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Awasthi A, Minin VM, Huang J, Chow D, Xu J. Fitting a stochastic model of intensive care occupancy to noisy hospitalization time series during the COVID-19 pandemic. Stat Med 2023; 42:5189-5206. [PMID: 37705508 DOI: 10.1002/sim.9907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/28/2023] [Accepted: 09/01/2023] [Indexed: 09/15/2023]
Abstract
Intensive care occupancy is an important indicator of health care stress that has been used to guide policy decisions during the COVID-19 pandemic. Toward reliable decision-making as a pandemic progresses, estimating the rates at which patients are admitted to and discharged from hospitals and intensive care units (ICUs) is crucial. Since individual-level hospital data are rarely available to modelers in each geographic locality of interest, it is important to develop tools for inferring these rates from publicly available daily numbers of hospital and ICU beds occupied. We develop such an estimation approach based on an immigration-death process that models fluctuations of ICU occupancy. Our flexible framework allows for immigration and death rates to depend on covariates, such as hospital bed occupancy and daily SARS-CoV-2 test positivity rate, which may drive changes in hospital ICU operations. We demonstrate via simulation studies that the proposed method performs well on noisy time series data and apply our statistical framework to hospitalization data from the University of California, Irvine (UCI) Health and Orange County, California. By introducing a likelihood-based framework where immigration and death rates can vary with covariates, we find, through rigorous model selection, that hospitalization and positivity rates are crucial covariates for modeling ICU stay dynamics and validate our per-patient ICU stay estimates using anonymized patient-level UCI hospital data.
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Affiliation(s)
- Achal Awasthi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA
| | - Volodymyr M Minin
- Department of Statistics, University of California, Irvine, Irvine, California, USA
| | - Jenny Huang
- Department of Statistical Science, Duke University, Durham, North Carolina, USA
| | - Daniel Chow
- School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Jason Xu
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA
- Department of Statistical Science, Duke University, Durham, North Carolina, USA
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2
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Xu H, Fan H, Luan Y, Yan S, Martin L, Miao R, Pauly F, Meyhofer E, Reddy P, Linke H, Wärnmark K. Electrical Conductance and Thermopower of β-Substituted Porphyrin Molecular Junctions─Synthesis and Transport. J Am Chem Soc 2023; 145:23541-23555. [PMID: 37874166 PMCID: PMC10623571 DOI: 10.1021/jacs.3c07258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Indexed: 10/25/2023]
Abstract
Molecular junctions offer significant potential for enhancing thermoelectric power generation. Quantum interference effects and associated sharp features in electron transmission are expected to enable the tuning and enhancement of thermoelectric properties in molecular junctions. To systematically explore the effect of quantum interferences, we designed and synthesized two new classes of porphyrins, P1 and P2, with two methylthio anchoring groups in the 2,13- and 2,12-positions, respectively, and their Zn complexes, Zn-P1 and Zn-P2. Past theory suggests that P1 and Zn-P1 feature destructive quantum interference in single-molecule junctions with gold electrodes and may thus show high thermopower, while P2 and Zn-P2 do not. Our detailed experimental single-molecule break-junction studies of conductance and thermopower, the latter being the first ever performed on porphyrin molecular junctions, revealed that the electrical conductance of the P1 and Zn-P1 junctions is relatively close, and the same holds for P2 and Zn-P2, while there is a 6 times reduction in the electrical conductance between P1 and P2 type junctions. Further, we observed that the thermopower of P1 junctions is slightly larger than for P2 junctions, while Zn-P1 junctions show the largest thermopower and Zn-P2 junctions show the lowest. We relate the experimental results to quantum transport theory using first-principles approaches. While the conductance of P1 and Zn-P1 junctions is robustly predicted to be larger than those of P2 and Zn-P2, computed thermopowers depend sensitively on the level of theory and the single-molecule junction geometry. However, the predicted large difference in conductance and thermopower values between Zn-P1 and Zn-P2 derivatives, suggested in previous model calculations, is not supported by our experimental and theoretical findings.
