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Drug discovery efforts at George Mason University

With over 39,000 students, and research expenditures in excess of $200 million, George Mason University (GMU) is the largest R1 (Carnegie Classification of very high research activity) university in Virginia. Mason scientists have been involved in the discovery and development of novel diagnostics and therapeutics in areas as diverse as infectious diseases and cancer. Below are highlights of the efforts being led by Mason researchers in the drug discovery arena. To enable targeted cellular delivery, and non-biomedical applications, Veneziano and colleagues have developed a synthesis strategy that enables the design of self-assembling DNA nanoparticles (DNA origami) with prescribed shape and size in the 10 to 100 nm range. The nanoparticles can be loaded with molecules of interest such as drugs, proteins and peptides, and are a promising new addition to the drug delivery platforms currently in use. The investigators also recently used the DNA origami nanoparticles to fine tune the spatial presentation of immunogens to study the impact on B cell activation. These studies are an important step towards the rational design of vaccines for a variety of infectious agents. To elucidate the parameters for optimizing the delivery efficiency of lipid nanoparticles (LNPs), Buschmann, Paige and colleagues have devised methods for predicting and experimentally validating the pKa of LNPs based on the structure of the ionizable lipids used to formulate the LNPs. These studies may pave the way for the development of new LNP delivery vehicles that have reduced systemic distribution and improved endosomal release of their cargo post administration. To better understand protein-protein interactions and identify potential drug targets that disrupt such interactions, Luchini and colleagues have developed a methodology that identifies contact points between proteins using small molecule dyes. The dye molecules noncovalently bind to the accessible surfaces of a protein complex with very high affinity, but are excluded from contact regions. When the complex is denatured and digested with trypsin, the exposed regions covered by the dye do not get cleaved by the enzyme, whereas the contact points are digested. The resulting fragments can then be identified using mass spectrometry. The data generated can serve as the basis for designing small molecules and peptides that can disrupt the formation of protein complexes involved in disease processes. For example, using peptides based on the interleukin 1 receptor accessory protein (IL-1RAcP), Luchini, Liotta, Paige and colleagues disrupted the formation of IL-1/IL-R/IL-1RAcP complex and demonstrated that the inhibition of complex formation reduced the inflammatory response to IL-1B. Working on the discovery of novel antimicrobial agents, Bishop, van Hoek and colleagues have discovered a number of antimicrobial peptides from reptiles and other species. DRGN-1, is a synthetic peptide based on a histone H1-derived peptide that they had identified from Komodo Dragon plasma. DRGN-1 was shown to disrupt bacterial biofilms and promote wound healing in an animal model. The peptide, along with others, is being developed and tested in preclinical studies. Other research by van Hoek and colleagues focuses on in silico antimicrobial peptide discovery, screening of small molecules for antibacterial properties, as well as assessment of diffusible signal factors (DFS) as future therapeutics. The above examples provide insight into the cutting-edge studies undertaken by GMU scientists to develop novel methodologies and platform technologies important to drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Life-Cycle Greenhouse Gas Emissions and Human Health Trade-Offs of Organic Waste Management Strategies

Waste-to-energy systems can play an important role in diverting organic waste from landfills. However, real-world waste management can differ from idealized practices, and emissions driven by microbial communities and complex chemical processes are poorly understood. This study presents a comprehensive life-cycle assessment, using reported and measured data, of competing management alternatives for organic municipal solid waste including landfilling, composting, dry anaerobic digestion (AD) for the production of renewable natural gas (RNG), and dry AD with electricity generation. Landfilling is the most greenhouse gas (GHG)-intensive option, emitting nearly 400 kg CO 2e per tonne of organic waste. Composting raw organics resulted in the lowest GHG emissions, at -41 kg CO 2e per tonne of waste, while upgrading biogas to RNG after dry AD resulted in -36 to -2 kg CO 2e per tonne. Monetizing the results based on social costs of carbon and other air pollutant emissions highlights the importance of ground-level NH3 emissions from composting nitrogen-rich organic waste or post-AD solids. However, better characterization of material-specific NH 3 emissions from landfills and land-application of digestate is essential to fully understand the trade-offs between alternatives.

