Biology subjects

Pigolotti, S.

Publications and source records attributed to Pigolotti, S..

15 recordsLinked to original sources

bioRxiv2026

Ultrasensitive response in bacterial replication initiation

In bacteria, the time at which genome replication initiates is carefully regulated, as precision in this timing is crucial for cell cycle stability. Theoretical and experimental studies have shown that the probability of replication initiation sharply depends on cell volume as the cell grows. Such sharp response is usually termed "ultrasensitive" in biology, and has been subject of extensive theoretical study. Nevertheless, the source of ultrasensitivity in this system remains unclear. In this work, we show how ultrasensitivity in replication initiation emerges from the dynamics of DnaA, the central protein regulating initiation in all bacterial species. To do so, we propose a mechanistic, thermodynamically consistent model of the dynamics of DnaA, and study the conditions under which an ultrasensitive response arises. We find that ultrasensitivity results from a combination of regulatory processes, that varies with growth conditions. In slow growth, we find an interplay between sequestration of DnaA on chromosomal binding sites and DnaA binding at the origin of replication. This mechanism requires a "sweet spot" of origin binding affinities, whose values are consistent with available experimental measurements. In fast growth, ultrasensitivity instead arises from rapid transition between an inactive and an active form of DnaA, and requires cooperative binding at the origin of replication to be effective. Our results point to ultrasensitivity as the organizing principle underlying regulation of bacterial replication initiation.

systems biology↗

bioRxiv2025

Cell-cell communication as underlying principle governing color pattern formation in fishes

The diverse pigmentation patterns of animals are crucial for predation avoidance and behavioral display, yet mechanisms underlying this diversity remain poorly understood. In zebrafish, Turing models have been proposed to explain stripe patterns, but it is unclear if they apply to other fishes. In anemonefish (Amphiprion ocellaris), we identified gja5b, a gene orthologous to zebrafish leopard and encoding a connexin involved in pigment cell communication, as responsible for the Snowflake phenotype. Using CRISPR/Cas9 and transgenesis, we recapitulate the Snowflake phenotype and show expression of gja5b in iridophores. A matching allele was recovered in zebrafish, revealing complementary requirements in both species. Our findings highlight conserved roles of gap junction mediated communication in pigment patterning across divergent teleosts.

developmental biology↗

bioRxiv2025

Amendable decisions in living systems

A distinct feature of living systems is their capacity to take decisions based on uncertain environmental signals. Examples span from the microscopic scale of cell differentiation guided by the concentration of a morphogen, to complex choices made by animals and humans. The current paradigm in decision theory assumes that decisions, once taken, cannot be revoked. However, living systems often amend their decisions if new evidence favors an alternative hypothesis. In this paper, we characterize the optimal strategy for such amendable decisions. We find that, unlike irrevocable decisions, optimal amendable decisions can be made in a finite average time with zero error probability. Our theory successfully predicts the outcome of a visual experiment involving human participants and the accuracy of cell-fate decisions in early development. Our study reveals that amendments lead to a substantial advantage in decision-making, that is likely to be widely exploited by living beings.

biophysics↗

bioRxiv2024

Single-molecule detection of transient dimerization of opioid receptors 1: Homodimers' effect on signaling and internalization

Opioid receptors (ORs) are critical for endogenous and synthetic analgesics. Their homodimerization is considered important for their pharmacological diversities, but whether they form homodimers remains controversial. Here, we established that the three classical ORs, -, {kappa}-, and {delta}-ORs (MOR, KOR, and DOR, respectively) undergo repeated transient (120-180 ms) homodimerizations every few seconds. This was done by using single-molecule imaging and developing theories for analyzing single-molecule colocalization data, which provide the key parameters, homodimer-monomer dissociation equilibrium constants and rate constants. Their 9-26 amino-acid C-terminal cytoplasmic domains, without sequence similarities, are involved in specific homodimerization, whereas the transmembrane domains provide less specific affinities. Using the membrane-permeable peptides mimicking the C-terminal homodimerization sequences which block homodimerizations, functions of monomers and homodimers were dissected. KOR and DOR homodimers, but not MOR homodimers, activate downstream G-proteins differently from monomers upon agonist addition, without influencing OR internalization. These findings could guide strategies to enhance OR-based analgesia.

