Biology subjects

Harris, E.

Publications and source records attributed to Harris, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Detection of diverse coronaviruses, paramyxoviruses, and rhabdoviruses from cave-dwelling bats in Eastern Uganda

Bats harbor a diversity of viruses, some of which have the potential to impact human and livestock health. Caves in Eastern Uganda are commonly inhabited by bats in the genera Rhinolophus, Hipposideros, Myonycteris, and others. Human encroachment into these caves for shelter, hunting, mineral harvesting, and tourism poses a risk of exposure to infectious agents these bats may carry, yet little is known about the viruses present in these bats. From 2021 - 2023, 635 unique bats were captured in caves by mist net, with 69 bats resampled over the study for a total of 706 sampling instances. A total of 1,394 oral and rectal swabs were collected non-destructively and screened using molecular techniques for coronaviruses, paramyxoviruses, rhabdoviruses, flaviviruses, and filoviruses. Of these samples, 399 (56.5%) were collected during the rainy season and 307 (43.5%) during the dry season. Coronavirus RNA was detected in 59/706 (8.36%) of samples from Rhinolophus spp. (n = 35), Hipposideros caffer (n = 12), Myonycteris angolensis (n = 6), and Miniopterus spp. (n = 6). Six bats (0.85%) were positive for paramyxoviruses. Finally, (3 H. caffer, 1 M. angolensis, 1 Rhinolophus spp. and 1 Nycteris thebaica) 3 Rhinolophus bats were positive for rhabdoviruses (0.42%, all Rhinolophus spp.). No samples were positive for filovirus or flavivirus RNA. This project has generated novel data on the association of bat species and different viral strains present in these bats, advancing our knowledge of viral ecology and spillover risk at the human/bat interface.

genomics↗

bioRxiv2026

Early resource scarcity drives persistent transcriptional changes and vascular remodeling in the female prefrontal cortex

Early childhood poverty is an environmental risk factor for psychiatric and neurodegenerative disorders, yet the cellular mechanisms by which resource scarcity produces persistent brain vulnerability remain poorly understood. The medial prefrontal cortex (mPFC), which regulates executive function and motivated behavior, is sensitive to early environmental conditions. To identify mechanisms linking early resource scarcity to lasting mPFC dysfunction, we used the rat limited bedding and nesting (LBN) model, which recapitulates key features of poverty. Prior work shows LBN disrupts mPFC-mediated behaviors in adulthood, often in a sex-specific manner. Here, we used single-nucleus RNA sequencing (snRNAseq) to identify sex- and cell-type-specific transcriptional alterations in the adult mPFC following brief postnatal LBN exposure or control housing. LBN induced more differentially expressed genes (DEGs) across multiple pyramidal neuron clusters in females than in males. Unexpectedly, the largest transcriptional changes due to LBN occurred in vascular cells in females, whereas male vascular cells exhibited no DEGs. These female-specific vascular genes were enriched for alterations of transcriptional programs regulating angiogenesis and endothelial structure. This molecular profile was orthogonally validated with 3D vascular reconstruction, revealing LBN reduced vascular coverage in the adult female mPFC, driven by decreased vessel volume and shortened vessel length, while males were unaffected. Reduced vascular coverage may constrain metabolic support to this region. The postnatal period is a critical window for vascular maturation, and, taken together, these findings identify persistent, female-specific vascular alterations as a novel and previously unrecognized mechanism through which early resource scarcity may persistently affect brain function and vulnerability.

neuroscience↗

bioRxiv2026

Brain Organoids, Lessons from Fetal Neocortex Formation, and Rational Design for Quality Control

Recent widespread adoption of cerebral organoid protocols has led to many new studies assessing the human-specific features of neural diseases. However, not all organoid studies employ proper quality control, which limits the physiological relevance of their findings. Here, we discuss the stages of in vivo neocortex formation and how those stages are recapitulated in organoid protocols. We then present the first guide for real-time operator removal of maldeveloped organoids in shaking culture. Finally, we show preliminary work on an organoid imaging and mesofluidic control platform for automated quality control of organoid development. Taken together, this approach for assessing the morphological features of organoids will improve the rigor and reproducibility of organoid studies, increase effect sizes of physiologically relevant disease etiology, and pave the way for cortical organoid GMP in high-throughput. Clinical RelevanceThis establishes high-throughput, visual brain organoid quality control for disease studies and preclinical testing.

neuroscience↗

bioRxiv2026

Dengue virus-specific memory B cell subsets differ as a function of infection history

