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DOE OSTI2025

Seasonal changes in occupancy and activity patterns in native Collared Peccary and non-native wild pig and Common Warthog in southern Texas, the United States

Abstract Southern Texas, USA, is home to native collared peccaries (Dicotyles tajacu) and introduced populations of invasive wild pigs (generally Sus scrofa × domesticus hybrids) and non-native African warthogs (Phacochoerus africanus). Although these ecologically similar mammals co-occur in this region, the potential impacts of invasive suids on collared peccaries are poorly understood. We examined co-occupancy and activity pattern overlap of collared peccaries, wild pigs, and warthogs across 3 seasons (fall, winter, and spring) using remote camera data collected from Chaparral Wildlife Management Area, Cotulla, Texas (November 2020 to June 2021). Using activity pattern analyses and single and 2-species occupancy models incorporating habitat and climate characteristics, we found evidence of extensive spatial overlap between all species pairs and varying degrees of temporal overlap depending on species pairs and season. Collared peccaries and wild pigs displayed moderate temporal overlap across all seasons. Collared peccaries appeared to alter fall activity in the presence of wild pigs to be active earlier in the morning and less active during the day. Collared peccaries and warthogs had low-to-moderate temporal overlap (low in fall, winter; moderate in spring). Wild pigs and warthogs had low temporal overlap (fall, spring) and wild pigs appeared to alter activity in the presence of warthogs (fall), becoming less active during the day during peak warthog activity. Overall, our results suggest that peccary, wild pig, and warthog interactions and activity are dynamic and vary seasonally according to the ecology and preferred environmental conditions of each species. Given the potential for interspecific competition and disease transmission with Collared Peccary and other native wildlife, resource partitioning between wild pigs and warthogs needs to be further examined to aid in effective management strategies.

Kupferman, Caitlin A. (ORCID:0009000953554860)↗

DOE OSTI2024

The CNK–HYP scaffolding complex promotes RAF activation by enhancing KSR–MEK interaction

The RAS–MAPK pathway regulates cell proliferation, differentiation and survival, and its dysregulation is associated with cancer development. The pathway minimally comprises the small GTPase RAS and the kinases RAF, MEK and ERK. Activation of RAF by RAS is notoriously intricate and remains only partially understood. There are three RAF isoforms in mammals (ARAF, BRAF and CRAF) and two related pseudokinases (KSR1 and KSR2). RAS-mediated activation of RAF depends on an allosteric mechanism driven by the dimerization of its kinase domain. Recent work on human RAFs showed that MEK binding to KSR1 promotes KSR1–BRAF heterodimerization, which leads to the phosphorylation of free MEK molecules by BRAF. Similar findings were made with the single Drosophila RAF homolog. Here we show that the fly scaffold proteins CNK and HYP stabilize the KSR–MEK interaction, which in turn enhances RAF–KSR heterodimerization and RAF activation. The cryogenic electron microscopy structure of the minimal KSR–MEK–CNK–HYP complex reveals a ring-like arrangement of the CNK–HYP complex allowing CNK to simultaneously engage KSR and MEK, thus stabilizing the binary interaction. Together, these results illuminate how CNK contributes to RAF activation by stimulating the allosteric function of KSR and highlight the diversity of mechanisms impacting RAF dimerization as well as the regulatory potential of the KSR–MEK interaction.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Macroscale Control of Reactivity using 3D Printed Materials with Intrinsic Catalytic Properties

The morphology of heterogeneous catalysts can impact their performance. However, standard manufacturing methods like extrusion or pelleting offer little options for tailoring catalyst shape. Herein, stereolithographic 3D printing is used to produce catalysts with controlled topologies to enhance their performance. A series of magnetic stir-bar compartments (SBC) were 3D printed and tested as catalysts for sucrose hydrolysis. The SBC were printed using acrylic acid (AA) and 1,6-hexanediol diacrylate (HDDA) as acid sites and hydrophobic crosslinking domains, respectively. Variations in the number and tilt direction of the SBC blades produced significant changes in their apparent catalytic activities. These changes resulted from differences in the fraction of active surface effectively interacting with the reactants in solution, as revealed by computational fluid dynamics simulations. Moreover, varying HDDA:AA ratios in SBC regulated reactant-surface interactions to control catalytic activity. Overall, 3D printing catalysts enables quick performance optimization by simultaneously controlling macroscopic structure and molecular composition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Exploring the Interaction Between Head-Supported Mass, Posture, and Visual Stress on Neck Muscle Activation

