Biology subjects

Li, D.

Publications and source records attributed to Li, D..

At least 523 records · Page 29Linked to original sources

bioRxiv2021

The functions of SARS-CoV-2 neutralizing and infection-enhancing antibodies in vitro and in mice and nonhuman primates

SARS-CoV-2 neutralizing antibodies (NAbs) protect against COVID-19. A concern regarding SARS-CoV-2 antibodies is whether they mediate disease enhancement. Here, we isolated NAbs against the receptor-binding domain (RBD) and the N-terminal domain (NTD) of SARS-CoV-2 spike from individuals with acute or convalescent SARS-CoV-2 or a history of SARS-CoV-1 infection. Cryo-electron microscopy of RBD and NTD antibodies demonstrated function-specific modes of binding. Select RBD NAbs also demonstrated Fc receptor-{gamma} (Fc{gamma}R)-mediated enhancement of virus infection in vitro, while five non-neutralizing NTD antibodies mediated Fc{gamma}R-independent in vitro infection enhancement. However, both types of infection-enhancing antibodies protected from SARS-CoV-2 replication in monkeys and mice. Nonetheless, three of 31 monkeys infused with enhancing antibodies had higher lung inflammation scores compared to controls. One monkey had alveolar edema and elevated bronchoalveolar lavage inflammatory cytokines. Thus, while in vitro antibody-enhanced infection does not necessarily herald enhanced infection in vivo, increased lung inflammation can occur in SARS-CoV-2 antibody-infused macaques.

immunology↗

bioRxiv2021

Increased theta/alpha synchrony in the habenula-prefrontal network with negative emotional stimuli in human patients

Lateral habenula is believed to encode negative motivational stimuli and plays key roles in the pathophysiology of psychiatric disorders. However, how habenula activities are modulated during the perception and processing of emotional information is still poorly understood. We recorded local field potentials from bilateral habenula areas with simultaneous cortical magnetoencephalography in nine patients with psychiatric disorders during an emotional picture viewing task. Oscillatory activity in the theta/alpha band (5-10 Hz) within the habenula and prefrontal cortical regions, as well as the coupling between these structures, are increased during the perception and processing of negative emotional stimuli compared to positive emotional stimuli. The evoked increase in theta/alpha band synchronization in the frontal cortex-habenula network correlated with the emotional valence not the arousal score of the stimuli. These results provide direct evidence for increased theta/alpha synchrony within the habenula area and prefrontal cortex-habenula network in the perception of negative emotion in human participants.

neuroscience↗

bioRxiv2020

Hsp70 chaperons TDP-43 in dynamic, liquid-like phase and prevents it from amyloid aggregation

TAR DNA binding protein 43 kDa (TDP-43) undergoes liquid-liquid phase separation (LLPS) and forms reversible, cytoprotective nuclear bodies (NBs) in response to stress in cells. Abnormal liquid-to-solid phase transition condenses TDP-43 into irreversible pathological fibrils, which is associated with neurodegenerative disorders including amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). However, the mechanisms how cells maintain the dynamics of TDP-43 NBs in stressed conditions are not well understood. Here, we show that the molecular chaperon heat shock protein 70 (Hsp70) is recruited into TDP-43 NBs in stressed cells. It co-phase separates with TDP-43 and delays the maturation of TDP-43 droplets in vitro. In cells, downregulation of Hsp70 not only diminishes the formation but also reduces the dynamics of TDP-43 NBs especially during prolonged stress, which potentiates the cytotoxicity of TDP-43. Using NMR, we reveal that Hsp70 binds to the highly aggregation-prone, transient -helix of TDP-43 via its nucleotide-binding domain, which keeps TDP-43 in the highly dynamic, liquid-like phase and prevents pathological aggregation of TDP-43 both in vitro and in cells. Collectively, our findings demonstrate a crucial role of Hsp70 in chaperoning TDP-43 in the liquid-like phase, which provides a novel layer of the molecular mechanism how chaperons help proteins to remain functional and protect cells from stressed and/or diseased conditions.

