Hepatitis C Virus Dysregulates Polyamine and Proline Metabolism and Perturbs the Urea Cycle.

Hepatitis C virus (HCV) is an oncogenic virus that causes chronic liver disease in more than 80% of patients. During the last decade, efficient direct-acting antivirals were introduced into clinical practice. However, clearance of the virus does not reduce the risk of end-stage liver diseases to the level observed in patients who have never been infected. So, investigation of HCV pathogenesis is still warranted. Virus-induced changes in cell metabolism contribute to the development of HCV-associated liver pathologies. Here, we studied the impact of the virus on the metabolism of polyamines and proline as well as on the urea cycle, which plays a crucial role in liver function. It was found that HCV strongly suppresses the expression of arginase, a key enzyme of the urea cycle, leading to the accumulation of arginine, and up-regulates proline oxidase with a concomitant decrease in proline concentrations. The addition of exogenous proline moderately suppressed viral replication. HCV up-regulated transcription but suppressed protein levels of polyamine-metabolizing enzymes. This resulted in a decrease in polyamine content in infected cells. Finally, compounds targeting polyamine metabolism demonstrated pronounced antiviral activity, pointing to spermine and spermidine as compounds affecting HCV replication. These data expand our understanding of HCV's imprint on cell metabolism.

Natural-Target-Mimicking Translocation-Based Fluorescent Sensor for Detection of SARS-CoV-2 PLpro Protease Activity and Virus Infection in Living Cells.

Papain-like protease PLpro, a domain within a large polyfunctional protein, nsp3, plays key roles in the life cycle of SARS-CoV-2, being responsible for the first events of cleavage of a polyprotein into individual proteins (nsp1-4) as well as for the suppression of cellular immunity. Here, we developed a new genetically encoded fluorescent sensor, named PLpro-ERNuc, for detection of PLpro activity in living cells using a translocation-based readout. The sensor was designed as follows. A fragment of nsp3 protein was used to direct the sensor on the cytoplasmic surface of the endoplasmic reticulum (ER) membrane, thus closely mimicking the natural target of PLpro. The fluorescent part included two bright fluorescent proteins-red mScarlet I and green mNeonGreen-separated by a linker with the PLpro cleavage site. A nuclear localization signal (NLS) was attached to ensure accumulation of mNeonGreen into the nucleus upon cleavage. We tested PLpro-ERNuc in a model of recombinant PLpro expressed in HeLa cells. The sensor demonstrated the expected cytoplasmic reticular network in the red and green channels in the absence of protease, and efficient translocation of the green signal into nuclei in the PLpro-expressing cells (14-fold increase in the nucleus/cytoplasm ratio). Then, we used PLpro-ERNuc in a model of Huh7.5 cells infected with the SARS-CoV-2 virus, where it showed robust ER-to-nucleus translocation of the green signal in the infected cells 24 h post infection. We believe that PLpro-ERNuc represents a useful tool for screening PLpro inhibitors as well as for monitoring virus spread in a culture.

Development of 225Ac-doped biocompatible nanoparticles for targeted alpha therapy.

Targeted alpha therapy (TAT) relies on chemical affinity or active targeting using radioimmunoconjugates as strategies to deliver α-emitting radionuclides to cancerous tissue. These strategies can be affected by transmetalation of the parent radionuclide by competing ions in vivo and the bond-breaking recoil energy of decay daughters. The retention of α-emitting radionuclides and the dose delivered to cancer cells are influenced by these processes. Encapsulating α-emitting radionuclides within nanoparticles can help overcome many of these challenges. Poly(lactic-co-glycolic acid) (PLGA) nanoparticles are a biodegradable and biocompatible delivery platform that has been used for drug delivery. In this study, PLGA nanoparticles are utilized for encapsulation and retention of actinium-225 ([225Ac]Ac3+). Encapsulation of [225Ac]Ac3+ within PLGA nanoparticles (Zave = 155.3 nm) was achieved by adapting a double-emulsion solvent evaporation method. The encapsulation efficiency was affected by both the solvent conditions and the chelation of [225Ac]Ac3+. Chelation of [225Ac]Ac3+ to a lipophilic 2,9-bis-lactam-1,10-phenanthroline ligand ([225Ac]AcBLPhen) significantly decreased its release (< 2%) and that of its decay daughters (< 50%) from PLGA nanoparticles. PLGA nanoparticles encapsulating [225Ac]AcBLPhen significantly increased the delivery of [225Ac]Ac3+ to murine (E0771) and human (MCF-7 and MDA-MB-231) breast cancer cells with a concomitant increase in cell death over free [225Ac]Ac3+ in solution. These results demonstrate that PLGA nanoparticles have potential as radionuclide delivery platforms for TAT to advance precision radiotherapy for cancer. In addition, this technology offers an alternative use for ligands with poor aqueous solubility, low stability, or low affinity, allowing them to be repurposed for TAT by encapsulation within PLGA nanoparticles.

