Biology subjects

Beckmann, J. F.

Publications and source records attributed to Beckmann, J. F..

5 recordsLinked to original sources

bioRxiv2026

Benchmarking Molecular Methods of Protein Engineering and Surveying Protein Search Space to Bolster Artificial Intelligence-Based Designs

Proteins are complex macromolecules that drive functionality in cells across all life on Earth. Protein engineering and AI-based designs facilitate exploration of the vast search space. Herein, we explore and compare mutagenic methodologies in combination with fast and efficient phenotypic evaluation of a pink fluorophore (Magenta) to map protein search space and inform AI-based designer algorithms. We binned mutated variants as neutral, deleterious, or catastrophic based on the observed phenotype and fitness measurement (relative fluorescent units, RFUs). Importantly, we found that for a given fluorophore, about 80% of random mutations were deleterious for the artificially selected phenotype resulting in decreased fitness, 20% were neutral mutations, and 0.8% enhanced the artificially selected phenotype. Using error prone PCR (epPCR), we were able to identify four candidates in the first round and one candidate in the second round of epPCR for enhanced fluorescence and in toto enhanced RFUs by 35% after two rounds of epPCR. We compared these rates of true positive enhanced RFU generated sequences against a state of the art evolutionary algorithm approach and found that biological computation beats it in its current state. We conclude with suggestions for key improvements to enhance algorithm performance in the future. Taken together, we demonstrated that iterative rounds of variant prediction improved our algorithm, and our study can serve as a reference point for future AI driven modeling studies in red fluorescent protein engineering.

bioinformatics↗

bioRxiv2023

CNC Knitting Micro-Resolution Mosquito Bite Blocking Textiles

Mosquitoes and other biting arthropods transmit diseases worldwide, causing over 700,000 deaths each year, and costing about 3 billion annually for Aedes species alone. These insects also pose a significant threat to agricultural animals. While clothing could provide a simple solution to vector-borne diseases, modern textiles do not effectively block mosquito bites. To address this issue, we have designed three micro-resolution knitted structures, with five adjustable parameters, that can block bites. These designs were integrated into a computer numerical control knitting robot for mass production of bite-blocking garments with minimal human labor. We then quantified the comfort of blocking garments. Our knits enable individuals to protect themselves from insects amidst their day-to-day activities without impacting the environment. One Sentence SummaryWe create micro-resolution mosquito bite blocking knits produced by robotic manufacturing to protect humans against vector-borne disease.

bioengineering↗

bioRxiv2023

Modelling Emergence of Wolbachia Toxin-Antidote Protein Functions with an Evolutionary Algorithm.

Evolutionary algorithms (EAs) simulate Darwinian evolution and adeptly mimic natural evolution. Most EA applications in biology encode high levels of abstraction in top-down ecological population models. In contrast, our research merges protein alignment algorithms from bioinformatics into codon based EAs that simulate molecular protein string evolution from the bottom up. We apply our EA to reconcile a problem in the field of Wolbachia induced cytoplasmic incompatibility (CI). Wolbachia is a microbial endosymbiont that lives inside insect cells. CI is conditional insect sterility that operates as a toxin antidote (TA) system. Although, CI exhibits complex phenotypes not fully explained under a single discrete model. We instantiate in-silico genes that control CI, CI factors (cifs), as strings within the EA chromosome. We monitor the evolution of their enzymatic activity, binding, and cellular localization by applying selective pressure on their primary amino acid strings. Our model helps rationalize why two distinct mechanisms of CI induction might coexist in nature. We find that nuclear localization signals (NLS) and Type IV secretion system signals (T4SS) are of low complexity and evolve fast, whereas binding interactions have intermediate complexity, and enzymatic activity is the most complex. Our model predicts that as ancestral TA systems evolve into eukaryotic CI systems, the placement of NLS or T4SS signals can stochastically vary, imparting effects that might impact CI induction mechanics. Our model highlights how preconditions, genetic diversity, and sequence length can bias evolution of cifs towards one mechanism or another.

bioinformatics↗

bioRxiv2023

Metagenome diversity illuminates origins of pathogen effectors

Recent metagenome assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. Discovery of basal lineages (Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles reveals an evolutionary timepoint for the transition to host dependency, which occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system (T4SS) and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for derived rickettsial pathogens. MAG analysis also substantially increased diversity for genus Rickettsia and delineated a basal lineage (Tisiphia) that stands to inform on the rise of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages indicates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, illuminating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role shaping the rvh effector landscape, as evinced by the discover of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can provide incredible insight on the origins of pathogen effectors and how their architectural modifications become tailored to eukaryotic host cell biology.

microbiology↗

bioRxiv2020

Evolution of Wolbachia Mutualism and Reproductive Parasitism: Insight from Two Novel Strains that Co-infect Cat Fleas

Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, wCfeT and wCfeJ, found co-infecting cat fleas (Ctenocephalides felis) of the Elward Laboratory colony (Soquel, CA). wCfeT is basal to nearly all described Wolbachia supergroups, while wCfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. wCfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, wCfeJ harbors a toxin-antidote operon analogous to the wPip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. wCfeJ cinB and immediate-5 end genes are syntenic to large modular toxins encoded in CI-like operons of certain Wolbachia strains and Rickettsia species, signifying that CI toxins streamline by fission of larger toxins. Remarkably, the C. felis genome itself contains two CI-like antidote genes, divergent from wCfeJ cinA, revealing episodic reproductive parasitism in cat fleas and evidencing mobility of CI loci independent of WO-phage. Additional screening revealed predominant co-infection (wCfeT/wCfeJ) amongst C. felis colonies, though occasionally wCfeJ singly infects fleas in wild populations. Collectively, genomes of wCfeT, wCfeJ, and their cat flea host supply instances of lateral gene transfers that could drive transitions between parasitism and mutualism. ImportanceMany arthropod and certain nematode species are infected with wolbachiae which are intracellular bacteria well known for reproductive parasitism (RP). Like other RP strategies, Wolbachia-induced cytoplasmic incompatibility, CI, increases prevalence and frequency in host populations. Mutualism is another strategy employed by wolbachiae to maintain host infection, with some strains synthesizing and supplementing certain B vitamins (particularly biotin) to invertebrate hosts. Curiously, we discovered two novel Wolbachia strains that co-infect cat fleas (Ctenocephalides felis): wCfeT carries biotin synthesis genes, while wCfeJ carries a CI-inducing toxin-antidote operon. Our analyses of these genes highlight their mobility across the Wolbachia phylogeny and source to other intracellular bacteria. Remarkably, the C. felis genome also carries two CI-like antidote genes divergent from the wCfeJ antidote gene, indicating episodic RP in cat fleas. Collectively, wCfeT and wCfeJ inform on the rampant dissemination of diverse factors that mediate Wolbachia strategies for persisting in invertebrate host populations.

genomics↗