Fungi Collection & Identification

Over the past eight years, I have developed expertise in the collection of fungi, mainly Basidiomycota, their establishment into microbial cultures, and identification by DNA barcoding using appropriate primers. By exploring different biotopes and environments in Minnesota (USA), I created a unique Basidiomycota strain library with more than 50 specimens, including several species with different strains from various locations.

• Collection of living specimens (Basidiomycota and Streptomyces).
• Establishment of microbial cultures.
• Identification of species and strains by DNA barcoding from fruiting bodies, liquid, or solid cultures.
• Creation of a field-to-laboratory Basidiomycota strain biobank (over 50 strains).

Natural Products Chemistry

My work and interest in natural product discovery have driven me to develop strong skills in the isolation and identification of bioactive secondary metabolites from microbial cultures.

• Fermentation in formats ranging from 96-deep well plates (1.2 mL) to large flasks (2 L).
• Preparation of extracts from microbial fermentations.
• Development of analytical methods using HPLC.
• Detection, quantification, and monitoring of secondary metabolites (HPLC, LC-MS).
• Isolation of compounds through liquid-liquid extraction, solid-phase extraction, flash chromatography, and (semi-) preparative HPLC.
• Structure elucidation using high-resolution mass spectrometry (HR-MS) and 1D/2D NMR spectroscopy (¹H, ¹³C, COSY, HSQC, HMBC).
• Discovery and identification of volatile natural products (terpenes) from fungal fermentations using GC-MS.

Screening | Cell Biology

I began my scientific career as a cancer biologist and have since gained extensive experience in the discovery and characterization of natural products from various origins (plants, semi-synthetic sources, and marine fungi) with applications as anticancer or antimicrobial agents.

• Human cancer cell culture (adherent and suspension cell lines).
• Development of protocols and bioassays for large-scale screening.
• Optimization and miniaturization of protocols (96-well plates).
• Cytotoxicity assays (manual methods and commercial kits) for anticancer activity discovery and identification of cell death mechanisms.
• Screening of fungal fermentations for enzymatic activity (e.g., lignocellulolytic, laccase, and peroxidase activities).
• Quantitative real-time PCR (qRT-PCR).
• Flow cytometry.
• Fluorescence microscopy.
• SDS-PAGE and Western blotting.

Synthetic Biology

After mining the genomes of several specimens from my Basidiomycota fungal strain library to isolate genes of interest, I have developed strong expertise in the isolation, cloning, and expression of genes with industrial and economic significance 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 using Gibson assembly.
• Development, optimization, and simplification of complex protocols and SOPs.
• Yeast homologous recombination.
• Constitutive or inducible expression of intracellular or secreted proteins and biocatalysts.
• Expression in appropriate model and non-model organisms, including Escherichia coli, Pseudomonas putida, Deinococcus radiodurans, Bacillus subtilis, and the yeast Pichia pastoris.
• Strain engineering and metabolic pathway engineering.

Bioinformatics

The various research projects in molecular biology and biochemistry I have worked on have led me to develop strong bioinformatics and computational biology skills, covering different aspects, such as:

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

Coding | Programming

I recently decided to learn and develop coding and programming skills in R, Python 3, HTML5, and CSS3. Using online resources, my objective was to develop new skills that would help automate recurring tasks, solve complex professional challenges, manage and visualize large datasets, and generate high-quality figures.

R Programming Language (R Studio)

• Data management and analysis of large datasets.
• Data visualization (plots, gene clusters, etc.) and design of high-quality figures for publications and presentations.

Python 3 Programming Language

• Creation and development of smart Python 3 scripts and programs to solve challenging and complex problems, automate time-consuming workflows, and manage and analyze large datasets for biotechnology research projects (e.g., extraction of large datasets from files or online resources and websites).

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

HTML5 - CSS3 - Bootstrap 5

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