Publications by authors named "Javier Muñoz-Garcia"

16 Publications

  • Page 1 of 1

The twin cytokines interleukin-34 and CSF-1: masterful conductors of macrophage homeostasis.

Theranostics 2021 1;11(4):1568-1593. Epub 2021 Jan 1.

Université de Nantes, Institut de Cancérologie de l'Ouest, Saint-Herblain, F-44805, France.

Macrophages are specialized cells that control tissue homeostasis. They include non-resident and tissue-resident macrophage populations which are characterized by the expression of particular cell surface markers and the secretion of molecules with a wide range of biological functions. The differentiation and polarization of macrophages relies on specific growth factors and their receptors. Macrophage-colony stimulating factor (CSF-1) and interleukine-34 (IL-34), also known as "twin" cytokines, are part of this regluatory landscape. CSF-1 and IL-34 share a common receptor, the macrophage-colony stimulating factor receptor (CSF-1R), which is activated in a similar way by both factors and turns on identical signaling pathways. However, there is some discrete differential activation leading to specific activities. In this review, we disscuss recent progress in understanding of the role of the twin cytokines in macrophage differentiation, from their interaction with CSF-1R and the activation of signaling pathways, to their implication in macrophage polarization of non-resident and tissue-resident macrophages. A special focus on IL-34, its involvement in pathophsyiological contexts, and its potential as a theranostic target for macrophage therapy will be proposed.
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http://dx.doi.org/10.7150/thno.50683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778581PMC
January 2021

Drug delivery and temperature control in microfluidic chips during live-cell imaging experiments.

Methods Cell Biol 2018 19;147:3-28. Epub 2018 Jul 19.

University of Rennes, Institute of Genetics and Development, CNRS, Rennes, France. Electronic address:

Microfluidic technologies have become a standard tool in cell biological studies, offering unprecedented control of the chemical and physical environment of cells grown in microdevices, the possibility of multiplexing assays, as well as the capacity to monitor the behavior of single cells in real time while dynamically manipulating their growth medium. However, the properties of the materials employed for the fabrication of microchips that are compatible with live-cell imaging has limited the use of these techniques for a broad range of experiments. In particular, the strong absorption of a large panel of small molecules by these materials prevents the accurate delivery of compounds of interest. Here we describe a novel microsystem dedicated to live-cell imaging that (1) uses alternative materials devoid of absorptive properties, and (2) allows for dynamic in-chip control of sample temperature. Based on a proof-of-concept design that we have routinely used with non-adherent fission yeast cells, this chapter details all the steps for the fabrication and utilization of these microdevices.
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http://dx.doi.org/10.1016/bs.mcb.2018.06.004DOI Listing
December 2018

Nonuniversality of front fluctuations for compact colonies of nonmotile bacteria.

Phys Rev E 2018 Jul;98(1-1):012407

Departamento de Matemáticas & GISC, Universidad Carlos III de Madrid, Leganés, Spain.

The front of a compact bacterial colony growing on a Petri dish is a paradigmatic instance of non-equilibrium fluctuations in the celebrated Eden, or Kardar-Parisi-Zhang (KPZ), universality class. While in many experiments the scaling exponents crucially differ from the expected KPZ values, the source of this disagreement has remained poorly understood. We have performed growth experiments with B. subtilis 168 and E. coli ATCC 25922 under conditions leading to compact colonies in the classically alleged Eden regime, where individual motility is suppressed. Non-KPZ scaling is indeed observed for all accessible times, KPZ asymptotics being ruled out for our experiments due to the monotonic increase of front branching with time. Simulations of an effective model suggest the occurrence of transient nonuniversal scaling due to diffusive morphological instabilities, agreeing with expectations from detailed models of the relevant biological reaction-diffusion processes.
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http://dx.doi.org/10.1103/PhysRevE.98.012407DOI Listing
July 2018

A drug-compatible and temperature-controlled microfluidic device for live-cell imaging.

