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A pilot-scale continuous tubular reactor increases enzymatic digestibility of four different feedstocks by removing xylan and effectively achieving economically viable ethanol concentrations.
This study demonstrates a method for determining the isotopic composition of low-level (sub-pg) plutonium (Pu) directly from a cotton swipe. Environmental sample (ES) swipes are routinely employed as a tool for monitoring activities in nuclear facilities. Traditional ES swipe analysis, as employed in nuclear safeguards, utilizes laborious ashing, digestion, and chemical separation procedures prior to mass spectrometric (MS) analysis. Here, an innovative sample introduction technique employing a microextraction probe to extract Pu directly from the swipe surface is described. The microextraction probe lowers onto the swipe surface, seals on a small area (8 mm 2 ), and delivers solvent (2% HNO 3 ) to extract actinide material that may be present. The extracted analyte is subsequently directed into a sector field inductively coupled plasma (ICP)-MS for isotope ratio determination. This microextraction-ICP-MS method successfully determined the isotopic composition ( 240 Pu/ 239 Pu and 242 Pu/ 239 Pu) of three Pu certified reference materials (CRM 136, 137, and 138) that were deposited (1 pg) onto ES swipes. The percent relative difference from the certified value, uncorrected for instrumental fractionation, was <2% for the 240 Pu/ 239 Pu ratio on all three CRMs and <10% for the 242 Pu/ 239 Pu ratio on CRM 136 and 138. Here, the percent relative standard deviation, an estimate of the sample-to-sample isotopic precision, was <4% for the 240 Pu/ 239 Pu and <15% for the 242 Pu/ 239 Pu. Method limits of detection were determined, based on measurements of an enriched 244 Pu material, to be ~7 fg. Additionally, a mixed uranium (U) and Pu deposition was made to determine the method's ability to simultaneously extract U and Pu and determine the isotopic composition of both analytes.
We report two ICP-MS methods were developed to measure the radiotoxic isotope 226 Ra in brain tissues from a radium dial painter worker. The first method was a direct analysis of acid digested samples using quadrupole ICP-MS. The instrumental LOD of 226 Ra was 0.1 ng kg -1 . Polyatomic interferences at m/z 226 were investigated and Pb was identified from a polyatomic interferent in an in-house sample prepared from bovine brain, with a 226/208 formation ratio of 4 × 10 -8 . The quadrupole ICP-MS method was also used to measure levels of beryllium, strontium, and uranium. A second method was developed that included cation-exchange chromatography to separate 226 Ra followed by analysis with sector field MC-ICP-MS. The instrumental LOD for the cation exchange method with MC-ICP-MS detection was 0.5 pg kg -1 (19 mBq kg -1 ). The measured concentrations of 226 Ra in different brain regions ranged from 0.09–0.72 ng kg -1 (3.3–27 Bq kg -1 ) and radium was non-uniformly distributed in the brain.
Here, we show for the first time that main-chain organometallic polymers (MCOPs) can be prepared from Janus N-heterocyclic carbene (NHC) linkers and polynuclear cluster nodes. The crosslinked framework Co 4 S 4 -MCOP is synthesized via ligand displacement reactions and undergoes reversible electron transfer in the solid state. Discrete molecular cluster species can be excised from the framework by digesting the solid in solutions of excess monocarbene. Lastly, we demonstrate a synthetic route to monodisperse framework particles via coordination modulation.
Spatial proteomics holds great promise for revealing tissue heterogeneity in both physiological and pathological conditions. However, one significant limitation of most spatial proteomics workflows is the requirement of large sample amounts that blurs cell-type-specific or microstructure-specific information. In this study, we developed an improved sample preparation approach for spatial proteomics and integrated it with our previously-established laser capture microdissection (LCM) and microfluidics sample processing platform. Specifically, we developed a hanging drop (HD) method to improve the sample recovery by positioning a nanowell chip upside-down during protein extraction and tryptic digestion steps. Compared with the commonly-used sitting-drop method, the HD method keeps the tissue pixel away from the container surface, and thus improves the accessibility of the extraction/digestion buffer to the tissue sample. The HD method can increase the MS signal by 7 fold, leading to a 66% increase in the number of identified proteins. An average of 721, 1489, and 2521 proteins can be quantitatively profiled from laser-dissected 10 μm-thick mouse liver tissue pixels with areas of 0.0025, 0.01, and 0.04 mm 2 , respectively. The improved system was further validated in the study of cell-type-specific proteomes of mouse uterine tissues.