54 ENVIRONMENTAL SCIENCES↗

Enhanced Softwood Cellulose Accessibility by H 3 PO 4 Pretreatment: High Sugar Yield without Compromising Lignin Integrity

Softwood lignocellulose is a potential feedstock for the production of biofuels and bioproducts. However, the highly cross-linked nature of softwood lignocellulose restricts enzyme access to its sugars. Thus, harsh pretreatment conditions (180–280 °C) and/or high enzyme loading are required to unlock sugars. These requirements negatively affect the economic viability of softwoods in biorefineries. Here we show that H 3 PO 4 pretreatment of pine and Douglas fir under a mild reaction temperature (50 °C) and atmospheric pressure enabled a high (~80%) glucan digestibility with low enzyme loading (5 filter paper units (FPU)/g glucan). The dissolution and regeneration of softwoods disrupted the hydrogen bonding between cellulose chains, thereby increasing the cellulose accessibility to cellulase (CAC) values by ~38-fold (from ~0.4 to 15 m 2 /g biomass). Examination of H 3 PO 4 -pretreated softwoods by cross-polarization/magic angle spin (CP/MAS), 13 C- nuclear magnetic resonance (NMR), and Fourier-transform infrared spectroscopy (FTIR) revealed that breaking of the orderly hydrogen bonding of crystalline cellulose caused the increase in CAC (higher than 11 m 2 /g biomass), which, in turn, was responsible for the high glucan digestibility of pretreated softwoods. The H 3 PO 4 pretreatment process was feedstock independent. Finally, 2D 13 C– 1 H heteronuclear single quantum coherence (HSQC) NMR showed that the lignin was depolymerized but not condensed; thus, the lignin can be available for producing high-value products.

09 BIOMASS FUELS↗

Electrochemical Nutrient Recovery for the Food–Energy–Water Nexus at Municipal Wastewater Facilities: Multivariate Analyses of Seasonal Sampling and Reactor Performance

Digester-equipped municipal wastewater facilities generate recycle streams with high nutrient loads that increase energy consumption and can cause environmental pollution. The reduction of these loads through electrochemical nutrient recovery (ENR) could enhance the food–energy–water nexus by producing fertilizer (struvite). This study investigated the recovery process through a 1 year sampling of recycle streams and the implementation of nutrient recovery. Time series analyses showed that P (as orthophosphate) concentration was time-variant in digester effluent streams, while N (as ammonia) concentration was time-variant in only the aerobic system. Furthermore, these two nutrient concentrations did not correlate in any of the recycle streams. Subsequent multivariate screening analyses identified anode type, NH 4 + concentration, cathodic potential, P concentration, and temperature as most significant for ENR. Finally, the optimum conditions of cathodic potential, anode area-to-volume ratio, and temperature applied to a real recycle stream resulted in 95% P recovery with 0.03 kWh/kg P. This energy consumption is significantly lower than process energy for conventional P fertilizers (1.1 kWh/kg P) and chemical recovery processes at scale (1.7–12.9 kWh/kg P). Overall, this study recommended specific process controls for nutrient recovery, expanded the variables evaluated for ENR, and demonstrated the ability to significantly impact energy demand associated with P-based fertilizers.

