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DOE OSTI2023

Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries

Type I modular polyketide synthases (PKSs) are multi-domain enzymes functioning like assembly lines. Many engineering attempts have been made for the last three decades to replace, delete and insert new functional domains into PKSs to produce novel molecules. However, inserting heterologous domains often destabilize PKSs, causing loss of activity and protein misfolding. To address this challenge, here we develop a fluorescence-based solubility biosensor that can quickly identify engineered PKSs variants with minimal structural disruptions. Using this biosensor, we screen a library of acyltransferase (AT)-exchanged PKS hybrids with randomly assigned domain boundaries, and we identify variants that maintain wild type production levels. We then probe each position in the AT linker region to determine how domain boundaries influence structural integrity and identify a set of optimized domain boundaries. Overall, we have successfully developed an experimentally validated, high-throughput method for making hybrid PKSs that produce novel molecules.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Engineering controllable alteration of malonyl-CoA levels to enhance polyketide production

Heterologous expression of polyketide synthase (PKS) genes in Escherichia coli has enabled the production of various valuable natural and synthetic products. However, the limited availability of malonyl-CoA (M-CoA) in E. coli remains a substantial impediment to high-titer polyketide production. Here we address this limitation by disrupting the native M-CoA biosynthetic pathway and introducing an orthogonal pathway comprising a malonate transporter and M-CoA ligase, enabling efficient M-CoA biosynthesis under malonate supplementation. This approach substantially increases M-CoA levels, enhancing fatty acid and polyketide titers while reducing the promiscuous activity of PKSs toward undesired acyl-CoA substrates. Subsequent adaptive laboratory evolution of these strains provides insights into M-CoA regulation and identifies mutations that further boost M-CoA and polyketide production. This strategy improves E. coli as a host for polyketide biosynthesis and advances understanding of M-CoA metabolism in microbial systems.

Klass, Sarah H↗

DOE OSTI2025

Engineering modular enzyme assembly: synthetic interface strategies for natural products biosynthesis applications

Covering: 2020 to 2025Natural products remain indispensable sources of therapeutic and bioactive compounds, yet traditional discovery strategies are constrained by compound rediscovery. Modular biosynthetic enzymes, such as type I polyketide synthases (PKSs) and type A non-ribosomal peptide synthetases (NRPSs), offer promising platforms for combinatorial biosynthesis owing to their programmable architectures. However, practical implementation is frequently limited by inter-modular incompatibility and domain-specific interactions. This review highlights recent advances in modular enzyme assembly enabled by synthetic interfaces-including cognate docking domains, synthetic coiled-coils, SpyTag/SpyCatcher, and split inteins-which function as orthogonal, standardized connectors to facilitate post-translational complex formation. These interfaces support rational investigations into substrate specificity, module compatibility, and pathway derivatization as well as general enzyme clustering applications beyond PKS and NRPS systems. Synthetic interfaces can be integrated with computational tools to support a more systematic and scalable framework for modular enzyme engineering by providing predictive insights into domain compatibility and interface design. These approaches within iterative design-build-test-learn workflows can accelerate the programmable assembly of biosynthetic systems and expand the accessible chemical space for natural products.

Kim, Gahyeon↗

DOE OSTI2020

Estimation of Body Fat Percentage for Clinical Pharmacokinetic Studies in Children

Obesity is a prevalent childhood condition and the degree of adiposity appears likely to be an important covariate in the pharmacokinetics (PKs) of many drugs. We undertook these studies to facilitate the evaluation and, where appropriate, quantification of the covariate effect of body fat percentage (BF%) on PK parameters in children. We examined two large databases to determine the values and variabilities of BF% in children with healthy body weights and in those with obesity, comparing the accuracy and precision of BF% estimation by both clinical methods and demographically derived techniques. Additionally, we conducted simulation studies to evaluate the utility of the several methods for application in clinical trials. BF% was correlated with body mass index (BMI), but was highly variable among both children with healthy body weights and those with obesity. Bio‐impedance and several demographically derived techniques produced mean estimates of BF% that differed from dual x‐ray absorptiometry by < 1% (accuracy) and a SD of 5% or less (precision). Simulation studies confirmed that when the differences in precision among the several methods were small compared with unexplained between‐subject variability of a PK parameter, the techniques were of similar value in assessing the contribution of BF%, if any, as a covariate for that PK parameter. The combination of sex and obesity stage explained 68% of the variance of BF% with BMI. The estimation of BF% from sex and obesity stage can routinely be applied to PK clinical trials to evaluate the contribution of BF% as a potential covariate.