The four dengue virus serotypes (DENV1-4) are a major global health threat. Infection generates protective immunity over multiple exposures with different serotypes. Virus-specific memory B cells (MBCs) can contribute to lasting protection, yet their development over multiple DENV infections remains undefined. We comprehensively evaluated frequencies of nine DENV-specific B cell subsets in 58 samples from dengue cases, comparing groups with primary (1{degrees}) versus secondary (2{degrees}) DENV infection history. Longitudinal sampling from acute infection to 18 months post-symptom onset enabled assessment of DENV-specific MBC temporal dynamics. Critically, we found that DENV-specific B cell frequency differed substantially at the level of phenotypic subsets in 1{degrees} versus 2{degrees} immunity, despite no significant difference in total frequency of DENV-specific B cells. In particular, DENV-specific IgG+, IgM+, atypical, and class-switched IgD-MBCs were durable until 18 months and accumulated with multiple exposures, representing a bona fide memory compartment against DENV. Also, naive-like IgD+/IgM+ DENV-specific B cells were found. Interestingly, the peak of certain DENV-specific MBCs occurred >3-months post-symptom onset in 2{degrees} DENV immunity, suggesting potential for long-term MBC maturation. We demonstrate that DENV-specific MBC subsets differ as a function of infection history, suggesting that 2{degrees} DENV immunity does not simply generate a quantitative boost, but a qualitative reprogramming of the memory pool. Significance StatementThe four dengue virus serotypes (DENV1-4) cause the most prevalent human mosquito-borne viral disease. Dengue is a febrile disease that often results in debilitating body pain and can rapidly progress to severe disease involving shock. People are generally protected after multiple exposures to different serotypes. Memory B cells (MBCs) can contribute to lasting protection against subsequent dengue. To understand how these rare DENV-specific MBCs develop over multiple exposures, we compared samples from cases with primary versus secondary (i.e., multiple) DENV infections. We found that instead of a higher frequency of total DENV-specific MBCs, particular subsets of DENV-specific MBCs were higher and peaked later after multiple exposures. This suggests that a qualitative shift in DENV-specific MBCs may contribute to protective immunity.

immunology↗

bioRxiv2025

Wee1 opposes APC/C(Cdh1) activity to promote S-phase entry

Wee1 phosphorylates and inhibits CDK activity to inhibit mitotic entry and establish a G2 DNA damage checkpoint. Consequently, Wee1 inhibitors are in clinical trials, developed to be synthetically lethal in TP53 mutant tumours that become reliant on a Wee1-mediated DNA damage checkpoint. However, Wee1 inhibitors have efficacy in TP53 wild-type tumours and many trials have been terminated due to high levels of toxic side-effects, suggesting that Wee1 has unknown functions. Here, we show that Wee1 promotes cell cycle re-entry from quiescence (G0) by opposing the activity of the E3 ubiquitin ligase, APC/CCdh1. Wee1 phosphorylates Cdh1 (FZR1) at key residues that mediate the interaction between Cdh1 and APC/C. Cells with loss-of-function of Wee1 during G0/G1 have delayed S-phase entry, an impaired G1/S transition, abnormal S-phase accumulation of the CDK inhibitor p21 and enter a p21-dependent G2 arrest. Reduced expression of APC/CCdh1 or p21 renders cells more sensitive to acute Wee1 inhibition and both pathways are downregulated in acquired Wee1 inhibitor resistance. Our study reveals a new cell cycle control mechanism that has implications for how Wee1 inhibitors should be used in the clinic.

cell biology↗

bioRxiv2025

Dengue Virus NS1 Binds Ephrin B1 to Trigger Endothelial Dysfunction

Dengue virus (DENV), a member of the Flaviviridae family, is the most prevalent and medically important mosquito-borne viral pathogen. Infected cells secrete the viral non-structural protein 1 (NS1) into the bloodstream, where it can interact with endothelial cells to induce vascular leak. Host factors involved in NS1-mediated endothelial dysfunction are incompletely understood, leading us to investigate the host interactome of DENV NS1 in endothelial cells via a comparative mass spectrometry approach. We identified ephrin B1 (EFNB1) as a critical host factor in NS1-mediated endothelial barrier dysfunction and show that phosphorylation of EFNB1 is necessary for induction of barrier dysfunction. Further, we map the interface of the EFNB1-NS1 complex through biochemical and computational approaches, and we show that EFNB1-Fc-fusion proteins can act as decoys to block NS1-induced barrier dysfunction in vitro and in vivo. This study provides insights into the mechanism of flavivirus NS1-mediated endothelial barrier dysfunction and new avenues to target vascular leak.

