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Tribby A, Bois JS, Montzka SA, Atlas EL, Vimont I, Lan X, Tans PP, Elkins JW, Blake DR, Wennberg PO. Hydrocarbon Tracers Suggest Methane Emissions from Fossil Sources Occur Predominately Before Gas Processing and That Petroleum Plays Are a Significant Source. Environ Sci Technol 2022; 56:9623-9631. [PMID: 35699285 PMCID: PMC9260955 DOI: 10.1021/acs.est.2c00927] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
We use global airborne observations of propane (C3H8) and ethane (C2H6) from the Atmospheric Tomography (ATom) and HIAPER Pole-to-Pole Observations (HIPPO), as well as U.S.-based aircraft and tower observations by NOAA and from the NCAR FRAPPE campaign as tracers for emissions from oil and gas operations. To simulate global mole fraction fields for these gases, we update the default emissions' configuration of C3H8 used by the global chemical transport model, GEOS-Chem v13.0.0, using a scaled C2H6 spatial proxy. With the updated emissions, simulations of both C3H8 and C2H6 using GEOS-Chem are in reasonable agreement with ATom and HIPPO observations, though the updated emission fields underestimate C3H8 accumulation in the arctic wintertime, pointing to additional sources of this gas in the high latitudes (e.g., Europe). Using a Bayesian hierarchical model, we estimate global emissions of C2H6 and C3H8 from fossil fuel production in 2016-2018 to be 13.3 ± 0.7 (95% CI) and 14.7 ± 0.8 (95% CI) Tg/year, respectively. We calculate bottom-up hydrocarbon emission ratios using basin composition measurements weighted by gas production and find their magnitude is higher than expected and is similar to ratios informed by our revised alkane emissions. This suggests that emissions are dominated by pre-processing activities in oil-producing basins.
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Affiliation(s)
- Ariana
L. Tribby
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Justin S. Bois
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Stephen A. Montzka
- National
Oceanic and Atmospheric Administration, Global Monitoring Laboratory, Boulder, Colorado 80305 United States
| | - Elliot L. Atlas
- Rosenstiel
School of Marine and Atmospheric Science, University of Miami, Miami, Florida 33149, United States
| | - Isaac Vimont
- National
Oceanic and Atmospheric Administration, Global Monitoring Laboratory, Boulder, Colorado 80305 United States
- Cooperative
Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309 United States
| | - Xin Lan
- National
Oceanic and Atmospheric Administration, Global Monitoring Laboratory, Boulder, Colorado 80305 United States
- Cooperative
Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309 United States
| | - Pieter P. Tans
- National
Oceanic and Atmospheric Administration, Global Monitoring Laboratory, Boulder, Colorado 80305 United States
| | - James W. Elkins
- National
Oceanic and Atmospheric Administration, Global Monitoring Laboratory, Boulder, Colorado 80305 United States
- Cooperative
Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309 United States
| | - Donald R. Blake
- Department
of Chemistry, University of California—Irvine, Irvine, California92697, United States
| | - Paul O. Wennberg
- Division
of Engineering and Applied Science, California
Institute of Technology, Pasadena, California 91125, United States
- Division
of Geological and Planetary Sciences, California
Institute of Technology, Pasadena, California 91125, United States
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2
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Gross P, Kumar KV, Goehring NW, Bois JS, Hoege C, Jülicher F, Grill SW. Guiding self-organized pattern formation in cell polarity establishment. Nat Phys 2019; 15:293-300. [PMID: 31327978 PMCID: PMC6640039 DOI: 10.1038/s41567-018-0358-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/23/2018] [Indexed: 05/25/2023]
Abstract
Spontaneous pattern formation in Turing systems relies on feedback. Patterns in cells and tissues however often do not form spontaneously, but are under control of upstream pathways that provide molecular guiding cues. The relationship between guiding cues and feedback in controlled biological pattern formation remains unclear. We explored this relationship during cell polarity establishment in the one-cell-stage C. elegans embryo. We quantified the strength of two feedback systems that operate during polarity establishment, feedback between polarity proteins and the actomyosin cortex, and mutual antagonism amongst polarity proteins. We characterized how these feedback systems are modulated by guiding cues from the centrosome. By coupling a mass-conserved Turing-like reaction-diffusion system for polarity proteins to an active gel description of the actomyosin cortex, we reveal a transition point beyond which feedback ensures self-organized polarization even when cues are removed. Notably, the baton is passed from a guide-dominated to a feedback-dominated regime significantly beyond this transition point, which ensures robustness. Together, this reveals a general criterion for controlling biological pattern forming systems: feedback remains subcritical to avoid unstable behaviour, and molecular guiding cues drive the system beyond a transition point for pattern formation.
