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Lopez, C. B.

Publications and source records attributed to Lopez, C. B..

At least 19 recordsLinked to original sources
bioRxiv2026

RIG-I-MAVS-NOXA axis coordinates antiviral defense and apoptosis during parahenipavirus infection

The Gamak virus (GAKV) is a recently identified shrew-borne paramyxovirus belonging to the genus Parahenipavirus, which also includes the zoonotic Langya virus (LayV). Despite the growing recognition of shrew-associated paramyxoviruses, the host pathways that detect infection and regulate antiviral responses remain poorly understood. In this study, we characterized host responses to GAKV infection using integrated in vitro and in vivo approaches. GAKV infection induced robust innate immune responses in A549 cells, characterized by activation of interferon regulatory factor 3 (IRF3) and signal transducer and activator of transcription 1 (STAT1), together with induction of type I interferon (IFN) and interferon-stimulated genes (ISGs). Transcriptomic analysis further revealed coordinated enrichment of antiviral and intrinsic apoptosis-associated pathways, suggesting a link between innate immune signaling and apoptosis during GAKV infection. Genetic analyses identified retinoic acid-inducible gene I (RIG-I) and mitochondrial antiviral signaling protein (MAVS) as essential mediators of antiviral signaling and apoptosis during GAKV infection. Furthermore, disruption of type I IFN-STAT1 signaling attenuated apoptosis. NOXA knockdown reduced apoptosis and enhanced viral replication, identifying NOXA as a downstream effector linking innate immune activation to apoptosis. Consistent with these in vitro findings, intranasal GAKV infection in six-week-old female wild-type BALB/c mice was associated with lung-restricted viral RNA detection and induction of antiviral responses without overt disease. Together, these findings identify a RIG-I-MAVS-IFN-NOXA signaling axis that integrates antiviral and apoptotic responses during GAKV infection, providing a mechanistic framework for understanding host defense against parahenipaviruses.

microbiology↗
bioRxiv2026

Circadian Clock Gene Modulation and Selective Reprogramming in Response to Virus Infection

The circadian clock regulates fundamental cellular processes that include the host response to infection. However, the intersection of the circadian clock and the mechanisms that drive antiviral immunity remains poorly understood. Copy-back viral genomes (cbVGs) generated during virus replication strongly stimulate immunity during infection with negative-sense RNA viruses. Here, we demonstrate at the single cell level that A549 lung epithelial cells, commonly used to model lung infections, sustain circadian rhythms and upon infection with Sendai virus (SeV) progressively remodel the circadian clock through an innate immune response driven primarily by cbVGs. Furthermore, we show that cbVG-driven changes in circadian gene expression are mediated through two distinct innate immune sensing pathways: the RIG-I adaptor MAVS is required for preferential induction of the BMAL1 paralog ARNTL2, whereas the double-stranded RNA sensor PKR is required for the cbVG-specific induction of the negative-feedback regulators NR1D1, NR1D2, and PER1. A similar cbVG-specific signature was observed during respiratory syncytial virus infection, suggesting that cbVG-driven circadian gene regulation is not unique to SeV. In addition, we established through gain- and loss-of-function experiments that ARNTL2 is functionally required for amplifying the transcriptional response to infection, with selective effects on the expression of specific antiviral genes, including CCL5. Together, these findings establish innate immune signaling triggered by cbVGs as selective driver of circadian clock gene expression during viral infection through distinct sensing pathways and identify ARNTL2 as a previously unrecognized regulator of virus-induced host transcriptional responses.

microbiology↗
bioRxiv2026

Detailed single-cell mapping of the transcriptional response to a virus infection driven by copy-back viral genomes

The antiviral response to several clinically significant viruses, including respiratory syncytial virus and parainfluenza virus, is driven by copy-back viral genomes (cbVGs) generated during virus replication. However, the broader impact of cbVGs on the functional states of host cells remains undefined. Here, we developed a single-cell RNA-sequencing and computational framework to map cbVG-driven host responses during Sendai virus infection. Unsupervised profiling identified distinct transcriptional states throughout the course of infection, highlighting a shift from early antiviral signaling to later inflammatory and remodeling programs. Stratifying infected cells by cbVG status demonstrated that cbVG-positive cells initiate interferon and chemokine programs, which later spread to cbVG-negative cells. At later stages, cbVG-positive cells acquire additional signaling, cytoskeletal, transcriptional, and stress-adaptation programs, which are absent in cbVG-clean infection. This work defines the broader cbVG-driven layered and dynamic host response and provides a valuable high-resolution resource of the temporal cellular response to a virus infection.