biophysics↗

bioRxiv2024

Single-molecule detection of transient dimerization of opioid receptors 2: Heterodimer blockage reduces morphine tolerance

Heterodimerization of opioid receptors (ORs), MOR, KOR, and DOR, is implied in their functional regulation and diversification, and thus its understanding is crucial for developing better analgesic treatments. However, our knowledge on OR heterodimerization/heterodimers remains limited. Here, using single-molecule imaging and functional analysis, we found that MOR, the main morphine receptor, repeatedly forms transient ({approx}250 ms) heterodimers with DOR every 1-10 seconds, but not with KOR, whereas DOR and KOR also form transient heterodimers. We obtained all the heterodimer-monomer equilibrium constants and rate constants with/without agonists. We identified the critical heterodimer binding sites in the extracellular domains, in addition to the less-specific transmembrane domains, and developed soluble peptide blockers for MOR-DOR and DOR-KOR heterodimerization, using amino-acid sequences mimicking the extracellular binding sites. With these peptide blockers, we dissected the monomer/dimer roles in OR internalization and signaling. The soluble MOR-DOR heterodimer blocker reduced the development of long-term morphine tolerance in mice.

biophysics↗

bioRxiv2024

Growth generates a hyperdisordered pattern of chromatophores on squid skin

While the physics of disordered packing in non-growing systems is well understood, unexplored phenomena can emerge when packing takes place in growing domains. We study the arrangements of pigment cells (chromatophores) on squid skin as a biological example of a packed system on an expanding surface. We find that relative density fluctuations in cell numbers grow with spatial scale. We term this behavior "hyperdisordered", in contrast with hyperuniform behavior in which relative fluctuations tend to zero at large scale. We find that hyperdisordered scaling, akin to that of a critical system, is quantitatively reproduced by a model in which hard disks are randomly inserted in a homogeneously growing surface. In addition, we find that chromatophores increase in size during animal development, but maintain a stationary size distribution. The physical mechanisms described in our work may apply to a broad class of growing dense systems.

biophysics↗

bioRxiv2024

Blocking uncertain errors of PCR

The polymerase chain reaction (PCR) plays a central role in genetic engineering and is routinely used in various applications, from biological and medical research to the diagnosis of viral infections. PCR is an extremely sensitive method for detecting target DNA sequences, but it is substantially error-prone. In particular, the mishybridization of primers to contaminating sequences can result in false positives for virus tests. The blocker method, also called the clamping method, has been developed to suppress mishybridization errors. However, its application is limited by the requirement that the contaminating template sequence must be known in advance. Here, we demonstrate that a mixture of multiple blocker sequences effectively suppresses the amplification of contaminating sequences even in the presence of uncertainty. The blocking effect was characterized by a simple model validated by experiments. Furthermore, the modeling allowed us to minimize the errors by optimizing the blocker concentrations. The results highlighted an inherent robustness of the blocker method, in that fine-tuning of the blocker concentrations is not necessary. Our method extends the applicability of PCR and other hybridization-based techniques, including genome editing, RNA interference, and DNA nanotechnology, by improving their fidelity. SignificanceThe applications of PCR are increasing day by day, and there is a need to suppress PCR errors to improve the accuracy of PCR-based techniques and broaden their applicability. The blocker method has been developed to substantially suppress mispriming. However, the method requires prior knowledge of the contaminating sequence, which limits its applicability. We successfully demonstrate that adding a combination of multiple blocker sequences can substantially suppress PCR errors, even when we have only partial information about the contaminating sequences. We also construct a biophysical model of the blocking effect, which allows us to find the optimal blocker combinations that minimize the PCR error. Since the method targets hybridization, it is readily applicable to a wide range of biotechnologies.

