Epigenetics: Biology's Quantum Mechanics

The perspective presented here is that modern genetics is at a similar stage of development as were early formulations of quantum mechanics theory in the 1920s and that in 2010 we are at the dawn of a new revolution in genetics that promises to enrich and deepen our understanding of the gene and the genome. The interrelationships and interdependence of two views of the gene – the molecular biological view and the epigenetic view – are explored, and it is argued that the classical molecular biological view is incomplete without incorporation of the epigenetic perspective and that in a sense the molecular biological view has been evolving to include the epigenetic view. Intriguingly, this evolution of the molecular view toward the broader and more inclusive epigenetic view of the gene has an intriguing, if not precise, parallel in the evolution of concepts of atomic physics from Newtonian mechanics to quantum mechanics that are interesting to consider

Function and misfunction of the two promoters of the Drosophila Antennapedia gene

Journal ArticleIn the Antennapedia (Antp) gene of Drosophila melanogaster, structurally distinct RNAs arise from different transcription initiation sites. When the two sites are separated by a chromosome inversion, transcripts are produced from each fragment of the split Antp locus, and these RNAs initiate at the same nucleotide as in wild-type animals. Thus, the initiation sites are regulated by independent promoters

The Assembly History of Field Spheroidals: Evolution of Mass-to-light Ratios and Signatures of Recent Star Formation

We present a comprehensive catalog of high signal-to-noise spectra obtained with the DEIMOS spectrograph on the Keck II telescope for a sample of F850LP<22.43 (AB) field spheroidal (E+S0s; 163) and bulge dominated disk (61) galaxies in the redshift range 0.2<z<1.2. We examine the zero point, tilt and scatter of the Fundamental Plane (FP) as a function of redshift and morphological properties, carefully accounting for luminosity-dependent biases via Montecarlo simulations. The evolution of the overall FP can be represented by a mean change in effective mass-to-light ratio given by <d \log (M/L_{\rm B})/dz>=-0.72^{+0.07}_{-0.05}\pm0.04. However, this evolution depends significantly on the dynamical mass, being slower for larger masses as reported in a previous letter. In addition, we separately show the intrinsic scatter of the FP increases with redshift as d(rms(M/L_{\rm B}))/dz=0.040\pm0.015. Although these trends are consistent with single burst populations which formed at $z_f>2$ for high mass spheroidals and z_{f}~1.2 for lower mass systems, a more realistic picture is that most of the stellar mass formed in all systems at z>2 with subsequent activity continuing to lower redshifts (z<1.2). The fraction of stellar mass formed at recent times depend strongly on galactic mass, ranging from <1% for masses above 10^{11.5} M_{\odot} to 20-40% below 10^{11} M_{\odot}. Independent support for recent activity is provided by spectroscopic ([\ion{O}{2}] emission, H\delta) and photometric (blue cores and broad-band colors) diagnostics. Via the analysis of a large sample with many independent diagnostics, we are able to reconcile previously disparate interpretations of the assembly history of field spheroidals. [Abridged]Comment: 26 pages including 24 figures, submitted to ApJ. Complete and compact version with full resolution images available at http://www.astro.ucla.edu/~ttreu/ms.pd

Dependence of the Fundamental Plane Scatter on Galaxy Age

The fundamental plane (FP) has an intrinsic scatter that can not be explained purely by observational errors. Using recently available age estimates for nearby early type galaxies, we show that a galaxy's position relative to the FP depends on its age. In particular, the mean FP corresponds to ellipticals with an age of ~10 Gyr. Younger galaxies are systematically brighter with higher surface brightness relative to the mean relation. Old ellipticals form an `upper envelope' to the FP. For our sample of mostly non-cluster galaxies, age can account for almost half of the scatter in the B band FP. Distance determinations based on the FP may have a systematic bias, if the mean age of the sample varies with redshift. We also show that fundamental plane residuals, B-V colors and Mg_2 line strength are consistent with an ageing central burst superposed on an old stellar population. This reinforces the view that these age estimates are tracing the last major episode of star formation induced by a gaseous merger event. We briefly discuss the empirical `evolutionary tracks' of merger-remnants and young ellipticals in terms of their key observational parameters.Comment: 14 pages, Latex, 2 figures, accepted by ApJ Letter

Composting hoop structure bedding/manure

Tom Richard has conducted composting research on ISU\u27s Rhodes Research Farm using cornstalk-bedded manure from a finishing hoop. The manure is partially composted in the building. Manure inside the hooped structure varies in moisture content and nitrogen. The wet areas where pigs dung are high in nitrogen; dry areas are low in nitrogen

Biogeochemie, Fluide, Gashydrate und Paläoklima des Schwarzen Meers = Biogeochemistry, fluids, gas hydrates and paleo climate of the Black Sea : Istanbul, Trabzon, Istanbul ; Forschungsschiff Meteor, Reise Nr. M72 ; 07.02.2007 – 04.06.2007

