Seasonal and inter-annual temperature variability in the bottom waters over the western Black Sea shelf

Long-term changes in the state of the Bottom Shelf Water (BSW) on the Western shelf of the Black Sea are assessed using analysis of intra-seasonal and inter-annual temperature variations. For the purpose of this study the BSW is defined as such shelf water mass between the seabed and the upper mixed layer (bounded by the σθ = 14.2 isopycnal) which has limited ability to mix vertically with oxygen-rich surface waters during the warm season due to formation of a seasonal pycnocline. A long-term time series of temperature anomalies in the BSW is constructed from in-situ observations taken over the 2nd half of the 20th century. The BSW is shown to occupy nearly half of the shelf area during the summer stratification period (May–November).The results reveal a warm phase in the 1960s/70s, followed by a cold phase between 1985 and 1995 and a further warming after 1995. The transition between the warm and cold periods coincides with a regime shift in the Black Sea ecosystem. While it was confirmed that the memory of winter convection is well preserved over the following months in the deep sea, the signal of winter cooling in the BSW significantly reduces during the warm season. The potential of the BSW to ventilate horizontally during the warm season with the deep-sea waters is assessed using isopycnic analysis of temperature variations. It is shown that temperature in the BSW is stronger correlated with the temperature of Cold Intermediate Waters (CIW) in the deep sea than with the severity of the previous winters, thus indicating that the isopycnal exchanges with the deep sea are more important for inter-annual/inter-decadal variability of the BSW on the western Black Sea shelf than effects of winter convection on the shelf itself

The dynamics of dense water cascades: from laboratory scales to the Arctic Ocean

The sinking of dense shelf waters down the continental slope (or “cascading”) contributes to oceanic water mass formation and carbon cycling. Cascading is therefore of significant importance for the global overturning circulation and thus climate. The occurrence of cascades is highly intermittent in space and time and observations of the process itself (rather than its outcomes) are scarce. Global climate models do not typically resolve cascading owing to numerical challenges concerning turbulence, mixing and faithful representation of bottom boundary layer dynamics. This work was motivated by the need to improve the representation of cascading in numerical ocean circulation models. Typical 3-D hydrostatic ocean circulation models are employed in a series of numerical experiments to investigate the process of dense water cascading in both idealised and realistic model setups. Cascading on steep bottom topography is modelled using POLCOMS, a 3-D ocean circulation model using a terrain-following s-coordinate system. The model setup is based on a laboratory experiment of a continuous dense water flow from a central source on a conical slope in a rotating tank. The descent of the dense flow as characterised by the length of the plume as a function of time is studied for a range of parameters, such as density difference, speed of rotation, flow rate and (in the model) diffusivity and viscosity. Very good agreement between the model and the laboratory results is shown in dimensional and non-dimensional variables. It is confirmed that a hydrostatic model is capable of reproducing the essential physics of cascading on a very steep slope if the model correctly resolves velocity veering in the bottom boundary layer. Experiments changing the height of the bottom Ekman layer (by changing viscosity) and modifying the plume from a 2-layer system to a stratified regime (by enhancing diapycnal diffusion) confirm previous theories, demonstrate their limitations and offer new insights into the dynamics of cascading outside of the controlled laboratory conditions. In further numerical experiments, the idealised geometry of the conical slope is retained but up-scaled to oceanic dimensions. The NEMO-SHELF model is used to study the fate of a dense water plume of similar properties to the overflow of brine-enriched shelf waters from the Storfjorden in Svalbard. The overflow plume, resulting from sea ice formation in the Storfjorden polynya, cascades into the ambient stratification resembling the predominant water masses of Fram Strait. At intermediate depths between 200-500m the plume encounters a layer of warm, saline AtlanticWater. In some years the plume ‘pierces’ the Atlantic Layer and sinks into the deep Fram Strait while in other years it remains ‘arrested’ at Atlantic Layer depths. It has been unclear what parameters control whether the plume pierces the Atlantic Layer or not. In a series of experiments we vary the salinity ‘S’ and the flow rate ‘Q’ of the simulated Storfjorden overflow to investigate both strong and weak cascading conditions. Results show that the cascading regime (piercing, arrested or ‘shaving’ - an intermediate case) can be predicted from the initial values of S and Q. In those model experiments where the initial density of the overflow water is considerably greater than of the deepest ambient water mass we find that a cascade with high initial S does not necessarily reach the bottom if Q is low. Conversely, cascades with an initial density just slightly higher than the deepest ambient layer may flow to the bottom if the flow rate Q is high. A functional relationship between S/Q and the final depth level of plume waters is explained by the flux of potential energy (arising from the introduction of dense water at shallow depth) which, in our idealised setting, represents the only energy source for downslope descent and mixing. Lastly, the influence of tides on the propagation of a dense water plume is investigated using a regional NEMO-SHELF model with realistic bathymetry, atmospheric forcing, open boundary conditions and tides. The model has 3 km horizontal resolution and 50 vertical levels in the sh-coordinate system which is specially designed to resolve bottom boundary layer processes. Tidal effects are isolated by comparing results from model runs with and without tides. A hotspot of tidally-induced horizontal diffusion leading to the lateral dispersion of the plume is identified at the southernmost headland of Spitsbergen which is in close proximity to the plume path. As a result the lighter fractions in the diluted upper layer of the plume are drawn into the shallow coastal current that carries Storfjorden water onto the Western Svalbard Shelf, while the dense bottom layer continues to sink down the slope. This bifurcation of the plume into a diluted shelf branch and a dense downslope branch is enhanced by tidally-induced shear dispersion at the headland. Tidal effects at the headland are shown to cause a net reduction in the downslope flux of Storfjorden water into deep Fram Strait. This finding contrasts previous results from observations of a dense plume on a different shelf without abrupt topography. The dispersive mechanism which is induced by the tides is identified as a mechanism by which tides may cause a relative reduction in downslope transport, thus adding to existing understanding of tidal effects on dense water overflows.NER