Encapsulating anaerobic microorganisms allows for the separation of the solids retention time from the hydraulic retention time during anaerobic wastewater treatment. The harsh chemistries involved in the process of encapsulation can have adverse effects on microorganisms for anaerobic digestion, especially methanogens, and can lead to lower methane yields after encapsulation. Improving the survival and maintaining activity of anaerobic communities during encapsulation will likely be the key to improving methane yield. In this study, we investigated the encapsulation of biomass grown as biofilms on two carbonaceous materials, biochar and powdered activated carbon (PAC), to improve methane yield. Microorganisms grown as biofilms on biochar and PAC were encapsulated in polyethylene glycol (PEG) and incubated for 10 days. After 10 days, the unamended control capsules produced 81.6 ± 5.4 μmol of methane, while PAC-amended capsules produced 129.8 ± 1.9 μmol and biochar-amended capsules produced 432.96 ± 20.8 μmol methane, with the differences being statistically significant (p < 0.05). In biochar, a higher relative abundance of methanogens led to increased methane production capacity. The ratio of the methyl coenzyme M reductase (mcrA) genes to total 16S rRNA genes in the encapsulated biochar-supported biofilms was significantly higher than that in the encapsulated unsupported (p = 4.9 × 10 −5 ) and the PAC-supported biofilms (p = 0.012). Biochar-supported biofilms also had higher methane output per mcrA or 16S rRNA gene copy number. For the PAC, biofilms were protected from ammonium persulfate (APS), a powerful oxidant used in the encapsulation process. PAC removed 92% of dissolved APS, reducing exposure of the methanogens to this chemical. Unfortunately, this removal of APS compromised capsule stability, limiting the amount of PAC that could be added to the capsules. Furthermore, amendments that improve survival and activity of methanogens should be used in the capsules instead of those that protect methanogens by interfering with encapsulant polymerization chemistry.
When attempting to obtain light-color lignin from lignocellulosic biomass or industrial lignin, the available options based on chemical or morphological modification suffer from low yield, high cost, and lack of availability at the required scales. In this study, we adopted a polyhydric-alcohol-based deep eutectic solvent (PA-DES) to directly extract light-color lignin from natural biomass, which is even whiter than native cellulolytic enzyme lignin (CEL). The isolated lignin possessed a high recovery yield (97.36%), regular micro-spherical morphology, enriched β-ether linkage of 58/100Ar, low phenolic hydroxyl content of 1.25 mmol g -1 , minimal carbonyl content of 0.70 mmol g -1 , and less condensed structures, thus yielding a lower content of chromophores. Further, this lignin showed excellent sunscreen effects, which could enhance the SPF of a commercial sunscreen from 15 to 40 with only 5 wt% addition. This study can provide essential guidance for the scale-up production of light-color lignin and obtaining near-complete digestible cellulose for further saccharification.
A microextraction (ME) sampling system, paired with inductively coupled plasma-mass spectrometry (ICP-MS), was employed to spatially analyze proteins tagged with lanthanum (La), gadolinium (Gd), or terbium (Tb) on the surface of western blot paper. The proteins were covalently tagged, separated via gel electrophoresis, and transferred to western blot paper for analysis by ME-ICP-MS. The ME-ICP-MS method enables the direct sampling of the tagged species on the western blot paper, without any sample preparation. Traditionally, the tagged analyte would need to be stained, excised, and digested to be analyzed by ICP-MS for its elemental and isotopic characterization. Preliminary detection limits for the ME-ICP-MS method applied to western blot paper were established to be 564, 54, and 2.5 fg for La, Gd, and Tb, respectively. The developed ME-ICP-MS method was compared to laser ablation (LA) ICP-MS, another direct solid sampling technique; it was readily determined that ME-ICP-MS can effectively map the elemental constituents on the western blot paper with comparable analysis time and measurement sensitivity. The analysis time per 2 × 4 mm extraction is ∼1 minute; if protein spots are directly targeted (rather than systematically mapping the entire blot paper), the analysis time per protein spot is ∼1 min. This developed method proved to be fast, effective, and accessible for correlating protein molecular weight with the detection of the inorganic tagant. The ME-ICP-MS approach could be widely applicable in research areas that involve metal-tagged protein bioconjugates, such as in the development of diagnostic and therapeutic agents and other biochemical probes.
Replacing biorefinery designs that use stepwise fractionation, depolymerization, and conversion processes with designed tandem process steps can greatly reduce a biorefinery's operating costs and environmental impact. Reductive Catalytic Fractionation (RCF) is a highly efficient lignin-first approach that combines biomass fractionation and lignin depolymerization to generate a hydrogenolysis oil and pulp. The oil is composed of a complex mixture of phenolic monomers, dimers, and oligomers. Intergrating this chemical deconstruction process with microbial funneling of phenolics can simplify the product mixture and make high-value products. We applied RCF to poplar biomass in a biomass-to-bioproduct processing chain in which the phenolics were funneled to 2-pyrone-4,6-dicarboxylic acid (PDC) by an engineered strain of Novosphingobium aromaticivorans DSM12444. The pulp was enzymatically digested and the glucose and xylose was funneled to ethanol by an engineered strain of Saccharomyces cerevisiae GLBRCY945. By combining biomass fractionation and lignin depolymerization we removed a costly processing step that directly translated into a 29% reduction in the minimum selling price of PDC. This work combines experimentation with process modeling of an integrated biorefinery design to show how utilizing tandem process steps can significantly reduce operating expenses and environmental impact of upgrading lignocellulosic biomass to a portfolio of high value products.