Photostasis and photosynthetic adaptation to polar life.

Photostasis is the light-dependent maintenance of energy balance associated with cellular homeostasis in photoautotrophs. We review evidence that illustrates how photosynthetic adaptation in polar photoautrophs such as aquatic green algae, cyanobacteria, boreal conifers as well as terrestrial angiosperms exhibit an astonishing plasticity in structure and function of the photosynthetic apparatus. This plasticity contributes to the maintenance of photostasis, which is essential for the long-term survival in the seemingly inhospitable Antarctic and Arctic habitats. However, evidence indicates that polar photoautrophic species exhibit different functional solutions for the maintenance of photostasis. We suggest that this reflects, in part, the genetic diversity symbolized by inherent genetic redundancy characteristic of polar photoautotrophs which enhances their survival in a thermodynamically challenging environment.

Comprehensive Micro-SPE-Based Bottom-Up Proteomic Workflow for Sensitive Analysis of Limited Samples.

Clinical and biological samples are often scarce and precious (e.g., rare cell isolates, microneedle tissue biopsies, small-volume liquid biopsies, and even single cells or organelles). Typical large-scale proteomic methods, where significantly higher protein amounts are analyzed, are not directly transferable to the analysis of limited samples due to their incompatibility with pg-, ng-, and low-µg-level protein sample amounts. Here, we report the on-microsolid-phase extraction tip (OmSET)-based sample preparation workflow for sensitive analysis of limited biological samples to address this challenge. The developed platform was successfully tested for the analysis of 100-10,000 typical mammalian cells and is scalable to allow for lower and larger protein amounts and more samples to be analyzed (i.e., higher throughput of analysis).

Composite "Crosslinked Polyvinyl Alcohol-Magnetite" as a Stimuli-Responsive Matrix for Optical Methods.

The preparation and application of the composite material "crosslinked polyvinyl alcohol-magnetite" as a sensitive matrix for use in digital colorimetry and optical micrometry methods are discussed. The material was synthesized in the form of spherical granules (for micrometry) and thin films (for digital colorimetry). The obtained composites were characterized by the registration of magnetization curves. It was shown that the amount of grown Fe3O4 particles in the polymer gel is in linear dependence with the iron salt concentrations in the impregnating solutions. The composite granules were applied to determining monosaccharides using optical micrometry. The optimal pH value for the total amount of monosaccharides' determination was 8.6. The study of the analytical response of composite granules and films performed with a low limit of detection (7.9 mmol/dm3) of both glucose and fructose and a possibility of the control of high alcohol contention in water media. The granules were used to determine the total carbohydrate content in samples of natural honey and syrups with high fructose contents, while the films were used to control the alcohol content in hand antiseptics. The results obtained are in good agreement with the data provided by the manufacturers.

Multimode chromatography-based techniques for high purity isolation of extracellular vesicles from human blood plasma.