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Affiliation(s)
- Peter Gross
- BIOTEC, TU Dresden, Tatzberg 47/49, 01307, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics,
Pfotenhauerstrasse 108, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems,
Nöthnitzer Strasse 38, 01187 Dresden, Germany
| | - K. Vijay Kumar
- Max Planck Institute for the Physics of Complex Systems,
Nöthnitzer Strasse 38, 01187 Dresden, Germany
- International Centre for Theoretical Sciences, Tata Institute of
Fundamental Research, Bengaluru 560089, India
| | - Nathan W. Goehring
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT,
UK
- Medical Research Council Laboratory for Molecular Cell Biology,
Gower Street, University College London, London WC1E 6BT, UK
| | - Justin S. Bois
- California Institute of Technology, 1200 E California Blvd,
Pasadena, CA 91125, USA
| | - Carsten Hoege
- Max Planck Institute of Molecular Cell Biology and Genetics,
Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems,
Nöthnitzer Strasse 38, 01187 Dresden, Germany
| | - Stephan W. Grill
- BIOTEC, TU Dresden, Tatzberg 47/49, 01307, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics,
Pfotenhauerstrasse 108, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems,
Nöthnitzer Strasse 38, 01187 Dresden, Germany
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3
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Nath RD, Bedbrook CN, Abrams MJ, Basinger T, Bois JS, Prober DA, Sternberg PW, Gradinaru V, Goentoro L. The Jellyfish Cassiopea Exhibits a Sleep-like State. Curr Biol 2017; 27:2984-2990.e3. [PMID: 28943083 DOI: 10.1016/j.cub.2017.08.014] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/17/2017] [Accepted: 08/04/2017] [Indexed: 12/28/2022]
Abstract
Do all animals sleep? Sleep has been observed in many vertebrates, and there is a growing body of evidence for sleep-like states in arthropods and nematodes [1-5]. Here we show that sleep is also present in Cnidaria [6-8], an earlier-branching metazoan lineage. Cnidaria and Ctenophora are the first metazoan phyla to evolve tissue-level organization and differentiated cell types, such as neurons and muscle [9-15]. In Cnidaria, neurons are organized into a non-centralized radially symmetric nerve net [11, 13, 15-17] that nevertheless shares fundamental properties with the vertebrate nervous system: action potentials, synaptic transmission, neuropeptides, and neurotransmitters [15-20]. It was reported that cnidarian soft corals [21] and box jellyfish [22, 23] exhibit periods of quiescence, a pre-requisite for sleep-like states, prompting us to ask whether sleep is present in Cnidaria. Within Cnidaria, the upside-down jellyfish Cassiopea spp. displays a quantifiable pulsing behavior, allowing us to perform long-term behavioral tracking. Monitoring of Cassiopea pulsing activity for consecutive days and nights revealed behavioral quiescence at night that is rapidly reversible, as well as a delayed response to stimulation in the quiescent state. When deprived of nighttime quiescence, Cassiopea exhibited decreased activity and reduced responsiveness to a sensory stimulus during the subsequent day, consistent with homeostatic regulation of the quiescent state. Together, these results indicate that Cassiopea has a sleep-like state, supporting the hypothesis that sleep arose early in the metazoan lineage, prior to the emergence of a centralized nervous system.
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Affiliation(s)
- Ravi D Nath
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA; Howard Hughes Medical Institute
| | - Claire N Bedbrook
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Michael J Abrams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Ty Basinger
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Justin S Bois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - David A Prober
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA; Howard Hughes Medical Institute
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Lea Goentoro
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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4
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Webster A, Li S, Hur JK, Wachsmuth M, Bois JS, Perkins EM, Patel DJ, Aravin AA. Aub and Ago3 Are Recruited to Nuage through Two Mechanisms to Form a Ping-Pong Complex Assembled by Krimper. Mol Cell 2016; 59:564-75. [PMID: 26295961 DOI: 10.1016/j.molcel.2015.07.017] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/26/2015] [Accepted: 07/20/2015] [Indexed: 02/08/2023]
Abstract
In Drosophila, two Piwi proteins, Aubergine (Aub) and Argonaute-3 (Ago3), localize to perinuclear "nuage" granules and use guide piRNAs to target and destroy transposable element transcripts. We find that Aub and Ago3 are recruited to nuage by two different mechanisms. Aub requires a piRNA guide for nuage recruitment, indicating that its localization depends on recognition of RNA targets. Ago3 is recruited to nuage independently of a piRNA cargo and relies on interaction with Krimper, a stable component of nuage that is able to aggregate in the absence of other nuage proteins. We show that Krimper interacts directly with Aub and Ago3 to coordinate the assembly of the ping-pong piRNA processing (4P) complex. Symmetrical dimethylated arginines are required for Aub to interact with Krimper, but they are dispensable for Ago3 to bind Krimper. Our study reveals a multi-step process responsible for the assembly and function of nuage complexes in piRNA-guided transposon repression.
