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194 records · Page 11

Kinetic Measurements in Heterogeneous Catalysis

This contribution is about the experimental determination of the rate of a heterogeneous catalytic reaction and the analysis of kinetic data. In this case, the reaction rate can be defined as the frequency at which the closed sequence of elementary steps transforming reactants into products is occurring. However, the rate of chemical reaction is not directly observed; rather, one records the rate of substance change. The rate of chemical reaction is calculated based on the rate of substance change and assumed stoichiometry of the reaction. In order to make this an intensive quantity (i.e., independent of the volume in which the reaction is performed, this frequency is divided by the latter or by a quantity proportional to the latter). As the focus of what follows is on heterogeneously catalyzed reactions this can be the catalyst mass, the catalyst surface area or the total number of active sites present in the reaction volume confined by the walls of a chemical reactor. For example, the rate may be reported as one of the following: Net rate of consumption/production of component i mol m-3 s-1 Net specific rate of consumption/production of component i mol kg-1 s-1 Rate of substance change (per unit volume of catalyst) mol m-3 s-1 Specific reaction rate (per unit mass of catalyst) mol kg-1 s-1 Net rate of consumption/production of component i mol m-2 s-1 The turnover frequency (TOF) is a characteristic originally introduced by Boudart [1] is expressed as TOF=R/G_tot , where R is the steady-state rate of reactant consumption or product generation and G_totis the total areal density of active sites [mol m-2]. The latter is typically taken from experimental chemisorption data obtained at low temperature. The advancement of a chemical reaction leads to changes in the amounts of reactants and products which, for a stoichiometric single reaction, are connected by the stoichiometric coefficients. In many cases, for the sake of simplicity, we will assume that the investigated reaction proceeds according to a single reaction pathway, so that the net production rate of a reaction component is directly proportional to the reaction rate and that the latter equals the net production rate of any of the involved components when divided by the appropriate stoichiometric coefficient. For complex stoichiometric reactions the net production rates of the involved components are linear combinations of the reaction rates. Different goals for kinetic measurements can be formulated: Catalyst testing, i.e., obtaining the kinetic dependences for the development and discrimination of efficient catalytic materials. Precise kinetic characterization of active materials via high-throughput screening is a part of such activity. Detailed kinetics, i.e., revealing the detailed mechanism of complex catalytic reaction via systematic kinetic studies, both steady-state and non-steady-state Industrial kinetics, i.e., obtaining data and relationships for describing and predicting the behaviour of catalytic reactors and processes at industrial scale Finally, mathematical modeling and analysis where kinetic measurements provide data for understanding complex kinetic phenomena, e.g., oscillations, non-linear self-organization, etc.

36 MATERIALS SCIENCE↗

Engineering and Application of a Thermostable MHETase for PET Depolymerization

Enzymatic hydrolysis of poly(ethylene terephthalate) (PET) releases mono(2-hydroxyethyl) terephthalate (MHET) as a major product, the accumulation of which can prolong reactor residence times and complicate downstream monomer separations. The use of a MHETase enzyme can enable MHET hydrolysis to the monomers, terephthalic acid and ethylene glycol, but industrial PETases typically operate at thermophilic temperatures and the well-known MHETase from Ideonella sakaiensis is a mesophilic enzyme, thus warranting the development of thermophilic MHETases. Here, we characterize thermostable MHET-active enzymes from a natural diversity screen by applying a hidden Markov model based on the previously reported, archaeal ferulic acid esterase, PET46. We identified enzymes with higher thermostability than PET46 and quantified their MHETase activity in reactions at 70 °C. The crystal structure of MHT077, the homologue with the highest MHETase activity and an apparent melting temperature (T m,app ) of 94.6 °C, informed site saturation mutagenesis in the active site and lid-domain interface. MHT077 exhibited a ∼100-fold slower unfolding rate at 65 °C than PET46, indicating substantially greater kinetic stability. In parallel, we applied evolution-informed design, a probabilistic model that leverages coevolutionary patterns in large multiple sequence alignments, to improve the activity and thermostability of five ferulic acid esterases. One design, EV-MHT043–5 was identified with a comparable thermostability (T m,app = 96.1 °C) and a 3-fold improvement in its MHETase activity relative to the wildtype enzyme, MHT043. Combination variants of beneficial mutations were screened and afforded a variant, MHT077 LFK , which reduced MHET accumulation in bioreactor experiments with postconsumer PET waste. Overall, this study expands the known MHET-hydrolyzing protein scaffolds available for enzymatic PET recycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data-Driven Discovery of Bimetallic Nanoparticles Catalysts for the Hydrogenolysis of Polyethylene

