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Articles 1 - 14 of 14
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Multivariate Analysis Of Open Field Exploration Identifies Latent Spatial And Social Behavioral Axes In Domestic Dogs, Budhaditya Chowdhury, Moira Van Staaden, Robert Huber
Multivariate Analysis Of Open Field Exploration Identifies Latent Spatial And Social Behavioral Axes In Domestic Dogs, Budhaditya Chowdhury, Moira Van Staaden, Robert Huber
Advanced Science Research Center
Recent methodological advances in studying large scale animal movements have let researchers gather rich datasets from behaving animals. Often collected in small sample sizes due to logistical constraints, these datasets are however, ideal for multivariate explorations into behavioral complexity. In behavioral studies of domestic dogs, although automated data loggers have recently seen increasing use, a comprehensive framework to identify complex behavioral axes is lacking. Dog behavioral studies frequently rely on subjective ratings, despite demonstrable evidence that these are insufficient for identifying behavioral variables. Taking advantage of dogs’ innate running abilities and readily available GPS data loggers, we extracted latitude-longitude coordinates …
Proximal And Distal Control For Ligand Binding In Neuroglobin: Role Of The Cd Loop And Evidence For His64 Gating, Cécile Exertier, Lisa Milazzo, Ida Freda, Linda Celeste Montemiglio, Antonella Scaglione, Gabriele Cerutti, Giacomo Parisi, Massimiliano Anselmi, Giulietta Smulevich, Carmelinda Savino, Beatrice Vallone
Proximal And Distal Control For Ligand Binding In Neuroglobin: Role Of The Cd Loop And Evidence For His64 Gating, Cécile Exertier, Lisa Milazzo, Ida Freda, Linda Celeste Montemiglio, Antonella Scaglione, Gabriele Cerutti, Giacomo Parisi, Massimiliano Anselmi, Giulietta Smulevich, Carmelinda Savino, Beatrice Vallone
Advanced Science Research Center
Neuroglobin (Ngb) is predominantly expressed in neurons of the central and peripheral nervous systems and it clearly seems to be involved in neuroprotection. Engineering Ngb to observe structural and dynamic alterations associated with perturbation in ligand binding might reveal important structural determinants, and could shed light on key features related to its mechanism of action. Our results highlight the relevance of the CD loop and of Phe106 as distal and proximal controls involved in ligand binding in murine neuroglobin. We observed the effects of individual and combined mutations of the CD loop and Phe106 that conferred to Ngb higher CO …
Viral Entry Properties Required For Fitness In Humans Are Lost Through Rapid Genomic Change During Viral Isolation, Sho Iketani, Ryan C. Shean, Marion Ferren, Negar Makhsous, Dolly B. Aquino, Amedee Des Georges, Bert Rima, Cyrille Mathieu, Matteo Porotto, Anne Moscona, Alexander L. Greninger
Viral Entry Properties Required For Fitness In Humans Are Lost Through Rapid Genomic Change During Viral Isolation, Sho Iketani, Ryan C. Shean, Marion Ferren, Negar Makhsous, Dolly B. Aquino, Amedee Des Georges, Bert Rima, Cyrille Mathieu, Matteo Porotto, Anne Moscona, Alexander L. Greninger
Advanced Science Research Center
Human parainfluenza viruses cause a large burden of human respiratory illness. While much research relies upon viruses grown in cultured immortalized cells, human parainfluenza virus 3 (HPIV-3) evolves in culture. Cultured viruses differ in their properties compared to clinical strains. We present a genome-wide survey of HPIV-3 adaptations to culture using metagenomic next-generation sequencing of matched pairs of clinical samples and primary culture isolates (zero passage virus). Nonsynonymous changes arose during primary viral isolation, almost entirely in the genes encoding the two surface glycoproteins—the receptor binding protein hemagglutinin-neuraminidase (HN) or the fusion protein (F). We recovered genomes from 95 HPIV-3 …
