A5013619177- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
- Advanced Fluorescence Microscopy Techniques
- Advanced biosensing and bioanalysis techniques
- Molecular Biology Techniques and Applications
- DNA and Nucleic Acid Chemistry
- Gamma-ray bursts and supernovae
- Orbital Angular Momentum in Optics
- Nanopore and Nanochannel Transport Studies
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- RNA Interference and Gene Delivery
- Force Microscopy Techniques and Applications
- Bacteriophages and microbial interactions
- Astronomy and Astrophysical Research
- Genomics and Phylogenetic Studies
- Diffusion and Search Dynamics
- Galaxies: Formation, Evolution, Phenomena
- Astrophysics and Cosmic Phenomena
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Astro and Planetary Science
- Radio Astronomy Observations and Technology
- Scientific Computing and Data Management
- Geology and Paleoclimatology Research
- Genomics and Rare Diseases
Lawrence Berkeley National Laboratory
2024
University of California, Berkeley
2024
The University of Texas Medical Branch at Galveston
2022-2024
Harvard University
2017-2021
Bar-Ilan University
2009-2018
Alzheimer's Association of Israel
2018
Chromosome organization is crucial for genome function. Here, we present a method visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the microscopy methods OligoSTORM OligoDNA-PAINT, trace 8 megabases human 19, structures ranging in size from few kilobases over megabase. Focusing on regions that contribute compartments, discover distinct that, spite considerable variability, can predict whether...
Significance FISH enables researchers to visualize the subcellular distribution of RNA and DNA molecules in individual cells. The recent development methods employing probes composed synthetic oligonucleotides (oligos) allows tightly control aspects probe design such as binding energy genomic specificity. Although oligo are central many recently developed massively multiplexed superresolution imaging methods, no dedicated computational utility exists facilitate on genome-wide scale. Here, we...
Abstract Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops generally studied a finer scale, the impact looping on proximal interactions remains enigmatic. Here, we critically examine nuclear and loop-proximal using combination in situ Hi-C unparalleled depth, algorithm development, biophysical modeling. Producing large map with 33 billion contacts conjunction an for performing...
Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, disease. Here, we focus on interactions Drosophila, where homologous chromosomes are paired somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach minimize misassignment thus robustly distinguish trans-homolog contacts. This...
Eukaryotic DNA is highly organized within nuclei and this organization important for genome function. Fluorescent in situ hybridization (FISH) approaches allow 3D architectures of genomes to be visualized. Scalable FISH technologies, which can applied whole animals, are needed help unravel how genomic architecture regulates, or regulated by, gene expression during development, growth, reproduction, aging. Here, we describe a multiplexed Oligopaint library that targets the entire...
Mosquito transmission of dengue viruses to humans starts with infection skin resident cells at the biting site. There is great interest in identifying transmission-enhancing factors mosquito saliva order counteract them. Here we report discovery high levels anti-immune subgenomic flaviviral RNA (sfRNA) virus 2-infected saliva. We established that sfRNA present using three different methods: northern blot, RT-qPCR and sequencing. next show salivary protected detergent-sensitive compartments,...
The dynamics of a diffusing particle in potential field is ubiquitous physics, and it plays pivotal role single-molecule studies. We present formalism for analyzing the particles harmonic potentials at low Reynolds numbers using time evolution probability distribution function. demonstrate power by simulation measuring nanobead tethered to single DNA molecule. It allows one simultaneously extract all parameters that describe system, namely, diffusion coefficient restoring-force constant.
Using an optimized combination of tethered particle motion method, total internal reflection, and a gold nanobead, we measured the three-dimensional distribution free end DNA molecule. The along axial $z$ direction (perpendicular to surface) is found be Rayleigh-like, in agreement with wormlike chain freely jointed simulations. these simulations, show that presence wall increases correlations between orientations neighboring segments compared DNA. While simulated planar ($\mathit{xy}$)...
