The triglyceride-synthesizing enzyme diacylglycerol acyltransferase 2 modulates the formation of the hepatitis C virus replication organelle.

The replication organelle of hepatitis C virus (HCV), called membranous web, is derived from the endoplasmic reticulum (ER) and mainly comprises double membrane vesicles (DMVs) that concentrate the viral replication complexes. It also tightly associates with lipid droplets (LDs), which are essential for virion morphogenesis. In particular acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1), a rate-limiting enzyme in triglyceride synthesis, promotes early steps of virus assembly. The close proximity between ER membranes, DMVs and LDs therefore permits the efficient coordination of the HCV replication cycle. Here, we demonstrate that exaggerated LD accumulation due to the excessive expression of the DGAT1 isozyme, DGAT2, dramatically impairs the formation of the HCV membranous web. This effect depended on the enzymatic activity and ER association of DGAT2, whereas the mere LD accumulation was not sufficient to hamper HCV RNA replication. Our lipidomics data indicate that both HCV infection and DGAT2 overexpression induced membrane lipid biogenesis and markedly increased phospholipids with long chain polyunsaturated fatty acids, suggesting a dual use of these lipids and their possible competition for LD and DMV biogenesis. On the other hand, overexpression of DGAT2 depleted specific phospholipids, particularly oleyl fatty acyl chain-containing phosphatidylcholines, which, in contrast, are increased in HCV-infected cells and likely essential for viral infection. In conclusion, our results indicate that lipid exchanges occurring during LD biogenesis regulate the composition of intracellular membranes and thereby affect the formation of the HCV replication organelle. The potent antiviral effect observed in our DGAT2 overexpression system unveils lipid flux that may be relevant in the context of steatohepatitis, a hallmark of HCV infection, but also in physiological conditions, locally in specific subdomains of the ER membrane. Thus, LD formation mediated by DGAT1 and DGAT2 might participate in the spatial compartmentalization of HCV replication and assembly factories within the membranous web.

Benzoyl Chloride Derivatization Advances the Quantification of Dissolved Polar Metabolites on Coral Reefs.

Extracellular chemical cues constitute much of the language of life among marine organisms, from microbes to mammals. Changes in this chemical pool serve as invisible signals of overall ecosystem health and disruption to this finely tuned equilibrium. In coral reefs, the scope and magnitude of the chemicals involved in maintaining reef equilibria are largely unknown. Processes involving small, polar molecules, which form the majority components of labile dissolved organic carbon, are often poorly captured using traditional techniques. We employed chemical derivatization with mass spectrometry-based targeted exometabolomics to quantify polar dissolved phase metabolites on five coral reefs in the U.S. Virgin Islands. We quantified 45 polar exometabolites, demonstrated their spatial variability, and contextualized these findings in terms of geographic and benthic cover differences. By comparing our results to previously published coral reef exometabolomes, we show the novel quantification of 23 metabolites, including central carbon metabolism compounds (e.g., glutamate) and novel metabolites such as homoserine betaine. We highlight the immense potential of chemical derivatization-based exometabolomics for quantifying labile chemical cues on coral reefs and measuring molecular level responses to environmental stressors. Overall, improving our understanding of the composition and dynamics of reef exometabolites is vital for effective ecosystem monitoring and management strategies.

A Negatively Curved Nanographene with Four Embedded Heptagons.

Negatively curved nanographenes are considered as cutouts of three-dimensional fully sp2-hybridized carbon allotropes such as Schwarzites. Here we present the synthesis of a C76 cut-out of the Schwarzite 8-4-1-p proposed by Lenosky et al. and investigate its optical as well as electrochemical properties. Furthermore, supramolecular interactions with fullerenes C60 and C70 were studied.

Microorganisms uniquely capture and predict stony coral tissue loss disease and hurricane disturbance impacts on US Virgin Island reefs.

