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We present draft genomes of two Paraburkholderia strains and two Burkholderia strains. Three strains were isolated from surrounding soils and one from roots of switchgrass (Panicum virgatum) in Michigan, USA.
The novel fungal strain, Fusarium sp. strain DS 682, was isolated from the rhizosphere of the perennial grass, Bouteloua gracilis , at the Konza Prairie Biological Station in Kansas. This fungal strain is common across North American grasslands and is resilient to environmental fluctuations. The draft genome is estimated to be 97.2% complete.
ABSTRACT RNA degradation is an important process that influences the ultimate concentration of individual proteins inside cells. While the main enzymes that facilitate this process have been identified, global maps of RNA turnover are available for only a few species. Even in these cases, there are few sequence elements that are known to enhance or destabilize a native transcript; even fewer confer the same effect when added to a heterologous transcript. To address this knowledge gap, we assayed genome-wide RNA degradation in the cyanobacterium Synechococcus sp. strain PCC 7002 by collecting total RNA samples after stopping nascent transcription with rifampin. We quantified the abundance of each position in the transcriptome as a function of time using RNA-sequencing data and later analyzed the global mRNA decay map using machine learning principles. Half-lives, calculated on a per-ORF (open reading frame) basis, were extremely short, with a median half-life of only 0.97 min. Despite extremely rapid turnover of most mRNA, transcripts encoding proteins involved in photosynthesis were both highly expressed and highly stable. Upon inspection of these stable transcripts, we identified an enriched motif in the 3′ untranslated region (UTR) that had similarity to Rho-independent terminators. We built statistical models for half-life prediction and used them to systematically identify sequence motifs in both 5′ and 3′ UTRs that correlate with stabilized transcripts. We found that transcripts linked to a terminator containing a poly(U) tract had a longer half-life than both those without a poly(U) tract and those without a terminator. IMPORTANCE RNA degradation is an important process that affects the final concentration of individual mRNAs, affecting protein expression and cellular physiology. Studies of how RNA is degraded increase our knowledge of this fundamental process as well as enable the creation of genetic tools to manipulate RNA stability. By studying global transcript turnover, we searched for sequence elements that correlated with transcript (in)stability and used these sequences to guide tool design. This study probes global RNA turnover in a cyanobacterium, Synechococcus sp. strain PCC 7002, that both has a unique array of RNases that facilitate RNA degradation and is an industrially relevant strain that could be used to convert CO 2 and sunlight into useful products.
We conducted a comprehensive comparative analysis of extracellular vesicles (EVs) from two Acanthamoeba castellanii strains, Neff (environmental) and T4 (clinical). Morphological analysis via transmission electron microscopy revealed slightly larger Neff EVs (average = 194.5 nm) compared to more polydisperse T4 EVs (average = 168.4 nm). Nanoparticle tracking analysis (NTA) and dynamic light scattering validated these differences. Proteomic analysis of the EVs identified 1,352 proteins, with 1,107 common, 161 exclusive in Neff, and 84 exclusively in T4 EVs. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) mapping revealed distinct molecular functions and biological processes and notably, the T4 EVs enrichment in serine proteases, aligned with its pathogenicity. Lipidomic analysis revealed a prevalence of unsaturated lipid species in Neff EVs, particularly triacylglycerols, phosphatidylethanolamines (PEs), and phosphatidylserine, while T4 EVs were enriched in diacylglycerols and diacylglyceryl trimethylhomoserine, phosphatidylcholine and less unsaturated PEs, suggesting differences in lipid metabolism and membrane permeability. Metabolomic analysis indicated Neff EVs enrichment in glycerolipid metabolism, glycolysis, and nucleotide synthesis, while T4 EVs, methionine metabolism. Furthermore, RNA-seq of EVs revealed differential transcript between the strains, with Neff EVs enriched in transcripts related to gluconeogenesis and translation, suggesting gene regulation and metabolic shift, while in the T4 EVs transcripts were associated with signal transduction and protein kinase activity, indicating rapid responses to environmental changes. In this novel study, data integration highlighted the differences in enzyme profiles, metabolic processes, and potential origins of EVs in the two strains shedding light on the diversity and complexity of A. castellanii EVs and having implications for understanding host-pathogen interactions and developing targeted interventions for Acanthamoeba-related diseases.
