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At least 217 records · Page 12

Regioselectivity mechanism of the Thunbergia alata Δ 6 -16:0-acyl carrier protein desaturase

Plant plastidial acyl–acyl carrier protein (ACP) desaturases are a soluble class of diiron-containing enzymes that are distinct from the diiron-containing integral membrane desaturases found in plants and other organisms. The archetype of this class is the stearoyl-ACP desaturase which converts stearoyl-ACP into oleoyl (18:1Δ 9 cis )-ACP. Several variants expressing distinct regioselectivity have been described including a Δ 6 -16:0-ACP desaturase from black-eyed Susan vine ( Thunbergia alata ). We solved a crystal structure of the T. alata desaturase at 2.05 Å resolution. Using molecular dynamics (MD) simulations, we identified a low-energy complex between 16:0-ACP and the desaturase that would position C6 and C7 of the acyl chain adjacent to the diiron active site. The model complex was used to identify mutant variants that could convert the T. alata Δ 6 desaturase to Δ 9 regioselectivity. Additional modeling between ACP and the mutant variants confirmed the predicted regioselectivity. Furthermore, to validate the in-silico predictions, we synthesized two variants of the T. alata desaturase and analyzed their reaction products using gas chromatography-coupled mass spectrometry. Assay results confirmed that mutants designed to convert T. alata Δ 6 to Δ 9 selectivity exhibited the predicted changes. In complementary experiments, variants of the castor desaturase designed to convert Δ 9 to Δ 6 selectivity lost some of their Δ9 desaturation ability and gained the ability to desaturate at the Δ 6 position. The computational workflow for revealing the mechanistic understanding of regioselectivity presented herein lays a foundation for designing acyl-ACP desaturases with novel selectivities to increase the diversity of monoenes available for bioproduct applications.

59 BASIC BIOLOGICAL SCIENCES↗

X-ray Emission Measurements following Charge Exchange between C 6+ and He

X-ray spectra following charge exchange collisions between C6+ and He are presented for collision energies between 460 eV/u and 32,000 eV/u. Spectra were obtained at the Oak Ridge National Laboratory ion-atom merged-beams apparatus, using a microcalorimeter X-ray detector capable of fully resolving the C VI Lyman series lines through Ly-gamma. These line ratios are sensitive to the initial electron l-distribution and test our understanding of the charge exchange process. In addition, these line ratios are important for identifying charge exchange in astrophysical contexts involving the interaction of solar wind ions with neutrals. Our measurements are performed at collision velocities (300 km/s to 2500 km/s) which overlap most of the solar wind range. Additional data of this type can hopefully be combined with computations to provide an extensive set of reliable line ratios and absolute cross sections for the interpretation of a variety of astrophysical situations.

Defay, X↗

Development of genetic tools for heterologous protein expression in a pentose‐utilizing environmental isolate of Pseudomonas putida

Abstract Pseudomonas putida has emerged as a promising host for the conversion of biomass‐derived sugars and aromatic intermediates into commercially relevant biofuels and bioproducts. Most of the strain development studies previously published have focused on P. putida KT2440, which has been engineered to produce a variety of non‐native bioproducts. However, P. putida is not capable of metabolizing pentose sugars, which can constitute up to 25% of biomass hydrolysates. Related P. putida isolates that metabolize a larger fraction of biomass‐derived carbon may be attractive as complementary hosts to P. putida KT2440. Here we describe genetic tool development for P. putida M2, a soil isolate that can metabolize pentose sugars. The functionality of five inducible promoter systems and 12 ribosome binding sites was assessed to regulate gene expression. The utility of these expression systems was confirmed by the production of indigoidine from C6 and C5 sugars. Chromosomal integration and expression of non‐native genes was achieved by using chassis‐independent recombinase‐assisted genome engineering (CRAGE) for single‐step gene integration of biosynthetic pathways directly into the genome of P. putida M2. These genetic tools provide a foundation to develop hosts complementary to P. putida KT2440 and expand the ability of this versatile microbial group to convert biomass to bioproducts.

