Moisés Santillán | Centro de Investigacion y Estudios Avanzados del IPN (original) (raw)
Papers by Moisés Santillán
The definitions of power and efficiency for energy-converting intracellular biochemical processes... more The definitions of power and efficiency for energy-converting intracellular biochemical processes, introduced by Caplan and Essig are studied. These definitions are recovered in the present work with the formalism of De Groot and Mazur for First-Order Irreversible Thermodynamics, rather than the formalism of Prigogine, as done by Caplan and Essig.
The term molecular biology is so familiar nowadays that nobody questions its meaning. However, th... more The term molecular biology is so familiar nowadays that nobody questions its meaning. However, there was no consensus in the beginning about that, and even some people disputed that such a term corresponded to a new science.
Abstract In the traditional statistical mechanics textbooks, the entropy concept is first introdu... more Abstract In the traditional statistical mechanics textbooks, the entropy concept is first introduced for the microcanonical ensemble and then extended to the canonical and grand-canonical cases. However, in the authors' experience, this procedure makes it difficult for the student to see the bigger picture and, although quite ingenuous, the subtleness of the demonstrations to pass from the microcanonical to the canonical and grand-canonical ensembles is hard to grasp.
Abstract Hill functions follow from the equilibrium state of the reaction in which n ligands simu... more Abstract Hill functions follow from the equilibrium state of the reaction in which n ligands simultaneously bind a single receptor. This result if often employed to interpret the Hill coefficient as the number of ligand binding sites in all kinds of reaction schemes. Here, we study the equilibrium states of the reactions in which n ligand bind a receptor sequentially, both non-cooperatively and in a cooperative fashion.
Multistability is an emergent dynamic property that has been invoked to explain multiple coexisti... more Multistability is an emergent dynamic property that has been invoked to explain multiple coexisting biological states. In this work, we investigate the origin of bistability in the lac operon. To do this, we develop a mathematical model for the regulatory pathway in this system and compare the model predictions with other experimental results in which a nonmetabolizable inducer was employed.
SE REALIZA LA APLICACION DEL PROGRAMA CABLECAD AM/FM/GIS PARA AUTOMATIZACION DE EMPRESA ELECTRICA... more SE REALIZA LA APLICACION DEL PROGRAMA CABLECAD AM/FM/GIS PARA AUTOMATIZACION DE EMPRESA ELECTRICAS. SE EXPLICA LAS CARACTERISTICAS, DISPOSITIVOS Y VENTAJAS DEL PROGRAMA CABLECAD EN EL PROCESO DE AUTOMATIZACION Y ANALISIS DE LOS PROGRAMAS APLICADOS A UN SISTEMA DE DISTRIBUCION. SE MUESTRA LOS DETALLES HISTORICOS, TECNICOS Y OPERACIONALES DE LA EMPRESA ELECTRICA DEL ECUADOR.
We present a brief review of some works addresed to a connection between concepts arising from bo... more We present a brief review of some works addresed to a connection between concepts arising from both finite-time thermodynamics (FTT) and first order irreversible thermodynamics (FOIT). While the first order irreversible thermodynamics formalism is based on the study of local variables, finite time thermodynamics mainly deals with net global process variables.
The hemoflagellate Trypanosoma cruzi is the causative agent of American trypanosomiasis. Despite ... more The hemoflagellate Trypanosoma cruzi is the causative agent of American trypanosomiasis. Despite the importance of motility in the parasite life cycle, little is known about T. cruzi motility, and there is no quantitative description of its flagellar beating. Using video microscopy and quantitative vectorial analysis of epimastigote trajectories, we find a forward parasite motility defined by tip-to-base symmetrical flagellar beats.
Abstract: This work extends a recently developed mathematical theory of thermodynamics for discre... more Abstract: This work extends a recently developed mathematical theory of thermodynamics for discrete-state, continuous-time Markov processes with, and more importantly without, detailed balance. We show that the Legendre transform in connection to ensemble changes in Gibbs' statistical mechanics can be derived from the stochastic theory. We consider the joint probability $ p_ {XY} $ of two random variables $ X $ and $ Y $ and the conditional probability $ p_ {X| Y= y^*} ,with, with ,with y^*=< Y> $ according to $ p_ {XY} $.
