Biology subjects

Lee, J. M.

Publications and source records attributed to Lee, J. M..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Injectable ventral spinal stimulator evokes programmable and biomimetic hindlimb motion

Spinal cord neuromodulation can restore partial to complete loss of motor functions associated with neuromotor disease and trauma. Current technologies have made substantial progress, but have limitations as dorsal epidural or intraspinal devices that are either remote to ventral motor neurons or subject to surgical intervention in the spinal tissue. Here, we describe a flexible and stretchable spinal stimulator design with nanoscale thickness that can be implanted by minimally-invasive injection through a polymeric catheter to target the ventral spinal space of mice. Ventrolaterally implanted devices exhibited substantially lower stimulation threshold currents and more precise recruitment of motor pools than comparable dorsal epidural implants. Functionally relevant and novel hindlimb movements were achieved via specific stimulation patterns of the electrodes. This approach holds translational potential for improving controllable limb function following spinal cord injury or neuromotor disease.

bioengineering↗

bioRxiv2023

Stitching flexible electronics into the brain

Understanding complex neuronal networks requires monitoring long-term neuronal activity in various regions of the brain. Significant progress has been made in multi-site implantations of well-designed probes, such as multi-site implantation of Si-based and polymer-based probes. However, these multi-probe strategies have been limited by the sizes and weights of interfaces to the multiple probes and the inability to track the activity of the same neurons and changes in neuronal activity over longer time periods. Here, we report a long single flexible probe that can be implanted by stitching into multiple regions of the mouse brain and subsequently transmit chronically-stable neuronal signals from the multiple sites via a single low-mass interface. We implanted the probe at four different sites using a glass capillary needle or two sites using an ultrathin metal needle. In-vitro tests in brain-mimicking hydrogel showed that multi-site probe implantations achieved a high connection yield of >86%. In-vivo histological images at each site of probes, implanted by stitching using either glass capillary or ultrathin metal insertion needles exhibit seamless tissue-probe interfaces with negligible chronic immune response. In addition, electrophysiology studies demonstrated the ability to track single neuron activities at every injection site with chronic stability over at least one month. Notably, the measured spike amplitudes and signal-to-noise ratios at different implantation sites showed no statistically significant differences. Multi-site stitching implantation of flexible electronics in the brain opens up new opportunities for both fundamental neuroscience research and electrotherapeutic applications.

bioengineering↗

bioRxiv2023

An Exploratory Multi-Session Study of Learning High-Dimensional Body-Machine Interfacing for Assistive Robot Control

Individuals who suffer from severe paralysis often lose the capacity to perform fundamental body movements and everyday activities. Empowering these individuals with the ability to operate robotic arms, in high-dimensions, helps to maximize both functional utility and human agency. However, high-dimensional robot teleoperation currently lacks accessibility due to the challenge in capturing high-dimensional control signals from the human, especially in the face of motor impairments. Body-machine interfacing is a viable option that offers the necessary high-dimensional motion capture, and it moreover is noninvasive, affordable, and promotes movement and motor recovery. Nevertheless, to what extent body-machine interfacing is able to scale to high-dimensional robot control, and whether it is feasible for humans to learn, remains an open question. In this exploratory multi-session study, we demonstrate the feasibility of human learning to operate a body-machine interface to control a complex, assistive robotic arm in reaching and Activities of Daily Living tasks. Our results suggest the manner of control space mapping, from interface to robot, to play a critical role in the evolution of human learning.

bioengineering↗

bioRxiv2023

GolpHCat (TMEM87A): a unique voltage-gated and pH-sensitive cation channel in the Golgi

The Golgi apparatus is a critical intracellular organelle that is responsible for modifying, packaging, and transporting proteins to their destinations. Golgi homeostasis involving the acidic pH, ion concentration, and membrane potential, is critical for proper functions and morphology of the Golgi. Although transporters and anion channels that contribute to Golgi homeostasis have been identified, the molecular identity of cation channels remains unknown. Here we identify TMEM87A as a novel Golgi-resident cation channel that contributes to pH homeostasis and rename it as GolpHCat (Golgi pH-sensitive Cation channel). The genetic ablation of GolpHCat exhibits an impaired resting pH in the Golgi. Heterologously expressed GolpHCat displays voltage- and pH-dependent, non-selective cationic, and inwardly rectifying currents, with potent inhibition by gluconate. Furthermore, reconstitution of purified GolpHCat in liposomes generates functional channel activities with unique voltage-dependent gating and ion permeation. GolpHCat is expressed in various cell types such as neurons and astrocytes in the brain. In the hippocampus, GolpHCat-knockout mice show dilated Golgi morphology and altered glycosylation and protein trafficking, leading to impaired spatial memory with significantly reduced long-term potentiation. We elucidate that GolpHCat, by maintaining Golgi membrane potential, regulates ionic and osmotic homeostasis, protein glycosylation/trafficking, and brain functions. Our results propose a new molecular target for Golgi-related diseases and cognitive impairment.

