Biology subjects

Kempf, I.

Publications and source records attributed to Kempf, I..

7 recordsLinked to original sources

bioRxiv2025

Microscopic PhotoSelection (MiPS) of single cells in mother machine microfluidic devices

Techniques for selecting or sorting single cells within large populations of genetic variants are central to synthetic biology and biotechnology. Widely-used methods such as Fluorescence Activated Cell Sorting (FACS) enable rapid processing of large libraries, but are restricted to low-dimensional measurements taken at a single time point. As a result, sorting based on dynamic or multi-trait phenotypes--such as transient properties and properties that occur on fast timescales or in response to dynamic actuating signals--remains fundamentally challenging. Here we introduce Microscopic PhotoSelection (MiPS) which employs an automated robotic platform for single-cell selection based on multiple dynamic criteria, directly on microfluidic mother machine devices. The system couples long-term single-cell imaging with real-time analysis and selective optical targeting, allowing fully automated enrichment using high-intensity UV light or alternative wavelengths with the addition of photosensitisers. By targeting many cells in parallel, our platform overcomes throughput limitations of existing microfluidic-based selection technologies such as optical tweezers or droplet-based methods and provides a direct approach to select cells based on time-resolved, multi-trait phenotypes. We demonstrate the ability to perform in vivo selection and outline how iterative, feedback-based selection strategies can refine enrichment across multiple rounds. Taken together, our work establishes a high-throughput selection framework integrated into microfluidic devices, enabling applications in directed evolution, biosensor optimisation, circuit engineering, and diagnostics, where selection based on dynamic, multi-trait phenotypes is essential.

bioengineering↗

bioRxiv2025

Sequence-free landscape inference for directed evolution

Directed evolution is a method for engineering biological systems or components, such as proteins, wherein desired traits are optimised through iterative rounds of mutagenesis and selection of fit variants. The process of protein directed evolution can be envisaged as navigation over high-dimensional landscapes with numerous local maxima. The performance of any strategy in navigating such a landscape is dependent on the ruggedness of that landscape. However, this information is generally unavailable at the outset of an experiment, and cannot currently be computed using analytical methods. Here we propose SLIDE, Sequence-free Landscape Inference for Directed Evolution, which consists of two parts. First, SLIDE provides an estimation for landscape ruggedness from a mutating population using only population-level phenotypic data and an estimation of mutation rate. Ruggedness information in itself is valuable in protein design, for instance in predicting evolutionary stability. Second, SLIDE offers a framework for using the estimated ruggedness metric to select high-performing parameters for directed evolution control. Using theoretical NK landscapes and four real-world protein fitness landscapes, we demonstrate improvement upon the performance of standard selection strategies, particularly on rugged landscapes, using a pipeline that could also be combined with emerging AI-based methods for driving direction evolution.

synthetic biology↗

bioRxiv2024

Quantum Correlations in Engineered Magneto-Sensitive Fluorescent Proteins Enables Multi-Modal Sensing in Living Cells

Quantum mechanical phenomena have been identified as fundamentally significant to an increasing number of biological processes. Simultaneously, quantum sensing is emerging as a cutting-edge technology for diverse applications across materials and biological science. However, until recently, biological based candidates for quantum sensors have been limited to in vitro systems, were prone to light induced degradation, and the experimental setups involved are typically not amenable to high-throughput study as would enable further engineering e.g. via directed evolution. We recently created a new class of magneto-sensitive fluorescent proteins (MFPs), which we show overcome these challenges and represent a new form of engineered biological quantum sensors that function both at physiological conditions and in living cells. Through directed evolution, we demonstrate the possibility of engineering these proteins to alter properties of their response to magnetic fields and radio frequencies. These effects are explained in terms of the radical pair mechanism (RPM), involving the protein backbone and a bound flavin cofactor. Using this engineered system we demonstrate the first observation of a fluorescent protein exhibiting Optically Detected Magnetic Resonance (ODMR) in living bacterial cells at room temperature, at sufficiently high signal-to-noise to be detected in a single cell. These magnetic resonance and magnetic field effects measured via fluorescence enable novel technologies; examples we demonstrate include spatial localisation of fluorescence signals using gradient fields (i.e. Magnetic Resonance Imaging (MRI) using a genetically encoded probe), sensing of the molecular microenvironment, multiplexing of bio-imaging, and lock-in detection, overcoming typical fluorescence imaging challenges of light scattering and autofluorescence. Taken together, our results represent a new range of sensing modalities for engineered biological systems, based on and designed around understanding the quantum mechanical properties of MFPs.

