Biology subjects

Ruoff, P.

Publications and source records attributed to Ruoff, P..

12 recordsLinked to original sources

bioRxiv2026

A DNA mass conservation mechanism underpins cellular mtDNA number regulation

The nucleoid, which houses mtDNA within the mitochondrial matrix, is a phase-separation-driven biomolecular condensate capable of carrying out a broad spectrum of complex functions, including DNA replication, transcription, and repair. Here, we show by data-driven computational modelling that the concept of a tightly regulated intranucleoid de-oxynucleoside triphoshate (dNTP) pool explains the observation that the number of mtDNA base pairs per cell is conserved in human hybrid cell lines regardless of the size of the introduced mitochondrial genome. This concept is then used to address the enigmatic observation that the synthesis rate of the short DNA strand called 7S DNA, which is part of the triple-stranded displacement loop (D-loop) found in the main noncoding region of mtDNA, increases dramatically during the cell cycle. Collectively, our quantitative analyses suggest that the mammalian mtDNA replisome uses a strictly controlled intranucleoid dNTP pool based predominantly on the synthesis and degradation of 7S DNA. One potential evolutionary explanation for this mechanism is that it offers an energetic advantage by enabling greater reliance on the salvage pathway for mtDNA replication.

molecular biology↗

bioRxiv2026

Intrinsic sodium regulation by Na,K-ATPase: The blue crab's salinity adaptation described by a single negative feedback loop

The term enantiostasis was introduced by Mangum and Towle to describe a functional relationship between environmental changes and an organisms adaptation, and furthermore, to distinguish this kind of adaptation from homeostatic control. The defining example of enantiostasis is the blue crabs blood salinity adaptation when the animal is exposed to different environmental salinities during its move between the ocean and upriver locations. In this paper a model for osmoregulation is suggested based on one of two identified negative feedbacks in the mechanism of Na,K-ATPase. Using a scheme suggested by Towle in 1997 the effect of the feedback is tested with respect to the blue crabs salinity adaptation. Not only does this single feedback model give a practically quantitative description of the blue crabs adaptation data, the model is also able to show other observed patterns of osmoregulation. In view of these results the relationship between enantiostasis and homeostasis is discussed. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=173 HEIGHT=200 SRC="FIGDIR/small/698424v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1d76ba5org.highwire.dtl.DTLVardef@1dc341forg.highwire.dtl.DTLVardef@1e20621org.highwire.dtl.DTLVardef@94c8_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITwo sodium-regulating feedbacks are identified in the operation of Na,K-ATPase. C_LIO_LIOne of these feedbacks is able to describe hypo- and hyperosmotic regulations. C_LIO_LIThe relationship between enantiostasis and homeostasis is discussed. C_LI

systems biology↗

bioRxiv2024

Background compensation revisited: Conserved phase response curves in frequency controlled homeostats with coherent feedback

Background compensation is the ability of a controlled variable to respond to an applied perturbation in an unchanged manner and independent of different but constant background signals which act in parallel to the perturbation. We found that background compensation occurs by coherent feedback mechanisms where additional control variables feed directly back to the controlled variable. This paper extends a previous study on background compensation to include phase responses in frequency controlled coherent feedback oscillators. While the frequency resetting amplitude in coherent feedback oscillators is found to be dependent on the inflow/outflow perturbation of the controlled variable and thereby become phase dependent, the frequency resetting itself and the corresponding phase response curves are found to be background compensated. It is speculated that this type of background compensation may be an additional way how ambient noise can be ignored by organisms.

systems biology↗

bioRxiv2023

Coherent feedback leads to robust background compensation in oscillatory and non-oscillatory homeostats

When in an integral feedback controller a step perturbation is applied at a constant background, the controlled variable (described here as A) will in general respond with decreased response amplitudes {Delta}A as backgrounds increase. The controller variable E will at the same time provide the necessary compensatory flux to move A back to its set-point. A typical example of decreased response amplitudes at increased backgrounds is found in retinal light adaptation. Due to remarks in the literature that retinal light adaptation would also involve a compensation of backgrounds we became interested in conditions how background compensation could occur. In this paper we describe how background influences can be robustly eliminated. When such a background compensation is active, oscillatory controllers will respond to a defined perturbation with always the same (damped or undamped) frequency profile, or in the non-oscillatory case, with the same response amplitude {Delta}A, irrespective of the background level. To achieve background compensation we found that two conditions need to apply: (i) an additional set of integral controllers (here described as I1 and I2) have to be employed to keep the manipulated variable E at a defined set-point, and (ii), I1 and I2 need to feed back to the A-E signaling axis directly through the controlled variable A. In analogy to a similar feedback applied in quantum control theory, we term these feedback conditions as coherent feedback. When analyzing retinal light adaptations in more detail, we find no evidence in the presence of background compensation mechanisms. Although robust background compensation, as described theoretically here, appears to be an interesting regulatory property, relevant biological or biochemical examples still need to be identified.

