Intracellular pathways for lignin catabolism in white-rot fungi.

Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in nature. While lignin depolymerization by WRF has been extensively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here, we employ 13C-isotope labeling, systems biology approaches, and in vitro enzyme assays to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel carbon from lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems and furthermore establish a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts-a key step toward enabling a sustainable bioeconomy.

Site-specific incorporation of phosphotyrosine using an expanded genetic code.

Access to phosphoproteins with stoichiometric and site-specific phosphorylation status is key to understanding the role of protein phosphorylation. Here we report an efficient method to generate pure, active phosphotyrosine-containing proteins by genetically encoding a stable phosphotyrosine analog that is convertible to native phosphotyrosine. We demonstrate its general compatibility with proteins of various sizes, phosphotyrosine sites and functions, and reveal a possible role of tyrosine phosphorylation in negative regulation of ubiquitination.

Mammalian target of rapamycin complex 1 (mTORC1) plays a role in Pasteurella multocida toxin (PMT)-induced protein synthesis and proliferation in Swiss 3T3 cells.

Pasteurella multocida toxin (PMT) is a potent mitogen known to activate several signaling pathways via deamidation of a conserved glutamine residue in the α subunit of heterotrimeric G-proteins. However, the detailed mechanism behind mitogenic properties of PMT is unknown. Herein, we show that PMT induces protein synthesis, cell migration, and proliferation in serum-starved Swiss 3T3 cells. Concomitantly PMT induces phosphorylation of ribosomal S6 kinase (S6K1) and its substrate, ribosomal S6 protein (rpS6), in quiescent 3T3 cells. The extent of the phosphorylation is time and PMT concentration dependent, and is inhibited by rapamycin and Torin1, the two specific inhibitors of the mammalian target of rapamycin complex 1 (mTORC1). Interestingly, PMT-mediated mTOR signaling activation was observed in MEF WT but not in Gα(q/11) knock-out cells. These observations are consistent with the data indicating that PMT-induced mTORC1 activation proceeds via the deamidation of Gα(q/11), which leads to the activation of PLCß to generate diacylglycerol and inositol trisphosphate, two known activators of the PKC pathway. Exogenously added diacylglycerol or phorbol 12-myristate 13-acetate, known activators of PKC, leads to rpS6 phosphorylation in a rapamycin-dependent manner. Furthermore, PMT-induced rpS6 phosphorylation is inhibited by PKC inhibitor, Gö6976. Although PMT induces epidermal growth factor receptor activation, it exerts no effect on PMT-induced rpS6 phosphorylation. Together, our findings reveal for the first time that PMT activates mTORC1 through the Gα(q/11)/PLCß/PKC pathway. The fact that PMT-induced protein synthesis and cell migration is partially inhibited by rapamycin indicates that these processes are in part mediated by the mTORC1 pathway.

Chemically Recyclable, High Molar Mass Polyoxazolidinones via Ring-Opening Metathesis Polymerization.

The development of robust methods for the synthesis of chemically recyclable polymers with tunable properties is necessary for the design of next-generation materials. Polyoxazolidinones (POxa), polymers with five-membered urethanes in their backbones, are an attractive target because they are strongly polar and have high thermal stability, but existing step-growth syntheses limit molar masses and methods to chemically recycle POxa to monomer are rare. Herein, we report the synthesis of high molar mass POxa via ring-opening metathesis polymerization of oxazolidinone-fused cyclooctenes. These novel polymers show <5% mass loss up to 382-411 °C and have tunable glass transition temperatures (14-48 °C) controlled by the side chain structure. We demonstrate facile chemical recycling to monomer and repolymerization despite moderately high monomer ring-strain energies, which we hypothesize are facilitated by the conformational restriction introduced by the fused oxazolidinone ring. This method represents the first chain growth synthesis of POxa and provides a versatile platform for the study and application of this emerging subclass of polyurethanes.

Targeted curation of the gut microbial gene content modulating human cardiovascular disease.

IMPORTANCE: One of the most-cited examples of the gut microbiome modulating human disease is the microbial metabolism of quaternary amines from protein-rich foods. By-products of this microbial processing promote atherosclerotic heart disease, a leading cause of human mortality globally. Our research addresses current knowledge gaps in our understanding of this microbial metabolism by holistically inventorying the microorganisms and expressed genes catalyzing critical atherosclerosis-promoting and -ameliorating reactions in the human gut. This led to the creation of an open-access resource, the Methylated Amine Gene Inventory of Catabolism database, the first systematic inventory of gut methylated amine metabolism. More importantly, using this resource we deliver here, we show for the first time that these gut microbial genes can predict human disease, paving the way for microbiota-inspired diagnostics and interventions.

