Publications by authors named "Gradinaru V"

Article Synopsis
  • Adeno-associated viruses (AAVs) are important tools used for delivering genes in research and clinical settings, but understanding how these viruses interact with cells can be challenging, especially for those that have been modified through directed evolution.
  • This study uses a human cell microarray platform to uncover how both natural and engineered AAVs connect with human cell receptors, discovering that AAV9 specifically interacts with interleukin 3 (IL3) and that engineered AAVs can interact with the low-density lipoprotein receptor-related protein 6 (LRP6), which might enhance their ability to cross the blood-brain barrier.
  • The findings also highlight potential side effects from engineered AAVs due to off-target tissue binding, paving the
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  • Deep-learning methods for protein structure prediction are highly accurate, but there's a gap in predicting which proteins can effectively bind to targets, limiting their practical applications in protein engineering.
  • To address this gap, a new tool called APPRAISE has been developed, which scores the target-binding ability of engineered proteins after their structures are predicted using tools like AlphaFold or ESMFold, doing so in less than a second per model.
  • APPRAISE has been successfully tested for various engineered proteins, including those targeting the SARS-CoV-2 spike and certain viral vectors, and is available online through Google Colaboratory, enhancing protein structure prediction and aiding biomedical research.
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A longstanding challenge in gene therapy is expressing a dosage-sensitive gene within a tight therapeutic window. For example, loss of function causes Rett syndrome, while its duplication causes duplication syndrome. Viral gene delivery methods generate variable numbers of gene copies in individual cells, creating a need for gene dosage-invariant expression systems.

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The gastrointestinal (GI) tract is innervated by intrinsic neurons of the enteric nervous system (ENS) and extrinsic neurons of the central nervous system and peripheral ganglia. The GI tract also harbors a diverse microbiome, but interactions between the ENS and the microbiome remain poorly understood. Here, we activate choline acetyltransferase (ChAT)-expressing or tyrosine hydroxylase (TH)-expressing gut-associated neurons in mice to determine effects on intestinal microbial communities and their metabolites as well as on host physiology.

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Currently, ultrashort oligopeptides consisting of fewer than eight amino acids represent a cutting-edge frontier in materials science, particularly in the realm of hydrogel formation. By employing solid-phase synthesis with the Fmoc/tBu approach, a novel pentapeptide, FEYNF-NH, was designed, inspired by a previously studied sequence chosen from hen egg-white lysozyme (FESNF-NH). Qualitative peptide analysis was based on reverse-phase high performance liquid chromatography (RP-HPLC), while further purification was accomplished using solid-phase extraction (SPE).

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In this study, a new strategy was adopted for obtaining polymer/protein hybrid hydrogels with shape stability and tunable mechanical or rheological characteristics by using non-toxic procedures. A chemical network was created using a poly(vinyl alcohol)(PVA)/bovine serum albumin (BSA) mixture in aqueous solution in the presence of genipin and reduced glutathione (GSH). Then, a second physical network was formed through PVA after applying freezing/thawing cycles.

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Article Synopsis
  • Integrating cell type-specific enhancers with recombinant adeno-associated viruses (AAVs) allows targeted genetic access to specific cell types, but AAVs have a limited capacity for the size of genetic material they can deliver.
  • The concept of transcriptional crosstalk involves separating large regulatory elements into a second AAV genome, offering a new way to achieve specific gene expression within a certain cell type.
  • The study identifies transcriptional crosstalk in AAVs with 11 mouse brain enhancers, using advanced spatial genomics to examine AAV behavior, and successfully demonstrates cell type-specific gene editing in tissues with minimal invasiveness.
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Background: Copy number variations, and particularly duplications of genomic regions, have been strongly associated with various neurodegenerative conditions including autism spectrum disorder (ASD). These genetic variations have been found to have a significant impact on brain development and function, which can lead to the emergence of neurological and behavioral symptoms. Developing strategies to target these genomic duplications has been challenging, as the presence of endogenous copies of the duplicate genes often complicates the editing strategies.

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Article Synopsis
  • Multi-wavelength analytical ultracentrifugation (MW-AUC) offers enhanced accuracy for characterizing and quantifying adeno-associated viruses compared to traditional methods.
  • Guidelines for experimental design in sedimentation velocity and buoyant density equilibrium AUC are provided.
  • MW-AUC effectively identifies capsid ratios and contaminants, detects partially filled capsids, and delivers more reliable results than dual-wavelength AUC, transmission electron microscopy, and mass photometry, reinforcing its status as the gold standard for analyzing viral vectors.
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The circadian rhythm pacemaker, the suprachiasmatic nucleus (SCN), mediates light entrainment via vasoactive intestinal peptide (VIP) neurons (SCN). Yet, how these neurons uniquely respond and connect to intrinsically photosensitive retinal ganglion cells (ipRGCs) expressing melanopsin (Opn4) has not been determined functionally in freely behaving animals. To address this, we first used monosynaptic tracing from SCN neurons in mice and identified two SCN subpopulations.

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Crossing the blood-brain barrier in primates is a major obstacle for gene delivery to the brain. Adeno-associated viruses (AAVs) promise robust, non-invasive gene delivery from the bloodstream to the brain. However, unlike in rodents, few neurotropic AAVs efficiently cross the blood-brain barrier in non-human primates.

