Biology subjects

Lee, S.

Publications and source records attributed to Lee, S..

At least 469 records · Page 26Linked to original sources

bioRxiv2022

The nervous system leverages the non-linear properties of the Achilles tendon to regulate ankle impedance during postural control

Regulating ankle impedance is essential for controlled interactions with the environment and rejecting unexpected disturbances. Ankle impedance in the sagittal plane depends strongly on the triceps surae and Achilles tendon, but their relative contributions remain unknown. It is commonly assumed that ankle impedance is controlled by changing muscle activation and, thereby, muscle impedance, but this ignores the fact that tendon impedance also changes with loading caused by increases in muscle activation. Thus, we sought to determine the relative contributions from the triceps surae and Achilles tendon during conditions relevant to postural control. We used a novel technique that combines B-mode ultrasound imaging with joint-level perturbations to quantify ankle, muscle, and tendon impedance simultaneously across activation levels from 0 - 30% of maximum voluntary contraction. We found that muscle and tendon stiffness, the static component of impedance, increased with voluntary plantarflexion contractions, but that muscle stiffness exceeded tendon stiffness at very low loads (21 {+/-} 7 N). Above these loads, corresponding to 1.3% of maximal strength for an average participant in our study, ankle stiffness was determined predominately by Achilles tendon stiffness. Hence, the nervous system leverages the non-linear properties of the Achilles tendon to increase ankle stiffness during postural conditions.

physiology↗

bioRxiv2022

All-optical observation on activity-dependent nanoscale dynamics of myelinated axons

In the mammalian brain, rapid conduction of neural information is supported by the myelin, whose functional efficacy shows steep dependence on its nanoscale cytoarchitecture. Although previous in vitro studies suggested that neural activity accompanies nanometer-scale cellular deformations, it has remained unexplored whether neural activity can dynamically remodel the myelinated axon due to the technical challenge in observing its nanostructural dynamics in living tissues. To this end, we introduced a novel all-optical approach combining a nanoscale dynamic readout based on spectral interferometry and optogenetic control of neural excitation on a living brain slice preparation. In response to optogenetically evoked neuronal burst firing, the myelinated axons exhibited progressive and reversible spectral redshifts, corresponding to the transient swelling at a subnanometer scale. We further revealed that the activity-dependent nanostructural dynamics was localized to the paranode. In summary, our novel all-optical studies substantiate that myelinated axon exhibits activity-dependent nanoscale swelling, which potentially serves to dynamically tune the transmission speed of neural information. RESEARCH SUMMARIESAs neural activity involves rapid ion flux across the cell membrane, researchers have long been tried to detect the accompanying nanoscale morphological dynamics. However, measuring the activity-dependent nanostructural dynamics in the living mammalian brain has been an enigma due to the technical limitations. By combining excitatory optogenetics and in situ nanoscale metrology based on spectral interference, we demonstrate the first direct observation that the mammalian axons exhibit transient activity-dependent swelling at subnanometer-scale.

neuroscience↗

bioRxiv2022

Engineered Serum Markers for Noninvasive Monitoring of Gene Expression in the Brain

Noninvasive efforts to map brain gene expression have been hampered by low sensitivity and limited access to the brain. Here, we introduce a new platform that enables multiplexed, noninvasive, and site-specific monitoring of brain gene expression through a novel class of engineered reporters called Released Markers of Activity (RMAs). Instead of detecting gene expression in the less accessible brain, RMA reporters exit from a known brain region into the blood, where they can be easily measured with biochemical techniques. Expressing RMAs at a single brain site, typically covering [~]1% of the brain volume, provides up to a 39,000-fold signal increase over the baseline in vivo. Further, expression of RMAs in as few as several hundred neurons was sufficient for their reliable detection. When placed under a promoter upregulated by neuronal activity, RMAs could be used to measure neuronal activity in specific brain regions with a simple blood draw. We found that chemogenetic activation of cells expressing Fos-responsive RMA increased serum levels of RMA over 4-fold compared to non-activated controls. By contrast, a control RMA expressed under a constitutive neuronal promoter did not show such upregulation, demonstrating multiplexed ratiometric measurement with RMAs and proving specificity of neuronal activity discrimination. Together, our study pioneers a new noninvasive paradigm for repeatable and multiplexed monitoring of gene expression in an intact brain with sensitivity that is currently unavailable through other noninvasive gene expression reporter systems.