Early Auditory Event Related Potentials Distinguish Higher-Order From First-Order Aversive Conditioning.

Stimuli in reality rarely co-occur with primary reward or punishment to allow direct associative learning of value. Instead, value is thought to be inferred through complex higher-order associations. Rodent research has demonstrated that the formation and maintenance of first-order and higher-order associations are supported by distinct neural substrates. In this study, we explored whether this pattern of findings held true for humans. Participants underwent first-order and subsequent higher-order conditioning using an aversive burst of white noise or neutral tone as the unconditioned stimuli. Four distinct tones, initially neutral, served as first-order and higher-order conditioned stimuli. Autonomic and neural responses were indexed by pupillometry and evoked response potentials (ERPs) respectively. Conditioned aversive values of first-order and higher-order stimuli led to increased autonomic responses, as indexed by pupil dilation. Distinct temporo-spatial auditory evoked response potentials were elicited by first-order and high-order conditioned stimuli. Conditioned first-order responses peaked around 260 ms and source estimation suggested a primary medial prefrontal and amygdala source. Conversely, conditioned higher-order responses peaked around 120 ms with an estimated source in the medial temporal lobe. Interestingly, pupillometry responses to first-order conditioned stimuli were diminished after higher order training, possibly signifying concomitant incidental extinction, while responses to higher-order stimuli remained. This suggests that once formed, higher order associations are at least partially independent of first order conditioned representations. This experiment demonstrates that first-order and higher-order conditioned associations have distinct neural signatures, and like rodents, the medial temporal lobe may be specifically involved with higher-order conditioning.

Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation.

BACKGROUND: Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. RESULTS: We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. CONCLUSIONS: These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells. Video Abstract.

Concentration-Dependent Solvation Structure and Dynamics of Aqueous Sulfuric Acid Using Multinuclear NMR and DFT.

Sulfuric acid is a ubiquitous compound for industrial processes, and aqueous sulfate solutions also play a critical role as electrolytes for many prominent battery chemistries. While the thermodynamic literature on it is quite well-developed, comprehensive studies of the solvation structure, particularly molecular-scale dynamical and transport properties, are less available. This study applies a multinuclear nuclear magnetic resonance (NMR) approach to the elucidation of the solvation structure and dynamics over wide temperature (-10 to 50 °C) and concentration (0-18 M) ranges, combining the 17O shift, line width, and T1 relaxation measurements, 33S shift and line width measurements, and 1H pulsed-field gradient NMR measurements of proton self-diffusivity. In conjunction, these results indicate a crossover between two regimes of solvation structure and dynamics, occurring above the concentration associated with the deep eutectic point (∼4.5 M), with the high-concentration regime dominated by a strong water-sulfate correlation. This description was borne out in detail by the activation energy trends with increasing concentration derived from the relaxation of both the H2O/H3O+ and H2SO4/HSO4-/SO42- 17O resonances and the 1H self-diffusivity. However, the 17O chemical shift difference between the H2O/H3O+ and H2SO4/HSO4-/SO42- resonances across the entire temperature range is nevertheless strikingly linear. A computational approach coupling molecular dynamics simulations and density functional theory NMR shift calculations to reproduce this trend is presented, which will be the subject of further development. This combination of multinuclear, dynamical NMR, and computational methods, and the results furnished by this study, will provide a platform for future studies on battery electrolytes where aqueous sulfate chemistry plays a central role in the solution structure.

Decrypting bacterial polyphenol metabolism in an anoxic wetland soil.

Microorganisms play vital roles in modulating organic matter decomposition and nutrient cycling in soil ecosystems. The enzyme latch paradigm posits microbial degradation of polyphenols is hindered in anoxic peat leading to polyphenol accumulation, and consequently diminished microbial activity. This model assumes that polyphenols are microbially unavailable under anoxia, a supposition that has not been thoroughly investigated in any soil type. Here, we use anoxic soil reactors amended with and without a chemically defined polyphenol to test this hypothesis, employing metabolomics and genome-resolved metaproteomics to interrogate soil microbial polyphenol metabolism. Challenging the idea that polyphenols are not bioavailable under anoxia, we provide metabolite evidence that polyphenols are depolymerized, resulting in monomer accumulation, followed by the generation of small phenolic degradation products. Further, we show that soil microbiome function is maintained, and possibly enhanced, with polyphenol addition. In summary, this study provides chemical and enzymatic evidence that some soil microbiota can degrade polyphenols under anoxia and subvert the assumed polyphenol lock on soil microbial metabolism.