cell biology↗

bioRxiv2020

AIE-nanoparticle assisted ultra-deep microscopy in the in vivo mouse brain under 1300-nm excitation

Aggregation-induced emission nanoparticles serve as promising fluorescence probes for multi-photon excitation microscopy due to the large absorption cross-section at NIR-IIb region. Here we present organic AIE nanoparticles that feature high aborption cross-section under three-photon excitation. We show that these enable ultra-deep NIR-IIa excited three-photon imaging in the in-vivo mouse brain.

neuroscience↗

bioRxiv2020

Fucoidan but not 2'-Fucosyllactose could inhibit human norovirus replication in zebrafish larvae

Human noroviruses (hNoVs) cause heavy disease burden worldwide and there is no clinically approved vaccination or antivirals hitherto. In this study, with the use of a zebrafish larvae in vivo platform, we investigated the anti-hNoV potentials of fucoidan and 2-Fucosyllactose (2-FL). As a result, although both fucoidan and 2-FL were able to block hNoV GII.4 virus-like particle (VLPs) from binding to type A saliva as expected, only fucoidan but not 2-FL was able to inhibit the replication of hNoV GII.P16-GII.4 in zebrafish larvae, indicating the possible needs of higher molecular weights for fucosylated carbohydrates to exert anti-hNoV effect.

microbiology↗

bioRxiv2020

Characterizing intra-tumor and inter-tumor variability of immune cell infiltrates in murine syngeneic tumors

By using serial-sectioning methodology combined with immunohistochemistry (IHC) and whole-slide digital image analysis (DIA), we present a systematic analysis of intra-tumor and inter-tumor variability in the abundance of nine immune cell biomarkers in multiple murine tumor models. Our analysis shows that inter-tumor variability is typically the dominant source of variation in measurements of immune cell densities. Statistical power analysis reveals how group size and variance in immune cell density estimates affect the predictive power for detecting a statistically meaningful fold-change in immune cell density. Inter-tumor variability in the ratio of immune cell densities show distinct patterns in select tumor models and reveal the existence of strong correlations between select biomarker pairs. Further, we show that the relative proportion of immune cells at different depths across tumor samples is preserved in some but not all tumor models thereby revealing the existence of compositional heterogeneity. The results and analyses presented here reveal the complex nature of immunologic heterogeneity that exists in murine tumor models and provide guidelines for designing preclinical studies for immuno-oncology research and drug development.

cancer biology↗

bioRxiv2020

Ppard is Essential in Acceleration of Pancreatic Ductal Adenocarcinoma Development by High-Fat Diet in Mutant Kras Mice

Pro-obesity high-fat diet is linked with an increased incidence of pancreatic cancers, but the molecular underpinnings of this association remain poorly understood. Here, we report that PPARD is upregulated in pancreatic intraepithelial neoplasia lesions (PanINs) at early stages of pancreatic tumorigenesis in humans and mutant Kras mice. Transgenic overexpression of Ppard in pancreatic epithelial cells drastically accelerates the development and progression of pancreatic ductal adenocarcinoma in mutant Kras mice when activated by feeding the mice with a high-fat diet or a diet containing GW501516 (50 mg/kg), a selective PPARD agonist. In contrast, pancreatic Ppard genetic deletion significantly suppressed the promotion of pancreatic tumorigenesis by these diets. Mechanistically, we found that this Ppard hyperactivation in pancreatic epithelial cells of mutant Kras mice increased production of chemokines and cytokines (e.g., CcI2, CcI4-5, CxcI5 and II6), leading to the robustly increased recruitment of myeloid-derived suppressor cells and macrophages into pancreata, which fostered an immune suppressive microenvironment and subsequently accelerated pancreatic ductal adenocarcinoma development and progression. Our findings demonstrate that PPARD plays an essential role in the promotion of pancreatic tumorigenesis by a high-fat diet. Targeted inhibition of PPARD activation is a potential interventive strategy for pancreatic cancer prevention and therapy.