Manipulation Of Ploidy In Caenorhabditis Elegans, Erlyana K. Clarke, Katherine A. Rivera Gomez, Zaki Mustachi, Mikaela C. Murph, Mara Schvarzstein
Manipulation Of Ploidy In Caenorhabditis Elegans, Erlyana K. Clarke, Katherine A. Rivera Gomez, Zaki Mustachi, Mikaela C. Murph, Mara Schvarzstein
Advanced Science Research Center
Mechanisms that involve whole genome polyploidy play important roles in development and evolution; also, an abnormal generation of tetraploid cells has been associated with both the progression of cancer and the development of drug resistance. Until now, it has not been feasible to easily manipulate the ploidy of a multicellular animal without generating mostly sterile progeny. Presented here is a simple and rapid protocol for generating tetraploid Caenorhabditis elegans animals from any diploid strain. This method allows the user to create a bias in chromosome segregation during meiosis, ultimately increasing ploidy in C. elegans. This strategy relies on the transient …
Journey To The Center Of The Protein: Allostery From Multitemperature Multiconformer X-Ray Crystallography, Daniel A. Keedy
Journey To The Center Of The Protein: Allostery From Multitemperature Multiconformer X-Ray Crystallography, Daniel A. Keedy
Advanced Science Research Center
Proteins inherently fluctuate between conformations to perform functions in the cell. For example, they sample product-binding, transition-state-stabilizing and product-release states during catalysis, and they integrate signals from remote regions of the structure for allosteric regulation. However, there is a lack of understanding of how these dynamic processes occur at the basic atomic level. This gap can be at least partially addressed by combining variable-temperature (instead of traditional cryogenic temperature) X-ray crystallography with algorithms for modeling alternative conformations based on electron-density maps, in an approach called multitemperature multiconformer X-ray crystallography (MMX). Here, the use of MMX to reveal alternative conformations at …
Improving Cartilage Phenotype From Differentiated Pericytes In Tunable Peptide Hydrogels, Enateri V. Alakpa, Vineetha Jayawarna, Karl E. V. Burgess, Christopher C. West, Bruno Péault, Rein V. Ulijn, Matthew J. Dalby
Improving Cartilage Phenotype From Differentiated Pericytes In Tunable Peptide Hydrogels, Enateri V. Alakpa, Vineetha Jayawarna, Karl E. V. Burgess, Christopher C. West, Bruno Péault, Rein V. Ulijn, Matthew J. Dalby
Advanced Science Research Center
Differentiation of stem cells to chondrocytes in vitro usually results in a heterogeneous phenotype. This is evident in the often detected over expression of type X collagen which, in hyaline cartilage structure is not characteristic of the mid-zone but of the deep-zone ossifying tissue. Methods to better match cartilage developed in vitro to characteristic in vivo features are therefore highly desirable in regenerative medicine. This study compares phenotype characteristics between pericytes, obtained from human adipose tissue, differentiated using diphenylalanine/serine (F2/S) peptide hydrogels with the more widely used chemical induced method for chondrogenesis. Significantly higher levels of type II collagen were …
Conserved Amino Acid Networks Modulate Discrete Functional Properties In An Enzyme Superfamily, Chitra Narayanan, Donald Gagne, Kimberly A. Reynolds, Nicolas Doucet
Conserved Amino Acid Networks Modulate Discrete Functional Properties In An Enzyme Superfamily, Chitra Narayanan, Donald Gagne, Kimberly A. Reynolds, Nicolas Doucet
Advanced Science Research Center