59 BASIC BIOLOGICAL SCIENCES↗

WE-AB-207B-10: On Spinal Nerve Toxicity from Single-Session SAbR in Pigs and the Translation of Small Animal NTCP Models

Purpose: The incidence of peripheral neuropathy has risen with increased utilization of SAbR. There is no consensus regarding the dose-tolerance of the peripheral nervous system. In 2015, we commenced an investigation to test the hypotheses that single-session irradiation to the pig spinal nerves exhibit a similar dose-tolerance as that of the spinal cord and that a dose-length effect exists. This work evaluates the direct application of small animal NTCP models to both large animal spinal cord and preliminary peripheral nerve data. Methods: To date, 16 of 25 Yucatan minipigs have received single-session SAbR to a 1.5cm length and 4 of 25 have received irradiation to a 0.5cm length of left-sided C6-C8 spinal nerves. Toxicity related gait change has been observed in 13 animals (9 from the long length group and 4 from the short). This preliminary data is overlaid on several dose-response models which have been fit to rodent spinal cord tolerance experiments. Model parameters define a toxicity profile between a completely serial or parallel behaving organ. Adequacy of model application, including how length effects are handled, to published minipig spinal cord dose-response data and to preliminary peripheral nerve response data was evaluated through residual analysis. Results: No rodent-derived dose-response models were directly applicable to all pig data for the different lengths irradiated. Several models fit the long-length irradiated spinal cord data well, with the more serial-like models fitting best. Preliminary data on the short-length irradiation suggests no length effect exists, disproving our hypothesis. Conclusion: Direct application of small-animal NTCP models to pig data suggests dose-length effect predictions from small animal data may not translate clinically. However, the small animal models used have not considered dose heterogeneity and it is expected that including the low-to-mid dose levels in the penumbral region will improve this match. This work was funded by the Cancer Prevention Research Institute of Texas (CPRIT).

60 APPLIED LIFE SCIENCES↗

Expanded genome and proteome reallocation in a novel, robust Bacillus coagulans strain capable of utilizing pentose and hexose sugars

Bacillus coagulans, a Gram-positive thermophilic bacterium, is recognized for its probiotic properties and recent development as a microbial cell factory. Despite its importance for biotechnological applications, the current understanding of B. coagulans’ robustness is limited, especially for undomesticated strains. To fill this knowledge gap, we characterized the metabolic capability and performed functional genomics and systems analysis of a novel, robust strain, B. coagulans B-768. Genome sequencing revealed that B-768 has the largest B. coagulans genome known to date (3.94 Mbp), about 0.63 Mbp larger than the average genome of sequenced B. coagulans strains, with expanded carbohydrate metabolism and mobilome. Functional genomics identified a well-equipped genetic portfolio for utilizing a wide range of C5 (xylose, arabinose), C6 (glucose, mannose, galactose), and C12 (cellobiose) sugars present in biomass hydrolysates, which was validated experimentally. For growth on individual xylose and glucose, the dominant sugars in biomass hydrolysates, B-768 exhibited distinct phenotypes and proteome profiles. Faster growth and glucose uptake rates resulted in lactate overflow metabolism, which makes B. coagulans a lactate overproducer; however, slower growth and xylose uptake diminished overflow metabolism due to the high energy demand for sugar assimilation. Carbohydrate Transport and Metabolism (COG-G), Translation (COG-J), and Energy Conversion and Production (COG-C) made up 60%–65% of the measured proteomes but were allocated differently when growing on xylose and glucose. The trade-off in proteome reallocation, with high investment in COG-C over COG-G, explains the xylose growth phenotype with significant upregulation of xylose metabolism, pyruvate metabolism, and tricarboxylic acid (TCA) cycle. Strain B-768 tolerates and effectively utilizes inhibitory biomass hydrolysates containing mixed sugars and exhibits hierarchical sugar utilization with glucose as the preferential substrate.

carbohydrate metabolism↗

Bromination of 1,2,3,4-Tetrahydro-1,10-phenanthroline: Synthesis and Crystal Structure of 6-Bromo-1,2,3,4-tetrahydro-1,10-phenanthroline and Its Bromide Salt