microbiology↗
bioRxiv2025

Variable and conserved features of copy-back viral genome populations generated de novo during Sendai virus infection

Copy-back viral genomes (cbVGs) are generated during the replication of negative-sense RNA viruses when the polymerase drops off from the genome and reattaches to the nascent strand. cbVGs have strong immunostimulatory properties and impact infection outcomes. Despite their importance, the composition and mechanisms of de novo cbVG generation and accumulation remain unclear due to challenges in obtaining cbVG-free virus stocks (clean stocks). Here, we obtained several clean stocks by independently rescuing recombinant Sendai virus (SeV) six times and verified their cleanliness through PCR, RNA sequencing, and absence of immunostimulatory activity. High multiplicity-of-infection passaging of clean stocks produced six high-MOI passaged stocks, each with distinct cbVG populations. Among them, polymerase drop-off (break) positions occurred throughout the genome, while polymerase reattachment (rejoin) positions preferentially occurred near the trailer end. Few common breaks were observed between stocks, while there was a hot rejoin region near the trailer end. In each stock, a few cbVG species dominated and remained stable across passages, all conforming to the rule of six, regardless of length. Low-abundance cbVGs were variable across passages, indicating the continuous generation of new cbVGs, despite the stabilization of a subset of species. Intriguingly, cbVG species which originated from polymerase drop-off at or close to nucleotide 1 were present in all stocks, suggesting that cbVG species originating at the 3 end of the genome are conserved products of SeV replication.

microbiology↗
bioRxiv2025

Terminal Loop Sequences in Viral Double-Stranded RNAs Modulate RIG-I Signaling

Detection of foreign RNAs is a crucial activation step for innate immunity pathways in response to viral infections. Retinoic acid-inducible gene I (RIG-I) is a cytoplasmic RNA sensor that triggers type I and III interferon (IFN) expression and activates the antiviral response in response to RNA virus infection. The activating ligand for RIG-I has been shown to be 5-triphosphated, blunt-ended, double-stranded (ds)RNA, but questions remain on the impact of other RNA motifs on RIG-I activation. Here we show that immune-activating copy-back viral genomes (cbVGs) contain RNA stem loops away from the 5 end of the RNA that enhance RIG-I signaling and IFN expression. Importantly, the sequence of the terminal loops of the activating motifs impacts the strength of IFN expression. Additionally, we show that synthetic versions of these cbVG-derived stem loops trigger innate immune responses in mice demonstrating their potential as immunostimulants in vivo.

microbiology↗
bioRxiv2025

Validation of diverse and previously untraceable Sendai virus copyback viral genomes by Direct RNA Sequencing