In this work, we applied the sequence-based statistical coupling analysis approach to characterize conserved amino acid networks important for biochemical function in the pancreatic-type ribonuclease (ptRNase) superfamily. This superfamily-wide analysis indicates a decomposition of the RNase tertiary structure into spatially distributed yet physically connected networks of co-evolving amino acids, termed sectors. Comparison of this statistics-based description with new NMR experiments data shows that discrete amino acid networks, termed sectors, control the tuning of distinct functional properties in different enzyme homologs. Further, experimental characterization of evolutionarily distant sequences reveals that sequence variation at sector positions can distinguish homologs with a conserved …
Photoassisted Oxidation Of Sulfides Catalyzed By Artificial Metalloenzymes Using Water As An Oxygen Source, Christian Herrero, Nhung Nguyen-Thi, Fabien Hammerer, Frédéric Banse, Donald Gagne, Nicolas Doucet, Jean-Pierre Mahy, Rémy Ricoux
Photoassisted Oxidation Of Sulfides Catalyzed By Artificial Metalloenzymes Using Water As An Oxygen Source, Christian Herrero, Nhung Nguyen-Thi, Fabien Hammerer, Frédéric Banse, Donald Gagne, Nicolas Doucet, Jean-Pierre Mahy, Rémy Ricoux
Advanced Science Research Center
The Mn(TpCPP)-Xln10A artificial metalloenzyme, obtained by non-covalent insertion of Mn(III)-meso-tetrakis(p-carboxyphenyl)porphyrin [Mn(TpCPP), 1-Mn] into xylanase 10A from Streptomyces lividans (Xln10A) as a host protein, was found able to catalyze the selective photo-induced oxidation of organic substrates in the presence of [RuII(bpy)3] 2+ as a photosensitizer and [CoIII(NH3)5Cl]2+ as a sacrificial electron acceptor, using water as oxygen atom source.
Nmrfx Processor: A Cross-Platform Nmr Data Processing Program, Michael Norris, Bayard Fetler, Jan Marchant, Bruce A. Johnson
Nmrfx Processor: A Cross-Platform Nmr Data Processing Program, Michael Norris, Bayard Fetler, Jan Marchant, Bruce A. Johnson
Advanced Science Research Center
NMRFx Processor is a new program for the processing of NMR data. Written in the Java programming language, NMRFx Processor is a cross-platform application and runs on Linux, Mac OS X and Windows operating systems. The application can be run in both a graphical user interface (GUI) mode and from the command line. Processing scripts are written in the Python programming language and executed so that the low-level Java commands are automatically run in parallel on computers with multiple cores or CPUs. Processing scripts can be generated automatically from the parameters of NMR experiments or interactively constructed in the GUI. …
Dynamic Surfaces For The Study Of Mesenchymal Stem Cell Growth Through Adhesion Regulation, Jemma N. Roberts, Jugal Kishore Sahoo, Laura E. Mcnamara, Karl V. Burgess, Jingli Yang, Enateri V. Alakpa, Hilary J. Anderson, Jake Hay, Lesley-Anne Turner, Stephen J. Yarwood, Mischa Zelzer, Richard O.C. Oreffo, Rein V. Ulijn, Matthew J. Dalby
Dynamic Surfaces For The Study Of Mesenchymal Stem Cell Growth Through Adhesion Regulation, Jemma N. Roberts, Jugal Kishore Sahoo, Laura E. Mcnamara, Karl V. Burgess, Jingli Yang, Enateri V. Alakpa, Hilary J. Anderson, Jake Hay, Lesley-Anne Turner, Stephen J. Yarwood, Mischa Zelzer, Richard O.C. Oreffo, Rein V. Ulijn, Matthew J. Dalby
Advanced Science Research Center
Out of their niche environment, adult stem cells, such as mesenchymal stem cells (MSCs), spontaneously differentiate. This makes both studying these important regenerative cells and growing large numbers of stem cells for clinical use challenging. Traditional cell culture techniques have fallen short of meeting this challenge, but materials science offers hope. In this study, we have used emerging rules of managing adhesion/ cytoskeletal balance to prolong MSC cultures by fabricating controllable nanoscale cell interfaces using immobilized peptides that may be enzymatically activated to change their function. The surfaces can be altered (activated) at will to tip adhesion/cytoskeletal balance and initiate …