The bromination reaction of 1,2,3,4-tetrahydro-1,10-phenanthroline (tphen) is investigated, which can afford a new heterocyclic compound, namely 6-bromo-1,2,3,4-tetrahydro-1,10-phenanthroline (1). The bromide salt of 1, i.e., 1 · (1H) · Br (2), can be isolated from the bromination system. The accurate structures of both compounds are confirmed and investigated by single-crystal X-ray diffraction. The result proves that the bromination reaction of tphen mainly affords its C6-substituted product. In compounds 1 and 2, the N−H···Br hydrogen bonds play an important role in intermolecular connection. Crystal data of 1: Monoclinic system, sp. gr. Pc, a = 4.6628(8) Å, b = 8.7980(15) Å, c = 13.1347(19) Å, β = 101.342(5)°, Z = 2, V = 528.31(15) Å{sup 3}. Crystal data of 2: Monoclinic system, sp. gr. P2{sub 1}/n, a = 16.6171(16) Å, b = 7.8323(8) Å, c = 18.6972(18) Å, β = 113.597(2)°, Z = 4, V = 2230.0(4) Å{sup 3}.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Condensation Reaction of 1,2,3,4-Tetrahydro-1,10-phenanthroline and Formaldehyde: Synthesis and Crystal Structures of Bis(1,2,3,4-tetrahydro-1,10-phenanthroline-6-yl)methane and Its p-Toluenesulfonate Salt

A new heterocyclic compound, bis(1,2,3,4-tetrahydro-1,10-phenanthroline-6-yl) methane (1), was obtained by the condensation reaction of 1,2,3,4-tetrahydro-1,10-phenanthroline (tphen) and formaldehyde (HCHO). The p-toluenesulfonate salt of 1, (ptsa){sub 2} · (1H{sub 2}) (2, ptsaH = p-toluenesulfonic acid), is also synthesized and characterized. Cystal structures of 1 and 2 are determined by X-ray single crystal diffraction. The molecules of 1 form a 1D helix supramolecular chain by weak N−H···N hydrogen bonds, while in crystal 2, the 1H{sub 2}{sup 2+} cations and ptsa{sup -} anions are alternately connected by strong N−H···O hydrogen bonds and generate a 1D zigzag supramolecular chain. The result also proves that the condensation reaction of tphen can provide its C6 condensation product with high regioselectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Impact of Polymer Electrolyte Membrane Degradation Products on Oxygen Reduction Reaction Activity for Platinum Electrocatalysts

The impact of model membrane degradation compounds on the relevant electrochemical parameters for the oxygen reduction reaction (i.e. electrochemical surface area and catalytic activity), was studied for both polycrystalline Pt and carbon supported Pt electrocatalysts. Model compounds, representing previously published, experimentally determined polymer electrolyte membrane degradation products, were in the form of perfluorinated organic acids that contained combinations of carboxylic and/or sulfonic acid functionality. Perfluorinated carboxylic acids of carbon chain length C1 – C6 were found to have an impact on electrochemical surface area (ECA). The longest chain length acid also hindered the observed oxygen reduction reaction (ORR) performance, resulting in a 17% loss in kinetic current (determined at 0.9 V). Model compounds containing sulfonic acid functional groups alone did not show an effect on Pt ECA or ORR activity. Lastly, greater than a 44% loss in ORR activity at 0.9V was observed for diacid model compounds DA-Naf (perfluoro(2-methyl-3-oxa-5-sulfonic pentanoic) acid) and DA-3M (perfluoro(4-sulfonic butanoic) acid), which contained both sulfonic and carboxylic acid functionalities.

30 DIRECT ENERGY CONVERSION↗

Heterologous expression of family 10 xylanases from Acidothermus cellulolyticus enhances the exoproteome of Caldicellulosiruptor bescii and growth on xylan substrates

