Biology subjects

Azpeitia, E.

Publications and source records attributed to Azpeitia, E..

5 recordsLinked to original sources

bioRxiv2026

Temporal variability and its effects on diversity maintenance in an agroecological matrix

Agroecosystems are dynamic ecosystems, constituted by patches of vegetation and agricultural use, where biodiversity is shaped by spatial and temporal variability. While most studies have focused on spatial composition and configuration, the role of temporal variability remains poorly understood. Yet, temporal dynamics can strongly modify species composition, abundance, and persistence in ecological communities. Temporal variability is particularly relevant in agroecosystems with rainfed agriculture where environmental conditions shift dramatically between rainy and dry seasons. In this paper, we assess the role of temporal variability on biodiversity maintenance in an agricultural matrix using a metacommunity model that simulates an agricultural landscape under rainfed conditions, that is, with abrupt seasonal changes in the agricultural patches. This model couples a local community network dynamic with a migration dynamic and is based on empirically documented features of rainfed agricultural matrices. Our results show that temporal variability provides new opportunities for species to recover from low densities. However, the effect of temporal variability is not straightforward. It depends on the initial and final conditions, the migration and mortality rates and the intensity of temporal variability. Overall, our findings highlight the need to further investigate temporal variability to better understand its role in shaping biodiversity in agricultural landscapes.

ecology↗

bioRxiv2026

Dose–Response Alignment Does Not Inherently Enhance Information Transmission in Signaling Pathways

Understanding how signaling pathways reliably transmit information is fundamental to explaining cellular decision-making. Several studies have suggested that Dose-Response Alignment (DoRA) --the overlapping of dose-response curves between receptor occupancy and downstream responses-- enhances information transmission by ensuring a linear mapping between occupancy and response. Here, we challenge this intuition using analytical and numerical analyses of a basic signaling mechanism. Our results show that DoRA, linearity and information transmission are fundamentally dissociable properties. We find that occupancy-response linearity is normalization-independent, whereas the measured degree of alignment depends on the normalization scheme used to compare dose-response curves. Specifically, normalization by maximal attained responses preferentially reflects occupancy-response linearity, whereas normalization by total response capacity preserves response dynamic range. Accordingly, under the first normalization, perfect alignment reflects linear occupancy-response mappings, whereas under the second normalization alignment can remain imperfect because it does not exclusively reflect linearity. Importantly, neither perfect alignment nor linearity necessarily maximize information transmission; instead, information transmission can increase through larger dynamic range or reduced noise. Our results show that efficient information transmission cannot be inferred from dose-response alignment or linearity alone, but emerges from the balance between dynamic range, biochemical noise, and input-output mapping.

Systems Biology↗

bioRxiv2021

The making of cauliflowers: the story of unsuccessful flowers

The arrangement of plant organs, called phyllotaxis, produce remarkable spiral or whorled patterns. Cauliflowers present a unique phyllotaxis with a multitude of spirals over a wide range of scales. How such a self-similar fractal organization emerges from developmental mechanisms has remained elusive. Combining experimental assays with modeling, we found that cauliflowers arise due to the hysteresis of the bistable floral network that generates inflorescences imprinted by a transient floral state. We further show how additional mutations affecting meristem growth dynamics can induce the production of conical phyllotactic structures reminiscent of the conspicuous fractal Romanesco shape. This study reveals how the spectacular morphological modification of the inflorescences in cauliflower and Romanesco shape arises from the hysteresis of the genetic programs controlling inflorescence development. One Sentence SummaryThe molecular making of cauliflowers

plant biology↗

bioRxiv2019

Short residence times of DNA-bound transcription factors can reduce gene expression noise and increase the transmission of information in a gene regulation system

Gene expression noise is not just ubiquitous but also variable, and we still do not understand some of the most elementary factors that affect it. Among them is the residence time of a transcription factor (TF) on DNA, the mean time that a DNA-bound TF remains bound. Here, we use a stochastic model of transcriptional regulation to study how this residence time affects gene expression. We find that the effect of residence time on gene expression depends on the level of induction of the gene. At high levels of induction, residence time has no effect on gene expression. However, as the level of induction decreases, short residence times reduce gene expression noise. The reason is that fast on-off TF binding dynamics prevent long periods where proteins are predominantly synthesized or degraded, which can cause excessive fluctuations in gene expression. As a consequence, short residence times can help a gene regulation system acquire information about the cellular environment it operates in. Our predictions are consistent with the observation that experimentally measured residence times are usually modest and lie between seconds to minutes.

systems biology↗

bioRxiv2019

The positive role of noise for information acquisition in biological signaling pathways

All living systems acquire information about their environment. At the cellular level, they do so through signaling pathways, which rely on interactions between molecules that detect and transmit the presence of an extracellular cue or signal to the cells interior. Such interactions are inherently stochastic and thus noisy. In classical information theory, a noisy communication channel degrades the amount of transmissible information relative to a noise-free channel. For this reason, one would expect that the kinetic parameters that determine a pathways operation minimize noise. We show that this is not the case under a wide range of biologically sensible parameter values. Specifically, we perform computational simulations of simple signaling systems, which show that a noisy molecular interaction dynamics is a necessary condition for information acquisition. Moreover, we show that optimal information acquisition, where a system reacts most sensitively to changes in the environment, can be obtained close to the maximal attainable level of noise in the system. Our work highlights the positive role that noise can have in biological information processing.\n\nAuthor summaryThe acquisition of information is fundamental for living systems, because the decisions they take based on such information directly affect survival and reproduction. The molecular mechanisms used by cells to acquire information are signaling pathways. The molecular interactions of signaling pathways, such as the binding of a signal to a receptor, are by nature noisy. This is important, because noise disrupts information. Hence, to maximize the acquisition of information, signaling pathways should minimize the noise of their molecular interactions. Here we show that a noisy dynamic of the molecular interactions can improve the acquisition of information, and that the maximal capacity to acquire information can be obtained with a close-to-maximal level of noise in a signaling pathway. Thus, contrary to expectations, noise can improve the acquisition of information in living systems.

systems biology↗