Open Biol 2016 08;6(8)

SyntheCell team, Institute of Genetics and Development, CNRS UMR 6290, 2 avenue du Pr. Léon Bernard, 35043 Rennes, France

Monitoring cellular responses to changes in growth conditions and perturbation of targeted pathways is integral to the investigation of biological processes. However, manipulating cells and their environment during live-cell-imaging experiments still represents a major challenge. While the coupling of microfluidics with microscopy has emerged as a powerful solution to this problem, this approach remains severely underexploited. Indeed, most microdevices rely on the polymer polydimethylsiloxane (PDMS), which strongly absorbs a variety of molecules commonly used in cell biology. This effect of the microsystems on the cellular environment hampers our capacity to accurately modulate the composition of the medium and the concentration of specific compounds within the microchips, with implications for the reliability of these experiments. To overcome this critical issue, we developed new PDMS-free microdevices dedicated to live-cell imaging that show no interference with small molecules. They also integrate a module for maintaining precise sample temperature both above and below ambient as well as for rapid temperature shifts. Importantly, changes in medium composition and temperature can be efficiently achieved within the chips while recording cell behaviour by microscopy. Compatible with different model systems, our platforms provide a versatile solution for the dynamic regulation of the cellular environment during live-cell imaging.
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http://dx.doi.org/10.1098/rsob.160156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5008015PMC
August 2016

Formation and maintenance of nitrogen-fixing cell patterns in filamentous cyanobacteria.

Proc Natl Acad Sci U S A 2016 May 9;113(22):6218-23. Epub 2016 May 9.

Grupo Interdisciplinar de Sistemas Complejos (GISC) and Departamento de Matemáticas, Universidad Carlos III de Madrid, 28911 Leganes, Spain

Cyanobacteria forming one-dimensional filaments are paradigmatic model organisms of the transition between unicellular and multicellular living forms. Under nitrogen-limiting conditions, in filaments of the genus Anabaena, some cells differentiate into heterocysts, which lose the possibility to divide but are able to fix environmental nitrogen for the colony. These heterocysts form a quasiregular pattern in the filament, representing a prototype of patterning and morphogenesis in prokaryotes. Recent years have seen advances in the identification of the molecular mechanism regulating this pattern. We use these data to build a theory on heterocyst pattern formation, for which both genetic regulation and the effects of cell division and filament growth are key components. The theory is based on the interplay of three generic mechanisms: local autoactivation, early long-range inhibition, and late long-range inhibition. These mechanisms can be identified with the dynamics of hetR, patS, and hetN expression. Our theory reproduces quantitatively the experimental dynamics of pattern formation and maintenance for wild type and mutants. We find that hetN alone is not enough to play the role as the late inhibitory mechanism: a second mechanism, hypothetically the products of nitrogen fixation supplied by heterocysts, must also play a role in late long-range inhibition. The preponderance of even intervals between heterocysts arises naturally as a result of the interplay between the timescales of genetic regulation and cell division. We also find that a purely stochastic initiation of the pattern, without a two-stage process, is enough to reproduce experimental observations.
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http://dx.doi.org/10.1073/pnas.1524383113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896711PMC
May 2016

Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli.

Nucleic Acids Res 2016 08 16;44(14):6707-20. Epub 2016 Apr 16.

Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel

Post-transcriptional regulatory processes may change transcript levels and affect cell-to-cell variability or noise. We study small-RNA downregulation to elucidate its effects on noise in the iron homeostasis network of Escherichia coli In this network, the small-RNA RyhB undergoes stoichiometric degradation with the transcripts of target genes in response to iron stress. Using single-molecule fluorescence in situ hybridization, we measured transcript numbers of the RyhB-regulated genes sodB and fumA in individual cells as a function of iron deprivation. We observed a monotonic increase of noise with iron stress but no evidence of theoretically predicted, enhanced stoichiometric fluctuations in transcript numbers, nor of bistable behavior in transcript distributions. Direct detection of RyhB in individual cells shows that its noise is much smaller than that of these two targets, when RyhB production is significant. A generalized two-state model of bursty transcription that neglects RyhB fluctuations describes quantitatively the dependence of noise and transcript distributions on iron deprivation, enabling extraction of in vivo RyhB-mediated transcript degradation rates. The transcripts' threshold-linear behavior indicates that the effective in vivo interaction strength between RyhB and its two target transcripts is comparable. Strikingly, the bacterial cell response exhibits Fur-dependent, switch-like activation instead of a graded response to iron deprivation.
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http://dx.doi.org/10.1093/nar/gkw273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001584PMC
August 2016

Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system.