neuroscience↗

bioRxiv2022

A membrane sensing mechanism couples local lipid metabolism to protein degradation at the inner nuclear membrane

Lipid composition is a determinant of organelle identity; however, whether the inner nuclear membrane (INM) domain of the endoplasmic reticulum (ER) harbors a unique lipid chemistry that contributes to its identity is not known. Here, we demonstrate that a unique INM lipid environment enriched in diacylglycerol protects the nucleo-cytoskeletal linker Sun2 from local degradation by the ubiquitin-proteasome system. A membrane binding amphipathic helix in the nucleoplasmic domain of Sun2 senses INM lipids and is essential to its protein stability. We show that the protein phosphatase CTDNEP1 localizes to the INM to maintain a distinct INM lipid environment necessary for Sun2 accumulation through regulation of the phosphatidic acid phosphatase lipin 1. Thus, the INM lipid environment sculpts the INM proteome via direct lipid-protein interactions that regulate protein stability, which has broad implications for mechanisms of diseases associated with the nuclear envelope.

cell biology↗

bioRxiv2022

Maternal immune activation alters social affective behavior and sensitivity to corticotropin releasing factor in male but not female rats

Prenatal infection increases risk for neurodevelopmental disorders such as autism in offspring. In the rodents, prenatal administration of the viral mimic Polyinosinic:polycytidylic acid (Poly I:C) allows for investigation of developmental consequences of gestational sickness on offspring social behavior and neural circuit function. Because maternal immune activation (MIA) disrupts cortical development and sociability, we examined social decision-making in a rat social affective preference (SAP) task. Following Poly I:C (0.5 mg/kg) on gestational day 12.5, male adult offspring (PN 50) exhibited atypical social interactions with stressed conspecifics whereas female SAP behavior was unaffected by maternal Poly I:C. Social responses to stressed conspecifics depend upon the insular cortex where corticotropin releasing factor (CRF) modulates synaptic transmission and SAP behavior. We characterized insular field excitatory postsynaptic potentials (fEPSP) in adult offspring of MIA or control treated dams. Male MIA offspring showed decreased sensitivity to CRF (300 nM) while female MIA offspring showed greater sensitivity to CRF compared to sham offspring. These sex specific effects appear to be behaviorally relevant as CRF injected into the insula of male and female rats prior to social exploration testing had no effect in MIA male offspring but increased social interaction in female MIA offspring. We examined the cellular distribution of CRF receptor mRNA but found no effect of maternal Poly I:C in the insula. Together these experiments reveal sex specific effects of prenatal infection on offspring social decision making and identify insular CRF signaling as a novel neurobiological substrate for autism risk.

neuroscience↗

bioRxiv2022

A novel hyper-parameter can increase the prediction accuracy in a single-step genetic evaluation

