Biology subjects

Benitez, M.

Publications and source records attributed to Benitez, M..

At least 19 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

Connexins are essential for the contribution of latent progenitors to self-repair after spinal cord injury

Gap junctions are important regulators of the biology of neural stem cells. Both in vertebrates with regenerative abilities and neonatal rodents, ependymal cells communicate via connexin (Cx) 43 and Cx26. Gap junction coupling and Cx26 are down-regulated as the ependyma becomes quiescent in adulthood, but injury overrules this developmental down-regulation suggesting a role for Cx signalling in the reactivation of ependymal cells. Here, we aim to explore the role of Cx26 and Cx43 in the response of ependymal cells to injury. We find that Cx26 is critical for the proliferative response to injury and thereby scar formation. Cx43 plays a key role in the communication between ependymal cells of Ca2+ signals induced by activation of P2X7 receptors that trigger downstream events. Our data show that Cxs are relevant targets to manipulate the ependymal stem cell niche to achieve a better self-repair after spinal cord injury.

neuroscience↗

bioRxiv2024

Cell Geometry and Membrane Protein Crowding Constrain Growth Rate, Overflow Metabolism, Respiration, and Maintenance Energy.

The rules of prokaryotic cell design remain elusive. Here, a theory is presented for interpreting growth rate, overflow metabolism, respiration efficiency, and maintenance energy flux based on cell dimensions, membrane protein crowding, and metabolism. The theory employs biophysical properties and systems analysis to successfully interpret phenotypes of Escherichia coli K-12 strains MG1655 and NCM3722. These strains are genetically similar but differ in surface area-to-volume (SA:V) ratios ([~]30%), growth rate on glucose ([~]40%), and overflow-inducing growth rates ([~]80%). Six predictions were tested and validated using experimental phenomics, proteomics, and mutant data. Analyses did not require assumptions regarding cytosolic macromolecular crowding highlighting the distinct properties of the theory. Cell geometry and membrane protein crowding are significant biophysical constraints of cell biology.

systems biology↗

bioRxiv2024

Unravelling a diversity of cellular structures and aggregation dynamics during the early development of Myxococcus xanthus

Aggregation underlies collective dynamics of a diversity of organisms, enabling the formation of complex structures and emergent behaviours in interaction with the environment. Myxococcus xanthus, a social bacterium, is a valuable model for studying aggregation, particularly in the development and evolution of multicellularity. While the collective behaviour of M. xanthus has been largely studied under very crowded, ideal, conditions, there is a lack of understanding at not crowded or sparse conditions. In this work, we study the early stages of emergent collective behaviour of M. xanthus under nutrient-poor and low density conditions, uncovering the formation of diverse cellular structures with different shapes and sizes, ranging from individual cells to networks comprising thousands of cells. We study their motility patterns and their prevalence along development, and argue over their cross-scale role on the populations exploratory dynamics. This work contributes to understanding key, yet largely understudied, aspects in the early stages of multicellular development in myxobacteria, shedding light on the dynamics underlying aggregative processes in this and other taxa and study systems.

developmental biology↗

bioRxiv2023

Harvesting trajectories in large-scale coffee plantations: ecological and management drivers and implications

CONTEXTCoffee is produced under different management systems and scales of production categorized as Syndromes of Production. The "Capitalist Syndrome" is characterized by the high use of capital and labor inputs to increase agricultural outputs. This syndrome results in practices like high planting densities that may promote the development and dispersal of plant pathogens like coffee leaf rust. The spatial arrangement of coffee trees drives the spatial movement of the harvesters, who can bear and disperse pathogens across and within plantations. In most capitalist coffee plantations, harvesters work multiple hours to maximize the daily harvest, which might increase their dispersal potential. However, their spatial movement has not yet been described, nor its relationship with the scale or management of the plantation, and even less its ecological implications for pathogens dispersal. OBJECTIVEWe describe and analyze the daily spatial movement of coffee harvesters in two large-scale capitalist plantations: an organic and a conventional plantation. METHODSUsing state-space models, we recorded and analyzed the spatial movements of harvesters. We then constructed a driver tree for harvest dynamics, which incorporated qualitative variables related to climate, coffee plants, and management aspects reported by the harvesters. RESULTS AND CONCLUSIONSOur model differentiated two kinds of movements: 1) when trees have berries, harvesters remain in the coffee rows or areas nearby (Collect state; 94-98% of the steps); 2) when not, harvesters make longer steps within the harvesting location or move to another area (Search state; 2-6% of the steps). In the organic plantation, the Search state had a longer-tailed step-length distribution than in the conventional plantation, resulting in a significantly higher visited area per worker (p<0.05). This might be related to a) a lower fruit load or percentage of trees with ripe fruits when we took the data or b) smaller harvesting locations ("pantes") per number of harvesters. Harvesting movements that explore a wider area, either by visiting more plants or by changing locations on the same day, could create more foci of CLR infection across the plantation. SIGNIFICANCEOur results highlight practices that can reduce the possible impact of human dispersal of pathogens like shorter harvesting trajectories by working fewer hours a day or avoiding harvesting at the end of the maturation season when few trees have berries and harvesters have to travel longer distances. This calls for organic coffee management that could prevent diseases, increase diversity, and guarantee just and safe conditions for workers.

