Biology subjects

Sebastian, A.

Publications and source records attributed to Sebastian, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Rice blast fungus hijacks a rice RALF peptide to initiate infection

Plant-derived peptides regulate immunity and host-microbe interactions, but whether fungal pathogens exploit endogenous plant peptides for infection-site selection remains largely unknown. Rapid alkalinization factors (RALFs) are a family of plant peptide hormones that contribute to plant development, reproduction, stress responses, and cell-wall organization. Here, we show that OsRALF7, which is an immune-activating peptide in rice (Oryza sativa), is co-opted by the rice blast fungus Magnaporthe oryzae as a host-derived cue for appressorium formation, specialized infection structures required for host penetration. While synthetic OsRALF7 peptide induced defense responses in rice suspension cells, the same peptide induced appressorium formation in M. oryzae. OsRALF7-induced appressorium formation was associated with activation of the cAMP/PKA and Pmk1 MAPK pathways and required a hydrophobic surface. M. oryzae inoculated onto Osralf7 knockout plants formed fewer appressoria, and the positioning of these appressoria relative to the boundaries between two adjacent plant epidermal cells was altered. These findings suggest that OsRALF7 provides positional information for infection initiation for M. oryzae. OsRALF7 localized to the plasma membrane and cell wall in rice, and its appressorium-inducing activity required a conserved YISY motif and cysteine residues. This activity was not conserved in Colletotrichum higginsianum, as RALF23 from Arabidopsis thaliana did not induce appressorium formation but instead showed antifungal activity. Together, these findings uncover a dual function of endogenous plant immune-modulating RALF peptides at the plant-pathogen interface, where they can be exploited by M. oryzae as a host-derived cue for infection initiation while also retaining antifungal activity against other fungal species.

plant biology↗

bioRxiv2026

Aging disrupts transcriptional programs for memory updating in the dorsal hippocampus and reveals a required role for Tent5a in reconsolidation

Existing memories can be updated with new information through a process known as reconsolidation, though the molecular mechanisms underlying this process are poorly understood. Additionally, memory updating is impaired with aging, but little is known about how this impairment occurs. Here, we used a hippocampus-dependent memory updating task alongside transcriptomics to identify which genes are upregulated in the dorsal hippocampus specifically during a memory update in both young adult mice, which show successful memory updating, and in old mice, which do not. In young mice, we observed that distinct transcriptional programs were activated by reconsolidation-dependent memory updating and memory retrieval without new information. In old mice, similar transcriptional programs were engaged by both memory updating and memory retrieval. From our sequencing results, we identified Tent5a as a novel regulator of reconsolidation-mediated memory updating, and we demonstrate that hippocampal expression of Tent5a is necessary for this process. Together, these results expand our understanding of both the underlying transcriptional mechanisms of memory updating and how these mechanisms go awry in the aged brain.

neuroscience↗

bioRxiv2026

Human CCR4-NOT suppresses pervasive transcription and retrotransposable elements

CCR4-NOT regulates multiple steps in gene regulation and has been well studied in budding yeast. Although primarily cytoplasmic, where it plays an essential role in mRNA degradation, the human complex has poorly characterized nuclear functions. Here, we used auxin-induced degradation to rapidly deplete the scaffold subunit CNOT1 and the E3 ligase CNOT4, and characterized the transcriptional functions of the human CCR4-NOT complex. Using transient transcriptome profiling (TT-Seq) to measure ongoing transcription, we found widespread activation of RNA synthesis in depleted cells across genic and intergenic regions. Interestingly, fewer genes were repressed, including KRAB-Zinc-Finger-protein (KZNF) genes, especially those on chromosome 19. KZNFs repress genes and retrotransposable elements (rTEs), and consistent with decreased KZNF expression, rTEs, mainly Long Interspersed Nuclear Elements (LINEs), were activated. Full-length active LINEs and rTEs lying outside of genes were activated, suggesting that the increased transcription is not the direct result of transcription of the genes the rTEs are embedded in. We found that most activated transcription events were in proximity to KZNF binding sites, suggesting that KZNF regulation contributes to the suppression of genic and rTE transcription. Finally, we demonstrate that CCR4-NOT regulates the stability of rTE RNAs, indicating that the complex tightly controls transposon expression by repressing transcription and targeting their RNAs for decay.

molecular biology↗

bioRxiv2025

Degradation factor 1, Def1, regulates mRNA translation and decay through Ccr4-Not-dependent ubiquitylation of the ribosome.