36 MATERIALS SCIENCE↗

Ice Nucleating Particle Connections to Regional Argentinian Land Surface Emissions and Weather During the Cloud, Aerosol, and Complex Terrain Interactions Experiment

Abstract Here, we present a multi‐season study of ice‐nucleating particles (INPs) active via the immersion freezing mechanism, which took place in north‐central Argentina, a worldwide hotspot for mesoscale convective storms. INPs were measured untreated, after heating to 95°C, and after hydrogen peroxide digestion. No seasonal cycle of INP concentrations was observed. Heat labile INPs, which we define as “biological” herein, dominated the population active at −5 to −20°C, while non‐heat‐labile organic INPs (decomposed by peroxide) dominated at lower temperatures, from −20 to −28°C. Inorganic INPs (remaining after peroxide digestion), were minor contributors to the overall INP activity. Biological INP concentration active around −12°C peaked during rain events and under high relative humidity, reflecting emission mechanisms independent of the background aerosol concentration. The ratio of non‐heat‐labile organic and inorganic INPs was generally constant, suggesting they originated from the same source, presumably from regional arable topsoil based on air mass histories. Single particle mass spectrometry showed that soil particles aerosolized from a regionally common agricultural topsoil contained known mineral INP sources (K‐feldspar and illite) as well as a significant organic component. The INP activity observed in this study correlates well with agricultural soil INP activities from this and other regions of the world, suggesting that the observed INP spectra might be typical of many arable landscapes. These results demonstrate the strong influence of regional continental landscapes, emitting INPs of types that are not yet well represented in global models.

54 ENVIRONMENTAL SCIENCES↗

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

Hagen, Live↗

Mild organosolv pretreatment of sugarcane bagasse with acetone/phenoxyethanol/water for enhanced sugar production

This study conducted mild organosolv pretreatment of sugarcane bagasse with acetone/phenoxyethanol/water (APW) solutions to improve sugar production in the subsequent enzymatic hydrolysis step. Here, the Box–Behnken design was used to optimize pretreatment conditions based on lignin removal. Further examination of the data revealed that lignin removal was positively correlated (R 2 > 0.95) with the combined severity factor (CSF). Pretreatment under the optimal conditions (125 °C–120 min, 0.17 M H 2 SO 4 , liquid–solid ratio of 15) led to 98.1% lignin removal and 74.5% cellulose digestibility compared to a low digestibility of 9.3% with raw sugarcane bagasse (SCB). Moreover, the APW process showed effective fractionation of pine, corn stalk and bamboo, and lignin removal was over 90%. The recovered lignin was characterized by 2D-HSQC NMR and 31P NMR, suggesting that the pretreatment resulted in breakage of β-O-4, total phenolic OH and H-units increased. However, the enzymatic hydrolysis efficiency (EHE) of samples with a lower lignin content (<4%) varied significantly. Correlations between various substrate-related factors of the pretreated SCB and EHE were analyzed to understand this observation. The results showed that the surface area of cellulose, lateral order index, CrI, and specific surface area were the predominant factors for enzymatic hydrolysis rather than lignin properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The importance of ester cleavage in the butylamine pretreatment of hybrid poplar

Butylamine is an effective in-and-out pretreatment solvent for hybrid poplar. It penetrates the cell walls and breaks ester cross-linkages, facilitating lignin release and improving enzymatic digestion. This work explores the “in-and-out” pretreatment of hybrid poplar with butylamine as a distillable protic solvent and reagent. The butylamine solvent can be removed by vacuum distillation with >95% solvent removal in all cases, providing a valuable scheme for efficient solvent recovery and recycling. Running the reaction with neat butylamine at 140 °C for 3 hours results in high yields of monosaccharides (90% glucose and 71% xylose) after enzymatic digestion, and a good tolerance to water content with no significant reduction in glucose yield up to an 8 : 1 water : butylamine ratio. We investigate the mechanisms of this pretreatment using powder X-ray diffraction, thermogravimetric analysis, fluorescence microscopy, elemental analysis, solid state and solution state nuclear magnetic spectroscopy to observe chemical and material markers of the pretreatment chemistry. The results suggest that the butylamine leaves the macro and microstructural properties of the lignocellulose relatively unaltered, but conducts targeted ester cleavage chemistry to remove cross-links between the various biopolymers and partially solubilize the lignin component of the biomass. These findings should act to guide future development of pretreatment chemistry for the development of biorefinery processes, and assist in the utilization of biomass as a starting point for chemical syntheses.