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Affiliation(s)
- Alexandre Webster
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sisi Li
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10021 USA
| | - Junho K Hur
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Malte Wachsmuth
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Justin S Bois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Edward M Perkins
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10021 USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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5
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Bor B, Poweleit N, Bois JS, Cen L, Bedree JK, Zhou ZH, Gunsalus RP, Lux R, McLean JS, He X, Shi W. Phenotypic and Physiological Characterization of the Epibiotic Interaction Between TM7x and Its Basibiont Actinomyces. Microb Ecol 2016; 71:243-55. [PMID: 26597961 PMCID: PMC4688200 DOI: 10.1007/s00248-015-0711-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/11/2015] [Indexed: 05/11/2023]
Abstract
Despite many examples of obligate epibiotic symbiosis (one organism living on the surface of another) in nature, such an interaction has rarely been observed between two bacteria. Here, we further characterize a newly reported interaction between a human oral obligate parasitic bacterium TM7x (cultivated member of Candidatus Saccharimonas formerly Candidate Phylum TM7), and its basibiont Actinomyces odontolyticus species (XH001), providing a model system to study epiparasitic symbiosis in the domain Bacteria. Detailed microscopic studies indicate that both partners display extensive morphological changes during symbiotic growth. XH001 cells manifested as short rods in monoculture, but displayed elongated and hyphal morphology when physically associated with TM7x. Interestingly, these dramatic morphological changes in XH001 were also induced in oxygen-depleted conditions, even in the absence of TM7x. Targeted quantitative real-time PCR (qRT-PCR) analyses revealed that both the physical association with TM7x as well as oxygen depletion triggered up-regulation of key stress response genes in XH001, and in combination, these conditions act in an additive manner. TM7x and XH001 co-exist with relatively uniform cell morphologies under nutrient-replete conditions. However, upon nutrient depletion, TM7x-associated XH001 displayed a variety of cell morphologies, including swollen cell body, clubbed-ends, and even cell lysis, and a large portion of TM7x cells transformed from ultrasmall cocci into elongated cells. Our study demonstrates a highly dynamic interaction between epibiont TM7x and its basibiont XH001 in response to physical association or environmental cues such as oxygen level and nutritional status, as reflected by their morphological and physiological changes during symbiotic growth.
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Affiliation(s)
- Batbileg Bor
- Section of Oral Biology, School of Dentistry, University of California, Los Angeles, CA, 90095, USA
| | - Nicole Poweleit
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Justin S Bois
- Division of Biology and Biological Engineering, California Institute of Technology, MC 114-96, Pasadena, CA, 91125, USA
| | - Lujia Cen
- Section of Oral Biology, School of Dentistry, University of California, Los Angeles, CA, 90095, USA
| | - Joseph K Bedree
- Section of Oral Biology, School of Dentistry, University of California, Los Angeles, CA, 90095, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Robert P Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Renate Lux
- Section of Oral Biology, School of Dentistry, University of California, Los Angeles, CA, 90095, USA
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA, 98195, USA
| | - Xuesong He
- Section of Oral Biology, School of Dentistry, University of California, Los Angeles, CA, 90095, USA.
| | - Wenyuan Shi
- Section of Oral Biology, School of Dentistry, University of California, Los Angeles, CA, 90095, USA.
