scholarly journals Approaches to Study Native Chromatin-Modifying Complex Activities and Functions

2021 ◽  
Vol 9 ◽  
Author(s):  
Maxime Galloy ◽  
Catherine Lachance ◽  
Xue Cheng ◽  
Félix Distéfano-Gagné ◽  
Jacques Côté ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Structural Components ◽  
Genome Expression ◽  
Novel Approach ◽  
Approaches To Study ◽  
Experimental Approaches ◽  
Epigenetic Signatures ◽  
Chromatin Modifying Complex ◽  
Complex Activities ◽  
Chromatin Modifiers

The modification of histones—the structural components of chromatin—is a central topic in research efforts to understand the mechanisms regulating genome expression and stability. These modifications frequently occur through associations with multisubunit complexes, which contain active enzymes and additional components that orient their specificity and read the histone modifications that comprise epigenetic signatures. To understand the functions of these modifications it is critical to study the enzymes and substrates involved in their native contexts. Here, we describe experimental approaches to purify native chromatin modifiers complexes from mammalian cells and to produce recombinant nucleosomes that are used as substrates to determine the activity of the complex. In addition, we present a novel approach, similar to the yeast anchor-away system, to study the functions of essential chromatin modifiers by quickly inducing their depletion from the nucleus. The step-by-step protocols included will help standardize these approaches in the research community, enabling convincing conclusions about the specificities and functions of these crucial regulators of the eukaryotic genome.

scholarly journals Advanced experimental approaches to marine water-column biogeochemical processes

2017 ◽  
Vol 75 (1) ◽  
pp. 30-42 ◽  
Author(s):  
Louis Legendre ◽  
Richard B Rivkin ◽  
Nianzhi Jiao
Keyword(s):  
Water Column ◽  
Numerical Models ◽  
Free Water ◽  
Sea Surface ◽  
Biogeochemical Processes ◽  
In Situ Experiments ◽  
Technological Developments ◽  
Approaches To Study ◽  
Experimental Approaches

Abstract This “Food for Thought” article examines the potential uses of several novel scientific and technological developments, which are currently available or being developed, to significantly advance or supplement existing experimental approaches to study water-column biogeochemical processes (WCB-processes). After examining the complementary roles of observation, experiments and numerical models to study WCB-processes, we focus on the main experimental approaches of free-water in situ experiments, and at-sea and on-land meso- and macrocosms. We identify some of the incompletely resolved aspects of marine WCB-processes, and explore advanced experimental approaches that could be used to reduce their uncertainties. We examine three such approaches: free-water experiments of lengthened duration using bioArgo floats and gliders, at-sea mesocosms deployed several 100s m below the sea-surface using new biogeochemical sensors, and 50 m-tall on-land macrocosms. These approaches could lead to significant progress in concepts related to marine WCB-processes.

Optimum Strain Gauge Application to Bladed Assemblies

2002 ◽  
Author(s):  
J. Szwedowicz ◽  
S. M. Senn ◽  
R. S. Abhari
Keyword(s):  
Strain Gauge ◽  
Element Model ◽  
Strain Gauges ◽  
Structural Components ◽  
Algorithm Optimization ◽  
Rotating Blades ◽  
Novel Approach ◽  
Present Technique ◽  
Optimization Function ◽  
Rotating Impeller

Optimum placements of the strain gauges assure reliable vibration measurements of structural components such as rotating blades. Within the framework of cyclic vibration theory, a novel approach has been developed for computation of the optimum gauge positions on tuned bladed discs regarding the determined sensitivity, orthogonality, gradient and distance criteria. The utilized genetic algorithm optimization tool allows for an effective numerical search of suitable solutions of the defined optimization function. A rotating impeller disc represented by a cyclic finite element model demonstrates the application of this method. The present technique can be easily applied to other structural components requiring optimal strain gauge instrumentation.

scholarly journals Multi-model inference of network properties from incomplete data

2006 ◽  
Vol 3 (2) ◽  
pp. 123-136 ◽  
Author(s):  
Michael P. H. Stumpf ◽  
Thomas Thorne
Keyword(s):  
Network Models ◽  
Network Data ◽  
Global Networks ◽  
New Approach ◽  
Model Inference ◽  
Novel Approach ◽  
Eukaryotic Species ◽  
Network Properties ◽  
Experimental Approaches ◽  
Saccaromyces Cerevisiae

