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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Integrating Intermediate Traits in Phylogenetic Genotype-to-Phenotype Studies

A major goal of research in evolution and genetics is linking genotype to phenotype. This work could be direct, such as determining the genetic basis of a phenotype by leveraging genetic variation or divergence in a developmental, physiological, or behavioral trait. The work could also involve studying the evolutionary phenomena (e.g., reproductive isolation, adaptation, sexual dimorphism, behavior) that reveal an indirect link between genotype and a trait of interest. When the phenotype diverges across evolutionarily distinct lineages, this genotype-to-phenotype problem can be addressed using phylogenetic genotype-to-phenotype (PhyloG2P) mapping, which uses genetic signatures and convergent phenotypes on a phylogeny to infer the genetic bases of traits. The PhyloG2P approach has proven powerful in revealing key genetic changes associated with diverse traits, including the mammalian transition to marine environments and transitions between major mechanisms of photosynthesis. However, there are several intermediate traits layered in between genotype and the phenotype of interest, including but not limited to transcriptional profiles, chromatin states, protein abundances, structures, modifications, metabolites, and physiological parameters. Each intermediate trait is interesting and informative in its own right, but synthesis across data types has great promise for providing a deep, integrated, and predictive understanding of how genotypes drive phenotypic differences and convergence. We argue that an expanded PhyloG2P framework (the PhyloG2P matrix) that explicitly considers intermediate traits, and imputes those that are prohibitive to obtain, will allow a better mechanistic understanding of any trait of interest. Furthermore, this approach provides a proxy for functional validation and mechanistic understanding in organisms where laboratory manipulation is impractical.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

National User Resource for Biological Accelerator Mass Spectrometry (Final Report)

The National User Resource for Biological Accelerator Mass Spectrometry (User Resource) will provide isotopic analysis (primarily radiocarbon or 14C) by accelerator mass spectrometry (AMS) for NIH- funded researchers across the United States and will be the only User Resource of its type in the United States. The User Resource will provide measurement capability and expertise to a research community that requires highly sensitive, quantitative isotope analyses. Since commissioning a new accelerator mass spectrometer in June 2014, we have measured over 4000 samples a year for collaborators and service users. The User Resource will enable us to continue to meet these research needs, as well as provide for new users whose research programs would benefit from AMS as a measurement tool. The User Resource’s forte will be ultra-high sensitivity quantitation of radiocarbon and selected other radioisotopes for research studies where isotopes are required. Radioisotope labeling studies have been and will continue to be an important tool for addressing many complex biomedical science problems. AMS is a specialized and unique type of mass spectrometry that provides absolute quantitation of radiocarbon and other relevant radioisotopes with extreme sensitivity, having limits of detection in real samples on the order of a few attomol/mg of sample at measurement precisions of ~3%. It is the only instrumental method capable of quantifying radioisotope-labeled agents routinely in real-world samples with such precision and sensitivity. The sensitivity of AMS allows for the quantification of radiolabeled metabolites in extremely complex matrices of cells and organisms at very low concentrations and in small samples. AMS allows studies to be conducted without perturbing metabolism leading to more relevant quantification of metabolic rates and pathways. In addition, it enables quantification of pharmacokinetic and metabolic properties of toxicants at environmentally relevant concentrations in model systems as well as the ability to quantify pharmacokinetics and other molecular endpoints directly in humans. Such quantitative assessments can 1) improve risk assessment for toxicants, 2) address safety and efficacy considerations for therapeutic entities, 3) deepen understanding of xenobiotic and intermediary metabolism, 4) help understand the interactions between critical molecular pathways, and 5) improve efforts to model and predict various metabolic and biological states. These capabilities have been applied in a number of areas including research in carcinogenesis, toxicology, nutrition, pharmacology/drug development and basic biological science. As a NIGMS National Resource the National User Resource for Biological Accelerator Mass Spectrometry will help NIH funded scientists achieve a deeper understanding of the etiology of human health concerns by (1) enabling the quantification of pharmacokinetics and other molecular endpoints directly in humans; (2) offering the ability to conduct quantitative studies using biologics such as proteins or lipids, and thereby reducing the amount of radioisotope usage in biomedical labs; and (3) enabling more relevant studies of metabolic pathways in health and disease through the use of much lower, more biologically-relevant, concentrations of metabolic substrates in cells and intact organisms. Such studies support NIGMS’s basic biomedical research areas that contribute to the understanding of fundamental cellular and physiological principles and enable research supported by the Biophysics, Biomedical Technology, and Computational Biosciences (BBCB); Genetics and Molecular, Cellular, and Developmental Biology (GMCDB); Pharmacology, Physiology, Biological Chemistry (PPBC) and Training, Workforce Development, and Diversity (TWD) Divisions. Over the next five years, our goals are to: 1. Improve the efficiency of operation for AMS measurements through installation of new interfaces to our AMS systems, technical modifications to improve gas accepting ion source efficiency and upgrading our data analysis software for improved ease of use and data reporting. 2. Increase the accessibility and visibility of ultra-sensitive 14C measurements for the biomedical research community by training of new investigators and expanding our national user base. 3. Provide high throughput, ultra-sensitive 14C analysis for the NIGMS and NIH user community.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Acetaminophen production in the edible, filamentous cyanobacterium Arthrospira platensis