Objective Assess neck muscle activity for varying interactions between helmet, posture, and visual stress in a simulated “helo-hunch” posture. Background Military aviators frequently report neck pain (NP). Risk factors for NP include head-supported mass, awkward postures, and mental workload. Interactions between these factors could induce constant low-level muscle activation during helicopter flight and better explain instances of NP. Method Interactions between physical loading (helmet doffed/donned), posture (symmetric/asymmetric), and visual stress (low/high contrast) were studied through neck muscle electromyography (EMG), head kinematics, subjective discomfort, perceived workload, and task performance. Subjects ( n = 16) performed eight 30-min test conditions (varied physical loading, posture, and visual stress) while performing a simple task in a simulated “helo-hunch” seating environment. Results Conditions with a helmet donned had fewer EMG median frequency cycles (which infer motor unit rotation for rest/recovery, where more cycles are better) in the left cervical extensor and left sternocleidomastoid. Asymmetric posture (to the right) resulted in higher normalized EMG activity in the right cervical extensor and left sternocleidomastoid and resulted in less lateral bending compared with neutral across all conditions. Conditions with high visual stress also resulted in fewer EMG cycles in the right cervical extensor. Conclusion A complex interaction exists between the physical load of the helmet, postural stress from awkward postures, and visual stress within a simulated “helo-hunch” seating environment. Application These results provide insight into how visual factors influence biomechanical loading. Such insights may assist future studies in designing short-term administrative controls and long-term engineering controls.

Behavioral Sciences↗

DOE OSTI2023

Microdynamics of active particles in defect-rich colloidal crystals

Hypothesis. Because they are self-propulsive, active colloidal particles can interact with their environment in ways that differ from passive, Brownian particles. Here, we explore how interactions in different microstructural regions may contribute to colloidal crystal annealing. Experiments. We investigate active particles propagating in a quasi-2D colloidal crystal monolayer produced by alternating current electric fields (active-to-passive particle ratio ~ 1:720). The active particle is a platinum Janus sphere propelled by asymmetric decomposition of hydrogen peroxide. Crystals are characterized for changes in void properties. The mean-squared-displacement of Janus particles are measured to determine how active microdynamics depend on the local microstructure, which is comprised of void regions, void-adjacent regions (defined as within three particle diameters of a void), and interstitial regions. Findings. At active particle energy E A = 2.55 k B T, the average void size increases as much as three times and the average void anisotropy increases about 40% relative to the passive case. Further, the average microdynamical enhancement, <δ(t)>, of Janus particles in the crystal relative to an equivalent passive Janus particle is reduced compared to that of a free, active particle (<δ(t) > is 1.88 ± 0.04 and 2.66 ± 0.08, respectively). The concentration of active particles is enriched in void and void-adjacent regions. Active particles exhibit the greatest change in dynamics relative to the passive control in void-adjacent regions (<δ(t)> = 2.58 ± 0.06). The results support the conjecture that active particle microdynamical enhancement in crystal lattices is affected by local defect structure.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Hydrogen in Nanocatalysis

Hydrogen is ubiquitous in catalysis. It is involved in many important reactions such as water splitting, N 2 reduction, CO 2 reduction, and alkane activation. In this Perspective, we focus on the hydrogen atom and follow its electron as it interacts with a catalyst or behaves as part of a catalyst from a computational point of view. In this work, we present recent examples in both nanocluster and solid catalysts to elucidate the parameters governing the strength of the hydrogen–surface interactions based on site geometry and electronic structure. We further show the interesting behavior of hydride in nanometal and oxides for catalysis. Overall, the key take-home messages are: (1) the in-the-middle electronegativity and small size of hydrogen give it great versatility in interacting with active sites on nanoparticles and solid surfaces; (2) the strength of hydrogen binding to an active site on a surface is an important descriptor of the chemical and catalytic properties of the surface; (3) the energetics of the hydrogen binding is closely related to the electronic structure of the catalyst; (4) hydrides in nanoclusters and oxides and on surfaces offer unique reactivity for reduction reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Donor–Acceptor Conjugated Copolymers Containing Transition-Metal Complex: Intrachain Magnetic Exchange Interactions and Magneto-Optical Activity