Copyback viral genomes (cbVGs) are truncated viral genomes with complementary ends produced when the viral negative-sense RNA virus polymerase detaches from the replication template and resumes elongation from the nascent strand. Despite advances in methods to identify cbVGs based on the site of polymerase break and rejoin, PCR-based tools cannot provide full length sequences of most cbVGs and/or can introduce errors and artifacts during cbVG amplification. These limitations have painted a limited picture of the diverse population of cbVGs generated during infection. To improve our ability to obtain native full-length sequences of cbVGs, we optimized Direct RNA Sequencing (DRS) as a fast and simple tool to sequence full-length cbVGs and designed a BLAST-based analysis approach to identify cbVGs from long-read sequencing data. We analyzed the DRS outputs of multiple Sendai virus stocks to highlight both the utility and limitations of this tool. We found that to capture the dominant 546 nucleotide cbVG produced by Sendai virus strain Cantell, the length of complementarity between the virus trailer and the DRS oligonucleotide should optimally be increased to up to 32 nucleotides. We also demonstrate comparable quality of cbVG sequences by DRS from as little RNA as 17.6ng from the media fraction or 50ng of from the cellular fraction of cells infected with SeV, in contrast to the recommended 1000ng. Importantly, we validated different cbVG species from two recombinant Sendai virus stocks, including for the first time cbVGs whose break positions occurred at or near position one in the reference genome. ImportanceMost viruses of the order Mononegavirales has been demonstrated to naturally generate copyback viral genomes. These genomes are critical determinants of infection outcomes; they interfere with standard virus replication by competing for viral resources, activate antiviral responses, and inhibit protein translation. Despite their critical roles in infection, current tools to study copyback viral genomes rely either on preexisting knowledge of the sequence of a target RNA or require reverse-transcription and amplification of the target RNA, biasing toward short cbVGs and introducing relatively high rates of errors. Our lab has long advocated for RNA virologists to sequence their stocks to assess the role cbVGs may have in their infections. Toward this effort, we detail the optimization of Direct RNA Sequencing to sequence full-length cbVGs while maintaining the integrity of the native cbVG RNA and present the Long-Read cbVG Analysis (LoCA; https://github.com/lopezlab-washu/LOCA.git) script as a highly accessible BLAST-based tool for cbVG detection.

microbiology↗
bioRxiv2024

IFNα Inhibits JAK2V617F-Driven Neoplastic Vasculogenesis and Endothelial-to-Mesenchymal Transition in a 3D iPSC-Based Bone Marrow Niche Model

The vascular niche is a critical regulator of hematopoiesis and disease progression in myeloproliferative neoplasms (MPN). The presence of JAK2V617F+ endothelial cells (EC) in MPN patients and their association with cardiovascular complications highlight the need to understand and therapeutically target this compartment. Using patient-specific induced pluripotent stem cells (iPSC) harboring JAK2WT or the MPN-driver JAK2V617F (heterozygous, JAK2V617FHET, or homozygous, JAK2V617FHOM), we identified zygosity-dependent transcriptional profiles in iPSC-derived EC (iEC) at baseline and following interferon-alpha (IFN) treatment. JAK2V617FHET iEC exhibited an endothelial-to-mesenchymal transition (EndMT) signature, while JAK2V617FHOM iEC showed suppression of translation and ribosome biogenesis. Leveraging iPSC-based 3D assembloids that mimic the bone marrow (BM) niche, we showed that JAK2V617F-driven EndMT is inhibited by tyrosine kinase inhibitors and IFN. In both JAK2V617F-driven polycythemia vera and TPO-driven myelofibrosis murine models, scRNA-seq analysis of the BM vascular niche consistently revealed inflammatory and EndMT-associated signatures in arterial and arteriolar EC. Notably, dysregulation of ribosome- and translation-related pathways emerged in the myelofibrosis model and at advanced disease stages in JAK2V617F-driven polycythemia vera, indicating progressive vascular remodeling with disease evolution. Chronic pegylated IFN treatment in vivo effectively reversed these pathological changes. IFNs anti-EndMT activity was further validated in BM biopsies from MPN patients undergoing IFN therapy. This is the first study to define MPN stage-dependent vascular remodeling and zygosity-specific endothelial effects of JAK2V617F, and to directly link IFN-mediated EndMT inhibition as a novel antifibrotic mechanism. Our 3D assembloids provide a translational platform for mechanistic studies and therapeutic targeting of the BM microenvironment in MPN. Bullet PointsO_LIArterial vascular remodeling emerges as a novel hallmark of MPN, characterized by TNF-inflammation, ribosomal dysregulation and EndMT. C_LIO_LIIFN restores neoplastic endothelial dysfunction, highlighting its role as a vascular niche-modulating and anti-fibrotic agent in MPN. C_LI

cancer biology↗
bioRxiv2024

DDO-adjuvanted influenza A virus nucleoprotein mRNA vaccine induces robust humoral and cellular type 1 immune responses and protects mice from challenge

