Biology subjects

Guy, L.

Publications and source records attributed to Guy, L..

9 recordsLinked to original sources

bioRxiv2026

PLAGUE: Improved confidence plasmid reconstruction from short read assemblies

As the vast majority of archival data is short-read based, reliable strategies for detecting and classifying plasmids out of these data are still needed. A widely adopted solution for binning plasmids with rich contextual data is MOB-Suite. However, a large portion of the available data has low coverage and results in fragmented assemblies. Under these circumstances, MOB-Suite delivers a high number of false positives, leading to wasteful follow-up experiments. To improve the reliability of MOB-Suite, while retaining and enriching its biological contextual output, we have developed PLAGUE. PLAGUE is a fast and low-memory consumption post-processing tool for MOB-Suite outputs, relying on checks of circularity, reads spanning the gap between the 3 and 5 ends and total coverage of the plasmid candidate. PLAGUE can reduce the number of false positives in MOB-Suite outputs by over 30%, while retaining almost full sensitivity. It is fully containerized and easy to use in clusters as well as locally.

microbiology↗

bioRxiv2025

FlashFold: a standalone command-line tool for accelerated protein structure prediction

AlphaFold has revolutionized the decades-old issue of precisely predicting protein structures. However, its high accuracy relies on a computationally intensive step that involves searching vast databases for homologous sequences as the query protein of interest. Additionally, predicting the quaternary structure of protein complexes requires prior knowledge of subunit counts, a prerequisite rarely met. To address these limitations, we introduce FlashFold - a fast, user-friendly tool for protein structure prediction. It accelerates homology searches using a compact built-in database, enabling structure predictions up to 3-fold faster than AlphaFold3, with sacrificing little or no accuracy. Unlike others, FlashFold features adaptable built-in databases that allow users to easily incorporate their own privately sequenced data - an option that can positively influence the prediction accuracy. Moreover, it allows users to estimate stoichiometry of protein complexes directly from sequence information. To support high-throughput workflows and streamline downstream decision-making, it generates interactive and filterable summary reports, enabling users to efficiently visualize protein structures, and interpret large volumes of prediction results. FlashFold runs locally on Linux and Mac, eliminating reliance on third-party servers. FlashFold is available at https://github.com/chayan7/flashfold.

bioinformatics↗

bioRxiv2024

Host-specific adaptation of Legionella pneumophila to single and multiple hosts

Legionella pneumophila is an endosymbiotic bacterial species able to infect and reproduce in various protist and human hosts. Upon entry in human lungs, they may infect lung macrophages, causing Legionnaires disease (LD), an atypical pneumonia, using similar mechanisms as in their protozoan hosts, despite the two hosts being separated by a billion years of evolution. In this study, we used experimental evolution to identify genes conferring host-specificity to L. pneumophila. To this end, we passaged L. pneumophila in two different hosts - Acanthamoeba castellanii and the human macrophage-like cells U937 - separately and by switching between the hosts twice a week for a year. In total, we identified 1518 mutations present in at least 5% of the population at the time of sampling. Half of these were localized in five groups of repeated sequences, likely to be recombination hotspots. Forty-nine mutations were fixed in the 18 populations at the end of the experiment, representing four different groups. The first two groups involve adaptation to the specific selection conditions, including (i) two specific mutations in the 30S ribosomal protein S12 (RpsL) that conferred resistance to streptomycin, to which the bacteria were unexpectedly exposed to during serial passage and (ii) two mutations, one in the 30S ribosomal protein S4 (RpsD), and one in the chaperonin GroES, both of which are likely to be fitness-restoring compensatory mutations to the original RpsL mutations. Two more interesting groups of mutations included (iii) mutations in 4 different strain-specific genes involved in LPS synthesis, found only in the lineages passaged with A. castellanii and (iv) mutations in the gene coding for LerC, a key regulator of protein effector expression, which was independently mutated in 6 lineages grown in presence of the U937 cells. We propose that the mutations degrading the function of the regulator LerC improve the fitness of L. pneumophila in human-derived cells, and that modifications in the LPS are beneficial for growth in A. castellanii. This study is a first step in further investigating determinants of host specificity in L. pneumophila.

