Publications by authors named "Brian Fox"

Article Synopsis
  • * The study introduces Sensor-seq, a high-throughput platform that allows for the design and identification of aTF biosensors that can bind to a variety of non-native ligands, testing 17,737 variants of aTF TtgR against multiple compounds.
  • * Sensor-seq successfully finds biosensors with high performance for various ligands and showcases their practical use through cell-free detection systems for specific drugs, enhancing the ability to create new biosensors beyond natural limitations.
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Enzyme replacement therapy (ERT) is the only approved disease-modifying treatment modality for Pompe disease, a rare, inherited metabolic disorder caused by a deficiency in the acid -glucosidase (GAA) enzyme that catabolizes lysosomal glycogen. First-generation recombinant human GAA (rhGAA) ERT (alglucosidase alfa) can slow the progressive muscle degeneration characteristic of the disease. Still, most patients experience diminished efficacy over time, possibly because of poor uptake into target tissues.

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Here, we report the draft genome sequence of sp. CAP02, which metabolizes caprolactam as a sole source of carbon and nitrogen. This bacterium was isolated from Dane County Landfill Site No.

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In mammals, l-cysteine (Cys) homeostasis is maintained by the mononuclear nonheme iron enzyme cysteine dioxygenase (CDO), which oxidizes Cys to cysteine sulfinic acid. CDO contains a rare post-translational modification, involving the formation of a thioether cross-link between a Cys residue at position 93 ( CDO numbering) and a nearby tyrosine at position 157 (Cys-Tyr cross-link). As-isolated CDO contains both the cross-linked and non-cross-linked isoforms, and formation of the Cys-Tyr cross-link during repeated enzyme turnover increases CDO's catalytic efficiency by ∼10-fold.

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Background: mutations are associated with an adverse prognosis in acute myeloid leukemia (AML) and higher-risk myelodysplastic syndromes (HR-MDS). However, the integrated genetic, epigenetic, and immunologic landscape of -mutated AML/HR-MDS is not well defined.

Objectives: To define the genetic, epigenetic, and immunologic landscape of mutant and wild-type AML and HR-MDS patients.

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Background: The minimal clinically important difference (MCID) is the smallest change in outcome that physicians or patients would consider meaningful and is relevant when evaluating disease progression or the efficacy of interventions. Studies of patients with late-onset Pompe disease (LOPD) have used the 6-min walk distance (6MWD) as an endpoint to assess motor function. However, an MCID for 6MWD (% predicted and meters) has yet to be established in LOPD.

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Article Synopsis
  • Allosteric transcription factors (aTFs) are important tools for detecting various molecules but designing them to work with new compounds is difficult due to potential disruptions in their allosteric properties.
  • The researchers developed a high-throughput platform called Sensor-seq that screened over 17,000 variants of the aTF TtgR to find biosensors that can bind to a range of non-native and native ligands.
  • The study resulted in the identification of new biosensors with excellent specificity and effectiveness, and practical applications were demonstrated through cell-free detection systems for naltrexone and quinine.
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Unlabelled: In normal cells, binding of the transmembrane protein CD47 to signal regulatory protein-α (SIRPα) on macrophages induces an antiphagocytic signal. Tumor cells hijack this pathway and overexpress CD47 to evade immune destruction. Macrophage antitumor activity can be restored by simultaneously blocking the CD47-SIRPα signaling axis and inducing a prophagocytic signal via tumor-opsonizing antibodies.

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Sterile alpha and toll/interleukin receptor motif-containing 1 (SARM1) is a critical regulator of axon degeneration that acts through hydrolysis of NAD following injury. Recent work has defined the mechanisms underlying SARM1's catalytic activity and advanced our understanding of SARM1 function in axons, yet the role of SARM1 signaling in other compartments of neurons is still not well understood. Here, we show in cultured hippocampal neurons that endogenous SARM1 is present in axons, dendrites, and cell bodies and that direct activation of SARM1 by the neurotoxin Vacor causes not just axon degeneration, but degeneration of all neuronal compartments.

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The treatment landscape for lysosomal storage disorders (LSDs) is rapidly evolving. An increase in the number of preclinical and clinical studies in the last decade has demonstrated that pharmacological chaperones are a feasible alternative to enzyme replacement therapy (ERT) for individuals with LSDs. A systematic search was performed to retrieve and critically assess the evidence from preclinical and clinical applications of pharmacological chaperones in the treatment of LSDs and to elucidate the mechanisms by which they could be effective in clinical practice.

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Kelp is an abundant, farmable biomass-containing laminarin and alginate as major polysaccharides, providing an excellent model substrate to study their deconstruction by simple enzyme mixtures. Our previous study showed strong reactivity of the glycoside hydrolase family 55 during hydrolysis of purified laminarin, raising the question of its reactivity with intact kelp. In this study, we determined that a combination of a single glycoside hydrolase family 55 β-1,3-exoglucanase with a broad-specificity alginate lyase from the polysaccharide lyase family 18 gives efficient hydrolysis of untreated kelp to a mixture of simple sugars, that is, glucose, gentiobiose, mannitol-end glucose, and mannuronic and guluronic acids and their soluble oligomers.

