Biology subjects

Daniels, J.

Publications and source records attributed to Daniels, J..

7 recordsLinked to original sources

bioRxiv2025

Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis

The increasing scale and complexity of neuroimaging datasets aggregated from multiple study sites present substantial analytic challenges, as existing statistical analysis tools struggle to handle missing voxel-data, suffer from limited computational speed and inefficient memory allocation, and are restricted in the types of statistical designs they are able to model. We introduce Image-Based Meta- & Mega-Analysis (IBMMA), a novel software package implemented in R and Python that provides a unified framework for analyzing diverse neuroimaging features, efficiently handles large-scale datasets through parallel processing, offers flexible statistical modeling options, and properly manages missing voxel-data commonly encountered in multi-site studies. IBMMA produced stronger effect sizes and revealed findings in brain regions that traditional software overlooked due to missing voxel-data resulting in gaps in brain coverage. IBMMA has the potential to accelerate discoveries in neuroscience and enhance the clinical utility of neuroimaging findings.

neuroscience↗

bioRxiv2025

Structural Plasticity of RRE Stem-Loop II Modulates Nuclear Export of HIV-1 RNA

The Rev Response Element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 infection. However, our structural understanding of this crucial virological process remains limited. In this study, we determined several crystal structures of an intact RRE stem-loop II in two distinct conformations, performed negative-staining electron microscopy and molecular dynamics simulations, and revealed that this three-way junction RNA exhibits remarkable structural plasticity. Through in vitro Rev-binding and in vivo Rev-activity assays using various stem-loop II mutants designed to favor one of the conformers, we demonstrated that the structural plasticity of stem-loop II modulates Rev binding and oligomerization. Our findings illuminate emerging perspectives on RRE dynamics-based regulation of HIV-1 RNA nuclear export and provide a framework for developing anti-HIV drugs that target specific RRE conformations.

biophysics↗

bioRxiv2024

Long-term population dynamics of an endangered butterfly are influenced by hurricane-mediated disturbance

Effective species conservation requires understanding an organisms population dynamics and natural history, but long-term data are challenging to collect and maintain. As a result, conservation management decisions are frequently made using short-term data, which are insufficient to accurately assess population trends in most species. For less-studied taxa, including most invertebrates, inadequate understanding of life and natural history also impedes conservation efforts. Long-term studies are highly valuable for improving conservation decisions for target species as they serve as a model for other understudied species. We use mark-recapture data collected over 35 years to examine weather drivers of population patterns for an endangered butterfly, Schaus swallowtail (Heraclides ponceana), and to enhance our understanding of its natural history. We show that the population size of Schaus swallowtail butterfly was highly variable, ranging from under 100 to over 10,000 individuals. Population size is influenced by weather events and population size in the previous year. Population size was lower immediately following high wind events but was positively influenced by high wind events four years prior, with notable population increases following tropical cyclone events. Precipitation during the dry season preceding the adult flight period was also associated with higher population sizes. This study reveals the potentially beneficial role of hurricane-mediated disturbance on Schaus swallowtail populations potentially due to increased treefall gaps and the resulting shifts in plant communities. This remarkable data set represents one of the longest-term studies on a tropical insect.

ecology↗

bioRxiv2023

Nectophore coordination and kinematics by physonect siphonophores

Siphonophores are ubiquitous and often highly abundant members of pelagic ecosystems throughout the open ocean. They are unique among animal taxa in that they use multiple jets for propulsion. Little is known about kinematics of the individual jets produced by nectophores or how the jets are coordinated during normal swimming behavior. Using remotely operated vehicles and SCUBA, we video recorded the swimming behavior of several physonect species in their natural environment. The pulsed kinematics of the individual nectophores that comprise the siphonophore nectosome were quantified and, based on these kinematics, we examined the coordination of adjacent nectophores. We found for all species that nectophores sharing the same side of the nectosomal axis were coordinated metachronally. However, this coordination was not shared with nectophores on the opposite side of the nectosomal axis. For most species, the metachronal contraction waves of nectophores were initiated by the apical nectophores and traveled dorsally. However, the metachronal wave of Apolemia rubriversa traveled in the opposite direction. Although nectophore groups on opposite sides of the nectosome were not coordinated, they pulsed with similar frequencies. This enabled siphonophores to maintain relatively linear trajectories during swimming. The timing and characteristics of the metachronal coordination of pulsed jets affects how the jet wakes interact and may provide important insight into how interacting jets may be optimized for efficient propulsion.

zoology↗

bioRxiv2022

Multimodal mass spectrometry imaging reveals single-cell metabolic states in mammalian liver