bioengineering↗

bioRxiv2023

Genome replication in asynchronously growing microbial populations

Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and genome stability. Qualitatively, in a growing cell culture, one expects that genomic regions that are replicated early should be more abundant than regions that are replicated late. This abundance pattern can be experimentally measured using deep sequencing. However, a general quantitative theory to explain these data is still lacking. In this paper, we predict the abundance of DNA fragments in asynchronously growing cultures from any given stochastic model of the DNA replication program. As key examples, we present stochastic models of the DNA replication programs in Escherichia coli and in budding yeast. In both cases, our approach leads to analytical predictions that are in excellent agreement with experimental data and permit to infer key information about the replication program. In particular, our method is able to infer the locations of known replication origins in budding yeast with high accuracy. These examples demonstrate that our method can provide insight into a broad range of organisms, from bacteria to eukaryotes.

biophysics↗

bioRxiv2022

Kinetic error suppression of PCR

The polymerase chain reaction (PCR) is a central technique in biotechnology. Its ability to amplify a specific target region of a DNA sequence has led to prominent applications, including virus tests, DNA sequencing, genotyping, and genome cloning. These applications rely on the specificity of the primer hybridization, and therefore require effective suppression of hybridization errors. A simple and effective method to achieve that is to add blocker strands, also called as clamp, to the PCR mixture. These strands bind to the unwanted target sequence, thereby blocking the primer mishybridization. Because of its simplicity, this method is applicable to a broad nucleic-acid-based biotechnology. However, the precise mechanism by which blocker strands suppress PCR error remains to be understood, limiting the applicability of this technique. Here, we combine experiments and theoretical modeling to reveal this mechanism. We find that the blocker strands both energetically destabilize the mishybridized complex and sculpt a kinetic barrier to suppress mishybridization. This combination of energetic and kinetic biasing extends the viable range of annealing temperatures, which reduces design constraint of the primer sequence and extends the applicability of PCR.

biophysics↗

bioRxiv2021

Speed fluctuations of bacterial replisomes

Replisomes are multi-protein complexes that replicate genomes with remarkable speed and accuracy. Despite their importance, their dynamics is poorly characterized, especially in vivo. In this paper, we present an approach to infer the replisome dynamics from the DNA abundance distribution measured in a growing bacterial population. Our method is sensitive enough to detect subtle variations of the replisome speed along the genome. As an application, we experimentally measured the DNA abundance distribution in Escherichia coli populations growing at different temperatures using deep sequencing. We find that the average replisome speed increases nearly five-fold between 17{degrees}C and 37{degrees}C. Further, we observe wave-like variations of the replisome speed along the genome. These variations correlate with previously observed variations of the mutation rate. We interpret this correlation as a speed-error trade-off in DNA replication. Our approach has the potential to elucidate replication dynamics in E. coli mutants and in other bacterial species.

biophysics↗

bioRxiv2021

Generalized Euler-Lotka equation for correlated cell divisions

Cell division times in microbial populations display significant fluctuations. These fluctuations impact the population growth rate in a non-trivial way. If fluctuations are uncorrelated among different cells, the population growth rate is predicted by the Euler-Lotka equation, which is a classic result in mathematical biology. However, cell division times can present significant correlations, due to physical properties of cells that are passed from mothers to daughters. In this paper, we derive an equation remarkably similar to the Euler-Lotka equation which is valid in the presence of correlations. Our exact result is based on large deviation theory and does not require particularly strong assumptions on the underlying dynamics. We apply our theory to a phenomenological model of bacterial cell division. We find that the discrepancy between the growth rate predicted by the Euler-Lotka equation and our generalized version is relatively small, but large enough to be measurable in experiments.

