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At least 55 records · Page 3

Evaluation of DNA Extraction Efficiency in Diverse Algae Strains Using Commercial Kits and Lysis Approaches

Efficient DNA extraction is essential for accurately monitoring microalgae communities in large-scale cultivation systems such as raceway ponds and wastewater ponds. Traditional phenol chloroform extracts are a staple in microbiology but are obsolete for routine sampling due to its high toxicity reagents and time intensive setups. Commercial DNA extraction kits are more favorable for the microbes found in these ponds, but lack specific kits made for these communities. Little is known about which kits perform the best, leading researchers to use a variety of different kits with inconsistent results. This project compared one precipitation based commercial kit (Lucigen Masterpure) and five wash based kits (Monarch, Zymo Quick-DNA, and three Qiagen DNeasy kits) using four brackish algae strains to determine which methods yield the greatest quantity and quality of genomic DNA. Extractions were evaluated using the manufacturers protocol, and additional pretreatment options were administered before a single kit to compare its potential in being added routinely before extractions. Pretreatment options included both cryogenic freeze-thawing and heat incubation using enzymes. DNA was quantified using Qubit fluorometry and NanoDrop purity ratios. Overall, the Qiagen PowerWater kit provided the highest DNA yield and purity, but at a significantly higher cost then the precipitation-based kit (MasterPure). It was also noted that while the precipitation-based kit was significantly cheaper, provided similar results, it took significantly more time to complete a single run. Cryogenic pretreatment (6x cycles) increased average DNA yields by up to 80%, whereas enzymatic pretreatment most improved purity ratios without substantially improving quantity. The results suggest that it may be more cost and time efficient to use Qiagen kits with the addition of lysis pretreatments to procure better results. Future works includes developing a better system to efficiently collect multi variable data, and to upscale to artificial polycultures using similar methodologies alongside sequencing to confirm kit results.

59 BASIC BIOLOGICAL SCIENCES

Solar Spectrum Conversion for an Algae Bioreactor (CRADA Final Report)

This project focused on developing advanced optical coatings to improve solar energy utilization. The research aimed to create lanthanide-doped upconversion nanoparticles (UCNPs) capable of capturing unused near-infrared (NIR) light from the sun and converting it into visible light (blue and red photons) that can be used for photosynthesis. The primary goal was to identify, synthesize, and integrate highly efficient UCNPs into a transparent thin-film device. Through a comprehensive workflow involving computer simulations, high-throughput robotic synthesis, and detailed optical characterization, the project successfully developed a high-performance material. The key technical achievement was the creation of a core-shell UCNP (NaYF₄:20%Yb³⁺, 2%Er³⁺ coated with a 10 nm NaYF₄ shell) that demonstrated a quantum yield of 3.2% for converting 980 nm NIR light into visible light. Transparent thin films fabricated from these nanoparticles showed excellent optical properties, confirming their potential for practical applications. This research adds to the scientific understanding of energy transfer in lanthanide materials and demonstrates a technically effective method for creating efficient light-converting coatings. The primary benefit to the public lies in the potential for these coatings to enhance the efficiency of solar-driven processes, such as boosting the growth of algae in photobioreactors for biofuel production.

14 SOLAR ENERGY

An Experimental and Computational Approach to Investigating CO 2 Uptake of Cellulose-producing Algae from Cellulosic Ethanol Production (Final Report)

This project combined experimental algal cultures with predictive quantum calculations to evaluate system-level CO 2 uptake and conversion efficiency of cellulose-producing Nannochloropsis sp. algae. Recently, Nannochloropsis sp. has garnered attention as a novel host organism for converting low-cost CO 2 produced from cellulosic ethanol fermentations into algal lipids for biodiesel production and microcrystalline cellulose as a high-value co-product. As depicted in the figure below, this project (1) optimized Nannochloropsis salina (N. salina) cultures on effluent gas produced directly from cellulosic ethanol fermentation, (2) characterized the fermentation products, quantify cellulose production, and calculate CO 2 uptake efficiency with predictive quantum calculations, (3) conducted a life cycle and techno economic analysis of the proposed integration, and (4) provided training opportunities to students attending UC Riverside.

09 BIOMASS FUELS

Algae Hydrothermal Liquefaction: End-of-Project Report

This document is a close-out report for two Pacific Northwest National Laboratory (PNNL) projects funded by the Alternative Fuels and Feedstocks Office (formerly the Bioenergy Technologies Office) of the Department of Energy (DOE). The two projects are: • Thermochemical Interface (DOE ref. no. 1.3.4.101, PNNL ref. no. 64490) • HTL Model Development (DOE ref. no. 1.3.5.202, PNNL ref. no. 71612) At the end of fiscal year 2025, both projects ended. Additional activities related to the topics of algae, hydrothermal liquefaction (HTL), and the techno-economic assessment of HTL of algal feedstocks will be studied in other projects. Key technical findings of the projects were published in early 2025 and highlights will be summarized in this document. A summary of recent technical findings from 2025 are also included herein. This close-out report summarizes key outcomes from both projects highlighting the value and technical impact achieved.

09 BIOMASS FUELS

Engineering-Scale Validation of Novel Algae CO 2 Capture and Bioproducts Technology

The purpose of this project was to advance and scale the algae-based technology Helios-NRG has been developing for capture of CO 2 from the flue gas of coal-burning power plants with conversion of the CO 2 to high-value products. In order to encourage the process becoming commercial and be adoptable, it is essential that the cost of CO 2 be close to net zero or slightly revenue positive. Two methods to achieve this are reducing the cost of operations through efficiencies and selling of products derived from conversion. Helios and the project team partners have accomplished the goals of furthering the technology to be more scalable and substantially lower cost with a defined pathway for commercialization.

