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1.
Nat Methods ; 2024 May 14.
Article in English | MEDLINE | ID: mdl-38744918

ABSTRACT

The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories. Here we report the summary of the outcomes to provide robust benchmarks and a valuable entry point for the scientific community.

2.
J Am Soc Mass Spectrom ; 35(5): 912-921, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38535992

ABSTRACT

Structure-based drug design, which relies on precise understanding of the target protein and its interaction with the drug candidate, is dramatically expedited by advances in computational methods for candidate prediction. Yet, the accuracy needs to be improved with more structural data from high throughput experiments, which are challenging to generate, especially for dynamic and weak associations. Herein, we applied native mass spectrometry (native MS) to rapidly characterize ligand binding of an allosteric heterodimeric complex of SARS-CoV-2 nonstructural proteins (nsp) nsp10 and nsp16 (nsp10/16), a complex essential for virus survival in the host and thus a desirable drug target. Native MS showed that the dimer is in equilibrium with monomeric states in solution. Consistent with the literature, well characterized small cosubstrate, RNA substrate, and product bind with high specificity and affinity to the dimer but not the free monomers. Unsuccessfully designed ligands bind indiscriminately to all forms. Using neutral gas collision, the nsp16 monomer with bound cosubstrate can be released from the holo dimer complex, confirming the binding to nsp16 as revealed by the crystal structure. However, we observed an unusual migration of the endogenous zinc ions bound to nsp10 to nsp16 after collisional dissociation. The metal migration can be suppressed by using surface collision with reduced precursor charge states, which presumably resulted in minimal gas-phase structural rearrangement and highlighted the importance of complementary techniques. With minimal sample input (∼µg), native MS can rapidly detect ligand binding affinities and locations in dynamic multisubunit protein complexes, demonstrating the potential of an "all-in-one" native MS assay for rapid structural profiling of protein-to-AI-based compound systems to expedite drug discovery.


Subject(s)
Mass Spectrometry , Methyltransferases , Protein Multimerization , SARS-CoV-2 , Viral Nonstructural Proteins , Viral Regulatory and Accessory Proteins , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , SARS-CoV-2/chemistry , Mass Spectrometry/methods , Allosteric Regulation , Protein Binding , Humans , Ligands , Models, Molecular
3.
Res Sq ; 2023 Aug 23.
Article in English | MEDLINE | ID: mdl-37674709

ABSTRACT

The combination of native electrospray ionisation with top-down fragmentation in mass spectrometry allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and co-factors. While this approach is powerful, both native mass spectrometry and top-down mass spectrometry are not yet well standardised, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics (CTDP) initiated a study to develop and test protocols for native mass spectrometry combined with top-down fragmentation of proteins and protein complexes across eleven instruments in nine laboratories. The outcomes are summarised in this report to provide robust benchmarks and a valuable entry point for the scientific community.

4.
J Opt Soc Am A Opt Image Sci Vis ; 40(5): 942-954, 2023 May 01.
Article in English | MEDLINE | ID: mdl-37133191

ABSTRACT

Medical imaging devices are becoming increasingly compact, necessitating optimization research into different methods of actuation. Actuation influences important parameters of the imaging device such as size, weight, frame rate, field of view (FOV), and image reconstruction for imaging devices point scanning techniques. Current literature around piezoelectric fiber cantilever actuators focuses on device optimization with a fixed FOV but neglects adjustability. In this paper, we introduce an adjustable FOV piezoelectric fiber cantilever microscope and provide a characterization and optimization procedure. To overcome calibration challenges, we utilize a position sensitive detector (PSD) and address trade-offs between FOV and sparsity with a novel inpainting technique. Our work demonstrates the potential for scanner operation when sparsity and distortion dominate the FOV, extending the usable FOV for this form of actuation and others that currently only operate under ideal imaging conditions.

5.
J Chem Inf Model ; 63(5): 1438-1453, 2023 03 13.
Article in English | MEDLINE | ID: mdl-36808989

ABSTRACT

Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic's evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (Mpro), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. This work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic "warhead" to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of Mpro with micromolar affinities (KI of 5.27 µM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.