A donor-acceptor conjugated copolymer containing thienothiophene (TT) (Donor) units and Co(II) complexes (Acceptor) has been synthesized and characterized. The studies of magnetic properties of the polymers by SQUID and EPR measurements showed antiferromagnetic exchange interaction between neighboring spin centers along with the polymer backbone through intrachain in-teractions. It is the first time that D-A conjugated polymer backbone serving as bridging ligands for magnetic couplings, making this type of polymers promising as magnetic materials. Moreover, the magneto-optical activity (MOA) of polymer LCP1 was char-acterized using magnetic circular dichroism (MCD) spectroscopy. It was found that the material exhibits a large magneto-optic rotation with a peak Verdet constant of 2980 deg*T -1 *m -1 at 590 nm.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Inverse design of pore wall chemistry and topology through active learning of surface group interactions

Design of next-generation membranes requires a nanoscopic understanding of the effect of biologically inspired heterogeneous surface chemistries and topologies (roughness) on local water and solute behavior. In particular, the rejection of small, neutral solutes, such as boric acid, poses a heretofore unsolved challenge. In prior work, a computational inverse design technique using an evolutionary optimization successfully uncovered new surface design strategies for optimized transport of water over solutes in smooth, model pores consisting of two surface chemistries. However, extending such an approach to more complex (and realistic) scenarios involving many surface chemistries as well as surface roughness is challenging due to the expanded design space. In this work, we develop a new approach that uses active learning to optimize in a reduced feature space of surface group interactions, finding parameters that lead to their assembly into ordered, optimal patterns. This approach rapidly identifies novel surface functionalizations that maximize the difference in water and boric acid transport through the nanopore. Moreover, we find that the roughness of the nanopore wall, independent of its chemistry, can be leveraged to enhance transport selectivity: oscillations in the pore wall diameter optimally inhibit boric acid transport by creating energetic wells from which the solute must escape to transport down the pore. Furthermore, this proof-of-concept demonstrates the potential for active learning strategies, in concert with molecular simulations, to rapidly navigate complex design spaces of aqueous interfaces and is promising as a tool for engineering water-mediated surface interactions for a broad range of applications.

36 MATERIALS SCIENCE↗

DOE OSTI2024

An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol γ

The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological diseases. Although not a catalytic residue, Pol γ arginine-853 mutants are void of polymerase activity. To identify the structural basis for the disease, we determined a crystal structure of the Pol γ mutant ternary complex with correct incoming nucleotide 2'-deoxycytidine 5'-triphosphate (dCTP). Opposite to the wild type that undergoes open-to-closed conformational changes when bound to a correct nucleotide that is essential for forming a catalytically competent active site, the mutant complex failed to undergo the conformational change, and the dCTP did not base pair with its Watson-Crick complementary templating residue. Our studies revealed that arginine-853 coordinates an interaction network that aligns the 3'-end of primer and dCTP with the catalytic residues. Disruption of the network precludes the formation of Watson-Crick base pairing and closing of the active site, resulting in an inactive polymerase.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Visualizing interfacial collective reaction behaviour of Li–S batteries

