The Experts below are selected from a list of 171825 Experts worldwide ranked by ideXlab platform
Kaustubh Bhalerao - One of the best experts on this subject based on the ideXlab platform.
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a modular Positive Feedback based gene amplifier
Journal of Biological Engineering, 2010Co-Authors: Goutam Nistala, Kang Wu, Kaustubh BhaleraoAbstract:Background: Positive Feedback is a common mechanism used in the regulation of many gene circuits as it can amplify the response to inducers and also generate binary outputs and hysteresis. In the context of electrical circuit design, Positive Feedback is often considered in the design of amplifiers. Similar approaches, therefore, may be used for the design of amplifiers in synthetic gene circuits with applications, for example, in cell-based sensors. Results: We developed a modular Positive Feedback circuit that can function as a genetic signal amplifier, heightening the sensitivity to inducer signals as well as increasing maximum expression levels without the need for an external cofactor. The design utilizes a constitutively active, autoinducer-independent variant of the quorumsensing regulator LuxR. We experimentally tested the ability of the Positive Feedback module to separately amplify the output of a one-component tetracycline sensor and a two-component aspartate sensor. In each case, the Positive Feedback module amplified the response to the respective inducers, both with regards to the dynamic range and sensitivity. Conclusions: The advantage of our design is that the actual Feedback mechanism depends only on a single gene and does not require any other modulation. Furthermore, this circuit can amplify any transcriptional signal, not just one encoded within the circuit or tuned by an external inducer. As our design is modular, it can potentially be used as a component in the design of more complex synthetic gene circuits.
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A modular Positive Feedback-based gene amplifier
Journal of biological engineering, 2010Co-Authors: Goutam Nistala, Christopher V. Rao, Kaustubh BhaleraoAbstract:Positive Feedback is a common mechanism used in the regulation of many gene circuits as it can amplify the response to inducers and also generate binary outputs and hysteresis. In the context of electrical circuit design, Positive Feedback is often considered in the design of amplifiers. Similar approaches, therefore, may be used for the design of amplifiers in synthetic gene circuits with applications, for example, in cell-based sensors. We developed a modular Positive Feedback circuit that can function as a genetic signal amplifier, heightening the sensitivity to inducer signals as well as increasing maximum expression levels without the need for an external cofactor. The design utilizes a constitutively active, autoinducer-independent variant of the quorum-sensing regulator LuxR. We experimentally tested the ability of the Positive Feedback module to separately amplify the output of a one-component tetracycline sensor and a two-component aspartate sensor. In each case, the Positive Feedback module amplified the response to the respective inducers, both with regards to the dynamic range and sensitivity. The advantage of our design is that the actual Feedback mechanism depends only on a single gene and does not require any other modulation. Furthermore, this circuit can amplify any transcriptional signal, not just one encoded within the circuit or tuned by an external inducer. As our design is modular, it can potentially be used as a component in the design of more complex synthetic gene circuits.
Carsten Wiuf - One of the best experts on this subject based on the ideXlab platform.
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Finding the Positive Feedback loops underlying multi-stationarity
BMC systems biology, 2015Co-Authors: Elisenda Feliu, Carsten WiufAbstract:Background Bistability is ubiquitous in biological systems. For example, bistability is found in many reaction networks that involve the control and execution of important biological functions, such as signaling processes. Positive Feedback loops, composed of species and reactions, are necessary for bistability, and generally for multi-stationarity, to occur. These loops are therefore often used to illustrate and pinpoint the parts of a multi-stationary network that are relevant (‘responsible’) for the observed multi-stationarity. However Positive Feedback loops are generally abundant in reaction networks but not all of them are important for understanding the network’s dynamics.
