Biology subjects

Shen, K.

Publications and source records attributed to Shen, K..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

Signal complexity indicators of health status in clinical-EEG

Brain signal variability changes across the lifespan in both health and disease, likely reflecting changes in information processing capacity related to development, aging and neurological disorders. While signal complexity, and multiscale entropy (MSE) in particular, has been proposed as a biomarker for neurological disorders, most observations of altered signal complexity have come from studies comparing patients with few to no comorbidities against healthy controls. In this study, we examined whether MSE of brain signals was distinguishable across individuals in a large and heterogeneous set of clinical-EEG data. Using a multivariate analysis, we found unique timescale-dependent differences in MSE across various neurological disorders. We also found MSE to differentiate individuals with non-brain comorbidities, suggesting that MSE is sensitive to brain signal changes brought about by metabolic and other non-brain disorders. Such changes were not detectable in the spectral power density of brain signals. Our findings suggest that brain signal complexity may offer complementary information to spectral power about an individuals health status and is a promising avenue for clinical biomarker development.

neuroscience↗

bioRxiv2021

mTOR-activating mutations in RRAGD cause kidney tubulopathy and cardiomyopathy (KICA) syndrome

BackgroundOver the last decaces, advances in genetic techniques have resulted in the identification of rare hereditary disorders of renal magnesium and salt handling. Nevertheless, {+/-}20% of all tubulopathy patients remain without genetic diagnosis. Here, we explore a large multicentric patient cohort with a novel inherited salt-losing tubulopathy, hypomagnesemia and dilated cardiomyopathy (DCM). MethodsWhole exome and genome sequencings were performed with various subsequent functional analyses of identified RRAGD variants in vitro. ResultsIn 8 children from unrelated families with a tubulopathy characterized by hypomagnesemia, hypokalemia, salt-wasting, and nephrocalcinosis, we identified heterozygous missense variants in RRAGD that mostly occurred de novo. Six of these patients additionally suffered from DCM requiring heart transplantation in 3 of them. An additional dominant variant in RRAGD was simultaneously identified in eight members of a large family with a similar renal phenotype. RRAGD encodes GTPase RagD mediating amino acid signaling to the mechanistic target of rapamycin complex 1 (mTORC1). RagD expression along the mammalian nephron include the thick ascending limb and the distal convoluted tubule. The identified RRAGD variants were shown to induce a constitutive activation of mTOR signaling in vitro, ConclusionsOur findings establish a novel disease phenotype combining kidney tubulopathy and cardiomyopathy (KICA) caused by an activation of mTOR signaling suggesting a critical role of Rag GTPase D for renal electrolyte handling and cardiac function. SIGNIFICANCE STATEMENTHere, we report on heterozygous variants in RRAGD in patients with profound hypomagnesemia, renal salt wasting, nephrocalcinosis, and dilated cardiomyopathy. The identified RagD variants induce a constitutive activation of mTOR signaling in vitro. These findings not only establish a novel monogenic disorder of the kidney tubule, but demonstrate the essential role of mTOR signaling for distal tubular electrolyte handling and cardiac function.

genetics↗

bioRxiv2020

Topological Insights into Mutant Huntingtin Exon 1 and PolyQ Aggregates by Cryo-Electron Tomography

Huntington disease (HD) is a neurodegenerative trinucleotide repeat disorder caused by an expanded poly-glutamine (polyQ) tract in the mutant huntingtin (mHTT) protein. The formation and topology of filamentous mHTT inclusions in the brain (hallmarks of HD implicated in neurotoxicity) remain elusive. Using cryo-electron tomography and subtomogram averaging, here we show that mHTT exon 1 and polyQ-only aggregates in vitro are structurally heterogenous and filamentous, similar to prior observations with other methods. Yet, we observed some filaments in both types of aggregates under [~]2 nm in width, thinner than previously reported, while other regions form large sheets. In addition, our data show a prevalent subpopulation of filaments exhibiting a lumpy, slab-shaped morphology in both aggregates, supportive of the "polyQ core" model. This provides a basis for future cryoET studies of various aggregated mHTT and polyQ constructs to improve their structure-based modeling and their identification in cells without fusion tags.