systems biology↗

bioRxiv2023

Homeostasis at different backgrounds: The roles of overlayed feedback structures in vertebrate photoadaptation

We have studied the resetting behavior of eight basic integral controller motifs with respect to different but constant backgrounds. We found that the controllers split symmetrically into two classes: one class, based on derepression of the compensatory flux, leads to more rapid resetting kinetics as backgrounds increase. The other class, which directly activates the compensatory flux, shows a slowing down in the resetting at increased backgrounds. We found a striking analogy between the resetting kinetics of vertebrate photoreceptors and controllers based on derepression, i.e. vertebrate rod or cone cells show decreased sensitivities and accelerated response kinetics as background illuminations increase. The central molecular model of vertebrate photoadaptation consists of an overlay of three negative feedback loops with cytosolic calcium [Formula], cyclic guanosine monophosphate (cGMP) and cyclic nucleotide-gated (CNG) channels as components. While in one of the feedback loops the extrusion of [Formula] by potassium-dependent sodium-calcium exchangers (NCKX) can lead to integral control with cGMP as the controlled variable, the expected robust perfect adaptation of cGMP is lost, because of the two other feedback loops. They avoid that [Formula] levels become too high and toxic. Looking at psychophysical laws, we found that in all of the above mentioned basic controllers Webers law is followed when a "just noticeable difference" (threshold) of 1% of the controlled variables set-point was considered. Applying comparable threshold pulses or steps to the photoadaptation model we find, in agreement with experimental results, that Webers law is followed for relatively high backgrounds, while Stephens power law gives a better description when backgrounds are low. Limitations of our photoadaption model, in particular with respect to potassium/sodium homeostasis, are discussed. Finally, we discuss possible implication of background perturbations in biological controllers when compensatory fluxes are based on activation.

systems biology↗

bioRxiv2022

A basic model of calcium homeostasis in non-excitable cells

The level of cytosolic calcium (Ca2+) in cells is tightly regulated to about 100 nM (pCa {approx} 7). Due to external stimuli, the basal cytosolic Ca2+ level can temporarily be raised to much higher values. The resulting Ca2+ transients take part in cell-intrinsic signals, which result in cellular responses. Because of its signaling importance and that high levels of Ca2+ can lead to apoptosis, regulation and homeostatic control of cytosolic Ca2+ is essential. Based on experimentally known molecular interactions and kinetic data together with control theoretic concepts (integral feedback) we developed a basic computational model describing robust cytosolic Ca2+ homeostasis. The aim of the model is to describe the integrative mechanisms involved in cytosolic Ca2+ homeostasis in non-excitable cells. From a model perspective, the cytosolic steady state value (set point) of 100 nM is determined by negative feedback loops (outflow controllers), one of these represented by the plasma membrane Ca2+ ATPase (PMCA) - calmodulin (CaM) pump and its activation by cytosolic Ca2+. Hysteretic behaviors of the Ca pumps and transporters have been added leading to improved kinetic behaviors indicating that hysteretic properties of the Ca2+ pumps appear important how cytosolic Ca2+ transients are formed. Supported by experimental data the model contains new findings that the activation of the inositol 1,4,5,-tris-phosphate receptor by cytosolic Ca2+ has a cooperativity of 1, while increased Ca2+ leads to a pronounced inhibition with a cooperativity of 2. The model further suggests that the capacitative inflow of Ca2+ into the cytosol at low Ca2+ storage levels in the ER undergoes a successive change in the cooperativity of the Store Operated calcium Channel (SOCC) as Ca2+ levels in the ER change. Integrating these aspects the model can show sustained oscillations with period lengths between 2 seconds and 30 hours. Author SummaryCytosolic calcium is subject to a general homeostatic regulation to about 100 nM against a ten thousand times larger extracellular calcium concentration. We investigated the conditions for robust cytosolic and luminal (endoplasmatic reticulum, ER) calcium homeostasis in non-excitable blood and epithelial cells and how external and internal calcium perturbations affect these homeostatic mechanisms. We found that gradual time-dependent (hysteretic) changes of calcium pumps and transporters and their associated cooperativities play an essential role in observed kinetics of the calcium flow in and out of the ER. Using a two-site calcium binding model we quantitatively describe the cytosolic calcium-induced calcium transport out of the ER with a cooperativity of 1, and its inhibition at higher cytosolic calcium concentrations with a cooperativity of 2. For the capacitative Ca entry by Store Operated Calcium Channels (SOCCs) when ER calcium needs to be refilled we find excellent agreement between experimental kinetic data and the model when the cooperativity of luminal calcium changes from 1.3 at 500 M to 0.8 at 20 M. Integrating these different aspects of cytosolic and store calcium regulation leads to a basic model for cellular calcium homeostasis, which can show oscillations with period lenths from a few seconds up to 30 hours!