Aluminum content of parenteral nutrition in neonates: measured versus calculated levels.

BACKGROUND AND OBJECTIVE: Aluminum (Al) is associated with significant central nervous system toxicity and bone and liver damage. Because Al is a contaminant of parenteral nutrition (PN) components including calcium and phosphate additives, premature infants are at potentially high risk for toxicity. The US Food and Drug Administration (FDA) has mandated PN component product labeling and recommended maximum Al daily exposure limits. The objective of this article is to determine the actual Al content of neonatal PN solutions, compare these values to the calculated amounts from manufacturers' PN product labels, and ascertain whether the actual Al exposure exceeds the FDA recommended maximum of 5 microg . kg(-1) . day(-1). MATERIALS AND METHODS: Samples from 40 neonatal patient PN solutions were selected for sampling and Al content determination. Samples were also taken from 16 manufacturer's component products used in PN formulation. All of the samples were sent to Mayo Laboratories for Al content measurement. The calculated Al concentrations in PN samples were determined from the manufacturer's labeled content. RESULTS: Both measured and calculated Al concentrations exceeded the FDA recommended safe limit of <5 microg . kg(-1) . day(-1). The actual measured Al content was significantly lower than the calculated Al content in both the patient PN solutions and the component product samples. CONCLUSIONS: Al exposure exceeded the FDA recommended maximum limit for all patient samples; however, the actual measured Al content of all the samples was significantly less than the calculated Al content based on manufacturer's labels. These findings suggest that manufacturers label their products with actual Al content at the time of product release rather than at time of expiration. Periodic monitoring of Al levels should be considered with prolonged PN therapy. Changes in manufacturing processes, including the use of better raw materials, are essential to reduce Al contamination to meet FDA mandates.

The Effects of Common Over-the-Counter Moisturizers on Skin Barrier Function: A Randomized, Observer-Blind, Within-Patient, Controlled Study.

BACKGROUND: Moisturizers possibly improve atopic dermatitis (AD) by restoration of skin barrier, although some have detrimental effects. OBJECTIVE: The aim of the study was to estimate the effects of several routine moisturizers on barrier functions. METHODS: This is a randomized, forearm-controlled, observer-blind study. Patients older than 12 years with clear to moderate AD were randomized to 1 of 4 moisturizers (Cetaphil Cream, Aveeno Eczema Therapy Moisturizing Cream, CeraVe Moisturizing Cream, Vaseline) applied to nonlesional skin of 1 forearm and no moisturizer to the opposite forearm for 4 weeks. Transepidermal water loss (TEWL), capacitance, pH, and TEWL after tape stripping were evaluated at weeks 0 and 4. In addition, participants without AD underwent baseline measurements only. RESULTS: Twenty patients with AD completed the study. Baseline measurements between the AD group and 10 non-AD controls were similar. After the intervention (AD group), mean TEWL improved in the treated forearm and worsened in the untreated one, but the difference was not significant. There was no significant change in pH or in TEWL after tape stripping. Capacitance significantly improved in the moisturizer forearm. The study was underpowered as recruitment fell short. CONCLUSIONS: The effects of moisturizers on nonlesional AD skin were small and need to be addressed when powering future studies. Broadening investigations beyond the classic barrier properties might be useful in future studies.

Effects of ingested nanocellulose on intestinal microbiota and homeostasis in Wistar Han rats.

Micron scale cellulose materials are "generally regarded as safe" (GRAS) as binders and thickeners in food products. However, nanocellulose materials, which have unique properties that can improve food quality and safety, have not received US-Food and Drug Administration (FDA) approval as food ingredients. In vitro and in vivo toxicological studies of ingested nanocellulose revealed minimal cytotoxicity, and no subacute in vivo toxicity. However, ingested materials may modulate gut microbial populations, or alter aspects of intestinal function not elucidated by toxicity testing, which could have important health implications. Here, we report the results of studies conducted in a rat gavage model to assess the effects of ingested cellulose nanofibrils (CNF) on the fecal microbiome and metabolome, intestinal epithelial expression of cell junction genes, and ileal cytokine production. Feces, plasma, and ilea were collected from Wistar Han rats before and after five weeks of biweekly gavages with water or cream, with or without 1% CNF. CNF altered microbial diversity, and diminished specific species that produce short chain fatty acids, and that are associated with increased serum insulin and IgA production. CNF had few effects on the fecal metabolome, with significant changes in only ten metabolites of 366 measured. Exposure to CNF also altered expression of epithelial cell junction genes, and increased production of cytokines that modulate proliferation of CD8 T cells. These perturbations likely represent initiation of an adaptive immune response, however, no associated pathology was seen within the duration of the study. Additional studies are needed to better understand the health implications of these changes in long term.

