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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Potential Biocontrol Activities of Populus Endophytes against Several Plant Pathogens Using Different Inhibitory Mechanisms

The plant microbiome can be used to bolster plant defense against abiotic and biotic stresses. Some strains of endophytes, the microorganisms within plants, can directly inhibit the growth of plant fungal pathogens. A previously isolated endophyte from wild Populus (poplar), WPB of the species Burkholderia vietnamiensis, had robust in vitro antifungal activity against pathogen strains that are highly virulent and of concern to Pacific Northwest agriculture: Rhizoctonia solani AG-8, Fusarium culmorum 70110023, and Gaemannomyces graminis var. tritici (Ggt) ARS-A1, as well as activity against the oomycete, Pythium ultimum 217. A direct screening method was developed for isolation of additional anti-fungal endophytes from wild poplar extracts. By challenging pathogens directly with dilute extracts, eleven isolates were found to be inhibitory to at least two plant pathogen strains and were therefore chosen for further characterization. Genomic analysis was conducted to determine if these endophyte strains harbored genes known to be involved in antimicrobial activities. The newly isolated Bacillus strains had gene clusters for production of bacillomycin, fengicyn, and bacillibactin, while the gene cluster for the synthesis of sessilin, viscosin and tolaasin were found in the Pseudomonas strains. The biosynthesis gene cluster for occidiofungin (ocf) was present in the Burkholderia vietnamiensis WPB genome, and an ocf deletion mutant lost inhibitory activity against 3 of the 4 pathogens. The new isolates lacked the gene cluster for occidiofungin implying they employ different modes of action. Other symbiotic traits including nitrogen fixation, phosphate solubilization, and the production of auxins and siderophores were investigated. Although it will be necessary to conduct in vivo tests of the candidates with pathogen-infected agricultural crops, the wild poplar tree microbiome may be a rich source of beneficial endophyte strains with potential for biocontrol applications against a variety of pathogens and utilizing varying modes of action.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Breaking $\mathrm{OER}$ and $\mathrm{CER}$ scaling relations via strain and its relaxation in $\mathrm{RuO}$ 2 (101)

Green hydrogen production from abundant water sources is an important component of renewable energy storage. Water oxidation catalysts are typically considered bound by adsorbate scaling relations, limiting their activity for the oxygen evolution reaction (OER) as well as selectivity between OER and the chlorine evolution reaction (CER) that compete in saline water streams. RuO 2 is highly active for both reactions, and recent measurements have shown the OER activity is greater on undercoordinated, high index facets compared to the lowest-energy (110) facet often studied. The growth of such orientations as epitaxial films, however, can result in appreciable strain and potential surface faceting via its relaxation. Here, we find the activity and selectivity towards OER and CER vary with thickness in epitaxial (101) RuO 2 thin films: OER activity decreases 4x as film thickness increases from 8 nm to 48 nm, while CER activity is comparable. Thus, strain and its relaxation can be used to break scaling relationships between OER and CER, highlighting the important role that defects play in selective oxidation processes on RuO 2 in chloride-containing media.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Residual lattice strain in quartzites as a potential palaeo-piezometer

SUMMARY If a crystal lattice is subjected to a stress, it becomes distorted and no longer represents the ideal crystal symmetry, and if the stress introduces defects such as dislocations, some of this distortion is preserved after the applied stress is removed. In this study, we investigate lattice distortion in quartz at the micron scale with synchrotron X-ray Laue diffraction. From Laue images the local deviatoric strain tensor is derived and corresponding stresses are calculated based on elastic properties. The method is applied to metasedimentary quartzites from the Bergell Alps that were deformed at conditions of greenschist facies metamorphism. The residual palaeostrain is represented in maps of the deviatoric strain tensor components and with deviatoric strain axis pole figures. Data suggest overall shortening perpendicular to the schistosity plane but with considerable asymmetry relative to foliation and lineation, probably attributed to simple shear. Crystallographic pole figures from Laue diffraction agree with neutron diffraction and EBSD measurements and display quartz c-axes girdle distributions with maxima also perpendicular to schistosity. The method shows promise to be used as a palaeo-piezometer to unravel the stress field during tectonic deformation.