molecular biology↗

bioRxiv2020

Repression of lysosomal transcription factors Tfeb and Tfe3 is essential for the development and function of microglia

As the primary phagocytic cells of the central nervous system, microglia exquisitely regulate their lysosomal activity to facilitate brain development and homeostasis. However, mechanisms that coordinate lysosomal activity with microglia development, migration, and function remain unclear. Here we show that embryonic macrophages require the lysosomal GTPase RagA and the GTPase-activating protein Folliculin to colonize the brain in zebrafish. We demonstrate that embryonic macrophages in rraga mutants show increased expression of lysosomal genes but display significant downregulation of immune and migration-related genes. Furthermore, we find that RagA and Folliculin repress the key lysosomal transcription factor Tfeb, and its homologs Tfe3a and Tfe3b, in the macrophage lineage. Using RNA-Sequencing, we establish that Tfeb and Tfe3 are required for activation of lysosomal target genes under conditions of stress but not for basal expression of lysosomal pathways. Collectively, our data define a lysosomal regulatory circuit essential for macrophage development and function in vivo. TeaserThe degradation machinery of the cell must be carefully controlled for the normal formation and function of key immune cells called microglia.

developmental biology↗

bioRxiv2020

An endoplasmic reticulum (ER) ATPase safeguards ER identity by removing ectopically localized mitochondrial proteins

Stringent targeting of membrane proteins to corresponding organelles is essential for organelle identity and functions. In addition to molecular pathways that target proteins to appropriate organelles, surveillance mechanisms clear mistargeted proteins from undesired destinations. While Msp1 functions on mitochondrial membrane to remove mistargeted proteins, the surveillance mechanism for the ER is not well understood. Here, we show that mitochondrial tail-anchored (TA) and signal-anchored (SA) proteins mislocalize to ER membrane in neurons and muscles in C. elegans catp-8 mutants. catp-8 encodes a conserved P5A type ATPase, which localizes to ER and removes ectopic mitochondrial TA/SA proteins from ER. In catp-8 mutant, mitochondria fission protein FIS-1 mislocalizes to ER membrane. Together with another mitochondria fission protein MFF-2, FIS-1 causes ER fragmentation in a Dynamin related protein (DRP-1) dependent manner. Additionally, CATP-8 is essential for dendrite development. catp-8 mutant dramatically reduces the level of the dendrite guidance receptor DMA-1, leading to diminished dendritic arbors. Hence, P5A ATPase safeguards ER morphology and functions by preventing mitochondrial proteins mislocalization. HIGHLIGHTSCATP-8, a P5A type ATPase, localizes to ER and functions as a surveillance mechanism to remove mistargeted mitochondrial proteins. Multiple mitochondria proteins are mistargeted to ER in catp-8 mutants. Ectopic recruitment of mitochondria fission mechinary to ER causes ER fragmentation in catp-8 mutants. CATP-8 is essential for PVD dendrite morphogenesis through modulating the level of transmembrane receptor DMA-1.

cell biology↗

bioRxiv2020

TAEL 2.0: An Improved Optogenetic Expression System for Zebrafish

Inducible gene expression systems are valuable tools for studying biological processes. We previously developed an optogenetic gene expression system called TAEL that is optimized for use in zebrafish. When illuminated with blue light, TAEL transcription factors dimerize and activate gene expression downstream of the TAEL-responsive C120 promoter. By using light as the inducing agent, the TAEL/C120 system overcomes limitations of traditional inducible expression systems by enabling fine spatial and temporal regulation of gene expression. Here, we describe ongoing efforts to improve the TAEL/C120 system. We made modifications to both the TAEL transcriptional activator and the C120 regulatory element, collectively referred to as TAEL 2.0. We demonstrate that TAEL 2.0 consistently induces higher levels of reporter gene expression and at a faster rate, but with comparable background and toxicity as the original TAEL system. With these improvements, we were able to create functional stable transgenic lines to express the TAEL 2.0 transcription factor either ubiquitously or with a tissue-specific promoter. We demonstrate that the ubiquitous line in particular can be used to induce expression at late embryonic and larval stages, addressing a major deficiency of the original TAEL system. This improved optogenetic expression system will be a broadly useful resource for the zebrafish community.

