bioRxiv Science⌕ Search

Biology subjects

Miller, S.

Publications and source records attributed to Miller, S..

At least 19 recordsLinked to original sources
bioRxiv2026

Survey of transcription initiation in the streamlined genomes of Paramecium

In the genus Paramecium, the macronuclear genome is remarkably compact and optimized for gene expression. As a means to explore eukaryotic transcription in the context of a streamlined genome and shed light on the role of sequence architecture on gene expression and loss, we analyzed the distribution and diversity of candidate transcription initiation sites (TISs) in Paramecium sexaurelia, Paramecium tetraurelia and their outgroup, Paramecium caudatum. Our analysis suggests that for Paramecium, most genes have very short 5 prime UTRs (40 bp or less) and their transcription initiation regions (TIRs) have a median dispersion (akin to width) of 8-10 bp. The TIRs for the three species have high AT content. TIR dispersion is not to gene expression. However, mean TIS position relative to the translation start site per gene does in gene expression for the three species, and is often conserved between them. While mean TIS position and gene expression are linked, gene expression itself is the main driver of paralog retention in the aurelias. As compared to other eukaryotes, Paramecium has a uniquely well-defined and short main TIS region, and sequence motifs that likely diverge from the consensus in multicellular eukaryotes.

genomics↗
bioRxiv2026

Diversity and community structure of anaerobic gut fungi in camels

Anaerobic gut fungi (AGF) are key members of the herbivorous gut microbiome. While AGF communities have been well-studied in foregut and hindgut fermenters, they remain poorly characterized in pseudoruminants such as camels. Here, we present a comprehensive culture-independent diversity survey of 142 fecal samples from all three extant camel species (Camelus dromedarius, Camelus bactrianus, and Camelus ferus). The AGF community in Camelus was highly diverse, with representatives of 42 AGF genera identified. However, this diversity was unevenly distributed, with three genera (Neocallimastix, Caecomyces, and Orpinomyces) accounting for 70.7% of sequences encountered, and only 12 genera exceeding 1% relative abundance in the entire dataset. While several of the genera identified as major components of the AGF community in camels are highly ubiquitous in all herbivores, others, such as Oontomyces, Aestipascuomyces, Liebetanzomyces, and the yet uncultured genera NY09, NY03, and JV-2025d are extremely rare in ruminants and hindgut fermenters, hinting at their preference and potential co-evolution with the Camelidae. Ordination approaches identified host species and biogeography as key determinants driving AGF community structure differences between various camel species. Comparative community structure analysis between AGF community in camels versus reference foregut and hindgut fermenters identified the relative enrichment of the genera Oontomyces and Aestipascuomyces in pseudoruminants datasets. Our results demonstrate a distinct AGF community composition in Camelidae, elucidate factors impacting AGF diversity and community structure variations in Camelus, and identify key distinct taxa differentially enriched in psuedoruminants compared to ruminants and hindgut fermenters. The ecological and evolutionary drivers of such patterns are discussed.

microbiology↗
bioRxiv2026

Oscillating Hypercapnia Induces Neural Abundant Protein Efflux and Potential Depletion in Health and Chronic Traumatic Brain Injury

Emerging preclinical and clinical evidence suggests that low frequency hemodynamic oscillations drive CSF flow, which in turn mediates glymphatic clearance. The current study investigated whether CO2-induced low frequency hemodynamic oscillations during magnetic resonance imaging would increase clearance of proteins (glial fibrillary acidic protein, neurofilament light chain, ptau217 and brain-derived tau) from brain to blood, and temporarily improve cognitive performance in individuals with chronic traumatic brain injury (TBI) and age/sex-matched healthy controls. Results indicated that cerebrovascular reactivity, normalized CSF volume, and predicted brain age significantly differed between chronic TBI and controls, while bulk CSF flow differed only at trend levels. Multiple protein concentrations were significantly increased at [~]45 minutes post-hypercapnia, decreased at [~]90 minutes, and returned to pre-hypercapnia levels by [~]150 minutes. Protein efflux was more strongly associated with total CSF volume and total white matter volume rather than cerebrovascular reactivity or bulk CSF flow. Both groups exhibited reduced cognitive interference post-hypercapnia, and hypercapnia associated symptoms quickly returned to baseline levels. In conclusion, hypercapnia temporarily increases clearance of multiple neural abundant proteins into blood, and this effect is moderated by atrophy. Current results suggest that hypercapnia may therapeutically combat pathological protein aggregation post-trauma, and prophylactically during normal aging.

