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Biology subjects

Chen, C.-H.

Publications and source records attributed to Chen, C.-H..

At least 19 recordsLinked to original sources

Harnessing historical collections to reconstruct the invasion history of Microstegium vimineum (Poaceae)

The evolutionary processes underlying successful invasions are often difficult to disentangle. Historical collections provide a temporal perspective, offering great potential to reconstruct invasion histories and identify the processes driving invasions. Japanese stiltgrass (Microstegium vimineum) is an invasive C4 grass introduced to eastern North America over a century ago and now established in 31 USA states. To reconstruct its invasion history, we leveraged low-coverage whole-genome sequencing of 142 herbarium and 330 contemporary samples spanning the temporal and spatial extent of the North American invasion and the native range in Asia. We identified three independent introductions in the USA: an awnless form in the South and two independent introductions of awned forms in the North, with limited admixture among introductions across space and time. In both regions, we observed high genetic diversity in the earliest available collections despite demographic bottlenecks and identified several putative selective sweeps in or near flowering-time genes, suggesting rapid evolution in the introduced range. Our analyses support separate invasions in the USA, likely facilitated by standing genetic variation and selection, but provide little support for admixture playing a major role. Our study highlights the power of historical collections to uncover the processes and mechanisms underlying successful biological invasions.

evolutionary biology↗

ALDH1B1 promotes mitochondrial γ-butyrobetaine biosynthesisand fatty acid oxidation in colorectal cancer

Metabolic reprogramming is a hallmark of cancer cells, and stem-like populations often upregulate aldehyde dehydrogenases (ALDHs). Functional studies have established essential roles for individual ALDH isoforms in tumor initiation, progression, and metastasis; however, the mechanisms by which these enzymes promote malignancy remain poorly understood. Here we show that aldehyde dehydrogenase 1B1 (ALDH1B1), a mitochondrial enzyme highly expressed in colorectal cancer (CRC) and pancreatic ductal adenocarcinoma (PDAC), generates {gamma}-butyrobetaine (GBB) and {gamma}-aminobutyric acid (GABA) in CRC cells. The biosynthesis of both aminocarboxylic acids has been attributed to the cytosolic enzyme ALDH9A1, and we demonstrate that mitochondrial GBB and GABA are functionally distinct from the cytosolic pools of these metabolites. We further demonstrate that mitochondrial GBB can function as an antiport substrate of carnitine-acylcarnitine translocase (CACT), the transporter that mediates fatty acid uptake into the mitochondrial inner matrix. This activity complements the role of cytosolic GBB as the biosynthetic precursor to carnitine. Accordingly, ALDH1B1 can markedly enhance mitochondrial fatty acid oxidation (FAO), a catabolic process that has been linked to CRC and PDAC stemness, progression, and metastasis. Our findings reveal an unexpected role for ALDH1B1 in carnitine metabolism, GABA biosynthesis, and FAO and illustrate how the compartmental reprogramming of metabolic pathways can promote tumor growth.

cancer biology↗

Pancreatic cancer fibrosis activates protumorigenic Schwann cells through a nuclear mechanosensing mechanism.

