Biology subjects

Tran, A.

Publications and source records attributed to Tran, A..

52 records · Page 3Linked to original sources

bioRxiv2021

An enveloped virus-like particle vaccine expressing a stabilized prefusion form of the SARS-CoV-2 spike protein elicits potent immunity after a single dose.

Development of efficacious single dose vaccines would substantially aid efforts to stop the uncontrolled spread of the COVID-19 pandemic. We evaluated enveloped virus-like particles (eVLPs) expressing various forms of the SARS-CoV-2 spike protein and several adjuvants in an effort to identify a COVID-19 vaccine candidate efficacious after a single dose. The eVLPs expressing a modified prefusion form of SARS-CoV-2 spike protein were selected as they induced the highest antibody binding titers and neutralizing activity after a single injection in mice. Formulation of SARS-CoV-2 S eVLPs with aluminum phosphate resulted in balanced induction of IgG2 and IgG1 isotypes and antibody binding and neutralization titers were undiminished for more than 3 months after a single immunization. A single dose of this candidate, VBI-2902a (prefusion S eVLPs formulated with aluminum phosphate), protected Syrian golden hamsters from challenge with SARS-CoV-2 and supports the on-going clinical evaluation of VBI-2902a as a potential single dose vaccine against COVID-19. HighlightsO_LIVBI-2902a is a VLP-based vaccine candidate against SARS-COV-2 C_LIO_LIVBI-2902a contains VLPs pseudotyped with a modified prefusion SARS-COV-2 S in Alum. C_LIO_LIVBI-2902a induces robust neutralization antibody response against SARS-COV-2 S C_LIO_LIVBI-2902a protects hamsters from SARS-CoV-2 induced lung inflammation C_LIO_LIA single dose of VBI-2902a provides protective benefit in hamsters C_LI

immunology↗

bioRxiv2021

Balanced Input from the tRNA Prenyltransferase MiaA Controls the Stress Resistance and Virulence Potential of Extraintestinal Pathogenic Escherichia coli

An ability to adapt to rapidly changing and often hostile environments is key to the success of many bacterial pathogens. In Escherichia coli, the highly conserved enzymes MiaA and MiaB mediate the sequential prenylation and methylthiolation of adenosine-37 within tRNAs that decode UNN codons. Here, we show that MiaA, but not MiaB, is critical to the fitness and virulence of extraintestinal pathogenic E. coli (ExPEC), a major cause of urinary tract and bloodstream infections. Deletion of miaA has pleiotropic effects, rendering ExPEC especially sensitive to stressors like nitrogen and oxygen radicals and osmotic shock. We find that stress can stimulate striking changes in miaA expression, which in turn can increase translational frameshifting and markedly alter the bacterial proteome. Cumulatively, these data indicate that ExPEC, and likely other organisms, can vary MiaA levels as a means to fine-tune translation and the spectrum of expressed proteins in response to changing environmental challenges.

microbiology↗

bioRxiv2020

Characterization of cell-cell communication in COVID-19 patients

COVID-19 patients display a wide range of disease severity, ranging from asymptomatic to critical symptoms with high mortality risk. Our ability to understand the interaction of SARS-CoV-2 infected cells within the lung, and of protective or dysfunctional immune responses to the virus, is critical to effectively treat these patients. Currently, our understanding of cell-cell interactions across different disease states, and how such interactions may drive pathogenic outcomes, is incomplete. Here, we developed a generalizable workflow for identifying cells that are differentially interacting across COVID-19 patients with distinct disease outcomes and use it to examine five public single-cell RNA-seq datasets with a total of 85 individual samples. By characterizing the cell-cell interaction patterns across epithelial and immune cells in lung tissues for patients with varying disease severity, we illustrate diverse communication patterns across individuals, and discover heterogeneous communication patterns among moderate and severe patients. We further illustrate patterns derived from cell-cell interactions are potential signatures for discriminating between moderate and severe patients.

systems biology↗

bioRxiv2020

Sleep is required for odor exposure to consolidate memory and remodel olfactory synapses.

