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https://www.readbyqxmd.com/read/28098827/shared-sulfur-mobilization-routes-for-trna-thiolation-and-molybdenum-cofactor-biosynthesis-in-prokaryotes-and-eukaryotes
#1
REVIEW
Silke Leimkühler, Martin Bühning, Lena Beilschmidt
Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm⁵s²U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure...
January 14, 2017: Biomolecules
https://www.readbyqxmd.com/read/28098257/a-comprehensive-platform-for-the-analysis-of-ubiquitin-like-protein-modifications-using-in-vivo-biotinylation
#2
Lucia Pirone, Wendy Xolalpa, Jón Otti Sigurðsson, Juanma Ramirez, Coralia Pérez, Monika González, Ainara Ruiz de Sabando, Félix Elortza, Manuel S Rodriguez, Ugo Mayor, Jesper V Olsen, Rosa Barrio, James D Sutherland
Post-translational modification by ubiquitin and ubiquitin-like proteins (UbLs) is fundamental for maintaining protein homeostasis. Efficient isolation of UbL conjugates is hampered by multiple factors, including cost and specificity of reagents, removal of UbLs by proteases, distinguishing UbL conjugates from interactors, and low quantities of modified substrates. Here we describe bioUbLs, a comprehensive set of tools for studying modifications in Drosophila and mammals, based on multicistronic expression and in vivo biotinylation using the E...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096941/transport-of-biomolecules-to-binding-partners-displayed-on-the-surface-of-microbeads-arrayed-in-traps-in-a-microfluidic-cell
#3
Xiaoxiao Chen, Thomas F Leary, Charles Maldarelli
Arrays of probe molecules integrated into a microfluidic cell are utilized as analytical tools to screen the binding interactions of the displayed probes against a target molecule. These assay platforms are useful in enzyme or antibody discovery, clinical diagnostics, and biosensing, as their ultraminiaturized design allows for high sensitivity and reduced consumption of reagents and target. We study here a platform in which the probes are first grafted to microbeads which are then arrayed in the microfluidic cell by capture in a trapping course...
January 2017: Biomicrofluidics
https://www.readbyqxmd.com/read/28090409/development-and-characterization-of-23-microsatellite-loci-for-rhododendron-ovatum-ericaceae
#4
De-Chen Liu, Yang Zhang, Si-Si Wang, Meng-Yu Liao, Xin-Yu Fan, Yuan-Yuan Li, Rong Wang
PREMISE OF THE STUDY: To estimate the genetic variation of Rhododendron ovatum (Ericaceae), a monoecious evergreen shrub, 23 microsatellite markers were identified from its nuclear genome. METHODS AND RESULTS: We developed 16 polymorphic and seven monomorphic microsatellite primers using the biotin-streptavidin capture method. The 16 polymorphic loci were investigated further using 89 individuals sampled from three populations in China. The number of alleles per locus ranged from four to 30, indicating a high level of polymorphism...
January 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28090407/development-of-15-polymorphic-microsatellite-markers-for-ficus-virens-moraceae
#5
Rong-Hua Fu, Yun-Xiang Li, Mei Liu, Qiu-Mei Quan
PREMISE OF THE STUDY: Ficus virens (Moraceae) is distributed widely in South and Southeast Asia, Melanesia, and northern Australia, and it is also cultivated outside its original northern range limit in southwestern China. Therefore, the species is well suited to explore the mechanism of range limits of Ficus species. However, little is known about its genetic background. METHODS AND RESULTS: Fifteen polymorphic microsatellite markers were developed using the biotin-streptavidin capture method...
