Biology subjects

Bakker, E.

Publications and source records attributed to Bakker, E..

6 recordsLinked to original sources

bioRxiv2025

TOWARDS CLIMATE-SMART REWILDING: AN INTEGRATED FRAMEWORK FOR BIODIVERSITY, CLIMATE CHANGE, AND SOCIETY

The UN Decade on Ecosystem Restoration and the Kunming-Montreal Global Biodiversity Framework aim to restore 30% of degraded ecosystems. Both the IPCC and IPBES highlight the crucial role of ecosystem restoration in addressing the interconnected crises of climate change and biodiversity loss. One key restoration strategy is rewilding, which enhances ecosystem complexity with minimal human intervention. While traditional rewilding strategies often focus on benefits for biodiversity, we propose a climate-smart rewilding framework as a new approach designed to deliver climate benefits alongside biodiversity restoration. This framework seeks to integrate biodiversity, climate change adaptation and mitigation, as well as socio-economic benefits and trade-offs. We illustrate how this framework can be utilized to identify areas across Europe where rewilding could increase carbon sequestration, enhance species abilities to adapt to the velocity of climate change, and maximize wildlife-watching benefits while minimizing the costs associated with livestock-wildlife conflict. Finally, we acknowledge some limitations of climate-smart rewilding, but we argue that its adaptability and low cost render it a promising solution to the challenges facing Europe and beyond.

ecology↗

bioRxiv2024

Temperature drives seagrass recovery across the Western North Atlantic

Climate-driven shifts in herbivores, temperature and nutrient runoff threaten coastal ecosystem resilience. However, our understanding of ecological resilience, particularly for foundation species, remains limited due to a rarity of field experiments that are conducted across appropriate spatial and temporal scales and that investigate multiple stressors. This study aimed to evaluate the resilience of a widespread tropical marine plant (turtlegrass) to disturbances across its geographic range and how this is impacted by environmental gradients in (a)biotic factors. We assessed the resilience (i.e. recovery) of turtlegrass to a simulated disturbance (complete above- and belowground biomass removal) over a year. Contrary to temperate studies, higher temperature generally enhanced seagrass recovery. While nutrients and light availability had minimal impact, combined high levels of nutrients and herbivore grazing (meso and megaherbivore) reduced aboveground recovery. Our results suggest that the resilience of some tropical species, especially in cooler subtropical waters, may initially increase with warming.

ecology↗

bioRxiv2023

The Arabidopsis Information Resource in 2024

Since 1999, The Arabidopsis Information Resource (www.arabidopsis.org) has been curating data about the Arabidopsis thaliana genome. Its primary focus is integrating experimental gene function information from the peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal is to produce a gold standard functional annotation set that reflects the current state of knowledge about the Arabidopsis genome. At the same time, the resource serves as a nexus for community-based collaborations aimed at improving data quality, access and reuse. For the past decade, our work has been made possible by subscriptions from our global user base. This update covers our ongoing biocuration work, some of our modernization efforts that contribute to the first major infrastructure overhaul since 2011, the introduction of JBrowse2, and the resources role in community activities such as organizing the structural reannotation of the genome. For gene function assessment, we used Gene Ontology annotations as a metric to evaluate: (1) what is currently known about Arabidopsis gene function, and (2) the set of unknown genes. Currently, 74% of the proteome has been annotated to at least one Gene Ontology term. Of those loci, half have experimental support for at least one of the following aspects: molecular function, biological process, or cellular component. Our work sheds light on the genes for which we have not yet identified any published experimental data and have no functional annotation. Drawing attention to these unknown genes highlights knowledge gaps and potential sources of novel discoveries. Article SummaryThe Arabidopsis Information Resource (TAIR, www.arabidopsis.org) is a comprehensive website about Arabidopsis thaliana, a small plant thats very easy to grow and analyze in the laboratory and is used to understand how many other plants function. We share our progress in data collection and organization, website and tool improvement, and our involvement in community projects.

plant biology↗

bioRxiv2022

Adrenal cortex size, homeostasis and tumorigenesis is regulated by gonadal hormones via androgen receptor/β-catenin signalling crosstalk.

Female bias is highly prevalent among adrenal cortex hyperplasia and neoplasia, but the reasons behind this phenomenon are poorly understood. In this article, we show that overexpression of the secreted WNT agonist R-spondin-1 leads to ectopic activation of WNT/{beta}-catenin signalling and causes sex-specific adrenocortical hyperplasia in mice. While female adrenals show ectopic proliferation, male adrenals display excessive immune system activation and cortical thinning. Using a combination of genetic manipulations and hormonal treatment, we show that gonadal androgens suppress ectopic proliferation in the adrenal cortex and determine the selective activation of WNT-related genes Axin2 and Wnt4. Notably, genetic removal of androgen receptor (AR) from adrenocortical cells restores the mitogenic effect of WNT/{beta}-catenin signalling. This is the first demonstration that AR activity in the adrenal cortex determines susceptibility to canonical WNT signalling-induced hyperplasia. TeaserActivation of R-spondin signaling in the adrenal cortex leads to a sexually dimorphic phenotype causing tumors in females and immune cell recruitment in males

cancer biology↗

bioRxiv2018

Estimating numbers of fluorescent molecules in single cells by analysing fluctuations in photobleaching

The impact of fluorescence microscopy has been limited by the difficulties of express-ing measurements of fluorescent proteins in numbers of molecules. Absolute numbers enable the integration of results from different laboratories, empower mathematical modelling, and are the bedrock for a quantitative, predictive biology. Here we develop a general algorithm to infer numbers of molecules from fluctuations in the photobleaching of proteins tagged with Green Fluorescent Protein. To untangle measurement noise from stochastic fluctuations, we use the linear noise approximation and Kalman filtering within a framework of Bayesian inference. Not only do our results agree with biochemical measurements for multiple proteins in budding yeast, but we also provide a statistically verified model of measurement noise for fluorescence microscopes. The experiments we require are straightforward and use only a wide-field fluorescence microscope. As such, our approach has the potential to become standard for those practising quantitative fluorescence microscopy.

systems biology↗

bioRxiv2017

Morphologically Constrained and Data Informed Cell Segmentation of Budding Yeast

MotivationAlthough high-content image cytometry is becoming increasingly routine, processing the large amount of data acquired during time-lapse experiments remains a challenge. The majority of approaches for automated single-cell segmentation focus on flat, uniform fields of view covered with a single layer of cells. In the increasingly popular microfluidic devices that trap individual cells for long term imaging, these conditions are not met. Consequently, most segmentation techniques perform poorly. Incorporating information about the microfluidic features, media flow and morphology of the cells can substantially improve performance, though it may constrain the generalizability of software.\n\nResultsHere we present DISCO (Data Informed Segmentation of Cell Objects), a framework for using the physical constraints imposed by microfluidic traps, the shape based morphological constraints of budding yeast and temporal information about cell growth and motion, to allow tracking and segmentation of cells in micrflouidic devices. Using manually curated data sets, we demonstrate substantial improvements in both tracking and segmentation for this approach when compared with existing software.\n\nAvailabilityThe MATLAB(R) code for the algorithm and for measuring performance is available at https://github.com/pswain/segmentation-software. The test images and the curated ground truth results used for comparing the algorithms are available at http://swainlab.bio.ed.ac.uk/.

bioinformatics↗