Kinetics of gene expression in bacteria — From models to measurements, and back again

2013 ◽  
Vol 91 (7) ◽  
pp. 487-494 ◽  
Author(s):  
Andre S. Ribeiro
Keyword(s):  
Gene Expression ◽  
Stochastic Process ◽  
Stochastic Model ◽  
Experimental Validation ◽  
Live Cells ◽  
Genetic Circuits ◽  
Future Developments ◽  
The One ◽  
Kinetics Of ◽  
Production Dynamics

Dennis Salahub has contributed to several scientific areas. Likely, one of the lesser known contributions is the one on the study of the kinetics of gene expression in prokaryotes, which resulted in a delayed stochastic model of transcription and translation dynamics in bacteria. The model has become the basis for modeling stochastic genetic circuits and has provided a framework for interpreting recent measurements of transcripts production dynamics in live cells, one event at a time. Here, we review the contributions by Salahub and colleagues to the modeling strategies of gene expression as a multi-delayed stochastic process. Next, we describe recent findings, which build upon this work and provide experimental validation of the models. Finally, we discuss potential future developments in this field of research.

Arrangement Of Monomeric Units In Fibrin

1979 ◽  
Author(s):  
Jan Hermans
Keyword(s):  
Fiber Axis ◽  
High Symmetry ◽  
Linear Polymers ◽  
Fiber Volume ◽  
High Fiber ◽  
Rotation Axes ◽  
Small Set ◽  
Helical Turn ◽  
The One ◽  
Kinetics Of

Measurements of light scattering have given much information about formation and properties of fibrin. These studies have determined mass-length ratio of linear polymers (protofibrils) and of fibers, kinetics of polymerization and of lateral association and volume-mass ratio of thick fibers. This ratio is 5 to 1. On the one hand, this high value suggests that the fiber contains channels that allow the diffusion of enzymes such as Factor XHIa and plasmin; on the other hand, the high value appears paradoxical for a stiff fiber made up of elongated units (fibrin monomers) arranged in parallel. Such a high fiber volume is a property of only a small set out of many high-symmetry models of fibrin, which may be constructed from overlapping three-domain monomers which are arranged into strands, are aligned nearly parallel to the fiber axis and make adequate longitudinal and lateral contacts. These models contain helical protofibrils related to each other by rotation axes parallel to the fiber axis. The protofibrils may contain 2, 3 or 4 monomers per helical turn and there are four possible symmetries. A large specific volume is achieved if the ends of each monomer are slightly displaced from the protofibril axis, either by a shift or by a tilt of the monomer. The fiber containing tilted monomers is more highly interconnected; the two ends of a tilted monomer form lateral contacts with different adjacent protofibrils, whereas the two ends of a non-tilted monomer contact the same adjacent protofibril(s).

scholarly journals Synthesis and Polymerization Kinetics of Rigid Tricyanate Ester

Polymers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1686
Author(s):  
Andrey Galukhin ◽  
Roman Nosov ◽  
Ilya Nikolaev ◽  
Elena Melnikova ◽  
Daut Islamov ◽  
...  
Keyword(s):  
Kinetic Analysis ◽  
Single Step ◽  
Polymerization Kinetics ◽  
Scanning Calorimetry ◽  
Modulated Differential Scanning Calorimetry ◽  
Diffusion Controlled ◽  
Polymerization Product ◽  
The One ◽  
Kinetics Of

A new rigid tricyanate ester consisting of seven conjugated aromatic units is synthesized, and its structure is confirmed by X-ray analysis. This ester undergoes thermally stimulated polymerization in a liquid state. Conventional and temperature-modulated differential scanning calorimetry techniques are employed to study the polymerization kinetics. A transition of polymerization from a kinetic- to a diffusion-controlled regime is detected. Kinetic analysis is performed by combining isoconversional and model-based computations. It demonstrates that polymerization in the kinetically controlled regime of the present monomer can be described as a quasi-single-step, auto-catalytic, process. The diffusion contribution is parameterized by the Fournier model. Kinetic analysis is complemented by characterization of thermal properties of the corresponding polymerization product by means of thermogravimetric and thermomechanical analyses. Overall, the obtained experimental results are consistent with our hypothesis about the relation between the rigidity and functionality of the cyanate ester monomer, on the one hand, and its reactivity and glass transition temperature of the corresponding polymer, on the other hand.

scholarly journals KD determination from time-resolved experiments on live cells with LigandTracer and reconciliation with end-point flow cytometry measurements

2021 ◽  
Author(s):  
Diana Spiegelberg ◽  
Jonas Stenberg ◽  
Pascale Richalet ◽  
Marc Vanhove
Keyword(s):  
Flow Cytometry ◽  
Live Cells ◽  
Time Resolved ◽  
Surface Receptors ◽  
Full Characterization ◽  
End Point ◽  
Titration Curves ◽  
Kinetics Of

AbstractDesign of next-generation therapeutics comes with new challenges and emulates technology and methods to meet them. Characterizing the binding of either natural ligands or therapeutic proteins to cell-surface receptors, for which relevant recombinant versions may not exist, represents one of these challenges. Here we report the characterization of the interaction of five different antibody therapeutics (Trastuzumab, Rituximab, Panitumumab, Pertuzumab, and Cetuximab) with their cognate target receptors using LigandTracer. The method offers the advantage of being performed on live cells, alleviating the need for a recombinant source of the receptor. Furthermore, time-resolved measurements, in addition to allowing the determination of the affinity of the studied drug to its target, give access to the binding kinetics thereby providing a full characterization of the system. In this study, we also compared time-resolved LigandTracer data with end-point KD determination from flow cytometry experiments and hypothesize that discrepancies between these two approaches, when they exist, generally come from flow cytometry titration curves being acquired prior to full equilibration of the system. Our data, however, show that knowledge of the kinetics of the interaction allows to reconcile the data obtained by flow cytometry and LigandTracer and demonstrate the complementarity of these two methods.