Summary It has previously been shown that subnets differ from global networks from which they are sampled for all but a very limited number of theoretical network models. These differences are of qualitative as well as quantitative nature, and the properties of subnets may be very different from the corresponding properties in the true, unobserved network. Here we propose a novel approach which allows us to infer aspects of the true network from incomplete network data in a multi-model inference framework. We develop the basic theoretical framework, including procedures for assessing confidence intervals of our estimates and evaluate the performance of this approach in simulation studies and against subnets drawn from the presently available PIN network data in Saccaromyces cerevisiae. We then illustrate the potential power of this new approach by estimating the number of interactions that will be detectable with present experimental approaches in sfour eukaryotic species, inlcuding humans. Encouragingly, where independent datasets are available we obtain consistent estimates from different partial protein interaction networks. We conclude with a discussion of the scope of this approaches and areas for further research

scholarly journals Novel in vitro Experimental Approaches to Study Myelination and Remyelination in the Central Nervous System

2021 ◽  
Vol 15 ◽  
Author(s):  
Davide Marangon ◽  
Nicolò Caporale ◽  
Marta Boccazzi ◽  
Maria P. Abbracchio ◽  
Giuseppe Testa ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Molecular Mechanisms ◽  
Disease Modeling ◽  
Brain Physiology ◽  
Pathological Conditions ◽  
Approaches To Study ◽  
The Central Nervous System ◽  
Experimental Approaches

Myelin is the lipidic insulating structure enwrapping axons and allowing fast saltatory nerve conduction. In the central nervous system, myelin sheath is the result of the complex packaging of multilamellar extensions of oligodendrocyte (OL) membranes. Before reaching myelinating capabilities, OLs undergo a very precise program of differentiation and maturation that starts from OL precursor cells (OPCs). In the last 20 years, the biology of OPCs and their behavior under pathological conditions have been studied through several experimental models. When co-cultured with neurons, OPCs undergo terminal maturation and produce myelin tracts around axons, allowing to investigate myelination in response to exogenous stimuli in a very simple in vitro system. On the other hand, in vivo models more closely reproducing some of the features of human pathophysiology enabled to assess the consequences of demyelination and the molecular mechanisms of remyelination, and they are often used to validate the effect of pharmacological agents. However, they are very complex, and not suitable for large scale drug discovery screening. Recent advances in cell reprogramming, biophysics and bioengineering have allowed impressive improvements in the methodological approaches to study brain physiology and myelination. Rat and mouse OPCs can be replaced by human OPCs obtained by induced pluripotent stem cells (iPSCs) derived from healthy or diseased individuals, thus offering unprecedented possibilities for personalized disease modeling and treatment. OPCs and neural cells can be also artificially assembled, using 3D-printed culture chambers and biomaterial scaffolds, which allow modeling cell-to-cell interactions in a highly controlled manner. Interestingly, scaffold stiffness can be adopted to reproduce the mechanosensory properties assumed by tissues in physiological or pathological conditions. Moreover, the recent development of iPSC-derived 3D brain cultures, called organoids, has made it possible to study key aspects of embryonic brain development, such as neuronal differentiation, maturation and network formation in temporal dynamics that are inaccessible to traditional in vitro cultures. Despite the huge potential of organoids, their application to myelination studies is still in its infancy. In this review, we shall summarize the novel most relevant experimental approaches and their implications for the identification of remyelinating agents for human diseases such as multiple sclerosis.

Towards astrobiological experimental approaches to study planetary UV surface environments

2018 ◽  
Vol 14 (S345) ◽  
pp. 222-226
Author(s):  
Ximena C. Abrevaya ◽  
Martin Leitzinger ◽  
Oscar J. Oppezzo ◽  
Petra Odert ◽  
G. Juan M. Luna ◽  
...  
Keyword(s):  
Ultraviolet Radiation ◽  
Laboratory Experiments ◽  
Lethal Dose ◽  
Action Spectrum ◽  
Interdisciplinary Approach ◽  
Accurate Estimation ◽  
Atmospheric Attenuation ◽  
Approaches To Study ◽  
Experimental Approaches ◽  
The Impact

AbstractThe stellar ultraviolet radiation (UVR) has been studied in the last decade and has been found to be an important factor to determine the habitability of planetary surfaces. It is known that UVR can be a constraint for life. However, most of the studies of UVR and habitability have missed some fundamental aspects: i) Accurate estimation of the planetary atmospheric attenuation, ii) The biological inferences used to represent the impact of the stellar UVR on life are theoretical and based on the action spectrum (for DNA or microorganisms) or considering parameters as the “lethal dose” obtained from non-astrobiological experiments. Therefore, the conclusions reached by previous studies about the UVR habitability of planetary bodies may be inaccurate. In this work, we propose how to address these studies in a more accurate way through an interdisciplinary approach that combines astrophysics, microbiology, and photobiology and by the use of specially designed laboratory experiments.