The ability to deconstruct plant biomass without conventional pretreatment has made members of the genus Caldicellulosiruptor the target of investigation for the consolidated processing of lignocellulosic biomass to biofuels and bioproducts. These Gram-positive bacteria are hyperthermophilic anaerobes and the most thermophilic cellulolytic organisms so far described. They use both C5 and C6 sugars simultaneously and have the ability to grow well on xylan, a major component of plant cell walls. This is an important advantage for their use to efficiently convert biomass at yields sufficient for an industrial process. For commodity chemicals, yield from substrate is perhaps the most important economic factor. In an attempt to improve even further the ability of C. bescii to use xylan, we introduced two xylanases from Acidothermus cellulolyticus. Acel_0180 includes tandem carbohydrate-binding modules (CBM2 and CBM3) located at the C-terminus, one of which, CBM2, is not present in C. bescii. Also, the sequences of Xyn10A and Acel_0180 have very little homology with the GH10 domains present in C. bescii . For these reasons, we selected these xylanases as potential candidates for synergistic interaction with those in the C. bescii exoproteome. As a result, heterologous expression of two xylanases from Acidothermus cellulolyticus in Caldicellulosiruptor bescii resulted in a modest, but significant increase in the activity of the exoproteome of C. bescii on xylan substrates. Even though the increase in extracellular activity was modest, the ability of C. bescii to grow on these substrates was dramatically improved suggesting that the xylan substrate/microbe interaction substantially increased deconstruction over the secreted free enzymes alone. In conclusion, we anticipate that the ability to efficiently use xylan, a major component of plant cell walls for conversion of plant biomass to products of interest, will allow the conversion of renewable, sustainable, and inexpensive plant feedstocks to products at high yields.

09 BIOMASS FUELS↗

Discovery of a Splicing Regulator Required for Cell Cycle Progression

In the G1 phase of the cell division cycle, eukaryotic cells prepare many of the resources necessary for a new round of growth including renewal of the transcriptional and protein synthetic capacities and building the machinery for chromosome replication. The function of G1 has an early evolutionary origin and is preserved in single and multicellular organisms, although the regulatory mechanisms conducting G1 specific functions are only understood in a few model eukaryotes. Here we describe a new G1 mutant from an ancient family of apicomplexan protozoans. Toxoplasma gondii temperature-sensitive mutant 12-109C6 conditionally arrests in the G1 phase due to a single point mutation in a novel protein containing a single RNA-recognition-motif (TgRRM1). The resulting tyrosine to asparagine amino acid change in TgRRM1 causes severe temperature instability that generates an effective null phenotype for this protein when the mutant is shifted to the restrictive temperature. Orthologs of TgRRM1 are widely conserved in diverse eukaryote lineages, and the human counterpart (RBM42) can functionally replace the missing Toxoplasma factor. Transcriptome studies demonstrate that gene expression is downregulated in the mutant at the restrictive temperature due to a severe defect in splicing that affects both cell cycle and constitutively expressed mRNAs. The interaction of TgRRM1 with factors of the tri-SNP complex (U4/U6 & U5 snRNPs) indicate this factor may be required to assemble an active spliceosome. Thus, the TgRRM1 family of proteins is an unrecognized and evolutionarily conserved class of splicing regulators. This study demonstrates investigations into diverse unicellular eukaryotes, like the Apicomplexa, have the potential to yield new insights into important mechanisms conserved across modern eukaryotic kingdoms.

Cell↗

Disruption of Retinol (Vitamin A) Signaling by Phthalate Esters: SAR and Mechanism Studies

A spectrum of reproductive system anomalies (cryptorchidism, hypospadias, dysgenesis of Wolffian duct-derived tissues and prostate, and reduced sperm production) in male rats exposed in utero to phthalate esters (PEs) are thought to be caused by PE inhibition of fetal testosterone production. Recently, dibutyl and dipentyl phthalate (DBuP, DPnP) were shown to disrupt the retinol signaling pathway (RSP) in mouse pluripotent P19 embryonal carcinoma cells in vitro. The RSP regulates the synthesis and cellular levels of retinoic acid (RA), the active metabolite of retinol (vitamin A). In this new study, a total of 26 di- and mono-esters were screened to identify additional phthalate structures that disrupt the RSP and explore their mechanisms of action. The most potent PEs, those causing > 50% inhibition, contained aryl and cycloalkane groups or C4-C6 alkyl ester chains and were the same PEs reported to cause malformations in utero. They shared similar lipid solubility; logP values were between 4 and 6 and, except for PEs with butyl and phenyl groups, were stable for prolonged periods in culture. Mono- and cognate di-esters varied in ability to disrupt the RSP; e.g., DEHP was inactive but its monoester was active while DBuP was active yet its monoester was inactive. DBuP and dibenzyl phthalate both disrupted the synthesis of RA from retinol but not the ability of RA to activate gene transcription. Both PEs also disrupted the RSP in C3H10T1/2 multipotent mesenchymal stem cells. Based on this in vitro study showing that some PEs disrupt retinol signaling and previous in vivo studies that vitamin A/ RA deficiency and PEs both cause strikingly similar anomalies in the male rat reproductive system, we propose that PE-mediated inhibition of testosterone and RA synthesis in utero are both causes of malformations in male rat offspring.