Abstract Spirulina is the common name for the edible, nonheterocystous, filamentous cyanobacteriumArthrospira platensisthat is grown industrially as a food supplement, animal feedstock, and pigment source. Although there are many applications for engineering this organism, until recently no genetic tools or reproducible transformation methods have been published. While recent work showed the production of a diversity of proteins inA. platensis, including single‐domain antibodies for oral delivery, there remains a need for a modular, characterized genetic toolkit. Here, we independently establish a reproducible method for the transformation ofA. platensisand engineer this bacterium to produce acetaminophen as proof‐of‐concept for small molecule production in an edible host. This work opensA. platensisto the wider scientific community for future engineering as a functional food for nutritional enhancement, modification of organoleptic traits, and production of pharmaceuticals for oral delivery.

Biotechnology & Applied Microbiology↗
DOE OSTI2025

Genetic and biochemical characterization of a radical SAM enzyme required for post-translational glutamine methylation of methyl-coenzyme M reductase

ABSTRACT Methyl-coenzyme M reductase (MCR), the key catalyst in the anoxic production and consumption of methane, contains an unusual 2-methylglutamine residue within its active site. In vitro data show that a B12-dependent radical SAM (rSAM) enzyme, designated MgmA, is responsible for this post-translational modification (PTM). Here, we show that two different MgmA homologs are able to methylate MCR in vivo when expressed in Methanosarcina acetivorans , an organism that does not normally possess this PTM. M. acetivorans strains expressing MgmA showed small, but significant, reductions in growth rates and yields on methylotrophic substrates. Structural characterization of the Ni(II) form of Gln-methylated M. acetivorans MCR revealed no significant differences in the protein fold between the modified and unmodified enzyme; however, the purified enzyme contained the heterodisulfide reaction product, as opposed to the free cofactors found in eight prior M. acetivorans MCR structures, suggesting that substrate/product binding is altered in the modified enzyme. Structural characterization of MgmA revealed a fold similar to other B12-dependent rSAMs, with a wide active site cleft capable of binding an McrA peptide in an extended, linear conformation. IMPORTANCE Methane plays a key role in the global carbon cycle and is an important driver of climate change. Because MCR is responsible for nearly all biological methane production and most anoxic methane consumption, it plays a major role in setting the atmospheric levels of this important greenhouse gas. Thus, a detailed understanding of this enzyme is critical for the development of methane mitigation strategies.

Rodriguez Carrero, Roy J. (ORCID:0000000184475641)↗
DOE OSTI2025

Revisiting synthetic lethality of Gcn5-related N-acetyltransferase (GNAT) family mutations in Haloferax volcanii

ABSTRACT Lysine acetylation is a post-translational modification that occurs in all domains of life, highlighting its evolutionary significance. Previous genome comparison identified three Gcn5-related N-acetyltransferase (GNAT) family members as lysine acetyltransferase homologs (Pat1, Pat2, and Elp3) and two deacetylase homologs (Sir2 and HdaI) in the halophilic archaeonHaloferax volcanii, withelp3andpat2proposed as a synthetic lethal gene pair. Here, we advance these findings by performing single and double mutagenesis ofelp3with thepat1andpat2lysine acetyltransferase gene homologs. Genome sequencing and PCR screens of these strains reveal successful generation of Δelp3,Δpat1Δelp3, and Δpat2Δelp3mutant strains. Although these mutant strains exhibited a reduced growth rate compared to the parent, they remained viable. Overall, this study provides genetic evidence thatelp3andpat2, while impacting cell growth, are not a synthetic lethal gene pair as previously reported. IMPORTANCE Here, we reveal by whole-genome sequencing that the GNAT family gene homologselp3andpat2can be deleted in the sameHaloferax volcaniistrain. Beyond the targeted deletions, minimal differences between the parent and Δelp3Δpat2mutant were observed, suggesting that suppressor mutations are not responsible for our ability to generate this double mutant strain. Elp3 and Pat2, thus, may not share as close a functional relationship as implied by earlier study. Our finding is significant as Elp3 is thought to function in acetylation in tRNA modification, while Pat2 likely functions in the lysine acetylation of proteins.

