An Eco-Friendly Synthesis Approach for Enhanced Photocatalytic and Antibacterial Properties of Copper Oxide Nanoparticles Using Coelastrella terrestris Algal Extract.

Background: In the current scenario, the synthesis of nanoparticles (NPs) using environmentally benign methods has gained significant attention due to their facile processes, cost-effectiveness, and eco-friendly nature. Methods: In the present study, copper oxide nanoparticles (CuO NPs) were synthesized using aqueous extract of Coelastrella terrestris algae as a reducing, stabilizing, and capping agent. The synthesized CuO NPs were characterized by X-ray diffraction (XRD), UV-visible spectroscopy (UV-Vis), Fourier transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), and field emission scanning electron microscopy (FE-SEM) coupled with energy-dispersive X-ray spectroscopy (EDS). Results: XRD investigation revealed that the biosynthesized CuO NPs were nanocrystalline with high-phase purity and size in the range of 4.26 nm to 28.51 nm. FTIR spectra confirmed the existence of secondary metabolites on the surface of the synthesized CuO NPs, with characteristic Cu-O vibrations being identified around 600 cm-1, 496 cm-1, and 440 cm-1. The FE-SEM images predicted that the enhancement of the algal extract amount converted the flattened rice-like structures of CuO NPs into flower petal-like structures. Furthermore, the degradation ability of biosynthesized CuO NPs was investigated against Amido black 10B (AB10B) dye. The results displayed that the optimal degradation efficacy of AB10B dye was 94.19%, obtained at 6 pH, 50 ppm concentration of dye, and 0.05 g dosage of CuO NPs in 90 min with a pseudo-first-order rate constant of 0.0296 min-1. The CuO-1 NPs synthesized through algae exhibited notable antibacterial efficacy against S. aureus with a zone of inhibition (ZOI) of 22 mm and against P. aeruginosa with a ZOI of 17 mm. Conclusion: Based on the findings of this study, it can be concluded that utilizing Coelastrella terrestris algae for the synthesis of CuO NPs presents a promising solution for addressing environmental contamination.

Ribosomal profiling of human endogenous retroviruses in healthy tissues.

Human endogenous retroviruses (HERVs) are the germline embedded proviral fragments of ancient retroviral infections that make up roughly 8% of the human genome. Our understanding of HERVs in physiology primarily surrounds their non-coding functions, while their protein coding capacity remains virtually uncharacterized. Therefore, we applied the bioinformatic pipeline "hervQuant" to high-resolution ribosomal profiling of healthy tissues to provide a comprehensive overview of translationally active HERVs. We find that HERVs account for 0.1-0.4% of all translation in distinct tissue-specific profiles. Collectively, our study further supports claims that HERVs are actively translated throughout healthy tissues to provide sequences of retroviral origin to the human proteome.

The brain-liver cholinergic anti-inflammatory pathway and viral infections.

Efferent cholinergic signaling is a critical and targetable source of immunoregulation. The vagus nerve (VN) is the primary source of cholinergic signaling in the body, and partially innervates hepatic functionality through the liver-brain axis. Virus-induced disruption of cholinergic signaling may promote pathogenesis in hepatotropic and neurotropic viruses. Therefore, restoring VN functionality could be a novel therapeutic strategy to alleviate pathogenic inflammation in hepatotropic and neurotropic viral infections alike. In this minireview, we discuss the physiological importance of cholinergic signaling in maintaining liver-brain axis homeostasis. Next, we explore mechanisms by which the VN is perturbed by viral infections, and how non-invasive restoration of cholinergic signaling pathways with bioelectronic medicine (BEM) might ameliorate hepatic inflammation and neuroinflammation in certain viral infections.

Acute Presentation of Asymptomatic Giant Endometrioma in Pregnancy: A Case Report.

Endometriomas are associated with severe endometriosis and are uncommon in asymptomatic women. Reported cases of giant endometriomas are few especially in pregnancy. Decidualization of endometriomas can mimic malignancies in pregnancy. Fetal outcomes can be good after excision of large endometriomas in the 2nd trimester. We present a case of giant endometrioma diagnosed in an asymptomatic woman who developed symptoms after becoming pregnant. Clinical findings, investigations, and histopathology were consistent with ovarian endometrioma. Maternal and fetal outcomes were good after the excision of the mass.