Supported platinum nanoparticles are known to convert polyolefins to high-quality liquid hydrocarbons with hydrogen under relatively mild conditions. However, no systematic study has been undertaken using bimetallic catalysts for polyethylene upcycling. Specifically, a total of 98 monometallic and bimetallic combinations (Ag, Cr, Co, Cu, Fe, Ga, In, Mn, Ni, Pd, Pt, Rh, Ru, Zr) on alumina were synthesized utilizing surface organometallic chemistry (SOMC) technique via robotic platform. These were investigated at a small scale (10 mg of catalyst and 50 mg of polyethylene) for their activity for the hydrogenolysis of polyethylene in a high-throughput batch reactor. Combinations of Ni and Co were selected as candidates with high activity toward conversion into paraffin oils. Reaction conditions were optimized with Ni/Co/Al 2 O 3 catalyst at a larger scale (300 mg catalyst and 3 g polyethylene) to obtain a high yield (93.1%) of paraffin wax with desired properties (M n = 380 Da) and low polydispersity (Đ = 1.2). Ni/Co/Al 2 O 3 was compared against Co/Ni/Al 2 O 3 to understand the role of the deposition sequence. When Co is deposited before Ni, a layer of cobalt aluminate is formed upon reduction, stabilizing the deposition of 5 nm metallic Ni particles. When nickel is deposited before Co, particles are larger (average >20 nm) and more oxidized (Ni δ+ in NiAl 2 O 4 ), decreasing the availability of the catalytically active metallic Ni. In conclusion, the difference in electronic environments was also described by DFT calculations, which revealed that smaller 3D clusters of Ni are preferred on CoAl2O4 over the 3D clusters on NiAl 2 O 4 and that these smaller clusters are more reducible, as confirmed experimentally.

Polymer↗

Multi-beam X-ray ptychography for high-throughput coherent diffraction imaging

X-ray ptychography is a rapidly developing coherent diffraction imaging technique that provides nanoscale resolution on extended field-of-view. However, the requirement of coherence and the scanning mechanism limit the throughput of ptychographic imaging. Herein, we propose X-ray ptychography using multiple illuminations instead of single illumination in conventional ptychography. Multiple locations of the sample are simultaneously imaged by spatially separated X-ray beams, therefore, the obtained field-of-view in one scan can be enlarged by a factor equal to the number of illuminations. We have demonstrated this technique experimentally using two X-ray beams focused by a house-made Fresnel zone plate array. Two areas of the object and corresponding double illuminations were successfully reconstructed from diffraction patterns acquired in one scan, with image quality similar with those obtained by conventional single-beam ptychography in sequence. Multi-beam ptychography approach increases the imaging speed, providing an efficient way for high-resolution imaging of large extended specimens.

47 OTHER INSTRUMENTATION↗

acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens

Abstract High throughput CRISPR screens are revolutionizing the way scientists unravel the genetic underpinnings of engineered and evolved phenotypes. One of the critical challenges in accurately assessing screening outcomes is accounting for the variability in sgRNA cutting efficiency. Poorly active guides targeting genes essential to screening conditions obscure the growth defects that are expected from disrupting them. Here, we develop acCRISPR, an end-to-end pipeline that identifies essential genes in pooled CRISPR screens using sgRNA read counts obtained from next-generation sequencing. acCRISPR uses experimentally determined cutting efficiencies for each guide in the library to provide an activity correction to the screening outcomes via calculation of an optimization metric, thus determining the fitness effect of disrupted genes. CRISPR-Cas9 and -Cas12a screens were carried out in the non-conventional oleaginous yeast Yarrowia lipolytica and acCRISPR was used to determine a high-confidence set of essential genes for growth under glucose, a common carbon source used for the industrial production of oleochemicals. acCRISPR was also used in screens quantifying relative cellular fitness under high salt conditions to identify genes that were related to salt tolerance. Collectively, this work presents an experimental-computational framework for CRISPR-based functional genomics studies that may be expanded to other non-conventional organisms of interest.