Subject(s)
COVID-19 , Hepatitis C, Chronic , Humans , SARS-CoV-2/metabolism , Antiviral Agents/pharmacology , Pandemics , Artificial Intelligence , Protease Inhibitors/pharmacology , Molecular Docking Simulation
6.
J Chromatogr A ; 1688: 463721, 2023 Jan 11.
Article in English | MEDLINE | ID: mdl-36565654

ABSTRACT

Hydrophilic-interaction liquid chromatography (HILIC) of intact proteins offers high-resolution separations of glycoforms of glycoproteins differing in the number of (neutral) glycans. However, to obtain efficient separations it is essential that the positively charged sites of the proteins are shielded by acidic (negative) ion-pair reagents (IPRs), so as to enhance the contribution of the hydroxyl groups of the (neutral) sugars in the glycoprotein. Here, we studied the influence of various IPRs that differ in physico-chemical properties, such as hydrophobicity and acidity, on the capillary-scale HILIC separation of intact (glyco)proteins. We evaluated the use of fluoroacetic acid (MFA), difluoroacetic acid (DFA), trifluoroacetic acid (TFA), and heptafluorobutyric acid (HFBA) as diluents for sample preparation, as solvents for sample loading on a reversed-phase trap prior to the HILIC separation, and as mobile-phase components for HILIC and HILIC-MS. To reduce the contribution of ion-exchange interaction with the (silica-based) stationary phase, we used an acrylamide-based monolithic column. We studied the influence of the different IPRs on each step of the separation of a mixture of proteins of different size and hydrophilicity and on the separation of the five glycoforms of ribonuclease B. The content of IPR in the sample was shown not to affect the separation and the MS detection. However, a low content of TFA and DFA in the mobile phase is favourable, as it reduces adduct formation and leads to higher signal intensity. The optimized HILIC conditions successfully resolved nine major glycoforms groups of a ∼40 kDa glycoprotein horseradish peroxidase (HRP), as an example of a complex glycoprotein.


Subject(s)
Glycoproteins , Indicators and Reagents , Chromatography, Liquid/methods , Glycoproteins/chemistry , Mass Spectrometry , Ions , Hydrophobic and Hydrophilic Interactions
7.
Methods Mol Biol ; 2500: 181-199, 2022.
Article in English | MEDLINE | ID: mdl-35657594

ABSTRACT

Protein encoding genes can undergo modifications posttranscriptionally and posttranslationally, yielding many different "proteoforms." The chemical diversity of such modifications is known to be important biomarkers of function within biological systems but is not completely understood. Top-down mass spectrometry is a valuable tool for the characterization of proteoforms, especially for histones that have complex combinations of posttranslational modifications (PTMs). In this chapter, we present a top-down liquid chromatography-mass spectrometry experimental and data analysis workflow for the identification of novel, unexpected modifications on histones. Proteoforms of interest are first discovered using the "open" modification search in TopPIC. Then target proteoforms are manually confirmed using the data visualization tool-LcMsSpectator, part of the Informed-Proteomics package. The workflow can be very helpful in targeted PTM analysis and can be expanded to other types of proteins for discovery of unknown PTMs.


Subject(s)
Histones , Tandem Mass Spectrometry , Chromatography, Liquid , Histones/genetics , Protein Processing, Post-Translational , Proteomics/methods , Tandem Mass Spectrometry/methods
8.
Biomed Opt Express ; 13(4): 2103-2116, 2022 Apr 01.
Article in English | MEDLINE | ID: mdl-35519286

ABSTRACT

Mitochondrial redox is an important indicator of cell metabolism and health, with implications in cancer, diabetes, aging, neurodegenerative diseases, and mitochondrial disease. The most common method to observe redox of individual cells and mitochondria is through fluorescence of NADH and FAD+, endogenous cofactors serve as electron transport inputs to the mitochondrial respiratory chain. Yet this leaves out redox within the respiratory chain itself. To a degree, the missing information can be filled in by exogenous fluorophores, but at the risk of disturbed mitochondrial permeability and respiration. Here we show that variations in respiratory chain redox can be detected up by visible-wavelength transient absorption microscopy (TAM). In TAM, the selection of pump and probe wavelengths can provide multiphoton imaging contrast between non-fluorescent molecules. Here, we applied TAM with a pump at 520nm and probe at 450nm, 490nm, and 620nm to elicit redox contrast from mitochondrial respiratory chain hemeproteins. Experiments were performed with reduced and oxidized preparations of isolated mitochondria and whole muscle fibers, using mitochondrial fuels (malate, pyruvate, and succinate) to set up physiologically relevant oxidation levels. TAM images of muscle fibers were analyzed with multivariate curve resolution (MCR), revealing that the response at 620nm probe provides the best redox contrast and the most consistent response between whole cells and isolated mitochondria.

