Organization of Highly Acetylated Chromatin around Sites of Heterogeneous Nuclear RNA Accumulation

Histones found within transcriptionally competent and active regions of the genome are highly acetylated. Moreover, these highly acetylated histones have very short half-lives. Thus, both histone acetyltransferases and histone deacetylases must enrich within or near these euchromatic regions of the interphase chromatids. Using an antibody specific for highly acetylated histone H3, we have investigated the organization of transcriptionally active and competent chromatin as well as nuclear histone acetyltransferase and deacetylase activities. We observe an exclusion of highly acetylated chromatin around the periphery of the nucleus and an enrichment near interchromatin granule clusters (IGCs). The highly acetylated chromatin is found in foci that may reflect the organization of highly acetylated chromatin into “chromonema” fibers. Transmission electron microscopy of Indian muntjac fibroblast cell nuclei indicates that the chromatin associated with the periphery of IGCs remains relatively condensed, most commonly found in domains containing chromatin folded beyond 30 nm. Using electron spectroscopic imaging, we demonstrate that IGCs are clusters of ribonucleoprotein particles. The individual granules comprise RNA-rich fibrils or globular regions that fold into individual granules. Quantitative analysis of individual granules indicates that they contain variable amounts of RNA estimated between 1.5 and >10 kb. We propose that interchromatin granules are heterogeneous nuclear RNA-containing particles, some of which may be pre-mRNA generated by nearby transcribed chromatin. An intermediary zone between the IGC and surrounding chromatin is described that contains factors with the potential to provide specificity to the localization of sequences near IGCs.

The future of coral reefs

Coral reefs, with their millions of species, have changed profoundly because of the effects of people, and will continue to do so for the foreseeable future. Reefs are subject to many of the same processes that affect other human-dominated ecosystems, but some special features merit emphasis: (i) Many dominant reef builders spawn eggs and sperm into the water column, where fertilization occurs. They are thus particularly vulnerable to Allee effects, including potential extinction associated with chronic reproductive failure. (ii) The corals likely to be most resistant to the effects of habitat degradation are small, short-lived “weedy” corals that have limited dispersal capabilities at the larval stage. Habitat degradation, together with habitat fragmentation, will therefore lead to the establishment of genetically isolated clusters of inbreeding corals. (iii) Increases in average sea temperatures by as little as 1°C, a likely result of global climate change, can cause coral “bleaching” (the breakdown of coral–algal symbiosis), changes in symbiont communities, and coral death. (iv) The activities of people near reefs increase both fishing pressure and nutrient inputs. In general, these processes favor more rapidly growing competitors, often fleshy seaweeds, and may also result in explosions of predator populations. (v) Combinations of stress appear to be associated with threshold responses and ecological surprises, including devastating pathogen outbreaks. (vi) The fossil record suggests that corals as a group are more likely to suffer extinctions than some of the groups that associate with them, whose habitat requirements may be less stringent.

Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.

The Zn(Scys)4 unit is present in numerous proteins, where it assumes structural, regulatory, or catalytic roles. The same coordination is found naturally around iron in rubredoxins, several structures of which have been refined at resolutions of, or near to, 1 A. The fold of the small protein rubredoxin around its metal ion is an excellent model for many zinc finger proteins. Zn-substituted rubredoxin and its Fe-containing counterpart were both obtained as the products of the expression in Escherichia coli of the rubredoxin-encoding gene from Clostridium pasteurianum. The structures of both proteins have been refined with an anisotropic model at atomic resolution (1.1 A, R = 8.3% for Fe-rubredoxin, and 1.2 A, R = 9.6% for Zn-rubredoxin) and are very similar. The most significant differences are increased lengths of the M-S bonds in Zn-rubredoxin (average length, 2.345 A) as compared with Fe-rubredoxin (average length, 2.262 A). An increase of the CA-CB-SG-M dihedral angles involving Cys-6 and Cys-39, the first cysteines of each of the Cys-Xaa-Xaa-Cys metal binding motifs, has been observed. Another consequence of the replacement of iron by zinc is that the region around residues 36-46 undergoes larger displacements than the remainder of the polypeptide chain. Despite these changes, the main features of the FeS4 site, namely a local 2-fold symmetry and the characteristic network of N-H...S hydrogen bonds, are conserved in the ZnS4 site. The Zn-substituted rubredoxin provides the first precise structure of a Zn(Scys)4 unit in a protein. The nearly identical fold of rubredoxin around iron or zinc suggests that at least in some of the sites where the metal has mainly a structural role-e.g., zinc fingers-the choice of the relevant metal may be directed by its cellular availability and mobilization processes rather than by its chemical nature.