microbiology↗

bioRxiv2025

rapunzel5 is necessary for normal hematopoietic development in zebrafish

The molecular mechanisms regulating the highly complex process of hematopoiesis in vertebrates is still enigmatic. This system begins with the controlled differentiation of adult hematopoietic stem and progenitor cells (HSPCs), which can proliferate and generate all types of mature blood cells. Identifying the underlying factors and mechanisms that allow HSPCs to differentiate and proliferate is an essential issue in stem cell biology and tissue homeostasis; disruptions in these processes can cause severe diseases. A transcriptomic screen of hematopoietic-supportive zebrafish stromal tissues identified rapunzel5 (rpz5) was likely involved in vertebrate hematopoiesis. We performed loss-of-function experiments in zebrafish embryos at the one-cell-stage with morpholinos to determine if blood cell production was affected by rpz5. rpz5 knockdown resulted in reduced amounts of red blood cells, myeloid cells, and thrombocytes, and adding back exogenous rpz5 rescued these deficiencies. Further analysis with methylcellulose assays indicated that there was also a significant reduction in HSPCs following rpz5 reduction. Together, these findings suggest that zebrafish rpz5 is essential for normal formation, differentiation, and proliferation of HSPCs, specifically down the erythroid and myeloid pathway. Fully understanding the roles of novel genes such as rpz5 is essential for understanding the evolution of vertebrate hematopoiesis and for treating hematological diseases in the future.

genetics↗

bioRxiv2025

Therapeutic Potential of Cyclodextrins Targeting Dengue Virus and SARS-CoV-2 Infection and Pathogenesis

Cyclodextrins (CDs) are cyclic oligosaccharides with promising therapeutic applications, including antiviral activity. During viral infections, pathogenesis arises not only from viral replication but also from viral proteins that act as "toxins", disrupting cellular barriers and inducing endothelial dysfunction, a hallmark of severe diseases such as dengue and COVID-19. Dengue virus (DENV) NS1 and SARS-CoV-2 Spike proteins induce endothelial hyperpermeability, contributing to severe complications. Here we explored the potential of a panel of 18 CDs in mitigating endothelial dysfunction caused by these viral proteins and evaluated the CDs antiviral activity in vitro and in vivo. The effect of CDs on endothelial hyperpermeability was assessed using a trans-endothelial electrical resistance assay with human pulmonary microvascular endothelial cells exposed to DENV NS1 and SARS-CoV-2 Spike proteins. Antiviral efficacy of CDs was evaluated in Vero cells infected with DENV2 and Calu-3 cells infected with SARS-CoV-2, and in vivo protection was assessed in a lethal DENV2 mouse model. CDs effectively inhibited DENV NS1-induced endothelial hyperpermeability in vitro, demonstrating their potential to counteract NS1-mediated barrier disruption. In the murine model, CD1 treatment provided partial protection against DENV-induced morbidity and mortality. Further, CDs significantly reduced SARS-CoV-2 infection in vitro and inhibited Spike-induced endothelial dysfunction. These findings indicate that CDs can prevent endothelial hyperpermeability induced by DENV NS1 and SARS-CoV-2 Spike proteins and exhibit antiviral activity against SARS-CoV-2, positioning them as promising candidates for mitigating endothelial complications associated with viral infections. Further research is needed to explore the clinical relevance of CDs and their mechanisms of action.

microbiology↗

bioRxiv2025

Cytoplasmic mRNA decay by the anti-viral nuclease RNase L promotes transcriptional repression

Ribonuclease (RNase) L is an antiviral factor that promiscuously degrades viral and cellular RNA in the cytoplasm. This results in extensive translational reprogramming, altering mRNA processing and export. Here, we reveal that another major consequence of cytoplasmic RNase L activity is the repression of nascent RNA synthesis in the nucleus. This is not associated with altered nuclear RNA stability but instead results from transcriptional repression. For RNA polymerase II, repression is primarily associated with reduced occupancy of serine 2-phosphorylated polymerase in gene bodies, indicating an elongation defect. Prominent among the transcriptionally downregulated loci are immune-related genes, supporting a role for RNase L in tempering innate immune and inflammatory responses. RNase L activation also caused disruption of nucleoli and reduced RNA polymerase I and III transcription. Crosstalk between RNA decay and transcription thereby contributes to the large-scale modulation of gene expression in RNase L-activated cells.