bioengineering↗

bioRxiv2024

Learning-Based Estimation of Fitness Landscape Ruggedness for Directed Evolution

Directed evolution is a method for engineering biological systems or components, such as proteins, wherein desired traits are optimised through iterative rounds of mutagenesis and selection of fit variants. The process of protein directed evolution can be envisaged as navigation over high-dimensional landscapes with numerous local maxima, mapping every possible variant of a protein to its fitness. The performance of any strategy in navigating such a landscape is dependent on several parameters, including its ruggedness. However, this information is generally unavailable at the outset of an experiment, and cannot be computed using analytical methods. Here we propose a learning-based method for estimating landscape ruggedness from a mutating population, using only population average performance data. This method uses a short period of exploration at the beginning of an experiment to predict the ruggedness, subsequently guiding the choice of high-performing parameters for directed evolution control. We then simulate this approach on two real-world protein fitness landscapes, demonstrating an improvement upon the performance of standard strategies, particularly on rugged landscapes. In addition to improving the overall outcomes of directed evolution, this method has the advantage of being readily deployable in laboratory settings, even in configurations that exclusively capture average population measures. Given the rapidly expanding application space of engineered proteins, the products of improved directed evolution are relevant in medicine, agriculture and manufacturing.

bioengineering↗

bioRxiv2023

Dissemination of IncI plasmid encoding blaCTX-M-1 is not hampered by its fitness cost in the pig's gut.

Multiresistance plasmids belonging to the IncI incompatibility group have become one of the most pervasive plasmid types in extended-spectrum beta-lactamase producing Escherichia coli of animal origin. The extent of the burden imposed on the bacterial cell by these plasmids seems to contribute to the emergence of "epidemic" plasmids. However, in vivo data in the natural environment of the strain are scarce. Here, we investigated the cost of a blaCTX-M-1-IncI1 epidemic plasmid in a commensal E. coli animal strain, UB12-RC, before and after oral inoculation of fifteen 6-to 8-week-old specific pathogen-free pigs. Growth rate in rich medium was determined on (i) UB12-RC and derivatives, with or without plasmid, in vivo and/or in vitro evolved, and (ii) strains that acquired the plasmid in the gut during the experiment. Although blaCTX-M-1-IncI1 plasmid imposed no measurable burden on the recipient strain after conjugation and during the longitudinal carriage in the pigs gut, we observed a significant difference in the bacterial growth rate between IncI1 plasmid-carrying and plasmid-free isolates collected during in vivo carriage. Only a few mutations on the chromosome of the UB12-RC derivatives were detected by whole-genome sequencing. RNA-Seq analysis of a selected set of these strains showed that transcriptional responses to the blaCTX-M-1-IncI1 acquisition were limited, affecting metabolism, stress response, and motility functions. Our data suggest that the effect of IncI plasmid on host cells is limited, fitness cost being insufficient to act as a barrier to IncI plasmid spread among natural population of E. coli in the gut niche.

microbiology↗

bioRxiv2022

Comparative genome analysis of Enterococcus cecorum reveals intercontinental spread of a lineage of clinical poultry isolates.

Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering, mortality, and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last ten years in 16 French broiler farms. Comparative genomics, genome-wide association study, and measured susceptibility to serum, biofilm forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate origin of the isolates or phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster in few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCEEnterococcus cecorum is an important pathogen in poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first dataset on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage probably also circulating elsewhere and which should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum-related diseases.

genomics↗

bioRxiv2022

Antimicrobial resistance of Enterococcus cecorum: ECOFF determination

Enterococcus cecorum, a commensal Gram-positive bacterium of the chicken gut, has emerged as a worldwide cause of lameness in poultry, particularly in fast-growing broilers. It is responsible for osteomyelitis, spondylitis and femoral head necrosis, causing animal suffering, mortality and antimicrobial use. Research on the antimicrobial resistance of E. cecorum clinical isolates in France is scarce, and epidemiological cut-off (ECOFF) values unknown. To determine tentative ECOFF (COWT) values for E. cecorum and to investigate the antimicrobial resistance patterns of isolates from mainly French broilers, we tested the susceptibility of a collection of commensal and clinical isolates (n=208) to 29 antimicrobials by the disc diffusion (DD) method. We also determined the minimum inhibitory concentrations (MICs) of 23 antimicrobials by the broth micro-dilution method. To detect chromosomal mutations conferring antimicrobial resistance, we investigated the genomes of 118 E. cecorum isolates mainly obtained from infectious sites and previously described in the literature. We determined the COWT values for more than 20 antimicrobials and identified two chromosomal mutations explaining fluoroquinolone resistance. The DD method appears better suited for detecting E. cecorum antimicrobial resistance. Although tetracycline and erythromycin resistances were persistent in clinical and non-clinical isolates, we found little or no resistance to medically important antimicrobials.

microbiology↗