Mechanism of photoreceptor cGMP phosphodiesterase inhibition by its gamma-subunits.

cGMP phosphodiesterase (PDE) is the key effector enzyme of vertebrate photoreceptor cells that regulates the level of the second messenger, cGMP. PDE consists of catalytic alpha and beta subunits (Palpha and Pbeta) and two inhibitory gamma subunits (Pgamma) that block PDE activity in the dark. The major inhibitory region has been localized to the C terminus of Pgamma. The last C-terminal residues -IleIle form an important hydrophobic domain critical for the inhibition of PDE activity. In this study, mutants of Pgamma were designed for cross-linking experiments to identify regions on Palpha and Pbeta subunits that bind to the Pgamma C terminus. In one of the mutants, the cysteine at position 68 was substituted with serine, and the last four C-terminal residues of Pgamma were replaced with a single cysteine. This mutant, Pgamma83Cys, was labeled with photoprobe 4-(N-maleimido) benzophenone (MBP) at the cysteine residue. The labeled Pgamma83CysMBP mutant was a more potent inhibitor of PDE activity than the unlabeled mutant, indicating that the hydrophobic MBP probe mimics the Pgamma hydrophobic C terminus. A specific, high-yield cross-linking of up to 70% was achieved between the Pgamma83CysMBP and PDE catalytic subunits. Palpha and the N-terminally truncated Pbeta (lacking 147 aa residues) cross-linked to Pgamma83CysMBP with the same efficiency. Using mass spectrometric analysis of tryptic fragments from the cross-linked PDE, we identified the site of cross-linking to aa residues 751-763 of Palpha. The corresponding region of Pbeta, Pbeta-749-761, also may bind to the Pgamma C terminus. Our data suggest that Pgamma blocks PDE activity through the binding to the catalytic site of PDE, near the NKXD motif, a consensus sequence for interaction with the guanine ring of cGMP.

Identification of the local productive systems in Spain: a new approach

Paper submitted to the 44th European Congress of the European Regional Science Association, Porto, 25-29 August 2004.

Consequences of Kondo exchange on quantum spins

When individual quantum spins are placed in close proximity to conducting substrates, the localized spin is coupled to the nearby itinerant conduction electrons via Kondo exchange. In the strong coupling limit this can result in the Kondo effect — the formation of a correlated, many body singlet state — and a resulting renormalization of the density of states near the Fermi energy. However, even when Kondo screening does not occur, Kondo exchange can give rise to a wide variety of other phenomena. In addition to the well known renormalization of the g factor and the finite spin decoherence and relaxation times, Kondo exchange has recently been found to give rise to a newly discovered effect: the renormalization of the single ion magnetic anisotropy. Here we put these apparently different phenomena on equal footing by treating the effect of Kondo exchange perturbatively. In this formalism, the central quantity is ρJ, the product of the density of states at the Fermi energy ρ and the Kondo exchange constant J. We show that perturbation theory correctly describes the experimentally observed exchange induced shifts of the single spin excitation energies, demonstrating that Kondo exchange can be used to tune the effective magnetic anisotropy of a single spin.

The International Competitiveness of the Biscayan Iron and Steel Industry (1880-1913)

This study has a double objective: to provide foreign colleagues with an insight into the controversy surrounding the international competitiveness of pig iron produced in Bilbao and also to present previously unpublished documentation regarding the European iron industry, which I have retrieved from the historical archive of Credit Lyonnais of Paris. This information includes the costs of Biscayan, French, British, German and Belgium pig iron broken down into five components (iron ore, coke, flux, labour and other costs), which is useful in determining the reasons why the pig iron from Bilbao became less competitive. The article is made up of three parts. Firstly, I will synthesise the controversy surrounding the competitiveness of the Basque iron and steel industry. Then I will present the itemised costs which provide information to illustrate how Biscayan pig iron was not competitive because it was produced with English coal which was more expensive than that consumed by the European factories located "on top of" or near coal seams. The article will finish with a section that, by way of conclusion, explains the comparative advantage and disadvantage of Bilbao, applying the first model of Alfred Weber's Theory of Industrial Location to three technological advances, occurring between the 1860s and 1913 (malleable iron, Bessemer steel and Thomas steel).