molecular biology↗

bioRxiv2024

Flavivirus NS1-triggered endothelial dysfunction promotes virus dissemination

The Flaviviridae are a family of viruses that include the important arthropod-borne human pathogens dengue virus (DENV), West Nile virus, Zika virus, Japanese encephalitis virus, and yellow fever virus. Flavivirus nonstructural protein 1 (NS1) is essential for virus replication but is also secreted from virus-infected cells. Extracellular NS1 acts as a virulence factor during flavivirus infection in multiple ways, including triggering endothelial dysfunction and vascular leak via interaction with endothelial cells. While the role of NS1 in inducing vascular leak and exacerbating pathogenesis is well appreciated, if and how NS1-triggered endothelial dysfunction promotes virus infection remains obscure. Flaviviruses have a common need to disseminate from circulation into specific tissues where virus-permissive cells reside. Tissue-specific dissemination is associated with disease manifestations of a given flavivirus, but mechanisms dictating virus dissemination are unclear. Here we show that NS1-mediated endothelial dysfunction promotes virus dissemination in vitro and in vivo. In mouse models of DENV infection, we show that anti-NS1 antibodies decrease virus dissemination, while the addition of exogenous NS1 promotes virus dissemination. Using an in vitro system, we show that NS1 promotes virus dissemination in two distinct ways: (1) promoting crossing of barriers and (2) increasing infectivity of target cells in a tissue- and virus-specific manner. The capacity of NS1 to modulate infectivity correlates with a physical association between virions and NS1, suggesting a potential NS1-virion interaction. Taken together, our study indicates that flavivirus NS1 promotes virus dissemination across endothelial barriers, providing an evolutionary basis for virus-triggered vascular leak. Author SummaryThe Flaviviridae contain numerous medically important human pathogens that cause potentially life-threatening infections. Over half of the worlds population is at risk of flavivirus infection, and this number is expected to increase as climate change expands the habitats of the arthropod vectors that transmit these flaviviruses. There are few effective vaccines and no therapeutics approved for prevention or treatment of flavivirus infection, respectively. Given these challenges, understanding how and why flaviviruses cause pathogenesis is critical for identifying targets for therapeutic intervention. The secreted nonstructural protein 1 (NS1) of flaviviruses is a conserved virulence factor that triggers endothelial dysfunction in a tissue-specific manner. It is unknown if this endothelial dysfunction provides any benefit for virus infection. Here we provide evidence that NS1-triggered endothelial dysfunction facilitates virus crossing of endothelial barriers and augments infection of target cells in vitro and promotes virus dissemination in vivo. This study provides an evolutionary explanation for flaviviruses evolving the capacity to trigger barrier dysfunction and highlights NS1 and the pathways governing endothelial dysfunction, as therapeutic targets to prevent flavivirus dissemination.

microbiology↗

bioRxiv2024

Identification of immunogenic and cross-reactive chikungunya virus-specific CD4+ T cell epitopes in chronic chikungunya viral arthritic disease in humans

Chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes acute febrile illness that can progress into chronic chikungunya virus disease (CHIKVD) marked by persistent debilitating arthralgia. At present, the exact cause of chronic CHIKVD is not understood, and in humans, the targets of CD4+ T cells in CHIKV are currently unknown. Here, by stimulating peripheral blood mononuclear cells (PBMCs) collected from patients suffering from chronic CHIKVD with peptides spanning the entire CHIKV genome, we provide a comprehensive landscape of CHIKV CD4+ T cell epitopes. We identified 123 novel CD4+ T cell epitopes and three immunodominant regions in E1, nsP1 and CP proteins. The immunodominance of these E1, nsP1 and CP regions was mapped to optimal epitopes, characterized by the capacity to bind to many common HLA class II allelic variants. In addition, we designed and validated a new CHIKV-specific CD4+ T cell epitope megapool, spanning both structural and non-structural proteins, which can be a useful tool to study CHIKV-specific T cell responses in small blood volumes, typically available in pediatric or clinical samples. Finally, by in silico assessment of the conservation of the CHIKV proteome in a diverse set of alphaviruses, we defined CHIKV epitopes conserved across arthritogenic and encephalitic viruses. Overall, our work is the first to identify CD4+ T cell targets of CHIKV in humans, expanding our capacity to study the role of T cells in CHIKV pathogenesis and mapping targets of alphaviruses for vaccine design.