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Affiliation(s)
- Hailiang Xu
- NanoLund, Lund University, Box 118, 22100 Lund, Sweden
- Department
of Chemistry, Centre of Analysis and Synthesis, Lund University, Box 121, 22100 Lund, Sweden
| | - Hao Fan
- Department
of Chemistry, Centre of Analysis and Synthesis, Lund University, Box 121, 22100 Lund, Sweden
| | - Yuxuan Luan
- Department
of Mechanical Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Shen Yan
- Department
of Mechanical Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - León Martin
- Institute
of Physics and Centre for Advanced Analytics and Predictive Sciences, University of Augsburg, 86159 Augsburg, Germany
| | - Ruijiao Miao
- Department
of Mechanical Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Fabian Pauly
- Institute
of Physics and Centre for Advanced Analytics and Predictive Sciences, University of Augsburg, 86159 Augsburg, Germany
| | - Edgar Meyhofer
- Department
of Mechanical Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Pramod Reddy
- Department
of Mechanical Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Materials Science and Engineering, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Heiner Linke
- NanoLund, Lund University, Box 118, 22100 Lund, Sweden
- Solid State
Physics, Lund University, Box 118, 22100 Lund, Sweden
| | - Kenneth Wärnmark
- NanoLund, Lund University, Box 118, 22100 Lund, Sweden
- Department
of Chemistry, Centre of Analysis and Synthesis, Lund University, Box 121, 22100 Lund, Sweden
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3
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Cai Z, Weinstein H, Aravind I, Li R, Weng S, Zhang B, Habif JL, Cronin SB. Dynamic Study of Intercalation/Deintercalation of Ionic Liquids in Multilayer Graphene Using an Alternating Current Raman Spectroscopy Technique. J Phys Chem Lett 2023; 14:7223-7228. [PMID: 37552573 PMCID: PMC10440811 DOI: 10.1021/acs.jpclett.3c01686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/31/2023] [Indexed: 08/10/2023]
Abstract
We report Raman spectra and infrared (IR) imaging collected during the intercalation-deintercalation half cycles in a multilayer graphene (MLG) device (∼100 layers) operating at 0.2-10 Hz. The device consists of a MLG/alumina membrane/copper stack, in which the alumina membrane is filled with ionic liquid [DEME][TFSI], forming an electrochemical cell. Upon the application of a positive voltage, the TFSI- anions intercalate into the interstitial spaces in the MLG. The incident laser light is modulated using an optical chopper wheel that is synchronized with (and delayed with respect to) a 0.2-10 Hz alternating current (AC) voltage signal. Raman spectra taken just 200 ms apart show the emergence and disappearance of the intercalated G band mode at around 1610 cm-1. By integration of over hundreds of cycles, a significant Raman signal can be obtained. The intercalation/deintercalation is also monitored with thermal imaging via voltage-induced changes in the carrier density, complex dielectric function ε(ω), and thermal emissivity of the device.
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Affiliation(s)
- Zhi Cai
- Mork
Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Haley Weinstein
- Ming
Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California 90089, United States
| | - Indu Aravind
- Department
of Physics and Astronomy, University of
Southern California, Los Angeles, California 90089, United States
| | - Ruoxi Li
- Mork
Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Sizhe Weng
- Ming
Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California 90089, United States
| | - Boxin Zhang
- Mork
Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Jonathan L. Habif
- Ming
Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California 90089, United States
| | - Stephen B. Cronin
- Department
of Physics and Astronomy, University of
Southern California, Los Angeles, California 90089, United States
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Ming
Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California 90089, United States
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4
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Jafari S, Henriksson J, Yan H, Alenius M. Stress and odorant receptor feedback during a critical period after hatching regulates olfactory sensory neuron differentiation in Drosophila. PLoS Biol 2021; 19:e3001101. [PMID: 33793547 PMCID: PMC8043390 DOI: 10.1371/journal.pbio.3001101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/13/2021] [Accepted: 03/02/2021] [Indexed: 11/19/2022] Open
Abstract
Here, we reveal that the regulation of Drosophila odorant receptor (OR) expression during the pupal stage is permissive and imprecise. We found that directly after hatching an OR feedback mechanism both directs and refines OR expression. We demonstrate that, as in mice, dLsd1 and Su(var)3-9 balance heterochromatin formation to direct OR expression. We show that the expressed OR induces dLsd1 and Su(var)3-9 expression, linking OR level and possibly function to OR expression. OR expression refinement shows a restricted duration, suggesting that a gene regulatory critical period brings olfactory sensory neuron differentiation to an end. Consistent with a change in differentiation, stress during the critical period represses dLsd1 and Su(var)3-9 expression and makes the early permissive OR expression permanent. This induced permissive gene regulatory state makes OR expression resilient to stress later in life. Hence, during a critical period OR feedback, similar to in mouse OR selection, defines adult OR expression in Drosophila.
