5430 research outputs found
Sort by
Günter Blobel\u27s publications
No full textArchive of Günter Blobel\u27s publications in his laboratory, 2018
Photo by Lubosh Stepanekhttps://digitalcommons.rockefeller.edu/blobel-molecular-biology/1031/thumbnail.jp
Blobel lab in Dresden
No full textGünter Blobel’s passion for the city was evident when members of his laboratory and about 80 ex-Blobelites participated in a 65th birthday Symposium held in his honor in May 2001 at the newly constructed magnificent Max Planck Institute for Molecular Cell Biology and Genetics. The participants were treated to several outstanding tours of the city by Günter, who acted as the passionate guide.
Photo by Lubosh Stepanekhttps://digitalcommons.rockefeller.edu/blobel-molecular-biology/1060/thumbnail.jp
Single Cell Analysis of the HIV-1 Latent Reservoir
Get PDFHuman immunodeficiency virus type 1 (HIV-1), the virus that causes acquired immune deficiency syndrome (AIDS), is one of the world\u27s most serious health and development challenges. Worldwide there are approximately 36.7 million people living with HIV, and tens of millions have died of AIDS-related causes since the beginning of the epidemic. Treatment of HIV-1 infection with combinations of antiretroviral drugs has significantly reduced the death rate and improved the quality of life of HIV-1 infected individuals. Despite over thirty years of HIV-1 research, however, both a cure and a vaccine remain elusive. Complete eradication of HIV-1 by antiretroviral drugs is prevented by the persistence of rare, long-lived, latently infected cells. These cells, called the latent reservoir, are thought to resist immune clearance and viral cytopathic effects by harboring a transcriptionally quiescent integrated HIV-1 provirus. As a result, interruption of suppressive therapy almost inevitably results in rapid viral rebound, which originates from these latently infected cells and prevents HIV-1 cure. It is thought that establishing the reservoir requires intact retroviral integration into the host cell genome and subsequent transcriptional silencing of the integrated provirus. These are rare events and these cells have no known distinguishing surface markers, which has made it difficult to define the precise cellular and molecular nature of the reservoir. The long half-life of the latent reservoir has been attributed to a stable pool of long-lived latently infected CD4+ T cells. An alternative explanation, consistent with the frequent occurrence of monotypic viral sequences, is that infected latent cells are maintained in part by cell proliferation. T cell division and productive HIV-1 transcription are mediated by shared metabolic and transcriptional pathways, and productive HIV-1 infection typically leads to CD4+ T cell death. Thus, how infected cells survive while dividing is unknown. I focused my thesis on characterizing this latent reservoir in virally suppressed, HIV-1 infected individuals and examining the mechanisms of HIV-1 latency. In the first part of this thesis, using a novel single-cell, high throughput integration site sequencing method, I demonstrate that HIV-1 infected cells are capable of cell division, but that the great majority of the largest expanded clones contain defective proviruses which cannot contribute to the replication competent rebound virus. In the second part of this thesis, using an assay to qualitatively and quantitatively characterize the latent reservoir, I suggest that the replication competent latent reservoir may, in fact, be maintained in part by rare cell division events. And finally, I developed a novel isolation strategy which allowed single cell characterization of recently reactivated latent cells. I was able to obtain reactivated latent T cells that produced intact, replication competent HIV-1. By sequencing the T cell receptors, I prove that these isolated latent cells are expanded T cell clones. Single cell gene expression analysis revealed that latent cells share a specific gene profile that prominently includes genes implicated in silencing the virus, T cell exhaustion markers, and genes that may aid in identification of specific CD4+ T cell subsets prone to latent infection. Together, the data supports a model for latency whereby infected T cells turn on a gene expression program that suppresses viral replication during cell division thereby preventing activation of the cell death pathways that are normally triggered by HIV-1 infection
Catalyst Quartet
No full text2018, December 14
Catalyst Quartet: Jessie Montgomery and Karla Donehew-Perez, violins; Paul Laraia, viola; Karlos Rodriguez, cello, Performing J.S. Bach: Goldberg Variations (arranged by the Catalyst Quartet).https://digitalcommons.rockefeller.edu/tri-institutional-noon-recitals/1049/thumbnail.jp