Locus specific human endogenous retroviruses reveal new lymphoma subtypes.

The heterogeneity of cancers are driven by diverse mechanisms underlying oncogenesis such as differential 'cell-of-origin' (COO) progenitors, mutagenesis, and viral infections. Classification of B-cell lymphomas have been defined by considering these characteristics. However, the expression and contribution of transposable elements (TEs) to B cell lymphoma oncogenesis or classification have been overlooked. We hypothesized that incorporating TE signatures would increase the resolution of B-cell identity during healthy and malignant conditions. Here, we present the first comprehensive, locus-specific characterization of TE expression in benign germinal center (GC) B-cells, diffuse large B-cell lymphoma (DLBCL), Epstein-Barr virus (EBV)-positive and EBV-negative Burkitt lymphoma (BL), and follicular lymphoma (FL). Our findings demonstrate unique human endogenous retrovirus (HERV) signatures in the GC and lymphoma subtypes whose activity can be used in combination with gene expression to define B-cell lineage in lymphoid malignancies, highlighting the potential of retrotranscriptomic analyses as a tool in lymphoma classification, diagnosis, and the identification of novel treatment groups.

Dealing with infodemic during COVID-19 pandemic: Role of effective health communication in facilitating outbreak response & actions - An ICMR experience.

Objectives: To highlight and assess the impact of intervention tools used by Indian Council of Medical Research (ICMR) against COVID19 associated infodemic in the world's largest democratic country, India. Study design: It is a retrospective cross sectional study. The impact of ICMR's multi-pronged strategy to address the infodemic during pandemic has been assessed through analysis of print media reportage and social media engagements. Methods: The impact of the interventions was assessed using cloud media mappers like MediaCloud and Meltwater using keywords. The data was analysed in terms of reportage, theme of reportage. A sub-section of media reportage (Feb 2020-June 2020) was analysed in details from 4 major dailies to understand the coverage and tonality of media reports. The data on COVID 19 related tweets, posts and uploads were taken from social media platforms of Indian Council of Medical Research (ICMR) particularly twitter, instagram, facebook and youtube and estimate of pre and post pandemic changes in followers or users were collected for analysis. The data was curated and analysed using MS excel. Results: There was a surge of 3800% reportage in media during pandemic as compared to same time frame in pre-pandemic times. A surge of followers on twitter from 26,823 on Feb 2020 (before pandemic) to 3,36,098 at March 2022 (after pandemic) was observed. A drastic increase in monthly followers was observed after start of Pandemic (after Feb 2020) in comparison to before pandemic (Before Feb 2020). Similar trends were observed on other social media platforms of ICMR. Conclusions: The Communications Unit at ICMR geared up with more robust plans and designed several interventions to mitigate the infodemic which helped in evidence based decision making towards outbreak response and action. This highlights the importance of evidence based, crisp, timely and effective communication during the epidemics/pandemics to buid trust and confidence in the community.

Evolving spike-protein N-glycosylation in SARS-CoV-2 variants.

Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune-response, both of which are impacted by host-installed N-glycans. Using highly-sensitive DeGlyPHER approach, we compared the N-glycan landscape on spikes of the SARS-CoV-2 Wuhan-Hu-1 strain to seven WHO-defined variants of concern/interest, using recombinantly expressed, soluble spike-protein trimers, sharing same stabilizing-mutations. We found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.

Endogenous Reverse Transcriptase Inhibition Attenuates TLR5-Mediated Inflammation.

