Biology subjects

Wu, J. Y.

Publications and source records attributed to Wu, J. Y..

12 recordsLinked to original sources

bioRxiv2026

The development of slow and fast theta oscillations in the human brain

Theta oscillations are pivotal for attention and memory, with developmental shifts in theta activity and connectivity tracking memory ability across the lifespan. Building on initial evidence that the theta band separates into slow and fast sub-bands across development within the medial temporal lobe (MTL) and the prefrontal cortex (PFC), this preregistered study (https://osf.io/gsru7) characterized the frequencies of slow (~1.5-4.5 Hz) and fast (~4.5-9.0 Hz) theta oscillations across the brain in a large developmental cohort. We analyzed intracranial EEG (iEEG) recordings from widespread brain regions in 101 children and adults (5.93-54.00 years, 63 males; n electrodes = 5691) using task-based (attention to to-be-remembered visual stimuli) and task-free (resting-state) data. We reveal distinct slow and fast theta oscillations in all regions and identify a spatial gradient in both frequency ranges, with slow theta oscillations speeding up and fast theta oscillations slowing down from posterior to anterior regions. The dissociation between slow and fast theta frequencies peaks during young adulthood, mirroring the developmental trajectory of attention and memory. In the hippocampus and PFC, attentional state (task-based, task-free) modulated age effects, and individual differences in task-based slow theta frequencies predicted individual differences in memory performance, linking the development of slow theta oscillations to the development of memory. Gray matter volume was not associated with age- or task-related differences in theta frequencies, suggesting that the development of theta oscillations is independent of regional brain structure. This study establishes developmental trajectories of slow and fast theta oscillations in localized brain regions and links the maturation of hippocampal and PFC slow theta oscillations to the development of attention and memory.

neuroscience↗

bioRxiv2025

Declarative Memory Through the Lens of Single-Trial Peaks in High-Frequency Power

Declarative memory depends on the coordination of local processing, indexed by high-frequency broadband (HFB) activity, with global network organization, indexed by theta oscillations. However, theta and HFB exhibit asynchronous timing, raising the question of how results of local processing are communicated throughout the network. Using intracranial EEG in patients performing a recognition memory task, we examined this coordination across the medial temporal lobe (MTL) and prefrontal cortex (PFC). HFB peak activity was earlier in the MTL than PFC. Anchoring analyses of theta phase clustering and connectivity to HFB peaks revealed strong phase clustering locked to HFB peaks in the PFC, as well as connectivity between the PFC and MTL that predicted individual memory performance. Graph analysis revealed specific connections amidst sparse network connectivity during memory success. This study demonstrates that transient brain states linked to internal physiological events support memory and refines our understanding of local and network-level process interactions. HighlightsO_LIMemory-linked theta activity is time-locked to internal brain events C_LIO_LINetwork connectivity changes dynamically during memory processing C_LIO_LISparse network connectivity supports successful memory C_LIO_LISpecific sequences of transient states may be critical for declarative memory C_LI

neuroscience↗

bioRxiv2024

The development of aperiodic neural activity in the human brain

The neurophysiological mechanisms supporting brain maturation are fundamental to attention and memory capacity across the lifespan. Human brain regions develop at different rates, with many regions developing into the third and fourth decades of life. Here, in this preregistered study (https://osf.io/gsru7), we analyzed intracranial EEG (iEEG) recordings from widespread brain regions in a large developmental cohort. Using task-based (i.e., attention to-be-remembered visual stimuli) and task-free (resting-state) data from 101 children and adults (5.93 - 54.00 years, 63 males; n electrodes = 5691), we mapped aperiodic (1/[f]-like) activity, a proxy of neural noise, with steeper slopes indexing less noise and flatter slopes indexing more noise. We reveal that aperiodic slopes flatten with age into young adulthood in both association and sensorimotor cortices, challenging models of early sensorimotor development based on brain structure. In prefrontal cortex (PFC), attentional state modulated age effects, revealing steeper task-based than task-free slopes in adults and the opposite in children, consistent with the development of cognitive control. Age-related differences in task-based slopes also explained age-related gains in memory performance, linking the development of PFC cognitive control to the development of memory. Last, with additional structural imaging measures, we reveal that age-related differences in gray matter volume are similarly associated with aperiodic slopes in association and sensorimotor cortices. Our findings establish developmental trajectories of aperiodic activity in localized brain regions and illuminate the development of PFC control during adolescence in the development of attention and memory.