9.
Anal Chem ; 94(15): 5909-5917, 2022 04 19.
Article in English | MEDLINE | ID: mdl-35380435

ABSTRACT

SARS-CoV-2 cellular infection is mediated by the heavily glycosylated spike protein. Recombinant versions of the spike protein and the receptor-binding domain (RBD) are necessary for seropositivity assays and can potentially serve as vaccines against viral infection. RBD plays key roles in the spike protein's structure and function, and thus, comprehensive characterization of recombinant RBD is critically important for biopharmaceutical applications. Liquid chromatography coupled to mass spectrometry has been widely used to characterize post-translational modifications in proteins, including glycosylation. Most studies of RBDs were performed at the proteolytic peptide (bottom-up proteomics) or released glycan level because of the technical challenges in resolving highly heterogeneous glycans at the intact protein level. Herein, we evaluated several online separation techniques: (1) C2 reverse-phase liquid chromatography (RPLC), (2) capillary zone electrophoresis (CZE), and (3) acrylamide-based monolithic hydrophilic interaction chromatography (HILIC) to separate intact recombinant RBDs with varying combinations of glycosylations (glycoforms) for top-down mass spectrometry (MS). Within the conditions we explored, the HILIC method was superior to RPLC and CZE at separating RBD glycoforms, which differ significantly in neutral glycan groups. In addition, our top-down analysis readily captured unexpected modifications (e.g., cysteinylation and N-terminal sequence variation) and low abundance, heavily glycosylated proteoforms that may be missed by using glycopeptide data alone. The HILIC top-down MS platform holds great potential in resolving heterogeneous glycoproteins for facile comparison of biosimilars in quality control applications.


Subject(s)
Biosimilar Pharmaceuticals , COVID-19 , Chromatography, Liquid , Chromatography, Reverse-Phase/methods , Glycoproteins/chemistry , Humans , Hydrophobic and Hydrophilic Interactions , Mass Spectrometry , Polysaccharides/analysis , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry
10.
J Phys Chem B ; 126(7): 1404-1412, 2022 02 24.
Article in English | MEDLINE | ID: mdl-35166549

ABSTRACT

Hemeproteins are frequent subjects for ultrafast transient absorption spectroscopy (TAS) because of biological importance, strong UV-vis absorption, high photostability, and interesting transient dynamics that depend on redox, conformation, and ligand binding. TAS on hemeproteins is usually performed on isolated, purified proteins, though their response is likely to be different in their native molecular environment, which involves the formation of protein complexes and supercomplexes. Recently, we reported a transient absorption microscopy (TAM) experiment which elicited a transient response from hemeproteins in intact biological tissue using a visible-wavelength pump (530 nm) and probe (490 nm). Here, we find that adaptive noise canceling plus resonant galvanometer scanning enables a high-repetition-rate fiber laser source to make redox-sensitive measurements of cytochrome c (Cyt-c). We investigate the origins of the visible-wavelength response of biological tissue through TAS of intact mitochondrial respiratory supercomplexes, separated via gel electrophoresis. We find that each of these high-molecular-weight gel bands yields a TAS response characteristic of cytochrome hemes, implying that the TAS response of intact cells and tissue originates from not just Cyt-c but a mixture of respiratory cytochromes. We also find differences in excited-state lifetime between wild-type (WT) and a tafazzin-deficient (TAZ) mouse model of mitochondrial disease.


Subject(s)
Cytochromes c , Heme , Animals , Cytochromes c/chemistry , Heme/chemistry , Humans , Mice , Mitochondrial Membranes/metabolism , Oxidation-Reduction , Spectrum Analysis
11.
Opt Lett ; 47(22): 5841-5844, 2022 Nov 15.
Article in English | MEDLINE | ID: mdl-37219129

ABSTRACT

Impulsive stimulated Raman scattering (ISRS) is a robust technique for studying low frequency (<300 cm-1) Raman vibrational modes, but ISRS has faced difficulty in translation to an imaging modality. A primary challenge is the separation of the pump and probe pulses. Here we introduce and demonstrate a simple strategy for ISRS spectroscopy and hyperspectral imaging that uses complementary steep edge spectral filters to separate the probe beam detection from the pump and enables simple ISRS microscopy with a single-color ultrafast laser source. ISRS spectra are obtained that span from the fingerprint region down to <50 cm-1 vibrational modes. Hyperspectral imaging and polarization-dependent Raman spectra are also demonstrated.