Das Schwarze Meer ist das größte anoxische Meeresbecken der Erde. Hohe biologische Produktion in der Deckschicht und ein tiefer anoxischer Wasserkörper unterhalb der Chemokline in 100-150 m Wassertiefe füh-ren zu einzigartigen Bedingungen für mikrobielles Leben, geochemische Kreis-läufe und Sedimentationsprozesse. Gas- und Fluidemissionen aus verschiedenen geolo-gischen Formationen wie z.B. Methanaus-tritt entlang der Schelfkante oder Ausstoß von kohlenwasserstoffhaltigen Fluiden aus Schlammvulkanen in Tiefseeregionen lie-fern ein einzigartiges Umfeld für die Erfor-schung von geologischen Tiefenprozessen, geochemischen Kreisläufen, mikrobiellen Habitaten und den kontrollierenden Bedin-gungen für mikrobielle Schlüsselprozesse der Elementkreisläufe in einer permanent anoxischen Welt. Fahrtabschnitt M72/1 untersucht unter der Leitung von Dr. R. Seifert geochemische Kreisläufe und mikrobielles Leben an akti-ven Gasquellen innerhalb der Statbilitäts-zone von Gashydrat ab ca. 700 m Wasser-tiefe im Paläo-Djnepr-Gebiet. Der anschlie-ßende Fahrtabschnitt M 72/2 findet im Rahmen des EU-Projekts HERMES und des deutschen Geotechnologien-Projekts MUMM II unter der Leitung von Prof. Dr. A. Boetius statt und untersucht die Kontrol-len und Mechanismen der mikrobiellen Transporte und Umsätze chemischer Ele-mente an Methanquellen auf der Schelfkante und an Fluidaustritten von Schlammvulka-nen. Als Aktivität eines weiteren Geotech-nologienprojekts METRO widmet sich Fahrtabschnitt M 72/3 unter der Leitung von Prof. Dr. G. Bohrmann der Erforschung von Herkunft, Verteilung und Dynamik von Methan und Gashydraten in Sedimenten sowie der Untersuchung von Methanflüssen von den Sedimenten in die Wassersäule. Anschließend wird Fahrtabschnitt M 72/4seismische Untersuchungen der Migrationswege von Fluiden in den tiefen Unter-gründen des Djnepr-seep-Systems und der Schlammvulkane im Sorokin Trog unter der Leitung von Dr. J. Bialas vornehmen. Den Abschluss bildet Fahrtabschnitt M 72/5 un-ter der Leitung von Dr. C. Borowski mit Untersuchungen der geochemischen und mikrobiellen Prozesse in der geschichteten Wassersäule und in Sedimenten um die Chemokline wie in den tiefen anoxischen Becken. Die Reise M 72 wird am 07. Februar 2007 in Istanbul (Türkei) beginnen und am 04. Juni 2007 ebenfalls in Istanbul enden.The Black Sea is the largest anoxic basin on earth. High biological productivity in the oxygenated surface waters and a deep anoxic water body below the chemocline at 100–150 m water depth provide unique conditions for anaerobic microbial life, geochemical cycling and sedimentation processes which make the present day Black Sea a modern type locality for TOC-rich sedimentation and element cycling processes in the geological past. Hydrocarbon emissions from various geological settings such as methane gas seepage along large stretches of the shelf break and fluid discharges from mud volcanoes in deep-sea regions provide unique environmental conditions for studying geological subsurface processes, geochemical cycling, microbial habitats and controls on microbial key processes for element cycling in a permanent anoxic world. Geochemical cycling and microbial life at active gas seeps located in the stability zone of gas hydrates below 700 m water depth in the paleo Dnepr area will be investigated by leg M 72/1 with Dr. R. Seifert as a chief scientist. In the frame of the EU project HERMES and the German “Geotechnologies” project MUMM II, leg M 72/2 with Prof. Dr. A. Boetius as a chief scientist will focus on the controls and mechanisms of chemical element transport and breakdown by seep microbiota at shelf break gas seeps and fluid discharges of mudvolcanoes in the Sorokin Trough. As an activity of another “Geotechnologies” project METRO, leg M 72/3 with Prof. Dr. G. Bohrmann as a chief scientist will study in various geological settings, mainly of the eastern Black Sea, the origins, distributions and dynamics of methane and gas hydrates in sediments and also methane fluxes from the sediment to the water column. This will be followed by seismic investigations of fluid migration pathways in the subsurface of Sorokin Trough mud volcanoes and the paleo-Dnepr seepage system during M 72/4 with Dr. J. Bialas as a chief scientist. The final leg M 72/5 with Dr. C. Borowski as a chief scientist will lead to various areas in the western and eastern Black Sea and will focus on geochemical and microbiological processes in the stratified water column and in sediments around the chemocline and in the anoxic basins. Cruise M 72 will start on 07th February in Istanbul (Turkey) and end on 04th June again in Istanbul