Green, Thomas P.↗

DOE OSTI2020

A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis

Persister cells are genetically identical variants in a bacterial population that have phenotypically modified their physiology to survive environmental stress. In bacterial pathogens, persisters are able to survive antibiotic treatment and reinfect patients in a frustrating cycle of chronic infection. To better define core persistence mechanisms for therapeutics development, we performed transcriptomics analyses of Burkholderia thailandensis populations enriched for persisters via three methods: flow sorting for low proton motive force, meropenem treatment, and culture aging. Although the three persister-enriched populations generally displayed divergent gene expression profiles that reflect the multimechanistic nature of stress adaptations, there were several common gene pathways activated in two or all three populations. These include polyketide and nonribosomal peptide synthesis, Clp proteases, mobile elements, enzymes involved in lipid metabolism, and ATP binding cassette (ABC) transporter systems. In particular, identification of genes that encode polyketide synthases (PKSs) and fatty acid catabolism factors indicates that generation of secondary metabolites, natural products, and complex lipids could be part of the metabolic program that governs the persistence state. We also found that loss-of-function mutations in the PKS-encoding gene locus BTH_I2366, which plays a role in biosynthesis of histone deacetylase (HDAC) inhibitors, resulted in increased sensitivity to antibiotics targeting DNA replication. Furthermore, treatment of multiple bacterial pathogens with a fatty acid synthesis inhibitor, CP-640186, potentiated the efficacy of meropenem against the persister populations. Altogether, our results suggest that bacterial persisters may exhibit an outwardly dormant physiology but maintain active metabolic processes that are required to maintain persistence.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

De novo transcriptome in roots of switchgrass ( Panicum virgatum L. ) reveals gene expression dynamic and act network under alkaline salt stress

Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress. Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes. Conclusions: Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Hyaloscypha finlandica Metabolome Repository

This repository provides the curated data tables, manuscript figure and table exports, dependency records, and workflow scripts supporting an integrated comparative genomics and untargeted LC-MS/MS metabolomics analysis of Hyaloscypha finlandica strain PMI 746, a root-associated dark septate endophyte of poplar. The repository includes genome-mining summaries from antiSMASH, FunBGCeX, BGC-Prophet, and BiG-SCAPE; processed metabolomics inputs; metabolite annotation evidence; statistical outputs; and publication-facing figures and tables. Raw LC-MS/MS spectra, full genome/protein downloads, and large generated tool outputs are referenced through public archive/accession records and are not stored in Git.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Search for Correlations of High-energy Neutrinos Detected in IceCube with Radio-bright AGN and Gamma-Ray Emission from Blazars

The IceCube Neutrino Observatory sends realtime neutrino alerts with a high probability of being astrophysical in origin. We present a new method to correlate these events and possible candidate sources using 2089 blazars from the Fermi-LAT 4LAC-DR2 catalog and with 3413 active galactic nuclei (AGNs) from the Radio Fundamental Catalog. No statistically significant neutrino emission was found in any of the catalog searches. The result suggests that a small fraction, <1%, of the studied AGNs emit neutrinos that pass the alert criteria, and is compatible with prior evidence for neutrino emission presented by IceCube and other authors from sources such as TXS 0506 + 056 and PKS 1502 + 106. We also present cross-checks to other analyses that claim a significant correlation using similar data samples.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

All-sky Neutrino Point-source Search with IceCube Combined Track and Cascade Data

Despite extensive efforts, discovery of high-energy astrophysical neutrino sources remains elusive. We present an event-level simultaneous maximum likelihood analysis of tracks and cascades using IceCube data collected from 2008 April 6 to 2022 May 23 to search the whole sky for neutrino sources, and using a source catalog, for coincidence of neutrino emission with gamma-ray emission. This is the first time a simultaneous fit of different detection channels is used to conduct a time-integrated all-sky scan with IceCube. Combining all-sky tracks, with superior pointing power and sensitivity in the northern sky, with all-sky cascades, with good energy resolution and sensitivity in the southern sky, we have developed the most sensitive point-source search to date by IceCube that targets the entire sky. The most significant point in the northern sky aligns with NGC 1068, a Seyfert II galaxy, which, from the catalog search, shows a 3.5σ excess over background after accounting for trials. The most significant point in the southern sky does not align with any source in the catalog and is not significant after accounting for trials. A search for the single most significant Gaussian flare at the locations of NGC 1068, PKS 1424+240, and the southern highest-significance point shows results consistent with expectations for steady emission. Notably, this is the first time that a flare shorter than four years has been excluded as being responsible for NGC 1068’s emergence as a neutrino source. Our results show that combining tracks and cascades when conducting neutrino source searches improves sensitivity and can lead to new discoveries.