neuroscience↗

bioRxiv2024

Loss of RREB1 reduces adipogenesis and improves insulin sensitivity in mouse and human adipocytes

There are multiple independent genetic signals at the Ras-responsive element binding protein 1 (RREB1) locus associated with type 2 diabetes risk, fasting glucose, ectopic fat, height, and bone mineral density. We have previously shown that loss of RREB1 in pancreatic beta cells reduces insulin content and impairs islet cell development and function. However, RREB1 is a widely expressed transcription factor and the metabolic impact of RREB1 loss in vivo remains unknown. Here, we show that male and female global heterozygous knockout (Rreb1+/-) mice have reduced body length, weight, and fat mass on high-fat diet. Rreb1+/- mice have sex- and diet-specific decreases in adipose tissue and adipocyte size; male mice on high-fat diet had larger gonadal adipocytes, while males on standard chow and females on high-fat diet had smaller, more insulin sensitive subcutaneous adipocytes. Mouse and human precursor cells lacking RREB1 have decreased adipogenic gene expression and activated transcription of genes associated with osteoblast differentiation, which was associated with Rreb1+/- mice having increased bone mineral density in vivo. Finally, human carriers of RREB1 T2D protective alleles have smaller adipocytes, consistent with RREB1 loss-of-function reducing diabetes risk.

physiology↗

bioRxiv2023

Sharp wave ripple coupling in zebrafish hippocampus and basolateral amygdala

The mammalian hippocampus exhibits sharp wave events (1-30 Hz) with an often-present superimposed fast ripple oscillation (120-200 Hz) forming a sharp wave ripple (SWR) complex. During slow wave sleep or consummatory behaviors, SWRs result from the sequential spiking of hippocampal cell assemblies initially activated during imagined or learned experiences. SWRs occur in tandem with cortical/subcortical assemblies critical to the long-term storage of specific memory types. Leveraging juvenile zebrafish, we show that SWR events in their hippocampal homologue, the anterodorsolateral lobe (ADL), in ex vivo whole-brains are locally generated and maintained. SWR events were also recorded in the basolateral amygdala (BLA). Concomitant single cell calcium imaging and local field potential (LFP) recordings showed that BLA SWs couple to ADL SWs. Calcium imaging recordings of whole-brains demonstrated that ADL and BLA SWRs are endogenously and spontaneously silenced by the activation of a more caudal population of putative cholinergic cells. Electrical stimulation of this caudal region silenced ADL SWs. Our results suggest that the SWR-generating circuit is evolutionarily conserved through shared acetylcholine modulating mechanisms. These findings further our understanding of neuronal population dynamics in the zebrafish brain and highlights their advantage for simultaneously recording SW/SWRs and single cell activity in diverse brain regions.

neuroscience↗

bioRxiv2022

SPNS1 is required for the transport of lysosphingolipids and lysoglycerophospholipids from lysosomes