BackgroundFibrosis and tumor innervation are two features of the tumor microenvironment (TME) that contribute directly to the lethality of pancreatic ductal adenocarcinoma (PDAC), but their potential interactions have not been explored. Moreover, although it is known that activated Schwann cells (SCs) stimulate cancer cell invasion, it remains unclear how SCs are activated. ObjectiveWe determined how SCs are activated in the pancreatic fibrotic microenvironment. DesignThe correlation between physical features of the microenvironment and SC activation was assessed in human patient samples and in mice by SC c-Jun phosphorylation monitoring, atomic force microscopy and multiphoton live imaging. Several in vitro models in which forces were applied to SCs expressing a reporter for c-Jun phosphorylation and RNA-Seq analysis were used to decipher the cellular and molecular mechanisms of SC activation. ResultsNerves surrounded by stiff stroma present higher SC activation. Intravital imaging shows a matrix dependent SC activation. Mechanical forces on SCs induce c-Jun phosphorylation in SCs in a non-canonical manner that involves a nuclear sensing machinery with the proinflammatory enzyme Phospholipase A2. ConclusionFibrosis enhances the protumorigenic impact of innervation by activating SCs via a mechanism in which nuclear compression triggers non-canonical activation of the AP-1 transcription factor complex. Pancreatic fibrosis alone, without cancer cells, is sufficient to activate SCs, suggesting this mechanism may be common across non-malignant pancreatic diseases. Notably, SCs are more sensitive to mechanical activation than PDAC cells. These findings reveal TME interactions that may guide future microenvironment-targeted PDAC therapies. What is already known on this topicThe pancreatic cancer tumor microenvironment is highly innervated and fibrotic, two components of the tumor microenvironment that regulate tumorigenesis. How they impact each other is unknown. Schwann cells have emerged as a significant protumorigenic player, but the triggers of Schwann cell activation remain undefined. What this study addsWe establish that fibrosis induces Schwann cell activation and characterize the mechanism by which it occurs. We uncovered a mechanical mode of action that deforms nuclear membrane and activates c-Jun in Schwann cells, which contradicts the traditional view of c-Jun activation through a stimulus detected at the plasma membrane. How this study might affect research, practice or policyThis study provides a better understanding of the biology of pancreatic ductal adenocarcinoma and supports the development of novel precision therapies that target the fibrotic microenvironment to impact the protumorigenic effect of tumor innervation.

cancer biology↗

Adaptive sampling-based enrichment enables genome reconstruction of intracellular symbionts despite host background and reference divergence

Recovering genomes of intracellular microbes from host-dominated samples remains a major challenge in microbial genomics, due to low target abundance, overwhelming host DNA, and the inability to culture these organisms independently. Despite extensive interest in Wolbachia, efficient genome recovery directly from host tissues remains limited by the inefficiency of host-dominated sequencing and the constraints of existing enrichment strategies. Here, we demonstrate that Oxford Nanopore adaptive sampling (AS) enables efficient, real-time enrichment of target DNA directly from complex host tissues, providing a culture-free approach for genome recovery in such systems. To our knowledge, this represents the first application of enrichment-mode adaptive sampling to achieve de novo reconstruction of an intracellular endosymbiont genome in a mosquito system. Using Aedes aegypti mosquitoes infected with a locally derived wAlbB-like strain, we applied enrichment-mode AS to selectively sequence Wolbachia DNA. This resulted in an increase from <1% Wolbachia reads in conventional shotgun data to [~]90% under adaptive sampling. De novo assembly of AS-enriched long reads yielded a near-complete genome ([~]1.5 Mb) in two contigs with >96-99% completeness. Comparative analyses revealed multiple large-scale chromosomal rearrangements relative to the reference wAlbB genome, demonstrating that adaptive sampling does not impose reference-dependent genome structure. Annotation further identified three prophage-associated regions, including two strain-specific expansions absent from the reference genome. Notably, cytoplasmic incompatibility genes (cifA and cifB) were identified adjacent to one of these regions, consistent with their known genomic association with prophage elements. Importantly, adaptive sampling remained effective despite substantial structural divergence between the reference and target genomes, revealing an unexpectedly robust application of this approach beyond its presumed operating conditions. Together, these results establish enrichment-mode adaptive sampling as a robust and scalable strategy for genome-resolved analysis of intracellular bacteria in host-associated systems.