cancer biology↗

bioRxiv2020

IgM Natural Antibodies Bind HLA-E-Leader Peptide Complexes and Modulate NK Cell Cytotoxicity

HLA-E is a non-classical class Ib molecule that has limited polymorphism and binds HLA class Ia leader peptides (VL9). HLA-E-VL9 complexes interact with the natural killer (NK) cell receptors NKG2A-C/CD94 and regulate NK cell-mediated cytotoxicity. Here we isolated a murine IgM antibody 3H4, that specifically recognized HLA-E-VL9 bound complexes and enhanced killing of HLA-E-VL9-expressing cells by an NKG2A+ NK cell line. Structural analysis revealed how 3H4 prevents CD94/NKG2A docking on HLA-E-VL9 by binding with an overlapping footprint. Upon in vitro maturation, an affinity-optimized 3H4 IgG showed enhanced NK killing of HLA-E-VL9-expressing cells. Remarkably, HLA-E-VL9-specific IgM autoantibodies with similar specificity and functions to 3H4 were subsequently isolated from naive B cells of cytomegalovirus (CMV)-negative, healthy male human donors. Thus, a repertoire of germline low affinity HLA-E-VL9-reactive antibodies are present in both naive human and murine B cell repertoires. These antibodies can enhance NK cell cytotoxicity and therefore have potential for therapeutic modulation of NK cell function.

immunology↗

bioRxiv2020

The SC-SNc pathway boosts appetitive locomotion in predatory hunting

Appetitive locomotion is essential for organisms to approach rewards, such as food and prey. How the brain controls appetitive locomotion is poorly understood. In a naturalistic goal-directed behavior--predatory hunting, we demonstrate an excitatory brain circuit from the superior colliculus (SC) to the substantia nigra pars compacta (SNc) to boost appetitive locomotion. The SC-SNc pathway transmitted locomotion-speed signals to dopamine neurons and triggered dopamine release in the dorsal striatum. Activation of this pathway increased the speed and frequency of approach during predatory hunting, an effect that depended on the activities of SNc dopamine neurons. Conversely, synaptic inactivation of this pathway impaired appetitive locomotion but not defensive or exploratory locomotion. Together, these data revealed the SC as an important source to provide locomotion-related signals to SNc dopamine neurons to boost appetitive locomotion.

neuroscience↗

bioRxiv2020

Photostimulation of lymphatic clearance of red blood cells from the mouse brain after intraventricular hemorrhage

Intraventricular hemorrhage (IVH) is the most fatal form of brain injury, yet a therapy directed at ameliorating intraventricular clot is very limited. There is accumulating evidence that an augmentation of the meningeal lymphatic (MLVs) functions might be a promising therapeutic target for IVH. In particular, the photostimulation (PS) of MLVs could be promising for non-invasive therapy of IVH via PS of clearance of red blood cells (RBCs) from the brain via MLVs. Indeed, we uncover that PS has therapeutic effects on IVH in mice reducing the mortality, improving the emotional status, accelerating the RBCs evacuation from the ventricles and increasing the ICP recovery. Our findings strongly suggest that the PS-mediated stimulation of drainage and clearing functions of MLVs can be a novel bedside, readily applicable and commercially viable technologies for treatment of IVH. These pilot results open new horizons in a non-invasive therapy of IVH via PS stimulation of regenerative lymphatic mechanisms.

neuroscience↗

bioRxiv2020

Counterfactual Hypothesis Testing of Tumor Microenvironment Scenarios Through Semantic Image Synthesis

AO_SCPLOWBSTRACTC_SCPLOWRecent multiplexed protein imaging technologies characterize cells, their spatial organization, and interactions within microenvironments at an unprecedented resolution. Although observational data can reveal spatial associations, it does not allow users to infer salient biological relationships and cellular interactions. To address this challenge, we develop a generative model that allows users to test hypotheses about the effect of cell-cell interactions on protein expression through in silico perturbation. Our Cell-Cell Interaction GAN (CCIGAN) model employs a generative adversarial network (GAN) architecture to generate high fidelity synthetic multiplexed images from semantic cell segmentations. Our approach is unique in that it learns relationships between all imaging channels simultaneously and yields biological insights from multiple imaging technologies in silico, capturing known tumor-immune cell interactions missed by other state-of-the-art GAN models.