ecology↗

bioRxiv2023

Interplay between harvesting, planting density and ripening time affects coffee leaf rust dispersal and infection

The relationship between the spatial structure of hosts and the individual movement of vectors is central to developing a comprehensive representation of pathogen dynamics. Here we focus on the dynamics of coffee leaf rust (CLR; Hemileia vastatrix), which is one of the principal coffee diseases around the globe. This fungus disperses between plants or regions through direct contact, water splash, or local turbulent wind conditions. Some studies have proposed that coffee harvesters can also bear CLR during harvesting. However, it is not clear how relevant these movements are for CLR dispersal and plot-level infection in plots with different planting densities. Besides, there are bidirectional interactions between the plantation characteristics (e.g. planting density and ripening synchronicity) and the movement of harvesters that might modify their dispersal potential. Overall, there is a lack of mechanistic models to represent these interactions. Here we present a computational model to explore the role of coffee ripening synchronicity in reproducing the different movement trajectories observed in the field. We then evaluate how these harvesting trajectories modify rust dispersal and change CLR infection in plots with increasing planting densities and a constant contact-mediated rust dispersal mechanism. For both synchronization scenarios, the distribution of step lengths is positively skewed. Interplant asynchronous ripening and scarcity of trees with berries generate trajectories with medium to long steps contrary to scenarios with synchronous ripening and without scarcity. The harvest dispersal significantly increases coffee plot infection (up to 15%) compared to scenarios where only local mechanisms for CLR dispersal are present. This effect is maximal for trajectories with medium to long steps from the asynchronous scenario and in plantations with medium planting densities. In particular, medium-sized steps are more likely to create new foci and networks of contact-mediated infected plants. The interaction between the proportion and the size of infected networks results in a nonlinear behavior of rust increase due to harvest. Our results aim to spur discussion on practices that could reduce the impact of harvesting and specific trajectories, in scenarios where one can benefit from asynchronous maturation of berries and shaded plantations. Some examples of practices include reducing the medium to long-distance movements during the same day, for instance, by avoiding harvesting at the end of the harvest season when trees ripening asynchronicity and CLR levels are higher.

ecology↗

bioRxiv2023

Cytokinins control secondary cell wall formation in the inflorescence stem of Arabidopsis

Spatiotemporal control over developmental programs is vital to all organisms. Here we show that cytokinin (signaling) deficiency leads to early secondary cell wall (SCW) formation in Arabidopsis inflorescence stem that associates with precocious upregulation of a SCW transcriptional cascade controlled by NAC TFs (NSTs). We demonstrate that cytokinin signaling through the AHK2/3 and the ARR1/10/12 suppresses the expression of several NSTs and SCW formation in the apical portions of stems. Exogenous cytokinin application reconstituted both proper development and apical-basal gradient of NST1 and NST3 in a cytokinin biosynthesis-deficient mutant. We show that AHK2 and AHK3 required functional NST1 or NST3 to control SCW initiation in the interfascicular fibers, further evidencing that cytokinins act upstream of NSTs transcription factors. The premature onset of a rigid SCW biosynthesis and altered expression of NST1/3 and VND6/7 due to cytokinin deficiency led to the formation of smaller tracheary elements (TEs) and impaired hydraulic conductivity. We conclude that cytokinins downregulate NSTs to inhibit premature SCW formation in the apical part of the inflorescence stem, facilitating thus the development of fully functional TEs and interfascicular fibers. Summary statementCytokinins attenuate premature secondary cell wall (SCW) formation via downregulating the expression of NAC TFs, the master switches of SCW transcriptional cascade, thus affecting the tracheary elements size and conductivity.

plant biology↗

bioRxiv2022

Dispersion and Plant Arrangement Condition the Timing and Magnitude of Coffee Rust Infection