Abstract In the present work we study the transcription-factor regulatory network that controls t... more Abstract In the present work we study the transcription-factor regulatory network that controls the synthesis of flagella in E. coli. Our objective is to address how the transcription-factor dynamics (in terms of their promoter activities and associated rates) correlate with their positions in the hierarchical organization of this regulatory network. Our results suggest that global-regulator promoters express at higher rates than those of local regulators, particularly when the bacterial populations are actively growing.
Understanding the regulation of gene control networks and their ensuing dynamics will be a critic... more Understanding the regulation of gene control networks and their ensuing dynamics will be a critical component in the understanding of the mountain of genomic data being currently collected. This paper reviews recent mathematical modeling work on the tryptophan and lactose operons which are, respectively, the classical paradigms for repressible and inducible operons. To cite this article: MC Mackey et al., CR Biologies 327 (2004).
In the last few years, the efforts to elucidate the mechanisms underlying the segmentation clock ... more In the last few years, the efforts to elucidate the mechanisms underlying the segmentation clock in various vertebrate species have multiplied. Early evidence suggested that oscillations are caused by one of the genes under the Notch signalling pathway (like those of the her or Hes families). Recently, Aulehla et al.[Wnt3a plays a major role in the segmentation clock controlling somitogenesis. Dev.
Resumen LYT1 es una molécula con actividad lítica en condiciones ácidas, que según se demostró ge... more Resumen LYT1 es una molécula con actividad lítica en condiciones ácidas, que según se demostró genéticamente, participa en el proceso de infección y transición de estadio de T. cruzi. Su diferente funcionalidad es resultado de la producción de dos proteínas, obtenidas por trans-empalme alternativo, que contienen una secuencia de secreción y una nuclear (LYT1s) o únicamente la secuencia nuclear (LYT1n).
Amigo lector, el trabajo que tienes en tus manos lo hemos realizado con el deseo de que te ayude ... more Amigo lector, el trabajo que tienes en tus manos lo hemos realizado con el deseo de que te ayude a aprobar el examen extraordinario, los autores se sentirán altamente recompensados en su labor educativa al saber que lo has aprovechado y que te ha sido de utilidad. Por tu parte el esfuerzo realizado te acercará a tu siguiente meta: tus estudios de licenciatura.
Transcriptional bursting, also known as transcriptional pulsing, is a fundamental property of gen... more Transcriptional bursting, also known as transcriptional pulsing, is a fundamental property of genes from bacteria to humans (Chubb et al., 2006; Golding et al., 2005; Raj et al., 2006). Transcription of genes, the process which transforms the stable code written in DNA into the mobile RNA message can occur in" bursts" or" pulses".
Proceedings of the National …, Jan 1, 2001
A mathematical model for regulation of the tryptophan operon is presented. This model takes into ... more A mathematical model for regulation of the tryptophan operon is presented. This model takes into account repression, feedback enzyme inhibition, and transcriptional attenuation. Special attention is given to model parameter estimation based on experimental data. The model's system of delay differential equations is numerically solved, and the results are compared with experimental data on the temporal evolution of enzyme activity in cultures of Escherichia coli after a nutritional shift (minimal ؉ tryptophan medium to minimal medium). Good agreement is obtained between the numeric simulations and the experimental results for wild-type E. coli, as well as for two different mutant strains.
Biophysical journal, Jan 1, 2004
A mathematical model of the lac operon which includes all of the known regulatory mechanisms, inc... more A mathematical model of the lac operon which includes all of the known regulatory mechanisms, including external-glucose-dependent catabolite repression and inducer exclusion, as well as the time delays inherent to transcription and translation, is presented. With this model we investigate the influence of external glucose, by means of catabolite repression and the regulation of lactose uptake, on the bistable behavior of this system.