immunology↗

bioRxiv2024

A novel method for characterizing cell-cell interactions at single-cell resolution reveals unique signatures in blood T cell-monocyte complexes during infection

Communication between immune cells through direct contact is a critical feature of immune responses. Here, we developed a novel high-throughput method to study the transcriptome and adaptive immune receptor repertoire of single cells forming complexes without needing bioinformatic deconvolution. We found that T cells and monocytes forming complexes in blood during active tuberculosis (TB) and dengue hold unique transcriptomic signatures indicative of TCR/MCH-II immune synapses. Additionally, T cells in complexes showed enrichment for effector phenotypes, imaging and transcriptomic features of active TCR signaling, and increased immune activity at diagnosis compared to after anti-TB therapy. We also found evidence for bidirectional RNA exchange between T cells and monocytes, since complexes were markedly enriched for "dual-expressing" cells (i.e., co-expressing T cell and monocyte genes). Thus, studying immune cell complexes at a single-cell resolution offers novel perspectives on immune synaptic interactions occurring in blood during infection. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=59 SRC="FIGDIR/small/612103v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@f90023org.highwire.dtl.DTLVardef@178007corg.highwire.dtl.DTLVardef@167e53corg.highwire.dtl.DTLVardef@1faff48_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Perturbed pediatric serum metabolome in mild and severe dengue disease

Dengue viruses (DENVs) are the most prevalent arboviruses affecting humans. Four billion people are at risk of infection and this burden is rapidly increasing due to geographic expansion of the mosquito vector. Infection with any of the four serotypes of DENV can result in a self-limiting disease but debilitating febrile illness (DF), and some infections progress to severe disease with manifestations such as hemorrhage and shock. DENV infection drives the metabolic state of host cells for viral benefit and induces a host-immune response that has metabolic implications that link to disease. In this study, a dynamic metabolic response to DENV infection and disease was measured in 535 pediatric patient sera using liquid chromatography-mass spectrometry. The metabolome was interrogated to discover biochemical pathways and identify key metabolites perturbed in severe dengue disease. A biomarker panel of thirty-two perturbed metabolites was utilized to classify DF, and severe dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) with high sensitivity and specificity equating to a balanced accuracy of 96.9%. Some metabolites that were structurally confirmed here belong to important biochemical pathways of omega-3 and omega-6 fatty acids, sphingolipids, purines, and tryptophan metabolism. A previously reported trend between serotonin and platelets in DHF patients has been expanded upon here to reveal a major depletion of serotonin, but not platelets, in DSS patients. This study differentiated and classified DF and DHF/DSS using a serum metabolic biomarker panel based on perturbed biochemical pathways that have potential implications for severe dengue disease. One sentence summary: Metabolic biomarkers distinguish dengue hemorrhagic fever and dengue shock syndrome from dengue fever and lend insight to severe disease pathology

systems biology↗

bioRxiv2024

Tracking the genetic diversity of SARS-CoV-2 variants in Nicaragua throughout the COVID-19 Pandemic

The global circulation of SARS-CoV-2 has been extensively documented, yet the dynamics within Central America, particularly Nicaragua, remain underexplored. This study characterizes the genomic diversity of SARS-CoV-2 in Nicaragua from March 2020 through December 2022, utilizing 1064 genomes obtained via next-generation sequencing. These sequences were selected nationwide and analyzed for variant classification, lineage predominance, and phylogenetic diversity. We employed both Illumina and Oxford Nanopore Technologies for all sequencing procedures. Results indicated a temporal and spatial shift in dominant lineages, initially from B.1 and A.2 in early 2020 to various Omicron subvariants towards the studys end. Significant lineage shifts correlated with changes in COVID-19 positivity rates, underscoring the epidemiological impact of variant dissemination. The comparative analysis with regional data underscored the low diversity of circulating lineages in Nicaragua and their delayed introduction compared to other countries in the Central American region. The study also linked specific viral mutations with hospitalization rates, emphasizing the clinical relevance of genomic surveillance. This research advances the understanding of SARS-CoV-2 evolution in Nicaragua and provide valuable information regarding its genetic diversity for public health officials in Central America. We highlight the critical role of ongoing genomic surveillance in identifying emergent lineages and informing public health strategies.

genomics↗

bioRxiv2024

Antibodies targeting Crimean-Congo hemorrhagic fever virus GP38 limit vascular leak and viral spread