58 GEOSCIENCES↗
DOE OSTI2021

Investigating the role of the transcriptional regulator Ure2 on the metabolism of Saccharomyces cerevisiae: a multi-omics approach

Ure2 regulates nitrogen catabolite repression in Saccharomyces cerevisiae. Deletion of URE2 induces a physiological state mimicking the nitrogen starvation and autophagic responses. Previous work has shown that deletion of URE2 increases the fermentation rate of some wine-producing strains of S. cerevisiae. In this work, we investigated the effect of URE2 deletion (ΔURE2) on the metabolism of S. cerevisiae. During growth on glucose, the ΔURE2 mutant grew less well than the wild type; however, it produced ethanol at higher rates. To better under the behavior of this mutant, we performed transcriptomics and metabolomics. Analysis of the RNA sequencing results and metabolite levels indicate that the mutant strain exhibited characteristics of both nitrogen starvation and autophagy. In addition, many pyruvate decarboxylase and alcohol dehydrogenase isoforms were expressed at higher rates than the wild type. The mutant also accumulated less trehalose and glycogen, and produced more lipids. These results suggest that URE2 may be a promising target for metabolic engineering in S. cerevisiae and potentially other strains of yeast as well for the production of lipid-based fuels and chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Electrons to Molecules by Engineering and Evolution: Biological Upgrading of Formate by Cupriavidus necator

Waste carbon from industrial point sources can be captured, stored, and/or transformed using electrochemical conversion or "electrons to molecules" technologies using low-cost renewable electricity. One such process involves electrocatalytic reduction of CO2 to generate formate/formic acid, a C1 carboxylic acid. Formate is a promising potential feedstock for microbial upgrading, as it is water soluble and can be consumed as the sole source of carbon and energy by some microbial species, such as the soil bacterium Cupriavidus necator. Here we will present progress toward improving C. necator as a host for biological conversion of formate to value-added products. Using the power of adaptive laboratory evolution, we were able to isolate mutants of C. necator with significantly faster growth rates on formate. We then sequenced the genomes of these strains, elucidated the metabolic role of the mutations we found, and then used these insights to build rationally engineered strains that outperform even the best evolved isolates. These results highlight the utility of "genome streamlining" as a route for generating platform strains with potential industrial applications.

adaptive laboratory evolution↗
DOE OSTI2023

NanoMechanics: Elasticity and Friction in Nano‐Objects

A large scientific and technological effort is underway to investigate the properties of two‐dimensional (2D) materials to become building blocks in integrated nano‐electronic and photonic circuits, composites, coatings, energy harvesting nano‐ systems, nano‐sensors, and nano‐electro‐mechanical systems (NEMS).While several experiments and calculations have revealed exciting novel phenomena in these nanostructures, many scientific and technological questions remain open. In particular, understanding and controlling the structure and mechanical properties of 2D materials at the interface with a solid surface is of key importance to enable the aforementioned nanotechnologies, as well as to fulfill the potential of strain engineering to tailor their properties. The vision of this DoE research program was to investigate novel mechanical properties and phenomena in 1D and 2D materials with the overarching goal of defining a new basic understanding of mechanical behavior in nano and quantum systems. The group of the PI has developed in the last years several studies on the mechanical properties of Carbon nanotubes and oxide nanobelts, more recently the PI has focused her attention on the properties of two‐dimensional materials, such as graphene and MoS 2 , which are a few‐atomic‐layer thick films and hold a great potential for technological and energy applications. The most studied 2D material is graphene, existing as a single layer of graphite or a few‐layer thick epitaxial graphene film. Graphene possesses a large in‐plane Young’s modulus as well as high intrinsic carrier mobility, and high in‐plane thermal conductivity. Besides graphene, also 2D films of graphene oxide (GO), hexagonal Boron Nitride (h‐BN), and transition metal dichalcogenides such as MoS 2 exhibit unique and excellent properties and hold great promise for nanotechnology applications. This research program was aimed at developing a new basic understanding of the mechanical properties of 1D and 2D materials at the interface with solid substrates, with a focus on the role of defects, materials structure, and substrate interaction. Ultimately, we aimed at developing the basic knowledge and experimental tools for manipulating 1D and 2D materials’ structure, stacking, substrate interaction, defects, and number of layers to realize an entirely new class of ultra‐hard, ultra‐thin, and ultra‐light active materials with ad‐ hoc mechanical properties for a variety of applications.