The H-matrix best linear unbiased prediction (HBLUP) method has been widely used in livestock breeding programs. It can integrate all information, including pedigree, genotypes, and phenotypes on both genotyped and non-genotyped individuals into one single evaluation that can provide reliable predictions of breeding values. The existing HBLUP method (e.g., that implemented in BLUPf90 software) requires hyper-parameters that should be adequately optimised as otherwise the genomic prediction accuracy may decrease. In this study, we assess the performance of HBLUP using various hyper-parameters such as blending, tuning and scale factor in simulated as well as real data on Hanwoo cattle. In both simulated and cattle data, we show that blending is not necessary, indicating that the prediction accuracy decreases when using a blending hyper-parameter < 1. The tuning process (adjusting genomic relationships accounting for base allele frequencies) improves prediction accuracy in the simulated data, confirming previous studies, although the improvement is not statistically significant in the Hanwoo cattle data. We also demonstrate that a scale factor, , which determines the relationship between allele frequency and per-allele effect size, can improve the HBLUP accuracy in both simulated and real data. Our findings suggest that an optimal scale factor should be considered to increase the prediction accuracy, in addition to blending and tuning processes, when using HBLUP. Author SummaryDespite significant advancements in genotyping technologies, the capability to predict the phenotypes of complex traits is still limited. H-matrix best linear unbiased prediction (HBLUP) method has been used to tackle this limitation to demonstrate a promising prediction accuracy. However, the performance of HBLUP depends heavily on the optimisation of hyper-parameters (e.g. blending and tuning). In this study, we introduce a scale factor (), as a new hyper-parameter in HBLUP, which accounts for the relationship between allele frequency and per-allele effect size. Using simulation and real data analysis, we investigate the impact of the hyper-parameters (blending, tuning, and scale factor) on the performance of HBLUP. In general, the blending process may not improve the prediction accuracy for simulation and cattle data although a marginally improved prediction accuracy is observed with a blending hyper-parameter = 0.86 for one of carcass traits in the cattle data. In contrast, the tuning process can increase the HBLUP accuracy particularly in simulated data. Furthermore, we observe that an optimal scale factor plays a significant role in improving the prediction accuracy in both simulated and real data, and the improvement is relatively large compared with blending and tuning processes. In this context, we propose considering the scale factor as a hyper-parameter to increase the predictive performance of HBLUP.

genomics↗

bioRxiv2022

Host-enemy interactions provide limited biotic resistance for a range-expanding species via reduced apparent competition

As species ranges shift in response to anthropogenic change, they lose coevolved or coadapted interactions and gain novel ones in recipient communities. Range-expanding species may lose or experience weak antagonistic interactions with competitors and enemies, and traits of interacting species will determine the strength of interactions. We leveraged a poleward range expansion of an oak gall wasp that co-occurs on its host plant with other gall wasp species and interacts with shared natural enemies (largely parasitoid wasps). We created quantitative host-parasitoid interaction networks by sampling galls on 400 trees. We compared network structure and function and traits of hosts and parasitoids in the native and expanded range. Interaction networks were less diverse in the expanded range, with low complementarity of parasitoid assemblages among hosts. While whole networks were more generalized in the expanded range, interactions with the range-expanding species were more specialized. This was not due to a loss of specialist enemies but weak apparent competition by shared generalist enemies. Phenological divergence of enemy assemblages attacking the novel and co-occurring hosts was greater in the expanded range that may contribute to weak apparent competition. Given the rate and extent of anthropogenic-driven range expansions, it is pressing to uncover how complex biotic interactions are reassembled.

ecology↗

bioRxiv2022

Paracrine signaling by pancreatic delta cells determines the glycemic set point in mice

Pancreatic islets contain several endocrine cell types that coordinate to maintain blood glucose homeostasis. While {beta} and cells are thought to be the main drivers of glucose homeostasis through insulin and glucagon secretion respectively, the contribution of {delta} cells and somatostatin (SST) secretion to establishing the glycemic set point remains unresolved. Here we remove local SST signaling from {delta} cells within the pancreatic islet to investigate their contribution to the glycemic set point. Our data demonstrate that ablating {delta} cells or SST leads to a sustained decrease in the glycemic set point. This coincides with a decreased glucose threshold for insulin response from {beta} cells, leading to increased insulin secretion to the same glucose challenge. In contrast, cell ablation had no effect on glycemic set point. Collectively, these data establish the physiological role of {delta} cells in determining the glycemic set point through their interaction with {beta} cells.