PLoS Comput Biol 2011 Dec 15;7(12):e1002317. Epub 2011 Dec 15.

Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.

In an active, self-ubiquitinated state, the Ring1B ligase monoubiquitinates histone H2A playing a critical role in Polycomb-mediated gene silencing. Following ubiquitination by external ligases, Ring1B is targeted for proteosomal degradation. Using biochemical data and computational modeling, we show that the Ring1B ligase can exhibit abrupt switches, overshoot transitions and self-perpetuating oscillations between its distinct ubiquitination and activity states. These different Ring1B states display canonical or multiply branched, atypical polyubiquitin chains and involve association with the Polycomb-group protein Bmi1. Bistable switches and oscillations may lead to all-or-none histone H2A monoubiquitination rates and result in discrete periods of gene (in)activity. Switches, overshoots and oscillations in Ring1B catalytic activity and proteosomal degradation are controlled by the abundances of Bmi1 and Ring1B, and the activities and abundances of external ligases and deubiquitinases, such as E6-AP and USP7.
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http://dx.doi.org/10.1371/journal.pcbi.1002317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240587PMC
December 2011

Integrating multiple signals into cell decisions by networks of protein modification cycles.

Biophys J 2011 Oct;101(7):1590-6

School of Mathematical Sciences, Complex Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland.

Posttranslational protein modifications play a key role in regulating cellular processes. We present a general model of reversible protein modification networks and demonstrate that a single protein modified by several enzymes is capable of integrating multiple signals into robust digital decisions by switching between multiple forms that can activate distinct cellular processes. First we consider two competing protein modification cycles and show that in the saturated regime, the protein is concentrated into a single form determined by the enzyme activities. We generalize this to protein modification networks with tree structure controlled by multiple enzymes that can be characterized by their phase diagram, which is a partition of the space of enzyme activities into regions corresponding to different dominant forms. We show that the phase diagram can be obtained analytically from the wiring diagram of the modification network by recursively solving a set of balance equations for the steady-state distributions and then applying a positivity condition to determine the regions corresponding to different responses. We also implement this method in a computer algebra system that automatically generates the phase diagram as a set of inequalities. Based on this theoretical framework, we determine some general properties of protein modification systems.
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http://dx.doi.org/10.1016/j.bpj.2011.08.046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183812PMC
October 2011

Signalling over a distance: gradient patterns and phosphorylation waves within single cells.

Biochem Soc Trans 2010 Oct;38(5):1235-41

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

Recent discoveries of phosphorylation gradients and microdomains with different protein activities have revolutionized our perception of information transfer within single cells. The different spatial localization of opposing reactions in protein-modification cycles has been shown to bring about heterogeneous stationary patterns and travelling waves of protein activities. We review spatial patterns and modes of signal transfer through phosphorylation/dephosphorylation and GDP/GTP exchange cycles and cascades. We show how switches between low-activity and high-activity states in a bistable activation-deactivation cycle can initiate the propagation of travelling protein-modification waves in the cytoplasm. Typically, an activation wave is initiated at the plasma membrane and propagates through the cytoplasm until it reaches the nucleus. An increase in deactivator activity is followed by the initiation of an inactivation wave that moves in the reverse direction from the nucleus. We show that the ratio of opposing enzyme rates is a key parameter that controls both the spread of activation through cascades and travelling waves.
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http://dx.doi.org/10.1042/BST0381235DOI Listing
October 2010

Formation of intracellular concentration landscapes by multisite protein modification.