The formation of metastable wurtzite-like CuInSe 2 nanocrystals remains poorly understood due to the structural complexity of copper selenide intermediates. Here, we demonstrate that weissite-like Cu 2−x Se can serve as a structural template for topotactic cation exchange to wurtzite-like CuInSe 2 . Time-resolved XRD and SEM/STEM-EDX analyses reveal progressive In 3+ incorporation within the preserved hexagonally close-packed Se 2− sublattice, accompanied by displacement and redistribution of Cu + ions. TEM and statistical size analysis show that cation exchange is coupled to an anisotropic Ostwald ripening, driving lateral growth of the nanoplates. Control experiments confirm that growth is mediated by In 3+ incorporation rather than thermal phase relaxation or digestion. Furthermore, these findings provide mechanistic insight into how hexagonal anion sublattices guide metastable ternary formation, clarifying the interplay between cation exchange and nanoplate growth.
Lignocellulosic biorefineries can generate various energy-rich side streams, including biogas from anaerobic digestion, a lignin stream from biomass pretreatment, and conversion residues. This study evaluates different chemical energy utilization strategies in lignocellulosic biorefineries based on energy and carbon efficiencies, cost, and greenhouse gas mitigation potential. Specifically, using modeling and optimization, we examine strategies that include electricity generation, biogas upgrade to biomethane, lignin valorization, and carbon capture and storage. We find that upgrading biogas to biomethane demonstrates the highest energy efficiency and leads to the lowest minimum fuel selling price for the main product, ethanol. The biorefinery with carbon capture and storage achieves the lowest net carbon footprint. Lignin valorization has the highest carbon footprint due to the additional materials required for lignin depolymerization, despite its potential to produce high value bioproducts.
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Here, using an OpenMP Application Programming Interface, the resolution-of-the-identity second-order Møller–Plesset perturbation (RI-MP2) method has been off-loaded onto graphical processing units (GPUs), both as a standalone method in the GAMESS electronic structure program and as an electron correlation energy component in the effective fragment molecular orbital (EFMO) framework. First, a new scheme has been proposed to maximize data digestion on GPUs that subsequently linearizes data transfer from central processing units (CPUs) to GPUs. Second, the GAMESS Fortran code has been interfaced with GPU numerical libraries (e.g., NVIDIA cuBLAS and cuSOLVER) for efficient matrix operations (e.g., matrix multiplication, matrix decomposition, and matrix inversion). The standalone GPU RI-MP2 code shows an increasing speedup of up to 7.5× using one NVIDIA V100 GPU with one IBM 42-core P9 CPU for calculations on fullerenes of increasing size from 40 to 260 carbon atoms using the 6-31G(d)/cc-pVDZ-RI basis sets. A single Summit node with six V100s can compute the RI-MP2 correlation energy of a cluster of 175 water molecules using the correlation consistent basis sets cc-pVDZ/cc-pVDZ-RI containing 4375 atomic orbitals and 14 700 auxiliary basis functions in ~0.85 h. In the EFMO framework, the GPU RI-MP2 component shows near linear scaling for a large number of V100s when computing the energy of an 1800-atom mesoporous silica nanoparticle in a bath of 4000 water molecules. The parallel efficiencies of the GPU RI-MP2 component with 2304 and 4608 V100s are 98.0% and 96.1%, respectively.
Lignocellulosic biomass offers a renewable carbon source which can be anaerobically digested to produce short-chain carboxylic acids. Here, we assess fuel properties of oxygenates accessible from catalytic upgrading of these acids a priori for their potential to serve as diesel bioblendstocks. Ethers derived from C 2 and C 4 carboxylic acids are identified as advantaged fuel candidates with significantly improved ignition quality (>56% cetane number increase) and reduced sooting (>86% yield sooting index reduction) when compared to commercial petrodiesel. The prescreening process informed conversion pathway selection toward a C 11 branched ether, 4-butoxyheptane, which showed promise for fuel performance and health- and safety-related attributes. A continuous, solvent-free production process was then developed using metal oxide acidic catalysts to provide improved thermal stability, water tolerance, and yields. Liter-scale production of 4-butoxyheptane enabled fuel property testing to confirm predicted fuel properties, while incorporation into petrodiesel at 20 vol % demonstrated 10% improvement in ignition quality and 20% reduction in intrinsic sooting tendency. Storage stability of the pure bioblendstock and 20 vol % blend was confirmed with a common fuel antioxidant, as was compatibility with elastomeric components within existing engine and fueling infrastructure. Technoeconomic analysis of the conversion process identified major cost drivers to guide further research and development. Life-cycle analysis determined the potential to reduce greenhouse gas emissions by 50 to 271% relative to petrodiesel, depending on treatment of coproducts.
