Biology subjects

Camacho, D. J.

Publications and source records attributed to Camacho, D. J..

3 recordsLinked to original sources

bioRxiv2025

A defined growth medium for trace metal limitation studies in Auxenochlorella sp. (UTEX 250-A) during mixotrophic growth with glucose.

Auxenochlorella sp. (strain UTEX 250-A) is a fast-growing, oleaginous alga that is an emerging reference organism for basic research, with broad biotechnological applications. Advancing UTEX 250-A as a biotechnological workhorse requires a deeper understanding of its nutritional demands, particularly under different trophic conditions. However, little is known about the specific acclimations that allow UTEX 250-A to thrive when essential nutrients are scarce. Here, we describe the formulation of a defined growth medium that supports the cultivation of UTEX 250-A with controlled trace levels of the essential micronutrients iron, copper, and zinc. Special attention was given to ensure that the medium was compatible with inductively coupled plasma mass spectrometry (ICP-MS) analysis, enabling the detection and minimization of metal contamination in the nanomolar range. The medium was designed to provide sufficient nutrients to support the mixotrophic growth of UTEX 250-A from an initial density of 105 cells/mL to a stationary density of 2.4x108 cells/mL, with additional nutrients supplied to accommodate metabolic and trophic transitions during stationary phase, when photosynthesis is restored due to carbon limitation. This replete medium provides a foundation for robust nutrient limitation studies in Auxenochlorella sp. (UTEX 250-A).

systems biology↗

bioRxiv2025

Allodiploid hybridization, loss-of-heterozygosity and aneuploidy in the green alga Auxenochlorella, an emerging model for discovery research and bioengineering

Auxenochlorella spp. are diploid oleaginous green algae whose streamlined genomes can be readily manipulated by homologous recombination, making them highly amenable to discovery research and bioengineering. Vegetatively diploid organisms experience specific evolutionary phenomena, including allodiploid hybridization, mitotic recombination, loss-of-heterozygosity and aneuploidy; however, studies of these forces have largely focused on yeasts. Here, we present a telomere-to-telomere phased diploid genome assembly of Auxenochlorella UTEX 250-A (haploid length 22 Mb) and introduce a genetic toolkit for site-specific manipulation of the nuclear genome in multiple strains, featuring several selectable markers, inducible promoters, and fluorescent reporters for protein localization. UTEX 250-A is an allodiploid hybrid of Auxenochlorella protothecoides and Auxenochlorella symbiontica, two species differentiated by extensive chromosomal rearrangements. UTEX 250-A haplotypes are a mosaic of each parental species following mitotic recombination, and two chromosomes are trisomic. Loss-of-heterozygosity events are pervasive across Auxenochlorella and can evolve rapidly in the laboratory. High-quality structural annotation yielded [~]7,500 genes per haplotype. Auxenochlorella have experienced gene family loss and reduction, including core photosynthesis genes, and exhibit periodic adenine and cytosine methylation at promoters and gene bodies, respectively. Approximately 10% of genes, especially those involved in DNA repair and sex, overlap antisense long noncoding RNAs, which may participate in a regulatory mechanism. We demonstrate the utility of Auxenochlorella for fundamental research by knockout of a chlorophyll biosynthesis enzyme, and confirm one trisomy by allele-specific transformation. These results demonstrate the generality of several evolutionary forces associated with vegetative diploidy and provide a foundation for use of Auxenochlorella as a reference organism. One-sentence summaryAuxenochlorella, green algae shaped by evolutionary forces acting on vegetative diploids, are amenable to discovery research and bioengineering via efficient site-specific homologous recombination

plant biology↗

bioRxiv2019

Varied effects of algal symbionts on transcription factor NF-κB in a sea anemone and a coral: possible roles in symbiosis and thermotolerance

Many cnidarians, including the reef-building corals, undergo symbiotic mutualisms with photosynthetic dinoflagellate algae of the family Symbiodiniaceae. These partnerships are sensitive to temperature extremes, which cause symbiont loss and increased coral mortality. Previous studies have implicated host immunity and specifically immunity transcription factor NF-{kappa}B as having a role in the maintenance of the cnidarian-algal symbiosis. Here we have further investigated a possible role for NF-{kappa}B in establishment and loss of symbiosis in various strains of the anemone Exaiptasia (Aiptasia) and in the coral Pocillopora damicornis. Our results show that NF-{kappa}B expression is reduced in Aiptasia larvae and adults that host certain algae strains. Treatment of Aiptasia larvae with a known symbiosis-promoting cytokine, transforming growth factor {beta}, also led to decreased NF-{kappa}B expression. We also show that aposymbiotic Aiptasia (with high NF-{kappa}B expression) have increased survival following infection with the pathogenic bacterium Serratia marcescens as compared to symbiotic Aiptasia (low NF-{kappa}B expression). Furthermore, a P. damicornis coral colony hosting Durusdinium spp. (formerly clade D) symbionts had higher basal NF-{kappa}B expression and decreased heat-induced bleaching as compared to two individuals hosting Cladocopium spp. (formerly clade C) symbionts. Lastly, genome-wide gene expression profiling and genomic promoter analysis identified putative NF-{kappa}B target genes that may be involved in thermal bleaching, symbiont maintenance, and/or immune protection in P. damicornis. Our results provide further support for the hypothesis that modulation of NF-{kappa}B and immunity plays a role in some, but perhaps not all, cnidarian-Symbiodiniaceae partnerships as well as in resistance to pathogens and bleaching.

molecular biology↗