Microbiology↗
DOE OSTI2025

Enhancing chemical bioproduction with rational control of bacterial post-translational modifications

Efficient conversion of inexpensive feedstocks to valuable chemicals by microbes is critical for a robust bioeconomy, but the ability to rationally design bacteria is hampered by insufficient knowledge of how post translational modifications (PTMs) control bacterial protein function and thus bioproduction phenotypes. Our study will focus on the lysine acetylation, a ubiquitous bacterial PTM that can affect the function of enzymes in central metabolism that are often critical for bioproduction processes, disrupt transcriptional regulation, and reduce translation. However, most lysine acetylation data is observational, which means that we do not know when, how, and what specific acetylated residues affect protein function and bacterial physiology. For our model host, we will use a Pseudomonas putida strain that we previously engineered to convert lignocellulosic feedstocks into chemicals such as itaconic acid (ITA). With this strain, we use a dynamic two-stage bioproduction process in which ITA is produced during a non-growth associated production phase. Production is highest during growth stages when lysine acetylation is low in other organisms (early stationary phase) and stalls in conditions where acetylation is highest (late stationary phase). The switch from high to stalled ITA production is also correlated with an unexpected increase in acetate levels – the precursor to non-enzymatic lysine acetylation. As such, we predict that lysine acetylation plays a substantial role in regulating the metabolic pathways required for ITA production. We will develop a generalizable approach that combines high-throughput genetic screens and cutting-edge genome engineering with state-of-the-art proteomics, metabolomics, and genetic code expansion methods to identify and modulate lysine acetylation patterns in bacteria. Ultimately, these strategies aim to manipulate protein expression and acetylation patterns to enhance bioproduction phenotypes (e.g., sustained ITA production in late stationary phase).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Structural features of xylan dictate reactivity and functionalization potential for bio-based materials

Plant-based materials have the potential to replace some petroleum-based products, offering compostability and biodegradability as critical advantages. Xylan-rich biomass sources are gaining recognition due to their abundance and underutilization in current industrial applications. Research of potential xylan applications has been complicated by the complex and heterogeneous structure that varies for different xylan feedstocks. Acylation is a broadly used reaction in functionalization of polysaccharides at an industrial scale. However, the efficiency of this reaction varies with the xylan source. To optimize xylan valorization, a systematic understanding of structure–reactivity relationships is essential. This study explores, characterizes, and compares various xylan feedstocks in the acylation process. Xylan feedstocks were analyzed for their chemical composition, degree of polymerization, branching, solubility, and presence of impurities. These features were correlated with xylan glycotypes’ reactivity toward functionalization with succinic anhydride in an optimized DMSO/KOH condition, achieving carboxyl contents of up to 1.46. We used principal component analysis and hierarchical clustering to identify key structural features of xylan that promote its reactivity. Our findings reveal that xylans with higher xylose content and lower degrees of branching exhibit enhanced reactivity, achieving higher carboxyl content and yields. Structural analyses confirmed successful modification, and light scattering analyses showed dramatic changes in the solution properties. Succinylation improves the solubility and film-forming properties of native xylans. This study shows key structure–reactivity relationships in xylan succinylation, establishing that low branching, high xylose content, and reduced lignin impurity enhance chemical functionalization. The results offer a framework for selecting optimal biomass feedstocks and support future efforts in genetic and synthetic biology to design plants with tunable xylan architectures. These findings advance the hemicellulose valorization for applications in coatings and packaging.