neuroscience↗
bioRxiv2026

Diatom Endosymbionts have Shrinking but Stable Genomes Despite Low Coding Density

Successful establishment of long-term, obligate endosymbiotic relationships requires integration of hosts and endosymbionts across multiple levels. For example, highly integrated, host-beneficial endosymbionts typically have extremely reduced genomes and metabolisms. However, we do not yet fully understand the specific mechanisms that drive this integration or if there is a specific order in which these changes must occur. To investigate the early stages of endosymbiont genome reduction, we greatly expanded available whole genome data for the nitrogen-fixing endosymbionts (spheroid bodies, SBs) of diatoms in the family Rhopalodiaceae. We used these data to reconstruct SB evolutionary history and to characterize SB core metabolic capacity. We found two key genes missing from all SB genomes, mltA and dnaA, which could provide points of host control over SB cell division. Although most of the SB core genome is experiencing moderately strong purifying selection, we identified 54 genes under positive selection. Eighteen of these are peripheral proteins or involved in cell wall and cell membrane metabolism and could be involved in direct interactions with the host. Unexpectedly, we also found three nif genes under positive selection that are core to the central nitrogen-fixing enzyme. Overall, our results provide early insights into how SBs and their hosts interact, showing that SBs are still in the early stages of endosymbiont genome reduction, but they differ in key ways from current models, including the early loss of all mobile elements.

evolutionary biology↗
bioRxiv2026

Sphingolipid regulation by yeast Mdm1 supports adaptive remodeling of the methionine transporter Mup1

Membrane lipid composition influences endocytic remodeling of nutrient transporters, yet how lipid metabolism is spatially coordinated to support sustained adaptation to nutrient limitations remains unclear. Here, we investigated whether the ER-vacuole tether Mdm1 links sphingolipid homeostasis to regulation of the high-affinity methionine permease Mup1 in budding yeast. To test this, we examined Mup1 trafficking, amino acid homeostasis, and sphingolipid composition in mdm1{Delta} cells during starvation. We found that loss of Mdm1 causes persistent retention of Mup1 at the plasma membrane, accompanied by reduced intracellular methionine and broad amino acid depletion. Lipidomic analyses revealed decreased sphingoid bases and altered ceramide composition in mdm1{Delta} cells. Importantly, supplementation with the sphingolipid precursor phytosphingosine restored sphingolipid pools, rescued Mup1 endocytosis, and improved amino acid homeostasis. Consistent with a chronic amino acid restriction-like state, mdm1{Delta} cells exhibited extended chronological lifespan. Together, these findings identify Mdm1 as a spatial organizer of sphingolipid metabolism required for adaptive endocytic remodeling of Mup1, thereby linking ER-vacuole contact site function to plasma membrane proteostasis and metabolic adaptation.

cell biology↗
bioRxiv2026

Behavior evolves as a correlated response to selection on cuticle color in Drosophila melanogaster and D. simulans

To predict adaptive evolution, we need to understand the degree to which selection on one trait can constrain or redirect evolutionary responses in other traits. We used artificial selection on cuticle color in Drosophila melanogaster and D. simulans to investigate whether color and behavior evolve in tandem. We selected for light and dark thoracic colors for 16 generations in two populations per species and measured correlated responses in aggression, basal activity, total activity, sleep, and geotaxis. Dark selected individuals consistently showed higher aggression and basal activity than light selected or control flies across both species and sexes, pointing to a modest but repeatable correlated response. In contrast, patterns for geotaxis, sleep, and total activity evolved unpredictably, often varying across species and populations, and showed no clear association with color. Within-population phenotypic correlations between color and aggression were significant but weak (rho = -0.035, rho{superscript 2} = 0.001), suggesting that color is a poor predictor of individual aggressive behavior. Populations evolving higher aggression also tended to evolve higher basal activity (rho = 0.52, p = 0.004), suggesting activity may have evolved as a correlated response rather than through a direct color-activity link. The persistence of correlated responses in aggression and basal activity in response to selection on color is consistent with a conserved genetic basis, such as pleiotropy or linkage disequilibrium, although our data do not distinguish between these mechanisms. Identifying the loci underlying variation in both color and behavior, and testing their effects experimentally, will clarify how multivariate genetic covariance shapes the direction and pace of adaptive evolution.