Animals with complex nervous systems demand sleep for memory consolidation and synaptic remodeling. Here we show that though the Caenorhabditis elegans nervous system has a limited number of neurons, sleep is necessary for both processes. In addition, it is unclear in any system if sleep collaborates with experience to alter synapses between specific neurons and whether this ultimately affects behavior. C. elegans neurons have defined connections and well-described contributions to behavior. We show that spaced odor-training and post-training sleep induce long-term memory. Memory consolidation, but not acquisition, requires a pair of interneurons, the AIYs, which play a role in odor-seeking behavior. In worms that consolidate memory, both sleep and odor conditioning are required to diminish inhibitory synaptic connections between the AWC chemosensory neurons and the AIYs. Thus, we demonstrate in a living organism that sleep is required for events immediately after training that drive memory consolidation and alter synaptic structures.

neuroscience↗

bioRxiv2020

Age-Associated Insolubility of Parkin in Human Midbrain is Linked to Redox Balance and Sequestration of Reactive Dopamine Metabolites

The mechanisms by which parkin protects the adult human brain from Parkinson disease remain incompletely understood. We hypothesized that parkin cysteines participate in redox reactions, which are reflected in its posttranslational modifications. We found that in human control brain, including the S. nigra, parkin is largely insoluble after age 40 years, which is linked to its oxidation, e.g., at Cys95 and Cys253. In mice, oxidative stress increases posttranslational modifications at parkin cysteines and reduces its solubility. Oxidation of recombinant parkin also promotes insolubility and aggregate formation, but in parallel, lowers hydrogen peroxide (H2O2). This thiol-based redox activity is diminished by parkin point mutants, e.g., p.C431F and p.G328E. Intriguingly, in parkin-deficient human brain H2O2 concentrations are elevated. In prkn-null mice, H2O2 levels are dysregulated under oxidative stress conditions, such as acutely by MPTP-toxin exposure or chronically due to a second genetic hit. In dopamine toxicity studies, wild-type parkin, but not disease-linked mutants, protects human dopaminergic M17 cells, in part through lowering H2O2. Parkin also neutralizes reactive, electrophilic dopamine metabolites via adduct formation, which occurs foremost at primate-specific Cys95. Further, wild-type but not p.C95A-mutant parkin augments melanin formation. In sections of normal, adult human midbrain, parkin specifically co-localizes with neuromelanin pigment, frequently within LAMP-3/CD63+ lysosomes. We conclude that oxidative modifications of parkin cysteines are associated with protective outcomes, which include the reduction of H2O2, conjugation of reactive dopamine metabolites, sequestration of radicals within insoluble aggregates, and increased melanin formation. The loss of these redox effects may augment oxidative stress in dopamine producing neurons of mutant PRKN allele carriers, thereby contributing to neurodegeneration.

neuroscience↗

bioRxiv2020

Extra-hypothalamic oxytocin neurons drive stress-induced social vigilance and avoidance

Oxytocin increases the salience of both positive and negative social contexts and it is thought that these diverse actions on behavior are mediated in part through circuit-specific action. This hypothesis is based primarily on manipulations of oxytocin receptor function, leaving open the question of whether different populations of oxytocin neurons mediate different effects on behavior. Here we inhibited oxytocin synthesis in a social stress-sensitive population of oxytocin neurons specifically within the medioventral bed nucleus of the stria terminalis (BNSTmv). Oxytocin knock-down prevented stress-induced increases in social vigilance and decreases in social approach. Viral tracing of BNSTmv oxytocin neurons revealed fibers in regions controlling defensive behaviors including lateral hypothalamus, anterior hypothalamus, and anteromedial BNST (BNSTam). Oxytocin infusion into BNSTam in stress naive mice increased social vigilance and reduced social approach. These results show that a population of extra-hypothalamic oxytocin neurons play a key role in controlling stress-induced social anxiety behaviors.

neuroscience↗

bioRxiv2020

Oxidative Modifications of Parkin Underlie its Selective Neuroprotection in Adult Human Brain