Establishment of pluripotent cell lines from vertebrate species - Present status and future prospects

Pluripotent embryonic stem (ES) cells are undifferentiated cell lines derived from early embryos and are capable of unlimited undifferentiated proliferation in vitro. They retain the ability to differentiate into all cell types including germ cells in chimeric animals in vivo, and can be induced to form derivatives of all three germ layers in vitro. Mouse ES cells represent one of the most important tools in genetic research. Major applications include the targeted mutation of specific genes by homologous recombination and the discovery of new genes by gene trap strategies. These applications would be of high interest for other model organisms and also for livestock species, However, in spite of tremendous research activities, no proven ES cells colonizing the germ line have been established for vertebrate species other than mouse a nd chicken thus far. This review summarizes the current status of deriving pluripotent embryonic stem cell lines from vertebrates and recent developments in nuclear transfer technology, which may provide an alternative tool for genetic modification of livestock animals. Copyright (C) 1999 S. Karger AG, Basel

Barley Genomics: An Overview

Barley (Hordeum vulgare), first domesticated in the Near East, is a well-studied crop in terms of genetics, genomics, and breeding and qualifies as a model plant for Triticeae research. Recent advances made in barley genomics mainly include the following: (i) rapid accumulation of EST sequence data, (ii) growing number of studies on transcriptome, proteome, and metabolome, (iii) new modeling techniques, (iv) availability of genome-wide knockout collections as well as efficient transformation techniques, and (v) the recently started genome sequencing effort. These developments pave the way for a comprehensive functional analysis and understanding of gene expression networks linked to agronomically important traits. Here, we selectively review important technological developments in barley genomics and related fields and discuss the relevance for understanding genotype-phenotype relationships by using approaches such as genetical genomics and association studies. High-throughput genotyping platforms that have recently become available will allow the construction of high-density genetic maps that will further promote marker-assisted selection as well as physical map construction. Systems biology approaches will further enhance our knowledge and largely increase our abilities to design refined breeding strategies on the basis of detailed molecular physiological knowledge