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Article Synopsis
  • Modern neuroscience tools, like optogenetics and calcium imaging, help researchers study specific brain circuits in rodents to understand neurological diseases.
  • Using viral vectors, scientists can deliver genetic material to target specific cells in engineered rodents, but applying these methods to nonhuman primates poses challenges due to limited viral vectors.
  • Recent advancements in adeno-associated viral vectors for nonhuman primates could enhance research capabilities, leading to better insights and potential treatments for neurological and neurodegenerative conditions.
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Delivering genes to and across the brain vasculature efficiently and specifically across species remains a critical challenge for addressing neurological diseases. We have evolved adeno-associated virus (AAV9) capsids into vectors that transduce brain endothelial cells specifically and efficiently following systemic administration in wild-type mice with diverse genetic backgrounds, and in rats. These AAVs also exhibit superior transduction of the CNS across non-human primates (marmosets and rhesus macaques), and in ex vivo human brain slices, although the endothelial tropism is not conserved across species.

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Hydrogels are three-dimensional networks with a variety of structures and functions that have a remarkable ability to absorb huge amounts of water or biological fluids. They can incorporate active compounds and release them in a controlled manner. Hydrogels can also be designed to be sensitive to external stimuli: temperature, pH, ionic strength, electrical or magnetic stimuli, specific molecules, etc.

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Copy number variations, and particularly duplications of genomic regions, have been strongly associated with various neurodegenerative conditions including autism spectrum disorder (ASD). These genetic variations have been found to have a significant impact on brain development and function, which can lead to the emergence of neurological and behavioral symptoms. Developing strategies to target these genomic duplications has been challenging, as the presence of endogenous copies of the duplicate genes often complicates the editing strategies.

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The blood-brain barrier (BBB) presents a major challenge for delivering large molecules to study and treat the central nervous system. This is due in part to the scarcity of targets known to mediate BBB crossing. To identify novel targets, we leverage a panel of adeno-associated viruses (AAVs) previously identified through mechanism-agnostic directed evolution for improved BBB transcytosis.

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In situ-forming gels with self-assembling and self-healing properties are materials of high interest for various biomedical applications, especially for drug delivery systems and tissue regeneration. The main goal of this research was the development of an innovative gel carrier based on dynamic inter- and intramolecular interactions between amphiphilic polyurethane and peptide structures. The polyurethane architecture was adapted to achieve the desired amphiphilicity for self-assembly into an aqueous solution and to facilitate an array of connections with peptides through physical interactions, such as hydrophobic interactions, dipole-dipole, electrostatic, π-π stacking, or hydrogen bonds.

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Tissue clearing combined with deep imaging has emerged as a powerful technology to expand classical histological techniques. Current techniques have been optimized for imaging sparsely pigmented organs such as the mammalian brain. In contrast, melanin-rich pigmented tissue, of great interest in the investigation of melanomas, remains challenging.

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Peptides and their related compounds can self-assemble into diverse nanostructures of different shapes and sizes in response to various stimuli such as pH, temperature or ionic strength. Here we report the synthesis and characterization of a lysozyme derived pentapeptide and its ability to build well-defined fibrillar structures. Lysozyme FESNF peptide fragment was synthesized by solid phase peptide synthesis using the Fmoc/t-Bu strategy, purified by analytical high-performance liquid chromatography (HPLC) and its molecular weight was confirmed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS).

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Adeno-associated viruses (AAVs) promise robust gene delivery to the brain through non-invasive, intravenous delivery. However, unlike in rodents, few neurotropic AAVs efficiently cross the blood-brain barrier in non-human primates (NHPs). Here we describe AAV.

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This paper reports new physical hydrogels obtained by the freezing/thawing method. They include pullulan (PULL) and poly(vinyl alcohol) (PVA) as polymers, bovine serum albumin (BSA) as protein, and a tripeptide, reduced glutathione (GSH). In addition, a sample containing PULL/PVA and lysozyme was obtained in similar conditions.

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Article Synopsis
  • Efficient delivery of genes across the brain's blood vessels is crucial for treating neurological diseases, and modified adeno-associated viruses (AAV9) have been developed to target brain endothelial cells effectively in various animal models.
  • These modified AAVs show enhanced ability to transduce cells in non-human primates and human brain tissue, although their targeting efficiency varies across species.
  • The research indicates that these mouse-specific capsids can be utilized to alter the blood-brain barrier, turning it into a functional biofactory that produces beneficial proteins, like Hevin, to improve synaptic function in mice with synaptic deficits.
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Article Synopsis
  • - The study addresses the challenges of using engineered adeno-associated viral vectors (AAVs) for targeting specific cell types by developing a new method called USeqFISH, which allows for high-resolution spatial profiling of RNA in tissues.
  • - USeqFISH was used to analyze the transduction patterns of six different systemic AAVs in mouse brain regions, revealing unique preferences for certain cell subtypes, such as AAV-PHP.N favoring excitatory neurons.
  • - The method also facilitates the profiling of regulatory elements within AAV genomes and shows promise for applications in studying gene delivery in non-human primates.
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