evolutionary biology↗
bioRxiv2026

Nvj3 regulates Dga1-mediated triacylglycerol synthesis and lipid droplet formation at ER contact sites

Lipid droplet (LD) biogenesis is essential for lipid homeostasis during nutrient stress, yet how lipid intermediates are spatially organized to support efficient triacylglycerol (TAG) synthesis remains unclear. Here, we identify Nvj3 as a nutrient-responsive regulator that links diacylglycerol (DAG) availability to TAG synthesis and LD formation at the endoplasmic reticulum (ER). Nvj3 is induced by glucose depletion and recruited to LD-associated ER domains. Loss of Nvj3 causes neutral lipid accumulation under steady state conditions but delays TAG synthesis under acute inducible metabolic transitions. Using controlled TAG induction systems, we show that Nvj3 is required to couple Dga1-dependent TAG synthesis to LD formation. In the absence of Nvj3, TAG accumulates but remains inefficiently packaged into LDs. Consistent with this defect, nvj3{Delta} cells exhibit altered phospholipid remodeling and mislocalization of DAG away from ER domains during starvation. Together, these findings establish Nvj3 as an organizer of lipid availability during metabolic stress and suggest that spatial control of DAG is a key determinant of LD biogenesis. SummaryThis study identifies Nvj3 as a spatial organizer of Dga1-dependent lipid droplet formation. Nvj3 promotes proper diacylglycerol positioning, and enables efficient triacylglycerol synthesis during metabolic stress. We propose that Nvj3 regulates lipid flux through spatial compartmentalization of diacylglycerol at membrane contact site-associated ER domains.

cell biology↗
bioRxiv2025

Networks of sexually dimorphic neurons that regulate social behaviors in Drosophila

Neural mechanisms underlying sexually dimorphic social behaviors remain enigmatic in most species. In Drosophila, sexually dimorphic P1/pC1x neurons have been described as a site of sensory integration that regulates mating and aggressive behaviors. We show that the male P1/pC1x population forms a highly intertwined network with male-specific mAL and aSP-a neurons that is poised to regulate male behavior. The 48 P1/pC1x cell types exhibit heterogeneous synaptic connections with a subset receiving strong input from identified sensory pathways. We also describe circuit motifs by which P1 and sexually dimorphic aIPg neurons co-regulate social behaviors. Genetic driver lines for these cell types were generated and used to discover distinct roles for P1/pC1x cell types in promoting social acoustic signaling and male-male interactions. Our results reveal unexpected diversity in the connectivity and behavioral roles of the P1/pC1x cell types and provide essential genetic tools for interrogating their neurophysiological and behavioral functions.

neuroscience↗
bioRxiv2025

Characterization of a Novel Transmembrane Activating STING Agonist using Genetically Humanized Mice

STING is a pattern recognition receptor that activates type I interferon and proinflammatory responses in addition to unrelated molecular processes following exposure of DNA to the cytosol. Its pharmacologic stimulation enhances vaccine potency and generates effective antitumor responses but clinical trials evaluating STING agonists have not led to approval for human use. STING activation can occur through ligand engagement of either cytosolic or transmembrane protein domains, processes to which distinct cellular phenotypes are attributed. However, the only transmembrane STING agonist identified is human selective and in vivo testing in conventional models is not feasible. Here we describe synthesis of novel STING agonists efficacious against allelic variants of the protein. We also describe genetically humanized STING mice and demonstrate their suitability as a model to evaluate in vivo responses following exogenous administration of human-selective agonists. Experiments demonstrate that the lead molecule (termed INI3069) functions through binding to the STING transmembrane region and its comparison with conventional agonists reveals significant differences in molecular and immune effects. INI3069 can also enhance antibody responses to co-administered antigens and antitumor responses. This work both represents the first in vivo examination of the effects of transmembrane STING agonism and demonstrates efficacy of a potential novel vaccine adjuvant and oncological therapeutic.