01 COAL, LIGNITE, AND PEAT

Iron-starvation induces photosystem I antenna remodeling in green algae

Dunaliella salina and Dunaliella tertiolecta are extremophile, marine algae that can survive in very low Fe conditions. In this study, we used TMT-proteomics to compare the Fe starvation responses to the Fe replete responses. Samples were digested with trypsin, labeled with TMT 10-Plex, then analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.

59 BASIC BIOLOGICAL SCIENCES

Algae, Wastewater Treatment and SAF

Microalgal biomass production has been proposed for many years for the low-cost production of foods, feeds, fuels and other bio-products, and to treat wastewaters, while reducing greenhouse gas emissions, with raceway ponds the most economical technology for cultivating microalgae.

09 BIOMASS FUELS

Algae, Wastewater Treatment and SAF

Microalgal biomass production has been proposed for many years for the low-cost production of foods, feeds, fuels and other bio-products, and to treat wastewaters, while reducing greenhouse gas emissions, with raceway ponds the most economical technology for cultivating microalgae.

09 BIOMASS FUELS

Algae, Wastewater Treatment and SAF

Microalgal biomass production has been proposed for many years for the low-cost production of foods, feeds, fuels and other bio-products, and to treat wastewaters, while reducing greenhouse gas emissions, with raceway ponds the most economical technology for cultivating microalgae.

09 BIOMASS FUELS

Domesticating the green alga Scenedesmus obliquus

Microalgae cultivation processes exist only for a few species used in commercial applications. Their domestication is still in its infancy, with major advances required, specifically to overcome limiting factors in microalgae production. The goal is to develop superior strains without the need of genetic technologies that would require lengthy regulatory permits, and often limit consumer acceptance. Adaptive Laboratory Evolution techniques, alone or in conjunction with sexual recombination, can allow for rapid develop of improved strains and their industrial production. Approaches include increased photon utilization efficiency by cultures operating under full sunlight conditions due to higher light saturation levels, allowing for higher productivities under outdoor conditions. Decades of research yielded some promising results under controlled conditions with a few specific mutant strains. However, these failed to achieve the anticipated higher productivities in actual algal mass cultures, in part due to the inability of mutations to overcome photoinhibition, reactive oxygen species, and other pleiotropic impacts on photosynthesis.

09 BIOMASS FUELS

Description of a novel extremophile green algae, Chlamydomonas pacifica , and its potential as a biotechnology host

We present the comprehensive characterization of a newly identified microalga, Chlamydomonas pacifica , originally isolated from a soil sample in San Diego, CA, USA. This species showcases remarkable biological versatility, including a broad pH range tolerance (6–11.5), high thermal tolerance (up to 42 °C), and salinity resilience (up to 2 % NaCl). Its amenability to genetic manipulation and sexual reproduction via mating, particularly between the two opposing strains CC-5697 & CC-5699, now publicly available through the Chlamydomonas Resource Center, underscores its potential as a biotechnological chassis. The biological assessment of C. pacifica revealed versatile metabolic capabilities, including diverse nitrogen assimilation capability, motility and phototaxis. Genomic and transcriptomic analyses identified 17,829 genes within a 121 Mb genome, featuring a GC content of 61 %. The codon usage of C. pacifica closely mirrors that of C. reinhardtii , indicating a conserved genetic architecture that supports a trend in codon preference with minor variations. Phylogenetic analyses position C. pacifica within the core-Reinhardtinia clade yet distinct from known Volvocales species. The lipidomic data revealed an abundance of triacylglycerols (TAGs), promising for biofuel applications and lipids for health-related benefits. Our investigation lays the groundwork for exploiting C. pacifica in biotechnological applications, from biofuel generation to synthesizing biodegradable plastics, positioning it as a versatile host for future bioengineering endeavors.

Alkali tolerant

Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae

Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous giant virus/virophage insertions. Together, these findings highlight Phaeocystales as an ecologically versatile and geographically widespread lineage shaped by evolutionary innovation and adaptation to contrasting environmental stressors.

Füssy, Zoltán

SISGR: The regulation of carbon fixation in plant and green algae: Rubisco activase and the origin of heat inactivation of CO 2 assimilation

Rubisco activase (Rca) is a critical AAA+ ATPase protein complex that remodels and promotes the Rubisco enzyme, a key player in photosynthetic performance and carbon fixation. The assembly and function of the Rca protein complex are regulated by a range of factors, including subunit concentration, nucleotide-binding states, thermal conditions, metal-ion coordination, and post-translational modifications, such as phosphorylation. Despite its importance in photosynthesis, the detailed molecular mechanisms underlying the regulation of plant Rca and how it activates Rubisco remain elusive. This project aims to bridge this knowledge gap by integrating sophisticated enzymology tools with single-molecule methods and high-resolution electron microscopy to elucidate the structure and function of plant Rca. Through these multiple approaches, we have systematically investigated how the activity of plant Rca is impacted by various factors, such as phosphorylation and metal-ion coordination. The Rca complex assembly/disassembly dynamics were captured using anti-Brownian electrokinetic (ABEL) trap-based measurements, providing unprecedented insight into its structural flexibility and diverse assembly states. Furthermore, the structural analysis of Rca through electron crystallography and single-particle cryogenic electron microscopy (cryo-EM) reveals novel assembly states of the spinach Rca, providing insight into the mechanistic action for Rubisco remodeling. By combining cutting-edge tools and approaches, this work uncovers critical aspects of Rca’s regulation and assembly, paving the way for a deeper understanding of its role in photosynthetic efficiency and the potential for enhancing carbon fixation in crops.

59 BASIC BIOLOGICAL SCIENCES