January 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28088285/plasmon-enhanced-fluorescence-imaging-with-silicon-based-silver-chips-for-protein-and-nucleic-acid-assay
#6
Bing Yuan, Xiangxu Jiang, Chu Yao, Meimei Bao, Jiaojiao Liu, Yujiang Dou, Yinze Xu, Yao He, Kai Yang, Yuqiang Ma
Metal-enhanced fluorescence shows great potential for improving the sensitivity of fluoroscopy, which has been widely used in protein and nucleic acid detection for biosensor and bioassay applications. In comparison with the traditional glass-supported metal nanoparticles (MNPs), the introduction of a silicon substrate has been shown to provide an increased surface-enhanced Raman scattering (SERS) effect due to the coupling between the MNPs and the semiconducting silicon substrate. In this work, we further study the fluorescence-enhanced effect of the silicon-supported silver-island (Ag@Si) plasmonic chips...
February 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28078594/exploration-of-fas-s-nitrosylation-by-the-biotin-switch-assay
#7
Ali Bettaieb, Catherine Paul, Stéphanie Plenchette
S-nitrosylation is the covalent attachment of nitric oxide radical to the thiol side chain of cysteine. The death receptor Fas/CD95 can be S-nitrosylated in cancer cell lines by NO donors or iNOS activation. This posttranslational modification (PTM) induces Fas aggregation into lipid rafts and enhances FasL-mediated signaling and apoptosis. In this report, we describe the detection of Fas S-nitrosylation by the most commonly used method, the biotin switch assay (BSA) technique, that allows the detection of this very labile covalent modification in cells or tissues...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28078593/detection-of-s-acylated-cd95-by-acyl-biotin-exchange
#8
Aurelie Rossin, Anne-Odile Hueber
S-acylation is the covalent addition of a fatty acid, most generally palmitate onto cysteine residues of proteins through a labile thioester linkage. The death receptor CD95 is S-palmitoylated and this post-translational modification plays a crucial role on CD95 organization in cellular membranes and thus on CD95-mediated signaling. Here, we describe the nonradioactive detection of CD95 S-acylation by acyl-biotin exchange chemistry in which a biotin is substituted for the CD95-linked fatty acid. This sensitive technique, which depends on the ability of hydroxylamine to specifically cleave the thioester linkage between fatty acids and proteins, relies on three chemical steps: (1) blockage of free thiols of non-modified cysteine residues, (2) hydroxylamine-mediated cleavage of thioester-linked fatty acids to restore free thiols and (3) biotinylation of free thiols with a thiol reactive biotinylation agent...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28071745/molecularly-imprinted-biodegradable-nanoparticles
#9
Mariacristina Gagliardi, Alice Bertero, Angelo Bifone
Biodegradable polymer nanoparticles are promising carriers for targeted drug delivery in nanomedicine applications. Molecu- lar imprinting is a potential strategy to target polymer nanoparticles through binding of endogenous ligands that may promote recognition and active transport into specific cells and tissues. However, the lock-and-key mechanism of molecular imprinting requires relatively rigid cross-linked structures, unlike those of many biodegradable polymers. To date, no fully biodegradable molecularly imprinted particles have been reported in the literature...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28069430/functional-characterization-of-avidins-in-amphioxus-branchiostoma-japonucum-evidence-for-a-dual-role-in-biotin-binding-and-immune-response
#10
Xiaomin Guo, Jiajing Xin, Peng Wang, Xiaoyuan Du, Guangdong Ji, Zhan Gao, Shicui Zhang
Avidin is well known for its high affinity to biotin and has been found in many egg-laying vertebrate species. However, little is known about avidin in invertebrate species to date. Here we clearly showed the presence of two avidin genes, Bjavidin1 and Bjavidin2, in the amphioxus Branchiostoma japonicum, the first ones in non-vertebrate animals. We also showed that the expression of both Bjavidin1 and Bjavidin2 were inducible by progesterone, LTA and LPS. Moreover, we demonstrated for the first time that in addition to biotin-binding, the recombinant proteins rBjAVIDIN1 and rBjAVIDIN2 were not only able to interact with Gram-positive and negative bacteria as well as their conserved surface components LTA and LPS but also to enhance phagocytosis of bacteria by macrophages, suggesting that BjAVIDIN1 and BjAVIDIN2 both function as pattern recognition receptors and opsonins...