12.
Intervention (Amstelveen) ; 19(1): 58-66, 2021.
Article in English | MEDLINE | ID: mdl-34642580

ABSTRACT

Problem Management Plus (PM+) is a low-intensity psychological intervention developed by the World Health Organization that can be delivered by nonspecialists to address common mental health conditions in people affected by adversity. Emerging evidence demonstrates the efficacy of PM+ across a range of settings. However, the published literature rarely documents the adaptation processes for psychological interventions to context or culture, including curriculum or implementation adaptations. Practical guidance for adapting PM+ to context while maintaining fidelity to core psychological elements is essential for mental health implementers to enable replication and scale. This paper describes the process of contextually adapting PM+ for implementation in Rwanda, Peru, Mexico and Malawi undertaken by the international nongovernmental organization Partners In Health. To our knowledge, this initiative is among the first to adapt PM+ for routine delivery across multiple public sector primary care and community settings in partnership with Ministries of Health. Lessons learned contribute to a broader understanding of effective processes for adapting low-intensity psychological interventions to real-world contexts.

13.
Trials ; 22(1): 630, 2021 Sep 16.
Article in English | MEDLINE | ID: mdl-34530894

ABSTRACT

BACKGROUND: Malawi is a low-income country in sub-Saharan Africa that has limited resources to address a significant burden of disease-including HIV/AIDS. Additionally, depression is a leading cause of disability in the country but largely remains undiagnosed and untreated. The lack of cost-effective, scalable solutions is a fundamental barrier to expanding depression treatment. Against this backdrop, one major success has been the scale-up of a network of more than 700 HIV clinics, with over half a million patients enrolled in antiretroviral therapy (ART). As a chronic care system with dedicated human resources and infrastructure, this presents a strategic platform for integrating depression care and responds to a robust evidence base outlining the bi-directionality of depression and HIV outcomes. METHODS: We will evaluate a stepped model of depression care that combines group-based Problem Management Plus (group PM+) with antidepressant therapy (ADT) for 420 adults with moderate/severe depression in Neno District, Malawi, as measured by the Patient Health Questionnaire-9 (PHQ-9) and Mini-International Neuropsychiatric Interview (MINI). Roll-out will follow a stepped-wedge cluster randomized design in which 14 health facilities are randomized to implement the model in five steps over a 15-month period. Primary outcomes (depression symptoms, functional impairment, and overall health) and secondary outcomes (e.g., HIV: viral load, ART adherence; diabetes: A1C levels, treatment adherence; hypertension: systolic blood pressure, treatment adherence) will be measured every 3 months through 12-month follow-up. We will also evaluate the model's cost-effectiveness, quantified as an incremental cost-effectiveness ratio (ICER) compared to baseline chronic care services in the absence of the intervention model. DISCUSSION: This study will conduct a stepped-wedge cluster randomized trial to compare the effects of an evidence-based depression care model versus usual care on depression symptom remediation as well as physical health outcomes for chronic care conditions. If determined to be cost-effective, this study will provide a model for integrating depression care into HIV clinics in additional districts of Malawi and other low-resource settings with high HIV prevalence. TRIAL REGISTRATION: ClinicalTrials.gov NCT04777006 . Registered on 1 March, 2021.


Subject(s)
Depression , HIV Infections , Adult , Cost-Benefit Analysis , Depression/diagnosis , Depression/therapy , HIV Infections/diagnosis , HIV Infections/drug therapy , Humans , Malawi , Randomized Controlled Trials as Topic , Viral Load
14.
Int J Mass Spectrom ; 4692021 Nov.
Article in English | MEDLINE | ID: mdl-34421332