One central issue in coffee-leaf rust (Hemileia vastatrix) epidemiology is to understand what determines the intensity and the timing of yearly infections in coffee plantations. However, most experimental and theoretical studies report infection as an average at the plot level, obscuring the role of potentially key factors like rust dispersal or the planting pattern. Here, we first review the rust epidemic patterns of different sites, which reveal large variability in the duration and magnitude of the different epidemiologic phases. We then present a spatially explicit and parametrised model, where the host population is subdivided into discrete patches linked through spore dispersal, modelled as simple diffusion. With this model, we study the role of the planting arrangement, the dispersal intensity and plant-level variables on the maximum average tree infection (MATI) and its timing. Our results suggest that the epidemic timeline can be divided into two phases: a time lag and a growth phase per se. The model shows that the combination of the dispersal magnitude and plant aggregation modifies the MATI and the time to MATI, mainly by preventing some plants from reaching their maximum peak during the epidemic. It also affects the epidemic curves, which can have a stepped, or a rather smooth pattern in plots with otherwise similar conditions. The initial rust infection modulates the time lag before the epidemic and the infected leaf-fall rate drastically changes the MATI. These findings highlight the importance of explicitly considering the spatial aspects of coffee agroecosystems when measuring and managing rust infection, and help us to further understand the spatio-temporal dynamics of ecological systems in general.

systems biology↗

bioRxiv2021

The environment topography alters the transition from single-cell populations to multicellular structures in Myxococcus xanthus

The social soil-dwelling bacteria Myxococcus xanthus can form multicellular structures, known as fruiting bodies. Experiments in homogeneous environments have shown that this process is affected by the physico-chemical properties of the substrate, but they have largely neglected the role of complex topographies. We experimentally demonstrate that the topography alters single-cell motility and multicellular organization in M. xanthus. In topographies realized by randomly placing silica particles over agar plates, we observe that the cells interaction with particles drastically modifies the dynamics of cellular aggregation, leading to changes in the number, size and shape of the fruiting bodies, and even to arresting their formation in certain conditions. We further explore this type of cell-particle interaction in a minimal computational model. These results provide fundamental insights into how the environment topography influences the emergence of complex multicellular structures from single cells, which is a fundamental problem of biological, ecological and medical relevance.

biophysics↗

bioRxiv2020

Interplay of mesoscale physics and agent-like behaviors in the parallel evolution of aggregative multicellularity

Myxobacteria and dictyostelids are prokaryotic and eukaryotic multicellular lineages, respectively, that after nutrient depletion aggregate and develop into structures called fruiting bodies. The developmental processes and the resulting morphological outcomes resemble one another to a remarkable extent despite their independent origins, the evolutionary distance between them and the lack of traceable levels of homology in the molecular mechanisms of the groups. We hypothesize that the morphological parallelism between the two lineages arises as the consequence of the interplay, within multicellular aggregates, between generic processes, physical and physicochemical processes operating similarly in living and non-living matter at the mesoscale (~10-3-10-1 m) and agent-like behaviors, unique to living systems, characteristic of the constituent cells. To this effect, we analyze the relative contribution of the generic and agent-like determinants in the main phenomena of myxobacteria and dictyostelid development, and their roles in the emergence of their shared traits. We show that as a consequence of aggregation collective cell-cell contacts mediate the emergence of liquid-like properties, making nascent multicellular masses subject to new sets of patterning and morphogenetic processes. In both lineages, this leads to behaviors such as streaming, rippling, and rounding up, similar to effects observed in non-living fluids. Later the aggregates solidify, leading them to exhibit additional generic properties and motifs. We consider evidence that the morphological phenotypes of the multicellular masses deviate from the predictions of generic physics due to the contribution of agent-like behaviors. These include directed migration, quiescence, and oscillatory signal transduction of the cells mediated by responses to external cues acting through species-specific regulatory and signaling mechanisms reflecting the evolutionary histories of the respective organisms. We suggest that the similar developmental trajectories of Myxobacteria and Dictyostelia are more plausibly due to shared generic physical processes in coordination with analogous agent-type behaviors than to convergent evolution under parallel selection regimes. Finally, we discuss the broader implications of the existence and synergy of these two categories of developmental factors for evolutionary theory.

developmental biology↗

bioRxiv2020

Linking coleopteran diversity with agricultural management of maize agroecosystems in Oaxaca, Mexico