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6
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Bor B, Bois JS, Quinlan ME. Regulation of the formin Cappuccino is critical for polarity of Drosophila oocytes. Cytoskeleton (Hoboken) 2015; 72:1-15. [PMID: 25557988 DOI: 10.1002/cm.21205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 12/19/2014] [Indexed: 11/06/2022]
Abstract
The Drosophila formin Cappuccino (Capu) creates an actin mesh-like structure that traverses the oocyte during midoogenesis. This mesh is thought to prevent premature onset of fast cytoplasmic streaming which normally happens during late-oogenesis. Proper cytoskeletal organization and cytoplasmic streaming are crucial for localization of polarity determinants such as osk, grk, bcd, and nanos mRNAs. Capu mutants disrupt these events, leading to female sterility. Capu is regulated by another nucleator, Spire, as well as by autoinhibition in vitro. Studies in vivo confirm that Spire modulates Capu's function in oocytes; however, how autoinhibition contributes is still unclear. To study the role of autoinhibition in flies, we expressed a Capu construct that is missing the Capu Inhibitory Domain, CapuΔN. Consistent with a gain of activity due to loss of autoinhibition, the actin mesh was denser in CapuΔN oocytes. Further, cytoplasmic streaming was delayed and fertility levels decreased. Localization of osk mRNA in early stages, and bcd and nanos in late stages, were disrupted in CapuΔN-expressing oocytes. Finally, evidence that these phenotypes were due to a loss of autoinhibition comes from coexpression of the N-terminal half of Capu with CapuΔN, which suppressed the defects in actin, cytoplasmic streaming and fertility. From these results, we conclude that Capu can be autoinhibited during Drosophila oocyte development.
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Affiliation(s)
- Batbileg Bor
- Molecular Biology Interdepartmental PhD Program, University of California, Los Angeles, California, 90095-1570
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7
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Rasson AS, Bois JS, Pham DSL, Yoo H, Quinlan ME. Filament assembly by Spire: key residues and concerted actin binding. J Mol Biol 2014; 427:824-839. [PMID: 25234086 DOI: 10.1016/j.jmb.2014.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 07/28/2014] [Accepted: 09/04/2014] [Indexed: 01/09/2023]
Abstract
The most recently identified class of actin nucleators, WASp homology domain 2 (WH2) nucleators, use tandem repeats of monomeric actin-binding WH2 domains to facilitate actin nucleation. WH2 domains are involved in a wide variety of actin regulatory activities. Structurally, they are expected to clash with interprotomer contacts within the actin filament. Thus, the discovery of their role in nucleation was surprising. Here we use Drosophila Spire (Spir) as a model system to investigate both how tandem WH2 domains can nucleate actin and what differentiates nucleating WH2-containing proteins from their non-nucleating counterparts. We found that the third WH2 domain in Spir (Spir-C or SC) plays a unique role. In the context of a short nucleation construct (containing only two WH2 domains), placement of SC in the N-terminal position was required for the most potent nucleation. We found that the native organization of the WH2 domains with respect to each other is necessary for binding to actin with positive cooperativity. We identified two residues within SC that are critical for its activity. Using this information, we were able to convert a weak synthetic nucleator into one with activity equal to a native Spir construct. Lastly, we found evidence that SC binds actin filaments, in addition to monomers.
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Affiliation(s)
- Amy S Rasson
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Justin S Bois
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Duy Stephen L Pham
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Haneul Yoo
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Margot E Quinlan
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California Los Angeles, Paul D. Boyer Hall, 611 Charles E. Young Drive East, Box 951570, Los Angeles, CA 90095-1570, USA.
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8
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Roth-Johnson EA, Vizcarra CL, Bois JS, Quinlan ME. Interaction between microtubules and the Drosophila formin Cappuccino and its effect on actin assembly. J Biol Chem 2013; 289:4395-404. [PMID: 24362037 DOI: 10.1074/jbc.m113.499921] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Formin family actin nucleators are potential coordinators of the actin and microtubule cytoskeletons, as they can both nucleate actin filaments and bind microtubules in vitro. To gain a more detailed mechanistic understanding of formin-microtubule interactions and formin-mediated actin-microtubule cross-talk, we studied microtubule binding by Cappuccino (Capu), a formin involved in regulating actin and microtubule organization during Drosophila oogenesis. We found that two distinct domains within Capu, FH2 and tail, work together to promote high-affinity microtubule binding. The tail domain appears to bind microtubules through nonspecific charge-based interactions. In contrast, distinct residues within the FH2 domain are important for microtubule binding. We also report the first visualization of a formin polymerizing actin filaments in the presence of microtubules. Interestingly, microtubules are potent inhibitors of the actin nucleation activity of Capu but appear to have little effect on Capu once it is bound to the barbed end of an elongating filament. Because Capu does not simultaneously bind microtubules and assemble actin filaments in vitro, its actin assembly and microtubule binding activities likely require spatial and/or temporal regulation within the Drosophila oocyte.
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10
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Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR, Dirks RM, Pierce NA. NUPACK: Analysis and design of nucleic acid systems. J Comput Chem 2011; 32:170-3. [PMID: 20645303 DOI: 10.1002/jcc.21596] [Citation(s) in RCA: 984] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
UNLABELLED The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables: ANALYSIS thermodynamic analysis of dilute solutions of interacting nucleic acid strands. DESIGN sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium.Utilities: evaluation, display, and annotation of equilibrium properties of a complex of nucleic acid strands. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.
