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At least 55 records · Page 3

Development, optimization, and application of an episomal plasmid system for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre- loxP -mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

CRISPR-Cas9

Data for Development, Optimization, and Application of an Episomal Plasmid System for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre-loxP-mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

Gene Editing

A matheuristic for design and dispatch of a utility-connected distributed energy system

Modeling distributed power generation systems often requires complicated mathematical expressions that present challenges for commercial optimization solvers. Here, this paper presents a matheuristic to solve a mixed-integer optimization model that informs decisions regarding the design and dispatch of a utility-connected microgrid. We deploy a genetic algorithm to search the system design space and a linear program to solve the economic dispatch problem. The model is a component of a web tool that requires solutions within a few minutes. Our method yields objective function values within 5% of an exogenously produced optimal in fewer than 30 seconds for 90% of our test cases compared to only 10% of our test cases by a traditional optimization solver in the same amount of time.

24 POWER TRANSMISSION AND DISTRIBUTION

Recovery of Oxpure 612C-50 Coconut Carbon Particles Using Bump Arrays

Cyanide is used to leach gold from crushed ore (solid matrix) into a gold cyanide solution. The gold is extracted from the cyanide solution by adsorption onto activated carbon. The gold extraction process occurs when the activated coconut carbon is placed into tanks that contain the gold cyanide solution either in a batch process or into a continuous flow circuit. The coconut carbon is then removed from the solution for gold recovery. The use of the mesofluidic separation system (a deterministic lateral displacement system) can significantly reduce costs and waste generated from the process of removing the coconut carbon from the solution. In the coconut carbon recovery process used at many gold mines in Nevada, the gold is attached to carbon particles that are still in the cyanide liquor. The mesofluidic system can rapidly remove the gold bearing carbon particles from the cyanide liquor quickly and with no operating costs. The benefits include: • Reduce operational costs related to filtration and hydro-cyclones • Reduced acid usage for the elution gold stripping phase as only 25% of the fluids will follow the carbon particles to the final express lane when two mesofluidic systems are used in series This alternative particle removal techniques would be advantageous. A promising technique for removing larger particles from slurries is mesofluidic separation, similar to deterministic lateral displacement arrays or “bump” arrays [1] but operates at much larger flow rates. As described by Pease, et al. [2], “Bump arrays in deterministic lateral displacement devices separate large particles from small particles using arrays of staggered posts. Large particles, defined as those with radii larger than the distance between the edge of a post and the stagnation streamline from the next downstream post, must bump toward one side of the device, whereas particles smaller than this distance slalom from entrance to exit without net lateral displacement.” Unlike filters or sieves, the posts in the arrays that cause separation do not block or occlude particle flow but work because particles go around the posts. Unlike hydrocyclones separation, separation is not driven by particle density, because gravitational forces are unimportant to mesofluidic separation. Burns, et al., and Pease, et al., have shown that particles may be separated from complex suspensions, under turbulent flow conditions, and at industrially important flow rates [3-5]. They have also recently shown that mesofluidic devices may be arranged in series to increase separation performance [6]. In this paper, we evaluate the mesofluidic system for the separation of commercial OxPure GR 612 Charred Coconut shell particles as a proof of principle test for the rapid separation using the 1500 micron cut mesofluidic separator. We first describe the experimental system and conditions. We then present the experimental results. [1] Huang, L.R., E.C. Cox, R.H. Austin, J.C. Sturm. 2004. Continuous particle separation through deterministic lateral displacement. Science, 304, 987–990. https://doi.org/10.1126/science.1094567. [2] Pease L.F., J.A. Bamberger, C.A. Burns, and M.J. Minette. 2021. Large Particle Separation from Non-Newtonian Slurries using Bump Arrays. In Proceedings of the ASME 2021 Fluids Engineering Division Summer Meeting FEDSM2021-65904, V003T08A023. New York, New York: ASME. doi:10.1115/FEDSM2021-65904 [3] Burns C.A., T.G. Veldman, J. Serkowski, R.C. Daniel, X.-Y. Yu, M.J. Minette, L.F. Pease. 2021. Mesofluidic separation versus dead-end filtration. Separation and Purification Technology, 254, 117256. https://doi.org/10.1016/j.seppur.2020.117256. [4] Pease L.F., J.E. Serkowski, T.G. Veldman, J. Williams, X.-Y. Yu, M.J. Minette, J.A. Bamberger, C.A. Burns. 2021. Can Bump Arrays Separate Particles from Turbulent Flows?. In Proceedings of the ASME 2021 Fluids Engineering Division Summer Meeting FEDSM2021-67696, V003T08A024. New York, New York: ASME. doi:10.11