2D Materials↗
DOE OSTI2020

Friction stir gradient alloying: A high-throughput method to explore the influence of V in enabling HCP to BCC transformation in a γ-FCC dominated high entropy alloy

The compositional possibilities in high entropy alloys (HEAs) is very vast and effective strategies are needed to establish potential alloy chemistries. In this study, friction stir gradient alloying (FSGA), a recently-introduced high-throughput (HT) technique incorporating compositional and microstructural gradients, was used to explore the possibility of introducing a bcc transformation domain in γ-fcc dominated TRIP HEA Fe 38.5 Mn 20 Cr 15 Co 20 Si 5 Cu 1.5 (at.%) by vanadium addition. FSGA has accelerated the process of attaining the composition-microstructure library and the results suggest that vanadium addition of ~1 at.% results in nucleation of α-bcc. Additionally, this is the first observation of ε-hcp to α-bcc transformation in a TRIP HEA and supports the Olson-Cohen model of martensitic transformation (γ-fcc → ε-hcp → α-bcc). ε-hcp is nucleated with a pyramidal orientation by the formation of planar faults on the {111} close-packed planes of γ-fcc, and α-bcc is nucleated in the vicinity of ε-hcp along the {111} γ-fcc trace. There are indications for the formation of basal orientated ε-hcp from intersecting ε-hcp planes orientated for the pyramidal slip. Thus, the study shows the nucleation and growth of the α-bcc phase attributed to the dual effects of chemistry and strain and potential co-existence of all the three phases.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Operando Investigation on the Role of Densification and Chemo-Mechanics on Solid-State Cathodes

All solid-state batteries are desirable for a range of energy storage applications which require high energy density. Achieving a high energy density in a solid-state battery requires the operation of an energy dense anode with a composite solid-state cathode. Pores and/or voids within a solid state cathode are ion-blocking and thus control over the concentration and distribution of pores in the initial electrode and cycled electrode is desirable. This study provides an understanding of the interplay between electrode microstructure and mechanics on active material utilization in solid state cathodes composed of NCM 811 and Li 6 PS 5 Cl. Decreasing the solid electrolyte particle size leads to greater active material-electrolyte contact and less total deformation when exposed to an external load. Composite cathodes with greater compliance can potentially decrease strain between the active material and solid electrolyte, decrease delamination events and result in higher overall active material utilization and high capacity retention.

25 ENERGY STORAGE↗
DOE OSTI2021

The mechanics of brittle granular materials with coevolving grain size and shape

The influence of particle shape on the mechanics of sand is widely recognized, especially in mineral processing and geomechanics. However, most existing continuum theories for engineering applications do not encompass the morphology of the grains and its evolution during comminution. Similarly, the relatively few engineering models accounting for grain-scale processes tend to idealize particles as spheres, with their diameters considered as the primary and sole geometric descriptor. This paper inspires a new generation of constitutive laws for crushable granular continua with arbitrary, yet evolving, particle morphology. We explore the idea of introducing multiple grain shape descriptors into Continuum Breakage Mechanics (CBM), a theory originally designed to track changes in particle size distributions during confined comminution. We incorporate the influence of these descriptors on the elastic strain energy potential and treat them as dissipative state variables. In analogy with the original CBM, and in light of evidence from extreme fragmentation in nature, the evolution of the additional shape descriptors is postulated to converge towards an attractor. Comparisons with laboratory experiments, discrete element analyses and particle-scale fracture models illustrate the encouraging performance of the theory. The theory provides insights into the feedback among particle shape, compressive yielding and inelastic deformation in crushable granular continua. These results inspire new questions that should guide future research into crushable granular systems using particle-scale imaging and computations.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Draft genome of Rosenbergiella nectarea strain 8N4 T provides insights into the potential role of this species in its plant host