genomics↗

Structural determination of the HIV-1 Variable Region 3 epitope of antibody 19b

The HIV-1 Envelope (Env) in its pre-receptor "closed" conformation is targeted by broadly neutralizing antibodies (bnAbs), while its receptor-bound "open" conformation, exposes immunodominant epitopes targeted by non-neutralizing antibodies. A human immunoglobin G (IgG) monoclonal antibody (mAb), 19b, binds an Env third variable (V3) loop epitope that is only exposed in the open Env conformation. Despite widespread use of 19b to detect the open Env conformation in immunoassays, its epitope has not yet been structurally defined. Here we determine crystal structures of ligand-free and V3 peptide-bound 19b Fab to visualize details of this interaction. 19b utilizes both its heavy and light chains to interact with the V3 loop. The 5-residue heavy chain complementarity-determining region (CDR H3) facilitates a hydrophobic pocket for V3 residues to associate with. 19b adopts a cradle binding mode with its CDRH1, CDRL2 and CDRL3 mediating interactions with V3 regions that flank the conserved GPGR/Q motif, without making substantial contacts with the GPGR arch region. Our high-resolution structures by elucidating the epitope, binding mode and the structural basis for the broad reactivity of 19b, fill a gap in our knowledge of a reagent that is widely used in immunoassays.

biochemistry↗

Synaptic MEMOIR: mapping individual synapses of neurons with protein barcodes

Obtaining wiring diagrams of brains has been a major achievement for neuroscience. However, an underlying challenge in connectomics is the fundamental tradeoff between the imaging resolution needed to resolve synapses and the volume of the brain that can be imaged. For example, electron microscopy (EM) visualizes synaptic sites with ~5 nm resolution, but is difficult to scale beyond volumes of 1 mm3. Here, we present Synaptic MEMOIR (Memory with Engineered Mutagenesis with Optical in situ Readout) that enables imaging of neuronal projections in animal brains with single-synapse resolution. Synaptic MEMOIR is built around three key design features. First, protein barcodes are transported to synapses to allow matching of synaptic barcodes to cell body barcodes without high resolution imaging and the error-prone process of tracing neuronal processes across long distances. Second, Synaptic MEMOIR uses continuous mutagenesis to generate a large diversity of barcodes to uniquely label cell bodies and synapses. Last, the timing of recombination and transport can be tuned to record synaptic age or projection information. Combining these features, we demonstrated projection mapping of 113 neurons in the Drosophila melanogaster optic lobe in a volume of 9.5 million m3. Because synapses are identified by transported barcodes with optical microscopy at 300 nm resolution, this approach can potentially scale to much larger volumes, similar at least to those imaged in recent mouse brain transcriptomics atlases. In addition, synaptic MEMOIR can match barcodes across brain sections, and does not require tissue clearing to track long-range projections. Together, these results provide the foundation for a scalable optical image-based system for reconstructing the neural wiring diagrams of brains across different developmental stages, genetic backgrounds and perturbations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=46 SRC="FIGDIR/small/690442v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@8363cdorg.highwire.dtl.DTLVardef@d3240org.highwire.dtl.DTLVardef@5e2793org.highwire.dtl.DTLVardef@1784f2a_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

Cerebral cortical structures linked to intelligence

Understanding the neural basis of intelligence in humans remains an ongoing scientific pursuit. Early studies with small samples identified potential regions but lacked consistency across findings. Recent large-scale magnetic resonance imaging (MRI) datasets, using intelligence measures focused on verbal-numerical reasoning, now offer more robust opportunities for discovery. In this study (N=11,289), we showed the dorsolateral prefrontal cortex as exhibiting the strongest effect size and a significant causal relationship with intelligence, where larger surface area predicts higher intelligence as revealed by Mendelian randomization analyses. Additional regions, including the orbitofrontal and temporal cortices, also showed causal links to intelligence. These regions are critical for working memory, executive function, and language. Reverse causality analyses further indicated that higher intelligence contributes to increased total surface area and greater cortical thickness in the perisylvian language region. Our findings replicate prior evidence of a bidirectional relationship between total surface area and intelligence and further offer novel insights into regional cortical associations and causal effect. Collectively, these findings support a polyregional cortical configuration of intelligence, highlighting the dorsolateral prefrontal cortex--a key hub for cognitive ability.

neuroscience↗

Restraint of TGFβ family signaling by SMAD7 is necessary for hematopoietic stem cell maturation in the embryo.

