Fungi Collection & Identification

Over the past 7 years, I have developped a good expertise in collect of Fungi, mainly Basidiomycota, their establishement into microbial cultures and identification by DNA barcoding using appropriate primers. By exploring different biotopes and environements in Minnesota (USA), I created a unique Basidiomycota strain library including more than 50 specimens whose several species with different strains from various locations.

• Collect of living specimens (Basidiomycota, Streptomyces).
• Establishement of microbial cultures.
• Identification (species and strain level) by DNA barcoding from fruiting body, liquid or solid culture.
• Creation of a field-to-laboratory Basidiomycota strain biobank (> 50 strains).

Natural Products Chemistry

My work and interest in natural products discovery have driven me to acquire good skills in isolation and identification of bioactive secondary metabolites from microbial cultures.

• Fermentation from 96-deep well plates format (1.2 mL) to large flasks (2L).
• Preparation of extracts from microbial fermentations.
• Development of methods by analytical HPLC.
• Detection, quantification and monitoring of secondary metabolites.
• Isolation of compounds by liquid - liquid, solid phase extraction, Flash chromatography and (semi-) preparative HPLC.
• Structure elucidation from high-resolution MS (mass spectrometry) and 1D/2D NMR (nuclear magnetic resonance) data.
• Discovery of volatile natural products (terpenes) from fungal fermentations by GC-MS.

Screening | Cell Biology

I started my scientific career as cancer biologist and has gained intensive experience in discovery and characterization of natural products from various origins (plant, hemi-synthetic, marine fungi) as anticancer agents.

• Human cancer cell culture (adherent and suspensions cancer cell lines).
• Development of protocols and bioassays for large screening.
• Optimization and miniaturization of protocols (96 well plates).
• Cytotoxicity assays (manual and commercial kits) for anticancer activity discovery and identification of cell death mechanisms.
• Screening of fungal fermentations for enzymatic activity (lignocellulolytic, laccase, peroxidase activities).
• qPCR.
• Flow cytometry.
• Fluorescent microscopy.
• Western Blotting.

Synthetic Biology

After mining the genome of several speciems from my Basidiomycota fungal strain library for isolation of genes of interest, I have acquired a strong exertise in isolation, cloning and expression of genes of industrial and economic interest in appropriate heterologous hosts.

• DNA/RNA isolation from fungal cultures.
• Polymerase chain reaction (Touchdown PCR, Gradient PCR, Colony PCR, Multiplex PCR, 2-step PCR).
• Isolation of genes of interest from unsequenced and unique Fungi.
• Sequence design, DNA assembly and plasmid creation.
• Molecular cloning (restriction enzyme-free) of large and/or multiple fragments and Gibson assembly.
• Development, optimization and simplification of complex protocols and SOPs.
• Yeast homologous recombination.
• Consitutive or inducible expression of intracellular or secreted proteins and biocatalysts.
• Expression in appropriate model and non-model organisms Escherichia coli, Pseudomonas putida, Deinococcus radiodurans, Bacillus subtilis strains and yeast Pichia pastoris.
• Strain engineering - metabolic pathway engineering.

Bioinformatics

The different research projects in molecular biology and biochemistry I have been working on lead me develop strong bioinformatics and computational biology skills covering different aspect, such as:

• Blast and sequence alignment.
• Phylogenetic analyzis.
• Genome mining, identification and description of biosynthetic gene clusters.
• Gene prediction for Basidiomycota phyllum.
• Python 3 programming and BioPython library.
• Protein structure modeling and prediction (Pymol, SWISS-MODEL, AlphaFold).
• Experience with various software (Aliview, CLC Genomics Workbench, Jalview, MEGA, SnapGene, UGENE).
• Experience on Linux (Ubuntu).

Coding | Programming

I recently decided to learn and develop coding and programming skills for R, Python 3, HTML 5 and CSS 3 languages. Using online ressources, my objective was to develop new skills that would help to automate reccuring tasks, solve complex profesional challenges, manage and visualize large sets of data and generate high-quality figures.

R programming language (R Studio)

• Data management and analyzis of large datasets.
• Data visualization (plots, gene clusters,...).
• Design of high-quality figures for publications and presentation.

Python 3 programming language

• Creation and development of Python 3 scripts and programs for extraction of large data sets from files or from online resources and websites, management and analysis of large data sets.
• Development of smart scripts and novel algorithms to solve challenging and complex problems and automate time-consuming worklows and multi-steps tasks for biotechnology research projects.

Python 3 scripts and programms I completed and on which I am currently working on have been deposited on my personal GitHub profile page.

HTML5 - CSS3

• Design of this responsive website from scratch using HTML5 and CSS3 languages.