developmental biology↗

bioRxiv2020

Mining the potential of VRS1-5 gene to raise barley grain yield

VRS1-5 genes determine spike row types during the early stages of spike development in barley (Hordeum vulgare), yet their functions for the determination of grain yield during the late stages of spike development are largely unknown. To assess the role of VRS1-5 genes in determining grain yield components, we sequenced VRS1-5 genes from 894 worldwide barley accessions and measured 19 spike morphology traits in four environments. Single nucleotide polymorphism SNP markers and gene marker-based haplotypes for VRS1-5 displayed close associations with spike morphology traits. We further developed a spatiote-temporal transcriptome atlas (255 samples) at 17 stages and five positions along the spike, that linked spike morphology to spikelet development and expression patterns of VRS1-5 genes. Phenotypic measurements demonstrated that mutations in VRS1-5 suppress the initiation of spikelet primordia and, trigger spikelet abortion by increasing cytokinin content and improving sensitivity of spikelet primordia to cytokinin. Our integrated results illustrate how breeding can globally alter spike morphology through diversity at the VRS1-5 genes, which show great potential in increasing barley grain yield.

developmental biology↗

bioRxiv2020

Proximity labeling at non-centrosomal microtubule-organizing centers reveals VAB-10B and WDR-62 as distinct microtubule regulators

Reorganization of microtubules from the centrosome to non-centrosomal subcellular sites is central to cell differentiation. To identify components of non-centrosomal microtubule organizing centers in differentiated cells of a living organism, we developed the biotin ligase-based proximity labeling approach TurboID for use in C. elegans. We identified proteins proximal to the non-centrosomal microtubule minus end protein PTRN-1/Patronin at the apical membrane of epithelial cells, focusing on two conserved proteins: spectraplakin protein VAB-10B and WDR-62, a protein we identify as homologous to vertebrate primary microcephaly disease gene WDR62. We found that WDR-62 and VAB-10B independently regulate the growth and localization of non-centrosomal microtubules and the apical targeting of microtubule minus end proteins. This regulation occurs downstream of cell polarity and in conjunction with actin. Our data suggest a division of labor where microtubule growth and anchoring are regulated by distinct complexes and uncover novel functions of spectraplakins and WDR62 family proteins.

cell biology↗

bioRxiv2020

SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain

The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and cells rendered permissive by ectopic expression of various mammalian ACE2 orthologs. Nonetheless, D614G affinity for ACE2 was reduced due to a faster dissociation rate. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts a critical interprotomer contact and that this dramatically shifts the S protein trimer conformation toward an ACE2-binding and fusion-competent state. Consistent with the more open conformation, neutralization potency of antibodies targeting the S protein receptor-binding domain was not attenuated. These results indicate that D614G adopts conformations that make virion membrane fusion with the target cell membrane more probable but that D614G retains susceptibility to therapies that disrupt interaction of the SARS-CoV-2 S protein with the ACE2 receptor.