Yeast Def1 is well known for its role in regulating RNA polymerase II elongation and degrading the large subunit of polymerase during transcriptional stress. It is an abundant cytoplasmic protein that undergoes stress-induced processing and is then transported to the nucleus. Previous research from our lab has shown that Def1 interacts with various proteins involved in mRNA decay and translation control, and that it regulates mRNA half-lives, suggesting an important role in the cytoplasm. In this study, we report that Def1 binds polyribosomes and that its null mutant strain exhibits phenotypes indicating a role in translation. Ribo-seq analysis revealed that deleting DEF1 altered ribosome footprints on mRNAs and increased the dwell time of ribosomes at non-optimal codons in the A-site. Additionally, results from a codon-optimality reporter assay suggest that Def1 facilitates the degradation of mRNAs containing non-optimal codons. The Ccr4-Not complex links codon optimality to mRNA decay, and Def1s binding to ribosomes depends on its ubiquitin-binding domain, as well as the ubiquitylation of eS7a in the small ribosomal subunit by the Ccr4-Not complex. Moreover, the polyglutamine-rich, unstructured C-terminus of Def1 is crucial for its interaction with RNA decay and translation factors. This indicates that Def1 functions as a ubiquitin-dependent scaffold, connecting translation status to mRNA decay. In summary, we have identified a cytoplasmic function for Def1 in translation and established it as a regulator of gene expression, spanning both transcription and translation processes.

molecular biology↗

bioRxiv2025

Epigenetic modifiers to treat retinal degenerative diseases

We have previously demonstrated the ability of inhibitors of LSD1 and HDAC1 to block rod degeneration, preserve vision, maintain rod-specific transcripts and downregulate those involved in inflammation, gliosis, and cell death in the rd10 mouse model of Retinitis Pigmentosa (RP). To extend our findings we tested the hypothesis that this effect was due to altered chromatin structure by using a range of inhibitors of chromatin condensation to prevent photoreceptor degeneration in the rd10 mouse model. We used inhibitors for G9A/GLP that catalyzes methylation of H3K9, for EZH2 that catalyzes trimethylation of H3K27, and compared them to the actions of inhibitors of LSD1 and HDAC. All the inhibitors decondense chromatin and all preserve, to different extents, retinas from degeneration in rd10 mice, but they act through different metabolic pathways. One group of inhibitors, modifiers for LSD1 and EZH2, demonstrate a high level of maintenance of rod-specific transcripts, activation of Ca+2 and Wnt signaling pathways with inhibition of antigen processing and presentation, immune response and microglia phagocytosis. Another group of inhibitors, modifiers for HDAC and G9A/GLP work through upregulation of NGF-stimulated transcription, while down-regulating genes belong to immune response, extracellular matrix, cholesterol signaling and programmed cell death. Our results provide robust support for our hypothesis that inhibition of chromatin condensation can be sufficient to prevent rod death in rd10 mice.

neuroscience↗

bioRxiv2024

Single-cell and spatiotemporal transcriptomic profiling of brain immune infiltration following Venezuelan equine encephalitis virus infection

