A5009896683- Photoreceptor and optogenetics research
- Retinal Development and Disorders
- Single-cell and spatial transcriptomics
- bioluminescence and chemiluminescence research
- Advanced biosensing and bioanalysis techniques
- Zebrafish Biomedical Research Applications
- Molecular Biology Techniques and Applications
- Axon Guidance and Neuronal Signaling
- CRISPR and Genetic Engineering
- Neuroinflammation and Neurodegeneration Mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Neurogenesis and neuroplasticity mechanisms
- RNA and protein synthesis mechanisms
- Neuroscience and Neuropharmacology Research
- Advanced Fluorescence Microscopy Techniques
- Mitochondrial Function and Pathology
- Cancer-related molecular mechanisms research
- Cell Image Analysis Techniques
- Biosensors and Analytical Detection
- Retinal Diseases and Treatments
- Photosynthetic Processes and Mechanisms
- Angiogenesis and VEGF in Cancer
- Genomics and Chromatin Dynamics
- interferon and immune responses
Boston VA Research Institute
2019-2024
Harvard University
2018-2024
Howard Hughes Medical Institute
2019-2022
University of California, San Diego
2019
University of Cambridge
1999
Abstract We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking barcodes onto complementary DNAs with a one-step stitching reaction to create pooled, indexed sequencing libraries. This enables selection multiple cell populations tissue full-transcriptome based on location, morphology or protein...
Abstract Dissecting the myriad regulatory mechanisms controlling eukaryotic transcripts from production to degradation requires quantitative measurements of mRNA flow across cell. We developed subcellular TimeLapse-seq measure rates at which RNAs are released chromatin, exported nucleus, loaded onto polysomes, and degraded within nucleus cytoplasm. These varied substantially, yet genes with related functions or targeted by same transcription factors RNA binding proteins flowed compartments...
Nrf2, a transcription factor that regulates the response to oxidative stress, has been shown rescue cone photoreceptors and slow vision loss in mouse models of retinal degeneration (rd). The pigment epithelium (RPE) is damaged these models, but whether it also could be rescued by Nrf2 not previously examined. We used an adeno-associated virus (AAV) with RPE-specific (Best1) promoter overexpress RPE rd mice. Control mice showed disruption regular array RPE, as well cells. Cones were lost...
Retinitis pigmentosa (RP) is an inherited retinal disease affecting >20 million people worldwide. Loss of daylight vision typically occurs due to the dysfunction/loss cone photoreceptors, cell type that initiates our color and high-acuity vision. Currently, there no effective treatment for RP, other than gene therapy a limited number specific genes. To develop gene-agnostic therapy, we screened 20 genes their ability prolong photoreceptor survival in vivo. Here, report adeno-associated...
How do neuronal subtypes emerge during development? Recent molecular studies have profiled existing diversity, but subtype genesis remains elusive. The 15 types of mouse retinal bipolar interneurons are characterized by distinct functions, morphologies, and transcriptional profiles. Here, we develop a comprehensive spatiotemporal map in the murine retina. Combining multiplexed detection 16 RNA markers with timed delivery 5-ethynyl uridine (EdU) bromodeoxyuridine (BrdU), analyze more than...
Recent transcriptional profiling technologies are uncovering previously-undefined cell populations and molecular markers at an unprecedented pace. While single RNA (scRNA) sequencing is attractive approach for unbiased of all types, a complementary method to isolate sequence specific from heterogeneous tissue remains challenging. Here, we developed Probe-Seq, which allows deep types isolated using as the defining feature. Dissociated cells labeled fluorescent in situ hybridization (FISH)...
The bipolar interneurons of the mammalian retina have evolved as a diverse set cells with distinct subtype characteristics, which reflect specialized contributions to visual circuitry. Fifteen subtypes been identified in mouse retina, each characteristic gene expression, morphology, and light responses. This review provides an overview developmental events that underlie generation cell class, summarizing current knowledge genetic programs establish maintain fates, well shape final...
SUMMARY Fluorescent in situ hybridization (FISH) reveals the abun-dance and positioning of nucleic acid sequences fixed sam-ples can be combined with cell segmentation to produce a powerful single gene expression assay. However, it re-mains difficult label more than few targets visu-alize acids environments such as thick tissue using conventional FISH technologies. Recently, meth-ods have been developed for multiplexed amplification signals, yet remains challenging achieve high lev-els...
ABSTRACT Recent transcriptional profiling technologies are uncovering previously-undefined cell populations and molecular markers at an unprecedented pace. While single RNA (scRNA) sequencing is attractive approach for unbiased of all types, a complementary method to isolate sequence specific from heterogeneous tissue remains challenging. Here, we developed Probe-Seq, which allows deep types isolated using as the defining feature. Dissociated cells labelled fluorescent in situ hybridization...
Abstract Retinitis pigmentosa (RP) is an inherited retinal disease, affecting >20 million people worldwide. Loss of daylight vision typically occurs due to the dysfunction/loss cone photoreceptors, cell type that initiates our color and high acuity vision. Currently, there no effective treatment for RP, other than gene therapy a limited number specific disease genes. To develop gene-agnostic therapy, we screened ≈20 genes their ability prolong photoreceptor survival in vivo . Here, report...
Most organs and tissues are composed of many types cells. To characterize cellular state, various transcription profiling approaches currently available, including whole-tissue bulk RNA sequencing, single cell sequencing (scRNA-Seq), type-specific sequencing. What is missing in this repertoire a simple, versatile method for transcriptional which genetic markers or antibodies not readily available. We therefore developed Probe-Seq, uses hybridization gene-specific probes to isolation specific...
Abstract Protocol for synthesis of the photocleavable hetero-dimerizer zapalog (TMP-DANB-SLF). Adapted from: Gutnick A., Banghart M. R., West E. Schwartz T. L., "The light-sensitive dimerizer reveals distinct modes immobilization axonal mitochondria.", Nature Cell Biology (2019) https://doi.org/10.1038/s41556-019-0317-2
Abstract How do neuronal subtypes emerge during development? Recent molecular studies have expanded our knowledge of existing diversity. However, the genesis remains elusive and previous been limited by a lack quantitative methods for simultaneous detection subtype diversity in situ . The bipolar interneurons mammalian retina represent diverse class, characterized distinct functions, morphologies, recently discovered transcriptional profiles. Here, we developed comprehensive spatiotemporal...