Nichlas Namoradze, Piano
No full text2018, September 21
Nichlas Namoradze, piano, performed Bac Partita no.6, Schumann Humoreske, Op. 2, Namoradze Etudes I-III, Schumann Arabeske, Op. 8https://digitalcommons.rockefeller.edu/tri-institutional-noon-recitals/1059/thumbnail.jp
Zorá String Quartet
No full text2018, April 13
Zorá String Quartet: Dechopol Kowintaweewat and Hsuan-Hao Hsu, violins; Pablo Muñoz Salido, viola; Zizai Ning, cello, performed Beethoven: String Quartet No. 15 in A Minor, Op. 132; Mendelssohn: String Quartet No. 2 in A Minor, Op. 13https://digitalcommons.rockefeller.edu/tri-institutional-noon-recitals/1069/thumbnail.jp
Blobel Laboratory. View no. 5, April 2018
No full textBlobel laboratory in the Rockefeller Research Building, 2018
Photo by Lubosh Stepanekhttps://digitalcommons.rockefeller.edu/blobel-laboratory/1004/thumbnail.jp
Characterizing Human Transfer RNAs by Hydro-tRNAseq and PAR-CLIP
Get PDFThe participation of tRNAs in fundamental aspects of biology and disease necessitates an accurate, experimentally confirmed annotation of tRNA genes, and curation of precursor and mature tRNA sequences. This has been challenging, mainly because RNA secondary structure and nucleotide modifications, together with tRNA gene multiplicity, complicate sequencing and read mapping efforts. To address these issues, I developed hydro-tRNAseq, a method based on partial alkaline RNA hydrolysis that generates fragments amenable for sequencing. To identify transcribed tRNA genes, I further complemented this approach with Photoactivatable Crosslinking and Immunoprecipitation (PAR-CLIP) of SSB/La, a conserved protein involved in pre-tRNA processing. My results show that approximately half of all predicted tRNA genes are transcribed in human cells, suggesting that the tRNA genomic space is more contracted than previously thought as a result of regulation of expression. I also report predominant nucleotide modification sites, their order of incorporation, and identify tRNA leader, trailer and intron sequences. By using complementary sequencing-based methodologies I present a human tRNA reference set, and determine expression levels of mature and processing intermediates of tRNAs in human cells. The technical advances provided by hydro-tRNAseq are applied towards the molecular diagnosis of a genetic neurodevelopmental syndrome, caused by mutations in the tRNA processing factor CLP1. Finally, I harness this novel experimental and computational expertise towards the identification of the endonuclease complex C3PO as a novel processing factor of human tRNAs. I carry out a transcriptome-wide analysis of C3PO targets, identify its binding sites and motifs, and provide insights into its biochemical and biological functions
Marjorie McCarty Oral History. Part 8: Theater and Music
No full textInterview recorded on September 14th, 2017. Part of the Rita and Frits Markus Library Oral History project.https://digitalcommons.rockefeller.edu/marjorie-mccarty/1008/thumbnail.jp
IGDB-2, an IG/FNIII Protein, Binds the ION Channel LGC-34 and Controls Sensory Compartment Morphogenesis in C. Elegans
Get PDFSensory organ glia surround neuronal receptive endings (NREs), forming a specialized extracellular space, or compartment, important for neuronal activity, and reminiscent of glia-ensheathed synapses in the central nervous system. Sensory organ glia are conserved across organisms, but our current understanding of how they form sensory compartments is generally lacking. To date, the Caenorhabditis elegans amphid sensory organ has provided critical insight into some of these developmental processes. DAF-6, a Patched-related protein, was previously shown to be required in amphid glia to restrict sensory compartment size. LIT-1, a Nemo-like kinase, and SNX-1, a retromer component, antagonize DAF-6 and promote compartment expansion. My work here further explores the machinery underlying compartment size control. In seeking genes whose inactivation restores normal compartment size to daf-6 mutants, I identify two novel regulators: IGDB-2, an Ig/FNIII protein, and LGC-34, a ligand-gated ion channel. First, igdb-2 mutations suppress daf-6 mutant defects. IGDB-2 acts in glia, where it localizes to glial membranes surrounding NREs, and, together with LIT-1 and SNX-1, regulates compartment morphogenesis. Second, immunoprecipitation followed by mass spectrometry demonstrates that IGDB-2 binds to LGC-34, and lgc-34 mutations inhibit igdb-2 suppression of daf-6. My findings thus reveal the novel IGDB-2/LGC-34 membrane protein complex and suggest new molecular mechanisms for how sensory compartment size is controlled