Bacillus cereus is a ubiquitous Gram-positive, spore-forming, rod-shaped saprophytic bacterium, occasionally reported to cause food-borne illnesses. However, instances of B. cereus strains harboring anthrax toxin and capsule genes have elevated certain strains as formidable pathogens and biothreats. This study focuses on the genomic analysis and the structural characterization of capsular material produced by the virulent B. cereus PATH2418 strain, isolated from the wound of a traumatic open fracture patient. The genome was sequenced using Nanopore MinION sequencing, revealing a chromosome of 5,270,283 bp and three plasmids. One plasmid, pATH1, was found to encode an operon for the biosynthesis of a bacterial capsule. This operon had sequence homology to the Bacillus anthracis capBCADE operon, which encodes the poly-γ-D-glutamate (PDGA) capsule. The capsule production in B. cereus PATH2418 was influenced by temperature and CO 2 levels. Structural analysis of the capsular material using a combined approach of nuclear magnetic resonance (NMR) and high-performance liquid chromatography (HPLC) techniques confirmed the presence of a high-molecular-weight poly-γ-glutamate capsule, with an enantiomeric composition of approximately 67% D-glutamic acid and 33% L-glutamic acid, matching that of B. anthracis.
Abstract Objective Adaptive laboratory evolution (ALE) is an effective approach to study the evolution behavior of bacterial cultures and to select for strains with desired metabolic features. In this study, we explored the possibility of evolving Thermotoga sp. strain RQ7 for cellulose-degrading abilities. Results Wild type RQ7 strain was subject to a series of transfers over six and half years with cellulose filter paper as the main and eventually the sole carbon source. Each transfer was accompanied with the addition of 50 μg of Caldicellulosiruptor saccharolyticus DSM 8903 genomic DNA. A total of 331 transfers were completed. No cellulose degradation was observed with the RQ7 cultures. Thirty three (33) isolates from six time points were sampled and sequenced. Nineteen (19) of the 33 isolates were unique, and the rest were duplicated clones. None of the isolates acquired C. saccharolyticus DNA, but all accumulated small-scale mutations throughout their genomes. Sequence analyses revealed 35 mutations that were preserved throughout the generations and another 15 mutations emerged near the end of the study. Many of the affected genes participate in phosphate metabolism, substrate transport, stress response, sensory transduction, and gene regulation.
Optical frequency domain reflectometry (OFDR) is a spectral measurement technique in which shifts in the local Rayleigh backscatter spectra can be used to perform distributed temperature or strain measurements relative to a reference measurement using ordinary single-mode optical fibers. Here, we demonstrate a data processing methodology for improving the resolvable range of temperature and strain by adaptively varying the reference measurement position by position, based on the time evolution of the local optical intensities and the correlation between the reference and active measurements. These methods nearly double the resolvable range of temperature and strain compared with that achieved using the traditional static reference approach.
The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.
Strains play a pivotal role in determining the phase equilibrium, domain configuration, and functional properties of the low-dimensional ferroelectrics. There is growing interest in the strain engineering of ferroelectric K x Na 1- x NbO 3 (KNN) epitaxial thin films, which exhibit excellent physical properties and promise as eco-friendly alternatives to lead-based ferroelectrics for microdevice applications. Further, advances have been made in understanding the phase equilibria and transitions, domains and domain walls, and their relations to the physical properties of KNN epitaxial thin films using a combination of experiments and theoretical modeling, particularly phase-field simulations. Here, we review recent progress in these aspects and showcase the phase-field method for establishing strain phase diagrams, elucidating the domain and domain wall structures at equilibrium, and predicting the structure–property relationships in ferroelectric KNN thin films. We also discuss challenges and opportunities to further advance our understanding of KNN thin films and potentially unlock new functionalities by leveraging phase-field simulations.