ABSTRACT

Native mass spectrometry analysis of membrane proteins has yielded many useful insights in recent years with respect to membrane protein-lipid interactions, including identifying specific interactions and even measuring binding affinities based on observed abundances of lipid-bound ions after collision-induced dissociation (CID). However, the behavior of non-covalent complexes subjected to extensive CID can in principle be affected by numerous factors related to gas-phase chemistry, including gas-phase basicity (GB) and acidity, shared-proton bonds, and other factors. A recent report from our group showed that common lipids span a wide range of GB values. Notably, phosphatidylcholine (PC) and sphingomyelin lipids are more basic than arginine, suggesting they may strip charge upon dissociation in positive ion mode, while phosphoserine lipids are slightly less basic than arginine and may form especially strong shared-proton bonds. Here, we use CID to probe the strength of non-specific gas-phase interactions between lipid head groups and several soluble proteins, used to deliberately avoid possible physiological protein-lipid interactions. The strengths of the protein-head group interactions follow the trend predicted based solely on lipid and amino acid GBs: phosphoserine (PS) head group forms the strongest bonds with these proteins and out-competes the other head groups studied, while glycerophosphocholine (GPC) head groups form the weakest interactions and dissociate carrying away a positive charge. These results indicate that gas-phase thermochemistry can play an important role in determining which head groups remain bound to protein ions with native-like structures and charge states in positive ion mode upon extensive collisional activation.

15.
Article in English | MEDLINE | ID: mdl-34168884

ABSTRACT

BACKGROUND: There is a growing literature in support of the effectiveness of task-shared mental health interventions in resource-limited settings globally. However, despite evidence that effect sizes are greater in research studies than actual care, the literature is sparse on the impact of such interventions as delivered in routine care. In this paper, we examine the clinical outcomes of routine depression care in a task-shared mental health system established in rural Haiti by the international health care organization Partners In Health, in collaboration with the Haitian Ministry of Health, following the 2010 earthquake. METHODS: For patients seeking depression care betw|een January 2016 and December 2019, we conducted mixed-effects longitudinal regression to quantify the effect of depression visit dose on symptoms, incorporating interaction effects to examine the relationship between baseline severity and dose. RESULTS: 306 patients attended 2052 visits. Each visit was associated with an average reduction of 1.11 in depression score (range 0-39), controlling for sex, age, and days in treatment (95% CI -1.478 to -0.91; p < 0.001). Patients with more severe symptoms experienced greater improvement as a function of visits (p = 0.04). Psychotherapy was provided less frequently and medication more often than expected for patients with moderate symptoms. CONCLUSIONS: Our findings support the potential positive impact of scaling up routine mental health services in low- and middle-income countries, despite greater than expected variability in service provision, as well as the importance of understanding potential barriers and facilitators to care as they occur in resource-limited settings.

16.
Bioinformatics ; 37(22): 4193-4201, 2021 11 18.
Article in English | MEDLINE | ID: mdl-34145874

ABSTRACT

MOTIVATION: Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion's collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. RESULTS: We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. AVAILABILITY AND IMPLEMENTATION: https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).


Subject(s)
Ion Mobility Spectrometry , Software , Mass Spectrometry/methods , Ions
17.
Environ Microbiol ; 23(6): 3225-3239, 2021 06.
Article in English | MEDLINE | ID: mdl-33928761

ABSTRACT

A multitude of concurrent biological and physical processes contribute to microbial community turnover, especially in highly dynamic coastal environments. Characterizing what factors contribute most to shifts in microbial community structure and the specific organisms that correlate with changes in the products of photosynthesis improves our understanding of nearshore microbial ecosystem functions. We conducted high frequency sampling in nearshore Southern California in order to capture sub-weekly microbial community dynamics. Microbial communities were characterized by flow cytometry and 16S rRNA gene sequencing, and placed in the context of physicochemical parameters. Within our time-series, season and nutrient availability corresponded to changes in dominant microbial community members. Concurrent aseasonal drivers with overlapping scales of variability were also apparent when we used network analysis to assess the microbial community as subsets of the whole. Our analyses revealed the microbial community as a mosaic, with overlapping groups of taxa that varied on different timescales and correlated with unique abiotic and biotic factors. Specifically, a subnetwork associated with chlorophyll a exhibited rapid turnover, indicating that ecologically important subsets of the microbial community can change on timescales different than and in response to factors other than those that govern turnover of most members of the assemblage.