Palasz, Joseph M↗

Direct and rapid uranium isotopic analysis of environmental sample swipes via microextraction – LS-APGD/Orbitrap mass spectrometry

Accurate and precise isotopic analysis of actinides collected on environmental sample swipes from within nuclear facilities is an important safeguarding measure for detecting undeclared materials and activities. Traditional isotope ratio (IR) analysis of actinides using a bulk digestion approach can be laborious and time-consuming. Recently, direct analysis of environmental swipe samples using a microextraction approach has been explored as an alternative to conventional bulk digestion methods. The present study further evaluates this approach for accurate and precise isotopic analysis of uranium (U) in cotton swipe samples using the liquid sampling-atmospheric pressure glow discharge (LS-APGD)/Orbitrap-FTMS Booster detection system. The instrumental parameters were optimized, and quantitative capabilities were demonstrated through excellent linearity (R2 = 0.99) across a deposited mass range of 1 to 500 ng, with a limit of detection of 90 pg (in a 2 × 4 mm region) for total U; well below typical U concentrations (ng–mg range) in environmental sample swipes. The 235U/238U ratio showed excellent accuracy (−0.3% relative difference from the certificate value), with ∼20× improvement over previous microextraction-Orbitrap methods. Precision (∼1% relative standard deviation) was also greatly enhanced by ∼5×. This study also demonstrates that figures of merit achieved with neat U solution were not highly degraded when various external interfering elements/matrices were introduced. Finally, the developed method was successfully applied to analyze practical swipe samples representative of laboratory and outdoor environments. The presented figures of merit and applicability to practical samples further validate the capability of the platform for rapid analysis (<7 minutes) of environmental swipe samples.

Shrestha, Suraj [Clemson University, SC]↗

Energy and nutrient recovery from municipal and industrial waste and wastewater—a perspective

This publication highlights the latest advancements in the field of energy and nutrient recovery from organics rich municipal and industrial waste and wastewater. Energy and carbon rich waste streams are multifaceted, including municipal solid waste, industrial waste, agricultural by-products and residues, beached or residual seaweed biomass from post-harvest processing, and food waste, and are valuable resources to overcome current limitations with sustainable feedstock supply chains for biorefining approaches. The emphasis will be on the most recent scientific progress in the area, including the development of new and innovative technologies, such as microbial processes and the role of biofilms for the degradation of organic pollutants in wastewater, as well as the production of biofuels and value-added products from organic waste and wastewater streams. The carboxylate platform, which employs microbiomes to produce mixed carboxylic acids through methane-arrested anaerobic digestion, is the focus as a new conversion technology. Nutrient recycling from conventional waste streams such as wastewater and digestate, and the energetic valorization of such streams will also be discussed. The selected technologies significantly contribute to advanced waste and wastewater treatment and support the recovery and utilization of carboxylic acids as the basis to produce many useful and valuable products, including food and feed preservatives, human and animal health supplements, solvents, plasticizers, lubricants, and even biofuels such as sustainable aviation fuel.

59 BASIC BIOLOGICAL SCIENCES↗

Circulating Current Reduction of Back-to-Back MMC with Advanced Grid-Support Functionalities for Medium-Voltage Applications

A Lyapunov energy function based circulating current reduction scheme for a back to back modular multilevel converter based system for a microgrid application has been proposed in this digest. In order to ensure no circulating or zero sequence currents within the modules, the dynamics from one leg of the converter to the other are evaluated. A Lyapunov energy function is then developed and utilizing the circulating current dynamics of the converter the overall control law is implemented. In this digest a decentralized hierarchical control architecture has been implemented for the main current control; where the outer loop or the central controller implements the higher level grid interconnection functions as per IEEE 1547-2018 standards and the inner loop based on synchronous reference frame implements the current control architecture. The inner loops' outputs are the commanded converter voltages either on either side which are augmented by the Lyapunov energy function based circulating current suppression architecture. To evaluate the efficacy of the overall system, the overall system is modeled around a 300kVA back to back SiC multilevel modular converter used as a direct-connected medium voltage (MV) grid intertie based on MATLAB/Simulink domain. Several important case studies are presented in this paper to prove the effectiveness of the proposed architecture. case study results are presented.