Biodiversity is known to be influenced by agricultural practices in many ways. However, it is necessary to understand how this relation takes place in particular agroecosystems, sociocultural contexts and for specific biological groups. Also, in order to systematically study and track how biodiversity responds or changes with agricultural practices, it is necessary to find groups that can be used as practical indicators. We conduct a study of beetle (Coleoptera) diversity in maize-based agricultural plots with heterogeneous management practices in the Central Valleys of Oaxaca, Mexico. First, we use a mixture of local knowledge and multivariate statistics to group the plots into two broad and contrasting management categories (traditional vs. industrialized). Then, we present an analysis of Coleopteran diversity for each category, showing higher levels across different diversity indexes for the traditional plots. Also, our results let us postulate the Curculionidae family as an indicator of both management type and overall Coleopteran diversity in the agricultural lands of the study site. We discuss our results in terms of the agricultural matrix quality and its role in joint productive and biodiversity conservation strategies.

ecology↗

bioRxiv2019

High density of white-faced capuchins (Cebus capucinus) and habitat quality in the Taboga Forest of Costa Rica

Across the globe, primate species and habitats are threatened by human activity. This is especially true for species found in tropical dry forests, which are widely distributed and comprise diverse habitats that remain largely unprotected. Evidence suggests that some primate species endemic to tropical dry forests may be more sensitive to anthropogenic disturbance than others, but our ability to predict primate abundance in the face of disturbance also depends on the specific variables for each site. Here, we consider the factors that explain the high density of white-faced capuchins (Cebus capucinus) found in the Taboga Forest, Costa Rica, a relatively small fragment of tropical dry forest surrounded by agricultural fields. Our analyses suggest that, for capuchins (and potentially for mantled howler monkeys, Alouatta palliata), the size and disturbance of a forest fragment may matter less than the composition and availability of key resources, like above-ground water. Group sightings for both species were higher near permanent water sources, but group sightings did not vary between edge and interior forest. These findings help explain why some primate species can flourish even alongside anthropogenic disturbance and thus carry important implications for conservation efforts. Smaller forest fragments, like Taboga, may be able to support high densities of some species because they provide a mosaic of habitats and key resources that buffer adverse ecological conditions. Future studies will assess the extent to which primates in the Taboga Forest rely on the canals versus the river and will consider how the high density of capuchins in Taboga influences ranging patterns, home range overlap, and the frequency and intensity of intergroup encounters.\n\nRESEARCH HIGHLIGHTSO_LIHere we introduce a new white-faced capuchin study site in the Taboga Forest, Costa Rica, a fragmented tropical dry forest.\nC_LIO_LIForest fragments like Taboga may support high primate densities because they provide a mosaic of habitats and key resources.\nC_LI

animal behavior and cognition↗

bioRxiv2019

Landscape heterogeneity of peasant-managed agricultural matrices

In agricultural landscapes, management practices and other environmental and social factors shape complex agroecological matrices. In turn, the structure of such matrices impacts both agricultural activities and biodiversity conservation, for instance, by mediating wildlife migration between agricultural and habitat patches. One way to characterize a matrix, its potential role in biodiversity conservation, and how its descriptors change across different spatial scales, is characterizing heterogeneity metrics and systematically examining how such metrics change with grain size and landscape extent. However, these methods have rarely been applied to tropical, peasant-managed landscapes, even though this type of landscape occupies most of the agricultural surface in or near biodiversity hotspots. We focus on a peasant-managed agricultural landscape in Oaxaca, Mexico, for which we mapped and quantified the land-use classes and evaluated heterogeneity metrics. We also examined the response of heterogeneity metrics to changes in grain and extent scales. This allowed us to further understand the structure and conservation potential of the agroecological matrix in this type of landscape, to broadly compare this landscape with other agricultural landscapes in North America, and to recommend specific landscape metrics for different types of studies involving agricultural matrices. We conclude that this type of agricultural matrix is ideal to pursue joint agricultural and conservation strategies in an integrated landscape.

ecology↗

bioRxiv2019

A Systems Biology perspective of Dynamical Patterning Modules in the transition to multicellularity: lessons from an aggregative bacteria

Development and evolution are dynamical processes under the continuous control of organismic and environmental factors. Generic physical processes, associated with biological materials and certain genes or molecules, provide a morphological template for the evolution and development of organism forms. Generic dynamical behaviors, associated with recurring network motifs, provide a temporal template for the regulation and coordination of biological processes. The role of generic physical processes and their associated molecules in development is the topic of the Dynamical Patterning Module (DPM) framework. The role of generic dynamical behaviors in biological regulation is studied via the identification of the associated Network Motifs (NM). We propose a joint DPM-NM perspective on the emergence and regulation of multicellularity focusing on a multicellular aggregative bacterium, Myxococcus xanthus. Understanding M. xanthus development as a dynamical process embedded in a physical substrate provides novel insights into the interaction between developmental regulatory networks and generic physical processes in the evolutionary transition to multicellularity.