Biophys J 2010 Jul;99(1):59-66

Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.

Multiple cellular proteins are covalently modified (e.g., phosphorylated/dephosphorylated) at several sites, which leads to diverse signaling activities. Here, we consider a signaling cascade that is activated at the plasma membrane and composed of two-site protein modification cycles, and we focus on the radial profile of the concentration landscapes created by different protein forms in the cytoplasm. We show that under proper conditions, the concentrations of modified proteins generate a series of peaks that propagate into the cell interior. Proteins modified at both sites form activity gradients with long plateaus that abruptly decay at successive locations along the path from the membrane to the nucleus. We demonstrate under what conditions signals generated at the membrane stall in the vicinity of that membrane or propagate into the cell. We derive analytical approximations for the main characteristics of the protein concentration profiles and demonstrate what we believe to be a novel steady-state pattern formation mechanism capable of generating precise spatial guidance for diverse cellular processes.
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http://dx.doi.org/10.1016/j.bpj.2010.04.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895390PMC
July 2010

Observation and modeling of interrupted pattern coarsening: surface nanostructuring by ion erosion.

Phys Rev Lett 2010 Jan 12;104(2):026101. Epub 2010 Jan 12.

Systems Biology Ireland and Grupo Interdisciplinar de Sistemas Complejos (GISC), University College Dublin, Belfield, Dublin 4, Ireland.

We report the experimental observation of interrupted coarsening for surface self-organized nanostructuring by ion erosion. Analysis of the target surface by atomic force microscopy allows us to describe quantitatively this intriguing type of pattern dynamics through a continuum equation put forward in different contexts across a wide range of length scales. The ensuing predictions can thus be consistently extended to other experimental conditions in our system. Our results illustrate the occurrence of nonequilibrium systems in which pattern formation, coarsening, and kinetic roughening appear, each of these behaviors being associated with its own spatiotemporal range.
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http://dx.doi.org/10.1103/PhysRevLett.104.026101DOI Listing
January 2010

Aggregation of chemotactic organisms in a differential flow.

Phys Rev E Stat Nonlin Soft Matter Phys 2009 Dec 4;80(6 Pt 1):061902. Epub 2009 Dec 4.

Complex and Adaptive Systems Laboratory, Systems Biology Ireland, School of Mathematical Sciences, University College Dublin, Belfield, Dublin 4, Ireland.

We study the effect of advection on the aggregation and pattern formation in chemotactic systems described by Keller-Segel-type models. The evolution of small perturbations is studied analytically in the linear regime complemented by numerical simulations. We show that a uniform differential flow can significantly alter the spatial structure and dynamics of the chemotactic system. The flow leads to the formation of anisotropic aggregates that move following the direction of the flow, even when the chemotactic organisms are not directly advected by the flow. Sufficiently strong advection can stop the aggregation and coarsening process that is then restricted to the direction perpendicular to the flow.
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http://dx.doi.org/10.1103/PhysRevE.80.061902DOI Listing
December 2009

Coupling of morphology to surface transport in ion-beam-irradiated surfaces: normal incidence and rotating targets.

J Phys Condens Matter 2009 Jun 12;21(22):224020. Epub 2009 May 12.

Grupo Interdisciplinar de Sistemas Complejos (GISC) and School of Mathematical Sciences and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Republic of Ireland.

Continuum models have proved their applicability to describe nanopatterns produced by ion-beam sputtering of amorphous or amorphizable targets at low and medium energies. Here we pursue the recently introduced 'hydrodynamic approach' in the cases of bombardment at normal incidence, or of oblique incidence onto rotating targets, known to lead to self-organized arrangements of nanodots. Our approach stresses the dynamical roles of material (defect) transport at the target surface and of local redeposition. By applying results previously derived for arbitrary angles of incidence, we derive effective evolution equations for these geometries of incidence, which are then numerically studied. Moreover, we show that within our model these equations are identical (albeit with different coefficients) in both cases, provided surface tension is isotropic in the target. We thus account for the common dynamics for both types of incidence conditions, namely formation of dots with short-range order and long-wavelength disorder, and an intermediate coarsening of dot features that improves the local order of the patterns. We provide for the first time approximate analytical predictions for the dependence of stationary dot features (amplitude and wavelength) on phenomenological parameters, that improve upon previous linear estimates. Finally, our theoretical results are discussed in terms of experimental data.
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http://dx.doi.org/10.1088/0953-8984/21/22/224020DOI Listing
June 2009

Positional information generated by spatially distributed signaling cascades.

