Biology subjects

Li, J. Y.

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

11 recordsLinked to original sources

bioRxiv2025

Oxygen uptake in human donor corneas: the centripetal gradient and its changes in culture and correlation with wounds and aminophylline treatment

Oxygen is a diatomic element abundant in the atmosphere and is essential for homeostatic and metabolic processes within the cornea. The avascular cornea uptakes oxygen from the atmosphere and performs refractory and protective functions that are essential for eyesight. However, the spatial-temporal profile of oxygen uptake (O2U) in human corneas remains uncharacterized in literature. Utilizing the micro optrode technique and donor corneas, we demonstrated that the limbus has a significantly higher O2U than the cornea center, exhibiting a pattern of centripetal gradient of O2U. This pattern is thus conserved in the corneas of mice, rats, non-human primates, and humans, representing a metabolic feature of physiological significance, which may have diagnostic and prognostic value. Being cultured at 37{degrees}C and 5% CO2, this centripetal pattern became more prominent in the first three days, and less so on day 4. The pattern remained in the corneas with injury, increased O2U appears to correlate with wound healing, similar to patterns observed in animal models with a dynamic increase of metabolism in the periphery, followed by the limbus, and subsequent return to baseline. Administration of the drug aminophylline prevented a decrease of O2U at day 4. We conclude that the centripetal pattern of O2U is conserved across species and in the human cornea. Combined, our results suggest the functional and clinical significance of the mesoscopic metabolism pattern for further study and the use of aminophylline as a therapeutic agent to increase O2U and enhance corneal wound healing.

cell biology↗

bioRxiv2025

Synaptic dynamics govern spatial integration in mouse visual cortex

Neurons in primary visual cortex are often suppressed by stimuli extending beyond their receptive fields. This surround suppression is proposed to reduce the redundancy of encoding large stimuli and support scene segmentation. We find that surround suppression decreases firing rates in mouse primary visual cortex by accelerating the decay of visually-evoked responses and reducing response duration. The rapid decay of visual responses at large sizes is enhanced by increased contrast, reduced by locomotion, and invariant to stimulus orientation, consistent with the engagement of a network mechanism. While fast-spiking interneurons have faster dynamics relative to neighboring pyramidal cells, the dynamics of somatostatin-expressing interneurons are delayed. At the subthreshold level, the rapid decay of visual responses with increasing size is due to a delayed removal of both synaptic excitation and inhibition below baseline levels following visual input. We propose that the delayed activation of somatostatin-expressing interneurons drives a network-wide suppression and accelerates the decay of the visual response. Thus, these data identify a key role for synaptic network dynamics in regulating both spatial and temporal integration in mouse visual cortex.

neuroscience↗

bioRxiv2024

Behavioral state and stimulus strength regulate the role of somatostatin interneurons in stabilizing network activity

Inhibition stabilization enables cortical circuits to encode sensory signals across diverse contexts. Somatostatin-expressing (SST) interneurons are well-suited for this role through their strong recurrent connectivity with excitatory pyramidal cells. We developed a cortical circuit model predicting that SST cells become increasingly important for stabilization as sensory input strengthens. We tested this prediction in mouse primary visual cortex by manipulating excitatory input to SST cells, a key parameter for inhibition stabilization, with a novel cell-type specific pharmacological method to selectively block glutamatergic receptors on SST cells. Consistent with our model predictions, we find antagonizing glutamatergic receptors drives a paradoxical facilitation of SST cells with increasing stimulus contrast. In addition, we find even stronger engagement of SST-dependent stabilization when the mice are aroused. Thus, we reveal that the role of SST cells in cortical processing gradually switches as a function of both input strength and behavioral state.

neuroscience↗

bioRxiv2023

Epigenetic regulation of Leukocyte associated immunoglobulin-like receptors 1 and 2 by interferon signaling in macrophages and T cells