Neurotropic alphaviruses such as Venezuelan equine encephalitis virus (VEEV) are critical human pathogens that continually expand to naive populations and for which there are no licensed vaccines or therapeutics. VEEV is highly infectious via the aerosol route and is a recognized weaponizable biothreat that causes neurological disease in humans. The neuropathology of VEEV has been attributed to an inflammatory immune response in the brain yet the underlying mechanisms and specific immune cell populations involved are not fully elucidated. This study uses single-cell RNA sequencing to produce a comprehensive transcriptional profile of immune cells isolated from the brain over a time course of infection in a mouse model of VEEV. Analyses reveal differentially activated subpopulations of microglia, including a distinct type I interferon-expressing subpopulation. This is followed by the sequential infiltration of myeloid cells and cytotoxic lymphocytes, also comprising subpopulations with unique transcriptional signatures. We identify a subpopulation of myeloid cells that form a distinct localization pattern in the hippocampal region whereas lymphocytes are widely distributed, indicating differential modes of recruitment, including that to specific regions of the brain. Altogether, this study provides a high-resolution analysis of the immune response to VEEV in the brain and highlights potential avenues of investigation for therapeutics that target neuroinflammation in the brain. Author SummaryVenezuelan equine encephalitis virus (VEEV) causes brain inflammation in both animals and humans when transmitted by mosquito bite or infectious aerosols. The mechanisms underlying disease caused by VEEV, including the role of the immune response in brain pathology, are not well understood. Here we performed a comprehensive assessment of the immune response to VEEV in the brain over time using two advanced sequencing techniques. Following infection, immune cells infiltrate the brain in a sequential fashion and display different activation profiles. Different types of immune cells also display strikingly different spatial patterns throughout the brain. This study provides the most comprehensive description of the immune response to VEEV in the brain performed to date and advances our understanding of immune-driven neuropathology and identification of therapeutic targets.

immunology↗

bioRxiv2024

Human CCR4-NOT is a global regulator of gene expression and is a novel silencer of retrotransposon activation

CCR4-NOT regulates multiple steps in gene regulation and has been well studied in budding yeast, but much less is known about the human complex. Auxin-induced degradation was used to rapidly deplete the scaffold subunit CNOT1, and CNOT4, to characterize the functions of human CCR4-NOT in gene regulation. Depleting CNOT1 increased RNA levels and caused a widespread decrease in RNA decay. In contrast, CNOT4 depletion only modestly changed steady-state RNA levels and, surprisingly, led to a global acceleration in mRNA decay. Further, depleting either subunit resulted in a global increase in RNA synthesis. In contrast to most of the genome, the transcription of KRAB-Zinc-Finger-protein (KZNFs) genes, especially those on chromosome 19, was repressed. KZNFs are transcriptional repressors of retrotransposable elements (rTEs), and consistent with the decreased KZNFs expression, rTEs, mainly Long Interspersed Nuclear Elements (LINEs), were activated. These data establish CCR4-NOT as a global regulator of gene expression and a novel silencer of rTEs.

molecular biology↗

bioRxiv2024

Targeting DLK1 improves survival in patient-derived xenograft models of myeloid leukemia associated with Down syndrome

Children with Down syndrome have a markedly increased risk of developing myeloid leukemia (ML-DS). Although having an excellent prognosis, 10-20% develop relapsed or refractory disease with poor survival, highlighting the need for new targeted approaches. The pathogenesis of ML-DS is tightly linked to fetal hematopoiesis and mutations in GATA1, generating the truncated GATA1short(s) isoform. We identified Delta-like non-canonical Notch ligand 1 (DLK1) as a direct GATA1s target. DLK1, a paternally imprinted transmembrane protein, is highly expressed in fetal liver CD34 cells but absent in adult hematopoiesis, making it an attractive immunotherapeutic target. Chromatin profiling revealed GATA1s occupancy at a distal enhancer within the DLK1-DIO3 locus, driving aberrant DLK1 upregulation in ML-DS. Functional studies demonstrated that DLK1 is a leukemia dependency, as its genetic ablation impaired proliferation and engraftment, induced apoptosis, and altered Notch and {beta}-catenin signaling. Therapeutically, a DLK1-directed antibody-drug conjugate (DLK1-ADC) induced selective cytotoxicity, abrogated colony formation, and significantly prolonged survival in refractory ML-DS PDX models, achieving durable remissions at higher doses. These findings establish DLK1 as a leukemia-specific vulnerability and provide preclinical proof-of-concept for DLK1-targeted therapies in ML-DS and other leukemias with fetal-like expression programs. Key PointsO_LIDLK1 is a GATA1s-driven leukemia dependency in ML-DS, linking fetal hematopoietic programs to leukemic stemness and refractory disease. C_LIO_LITherapeutic targeting of DLK1 with an antibody-drug conjugate selectively eradicates leukemia cells and prolongs survival in ML-DS PDX models C_LI