evolutionary biology↗

bioRxiv2022

High-efficiency transfection of Acanthamoeba castellanii using a cationic polymer

The free-living amoeba Acanthamoeba castellanii is an ecologically, clinically, and evolutionarily important microorganism. A. castellanii amoebae are directly pathogenic to humans and serve as reservoirs for bacterial pathogens (e.g., Legionella pneumophila) but also regulate the proliferation of other microorganisms in the soil. Despite their importance, no reliable genetic system has been developed, hampering the use of A. castellanii and related species as model organisms. Transfecting A. castellanii with plasmids is possible with commercial kits, but it is expensive, inefficient, and vulnerable to product discontinuation. In this contribution, we present a method for efficient transfection of A. castellanii with readily available and inexpensive polyethylenimines. We systematically explore the methods parameters, obtaining up to 100-fold higher efficiency than currently used protocols. The method presented here provides a robust step towards a complete genetic toolbox for A. castellanii, hence expanding its use as a model organism.

microbiology↗

bioRxiv2022

Rapid, in-patient adaptations of Legionella pneumophila to the human host

Legionella pneumophila are host-adapted bacteria that infect and reproduce primarily in amoeboid protists. Using similar infection mechanisms, they infect human macrophages, and cause Legionnaires disease, an atypical pneumonia, and the milder Pontiac fever. We hypothesized that, despite these similarities, the hosts are different enough so that there exist high-selective value mutations that would dramatically increase the fitness of Legionella inside the human host. By comparing a large number of isolates from independent infections, we identified two genes, mutated in three unrelated patients, despite the short duration of the incubation period (2-14 days). One is a gene coding for an outer membrane protein (OMP) belonging to the OmpP1/FadL family. The clinical strain, carrying the mutated OMP homolog, grows faster in macrophages than the wild type strain, and thus appears to be better adapted to the human host. The other is a gene coding for a protein involved in cyclic-di-GMP regulation, which in turn modulates flagellar activity. As human-to-human transmission is very rare, fixation of these mutations into the population and spread into the environment is unlikely. Therefore, convergent evolution - here mutations in the same genes observed in independent human infections - could point to adaptations to the accidental human host. These results suggest that despite its ability to infect, replicate, and disperse from amoebae, L. pneumophila is not well adapted to the human host. Impact statementLegionella pneumophila is primarily infecting amoeboid protists, but occasionally infects human lung macrophages, causing Legionnaires disease, an atypical pneumonia. By comparing 171 isolates from patients to their probable environmental source, we identified 119 mutations that presumably occurred in-patient. Among these, several mutations occurred in the gene. In particular, two genes were mutated thrice, significantly more often than expected by chance alone, and are likely to represent adaptations to the human host. We experimentally show that, for one mutation at least, the mutated strain grows faster in human macrophages than in amoebae. By specifically investigating in-patient mutations, we were able to identify two genes that might be involved in human host-specific adaptations of L. pneumophila. This result suggests that L. pneumophila is not particularly well adapted to the human host, as mutations get fixed in-patient, during the short course of an infection (2-14 days), indicating a very high selective value. Data SummaryThe sequencing data generated in this study are available in the NCBI database under the BioProject accession number: PRJEB52976.

