in nature and attractive biocatalysts due to their ability to use readily available molecular oxygen as sole cofactor for their catalytic elimination of a large number of chemicals...
March 22, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28330159/in-silico-characterization-and-differential-expression-pattern-analysis-of-conserved-hmg-coa-reductase-domain-isolated-from-aconitum-balfourii-stapf
#13
Eti Sharma, Saurabh Pandey, A K Gaur
The 3-hydroxy-3-methyl glutaryl CoA reductase (HMGR) is the key enzyme of mevalonate pathway in plants. A partial genomic DNA fragment encoding HMGR conserved domain (denoted as AbHMGR) is isolated from Aconitum balfourii Stapf. It comprises 871 bp encoding 290 amino acids. In silico analysis reveals that it had extensive similarities to other plant HMGR gene. Domain analysis of AbHMGR showed two highly conserved NADPH and HMG CoA domains. Docking study predicted inhibitor, substrate and cofactor binding sites in the protein...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329912/structural-and-mechanistic-insights-into-homocysteine-degradation-by-a-mutant-of-methionine-%C3%AE-lyase-based-on-substrate-assisted-catalysis
#14
Dan Sato, Tomoo Shiba, Shunsuke Yunoto, Kazuo Furutani, Mitsuki Fukumoto, Daizou Kudou, Takashi Tamura, Kenji Inagaki, Shigeharu Harada
Methionine γ-lyse (MGL) catalyzes the α, γ-elimination of l-methionine and its derivatives as well as the α, β-elimination of l-cysteine and its derivatives to produce α-keto acids, volatile thiols, and ammonia. The reaction mechanism of MGL has been characterized by enzymological studies using several site-directed mutants. The Pseudomonas putida MGL C116H mutant showed drastically reduced degradation activity toward methionine while retaining activity toward homocysteine. To understand the underlying mechanism and to discern the subtle differences between these substrates, we analyzed the crystal structures of the reaction intermediates...
March 22, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28329449/behavioural-and-neurochemical-effects-of-alpha-lipoic-acid-associated-with-omega-3-in-tardive-dyskinesia-induced-by-chronic-haloperidol-in-rats
#15
Dayane Pessoa Araújo, Thaisa Camboim, Ana Silva, Caio Fonseca, Rebeca Sousa, Mabson Barbosa, Lucidio Oliveira, José Cavalcanti, Eudes Lucena, Fausto Guzen
Tardive dyskinesia (TD) is characterized by involuntary movements of the lower portion of the face being related to typical antipsychotic therapy. TD is associated with the oxidative imbalance in the basal ganglia. Lipoic acid (LA) and omega 3 (ω-3) are antioxidants acting as enzyme cofactors, regenerating antioxidant enzymes. This study aimed to investigate behavioral and neurochemical effects of supplementation with of LA (100mg/Kg) and ω-3 (1g/Kg) in the treatment of TD-induced by chronic use haloperidol (HAL) (1mg/Kg) in rats...
March 22, 2017: Canadian Journal of Physiology and Pharmacology
https://www.readbyqxmd.com/read/28327288/atrophin-controls-developmental-signaling-pathways-via-interactions-with-trithorax-like
#16
Kelvin Yeung, Ann Boija, Edvin Karlsson, Per-Henrik Holmqvist, Yonit Tsatskis, Ilaria Nisoli, Damian B Yap, Alireza Lorzadeh, Michelle Moksa, Martin Hirst, Samuel Aparicio, Manolis Fanto, Per Stenberg, Mattias Mannervik, Helen McNeill
Mutations in human Atrophin1, a transcriptional corepressor, cause dentatorubral-pallidoluysian atrophy, a neurodegenerative disease. Drosophila Atrophin (Atro) mutants display many phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Despite Atro's critical role in development and disease, relatively little is known about Atro's binding partners and downstream targets. We present the first genomic analysis of Atro using ChIP-seq against endogenous Atro. ChIP-seq identified 1300 potential direct targets of Atro including engrailed, and components of the Dpp and Notch signaling pathways...
March 22, 2017: ELife
https://www.readbyqxmd.com/read/28326616/high-prevalence-of-sensitization-to-gibberellin-regulated-protein-peamaclein-in-fruit-allergies-with-negative-immunoglobulin-e-reactivity-to-bet-v-1-homologs-and-profilin-clinical-pattern-causative-fruits-and-cofactor-effect-of-gibberellin-regulated-protein
#17
Naoko Inomata, Mami Miyakawa, Michiko Aihara
Gibberellin-regulated protein (GRP) is a new allergen in peach allergy, with an amino acid sequence very well conserved through several botanical species. We investigated the allergenicity of GRP in fruit allergies other than peaches and identified the clinical characteristics of fruit allergy patients with GRP sensitization. One hundred consecutive Japanese patients with fruit allergies were enrolled in the present study. To identify the features of GRP sensitization, we selected patients with negative ImmunoCAP results for Bet v 1 homologs and profilin, which are marker allergens for pollen-food allergy syndrome (PFAS), or lipid transfer protein...
March 22, 2017: Journal of Dermatology
https://www.readbyqxmd.com/read/28323419/the-role-of-sufs-is-restricted-to-fes-cluster-biosynthesis-in-escherichia-coli
#18
Martin Bühning, Angelo Valleriani, Silke Leimkühler
In Escherichia coli two different systems have been identified that are important for the coordinate formation of Fe-S clusters, namely the ISC and SUF systems. The ISC system is the housekeeping Fe-S machinery, which provides Fe-S clusters for numerous cellular proteins. The IscS protein of this system was additionally revealed to be the primary sulfur donor for numerous sulfur-containing molecules with important biological functions, among which are the molybdenum cofactor (Moco) and thiolated nucleosides in tRNA...
March 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28322784/flaviviridae-viruses-use-a-common-molecular-mechanism-to-escape-nucleoside-analogue-inhibitors
#19
James J Valdés, Philip T Butterill, Daniel Růžek
The RNA-dependent RNA polymerases of Flaviviridae viruses are crucial for replication. The Flaviviridae polymerase is organized into structural motifs (A-G), with motifs F, A, C and E containing interrogating, priming and catalytic substrate-interacting sites. Modified nucleoside analogues act as antiviral drugs by targeting Flaviviridae polymerases and integrating into the synthesized product causing premature termination. A threonine mutation of a conserved serine residue in motif B of Flaviviridae polymerases renders resistance to 2'-C-methylated nucleoside analogues...
March 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28322781/characterization-of-akr1b16-a-novel-mouse-aldo-keto-reductase
#20
Joan Giménez-Dejoz, Susanne Weber, Oleg A Barski, Gabriele Möller, Jerzy Adamski, Xavier Parés, Sergio Porté, Jaume Farrés
Aldo-keto reductases (AKRs) are distributed in three families and multiple subfamilies in mammals. The mouse Akr1b3 gene is clearly orthologous to human AKR1B1, both coding for aldose reductase, and their gene products show similar tissue distribution, regulation by osmotic stress and kinetic properties. In contrast, no unambiguous orthologs of human AKR1B10 and AKR1B15.1 have been identified in rodents. Although two more AKRs, AKR1B7 and AKR1B8, have been identified and characterized in mouse, none of them seems to exhibit properties similar to the human AKRs...
March 17, 2017: Chemico-biological Interactions
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