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Affiliation(s)
- Joseph N Zadeh
- Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA
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11
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Bois JS. Dimensional Analysis as a Tool to Introduce Biology Students to Physical Reasoning. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.1974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Abstract
We discuss pattern formation in active fluids in which active stress is regulated by diffusing molecular components. Nonhomogeneous active stress profiles create patterns of flow which transport stress regulators by advection. Our work is motivated by the dynamics of the actomyosin cell cortex in which biochemical pathways regulate active stress. We present a mechanism in which a single diffusing species up regulates active stress, resulting in steady flow and concentration patterns. We also discuss general pattern-formation behaviors of reaction-diffusion systems placed in active fluids.
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Affiliation(s)
- Justin S Bois
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, D-01187 Dresden, Germany
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13
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Mayer M, Depken M, Bois JS, Jülicher F, Grill SW. Anisotropies in cortical tension reveal the physical basis of polarizing cortical flows. Nature 2010; 467:617-21. [DOI: 10.1038/nature09376] [Citation(s) in RCA: 379] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 07/16/2010] [Indexed: 12/22/2022]
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14
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Klopper AV, Bois JS, Grill SW. Influence of secondary structure on recovery from pauses during early stages of RNA transcription. Phys Rev E Stat Nonlin Soft Matter Phys 2010; 81:030904. [PMID: 20365690 DOI: 10.1103/physreve.81.030904] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 10/29/2009] [Indexed: 05/29/2023]
Abstract
The initial stages of transcription by RNA polymerase are frequently marked by pausing and stalling events. These events have been linked to an inactive backtracked state in which the polymerase diffuses along the template DNA. We investigate theoretically the influence of RNA secondary structure in confining this diffusion. The effective confinement length peaks at transcript lengths commensurate with early stalling. This finite-size effect accounts for slow progress at the beginning of transcription, which we illustrate via stochastic hopping models for backtracking polymerases.
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Affiliation(s)
- A V Klopper
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
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15
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Carvalho L, Stühmer J, Bois JS, Kalaidzidis Y, Lecaudey V, Heisenberg CP. Control of convergent yolk syncytial layer nuclear movement in zebrafish. Development 2009; 136:1305-15. [PMID: 19279138 DOI: 10.1242/dev.026922] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nuclear movements play an essential role in metazoan development. Although the intracellular transport mechanisms underlying nuclear movements have been studied in detail, relatively little is known about signals from surrounding cells and tissues controlling these movements. Here, we show that, in gastrulating zebrafish embryos, convergence movements of nuclei within the yolk syncytial layer (YSL) are guided by mesoderm and endoderm progenitors migrating along the surface of the yolk towards the dorsal side of the developing gastrula. Progenitor cells direct the convergence movements of internal yolk syncytial nuclei (iYSN) by modulating cortical flow within the YSL in which the iYSN are entrained. The effect of mesoderm and endoderm progenitors on the convergence movement of iYSN depends on the expression of E-cadherin, indicating that adhesive contact between the cells and the YSL is required for the mesendoderm-modulated YSL cortical flow mediating nuclear convergence. In summary, our data reveal a crucial function for cortical flow in the coordination of syncytial nuclear movements with surrounding cells and tissues during zebrafish gastrulation.
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Affiliation(s)
- Lara Carvalho
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
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Abstract
A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures suggests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechanism of ‘helix-driven wrapping’. Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates the potential for topological effects to influence the kinetics and function of nucleic acid strands. An experimental study of metastable complementary ‘kissing hairpins’ demonstrates that the topological constraint of zero linking number between the loops effectively prevents conversion to the minimum free energy helical state. Introduction of short catalyst strands that break the topological constraint causes rapid conversion to full duplex.
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Affiliation(s)
| | - Suvir Venkataraman
- Department of Bioengineering, California Institute of TechnologyPasadena, CA 91125, USA
| | - Harry M. T. Choi
- Department of Bioengineering, California Institute of TechnologyPasadena, CA 91125, USA
| | | | | | - Niles A. Pierce
- Department of Bioengineering, California Institute of TechnologyPasadena, CA 91125, USA
- Department of Applied and Computational Mathematics, California Institute of TechnologyPasadena, CA 91125, USA
- To whom correspondence should be addressed at Caltech, Mail Code 114-96, Pasadena, CA 91125, USA. Tel: +1 626 395 8086; Fax: +1 626 395 8845;
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