Hematopoietic stem cells (HSCs), defined as cells that can engraft an adult when transplanted, mature from precursors (pre-HSCs) that differentiate from hemogenic endothelial cells (HECs) in the embryo. Many signaling pathways required to generate the first hematopoietic stem and progenitor cells in the embryo are well-characterized, but how HSCs mature from pre-HSCs is poorly understood. Here we show that "mothers against decapentaplegic homolog 7" (SMAD7), a negative regulator of transforming growth factor beta (TGF{beta}) and bone morphogenetic protein (BMP) signaling, is required for pre-HSC to HSC maturation. Deletion of Smad7 in endothelial cells allows the formation of pre-HSCs from HECs but impairs their maturation into HSCs. The data indicate that although TGF{beta} and BMP signaling are required for the generation of HECs and for HECs to undergo an endothelial-to-hematopoietic transition to generate pre-HSCs, one or both pathways must be subsequently down-regulated for effective pre-HSC to HSC maturation.

developmental biology↗

CASTLE: a training-free foundation-model pipeline for cross-species behavioral classification

Accurately and efficiently quantifying animal behavior at scale without intensive manual labeling is a long-standing challenge for neuroscience and ethology. Keypoint-based tracking emphasizes simplicity and efficiency but loses the richness of posture and context, while emerging foundation models capture pixel-level details, yet often require nontrivial efforts of retraining and can be more sensitive to backgrounds or lighting. Here, we present CASTLE, a training-free pipeline that addresses all these issues by synergistically combining foundation models for segmentation, tracking, and feature extraction. By isolating regions-of-interest (ROI), CASTLE first generates "focused (ROI-masked)" and orientation-invariant latent features, capturing rich postural details in zero-shot, fine-tuning-free manners. Following ROI isolation, CASTLE, through an interactive "Behavior Microscope" module, supports hierarchical clustering, for progressive, human-in-the-loop embedding and clustering. This enables raw-image-assisted discovery of behavioral classes without predefined categories. Across mice, Drosophila and C. elegans, CASTLE matches expert class annotations (>90%), reveals disease-relevant phenotypes in Parkinsonian mouse models. By eliminating purpose-specific model training and providing a raw-image-informed accessible workflow, CASTLE offers a scalable framework for interpretable, cross-species behavioral phenotyping.

neuroscience↗

An Enantioselective Chemical Probe for Chikungunya nsP2 Helicase with Antialphaviral Activity

Chikungunya virus (CHIKV) replication relies on the multifunctional nsP2 protein, making it an attractive target for antiviral drug discovery. Here, we report the resolution of oxaspiropiperidine 1, a first-in-class inhibitor of the CHIKV nsP2 RNA helicase (nsP2hel), into its constitutive enantiomers and characterization of their antiviral activity. The enantiomer (R)-1 exhibited potent inhibition of viral replication, nsP2hel ATPase activity, and dsRNA unwinding, while the (S)-1 enantiomer was >100-fold less active. The (R)-1 enantiomer also demonstrated high selectivity for CHIKV over other RNA viruses and for nsP2hel over other RNA helicases. Direct binding of (R)-1 to nsP2hel protein was confirmed by 19F NMR. Biophysical and structural studies revealed conformational polymorphism in the spirocyclic scaffold of (R)-1, suggesting a potential role of thermal mobility of the ligand in allosteric inhibition of nsP2hel. Collectively, these findings designate (R)-1 (RA-NSP2-1) as a high-quality chemical probe and (S)-1 (RA-NSP2-1N) as a negative control for probing the biology of alphavirus RNA helicases.

pharmacology and toxicology↗

Brainstem circuit for sickness-induced sleep

Increased sleep induced by immune activation plays a crucial role in facilitating recovery from illness. However, the neural mechanisms underlying sickness-induced sleep remain poorly understood. Here, we identify a brainstem circuit originating in the nucleus of the solitary tract (NST) that mediates sickness-induced sleep. Using activity-dependent genetic labeling, we tagged NST neurons activated by lipopolysaccharide (LPS) injection and showed that their chemogenetic activation strongly promotes non-rapid eye movement (NREM) sleep. These NST neurons project extensively to the parabrachial nucleus (PB), where LPS-activated neurons also promote NREM sleep. Fiber photometry imaging of several wake-promoting neuromodulators using their biosensors showed that evoked norepinephrine (NE) release from locus coeruleus (LC) neurons is markedly reduced by either LPS injection or direct activation of NST or PB sickness neurons. These results suggest that sickness-induced sleep is mediated in part by a brainstem circuit that regulates neuromodulator signaling.