A challenge in viral vaccine development is to produce vaccines that generate both neutralizing antibodies to prevent infection and cytotoxic CD8+ T-cells that target conserved viral proteins and can eliminate infected cells to control virus spread. mRNA vaccines offer an opportunity to design vaccines based on conserved CD8-targeting epitopes, but achieving robust antigen-specific CD8+ T-cells remains a challenge. Here we tested the viral-derived oligonucleotide DDO268 as an adjuvant in the context of a model influenza A virus (IAV) nucleoprotein (NP) mRNA vaccine in C57BL/6 mice. DDO268 safely induced local type I interferon (IFN) production, stimulated dendritic cells type 1 (DC1) activation and migration to the draining lymph nodes, and improved the generation of IgG2c antibodies and antigen-specific effector Th1 CD4+ and CD8+ T-cells (IFN{gamma}+TNF+IL2+) when co-packaged with NP mRNA. The DDO268 adjuvanted vaccine provided enhanced protection against lethal IAV challenge and reduced the antigen dose required to achieve this protection. These results highlight the potential of DDO268 as an effective mRNA vaccine adjuvant and show that an IAV NP mRNA/DDO268 vaccine is a promising approach for generating protective immunity against conserved IAV epitopes. IMPORTANCEVaccines that generate neutralizing antibodies and cytotoxic CD8+ T-cells targeting conserved epitopes are ideal for effective protection against viruses. mRNA vaccines combined with the right adjuvant offer a promising solution to this challenge. We show that the virus-derived oligonucleotide DDO268 enhances antibody and T cell responses to an influenza A virus (IAV) nucleoprotein (NP) mRNA vaccine in mice. DDO268 safely induces local type I interferon production and stimulates dendritic cell activation providing enhanced protection against IAV challenge. In addition, the adjuvant activity of DDO268 allows for the use of lower antigen doses during vaccination.

immunology↗
bioRxiv2024

A chronic murine model of pulmonary Acinetobacter baumannii infection enabling the investigation of late virulence factors, long-term antibiotic treatments, and polymicrobial infections

Acinetobacter baumannii can cause prolonged infections that disproportionately affect immunocompromised populations. Our understanding of A. baumannii respiratory pathogenesis relies on an acute murine infection model with limited clinical relevance that employs an unnaturally high number of bacteria and requires the assessment of bacterial load at 24-36 hours post-infection. Here, we demonstrate that low intranasal inoculums in immunocompromised mice with a tlr4 mutation leads to reduced inflammation, allowing for persistent infections lasting at least 3 weeks. Using this "chronic infection model," we determined the adhesin InvL is an imperative virulence factor required during later stages of infection, despite being dispensable in the early phase. We also demonstrate that the chronic model enables the distinction between antibiotics that, although initially reduce bacterial burden, either lead to complete clearance or result in the formation of bacterial persisters. To illustrate how our model can be applied to study polymicrobial infections, we inoculated mice with an active A. baumannii infection with Staphylococcus aureus or Klebsiella pneumoniae. We found that S. aureus exacerbates the infection, while K. pneumoniae enhances A. baumannii clearance. In all, the chronic model overcomes some limitations of the acute pulmonary model, expanding our capabilities to study of A. baumannii pathogenesis and lays the groundwork for the development of similar models for other important opportunistic pathogens.

microbiology↗
bioRxiv2024

SLC35A2 modulates paramyxovirus fusion events during infection

Paramyxoviruses are significant human and animal pathogens that include mumps virus (MuV), Newcastle disease virus (NDV) and the murine parainfluenza virus Sendai (SeV). Despite their importance, few host factors implicated in paramyxovirus infection are known. Using a recombinant SeV expressing destabilized GFP (rSeVCdseGFP) in a loss-of-function CRISPR screen, we identified the CMP-sialic acid transporter (CST) gene SLC35A1 and the UDP-galactose transporter (UGT) gene SLC35A2 as essential for paramyxovirus infection. SLC35A1 knockout (KO) cells showed significantly reduced binding and infection of SeV, NDV and MuV due to the lack of cell surface sialic acids, which act as their receptors. However, SLC35A2 KO cells revealed unknown critical roles for this factor in virus-cell and cell-to-cell fusion events during infection with different paramyxoviruses. While the UGT was essential for virus-cell fusion during SeV entry to the cell, it was not required for NDV or MuV entry. Importantly, the UGT promoted the formation of larger syncytia during MuV infection, suggesting a role in cell-to-cell virus spread. Our findings demonstrate that paramyxoviruses can bind to or enter A549 cells in the absence of canonical galactose-bound sialic-acid decorations and show that the UGT facilitates paramyxovirus fusion processes involved in entry and spread.