immunology↗
bioRxiv2025

Proactive Coral Reef Restoration Using Thermally Tolerant Corals in Hawaii

Effective conservation of degraded ecosystems requires mitigation of the original cause of decline, but this step can be difficult in the context of global climate change. On coral reefs, persistent environmental stress which causes coral bleaching may be addressed by using coral restoration stock which is naturally more resilient, often termed "proactive restoration" in terrestrial management. To explore the feasibility and consequences of this approach, we outplanted 391 colonies of 7 species of reef-building coral designated as thermally tolerant or thermally sensitive during stress testing and monitored them for 2 years using photogrammetry to evaluate tradeoffs and return-on-effort. We found no growth, complexity or effort tradeoffs when using thermally tolerant corals, but tolerant corals had lower survivorship during our monitoring period, driven primarily by one genus. These data illustrate nuanced tradeoffs and consequences to proactive reef restoration and suggest that the potential benefits of this approach may only be fully realized during future coral bleaching events.

ecology↗
bioRxiv2025

Neotenic expansion of adult-born dentate granule cells reconfigures GABAergic inhibition to enhance social memory consolidation

Adult-born dentate granule cells (abDGCs) contribute to hippocampal dentate gyrus (DG)-CA3/CA2 circuit functions in memory encoding, retrieval and consolidation. Heightened synaptic and structural plasticity of immature abDGCs is thought to govern their distinct contributions to circuit and network mechanisms of hippocampal-dependent memory operations. Protracted maturation or neoteny of abDGCs in higher mammals is hypothesized to offset decline in adult hippocampal neurogenesis by expanding the capacity for circuit and network plasticity underlying different memory operations. Here, we provide evidence for this hypothesis by genetically modelling the effective impact of neoteny of abDGCs on circuitry, network properties and social cognition in mice. We show that selective synchronous expansion of a single cohort of 4 weeks old immature, but not 8 weeks old mature abDGCs, increases functional recruitment of fast spiking parvalbumin expressing inhibitory interneurons (PV INs) in CA3/CA2, number of PV IN-CA3/CA2 synapses, and GABAergic inhibition of CA3/CA2. This transient increase in feed-forward inhibition in DG-CA2 decreased social memory interference and enhanced social memory consolidation. In vivo local field potential recordings revealed that the expansion of a single cohort of 4-week-old abDGCs increased baseline power, amplitude, and duration, as well as sensitivity to social investigation-dependent rate changes of sharp-wave ripples (SWRs) in CA1 and CA2, a neural substrate for memory consolidation. Inhibitory neuron-targeted chemogenetic manipulations implicate CA3/CA2 INs, including PV INs, as necessary and sufficient for social memory consolidation following neotenic expansion of the abDGC population and in wild-type mice, respectively. These studies suggest that neoteny of abDGCs may represent an evolutionary adaptation to support cognition by reconfiguring PV IN-CA3/CA2 circuitry and emergent network properties underlying memory consolidation.

neuroscience↗
bioRxiv2025

The encoding of interoceptive-based predictions by the paraventricular nucleus of the thalamus D2+ neurons

Understanding how the brain integrates internal physiological states with external sensory cues to guide behavior is a fundamental question in neuroscience. This process relies on interoceptive predictions, which are internal models that anticipate changes in the bodys physiological state based on sensory inputs and prior experiences. Despite recent advances in identifying the neural substrates of interoceptive predictions, the precise neuronal circuits involved remain elusive. In our study, we demonstrate that Dopamine 2 Receptor (D2R+) expressing neurons in the paraventricular nucleus of the thalamus (PVT) play key roles in interoception and interoceptive predictions. Specifically, these neurons are engaged in behaviors leading to physiologically relevant outcomes, with their activity highly dependent on the interoceptive state of the mice and the expected outcome. Furthermore, we show that chronic inhibition of PVTD2R+ neurons impairs the long-term performance of interoceptive-guided motivated behavior. Collectively, our findings provide insights into the role of PVTD2R+ neurons in learning and updating state-dependent predictions by integrating past experiences with current physiological conditions to optimize goal-directed behavior.