systems biology↗

bioRxiv2019

Role of aggregate size, multistability and communication in determining cell fate and patterning in M. xanthus

1.The emergence of multicellular organisms that exhibit cell differentiation and stereotypic spatial arrangements has been recognized as one of the major transitions in evolution. Myxobacteria have emerged as a useful study model to investigate multicellular evolution and development. Here, we propose a multiscale model that considers cellular adhesion and movement, molecular regulatory networks (MRNs), and cell-to-cell communication to study the emergence of cell fate determination and spatial patterning of Myxococcus xanthus fruiting bodies. The model provides a dynamic accounting of the roles of MRN multistability, intercellular communication and conglomerate size in determining cell fate and patterning during M. xanthus development. It also suggests that for cell fate determination and patterning to occur, the cell aggregate must surpass a minimum size. The model also allows us to contrast alternative scenarios for the C-signal mechanism and provides stronger support for an indirect effect (as a diffusible molecule) than a direct one (as a membrane protein).

developmental biology↗

bioRxiv2018

Plastic multicellular development of Myxococcus xanthus: genotype-environment interactions in a physical gradient

In order to investigate the contribution of the physical environment to variation in multicellular development of Myxococcus xanthus, phenotypes developed by different genotypes in a gradient of substrate stiffness conditions were quantitatively characterized. Statistical analysis showed that plastic phenotypes result from the genotype, the substrate conditions and the interaction between them. Also, phenotypes were expressed with scale- and trait-specificity. Overall, the presented information highlights the constructive role of the physical context in the development of microbial multicellularity, with both ecological and evolutionary implications.

developmental biology↗

bioRxiv2018

Drosophila anion exchanger 2 is required for proper ovary development and oogenesis

Understanding how cell fate decisions are regulated is a central question in stem cell biology. Recent studies have demonstrated that intracellular pH (pHi) dynamics contribute to this process. Indeed, the pHi of cells within a tissue is not simply a consequence of chemical reactions in the cytoplasm and other cellular activity, but is actively maintained at a specific setpoint in each cell type. We found previously that the pHi of cells in the follicle stem cell (FSC) lineage in the Drosophila ovary increases progressively during differentiation from an average of 6.8 in the FSCs, to 7.0 in newly produced daughter cells, to 7.3 in more differentiated cells. Two major regulators of pHi in this lineage are Drosophila sodium-proton exchanger 2 (dNhe2) and a previously uncharacterized gene, CG8177, that is homologous to mammalian anion exchanger 2 (AE2). Based on this homology, we named the gene ae2. Here, we generated null alleles of ae2 and found that homozygous mutant flies are viable but have severe defects in ovary development and adult oogenesis. Specifically, we find that ae2 null flies have smaller ovaries, reduced fertility, and impaired follicle formation. In addition, we find that the follicle formation defect can be suppressed by a decrease in dNhe2 copy number and enhanced by the overexpression of dNhe2, suggesting that this phenotype is due to the dysregulation of pHi. These findings support the emerging idea that pHi dynamics regulate cell fate decisions and our studies provide new genetic tools to investigate the mechanisms by which this occurs.

developmental biology↗

bioRxiv2018

Combined effect of matrix quality and spatial heterogeneity on biodiversity decline

The land-sparing/land-sharing debate remains an oversimplified framework to evaluate landscape management strategies that aim to reconcile food production and biodiversity conservation. Still, biodiversity-yield curves, on which the framework has relied, provide valuable qualitative information on biodiversitys sensitivity to agricultural practices, and much research has studied this relationship. But the potential effect of landscape configuration on biodiversitys response to intensification has rarely been considered; besides, studies have often taken yield as an indicator of agricultural management and have generalized conclusions from studying particular taxonomic groups. In this work we adapt a metacommunity model to analyze factors that shape biodiversitys response to agricultural intensification while addressing some of the simplifications of the land-sparing/land-sharing dichotomy. In particular, we study species richness decline in landscapes encompassing a combined gradient in matrix quality and configurational heterogeneity of habitat patches, and considering community dynamics. We found that species richness along an intensification gradient shifts from following a robust response to presenting an abrupt decline, as landscape heterogeneity increases, as stricter survival thresholds are applied to species or as habitat area is reduced. Our work highlights the interdependent effects of heterogeneity, habitat availability and matrix quality on biodiversity and contributes to a nuanced understanding of ecological and landscape factors that enable a robust response of biodiversity in the face of spatiotemporal perturbations.

ecology↗