microbiology↗
bioRxiv2024

Identification of distinct genotypes in circulating RSV A strains based on variants on the virus replication-associated genes

Respiratory syncytial virus is a common cause of respiratory infection that often leads to hospitalization of infected younger children and older adults. RSV is classified into two strains, A and B, each with several subgroups or genotypes. One issue with the definition of these subgroups is the lack of a unified method of identification or genotyping. We propose that genotyping strategies based on the genes coding for replication-associated proteins could provide critical information on the replication capacity of the distinct subgroup, while clearly distinguishing genotypes. Here, we analyzed the virus replication-associated genes N, P, M2, and L from de novo assembled RSV A sequences obtained from 31 newly sequenced samples from hospitalized patients in Philadelphia and 78 additional publicly available sequences from different geographic locations within the US. In-depth analysis and annotation of the protein variants in L and the other replication-associated proteins N, P, M2-1, and M2-2 identified the polymerase protein L as a robust target for genotyping RSV subgroups. Importantly, our analysis revealed non-synonymous variations in L that were consistently accompanied by conserved changes in its co-factor P or the M2-2 protein, suggesting associations and interactions between specific domains of these proteins. These results highlight L as an alternative to other RSV genotyping targets and demonstrate the value of in-depth analyses and annotations of RSV sequences as it can serve as a foundation for subsequent in vitro and clinical studies on the efficiency of the polymerase and fitness of different virus isolates. IMPORTANCEGiven the historical heterogeneity of Respiratory Syncytial Virus (RSV) and the disease it causes, there is a need to understand the circulating RSV strains each season. This requires an informative and consensus method of genotype definition. Here, we carried out a variant analysis that shows a pattern of specific variations among the replication-associated genes of RSV A across different seasons. Interestingly, these variation patterns point to previously defined interactions of domains within these genes, suggesting co-variation in the replication-associated genes. Our results also suggest a genotyping strategy that can prove to be particularly important in understanding the genotype-phenotype correlation in the era of RSV vaccination, where selective pressure on the virus to evolve is anticipated. More importantly, the categorization of RSV strains based on these patterns may prove to be of prognostic value.

microbiology↗
bioRxiv2024

Indiscriminate activities of different Henipavirus polymerase complex proteins allow for efficient minigenome replication in hybrid systems

The henipaviruses, including Nipah virus (NiV) and Hendra virus (HeV), are biosafety level 4 (BSL-4) zoonotic pathogens that cause severe neurological and respiratory disease in humans. To study the replication machinery of these viruses we developed robust minigenome systems that can be safely used in BSL-2 conditions. The nucleocapsid (N), phosphoprotein (P), and large protein (L) of henipaviruses are critical elements of their replication machinery and thus essential support components of the minigenome systems. Here, we tested the effects of diverse combinations of the replication support proteins on the replication capacity of the NiV and HeV minigenomes by exchanging the helper plasmids coding for these proteins among the two viruses. We demonstrate that all combinations including one or more heterologous proteins were capable of replicating both the NiV and HeV minigenomes. Sequence alignment showed identities of 92% for the N protein, 67% for P, and 87% for L. Notably, variations in amino acid residues were not concentrated in the N-P and P-L interacting regions implying that dissimilarities in amino acid composition among NiV and HeV polymerase complex proteins may not impact their interactions. The observed indiscriminate activity of NiV and HeV polymerase complex proteins is different from related viruses, which can support replication of heterologous genomes only when the whole polymerase complex belongs to the same virus. This newly observed promiscuous property of the henipavirus polymerase complex proteins could potentially be harnessed to develop universal anti-henipavirus antivirals. IMPORTANCEGiven the severity of disease induced by Hendra and Nipah viruses in humans and the continuous emergence of new henipaviruses as well as henipa-like viruses, it is necessary to conduct more comprehensive investigation of the biology of henipaviruses and their interaction with the host. The replication of henipaviruses and the development of antiviral agents can be studied in systems that allow experiments to be performed under biosafety level 2 conditions. Here, we developed two robust minigenome systems for Nipah virus (NiV) and Hendra virus (HeV) that provide a convenient alternative system for studying NiV and HeV replication. Using these systems, we demonstrate that any combinations of the three polymerase complex proteins of NiV and HeV could effectively initiate the replication of both viral minigenomes, which suggest that the interaction regions of the polymerase complex proteins could be effective targets for universal and effective anti-henipavirus interventions.