We have developed a powerful workflow to imaging endogenous metabolism in single cells on frozen tissue, allowing us to discover new cell subtypes in human liver. Performing spatially integrated multiomics in single cells within tissues is at the leading frontier in biology but has been prevented by technological challenges. We developed a critical new technology, cryogenic water cluster ion beam secondary ion mass spectrometry imaging ((H2O)n>28K-GCIB-SIMS)) at 1 {micro}m single-cell resolution. This allowed us to perform multi-modal mass spectrometry imaging (MSI) to detect metabolites, lipids, and proteins in single cells within functional liver zones and diverse cell types in the native tissue state. Our workflow utilizes the desorption electrospray ionization (DESI) mass spectrometry imaging (MSI) to build a reference map of metabolic heterogeneity and zonation across liver functional units. Then cryogenic (H2O)n>28K-GCIB-SIMS and C60-SIMS integrated metabolomics, lipidomic and proteomics, - characterizing the metabolic state in single cells on the same tissue section. We found for the first time that lipids and metabolites can classify liver metabolic zones and liver cell types beyond histological and protein-marker annotation. This provides a multi-modal workflow to define single-cell states in normal physiology and disease in mammalian tissue.

cell biology↗

bioRxiv2021

Lonely in the dark: trauma memory and sex-specific dysregulation of amygdala reactivity to fear signals

Loneliness exacerbates psychological distress and increases the risk of psychopathology after trauma exposure. The prevalence of trauma-associated disorders varies substantially between sexes, and accumulating evidence indicates sex-specific effects of loneliness. However, it is still unclear whether a lack of social connectedness affects trauma-induced intrusions and the neural processing of fear signals. Moreover, it is uncertain, whether loneliness plays a different role in women and men. We used a prestratification strategy and recruited n=47 (n=20 women) healthy individuals with high loneliness and n=35 controls (n=18 women). Participants were exposed to an experimental trauma and evoked intrusive thoughts in daily life were monitored for three consecutive days. Functional magnetic resonance imaging was used to assess neural habituation to fearful faces and fear learning (conditioning and extinction) prior to trauma exposure. The total number of intrusions and amygdala reactivity in neural fear processing served as the primary study outcomes. Our results revealed a significant interaction between loneliness and sex such that loneliness was associated with more intrusions in men, but not in women. A similar pattern emerged at the neural level, with both reduced amygdala habituation to repeated fearful faces and amygdala hyperreactivity during the conditioning of fear signals in lonely men, but not in women. Our findings indicate that loneliness may confer vulnerability to intrusive memories after trauma exposure in healthy men and that this phenotype relates to altered limbic processing of fear signals. Collectively, interventions targeting social connectedness may mitigate the sequelae of traumatic experiences.

neuroscience↗

bioRxiv2018

Crowdsourced study of children with autism and their typically developing siblings identifies differences in taxonomic and predicted function for stool-associated microbes using exact sequence variant analysis.

BackgroundThe existence of a link between the gut microbiome and autism spectrum disorder (ASD) is well established in mice, but in human populations efforts to identify microbial biomarkers have been limited due to problems stratifying participants within the broad phenotype of ASD and a lack of appropriately matched controls. To overcome these limitations and investigate the relationship between ASD and the gut microbiome, we ran a crowdsourced study of families 2-7 year old sibling pairs, where one child of the pair had a diagnosis of ASD and the other child did not.\n\nMethodsParents of age-matched sibling pairs electronically consented and completed study procedures via a secure web portal (microbiome.stanford.edu). Parents collected stool samples from each child, responded to behavioral questionnaires about the ASD childs typical behavior, and whenever possible provided a home video of their ASD childs natural social behavior. We performed DNA extraction and 16S rRNA amplicon sequencing on 117 stool samples (60 ASD and 57 NT) that met all study design eligibility criteria. Using DADA2, Exact Sequence Variants (ESVs) were identified as taxonomic units, and three statistical tests were performed on ESV abundance counts: (1) permutation test to determine differences between sibling pairs, (2) differential abundance test using a zero-inflated gaussian mixture model to account for the sparse abundance matrix, and (3) differential abundance test after modeling under a negative binomial distribution. The potential functional gene abundance for each sample was also inferred from the 16S rRNA data, providing KEGG Ortholog (KO), which were analyzed for differential abundance.\n\nResultsIn total, 21 ESVs had significantly differentially proportions in stool of children with ASD and their neurotypical siblings. Of these 21 ESVs, 11 were enriched in neurotypical children and ten were enriched in children with ASD. ESVs enriched in the ASD cohort were predominantly associated with Ruminococcaceae and Bacteroidaceae; while those enriched in controls were more diverse including taxa associated with Bifidobacterium, Porphyromonas, Slackia, Desulfovibrio, Acinetobacter johnsonii, and Lachnospiraceae. Exact Variant Analysis suggested that Lachnospiraceae was specific to the control cohort, while Ruminococcaceae, Tissierellaceae and Bacteroidaceae were significantly enriched in children with ASD. Metabolic gene predictions determined that while both cohorts harbor the butyrogenic pathway, the ASD cohort was more likely to use the 4-aminobutanoate (4Ab) pathway, while the control cohort was more likely to use the pyruvate pathway. The 4Ab pathway releases harmful by-products like ammonia and can shunt glutamate, affecting its availability as an excitatory neurotransmitter. Finally, we observed differences in the carbohydrate uptake capabilities of various ESVs identified between the two cohorts.

microbiology↗