neuroscience↗

An epigenetic basis for sustained inflammatory epithelial progenitor cell states in Crohn's disease

Defining consequential differences in intestinal epithelial stem cells in healthy humans versus those with inflammatory bowel disease (Crohns disease and ulcerative colitis) is essential for the development of much needed therapies to restore the epithelial barrier and maintain its fidelity. Employing single cell transcriptomic/epigenomic approaches and colonoid models from children and adults with Crohns disease led us to identify an inflammatory secretory progenitor (ISP) cell state present almost exclusively in patients with Crohns disease compared to control subjects. ISPs exhibit gene expression profiles consistent with normal secretory progenitor cells but concomitantly express a suite of distinguishing pro-inflammatory genes. Mechanistically, ISPs exhibit open chromatin and gene expression of ISP signature genes. While these ISP-specific genes are not expressed in intestinal stem cells, their chromatin is accessible in Crohns disease stem cells suggesting that ISP genes are epigenetically poised in stem cells and are transcriptionally activated in ISP cells in the presence of inflammatory stimuli. Consistently, Crohns disease colonoids exhibit sustained ISP gene expression that can be elicited further with pro-inflammatory cytokines or via co-culture with pro-inflammatory macrophages. In summary, we define differences in the epithelial stem and progenitor compartment of patients with Crohns disease suggesting aberrant stem cell differentiation and inflammatory gene expression arises during disease. HIGHLIGHTSO_LIWe identify an inflammatory secretory progenitor cell state in endoscopically non-inflamed tissue from pediatric and adult patients with Crohns disease. C_LIO_LICrohns disease epithelial stem and progenitor cells display increased chromatin accessibility preceding the emergence of inflammatory secretory progenitor cell states. C_LIO_LICrohns disease colonoids from non-inflamed regions contain inflammatory secretory progenitor cells in the absence of inflammatory stimuli C_LIO_LIInflammatory secretory progenitor cells expand in colonoid culture in response to cytokine stimulation or co-culture with pro-inflammatory macrophages C_LI

physiology↗

Living xylem cells encode a large number of conserved gene families responsible for vascular sap peptides

Plant long-distance signaling peptides travel through the vascular system to coordinate development and respond to environmental cues, yet their precursor genes and expression origins remain elusive. We characterized 4,804 sap peptide precursor genes in Populus trichocarpa using an integrated approach that combined liquid chromatography tandem mass spectrometry (LC-MS/MS) peptidomics, transcriptomics, and comparative genomics. This study expands the known precursor families from approximately 50 to thousands, the majority of which are conserved across angiosperms. Transcriptome analysis across xylem developmental stages revealed that living xylem cells, typically viewed as precursors to non-living structures, predominantly express these specifically at transitions between primary and secondary growth stages, indicating an active role in plant-wide signaling coordination. The precursor genes show conservation at the transcriptome level and are under strong purifying selection. Our findings provide a comprehensive overview of the gene families encoding sap peptides, redefining xylem as an active participant in plant communication and adaptation.