Biophysical journal, Jan 1, 2004
We develop a mathematical model of the phage λ lysis/lysogeny switch, taking into account recent ... more We develop a mathematical model of the phage λ lysis/lysogeny switch, taking into account recent experimental evidence demonstrating enhanced cooperativity between the left and right operator regions. Model parameters are estimated from available experimental data. The model is shown to have a single stable steady state for these estimated parameter values, and this steady state corresponds to the lysogenic state. When the CI degradation rate (γcI) is slightly increased from its normal value (γcI≃ 0.0 min− 1), two additional ...
… Interdisciplinary Journal of …, Jan 1, 2004
Cell motility and the …, Jan 1, 1992
Spores of the microsporidium Nosema algerae were stimulated to germinate in vitro while observed ... more Spores of the microsporidium Nosema algerae were stimulated to germinate in vitro while observed with video-enhanced contrast microscopy. Field-by-field playback of tape-recorded sequences yielded the first serial illustrations and kinematic analysis of the explosive discharge of the polar filament and the sporoplasm. The filament emerges from the anterior pole of the spore in a regularly pitched helicoidal course along a nearly straight axis, with a mean maximum instant velocity of 105 p d s . Just before elongation is completed the filament tip follows a tortuous path that often results in a curved or spiralling terminal configuration. Then elongation stops and, after a lag that may vary from less than 15 to over 500 ms, the sporoplasm pours out at the filament tip forming a globule that quickly grows up to a size larger than its original volume within the spore. Concomitantly, the helical filament becomes straightened and frequently the spore body is pulled forward. Thereafter a relaxed filament, usually 5-10% shorter than when maximally extended, remains connecting the empty spore case and the sporoplasmic droplet. Experiments with hyperosmolar media produced a considerable slowdown of filament extrusion and often precluded sporoplasm discharge. The present results are fully consistent with the hypothesis of a hydrostatic pressure-triggered mechanism of spore germination, and revealed that the process is composed of two discrete phases separated by a variable lag: 1) complete eversion of the polar filament, and 2 ) passage of the main sporoplasm mass along the tube.
The definitions of power and efficiency for energy-converting intracellular biochemical processes... more The definitions of power and efficiency for energy-converting intracellular biochemical processes, introduced by Caplan and Essig are studied. These definitions are recovered in the present work with the formalism of De Groot and Mazur for First-Order Irreversible Thermodynamics, rather than the formalism of Prigogine, as done by Caplan and Essig.
The term molecular biology is so familiar nowadays that nobody questions its meaning. However, th... more The term molecular biology is so familiar nowadays that nobody questions its meaning. However, there was no consensus in the beginning about that, and even some people disputed that such a term corresponded to a new science.
Abstract In the traditional statistical mechanics textbooks, the entropy concept is first introdu... more Abstract In the traditional statistical mechanics textbooks, the entropy concept is first introduced for the microcanonical ensemble and then extended to the canonical and grand-canonical cases. However, in the authors' experience, this procedure makes it difficult for the student to see the bigger picture and, although quite ingenuous, the subtleness of the demonstrations to pass from the microcanonical to the canonical and grand-canonical ensembles is hard to grasp.
Abstract Hill functions follow from the equilibrium state of the reaction in which n ligands simu... more Abstract Hill functions follow from the equilibrium state of the reaction in which n ligands simultaneously bind a single receptor. This result if often employed to interpret the Hill coefficient as the number of ligand binding sites in all kinds of reaction schemes. Here, we study the equilibrium states of the reactions in which n ligand bind a receptor sequentially, both non-cooperatively and in a cooperative fashion.
Multistability is an emergent dynamic property that has been invoked to explain multiple coexisti... more Multistability is an emergent dynamic property that has been invoked to explain multiple coexisting biological states. In this work, we investigate the origin of bistability in the lac operon. To do this, we develop a mathematical model for the regulatory pathway in this system and compare the model predictions with other experimental results in which a nonmetabolizable inducer was employed.
