Biology subjects

Lu, R.

Publications and source records attributed to Lu, R..

9 recordsLinked to original sources

bioRxiv2026

Cortical Hierarchy Dynamically Organizes Large-Scale Neural Propagation

Flexible behaviour depends on the continuous coordination of sensory-driven and internally guided processing, yet whether the cortical hierarchy spanning lower-order sensory to higher-order association systems dynamically organizes large-scale cortical propagation over time remains unclear. Here we combined source-resolved magnetoencephalography with Riemannian cortical-flow modelling to derive hierarchy consistency, a moment-to-moment measure of the alignment between cortical propagation and the principal sensory-to-association functional gradient. We found that large-scale cortical propagation was dynamically organized by the cortical hierarchy. Hierarchy consistency exhibited a reproducible low-frequency periodic component that defined a characteristic timescale for the continuous updating of propagation direction. This dynamic organization was coordinated by a distributed cortical switchboard spanning the default-mode, salience, control and limbic systems, and was constrained by structural connectivity and network-control architecture. It flexibly adapted to behavioural demands, with hierarchy consistency increasing across both sensorimotor and working-memory states, while its characteristic periodicity shifted in a task-dependent manner. Moreover, hierarchy-related propagation dynamics were systematically reorganized across ageing and associated with higher-order cognitive function. Together, these findings establish the cortical hierarchy as a dynamic organizing principle that continuously shapes the direction and temporal evolution of large-scale cortical propagation to support adaptive behaviour.

neuroscience↗

bioRxiv2018

Spatial and temporal inhibition of FGFR2b ligands reveals continuous requirements and novel targets in mouse inner ear morphogenesis

Morphogenesis of the inner ear epithelium requires coordinated deployment of several signaling pathways and disruptions cause abnormalities of hearing and/or balance. The FGFR2b ligands, FGF3 and FGF10, are expressed throughout otic development and are required individually for normal morphogenesis, but their prior and redundant roles in otic placode induction complicates investigation of subsequent combinatorial functions in morphogenesis. To interrogate these roles and identify new effectors of FGF3 and FGF10 signaling at the earliest stages of otic morphogenesis, we used conditional gene ablation after otic placode induction and temporal inhibition of signaling with a secreted, dominant-negative FGFR2b ectodomain. We show that both ligands are required continuously after otocyst formation for maintenance of the otic ganglion and patterning and proliferation of the epithelium, leading to normal morphogenesis of both the cochlear and vestibular domains. Furthermore, the first genomewide identification of proximal targets of FGFR2b signaling in the early otocyst reveals novel candidate genes for inner ear development and function.

developmental biology↗

bioRxiv2018

Penalized matrix decomposition for denoising, compression, and improved demixing of functional imaging data

Calcium imaging has revolutionized systems neuroscience, providing the ability to image large neural populations with single-cell resolution. The resulting datasets are quite large (with scales of TB/hour in some cases), which has presented a barrier to routine open sharing of this data, slowing progress in reproducible research. State of the art methods for analyzing this data are based on non-negative matrix factorization (NMF); these approaches solve a non-convex optimization problem, and are highly effective when good initializations are available, but can break down e.g. in low-SNR settings where common initialization approaches fail.\n\nHere we introduce an improved approach to compressing and denoising functional imaging data. The method is based on a spatially-localized penalized matrix decomposition (PMD) of the data to separate (low-dimensional) signal from (temporally-uncorrelated) noise. This approach can be applied in parallel on local spatial patches and is therefore highly scalable, does not impose non-negativity constraints or require stringent identifiability assumptions (leading to significantly more robust results compared to NMF), and estimates all parameters directly from the data, so no hand-tuning is required. We have applied the method to a wide range of functional imaging data (including one-photon, two-photon, three-photon, widefield, somatic, axonal, dendritic, calcium, and voltage imaging datasets): in all cases, we observe ~2-4x increases in SNR and compression rates of 20-300x with minimal visible loss of signal, with no adjustment of hyperparameters; this in turn facilitates the process of demixing the observed activity into contributions from individual neurons. We focus on two challenging applications: dendritic calcium imaging data and voltage imaging data in the context of optogenetic stimulation. In both cases, we show that our new approach leads to faster and much more robust extraction of activity from the video data.

neuroscience↗

bioRxiv2018

Clustered, information-dense transcription factor binding sites identify genes with similar tissue-wide expression profiles

BackgroundThe distribution and composition of cis-regulatory modules (e.g. transcription factor binding site (TFBS) clusters) in promoters substantially determine gene expression patterns and TF targets, whose expression levels are significantly regulated by TF binding. TF knockdown experiments have revealed correlations between TF binding profiles and gene expression levels. We present a general framework capable of predicting genes with similar tissue-wide expression patterns from activated or repressed TF targets using machine learning to combine TF binding and epigenetic features.\n\nMethodsGenes with correlated expression patterns across 53 tissues were identified according to their Bray-Curtis similarity. DNase I HyperSensitive region (DHS) -accessible promoter intervals of direct TF target genes were scanned with previously derived information theory-based position weight matrices (iPWMs) of 82 TFs. Features from information density-based TFBS clusters were used to predict target genes with machine learning classifiers. The accuracy, specificity and sensitivity of the classifiers were determined for different feature sets. Mutations in TFBSs were also introduced to examine their impact on cluster densities and the regulatory states of predicted target genes.\n\nResultsWe initially chose the glucocorticoid receptor gene (NR3C1), whose regulation has been extensively studied, to test this approach. SLC25A32 and TANK were found to exhibit the most similar expression patterns to this gene across 53 tissues. Prediction of other genes with similar expression profiles was significantly improved by eliminating inaccessible promoter intervals based on DHSs. A Random Forest classifier exhibited the best performance in detecting such coordinately regulated genes (accuracy was 0.972 for training, 0.976 for testing). Target gene prediction was confirmed using CRISPR knockdown data of TFs, which was more accurate than siRNA inactivation. Mutation analyses of TFBSs also revealed that one or more information-dense TFBS clusters in promoters are required for accurate target gene prediction.\n\nConclusionsMachine learning based on TFBS information density, organization, and chromatin accessibility accurately identifies gene targets with comparable tissue-wide expression patterns. Multiple, information-dense TFBS clusters in promoters appear to protect promoters from the effects of deleterious binding site mutations in a single TFBS that would effectively alter the expression state of these genes.