mesofluidic separation, slurry, bump array

Profiling expression strategies for a type III polyketide synthase in a lysate-based, cell-free system

Abstract Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli . Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli often results in a myriad of unpredictable issues with regard to protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as a valuable expression platform as a testbed for rapid prototyping expression parameters. Here, we use a type III polyketide synthase from Streptomyces griseus , RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We applied a library of constructs with different combinations of promoters and rppA coding sequences to investigate the synergies between promoter and codon usage. Subsequently, we assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. More importantly, the choice of coding sequences and promoters impact protein expression synergistically, which should be considered for future efforts to use CFE for high-yield protein expression. The promoter strategy when applied to RppA was not completely correlated with that observed with GFP, indicating that different promoter strategies should be applied for different proteins. In vivo experiments suggest that there is correlation, but not complete alignment between expressing in cell free and in vivo. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs, which advances CFE as a tool for natural product research.

59 BASIC BIOLOGICAL SCIENCES

A two-and-a-half dimensional symplectic space-charge solver

The nonlinear space-charge effect plays a significant role in high-intensity accelerators and has been extensively studied using multi-particle tracking methods. In this paper, we present a novel 2.5- dimensional symplectic space-charge solver specifically designed for long beam bunches. We begin by detailing its application to a transverse Gaussian density distribution under open boundary conditions in a straight system, where a semi-analytical expression is derived. We then demonstrate the solver’s adaptation to arbitrary distributions in open space, as well as within rectangular and round conducting pipes. Finally, we discuss the extension of this solver to circular accelerator systems. This study shows that the fast 2.5-dimensional solver can be a good approximation to the fully three-dimensional solver for long bunches in large circular accelerators.

Beam code development & simulation techniques

A Corrected Score Function Framework for Modelling Circadian Gene Expression

Many biological processes display oscillatory behaviour based on an approximately 24 h internal timing system specific to each individual. One process of particular interest is gene expression, for which several circadian transcriptomic studies have identified associations between gene expression during a 24 h period and an individual's health. A challenge with analysing data from these studies is that each individual's internal timing system is offset relative to the 24 h day-night cycle, where day–night cycle time is recorded for each collected sample. Laboratory procedures can accurately determine each individual's offset and determine the internal time of sample collection. However, these laboratory procedures are labour-intensive and expensive. Here, in this paper, we propose a corrected score function framework to obtain a regression model of gene expression given internal time when the offset of each individual is too burdensome to determine. A feature of this framework is that it does not require the probability distribution generating offsets to be symmetric with a mean of zero. Simulation studies validate the use of this corrected score function framework for cosinor regression, which is prevalent in circadian transcriptomic studies. Illustrations with data from three circadian transcriptomic studies further demonstrate that the proposed framework consistently mitigates bias relative to using a score function that does not account for this offset.