molecular biology↗

bioRxiv2022

Diversity of Learning to Control Complex Rehabilitation Robots Using High-Dimensional Interfaces

Upper body function is lost when injuries are sustained to the cervical spinal cord. Assistive machines can support the loss in upper body motor function. To regain functionality at the level of performing activities of daily living (e.g., self-feeding), though, assistive machines need to be able to operate in high dimensions. This means there is a need for interfaces with the capability to match high-dimensional operation. The body-machine interface provides this capability and has shown to be a suitable interface even for individuals with limited mobility. This is because it can take advantage of peoples available residual body movements. Previous studies using this interface have only shown that the interface can control low-dimensional assistive machines. In this pilot study, we demonstrate the interface can scale to high-dimensional robots, can be learned to control a 7-dimensional assistive robotic arm, to perform complex reaching and functional tasks, by an uninjured population. We also share results from various analyses that hint at learning, even when performance is extremely low. Decoupling intrinsic correlations between robot control dimensions seem to be a factor in learning--that is, proficiency in activating each control dimension independently may contribute to learning and skill acquisition of high-dimensional robot control. In addition, we show that learning to control the robot and learning to perform complex movement tasks can occur simultaneously.

bioengineering↗

bioRxiv2022

Highly efficient protein expression of Plasmodium vivax surface antigen, Pvs25 by silkworm, Bombyx mori, and its biochemical analysis.

Plasmodium vivax ookinete surface protein, Pvs25 is a transmission-blocking vaccine (TBV) candidate for malaria. Pvs25 has four EGF-like domains containing 22 cysteine residues forming 11 intramolecular disulfide bonds and this structural feature makes recombinant expression of Pvs25 difficult. In this study, we report the high expression of recombinant Pvs25 as a soluble form in silkworm, Bombyx mori. The Pvs25 protein was purified from hemolymphs of larvae and pupae by affinity chromatography. In the Pvs25 expressed by silkworm, no isoform with inappropriate disulfide bonds was found, requiring no further purification step which is necessary in case of Pichia pastoris based expressions systems. The Pvs25 from silkworm were confirmed to be the molecularly uniform by sodium dodecyl sulfate gel electrophoresis analysis and size exclusion chromatography analysis. To examine the immunogenicity, the Pvs25 from B. mori, was administered to BALB/c mice by the subcutaneous (s.c.) route with the oil adjuvant. The Pvs25 produced by silkworm induced potent and robust immune response, and the induced antisera correctly recognized P. vivax ookinetes in vitro, demonstrating the potency of Pvs25 from silkworm as a TBV candidate for malaria. This is the first study that to construct a mass production system for malaria TBV antigens by the silkworm to the best of our knowledge.

biochemistry↗

bioRxiv2022

SUMOylation of ABCD3 restricts bile acid synthesis and regulates metabolic homeostasis

Mitochondrial anchored protein ligase (MAPL) has been shown to function as both a SUMO and ubiquitin ligase with multiple roles in mitochondrial quality control, cell death pathways and inflammation. To examine the global function of MAPL we generated a knock-out mouse model and sought functional insight through unbiased BioID, transcriptomics and metabolic analysis. MAPL KO mice are lean and highly insulin sensitive, ultimately developing fully penetrant, spontaneous hepatocellular carcinoma after 18 months. BioID revealed the peroxisomal bile acid transporter ABCD3 as a primary MAPL interacting partner, which we show is SUMOylated in a MAPL-dependent manner. MAPL KO animals showed increased bile acid secretion in vivo and in isolated primary hepatocytes, along with robust compensatory changes in the expression of enzymes synthesizing and detoxifying bile acid. In addition, MAPL KO livers showed signs of ER stress and secreted high levels of Fgf21, the starvation hormone known to drive the reduction of white fat stores and promote insulin sensitivity. Lastly, during aging all MAPL KO mice developed hepatocellular carcinomas. These data reveal a major function for MAPL in the regulation of bile acid synthesis leading to profound changes in whole body metabolism and the ultimate generation of liver cancer when MAPL is lost.