59 BASIC BIOLOGICAL SCIENCES↗

Integrating continuous hypermutation with high–throughput screening for optimization of cis,cis –muconic acid production in yeast

Directed evolution is a powerful method to optimize proteins and metabolic reactions towards user-defined goals. It usually involves subjecting genes or pathways to iterative rounds of mutagenesis, selection and amplification. While powerful, systematic searches through large sequence-spaces is a labour-intensive task, and can be further limited by a priori knowledge about the optimal initial search space, and/or limits in terms of screening throughput. Here, we demonstrate an integrated directed evolution workflow for metabolic pathway enzymes that continuously generate enzyme variants using the recently developed orthogonal replication system, OrthoRep and screens for optimal performance in high-throughput using a transcription factor-based biosensor. We demonstrate the strengths of this workflow by evolving a rate-limiting enzymatic reaction of the biosynthetic pathway for cis,cis-muconic acid (CCM), a precursor used for bioplastic and coatings, in Saccharomyces cerevisiae. After two weeks of simply iterating between passaging of cells to generate variant enzymes via OrthoRep and high-throughput sorting of best-performing variants using a transcription factor-based biosensor for CCM, we ultimately identified variant enzymes improving CCM titers > 13-fold compared with reference enzymes. Taken together, the combination of synthetic biology tools as adopted in this study is an efficient approach to debottleneck repetitive workflows associated with directed evolution of metabolic enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Root system architecture in cereals: progress, challenges and perspective

We report roots are essential multifunctional plant organs involved in water and nutrient uptake, metabolite storage, anchorage, mechanical support, and interaction with the soil environment. Understanding of this ‘hidden half’ provides potential for manipulation of root system architecture (RSA) traits to optimize resource use efficiency and grain yield in cereal crops. Unfortunately, root traits are highly neglected in breeding due to the challenges of phenotyping, but could have large rewards if the variability in RSA traits can be fully exploited. Until now, a plethora of genes have been characterized in detail for their potential role in improving RSA. The use of forward genetics approaches to find sequence variations in genes underpinning desirable RSA would be highly beneficial. Advances in computer vision applications have allowed image-based approaches for high-throughput phenotyping of RSA traits that can be used by any laboratory worldwide to make progress in understanding root function and dissection of the genetics. At the same time, the frontiers of root measurement include non-invasive methods like X-ray computer tomography and magnetic resonance imaging that facilitate new types of temporal studies. Root physiology and ecology are further supported by spatiotemporal root simulation modeling. The discovery of component traits providing improved resilience and yield advantage in target environments is a key necessity for mainstreaming root-based cereal breeding. The integrated use of pan-genome resources, now available in most cereals, coupled with new in-field phenotyping platforms has the potential for precise selection of superior genotypes with improved RSA.

59 BASIC BIOLOGICAL SCIENCES↗

High-throughput 16S informatics (HTP16S) v1.0

Command-line application to do the informatics to support a high-throughout 16S sequencing run using LBL robotics and sequencing technology.

McCauley, Joshua [Lawrence Berkeley National Labor↗

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Abstract Background Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing—SIP—remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance—the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling. Results Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13 C-AMF hyphosphere DNA from a 13 CO 2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10–33 atom% 13 C), even though the soils’ overall enrichment was low (1.8 atom% 13 C). We assembled 212 13 C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13 C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera . Conclusions Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP—fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat—generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs’ phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling.