plant biology↗

The Taiwan Precision Medicine Initiative: A Cohort for Large-Scale Studies

The Taiwan Precision Medicine Initiative (TPMI), a project initiated by the Academia Sinica in collaboration with 16 major medical centers around Taiwan, has recruited 565,390 participants who consented to provide DNA samples for genetic profiling and grant access to their electronic medical records (EMR) for studies to develop precision medicine. Access to the EMR is both retrospective and prospective, allowing researchers to conduct prospective studies over time. Genetic profiling is done with population-optimized SNP arrays for the Han Chinese populations that enable genetic analyses such as genome-wide association, phenome-wide association, and polygenic risk score studies to evaluate common disease risk and pharmacogenetic response. Furthermore, the TPMI participants agree to be contacted for future research opportunities related to their genetic risks and receive personalized genetic risk profiles with health management recommendations. TPMI has established the TPMI Data Access Platform (TDAP), a central database and analysis platform that both safeguards the security of the data and facilitates academic research. The TPMI is the largest non-European cohort that merges genetic profiles with EMR in the world. With a cohort that can be followed over time, it can be utilized to validate genetic risk prediction models, conduct clinical trials to show the efficacy of risk-based health management, and optimize health policies based on genetic risks. In this report, we describe the TPMI study design, the population and genetic characteristics of the TPMI cohort, and the power it provides to conduct crucial studies in developing precision medicine on a population and personal level. As Han Chinese represent almost 20% of the worlds population, the results of TPMI studies will benefit >1.4 billion people around the world and serve as a model for developing population-based precision medicine.

genetics↗

Evolutionary conserved sap peptides derived from xylem-specific peptide precursors in woody angiosperms

Peptides act as long-distance mobile signals, transported through vascular sap to coordinate complex developmental processes. Since the tissue-specificity of peptide precursor gene expression is critical in determining peptide signaling function, we integrated vascular sap peptidomes with tissue-level transcriptomes to investigate the roles of sap peptides in two economically important woody plants, Populus trichocarpa and Eucalyptus grandis. Xylem exhibited the highest ratio of tissue-specific sap peptide precursor genes. Most of the sap peptides derived from xylem-specific precursor genes of P. trichocarpa and E. grandis were highly conserved throughout woody species selected from different clades in angiosperms, including magnoliids, rosids and asterids in eudicots. To further explore the conservation of these peptides, we examined the sap peptidome of Cinnamomum kanehirae (camphor tree), from the ancient clade with three xylem cell types. Approximately 90% of the peptides from xylem-specific precursors that were conserved between P. trichocarpa and E. grandis, were also conserved in the vascular sap of C. kanehirae, demonstrating a remarkably high conservation of these peptides across woody angiosperms. Most of the sap peptides conserved in these three woody species are also highly conserved across land plants, suggesting that these peptides may contribute to plant terrestrialization. Within the sap peptides from xylem- specific precursor genes, a total of 10 peptides were identical across all three woody plants. This substantial enrichment of xylem-specific precursor-derived peptides, along with their high conservation, suggests that these long-distance mobile peptides play a crucial role in secondary xylem development. One sentence summaryIntegration of sap peptidomic and tissue-level transcriptomic data revealed highly conserved long-distance mobile peptides derived from xylem- specific precursors across woody angiosperms.

evolutionary biology↗

Transcriptome analysis of Drosophila suzukii reveals molecular mechanisms conferring pyrethroid and spinosad resistance

Drosophila suzukii lay eggs in soft-skinned, ripening fruits, making this insect a serious threat to berry production. Since its 2008 introduction into North America, growers have used insecticides, such as pyrethroids and spinosads, as the primary approach for D. suzukii management, resulting in detections of insecticide resistance in this pest. This study sought to identify the molecular mechanisms conferring insecticide resistance in these populations. We sequenced the transcriptomes of two pyrethroid- and two spinosad-resistant isofemale lines. In both pyrethroid-resistant lines and one spinosad-resistant line, we identified overexpression of metabolic genes that are implicated in resistance in other insect pests. In the other spinosad-resistant line, we observed an overexpression of cuticular genes that have been linked to resistance. Our findings enabled the development of molecular diagnostics that we used to confirm persistence of insecticide resistance in California, U.S.A. To validate these findings, we leveraged D. melanogaster mutants with reduced expression of metabolic or cuticular genes that were found to be upregulated in resistant D. suzukii to demonstrate that these genes are involved in promoting resistance. This study is the first to characterize the molecular mechanisms of insecticide resistance in D. suzukii and provides insights into how current management practices can be optimized.