neuroscience↗
bioRxiv2025

Sequencing by Expansion (SBX) -- a novel, high-throughput single-molecule sequencing technology

Remarkable advances in high-throughput sequencing have enabled major biological discoveries and clinical applications, but achieving wider distribution and use depends critically on further improvements in scale and cost reduction. Nanopore sequencing has long held the promise for such progress, but has had limited market penetration. This is because efficient and accurate nanopore sequencing of nucleic acids has been challenged by fundamental signal-to-noise limitations resulting from the poor spatial resolution and molecular distinction of nucleobases. Here, we describe Sequencing by Expansion (SBX), a single-molecule sequencing technology that overcomes these limitations by using a biochemical conversion process to encode the sequence of a target nucleic acid molecule into an Xpandomer, a highly measurable surrogate polymer. Expanding over 50 times longer than the parent DNA templates, Xpandomers are engineered with high signal-to-noise reporter codes to enable facile, high-accuracy nanopore sequencing. We demonstrate the performance of SBX and present the specialized molecular structures, chemistries, enzymes and methods that enable it. The innovative molecular and systems engineering in SBX create a transformative technology to address the needs of existing and emerging sequencing applications.

genomics↗
bioRxiv2025

Senolytics Restore Hematopoietic Stem Cells Function in Sickle Cell Disease

Sickle Cell Disease (SCD) is a blood disorder affecting millions worldwide. Emerging evidence reveals that SCD pathophysiology increases risk of myeloid malignancies and hematopoietic stem cell (HSC) dysfunction, possibly due to pathological stress on bone marrow. To investigate this further, we interrogated mice and individuals with SCD and observed extended cell cycle times, oxidative stress, DNA damage, senescence, and dysregulation of molecular programs associated with these processes in bone marrow hematopoietic stem and progenitor cells (HSPCs). Human SCD HSPCs displayed poor hematopoietic potential ex vivo. SCD mice displayed a dramatic loss of transplantable bone marrow HSPCs, which was reversed upon treatment of SCD mice with the senolytic agent, ABT-263 (navitoclax). Thus, senolytics restore bone marrow function during SCD in mice and represent a novel strategy to improve bone marrow health in individuals with SCD and improve the safety of potentially curative gene therapies that utilize autologous HSPCs from individuals with SCD.

cell biology↗
bioRxiv2025

Positive associations between growth and thermal tolerance in the reef-building coral Montipora capitata

Relationships between ecologically important traits are increasingly important for the future of coral reefs, which are declining globally due to a variety of stressors. Corals that resist and recover from bleaching will be selected under future climates, which may negatively or positively impact a range of associated traits important for the structure and function of contemporary and future reefs. Using standardized assays, we investigated growth under ambient conditions, bleaching resistance and recovery after bleaching in a model population of 60 Montipora capitata colonies harboring diverse symbiont communities. We found significantly higher trait variance within Durusdinium-dominated colonies, highlighting the interaction of host and symbiont. We also show that symbiont community impacted thermal tolerance and survivorship during the thermal stress assay, but not recovery or growth. There was also a positive relationship between thermal tolerance and change in surface area and thermal tolerance and recovery from equivalent amounts of stress. These results demonstrate limited tradeoffs to thermal tolerance and suggest that bleaching tolerant corals in this model system are suited to recover from stress and maintain high growth rates under ambient conditions, providing insight into the adaptive capacity of thermally tolerant corals in the Anthropocene.

ecology↗
bioRxiv2025

AA147 Alleviates Symptoms in a Mouse Model of Multiple Sclerosis by Reducing Oligodendrocyte Loss