Russia and its Near Neighborhood: Competition and Conflict within the EU. Natolin Research Paper 04/May 2011

Russia in 2004 politely rejected the offer to become a participant in the European Neighbourhood Policy, preferring instead to pursue bilateral relations with the EU under the heading of ‘strategic partnership’. Five years later, its officials first reacted with concern to the ENP’s eastern dimension, the Eastern Partnership initiative. Quickly, however, having become convinced that the project would not amount to much, their concern gave way to indifference and derision. Furthermore, Russian representatives have failed to support idealistic or romantic notions of commonality in the area between Russia and the EU, shunned the terminology of ‘common European neighbourhood’ and replaced it in EU-Russian documents with the bland reference to ‘regions adjacent to the EU and Russian borders’. Internally, the term of the ‘near abroad’ was the official designation of the area in the Yeltsin era, and unofficially it is still in use today. As the terminological contortions suggest, Moscow officials consider the EU’s eastern neighbours as part of a Russian sphere of influence and interest. Assurances to the contrary notwithstanding, they look at the EU-Russia relationship as a ‘zero-sum game’ in which the gain of one party is the loss of the other. EU attempts to persuade the Russian power elite to regard cooperation in the common neighbourhood not as a competitive game but providing ‘win-win’ opportunities have been to no avail. In fact, conceptual approaches and practical policies conducted vis-à-vis the three Western CIS countries (Belarus, Ukraine and Moldova) and the southern Caucasus (Georgia, Armenia and Azerbaijan) confirm that, from Moscow’s perspective, processes of democratisation, liberalisation and integration with Western institutions in that region are contrary to Russian interests. In each and every case, therefore, the area’s ‘frozen conflicts’ have not been regarded by the Kremlin as an opportunity to promote stability and prosperity in the countries concerned but as an instrument to prevent European choices in their domestic and foreign policy. The current ‘reset’ in Russia’s relations with the United States and the ‘modernisation partnership’ with the EU have as yet failed to produce an impact on Russia’s policies in ‘its’ neighbourhood. The EU is nevertheless well advised to maintain its course of attempting to engage that country constructively, including in the common neighbourhood. However, its leverage is small. For any reorientation to occur in Moscow towards perceptions and policies of mutual benefit in the region, much would depend on Russia’s internal development.

Sedimentology of cores from the shelf of Lazarev Sea, East Antarctica

Distinct facies types, classified in radiocarbon-dated sediments from the shelf of the Lazarev Sea, East Antarctica, reveal a detailed history of processes that have controlled sedimentation during the deglaciation over the last 10,000 yr. The ice retreat on this part of the Antarctic shelf started 9500 yr BP, marked by the deposition of laminated sediments, deposited from a floating ice shelf. These laminites, which occur on top of diamictons laid down from a grounded ice sheet, are the basal sediments of the postglacial sequence. The intensity of the Antarctic Coastal Current (ACC), directed by shelf morphology, controlled sedimentation of the postglacial facies. A residual glaciomarine sediment with the fine fraction winnowed by strong currents developed from 9000-8000 yr BP in the western part of the investigation area and from 9000-5000 yr BP in the eastern part, closer to the prominent 'Fenno Deep' trough. Current velocities apparently decreased between 8000 and 2000 yr BP due to a deflection of the ACC by advancing ice tongues to the east of the investigation area during the 'Hypsithermal'. This led to a deposition of fine-grained sediments, and clay mineralogy suggests a continental source, possibly near the grounding line of the Nivl Ice Shelf, rather than a winnowing of sediments near the shelf break or advection from deeper water. Current velocities intensified after 2000 yr BP, removed fine material from these sediments and led to a relict sediment, consisting of coarse bryozoan and molluscan debris.

Particulate concentrations and vertical fluxes of sedimentary material and chemical elements, composition of particulate and sinking material in the water column of the Bear Island Trough, Norwegian Sea, July 1995

CTD and nephelometric sounding data are considered along with parameters of the near-bottom currents and particulate fluxes measured by a subsurface mooring station in the northern part of the Bear Island Trough. It is shown that the near-bottom current is characterized by highly variable parameters, while distribution of suspended particulate matter demonstrates surface and bottom maxima. Horizontal and vertical fluxes of sedimentary material in the nepheloid layer are studied.

Iran and the United States, 1979-1981 : three years of confrontation : a selected list of references /

Mode of access: Internet.

Performance characterization and relative dispersion of drogued drifters deployed in the fjords of Nootka Sound

Senior thesis written for Oceanography 445

Modulation of Translation Efficiency in S. cerevisiae by Codon Pairs and mRNA Structure

Thesis (Ph.D.)--University of Washington, 2016-06