January 6, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28068317/cryogenic-optical-localization-provides-3d-protein-structure-data-with-angstrom-resolution
#11
Siegfried Weisenburger, Daniel Boening, Benjamin Schomburg, Karin Giller, Stefan Becker, Christian Griesinger, Vahid Sandoghdar
We introduce Cryogenic Optical Localization in 3D (COLD), a method to localize multiple fluorescent sites within a single small protein with Angstrom resolution. We demonstrate COLD by determining the conformational state of the cytosolic Per-ARNT-Sim domain from the histidine kinase CitA of Geobacillus thermodenitrificans and resolving the four biotin sites of streptavidin. COLD provides quantitative 3D information about small- to medium-sized biomolecules on the Angstrom scale and complements other techniques in structural biology...
January 9, 2017: Nature Methods
https://www.readbyqxmd.com/read/28067471/traditional-and-novel-tools-to-probe-the-mitochondrial-metabolism-in-health-and-disease
#12
REVIEW
Yanfei Zhang, José L Avalos
Mitochondrial metabolism links energy production to other essential cellular processes such as signaling, cellular differentiation, and apoptosis. In addition to producing adenosine triphosphate (ATP) as an energy source, mitochondria are responsible for the synthesis of a myriad of important metabolites and cofactors such as tetrahydrofolate, α-ketoacids, steroids, aminolevulinic acid, biotin, lipoic acid, acetyl-CoA, iron-sulfur clusters, heme, and ubiquinone. Furthermore, mitochondria and their metabolism have been implicated in aging and several human diseases, including inherited mitochondrial disorders, cardiac dysfunction, heart failure, neurodegenerative diseases, diabetes, and cancer...
January 9, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28066939/the-nutrition-of-poultry-as-a-factor-affecting-litter-quality-and-foot-pad-dermatitis-an-updated-review
#13
REVIEW
S Swiatkiewicz, A Arczewska-Wlosek, D Jozefiak
Foot pad dermatitis (FPD), a condition of inflammation and necrotic lesions on the plantar surface of the footpads, is commonly observed in fast-growing broiler chickens and turkeys. FPD negatively affects the welfare of birds, performance indices and the economic profit of poultry meat production. Nutrition is an important factor affecting water intake, excreta moisture and litter quality and, in this way, the occurrence and intensity of FPD in birds. This article reviews and discusses the recent results published in the literature on the effects of nutritional factors on litter quality and FPD severity in broiler chickens and turkeys...
January 8, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28065858/role-of-transglutaminase-2-in-pac1-receptor-mediated-protection-against-hypoxia-induced-cell-death-and-neurite-outgrowth-in-differentiating-n2a-neuroblastoma-cells
#14
Alanood S Algarni, Alan J Hargreaves, John M Dickenson
The PAC1 receptor and tissue transglutaminase (TG2) play important roles in neurite outgrowth and modulation of neuronal cell survival. In this study, we investigated the regulation of TG2 activity by the PAC1 receptor in retinoic acid-induced differentiating N2a neuroblastoma cells. TG2 transamidase activity was determined using an amine incorporation and a peptide cross linking assay. In situ TG2 activity was assessed by visualising the incorporation of biotin-X-cadaverine using confocal microscopy. TG2 phosphorylation was monitored via immunoprecipitation and Western blotting...
January 5, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28064476/chemoselective-coupling-preserves-the-substrate-integrity-of-surface-immobilized-oligonucleotides-for-emulsion-pcr-based-gene-library-construction
#15
Marie L Malone, Valerie J Cavett, Brian M Paegel
Combinatorial bead libraries figure prominently in next-generation sequencing and are also important tools for in vitro evolution. The most common methodology for generating such bead libraries, emulsion PCR (emPCR), enzymatically extends bead-immobilized oligonucleotide PCR primers in emulsion droplets containing a single progenitor library member. Primers are almost always immobilized on beads via noncovalent biotin-streptavidin binding. Here, we describe covalent bead functionalization with primers (∼10(6) primers/2...