genomics↗

Mealtime alters daily rhythm in nuclear O-GlcNAcome to regulate hepatic gene expression

The liver circadian clock and hepatic transcriptome are highly responsive to metabolic signals generated from feeding-fasting rhythm. Previous studies have identified a number of nutrient-sensitive signaling pathways that could interpret metabolic input to regulate rhythmic hepatic biology. Here, we investigated the role of O-GlcNAcylation, a nutrient-sensitive post-translational modification (PTM) in mediating metabolic regulation of rhythmic biology in the liver. We observe daily oscillation of global nuclear protein O-GlcNAcylation in the liver of mice subjected to night-restricted feeding (NRF) using label-free global O-GlcNAc proteomics. Additional site-specific O-GlcNAc analysis by tandem mass tag mass spectrometry further supports temporal differences in O-GlcNAcylation by revealing day-night differences. Proteins involved in gene expression are enriched among rhythmically O-GlcNAcylated proteins, suggesting rhythmic O-GlcNAcylation may directly regulate the daily rhythmicity of the hepatic transcriptome. We show that rhythmic O-GlcNAcylation can also indirectly modulate the hepatic transcriptome by interacting with phosphorylation. Several proteins harboring O-GlcNAcylation-phosphorylation interplay motif exhibit rhythmic O-GlcNAcylation and phosphorylation. Specifically, we show that O-GlcNAcylation occurs at a phospho-degron of a key circadian transcriptional activator, circadian locomotor output cycles kaput (CLOCK), thus regulating its stability and transcriptional output. Finally, we report that day-restricted feeding (DRF) in the nocturnal mouse significantly alters O-GlcNAcylation rhythm. Whereas global O-GlcNAcylation analysis indicates dampening of global O-GlcNAcylation rhythm in mice fed under DRF, site-specific analysis reveals differential responses of O-GlcNAc sites when timing of food intake is altered. Notably, a substantial number of O-GlcNAcylation sites exhibit inverted day-night profiles when mice are subjected to DRF. This suggests the dysregulation of daily nuclear protein O-GlcNAcylation rhythm may contribute to the disruption in liver transcriptomic rhythm previously observed in DRF condition. In summary, our results provide new mechanistic insights into metabolic regulation of daily hepatic transcriptomic rhythm via interplay between O-GlcNAcylation and phosphorylation and shed light on the deleterious effects of improper mealtimes.

physiology↗

Global genomics of Aedes aegypti unveils widespread and novel persistent infectious viruses capable of triggering a small RNA response

The mosquito Aedes aegypti is a prominent vector for arboviruses, but the breadth of mosquito viruses that infects this specie is not fully understood. In the broadest global survey to date of over 200 Ae. aegypti small RNA samples, we detected viral small interfering RNAs (siRNAs) and Piwi interacting RNAs (piRNAs) arising from mosquito viruses. We confirmed that most academic laboratory colonies of Ae. aegypti lack persisting viruses, yet two commercial strains were infected by a novel tombus-like virus. Ae. aegypti from North to South American locations were also teeming with multiple insect viruses, with Anphevirus and a bunyavirus displaying geographical boundaries from the viral small RNA patterns. Asian Ae. aegypti small RNA patterns indicate infections by similar mosquito viruses from the Americas and reveal the first wild example of dengue virus infection generating viral small RNAs. African Ae. aegypti also contained various viral small RNAs including novel viruses only found in these African substrains. Intriguingly, viral long RNA patterns can differ from small RNA patterns, indicative of viral transcripts evading the mosquitoes RNA interference (RNAi) machinery. To determine whether the viruses we discovered via small RNA sequencing were replicating and transmissible, we infected C6/36 and Aag2 cells with Ae. aegypti homogenates. Through blind passaging, we generated cell lines stably infected by these mosquito viruses which then generated abundant viral siRNAs and piRNAs that resemble the native mosquito viral small RNA patterns. This mosquito small RNA genomics approach augments surveillance approaches for emerging infectious diseases.

genomics↗