systems biology↗

bioRxiv2021

Kinetics and mechanisms of catalyzed dual-E (antithetic) controllers

Homeostasis plays a central role in our understanding how cells and organisms are able to oppose environmental disturbances and thereby maintain an internal stability. During the last two decades there has been an increased interest in using control engineering methods, especially integral control, in the analysis and design of homeostatic networks. Several reaction kinetic mechanisms have been discovered which lead to integral control. In two of them integral control is achieved, either by the removal of a single control species E by zero-order kinetics ("single-E controllers"), or by the removal of two control species by second-order kinetics ("antithetic or dual-E control"). In this paper we show results when the control species E1 and E2 in antithetic control are removed enzymatically by ping-pong or ternary-complex mechanisms. Our findings show that enzyme-catalyzed dual-E controllers can work in two control modes. In one mode, one of the two control species is active, but requires zero-order kinetics in its removal. In the other mode, both controller species are active and both are removed enzymatically. Conditions for the two control modes are put forward and biochemical examples with the structure of enzyme-catalyzed dual-E controllers are discussed.

systems biology↗

bioRxiv2020

An amplified derepression controller with multisite inhibition and positive feedback

How organisms are able to maintain robust homeostasis has in recent years received increased attention by the use of combined control engineering and kinetic concepts, which led to the discovery of robust controller motifs. While these motifs employ kinetic conditions showing integral feedback and homeostasis for step-wise perturbations, the motifs performance differ significantly when exposing them to time dependent perturbations. One type of controller motifs which are able to handle exponentially and even hyperbolically growing perturbations are based on derepression. In these controllers the compensatory reaction, which neutralizes the perturbation, is derepressed, i.e. its reaction rate is increased by the decrease of an inhibitor acting on the compensatory flux. While controllers in this category can deal well with different time-dependent perturbations they have the disadvantage that they break down once the concentration of the regulatory inhibitor becomes too low and the compensatory flux has gained its maximum value. We wondered whether it would be possible to bypass this restriction, while still keeping the advantages of derepression kinetics. In this paper we show how the inclusion of multisite inhibition and the presence of positive feedback loops lead to an amplified controller which is still based on derepression kinetics but without showing the breakdown due to low inhibitor concentrations. By searching for the amplified feedback motif in natural systems, we found it as a part of the plant circadian clock where it is highly interlocked with other feedback loops.

systems biology↗

bioRxiv2020

Exploring Mechanisms of Glucose Uptake Regulation and Dilution Resistance in Growing Cancer Cells

Most cancer cells rely on aerobic glycolysis and increased glucose uptake for the production of biosynthetic precursors needed to support rapid proliferation. Increased glucose uptake and glycolytic activity may result in intracellular acidosis and increase of osmotically active substances, leading to cell swelling. This causes dilution of cellular constituents, which can markedly influence cellular reactions and the function of proteins, and hence, control mechanisms used by cancer cells to maintain a highly glycolytic phenotype must be robust to dilution. In this paper, we review the literature on cancer cell metabolism and glucose uptake, and employ mathematical modeling to examine control mechanisms in cancer cell metabolism that show robust homeostatic control in the presence of dilution. Using differential gene expression data from the Expression Atlas database, we identify the key components of glucose uptake in cancer, in order to guide the construction of a mathematical model. By simulations of this model we show that while negative feedback from downstream glycolytic metabolites to glucose transporters is sufficient for homeostatic control of glycolysis in a constant cellular volume, it is necessary to control intermediate glycolytic enzymes in order to achieve homeostatic control during growth. With a focus on glucose uptake in cancer, we demonstrate a systems biology approach to the identification, reduction, and analysis of complex regulatory systems. SIGNIFICANCERapid proliferation and increased glycolytic activity in cancer cells lead to dilution of cellular constituents, which can markedly influence cellular reactions and the function of proteins. Therefore, control mechanisms used by cancer cells to maintain a highly glycolytic phenotype must be robust to dilution. We construct a mathematical model of glucose uptake in cancer, and using a systems biology approach to the analysis of regulatory networks, identify the presence of integral control motifs as a means for achieving dilution resistance. Furthermore, we show that while negative feedback from downstream glycolytic metabolites to glucose transporters is sufficient for homeostatic control of glycolysis in a constant cellular volume, it is necessary to control intermediate glycolytic enzymes to achieve homeostatic control during growth.