cancer biology↗

bioRxiv2020

Parabacteroides distasonis insulin B:9-23 epitope mimic stimulates insulin specific T-cells and enhances Type 1 Diabetes in NOD mice

Type 1 Diabetes (T1D) is an autoimmune disease characterized by the destruction of pancreatic {beta}-cells. One of the earliest aspects of this process is development of autoantibodies and T-cells directed at an epitope in the B-chain of insulin (insB:9-23). Analysis of microbial protein sequences with homology to insB:9-23 sequence revealed 17 peptides showing >50% identity to insB:9-23. Of these, one peptide, found in the normal human gut commensal Parabacteroides distasonis, activated both human T cell clones from T1D patients and T-cell hybridomas from non-obese diabetic (NOD) mice specific to insB:9-23. Immunization of NOD mice with P. distasonis insB:9-23 peptide mimic or insB:9-23 peptide verified immune cross-reactivity. Colonization of female NOD mice with P. distasonis accelerated the development of T1D, increasing macrophages, dendritic cells and destructive CD8+ T-cells, while decreasing FoxP3+ regulatory T-cells. Western blot analysis identified P. distasonis reacting antibodies in sera of NOD mice colonized with P. distasonis and human T1D patients. Furthermore, adoptive transfer of splenocytes from P. distasonis treated mice to NOD/SCID mice enhanced disease phenotype in the recipients. Finally, analysis of human infant gut microbiome data revealed that exposure of infants to P. distasonis may modulate disease pathogenesis. Taken together, these data demonstrate the potential role for an insB:9-23-mimimetic peptide from gut microbiota as a molecular trigger or modifier of T1D pathogenesis. SIGNIFICANCE STATEMENTIn Type 1 diabetes (T1D), immune cells destroy pancreatic {beta}-cells. The trigger of this response, however, is unknown. Some sequences (epitopes) in the insulin molecule form a major target for this autoimmune response. We have identified a sequence in a human gut bacterium that can mimetic this insulin epitope. Immune cells specific to insulin cross-react with this bacterial mimetic. Further, this bacterium can accelerate diabetes onset in a mouse model of T1D, inducing destructive and decreasing protective immune cells. We found this mimetic in the gut of children developing T1D. Furthermore, T1D patients have a stronger immune response to this bacterium compared to healthy individuals. Taken together, this bacterial mimetic in human gut has the potential to trigger/modify T1D onset.

immunology↗

bioRxiv2020

Glutamatergic neurons in the preoptic hypothalamus promote wakefulness, destabilize NREM sleep, suppress REM sleep, and regulate cortical dynamics

Clinical and experimental data from the last nine decades indicate that the preoptic area of the hypothalamus is a critical node in a brain network that controls sleep onset and homeostasis. By contrast, we recently reported that a group of glutamatergic neurons in the lateral and medial preoptic area increases wakefulness, challenging the long-standing notion in sleep neurobiology that the preoptic area is exclusively somnogenic. However, the precise role of these subcortical neurons in the control of behavioral state transitions and cortical dynamics remains unknown. Therefore, in this study we used conditional expression of excitatory hM3Dq receptors in these preoptic glutamatergic (Vglut2+) neurons and show that their activation initiates wakefulness, decreases non-rapid eye movement (NREM) sleep, and causes a persistent suppression of rapid eye movement (REM) sleep. Activation of preoptic glutamatergic neurons also causes a high degree of NREM sleep fragmentation, promotes state instability with frequent arousals from sleep, and shifts cortical dynamics (including oscillations, connectivity, and complexity) to a more wake-like state. We conclude that a subset of preoptic glutamatergic neurons may initiate -but not maintain- arousals from sleep, and their inactivation may be required for NREM stability and REM sleep generation. Further, these data provide novel empirical evidence supporting the conclusion that the preoptic area causally contributes to the regulation of both sleep and wakefulness.