Acylation↗
DOE OSTI2025

Viral delivery of recombinases activates heritable genetic switches in plants

Viral vectors provide an increasingly versatile platform for transformation-free reagent delivery to plants. RNA viral vectors can be used to induce gene silencing, overexpress proteins, or introduce gene editing reagents; however, they are often constrained by carrying capacity or restricted tropism in germline cells. Site-specific recombinases that catalyze precise genetic rearrangements are powerful tools for genome engineering that vary in size and, potentially, efficacy in plants. In this work, we show that viral vectors based on tobacco rattle virus (TRV) deliver and stably express four recombinases ranging in size from ~0.6kb to ~1.5kb and achieve simultaneous marker removal and reporter activation through targeted excision in transgenic Nicotiana benthamiana lines. TRV vectors with Cre, FLP, CinH, and Integrase13 efficiently mediated recombination in infected somatic tissue and led to heritable modifications at high frequency. Here, an excision-activated Ruby reporter enabled simple and high-resolution tracing of infected cell lineages without the need for molecular genotyping. Together, our experiments broaden the scope of viral recombinase delivery and offer insights into infection dynamics that may be useful in developing future viral vectors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multi-scale signaling and tumor evolution in high-grade gliomas

Although genomic anomalies in glioblastoma (GBM) have been well studied for over a decade, its 5-year survival rate remains lower than 5%. We seek to expand the molecular landscape of high-grade glioma, composed of IDH-wildtype GBM and IDH-mutant grade 4 astrocytoma, by integrating proteomic, metabolomic, lipidomic, and post-translational modifications (PTMs) with genomic and transcriptomic measurements to uncover multi-scale regulatory interactions governing tumor development and evolution. Applying 14 proteogenomic and metabolomic platforms to 228 tumors (212 GBM and 16 grade 4 IDH-mutant astrocytoma), including 28 at recurrence, plus 18 normal brain samples and 14 brain metastases as comparators, reveals heterogeneous upstream alterations converging on common downstream events at the proteomic and metabolomic levels and changes in protein-protein interactions and glycosylation site occupancy at recurrence. Recurrent genetic alterations and phosphorylation events on PTPN11 map to important regulatory domains in three dimensions, suggesting a central role for PTPN11 signaling across high-grade gliomas.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Arabidopsis trigalactosyldiacylglycerol1 mutants reveal a critical role for phosphtidylcholine remodeling in lipid homeostasis

Lipid remodeling plays a critical role in plant response to abiotic stress and metabolic perturbations. Key steps in this process involve modifications of phosphatidylcholine (PC) acyl chains mediated by lysophosphatidylcholine: acyl-CoA acyltransferases (LPCATs) and phosphatidylcholine: diacylglycerol cholinephosphotransferase (ROD1). To assess their importance in lipid homeostasis, we took advantage of the trigalactosyldiacylglycerol1 (tgd1) mutant that exhibits marked increases in fatty acid synthesis and fatty acid flux through PC due to a block in inter-organelle lipid trafficking. Here, we showed that the increased fatty acid synthesis in tgd1 is due to posttranslational activation of the plastidic acetyl-coenzyme A carboxylase. Genetic analysis showed that knockout of LPCAT1 and 2 resulted in a lethal phenotype in tgd1. In addition, plants homozygous for lpcat2 and heterozygous for lpcat1 in the tgd1 background showed reduced levels of PC and triacylglycerols (TAG) and alterations in their fatty acid profiles. We further showed that disruption of ROD1 in tgd1 resulted in changes in fatty acid composition of PC and TAG, decreased leaf TAG content and reduced seedling growth. Combined, our results reveal a critical role of LPCATs and ROD1 in maintaining cellular lipid homeostasis under conditions, in which fatty acid production largely exceeds the cellular demand for membrane lipid synthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Computationally evaluating high-yield metabolites for sustainable aviation fuel (SAF) using machine learning

The computational tool described in this report helps identify promising biological pathways that produce SAF platform molecules (either a drop-in SAF, or a precursor that can be easily converted to a drop-in SAF). The workflow the computational tool follows first identifies possible biological pathways from a user-defined metabolite. These pathways may, or may not lead to a SAF platform molecule, thus the second step involves insilico testing of the end product of each pathway to assess whether it is, or is not, a SAF platform molecule. The identification of biological pathways performed in the first step is facilitated by linking the metabolite to a biological reaction database. Pathways are found by identifying pathways in the reaction database that include the metabolite. The computational tool includes an alternative way to find pathways. The alternative way develops a Flux Balanced Analysis (FBA), and modifying the FBA to include reactions that transform the metabolite. These modifications serve as a basis for understanding, in a semi-quantitative way, if there is an increase in the flux to desirable products. The second step, in silico testing of the end-products, is accomplished by estimating key physical properties relevant to SAF. When good models are available, we have integrated those models into the computational tool. In a few instances, we have developed our own models. In all instances, we have validated the models against available measured data. Finally, we have evaluated the effectiveness of our computational tool by genetically engineering Rhodosporidium toruloides. Validation occurred without the use of a FBA, and further validation is required.