Accumulation of sphingolipids, especially sphingosines, in the lysosomes is attributed to the pathogenesis of several lysosomal storage diseases. In search for a lysosomal protein that mediates the release of sphingosines, we identified SPNS1 which shares the highest homology to SPNS2, a sphingosine-1-phosphate (S1P) transporter. We generated knockout cells and mice for Spns1 and employed lipidomics and metabolomics to identify SPNS1 ligands. We found that knockouts of Spns1 resulted in the accumulation of sphingolipids, including sphingosines in embryonic brains and cell lines. These results suggest that deficiency of SPNS1 affects the clearance of sphingolipids in lysosomes. Biochemical assays demonstrated that sphingosines released from lysosomes required SPNS1. Furthermore, by performing a comprehensive analysis of metabolites from livers of postnatal Spns1 knockout mice (gSpns1-cKO), we detected a striking accumulation of lysoglycerophospholipids including LPC, LPE, LPG, and lysoplasmalogens. Interestingly, the release of these lysoglycerophospholipids also required SPNS1. Global knockout of Spns1 (gSpns1-KO) resulted in embryonic lethality between E12.5-E13.5 with developmental defects. Postnatal deletion of Spns1 in mice caused lipid accumulation in the lysosomes and pathological conditions reminiscent of lysosomal storage diseases. These results reveal a critical molecular role of SPNS1 as a transporter for lysosphingolipids and lysoglyerophospholipids from the lysosomes and link its physiological functions with lysosomal storage diseases. SignificancePhospholipids, including glycerophospholipids and sphingolipids, are delivered to the lysosomes for recycling. The hydrolysis of these lipids by lysosomal enzymes generates the corresponding lysoglycerophospholipids, such as lysophosphatidylcholine and lysosphingolipids, such as sphingosine, which are believed to be exported out of the lysosomes for recycling in the cytoplasm. However, it is unknown how these lysophospholipids are released from the lysosomes. The current study utilized genetic knockout models in combination with mass spectrometry analysis of complex phospholipids and sphingolipids to characterize the roles of an orphan lysosomal transporter, namely SPNS1. These findings show that deficiency of SPNS1 results in the accumulation of lysophospholipids in cells and animal tissues and that the transporter is required to transport both lysoglycerophospholipids and lysosphingolipids out of the lysosomes. SPNS1 is critical for early development in mice. Ablation of SPNS1 at postnatal life causes pathological conditions reminiscent of lysosomal storage diseases in mice. These findings reveal the molecular functions of SPNS1 as a lysophospholipid transporter and provide a foundation for studying the transport of these lysolipids in lysosomal storage diseases.

biochemistry↗

bioRxiv2022

Optical Metabolic Imaging Uncovers Sex- and Diet-dependent Lipid Changes in Aging Drosophila Brain

Aging is associated with progressive declines in physiological integrity and functions alongside increases in vulnerability to develop a number of diseases. The brain regulates sensory and motor functions as well as endocrine functions, and age-associated changes in brain are likely prerequisite for the organismal aging. Lipid metabolism has been associated with brain aging, which could be easily intervened by diets and lifestyles. However, the underlying mechanism through which brain lipid metabolism is regulated by diet during aging is elusive. Using stimulated Raman scattering (SRS) imaging combined with deuterium water (D2O) labeling, we visualized that lipid metabolic activities were changed by diet manipulation in aging Drosophila brain. Furthermore, we illuminated that insulin/IGF-1 signaling (IIS) pathway mediates the transformation of brain lipid metabolic changes in both an aging- and a diet-dependent manner. The lipid droplets (LDs) in the brain gradually became inert in both activities of lipid synthesis and mobilization with aging. High sugar diets enhanced the metabolic activity through promoting lipogenesis while dietary restriction increased the metabolic activity in both lipogenesis and lipolysis in brain LDs. However, these effects were impaired in both chico1/+ and dfoxo Drosophila mutants. We also observed that old chico1/+ brains maintained high metabolic activities, whilst the aged dfoxo brains acted exactly the opposite. More interestingly, the sexual dimorphism in brain lipid metabolism was impaired under diet regulation in both chico1/+ and dfoxo mutants. Locally reduced IIS activity in glial cells can mimic the systemic changes in systematic IIS mutants to maintain lipogenesis and lipolysis in aged brains, providing mechanistic insight into the anti-aging effects of IIS pathway. Our results highlight the manipulation of glia-specific IIS activity as a promising strategy in anti-aging treatments.

bioengineering↗

bioRxiv2022

Multi-Molecular Hyperspectral PRM-SRS Imaging

Lipids play crucial roles in many biological processes under physiological and pathological conditions. Mapping spatial distribution and examining metabolic dynamics of different lipids in cells and tissues in situ are critical for understanding aging and diseases. Commonly used imaging methods, including mass spectrometry-based technologies or labeled imaging techniques, tend to disrupt the native environment of cells/tissues and have limited spatial or spectral resolution, while traditional optical imaging techniques still lack the capacity to distinguish chemical differences between lipid subtypes. To overcome these limitations, we developed a new hyperspectral imaging platform that integrates a Penalized Reference Matching algorithm with Stimulated Raman Scattering (PRM-SRS) microscopy. With this new approach, we directly visualized and identified multiple lipid species in cells and tissues in situ with high chemical specificity and subcellular resolution. High density lipoprotein (HDL) particles containing non-esterified cholesterol was observed in the kidney, indicating that these pools of cholesterol are ectopic deposits, or have yet to be enriched. We detected a higher Cholesterol to phosphatidylethanolamine (PE) ratio inside the granule cells of hippocampal samples in old mice, suggesting altered membrane lipid synthesis and metabolism in aging brains. PRM-SRS imaging also revealed subcellular distributions of sphingosine and cardiolipin in the human brain sample. Compared with other techniques, PRM-SRS demonstrates unique advantages, including faster data processing and direct user-defined visualization with enhanced chemical specificity for distinguishing clinically relevant lipid subtypes in different organs and species. Our method has broad applications in multiplexed cell and tissue imaging.

