Biology subjects

Foldi, C.

Publications and source records attributed to Foldi, C..

3 recordsLinked to original sources

bioRxiv2023

Temporal regulation of AgRP neurons mediates context-induced feeding

An environment can have a powerful influence over appetite and feeding behaviour. For example, an environmental context, which reliably predicts food, will increase the appetitive food drive to the same environment context. Interestingly, mice are required to be hungry to develop such a context-induced feeding (CIF) response, suggesting the neural circuits sensitive to hunger play an important role to associate an internal energy state with a particular environment context. Hunger-sensing Agouti related peptide (AgRP) neurons are activated by circulating signals of energy deficit and reset to a silenced state by gut feedback mechanisms following food consumption. We hypothesised that AgRP neurons are both necessary and sufficient to drive CIF in the absence of hunger. While fasting increased CIF, chemogenetic inhibition of AgRP neurons during context acquisition prevented this effect. Intriguingly, chemogenetic activation of AgRP neurons during context acquisition did not increase CIF, suggesting precise temporal firing properties may be required. Indeed, photostimulation of AgRP neurons, only during context exposure (ON-OFF in context), increased CIF. Moreover, AgRP photostimulation prior to context exposure, coupled with the termination of photostimulation in the context in the absence of food consumption, was sufficient to drive a subsequent CIF. Our results suggest that AgRP neurons regulate the acquisition of CIF when the temporal firing properties are matched to context exposure. These results further highlight that acute AgRP inhibition is a salient neural event underscoring the effect of hunger on associative learning.

neuroscience↗

bioRxiv2022

Purging genomes of contamination eliminates systematic bias from evolutionary analyses of ancestral genomes

Contamination of genomes and sequence databases is an increasingly recognized problem, however, efficient tools for removing alien sequences are still sparse and the impact of impure data on downstream analyses remains to be fully explored. Here, we present a new, highly sensitive tool, ContScout, for removing contamination from genomes, evaluate the level of contamination in 844 published eukaryotic genomes and show that contaminating proteins can severely impact analyses of genome evolution. Via benchmarking against synthetic data, we demonstrate that ContScout achieves high specificity and sensitivity when separating sequences of different high level taxa from each other. Furthermore, by testing on manually curated data we show that ContScout by far outperforms pre-existing tools. In the context of ancestral genome reconstruction, an increasingly common approach in evolutionary genomics, we show that contamination leads to spurious early origins for gene families and inflates gene loss rates several fold, leading to false notions of complex ancestral genomes. Using early eukaryotic ancestors (including LECA) as a test case, we assess the magnitude of bias and identify mechanistic bases of the estimation problems. Based on these results, we advocate the incorporation of contamination filtering as a routine step of reporting new draft genomes and caution against the outright interpretation of complex ancestral genomes and subsequent gene loss without accounting for contamination.

bioinformatics↗

bioRxiv2021

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates tissue differentiation, growth and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim to comprehensively identify conserved genes related to fruiting body morphogenesis and distill novel functional hypotheses for functionally poorly characterized genes. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide informed hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defense, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for [~]10% of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi.

evolutionary biology↗