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Finding the Positive Feedback loops underlying multi-stationarity
arXiv: Molecular Networks, 2014Co-Authors: Elisenda Feliu, Carsten WiufAbstract:Bistability is ubiquitous in biological systems. For example, bistability is found in many reaction networks that involve the control and execution of important biological functions, such as signalling processes. Positive Feedback loops, composed of species and reactions, are necessary for bistability, and generally for multi-stationarity, to occur. These loops are therefore often used to illustrate and pinpoint the parts of a multi-stationary network that are relevant (`responsible') for the observed multi-stationarity. However Positive Feedback loops are generally abundant in reaction networks but not all of them are important for subsequent interpretation of the network's dynamics. We present an automated procedure to determine the relevant Positive Feedback loops of a multi-stationary reaction network. The procedure only reports the loops that are relevant for multi-stationarity (that is, when broken multi-stationarity disappears) and not all Positive Feedback loops of the network. We show that the relevant Positive Feedback loops must be understood in the context of the network (one loop might be relevant for one network, but cannot create multi-stationarity in another). Finally, we demonstrate the procedure by applying it to several examples of signaling processes, including a ubiquitination and an apoptosis network, and to models extracted from the Biomodels database. We have developed and implemented an automated procedure to find relevant Positive Feedback loops in reaction networks. The results of the procedure are useful for interpretation and summary of the network's dynamics.
Goutam Nistala - One of the best experts on this subject based on the ideXlab platform.
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a modular Positive Feedback based gene amplifier
Journal of Biological Engineering, 2010Co-Authors: Goutam Nistala, Kang Wu, Kaustubh BhaleraoAbstract:Background: Positive Feedback is a common mechanism used in the regulation of many gene circuits as it can amplify the response to inducers and also generate binary outputs and hysteresis. In the context of electrical circuit design, Positive Feedback is often considered in the design of amplifiers. Similar approaches, therefore, may be used for the design of amplifiers in synthetic gene circuits with applications, for example, in cell-based sensors. Results: We developed a modular Positive Feedback circuit that can function as a genetic signal amplifier, heightening the sensitivity to inducer signals as well as increasing maximum expression levels without the need for an external cofactor. The design utilizes a constitutively active, autoinducer-independent variant of the quorumsensing regulator LuxR. We experimentally tested the ability of the Positive Feedback module to separately amplify the output of a one-component tetracycline sensor and a two-component aspartate sensor. In each case, the Positive Feedback module amplified the response to the respective inducers, both with regards to the dynamic range and sensitivity. Conclusions: The advantage of our design is that the actual Feedback mechanism depends only on a single gene and does not require any other modulation. Furthermore, this circuit can amplify any transcriptional signal, not just one encoded within the circuit or tuned by an external inducer. As our design is modular, it can potentially be used as a component in the design of more complex synthetic gene circuits.
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A modular Positive Feedback-based gene amplifier
Journal of biological engineering, 2010Co-Authors: Goutam Nistala, Christopher V. Rao, Kaustubh BhaleraoAbstract:Positive Feedback is a common mechanism used in the regulation of many gene circuits as it can amplify the response to inducers and also generate binary outputs and hysteresis. In the context of electrical circuit design, Positive Feedback is often considered in the design of amplifiers. Similar approaches, therefore, may be used for the design of amplifiers in synthetic gene circuits with applications, for example, in cell-based sensors. We developed a modular Positive Feedback circuit that can function as a genetic signal amplifier, heightening the sensitivity to inducer signals as well as increasing maximum expression levels without the need for an external cofactor. The design utilizes a constitutively active, autoinducer-independent variant of the quorum-sensing regulator LuxR. We experimentally tested the ability of the Positive Feedback module to separately amplify the output of a one-component tetracycline sensor and a two-component aspartate sensor. In each case, the Positive Feedback module amplified the response to the respective inducers, both with regards to the dynamic range and sensitivity. The advantage of our design is that the actual Feedback mechanism depends only on a single gene and does not require any other modulation. Furthermore, this circuit can amplify any transcriptional signal, not just one encoded within the circuit or tuned by an external inducer. As our design is modular, it can potentially be used as a component in the design of more complex synthetic gene circuits.
Elisenda Feliu - One of the best experts on this subject based on the ideXlab platform.
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Finding the Positive Feedback loops underlying multi-stationarity
BMC systems biology, 2015Co-Authors: Elisenda Feliu, Carsten WiufAbstract:Background Bistability is ubiquitous in biological systems. For example, bistability is found in many reaction networks that involve the control and execution of important biological functions, such as signaling processes. Positive Feedback loops, composed of species and reactions, are necessary for bistability, and generally for multi-stationarity, to occur. These loops are therefore often used to illustrate and pinpoint the parts of a multi-stationary network that are relevant (‘responsible’) for the observed multi-stationarity. However Positive Feedback loops are generally abundant in reaction networks but not all of them are important for understanding the network’s dynamics.