microbiology↗

bioRxiv2020

Ceramic Packaging in Neural Implants

The lifetime of neural implants is strongly dependent on packaging due to the aqueous and biochemically aggressive nature of the body. Over the last decade, there has been a drive towards neuromodulatory implants which are wireless and approaching millimeter-scales with increasing electrode count. A so-far unrealized goal for these new types of devices is an in-vivo lifetime comparable to a sizable fraction of a healthy patient’s lifetime (>10-20 years). Existing, approved medical implants commonly encapsulate components in metal enclosures (e.g. titanium) with brazed ceramic inserts for electrode feedthrough. It is unclear how amenable the traditional approach is to the simultaneous goals of miniaturization, increased channel count, and wireless communication. Ceramic materials have also played a significant role in traditional medical implants due to their dielectric properties, corrosion resistance, biocompatibility, and high strength, but are not as commonly used for housing materials due to their brittleness and the difficulty they present in creating complex housing geometries. However, thin film technology has opened new opportunities for ceramics processing. Thin films derived largely from the semiconductor industry can be deposited and patterned in new ways, have conductivities which can be altered during manufacturing to provide conductors as well as insulators, and can be used to fabricate flexible substrates. In this review, we give an overview of packaging for neural implants, with an emphasis on how ceramic materials have been utilized in medical device packaging, as well as how ceramic thin film micromachining and processing may be further developed to create truly reliable, miniaturized, neural implantsCompeting Interest StatementThe authors have declared no competing interest.View Full Text

bioengineering↗

bioRxiv2020

SWELL1-LRRC8 complex regulates skeletal muscle cell size, intracellular signalling, adiposity and glucose metabolism

Maintenance of skeletal muscle is beneficial in obesity and Type 2 diabetes. Mechanical stimulation can regulate skeletal muscle differentiation, growth and metabolism, however the molecular mechanosensor remains unknown. Here, we show that SWELL1 (LRRC8a) functionally encodes a swell-activated anion channel that regulates PI3K-AKT, ERK1/2, mTOR signaling, muscle differentiation, myoblast fusion, cellular oxygen consumption, and glycolysis in skeletal muscle cells. SWELL1 over-expression in SWELL1 KO myotubes boosts PI3K-AKT-mTOR signaling to supra-normal levels and fully rescues myotube formation. Skeletal muscle targeted SWELL1 KO mice have smaller myofibers, generate less force ex vivo, and exhibit reduced exercise endurance, associated with increased adiposity under basal conditions, and glucose intolerance and insulin resistance when raised on a high-fat diet, compared to WT mice. These results reveal that the SWELL1-LRRC8 complex regulates insulin-PI3K-AKT-mTOR signalling in skeletal muscle to influence skeletal muscle differentiation in vitro and skeletal myofiber size, muscle function, adiposity and systemic metabolism in vivo.

cell biology↗

bioRxiv2020

Superior Colliculus-Projected GABAergic Retinal Ganglion Cells Mediate Looming-Evoked Flight Response

The looming stimulus-evoked flight response is an experimental paradigm for studying innate defensive behaviors. However, how the visual looming stimulus is transmitted from the retina to the brain remains poorly understood. Here, we report that superior colliculus (SC)-projecting RGCs transmit the looming signal from the retina to the brain to mediate the looming-evoked flight behavior by releasing GABA. In the mouse retina, GABAergic RGCs are capable of projecting to many brain areas, including the SC. Superior colliculus (SC)-projecting GABAergic RGCs (spgRGCs) are mono-synaptically connected to the parvalbumin-positive SC neurons known to be required for the looming-evoked flight response. Optogenetic activation of spgRGCs triggers GABA-mediated inhibition in SC neurons. The ablation or silence of spgRGCs compromises looming-evoked flight response but not image-forming functions. Therefore, this study shows that spgRGCs control the looming-evoked flight response by regulating SC neurons via GABA, providing novel insight into the regulation of innate defensive behaviors.

neuroscience↗

bioRxiv2020

PDH Mediated Mitochondrial Respiration Controls the Speed of Muscle Stem Cell Activation in Muscle Repair and Aging