59 BASIC BIOLOGICAL SCIENCES↗

Enabling AI in synthetic biology through Construction File specification

The Construction File (CF) specification establishes a standardized interface for molecular biology operations, laying a foundation for automation and enhanced efficiency in experiment design. It is implemented across three distinct software projects: PyDNA_CF_Simulator, a Python project featuring a ChatGPT plugin for interactive parsing and simulating experiments; ConstructionFileSimulator, a field-tested Java project that showcases 'Experiment' objects expressed as flat files; and C6-Tools, a JavaScript project integrated with Google Sheets via Apps Script, providing a user-friendly interface for authoring and simulation of CF. The CF specification not only standardizes and modularizes molecular biology operations but also promotes collaboration, automation, and reuse, significantly reducing potential errors. The potential integration of CF with artificial intelligence, particularly GPT-4, suggests innovative automation strategies for synthetic biology. While challenges such as token limits, data storage, and biosecurity remain, proposed solutions promise a way forward in harnessing AI for experiment design. This shift from human-driven design to AI-assisted workflows, steered by high-level objectives, charts a potential future path in synthetic biology, envisioning an environment where complexities are managed more effectively.

59 BASIC BIOLOGICAL SCIENCES↗

PW2 Pumping: March 18 thru March 22, 2020

Processed Coherence-length-gated Microwave Photonics Interferometry (CMPI) distributed vertical strain on March 18 through March 22, 2020 at the hydromechanical test facility located at the Clemson University Simpson Station research facility in Central, South Carolina, USA. This includes ambient data in addition to a pumping test performed between 14:31-20:31 EST on 3/22/2020 from Pumping Well 2 (PW2). These data are from a strain ribbon that was deployed in the vadose zone at approximately 34.670130°N, -82.729524°E from the ground surface to a depth of 8m in saprolite containing weak reflectors pairs were placed every 0.85 m along the fiber. Each weak reflector pair forms a 15 cm cavity strain meter. Strain unit: meters/meter (strain). Sampling rate 0.1 Hz. Each column corresponds to the strain data taken at a depth d from the ground surface. c1: d = 1.00m c2: d = 1.85m c3: d = 2.70m c4: d = 3.55m (large demodulation error) c5: d = 4.40m c6: d = 5.25m c7: d = 6.10m (large demodulation error) c8: d = 6.95m

Distributed Strain Sensing↗

Biorefinery and Carbon Cycling Research Project

In this project we focused on several aspects of technology development that advances the formation of an integrated biorefinery. These focus areas include: pretreatment of biomass to enhance quality of products from thermochemical conversion; characterization of and development of coproduct uses; advancement in fermentation of lignocellulosics and particularly C5 and C6 sugars simultaneously, and development of algal biomass as a potential substrate for the biorefinery. These advancements are intended to provide a diverse set of product choices within the biorefinery, thus improving the cost effectiveness of the system. Technical effectiveness was demonstrated in the thermochemical product quality in the form of lower tar production, simultaneous of use of multiple sugars in fermentation, use of biochar in environmental (ammonia adsorption) and agricultural applications, and production of algal biomass in wastewaters. Economic feasibility of algal biomass production systems seems attractive, relative to the other options. However, further optimization in all paths, and testing/demonstration at larger scales are required to fully understand the economic viabilities. The coproducts provide a clear picture that multiple streams of value can be generated within an integrated biorefinery, and these include fuels and products.