physiology↗

bioRxiv2022

ANTHRACNOSE RESISTANCE GENE2 confers fungal resistance in sorghum

Sorghum is an important food and feed crop globally; its production is hampered by anthracnose disease caused by the fungal pathogen Colletotrichum sublineola (Cs). Here, we report identification and characterization of ANTHRACNOSE RESISTANCE GENE 2 (ARG2) encoding a nucleotide-binding leucine-rich repeat (NLR) protein that confers race-specific resistance to Cs strains. ARG2 is one of a cluster of several NLR genes in the sorghum differential line SC328C that is resistant to some Cs strains. This cluster shows structural and copy number variations in different sorghum genotypes. Different sorghum variants carrying independent ARG2 alleles provided the genetic validation for the identity of the ARG2 gene. ARG2 expression is induced by Cs, and chitin induce ARG2 expression in resistant but not in susceptible lines. ARG2-mediated resistance is accompanied by higher expression of defense and secondary metabolite genes at early stages of infection, and anthocyanin and zeatin metabolisms are upregulated in resistant plants. Interestingly, ARG2 localizes to the plasma membrane when transiently expressed in Nicotiana benthamiana. Importantly, ARG2 plants produced higher shoot dry matter than near-isogenic lines carrying the susceptible allele suggesting absence of an ARG2 associated growth trade-off. Further, ARG2-mediated resistance is stable at a wide range of temperatures. Our observations open avenues for resistance breeding and for dissecting mechanisms of resistance.

plant biology↗

bioRxiv2022

Patterning Fluid Shear Stress Landscapes with Multiphoton Inner Laser Lithography (MILL) for Live Cell Adhesion and Translocation

Heterogenous fluid shear stress is known to provide mechanical cues for cell adhesion and translocation. To assemble 3D microstructures using current fabrication methods in a single channel and recapitulate in vivo heterogenous fluid flow would require hours of fabrication and specialized equipment. Inspired by the traditional art form of inside painting, we developed a technique for 3D fabrication of micro-patterned flow channels and mixed in vivo fluid flow in a matter of minutes. We termed this technique Multiphoton Inner Laser Lithography (MILL). We further showed that when combined with adaptive optics, MILL is compatible with both flat and curved channel shapes. MILL recapitulated in vivo tissue topology and 3D fluid flow within tissue stroma (low fluid shear, 0 - 3.5 dynes/cm2) and blood vessel (high fluid shear, 0 - 80 dynes/cm2). We demonstrate fibroblast cell and platelets adhere and translocate differently between laminar flow patterns that are homogenous versus heterogeneous in real time. Parallel strips of MILL channels were assembled for simultaneous platelet function test to quantify the efficacy of an antithrombotic GPVI Fab (~2000 microthrombi per test). The MILL technique can be readily reproduced in vivo fluid flow in minutes and benefit preclinical screening of drug pharmacokinetics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/496569v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1efbe9eorg.highwire.dtl.DTLVardef@cbab5aorg.highwire.dtl.DTLVardef@15ed255org.highwire.dtl.DTLVardef@42d14e_HPS_FORMAT_FIGEXP M_FIG C_FIG Significant pointsO_LIMILL channels are made from commercially available off the shelf components using a standard multiphoton imaging system C_LIO_LIVarying degrees of in vivo heterogenous laminar flow is shown to directly influence cells translocating on thinly coated collagen surfaces C_LIO_LIParallel strips of MILL channels were assembled for simultaneous platelet function tests (~2000 microthrombi per test). C_LI

bioengineering↗

bioRxiv2022

Effective Representation Learning via The Integrated Self-Supervised Pre-training models of StyleGAN2-ADA and DINO for Colonoscopy Images

In order to reach better performance in visual representation learning from image or video dataset, huge amount of annotated data are on demand. However, collecting and annotating large-scale datasets are costly and time-consuming tasks. Especially, in a domain like medical, it is hard to access patient images because of the privacy concerns and also not knowing what exactly to annotate without expert effort. One of the solutions to obviate the hassle is to use Self-Supervised learning methods (SSL) and Generative Adversarial Networks (GANs) together. SSL and GANs are quickly advancing fields. GANs have unique capability to create unlabeled data sources containing photo-realistic images while SSL methods are able to learn general image and video features from large-scale data without using any human-annotated labels. In this work, we explore leveraging the power of recently introduced StyleGAN2-ada and Self-Supervised Pre-Training of Dino together for the pretext task. Our underlying insight is also that leveraging the current approaches with Transfer Learning (TF) together brings benefit on doing pretext task in medical domain. By the strategy of unifying these two approaches, we propose the integrated version and use it derive representation learning on polyp dataset.