Inflammation induced oligodendrocyte death and CNS demyelination, are key features of multiple sclerosis (MS). Inflammation-triggered endoplasmic reticulum (ER) stress and oxidative stress promote tissue damage in MS and in its preclinical animal model, experimental autoimmune encephalitis (EAE). Compound AA147 is a potent activator of the ATF6 signaling arm of the unfolded protein response (UPR) that can also induce antioxidant signaling through activation of the NRF2 pathway in neuronal cells. Previous work showed that AA147 protects multiple tissues against ischemia/reperfusion damage through ATF6 and/or NRF2 activation; however, its therapeutic potential in neuroinflammatory disorders remains unexplored. Here, we demonstrate that AA147 ameliorated the clinical symptoms of EAE and reduced ER stress, oligodendrocyte loss, and demyelination. Additionally, AA147 suppressed T cells in the CNS without altering the peripheral immune response. Importantly, AA147 significantly increased the expressions of Grp78, an ATF6 target gene, in oligodendrocytes, while enhancing levels of Grp78 as well as Ho-1, an NRF2 target gene, in microglia. In cultured oligodendrocytes, AA147 promoted nuclear translocation of ATF6, but not NRF2. Intriguingly, AA147 altered the microglia activation profile, possibly by triggering the NRF2 pathway. AA147 was not therapeutically beneficial during the acute EAE stage in mice lacking ATF6 in oligodendrocytes, indicating that protection primarily involves ATF6 activation in these cells. Overall, our results suggest AA147 as a potential therapeutic opportunity for MS by promoting oligodendrocyte survival and regulating microglia status through distinct mechanisms.

neuroscience↗
bioRxiv2024

Human and Mouse Models for Kabuki Syndrome Reveal Increase in Inhibitory Synapse Development.

Intellectual disability, affecting 2-3% of the general population, often co-occurs with neurodevelopmental disorders and is frequently caused by mutations that impair synaptic function. Kabuki syndrome (KS), a rare multisystem disorder associated with developmental delay and intellectual disability, results from mutations in either KMT2D (KS1) or KDM6A (KS2), encoding a histone methyltransferase and demethylase, respectively. The mechanisms underlying intellectual disability in KS remain poorly understood. Here, we generated human iPS cells carrying conditional Cre/lox-dependent loss-of-function mutations in KMT2D or KDM6A and differentiated them into excitatory or inhibitory neurons. Analysis revealed that KS1 and KS2 inhibitory neurons unexpectedly showed increased GABAergic synapse formation, whereas excitatory neurons displayed reduced synapse development and impaired synaptic transmission. We confirmed these findings in hippocampal neurons in vitro and in vivo using a mouse model for KS1 demonstrating a bidirectional shift: increase in inhibition and decrease in excitation. Synapse numbers and synaptic transmission in brain slices were shifted to increased inhibition/excitation ratio. Mechanistically, KS1 mutations activated neuroinflammatory signaling, impaired astrocytic function, and promoted glia-driven inhibitory synapse formation in human neurons. By integrating human neuron models with conditional KMT2D/KDM6A deletions and a Kmt2d-mutant mouse model, we identify a novel synaptic disease mechanism in KS that links chromatin remodeling defects to disrupted information transfer in neural circuits, providing a mechanistic explanation for intellectual disability. Significance StatementKabuki syndrome, a rare disorder with intellectual disability, is caused by mutations in the chromatin regulators KMT2D and KDM6A, yet its cellular pathophysiology has remained unclear. Using new Cre/lox-inducible human neuron models together with a mouse model, we reveal a conserved excitation-inhibition imbalance characterized by increased inhibitory and decreased excitatory synapse formation. Our findings establish the first mechanistic framework linking KMT2D/KDM6A mutations to synaptic dysfunction, uncover glial contributions to disease pathogenesis, and suggest potential therapeutic avenues for restoring synaptic balance. HighlightsO_LIKS1 and KS2 mutations cause decrease in excitatory synapses in human neurons C_LIO_LIKS1 and KS2 mutations cause increase in inhibitory synapses in human neurons C_LIO_LIKS1 mutation causes decrease in excitatory and increase in inhibitory synapses in mice C_LIO_LIKS1 mutant mouse astrocytes facilitate increase in inhibitory synapses in human neurons C_LI

neuroscience↗