Background: Rosenbergiella nectarea strain 8N4 T , the type species of the genus Rosenbergiella, was isolated from Amygdalus communis (almond) floral nectar. Other strains of this species were isolated from the floral nectar of Citrus paradisi (grapefruit), Nicotiana glauca (tobacco tree) and from Asphodelus aestivus. R. nectarea strain 8N4 T is a Gram-negative, oxidase-negative, facultatively anaerobic bacterium in the family Enterobacteriaceae. Results: Here we describe features of this organism, together with its genome sequence and annotation. The DNA GC content is 47.38%, the assembly size is 3,294,717 bp, and the total number of genes are 3,346. The genome discloses the possible role that this species may play in the plant. The genome contains both virulence genes, like pectin lyase and hemolysin, that may harm plant cells and genes that are predicted to produce volatile compounds that may impact the visitation rates by nectar consumers, such as pollinators and nectar thieves. Conclusions: The genome of R. nectarea strain 8N4T reveals a mutualistic interaction with the plant host and a possible effect on plant pollination and fitness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evaluating the Feasibility of Measuring and Analyzing Strain Caused by Changes in Barometric Pressure in the Vadose Zone

Changes in barometric pressure propagate into the subsurface where they can affect water level measurements in wells and cause vertical strain. Previous strain sensors were developed to measure vertical strain, but they were limited to measurements at a single depth, making it difficult to evaluate strains from a migrating pressure wave. Technology known as Coherence-length-gated Microwave Photonics Interferometry (CMPI) uses optical fiber sensors to measure strain at multiple locations. It has the potential to detect strain caused by variations in barometric pressure at multiple depths in the subsurface. The goal of this study is to evaluate the feasibility of using this technology to record the changes in vertical strain in the vadose zone from small fluctuations in air pressure. Propagation of these air pressure fluctuations is affected by hydrogeological properties such as water content and permeability. A second goal of this study is to evaluate how these properties affect the air pressure distribution, strain, and gas-phase diffusivity with a long-term goal of using strain to monitor the vadose zone. The focus of this study is on a suite of laboratory experiments that used a sand-filled column with an open head space. The CMPI fiber was packaged and embedded along the axis of the column to measure the strain at multiple locations while air pressure transducers were installed through the wall of the column. Small periodic fluctuations in air pressure, similar to barometric pressure fluctuations, were created in the head space of the column using an audio driven speaker driven at 4 Hz using a sinusoidal signal created by a function generator. Then, the fluctuations propagated along the column where they were measured by the transducers and recorded as functions of time. Initial tests were conducted using dry sand, but then additional tests were conducted after injecting water into the column, which changed the hydrologic and mechanical properties. Another experiment was conducted after creating a thin barrier to air flow, which was designed to simulate a thin layer of saturated ground during rainfall. A final experiment was conducted by changing the grain size of the material to create a heterogeneity in the upper half of the column. The suite of six experiments was conducted to highlight effects of variations in water content and heterogeneities on air pressure and vertical strain. Numerical simulations were also created to evaluate the laboratory data and to provide a baseline analysis for the results. The numerical simulations used the governing equations to linear poroelasticity and two-phase flow with boundary conditions representing the experiments. The conceptual model for strain caused by barometric pressure recognizes that a fluctuating barometric pressure causes fluctuations in the air pore pressure that decrease in amplitude and lag in time with increase depth. The pressure distribution results in two different loads that cause strain: 1.) a mechanical load as the barometric pressure acts on the ground surface; and 2.) pressure loading in the pore space. The results show that the total vertical strain is a contribution of both of these loads, and this is the strain that was observed in the laboratory. The lab experiments show that both air pressure and strain vary as sinusoids that propagate with depth. The amplitude of the air pressure and strain decrease as a function of depth in all the conditions that were evaluate. For example, in the dry sand, the amplitude of the air pressure decreases from 25 Pa at the head space to 5 Pa at a depth of 70 cm, whereas the amplitude of the strain decreases from 0.15 to 0.06 µε over the same depth interval. In many cases the amplitudes decrease is approximately negative exponential functions of depth. When water was injected into the sand and the saturation increased, the amplitude of the air pressure increased in the partially saturated sand but decreased sharply to zero where the soil was saturated. The strain decreased with depth, but the transition from partially to fully saturated conditions had little effect on the strain profile, even though it had a major effect on the air pressure. This apparently is because strain is caused by variations in both water and air pressure. The fluctuating air pressure caused the water pressure to fluctuate, which caused strain throughout the column. Phase delay of the air pressure and the strain both increase as linear to bi-linear functions of depth. The phase delays indicate that pressure propagates at a velocity of 7 to 8 m/s in dry or partially saturated sand, but it drops by more than an order of magnitude in the vicinity of the capillary fringe. The phase delays indicate the strain propagates faster than the pressure. The data indicate that the strain propagates from 1.2 to more than 4x faster than the pressure. Switching from sand to silt in the column caused the velocity of the pressure to drop by roughly half for both pressures, but curiously, it had little effect on the velocity of the strain.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