circulating current↗

Altering the substitution and cross‐linking of glucuronoarabinoxylans affects cell wall architecture in Brachypodium distachyon

Summary The Poaceae family of plants provides cereal crops that are critical for human and animal nutrition, and also, they are an important source of biomass. Interacting plant cell wall components give rise to recalcitrance to digestion; thus, understanding the wall molecular architecture is important to improve biomass properties. Xylan is the main hemicellulose in grass cell walls. Recently, we reported structural variation in grass xylans, suggesting functional specialisation and distinct interactions with cellulose and lignin. Here, we investigated the functions of these xylans by perturbing the biosynthesis of specific xylan types. We generated CRISPR/Cas9 knockout mutants in Brachypodium distachyon XAX1 and GUX2 genes involved in xylan substitution. Using carbohydrate gel electrophoresis, we identified biochemical changes in different xylan types. Saccharification, cryo‐SEM, subcritical water extraction and ssNMR were used to study wall architecture. Bd XAX1A and Bd GUX2 enzymes modify different types of grass xylan. Brachypodium mutant walls are likely more porous, suggesting the xylan substitutions directed by both Bd XAX1A and GUX2 enzymes influence xylan‐xylan and/or xylan–lignin interactions. Since xylan substitutions influence wall architecture and digestibility, our findings open new avenues to improve cereals for food and to use grass biomass for feed and the production of bioenergy and biomaterials.

59 BASIC BIOLOGICAL SCIENCES↗

Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish

ABSTRACT Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce genomic information about the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) from previously described Kyphosus gut metagenomes and newly sequenced bioreactor enrichments reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzyme collections able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea ) and Verrucomicrobiota (order Kiritimatiellales ) highlight the importance of metabolic contributions from multiple phyla to broaden polysaccharide degradation capabilities. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors. IMPORTANCE Seaweed has long been considered a promising source of sustainable biomass for bioenergy and aquaculture feed, but scalable industrial methods for decomposing terrestrial compounds can struggle to break down seaweed polysaccharides efficiently due to their unique sulfated structures. Fish of the genus Kyphosus feed on seaweed by leveraging gastrointestinal bacteria to degrade algal polysaccharides into simple sugars. This study reconstructs metagenome-assembled genomes for these gastrointestinal bacteria to enhance our understanding of herbivorous fish digestion and fermentation of algal sugars. Investigations at the gene level identify Kyphosus guts as an untapped source of seaweed-degrading enzymes ripe for further characterization. These discoveries set the stage for future work incorporating marine enzymes and microbial communities in the industrial degradation of algal polysaccharides.

59 BASIC BIOLOGICAL SCIENCES↗

Effect of Natural Fermentation of Sorghum on Resistant Starch Molecular Structure and Fermentation Property

Relevant research results have suggested that fermentation can increase the content of sorghum amylose chains and their retrogradation value. Therefore, this study explored the effect of fermentation pretreatment on the yield, digestibility, molecular structure, and in vitro fermentation property of sorghum-resistant starch by conducting fermentation pretreatment of sorghum and extracting the resistant starch from fermented sorghum with pressure-heat compound enzyme method. The results were as follows. After fermentation pretreatment, the yield of sorghum-resistant starch increased, the digestibility of sorghum-resistant starch reduced, the laminated structure size on the surface of the particles became more uniform, and the stacking mode became more neat and denser. The sorghum-resistant starch prepared before and after fermentation did not produce new chemical groups, and its functional group peak remained unchanged. After fermentation, the weight-average molecular weight of sorghum-resistant starch was elevated, and the percentage content of high- and low-molecular substances increased and decreased, respectively, compared with that of the unfermented sorghum-resistant starch. The percentage content of short-chain branches in the branched chain increased, whereas that of the long-chain branches decreased; the crystallinity of sorghum-resistant starch after fermentation decreased, and the intensity of X-diffraction peak changed slightly before and after fermentation. According to the results of the in vitro fermentation experiments, the fermentation broth of sorghum-resistant starch had the highest content of butyric acid and short-chain fatty acid. Research results reveal that, after fermentation pretreatment, sorghum-resistant starch presented increased yield, more complex molecular structure, heavier molecular weight and more uniform surface morphology, more efficient butyric acid generation, and greater fermentation rate than unfermented sorghum-resistant starch.