09 BIOMASS FUELS↗
DOE OSTI2024

A novel electro-hydraulic unit design based on a shaftless integration of an internal gear machine and a permanent magnet electric machine

In recent years, increasingly stringent emission regulations have spurred an electrification trend in off-highway vehicle technology. To address challenges such as the high cost of power electronics components, limited battery capacity, and the substantial modifications required for the vehicles, there is a pressing need to develop high-speed, cost-effective, compact, and efficient electro-hydraulic units capable of powering vehicle functions. In response to these demands, this paper introduces an innovative morphology for an electro-hydraulic unit and outlines the integration method for a crescent-type internal gear machine with a permanent magnet synchronous electric machine. The proposed morphology aims to minimize component count through a shaftless solution while incorporating a cooling system that utilizes the same working fluid as the hydraulic machine. The design approach utilizes a genetic algorithm optimization process to maximize overall energy efficiency and compactness. Insights gained from the optimization results shed light on the relationship between key design parameters and unit performance, enhancing the understanding of this electro-hydraulic unit. A prototype of the unit was manufactured and tested, demonstrating a volumetric efficiency ranging from 81 % to 97 % at a maximum rotational velocity of the pinion of 6000 rpm. Finally, these results validate both the morphology and the design approach, indicating the feasibility of designing compact electro-hydraulic units that leverage hydraulic machines with higher maximum rotational velocities than commercially available counterparts as a mean to enhance efficiency and compactness.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2024

Phytosulfokine downregulates defense‐related WRKY transcription factors and attenuates pathogen‐associated molecular pattern‐triggered immunity

SUMMARY Phytosulfokine (PSK) is a plant growth‐promoting peptide hormone that is perceived by its cell surface receptors PSKR1 and PSKR2 in Arabidopsis. Plants lacking the PSK receptors show phenotypes consistent with PSK signaling repressing some plant defenses. To gain further insight into the PSK signaling mechanism, comprehensive transcriptional profiling of Arabidopsis treated with PSK was performed, and the effects of PSK treatment on plant defense readouts were monitored. Our study indicates that PSK's major effect is to downregulate defense‐related genes; it has a more modest effect on the induction of growth‐related genes. WRKY transcription factors (TFs) emerged as key regulators of PSK‐responsive genes, sharing commonality with a pathogen‐associated molecular pattern (PAMP) responses, flagellin 22 (flg22), but exhibiting opposite regulatory directions. These PSK‐induced transcriptional changes were accompanied by biochemical and physiological changes that reduced PAMP responses, notably mitogen‐activated protein kinase (MPK) phosphorylation (previously implicated in WRKY activation) and the cell wall modification of callose deposition. Comparison with previous studies using other growth stimuli (the sulfated plant peptide containing sulfated tyrosine [PSY] and Pseudomonas simiae strain WCS417) also reveals WRKY TFs' overrepresentations in these pathways, suggesting a possible shared mechanism involving WRKY TFs for plant growth–defense trade‐off.

Liu, Dian [Biochemistry and Molecular Biophysics T↗
DOE OSTI2024

A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders

Abstract Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modification, and gene expression assays to discover cranial motor neuron (cMN)cis-regulatory elements and subsequently nominate candidate non-coding variants in the congenital cranial dysinnervation disorders (CCDDs), a set of Mendelian disorders altering cMN development. We generate single cell epigenomic profiles for ~86,000 cMNs and related cell types, identifying ~250,000 accessible regulatory elements with cognate gene predictions for ~145,000 putative enhancers. We evaluate enhancer activity for 59 elements using an in vivo transgenic assay and validate 44 (75%), demonstrating that single cell accessibility can be a strong predictor of enhancer activity. Applying our cMN atlas to 899 whole genome sequences from 270 genetically unsolved CCDD pedigrees, we achieve significant reduction in our variant search space and nominate candidate variants predicted to regulate known CCDD disease genesMAFB, PHOX2A, CHN1, andEBF3– as well as candidates in recurrently mutated enhancers through peak- and gene-centric allelic aggregation. This work delivers non-coding variant discoveries of relevance to CCDDs and a generalizable framework for nominating non-coding variants of potentially high functional impact in other Mendelian disorders.