SE REALIZA LA APLICACION DEL PROGRAMA CABLECAD AM/FM/GIS PARA AUTOMATIZACION DE EMPRESA ELECTRICA... more SE REALIZA LA APLICACION DEL PROGRAMA CABLECAD AM/FM/GIS PARA AUTOMATIZACION DE EMPRESA ELECTRICAS. SE EXPLICA LAS CARACTERISTICAS, DISPOSITIVOS Y VENTAJAS DEL PROGRAMA CABLECAD EN EL PROCESO DE AUTOMATIZACION Y ANALISIS DE LOS PROGRAMAS APLICADOS A UN SISTEMA DE DISTRIBUCION. SE MUESTRA LOS DETALLES HISTORICOS, TECNICOS Y OPERACIONALES DE LA EMPRESA ELECTRICA DEL ECUADOR.
We present a brief review of some works addresed to a connection between concepts arising from bo... more We present a brief review of some works addresed to a connection between concepts arising from both finite-time thermodynamics (FTT) and first order irreversible thermodynamics (FOIT). While the first order irreversible thermodynamics formalism is based on the study of local variables, finite time thermodynamics mainly deals with net global process variables.
The hemoflagellate Trypanosoma cruzi is the causative agent of American trypanosomiasis. Despite ... more The hemoflagellate Trypanosoma cruzi is the causative agent of American trypanosomiasis. Despite the importance of motility in the parasite life cycle, little is known about T. cruzi motility, and there is no quantitative description of its flagellar beating. Using video microscopy and quantitative vectorial analysis of epimastigote trajectories, we find a forward parasite motility defined by tip-to-base symmetrical flagellar beats.
Abstract: This work extends a recently developed mathematical theory of thermodynamics for discre... more Abstract: This work extends a recently developed mathematical theory of thermodynamics for discrete-state, continuous-time Markov processes with, and more importantly without, detailed balance. We show that the Legendre transform in connection to ensemble changes in Gibbs' statistical mechanics can be derived from the stochastic theory. We consider the joint probability $ p_ {XY} $ of two random variables $ X $ and $ Y $ and the conditional probability $ p_ {X| Y= y^*} ,with, with ,with y^*=< Y> $ according to $ p_ {XY} $.
Abstract In the present work we study the transcription-factor regulatory network that controls t... more Abstract In the present work we study the transcription-factor regulatory network that controls the synthesis of flagella in E. coli. Our objective is to address how the transcription-factor dynamics (in terms of their promoter activities and associated rates) correlate with their positions in the hierarchical organization of this regulatory network. Our results suggest that global-regulator promoters express at higher rates than those of local regulators, particularly when the bacterial populations are actively growing.
Understanding the regulation of gene control networks and their ensuing dynamics will be a critic... more Understanding the regulation of gene control networks and their ensuing dynamics will be a critical component in the understanding of the mountain of genomic data being currently collected. This paper reviews recent mathematical modeling work on the tryptophan and lactose operons which are, respectively, the classical paradigms for repressible and inducible operons. To cite this article: MC Mackey et al., CR Biologies 327 (2004).
In the last few years, the efforts to elucidate the mechanisms underlying the segmentation clock ... more In the last few years, the efforts to elucidate the mechanisms underlying the segmentation clock in various vertebrate species have multiplied. Early evidence suggested that oscillations are caused by one of the genes under the Notch signalling pathway (like those of the her or Hes families). Recently, Aulehla et al.[Wnt3a plays a major role in the segmentation clock controlling somitogenesis. Dev.
Resumen LYT1 es una molécula con actividad lítica en condiciones ácidas, que según se demostró ge... more Resumen LYT1 es una molécula con actividad lítica en condiciones ácidas, que según se demostró genéticamente, participa en el proceso de infección y transición de estadio de T. cruzi. Su diferente funcionalidad es resultado de la producción de dos proteínas, obtenidas por trans-empalme alternativo, que contienen una secuencia de secreción y una nuclear (LYT1s) o únicamente la secuencia nuclear (LYT1n).
