Recursos de colección

Caltech Authors (171.365 recursos)

Repository of works by Caltech published authors.

Group = Heritage Medical Research Institute

Mostrando recursos 1 - 20 de 72

  1. Structural and functional analysis of mRNA export regulation by the nuclear pore complex

    Lin, Daniel H.; Correia, Ana R.; Cai, Sarah W.; Huber, Ferdinand M.; Jette, Claudia A.; Hoelz, André
    The nuclear pore complex (NPC) controls the passage of macromolecules between the nucleus and cytoplasm, but how the NPC directly participates in macromolecular transport remains poorly understood. In the final step of mRNA export, the DEAD-box helicase DDX19 is activated by the nucleoporins Gle1, Nup214, and Nup42 to remove Nxf1•Nxt1 from mRNAs. Here, we report crystal structures of Gle1•Nup42 from three organisms that reveal an evolutionarily conserved binding mode. Biochemical reconstitution of the DDX19 ATPase cycle establishes that human DDX19 activation does not require IP_6, unlike its fungal homologs, and that Gle1 stability affects DDX19 activation. Mutations linked to motor...

  2. An Oxidative Dearomatization Approach To Prepare the Pentacyclic Core of Ryanodol

    Xu, Chen; Han, Arthur; Reisman, Sarah E.
    An approach to synthesize the pentacyclic framework of the polyol diterpenoid ryanodol is reported. The ABC tricycle was constructed by a Co-mediated Pauson–Khand reaction, and both radical and anionic cyclization pathways were developed to form the E-ring. In addition, a reaction sequence involving SeO_2-mediated enone oxidation and hydroxyl-directed oxy-Michael addition was developed to introduce the A-ring oxidation. The feasibility of forming the bridging D-ring by an oxidative dearomatization was established.

  3. Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors

    Patriarchi, Tommaso; Cho, Jounhong Ryan; Merten, Katharina; Howe, Mark W.; Marley, Aaron; Xiong, Wei-Hong; Folk, Robert W.; Broussard, Gerard Joey; Liang, Ruqiang; Jang, Min Jee; Zhong, Haining; Dombeck, Daniel; von Zastrow, Mark; Nimmerjahn, Axel; Gradinaru, Viviana; Williams, John T.; Tian, Lin
    Neuromodulatory systems exert profound influences on brain function. Understanding how these systems modify the operating mode of target circuits requires measuring spatiotemporally precise neuromodulator release. We developed dLight1, an intensity-based genetically encoded dopamine indicator, to enable optical recording of dopamine dynamics with high spatiotemporal resolution in behaving mice. We demonstrated the utility of dLight1 by imaging dopamine dynamics simultaneously with pharmacological manipulation, electrophysiological or optogenetic stimulation, and calcium imaging of local neuronal activity. dLight1 enabled chronic tracking of learning-induced changes in millisecond dopamine transients in striatum. Further, we used dLight1 to image spatially distinct, functionally heterogeneous dopamine transients relevant to...

  4. Hydrogel-Tissue Chemistry: Principles and Applications

    Gradinaru, Viviana; Treweek, Jennifer; Overton, Kristin; Deisseroth, Karl
    Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons—even within vertebrate brains. This new approach and its variants, as...

  5. A wireless, low-drift, implantable intraocular pressure sensor with parylene-on-oil encapsulation

    Agarwal, Abhinav; Shapero, Aubrey; Rodger, Damien; Humayun, Mark; Tai, Yu-Chong; Emami, Azita
    This paper presents a wireless, implantable continuous intraocular pressure (IOP) monitoring system that features a parylene-on-oil sensor encapsulation method for achieving long-term low-drift in vivo. The system is implanted in the superotemporal quadrant of the eye between the sclera and conjunctiva. It consists of a commercial pressure sensor (STMicroelectronics LPS25H) with digital readout, a 65nm CMOS chip that supports wireless power/data telemetry and the I2C serial communication interface with the pressure sensor. The chip and pressure sensor are assembled on a flexible polyimide PCB, and then the sensor is submerged in biocompatible silicone oil and coated with parylene in situ....