cancer biology↗

bioRxiv2024

Early immune response to Coccidioides is characterized by robust neutrophil and fibrotic macrophage recruitment and differentiation

Coccidioidomycosis, or Valley fever, is an emerging respiratory disease caused by soil dwelling fungi of the Coccidioides genus that is expected to spread from the southwest into the central U.S. by 2050. While 60% of infections are asymptomatic, the other 40% of patients experience a range of symptoms, from self-limiting pneumonia to life-threatening disseminated disease. The immunological events that underlie the progression to severe disease remain under defined. Here, we probed the early immune response to Coccidioides using a high dose of an attenuated strain of C. posadasii in a mouse model of infection coupled with single-cell RNA sequencing. At 24 hours post-infection, robust immune infiltration is detected in the lung, marked by high levels of inflammatory PD-L1+ neutrophils and fungal-contact dependent pro-fibrotic Spp1+ macrophages. These findings elucidate the early dynamics of the host response to Coccidioides and provide a deeper understanding of host-pathogen interactions in the lung. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/609001v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@198a77forg.highwire.dtl.DTLVardef@11c9207org.highwire.dtl.DTLVardef@b71257org.highwire.dtl.DTLVardef@115447d_HPS_FORMAT_FIGEXP M_FIG C_FIG ImportanceBy examining early immune dynamics in the lungs, we uncover critical insights into how myeloid cells, particularly neutrophils and macrophages, are recruited and differentiated during Coccidioides infection. The discovery of specific immune cell subsets, such as PD-L1+ neutrophils and Spp1+ macrophages, which are associated with inflammation and fibrosis, highlights potential targets for therapeutic intervention. These findings provide a deeper understanding of the host-pathogen interactions that occur during Coccidioides infection, offering valuable directions for developing more effective treatments and preventive strategies against this increasingly prevalent disease.

immunology↗

bioRxiv2024

Spatiotemporal Analysis of Lung Immune Dynamics in Lethal Coccidioides posadasii Infection

Coccidioidomycosis, or Valley Fever, is a lung disease caused by inhalation of Coccidioides fungi, prevalent in the Southwestern U.S., Mexico, and parts of Central and South America. 350,000 cases are reported annually in the U.S., although that number is expected to increase as climate change expands fungal geographic range. While 60% of infections are asymptomatic, the symptomatic 40% are often misdiagnosed due to similarities with bronchitis or pneumonia. A small subset of infection progress to severe illness, necessitating a better understanding of immune responses during lethal infection. Using single-cell RNA sequencing and spatial transcriptomics, we characterized lung responses during Coccidioides infection. We identified monocyte-derived Spp1-expressing macrophages as potential mediators of tissue remodeling and fibrosis, marked by high expression of profibrotic and proinflammatory transcripts. These macrophages showed elevated TGF-{beta} and IL-6 signaling, pathways involved in fibrosis pathogenesis. Additionally, we observed significant neutrophil infiltration and defective lymphocyte responses, indicating severe adaptive immunity dysregulation in lethal, acute infection. These findings enhance our understanding of Coccidioides infection and suggest new therapeutic targets. ImportanceCoccidioidomycosis, commonly known as Valley Fever, is a lung disease caused by the inhalation of Coccidioides fungi, which is prevalent in the Southwestern U.S., Mexico, and parts of Central and South America. With climate change potentially expanding the geographic range of this fungus, understanding the immune responses during severe infections is crucial. Our study used advanced techniques to analyze lung responses during Coccidioides infection, identifying specific immune cells that may contribute to tissue damage and fibrosis. These findings provide new insights into the disease mechanisms and suggest potential targets for therapeutic intervention, which could improve outcomes for patients suffering from severe Valley Fever.