The dense array of N-linked glycans on the HIV-1 envelope glycoprotein (Env), known as the “glycan shield,” is a key determinant of immunogenicity, yet intrinsic heterogeneity confounds typical structure–function analysis. Here, we present an integrated approach of single-particle electron cryomicroscopy (cryo-EM), computational modeling, and site-specific mass spectrometry (MS) to probe glycan shield structure and behavior at multiple levels. We found that dynamics lead to an extensive network of interglycan interactions that drive the formation of higher-order structure within the glycan shield. This structure defines diffuse boundaries between buried and exposed protein surface and creates a mapping of potentially immunogenic sites on Env. Analysis of Env expressed in different cell lines revealed how cryo-EM can detect subtle changes in glycan occupancy, composition, and dynamics that impact glycan shield structure and epitope accessibility. Importantly, this identified unforeseen changes in the glycan shield of Env obtained from expression in the same cell line used for vaccine production. Finally, by capturing the enzymatic deglycosylation of Env in a time-resolved manner, we found that highly connected glycan clusters are resistant to digestion and help stabilize the prefusion trimer, suggesting the glycan shield may function beyond immune evasion.
Lignocellulose, the structural component of plant cells, is a major agricultural byproduct and the most abundant terrestrial source of biopolymers on Earth. The complex and insoluble nature of lignocellulose limits its conversion into value-added commodities, and currently, efficient transformation requires expensive pretreatments and high loadings of enzymes. In this work, we report on a fungus from the Parascedosporium genus, isolated from a wheat-straw composting community, that secretes a large and diverse array of carbohydrate-active enzymes (CAZymes) when grown on lignocellulosic substrates. We describe an oxidase activity that cleaves the major β-ether units in lignin, thereby releasing the flavonoid tricin from monocot lignin and enhancing the digestion of lignocellulose by polysaccharidase mixtures. We show that the enzyme, which holds potential for the biorefining industry, is widely distributed among lignocellulose-degrading fungi from the Sordariomycetes phylum.
Anaerobic fungi (class Neocallimastigomycetes) thrive as low-abundance members of the herbivore digestive tract. The genomes of anaerobic gut fungi are poorly characterized and have not been extensively mined for the biosynthetic enzymes of natural products such as antibiotics. Here, we investigate the potential of anaerobic gut fungi to synthesize natural products that could regulate membership within the gut microbiome. Here, complementary 'omics' approaches were combined to catalog the natural products of anaerobic gut fungi from four different representative species: Anaeromyces robustus (A. robustus), Caecomyces churrovis (C. churrovis), Neocallimastix californiae (N. californiae), and Piromyces finnis (P. finnis). In total, 146 genes were identified that encode biosynthetic enzymes for diverse types of natural products, including nonribosomal peptide synthetases and polyketide synthases.
Detecting viral infection is a key role of the innate immune system. The genomes of some RNA viruses have a high CpG dinucleotide content relative to most vertebrate cell RNAs, making CpGs a molecular marker of infection. The human zinc-finger antiviral protein (ZAP) recognizes CpG, mediates clearance of the foreign CpG-rich RNA, and causes attenuation of CpG-rich RNA viruses. While ZAP binds RNA, it lacks enzymatic activity that might be responsible for RNA degradation and thus requires interacting cofactors for its function. One of these cofactors, KHNYN, has a predicted nuclease domain. Using biochemical approaches, we found that the KHNYN NYN domain is a single-stranded RNA ribonuclease that does not have sequence specificity and digests RNA with or without CpG dinucleotides equivalently in vitro. We show that unlike most KH domains, the KHNYN KH domain does not bind RNA. Indeed, a crystal structure of the KH region revealed a double-KH domain with a negatively charged surface that accounts for the lack of RNA binding. Rather, the KHNYN C-terminal domain (CTD) interacts with the ZAP RNA-binding domain (RBD) to provide target RNA specificity. We define a minimal complex composed of the ZAP RBD and the KHNYN NYN-CTD and use a fluorescence polarization assay to propose a model for how this complex interacts with a CpG dinucleotide-containing RNA. In the context of the cell, this module would represent the minimum ZAP and KHNYN domains required for CpG-recognition and ribonuclease activity essential for attenuation of viruses with clusters of CpG dinucleotides.