Science & Technology - Other Topics↗
DOE OSTI2025

Gene editing to enhance biotic stress tolerance in sugarcane

Sugarcane (Saccharum spp.) contributes approximately 80% of global sugar production and 40% of biofuel while serving as a promising feedstock for bioproducts (Brant et al., 2025). However, productivity faces mounting challenges from biotic threats including fungal, viral and bacterial diseases (Rott, 2018). Traditional breeding approaches are severely constrained by sugarcane’s complex polyploid genome containing 10–12 copies of "hom(oe)ologous genes within an approximately 10 Gb genome (Healey et al., 2024), extending breeding cycles to 12–15 years. Genome editing has revolutionized crop improvement by enabling targeted modifications without necessarily introducing foreign DNA, potentially circumventing regulatory hurdles while accelerating variety development (Li et al., 2022a). For sugarcane, these technologies offer unprecedented opportunities to enhance biotic stress resilience while improving yield and quality. This article examines current progress and prospects for developing biotic stress-tolerant sugarcane through gene editing, emphasizing technical advances, promising gene targets, and strategic approaches for trait stacking.

CRISPR-Cas systems↗
DOE OSTI2026

Convergent evolution of aerobic fermentation through divergent mechanisms acting on the same key glycolytic genes

Expression profiling by high throughput sequencing The model yeast Saccharomyces cerevisiae has evolved aerobic fermentation in part through a whole genome duplication and subsequent retention of glycolytic genes. To identify independent yeast lineages with a high glycolytic rate phenotype we developed an assay measuring extracellular acidification rates (ECAR) to evaluate the glycolytic rates across diverse yeast species. This assay identified a novel group of yeasts in the genus Saturnispora with rapid glycolytic rates. Through comparative approaches, we found that several glycolytic genes encoding hexokinases and enzymes in lower glycolysis had higher expression and modifications in promoter sequences in rapid ECAR species. Intriguingly, many of the upregulated genes are the same genes that are duplicated in S. cerevisiae. When the transcription factor required for their activation was deleted, the mutants had a slow glycolytic rate and more respiratory phenotype. This work shows how the aerobic fermentation phenotype has convergently evolved in Saturnispora through transcriptional rewiring. This divergent mechanism nevertheless impacts the same glycolytic genes, which suggests that there are evolutionary constraints on how aerobic fermentation can arise.

Horianopoulos, Linda C. [Department of Food Scienc↗
DOE OSTI2025

Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community

ABSTRACT Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein‐coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer‐term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non‐coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency‐inverse document frequency (TF‐IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high‐quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within‐domain and involve non‐coding DNA. A relatively high proportion of the predicted protein‐coding HGTs appear to encode transposase activity, restriction‐modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF‐IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.

Microbiology↗
DOE OSTI2025

Analysis of biofilm assembly by large area automated AFM

Biofilms are complex microbial communities critical in medical, industrial, and environmental contexts. Understanding their assembly, structure, genetic regulation, interspecies interactions, and environmental responses is key to developing effective control and mitigation strategies. While atomic force microscopy (AFM) offers critically important high-resolution insights on structural and functional properties at the cellular and even sub-cellular level, its limited scan range and labor-intensive nature restricts the ability to link these smaller scale features to the functional macroscale organization of the films. We begin to address this limitation by introducing an automated large area AFM approach capable of capturing high-resolution images over millimeter-scale areas, aided by machine learning for seamless image stitching, cell detection, and classification. Large area AFM is shown to provide a very detailed view of spatial heterogeneity and cellular morphology during the early stages of biofilm formation which were previously obscured. Using this approach, we examined the organization of Pantoea sp. YR343 on PFOTS-treated glass surfaces. Our findings reveal a preferred cellular orientation among surface-attached cells, forming a distinctive honeycomb pattern. Detailed mapping of flagella interactions suggests that flagellar coordination plays a role in biofilm assembly beyond initial attachment. Additionally, we use large-area AFM to characterize surface modifications on silicon substrates, observing a significant reduction in bacterial density. This highlights the potential of this method for studying surface modifications to better understand and control bacterial adhesion and biofilm formation.

59 BASIC BIOLOGICAL SCIENCES↗