Subject(s)
Microbiota , California , Chlorophyll A , Microbiota/genetics , RNA, Ribosomal, 16S/genetics , Seasons
18.
PLoS One ; 16(4): e0250019, 2021.
Article in English | MEDLINE | ID: mdl-33886614

ABSTRACT

SARS-CoV-2 has caused a global pandemic, and has taken over 1.7 million lives as of mid-December, 2020. Although great progress has been made in the development of effective countermeasures, with several pharmaceutical companies approved or poised to deliver vaccines to market, there is still an unmet need of essential antiviral drugs with therapeutic impact for the treatment of moderate-to-severe COVID-19. Towards this goal, a high-throughput assay was used to screen SARS-CoV-2 nsp15 uracil-dependent endonuclease (endoU) function against 13 thousand compounds from drug and lead repurposing compound libraries. While over 80% of initial hit compounds were pan-assay inhibitory compounds, three hits were confirmed as nsp15 endoU inhibitors in the 1-20 µM range in vitro. Furthermore, Exebryl-1, a ß-amyloid anti-aggregation molecule for Alzheimer's therapy, was shown to have antiviral activity between 10 to 66 µM, in Vero 76, Caco-2, and Calu-3 cells. Although the inhibitory concentrations determined for Exebryl-1 exceed those recommended for therapeutic intervention, our findings show great promise for further optimization of Exebryl-1 as an nsp15 endoU inhibitor and as a SARS-CoV-2 antiviral.


Subject(s)
Antiviral Agents/pharmacology , COVID-19 Drug Treatment , Drug Repositioning , Endoribonucleases/antagonists & inhibitors , SARS-CoV-2/drug effects , Small Molecule Libraries/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Animals , Antiviral Agents/chemistry , COVID-19/virology , Caco-2 Cells , Chlorocebus aethiops , Drug Repositioning/methods , Endoribonucleases/metabolism , High-Throughput Screening Assays/methods , Humans , Molecular Docking Simulation , SARS-CoV-2/metabolism , Small Molecule Libraries/chemistry , Vero Cells , Viral Nonstructural Proteins/metabolism
19.
Rev Sci Instrum ; 92(2): 023704, 2021 Feb 01.
Article in English | MEDLINE | ID: mdl-33648049

ABSTRACT

Relative intensity noise (RIN) inherent in fiber lasers poses a serious obstacle to their use in pump-probe spectroscopy and imaging. RIN can be removed through an analog balanced detector, or, as we have previously shown, software adaptive noise cancellation (ANC) on digitized signals. One major drawback to software ANC is the added time required for digitizing and post-processing. In this article, we describe a design for ANC on a field-programmable gate array (FPGA), making use of high-level synthesis tools and fixed-point arithmetic to achieve real-time laser RIN suppression at 25 MHz sample rates. Unlike the software-ANC approach, the FPGA-ANC device can serve as a dedicated drop-in denoiser, placed between the detectors and a commercial lock-in amplifier. We demonstrate its application to transient absorption spectroscopy and microscopy, lowering the noise floor to ∼17 dB above the shot noise limit. Furthermore, we demonstrate a dramatic improvement in data acquisition time from ∼6 h to ∼5 min in a real-time imaging scenario.

20.
Environ Microbiol ; 23(7): 3825-3839, 2021 07.
Article in English | MEDLINE | ID: mdl-33621409

ABSTRACT

Concurrent osmotic and chaotropic stress make MgCl2 -rich brines extremely inhospitable environments. Understanding the limits of life in these brines is essential to the search for extraterrestrial life on contemporary and relict ocean worlds, like Mars, which could host similar environments. We sequenced environmental 16S rRNA genes and quantified microbial activity across a broad range of salinity and chaotropicity at a Mars-analogue salt harvesting facility in Southern California, where seawater is evaporated in a series of ponds ranging from kosmotropic NaCl brines to highly chaotropic MgCl2 brines. Within NaCl brines, we observed a proliferation of specialized halophilic Euryarchaeota, which corresponded closely with the dominant taxa found in salterns around the world. These communities were characterized by very slow growth rates and high biomass accumulation. As salinity and chaotropicity increased, we found that the MgCl2 -rich brines eventually exceeded the limits of microbial activity. We found evidence that exogenous genetic material is preserved in these chaotropic brines, producing an unexpected increase in diversity in the presumably sterile MgCl2 -saturated brines. Because of their high potential for biomarker preservation, chaotropic brines could therefore serve as repositories of genetic biomarkers from nearby environments (both on Earth and beyond) making them prime targets for future life-detection missions.


Subject(s)
Salinity , Seawater , Oceans and Seas , RNA, Ribosomal, 16S/genetics , Sodium Chloride/analysis
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