scholarly journals Stimulation of Innate Immunity byIn VivoCyclic di-GMP Synthesis Using Adenovirus

2014 ◽  
Vol 21 (11) ◽  
pp. 1550-1559 ◽  
Author(s):  
Benjamin J. Koestler ◽  
Sergey S. Seregin ◽  
David P. W. Rastall ◽  
Yasser A. Aldhamen ◽  
Sarah Godbehere ◽  
...  
Keyword(s):  
Innate Immunity ◽  
Mammalian Cells ◽  
Immune Cell ◽  
Innate Immune ◽  
Host Cells ◽  
Content Type ◽  
Cytokines And Chemokines ◽  
Novel Approach

ABSTRACTThe bacterial second messenger cyclic di-GMP (c-di-GMP) stimulates inflammation by initiating innate immune cell recruitment and triggering the release of proinflammatory cytokines and chemokines. These properties make c-di-GMP a promising candidate for use as a vaccine adjuvant, and numerous studies have demonstrated that administration of purified c-di-GMP with different antigens increases protection against infection in animal models. Here, we have developed a novel approach to produce c-di-GMP inside host cells as an adjuvant to exploit a host-pathogen interaction and initiate an innate immune response. We have demonstrated that c-di-GMP can be synthesizedin vivoby transducing a diguanylate cyclase (DGC) gene into mammalian cells using an adenovirus serotype 5 (Ad5) vector. Expression of DGC led to the production of c-di-GMPin vitroandin vivo, and this was able to alter proinflammatory gene expression in murine tissues and increase the secretion of numerous cytokines and chemokines when administered to animals. Furthermore, coexpression of DGC modestly increased T-cell responses to aClostridium difficileantigen expressed from an adenovirus vaccine, although no significant differences in antibody titers were observed. This adenovirus c-di-GMP delivery system offers a novel method to administer c-di-GMP as an adjuvant to stimulate innate immunity during vaccination.

Optimum Strain Gage Application to Bladed Assemblies

2002 ◽  
Vol 124 (4) ◽  
pp. 606-613 ◽  
Author(s):  
J. Szwedowicz ◽  
S. M. Senn ◽  
R. S. Abhari
Keyword(s):  
Strain Gage ◽  
Element Model ◽  
Strain Gages ◽  
Structural Components ◽  
Algorithm Optimization ◽  
Rotating Blades ◽  
Novel Approach ◽  
Present Technique ◽  
Optimization Function ◽  
Rotating Impeller

Optimum placements of the strain gages assure reliable vibration measurements of structural components such as rotating blades. Within the framework of cyclic vibration theory, a novel approach has been developed for computation of the optimum gage positions on tuned bladed disks regarding the determined sensitivity, orthogonality, gradient and distance criteria. The utilized genetic algorithm optimization tool allows for an effective numerical search of suitable solutions of the defined optimization function. A rotating impeller disk represented by a cyclic finite element model demonstrates the application of this method. The present technique can be easily applied to other structural components requiring optimal strain gage instrumentation.

scholarly journals Alteration of nuclear lamin organization inhibits RNA polymerase II–dependent transcription

2002 ◽  
Vol 156 (4) ◽  
pp. 603-608 ◽  
Author(s):  
Timothy P. Spann ◽  
Anne E. Goldman ◽  
Chen Wang ◽  
Sui Huang ◽  
Robert D. Goldman
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Mammalian Cells ◽  
Protein A ◽  
Selective Inhibition ◽  
Chromatin Organization ◽  
Dominant Negative ◽  
Gene Activity ◽  
Structural Components ◽  
Nuclear Lamins

RTegulation of gene activity is mediated by alterations in chromatin organization. In addition, chromatin organization may be governed in part by interactions with structural components of the nucleus. The nuclear lamins comprise the lamina and a variety of nucleoplasmic assemblies that together are major structural components of the nucleus. Furthermore, lamins and lamin-associated proteins have been reported to bind chromatin. These observations suggest that the nuclear lamins may be involved in the regulation of gene activity. In this report, we test this possibility by disrupting the normal organization of nuclear lamins with a dominant negative lamin mutant lacking the NH2-terminal domain. We find that this disruption inhibits RNA polymerase II activity in both mammalian cells and transcriptionally active embryonic nuclei from Xenopus laevis. The inhibition appears to be specific for polymerase II as disruption of lamin organization does not detectably inhibit RNA polymerases I and III. Furthermore, immunofluorescence observations indicate that this selective inhibition of polymerase II–dependent transcription involves the TATA binding protein, a component of the basal transcription factor TFIID.

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