  6. Evolution of a Strategy for the Enantioselective Total Synthesis of (+)-Psiguadial B

    Chapman, Lauren M.; Beck, Jordan C.; Lacker, Caitlin R.; Wu, Linglin; Reisman, Sarah E.
    (+)-Psiguadial B is a diformyl phloroglucinol meroterpenoid that exhibits antiproliferative activity against the HepG2 human hepatoma cancer cell line. This full account details the evolution of a strategy that culminated in the first enantioselective total synthesis of (+)-psiguadial B. A key feature of the synthesis is the construction of the trans-cyclobutane motif by a Wolff rearrangement with in situ catalytic, asymmetric trapping of the ketene. An investigation of the substrate scope of this method to prepare enantioenriched 8-aminoquinolinamides is disclosed. Three routes toward (+)-psiguadial B were evaluated that featured the following key steps: (1) an ortho-quinone methide hetero-Diels–Alder cycloaddition to...

  7. Viral Strategies for Targeting the Central and Peripheral Nervous Systems

    Bedbrook, Claire N.; Deverman, Benjamin E.; Gradinaru, Viviana
    Recombinant viruses allow for targeted transgene expression in specific cell populations throughout the nervous system. The adeno-associated virus (AAV) is among the most commonly used viruses for neuroscience research. Recombinant AAVs (rAAVs) are highly versatile and can package most cargo composed of desired genes within the capsid’s ∼5-kb carrying capacity. Numerous regulatory elements and intersectional strategies have been validated in rAAVs to enable cell type–specific expression. rAAVs can be delivered to specific neuronal populations or globally throughout the animal. The AAV capsids have natural cell type or tissue tropism and trafficking that can be modified for increased specificity. Here, we...

  8. Gut microbiota utilize immunoglobulin A for mucosal colonization

    Donaldson, G. P.; Ladinsky, M. S.; Yu, K. B.; Sanders, J. G.; Yoo, B. B.; Chou, W.-C.; Conner, M. E.; Earl, A. M.; Knight, R.; Bjorkman, P. J.; Mazmanian, S. K.
    The immune system responds vigorously to microbial infection while permitting lifelong colonization by the microbiome. Mechanisms that facilitate the establishment and stability of the gut microbiota remain poorly described. We found that a regulatory system in the prominent human commensal Bacteroides fragilis modulates its surface architecture to invite binding of immunoglobulin A (IgA) in mice. Specific immune recognition facilitated bacterial adherence to cultured intestinal epithelial cells and intimate association with the gut mucosal surface in vivo. The IgA response was required for B. fragilis (and other commensal species) to occupy a defined mucosal niche that mediates stable colonization of the...

  9. Multifunctional biophotonic nanostructures inspired by the longtail glasswing butterfly for medical devices

    Narasimhan, Vinayak; Siddique, Radwanul Hasan; Lee, Jeong Oen; Kumar, Shailabh; Ndjamen, Blaise; Du, Juan; Hong, Natalie; Sretavan, David; Choo, Hyuck
    Numerous living organisms possess biophotonic nanostructures that provide colouration and other diverse functions for survival. While such structures have been actively studied and replicated in the laboratory, it remains unclear whether they can be used for biomedical applications. Here, we show a transparent photonic nanostructure inspired by the longtail glasswing butterfly (Chorinea faunus) and demonstrate its use in intraocular pressure (IOP) sensors in vivo. We exploit the phase separation between two immiscible polymers (poly(methyl methacrylate) and polystyrene) to form nanostructured features on top of a Si3_N_4 substrate. The membrane thus formed shows good angle-independent white-light transmission, strong hydrophilicity and anti-biofouling...

  10. Effect of optical aberrations on intraocular pressure measurements using a microscale optical implant in ex vivo rabbit eyes

    Han, Samuel J.; Park, Haeri; Lee, Jeong Oen; Choo, Hyuck
    Elevated intraocular pressure (IOP) is the only modifiable major risk factor of glaucoma. Recently, accurate and continuous IOP monitoring has been demonstrated in vivo using an implantable sensor based on optical resonance with remote optical readout to improve patient outcomes. Here, we investigate the relationship between optical aberrations of ex vivo rabbit eyes and the performance of the IOP sensor using a custom-built setup integrated with a Shack–Hartmann sensor. The sensor readouts became less accurate as the aberrations increased in magnitude, but they remained within the clinically acceptable range. For root-mean-square wavefront errors of 0.10 to 0.94  μm, the accuracy and...