In Vitro Evolution and Computational Approaches to Predict, Prevent and Control Future Pandemics

The natural tendency of virus to mutate and the under-sampling of the environment makes it difficult to become aware of the emergence of new viral strains with pandemic potential. Being able to predict what mutations make a virus more infective might allow to spot such strains with minimal sampling and potentially allow to predict/prevent the next pandemic. The team attempted to mimic natural viral mutations and recombination through computational and experimental methods producing a variety of mutants of a SARS-COV-2 protein (receptor binding domain, RBD, of spike protein) responsible for viral entry in mammalian cells. The library of mutants was then interrogated for ability and lack-there-of to interact with the host cell receptor ushering viral entry, Angiotensin-converting enzyme 2 (ACE2). The negative and positive data set is intended to “teach the rules” of virus-host receptor interaction. Additionally, the positive clones were used to screen a set of antibody mutants designed to widen the breadth of viral mutants recognition, to demonstrate that this kind of libraries could also be a tool to produce antibody therapeutics impervious to viral mutation, even before a pandemic strain is discovered.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cranberry Arabino-Xyloglucan and Pectic Oligosaccharides Induce Lactobacillus Growth and Short-Chain Fatty Acid Production

Numerous health benefits have been reported from the consumption of cranberry-derived products, and recent studies have identified bioactive polysaccharides and oligosaccharides from cranberry pomace. This study aimed to further characterize xyloglucan and pectic oligosaccharide structures from pectinase-treated cranberry pomace and measure the growth and short-chain fatty acid production of 86 Lactobacillus strains using a cranberry oligosaccharide fraction as the carbon source. In addition to arabino-xyloglucan structures, cranberry oligosaccharides included pectic rhamnogalacturonan I which was methyl-esterified, acetylated and contained arabino-galacto-oligosaccharide side chains and a 4,5-unsaturated function at the non-reducing end. When grown on cranberry oligosaccharides, ten Lactobacillus strains reached a final culture density (ΔOD) ≥ 0.50 after 24 h incubation at 32 °C, which was comparable to L. plantarum ATCC BAA 793. All strains produced lactic, acetic, and propionic acids, and all but three strains produced butyric acid. This study demonstrated that the ability to metabolize cranberry oligosaccharides is Lactobacillus strain specific, with some strains having the potential to be probiotics, and for the first time showed these ten strains were capable of growth on this carbon source. The novel cranberry pectic and arabino-xyloglucan oligosaccharide structures reported here combined with the Lactobacillus strains that can metabolize cranberry oligosaccharides and produce short-chain fatty acids, have excellent potential as health-promoting synbiotics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Phylogenetic analyses and reclassification of the oleaginous marine species Nannochloris sp. “desiccata" (Trebouxiophyceae, Chlorophyta), formerly Chlorella desiccata , supported by a high-quality genome assembly