bioinformatics↗

bioRxiv2022

Significance tests for R2 of out-of-sample prediction using polygenic scores

The coefficient of determination (R2) is a well-established measure to indicate the predictive ability of polygenic scores (PGS). However, the sampling variance of R2 is rarely considered so that 95% confidence intervals (CI) are not usually reported. Moreover, when comparisons are made between PGS based on different discovery samples, the sampling covariance of R2 is necessary to test the difference between them. Here, we show how to estimate the variance and covariance of R2 values to assess the 95% CI and p-value of the R2 difference. We apply this approach to real data to predict into 28,880 European participants using UK Biobank (UKBB) and Biobank Japan (BBJ) GWAS summary statistics for cholesterol and BMI. We quantify the significantly higher predictive ability of UKBB PGS compared to BBJ PGS (p-value 7.6e-31 for cholesterol and 1.4e-50 for BMI). A joint model of UKBB and BBJ PGS significantly improves the predictive ability, compared to a model of UKBB PGS only (p-value 3.5e-05 for cholesterol and 1.3e-28 for BMI). The proposed approach can also be applied to testing a significant difference between R2 values across different p-value thresholds. We also show that the predictive ability of regulatory SNPs is significantly enriched than non-regulatory SNPs for cholesterol (p-value 2.6e-19 for UKBB and 8.7e-08 for BBJ). We suggest that the proposed approach (available in R package r2redux) should be used to test the statistical significance of difference between pairs of PGS, which may help to draw a correct conclusion about the predictive ability of PGS.

genetics↗

bioRxiv2022

Linearization Autoencoder: an autoencoder-based regression model with latent space linearization

Regression analysis is one of the most widely applied methods in many fields including bio-medical study. Dimensionality reduction is also widely used for data preprocessing and feature selection analysis, to extract high-impact features from the predictions. As the complexity of both data and prediction models increases, it becomes important and difficult to interpret the model. We suggested a novel method, linearizing autoencoder, for regression analysis with high-dimensional data. Based on the autoencoder model, we introduce a novel loss function to make data points aggregate corresponding to their known labels and align them preserving linear relations of the known feature. This model can align data points to the linear relations of labels, and achieve both the prediction and feature selection performances by extracting features that are important to the label we want to predict. Also, we applied this method to the real-world data and the result indicates that this method can successfully disentangle the latent space with given centroids in a supervised manner. This method can be applied to various prediction problems in biomedical fields.

bioinformatics↗

bioRxiv2022

Dynamic decoupling of salience and default mode networks by optogenetic manipulation of anterior insular cortex

The salience network (SN) and default mode network (DMN) play a crucial role in cognitive function. The SN, anchored in the anterior insular cortex (AI), has been hypothesized to modulate DMN activity during stimulus-driven cognition. However, the causal neural mechanisms underlying changes in DMN activity and its functional connectivity with the SN are poorly understood. Here we combine feedforward optogenetic stimulation with fMRI and computational modeling to dissect the causal role of AI neurons in dynamic functional interactions between SN and DMN nodes in the rat brain. Optogenetic stimulation of Chronos-expressing AI neurons in rats suppressed DMN activity, and decreased AI-DMN and intra-DMN functional connectivity. Our findings demonstrate that feedforward optogenetic stimulation of AI neurons induces dynamic suppression and decoupling of the DMN and elucidates previously unknown features of rodent brain network organization. Our study advances foundational knowledge of causal mechanisms underlying dynamic cross-network interactions and brain network switching. TeaserInsular cortex stimulation reveals causal mechanisms underlying default mode network suppression by the salience network

neuroscience↗

bioRxiv2022

ECPAS/Ecm29-Mediated 26S Proteasome Disassembly Is an Adaptive Response to Glucose Starvation