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Affiliation(s)
- Shadi Jafari
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Johan Henriksson
- Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Hua Yan
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Mattias Alenius
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
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5
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Stachowski TR, Snell ME, Snell EH. SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique. PLoS One 2020; 15:e0239702. [PMID: 33201877 PMCID: PMC7671560 DOI: 10.1371/journal.pone.0239702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/12/2020] [Indexed: 12/17/2022] Open
Abstract
A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been successful in mitigating damage but not eliminating it altogether; however, cryo-cooling can be difficult in some cases and has also been shown to limit functionally relevant protein conformations. The doses used for X-ray crystallography are typically in the kilo-gray to mega-gray range. While disulfide bonds are among the most significantly affected species in proteins in the crystalline state at both cryogenic and higher temperatures, there is limited information on their response to low X-ray doses in solution, the details of which might inform biomedical applications of X-rays. In this work we engineered a protein that dimerizes through a susceptible disulfide bond to relate the radiation damage processes seen in cryo-cooled crystals to those closer to physiologic conditions. This approach enables a low-resolution technique, small angle X-ray scattering (SAXS), to detect and monitor a residue specific process. A dose dependent fragmentation of the engineered protein was seen that can be explained by a dimer to monomer transition through disulfide bond cleavage. This supports the crystallographically derived mechanism and demonstrates that results obtained crystallographically can be usefully extrapolated to physiologic conditions. Fragmentation was influenced by pH and the conformation of the dimer, providing information on mechanism and pointing to future routes for investigation and potential mitigation. The novel engineered protein approach to generate a large-scale change through a site-specific interaction represents a promising tool for advancing radiation damage studies under solution conditions.
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Affiliation(s)
- Timothy R. Stachowski
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Mary E. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Materials Design and Innovation, State University at New York at Buffalo, Buffalo, New York, United States of America
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6
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Tang Y, Saul J, Nagaratnam N, Martin-Garcia JM, Fromme P, Qiu J, LaBaer J. Construction of gateway-compatible baculovirus expression vectors for high-throughput protein expression and in vivo microcrystal screening. Sci Rep 2020; 10:13323. [PMID: 32770037 PMCID: PMC7414197 DOI: 10.1038/s41598-020-70163-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
Baculovirus mediated-insect cell expression systems have been widely used for producing heterogeneous proteins. However, to date, there is still the lack of an easy-to-manipulate system that enables the high-throughput protein characterization in insect cells by taking advantage of large existing Gateway clone libraries. To resolve this limitation, we have constructed a suite of Gateway-compatible pIEx-derived baculovirus expression vectors that allow the rapid and cost-effective construction of expression clones for mass parallel protein expression in insect cells. This vector collection also supports the attachment of a variety of fusion tags to target proteins to meet the needs for different research applications. We first demonstrated the utility of these vectors for protein expression and purification using a set of 40 target proteins of various sizes, cellular localizations and host organisms. We then established a scalable pipeline coupled with the SONICC and TEM techniques to screen for microcrystal formation within living insect cells. Using this pipeline, we successfully identified microcrystals for ~ 16% of the tested protein set, which can be potentially used for structure elucidation by X-ray crystallography. In summary, we have established a versatile pipeline enabling parallel gene cloning, protein expression and purification, and in vivo microcrystal screening for structural studies.
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Affiliation(s)
- Yanyang Tang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Justin Saul
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Nirupa Nagaratnam
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Jose M Martin-Garcia
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA.
| | - Joshua LaBaer
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA.
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7
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Patel N, Huang XP, Grandner JM, Johansson LC, Stauch B, McCorvy JD, Liu Y, Roth B, Katritch V. Structure-based discovery of potent and selective melatonin receptor agonists. eLife 2020; 9:e53779. [PMID: 32118583 PMCID: PMC7080406 DOI: 10.7554/elife.53779] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/26/2020] [Indexed: 12/12/2022] Open
Abstract
Melatonin receptors MT1 and MT2 are involved in synchronizing circadian rhythms and are important targets for treating sleep and mood disorders, type-2 diabetes and cancer. Here, we performed large scale structure-based virtual screening for new ligand chemotypes using recently solved high-resolution 3D crystal structures of agonist-bound MT receptors. Experimental testing of 62 screening candidates yielded the discovery of 10 new agonist chemotypes with sub-micromolar potency at MT receptors, with compound 21 reaching EC50 of 0.36 nM. Six of these molecules displayed selectivity for MT2 over MT1. Moreover, two most potent agonists, including 21 and a close derivative of melatonin, 28, had dramatically reduced arrestin recruitment at MT2, while compound 37 was devoid of Gi signaling at MT1, implying biased signaling. This study validates the suitability of the agonist-bound orthosteric pocket in the MT receptor structures for the structure-based discovery of selective agonists.