Extracellular vesicles (EVs) play a pivotal role in various biological pathways, such as immune responses and the progression of diseases, including cancer. However, it is challenging to isolate EVs at high purity from blood plasma and other biofluids due to their low abundance compared to more predominant biomolecular species such as lipoprotein particles and free protein complexes. Ultracentrifugation-based EV isolation, the current gold standard technique, cannot overcome this challenge due to the similar biophysical characteristics of such species. We developed several novel approaches to enrich EVs from plasma while depleting contaminating molecular species using multimode chromatography-based strategies. On average, we identified 716 ± 68 and 1054 ± 35 protein groups in EV isolates from 100 µL of plasma using multimode chromatography- and ultracentrifugation-based techniques, respectively. The developed methods resulted in similar EV isolates purity, providing significant advantages in simplicity, throughput, scalability, and applicability for various downstream analytical and potential clinical applications.

Improved Data Acquisition Settings on Q Exactive HF-X and Fusion Lumos Tribrid Orbitrap-Based Mass Spectrometers for Proteomic Analysis of Limited Samples.

Deep proteomic profiling of complex biological and medical samples available at low nanogram and subnanogram levels is still challenging. Thorough optimization of settings, parameters, and conditions in nanoflow liquid chromatography-tandem mass spectrometry (MS)-based proteomic profiling is crucial for generating informative data using amount-limited samples. This study demonstrates that by adjusting selected instrument parameters, e.g., ion injection time, automated gain control, and minimally altering the conditions for resuspending or storing the sample in solvents of different compositions, up to 15-fold more thorough proteomic profiling can be achieved compared to conventionally used settings. More specifically, the analysis of 1 ng of the HeLa protein digest standard by Q Exactive HF-X Hybrid Quadrupole-Orbitrap and Orbitrap Fusion Lumos Tribrid mass spectrometers yielded an increase from 1758 to 5477 (3-fold) and 281 to 4276 (15-fold) peptides, respectively, demonstrating that higher protein identification results can be obtained using the optimized methods. While the instruments applied in this study do not belong to the latest generation of mass spectrometers, they are broadly used worldwide, which makes the guidelines for improving performance desirable to a wide range of proteomics practitioners.

Ionic Pairs-Engineered Fluorinated Covalent Organic Frameworks Toward Direct Air Capture of CO2.

The covalent organic frameworks (COFs) possessing high crystallinity and capability to capture low-concentration CO2 (400 ppm) from air are still underdeveloped. The challenge lies in simultaneously incorporating high-density active sites for CO2 insertion and maintaining the ordered structure. Herein, a structure engineering approach is developed to afford an ionic pair-functionalized crystalline and stable fluorinated COF (F-COF) skeleton. The ordered structure of the F-COF is well maintained after the integration of abundant basic fluorinated alcoholate anions, as revealed by synchrotron X-ray scattering experiments. The breakthrough test demonstrates its attractive performance in capturing (400 ppm) CO2 from gas mixtures via O─C bond formation, as indicated by the in situ spectroscopy and operando nuclear magnetic resonance spectroscopy using 13C-labeled CO2 sources. Both theoretical and experimental thermodynamic studies reveal the reaction enthalpy of ≈-40 kJ mol-1 between CO2 and the COF scaffolds. This implies weaker interaction strength compared with state-of-the-art amine-derived sorbents, thus allowing complete CO2 release with less energy input. The structure evolution study from synchrotron X-ray scattering and small-angle neutron scattering confirms the well-maintained crystalline patterns after CO2 insertion. The as-developed proof-of-concept approach provides guidance on anchoring binding sites for direct air capture (DAC) of CO2 in crystalline scaffolds.

Observation of a promethium complex in solution.

Lanthanide rare-earth metals are ubiquitous in modern technologies1-5, but we know little about chemistry of the 61st element, promethium (Pm)6, a lanthanide that is highly radioactive and inaccessible. Despite its importance7,8, Pm has been conspicuously absent from the experimental studies of lanthanides, impeding our full comprehension of the so-called lanthanide contraction phenomenon: a fundamental aspect of the periodic table that is quoted in general chemistry textbooks. Here we demonstrate a stable chelation of the 147Pm radionuclide (half-life of 2.62 years) in aqueous solution by the newly synthesized organic diglycolamide ligand. The resulting homoleptic PmIII complex is studied using synchrotron X-ray absorption spectroscopy and quantum chemical calculations to establish the coordination structure and a bond distance of promethium. These fundamental insights allow a complete structural investigation of a full set of isostructural lanthanide complexes, ultimately capturing the lanthanide contraction in solution solely on the basis of experimental observations. Our results show accelerated shortening of bonds at the beginning of the lanthanide series, which can be correlated to the separation trends shown by diglycolamides9-11. The characterization of the radioactive PmIII complex in an aqueous environment deepens our understanding of intra-lanthanide behaviour12-15 and the chemistry and separation of the f-block elements16.