immunology↗

bioRxiv2024

Single cell RNA sequencing reveals a shift in cell function and maturation of endogenous and infiltrating cell types in response to acute intervertebral disc injury

Intervertebral disc (IVD) degeneration contributes to disabling back pain. Degeneration can be initiated by injury, and progressively leads to irreversible cell loss and loss of IVD function. Attempts to restore IVD function through cell replacement therapies have had limited success due to knowledge gaps in the critical cell populations and molecular crosstalk after injury. Here, we used single cell RNA sequencing to identify the transcriptional changes of endogenous cells of the IVD and infiltrating cell populations following IVD injury. Control and Injured coccygeal IVDs were extracted from 12 week old female C57BL/6J mice 7 days post injury and subjected to single-cell resolution transcriptomic sequencing. Clustering, gene ontology, and pseudotime trajectory analyses determined transcriptomic divergences in the cells of the Injured IVD, flow cytometry identified they types of infiltrating immune cells, and immunofluorescence was utilized to define mesenchymal stem cell (MSC) localization. Clustering analysis revealed 11 distinct cell populations that included IVD, immune, vascular cells, and MSCs. Differential gene expression analysis determined that Outer Annulus Fibrosus, Neutrophils, Saa2-High MSCs, Macrophages, and Krt18+ Nucleus Pulposus (NP) cells were the major drivers of transcriptomic differences between Control and Injured cells. Gene ontology revealed that the most upregulated biological pathways were angiogenesis and T cell-related while wound healing and ECM regulation categories were downregulated. Pseudotime trajectory analyses revealed that IVD injury directed cells towards increased differentiation in all clusters, except for Krt18+ NP cells which remained in a less mature cell state. Saa2-High and Grem1-High MSCs populations drifted towards more differentiated IVD cells profiles with injury and localized distinctly within the IVD. This study revealed novel MSC populations in a heterogeneous landscape of IVD cell populations during injury, and these cells may be leveraged for future IVD repair studies. Lay SummaryThe intervertebral disc (IVD) is a spinal joint that accumulates damage with age but has limited tissue repair capabilities. IVD injuries progress into degeneration, and IVD degeneration is a leading cause of lower back pain. Understanding the cell populations that change and respond to injury will uncover targets to restore IVD function. Mesenchymal stem cells (MSCs) are cells within the IVD that can potentially replenish the cells lost after IVD damage. To better understand how IVD cell populations are affected by tissue damage, we performed single cell RNA sequencing of IVD tissue 7 days post injury and analyzed the differences in gene regulation. We identified diverse cells populations such as IVD, immune cells, vascular cells, and MSCs. We discovered the presence of Saa2 and Grem1 expressing MSCs that become less stem cell-like and express higher levels of IVD gene markers after injury. We also determined that Saa2 and Grem1 have varying gene expression patterns in IVD tissues that becomes attenuated after injury. These MSCs could be targeted for future stem cell therapies to prevent IVD degeneration.