Chemo-Enzymatic Synthesis Of Site-Specific Isotopically Labeled Nucleotides For Use In Nmr Resonance Assignment, Dynamics And Structural Characterizations, Andrew P. Longhini, Regan M. Leblanc, Owen Becette, Carolina Salguero, Christoph H. Wunderlich, Bruce A. Johnson, Victoria M. D'Souza, T. Kwaku Dayie
Chemo-Enzymatic Synthesis Of Site-Specific Isotopically Labeled Nucleotides For Use In Nmr Resonance Assignment, Dynamics And Structural Characterizations, Andrew P. Longhini, Regan M. Leblanc, Owen Becette, Carolina Salguero, Christoph H. Wunderlich, Bruce A. Johnson, Victoria M. D'Souza, T. Kwaku Dayie
Advanced Science Research Center
Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%. We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride …
Analysis Of Enzyme-Responsive Peptide Surfaces By Raman Spectroscopy, Jugal Kishore Sahoo, Narayana M.S. Sirimuthu, Anne Canning, Mischa Zelzer, Duncan Graham, Rein V. Ulijn
Analysis Of Enzyme-Responsive Peptide Surfaces By Raman Spectroscopy, Jugal Kishore Sahoo, Narayana M.S. Sirimuthu, Anne Canning, Mischa Zelzer, Duncan Graham, Rein V. Ulijn
Advanced Science Research Center
We report on the use of Raman spectroscopy as a tool to characterize model peptide functionalised surfaces. By taking advantage of Raman reporters built into the peptide sequence, the enzymatic hydrolysis of these peptides could be determined.
Chemo-Enzymatic Synthesis Of Site-Specific Isotopically Labeled Nucleotides For Use In Nmr Resonance Assignment, Dynamics And Structural Characterizations, Andrew P. Longhini, Regan M. Leblanc, Owen Becette, Carolina Salguero, Christoph H. Wunderlich, Bruce A. Johnson, Victoria M. D'Souza, Christoph Kreutz, T. Kwaku Dayle
Chemo-Enzymatic Synthesis Of Site-Specific Isotopically Labeled Nucleotides For Use In Nmr Resonance Assignment, Dynamics And Structural Characterizations, Andrew P. Longhini, Regan M. Leblanc, Owen Becette, Carolina Salguero, Christoph H. Wunderlich, Bruce A. Johnson, Victoria M. D'Souza, Christoph Kreutz, T. Kwaku Dayle
Advanced Science Research Center
Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%.We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride riboswitch …
An Optogenetic Gene Expression System With Rapid Activation And Deactivation Kinetics, Laura B. Motta-Mena, Anna Reade, Michael J. Mallory, Spencer Glantz, Orion D. Weiner, Kristen W. Lynch, Kevin H. Gardner
An Optogenetic Gene Expression System With Rapid Activation And Deactivation Kinetics, Laura B. Motta-Mena, Anna Reade, Michael J. Mallory, Spencer Glantz, Orion D. Weiner, Kristen W. Lynch, Kevin H. Gardner
Advanced Science Research Center
Optogenetic gene expression systems can control transcription with spatial and temporal detail unequaled with traditional inducible promoter systems. However, current eukaryotic light-gated transcription systems are limited by toxicity, dynamic range, or slow activation/deactivation. Here we present an optogenetic gene expression system that addresses these shortcomings and demonstrate its broad utility. Our approach utilizes an engineered version of EL222, a bacterial Light-Oxygen-Voltage (LOV) protein that binds DNA when illuminated with blue light. The system has a large (>100-fold) dynamic range of protein expression, rapid activation (< 10 s) and deactivation kinetics (< 50 s), and a highly linear response to light. With this system, we achieve light-gated transcription in several mammalian cell lines and intact zebrafish embryos with minimal basal gene activation and toxicity. Our approach provides a powerful new tool for optogenetic control of gene expression in space and time.