59 BASIC BIOLOGICAL SCIENCES

Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP

Abstract Bacterial DNA methylation is involved in diverse cellular functions, including modulation of gene expression, DNA repair, and restriction–modification systems for defense against viruses and other foreign DNA. Restriction systems hinder efforts to engineer organisms to produce fuels and chemicals from waste and renewable feedstocks by degrading DNA during transformation. Methylome analysis allows identification of motifs within a bacterial chromosome that may be targeted by native restriction enzymes. Further expression of the corresponding methyltransferases in Escherichia coli allows plasmid DNA to be protected from restriction in the target organism, thereby drastically enhancing transformation efficiency. Nanopore sequencing can detect methylated bases, but software is needed to transform modified base coordinates into methylated motifs. Here, we develop MIJAMP (MIJAMP Is Just A MethylBED Parser), a software package that was developed to discover methylated motifs from the output of ONT’s Modkit or other data in the methylBED format. MIJAMP employs a human-driven refinement strategy that empirically validates all motifs against genome-wide methylation data, thus eliminating incorrect motifs. MIJAMP also reports methylation data on specific, user-defined motifs. Using MIJAMP, we determined the methylated motifs both in a control strain (wild-type E. coli) and in Synecococcus sp. strain PCC7002, laying the foundation for improved transformation in this organism. MIJAMP is available at https://code.ornl.gov/alexander-public/mijamp/. One Sentence Summary: Here we describe software written to discover DNA methylation motifs from nanopore sequencing data.

59 BASIC BIOLOGICAL SCIENCES

Heat Transport Hysteresis Generated Through Frequency Switching of a Time-Dependent Temperature Gradient

A stochastic energetics framework is applied to examine how periodically shifting the frequency of a time-dependent oscillating temperature gradient affects heat transport in a nanoscale molecular model. We specifically examine the effects that frequency switching, i.e., instantaneously changing the oscillation frequency of the temperature gradient, has on the shape of the heat transport hysteresis curves generated by a particle connected to two thermal baths, each with a temperature that is oscillating in time. Analytical expressions are derived for the energy fluxes in/out of the system and the baths, with excellent agreement observed between the analytical expressions and the results from nonequilibrium molecular dynamics simulations. We find that the shape of the heat transport hysteresis curves can be significantly altered by shifting the frequency between fast and slow oscillation regimes. We also observe the emergence of features in the hysteresis curves such as pinched loops and complex multi-loop patterns due to the frequency shifting. The presented results have implications in the design of thermal neuromorphic devices such as thermal memristors and thermal memcapacitors.

36 MATERIALS SCIENCE

Modeling Cyber Supply Chain Incidents with Multilayered Graph Motifs

As noted within the literature, supply chain includes people and organizations---manufacturers, integrators, and third-party vendors---that are involved in one or more stages of a product lifecycle. Since supply chains, by definition, include organizations and people, supply chain risk management activities must consider dependencies between an organization's business processes and third-party resources. Just as adversarial tactics can be implemented via techniques implemented via networked computer systems, so can such tactics be expressed via legal business relationships. A cyber incident may have an exponential impact downstream, for example, by leveraging a product's distribution channel (e.g. malicious updates in SolarWinds, buggy updates in CrowdStrike). Similarly, legitimate and legal business relationships also affect the attack surface exposure of systems, enabling long-term persistence and/or unknown impacts to product quality that are hard to detect. This paper catalogs several recent digital supply chain incidents and applies a multilayered network formalism to develop structural indicators (graph motifs) that reflect potentially-adversarial behavior. Finally, we compare and contrast the characteristics of adversarial tactics (e.g. Loss of Availability, Data Collection) that leverage cyber-physical dependencies to those that leverage legal organizational relationships.

97 - MATHEMATICS AND COMPUTING

Identifying stochastic dynamics via finite expression methods

Modeling stochastic differential equations (SDEs) is crucial for understanding complex dynamical systems in various scientific fields. Recent methods often employ neural network-based models, which typically represent SDEs through a combination of deterministic and stochastic terms. However, these models usually lack interpretability and have difficulty in generalizing beyond their training domain. Here, this paper introduces the Finite Expression Method (FEX), a symbolic learning approach designed to derive interpretable mathematical representations of the deterministic component of SDEs. For the stochastic component, we integrate FEX with advanced generative modeling techniques to provide a comprehensive representation of SDEs. The numerical experiments on linear, nonlinear, and multidimensional SDEs demonstrate that FEX generalizes well beyond the training domain and delivers more accurate long-term predictions compared to neural network-based methods. The symbolic expressions identified by FEX not only improve prediction accuracy but also offer valuable scientific insights into the underlying dynamics of the systems.