Microalgae are diverse, with many gaps remaining in phylogenetic and physiological understanding. Thus, studying new microalgae species increases our broader comprehension of biological diversity, and evaluation of new candidates as algal production platforms can lead to improved productivity under a variety of cultivation conditions. Chlorella is a genus of fast-growing species often isolated from freshwater habitats and cultivated as a source of nutritional supplements. However, the use of freshwater increases competition with other freshwater needs. We identified Chlorella desiccata to be worthy of further investigation as a potential algae production strain, due to its isolation from a marine environment and its promising growth and biochemical composition properties. Long-read genomic sequencing was conducted for C. desiccata UTEX 2526, resulting in a high-quality, near chromosome level, diploid genome with an assembly length of 21.55 Mbp in only 18 contigs. We also report complete circular mitochondrial and chloroplast genomes. Phylogenomic and phylogenetic analyses using nuclear, chloroplast, 18S rRNA, and actin sequences revealed that this species clades within strains currently identified as Nannochloris (Trebouxiophyceae, Chlorophyta), leading to its reclassification as Nannochloris sp. “desiccata” UTEX 2526. The mode of cell division for this species is autosporulation, differing from the type species N. bacillaris. As has occurred across multiple microalgae genera, there are repeated examples of Nannochloris species reclassification in the literature. This high-quality genome assembly and phylogenetic analysis of the potential algal production strain Nannochloris sp. “desiccata” UTEX 2526 provides an important reference and useful tool for further studying this region of the phylogenetic tree.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Contrasting effects of glutamate and branched-chain amino acid metabolism on acid tolerance in a Castellaniella isolate from acidic groundwater

Groundwater acidification co-occurring with nitrate pollution is a common, global environmental health hazard. Denitrifying bacteria have been leveraged for the in situ removal of nitrate in groundwater. However, co-existing stressors—such as low pH—reduce the efficacy of biological removal processes. Castellaniella sp. str. MT123 is a complete denitrifier that was isolated from acidic, nitrate-contaminated groundwater. The strain grows robustly by nitrate respiration at pH < 6.0, completely reducing nitrate to dinitrogen gas. Genomic analyses of MT123 revealed few previously characterized acid tolerance genes. Thus, we utilized a combination of proteomics, metabolomics, and competitive mutant fitness to characterize the genetic mechanisms of MT123 acclimation to growth under mildly acidic conditions. We found that glutamate accumulation is critical in the acid acclimation of MT123, possibly through consumption of intracellular protons via glutamate decarboxylation to GABA. This is despite the fact that MT123 lacks the canonical glutamate decarboxylase-glutamate/GABA antiporter system implicated in acid tolerance in other bacteria. In contrast, branched-chain amino acid (BCAA) accumulation was detrimental to cell growth at lower pHs, possibly through indirect mechanisms impacting the cellular glutamate pool. Genetic analysis previously linked MT123 to a population of Castellaniella that bloomed—concurrent to nitrate removal—during a biostimulation effort to reduce groundwater nitrate concentrations at MT123’s location of origin. Thus, our analyses provide novel insight into mechanisms of acclimation to acidic conditions in a strain with significant potential for nitrate bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Enhancing functionalities in carbon fiber composites by titanium dioxide nanoparticles

