Nuria Conde-Pueyo

Nuria Conde-Pueyo
University Pompeu Fabra | UPF · Department of Experimental and Health Sciences

Núria Conde

About

50
Publications
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April 2009 - present
Institute of Evolutionary Biology
Position
  • PhD Student

Publications

Publications (50)
Article
Full-text available
Cognitive networks have evolved to cope with uncertain environments in order to make reliable decisions. Such decision making circuits need to respond to the external world in efficient and flexible ways, and one potentially general mechanism of achieving this is grounded in critical states. Mounting evidence has shown that brains operate close to...
Preprint
Cognitive networks have evolved to cope with uncertain environments in order to make reliable decisions. Such decision making circuits need to respond to the external world in efficient and flexible ways, and one potentially general mechanism of achieving this is grounded in critical states. Mounting evidence has shown that brains operate close to...
Article
Full-text available
Complex dynamical fluctuations, from intracellular noise, brain dynamics or computer traffic display bursting dynamics consistent with a critical state between order and disorder. Living close to the critical point has adaptive advantages and it has been conjectured that evolution could select these critical states. Is this the case of living cells...
Article
Full-text available
Multicellular entities are characterized by intricate spatial patterns, intimately related to the functions they perform. These patterns are often created from isotropic embryonic structures, without external information cues guiding the symmetry breaking process. Mature biological structures also display characteristic scales with repeating distri...
Preprint
Full-text available
Complex dynamical fluctuations, from molecular noise within cells, collective intelligence, brain dynamics or computer traffic have been shown to display noisy behaviour consistent with a critical state between order and disorder. Living close to the critical point can have a number of adaptive advantages and it has been conjectured that evolution...
Preprint
Full-text available
Complex dynamical fluctuations, from molecular noise within cells, collective intelligence, brain dynamics or computer traffic have been shown to display noisy behaviour consistent with a critical state between order and disorder. Living close to the critical point can have a number of adaptive advantages and it has been conjectured that evolution...
Preprint
Full-text available
Complex dynamical fluctuations, from molecular noise within cells, collective intelligence, brain dynamics or computer traffic have been shown to display noisy behaviour consistent with a critical state between order and disorder. Living close to the critical point can have a number of adaptive advantages and it has been conjectured that evolution...
Preprint
Full-text available
Multicellular entities are characterized by exquisite spatial patterns, intimately related to the functions they perform. Oftentimes these patterns emerge as periodic structures with a well-defined characteristic scale. A candidate mechanism to explain their origins was early introduced by Alan Turing through the interaction and diffusion of two so...
Article
Full-text available
What is the potential for synthetic biology as a way of engineering, on a large scale, complex ecosystems? Can it be used to change endangered ecological communities and rescue them to prevent their collapse? What are the best strategies for such ecological engineering paths to succeed? Is it possible to create stable, diverse synthetic ecosystems...
Preprint
Full-text available
What is the potential for synthetic biology as a way of engineering, on a large scale, complex ecosystems? Can it be used to change endangered ecological communities and rescue them to prevent their collapse? What are the best strategies for such ecological engineering paths to succeed? Is it possible to create stable, diverse synthetic ecosystems...
Poster
Full-text available
Climate change is pushing ecosystems towards extreme conditions and possibly towards tipping points. In drylands, this means to shift from vegetated to desert landscapes. In this poster, we present two approaches to stop the advances of the deserts across the nowadays vegetated semiarid ecosystems. First, replanting vegetation from time to time. Se...
Article
Full-text available
Photobioelectrochemical systems are an emerging possibility for renewable energy. By exploiting photosynthesis, they transform the energy of light into electricity. This study evaluates a simple, scalable bioelectrochemical system built from recycled plastic bottles, equipped with an anode made from recycled aluminum, and operated with the green al...
Article
Full-text available
Multicellularity is a crucial innovation that has taken place independently at least 25 times in the evolution of life on our planet. Uncovering the evolutionary rules associated to the emergence of this transition has been partially achieved thanks to a combination of comparative cell biology,phylogenetic, paleobiology and genomic studies of primi...