neuroscience↗

bioRxiv2020

Cross-reactive anti-hemagglutinin (HA) IgG responses are shaped by previous long-interval monovalent H5 vaccination and highly correlated with HA antigenic distance

Avian H5 influenza is an emerging influenza strain with the potential for human pandemic spread. One unresolved issue in pandemic vaccine preparedness is to what extent a vaccine recall response depends on the interval between the priming and boosting vaccinations. In this study, we analyzed the anti-H5 HA IgG responses to an H5 A/Indonesia/5/2005 boosting vaccination in three cohorts: (1) a short interval boosting cohort that received a prime and boost 28 days apart, (2) a long-interval boosting cohort that received an H5 A/Vietnam/203/2004 priming vaccination 5 years before boosting, and (3) a double long-boost cohort that received single doses of all three vaccines separated by 5-6 year intervals. Anti-HA IgG levels were measured using a multiple-plex assay against 21 H5 and 16 seasonal strains covering both influenza phylogenetic groups. We used the antigentic distance between the vaccine strain and each HA in the assay panel to de1ne the antibody response landscape. Both single and double long-interval boosting with the H5 variant vaccine elicited a broad antibody response to all H5 subtype strains, and double boosting resulted in sustained, vaccine-speci1c, anti-HA IgG levels over a six month period. Antibody-mediated immune responses were shaped by prior H5 exposure history, and the magnitude of both vaccine speci1c and cross-reactive anti-H5 HA IgG responses was highly correlated with the relative antigenic distance between the measured and the vaccine HAs. We conclude that the relative antibody landscape method can be used to quantify the phenomenon of antigenic imprinting on human influenza vaccine immune responses. IMPORTANCEA signi1cant obstacle to development of a universal influenza vaccine is understanding the relationship between multidimensional host humoral immunity, prior antigen exposure, and viral antigenicity. In this study, we used a multiplexed antibody assay to measure antibody cross-reactivities against antigenically similar H5 influenza virus strains. This work uses a novel method, relative antibody landscapes, to analyze the relationship between immune response and antigenic distance between the target H5 vaccine HA and other HAs in the assay after a boosting vaccination. This method improves analysis of immune responses by relating antigen exposure history to the influenza vaccination antibody response. This study also revealed that multiple vaccine boosting over several years can generate high levels of long-lasting cross-reactive antibodies against the priming H5 strains vaccine that subjects received, suggesting the HA imprinting mechanism(s) have a strong influence in the adult antibody response to H5 MIV vaccination.

immunology↗

bioRxiv2020

Asymmetrical pegs in square holes? Functional and phylogenetic determinants of plant community assembly in temperate forest understories

Despite advances in community assembly theory, uncertainties remain regarding how ecological and evolutionary processes shape species distributions and communities. We analyzed patterns of occurrence for 139 herbaceous plant species across 257 forest stands in Wisconsin (USA) to test predictions from community assembly theory. Specifically, we applied Bayesian phylogenetic linear mixed effects models (PGLMMs) to examine how functional traits and phylogenetic relationships influence plant distributions along environmental gradients and how functional similarity and phylogenetic relatedness affect local species co-occurrence. Leaf height, specific leaf area, and seed mass mediate species distributions along edaphic, climatic, and light gradients. In contrast, functional trait similarity and phylogenetic relationships only weakly affect patterns of local co-occurrence. These results confirm that broad-scale plant distributions are largely shaped by ecological sorting along environmental gradients but suggest deterministic assembly rules based on niche differentiation and complementary resource use may not govern local species co-occurrence in homogeneous environments. Statement of authorshipJB conceived the idea for the study. DL, SJ, and DR collected the vegetation and functional trait data. JB analyzed the data with assistance from DL. KC, KS, TG, and DW secured funding for research and oversaw data collection. JB wrote the first draft of the manuscript, all authors contributed to manuscript revisions. Data accessibility statementUpon acceptance, data will be archived at Figshare (https://figshare.com/) and scripts used to analyze the data will be shared on Github (https://github.com/jaredjbeck/).