The mechanisms by which Parkinson disease-linked parkin confers neuroprotection of human dopamine cells remain elusive. We hypothesized that its cysteines mediate multiple anti-oxidant effects in the midbrain. By studying >60 control specimens, we found that in adult human brain - but not in skeletal muscle- parkin is mostly aggregated and insoluble due to oxidative modifications, such as at C253. In vitro, parkins oxidation directly reduces hydrogen peroxide (H2O2) to water. In parkin-deficient human brain, H2O2 concentrations are elevated. In dopamine toxicity studies, wild-type parkin -but not disease-associated mutants-prevents neural death by lowering H2O2 and sequestering radicals within insoluble aggregates. Parkin conjugates dopamine metabolites at the human-specific residue C95 and augments melanin formation in vitro. Using epitope-mapped antibodies, we found that in adult Substantia nigra neurons parkin localizes to neuromelanin within LAMP-3/CD63-positive lysosomes. We conclude that parkins own oxidation, previously considered a loss-of-function event, underlies three neuroprotective effects in adult midbrain: its cysteines participate in H2O2 reduction, dopamine radical conjugation and the formation of neuromelanin.

neuroscience↗

bioRxiv2020

Mucosal-associated invariant T (MAIT) cells mediate protective host responses in sepsis

Sepsis is a systemic inflammatory response to infection and a leading cause of death. Mucosal-associated invariant T (MAIT) cells are innate-like T cells enriched in mucosal tissues that recognize bacterial ligands. We investigated MAIT cells during clinical and experimental sepsis, and their contribution to host responses. In experimental sepsis, MAIT-deficient mice had significantly increased mortality and bacterial load, and reduced tissue-specific cytokine responses. MAIT cells of WT mice expressed lower levels of IFN-{gamma} and IL-17a during sepsis compared to sham surgery, changes not seen in non-MAIT T cells. MAIT cells of patients presenting with sepsis were significantly reduced in frequency, more activated, and had decreased IFN-{gamma} production when stimulated, compared to healthy donors and paired 90-day post-sepsis samples. Our data suggest that MAIT cells are highly activated and become dysfunctional during clinical sepsis, and contribute to tissue-specific cytokine responses that are protective against mortality during experimental sepsis.

physiology↗

bioRxiv2019

Rift Valley fever in northern Senegal : a modelling approach to analyse the processes underlying virus circulation recurrence

Rift Valley fever (RVF) is endemic in northern Senegal, a Sahelian area characterized by a temporary pond network that drive both RVF mosquito population dynamics and nomadic herd movements. To investigate the mechanisms that explain RVF recurrent circulation, we modelled a realistic epidemiological system at the pond level integrating vector population dynamics, resident and nomadic ruminant herd population dynamics, and nomadic herd movements recorded in Younoufere area [1]. To calibrate the model, serological surveys were performed in 2015-2016 on both resident and nomadic herds in the same area. Mosquito population dynamics were obtained from a published model trained in the same region [2]. Model comparison techniques were used to compare five different scenarios of virus introduction by nomadic herds associated or not with vertical transmission in Aedes vexans. Our serological results confirmed a long lasting RVF endemicity in resident herds (IgG seroprevalence rate of 15.3%, n=222), and provided the first estimation of RVF IgG seroprevalence in nomadic herds in West Africa (12.4%, n=660). Multivariate analysis of serological data suggested an amplification of the transmission cycle during the rainy season with a peak of circulation at the end of that season. The best scenario of virus introduction combined yearly introductions of RVFV from 2008 to 2015 (the study period) by nomadic herds, with a proportion of viraemic individuals predicted to be larger in animals arriving during the 2nd half of the rainy season (3.4%). This result is coherent with the IgM prevalence rate (4%) found in nomadic herds sampled during the 2nd half of the rainy season. Although the existence of a vertical transmission mechanism in Aedes cannot be ruled out, our model demonstrates that nomadic movements are sufficient to account for this endemic circulation in northern Senegal. Author summaryRift Valley fever (RVF) is one of the most important vector borne disease in Africa, seriously affecting the health of domestic ruminants and humans and leading to severe economic consequences. This disease is endemic in northern Senegal, a Sahelian area characterized by a temporary pond network that drive both RVF mosquito population dynamics and nomadic herd movements. Two non-exclusive mechanisms may support this endemicity: recurrent introductions of the virus by nomadic animals, and vertical transmission of the virus (i.e. from infected female mosquito to eggs) in local Aedes populations. The authors followed up during 1 year resident and nomadic herds. They used the data thus obtained to model a realistic epidemiological system at the pond level integrating vector population dynamics, resident and nomadic ruminant herd population dynamics. They found that the best scenario explaining RVF remanence combined yearly introductions of RVFV by nomadic herds, with a proportion of viraemic predicted to be larger in animals arriving during the 2nd half of the rainy season, which is consistent with an amplification of virus circulation in the area during the rainy season. Although the existence of a vertical transmission mechanism in Aedes cannot be ruled out, their results demonstrates that nomadic movements are sufficient to account for this endemic circulation in northern Senegal.