cell biology↗

bioRxiv2024

Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections

Twister ribozymes are an extensively studied class of nucleolytic RNAs. Thousands of natural twisters have been proposed using sequence homology and structural descriptors. Yet, most of these candidates have not been validated experimentally. To address this gap, we developed CHiTA (Cleavage High-Throughput Assay), a high-throughput pipeline utilizing massively parallel oligonucleotide synthesis and next-generation sequencing to test putative ribozymes en masse in a scarless fashion. As proof of principle, we applied CHiTA to a small set of known active and mutant ribozymes. We then used CHiTA to test two large sets of naturally occurring twister ribozymes: over 1, 600 previously reported putative twisters and [~]1, 000 new candidate twisters. The new candidates were identified computationally in [~]1, 000 organisms, representing a massive increase in the number of ribozyme-harboring organisms. Approximately 94% of the twisters we tested were active and cleaved site-specifically. Analysis of their structural features revealed that many substitutions and helical imperfections can be tolerated. We repeated our computational search with structural descriptors updated from this analysis, whereupon we identified and confirmed the first intrinsically active twister ribozyme in mammals. CHiTA broadly expands the number of active twister ribozymes found in nature and provides a powerful method for functional analyses of other RNAs. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/603121v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@a9cc05org.highwire.dtl.DTLVardef@1917d6dorg.highwire.dtl.DTLVardef@c1a5ddorg.highwire.dtl.DTLVardef@1706f54_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Global Release of Translational Repression Across Plasmodiums Host-to-Vector Transmission Event

Malaria parasites must be able to respond quickly to changes in their environment, including during their transmission between mammalian hosts and mosquito vectors. Therefore, before transmission, female gametocytes proactively produce and translationally repress mRNAs that encode essential proteins that the zygote requires to establish a new infection. This essential regulatory control requires the orthologues of DDX6 (DOZI), LSM14a (CITH), and ALBA proteins to form a translationally repressive complex in female gametocytes that associates with many of the affected mRNAs. However, while the release of translational repression of individual mRNAs has been documented, the details of the global release of translational repression have not. Moreover, the changes in spatial arrangement and composition of the DOZI/CITH/ALBA complex that contribute to translational control are also not known. Therefore, we have conducted the first quantitative, comparative transcriptomics and DIA-MS proteomics of Plasmodium parasites across the host-to-vector transmission event to document the global release of translational repression. Using female gametocytes and zygotes of P. yoelii, we found that nearly 200 transcripts are released for translation soon after fertilization, including those with essential functions for the zygote. However, we also observed that some transcripts remain repressed beyond this point. In addition, we have used TurboID-based proximity proteomics to interrogate the spatial and compositional changes in the DOZI/CITH/ALBA complex across this transmission event. Consistent with recent models of translational control, proteins that associate with either the 5 or 3 end of mRNAs are in close proximity to one another during translational repression in female gametocytes and then dissociate upon release of repression in zygotes. This observation is cross-validated for several protein colocalizations in female gametocytes via ultrastructure expansion microscopy and structured illumination microscopy. Moreover, DOZI exchanges its interaction from NOT1-G in female gametocytes to the canonical NOT1 in zygotes, providing a model for a trigger for the release of mRNAs from DOZI. Finally, unenriched phosphoproteomics revealed the modification of key translational control proteins in the zygote. Together, these data provide a model for the essential translational control mechanisms used by malaria parasites to promote their efficient transmission from their mammalian host to their mosquito vector.

microbiology↗

bioRxiv2023

Vhl deletion in Dmp1-expressing cells alters MEP metabolism and promotes stress erythropoiesis

In recent years, general hypoxia-inducible factor (HIF)-prolyl hydroxylase (PHD) enzyme inhibitors have been developed for the treatment of anemia due to renal disease and osteoporosis. However, it remains a challenge to target the HIF signaling pathway without dysregulating the skeletal and hematopoietic system. Here, we examined the effects of Vhl deletion in bone by performing longitudinal analyses of VhlcKO mice at 3, 6, 10, and 24 weeks of age, where at 10 and 24 weeks of age, high bone mass and splenomegaly are present. Using flow cytometry, we observed increased frequency (%) of CD71loTER119hiFSClo orthochromatophilic erythroblasts and reticulocytes in 10- and 24-week-old VhlcKO bone marrow (BM), which correlated with elevated erythropoietin levels in the BM and increased number of red blood cells in circulation. The absolute numbers of myeloerythroid progenitors (MEPs) in the BM were significantly reduced at 24 weeks. Bulk RNA-Seq of the MEPs showed upregulation of Epas1 (Hif1a) and Efnb2 (Hif2a) in VhlcKO MEPs, consistent with a response to hypoxia, and genes involved in erythrocyte development, actin filament organization, and response to glucose. Additionally, histological analysis of VhlcKO spleens revealed red pulp hyperplasia and the presence of megakaryocytes, both of which are features of extramedullary hematopoiesis (EMH). EMH in the spleen was correlated with the presence of mature stress erythroid progenitors, suggesting that stress erythropoiesis is occurring to compensate for the BM microenvironmental irregularities. Our studies implicate that HIF-driven alterations in skeletal homeostasis can accelerate erythropoiesis. Key Points* Dysregulation of HIF signaling in Dmp1+ bone cells induces stress erythropoiesis. * Skeletal homeostasis modulates erythropoiesis.