Der Beitrag apoplastischer Peroxidasen der Blätter

Die für den ökologisch orientierten Waldumbau im Osterzgebirge bedeutsamen Baumarten Fagus sylvatica, Betula pendula und Sorbus aucuparia wurden in Open-Top-Kammern einer Langzeitbelastung (zweieinhalb Jahre) mit Schwefeldioxid oder einer Mischung aus Schwefeldioxid und Ozon ausgesetzt und deren Streßreaktionen untersucht. Am Beispiel von Fagus sylvatica wurden ergänzend die Auswirkungen von Blattverwundung, Blattlaus-Befall und Trockenheit betrachtet. Neben der Erfassung verschiedener biochemischer, blattanatomischer und morphologischer Parameter war es dabei ein besonderes Anliegen der Studie, die Prozesse in der Zellwandphase der Blätter genauer zu untersuchen. Hierbei war das Hauptaugenmerk auf die extrazellulären Peroxidasen gerichtet, da diese Enzyme das Potential besitzen, verschiedene an der Streßabwehr beteiligte Reaktionen zu katalysieren, und in der Zellwandphase in hohen Konzentrationen vorkommen. Die löslichen Zellwand-Peroxidasen aus den Blättern der drei Laubbaumarten wurden isoliert und deren Sulfit- und Indolessigsäure-Oxidationsaktivität in vitro gemessen. Die Enzyme wurden zudem hinsichtlich ihrer katalytischen Eigenschaften und des Vorkommens von Enzym-Isoformen untersucht. Aus den gewonnenen Ergebnissen konnten Aussagen über die mögliche Funktion der Peroxidasen unter den applizierten Streßbedingungen abgeleitet werden. Die Untersuchung zeigte, daß alle drei Baumarten intensiv auf die verschiedenen Streßfaktoren reagierten, z.B. mit Chlorophyllabbau, Nekrotisierung, allgemeiner Wuchsdepression, Veränderung der Peroxidaseaktivität. Es wurde deutlich, daß große artspezifische Unterschiede in der Reaktion auf die Luftschadstoffe bestanden, die auf eine unterschiedliche Schadstofftoleranz und unterschiedliche Strategien bei der Streßbewältigung schließen lassen. Anhand der Befunde bei Fagus sylvatica über die Folgen von Trockenheit, Blattverwundung und Blattlausbefall konnte zudem nachgewiesen werden, daß die Pflanzen einer Art auf die unterschiedlich rasch und mit unterschiedlicher Intensität einsetzenden Streßsituationen sehr differenziert zu reagieren vermochten. Dies galt sowohl unter zeitlichen als auch quantitativen und qualitativen Gesichtspunkten. Die Peroxidasen waren bei Belastungssituationen, an die sich die Pflanzen im Verlauf der Evolution anpassen konnten (mech. Schädigung, Wassermangel, Insektenbefall), an frühen Abwehrreaktionen beteiligt. Dagegen erfolgte unter Einwirkung von Luftschadstoffen keine rasche Aktivierung der Zellwandperoxidasen. Dies deutet an, daß die evolutiv erworbenen Abwehrmechanismen der Pflanzen gestört waren bzw. nicht in vollem Umfang wirksam werden konnten

VPg of murine norovirus binds translation initiation factors in infected cells

BACKGROUND: Norovirus genomic and subgenomic RNAs are covalently linked at the 5' nucleotide to a 15 kD protein called VPg. VPg of two human norovirus strains binds translation initiation factor eIF3 and other eIFs in vitro, suggesting VPg functions in initiation of protein synthesis on viral RNA. Human norovirus strains are not cultivable, and thus experimental evidence of interactions between VPg and eIFs in infected cells has been lacking. We used the cultivable murine norovirus MNV-1 as a model to study interactions between VPg and eIFs in infected cells. RESULTS: As shown previously for human norovirus VPg, MNV-1 VPg bound eIF3, eIF4GI, eIF4E, and S6 ribosomal protein in cell extracts by GST pull-down assay. Importantly, MNV-1 VPg co-precipitated eIF4GI and eIF4E from infected macrophages, providing evidence that VPg interacts with components of the translation machinery in norovirus infected cells. CONCLUSION: The interactions between MNV-1 VPg and eIFs completely mimic those reported for the human norovirus VPg, illustrating the utility of MNV-1 as a relevant molecular model to study mechanisms of human norovirus replication

Linkage mapping of putative regulator genes of barley grain development characterized by expression profiling