Coral reef ecosystems are now commonly affected by major climate and disease disturbances. Disturbance impacts are typically recorded using reef benthic cover, but this may be less reflective of other ecosystem processes. To explore the potential for reef water-based disturbance indicators, we conducted a 7-year time series on US Virgin Island reefs where we examined benthic cover and reef water nutrients and microorganisms from 2016 to 2022, which included two major disturbances: hurricanes Irma and Maria in 2017 and the stony coral tissue loss disease outbreak starting in 2020. The disease outbreak coincided with the largest changes in the benthic habitat, with increases in the percent cover of turf algae and Ramicrusta, an invasive alga. While sampling timepoint contributed most to changes in reef water nutrient composition and microbial community beta diversity, both disturbances led to increases in ammonium concentration, a mechanism likely contributing to observed microbial community shifts. We identified 10 microbial taxa that were sensitive and predictive of increasing ammonium concentration. This included the decline of the oligotrophic and photoautotrophic Prochlorococcus and the enrichment of heterotrophic taxa. As disturbances impact reefs, the changing nutrient and microbial regimes may foster a type of microbialization, a process that hastens reef degradation.

Arduino-Based Readout Electronics for Nuclear and Particle Physics.

Open Hardware-based microcontrollers, especially the Arduino platform, have become a comparably easy-to-use tool for rapid prototyping and implementing creative solutions. Such devices in combination with dedicated front-end electronics can offer low-cost alternatives for student projects, slow control and independently operating small-scale instrumentation. The capabilities can be extended to data taking and signal analysis at mid-level rates. Two detector realizations are presented, which cover the readouts of proportional counter tubes and of scintillators or wavelength-shifting fibers with silicon photomultipliers (SiPMs). The SiPMTrigger realizes a small-scale design for coincidence readout of SiPMs as a trigger or veto detector. It consists of a custom mixed signal front-end board featuring signal amplification, discrimination and a coincidence unit for rates of up to 200 kHz. The nCatcher transforms an Arduino Nano to a proportional counter readout with pulse shape analysis: time over threshold measurement and a 10-bit analog-to-digital converter for pulse heights. The device is suitable for low-to-medium-rate environments up to 5 kHz, where a good signal-to-noise ratio is crucial. We showcase the monitoring of thermal neutrons. For data taking and slow control, a logger board is presented that features an SD card and GSM/LoRa interface.

Proteomic Analysis of Salivary Extracellular Vesicles from COVID-19 Patients Reveals a Specific Anti-COVID-19 Response Protein Signature.

Despite the understanding of the coronavirus disease-19 (COVID-19), the role of salivary extracellular vesicles (sEVs) in COVID-19 remains unclear. Exploring the proteomic cargo of sEVs could prove valuable for diagnostic and prognostic purposes in assessing COVID-19. The proteomic cargo of sEVs from COVID-19(+) subjects and their healthy close contacts (HCC) was explored. sEVs were isolated by ultracentrifugation from unstimulated saliva samples, and subsequently characterized through nanoparticle tracking, transmission electron microscopy, and Western blot analyses. The proteomic cargo of sEVs was processed by LC-MS/MS. sEVs were morphologically compatible with EVs, with the presence of Syntenin-1 and CD81 EV markers. The sEV pellet showed 1417 proteins: 1288 in COVID-19(+) cases and 1382 in HCC. In total, 124 proteins were differentially expressed in sEVs from COVID-19(+) subjects. "Coronavirus-disease response", "complement and coagulation cascades", and "PMN extracellular trap formation" were the most enriched KEGG pathways in COVID-19(+) cases. The most represented biological processes were "Hemoglobin and haptoglobin binding" and "oxygen carrier activity", and the best-denoted molecular functions were "regulated exocytosis and secretion" and "leucocyte and PMN mediated immunity". sEV proteomic cargo in COVID-19(+) suggests activity related to immune response processes, oxygen transport, and antioxidant mechanisms. In contrast, in HCC, sEV signature profiles are mainly associated with epithelial homeostasis.

Comparison of surgery rates in biologic-naïve patients with Crohn's disease treated with vedolizumab or ustekinumab: findings from SOJOURN.