The 26S proteasome consists of loosely associated 20S catalytic and 19S regulatory complexes. Approximately half of the proteasomes in eukaryotic cells exist as free 20S complexes; however, our mechanistic and physiological understanding of what determines the ratio of 26S to 20S species remains incomplete. Here, we show that glucose starvation in mammalian cells results in the uncoupling of 26S holoenzymes into intact 20S and 19S subcomplexes. Subcomplex affinity-purification and quantitative mass spectrometry revealed that Ecm29 proteasome adaptor and scaffold (ECPAS) is a crucial mediator of this structural remodeling. The loss of ECPAS abrogated 26S dissociation, leading to decreased degradation of 20S proteasome substrates such as puromycylated polypeptides and lysine-less cyclin B. In silico modeling analysis suggested that the conformational changes of ECPAS may commence the disassembly process. ECPAS was also essential for proper endoplasmic reticulum stress response and cell survival during glucose starvation. In addition, we evaluated the role of ECPAS in vivo using the mouse xenograft model and observed that glucose-deprived tumor tissues had significantly elevated 20S proteasome levels. Collectively, our results indicate that the 20S-19S disassembly mediated by ECPAS is a novel mechanism adapting global proteolysis to physiological needs and an effective cellular strategy against proteotoxic stress.

biochemistry↗

bioRxiv2022

APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge

The E4 allele of Apolipoprotein E (APOE) is associated with both metabolic dysfunction and a heightened pro-inflammatory response - two findings that may be intrinsically linked through the concept of immunometabolism. Here, we combined bulk, single-cell, and spatial transcriptomics with cell-specific and spatially resolved metabolic analyses to systematically address the role of APOE across age, neuroinflammation, and AD pathology. RNAseq highlighted immunometabolic changes across the APOE4 glial transcriptome, specifically in subsets of metabolically distinct microglia enriched in the E4 brain during aging or following an inflammatory challenge. E4 microglia display increased Hif1 expression, a disrupted TCA cycle, and are inherently pro-glycolytic, while spatial transcriptomics and MALDI mass spectrometry imaging highlight an E4-specific response to amyloid that is characterized by widespread alterations in lipid metabolism. Taken together, our findings emphasize a central role for APOE in regulating microglial immunometabolism.

neuroscience↗

bioRxiv2022

Myriocin remodels sphingolipids and modulates proteostasis networks to enhance longevity

As the elderly population increases, chronic, age-associated diseases are challenging healthcare systems around the world. Nutrient limitation is well known to slow the aging process and improve health. Regrettably, practicing nutrient restriction to improve health is unachievable for most people. Alternatively, pharmacological strategies are being pursued including myriocin which increases lifespan in budding yeast. Myriocin impairs sphingolipid synthesis, resulting in lowered amino acid pools which promote entry into a quiescent, long-lived state. Here we present transcriptomic data during the first 6 hours of drug treatment that improves our mechanistic understanding of the cellular response to myriocin and reveals a new role for ubiquitin in longevity. Previously we found that the methionine transporter Mup1 traffics to the plasma membrane normally in myriocin-treated cells but is not active and undergoes endocytic clearance. We now show that UBI4, a gene encoding stressed-induced ubiquitin, is vital for myriocin-enhanced lifespan. Furthermore, we show that Mup1 fused to a deubiquitinase domain impairs myriocin-enhanced longevity. Broader effects of myriocin treatment on ubiquitination are indicated by our finding of a significant increase in K63-linked ubiquitin polymers following myriocin treatment. Although proteostasis is broadly accepted as a pillar of aging, our finding that ubiquitination of an amino acid transporter promotes longevity in myriocin-treated cells is novel. Addressing the role of ubiquitination/deubiquitination in longevity has the potential to reveal new strategies and targets for promoting healthy aging.

molecular biology↗

bioRxiv2022

High-fidelity optical diffraction tomography of live organisms using non-toxic tunable refractive index media

Optical diffraction tomography (ODT) enables the three-dimensional (3D) refractive index (RI) reconstruction. However, when the RI difference between a sample and a medium increases, effects of light scattering become significant, preventing the acquisition of high-quality and accurate RI reconstructions. Herein, we present a method for high-fidelity ODT by introducing non-toxic RI matching media. Optimally reducing the RI contrast enhances the fidelity and accuracy of 3D RI reconstruction, enabling visualization of the morphology and intra-organization of live biological samples without producing toxic effects. We validate our method using various biological organisms, including C. albicans and C. elegans. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/492426v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@a6b4d4org.highwire.dtl.DTLVardef@a9ec7borg.highwire.dtl.DTLVardef@1e4a795org.highwire.dtl.DTLVardef@b663aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