BackgroundInhibitory immune receptors are important for maintaining immune homeostasis. We recently identified epigenetic alterations in two members of this group, LAIR1 and LAIR2, in patients with inflammatory tissue damage and recurrent skin and soft tissue infections. We therefore hypothesized that the expression of LAIR1 and LAIR2 may be controlled by immune stimuli acting on discrete transcriptional regulatory elements. MethodsWe used flow cytometry, qRT-PCR, and RNAseq to assay LAIR1 and LAIR2 expression in human and murine immune cell subsets at baseline and post-treatment with immune mediators, including type I and II interferons, tumor necrosis factor-alpha (TNF-[a]), and lipopolysaccharide (LPS). Using chromatin immunoprecipitation sequencing (ChIP-seq), we identified candidate transcriptional regulatory elements of LAIR genes and evaluated their regulatory activity using luciferase reporters. ResultsBoth human and murine macrophages significantly upregulate LAIR1 expression as they differentiate from monocytes to macrophages. In response to interferons, LAIR1 protein levels increase, while LPS causes a relative reduction. Regulatory elements flanking LAIR genes exhibit distinct patterns of enhancer activity with variable responses to immune stimuli. These responses are related to discrete sets of transcription factors in inflammatory pathways that correlate with cell-specific LAIR expression patterns. In addition, we identified LAIR1 and LAIR2 regulatory elements that act as foci of 3D genome interactions with other highly active regulatory elements. ConclusionsOur findings define the complex regulatory landscapes of human and mouse LAIR genes and reveal new insights into the transcriptional regulatory mechanisms that control the expression of these important immune modulatory proteins.

immunology↗

bioRxiv2023

Input-specific synaptic depression shapes temporal integration in mouse visual cortex

Efficient sensory processing requires the nervous system to adjust to ongoing features of the environment. In primary visual cortex (V1), neuronal activity strongly depends on recent stimulus history. Existing models can explain effects of prolonged stimulus presentation, but remain insufficient for explaining effects observed after shorter durations commonly encountered under natural conditions. We investigated the mechanisms driving adaptation in response to brief (100 ms) stimuli in L2/3 V1 neurons by performing in vivo whole-cell recordings to measure membrane potential and synaptic inputs. We find that rapid adaptation is generated by stimulus-specific suppression of excitatory and inhibitory synaptic inputs. Targeted optogenetic experiments reveal that these synaptic effects are due to input-specific short-term depression of transmission between layers 4 and 2/3. Thus, distinct mechanisms are engaged following brief and prolonged stimulus presentation and together enable flexible control of sensory encoding across a wide range of time scales.

neuroscience↗

bioRxiv2022

Maternal immune activation and adolescent alcohol exposure increases alcohol drinking and disrupts cortical-striatal-hippocampal oscillations in adult offspring

Maternal immune activation (MIA) is strongly associated with an increased risk of developing mental illness in adulthood, which often co-occurs with alcohol misuse. The current study aimed to begin to determine whether MIA, combined with adolescent alcohol exposure (AE), could be used as a model with which we could study the neurobiological mechanisms behind such co-occurring disorders. Pregnant Sprague-Dawley rats were treated with PolyI:C or saline on gestational day 15. Half of the offspring were given continuous access to alcohol during adolescence, leading to four experimental groups: controls, MIA, AE, and Dual (MIA + AE). We then evaluated whether MIA and/or AE alters: 1) alcohol consumption; and 2) cortical-striatal-hippocampal oscillations in adult offspring. Dual rats, particularly females, drank significantly more alcohol in adulthood compared to all other groups. Using machine learning to build predictive models from oscillations, we were able to differentiate Dual rats from control rats and AE rats in both sexes, and Dual rats from MIA rats in females. The current data suggest that MIA+AE (Dual "hits") is a valuable model that we can use to study the neurobiological underpinnings of co-occurring disorders. Our future work aims to extend these findings to other addictive substances to enhance the translational relevance of this model.

neuroscience↗

bioRxiv2021

OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization

Elucidating the wiring diagram of the human cell is a central goal of the post-genomic era. We combined genome engineering, confocal live-cell imaging, mass spectrometry and data science to systematically map the localization and interactions of human proteins. Our approach provides a data-driven description of the molecular and spatial networks that organize the proteome. Unsupervised clustering of these networks delineates functional communities that facilitate biological discovery, and uncovers that RNA-binding proteins form a specific sub-group defined by unique interaction and localization properties. Furthermore, we discover that remarkably precise functional information can be derived from protein localization patterns, which often contain enough information to identify molecular interactions. Paired with a fully interactive website opencell.czbiohub.org, we provide a resource for the quantitative cartography of human cellular organization.

cell biology↗

bioRxiv2020

Distinct recruitment of feed-forward and recurrent pathways across higher-order areas of mouse visual cortex