BACKGROUND: Crohn's disease (CD) is a chronic inflammatory bowel disease characterized by relapsing and remitting inflammation that leads to progressive bowel damage. Despite advances in medical treatment for CD, many patients require surgical intervention. Most studies of surgery rates are from patients treated with anti-tumor necrosis factor alpha (anti-TNFα) treatments, with comparatively little data on the surgery rates of patients treated with vedolizumab and ustekinumab. SOJOURN aimed to estimate the hazard rate and incidence of the first CD-related surgery following initiation of treatment with vedolizumab or ustekinumab in biologic-naïve patients with CD. METHODS: SOJOURN was a retrospective, observational cohort study examining administrative claims data from the Optum® Research Database between July 1, 2017 and March 31, 2020. Included participants were adults with a diagnosis of CD and a claim for vedolizumab or ustekinumab (defined as the index treatment) between January 1, 2018 and December 31, 2019, with no claims for a biologic in the 6 months before initiation of this treatment. The variable follow-up started on the day after the index date and continued until whichever came first of discontinuation of the index treatment, surgery event, switching of the index treatment, initiation of combination biologic treatment, disenrollment, or March 31, 2020. The time to the first CD-related surgery on biologic treatment was estimated by Kaplan-Meier analysis. The hazard ratio and incidence rate ratio of CD-related surgery for each treatment cohort was compared using a Cox proportional hazards model and a Poisson regression model, respectively. RESULTS: Of the 1,122 included patients, 578 received vedolizumab and 544 received ustekinumab. After 1 year of the variable follow-up, 7.7% of patients receiving vedolizumab and 11.6% of patients receiving ustekinumab had undergone a CD-related surgery. Vedolizumab was associated with a 34.2% lower hazard rate of surgery (hazard ratio 0.658, 95% confidence interval [CI] 0.436-0.994, p = 0.047) and a 34.5% lower incidence of surgery (rate ratio 0.655, 95% CI 0.434-0.988, p = 0.044) than ustekinumab. CONCLUSIONS: This real-world analysis of biologic-naïve patients with CD suggests that vedolizumab is associated with greater effectiveness in reducing the rate of CD-related surgery than ustekinumab.

Obesity is related to maternal periodontitis severity in pregnancy: a cross-sectional study.

OBJECTIVES: To evaluate the relationship between obesity and periodontitis staging compared with periodontal healthy or gingivitis in pregnant women. MATERIALS AND METHODS: An analytical cross-sectional study was conducted on pregnant women between 11 and 14 weeks of pregnancy. Sociodemographic, clinical, obstetric, and periodontal variables were studied. The exposure variable was obesity (body mass index [BMI] ≥ 30), and the primary outcome was periodontitis staging versus periodontal healthy/gingivitis. Data were analysed and estimated by multinomial logistic regression models. RESULTS: The present study screened 1086 pregnancies and analysed 972 women with a median age of 29 years; 36.8% were diagnosed as obese. 26.9% of patients were diagnosed as periodontal healthy or gingivitis, 5.5% with stage I periodontitis, 38.6% with stage II periodontitis, 24% with stage III periodontitis, and 5.1% with stage IV periodontitis. After identifying and adjusting for confounding variables (educational level and plaque index), obesity had a relative risk ratio (RRR) of 1.66 (95% CI: 1.05-2.64; p = 0.03) and 1.57 (95% CI: 1.09-2.27; p = 0.015) for stage III periodontitis compared to periodontal healthy/gingivitis and stage II periodontitis, respectively. CONCLUSION: Besides the already known risk indicators for periodontitis (age, smoking, and educational level), our study suggests a relationship between obesity and periodontitis staging in pregnancy. CLINICAL RELEVANCE: Obesity can alter host immune responses, leading to increased susceptibility to infections and overactive host immunity, which could influence the prevalence and severity of maternal periodontitis in pregnancy.

Unstable environment of coastal lagoons drives genetic variation in the amphipod Quadrivisio lutzi.