ecology↗

bioRxiv2019

Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

The Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromere, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome [~]15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

genomics↗

bioRxiv2019

De novo EIF2AK1 and EIF2AK2 variants are associated with developmental delay, leukoencephalopathy, and neurologic decompensation

EIF2AK1 and EIF2AK2 encode members of the Eukaryotic Translation Initiation Factor 2 Alpha Kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of eight unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/8) or EIF2AK2 (7/8). Features seen in these eight individuals include white matter alterations (8/8), developmental delay (8/8), impaired language (8/8), cognitive impairment (7/8), ataxia (6/8), dysarthria in probands with verbal ability (6/6), hypotonia (6/8), hypertonia (5/8), and involuntary movements (3/8). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and patient-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate Eukaryotic Translation Initiation Factor 2 Subunit 1, (EIF2S1, also known as EIF2), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter disease (CACH/VWM), a leukoencephalopathy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.

genetics↗

bioRxiv2019

Label-retention expansion microscopy

Expansion microscopy (ExM) increases the effective resolving power of any microscope by expanding the sample with swellable hydrogel. Since its invention, ExM has been successfully applied to a wide range of cell, tissue and animal samples. Still, fluorescence signal loss during polymerization and digestion limits molecular-scale imaging using ExM. Here we report the development of label-retention ExM (LR-ExM) with a set of trifunctional anchors that not only prevent signal loss but also enable high-efficiency labeling using SNAP and CLIP tags. We have demonstrated multicolor LR-ExM for a variety of subcellular structures. Combining LR-ExM with super-resolution Stochastic Optical Reconstruction Microscopy (STORM), we have achieved molecular resolution in the visualization of polyhedral lattice of clathrin-coated pits in situ.

bioengineering↗

bioRxiv2018

Pseudo-Symmetry and Conformational Plasticity in 7 Transmembrane Helix (7TMH) Proteins: Intragenic Duplication and Assembly of 3TMH or 4TMH Protodomains with Evolutionary Balance of Structural Constraints and Functional Divergence

Membrane proteins sharing 7 transmembrane helices (7-TMH) dominate the polytopic TMH proteome. They cannot be grouped under a monolithic fold or superfold, however, a parallel structural analysis of folds around that magic number of 7-TMH in distinct 6/7/8-TMH protein superfamilies (SWEET, PnuC, TRIC, FocA, Aquaporin, GPCRs, AND MFS), reveals a common homology, not in their structural fold, but in their systematic pseudo-symmetric construction. Our analysis leads to guiding principles of intragenic duplication and pseudo-symmetric assembly of ancestral 3 or 4 Transmembrane Helix (3/4-TMH) protodomains/protofolds. A parallel deconstruction and reconstruction of these domains provides a structural and mechanistic framework for the evolution path of current pseudo-symmetrical transmembrane helical (TMH) proteins. It highlights the conformational plasticity inherent to fold formation itself. The sequence/structure analysis of different 6/7/8-TMH superfamilies provides a unifying theme of their evolutionary process involving the intragenic duplication of protodomains with varying degrees of sequence and fold divergence under conformational and functional constraints.

bioinformatics↗

bioRxiv2018

Robust and sensitive GFP-based cGMP sensor for real time imaging in intact Caenorhabditis elegans