cancer biology↗

bioRxiv2020

Frequency switching between oscillatory homeostats and the regulation of p53

Homeostasis is an essential concept to understand the stability of organisms and their adaptive behaviors when coping with external and internal assaults. Many hormones that take part in homeostatic control come in antagonistic pairs, such as glucagon and insulin reflecting the inflow and outflow compensatory mechanisms to control a certain internal variable, such as blood sugar levels. By including negative feedback loops homeostatic controllers can exhibit oscillations with characteristic frequencies. In this paper we demonstrate the associated frequency changes in homeostatic systems when individual controllers in a set of interlocked feedback loops gain control in response to environmental changes. Taking p53 as an example, we show how the Per2, ATM and Mdm2 feedback loops -interlocked with p53-gain individual control in dependence to DNA damage and how each of these controllers provide certain functionalities in their regulation of p53. In unstressed cells, the circadian regulator Per2 ensures a basic p53 level to allow its rapid up-regulation in case of DNA damage. When DNA damage occurs the ATM controller increases the level of p53 and defends it towards uncontrolled degradation, which despite DNA damage, would drive p53 to lower values and p53 dysfunction. Mdm2 on its side keeps p53 at a maximum level to avoid premature apoptosis. However, with on-going DNA damage the Mdm2 set-point is increased by HSP90 and other p53 stabilizers leading finally to apoptosis. An essential aspect in p53 regulation at occurring cell stress is the coordinated inhibition of ubiquitin-independent and ubiquitin-dependent degradation reactions and the increasing stabilizing mechanisms of p53. Whether oscillations serve a function or are merely a by-product of the controllers are discussed in view of the finding that homeostatic control of p53, as indicated above, does in principle not require oscillatory homeostats.

systems biology↗

bioRxiv2018

Homeostatic Controllers Compensating for Growth and Perturbations

Cells and organisms have developed homeostatic mechanisms to maintain internal stabilities which protect them against a changing environment. How cellular growth and homeostasis interact is still not well understood, but of increasing interest to the synthetic and molecular biology community where molecular control circuits are sought and tried to maintain homeostasis that opposes the diluting effects of cell growth. In this paper we describe the performance of four negative feedback (inflow) controllers, which, for different observed growth laws (time-dependent increase in the cellular volume V) are able to compensate for various time-dependent removals of the controlled variable A. The four implementations of integral control are based on zero-order, first-order autocatalytic, second-order (antithetic), and derepressing inhibition kinetics. All controllers behave ideal in the sense that they for step-wise perturbations in V and A are able to drive the controlled variable precisely back to the controllers theoretical set-point [Formula] The applied increase in cellular volume includes linear, exponential and saturating growth and reflect experimentally observed growth laws of single cell organisms and other cell types. During the increase in V, additional linear or exponential time-dependent perturbations which remove A are applied, and controllers are tested with respect to their ability to compensate for both the increase in volume V and the applied perturbations removing A. Our results show that the way how integral control is kinetically implemented and the structure of the negative feedback loop are essential determinants of a controllers performance. The results provide a ranking between the four tested controller types. Considering exponential volume increases together with an exponentially increasing removal rate of A controllers based on derepression kinetics perform best, but break down when the control-inhibitors concentration gets too low. The first-order autocatalytic controller is able to defend time-dependent exponential growth and removals in A, but generally with a certain offset below its theoretical set-point [Formula] The controllers based on zero-order and second-order (antithetic) integral feedback can only manage linear increases in V and removals in A, in dependence of the controllers aggressiveness. Our results provide a theoretical basis what controller kinetics are needed in order to compensate for different growth laws.

biophysics↗

bioRxiv2018

Antagonistic regulation with a unique setpoint, integral and double integral action

Several biochemical species are in organisms controlled in a pairwise manner i.e., two different species (e.g., hormone, enzyme, transporter protein) work to control the concentration of a third chemical species. Such pairs are often antagonistic, meaning that one of the controller species acts to increase whereas the other controller species acts to decrease the amount of the controlled species. How antagonistic systems interact to achieve regulation and to avoid competing against each other is not fully understood. An issue is how two antagonistic hormones can agree upon one common setpoint. We present here a new type of antagonistic regulatory system that has a single unique setpoint inherently defined by the system. The regulatory system controls the concentration of a chemical species with both integral and double integral action, achieving tight control. We show by the use of an analytical stability analysis, using the principle of vanishing perturbations, that the setpoint is asymptotically stable. Finally the prospect of treating the presented system as a part of a larger family of antagonistic regulatory systems with unique setpoints, integral and double integral action is discussed.

systems biology↗