The freshwater/brackish amphipod Quadrivisio lutzi inhabits coastal lagoons, highly unstable environments subject to sudden inflow of marine water. Our aim was to evaluate how the genetic composition varies in these populations. Brazilian populations were compared by 16S rRNA and COI gene sequences. The genetic structure of four Rio de Janeiro amphipod populations was evaluated during the period of 2011-2019 by COI. Rio de Janeiro population was compared with Alagoas and São Paulo populations, which was genetically distinct, at species level (16S, d > 7%; COI, d >14%). The genetic structure in Rio de Janeiro showed the Imboassica subpopulation as the most divergent (Imboassica & Carapebus, F ST = 0.238), followed by Lagamar population (Lagamar & Carapebus, F ST = 0.049). The geographic distance and urbanization around these lagoons explain the degree of genetic isolation of these amphipod subpopulations. Paulista and Carapebus populations were not structured. Temporal variation in haplotype number and frequency were evident in both populations that were evaluated (Carapebus and Imboassica). Changes in salinity and water volume variation at these lagoons may be responsible for the observed changes in genetic composition, which may be the results of genetic drift effects over temporally fluctuating size subpopulations, without loss of genetic diversity.

Molecular and morphometric analysis of nominal Brachidontes exustus (Mollusca, Mytilidae) in Brazilian waters.

Brachidontes exustus (Mollusca, Mytilidae) is mainly distributed in Central America, where it has been recognized as a _lataforma species. This study aimed to determine whether B. exustus extends beyond the Amazon Barrier and southward along the Brazilian West Atlantic coast. Mitochondrial genes coding for cytochrome-c oxidase, subunit I (COI) and 16S subunit of ribosomal _lataforma__ cid (16S rRNA) were analyzed with _lata parameters on Brazilian populations (Salvador, Arraial do Cabo and Fernando de Noronha) of scorched mussels previously recorded as B. exustus. Multivariate morphometric _latafor showed partial discrimination of species. Molecular _latafor confirmed B. exustus at Salvador, a population highly similar to Cartagena (Colombia), both belonging to the Atlantic Clade of the B. exustus complex. This fact adds evidence to the idea of the Amazon outflow as a semipermeable barrier. In the southeast of Brazil, B. exustus was not found; instead, B. darwinianus is the species represented at Arraial do Cabo (state of Rio de Janeiro), associated with brackish _lataf. Scorched mussels from Fernando de Noronha are most closely related to B. puniceus from Cape Verde with 4.4% differentiation. Demonstrating an independent evolutionary history since at least the beginning of the Pleistocene, its proposed new name is B. noronhensis.

Rapid Response to Pandemic Threats: Immunogenic Epitope Detection of Pandemic Pathogens for Diagnostics and Vaccine Development Using Peptide Microarrays.

Emergence and re-emergence of pathogens bearing the risk of becoming a pandemic threat are on the rise. Increased travel and trade, growing population density, changes in urbanization, and climate have a critical impact on infectious disease spread. Currently, the world is confronted with the emergence of a novel coronavirus SARS-CoV-2, responsible for yet more than 800 000 deaths globally. Outbreaks caused by viruses, such as SARS-CoV-2, HIV, Ebola, influenza, and Zika, have increased over the past decade, underlining the need for a rapid development of diagnostics and vaccines. Hence, the rational identification of biomarkers for diagnostic measures on the one hand, and antigenic targets for vaccine development on the other, are of utmost importance. Peptide microarrays can display large numbers of putative target proteins translated into overlapping linear (and cyclic) peptides for a multiplexed, high-throughput antibody analysis. This enabled for example the identification of discriminant/diagnostic epitopes in Zika or influenza and mapping epitope evolution in natural infections versus vaccinations. In this review, we highlight synthesis platforms that facilitate fast and flexible generation of high-density peptide microarrays. We further outline the multifaceted applications of these peptide array platforms for the development of serological tests and vaccines to quickly encounter pandemic threats.

Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys.