physiology↗

bioRxiv2023

Long-Read Genome Assembly and Gene Model Annotations for the Rodent Malaria Parasite Plasmodium yoelii 17XNL

Malaria causes over 200 million infections and over 600 thousand fatalities each year, with most cases attributed to a human-infectious Plasmodium species, Plasmodium falciparum. Many rodent-infectious Plasmodium species, like Plasmodium berghei, Plasmodium chabaudi, and Plasmodium yoelii, have been used as genetically tractable model species that can expedite studies of this pathogen. In particular, P. yoelii is an especially good model for investigating the mosquito and liver stages of parasite development because key attributes closely resemble those of P. falciparum. Because of its importance to malaria research, in 2002 the 17XNL strain of P. yoelii was the first rodent malaria parasite to be sequenced. While sequencing and assembling this genome was a breakthrough effort, the final assembly consisted of >5000 contiguous sequences that impacted the creation of annotated gene models. While other important rodent malaria parasite genomes have been sequenced and annotated since then, including the related P. yoelii 17X strain, the 17XNL strain has not. As a result, genomic data for 17X has become the de facto reference genome for the 17XNL strain while leaving open questions surrounding possible differences between the 17XNL and 17X genomes. In this work, we present a high-quality genome assembly for P. yoelii 17XNL using HiFi PacBio long-read DNA sequencing. In addition, we use Nanopore long-read direct RNA-seq and Illumina short-read sequencing of mixed blood stages to create complete gene models that include not only coding sequences but also alternate transcript isoforms, and 5 and 3 UTR designations. A comparison of the 17X and this new 17XNL assembly revealed biologically meaningful differences between the strains due to the presence of coding sequence variants. Taken together, our work provides a new genomic and gene expression framework for studies with this commonly used rodent malaria model species.

microbiology↗

bioRxiv2022

The clock gene Per1 expression may exert diurnal control over hippocampal memory consolidation

The circadian system influences many different biological processes, including memory performance. While the suprachiasmatic nucleus (SCN) functions as the brains central pacemaker, satellite clocks have also been identified in other brain regions, such as the memory-relevant dorsal hippocampus. Although it is unclear how these satellite clocks contribute to brain function, one possibility is that they may serve to exert diurnal control over local processes. Within the hippocampus, for example, the local clock may contribute to time-of-day effects on memory. Here, we used the hippocampus-dependent Object Location Memory task to determine how memory is regulated across the day/night cycle in mice. First, we systematically determined which phase of memory (acquisition, consolidation, or retrieval) is modulated across the 24h day. We found that mice show better long-term memory performance during the day than at night, an effect that was specifically attributed to diurnal changes in memory consolidation, as neither memory acquisition nor memory retrieval fluctuated across the day/night cycle. Using RNA-sequencing we identified the circadian clock gene Period1 (Per1) as a key mechanism capable of supporting this diurnal fluctuation in memory consolidation, as Per1 oscillates in tandem with memory performance. We then show that local knockdown of Per1 within the dorsal hippocampus has no effect on either the circadian rhythm or sleep behavior, although previous work has shown this manipulation impairs memory. Thus, Per1 may independently function within the dorsal hippocampus to regulate memory in addition to its known role in regulating the circadian rhythm within the SCN. Per1 may therefore exert local diurnal control over memory consolidation within the dorsal hippocampus.