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Finding the Positive Feedback loops underlying multi-stationarity
arXiv: Molecular Networks, 2014Co-Authors: Elisenda Feliu, Carsten WiufAbstract:Bistability is ubiquitous in biological systems. For example, bistability is found in many reaction networks that involve the control and execution of important biological functions, such as signalling processes. Positive Feedback loops, composed of species and reactions, are necessary for bistability, and generally for multi-stationarity, to occur. These loops are therefore often used to illustrate and pinpoint the parts of a multi-stationary network that are relevant (`responsible') for the observed multi-stationarity. However Positive Feedback loops are generally abundant in reaction networks but not all of them are important for subsequent interpretation of the network's dynamics. We present an automated procedure to determine the relevant Positive Feedback loops of a multi-stationary reaction network. The procedure only reports the loops that are relevant for multi-stationarity (that is, when broken multi-stationarity disappears) and not all Positive Feedback loops of the network. We show that the relevant Positive Feedback loops must be understood in the context of the network (one loop might be relevant for one network, but cannot create multi-stationarity in another). Finally, we demonstrate the procedure by applying it to several examples of signaling processes, including a ubiquitination and an apoptosis network, and to models extracted from the Biomodels database. We have developed and implemented an automated procedure to find relevant Positive Feedback loops in reaction networks. The results of the procedure are useful for interpretation and summary of the network's dynamics.
Marion Saint-lu - One of the best experts on this subject based on the ideXlab platform.
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Positive Feedback in Climate: Stabilization or Runaway, Illustrated by a Simple Experiment
Bulletin of the American Meteorological Society, 2016Co-Authors: Jean-louis Dufresne, Marion Saint-luAbstract:AbstractThe response of the various climatic processes to climate change can amplify (Positive Feedback) or damp (negative Feedback) the initial temperature perturbation. An example of a Positive Feedback is the surface albedo Feedback: when the surface temperature rises, part of the ice and snow melts, leading to an increase in the solar radiation absorbed by the surface and to an enhanced surface warming. Positive Feedbacks can lead to instability. On Venus, for example, a Positive Feedback is thought to have evolved into a runaway greenhouse effect. However, Positive Feedbacks can exist in stable systems. This paper presents a simple representation of a Positive Feedback in both a stable and an unstable system. A simple experimental device based on a scale principle is introduced to illustrate the Positive Feedback and its stabilization or runaway regimes. Stabilization can be achieved whether the amplitude of the Positive Feedback declines (e.g., “saturation” of the Feedback) or remains constant. The ...
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Positive Feedback in climate: stabilization or runaway, illustrated by a simple experiment
Bulletin of the American Meteorological Society, 2016Co-Authors: Jean-louis Dufresne, Marion Saint-luAbstract:The response of the various climatic processes to climate change can amplify (Positive Feedback) or damp (negative Feedback) the initial temperature perturbation. An example of a Positive Feedback is the surface albedo Feedback: when the surface temperature rises, part of the ice and snow melts leading to an increase in the solar radiation absorbed by the surface and to an enhanced surface warming. Positive Feedbacks can lead to instability. On Venus for example, a Positive Feedback is thought to have evolved into a runway greenhouse effect. However, Positive Feedbacks can exist in stable systems. This paper presents a simple representation of a Positive Feedback in both a stable and an unstable system. A simple experimental device based on a scale principle is introduced to illustrate the Positive Feedback and its stabilization or runaway regimes. Stabilization can be achieved whether the amplitude of the Positive Feedback declines (e.g. "saturation" of the Feedback) or remains constant. The device can also be used to illustrate the existence of tipping points, which are threshold values beyond which the amplification due to Feedbacks or the stability of the system suddenly changes. The physical equations of the device are established in the framework of the Feedback analysis. Key features to understand why a Positive Feedback does not necessarily lead to a runaway effect are described. The analogy between the different components of the device and those of the climate system is established. Finally, the contribution of individual Feedbacks to the total climate response is addressed. (Capsule Summary)To illustrate the concepts of Positive Feedback, stability, instability, tipping point and saturated Feedback we conceive a very simple device based on a scale with two water reservoirs.