Decline in the skeletal muscle stem cell (MuSC) function is a major contributor to age-associated impairments in muscle regeneration and function. The ability of MuSCs to activate (i.e. exit quiescence, enter the cell cycle, and divide) following injury is a critical step that initiates muscle regeneration. However, the mechanisms that regulate MuSC activation function are poorly understood. Here, we show that the activation function, specifically the speed by which cells progress through G0-G1, declines tremendously with age in mouse MuSCs. Using a number of in vivo models and ex vivo assays of MuSC activation and muscle regenerative functions, live cell metabolic flux analyses, and metabolomics we present data indicating that changes in MuSC mitochondrial flux underlie age-associated changes in MuSC activation. We show that, in the course of MuSC activation, there is a profound,16-fold, increase in ATP production rates, which is fueled largely by increases in pyruvate flux into mitochondria. We found that MuSCs from aged mice display progressive defects in the ability to increase mitochondrial flux during activation and that this correlates with higher levels of phosphorylated, inactivated, pyruvate dehydrogenase (PDH). Importantly, we demonstrate that pharmacologic and physiologic methods to induce dephosphorylation and activation of PDH in MuSCs are sufficient to rescue the activation and muscle regenerative functions of MuSCs in aged mice. Collectively the data presented show that MuSC mitochondrial function is a central regulator of MuSC activation and muscle regenerative functions. Moreover, our results suggest that approaches to increase MuSC pyruvate oxidation may have therapeutic potential to promote muscle repair and regeneration.

cell biology↗

bioRxiv2020

Completion and augmentation of connectomic datasets in dementia and Alzheimer's Disease using Virtual Patient Cohorts

Large neuroimaging datasets, including information about structural (SC) and functional connectivity (FC), play an increasingly important role in clinical research, where they guide the design of algorithms for automated stratification, diagnosis or prediction. A major obstacle is, however, the problem of missing features (e.g., lack of concurrent DTI SC and resting-state fMRI FC measurements for many of the subjects). We propose here to address the missing connectivity features problem by introducing strategies based on computational whole-brain network modeling. Using two datasets, the ADNI dataset and a healthy aging dataset, for proof-of-concept, we demonstrate the feasibility of virtual data completion (i.e., inferring "virtual FC" from empirical SC or "virtual SC" from empirical FC), by using self-consistent simulations of linear and nonlinear brain network models. Furthermore, by performing machine learning classification (to separate age classes or control from patient subjects) we show that algorithms trained on virtual connectomes achieve discrimination performance comparable to when trained on actual empirical data; similarly, algorithms trained on virtual connectomes can be used to successfully classify novel empirical connectomes. Completion algorithms can be combined and reiterated to generate realistic surrogate connectivity matrices in arbitrarily large number, opening the way to the generation of virtual connectomic datasets with network connectivity information comparable to the one of the original data. Significance statementPersonalized information on anatomical connectivity ("structural connectivity", SC) or coordinated resting state activation patterns ("functional connectivity, FC) is a source of powerful neuromarkers to detect and track the development of neurodegenerative diseases. However, there are often "gaps" in the available information, with only SC (or FC) being known but not FC (or SC). Exploiting whole-brain modelling, we show that gap in databases can be filled by inferring the other connectome through computational simulations. The generated virtual connectomic data carry information analogous to the one of empirical connectomes, so that machine learning algorithms can be trained on them. This opens the way to the release in the future of cohorts of "virtual patients", complementing traditional datasets in data-driven predictive medicine.

neuroscience↗

bioRxiv2019

Growth Cone-Localized Microtubule Organizing Center Establishes Microtubule Orientation in Dendrites

A polarized arrangement of neuronal microtubule arrays is the foundation of membrane trafficking and subcellular compartmentalization. Conserved among both invertebrates and vertebrates, axons contain exclusively "plus-end-out" microtubules while dendrites contain a high percentage of "minus-end-out" microtubules, the origins of which have been a mystery. Here we show that the dendritic growth cone contains a non-centrosomal microtubule organizing center (ncMTOC), which generates minus-end-out microtubules along outgrowing dendrites and plus-end-out microtubules in the growth cone. RAB-11-positive recycling endosomes accumulate in this region and are responsible for localizing the microtubule nucleation complex {gamma}-TuRC. The MTOC tracks the extending growth cone by kinesin-1/UNC-116-mediated endosome movements on distal plus-end-out microtubules and dynein-mediated endosome clustering near MTOC. Critically, perturbation of the function or localization of the MTOC causes reversed microtubule polarity in dendrites. These findings unveil the dendritic MTOC as a critical organelle for establishing axon-dendrite polarity.