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Article Synopsis
  • Mass spectrometry (MS) is a powerful tool for detecting chemical species but has limitations in processing speed, which can be improved by integrating it with microfluidics.
  • The Drop-NIMS platform combines a microfluidic device with a unique MS technique that allows for the random mixing of droplets to create a library of enzymatic reactions directly on the NIMS surface, minimizing handling.
  • This method was successfully used to quickly screen low-volume enzymatic reactions, identifying various glycoside hydrolases relevant to industries like food and biofuels, demonstrating its versatility and ease of use for analyzing small molecule metabolites.
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Article Synopsis
  • Cysteine dioxygenase (CDO) is an enzyme that converts cysteine into cysteine sulfinic acid, with a unique crosslink enhancing its catalytic efficiency.
  • The study focused on creating a variant of bacterial CDO (G82C) to test if a single DNA mutation could allow crosslink formation, showing that it indeed can form the crosslink but with lower efficiency than the wild-type enzyme.
  • Bioinformatics revealed many potential crosslinked CDOs in Gram-negative pathogenic bacteria, indicating a broader biological significance for this crosslink formation.
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To examine the potential impact of contact tracing to identify contacts and prevent mpox transmission among gay, bisexual, and other men who have sex with men (MSM) as the outbreak expanded. We assessed contact tracing outcomes from 10 US jurisdictions before and after access to the mpox vaccine was expanded from postexposure prophylaxis for persons with known exposure to include persons at high risk for acquisition (May 17-June 30, 2022, and July 1-31, 2022, respectively). Overall, 1986 mpox cases were reported in MSM from included jurisdictions (240 before expanded vaccine access; 1746 after expanded vaccine access).

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Enzymatic deconstruction of lignocellulosic biomass is crucial to establishment of the renewable biofuel and bioproduct economy. Better understanding of these enzymes, including their catalytic and binding domains, and other features offer potential avenues for improvement. Glycoside hydrolase family 9 (GH9) enzymes are attractive targets because they have members that exhibit exo- and endo-cellulolytic activity, processivity of reaction, and thermostability.

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Polyhydroxyalkanoate (PHA) production from plant biomass is an ideal way to realize sustainable PHA-based bioplastic. The present study demonstrated consolidated bioconversion of plant biomass to PHA by co-culturing two specialized bacteria, cellulolytic Streptomyces sp. SirexAA-E and PHA producing Priestia megaterium.

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Chemically labile ester linkages can be introduced into lignin by incorporation of monolignol conjugates, which are synthesized in planta by acyltransferases that use a coenzyme A (CoA) thioester donor and a nucleophilic monolignol alcohol acceptor. The presence of these esters facilitates processing and aids in the valorization of renewable biomass feedstocks. However, the effectiveness of this strategy is potentially limited by the low steady-state levels of aromatic acid thioester donors in plants.

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In the TRANSCEND NHL 001 study, 53% of patients with relapsed/refractory large B-cell lymphoma (LBCL) treated with lisocabtagene maraleucel (liso-cel) achieved a complete response (CR). To determine characteristics of patients who did and did not achieve a CR, we examined the tumor biology and microenvironment from lymph node tumor biopsies. LBCL biopsies from liso-cel-treated patients were taken pretreatment and ∼11 days posttreatment for RNA sequencing (RNA-seq) and multiplex immunofluorescence (mIF).

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Lactones are prevalent in biological and industrial settings, yet there is a lack of information regarding enzymes used to metabolize these compounds. One compound, γ-valerolactone (GVL), is used as a solvent to dissolve plant cell walls into sugars and aromatic molecules for subsequent microbial conversion to fuels and chemicals. Despite the promise of GVL as a renewable solvent for biomass deconstruction, residual GVL can be toxic to microbial fermentation.

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Dual leucine zipper kinase (DLK) and leucine zipper-bearing kinase (LZK) are regulators of neuronal degeneration and axon growth. Therefore, there is a considerable interest in developing DLK/LZK inhibitors for neurodegenerative diseases. Herein, we use ligand- and structure-based drug design approaches for identifying novel amino-pyrazine inhibitors of DLK/LZK.

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The ability to predict individual differences in motor learning has significant implications from both theoretical and applied perspectives. However, there is high variability in the methodological and analytical strategies employed as evidence for such predictions. Here, we critically examine the evidence for predictions of individual differences in motor learning by reviewing the literature from a 20-year period (2000-2020).

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Background: Studies suggest that immune checkpoint inhibitors may represent a promising strategy for boosting immune responses and improving the antitumor activity of standard therapies in patients with relapsed/refractory hematologic malignancies.

Aims: Phase 1/2 FUSION NHL 001 was designed to determine the safety and efficacy of durvalumab, an anti-programmed death ligand 1 (PD-L1) antibody, combined with standard-of-care therapies for lymphoma or chronic lymphocytic leukemia (CLL).

Methods And Results: The primary endpoints were to determine the recommended phase 2 dose of the drugs used in combination with durvalumab (durvalumab was administered at the previously recommended dose of 1500 mg every 4 weeks) and to assess safety and tolerability.

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RIPK1 is a master regulator of inflammatory signaling and cell death and increased RIPK1 activity is observed in human diseases, including Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS). RIPK1 inhibition has been shown to protect against cell death in a range of preclinical cellular and animal models of diseases. SAR443060 (previously DNL747) is a selective, orally bioavailable, central nervous system (CNS)-penetrant, small-molecule, reversible inhibitor of RIPK1.

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