09 BIOMASS FUELS↗

Analysis of Waste Isolation Pilot Plan (WIPP) Underground and MGO Samples by the Savannah River National Laboratory (SRNL)

Analysis of the recent WIPP samples are summarized in this report; WIPP Cam Filters 4, 6, 9 (3, 7, 11 were analyzed with FAS-118 in a separate campaign); WIPP Drum Lip R16 C4; WIPP Standard Waste Box R15 C5; WIPP MgO R16 C2; WIPP MgO R16 C4; WIPP MgO R16 C6; LANL swipes of parent drum; LANL parent drum debris; LANL parent drum; IAEA Swipe; Unused “undeployed” Swheat; Unused “undeployed” MgO; and Masselin cloth “smears”. Analysis showed that the MgO samples were very pure with low carbonate and water content. Other samples showed the expected dominant presence of Mg, Na and Pb. Parent drum debris sample was mildly acidic. Interpretation of results is not provided in this document, but rather to present and preserve the analytical work that was performed. The WIPP Technical Analysis Team is responsible for result interpretation which will be written separately.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Oak Ridge National Laboratory Analysis of Waste Isolation Pilot Plant Samples: Integrated Summary Report

Nondestructive and destructive analytical methods were used to analyze samples of debris collected from the top of R15 C5, the lip of R16 C4, the parent drum, and the continuous air monitor (CAM) and fixed air sampler (FAS) filters in addition to MgO samples collected from the tops of R14 C2, R14 C4, R14 C6 and R16 C4. The analytical evidence supports the conclusion that an exothermic oxidation reaction of Swheat Scoop® by metal nitrate salts produced sufficient quantities of gas to breach drum 68660. The metals and the acidic environment found in drum 68660 are known to accelerate these oxidation reactions. Moreover, the ratio of metal nitrate salts in drum 68660 was in a range in which a low melting eutectic mixture could form, which would also accelerate the oxidation reactions. Nitrated organics were not detected and they are not necessary to produce the exothermic reaction leading to the breach of drum 68660. All the contents of the drum were not consumed and the material ejected from drum 68660 either did not experience temperatures over 200 °C, or their exposure to elevated temperatures was very limited in duration (<seconds).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Development of an Integrated Biofuel and Chemical Refinery

This project has demonstrated the level of commercial readiness for production of the industrial chemical, 1,4-butanediol (BDO), from lignocellulosic biomass by engineered E. coli. Targets were BDO titer, rate, and yield (TRY) and growth in lignocellulosic hydrolysates (Hz). A range of Hzs were used to assess limitations for biomass-to-BDO. Via adaptive evolution methods, whole-genome sequencing, and introduction of identified target genes, strains co-utilizing C5/ C6 sugars were made. The composition of Hz versus TRY led to a modified Hz composition. This was used in partnership with the DOE to redirect the project to focus on 1) several biomass Hz from new suppliers, 2) Hz specification due to the characteristics of the Genomatica BDO process, 3) a gene cassette to engineer any BDO producing strain for biomass, and 4) modified BDO recovery to more economically recover BDO at industry specifications. BDO TRY and growth of the E. coli strains were predictable based on Hz composition from several suppliers. This defined metrics for biomass Hz composition to achieve BDO TRY along with internal TEA to evaluate the economic potential of each modification to strain, Hz feed, and process. An improved biomass-to-BDO production strain reached BDO T-R in a 30 L fermentation above original objectives. Yield approached the proposed Y and modifications to BDO recovery were demonstrated. Genomatica is now in the position of being able to incorporate biomass feedstocks into the commercial GENO BDO process.

09 BIOMASS FUELS↗

High Performance Polymers from Biomass

The objective of this study was to demonstrate feasibility and scale-up of cellulosic feedstocks for the production of a commercial C6 lactone. Visolis, Inc. has developed a fermentation platform for production of the lactone at high titers and yields. The lactone is used in high-end cosmetics industry and also serves as a valuable intermediate for production of biopolymers and biofuels. Strains employed by Visolis are capable of metabolizing both glucose and xylose, enabling full utilization of cellulosic hydrolysates as feedstock. Visolis and ABPDU conducted a 2L proof-of-concept fermentation campaign followed by a 50L scale-up campaign.

09 BIOMASS FUELS↗