Native N-glycome profiling of single cells and ng-level blood isolates using label-free capillary electrophoresis-mass spectrometry.

The development of reliable single-cell dispensers and substantial sensitivity improvement in mass spectrometry made proteomic profiling of individual cells achievable. Yet, there are no established methods for single-cell glycome analysis due to the inability to amplify glycans and sample losses associated with sample processing and glycan labeling. In this work, we present an integrated platform coupling online in-capillary sample processing with high-sensitivity label-free capillary electrophoresis-mass spectrometry for N-glycan profiling of single mammalian cells. Direct and unbiased quantitative characterization of single-cell surface N-glycomes are demonstrated for HeLa and U87 cells, with the detection of up to 100 N-glycans per single cell. Interestingly, N-glycome alterations are unequivocally detected at the single-cell level in HeLa and U87 cells stimulated with lipopolysaccharide. The developed workflow is also applied to the profiling of ng-level amounts (5-500 ng) of blood-derived protein, extracellular vesicle, and total plasma isolates, resulting in over 170, 220, and 370 quantitated N-glycans, respectively.

Heterogeneous Structure, Mechanisms of Counterion Exchange, and the Spacer Salt Effect in Complex Molten Salt Mixtures Including LaCl3.

Complex molten chloride salt mixtures of uranium, magnesium, and sodium are top candidates for promising nuclear energy technologies to produce electricity based on molten salt reactors. From a local structural perspective, LaCl3 is similar to UCl3 and hence a good proxy to study these complex salt mixtures. As fission products, lanthanide salts and their mixtures are also very important in their own right. This article describes from an experimental and theory perspective how very different the structural roles of MgCl2 and NaCl are in mixtures with LaCl3. We find that, whereas MgCl2 becomes an integral part of multivalent ionic networks, NaCl separates them. In a recent article (J. Am. Chem. Soc. 2022, 144, 21751-21762) we have called the disruptive behavior of NaCl "the spacer salt effect". Because of the heterogeneous nature of these salt mixtures, there are multiple structural motifs in the melt, each with its particular free energetics. Our work identifies and quantifies these; it also elucidates the mechanisms through which Cl- ions exchange between Mg2+-rich and La3+-rich environments.

Correction: Zhitkevich et al. HIV-1 Reverse Transcriptase Expression in HPV16-Infected Epidermoid Carcinoma Cells Alters E6 Expression and Cellular Metabolism, and Induces a Hybrid Epithelial/Mesenchymal Cell Phenotype. Viruses 2024, 16, 193.

Author Juris Jansons requested his exclusion from the authors of the original publication [...].

Transformative vaccination: A pentavalent shield against COVID-19 and influenza with betulin-based adjuvant for enhanced immunity.

The development of an effective combined vaccine represents a crucial strategy for preventing outbreaks of infectious diseases and reducing the burden on healthcare resources. Developing a combined vaccine against both influenza and the coronavirus is a promising approach, but it is still in the early stages of development. This paper reports on a novel combined pentavalent candidate vaccine that has shown promising results in mice, with statistically significant differences in mean antibody titer against the coronavirus and the influenza antigens compared to placebo. We have shown that the coronavirus antigen is capable of inducing an immune response autonomously, regardless of the presence of the influenza antigens in a combined vaccine. On the other hand, the presence of the coronavirus antigen in a combined vaccine showed to enhance the immune response against some of the studied influenza antigens, suggesting that these antigens may act in synergy and elicit an enhanced immune response. The absence of dose-dependent difference in mean antibody titer within the same antigenic groups of vaccine preparations suggested that even small amounts of the coronavirus and the influenza antigens could induce an immune response just as good as high-dose vaccine preparations, which certainly has important safety and cost implications. The vaccine is soon to be ready for clinical trials and mass production.

