Biology subjects

Fumey, J.

Publications and source records attributed to Fumey, J..

6 recordsLinked to original sources

bioRxiv2025

InSillyClo, a user-friendly web application to assist large-scale Golden Gate Cloning and MoClo workflows

Systems and synthetic biology developments often require the construction of many variants of a genetic circuit of interest, resulting in large-scale cloning campaigns. Golden Gate and Modular Cloning (MoClo), two powerful technologies enabling the scale-up of cloning workflows, play a central role for efficient circuit construction. These workflows include a number of dry-lab tasks, which are time-consuming and error-prone at scale. Currently, no software tool is available to handle these tasks in a dedicated, time-saving, and user-friendly manner. We present InSillyClo, an open-source web application to assist large-scale Golden Gate cloning and MoClo workflows. It supports an easy specification of genetic designs at any scale, followed by the automated generation of comprehensive workflow-related data. Moreover, InSillyClo leverages Modular Cloning with a versatile typing system of parts to generate user-defined workflows. InSillyClo is open source, accessible with or without user registration, and can also be used locally.

synthetic biology↗

bioRxiv2025

Paratyphoid Fever and Relapsing Fever in 1812 Napoleon's Devastated Army

During Napoleons retreat from Russia in 18121, countless soldiers of the French army succumbed to infectious diseases, but the responsible pathogen or pathogens remain debated2-5. We recovered and sequenced ancient DNA from the teeth of 13 soldiers who, based on historical records, likely died from infectious diseases, aiming to identify the pathogens responsible for their deaths6. Our results confirmed the presence of Salmonella enterica subsp enterica belonging to the lineage Para C, the causative agent of paratyphoid fever7 ; and Borrelia recurrentis, responsible for relapsing fever transmitted by body lice8. We were not able to detect Rickettsia prowazekii (the agent of typhus) and Bartonella quintana (the cause of trench fever), which had previously been associated with this deadly event, based on PCR results and historical symptom descriptions3. The presence of these previously unsuspected pathogens in these soldiers reveals that they could have contributed to the devastation of Napoleons Grande Armee during its disastrous retreat in 1812. HighlightsO_LIGenetic evidence of S. Paratyphi C and B. recurrentis in Napoleonic soldiers C_LIO_LIPhylogeny-driven authentication workflow for ultra-low-coverage pathogen aDNA C_LIO_LIHistorical descriptions of Napoleons army illness match paratyphoid fever symptoms C_LIO_LIMultiple infections likely contributed to the collapse of Napoleons 1812 campaign C_LI

microbiology↗

bioRxiv2022

Genetic identification and reiterated captures suggests that the Astyanax mexicanus El Pachon cavefish population is closed and declining

The size of Astyanax mexicanus blind cavefish populations of North-East Mexico is a demographic parameter of great importance for investigating a variety of ecological, evolutionary and conservation issues. However, very few estimates have been obtained. For these mobile animals living in an environment difficult to explore as a whole, methods based on capture-mark-recapture are appropriate, but the feasibility of such approach and the interpretation of the results depend on several assumptions that must be carefully examined. Here, we provide evidence that minimally invasive genetic identification from captures at different time intervals can give insights on cavefish population size dynamics as well as other important demographic parameters of interest. We also provide tools to calibrate sampling and genotyping efforts necessary to reach a given level of precision. Our results suggest that the El Pachon cave population is currently very small, of an order of magnitude of a few hundreds of individuals, and is distributed in a relatively isolated area. The probable decline in population size in the El Pachon cave since the last census in 1971 raises serious conservation issues.

zoology↗

bioRxiv2020

Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals

Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxing functional constraints. Gene decay can serve as a read-out of this evolutionary process. Animals living in the dark are outstanding models, in particular cavefishes as hundreds of species evolved independently during very different periods of time in absence of light. Here, we sought to understand some general principals on the extent and tempo of decay of several gene sets in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provides evidence for the most massive loss of eye genes reported so far in cavefishes. Comparisons with a recently-evolved cave population of Astyanax mexicanus and three species belonging to the tetraploid Chinese genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time and genome ploidy on the number of eye pseudogenes. In sharp contrast, most circadian clock and pigmentation genes appeared under strong selection. In cavefishes for which complete genomes are available, the limited extent of eye gene decay and the very small number of loss of function (LoF) mutations per pseudogene suggest that eye degeneration is never very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several eye pseudogenes carrying many LoF mutations in ancient fossorial mammals. Our analyses support the hypothesis that blind fishes cannot thrive more than a few millions of years in cave ecosystems.

evolutionary biology↗

bioRxiv2019

Diachronic monitoring of snow leopards at Sarychat-Ertash State Reserve (Kyrgyzstan) through scat genotyping: a pilot study

Snow leopards (Panthera uncia) are a keystone species of Central Asias high mountain ecosystem. The species is listed as vulnerable and is elusive, preventing accurate population assessments that could inform conservation actions. Non-invasive genetic monitoring conducted by citizen scientists offers avenues to provide key data on this species that would otherwise be inaccessible. From 2011 to 2015, OSI-Panthera citizen science expeditions tracked signs of presence of snow leopards along transects in the main valleys and crests of the Sarychat-Ertash State Reserve (Kyrgyzstan). Scat samples were genotyped at seven autosomal microsatellite loci and at a X/Y locus for sex identification, which allowed estimating a minimum of 11 individuals present in the reserve from 2011 to 2015. The genetic recapture of 7 of these individuals enabled diachronic monitoring, providing indications of individuals movements throughout the reserve. We found putative family relationships between several individuals. Our results demonstrate the potential of this citizen science program to get a precise description of a snow leopard population through time.

genetics↗

bioRxiv2016

Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish

BackgroundCavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They share similar phenotypic changes such as blindness and depigmentation resulting from independent and convergent evolution. As such they allow examining whether their evolution involved the fixation of preexisting standing genetic variations and/or de novo mutations. Cavefish populations are currently assigned to two main groups, the so-called \"old\" and \"new\" lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations.\n\nResultsFirst, we reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages, neither the ancient origin of the \"old\" lineage. Using IMa2, a program based on a method that does not assume that populations are at mutation/migration/drift equilibrium and thus allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (i.e. less than 20,000 years). Second, we identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of pools of embryos (Pool-seq) belonging to the \"old\" Pachon cave population and a surface population from Texas. Pachon cave population has accumulated more neutral substitutions than the surface population and we showed that it could be another signature of its recent origin. Based on summary statistics that can be computed with this SNP data set together with simulations of evolution of SNP polymorphisms in two recently isolated populations, we looked for sets of demographic parameters that allow the computation of summary statistics with simulated populations that are similar to the ones with the sampled populations. In most simulations for which we could find a good fit between the summary statistics of observed and simulated data, the best fit occurred when the divergence between simulated populations was less than 30,000 years.\n\nConclusionsAlthough it is often assumed that some cave populations such as Pachon cavefish have a very ancient origin, within the range of the late Miocene to the middle Pleistocene, a recent origin of these populations is strongly supported by our analyses of two independent sets of nuclear DNA polymorphism using two very different methods of analysis. Moreover, the observation of two divergent haplogroups of mitochondrial and nuclear genes with different geographic distributions support a recent admixture of two divergent surface populations before the isolation of cave populations. If cave populations are indeed only several thousand years old, many phenotypic changes observed in cavefish would thus have mainly involved the fixation of genetic variants present in surface fish populations and within a very short period of time.

evolutionary biology↗