scholarly journals High-performance chemical- and light-inducible recombinases in mammalian cells and mice

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Benjamin H. Weinberg ◽  
Jang Hwan Cho ◽  
Yash Agarwal ◽  
N. T. Hang Pham ◽  
Leidy D. Caraballo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mammalian Cells ◽  
High Performance ◽  
Genome Engineering ◽  
Genetic Circuits ◽  
Control Of Gene Expression ◽  
Expression Control ◽  
Gene Expression Control ◽  
High Performance Systems ◽  
Spatiotemporal Control

Abstract Site-specific DNA recombinases are important genome engineering tools. Chemical- and light-inducible recombinases, in particular, enable spatiotemporal control of gene expression. However, inducible recombinases are scarce due to the challenge of engineering high performance systems, thus constraining the sophistication of genetic circuits and animal models that can be created. Here we present a library of >20 orthogonal inducible split recombinases that can be activated by small molecules, light and temperature in mammalian cells and mice. Furthermore, we engineer inducible split Cre systems with better performance than existing systems. Using our orthogonal inducible recombinases, we create a genetic switchboard that can independently regulate the expression of 3 different cytokines in the same cell, a tripartite inducible Flp, and a 4-input AND gate. We quantitatively characterize the inducible recombinases for benchmarking their performances, including computation of distinguishability of outputs. This library expands capabilities for multiplexed mammalian gene expression control.

A semi-hybrid model for malaria with limited superinfection

1998 ◽  
Vol 30 (04) ◽  
pp. 1027-1057 ◽  
Author(s):  
Philippe Picard
Keyword(s):  
Stochastic Model ◽  
Population Size ◽  
Hybrid Model ◽  
Human Population ◽  
Threshold Level ◽  
The Other ◽  
The Difference ◽  
The One

Modelling malaria with consistency necessitates the introduction of at least two families of interconnected processes. Even in a Markovian context the simplest fully stochastic model is intractable and is usually transformed into a hybrid model, by supposing that these two families are stochastically independent and linked only through two deterministic connections. A model closer to the fully stochastic model is presented here, where one of the two families is subordinated to the other and just a unique deterministic connection is required. For this model a threshold theorem can be proved but the threshold level is not the one obtained in a hybrid model. The difference disappears only when the human population size approaches infinity.

scholarly journals Linking Ligand-Induced Alterations in Androgen Receptor Structure to Differential Gene Expression: A First Step in the Rational Design of Selective Androgen Receptor Modulators

2006 ◽  
Vol 20 (6) ◽  
pp. 1201-1217 ◽  
Author(s):  
Dmitri Kazmin ◽  
Tatiana Prytkova ◽  
C. Edgar Cook ◽  
Russell Wolfinger ◽  
Tzu-Ming Chu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Androgen Receptor ◽  
Rational Design ◽  
Dynamic Structure ◽  
Rational Approach ◽  
Peptide Phage Display ◽  
Differential Gene ◽  
Receptor Modulators ◽  
Kinetics Of

Abstract We have previously identified a family of novel androgen receptor (AR) ligands that, upon binding, enable AR to adopt structures distinct from that observed in the presence of canonical agonists. In this report, we describe the use of these compounds to establish a relationship between AR structure and biological activity with a view to defining a rational approach with which to identify useful selective AR modulators. To this end, we used combinatorial peptide phage display coupled with molecular dynamic structure analysis to identify the surfaces on AR that are exposed specifically in the presence of selected AR ligands. Subsequently, we used a DNA microarray analysis to demonstrate that differently conformed receptors facilitate distinct patterns of gene expression in LNCaP cells. Interestingly, we observed a complete overlap in the identity of genes expressed after treatment with mechanistically distinct AR ligands. However, it was differences in the kinetics of gene regulation that distinguished these compounds. Follow-up studies, in cell-based assays of AR action, confirmed the importance of these alterations in gene expression. Together, these studies demonstrate an important link between AR structure, gene expression, and biological outcome. This relationship provides a firm underpinning for mechanism-based screens aimed at identifying SARMs with useful clinical profiles.

scholarly journals Effects of embryo culture on global pattern of gene expression in preimplantation mouse embryos

Reproduction ◽  
2004 ◽  
Vol 128 (3) ◽  
pp. 301-311 ◽  
Author(s):  
Paolo Rinaudo ◽  
Richard M Schultz
Keyword(s):  
Gene Expression ◽  
Preimplantation Embryos ◽  
Expression Analysis Systematic Explorer ◽  
Cell Stage ◽  
Global Pattern ◽  
Preimplantation Mouse Embryos ◽  
Preimplantation Mouse ◽  
Global Patterns ◽  
The One

Culture of preimplantation embryos affects gene expression. The magnitude of the effect on the global pattern of gene expression, however, is not known. We compared global patterns of gene expression in blastocysts cultured from the one-cell stage in either Whitten’s medium or KSOM + amino acids (KSOM/AA) with that of blastocysts that developed in vivo, using the Affymetrix MOE430A chip. The analysis revealed that expression of 114 genes was affected after culture in Whitten’s medium, whereas only 29 genes were mis-expressed after culture in KSOM/AA. Expression Analysis Systematic Explorer was used to identify biological and molecular processes that are perturbed after culture and indicated that genes involved in protein synthesis, cell proliferation and transporter function were down-regulated after culture in Whitten’s medium. A common set of genes involved in transporter function was also down-regulated after culture in KSOM/AA. These results provide insights as to why embryos develop better in KSOM/AA than in Whitten’s medium, and highlight the power of microarray analysis to assess global patterns of gene expression.

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