microbiology↗
bioRxiv2023

Murine Parainfluenza Virus Persists in Lung Innate Immune Cells Sustaining Chronic Lung Pathology

Respiratory viruses including the human parainfluenza viruses (hPIVs) are a constant burden to human health, with morbidity and mortality frequently increased after the acute phase of the infection. Although is proven that respiratory viruses can persist in vitro, the mechanisms of virus or viral products persistence, their sources, and their impact on chronic respiratory diseases in vivo are unknown. Here, we used Sendai virus (SeV) to model hPIV infection in mice and test whether virus persistence associates with the development of chronic lung disease. Following SeV infection, virus products were detected in lung macrophages, type 2 innate lymphoid cells (ILC2s) and dendritic cells for several weeks after the infectious virus was cleared. Cells containing viral protein showed strong upregulation of antiviral and type 2 inflammation-related genes that associate with the development of chronic post-viral lung diseases, including asthma. Lineage tracing of infected cells or cells derived from infected cells suggests that distinct functional groups of cells contribute to the chronic pathology. Importantly, targeted ablation of infected cells or those derived from infected cells significantly ameliorated chronic lung disease. Overall, we identified persistent infection of innate immune cells as a critical factor in the progression from acute to chronic post viral respiratory disease.

microbiology↗
bioRxiv2023

S RNA Intergenic Deletions Drive Viral Interference during Arenavirus Infections

Arenaviruses, a family of negative-sense RNA viruses spread by rodents, are a leading cause of severe hemorrhagic fever in humans. Due to a paucity of antivirals and vaccines for arenaviruses, there is a need to identify new mechanisms for interfering with arenavirus replication. In several negative-sense RNA viruses, natural viral interference results from the production of non-standard viral genomes (nsVGs) that activate the innate immune system and/or compete for essential viral products. Although it is well established that arenaviruses produce strong interfering activities, it is unknown if they produce interfering nsVGs. Here we show that arenaviruses produce deletions within the intergenic region of their Small (S) RNA genome, which prevents the production of viral mRNA and protein. These deletions are more abundant when arenaviruses are grown in high-interfering conditions and are associated with inhibited viral replication. Overall, we found that arenaviruses produce internal deletions within the S RNA intergenic region that are produced by arenaviruses and can block viral replication. These natural arenavirus interfering molecules provide a new target for the generation of antivirals as well as an alternative strategy for producing attenuated arenaviruses for vaccines. AUTHOR SUMMARYArenaviruses are hemorrhagic fever-causing pathogens that infect millions of people a year. There are currently no approved antivirals that target arenaviruses and understanding natural mechanisms that inhibit arenavirus replication is crucial for the development of effective therapeutics. Here, we identify multiple deletions within arenavirus genomes that are associated with the inhibition of viral replication. We show that these deletions prevent viral protein production through the removal of the intergenic region of the viral genome. These deletions were found in all arenaviruses tested in this study representing a novel mechanism for development of new antivirals and vaccines that broadly target the arenavirus family.

microbiology↗
bioRxiv2023

Copyback viral genomes trigger stress granule formation independent of the antiviral response to interfere with viral translation in acute and persistent infections