cell biology↗

bioRxiv2021

Clomipramine suppresses ACE2-mediated SARS-CoV-2 entry

Myocardial damage caused by the newly emerged coronavirus (SARS-CoV-2) infection is one of key determinants of COVID-19 severity and mortality. SARS-CoV-2 entry to host cells are initiated by binding with its receptor, angiotensin converting enzyme (ACE) 2, and the ACE2 abundance is thought to reflect the susceptibility to infection. Here, we found that clomipramine, a tricyclic antidepressant, potently inhibits SARS-CoV-2 infection and metabolic disorder in human iPS-derived cardiomyocytes. Among 13 approved drugs that we have previously identified as potential inhibitor of doxorubicin-induced cardiotoxicity, clomipramine showed the best potency to inhibit SARS-CoV-2 spike glycoprotein pseudovirus-stimulated ACE2 internalization. Indeed, SARS-CoV-2 infection to human iPS-derived cardiomyocytes (iPS-CMs) and TMPRSS2-expressing VeroE6 cells were dramatically suppressed even after treatment with clomipramine. Furthermore, the combined use of clomipramine and remdesivir was revealed to synergistically suppress SARS-CoV-2 infection. Our results will provide the potentiality of clomipramine for the breakthrough treatment of severe COVID-19.

pharmacology and toxicology↗

bioRxiv2020

TRANsCre-DIONE transdifferentiates scar-forming reactive astrocytes into functional motor neurons

In spinal cord injury (SCI), the scar-forming reactive astrocytes with upregulated GFAP proliferate aberrantly near the injury site, allowing themselves as a prime target for transdifferentiation into neurons to replenish dead neurons. However, the conventional use of GFAP promoter to target reactive astrocytes has two inherent problems: inadvertent conversion of normal astrocytes and low efficiency due to progressive weakening of promoter activity during transdifferentiation. Here, we report that the scar-forming reactive astrocytes are selectively transdifferentiated into neurons with 87% efficiency and 96% specificity via TRANsCre-DIONE, a combination of the split-Cre system under two different promoters of GFAP and Lcn2 and a Cre-loxP-dependent inversion and expression of Neurog2 under the strong EF1 promoter. After SCI, TRANsCre-DIONE caused transdifferentiation into Isl1-positive motor neurons, reduced astrogliosis, enhanced regeneration in surrounding cells, and a significant motor recovery. Our study proposes TRANsCre-DIONE as the next-generation therapeutic approach for patients suffering from SCI. HighlightsTRANsCre-DIONE converts reactive astrocyte into neuron by over-expression of Neurog2 Reactive astrocytes are targeted using split-Cre under two promoters, GFAP and Lcn2 TRANsCre-DIONE reduces reactivity, replaces dead neurons and alleviates symptom of SCI Transdifferentiated-neurons are GABA+ in the striatum and Isl1+ in the spinal cord

neuroscience↗

bioRxiv2019

Influenza H3 and H1 hemagglutinins have different genetic barriers for resistance to broadly neutralizing stem antibodies

In the past decade, the discovery and characterization of broadly neutralizing antibodies (bnAbs) to the highly conserved stem region of influenza hemagglutinin (HA) have provided valuable insights for development of a universal influenza vaccine. However, the genetic barrier for resistance to stem bnAbs has not been thoroughly evaluated. Here, we performed a series of deep mutational scanning experiments to probe for resistance mutations. We found that the genetic barrier to resistance to stem bnAbs is generally very low for the H3 subtype but substantially higher for the H1 subtype. Several resistance mutations in H3 cannot be neutralized by stem bnAbs at the highest concentration tested, do not reduce in vitro viral fitness and in vivo pathogenicity, and are often present in circulating strains as minor variants. Thus, H3 HAs have a higher propensity than H1 HAs to escape major stem bnAbs and creates a potential challenge in the development of a bona fide universal influenza vaccine. ONE SENTENCE SUMMARYAcquisition of resistance by influenza virus to broadly neutralizing hemagglutinin stem antibodies varies tremendously depending on subtype.

microbiology↗

bioRxiv2019

Mitochondria tether to Focal Adhesions during cell migration and regulate their size.

