Biology subjects

Deravi, L. F.

Publications and source records attributed to Deravi, L. F..

3 recordsLinked to original sources

bioRxiv2026

Cephalopod Genome Expansion Drives Broader Reflectin Domain Boundaries

As more genome libraries become accessible across multiple cephalopod species, long standing assumptions about the molecular basis of their dynamic optical systems are being revisited. For example, cephalopod-specific reflectin proteins now appear far more variable as newly annotated sequences diverge from the canonical features that have long defined this protein family. In this perspective, we discuss these nuances and introduce a theoretical framework that expands the reflectin domain classification while preserving specificity across 141 known and previously uncharacterized reflectin sequences from ten cephalopod species. By combining this broadened domain architecture with quantitative, bioinformatics-driven metrics, we establish a generalizable framework that reliably identifies reflectins across their full sequence diversity, allowing for deeper structural comparisons and future functional discovery.

biochemistry↗

bioRxiv2024

Growth-coupled microbial biosynthesis of the animal pigment xanthommatin

The mining of genomes across life has unearthed a bounty of biosynthetic potential to diverse molecules key to a biobased future. While the heterologous expression of metabolic pathways has achieved broad success, most approaches suffer a similar fate in low initial production levels that require extensive, resource-heavy iterative strain engineering refinement. Herein we introduce a growth-coupled biosynthetic (GrowBio) strategy that irrevocably connects microbial growth with specialized compound production. We demonstrate the plug-and-play versatility of GrowBio in the production of the structurally complex animal biopigment xanthommatin, a color-changing ommochrome with material and cosmetic potential. Xanthommatin biosynthesis directly fuels growth of a newly designed Pseudomonas putida 5,10-methylenetetrahydrofolate auxotroph (PUMA). Aided by genome-scale metabolic modeling, PUMA was designed and built to be controlled by endogenous formate co-produced as a coupled biosynthetic byproduct in the multistep conversion of tryptophan to xanthommatin. Adaptive laboratory evolution was utilized to streamline xanthommatins gram-scale bioproduction via growth rate selection, establishing GrowBio as a promising biotechnological approach for establishing and optimizing the microbial production of value-added molecules.

synthetic biology↗

bioRxiv2023

Microbially Driven Reversible Actuation and Color Changing Materials

A common feature of natural living systems that is underexplored in the field of engineered living materials (ELMs) is macroscale mechanical actuation, as driven by active cellular processes. Here we demonstrate an ELM wherein Escherichia coli drives the reversible swelling and de-swelling actuation of a pH-responsive hydrogel by producing or consuming acidic metabolites. We covalently incorporated a novel synthetic pH indicator dye into the hydrogel network that complements the hydrogel actuation with coordinated color change. Acid production or consumption is controlled by media composition and multiple hydrogel form factors are explored. This approach represents a new form of biologically driven actuation that could be compatible with a range of responsive hydrogel applications.

bioengineering↗