Ge, YunFei↗

Prebiotic properties of Bacillus coagulans MA-13: production of galactoside hydrolyzing enzymes and characterization of the transglycosylation properties of a GH42 β-galactosidase

The spore-forming lactic acid bacterium Bacillus coagulans MA-13 has been isolated from canned beans manufacturing and successfully employed for the sustainable production of lactic acid from lignocellulosic biomass. Among lactic acid bacteria, B. coagulans strains are generally recognized as safe (GRAS) for human consumption. Low-cost microbial production of industrially valuable products such as lactic acid and various enzymes devoted to the hydrolysis of oligosaccharides and lactose, is of great importance to the food industry. Specifically, α- and β-galactosidases are attractive for their ability to hydrolyze not-digestible galactosides present in the food matrix as well as in the human gastrointestinal tract. In this work we have explored the potential of B. coagulans MA-13 as a source of metabolites and enzymes to improve the digestibility and the nutritional value of food. A combination of mass spectrometry analysis with conventional biochemical approaches has been employed to unveil the intra- and extra- cellular glycosyl hydrolase (GH) repertoire of B. coagulans MA-13 under diverse growth conditions. The highest enzymatic activity was detected on β-1,4 and α-1,6-glycosidic linkages and the enzymes responsible for these activities were unambiguously identified as β-galactosidase (GH42) and α-galactosidase (GH36), respectively. Whilst the former has been found only in the cytosol, the latter is localized also extracellularly. The export of this enzyme may occur through a not yet identified secretion mechanism, since a typical signal peptide is missing in the α-galactosidase sequence. A full biochemical characterization of the recombinant β-galactosidase has been carried out and the ability of this enzyme to perform homo- and hetero-condensation reactions to produce galacto-oligosaccharides, has been demonstrated. Probiotics which are safe for human use and are capable of producing high levels of both α-galactosidase and β-galactosidase are of great importance to the food industry. In this work we have proven the ability of B. coagulans MA-13 to over-produce these two enzymes thus paving the way for its potential use in treatment of gastrointestinal diseases.

59 BASIC BIOLOGICAL SCIENCES↗

Use of the lignocellulose-degrading bacterium Caldicellulosiruptor bescii to assess recalcitrance and conversion of wild-type and transgenic poplar