Benefiting from high energy density (2,600 Wh kg -1 )) and low cost, lithium-sulfur (Li-S) batteries are considered promising candidates for advanced energy-storage systems. Despite tremendous efforts in suppressing the long-standing shuttle effect of lithium polysulfides, understanding of the interfacial reactions of lithium polysulfides at the nanoscale remains elusive. This is mainly because of the limitations of in situ characterization tools in tracing the liquid-solid conversion of unstable lithium polysulfides at high temporal-spatial resolution. There is an urgent need to understand the coupled phenomena inside Li-S batteries, specifically, the dynamic distribution, aggregation, deposition and dissolution of lithium polysulfides. Here, by using in situ liquid-cell electrochemical transmission electron microscopy, we directly visualized the transformation of lithium polysulfides over electrode surfaces at the atomic scale. Notably, an unexpected gathering-induced collective charge transfer of lithium polysulfides was captured on the nanocluster active-centre-immobilized surface. It further induced an instantaneous deposition of nonequilibrium Li2S nanocrystals from the dense liquid phase of lithium polysulfides. Without mediation of active centres, the reactions followed a classical single-molecule pathway, lithium polysulfides transforming into Li 2 S 2 and Li 2 S step by step. Molecular dynamics simulations indicated that the long-range electrostatic interaction between active centres and lithium polysulfides promoted the formation of a dense phase consisting of Li + and S n 2- (2 < n ≤ 6), and the collective charge transfer in the dense phase was further verified by ab initio molecular dynamics simulations. Finally, the collective interfacial reaction pathway unveils a new transformation mechanism and deepens the fundamental understanding of Li-S batteries.

25 ENERGY STORAGE↗

DOE OSTI2023

Large-Eddy Simulations of Marine Boundary Layer Clouds Associated with Cold-Air Outbreaks during the ACTIVATE Campaign. Part II: Aerosol–Meteorology–Cloud Interaction

Aerosol effects on micro/macrophysical properties of marine stratocumulus clouds over the western North Atlantic Ocean (WNAO) are investigated using in situ measurements and large-eddy simulations (LES) for two cold-air outbreak (CAO) cases (28 February and 1 March 2020) during the Aerosol Cloud Meteorology Interactions over the Western Atlantic Experiment (ACTIVATE). The LES is able to reproduce the vertical profiles of liquid water content (LWC), effective radius r eff and cloud droplet number concentration N c from fast cloud droplet probe (FCDP) in situ measurements for both cases. Furthermore, we show that aerosols affect cloud properties (N c , r eff , and LWC) via the prescribed bulk hygroscopicity of aerosols ($\bar{κ}$) and aerosol size distribution characteristics. N c , r eff , and liquid water path (LWP) are positively correlated to $\bar{κ}$ and aerosol number concentration (N a ) while cloud fractional cover (CFC) is insensitive to $\bar{κ}$ and aerosol size distributions for the two cases. The realistic changes to aerosol size distribution (number concentration, width, and the geometrical diameter) with the same meteorology state allow us to investigate aerosol effects on cloud properties without meteorological feedback. We also use the LES results to evaluate cloud properties from two reanalysis products, ERA5 and MERRA-2. Compared to LES, the ERA5 is able to capture the time evolution of LWP and total cloud coverage within the study domain during both CAO cases while MERRA-2 underestimates them.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Structural insights into isoform-specific RAS-PI3Kα interactions and the role of RAS in PI3Kα activation

Abstract Mutations in RAS and PI3Kα are major drivers of human cancer. Their interaction plays a crucial role in activating PI3Kα and amplifying the PI3K-AKT-mTOR pathway. Disrupting RAS-PI3Kα interaction enhances survival in lung and skin cancer models and reduces tumor growth and angiogenesis, although the structural details of this interaction remain unclear. Here, we present structures of KRAS, RRAS2, and MRAS bound to the catalytic subunit (p110α) of PI3Kα, elucidating the interaction interfaces and local conformational changes upon complex formation. Structural and mutational analyses highlighted key residues in RAS and PI3Kα impacting binding affinity and revealed isoform-specific differences at the interaction interface in RAS and PI3K isoforms, providing a rationale for their differential affinities. Notably, in the RAS-p110α complex structures, RAS interaction with p110α is limited to the RAS-binding domain and does not involve the kinase domain. This study underscores the pivotal role of the RAS-PI3Kα interaction in PI3Kα activation and provides a blueprint for designing PI3Kα isoform-specific inhibitors to disrupt this interaction.

