Repository of works by Caltech published authors.
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MORC1 represses transposable elements in the mouse male germline - Pastor, William A.; Stroud, Hume; Nee, Kevin; Liu, Wanlu; Pezic, Dubravka; Manakov, Sergei A.; Lee, Serena A.; Moissiard, Guillaume; Zamudio, Natasha; Bourc'his, Déborah; Aravin, Alexei A.; Clark, Amander T.; Jacobsen, Steven E.
The Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA-methylated and silent genes. MORC1-deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homologue DNMT3L. Morc1 mutants show highly localized defects in the establishment of...
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project - Bergmann, Frank T.; Adams, Richard; Moodie, Stuart; Cooper, Jonathan; Glont, Mihai; Golebiewski, Martin; Hucka, Michael; Laibe, Camille; Miller, Andrew K.; Nickerson, David P.; Olivier, Brett G.; Rodriguez, Nicolas; Sauro, Herbert M.; Scharm, Martin; Soiland-Reyes, Stian; Waltemath, Dagmar; Yvon, Florent; Le Novère, Nicolas
Background: With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. Results: We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the...
Microwave Measurements of Carbon Monoxide on Titan - Muhleman, D. O.; Berge, G. L.; Clancy, R. T.
The ratio of the flux density of Titan was measured in two 200-megahertz bands, one centered on the (1-0) rotation line of carbon monoxide at 115.3 gigahertz and the other 2600 megahertz lower. The measurements were made with a complex-correlation technique on the new millimeter-wavelength interferometer at the Owens Valley Radio Observatory, Big Pine, California. The excess flux in the carbon monoxide band is interpreted as a strong detection of carbon monoxide and a mixing ratio, assumed constant, of 6 x 10^(-5). The brightness temperature of Titan at 112.6 gigahertz is 69 ± 10 kelvins, consistent with atmospheric emission from...
Nucleotide sequence of yellow fever virus: implications for flavivirus gene expression and evolution - Rice, Charles M.; Lenches, Edith M.; Eddy, Sean R.; Shin, Se Jung; Sheets, Rebecca L.; Strauss, James H.
The sequence of the entire RNA genome of the type flavivirus, yellow fever virus, has been obtained. Inspection of this sequence reveals a single long open reading frame of 10,233 nucleotides, which could encode a polypeptide of 3411 amino acids. The structural proteins are found within the amino-terminal 780 residues of this polyprotein; the remainder of the open reading frame consists of nonstructural viral polypeptides. This genome organization implies that mature viral proteins are produced by posttranslational cleavage of a polyprotein precursor and has implications for flavivirus RNA replication and for the evolutionary relation of this virus family to other...
On the Intermediate-redshift Central Stellar Mass-Halo Mass Relation, and Implications for the Evolution of the Most Massive Galaxies Since z ~ 1 - Shankar, Francesco; Guo, Hong; Bouillot, Vincent; Rettura, Alessandro; Meert, Alan; Buchan, Stewart; Kravtsov, Andrey; Bernardi, Mariangela; Sheth, Ravi; Vikram, Vinu; Marchesini, Danilo; Behroozi, Peter; Zheng, Zheng; Maraston, Claudia; Ascaso, Begoña; Lemaux, Brian C.; Capozzi, Diego; Huertas-Company, Marc; Gal, Roy R.; Lubin, Lori M.; Conselice, Christopher J.; Carollo, Marcella; Cattaneo, Andrea
The stellar mass-halo mass relation is a key constraint in all semi-analytic, numerical, and semi-empirical models of galaxy formation and evolution. However, its exact shape and redshift dependence remain under debate. Several recent works support a relation in the local universe steeper than previously thought. Based on comparisons with a variety of data on massive central galaxies, we show that this steepening holds up to z ~ 1 for stellar masses M_(star)≳2 × 10^(11) M_☉. Specifically, we find significant evidence for a high-mass end slope of β ≳ 0.35-0.70 instead of the usual β ≾ 0.20-0.30 reported by a number...