Article
Monitoring microbes that live deep inside the gut is a challenge. Engineering bacteria to express structures that can be tracked by ultrasound offers a way to locate such cells in vivo, and might have clinical implications.
Article
Full-text available
Changing environments pose a challenge to living organisms. Cells need to gather and process incoming information, adapting to changes in predictable ways. This requires in particular the presence of memory, which allows to store different internal states. Biological memory can be stored by switches that retain information of past and present event...
Article
Full-text available
Efforts in evolutionary developmental biology have shed light on how organs are developed and why evolution has selected some structures instead of others. These advances in the understanding of organogenesis along with the most recent techniques of organotypic cultures, tissue bioprinting and synthetic biology provide the tools to hack the physica...
Article
Full-text available
Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success...
Data
Fitting parameters and correlation coefficient r. (DOCX)
Data
Representative FACS analysis using quantitative single cell output. Fluorescence from Output Layer and Buffer Layer cells was assessed by flow cytometry. A total of 10.000 cells were analyzed. (A) Representative FACS plot of a wild type W303 cells. (B) Panel shows mCherry intensity (Y axis) versus autofluorescence (X axis) and allows selecting the...
Data
Theoretical implementation in single cell of a MUX4to1 multiplexer circuit according to standard methodology for circuit design. This circuit requires 10 different promoters, 6 regulated by the external inputs A, B, C, D, E, and F, and 4 for internal connections. Additionally, 8 different wires are necessary (dashed lines), implemented by 8 differe...
Data
Example of computational output detection and data quantification. (A) The quantification of one majority rule experiment is showed as an illustrative example of all circuits’ quantification and data treatment. For every chamber, and for each combination of inputs, fluorescence intensity of the subsets of OL cells was measured versus autofluorescen...
Data
Yeast strains used in this study. (DOCX)
Data
Graphic representation of the architecture of the Input, Output and Buffer Layers cells. (A) Identity cells (ID; top) express the S. cerevisiae alpha factor pheromone under the control of an input-inducible promoter. NOT cells (NOT; bottom) constitutively express this pheromone under the control of a modified TEF1 promoter (TEF1-OplacI). In the pre...
Data
Transfer Function analyses of the Input Layer cell library. Input Layer cells were mixed with the Output Layer GFP cells (OL1) and treated with different inputs concentrations. Samples were incubated for 4h at 30°C and analyzed by FACS. Data are expressed as the percentage of GFP positive cells and represent the mean and standard deviation of three...
Data
Growth curve of the Output Layer and Buffer Layer cells. (A) Output Layer cells OL1 (upper left), OL2 (upper right) and OL3 (lower left) growth curve was measured as in S8 Fig. (B) Buffer Layer cells growth curve was measured as in S8 Fig. (TIF)
Data
Examples of 2-inputs logic gates implemented with the library of cells. (A) AND gate. (B) NOR gate. C) N-IMPLIES gate. Schematic representation of the cells used in the circuits (left). Truth table (middle). Percentage of OL1 GFP-positive cells (right). Cells were mixed proportionally and treated with different combinations of inputs. After computi...
Data
Logic representation of the circuits implemented according to the standard methodology or the novel approach based on ILF. Despite the logic representation of circuits based on ILF involves NOT and OR logic gates, only NOT gates are genetically implemented. OR logic is implicitly implemented by spatial segregation of the consortia. In each consorti...
Data
Supporting information including: Design of minimal logic circuits based on inverted logic formulation (ILF), transfer function fitting, fluorescence data analysis, full description of each cell used in the biological circuits and Engineered Input Layer cells that respond to hormones. (DOCX)
Data
Plasmids strains used in this study. (DOCX)
Data
Relationship between the number of implementable functions and the number of cells and modules required. (A, B, C) Dependence of the number of possible implementable functions with respect to the number of different cells required. Data for functions with 2, 3 and 4 inputs are shown. (D, E, F) Dependence of the number of possible implementable func...
Data
Schematic representation and basic genetic information of the Input Layer cells. Cells in the library respond to six different inputs (DOX; doxycycline, PRO; progesterone, ALD; aldosterone, αCa; C. albicans alpha factor, EST; 17-β-estradiol, DEX; dexamethasone) with two different logics. In the presence of the input, Identity cells (ID, left) expre...
Data
Schematic representation and basic genetic information of the Output Layer and Buffer Layer cells. (A) The Output Layer cells sense S. cerevisiae alpha factor and shut down the expression of a fluorescent protein (GFP, mCherry) or the production of C. albicans alpha factor. All cells are W303 derivatives. (B) The Buffer Layer cell sense C. albicans...