  11. A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model

    Skubák, Pavol; Araç, Demet; Bowler, Matthew W.; Correia, Ana R.; Hoelz, Andre; Larsen, Sine; Leonard, Gordon A.; McCarthy, Andrew A.; McSweeney, Sean; Mueller-Dieckmann, Christoph; Otten, Harm; Salzman, Gabriel; Pannu, Navraj S.
    Determining macromolecular structures from X-ray data with resolution worse than 3 Å remains a challenge. Even if a related starting model is available, its incompleteness or its bias together with a low observation-to-parameter ratio can render the process unsuccessful or very time-consuming. Yet, many biologically important macromolecules, especially large macromolecular assemblies, membrane proteins and receptors, tend to provide crystals that diffract to low resolution. A new algorithm to tackle this problem is presented that uses a multivariate function to simultaneously exploit information from both an initial partial model and low-resolution single-wavelength anomalous diffraction data. The new approach has been used for...

  12. Biomolecular Ultrasound and Sonogenetics

    Maresca, David; Lakshmanan, Anupama; Abedi, Mohamed; Bar-Zion, Avinoam; Farhadi, Arash; Lu, George J.; Szablowski, Jerzy O.; Wu, Di; Yoo, Sangjin; Shapiro, Mikhail G.
    Visualizing and modulating molecular and cellular processes occurring deep within living organisms is fundamental to our study of basic biology and disease. Currently, the most sophisticated tools available to dynamically monitor and control cellular events rely on light-responsive proteins, which are difficult to use outside of optically transparent model systems, cultured cells, or surgically accessed regions owing to strong scattering of light by biological tissue. In contrast, ultrasound is a widely used medical imaging and therapeutic modality that enables the observation and perturbation of internal anatomy and physiology but has historically had limited ability to monitor and control specific cellular...

  13. Proteins, air and water: reporter genes for ultrasound and magnetic resonance imaging

    Lu, George J.; Farhadi, Arash; Mukherjee, Arnab; Shapiro, Mikhail G.
    A long-standing goal of molecular imaging is to visualize cellular function within the context of living animals, necessitating the development of reporter genes compatible with deeply penetrant imaging modalities such as ultrasound and magnetic resonance imaging (MRI). Until recently, no reporter genes for ultrasound were available, and most genetically encoded reporters for MRI were limited by metal availability or relatively low sensitivity. Here we review how these limitations are being addressed by recently introduced reporter genes based on air-filled and water-transporting biomolecules. We focus on gas-filled protein nanostructures adapted from buoyant microbes, which scatter sound waves, perturb magnetic fields and...

  14. Recombinantly Expressed Gas Vesicles as Nanoscale Contrast Agents for Ultrasound and Hyperpolarized MRI

    Farhadi, Arash; Ho, Gabrielle; Kunth, Martin; Ling, Bill; Lakshmanan, Anupama; Lu, George; Bourdeau, Raymond W.; Schröder, Leif; Shapiro, Mikhail G.
    Ultrasound and hyperpolarized magnetic resonance imaging enable the visualization of biological processes in deep tissues. However, few molecular contrast agents are available to connect these modalities to specific aspects of biological function. We recently discovered that a unique class of gas-filled protein nanostructures known as gas vesicles could serve as nanoscale molecular reporters for these modalities. However, the need to produce these nanostructures via expression in specialized cultures of cyanobacteria or haloarchaea limits their broader adoption by other laboratories and hinders genetic engineering of their properties. Here, we describe recombinant expression and purification of Bacillus megaterium gas vesicles using a...

  15. Acoustically modulated magnetic resonance imaging of gas-filled protein nanostructures

    Lu, George Jiaozhi; Farhadi, Arash; Szablowski, Jerzy O.; Lee-Gosselin, Audrey; Barnes, Samuel R.; Lakshmanan, Anupama; Bourdeau, Raymond W.; Shapiro, Mikhail G.
    Non-invasive biological imaging requires materials capable of interacting with deeply penetrant forms of energy such as magnetic fields and sound waves. Here, we show that gas vesicles (GVs), a unique class of gas-filled protein nanostructures with differential magnetic susceptibility relative to water, can produce robust contrast in magnetic resonance imaging (MRI) at sub-nanomolar concentrations, and that this contrast can be inactivated with ultrasound in situ to enable background-free imaging. We demonstrate this capability in vitro, in cells expressing these nanostructures as genetically encoded reporters, and in three model in vivo scenarios. Genetic variants of GVs, differing in their magnetic or...