Silicon is a promising candidate as a next generation anode to replace or complement graphite electrodes due to its high energy density and low lithiation potential. When silicon is lithiated, it experiences over 300% expansion which stresses the silicon as well as its solid electrolyte interphase (SEI) leading to poor performance. The use of nano-sized silicon has helped to mitigate volume expansion and stress in the silicon, yet the silicon SEI is still both mechanically and chemically unstable. Identifying the mechanical failure mechanism of the SEI will help enhance calendar and cycle life performance through improved SEI design. In situ moiré interferometry was investigated to try and track the in-plane strain in the SEI and silicon electrode for this purpose. Moiré can detect on the order of 10 nm changes in displacement and is therefore a useful tool in the measurement of strain. As the sample undergoes small deformations, large changes in the moiré fringe allow for measurements of displacement below the diffraction limit of light. Figure 1a shows how the moiré fringe changes as the sample grating deforms. As the sample contracts or expands, the frequency of the moiré fringe changes, and this change is proportional to the strain in the sample.
As the project titles indicate, the work focused on Group IV nanomembranes (NMs), thin functional layers, and interfaces, all with one or more dimensions at the nanoscale. The primary focus was discovery driven fundamental science. This approach led to surprising new, unexpected results that ended up being patentable and creating commercial value, but that were also high-impact science. Our effort divided into several overlapping thrusts: 1) strain engineering of NMs, via both lattice strain and externally applied strain, 2) interfaces between crystalline semiconductor NMs and other 2D sheets that are stacked or grown on each other, and 3) charge transport (electronics and optoelectronics) in thin layers, sheets, and surfaces. We accomplish these goals via 1) fabrication of new or higher-quality materials using NM approaches, 2) growth of new combinations, or 3) transfer and stacking to create new composites. The range of materials included combinations of Si, Ge, graphene, and several III-V compounds. The work has foundations in both nano- and mesoscale science.
Optomechanical strain sensing provides attractive opportunities for novel particle detection schemes, as well as studying stress-induced (i.e. non-radiogenic) phonon bursts, which have been demonstrated to limit the coherence times of superconducting qubits and are a suspected culprit in the low energy excesses observed by many dark matter direct detection experiments. We are investigating SiN microring optical resonator strain sensors, developed at Purdue University, for applications in fundamental particle sensing and QIS. These sensors can be embedded in the substrate upon which superconducting qubits are patterned, providing a handle to distinguish decoherence events of radiogenic origin from those due to crystal stress. In a similar way, these sensors can be operated in conjunction with superconducting detectors (e.g., MKIDs, TES) to enable multi-channel readout of particle interactions in the device substrate or serve as anticoincidence detectors, which may be required to ident ify low-energy interactions from dark matter particles down to the fermionic thermal relic mass limit of a few keV. Such sensors can potentially be used to directly observe resonant scattering processes of gamma rays (and perhaps neutrinos) where no detectable quanta are produced in the target, via the microscopic stress induced by the momentum transfer to the (fixed-in-place) crystal lattice as a whole. These strain sensors have so far found application in photonics and communications, but have yet to be adopted for HEP uses, where they can provide unique capabilities in the search for dark matter as well as understanding and improving the coherence times of superconducting qubits.