Abstract Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, disease. Here, we focused on interactions Drosophila , where homologous chromosomes are paired somatic cells from embryogenesis through adulthood. We first addressed the long-standing question of whether pairing extends genome-wide and, to this end, developed a haplotype-resolved Hi-C approach that uses new strategy minimize homolog misassignment thus robustly...
Abstract Single molecule studies make possible the characterization of molecular processes and identification biophysical sub‐populations that are not accessible through ensemble studies. We describe tethered particle motion, a method allows one to study single molecules in their natural form without having apply any external forces. The combines darkfield microscopy with metal nano‐bead. It permits properties particles, as well protein–DNA interactions. is suitable for vivo studies, we...
Abstract Chromosome structure is thought to be crucial for proper functioning of the nucleus. Here, we present a method visualizing chromosomal DNA at super-resolution and then integrating Hi-C data produce three-dimensional models chromosome organization. We begin by applying Oligopaint probes single-molecule localization microscopy methods OligoSTORM OligoDNA-PAINT image 8 megabases human 19, discovering that regions contributing compartments can form distinct structures. Intriguingly, our...
We utilized single-molecule tethered particle motion (TPM) tracking, optimized for studying the behavior of short (0.922 μm) dsDNA molecules under shear flow conditions, in proximity a wall (surface).
Abstract Genome organization in humans is governed by two major mechanisms: loop extrusion cohesin and CTCF the spatial compartmentalization of chromosomes. These folding mechanisms have been shown to regulate several genomic functions, including gene expression. However, how transcription might chromatin structure remains a subject many ongoing investigations. In this study, we use Integrator protein complex as tool understand impact aberrant on 3D genome. During initiation, RNA...
The rise of time-domain astronomy including electromagnetic counterparts to gravitational waves, microlensing, explosive phenomena, and even astrometry with Gaia, are showing the power need for surveys high-cadence, large area, long time baselines study transient universe. A constellation SmallSats or CubeSats providing wide, instantaneous sky coverage down 21 Vega mag at optical wavelengths would be ideal addressing this need. We assembling CuRIOS-ED (CubeSats Rapid Infrared Optical...
Abstract Philadelphia-positive leukemia is characterized by the translocation t(9;22)(q34;q11), which results in oncogene BCR-ABL1 and a chromosome called Philadelphia (Ph) (chr). The best Chronic Myeloid Leukemia (CML); however, also found Acute Lymphoblastic (ALL). ALL has been historically understudied, especially minority populations. Genome organization highly complex process chromatin segregated within nucleus into specific domains, making stable translocations unfavorable. How are...
We study a magnitude-limited sample of 36 Broad-lined Type Ic Supernovae (SNe Ic-BL) from the Zwicky Transient Facility Bright Survey, detected between March 2018 and August 2021. present light curves (LCs) for each SNe, analyze shape LCs to derive empirical parameters, along with explosion epochs every event. The has an average absolute peak magnitude in r band $M_r^{max}$ = -18.51 $\pm$ 0.15 mag. Using spectra obtained around light, we compute expansion velocities Fe II 5169 Angstrom line...
ABSTRACT In this second paper on the DECam deep-drilling field (DDF) program, we release 2020 optical $gri$-band light curves for transients and variables in extragalactic COSMOS ELAIS fields based time series observations with a 3-d cadence from semester 2021A through 2023A. order to demonstrate wide variety of domain events detected by program encourage others use data set, characterize sample presenting brief analysis light-curve parameters such as span, amplitude, peak brightness. We...
In this second paper on the DECam deep drilling field (DDF) program we release 2,020 optical gri-band light curves for transients and variables in extragalactic COSMOS ELAIS fields based time series observations with a 3-day cadence from semester 2021A through 2023A. order to demonstrate wide variety of domain events detected by encourage others use data set, characterize sample presenting brief analysis curve parameters such as span, amplitude, peak brightness. We also present preliminary...