Evaluation of SARS-CoV-2 serology assays reveals a range of test performance.

Appropriate use and interpretation of serological tests for assessments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure, infection and potential immunity require accurate data on assay performance. We conducted a head-to-head evaluation of ten point-of-care-style lateral flow assays (LFAs) and two laboratory-based enzyme-linked immunosorbent assays to detect anti-SARS-CoV-2 IgM and IgG antibodies in 5-d time intervals from symptom onset and studied the specificity of each assay in pre-coronavirus disease 2019 specimens. The percent of seropositive individuals increased with time, peaking in the latest time interval tested (>20 d after symptom onset). Test specificity ranged from 84.3% to 100.0% and was predominantly affected by variability in IgM results. LFA specificity could be increased by considering weak bands as negative, but this decreased detection of antibodies (sensitivity) in a subset of SARS-CoV-2 real-time PCR-positive cases. Our results underline the importance of seropositivity threshold determination and reader training for reliable LFA deployment. Although there was no standout serological assay, four tests achieved more than 80% positivity at later time points tested and more than 95% specificity.

Test performance evaluation of SARS-CoV-2 serological assays.

BACKGROUND: Serological tests are crucial tools for assessments of SARS-CoV-2 exposure, infection and potential immunity. Their appropriate use and interpretation require accurate assay performance data. METHOD: We conducted an evaluation of 10 lateral flow assays (LFAs) and two ELISAs to detect anti-SARS-CoV-2 antibodies. The specimen set comprised 128 plasma or serum samples from 79 symptomatic SARS-CoV-2 RT-PCR-positive individuals; 108 pre-COVID-19 negative controls; and 52 recent samples from individuals who underwent respiratory viral testing but were not diagnosed with Coronavirus Disease 2019 (COVID-19). Samples were blinded and LFA results were interpreted by two independent readers, using a standardized intensity scoring system. RESULTS: Among specimens from SARS-CoV-2 RT-PCR-positive individuals, the percent seropositive increased with time interval, peaking at 81.8-100.0% in samples taken >20 days after symptom onset. Test specificity ranged from 84.3-100.0% in pre-COVID-19 specimens. Specificity was higher when weak LFA bands were considered negative, but this decreased sensitivity. IgM detection was more variable than IgG, and detection was highest when IgM and IgG results were combined. Agreement between ELISAs and LFAs ranged from 75.7-94.8%. No consistent cross-reactivity was observed. CONCLUSION: Our evaluation showed heterogeneous assay performance. Reader training is key to reliable LFA performance, and can be tailored for survey goals. Informed use of serology will require evaluations covering the full spectrum of SARS-CoV-2 infections, from asymptomatic and mild infection to severe disease, and later convalescence. Well-designed studies to elucidate the mechanisms and serological correlates of protective immunity will be crucial to guide rational clinical and public health policies.

Chemically reprogramming the phospho-transfer reaction to crosslink protein kinases to their substrates.

The proteomic mapping of enzyme-substrate interactions is challenged by their transient nature. A method to capture interacting protein kinases in complexes with a single substrate of interest would provide a new tool for mapping kinase signaling networks. Here, we describe a nucleotide-based substrate analog capable of reprogramming the wild-type phosphoryl-transfer reaction to produce a kinase-acrylamide-based thioether crosslink to mutant substrates with a cysteine nucleophile substituted at the native phosphorylation site. A previously reported ATP-based methacrylate crosslinker (ATP-MA) was capable of mediating kinase crosslinking to short peptides but not protein substrates. Exploration of structural variants of ATP-MA to enable crosslinking of protein substrates to kinases led to the discovery that an ADP-based methacrylate (ADP-MA) crosslinker was superior to the ATP scaffold at crosslinking in vitro. The improved efficiency of ADP-MA over ATP-MA is due to reduced inhibition of the second step of the kinase-substrate crosslinking reaction by the product of the first step of the reaction. The new probe, ADP-MA, demonstrated enhanced in vitro crosslinking between the Src tyrosine kinase and its substrate Cortactin in a phosphorylation site-specific manner. The kinase-substrate crosslinking reaction can be carried out in a complex mammalian cell lysate setting, although the low abundance of endogenous kinases remains a significant challenge for efficient capture.