There are a few baseline reef-systems available for understanding the microbiology of healthy coral reefs and their surrounding seawater. Here, we examined the seawater microbial ecology of 25 Northern Caribbean reefs varying in human impact and protection in Cuba and the Florida Keys, USA, by measuring nutrient concentrations, microbial abundances, and respiration rates as well as sequencing bacterial and archaeal amplicons and community functional genes. Overall, seawater microbial composition and biogeochemistry were influenced by reef location and hydrogeography. Seawater from the highly protected 'crown jewel' offshore reefs in Jardines de la Reina, Cuba had low concentrations of nutrients and organic carbon, abundant Prochlorococcus, and high microbial community alpha diversity. Seawater from the less protected system of Los Canarreos, Cuba had elevated microbial community beta-diversity whereas waters from the most impacted nearshore reefs in the Florida Keys contained high organic carbon and nitrogen concentrations and potential microbial functions characteristic of microbialized reefs. Each reef system had distinct microbial signatures and within this context, we propose that the protection and offshore nature of Jardines de la Reina may preserve the oligotrophic paradigm and the metabolic dependence of the community on primary production by picocyanobacteria.

Patientenantikörper als Informationsquelle.

Since decades antibodies are used for diagnosis e. g. by detecting patient antibodies that specifically bind to Influenza virus proteins. We predict these diagnostic questions will be parallelized to diagnose all known disease specific antibodies at once. These tests will ask in addition, which unknown antibodies patrol in a patient's blood, and what exactly they bind to. Thereby, we expect to find antibody species that correlate to hitherto enigmatic diseases or have specialized functions.

The Development of a Macromolecular Analgesic for Arthritic Pain.

The addictive potential of clinically used opioids as a result of their direct action on the dopaminergic reward system in the brain has limited their application. In an attempt to reduce negative side effects as well as to improve the overall effectiveness of these analgesics, we have designed, synthesized, and evaluated an N-(2-hydroxypropyl)methacrylamide (HPMA)-based macromolecular prodrug of hydromorphone (HMP), a commonly used opioid. To this end, P-HMP was synthesized via RAFT polymerization and a subsequent polymer analogous reaction. Its interaction with inflammatory cells in arthritic joints was evaluated in vitro using a RAW 264.7 cell culture, and subsequent confocal microscopy analysis confirmed that P-HMP could be internalized by the cells via endocytosis. In vivo imaging studies indicated that the prodrug can passively target the arthritic joint after systemic administration in a rodent model of monoarticular adjuvant-induced arthritis (MAA). The inflammatory pain-alleviating properties of the prodrug were assessed in MAA rats using the incapacitance test and were observed to be similar to dose-equivalent HMP. Analgesia through mechanisms at the spinal cord level was further measured using the tail flick test, and it was determined that the prodrug significantly reduced spinal cord analgesia versus free HMP, further validating the peripheral restriction of the macromolecular prodrug. Immunohistochemical analysis of cellular uptake of the P-HMP within the MAA knee joint proved the internalization of the prodrug by phagocytic synoviocytes, colocalized with HMP's target receptor as well as with pain-modulating ion channels. Therefore, it can be concluded that the novel inflammation-targeting polymeric prodrug of HMP (P-HMP) has the potential to be developed as an effective and safe analgesic agent for musculoskeletal pain.

Genotoxicity Biomonitoring Along a Coastal Zone Under Influence of Offshore Petroleum Exploration (Southeastern Brazil).

Offshore oil exploration creates threats to coastal ecosystems, including increasing urbanization and associated effluent releases. Genotoxicity biomarkers in mussels were determined across a gradient of coastal zone influences of offshore petroleum exploration in southeastern Brazil. Coastal ecosystems such as estuaries, beaches and islands were seasonally monitored for genotoxicity evaluation using the brown mussel Perna perna. The greatest DNA damage (5.2% ± 1.9% tail DNA and 1.5‰  ± 0.8‰ MN) were observed in urban estuaries, while Santana Archipelago showed levels of genotoxicity near zero and is considered a reference site. Mussels from urban and pristine beaches showed intermediate damage levels, but were also influenced by urbanization. Thus, mussel genotoxicity biomarkers greatly indicated the proposed oil exploration and urbanization scenarios that consequently are genetically affecting coastal organisms.

Coral Reef Water Microbial Communities of Jardines de la Reina, Cuba.

Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean's 'Crown Jewel' reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms.

Corrigendum: Identifying predictors of clinical outcomes using the projection-predictive feature selection-a proof of concept on the example of Crohn's disease.

[This corrects the article DOI: 10.3389/fped.2023.1170563.].

Colostrum as a source of ESBL-Escherichia coli in feces of newborn calves.

The aim of the present study was to determine if colostrum and the equipment for harvesting and feeding colostrum are sources of fecal ESBL/AmpC-producing Escherichia coli (ESBL/AmpC-E. coli) in calves. Therefore, 15 male calves fed with pooled colostrum on a dairy farm and held individually in an experimental barn, the colostrum pool and the equipment for harvesting and feeding colostrum were sampled and analyzed for the occurrence of ESBL/AmpC-E. coli. The ESBL-AmpC-E. coli suspicious isolates were subjected to whole-genome sequence analysis. Forty-three of 45 fecal samples were tested positive for ESBL/AmpC-E. coli. In the colostrum sample and in the milking pot, we also found ESBL/AmpC-E. coli. All 45 E. coli isolates were ESBL-producers, mainly commensal sequence type (ST) 10, but also human-extraintestinal pathogenic E. coli ST131 and ST117 were found. The clonal identity of six fecal isolates with the ESBL-E. coli isolate from the colostrum and of five fecal isolates with the strain from the milking pot demonstrates that the hygiene of colostrum or the colostrum equipment can play a significant role in the spread of ESBL-E. coli. Effective sanitation procedures for colostrum harvesting and feeding equipment are crucial to reduce the ESBL-E. coli shedding of neonatal dairy calves.

Digital Microbe: a genome-informed data integration framework for team science on emerging model organisms.

The remarkable pace of genomic data generation is rapidly transforming our understanding of life at the micron scale. Yet this data stream also creates challenges for team science. A single microbe can have multiple versions of genome architecture, functional gene annotations, and gene identifiers; additionally, the lack of mechanisms for collating and preserving advances in this knowledge raises barriers to community coalescence around shared datasets. "Digital Microbes" are frameworks for interoperable and reproducible collaborative science through open source, community-curated data packages built on a (pan)genomic foundation. Housed within an integrative software environment, Digital Microbes ensure real-time alignment of research efforts for collaborative teams and facilitate novel scientific insights as new layers of data are added. Here we describe two Digital Microbes: 1) the heterotrophic marine bacterium Ruegeria pomeroyi DSS-3 with > 100 transcriptomic datasets from lab and field studies, and 2) the pangenome of the cosmopolitan marine heterotroph Alteromonas containing 339 genomes. Examples demonstrate how an integrated framework collating public (pan)genome-informed data can generate novel and reproducible findings.

Genotoxic effects of the water-soluble fraction of heavy oil in the brackish/freshwater amphipod Quadrivisio aff. lutzi (Gammaridea) as assessed using the comet assay.

Amphipod crustaceans have been widely used as invertebrate models in ecotoxicology due to their importance in the food chain. However, few studies have evaluated the genotoxic effects of pollutants in this model using the comet assay. The main obstacle to using amphipods in the comet assay is the difficulty in obtaining enough blood cells from a single individual. In this study, we evaluated the genotoxic effects of the water-soluble fraction (WSF) of heavy oil on the brackish/freshwater amphipod Quadrivisio aff. lutzi, which is common in the coastal lagoons of southeastern Brazil, using hemocytes obtained from single amphipods (without pooling) after optimizing hemolymph extraction. The comet assay revealed significantly higher DNA damage levels (2- to 6-fold higher) in treated amphipods compared to untreated ones with a sublethal concentration of 17.6 % of the WSF within 72 h of treatment. Two independent experiments confirmed an "up and down" pattern of DNA damage, measured as the % of DNA contained in the tail of the comets. Elevations in DNA damage levels were observed at the 6 and 48 h time points, while very low levels of DNA damage were observed at the 24 and 72 h time points. Furthermore, the comet assay revealed gender variability in the levels of DNA damage after short-term exposure.