Carbon fiber composite's high specific strength makes it incredibly useful for structural applications. However, their low strain-to-failure can be problematic in structural applications that can potentially see high strain conditions or high fatigue cycles resulting in sudden, catastrophic failure. This is further complicated by damage manifesting within the composite thus not showing damage indicators on the surface. Therefore, monitoring the structural integrity and strain history of the composite in application by itself—while maintaining positive composite performance—is vital to ensure safe operation. In this study, a homogeneous dispersion of TiO 2 nanoparticles on carbon fiber is demonstrated to generate a piezoresistive carbon fiber polymer matrix composite with enhanced self-sensing capabilities. The nanoparticle-embedded composites also exhibited superior strength and damping potential compared to the nanoparticle-free composites. The apparent interlaminar shear strength increased by up to 15% and the damping loss factor increased by an average of 150% while the piezoresistive sensitivity increased by up to 180% with the addition of a small weight fraction of nanoparticles to the fiber surface. These results demonstrate an approach to simultaneously improve the sensing capabilities, damping behavior and mechanical strength of carbon fiber composites by simply adding nanoparticles in the fiber sizing using a commercially scalable deposition method.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Antibacterial and antioxidant activities of Streptomyces sp. strain FR7 isolated from forest soil

Abstract Actinomycetes produce secondary metabolites with many bioactivities such as antimicrobial, which can be useful as alternatives against resistant bacterial strains. Therefore, the screening of new habitats is likely to provide new strains with high potential. In this work, the antimicrobial capacity was used to select Streptomyces sp. strains isolated from Raf Raf forest (Tunisia). From the strain displaying higher activity, FR7, an ethyl acetate extract was prepared under optimized culturing conditions (10 days at 30°C in ISP2 medium with initial pH 8), showing significant antimicrobial activity against Micrococcus luteus and Staphylococcus aureus (MIC = 5 μg ml−1), and Listeria monocytogenes and Pseudomonas aeruginosa (MIC = 20 μg ml−1). The extract displayed strong DPPH radical scavenging activity (IC50 = 1.3 μg ml−1) and protection of yeast cells from H2O2-induced oxidative stress determined by flow cytometry with dichlorofluorescein diacetate. The crude extract showed the presence of polyketides, with methylsalicylic acid as moiety, a large and diverse group of secondary metabolites with a wide range of bioactivities, including antioxidant and antibacterial. Based on 16S RNA gene sequences, strain FR7 was identified as belonging to genus Streptomyces with high resemblance to S. iakyrus. Streptomyces sp. FR7 has great potential as a source of antibacterial and antioxidant metabolites.

Weslati, Imen↗
DOE OSTI2025

Combining computational modeling and experimental library screening to affinity-mature VEEV-neutralizing antibody F5

Engineered monoclonal antibodies have proven to be highly effective therapeutics in recent viral outbreaks. However, despite technical advancements, an ability to rapidly adapt or increase antibody affinity and by extension, therapeutic efficacy, has yet to be fully realized. We endeavored to stand-up such a pipeline using molecular modeling combined with experimental library screening to increase the affinity of F5, a monoclonal antibody with potent neutralizing activity against Venezuelan Equine Encephalitis Virus (VEEV), to recombinant VEEV (IAB) E1E2 antigen. We modeled the F5/E1E2 binding interface and generated predictions for mutations to improve binding using a Rosetta-based approach and dTERMen, an informatics approach. The modeling was complicated by the fact that a high-resolution structure of F5 is not available and the H3 loop of F5 exceeds the length for which current modeling approaches can determine a unique structure. A subset of the predicted mutations from both methods were incorporated into a phage display library of scFvs. This library and a library generated by error-prone PCR were screened for binding affinity to the recombinant antigen. Results from the screens identified favorable mutations which were incorporated into 12 human-IgG1 variants. The best variant, containing eight mutations, improved KD from 0.63 nM (parental) to 0.01 nM. While this did not improve neutralization or therapeutic potency of F5 against IAB, it did increase cross-reactivity to other closely related VEEV epizootic and enzootic strains, demonstrating the potential of this method to rapidly adapt existing therapeutics to emerging viral strains.

affinity-maturation↗