Science & Technology - Other Topics↗

DOE OSTI2025

Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H 2 O 2 and O 2 . This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Controllable Emergent Spatial Spin Modulation in Sr 2 IrO 4 by In Situ Shear Strain

Symmetric anisotropic interaction can be ferromagnetic and antiferromagnetic at the same time but for different crystallographic axes. We show that the competition of anisotropic interactions of orthogonal irreducible representations can be a general route to obtain new exotic magnetic states. We demonstrate it here by observing the emergence of a continuously tunable 12-layer spatial spin modulation when distorting the square-lattice planes in the quasi-two-dimensional antiferromagnetic Sr 2 IrO 4 under in situ shear strain. Furthermore, this translation-symmetry-breaking phase is a result of an unusual strain-activated anisotropic interaction which is at the fourth order and competing with the inherent quadratic anisotropic interaction. Such a mechanism of competing anisotropy is distinct from that among the ferromagnetic, antiferromagnetic, and/or the Dzyaloshinskii-Moriya interactions, and it could be widely applicable and highly controllable in low-dimensional magnets.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

UrbanPop: A spatial microsimulation framework for exploring demographic influences on human dynamics

Ensuring the social equity of planning measures in social systems requires an understanding of human dynamics, particularly how individual relationships, activities, and interactions intersect with individual needs. Spatial microsimulation models (SMSMs) support planning for human security goals by representing human dynamics through realistic, georeferenced synthetic populations, that a) provide a complete representation of social systems while b) also protecting individual privacy. In this paper, we present UrbanPop, an open and reproducible SMSM framework for analysis of human dynamics with high spatial, temporal, and demographic resolution. UrbanPop creates synthetic populations of demographically detailed worker and student agents, positioning them first at probable nighttime locations (home), then moving them to probable daytime locations (work/school). Summary aggregations of these populations match the granular detail available at the census block group level in the American Community Survey Summary File (SF), providing realistic approximations of the actual population. UrbanPop users can select particular demographic traits important in their application, resulting in a highly tailored agent population. We first lay out UrbanPop's baseline methodology, including population synthesis, activity modeling, and diagnostics, then demonstrate these capabilities by developing case studies of shifting population distributions and high-risk populations in Knox County, TN during the global COVID-19 pandemic.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Cell to Ecosystem: Understanding Methane and Associated Nutrient Cycling by Sediment Hosted Syntrophic Consortia and Their Viral Predators

The anaerobic oxidation of methane (AOM) is a significant worldwide microbial process in anoxic lake and ocean sediments, responsible for sequestering up to 80% of this greenhouse gas. Often considered a metabolism on the edge of thermodynamic probability, the impact of ANaerobic MEthane-oxidizing ‘ANME’ archaea on carbon and nutrient cycling in sediment ecosystems is far reaching. They not only serve as a sink for methane coupled to diverse electron acceptors, but also catalyze the transformation of many important nutrients including nitrogen, phosphate, and iron. While information about the potential mechanisms supporting metabolism in AOM is now available, remarkably little has been learned about their nutritional requirements, their dependencies on bacterial partners, and consequentially their ultimate impact on nutrient transformation and bioavailability within sedimentary ecosystems, and beyond. Further, the role of viruses within sediment ecosystems represents an essential but vastly understudied aspect of the transformation of carbon and nutrients by AOM. Viruses are now widely appreciated as central players in biogeochemical cycles across diverse ecosystems. These nanoscale predators have been shown to enhance the turnover of essential nutrients, thus stimulating microbial growth and environmental viruses themselves may constitute an important reservoir of nitrogen and phosphorous. Little is known about the role of viruses in methane-impacted sedimentary ecosystems, however prior genomic and microscopy evidence suggests that AOM consortia are susceptible to phage infection. The overarching scientific goal of this multi-disciplinary research proposal is to build on these recent discoveries and expand our understanding of interactions and fundamental activities involved in cycling of carbon and nutrients by syntrophic methanotrophic archaeal-bacterial consortia and associated viruses in anoxic sedimentary environments. Our three specific objectives are to 1) Quantify energy and nutrient exchange (e.g. N, P, Fe and vitamins) within AOM consortia and between ANME-bacterial partners; 2) Identify virus-host interactions associated with AOM and assess C and N transfer through viruses in methane-impacted sediment ecosystems; 3) Model energy and nutrient exchange in AOM consortia and viral-host interactions (i.e. viral activity), and their environmental distribution patterns. Our experimental emphasis cuts across scales that are important for understanding microbial and viral interactions and activities within their habitats, as well as community wide biogeochemical transformations. These research goals will be accomplished through the application of novel molecular techniques targeting DNA, RNA, proteins, and metabolites combined with a unique multi-modal analytical imaging pipeline. We will then model the ecophysiological capabilities of diverse sediment-hosted methanotrophic consortia to develop a more comprehensive understanding of the energetic and nutritional interactions between different AOM partner couplings that occur in sediments.