bioinformatics↗

bioRxiv2018

Clonal Level Lineage Commitment Pathways of Hematopoietic Stem Cells In Vivo

While hematopoietic stem cells (HSCs) have been extensively studied at the population level, little is known about the lineage commitment of individual clones. Here, we provide comprehensive maps of in vivo HSC clonal development in mice under homeostasis and after depletion of the endogenous hematopoietic system. Under homeostasis, all donor-derived HSC clones regenerate blood homogeneously throughout all measured stages and lineages of hematopoiesis. In contrast, after the hematopoietic system has been depleted by irradiation or by an anti-ckit antibody, only a small fraction of donor-derived HSC clones differentiates while dominantly expanding and exhibiting lineage bias. We identified the cellular origins of clonal dominance and lineage bias, and uncovered the lineage commitment pathways that lead HSC clones to differential blood production. This study reveals surprising alterations in HSC regulation by irradiation, and identifies the key hematopoiesis stages that may be manipulated to control blood production and balance.\n\nSIGNIFICANCE STATEMENTHematopoietic stem cells (HSCs) sustain daily blood production through a complex step-wise lineage commitment process. In this work, we present the first comprehensive study of HSC lineage commitment at the clonal level and identify new HSC regulatory mechanisms that are undetectable by conventional population level studies. First, we uncover distinct HSC clonal pathways that lead to differential blood production and imbalances. Second, we reveal that HSC regulation under physiological conditions is strikingly different from that after injury. Third, we present a comprehensive map of HSC activities in vivo at the clonal level.

systems biology↗

bioRxiv2017

Three-photon fluorescence microscopy with an axially elongated Bessel focus

Volumetric imaging tools that are simple to adopt, flexible, and robust, are in high demand in the field of neuroscience, where the ability to image neurons and their networks with high spatiotemporal resolution is essential. Using an axially elongated focus approximating a Bessel beam, in combination with two-photon fluorescence microscopy, has proven successful at such an endeavor. Here we demonstrate three-photon fluorescence imaging with an axially extended Bessel focus. We use an axicon-based module which allowed for the generation of Bessel foci of varying numerical aperture and axial length, and apply this volumetric imaging tool to image mouse brain slices and for in vivo imaging of the mouse brain.

neuroscience↗

bioRxiv2017

50 Hz volumetric functional imaging with continuously adjustable depth of focus

Understanding how neural circuits control behavior requires monitoring a large population of neurons with high spatial resolution and volume rate. Here we report an axicon-based Bessel beam module with continuously adjustable depth of focus (CADoF), which turns frame rate into volume rate by extending the excitation focus in axial direction while maintaining high lateral resolutions. Cost-effective and compact, this CADoF Bessel module can be easily integrated into existing two-photon fluorescence microscopes. Simply translating one of the relay lenses along its optical axis enabled continuous adjustment of the focal length. We used this module to simultaneously monitor activity of spinal projection neurons extending over 60 m depth in larval zebrafish at 50 Hz volume rate with adjustable imaging thickness.

neuroscience↗

bioRxiv2017

Functional Compensation Between Hematopoietic Stem Cells In Vivo

In most organ systems, regeneration is a coordinated effort that involves many stem cells, but little is known about whether and how individual stem cells compensate for the functional deficiencies of other stem cells. Functional compensation between stem cells is critically important during disease progression and treatment. Here, we show how individual hematopoietic stem cells (HSCs) in a mouse heterogeneously compensate for the deficiencies of other HSCs during lymphopoiesis by increasing their clonal expansion at specific differentiation stages. This compensation rescues the overall blood supply and influences blood cell types outside of the deficient lineages in distinct patterns. We have identified the molecular regulators and signaling pathways in HSCs that are involved in this process. Our data demonstrate how stem cells interact with each other to constitute a coordinated network that is robust enough to withstand minor functional disruptions. Exploiting the innate compensation capacity of stem cell networks may improve the prognosis and treatment of many diseases.

systems biology↗

bioRxiv2017

A general method to fine-tune fluorophores for live-cell and in vivo imaging

AO_SCPCAPBSTRACTC_SCPCAPPushing the frontier of fluorescence microscopy requires the design of enhanced fluorophores with finely tuned properties. We recently discovered that incorporation of four-membered azetidine rings into classic fluorophore structures elicits substantial increases in brightness and photostability, resulting in the Janelia Fluor (JF) series of dyes. Here, we refine and extend this strategy, showing that incorporation of 3-substituted azetidine groups allows rational tuning of the spectral and chemical properties with unprecedented precision. This strategy yields a palette of new fluorescent and fluorogenic labels with excitation ranging from blue to the far-red with utility in live cells, tissue, and animals.

cell biology↗