Mitochondria are the key generators of ATP in a cell. Visually, they are highly dynamic organelles that undergo cellular fission and fusion events in response to changing cellular energy requirements. Mitochondria are now emerging as regulators of mammalian cell motility. Here we show that mitochondria infiltrate the leading edge of NIH3T3 fibroblasts during migration. At the leading edge, we find that mitochondria move to and tether to Focal Adhesions (FA). FA regulate cell migration by coupling the cytoskeleton to the Extracellular Matrix through integrin receptors. Importantly, we find that inhibition of mitochondrial ATP generation concomitantly inhibits FA size. This suggests that mitochondrial energy production regulates migration through FA control.

cell biology↗

bioRxiv2019

Albumin inhibits the activation of hepatic stellate cells by suppressing TGF-β/Smad3 signaling via IL-1β

Activated hepatic stellate cells (HSCs) play a key role in liver fibrosis and inactivating HSCs has been considered a promising therapeutic approach. We previously showed that albumin and its derivative, retinol binding protein (RBP)-albumin domain III fusion protein (named R-III), inhibit HSC activation. Here, we investigate the mode of action of albumin and R-III. NF-{kappa}B in activated HSCs was evenly distributed in the cytoplasm, but albumin expression and R-III treatment (albumin/R-III) induced NF-{kappa}B nuclear translocation via retinoic acid (RA) sequestration, resulting in increased expression of interleukin-1{beta} (IL-1{beta}). In an IL-1{beta} dependent manner, albumin/R-III inhibited Smad3 nuclear translocation via TAK1-, JNK-mediated Smad3 linker phosphorylation and decreased expression of Smad3 target genes, such as -smooth muscle actin and collagen type I. Mutation of the Smad3 linker phosphorylation sites abolished R-III effects on Smad3. In conclusion, our data suggest that the anti-fibrotic effects of albumin/R-III are due to RA sequestration which downregulates RAR-mediated signaling and also TGF-{beta}/Smad3 signaling. This mechanistic elucidation of albumin function in HSCs provides clues to understanding the frequent albumin mutations found in hepatocellular carcinoma.

molecular biology↗

bioRxiv2019

Single-cell profiles of retinal neurons differing in resilience to injury reveal neuroprotective genes

Neuronal types in the central nervous system differ dramatically in their resilience to injury or insults. Here we studied the selective resilience of mouse retinal ganglion cells (RGCs) following optic nerve crush (ONC), which severs their axons and leads to death of ~80% of RGCs within 2 weeks. To identify expression programs associated with differential resilience, we first used single-cell RNA-seq (scRNA-seq) to generate a comprehensive molecular atlas of 46 RGC types in adult retina. We then tracked their survival after ONC, characterized transcriptomic, physiological, and morphological changes that preceded degeneration, and identified genes selectively expressed by each type. Finally, using loss- and gain-of-function assays in vivo, we showed that manipulating some of these genes improved neuronal survival and axon regeneration following ONC. This study provides a systematic framework for parsing type-specific responses to injury, and demonstrates that differential gene expression can be used to reveal molecular targets for intervention.

neuroscience↗

bioRxiv2019

Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin

A longstanding question is how influenza evolves to escape human immunity, which is polyclonal and can target many distinct epitopes on the virus. Here we map how all amino-acid mutations to influenzas major surface protein affect viral neutralization by polyclonal human sera. The serum of some individuals is so focused that it selects single mutations that reduce viral neutralization by over an order of magnitude. However, different viral mutations escape the sera of different individuals. This individual-to-individual variation in viral escape mutations is not present among ferrets, which are frequently used as a model in influenza studies. Our results show how different single mutations help influenza escape the immunity of different members of the human population, a phenomenon that could shape viral evolution and disease susceptibility.

microbiology↗

bioRxiv2018

Chlamydia muridarum infection differentially changes smooth muscle contractility and responses to prostaglandins in uterus and cervix

Chlamydia trachomatis infection is a primary cause of reproductive tract diseases including chronic pelvic pain and infertility. Previous studies showed that this infection alters physiological activities in mouse oviducts. Whether this occurs in the uterus and cervix has never been investigated. This study characterized the physiological activity of the uterus and the cervix in a Chlamydia muridarum (Cmu) mouse model of reproductive tract infection. Uterine or cervix smooth muscle contractility, responses to oxytocin or prostaglandins (PGF2 and PGE2) and mRNA expression of oxytocin and PG receptors were assessed 14 days post infection. Cmu infection did not affect the contractions of the uterine horn but significantly decreased the contraction amplitude of the cervix. Cmu infection did not alter the responses of uterine horn or cervix to oxytocin, however PGF2 induced contractions of the uterine horn, but not the cervix, were significantly increased following Cmu infection. PGE2 contraction amplitude in both the uterine horn and cervix was unaffected by Cmu infection. An upregulation of Ptgfr and a down-regulation of Ptegr4 mRNA expression was observed in the uterine horn following Cmu infection. These results indicate that Cmu infection alters contractility and prostaglandin signalling in the female reproductive tract but the effects are localised to specific regions.