Abbasi, R. [Loyola University, Chicago, IL (United↗

DOE OSTI2021

Search for Multi-flare Neutrino Emissions in 10 yr of IceCube Data from a Catalog of Sources

A recent time-integrated analysis of a catalog of 110 candidate neutrino sources revealed a cumulative neutrino excess in the data collected by IceCube between 2008 April 6 and 2018 July 10. This excess, inconsistent with the background hypothesis in the Northern Hemisphere at the 3.3σ level, is associated with four sources: NGC 1068, TXS 0506+056, PKS 1424+240, and GB6 J1542+6129. Here, this Letter presents two time-dependent neutrino emission searches on the same data sample and catalog: a point-source search that looks for the most significant time-dependent source of the catalog by combining space, energy, and time information of the events, and a population test based on binomial statistics that looks for a cumulative time-dependent neutrino excess from a subset of sources. Compared to previous time-dependent searches, these analyses enable a feature to possibly find multiple flares from a single direction with an unbinned maximum-likelihood method. M87 is found to be the most significant time-dependent source of this catalog at the level of 1.7σ post-trial, and TXS 0506+056 is the only source for which two flares are reconstructed. The binomial test reports a cumulative time-dependent neutrino excess in the Northern Hemisphere at the level of 3.0σ associated with four sources: M87, TXS 0506+056, GB6 J1542+6129, and NGC 1068.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Comparing XRISM Cluster Velocity Dispersions with Predictions from Cosmological Simulations: Are Feedback Models Too Ejective?

The dynamics of the intracluster medium (ICM), the hot plasma that fills galaxy clusters, are shaped by gravity-driven cluster mergers and feedback from supermassive black holes (SMBHs) in the cluster cores. XRISM measurements of ICM velocities in several clusters offer insights into these processes. We compare XRISM measurements for nine galaxy clusters (Virgo, Perseus, Centaurus, Hydra-A, PKS 0745–19, A2029, Coma, A2319, and Ophiuchus) with predictions from three state-of-the-art cosmological simulation suites, TNG-Cluster, the Three Hundred Project GADGET-X, and GIZMO-SIMBA, that employ different models of feedback. In cool cores, XRISM reveals systematically lower velocity dispersions than the simulations predict, with all 10 measurements below the median simulated values by a factor of 1.5–1.7 on average and all falling within the bottom 10% of the predicted distributions. The observed kinetic-to-total pressure ratio is also lower, with a median value of 2.2%, compared to the predicted 5.0%–6.5% for the three simulations. Outside the cool cores and in non-cool-core (NCC) clusters, simulations show better agreement with XRISM measurements, except for the outskirts of the relaxed, cool-core cluster A2029, which exhibits an exceptionally low kinetic pressure support (<1%), with none of the simulated systems in either of the three suites reaching such low levels. The NCC Coma and A2319 exhibit dispersions at the lower end but within the simulated spread. Our comparison suggests that the three numerical models may overestimate the kinetic effects of SMBH feedback in cluster cores. Additional XRISM observations of NCC clusters will clarify if there is a systematic tension in the gravity-dominated regime as well.

galaxy clusters↗

DOE OSTI2020

Kinetic beaming in radiative relativistic magnetic reconnection: a mechanism for rapid gamma-ray flares in jets

ABSTRACT Rapid gamma-ray flares pose an astrophysical puzzle, requiring mechanisms both to accelerate energetic particles and to produce fast observed variability. These dual requirements may be satisfied by collisionless relativistic magnetic reconnection. On the one hand, relativistic reconnection can energize gamma-ray emitting electrons. On the other hand, as previous kinetic simulations have shown, the reconnection acceleration mechanism preferentially focuses high energy particles – and their emitted photons – into beams, which may create rapid blips in flux as they cross a telescope’s line of sight. Using a series of 2D pair-plasma particle-in-cell simulations, we explicitly demonstrate the critical role played by radiative (specifically inverse Compton) cooling in mediating the observable signatures of this ‘kinetic beaming’ effect. Only in our efficiently cooled simulations do we measure kinetic beaming beyond one light crossing time of the reconnection layer. We find a correlation between the cooling strength and the photon energy range across which persistent kinetic beaming occurs: stronger cooling coincides with a wider range of beamed photon energies. We also apply our results to rapid gamma-ray flares in flat-spectrum radio quasars, suggesting that a paradigm of radiatively efficient kinetic beaming constrains relevant emission models. In particular, beaming-produced variability may be more easily realized in two-zone (e.g. spine-sheath) set-ups, with Compton seed photons originating in the jet itself, rather than in one-zone external Compton scenarios.

79 ASTRONOMY AND ASTROPHYSICS↗