Development and validation of an electrocardiographic artificial intelligence model for detection of peripartum cardiomyopathy.

BACKGROUND: This study used electrocardiogram data in conjunction with artificial intelligence methods as a noninvasive tool for detecting peripartum cardiomyopathy. OBJECTIVE: This study aimed to assess the efficacy of an artificial intelligence-based heart failure detection model for peripartum cardiomyopathy detection. STUDY DESIGN: We first built a deep-learning model for heart failure detection using retrospective data at the University of Tennessee Health Science Center. Cases were adult and nonpregnant female patients with a heart failure diagnosis; controls were adult nonpregnant female patients without heart failure. The model was then tested on an independent cohort of pregnant women at the University of Tennessee Health Science Center with or without peripartum cardiomyopathy. We also tested the model in an external cohort of pregnant women at Atrium Health Wake Forest Baptist. Key outcomes were assessed using the area under the receiver operating characteristic curve. We also repeated our analysis using only lead I electrocardiogram as an input to assess the feasibility of remote monitoring via wearables that can capture single-lead electrocardiogram data. RESULTS: The University of Tennessee Health Science Center heart failure cohort comprised 346,339 electrocardiograms from 142,601 patients. In this cohort, 60% of participants were Black and 37% were White, with an average age (standard deviation) of 53 (19) years. The heart failure detection model achieved an area under the curve of 0.92 on the holdout set. We then tested the ability of the heart failure model to detect peripartum cardiomyopathy in an independent University of Tennessee Health Science Center cohort of pregnant women and an external Atrium Health Wake Forest Baptist cohort of pregnant women. The independent University of Tennessee Health Science Center cohort included 158 electrocardiograms from 115 patients; our deep-learning model achieved an area under the curve of 0.83 (0.77-0.89) for this data set. The external Atrium Health Wake Forest Baptist cohort involved 80 electrocardiograms from 43 patients; our deep-learning model achieved an area under the curve of 0.94 (0.91-0.98) for this data set. For identifying peripartum cardiomyopathy diagnosed ≥10 days after delivery, the model achieved an area under the curve of 0.88 (0.81-0.94) for the University of Tennessee Health Science Center cohort and of 0.96 (0.93-0.99) for the Atrium Health Wake Forest Baptist cohort. When we repeated our analysis by building a heart failure detection model using only lead-I electrocardiograms, we obtained similarly high detection accuracies, with areas under the curve of 0.73 and 0.93 for the University of Tennessee Health Science Center and Atrium Health Wake Forest Baptist cohorts, respectively. CONCLUSION: Artificial intelligence can accurately detect peripartum cardiomyopathy from electrocardiograms alone. A simple electrocardiographic artificial intelligence-based peripartum screening could result in a timelier diagnosis. Given that results with 1-lead electrocardiogram data were similar to those obtained using all 12 leads, future studies will focus on remote screening for peripartum cardiomyopathy using smartwatches that can capture single-lead electrocardiogram data.

Epidemiology of Orbital Inflammatory Disease: An AAO IRIS Registry Study.

PURPOSE: The current study queries the American Academy of Ophthalmology (AAO) Intelligent Research in Sight (IRIS) registry for data on the epidemiology, work-up, and management patterns of autoimmune orbital inflammation. METHODS: Analysis and description of patient data from the IRIS registry between 2013 and 2019 reviewing patients with autoimmune or idiopathic orbital inflammation with filters based on International Classification of Disease (ICD) and Current Procedural Terminology (CPT) codes. Patients with thyroid eye disease, orbital cellulitis, and orbital abscess were excluded. MAIN OUTCOME MEASURES: Demographic descriptions included gender, age, geographic region, and treatment. Sub-analysis was performed by assessing rates of imaging, biopsy, lab work-up, and diagnostic categories. RESULTS: In a final cohort of 20,584 patients, the mean age of onset of orbital inflammation was 51.7 years; 67% female; and 63% Caucasian, 21% unknown, 12% Black, 2.6% Asian, and 1.5% other. Only 49 had imaging, 78 had laboratory work-up, and 1,411 had biopsy codes. Treatment results showed 166 patients receiving antibiotics, 224 patients receiving steroids, and 35 patients receiving both. CONCLUSIONS: This study assessed the epidemiology, diagnostic patterns, and treatment patterns for orbital inflammation through the AAO IRIS registry. Practise patterns suggest a relatively low overall rate of imaging and laboratory studies compared to biopsies, although this certainly under-represents the actual number of imaging and laboratory studies and exemplifies the inherent imprecision of using a large database. However, the methodology of this study provides a framework of approaching the IRIS registry for oculoplastic research.