physiology↗

bioRxiv2018

Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants

Human influenza virus rapidly accumulates mutations in its major surface protein hemagglutinin (HA). The evolutionary success of influenza virus lineages depends on how these mutations affect HAs functionality and antigenicity. Here we experimentally measure the effects on viral growth in cell culture of all single amino-acid mutations to the HA from a recent human H3N2 influenza virus strain. We show that mutations that are measured to be more favorable for viral growth are enriched in evolutionarily successful H3N2 viral lineages relative to mutations that are measured to be less favorable for viral growth. Therefore, despite the well-known caveats about cell-culture measurements of viral fitness, such measurements can still be informative for understanding evolution in nature. We also compare our measurements for H3 HA to similar data previously generated for a distantly related H1 HA, and find substantial differences in which amino acids are preferred at many sites. For instance, the H3 HA has less disparity in mutational tolerance between the head and stalk domains than the H1 HA. Overall, our work suggests that experimental measurements of mutational effects can be leveraged to help understand the evolutionary fates of viral lineages in nature -- but only when the measurements are made on a viral strain similar to the ones being studied in nature.\n\nSignificance StatementA key goal in the study of influenza virus evolution is to forecast which viral strains will persist and which ones will die out. Here we experimentally measure the effects of all amino-acid mutations to the hemagglutinin protein from a human H3N2 influenza strain on viral growth in cell culture. We show that these measurements have utility for distinguishing among viral strains that do and do not succeed in nature. Overall, our work suggests that new high-throughput experimental approaches may be useful for understanding virus evolution in nature.

evolutionary biology↗

bioRxiv2017

Quantifying the ease of viral escape from broad and narrow antibodies to influenza hemagglutinin

Influenza virus can completely escape most antibodies with single mutations. However, rare antibodies broadly neutralize many viral strains. It is unclear how easily influenza virus might escape such antibodies if it was under strong pressure to do so. Here we map all single amino-acid mutations that increase resistance to broad antibodies targeting an H1 hemagglutinin. Crucially, our approach not only identifies antigenic mutations but also quantifies their effect sizes. All antibodies select mutations, but the effect sizes vary widely. The virus can escape a broad antibody that targets residues in hemagglutinins receptor-binding site the same way it escapes narrow strain-specific antibodies: via single mutations with huge effects. In contrast, broad antibodies targeting hemagglutinins stalk only select mutations with small effects. Therefore, among the antibodies we have examined, breadth is an imperfect indicator of the potential for viral escape via single mutations. Broadly neutralizing antibodies targeting the H1 hemagglutinin stalk are quantifiably harder to escape than the other antibodies tested here.

microbiology↗

bioRxiv2017

Uncovering Medical Insights from Vast Amounts of Biomedical Data in Clinical Case Reports

Clinical case reports (CCRs) have a time-honored tradition in serving as an important means of sharing clinical experiences on patients presenting with atypical disease phenotypes or receiving new therapies. However, the huge amount of accumulated case reports are isolated, unstructured, and heterogeneous clinical data, posing a great challenge to clinicians and researchers in mining relevant information through existing indexing tools. In this investigation, in order to render CCRs more findable, accessible, interoperable, and reusable (FAIR) by the biomedical community, we created a resource platform, including the construction of a test dataset consisting of 1000 CCRs spanning 14 disease phenotypes, a standardized metadata template and metrics, and a set of computational tools to automatically retrieve relevant medical information and to analyze all published PubMed clinical case reports with respect to trends in publication journals, citations impact, MeSH Terms, drug use, distributions of patient demographics, and relationships with other case reports and databases. Our standardized metadata template and CCR test dataset may be valuable resources to advance medical science and improve patient care for researchers who are using machine learning approaches with a high-quality dataset to train and validate their algorithms. In the future, our analytical tools may be applied towards other large clinical data sources as well.

bioinformatics↗