  16. Searching for the gut microbial contributing factors to social behavior in rodent models of autism spectrum disorder

    Needham, Brittany D.; Tang, Weiyi; Wu, Wei-Li
    Social impairment is one of the major symptoms in multiple psychiatric disorders, including autism spectrum disorder (ASD). Accumulated studies indicate a crucial role for the gut microbiota in social development, but these mechanisms remain unclear. This review focuses on two strategies adopted to elucidate the complicated relationship between gut bacteria and host social behavior. In a top-down approach, researchers have attempted to correlate behavioral abnormalities with altered gut microbial profiles in rodent models of ASD, including BTBR mice, maternal immune activation (MIA), maternal valproic acid (VPA) and maternal high-fat diet (MHFD) offspring. In a bottom-up approach, researchers use germ-free (GF)...

  17. Surface-Enhanced Raman Spectroscopy-Based Label-Free Insulin Detection at Physiological Concentrations for Analysis of Islet Performance

    Cho, Hyunjun; Kumar, Shailabh; Yang, Daejong; Vaidyanathan, Sagar; Woo, Kelly; Garcia, Ian; Shue, Hao J.; Yoon, Youngzoon; Ferreri, Kevin; Choo, Hyuck
    Label-free optical detection of insulin would allow in vitro assessment of pancreatic cell functions in their natural state and expedite diabetes-related clinical research and treatment; however, no existing method has met these criteria at physiological concentrations. Using spatially uniform 3D gold-nanoparticle sensors, we have demonstrated surface-enhanced Raman sensing of insulin in the secretions from human pancreatic islets under low and high glucose environments without the use of labels such as antibodies or aptamers. Label-free measurements of the islet secretions showed excellent correlation among the ambient glucose levels, secreted insulin concentrations, and measured Raman-emission intensities. When excited at 785 nm, plasmonic...

  18. Total Synthesis of (+)-Pleuromutilin

    Farney, Elliot P.; Feng, Sean S.; Schäfers, Felix; Reisman, Sarah E.
    An 18-step synthesis of the antibiotic (+)-pleuromutilin is disclosed. The key steps of the synthesis include a highly stereoselective SmI2-mediated cyclization to establish the eight-membered ring and a stereospecific transannular [1,5]-hydrogen atom transfer to set the C10 stereocenter. This strategy was also used to prepare (+)-12-epi-pleuromutilin. The chemistry described here will enable efforts to prepare new mutilin antibiotics.

  19. Surface-Enhanced Raman Spectroscopy-Based Label-Free Insulin Detection at Physiological Concentrations for Analysis of Islet Performance

    Cho, Hyunjun; Kumar, Shailabh; Yang, Daejong; Vaidyanathan, Sagar R.; Woo, Kelly; Garcia, Ian; Shue, Hao Jan; Yoon, Youngzoon; Ferreri, Kevin; Choo, Hyuck
    Label-free optical detection of insulin would allow in vitro assessment of pancreatic cell functions in their natural state and expedite diabetes-related clinical research and treatment; however, no existing method has met these criteria at physiological concentrations. Using spatially uniform 3D gold-nanoparticle sensors, we have demonstrated surface-enhanced Raman sensing of insulin in the secretions from human pancreatic islets under low and high glucose environments without the use of labels such as antibodies or aptamers. Label-free measurements of the islet secretions showed excellent correlation among the ambient glucose levels, secreted insulin concentrations, and measured Raman-emission intensities. When excited at 785 nm, plasmonic...

  20. Acoustically Targeted Chemogenetics for Noninvasive Control of Neural Circuits

    Szablowski, Jerzy O.; Lee-Gosselin, Audrey; Lue, Brian; Malounda, Dina; Shapiro, Mikhail G.
    Neurological and psychiatric disorders are often characterized by dysfunctional neural circuits in specific regions of the brain. Existing treatment strategies, including the use of drugs and implantable brain stimulators, aim to modulate the activity of these circuits. However, they are not cell-type-specific, lack spatial targeting or require invasive procedures. Here, we report a cell-type-specific and non-invasive approach based on acoustically targeted chemogenetics that enables the modulation of neural circuits with spatiotemporal specificity. The approach uses ultrasound waves to transiently open the blood–brain barrier and transduce neurons at specific locations in the brain with virally encoded engineered G-protein-coupled receptors. The engineered...

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