bioengineering↗

bioRxiv2022

Super-resolution stimulated Raman Scattering microscopy with A-PoD

Unlike traditionally-mapped Raman imaging, stimulated Raman scattering (SRS) imaging achieved the capability of imaging metabolic dynamics and a greatly improved signal-noise-ratio. However, its spatial resolution is still limited by the numerical aperture or scattering cross-section. To achieve super-resolved SRS imaging, we developed a new deconvolution algorithm - Adam optimization-based Pointillism Deconvolution (A-PoD) - for SRS imaging, and demonstrated a spatial resolution of 52 nm on polystyrene beads. By changing the genetic algorithm to A-PoD, the image deconvolution process was shortened by more than 3 orders of magnitude, from a few hours to a few seconds. By applying A-PoD to spatially correlated multi-photon fluorescence (MPF) imaging and deuterium oxide (D2O)-probed SRS (DO-SRS) imaging data from diverse samples, we compared nanoscopic distributions of proteins and lipids in cells and subcellular organelles. We successfully differentiated newly synthesized lipids in lipid droplets using A-PoD coupled with DO-SRS. The A-PoD-enhanced DO-SRS imaging method was also applied to reveal the metabolic change in brain samples from Drosophila on different diets. This new approach allows us to quantitatively measure the nanoscopic co-localization of biomolecules and metabolic dynamics in organelles. We expect that the A-PoD algorithm will have a wide range of applications, from nano-scale measurements of biomolecules to processing astronomical images.

bioengineering↗

bioRxiv2020

Scalp EEG interictal high frequency oscillations as an objective EEG biomarker of infantile spasms

ObjectiveTo investigate the diagnostic utility of high frequency oscillations (HFOs) via scalp electroencephalogram (EEG) in infantile spasms. MethodsWe retrospectively analyzed interictal slow-wave sleep EEGs sampled at 2,000 Hz recorded from 30 consecutive patients who were suspected of having infantile spasms. We measured the rate of HFOs (80-500 Hz) and the strength of the cross-frequency coupling between HFOs and slow-wave activity (SWA) at 3-4 Hz and 0.5-1 Hz as quantified with modulation indices (MIs). ResultsTwenty-three patients (77%) exhibited active spasms during the overnight EEG recording. Although the HFOs were detected in all children, increased HFO rate and MIs correlated with the presence of active spasms (p < 0.001 by HFO rate; p < 0.01 by MIs at 3-4 Hz; p = 0.02 by MIs at 0.5-1 Hz). The presence of active spasms was predicted by the logistic regression models incorporating HFO-related metrics (AUC: 0.80-0.98) better than that incorporating hypsarrhythmia (AUC: 0.61). The predictive performance of the best model remained favorable (87.5% accuracy) after a cross-validation procedure. ConclusionsIncreased rate of HFOs and coupling between HFOs and SWA are associated with active epileptic spasms. SignificanceScalp-recorded HFOs may serve as an objective EEG biomarker for active epileptic spasms. HighlightsO_LIObjective analyses of scalp high frequency oscillations and its coupling with slow-wave activity in infantile spasms were feasible. C_LIO_LIIncreased rate of high frequency oscillations and its coupling with slow-wave activity correlated with active epileptic spasms. C_LIO_LIThe scalp high frequency oscillations were also detected in neurologically normal children (although at the low rate). C_LI