ecology↗

bioRxiv2020

Ocean currents promote rare species diversity in protists

Oceans host communities of plankton composed of relatively few abundant species and many rare species. The number of rare protists species in these communities, as estimated in metagenomic studies, decays as a steep power law of their abundance. The ecological factors at the origin of this pattern remain elusive. We propose that oceanic currents affect biodiversity patterns of rare species. To test this hypothesis, we introduce a spatially-explicit coalescence model able to reconstruct the species diversity in a sample of water. Our model predicts, in the presence of oceanic currents, a steeper power law decay of the species abundance distribution and a steeper increase of the number of observed species with sample size. A comparison of two metagenomic studies of planktonic protist communities in oceans and in lakes quantitatively confirms our prediction. Our results support that oceanic currents positively impact the diversity of rare aquatic microbes.

ecology↗

bioRxiv2019

Hierarchical domain model explains multifractal scaling of chromosome contact maps

Modern biological techniques such as Hi-C permit to measure probabilities that different chromosomal regions are close in space. These probabilities can be visualised as matrices called contact maps. In this paper, we introduce a multifractal analysis of chromosomal contact maps. Our analysis reveals that Hi-C maps are bifractal, i.e. complex geometrical objects characterized by two distinct fractal dimensions. To rationalize this observation, we introduce a model that describes chromosomes as a hierarchical set of nested domains and we solve it exactly. The predicted multifractal spectrum is in excellent quantitative agreement with experimental data. Moreover, we show that our theory yields to a more robust estimation of the scaling exponent of the contact probability than existing methods. By applying this method to experimental data, we detect subtle conformational changes among chromosomes during differentiation of human stem cells.

biophysics↗

bioRxiv2019

Error-speed correlations in biopolymer synthesis

Synthesis of biopolymers such as DNA, RNA, and proteins are biophysical processes aided by enzymes. Performance of these enzymes is usually characterized in terms of their average error rate and speed. However, because of thermal fluctuations in these single-molecule processes, both error and speed are inherently stochastic quantities. In this paper, we study fluctuations of error and speed in biopolymer synthesis and show that they are in general correlated. This means that, under equal conditions, polymers that are synthesized faster due to a fluctuation tend to have either better or worse errors than the average. The error-correction mechanism implemented by the enzyme determines which of the two cases holds. For example, discrimination in the forward reaction rates tends to grant smaller errors to polymers with faster synthesis. The opposite occurs for discrimination in monomer rejection rates. Our results provide an experimentally feasible way to identify error-correction mechanisms by measuring the error-speed correlations.

biophysics↗

bioRxiv2018

Bet-hedging strategies in expanding populations

In ecology, species can mitigate their extinction risks in uncertain environments by diversifying individual phenotypes. This observation is quantified by the theory of bet-hedging, which provides a reason for the degree of phenotypic diversity observed even in clonal populations. The theory of bet-hedging in well-mixed populations is rather well developed. However, many species underwent range expansions during their evolutionary history, and the importance of phenotypic diversity in such scenarios still needs to be understood. In this paper, we develop a theory of bet-hedging for populations colonizing new, unknown environments that fluctuate either in space or time. In this case, we find that bet-hedging is a more favorable strategy than in well-mixed populations. For slow rates of variation, temporal and spatial fluctuations lead to different outcomes. In spatially fluctuating environments, bet-hedging is favored compared to temporally fluctuating environments. In the limit of frequent environmental variation, no opportunity for bet-hedging exists, regardless of the nature of the environmental fluctuations. For the same model, bet-hedging is never an advantageous strategy in the well-mixed case, supporting the view that range expansions strongly promote diversification. These conclusions are robust against stochasticity induced by finite population sizes. Our findings shed light on the importance of phenotypic heterogeneity in range expansions, paving the way to novel approaches to understand how biodiversity emerges and is maintained.\n\nAuthor summaryEcological populations are often exposed to unpredictable and variable environmental conditions. A number of strategies have evolved to cope with such uncertainty. One of them is stochastic phenotypic switching, by which some individuals in the community are enabled to tackle adverse conditions, even at the price of reducing overall growth in the short term. In this paper, we study the effectiveness of these \"bet-hedging\" strategies for a population in the process of colonizing new territory. We show that bet-hedging is more advantageous when the environment varies spatially rather than temporally, and infrequently rather than frequently.

ecology↗