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Andrade, R.

Publications and source records attributed to Andrade, R..

3 recordsLinked to original sources

Diversity-stability relationships become decoupled across spatial scales: a synthesis of organism and ecosystem types

The relationship between biodiversity and stability, or its inverse, temporal variability, is multidimensional and complex. Temporal variability in aggregate properties, like total biomass or abundance, is typically lower in communities with higher species diversity (i.e., the diversity-stability relationship or DSR). Recent work has shown that, at broader spatial extents, regional-scale aggregate variability is also lower with higher regional diversity (in plant systems) and with lower spatial synchrony. However, it is not yet clear whether regional DSRs hold across a broad range of organisms and ecosystem types. Furthermore, focusing exclusively on aggregate properties of communities may overlook potentially destabilizing compositional shifts. To test these questions, we compiled a large collection of long-term spatial metacommunity data spanning a wide range of taxonomic groups (e.g., birds, fish, plants, invertebrates) and ecosystem types (e.g., deserts, forests, oceans). We applied a newly developed quantitative framework for jointly analyzing aggregate and compositional variability across scales. We quantified DSRs for composition and total abundance in local communities and metacommunities. At the local scale, compositional DSRs suggested that higher local () diversity was associated with lower variability in animal populations but higher variability in plant populations, while aggregate DSRs supported the classic stabilizing effects of diversity. Spatial synchrony differed among taxa (birds had the lowest, plants the highest), suggesting differences in stabilization by spatial processes. Spatial synchrony declined with higher diversity among sites ({beta}) for both compositional and aggregate properties. However, at the regional ({gamma}) scale, we found no aggregate DSR, but a positive compositional DSR. Across a broader range of taxa, our results suggest that high {gamma}-diversity does not consistently stabilize aggregate properties at regional scales without sufficient spatial {beta}-diversity to reduce spatial synchrony. Open research statementAll data sets are accessible via the Environmental Data Initiative, and a specific data package of the data sets used in this analysis will be made publicly available (doi: pending). Citations to original sources are included in Appendix S1. Code to reproduce the analyses is found in a Zenodo archive (doi: pending) of the GitHub repository for this project (https://github.com/sokole/ltermetacommunities/tree/master/Manuscripts/MS3).

ecology↗

LUZP1, a novel regulator of primary cilia and the actin cytoskeleton, is altered in Townes-Brocks Syndrome

Primary cilia are sensory organelles that are crucial for cell signaling during development and organ homeostasis. Cilia arise from the centrosome and their formation is governed by numerous regulatory factors. We show that the leucine-zipper protein LUZP1 localizes to the pericentriolar material and actin cytoskeleton. Using TurboID proximity labeling and pulldowns, LUZP1 associates with factors linked to centrosome and actin filaments. Loss of LUZP1 reduces F-actin levels, facilitating ciliogenesis and altering Sonic Hedgehog signaling, pointing to a key role in the cytoskeleton-cilia interdependency. Moreover, we show that LUZP1 interacts with a truncated form of the transcription factor SALL1 that causes Townes-Brocks Syndrome. TBS is characterized by digit, heart and kidney malformations and is linked in part to defective cilia. Truncated SALL1 increases the ubiquitin proteasome-mediated degradation of LUZP1. Alteration of LUZP1 levels may be a contributing factor to TBS, suggesting possible therapies using modulators of cilia and cytoskeletal function.

cell biology↗

MOMO - Multi-Objective Metabolic mixed integer Optimization: application to yeast strain engineering

In this paper, we explore the concept of multi-objective optimization in the field of metabolic engineering when both continuous and integer decision variables are involved in the model. In particular, we propose a multi-objective model that may be used to suggest reaction deletions that maximize and/or minimize several functions simultaneously. The applications may include, among others, the concurrent maximization of a bioproduct and of biomass, or maximization of a bioproduct while minimizing the formation of a given by-product, two common requirements in microbial metabolic engineering.\n\nProduction of ethanol by the widely used cell factory Saccharomyces cerevisiae was adopted as a case study to demonstrate the usefulness of the proposed approach in identifying genetic manipulations that improve productivity and yield of this economically highly relevant bioproduct. We did an in vivo validation and we could show that some of the predicted deletions exhibit increased ethanol levels in comparison with the wild-type strain. The multi-objective programming framework we developed, called Momo, is open-source and uses PolySCIP{ddagger} as underlying multi-objective solver. Momo is available at http://momo-sysbio.gforge.inria.fr

systems biology↗