Abstract Background Biological conversion of lignocellulosic biomass is significantly hindered by feedstock recalcitrance, which is typically assessed through an enzymatic digestion assay, often preceded by a thermal and/or chemical pretreatment. Here, we assay 17 lines of unpretreated transgenic black cottonwood ( Populus trichocarpa ) utilizing a lignocellulose-degrading, metabolically engineered bacterium, Caldicellulosiruptor bescii . The poplar lines were assessed by incubation with an engineered C. bescii strain that solubilized and converted the hexose and pentose carbohydrates to ethanol and acetate. The resulting fermentation titer and biomass solubilization were then utilized as a measure of biomass recalcitrance and compared to data previously reported on the transgenic poplar samples. Results Of the 17 transgenic poplar lines examined with C. bescii , a wide variation in solubilization and fermentation titer was observed. While the wild type poplar control demonstrated relatively high recalcitrance with a total solubilization of only 20% and a fermentation titer of 7.3 mM, the transgenic lines resulted in solubilization ranging from 15 to 79% and fermentation titers from 6.8 to 29.6 mM. Additionally, a strong inverse correlation ( R 2 = 0.8) between conversion efficiency and lignin content was observed with lower lignin samples more easily converted and solubilized by C. bescii . Conclusions Feedstock recalcitrance can be significantly reduced with transgenic plants, but finding the correct modification may require a large sample set to identify the most advantageous genetic modifications for the feedstock. Utilizing C. bescii as a screening assay for recalcitrance, poplar lines with down-regulation of coumarate 3-hydroxylase 3 (C3H3) resulted in the highest degrees of solubilization and conversion by C. bescii . One such line, with a growth phenotype similar to the wild-type, generated more than three times the fermentation products of the wild-type poplar control, suggesting that excellent digestibility can be achieved without compromising fitness of the tree.

09 BIOMASS FUELS↗

Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes

Abstract Background Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration of longitudinal microbial and chemical data is necessary to illuminate how gut microorganisms supplement the energetic and nutritional requirements of animals. Although mammalian gut systems are well-studied in this capacity, the role of microbes in the breakdown and utilization of recalcitrant marine macroalgae in herbivorous fish is relatively understudied and an emerging priority for bioproduct extraction. Here we use a comprehensive survey of the marine herbivorous fish gut microbial ecosystem via parallel 16S rRNA gene amplicon profiling (microbiota) and untargeted tandem mass spectrometry (metabolomes) to demonstrate consistent transitions among 8 gut subsections across five fish of the genus of Kyphosus . Results Integration of microbial phylogenetic and chemical diversity data reveals that microbial communities and metabolomes covaried and differentiated continuously from stomach to hindgut, with the midgut containing multiple distinct and previously uncharacterized microenvironments and a distinct hindgut community dominated by obligate anaerobes. This differentiation was driven primarily by anaerobic gut endosymbionts of the classes Bacteroidia and Clostridia changing in concert with bile acids, small peptides, and phospholipids: bile acid deconjugation associated with early midgut microbiota, small peptide production associated with midgut microbiota, and phospholipid production associated with hindgut microbiota. Conclusions The combination of microbial and untargeted metabolomic data at high spatial resolution provides a new view of the diverse fish gut microenvironment and serves as a foundation to understand functional partitioning of microbial activities that contribute to the digestion of complex macroalgae in herbivorous marine fish.

Sparagon, Wesley J. (ORCID:0000000296274174)↗

Modular automated bottom-up proteomic sample preparation for high-throughput applications

Manual proteomic sample preparation methods limit sample throughput and often lead to poor data quality when thousands of samples must be analyzed. Automated liquid handler systems are increasingly used to overcome these issues for many of the sample preparation steps. Here, we detail a step-by-step protocol to prepare samples for bottom-up proteomic analysis for Gram-negative bacterial and fungal cells. The full modular protocol consists of three optimized protocols to: (A) lyse Gram-negative bacteria and fungal cells; (B) quantify the amount of protein extracted; and (C) normalize the amount of protein and set up tryptic digestion. These protocols have been developed to facilitate rapid, low variance sample preparation of hundreds of samples, be easily implemented on widely-available Beckman-Coulter Biomek automated liquid handlers, and allow flexibility for future protocol development. By using this workflow 50 micrograms of protein from 96 samples can be prepared for tryptic digestion in under an hour. We validate these protocols by analyzing 47 Pseudomonas putida and Rhodosporidium toruloides samples and show that this modular workflow provides robust, reproducible proteomic samples for high-throughput applications. The expected results from these protocols are 94 peptide samples from Gram-negative bacterial and fungal cells prepared for bottom-up quantitative proteomic analysis without the need for desalting column cleanup and with protein relative quantity variance (CV%) below 15%.

59 BASIC BIOLOGICAL SCIENCES↗