Fellow Eyes Conversion Rates in Patients With Unilateral Exudative Age-Related Macular Degeneration: An Academy IRIS® Registry Analysis.

BACKGROUND AND OBJECTIVE: This study aimed to examine conversion rates from non-exudative to exudative age-related macular degeneration (AMD) in the fellow eye of patients with unilateral exudative AMD using the Academy IRIS® Registry. PATIENTS AND METHODS: This study was a retrospective, cohort analysis from 2016 to 2019. Patient and disease characteristics including initial AMD stage were collected. Cox proportional-hazard (PH) and logistic regression modeling were performed. RESULTS: The risk of conversion was lower for men relative to women and for Asians and Blacks relative to Whites. Compared to never-smokers, active smokers were at increased risk of conversion, and compared to initially early non-exudative AMD eyes, intermediate and advanced non-exudative AMD eyes had higher rates of conversion. Compared to active choroidal neovascularization eyes, eyes with inactive choroidal neovascularization and inactive scars had lower rates of fellow eye conversion. CONCLUSIONS: In this cohort analysis of unilateral exudative AMD patients, women, Whites, and active smokers had higher rates of non-exudative to exudative AMD conversion in the fellow eye. [Ophthalmic Surg Lasers Imaging Retina 2024;55:220-226.].

Experimental and data analysis advances in thermal proteome profiling.

Method development for mass spectrometry (MS)-based thermal shift proteomic assays have advanced to probe small molecules with known and unknown protein-ligand interaction mechanisms and specificity, which is predominantly used in characterization of drug-protein interactions. In the discovery of target and off-target protein-ligand interactions, a thorough investigation of method development and their impact on the sensitivity and accuracy of protein-small molecule and protein-protein interactions is warranted. In this review, we discuss areas of improvement at each stage of thermal proteome profiling data analysis that includes processing of MS-based data, method development, and their effect on the overall quality of thermal proteome profiles. We also overview the optimization of experimental strategies and prioritization of an increased number of independent biological replicates over the number of evaluated temperatures.

Open-tubular trap columns: towards simple and robust liquid chromatography separations for single-cell proteomics.

Nanoflow liquid chromatography-mass spectrometry is key to enabling in-depth proteome profiling of trace samples, including single cells, but these separations can lack robustness due to the use of narrow-bore columns that are susceptible to clogging. In the case of single-cell proteomics, offline cleanup steps are generally omitted to avoid losses to additional surfaces, and online solid-phase extraction/trap columns frequently provide the only opportunity to remove salts and insoluble debris before the sample is introduced to the analytical column. Trap columns are traditionally short, packed columns used to load and concentrate analytes at flow rates greater than those employed in analytical columns, and since these first encounter the uncleaned sample mixture, trap columns are also susceptible to clogging. We hypothesized that clogging could be avoided by using large-bore porous layer open tubular trap columns (PLOTrap). The low back pressure ensured that the PLOTraps could also serve as the sample loop, thus allowing sample cleanup and injection with a single 6-port valve. We found that PLOTraps could effectively remove debris to avoid column clogging. We also evaluated multiple stationary phases and PLOTrap diameters to optimize performance in terms of peak widths and sample loading capacities. Optimized PLOTraps were compared to conventional packed trap columns operated in forward and backflush modes, and were found to have similar chromatographic performance of backflushed traps while providing improved debris removal for robust analysis of trace samples.

Chronic Viral Infections and Cancer, Openings for Therapies and Vaccines.

Infections are responsible for approximately one out of six cases of cancer worldwide [...].