High polarization electron beams for accelerators are generated using strained superlattice GaAs-based photocathodes. A collaboration of researchers at University of California Santa Barbara and Jefferson Lab has been investigating growth of SSL photocathodes using either chemical- or molecular-beam epitaxy (CBE or MBE) to re-establish a source of high polarization photocathode material. While calibrating growth parameters for the now standard GaAs/GaAsP strained superlattice structure, the UCSB personnel encountered the drawbacks of growing structures with phosphorus in a MBE or CBE system, including high vapor pressure byproducts, phosphorus contamination in both the GaAs layer and all subsequent materials grown in that chamber, and highly flammable and toxic chamber residues. For these reasons, the UCSB team began additionally investigating strained superlattices of InAlGaAs/AlGaAs, which has been successfully demonstrated in the literature1, to be a high QE, high polarization photocathode material. For GaAs/GaAsP, varying phosphorus content affects both the band gap and polarization. However for InAlGaAs/AlGaAs, In and Al content can be varied independently and allows optimization of both polarization and bandgap. Several variations on InAlGaAs/AlGaAs superlattice photocathodes, including those with distributed Bragg reflector (DBR) structures to enhance QE, have been grown at UCSB and sent to Jefferson Lab for testing. The initial results are quite promising, with polarization over 80% and QE about 0.3%, and ongoing test results will be presented.
Understanding temperature-dependent material decomposition and structural deformation induced by combined thermal-mechanical environments is critical for safety qualification of hardware under accident scenarios. Seeing in with X-rays elucidated the physics necessary to develop X-ray strain and thermometry diagnostics for use in optically opaque environments. Two parallel thermometry schemes were explored: X-ray fluorescence and X-ray diffraction of inorganic doped ceramics– colloquially known as thermographic phosphors. Two parallel surface strain techniques–Path-Integrated Digital Image Correlation and Frequency Multiplexed Digital Image Correlation–were demonstrated. Finally, preliminary demonstration of time-resolved digital volume correlation was performed by taking advantage of limited view reconstruction techniques. Additionally, research into blended ceramic-metal coatings was critical to generating intrinsic thermographic patterns for the future combination of X-ray strain and thermometry measurements.
This project seeks to elucidate and harness the exceptional robustness of novel and undomesticated Y. lipolytica isolates, which were identified from a genetic diversity screening for compatibility with bioenergy development. Bioenergy-relevant isolates were further developed as microbial platforms for efficient conversion of undetoxified biomass hydrolysates into designer bio-esters continuously recovered by solvent extraction. The project has three major goals. Goal 1. Elucidate and enhance the endogenous metabolism of Y. lipolytica for superior growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates under hypoxic conditions. Goal 2. Understand and enhance the underlying mechanism of exceptional tolerance of Y. lipolytica to organic solvents. Goal 3. Elucidate and rewire endogenous metabolism of the most robust Y. lipolytica strains for effective conversion of accumulating lipids to designer bio-esters. Significant progress has been made toward completing all research goals. We elucidated and optimized the robustness of Y. lipolytica by utilizing mixed C5 and C6 sugars in switchgrass hydrolysates (SGH) for lipid production (Aim 1). We conducted extensive omics analysis to investigate how genetic diversity among Yarrowia strains, derived from natural isolates or developed through adaptive laboratory evolution, influences lipid production when utilizing SGH. In Aim 2, novel mechanisms and underlying genetics were discovered that enabled Yarrowia strains to thrive in cultures containing high ionic liquid (IL) concentrations. Amongst other novel findings, it was found that sterols strengthened cell membranes to confer IL toxicity resistance, specifically via increased ergosterol content upon exposure to IL. In Aim 3, mechanistic studies elucidated how Y. lipolytica utilized intracellular lipids and alkanes/alkenes, leading to our discovery of novel enzymes and pathways for making short-chain esters. Most notably, thermostable chloramphenicol transferases were repurposed to function as alcohol acetyltransferases in Y. lipolytica, as well as the Gram-negative and Gram-positive bacteria Escherichia coli and thermophile Clostridium thermocellum, respectively.
This report details an analysis package, Ring Pull Strain Analysis (RPSA), that can be used to present and quantify digital image correlation (DIC) data as it relates to a gaugeless ring pull test. Gaugeless ring pull is a testing technique for mechanical testing of small annular samples, usually cut from a thin-walled tube. DIC data is often necessary for this kind of test because bending moments present on the ring cause a non-uniform strain distribution and localized measurements are necessary. In addition, the annular geometry of a ring lends itself to a polar representation, which is not present with typical DIC analysis methods. RPSA was made to calculate and plot the polar representation of strain from standard pre-processed DIC data of a gaugeless ring pull test. Further analysis can be done on ring pull including a quasi-uniaxial tensile analysis and coating analysis, which are also performed by RPSA. In addition, due to the universality of DIC plotting and ring pull test analysis, RPSA can accommodate a wide variety of tests, though it is tailored for ring pull testing. This report details how RPSA works, including the theory, assumptions, and logic behind the calculations and the structure of the program.