Complex dynamical systems

Generating entangled steady states in multistable open quantum systems via initial state control

Entanglement underpins the power of quantum technologies, yet it is fragile and typically destroyed by dissipation. Paradoxically, the same dissipation, when carefully engineered, can drive a system toward robust entangled steady states. However, this engineering task is nontrivial, as dissipative many-body systems are complex, particularly when they support multiple steady states. Here, we derive analytic expressions that predict how the steady state of a system evolving under a Lindblad equation depends on the initial state, without requiring integration of the dynamics. These results extend Refs. [V. V. Albert and L. Jiang, Phys. Rev. A 89, 022118 (2014); V. V. Albert et al., Phys. Rev. X 6, 041031 (2016)], showing that while the steady-state manifold is determined by the Liouvillian kernel, the weights within it depend on both the Liouvillian and the initial state. We identify a special class of Liouvillians for which the steady state depends only on the initial overlap with the kernel. Our framework provides analytical insight and a computationally efficient tool for predicting steady states in open quantum systems. As an application, we propose schemes to generate metrologically useful entangled steady states in spin ensembles via balanced collective decay.

Dissipative dynamics

Advances in genetic tools for metabolic engineering of non-conventional yeasts

Non-conventional yeasts are emerging as powerful alternatives to Saccharomyces cerevisiae for metabolic engineering, owing to their innate stress tolerance, broad substrate utilization, and distinctive metabolic capabilities. These attributes position them as promising chassis for producing biofuels, pharmaceuticals, and specialty chemicals. This review synthesizes recent advances in genetic toolkits for four such species—Pichia kudriavzevii (Issatchenkia orientalis), Starmerella bombicola, Debaryomyces hansenii, and Pachysolen tannophilus—highlighting progress across plasmid architectures (episomal and integrative), identification of autonomously replicating sequences and centromeric elements, and the development of safe-harbor genomic loci. We summarize promoter and terminator libraries enabling tunable expression, the expansion of auxotrophic and antifungal selection markers with recycling strategies, and the rapid adaptation of CRISPR-based systems (Cas9 and Cas12a) with optimized guide RNA expression, multiplex editing, and approaches that enhance homologous recombination (e.g., KU70/80 disruption). We also review landing-pad platforms for modular, repeated integrations and transposon-based tools (e.g., piggyBac) that facilitate multigene pathway assembly. Collectively, these innovations are accelerating design-build-test-learn cycles and enabling precise, scalable engineering of non-conventional yeasts. Remaining challenges—including limited species-specific episomal systems, variable transformation efficiencies, genome-stability concerns, and alternative codon usage—define clear priorities for future toolkit development. Together, these advances and open needs chart a path toward robust, sustainable biomanufacturing using diverse non-conventional yeast chassis.

59 BASIC BIOLOGICAL SCIENCES

Conditional guide RNA deactivation by mRNA and small molecule triggers in Saccharomyces cerevisiae

CRISPR interference (CRISPRi) technologies have revolutionized bioengineering by providing precise tools for gene expression modulation, enabling targeted gene perturbation and metabolic pathway optimization. Despite these advances, achieving dynamic control over gene expression by CRISPR-based regulation remains a challenge due to its inherently static nature. Utilizing toehold-mediated strand displacement and ligand-responsive ribozymes (aptazymes), this study introduces switchable guide RNAs (gRNAs) that facilitate tunable gene expression mediated by mRNA or small molecule signals. We demonstrate complete silencing of gRNA via strategically designed 5’ or 3’ extensions that impede the gRNA spacer or the dCas9 handle, with subsequent restoration of function through sequestration or cleavage of the obstructive sequence. The resulting toehold-embedded or aptazyme-embedded gRNAs can be deactivated by specific signals, including two full-length translatable mRNAs and two small molecule triggers, thereby lifting CRISPRi repression on targeted genes. This modular approach allows for gRNA-based biocomputing through multi-layer or multi-input genetic logic gates in Saccharomyces cerevisiae . Offering a versatile strategy for post-CRISPR regulation in response to environmental signals or cellular states, this methodology expands the toolkit in eukaryotic systems for reversible control of gene expression.