59 BASIC BIOLOGICAL SCIENCES↗

Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies

Genome-wide association studies are powerful tools to elucidate the genome-to-phenome relationship. In order to explain most of the observed heritability of a phenotypic trait, a sufficient number of individuals and a large set of genetic variants must be examined. The development of high-throughput technologies and cost-efficient resequencing of complete genomes have enabled the genome-wide identification of genetic variation at large scale. As such, almost all existing genetic variation becomes available, and it is now possible to identify rare genetic variants in a population sample. Rare genetic variants that were usually filtered out in most genetic association studies are the most numerous genetic variations across genomes and hold great potential to explain a significant part of the missing heritability observed in association studies. Rare genetic variants must be identified with high confidence, as they can easily be confounded with sequencing errors. In this study, we used a pre-filtered data set of 1,014 pure Populus trichocarpa entire genomes to identify rare and common small genetic variants across individual genomes. We compared variant calls between Platypus and HaplotypeCaller pipelines, and we further applied strict quality filters for improved genetic variant identification. Finally, we only retained genetic variants that were identified by both variant callers increasing calling confidence. Based on these shared variants and after stringent quality filtering, we found high genomic diversity in P. trichocarpa germplasm, with 7.4 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. We highlight the importance of genomic diversity and the potential of rare defective genetic variants in explaining a significant portion of P. trichocarpa's phenotypic variability in association genetics. The ultimate goal is to associate both rare and common alleles with poplar's wood quality traits to support selective breeding for an improved bioenergy feedstock.

Genetics & Heredity↗

Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.

16S rRNA gene amplicon Illumina sequencing↗

Mapping the functional landscape of the receptor binding domain of T7 bacteriophage by deep mutational scanning

The interaction between a bacteriophage and its host is mediated by the phage's receptor binding protein (RBP). Despite its fundamental role in governing phage activity and host range, molecular rules of RBP function remain a mystery. Here, we systematically dissect the functional role of every residue in the tip domain of T7 phage RBP (1660 variants) by developing a high-throughput, locus-specific, phage engineering method. This rich dataset allowed us to cross compare functional profiles across hosts to precisely identify regions of functional importance, many of which were previously unknown. Substitution patterns showed host-specific differences in position and physicochemical properties of mutations, revealing molecular adaptation to individual hosts. We discovered gain-of-function variants against resistant hosts and host-constricting variants that eliminated certain hosts. To demonstrate therapeutic utility, we engineered highly active T7 variants against a urinary tract pathogen. Our approach presents a generalized framework for characterizing sequence–function relationships in many phage–bacterial systems.

59 BASIC BIOLOGICAL SCIENCES↗

High-Density Automated Vertiport Concept of Operations

The National Aeronautics and Space Administration (NASA) vision for Advanced Air Mobility (AAM) includes Urban Air Mobility (UAM) – a concept involving vertical takeoff and landing (VTOL) aircraft, decentralized (or federated) traffic management, and new infrastructure to support urban, suburban, and rural flight operations. High-density performance-based routes or corridors enable prompt transportation of people and goods from node to node, where each node represents a vertiport, defined as an identifiable ground or elevated area used for the takeoff and landing of VTOL aircraft. In the presence of uncertainty surrounding aircraft turnaround time on the ground, vertiports are the critical end points in scheduling, sequencing, and spacing (SSS) of aircraft in dense metropolitan environments. This Concept of Operations (ConOps) includes vertiports of varying sizes, configurations, service offerings, and locations. UAM air vehicles include conventional rotorcraft, unmanned VTOL aircraft, and novel piloted VTOL aircraft. This ConOps focuses on operations at a high-density vertiport, supported by a Vertiport Automation System (VAS) with high-throughput operation capabilities under conditions defined as NASA’s Urban Air Mobility Maturity Level Four (UML-4).

UAM↗

High-Density Automated Vertiport Concept of Operations

The National Aeronautics and Space Administration (NASA) vision for Advanced Air Mobility (AAM) includes Urban Air Mobility (UAM) – a concept involving vertical takeoff and landing (VTOL) aircraft, decentralized (or federated) traffic management, and new infrastructure to support urban, suburban, and rural flight operations. High-density performance-based routes or corridors enable prompt transportation of people and goods from node to node, where each node represents a vertiport, defined as an identifiable ground or elevated area used for the takeoff and landing of VTOL aircraft. In the presence of uncertainty surrounding aircraft turnaround time on the ground, vertiports are the critical end points in scheduling, sequencing, and spacing (SSS) of aircraft in dense metropolitan environments. This Concept of Operations (ConOps) includes vertiports of varying sizes, configurations, service offerings, and locations. UAM air vehicles include conventional rotorcraft, unmanned VTOL aircraft, and novel piloted VTOL aircraft. This ConOps focuses on operations at a high-density vertiport, supported by a Vertiport Automation System (VAS) with high-throughput operation capabilities under conditions defined as NASA’s Urban Air Mobility Maturity Level Four (UML-4).

Urban Air Mobility↗