Antiviral responses are often accompanied by translation inhibition and formation of stress granules (SG) in infected cells. However, the triggers for these processes and their role during infection remain subjects of active investigation. Copy-back viral genomes (cbVGs) are the primary inducers of the Mitochondrial Antiviral Signaling (MAVS) pathway and antiviral immunity during Sendai Virus (SeV) and Respiratory Syncytial virus (RSV) infections. The relationship between cbVGs and cellular stress during viral infections is unknown. Here we show that SG form during infections containing high levels of cbVGs, and not during infections with low levels of cbVGs. Moreover, using RNA fluorescent in situ hybridization to differentiate accumulation of standard viral genomes from cbVGs at a single-cell level during infection, we show that SG form exclusively in cells that accumulate high levels of cbVGs. PKR activation is increased during high cbVG infections and, as expected, PKR is necessary to induce virus-induced SG. However, SG form independent of MAVS signaling, demonstrating that cbVGs induce antiviral immunity and SG formation through two independent mechanisms. Furthermore, we show that translation inhibition and SG formation do not affect the overall expression of interferon and interferon stimulated genes during infection, making the stress response dispensable for antiviral immunity. Using live-cell imaging, we show that SG formation is highly dynamic and correlates with a drastic reduction of viral protein expression even in cells infected for several days. Through analysis of active protein translation at a single cell level, we show that infected cells that form SG show inhibition of protein translation. Together, our data reveal a new cbVG-driven mechanism of viral interference where cbVGs induce PKR-mediated translation inhibition and SG formation leading to a reduction in viral protein expression without altering overall antiviral immunity. One Sentence SummarycbVGs trigger the cellular stress response independent of the antiviral response during RSV and parainfluenza virus infection leading to a reduction of virus protein expression.

microbiology↗
bioRxiv2023

Activity of brain stem glucagon neurons are modulated by energy state and encode sex and frequency-dependent negative valence and anxiety.

The glucagon-like peptide 1 (GLP-1) system has emerged as an important drug target for the treatment of obesity and diabetes. Preclinical and clinical studies demonstrate that the activation of GLP-1 receptors (GLP-1Rs) directly in the brain through overexpression of GLP-1 or GLP-1R agonists produces potent anorexigenic effects, yet the behavioral role and modulation of the endogenous GLP-1 producing system in the brain by energy status is unclear. In this study, we examined the anatomical, physiological, and behavioral properties of preproglucagon-expressing neurons in the nucleus of the solitary tract, GcgNTS neurons, which serve as the primary source of GLP-1 in the brain. Using transgenic laboratory mice, we observed no sex differences in the density and distribution of GcgNTS neurons in male and female mice. Fos immunolabeling experiments show that GcgNTS neurons are not significantly activated after intermittent access to palatable food, but the magnitude of Fos activation was linearly related to the amount of food intake in mice provided with ad libitum intermittent access to palatable food. Electrophysiological examination of GcgNTS neurons revealed that these neurons show energy-status and sex-dependent changes in neuronal firing and intrinsic excitability. Twenty-four hour food deprivation produced a significant reduction in excitability and firing in male, but not female mice. We then used optogenetics to investigate the causal behavioral role of GcgNTS neurons. High frequency optogenetic activation of GcgNTS neurons using the red light-gated opsin ChrimsonR produced female-specific anxiety-like behavior and real-time place aversion. For feeding, we observed that reversible optogenetic stimulation at high frequencies produced a significant reduction in homeostatic refeeding that did not differ by sex. Using operant conditioning, we found that reversible optogenetic activation of GcgNTS neurons at 20 Hz, but not 5, also reduces appetitive behavior. These data demonstrate that GcgNTS neurons exert control over motivation and food-seeking behavior in addition to consumption.

neuroscience↗
bioRxiv2023

VODKA2: An accurate method to detect copy-back and deletion viral genomes from next-generation sequencing data

During viral replication, viruses carrying an RNA genome produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication and pathogenesis. Because of their critical roles in determining the outcome of RNA virus infections, the study of nsVGs has flourished in recent years exposing a need for bioinformatic tools that can accurately identify them within Next-Generation Sequencing data obtained from infected samples. Here, we present our data analysis pipeline, Viral Opensource DVG Key Algorithm2 (VODKA2), that is optimized to run on a High Performance Computing (HPC) environment for fast and accurate detection of nsVGs from large data sets. Availability and implementationVODKA2 is freely available at GitHub (https://github.com/lopezlab-washu/VODKA2)

bioinformatics↗