cell biology↗

bioRxiv2019

Design of Ceramic Packages for Acoustically Coupled Implantable Medical Devices

ObjectiveUltrasonic acoustic power transfer is an efficient mechanism for coupling energy to millimeter and sub-millimeter implants in the body. To date, published ultrasonically powered implants have been encapsulated with thin film polymers that are susceptible to well-documented failure modes in vivo, including water penetration and attack by the body. As with all medical implants, packaging with ceramic or metallic materials can reduce water vapor transmission and improve biostability to provide decadal device lifetime. In this paper, we evaluate methods of coupling acoustic energy to the interior of ceramic packages. MethodsThe classic wave approach and modal expansion are used to obtain analytical expressions for acoustic transmission through two different package designs and these approaches are validated experimentally. A candidate package design is demonstrated using alumina packages and titanium lids, designed to be acoustically transparent. ResultsBulk modes are shown to be more effective at coupling acoustic energy to a piezoelectric receiver than flexural modes. Using bulk modes, packaged motes have an overall link efficiency of roughly 10%, compared to 25% for unpackaged motes. Packaging does not have a significant effect on translational misalignment penalties, but does increase angular misalignment penalties. Passive amplitude-modulated backscatter communication is demonstrated. ConclusionThin lids enable the use of acoustically coupled devices even with package materials of very different acoustic impedance. Significance: This work provides an analysis and method for designing packages that enable acoustic coupling with implantable medical devices, which could facilitate clinical translation.

bioengineering↗

bioRxiv2019

Complexity matching: brain signals mirror environment information patterns during music listening and reward

Understanding how the human brain integrates information from the environment with ongoing, internal brain signals in order to produce individual perspective is an essential element of understanding the human mind. Brain signal complexity, measured with multiscale entropy, has been employed as a measure of information processing in the brain (Carpentier et al., 2016), and we propose that it can also be used to measure the information available from a stimulus. We can directly assess the correspondence, or functional isomorphism, between brain signal complexity and stimulus complexity as an indication of how well the brain reflects the content of the environment in an analysis that we termed complexity matching. Music makes an ideal stimulus input because it is a multidimensional, complex signal, and because of its emotion and reward-inducing potential. We found that electroencephalography (EEG) complexity was lower and more closely resembled the musical complexity when participants performed a perceptual task that required them to closely track the acoustics, compared to an emotional task that asked them to think about how the music made them feel. Music-derived reward scores on the Barcelona Music Reward Questionnaire (Mas-Herrero et al., 2013) correlated with worse complexity matching and higher EEG complexity. Compared to perceptual-level processing, emotional and reward responses are associated with additional internal information processes above and beyond those in the external stimulus.\n\nSignificance StatementExperience of our world is combination of the input from the environment, our expectations, and individual responses. For example, the same piece of music can elict happiness in one person and sadness in another. We researched this by measuring the information in pieces of music and whether listeners brain more closely followed that, or whether additional information was added by the brain. We noted when listeners were reacting to how music made them feel, their brains added more information and the degree to which this occurred related to how much they find music rewarding. Thus, we were able to provide clues as to how the brain integrates incoming information, adding to it to provide a richer perceptual and emotional experience.

neuroscience↗

bioRxiv2018

A macaque connectome for large-scale network simulations in TheVirtualBrain

Models of large-scale brain networks that are informed by the underlying anatomical connectivity contribute to our understanding of the mapping between the structure of the brain and its dynamical function. Connectome-based modelling is a promising approach to a more comprehensive understanding of brain function across spatial and temporal scales, but it must be constrained by multi-scale empirical data from animal models. Here we describe the construction of a macaque connectome for whole-cortex simulations in TheVirtualBrain, an open-source simulation platform. We take advantage of available axonal tract-tracing datasets and enhance the existing connectome data using diffusion-based tractography in macaques. We illustrate the utility of the connectome as an extension of TheVirtualBrain by simulating resting-state BOLD-fMRI data and fitting it to empirical resting-state data.

neuroscience↗