neuroscience↗

bioRxiv2019

Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data

*Seq techniques (e.g. RNA-Seq) generate compositional datasets, i.e. the number of fragments sequenced is not proportional to the samples total RNA content. Thus, datasets carry only relative information, even though absolute RNA copy numbers are of interest. Current normalization methods assume most features do not change, which can lead to misleading conclusions when there are many changes. Furthermore, there are few real datasets and no simulation protocols currently available that can directly benchmark methods when many changes occur. We present absSimSeq, an R package that simulates compositional data in the form of RNA-Seq reads. We compared absSimSeq with several existing tools used for RNA-Seq differential analysis: sleuth, DESeq2, edgeR, limma, sleuth and ALDEx2 (which explicitly takes a compositional approach). We compared the standard normalization of these tools to either "compositional normalization", which uses log-ratios to anchor the data on a set of negative control features, or RUVSeq, another tool that directly uses negative control features. Our analysis shows that common normalizations result in reduced performance with current methods when there is a large change in the total RNA per cell. Performance improves when spike-ins are included and used with a compositional approach, even if the spike-ins have substantial variation. In contrast, RUVSeq, which normalizes count data rather than compositional data, has poor performance. Further, we show that previous criticisms of spike-ins did not take into consideration the compositional nature of the data. We demonstrate that absSimSeq can generate more representative datasets for testing performance, and that spike-ins should be more frequently used in a compositional manner to minimize misleading conclusions in differential analyses. Author SummaryA critical question in biomedical research is "Is there any change in the RNA transcript abundance when cellular conditions change?" RNA Sequencing (RNA-Seq) is a powerful tool that can help answer this question, but two critical parts of obtaining accurate measurements are (A) understanding the kind of data that RNA-Seq produces, and (B) "normalizing" the data between samples to allow for a fair comparison. Most tools assume that RNA-Seq data is count data, but in reality it is "compositional" data, meaning only percentages/proportions are available, which cannot directly answer the critical question. This leads to distorted results when attempting to simulate or analyze data that has a large global change. To address this problem, we designed a new simulation protocol called absSimSeq that can more accurately represent RNA-Seq data when there are large changes. We also proposed a "compositional normalization" method that can utilize "negative control" features that are known to not change between conditions to anchor the data. When there are many features changing, this approach improves performance over commonly used normalization methods across multiple tools. This work highlights the importance of having negative controls features available and of treating RNA-Seq data as compositional.

bioinformatics↗

bioRxiv2018

Venlafaxine stimulates PNN proteolysis and MMP-9 dependent enhancement of gamma power; relevance to antidepressant efficacy

Drugs that target monoaminergic transmission represent a first-line treatment for major depression. Though a full understanding of the mechanisms that underlie antidepressant efficacy is lacking, evidence supports a role for enhanced excitatory transmission. This can occur through two non-mutually exclusive mechanisms. The first involves increased function of excitatory neurons through relatively direct mechanisms such as enhanced dendritic arborization. Another mechanism involves reduced inhibitory function, which occurs with the rapid antidepressant ketamine. Consistent with this, GABAergic interneuron-mediated cortical inhibition is linked to reduced gamma oscillatory power, a rhythm also diminished in depression. Remission of depressive symptoms correlates with restoration of gamma power.\n\nDue to strong excitatory input, reliable GABA release and fast firing, PV neurons represent critical pacemakers for synchronous oscillations. PV neurons also represent the predominant GABAergic population enveloped by perineuronal nets (PNNs), lattice-like structures that localize glutamatergic input. Disruption of PNNs enhances lateral diffusion of glutamate receptors, reduces PV excitability, and enhances gamma activity.\n\nStudies suggest that monoamine reuptake inhibitors reduce integrity of the PNN. Mechanisms by which these inhibitors reduce PNN integrity, however, remain largely unexplored. A better understanding of these issues might encourage development of therapeutics that best upregulate PNN modulating proteases.\n\nWe observe that the serotonin/norepinephrine reuptake inhibitor venlafaxine reduces PNN integrity in murine brain. Moreover, venlafaxine treated mice (30 mg/kg/day) show an increase in carbachol-induced gamma power in hippocampal slices. Studies with mice deficient in matrix metalloproteinase-9 (MMP-9), a protease linked to PNN disruption in other settings, suggest that MMP-9 contributes to venlafaxine-enhanced gamma activity.

neuroscience↗