03 NATURAL GAS↗

DOE OSTI2026

Modulating Operational Conditions to Mitigate Deactivation in Formate Dehydrogenation on Pd Phases

In heterogeneous catalysis, poisoning by surface-bound intermediates poses a major barrier to sustained catalyst performance in (de)hydrogenation reactions. Formate/bicarbonate systems, as liquid organic hydrogen carriers (LOHCs), offer a CO 2 -integrated, low-temperature pathway for hydrogen storage and release, making them attractive for circular energy applications. However, their lower hydrogen density and susceptibility to catalyst deactivation limit their competitiveness compared to conventional LOHCs like methylcyclohexane. Here, this study investigates the mechanistic origins of formate (HCOO – ) dehydrogenation and associated deactivation on Pd interfaces. Using density functional theory (DFT) simulations, we show that under thermocatalytic conditions, strongly bound formate accumulates on the catalyst surface (Pd(111)), blocking active sites, raising activation barriers, and leading to progressive performance loss. Because formate adsorption involves charge transfer, we exploit its sensitivity to electronic structure by modulating the electrochemical potential of the catalyst. Our results reveal that hydrogen transfer from water and formate exhibits opposing potential dependencies, providing insights into the opposing driving forces behind both catalytic activity and poisoning. To further probe this phenomenon, we examine electrochemically induced phase transitions in Pd, focusing on PdO(100) and PdH(110), which are stable under oxidizing and reducing potentials, respectively, and demonstrate enhanced dehydrogenation activity between −0.4 and 0.2 V vs standard hydrogen electrode (SHE). Complementary thermal treatments help decouple kinetic and thermodynamic contributions to intermediate binding. These findings underscore the critical role of the catalyst phase and external stimuli in dictating poison-active site interactions and highlight phase engineering as a promising strategy to mitigate deactivation. This work offers mechanistic insights and design principles for developing more resilient and efficient catalysts for LOHC applications under realistic operating conditions.

Pd phase↗

DOE OSTI2025

Exploring phage–host interactions in Burkholderia cepacia complex bacterium to reveal host factors and phage resistance genes using CRISPRi functional genomics and transcriptomics

Complex interactions of bacteriophages with their bacterial hosts determine phage host range and infectivity. While phage defense systems and host factors have been identified in model bacteria, they remain challenging to predict in non-model bacteria. In this paper, we integrate functional genomics and transcriptomics to investigate phage–host interactions, revealing active phage resistance and host factor genes in Burkholderia cenocepacia K56-2. Burkholderia cepacia complex species are commonly found in soil and are opportunistic pathogens in immunocompromised patients. We studied infection of B. cenocepacia K56-2 with Bcep176, a temperate phage isolated from Burkholderia multivorans. A genome-wide dCas9 knockdown library targeting B. cenocepacia K56-2 was constructed, and a pooled infection experiment identified 63 novel genes or operons coding for candidate host factors or phage resistance genes. The activities of a subset of candidate host factor and resistance genes were validated via single-gene knockdowns. Transcriptomics of B. cenocepacia K56-2 during Bcep176 infection revealed that expression of genes coding for host factor and resistance candidates identified in this screen was significantly altered during infection by 4 h post-infection. Identifying which bacterial genes are involved in phage infection is important to understand the ecological niches of B. cenocepacia and its phages, and for designing phage therapies.

Bacterial Pathogenesis↗