Aptazyme

Inducible flippase-mediated metabolic engineering of Rhodosporidium toruloides for enhanced 3-hydroxypropionic acid production from corn stover hydrolysate

Rhodosporidium toruloides has gained increasing interests as a promising non-model host organism to produce a wide range of bioproducts from lignocellulosic biomass. Increasing the bioproduct titers, rates, and yields remains a challenge, largely due to a lack of robust and well-characterized genetic tools in this host. Here we developed an inducible flippase (FLP) and flippase recognition target (FRT) system that enables genetic manipulations without the need for additional selection markers. Synthetic inducible promoters were established, enabling regulation of FLP expression and efficient antibiotic marker removal. Leveraging this system, we engineered a strain to optimize 3-hydroxypropionic acid (3HP) production. Over four rounds of iterative genomic editing to resolve pathway bottlenecks, we achieved a 3HP titer of 69.4 g/L in fed-batch fermentation - the highest level reported in yeast from lignocellulosic hydrolysates. The engineered high 3HP producing strain offers a robust platform for sustainable bio-based chemical production from lignocellulosic feedstocks.

3-hydroxypropionic acid

Antitoxin control of optimal transcriptional repression in the atypical HigB–HigA toxin–antitoxin system from Proteus vulgaris

Abstract Bacterial toxin–antitoxin (TA) pairs transcriptionally autoregulate their expression via a repression/derepression mechanism in response to changing environmental conditions. The structural diversity of TA systems influences the mechanisms of transcriptional regulation. Here, we define the molecular mechanism for the plasmid-encoded HigB–HigA TA pair originally identified in a post-operative infection with antibiotic-resistant Proteus vulgaris. We determine DNA binding and promoter activity by the HigB–HigA complex supported by structural biology and molecular dynamics simulations of an elusive DNA operator–TA repressor complex. To define the optimal oligomeric TA repressor–DNA operator complex required for derepression, we engineered a dedicated trimeric HigB–HigA2 complex that represses transcription more than 26-fold as compared to the tetrameric HigB2–HigA2. These results expand the known diversity of how the HigB–HigA TA family is autoregulated.

Biochemistry & Molecular Biology

Temporally-consistent koopman autoencoders for forecasting dynamical systems

Absence of sufficiently high-quality data often poses a key challenge in data-driven modeling of high-dimensional spatio-temporal dynamical systems. Koopman Autoencoders (KAEs) harness the expressivity of deep neural networks (DNNs), the dimension reduction capabilities of autoencoders, and the spectral properties of the Koopman operator to learn a reduced-order feature space with simpler, linear dynamics. However, the effectiveness of KAEs is hindered by limited and noisy training datasets, leading to poor generalizability. To address this, we introduce the Temporally-Consistent Koopman Autoencoder (tcKAE), designed to generate accurate long-term predictions even with limited and noisy training data. This is achieved through a consistency regularization term that enforces prediction coherence across different time steps, thus enhancing the robustness and generalizability of tcKAE over existing models. We provide analytical justification for this approach based on Koopman spectral theory and empirically demonstrate tcKAE’s superior performance over state-of-the-art KAE models across a variety of test cases, including simple pendulum oscillations, kinetic plasma, and fluid flow data.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into theAtabeyarchaeum deiterrae-1chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

Biochemistry & Molecular Biology