ecology↗

bioRxiv2020

Single-cell data and correlation analysis support the independent double adder model in both Escherichia coli and Bacillus subtilis

The reference point for cell-size control in the cell cycle is a fundamental biological question. We previously reported that we were unable to reproduce the conclusions of Witz et al.s eLife paper (Witz, van Nimwegen, and Julou 2019) entitled, "Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism", despite extensive efforts. In this replication double adder (RDA) model, both replication and division cycles are determined via replication initiation as the sole implementation point of size control. Witz et al. justified the RDA model using a type of correlation analysis (the "I-value analysis") that they developed. By contrast, we previously showed that, in both Escherichia coli and Bacillus subtilis, replication initiation and cell division are determined by balanced biosynthesis of key cell cycle proteins (e.g., DnaA for initiation and FtsZ for cell division) and their accumulation to their respective threshold numbers, which Witz et al. coined the independent double adder (IDA) model. The adder phenotype is a natural quantitative consequence of these mechanistic principles. In a recent bioRxiv response to our report, Witz and colleagues explicitly confirmed two important limitations of the I-value analysis: (1) it is only applicable to non-overlapping cell cycles, wherein E. coli is known to deviate from the adder principle, and (2) it is only applicable to select biological models and, for example, cannot evaluate the IDA model. These limitations of the I-value analysis were not explained in the original eLife paper and were overlooked during the review process. In this report, we show using data analysis, mathematical modeling, and experiments why the I-value analysis - in its current implementation - cannot compare different biological models. Furthermore, the RDA model is incompatible with the adder principle and is not broadly supported by experimental data. For completeness, we also provide a detailed point-by-point response to Witz et al.s response (Witz, Julou, and van Nimwegen 2020) in the Supplemental Information.

systems biology↗

bioRxiv2020

An evolutionarily diverged mitochondrial protein controls biofilm growth and virulence in Candida albicans

A forward genetic screening approach identified orf19.2500, as a gene controlling Candida albicans biofilm dispersal and biofilm detachment. Three-dimensional (3-D) protein modeling and bioinformatics revealed that orf19.2500 is a conserved mitochondrial protein, structurally similar to, but functionally diverged from, the squalene/phytoene synthases family. The C. albicans orf19.2500 is distinguished by three evolutionarily acquired stretches of amino acid inserts, absent from all other eukaryotes except a small number of ascomycete fungi. Biochemical assays showed that orf19.2500 is required for the assembly and activity of the NADH ubiquinone oxidoreductase Complex I of the respiratory electron transport chain, and was thereby named NDU1. NDU1 is essential for respiration and growth on alternative carbon sources, important for immune evasion, required for virulence in a mouse model of hematogenously disseminated candidiasis, and for potentiating resistance to antifungal drugs. Our study is the first report on a protein that sets the Candida-like fungi phylogenetically apart from all other eukaryotes, based solely on evolutionary "gain" of new amino acid inserts that are also the functional hub of the protein.

microbiology↗

bioRxiv2020

Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach

SARS-CoV-2 neutralizing antibodies represent an important component of the ongoing search for effective treatment of and protection against COVID-19. We report here on the use of a naive phage display antibody library to identify a panel of fully human SARS-CoV-2 neutralizing antibodies. Following functional profiling in vitro against an early pandemic isolate as well as a recently emerged isolate bearing the D614G Spike mutation, the clinical candidate antibody, STI-1499, and the affinity-engineered variant, STI-2020, were evaluated for in vivo efficacy in the Syrian golden hamster model of COVID-19. Both antibodies demonstrated potent protection against the pathogenic effects of the disease and a dose-dependent reduction of virus load in the lungs, reaching undetectable levels following a single dose of 500 micrograms of STI-2020. These data support continued development of these antibodies as therapeutics against COVID-19 and future use of this approach to address novel emerging pandemic disease threats.

microbiology↗