Alternative oxidase is a terminal oxidase in the branched mitochondrial electron transport chain of most fungi including Aspergillus niger (subgenus Circumdati, section Nigri). A second, paralogous aox gene (aoxB) is extant in some A. niger isolates but also present in two divergent species of the subgenus Nidulantes—A. calidoustus and A. implicatus—as well as in Penicillium swiecickii. Black aspergilli are cosmopolitan opportunistic fungi that can cause diverse mycoses and acute aspergillosis in immunocompromised individuals. Amongst the approximately 75 genome-sequenced A. niger strains, aoxB features considerable sequence variation. Five mutations were identified that rationally affect transcription or function or terminally modify the gene product. One mutant allele that occurs in CBS 513.88 and A. niger neotype strain CBS 554.65 involves a chromosomal deletion that removes exon 1 and intron 1 from aoxB. Another aoxB allele results from retrotransposon integration. Three other alleles result from point mutations: a missense mutation of the start codon, a frameshift, and a nonsense mutation. A. niger strain ATCC 1015 has a full-length aoxB gene. The A. niger sensu stricto complex can thus be subdivided into six taxa according to extant aoxB allele, which may facilitate rapid and accurate identification of individual species
Primary production in Mono Lake, a hypersaline soda lake rich in dissolved inorganic arsenic, is dominated by Picocystis strain ML. We set out to determine if this photoautotrophic picoplankter could metabolize inorganic arsenic and in doing so form unusual arsenolipids (e.g., arsenic bound to 2-O-methyl ribosides) as reported in other saline ecosystems and by halophilic algae. We cultivated Picocystis strain ML on a seawater-based medium with either low (37 µM) or high (1000 µM) phosphate in the presence of arsenite (400 µM), arsenate (800 µM), or without arsenic additions (ca 0.025 µM). Cultivars formed a variety of organoarsenic compounds, including a phytyl 2-O-methyl arsenosugar, depending upon the cultivation conditions and arsenic exposure. When the cells were grown at low P, the organoarsenicals they produced when exposed to both arsenite and arsenate were primarily arsenolipids (~88%) with only a modest content of water-soluble organoarsenic compounds (e.g., arsenosugars). When grown at high P, sequestration shifted to primarily water-soluble, simple methylated arsenicals such as dimethylarsinate; arsenolipids still constituted ~32% of organoarsenic incorporated into cells exposed to arsenate but < 1% when exposed to arsenite. Curiously, Picocystis strain ML grown at low P and exposed to arsenate sequestered huge amounts of arsenic into the cells accounting for 13.3% of the dry biomass; cells grown at low P and arsenite exposure sequestered much lower amounts, equivalent to 0.35% of dry biomass. Extraction of a resistant phase with trifluoroacetate recovered most of the sequestered arsenic in the form of arsenate. Uptake of arsenate into low P-cultivated cells was confirmed by X-ray fluorescence, while XANES/EXAFS spectra indicated the sequestered arsenic was retained as an inorganic iron precipitate, similar to scorodite, rather than as an As-containing macromolecule. Samples from Mono Lake demonstrated the presence of a wide variety of organoarsenic compounds, including arsenosugar phospholipids, most prevalent in zooplankton (Artemia) and phytoplankton samples, with much lower amounts detected in the bottom sediments. These observations suggest a trophic transfer of organoarsenicals from the phytoplankton (Picocystis) to the zooplankton (Artemia) community, with efficient bacterial mineralization of any lysis-released organoarsenicals back to inorganic oxyanions before they sink to the sediments.