Spectral characteristic evolution: a new algorithm for gravitational wave propagation - Handmer, Casey J.; Szilágyi, Béla
We present a spectral algorithm for solving the full nonlinear vacuum Einstein field equations in the Bondi framework. Developed within the Spectral Einstein Code, we demonstrate spectral characteristic evolution as a technical precursor to Cauchy characteristic extraction, a rigorous method for obtaining gauge-invariant gravitational waveforms from existing and future astrophysical simulations. We demonstrate the new algorithm's stability, convergence, and agreement with existing evolution methods. We explain how an innovative spectral approach enables a two orders of magnitude improvement in computational efficiency.
Noise and control decoupling of Advanced LIGO suspensions - Shapiro, B. N.; Adhikari, R.; Driggers, J.; Kissel, J.; Lantz, B.; Rollins, J.; Youcef-Toumi, K.
Ground-based interferometric gravitational wave observatories such as Advanced LIGO must isolate their optics from ground vibrations with suspension systems to meet their stringent noise requirements. These suspensions typically have very high quality-factor resonances that require active damping. The sensor noise associated with this damping is a potential significant contributor to the sensitivity of these interferometers. This paper introduces a novel scheme for suspension damping that isolates much of this noise and permits greater amounts of damping. It also decouples the damping feedback design from the interferometer control. The scheme works by invoking a change from a local coordinate frame associated...
Atmospheric mass loss during planet formation: The importance of planetesimal impacts - Schlichting, Hilke E.; Sari, Re'em; Yalinewich, Almong
Quantifying the atmospheric mass loss during planet formation is crucial for understanding the origin and evolution of planetary atmospheres. We examine the contributions to atmospheric loss from both giant impacts and planetesimal accretion. Giant impacts cause global motion of the ground. Using analytic self-similar solutions and full numerical integrations we find (for isothermal atmospheres with adiabatic index γ=5/3) that the local atmospheric mass loss fraction for ground velocities v_g ≲ 0.25v_esc is given by χ_loss = (1.71v_g/v_esc)^4.9, where v_esc is the escape velocity from the target. Yet, the global atmospheric mass loss is a weaker function of the impactor velocity...
A model coupling plasticity and phase transformation with application to dynamic shear deformation of iron - Sadjadpour, Amir; Rittel, Daniel; Ravichandran, Guruswami; Bhattacharya, Kaushik
A simple model that brings together well-established thermo-mechanical models of plasticity with those of martensitic phase transformation into a single thermodynamic framework is proposed. The presentation is in one space dimension, but the framework is general so that the model may be extended to higher dimensions. The model is used to study recent experiments on the α⇔∊ martensitic phase transformation of pure iron under dynamic, shear-dominant loading conditions. It is shown that the model fitted to established thermodynamic data and selected experiments is able to reproduce the experimental observations in a wide range of loading rates ranging from quasistatic to...
NEOWISE Observations of Comet C/2013 A1 (Siding Spring) as It Approaches Mars - Stevenson, R.; Bauer, J. M.; Cutri, R. M.; Mainzer, A. K.; Masci, F. J.
The Near-Earth Object Wide-field Infrared Survey Explorer mission observed comet C/2013 A1 (Siding Spring) three times at 3.4 μm and 4.6 μm as the comet approached Mars in 2014. The comet is an extremely interesting target since its close approach to Mars in late 2014 will be observed by various spacecraft in situ. The observations were taken in 2014 January, July, and September when the comet was at heliocentric distances of 3.82 AU, 1.88 AU, and 1.48 AU. The level of activity increased significantly between the January and July visits but then decreased by the time of the observations in...