microbiology↗

bioRxiv2022

The origin and evolution of mitochondrial tropism in Midichloria bacteria

Midichloria are intracellular bacterial symbionts of ticks. Some representatives of this genus have the unique capability to colonize mitochondria in the cells of their hosts. Hypotheses on the nature of this interaction have proven difficult to test, partly due to a lack of data. Indeed, until now, mitochondrial tropism information and genomes were available only for symbionts of three and two tick host species, respectively. Here we analyzed the mitochondrial tropism of three additional Midichloria and sequenced nine novel genomes, showing that the tropism is pnon-monophyletic, either due to losses of the trait or multiple parallel acquisitions. Comparative genome analyses support the first hypothesis, as the genomes of non-mitochondrial symbionts appear to be reduced subsets of those capable of colonizing the organelles. We detect genomic signatures of mitochondrial tropism, showing a set of candidate genes characteristic of the strains capable of mitochondrial colonization. These include the type IV secretion system and the flagellum, which could allow the secretion of unique effectors, direct interaction with, or invasion of the mitochondria. Other genes, including putative adhesion molecules, proteins possibly involved in actin polymerization, cell wall and outer membrane proteins, are only present in mitochondrial symbionts. The bacteria could use these to manipulate host structures, including mitochondrial membranes, in order to fuse with the organelles or manipulate the mitochondrial network.

evolutionary biology↗

bioRxiv2019

Host-adaptation in Legionellales is 2.4 Gya, coincident with eukaryogenesis

Bacteria adapting to living in a host cell caused the most salient events in the evolution of eukaryotes, namely the seminal fusion with an archaeon 1, and the emergence of both the mitochondrion and the chloroplast 2. A bacterial clade that may hold the key to understanding these events is the deep-branching gammaproteobacterial order Legionellales - containing among others Coxiella and Legionella - of which all known members grow inside eukaryotic cells 3. Here, by analyzing 35 novel Legionellales genomes mainly acquired through metagenomics, we show that this group is much more diverse than previously thought, and that key host-adaptation events took place very early in its evolution. Crucial virulence factors like the Type IVB secretion (Dot/Icm) system and two shared effector proteins were gained in the last Legionellales common ancestor (LLCA), while many metabolic gene families were lost in LLCA and its immediate descendants. We estimate that LLCA lived circa 2.4 Ga ago, predating the last eukaryotic common ancestor (LECA) by at least 0.5 Ga 4. These elements strongly indicate that host-adaptation arose only once in Legionellales, and that these bacteria were using advanced molecular machinery to exploit and manipulate host cells very early in eukaryogenesis.

evolutionary biology↗

bioRxiv2018

Sensitivity to Affective Touch Depends on Adult Attachment Style

Affective touch supports affiliative bonds and social cognition. However, it remains unknown whether pre-existing models of social relating influence the perception of affective touch. Here, we present the first study (N=44) to examine how individual differences in attachment styles relate to the perception of affective touch, as well as to a different non-social modality of interoception, namely cardiac perceived accuracy. Using the gold standard assessment of adult attachment (Adult Attachment Interview), we found that insecure attachment was associated with reduced pleasantness discrimination between affective vs. non-affective, neutral touch. Acknowledging the different traditions in measuring attachment, we also used a well-validated self-report questionnaire that pertains to explicit representations of current close relationships. Using this measure, we found that higher scores on an attachment anxiety dimension (but not an attachment avoidance) were associated with reduced pleasantness discrimination between affective vs. non-affective, neutral touch. Attachment patterns (in both measures) were not related to cardiac perception accuracy. These results corroborate and extend previous literature on the affectivity of touch and its relation with affiliative bonds and social cognition. Given that attachment was not related to perceived cardiac accuracy, these findings point to the specificity of the relationship between affective touch and attachment.

neuroscience↗

bioRxiv2017

Paleophenotype Reconstruction Of Carbon Fixation Proteins As A Window Into Historic Biological States

Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physicochemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its [~]3.8 billion years of history on Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behavior of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can identify a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can extant life be used to reconstruct ancestral phenotypes? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the lab to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and to then link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first-step beyond single molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the beta-carbonic anhydrase protein. We assess how carbonic anhydrase proteins meet our selection criteria for reconstructing ancient biosignatures in the lab, which we term paleophenotype reconstruction.

evolutionary biology↗