Amigo lector, el trabajo que tienes en tus manos lo hemos realizado con el deseo de que te ayude ... more Amigo lector, el trabajo que tienes en tus manos lo hemos realizado con el deseo de que te ayude a aprobar el examen extraordinario, los autores se sentirán altamente recompensados en su labor educativa al saber que lo has aprovechado y que te ha sido de utilidad. Por tu parte el esfuerzo realizado te acercará a tu siguiente meta: tus estudios de licenciatura.
Transcriptional bursting, also known as transcriptional pulsing, is a fundamental property of gen... more Transcriptional bursting, also known as transcriptional pulsing, is a fundamental property of genes from bacteria to humans (Chubb et al., 2006; Golding et al., 2005; Raj et al., 2006). Transcription of genes, the process which transforms the stable code written in DNA into the mobile RNA message can occur in" bursts" or" pulses".
Proceedings of the National …, Jan 1, 2001
A mathematical model for regulation of the tryptophan operon is presented. This model takes into ... more A mathematical model for regulation of the tryptophan operon is presented. This model takes into account repression, feedback enzyme inhibition, and transcriptional attenuation. Special attention is given to model parameter estimation based on experimental data. The model's system of delay differential equations is numerically solved, and the results are compared with experimental data on the temporal evolution of enzyme activity in cultures of Escherichia coli after a nutritional shift (minimal ؉ tryptophan medium to minimal medium). Good agreement is obtained between the numeric simulations and the experimental results for wild-type E. coli, as well as for two different mutant strains.
Biophysical journal, Jan 1, 2004
A mathematical model of the lac operon which includes all of the known regulatory mechanisms, inc... more A mathematical model of the lac operon which includes all of the known regulatory mechanisms, including external-glucose-dependent catabolite repression and inducer exclusion, as well as the time delays inherent to transcription and translation, is presented. With this model we investigate the influence of external glucose, by means of catabolite repression and the regulation of lactose uptake, on the bistable behavior of this system.
Biophysical journal, Jan 1, 2004
We develop a mathematical model of the phage λ lysis/lysogeny switch, taking into account recent ... more We develop a mathematical model of the phage λ lysis/lysogeny switch, taking into account recent experimental evidence demonstrating enhanced cooperativity between the left and right operator regions. Model parameters are estimated from available experimental data. The model is shown to have a single stable steady state for these estimated parameter values, and this steady state corresponds to the lysogenic state. When the CI degradation rate (γcI) is slightly increased from its normal value (γcI≃ 0.0 min− 1), two additional ...
… Interdisciplinary Journal of …, Jan 1, 2004
Cell motility and the …, Jan 1, 1992
Spores of the microsporidium Nosema algerae were stimulated to germinate in vitro while observed ... more Spores of the microsporidium Nosema algerae were stimulated to germinate in vitro while observed with video-enhanced contrast microscopy. Field-by-field playback of tape-recorded sequences yielded the first serial illustrations and kinematic analysis of the explosive discharge of the polar filament and the sporoplasm. The filament emerges from the anterior pole of the spore in a regularly pitched helicoidal course along a nearly straight axis, with a mean maximum instant velocity of 105 p d s . Just before elongation is completed the filament tip follows a tortuous path that often results in a curved or spiralling terminal configuration. Then elongation stops and, after a lag that may vary from less than 15 to over 500 ms, the sporoplasm pours out at the filament tip forming a globule that quickly grows up to a size larger than its original volume within the spore. Concomitantly, the helical filament becomes straightened and frequently the spore body is pulled forward. Thereafter a relaxed filament, usually 5-10% shorter than when maximally extended, remains connecting the empty spore case and the sporoplasmic droplet. Experiments with hyperosmolar media produced a considerable slowdown of filament extrusion and often precluded sporoplasm discharge. The present results are fully consistent with the hypothesis of a hydrostatic pressure-triggered mechanism of spore germination, and revealed that the process is composed of two discrete phases separated by a variable lag: 1) complete eversion of the polar filament, and 2 ) passage of the main sporoplasm mass along the tube.