Data
Transfer Function analyses of the Output Layer and Buffer Layer cells. (A) Output Layer cells OL1 (upper left) and OL2 (upper right) were incubated with different concentrations of S. cerevisiae alpha-factor and analyzed as in S6 Fig. Output Layer cells OL3 (lower left) were incubated with Buffer Layer cells in the presence of different concentrati...
Data
Growth curve of the Input Layer cells library. Exponential cultures of Input Layer cells were diluted to OD660 nm ≈ 0.02 and their growth curve was measured using Synergy H1 BioTeK for 24 h. Data represent the mean and standard deviation of three independent experiments. (TIF)
Data
GFP data analysis. (A) Transfer function data of the OL1 cells expressed as GFP a.u. Values ranges from maximum of 1600 to a minimum of 450 GFP a.u and the curve presents a step like shape. Experimental transfer function data were fitted to a Hill equation as described in S1 Text. (B) Normalized GFP (a.u.) transfer function of OL1 cells (round circ...
Data
Design and in vivo implementation of a 3-input majority rule. (A) Schematic representation and spatial distribution of the cells used in the majority rule circuit. The circuit is the same as in Fig 3 except here we used IL7 cells, which respond to DOX (right), instead of the previously used IL12 cells, which respond to DEX (left). (B) Truth table (...
Article
Full-text available
Intelligent systems have emerged in our biosphere in different contexts and achieving different levels of complexity. The requirement of communication in a social context has been in all cases a determinant. The human brain, probably co-evolving with language, is an exceedingly successful example. Similarly, social insects complex collective decisi...
Article
Full-text available
Do-It-Yourself Biologist (DIYbio) és una branca del moviment de la ciència oberta que fomenta l'intercanvi obert de materials, dades i publicacions, i té el seu origen en l'auge viscut la dècada del 2000 per l'electrònica de codi obert i els tallers oberts. DIYbio ha recollit l'impuls i l'estigma d'aquest camp de manera que ha estat de manera alter...
Working Paper
Full-text available
Intelligent systems have emerged in our biosphere in different contexts and achieving different levels of complexity. The requirement of communication in a social context have been in all cases a determinant. The human brain, probably co-evolving with language, is an exceedingly successful example. Similarly, social insects complex collective decis...
Article
Full-text available
Cells are complex machines capable of processing information by means of an entangled network of molecular interactions. A crucial component of these decision-making systems is the presence of memory and this is also a specially relevant target of engineered synthetic systems. A classic example of memory devices is a 1-bit memory element known as t...
Article
Full-text available
Background Cells are subjected to dramatic changes of gene expression upon environmental changes. Stress causes a general down-regulation of gene expression together with the induction of a set of stress-responsive genes. The p38-related stress-activated protein kinase Hog1 is an important regulator of transcription upon osmostress in yeast. Resul...
Data
Full-text available
Supplementary Figure S1 to S9.
Data
Full-text available
Supplemetary Table 1. List of all the genes considered in the manuscript as Hog1-dependent (top 100 Hog1-depedent osmoresponsive genes), Hog1-independent (top 100 Hog1-independent osmoresponsive genes) and a list of all osmoresponsive genes from the microarray analysis (see the 'Gene expression studies' section in Materials and methods for the crit...
Article
Full-text available
Ongoing efforts within synthetic and systems biology have been directed towards the building of artificial computational devices using engineered biological units as basic building blocks. Such efforts, inspired in the standard design of electronic circuits, are limited by the difficulties arising from wiring the basic computational units (logic ga...
Article
Full-text available
Two genes are called synthetic lethal (SL) if mutation of either alone is not lethal, but mutation of both leads to death or a significant decrease in organism's fitness. The detection of SL gene pairs constitutes a promising alternative for anti-cancer therapy. As cancer cells exhibit a large number of mutations, the identification of these mutate...
Article
Full-text available
Appropriate regulation of the Hog1 mitogen-activated protein kinase (MAPK) pathway is essential for cells to survive osmotic stress. Here, we show that the two sensing mechanisms upstream of Hog1 display different signaling properties. The Sho1 branch is an inducible nonbasal system, whereas the Sln1 branch shows high basal signaling that is restri...
Chapter
Full-text available
This work has been supported by 6th EU framework SYNLET (NEST-043312), ComplexDis (NEST-043241) and NHI CA 113004 projects. We thank Dr Ricard Solé and Complex

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