January 9, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28062376/a-biotin-enrichment-strategy-identifies-novel-carbonylated-amino-acids-in-proteins-from-human-plasma
#16
Jesper F Havelund, Katarzyna Wojdyla, Michael J Davies, Ole N Jensen, Ian Max Møller, Adelina Rogowska-Wrzesinska
: Protein carbonylation is an irreversible protein oxidation correlated with oxidative stress, various diseases and ageing. Here we describe a peptide-centric approach for identification and characterisation of up to 14 different types of carbonylated amino acids in proteins. The modified residues are derivatised with biotin-hydrazide, enriched and characterised by tandem mass spectrometry. The strength of the method lies in an improved elution of biotinylated peptides from monomeric avidin resin using hot water (95°C) and increased sensitivity achieved by reduction of analyte losses during sample preparation and chromatography...
January 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28062280/biotin-independent-strains-of-escherichia-coli-for-enhanced-streptavidin-production
#17
Markus Jeschek, Maximilian O Bahls, Veronika Schneider, Philippe Marlière, Thomas R Ward, Sven Panke
Biotin is an archetypal vitamin used as cofactor for carboxylation reactions found in all forms of life. However, biotin biosynthesis is an elaborate multi-enzymatic process and metabolically costly. Moreover, many industrially relevant organisms are incapable of biotin synthesis resulting in the requirement to supplement defined media. Here we describe the creation of biotin-independent strains of Escherichia coli and Corynebacterium glutamicum through installation of an optimized malonyl-CoA bypass, which re-routes natural fatty acid synthesis, rendering the previously essential vitamin completely obsolete...
January 3, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28059871/modified-nanoantibodies-increase-sensitivity-in-avidin-biotin-immunohistochemistry
#18
Anthony Wong, Chelsea Sykora, Lewis Rogers, Jennifer Higginbotham, Jiwu Wang
Revealing the spatial arrangement of molecules within a tissue through immunohistochemistry (IHC) is an invaluable tool in biomedical research and clinical diagnostics. Choosing both the appropriate antibody and amplification system is paramount to the pathologic interpretation of the tissue at hand. The use of single domain VHH nanoantibodies (nAbs) promise more robust and consistent results in IHC, but are rarely used as an alternative to conventional immunoglobulin G (IgG) antibodies. nAbs are originally obtained from llamas and are the smallest antigen-binding fragments available...
January 4, 2017: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/28058293/quantification-of-small-molecule-protein-interactions-using-fret-between-tryptophan-and-the-pacific-blue-fluorophore
#19
Molly M Lee, Blake R Peterson
We report a new method to quantify the affinity of small molecules for proteins. This method is based on Förster resonance energy transfer (FRET) between endogenous tryptophan (Trp) residues and the coumarin-derived fluorophore Pacific Blue (PB). Tryptophan residues are frequently found in proteins near ligand-binding sites, making this approach potentially applicable to a wide range of systems. To improve access to PB, we developed a scalable multigram synthesis of this fluorophore, starting with inexpensive 2,3,4,5-tetrafluorobenzoic acid...
December 31, 2016: ACS Omega
https://www.readbyqxmd.com/read/28057523/surface-engineering-tumor-cells-with-adjuvant-loaded-particles-for-use-as-cancer-vaccines
#20
Kawther K Ahmed, Sean M Geary, Aliasger K Salem
Cell surface engineering is an expanding field and whilst extensive research has been performed decorating cell surfaces with biomolecules, the engineering of cell surfaces with particles has been a largely unexploited area. This study reports on the assembly of cell-particle hybrids where irradiated tumor cells were surface engineered with adjuvant-loaded, biodegradable, biocompatible, polymeric particles, with the aim of generating a construct capable of functioning as a therapeutic cancer vaccine. Successfully assembled cell-particle hybrids presented here comprised either melanoma cells or prostate cancer cells stably adorned with Toll-like receptor-9 ligand-loaded particles using streptavidin-biotin cross-linking...
January 3, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
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