Transposable elements (TEs) are mobile genomic sequences that encompass roughly 50% of the human genome. Class 1 TEs, or "retrotransposons," mobilize through the production of an RNA intermediate that is then reverse transcribed to form complementary DNA (cDNA) molecules capable of genomic reinsertion. While TEs are traditionally silenced to maintain genomic integrity, the recognition of immunostimulatory cues, such as those provided by microorganisms, drastically alters host transcription to induce the differential expression of TEs. Emerging evidence demonstrates that the inducible production of TE cDNA is not an inert phenomenon but instead has been coopted by host immunity to facilitate cross talk between host and constituents of the microbiota by agonizing intrinsic antiviral receptors. Here, we demonstrate that immunostimulation of toll-like receptor 4 (TLR4) with lipopolysaccharide (LPS) and TLR5 with bacterial flagella (FLA) alters the expression of retrotransposons, such as human endogenous retroviruses (HERVs) and long interspersed nuclear elements (LINEs). Next, we demonstrate that reverse transcriptase inhibitor (RTi) delivery ameliorates the acute production of the proinflammatory cytokine "tumor necrosis factor alpha" (TNF-α) in response to FLA in a monocytic cell line (THP-1). Collectively, our findings demonstrate that TLR5-mediated cross talk between the host and microbiota is partially dependent on the reverse transcription (RT) of retrotransposons. IMPORTANCE The microbiota is a potent reservoir of immunostimulatory and immunosuppressive motifs that fundamentally shape host immunity. Despite broad associations between microbial composition and host immunity, the mechanisms underlying host microbiota-induced immunoregulation remain poorly defined. Here, we demonstrate a novel mechanism by which motifs overabundant during dysbiotic conditions influence host immunity through the upregulation of endogenous RT to produce motifs that agonize antiviral receptors.

A single-cell transposable element atlas of human cell identity.

Single cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex biological systems. However, most sequencing studies overlook the contribution of transposable element (TE) expression to the transcriptome. In both scRNA-seq and bulk tissue RNA sequencing (RNA-seq), quantification of TE expression is challenging due to repetitive sequence content and poorly characterized TE gene models. Here, we developed a tool and analysis pipeline for Single cell Transposable Element Locus Level Analysis of scRNA Sequencing (Stellarscope) that reassigns multi-mapped reads to specific genomic loci using an expectation-maximization algorithm. Using Stellarscope, we built an atlas of TE expression in human PBMCs. We found that locus-specific TEs delineate cell types and define new cell subsets not identified by standard mRNA expression profiles. Altogether, this study provides comprehensive insights into the influence of transposable elements in human biology.

How human endogenous retroviruses interact with the microbiota in health and disease.

The microbiota is a collective of microorganisms whose composition is intimately linked with human health and disease. Emerging evidence demonstrates that endogenous retroviruses facilitate crosstalk between the host and microbiota to fundamentally shape immunity.

Naso-oropharyngeal microbiome from breast cancer patients diagnosed with COVID-19.

Due to immunosuppressive cancer therapies, cancer patients diagnosed with COVID-19 have a higher chance of developing severe symptoms and present a higher mortality rate in comparison to the general population. Here we show a comparative analysis of the microbiome from naso-oropharyngeal samples of breast cancer patients with respect to SARS-CoV-2 status and identified bacteria associated with symptom severity. Total DNA of naso-oropharyngeal swabs from 74 women with or without breast cancer, positive or negative for SARS-CoV-2 were PCR-amplified for 16S-rDNA V3 and V4 regions and submitted to massive parallel sequencing. Sequencing data were analyzed with QIIME2 and taxonomic identification was performed using the q2-feature-classifier QIIME2 plugin, the Greengenes Database, and amplicon sequence variants (ASV) analysis. A total of 486 different bacteria were identified. No difference was found in taxa diversity between sample groups. Cluster analysis did not group the samples concerning SARS-CoV-2 status, breast cancer diagnosis, or symptom severity. Three taxa (Pseudomonas, Moraxella, and Klebsiella,) showed to be overrepresented in women with breast cancer and positive for SARS-CoV-2 when compared to the other women groups, and five bacterial groups were associated with COVID-19 severity among breast cancer patients: Staphylococcus, Staphylococcus epidermidis, Scardovia, Parasegitibacter luogiensis, and Thermomonas. The presence of Staphylococcus in COVID-19 breast cancer patients may possibly be a consequence of nosocomial infection.

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.

The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD's Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.