<p>Abstract</p> <p>Background</p> <p>Barley (<it>Hordeum vulgare </it>L.) seed development is a highly regulated process with fine-tuned interaction of various tissues controlling distinct physiological events during prestorage, storage and dessication phase. As potential regulators involved within this process we studied 172 transcription factors and 204 kinases for their expression behaviour and anchored a subset of them to the barley linkage map to promote marker-assisted studies on barley grains.</p> <p>Results</p> <p>By a hierachical clustering of the expression profiles of 376 potential regulatory genes expressed in 37 different tissues, we found 50 regulators preferentially expressed in one of the three grain tissue fractions pericarp, endosperm and embryo during seed development. In addition, 27 regulators found to be expressed during both seed development and germination and 32 additional regulators are characteristically expressed in multiple tissues undergoing cell differentiation events during barley plant ontogeny. Another 96 regulators were, beside in the developing seed, ubiquitously expressed among all tissues of germinating seedlings as well as in reproductive tissues. SNP-marker development for those regulators resulted in anchoring 61 markers on the genetic linkage map of barley and the chromosomal assignment of another 12 loci by using wheat-barley addition lines. The SNP frequency ranged from 0.5 to 1.0 SNP/kb in the parents of the various mapping populations and was 2.3 SNP/kb over all eight lines tested. Exploration of macrosynteny to rice revealed that the chromosomal orders of the mapped putative regulatory factors were predominantly conserved during evolution.</p> <p>Conclusion</p> <p>We identified expression patterns of major transcription factors and signaling related genes expressed during barley ontogeny and further assigned possible functions based on likely orthologs functionally well characterized in model plant species. The combined linkage map and reference expression map of regulators defined in the present study offers the possibility of further directed research of the functional role of regulators during seed development in barley.</p

Tidally induced lateral dispersion of the Storfjorden overflow plume

We investigate the flow of brine-enriched shelf water from Storfjorden (Svalbard) into Fram Strait and onto the western Svalbard Shelf using a regional set-up of NEMO-SHELF, a 3-D numerical ocean circulation model. The model is set up with realistic bathymetry, atmospheric forcing, open boundary conditions and tides. The model has 3 km horizontal resolution and 50 vertical levels in the sh-coordinate system which is specially designed to resolve bottom boundary layer processes. In a series of modelling experiments we focus on the influence of tides on the propagation of the dense water plume by comparing results from tidal and non-tidal model runs. Comparisons of non-tidal to tidal simulations reveal a hotspot of tidally induced horizontal diffusion leading to the lateral dispersion of the plume at the southernmost headland of Spitsbergen which is in close proximity to the plume path. As a result the lighter fractions in the diluted upper layer of the plume are drawn into the shallow coastal current that carries Storfjorden water onto the western Svalbard Shelf, while the dense bottom layer continues to sink down the slope. This bifurcation of the plume into a diluted shelf branch and a dense downslope branch is enhanced by tidally induced shear dispersion at the headland. Tidal effects at the headland are shown to cause a net reduction in the downslope flux of Storfjorden water into the deep Fram Strait. This finding contrasts previous results from observations of a dense plume on a different shelf without abrupt topography

A pure population of lung alveolar epithelial type II cells derived from human embryonic stem cells.

Alveolar epithelial type II (ATII) cells are small, cuboidal cells that constitute approximately 60% of the pulmonary alveolar epithelium. These cells are crucial for repair of the injured alveolus by differentiating into alveolar epithelial type I cells. ATII cells derived from human ES (hES) cells are a promising source of cells that could be used therapeutically to treat distal lung diseases. We have developed a reliable transfection and culture procedure, which facilitates, via genetic selection, the differentiation of hES cells into an essentially pure (\u3e99%) population of ATII cells (hES-ATII). Purity, as well as biological features and morphological characteristics of normal ATII cells, was demonstrated for the hES-ATII cells, including lamellar body formation, expression of surfactant proteins A, B, and C, alpha-1-antitrypsin, and the cystic fibrosis transmembrane conductance receptor, as well as the synthesis and secretion of complement proteins C3 and C5. Collectively, these data document the successful generation of a pure population of ATII cells derived from hES cells, providing a practical source of ATII cells to explore in disease models their potential in the regeneration and repair of the injured alveolus and in the therapeutic treatment of genetic diseases affecting the lung