neuroscience↗

bioRxiv2021

MAVS mediates a protective immune response in the brain to Rift Valley fever virus

Rift Valley fever virus (RVFV) is a highly pathogenic mosquito-borne virus capable of causing hepatitis, encephalitis, blindness, hemorrhagic syndrome, and death in humans and livestock. Upon aerosol infection with RVFV, the brain is a major site of viral replication and tissue damage, yet pathogenesis in this organ has been understudied. Here, we investigated the immune response in the brain of RVFV infected mice. In response to infection, microglia initiate robust transcriptional upregulation of antiviral immune genes, as well as increased levels of activation markers and cytokine secretion that is dependent on mitochondrial antiviral-signaling protein (MAVS) and independent of toll-like receptors 3 and 7. In vivo, Mavs-/- mice displayed enhanced susceptibility to RVFV as determined by increased brain viral burden and higher mortality. Single-cell RNA sequence analysis identified microglia-specific defects in type I interferon and interferon responsive gene expression in Mavs-/- mice, as well as dysregulated lymphocyte infiltration. The results of this study provide a crucial step towards understanding the precise molecular mechanisms by which RVFV infection is controlled in the brain and will help inform the development of vaccines and antiviral therapies that are effective in preventing encephalitis. Author SummaryRift Valley fever virus causes severe disease in humans and livestock and in some cases can be fatal. There is concern about the use of Rift Valley fever virus as a bioweapon since it can be transmitted through the air, and there are no vaccines or antiviral treatments. Airborne transmission of the virus causes severe inflammation of the brain, yet little is known about the immune response against the virus in this organ. Here, we investigated the immune response in the brain to Rift Valley fever virus following intranasal infection. We determined that microglia, the resident immune cells of the brain, initiate a robust response to Rift Valley fever virus infection and identified a key immune pathway that is critical for the ability of microglia to respond to infection. When this immune pathway is rendered non-functional, mice have a dysregulated response to infection in the brain. This study provides insight into how the immune response can control Rift Valley fever virus infection of the brain.

immunology↗

bioRxiv2021

The Plasmodium NOT1-G Paralogue Acts as an Essential Nexus for Sexual Stage Maturation and Parasite Transmission

Productive transmission of malaria parasites hinges upon the execution of key transcriptional and post-transcriptional regulatory events. While much is now known about how specific transcription factors activate or repress sexual commitment programs, far less is known about the production of a preferred mRNA homeostasis following commitment and through the host-to-vector transmission event. Here we show that Plasmodium parasites have taken the unique approach to duplicate the NOT1 scaffold protein of the CAF1/CCR4/Not complex in order to dedicate one paralogue for essential transmission functions. Moreover, this NOT1-G paralogue is central to the sex-specific functions previously associated with its interacting partners, as deletion of not1-g in Plasmodium yoelii leads to a comparable or complete arrest phenotype for both male and female parasites. We show that, consistent with its role in other eukaryotes, PyNOT1-G localizes to cytosolic puncta throughout much of the Plasmodium life cycle. PyNOT1-G is essential to both the complete maturation of male gametes and to the continued development of the fertilized zygote originating from female parasites. Comparative transcriptomics of wild-type and pynot1-g- parasites shows that loss of PyNOT1-G leads to transcript dysregulation preceding and during gametocytogenesis, and shows that PyNOT1-G acts to preserve mRNAs that are critical to sexual and early mosquito stage development. Finally, we demonstrate that the tristetraprolin-binding domain, which acts as the typical organization platform for RNA decay (TTP) and RNA preservation (ELAV/HuR) factors is dispensable for PyNOT1-Gs essential blood stage functions but impacts host-to-vector transmission. Together, we conclude that Plasmodium has created and adapted a NOT1-G paralogue to fulfill the complex transmission requirements of both male and female parasites.

microbiology↗