Crimean-Congo hemorrhagic fever virus (CCHFV) is a priority pathogen transmitted by tick bites, with no vaccines or specific therapeutics approved to date. Severe disease manifestations include hemorrhage, endothelial dysfunction, and multiorgan failure. Infected cells secrete the viral glycoprotein GP38, whose extracellular function is presently unknown. GP38 is considered an important target for vaccine and therapeutic design as GP38-specific antibodies can protect against severe disease in animal models, albeit through a currently unknown mechanism of action. Here, we show that GP38 induces endothelial barrier dysfunction in vitro, and that CCHFV infection, and GP38 alone, can trigger vascular leak in a mouse model. Protective antibodies that recognize specific antigenic sites on GP38, but not a protective neutralizing antibody binding the structural protein Gc, potently inhibit endothelial hyperpermeability in vitro and vascular leak in vivo during CCHFV infection. This work uncovers a function of the secreted viral protein GP38 as a viral toxin in CCHFV pathogenesis and elucidates the mode of action of non-neutralizing GP38-specific antibodies.

microbiology↗

bioRxiv2024

A numbers game: Mosquito-based arbovirus surveillance in two distinct geographic regions of Latin America

Aedes mosquitoes, as vectors of medically important arthropod-borne viruses (arboviruses), constitute a major public health threat that requires entomological and epidemiological surveillance to guide vector control programs to prevent and reduce disease transmission. In this study, we present the collaborative effort of one year of mosquito-based arbovirus surveillance in two geographically distinct regions of Latin America (Nicaragua and Ecuador). Adult female mosquitoes were collected using backpack aspirators in over 2,800 randomly selected households (Nicaragua, Ecuador) and 100 key sites (Nicaragua) from eight distinct communities (Nicaragua: 2, Ecuador: 6). A total of 1,358 mosquito female pools were processed for RNA extraction and viral RNA detection using real-time RT-PCR. Ten positive dengue virus (DENV) pools were detected (3 in Nicaragua and 7 in Ecuador), all of which were found during the rainy season and matched the serotypes found in humans (Nicaragua: DENV-1 and DENV-4; Ecuador: DENV-2). Infection rates ranged from 1.13 to 23.13, with the Nicaraguan communities having the lowest infection rates. Our results demonstrate the feasibility of detecting DENV-infected Aedes mosquitoes in low-resource settings and underscore the need for targeted mosquito arbovirus sampling and testing, providing valuable insights for future surveillance programs in the Latin American region.

ecology↗

bioRxiv2023

The Inflammasome Pathway is Activated by Dengue Virus Non-structural Protein 1 and is Protective During Dengue Virus Infection

Dengue virus (DENV) is a medically important flavivirus causing an estimated 50-100 million dengue cases annually, some of whom progress to severe disease. DENV non-structural protein 1 (NS1) is secreted from infected cells and has been implicated as a major driver of dengue pathogenesis by inducing endothelial barrier dysfunction. However, less is known about how DENV NS1 interacts with immune cells and what role these interactions play. Here we report that DENV NS1 can trigger activation of inflammasomes, a family of cytosolic innate immune sensors that respond to infectious and noxious stimuli, in mouse and human macrophages. DENV NS1 induces the release of IL-1{beta} in a caspase-1 dependent manner. Additionally, we find that DENV NS1-induced inflammasome activation is independent of the NLRP3, Pyrin, and AIM2 inflammasome pathways, but requires CD14. Intriguingly, DENV NS1-induced inflammasome activation does not induce pyroptosis and rapid cell death; instead, macrophages maintain cellular viability while releasing IL-1{beta}. Lastly, we show that caspase-1/11-deficient, but not NLRP3-deficient, mice are more susceptible to lethal DENV infection. Together, these results indicate that the inflammasome pathway acts as a sensor of DENV NS1 and plays a protective role during infection.

immunology↗

bioRxiv2022

Retention time prediction to facilitate molecularstructure identification with tandem mass spectrometry

Comparing measured and predicted chromatographic retention time can improve molecular structure assignment in applications such as coupled liquid chromatography-tandem mass spectrometry. We assess a range of different machine learning methods to predict hydrophobicity, a molecular property that can be used as a proxy for retention time. The performance of the models is evaluated on the benchmark Martel and SAMPL7 datasets. We find that more powerful models perform better when predicting in-sample but not necessarily when generalizing to out-of-sample molecular families. We also find that ensemble methods can outperform individual models. Additionally, a multitask learning model shows promise for improving the generalization ability of graph neural networks for hydrophobicity prediction. Finally, we discuss how the ability of graph neural networks to generalize for molecular property prediction could be improved further.

bioinformatics↗