PLoS Comput Biol 2009 Mar 20;5(3):e1000330. Epub 2009 Mar 20.

School of Mathematical Sciences and Complex Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland.

The temporal and stationary behavior of protein modification cascades has been extensively studied, yet little is known about the spatial aspects of signal propagation. We have previously shown that the spatial separation of opposing enzymes, such as a kinase and a phosphatase, creates signaling activity gradients. Here we show under what conditions signals stall in the space or robustly propagate through spatially distributed signaling cascades. Robust signal propagation results in activity gradients with long plateaus, which abruptly decay at successive spatial locations. We derive an approximate analytical solution that relates the maximal amplitude and propagation length of each activation profile with the cascade level, protein diffusivity, and the ratio of the opposing enzyme activities. The control of the spatial signal propagation appears to be very different from the control of transient temporal responses for spatially homogenous cascades. For spatially distributed cascades where activating and deactivating enzymes operate far from saturation, the ratio of the opposing enzyme activities is shown to be a key parameter controlling signal propagation. The signaling gradients characteristic for robust signal propagation exemplify a pattern formation mechanism that generates precise spatial guidance for multiple cellular processes and conveys information about the cell size to the nucleus.
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http://dx.doi.org/10.1371/journal.pcbi.1000330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654021PMC
March 2009

Short-range stationary patterns and long-range disorder in an evolution equation for one-dimensional interfaces.

Phys Rev E Stat Nonlin Soft Matter Phys 2006 Nov 30;74(5 Pt 1):050103. Epub 2006 Nov 30.

Departamento de Matemáticas and Grupo Interdisciplinar de Sistemas Complejos (GISC), Universidad Carlos III de Madrid, Avenida de la Universidad 30, E-28911 Leganés, Spain.

A local evolution equation for one-dimensional interfaces is derived in the context of erosion by ion beam sputtering. We present numerical simulations of this equation which show interrupted coarsening in which an ordered cell pattern develops with constant wavelength and amplitude at intermediate distances, while the profile is disordered and rough at larger distances. Moreover, for a wide range of parameters the lateral extent of ordered domains ranges up to tens of cells. We also provide analytical estimates for the stationary pattern wavelength and mean growth velocity.
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http://dx.doi.org/10.1103/PhysRevE.74.050103DOI Listing
November 2006

Nonlinear ripple dynamics on amorphous surfaces patterned by ion beam sputtering.

Phys Rev Lett 2006 Mar 27;96(8):086101. Epub 2006 Feb 27.

Departamento de Matemáticas and Grupo Interdisciplinar de Sistemas Complejos (GISC), Universidad Carlos III de Madrid, Avenida de la Universidad 30, E-28911 Leganés, Spain.

Erosion by ion-beam sputtering (IBS) of amorphous targets at off-normal incidence frequently produces a (nanometric) rippled surface pattern, strongly resembling macroscopic ripples on aeolian sand dunes. A suitable generalization of continuum descriptions of the latter allows us to describe theoretically for the first time the main nonlinear features of ripple dynamics by IBS, namely, wavelength coarsening and nonuniform translation velocity, that agree with similar results in experiments and discrete models. These properties are seen to be the anisotropic counterparts of in-plane ordering and (interrupted) pattern coarsening in IBS experiments on rotating substrates and at normal incidence.
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http://dx.doi.org/10.1103/PhysRevLett.96.086101DOI Listing
March 2006