cGMP is a ubiquitous second messenger that plays a role in sensory signaling and plasticity through its regulation of ion channels and kinases. Previous studies that primarily used genetic and biochemical tools suggest that cGMP is spatiotemporally regulated in multiple sensory modalities, including light, heat, gases, salt and odor. FRET- and GFP-based cGMP sensors were developed to visualize cGMP in primary cell culture and Caenorhabditis elegans to corroborate these findings. While a FRET-based sensor has been used in an intact animal to visualize cGMP, the requirement of a multiple emission system limits its ability to be used on its own as well as with other sensors and fluorescent markers. Here, we demonstrate that WincG2, a codon-optimized version of the cpEGFP-based cGMP sensor FlincG3, can be used in C. elegans to visualize rapidly changing cGMP levels in living, behaving animals using a single fluorophore. We coexpressed the sensor with the blue light-activated guanylyl cyclases BeCyclOp and bPGC in body wall muscles and found that the rate of WincG2 fluorescence correlated with the rate of cGMP production by each cyclase. Furthermore, we show that WincG2 responds linearly upon NaCl concentration changes and SDS presentation in the cell bodies of the gustatory neuron ASER and the nociceptive phasmid neuron PHB, respectively. Intriguingly, WincG2 fluorescence in the ASER cell body decreased in response to a NaCl concentration downstep and either stopped decreasing or increased in response to a NaCl concentration upstep, which is opposite in sign to previously published calcium recordings. These results illustrate that WincG2 can be used to report rapidly changing cGMP levels in an intact animal and that the reporter can potentially reveal unexpected spatiotemporal landscapes of cGMP in response to stimuli.\n\nAuthor SummarycGMP is a second messenger that plays an important role in sensory signaling and neural plasticity. Previous genetic and biochemical studies indirectly suggest that cGMP is spatiotemporally regulated in neurons to modulate neural activity. While a FRET-based sensor for cGMP has been used in intact Caenorhabditis elegans to examine its spatiotemporal regulation in neurobiological processes, its use has been limited due to the complicated setup required to image this type of sensor. Here, we describe a GFP-based cGMP sensor that has been codon optimized for use in C. elegans and demonstrate that it responds robustly and reliably to endogenously changing cGMP levels. We show that the sensor responds to cGMP production by coexpressing it with blue light-activated guanylyl cyclases, and we show that it responds to NaCl and sodium dodecyl sulfate when expressed in a gustatory and nociceptive neuron, respectively. We think that this sensor can be used to investigate the spatiotemporal regulation of cGMP in neurons and its relationship to neural activity.

neuroscience↗

bioRxiv2018

The N-end Rule Pathway and Ubr1 mediate clearance of mis-translocated proteins from the cytosol via P2-encoded cellular location signals

The Arg/N-end rule pathway, a mechanism of protein degradation conserved from yeast to humans, is involved in cellular protein quality control, but its role has only been vaguely understood. Through systematic examination of single residue mutants of model misfolded substrates, and global analyses of yeast proteins, we discovered that Ubr1, an E3 ligase of the Arg/N-end rule, degrades organellar proteins that fail to reach their intended subcellular compartments. We determined that recognition by Ubr1 is dependent on location signals that are naturally embedded into the 2nd amino acid residue of the majority of proteins. The N-end rule pathway is thus likely to have been critical to the evolution of endosymbiotic relationships which paved the way for advanced eukaryotic cellular life. Significance StatementThis work elucidates a novel role for the N-end Rule Pathway, a protein degradation pathway highly conserved from yeast to humans. We demonstrate that the N-end rule pathway enforces the cellular compartmentalization of ER and mitochondrial proteins by degrading them when they fail to successfully translocate into their intended destinations and thus become mislocalized to the cytosol. This mechanism prevents the accumulation of toxic foreign proteins within the cytosol. Recognition of the displaced proteins is dependent on cellular location signals programmed into the 2nd residue of the target proteins, as well as the tendency for the proteins to misfold in a foreign environment. These findings have significant relevance to research on the mechanisms causing human diseases involving protein misfolding.

cell biology↗

bioRxiv2018

Scarless repair of acute and chronic kidney injury in African Spiny mice (Acomys cahirinus)

Solid organ fibrosis is a major burden on global health and medical care costs. Muroid rodents of the genus Acomys (African Spiny mice) are terrestrial mammals that evolved remarkable abilities to regenerate severe skin wounds without scar formation. However, whether scar-free wound repair in Acomys extends beyond skin to vital internal organs is not known. Here, we used two aggressive kidney injury models known to produce severe renal fibrosis and show that despite equivalent acute kidney injury, there was rapid restoration of nephron structure and function without fibrosis in Acomys compared to extensive fibrosis leading to renal failure in Mus musculus. These results suggest Acomys species have evolved genomic adaptations for wound healing that activate regenerative repair pathways not only in skin, but also in vital internal organs. Our findings have important implications for discovering a long-sought evolutionary solution to internal organ injury and regeneration.

pathology↗