Direct Spectrum of the Benchmark T Dwarf HD 19467 B - Crepp, Justin R.; Rice , Emily L.; Veicht, Aaron; Aguilar, Jonathan; Pueyo, Laurent; Giorla, Paige; Nilsson, Ricky; Luscz-Cook, Statia H.; Oppenheimer, Rebecca; Hinkley, Sasha; Brenner, Douglas; Vasisht, Gautam; Cady, Eric; Beichman, Charles A.; Hillenbrand, Lynne A.; Lockhart, Thomas; Matthews, Christopher T.; Roberts, Lewis C., Jr.; Sivaramakrishnan, Anand; Soummer, Rémi; Zhai, Chengxing
HD 19467 B is presently the only directly imaged T dwarf companion known to induce a measurable Doppler acceleration around a solar-type star. We present spectroscopy measurements of this important benchmark object taken with the Project 1640 integral field unit at Palomar Observatory. Our high-contrast R ≈ 30 observations obtained simultaneously across the JH bands confirm the cold nature of the companion as reported from the discovery article and determine its spectral type for the first time. Fitting the measured spectral energy distribution to SpeX/IRTF T dwarf standards and synthetic spectra from BT-Settl atmospheric models, we find that HD 19467...
Extraction of energy from gravitational waves by laser interferometer detectors - Ma, Yiqiu; Blair, David G.; Zhao, Chunnong; Kells, William
In this paper, we discuss the energy interaction between gravitational waves and laser interferometer gravitational wave detectors. We show that the widely held view that the laser interferometer gravitational wave detector absorbs no energy from gravitational waves is only valid under the approximation of a frequency-independent optomechanical coupling strength and a pump laser without detuning with respect to the resonance of the interferometer. For a strongly detuned interferometer, the optical-damping dynamics dissipates gravitational wave energy through the interaction between the test masses and the optical field. For a non-detuned interferometer, the frequency-dependence of the optomechanical coupling strength causes a tiny...
Regulation of mitochondrial fission by MiD51 - Losn, Oliver; Rome, Michael; Kaiser, Jens; Shan, Shu-ou; Chan, David
Mitochondrial fission requires the recruitment of dynamin-related protein 1 (Drp1) to mitochondria and activation of its GTP-dependent scission function. In mammals, the recruitment of Drp1 is primarily regulated by the outer membrane receptors Mff, MiD49 and MiD51, while Fis1 plays a minor role. We recently demonstrated that these receptors can function independently of one another to recruit Drp1 and mediate mitochondrial division. Intriguingly, exogenous expression of MiD49 and MiD51 causes constitutive recruitment of Drp1 but inhibits its scission activity. With mitochondrial stress, however, these receptors can rapidly activate pre-recruited Drp1 and cause rapid mitochondrial fragmentation independently of Fis1 and Mff....
Drugs and the brain, the MOOC - Lester, Henry; Cohen, Bruce
How does a MOOC differ in value and impact from previous "distance-learning" technologies? (1) A major additional possibility is the online community that springs up around the course. "Drugs and the Brain" brought some people with real-life interest in drug mechanisms, and others with detailed scientific experience. Quantifying the letter group: of the students who finished the 2012-2013 course and earned "statements of accomplishment", ~ 10% of the students had PHD degrees and 7% had MD degrees, and ~ 7% had professional degrees in pharmacy. This online community requires detailed curation, moderation, and judgment. For the 2013-2014 rendition, we plan...
The Near-ultraviolet Luminosity Function of Young, Early M-type Dwarf Stars - Ansdell, Megan; Gaidos, Eric; Mann, Andrew W.; Lepine, Sebastien; James, David; Buccino, Andrea; Baranec, Christoph; Law, Nicholas M.; Riddle, Reed; Mauas, Pablo; Petrucci, Romina
Planets orbiting within the close-in habitable zones of M dwarf stars will be exposed to elevated high-energy radiation driven by strong magnetohydrodynamic dynamos during stellar youth. Near-ultraviolet (NUV) irradiation can erode and alter the chemistry of planetary atmospheres, and a quantitative description of the evolution of NUV emission from M dwarfs is needed when modeling these effects. We investigated the NUV luminosity evolution of early M-type dwarfs by cross-correlating the Lépine & Gaidos catalog of bright M dwarfs with the Galaxy Evolution Explorer (GALEX) catalog of NUV (1771-2831 angstrom) sources. Of the 4805 sources with GALEX counterparts, 797 have NUV...