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Affiliation(s)
- Nilkanth Patel
- Department of Biological Sciences and Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern CaliforniaLos AngelesUnited States
| | - Xi Ping Huang
- Department of Pharmacology, University of North Carolina Chapel Hill Medical SchoolChapel HillUnited States
- National Institute of Mental Health Psychoactive Drug Screening Program, Department of Pharmacology, University of North Carolina Chapel Hill Medical SchoolChapel HillUnited States
| | - Jessica M Grandner
- Department of Biological Sciences and Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern CaliforniaLos AngelesUnited States
| | - Linda C Johansson
- Department of Biological Sciences and Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern CaliforniaLos AngelesUnited States
| | - Benjamin Stauch
- Department of Biological Sciences and Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern CaliforniaLos AngelesUnited States
| | - John D McCorvy
- Department of Pharmacology, University of North Carolina Chapel Hill Medical SchoolChapel HillUnited States
- National Institute of Mental Health Psychoactive Drug Screening Program, Department of Pharmacology, University of North Carolina Chapel Hill Medical SchoolChapel HillUnited States
| | - Yongfeng Liu
- Department of Pharmacology, University of North Carolina Chapel Hill Medical SchoolChapel HillUnited States
- National Institute of Mental Health Psychoactive Drug Screening Program, Department of Pharmacology, University of North Carolina Chapel Hill Medical SchoolChapel HillUnited States
| | - Bryan Roth
- Department of Pharmacology, University of North Carolina Chapel Hill Medical SchoolChapel HillUnited States
- National Institute of Mental Health Psychoactive Drug Screening Program, Department of Pharmacology, University of North Carolina Chapel Hill Medical SchoolChapel HillUnited States
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Chapel Hill Medical SchoolChapel HillUnited States
| | - Vsevolod Katritch
- Department of Biological Sciences and Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern CaliforniaLos AngelesUnited States
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Diaz U, Bergman ZJ, Johnson BM, Edington AR, de Cruz MA, Marshall WF, Riggs B. Microtubules are necessary for proper Reticulon localization during mitosis. PLoS One 2019; 14:e0226327. [PMID: 31877164 PMCID: PMC6932760 DOI: 10.1371/journal.pone.0226327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 11/25/2019] [Indexed: 01/04/2023] Open
Abstract
During mitosis, the structure of the Endoplasmic Reticulum (ER) displays a dramatic reorganization and remodeling, however, the mechanism driving these changes is poorly understood. Hairpin-containing ER transmembrane proteins that stabilize ER tubules have been identified as possible factors to promote these drastic changes in ER morphology. Recently, the Reticulon and REEP family of ER shaping proteins have been shown to heavily influence ER morphology by driving the formation of ER tubules, which are known for their close proximity with microtubules. Here, we examine the role of microtubules and other cytoskeletal factors in the dynamics of a Drosophila Reticulon, Reticulon-like 1 (Rtnl1), localization to spindle poles during mitosis in the early embryo. At prometaphase, Rtnl1 is enriched to spindle poles just prior to the ER retention motif KDEL, suggesting a possible recruitment role for Rtnl1 in the bulk localization of ER to spindle poles. Using image analysis-based methods and precise temporal injections of cytoskeletal inhibitors in the early syncytial Drosophila embryo, we show that microtubules are necessary for proper Rtnl1 localization to spindles during mitosis. Lastly, we show that astral microtubules, not microfilaments, are necessary for proper Rtnl1 localization to spindle poles, and is largely independent of the minus-end directed motor protein dynein. This work highlights the role of the microtubule cytoskeleton in Rtnl1 localization to spindles during mitosis and sheds light on a pathway towards inheritance of this major organelle.
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Affiliation(s)
- Ulises Diaz
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
- Department of Biochemistry & Biophysics, UCSF Mission Bay, San Francisco, California, United States of America
| | - Zane J. Bergman
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Brittany M. Johnson
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Alia R. Edington
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Matthew A. de Cruz
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Wallace F. Marshall
- Department of Biochemistry & Biophysics, UCSF Mission Bay, San Francisco, California, United States of America
| | - Blake Riggs
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
- * E-mail:
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