Uncovering the Diversity and Activity of Methylotrophic Methanogens in Freshwater Wetland Soils.

Wetland soils are one of the largest natural contributors to the emission of methane, a potent greenhouse gas. Currently, microbial contributions to methane emissions from these systems emphasize the roles of acetoclastic and hydrogenotrophic methanogens, while less frequently considering methyl-group substrates (e.g., methanol and methylamines). Here, we integrated laboratory and field experiments to explore the potential for methylotrophic methanogenesis in Old Woman Creek (OWC), a temperate freshwater wetland located in Ohio, USA. We first demonstrated the capacity for methylotrophic methanogenesis in these soils using laboratory soil microcosms amended with trimethylamine. However, subsequent field porewater nuclear magnetic resonance (NMR) analyses to identify methanogenic substrates failed to detect evidence for methylamine compounds in soil porewaters, instead noting the presence of the methylotrophic substrate methanol. Accordingly, our wetland soil-derived metatranscriptomic data indicated that methanol utilization by the Methanomassiliicoccaceae was the likely source of methylotrophic methanogenesis. Methanomassiliicoccaceae relative contributions to mcrA transcripts nearly doubled with depth, accounting for up to 8% of the mcrA transcripts in 25-cm-deep soils. Longitudinal 16S rRNA amplicon and mcrA gene surveys demonstrated that Methanomassiliicoccaceae were stably present over 2 years across lateral and depth gradients in this wetland. Meta-analysis of 16S rRNA sequences similar (>99%) to OWC Methanomassiliicoccaceae in public databases revealed a global distribution, with a high representation in terrestrial soils and sediments. Together, our results demonstrate that methylotrophic methanogenesis likely contributes to methane flux from climatically relevant wetland soils.IMPORTANCE Understanding the sources and controls on microbial methane production from wetland soils is critical to global methane emission predictions, particularly in light of changing climatic conditions. Current biogeochemical models of methanogenesis consider only acetoclastic and hydrogenotrophic sources and exclude methylotrophic methanogenesis, potentially underestimating microbial contributions to methane flux. Our multi-omic results demonstrated that methylotrophic methanogens of the family Methanomassiliicoccaceae were present and active in a freshwater wetland, with metatranscripts indicating that methanol, not methylamines, was the likely substrate under the conditions measured here. However, laboratory experiments indicated the potential for other methanogens to become enriched in response to trimethylamine, revealing the reservoir of methylotrophic methanogenesis potential residing in these soils. Collectively, our approach used coupled field and laboratory investigations to illuminate metabolisms influencing the terrestrial microbial methane cycle, thereby offering direction for increased realism in predictive process-oriented models of methane flux in wetland soils.

Laboratory evaluation of inflammatory bowel disease.

PURPOSE OF REVIEW: Recognizing inflammatory bowel disease (IBD) is straightforward when alarm symptoms are present, such as bloody diarrhea and weight loss. When the presentation is subtle or atypical, physicians must determine which patients warrant evaluation for IBD. Appropriate use of noninvasive tests can help identify which patients should undergo further investigation. RECENT FINDINGS: Currently IBD serologies lack high enough sensitivity and specificity to make them useful as a screening test for distinguishing IBD from other disorders, but they may have a role in classifying subtypes of IBD. Fecal markers seem promising for helping to differentiate IBD from irritable bowl syndrome and for monitoring disease activity. Pharmacogenetically guided dosing is recommended for safe use of thiopurines but ongoing routine laboratory monitoring remains important. Thiopurine metabolite measurement can be useful but may not be needed in all cases. SUMMARY: Primary care physicians should continue to rely on routine laboratory tests and clinical suspicion to decide which patients with abdominal pain to refer to a gastroenterologist. Serology panels are not useful for IBD screening as the results may lead to unnecessary procedures. Although fecal markers do show promise as a screening test for IBD, patient resistance to providing stool samples may limit its usefulness in disease monitoring. Thiopurine metabolite levels are best used in conjunction with clinical status and routine laboratory tests to monitor clinical response and adverse events.

Acute dislocation of the elbow caused by a solitary osteochondroma of the proximal radius.

A young man presented with acute dislocation of the left elbow at the radio-capitellar articulation caused by trapping of the biceps tendon at the stalk of a solitary osteochondroma. There was no deformity of the ulna and radius shaft suggestive of a developmental growth disturbance of the forearm bones. Good reduction could be achieved by simple relocation of the biceps tendon. The osteochondroma was excised.