Star Formation Properties in Barred Galaxies. III. Statistical Study of Bar-Driven Secular Evolution Using a Sample of Nearby Barred Spirals - Zhou, Zhi-Min; Cao, Chen; Wu, Hong
Stellar bars are important internal drivers of secular evolution in disk galaxies. Using a sample of nearby spiral galaxies with weak and strong bars, we explore the relationships between the star formation feature and stellar bars in galaxies. We find that galaxies with weak bars tend coincide with low concentrical star formation activity, while those with strong bars show a large scatter in the distribution of star formation activity. We find enhanced star formation activity in bulges toward stronger bars, although not predominantly, consistent with previous studies. Our results suggest that different stages of the secular process and many other...
Textpresso for oro-pharyngeal anatomy: a system for searching the full text of anatomy literatures - Van Auken, Kimberly; Druzinsky, Robert; Done, James; Sternberg, Paul; Mueller, Hans-Michael
Biological databases are a useful resource for parlaying existing data into new experimental hypotheses. Populating such databases with information from the published literature, however, can be labor intensive and thus is aided greatly by text mining tools capable of retrieving key facts from full text. The Textpresso information retrieval system (http://www.textpresso.org) is used by several Model Organism Database (MOD) communities to assist in curation [Müller HM, Kenny EE, Sternberg PW. 2004. PLoS Biol. Nov;2(11):e309; Van Auken KM, Fey P, Berardini TZ, et al. 2012. Database (Oxford). Nov 17;2012:bas040.] Textpresso searches the full text of literature using keywords and/or categories, groups...
Organizing signal transduction in the postsynaptic density - Kennedy, Mary
Excitatory neurons in the CNS receive thousands of synaptic contacts from other excitatory neurons. An increase in the strength of a relatively small number of these synapses can store a memory by binding connected neurons into a circuit in which all of the neurons fire each time the specific memory is evoked. An increase in synaptic strength involves addition of new glutamate receptors to the synaptic membrane, and re-arrangement of the cytoskeleton to support a larger synapse. Biochemical signaling enzymes that control this process, which is called “activity-dependent synaptic plasticity,” are organized near the postsynaptic membrane. The enzymes include several...
HST Rotational Spectral Mapping of Two L-type Brown Dwarfs: Variability in and out of Water Bands indicates High-altitude Haze Layers - Yang, Hao; Apai, Daniel; Marley, Mark S.; Saumon, Didier; Morley, Caroline V.; Buenzli, Esther; Artigau, Étienne; Radigan, Jacqueline; Metchev, Stanimir; Burgasser, Adam J.; Mohanty, Subhanjoy; Lowrance, Patrick J.; Showman, Adam P.; Karalidi, Theodora; Flateau, Davin; Heinze, Aren N.
We present time-resolved near-infrared spectroscopy of two L5 dwarfs, 2MASS J18212815+1414010 and 2MASS J15074759−1627386, observed with the Wide Field Camera 3 instrument on the Hubble Space Telescope (HST). We study the wavelength dependence of rotation-modulated flux variations between 1.1 μm and 1.7 μm. We find that the water absorption bands of the two L5 dwarfs at 1.15 μm and 1.4 μm vary at similar amplitudes as the adjacent continuum. This differs from the results of previous HST observations of L/T transition dwarfs, in which the water absorption at 1.4 μm displays variations of about half of the amplitude at other wavelengths. We find that the...
On the Progenitor System of the Type Iax Supernova 2014dt in M61 - Foley, Ryan J.; Van Dyk, Schuyler D.; Jha, Saurabh; Clubb, Kelsey I.; Filippenko, Alexei V.; Mauerhan, Jon C.; Miller, Adam A.; Smith, Nathan
We present pre-explosion and post-explosion Hubble Space Telescope images of the Type Iax supernova (SN Iax) 2014dt in M61. After astrometrically aligning these images, we do not detect any stellar sources at the position of the SN in the pre-explosion images to relatively deep limits (3σ limits of M_F438W > –5.0 mag and M_F814W > –5.9 mag). These limits are similar to the luminosity of SN 2012Z's progenitor system (M F435W = –5.43 ± 0.15 and M_F814W = –5.24 ± 0.16 mag), the only probable detected progenitor system in pre-explosion images of a SN Iax, and indeed, of any white-dwarf...