Cortical visual processing transforms features of the external world into increasingly complex and specialized neuronal representations. These transformations arise in part through target-specific routing of information; however, within-area computations may also contribute to area-specific function. Here, we sought to determine whether higher-order visual cortical areas LM, AL, PM, and AM have specialized anatomical and physiological properties by using a combination of whole-cell recordings and optogenetic stimulation of V1 axons in vitro. We discovered area-specific differences in the strength of recruitment of interneurons through feed-forward and recurrent pathways, as well as differences in cell-intrinsic properties and interneuron densities. These differences were most striking when comparing across medial and lateral areas, suggesting that these areas have distinct profiles for net excitability and integration of V1 inputs. Thus, cortical areas are not defined simply by the information they receive, but also by area-specific circuit properties that enable specialized filtering of these inputs.

neuroscience↗

bioRxiv2020

Therapy-induced transdifferentiation promotes glioma growth independent of EGFR signaling

Epidermal growth factor receptor (EGFR) is frequently amplified, mutated and overexpressed in malignant gliomas. Yet the EGFR-targeted therapies have thus far produced only marginal clinical response, and the underlying mechanism remains poorly understood. Through analyses of an inducible oncogenic EGFR-driven glioma mouse model system, our current study reveals a small population of glioma cells that can evade therapy-initiated apoptosis and potentiate relapse development by adopting a mesenchymal-like phenotypic state that no longer depends on oncogenic EGFR signaling. Transcriptome analyses of proximal and distal treatment responses further identify TGF{beta}/YAP/Slug signaling cascade activation as major regulatory mechanism that promotes therapy-induced glioma mesenchymal lineage transdifferentiation. Following anti-EGFR treatment, the TGF{beta} secreted from the stressed glioma cells acts to promote YAP nuclear translocation and activation, which subsequently stimulates upregulation of the pro-mesenchymal transcriptional factor Slug and then glioma lineage transdifferentiation towards a stable therapy-refractory state. Blockade of this adaptive response through enforced dominant negative YAP expression significantly delayed anti-EGFR relapse and significantly prolonged animal survival. Together, our findings shed new insight into EGFR-targeted therapy resistance and suggest that combinatorial therapies of targeting both EGFR and mechanisms underlying glioma lineage transdifferentiation could ultimately lead to deeper and more durable responses. SignificanceThis study demonstrates that molecular reprogramming and lineage transdifferentiation underlie anti-EGFR therapy resistance and is clinically relevant to the development of new combinatorial targeting strategies against malignant gliomas carrying aberrant EGFR signaling.

cancer biology↗

bioRxiv2019

Protocol development for discovery of angiogenesis inhibitors via automated methods using zebrafish

Their optical clarity as larvae and embryos, small size, and high fecundity make zebrafish ideal for whole animal high throughput screening. A high-throughput drug discovery platform (HTP) has been built to perform fully automated screens of compound libraries with zebrafish embryos. A Tg(Flk1:EGFP) line, marking endothelial cell cytoplasm, was used in this work to help develop protocols and functional algorithms for the system, with the intent of screening for angiogenesis inhibitors. Indirubin 3 Monoxime (I3M), a known angiogenesis inhibitor, was used at various concentrations to validate the protocols. Consistent with previous studies, a dose dependant inhibitory effect of I3M on angiogenesis was confirmed. The methods and protocols developed here could significantly increase the throughput of drug screens, while limiting human errors. These methods are expected to facilitate the discovery of novel anti-angiogenesis compounds and can be adapted for many other applications in which samples have a good fluorescent signal.

developmental biology↗

bioRxiv2018

Specification of diverse cell types during early neurogenesis of the mouse cerebellum

We applied single-cell RNA sequencing to profile genome-wide gene expression in about 9,400 individual cerebellar cells from the mouse embryo at embryonic day 13.5. Reiterative clustering identified the major cerebellar cell types and subpopulations of different lineages. Through pseudotemporal ordering to reconstruct developmental trajectories, we identified novel transcriptional programs controlling cell fate specification of populations arising from the ventricular zone and the anterior rhombic lip, two distinct germinal zones of the embryonic cerebellum. Together, our data revealed cell-specific markers for studying the cerebellum, important specification decisions, and a number of previously unknown subpopulations that may play an integral role in the formation and function of the cerebellum. Importantly, we identified a potential mechanism of vermis formation, which is affected by multiple congenital cerebellar defects. Our findings will facilitate new discovery by providing insights into the molecular and cell type diversity in the developing cerebellum.

developmental biology↗