Structuring of turbulence and its impact on basic features of Ekman boundary layers

The turbulent Ekman boundary layer (EBL) has been studied in a large number of theoretical, laboratory and modeling works since F. Nansen's observations during the Norwegian Polar Expedition 1893–1896. Nevertheless, the proposed analytical models, analysis of the EBL instabilities, and turbulence-resolving numerical simulations are not fully consistent. In particular, the role of turbulence self-organization into longitudinal roll vortices in the EBL and its dependence on the meridional component of the Coriolis force remain unclear. A new set of large-eddy simulations (LES) are presented in this study. LES were performed for eight different latitudes (from 1° N to 90° N) in the domain spanning 144 km in the meridional direction. Geostrophic winds from the west and from the east were used to drive the development of EBL turbulence. The emergence and growth of longitudinal rolls in the EBL was simulated. The simulated rolls are in good agreement with EBL stability analysis given in Dubos et al. (2008). The destruction of rolls in the westerly flow at low latitude was observed in simulations, which agrees well with the action of secondary instability on the rolls in the EBL. This study quantifies the effect of the meridional component of the Coriolis force and the effect of rolls in the EBL on the internal EBL parameters such as friction velocity, cross-isobaric angle, parameters of the EBL depth and resistance laws. A large impact of the roll development or destruction is found. The depth of the EBL in the westerly flow is about five times less than it is in the easterly flow at low latitudes. The EBL parameters, which depend on the depth, also exhibit large difference in these two types of the EBL. Thus, this study supports the need to include the horizontal component of the Coriolis force into theoretical constructions and parameterizations of the boundary layer in models

Promiscuity and preferences of metallothioneins: the cell rules

Metalloproteins are essential for many cellular functions, but it has not been clear how they distinguish between the different metals to bind the correct ones. A report in BMC Biology finds that preferences of two metallothionein isoforms for two different cations are due to inherent properties of these usually less discriminating proteins. Here these observations are discussed in the context of the cellular mechanisms that regulate metal binding to proteins

Northern Bering Sea tip jets

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 39 (2012): L08807, doi:10.1029/2012GL051537.Low-level regions of high wind speed known as tip jets have been identified near Cape Farewell, Greenland's southernmost point. These wind systems contribute to this area being the windiest location on the ocean's surface and play an important role in the regional weather and climate. Here we present the first analysis of the wind systems that make the Siberian coast of the northern Bering Sea the windiest location in the North Pacific Ocean during the boreal winter. In particular we show that tips jets characterized by enhanced northeasterly winds occur in the vicinity of the two prominent headlands along the coast, Cape Navarin and Cape Olyutorsky. The advance of sea ice in the region is shown to impact the frequency and location of the high speed winds in the vicinity of these two capes. Furthermore, we show that these jets are associated with the interaction of extra-tropical cyclones with the high topography of the Koryak Mountain range, situated just inland of the capes. The windstress imparted to the ocean via the tip jets is argued to help drive the formation of dense water in winter in the northern Bering Sea, thus playing an important role in the regional oceanic circulation.GWKM was supported by the Natural Science and Engineering Research Council of Canada. RSP was funded by grant NA08OAR43200895 from the National Oceanic and Atmospheric Administration.2012-10-2

Dynamics of Uptake and Metabolism of Small Molecules in Cellular Response Systems

BACKGROUND: Proper cellular function requires uptake of small molecules from the environment. In response to changes in extracellular conditions cells alter the import and utilization of small molecules. For a wide variety of small molecules the cellular response is regulated by a network motif that combines two feedback loops, one which regulates the transport and the other which regulates the subsequent metabolism. RESULTS: We analyze the dynamic behavior of two widespread but logically distinct two-loop motifs. These motifs differ in the logic of the feedback loop regulating the uptake of the small molecule. Our aim is to examine the qualitative features of the dynamics of these two classes of feedback motifs. We find that the negative feedback to transport is accompanied by overshoot in the intracellular amount of small molecules, whereas a positive feedback to transport removes overshoot by boosting the final steady state level. On the other hand, the negative feedback allows for a rapid initial response, whereas the positive feedback is slower. We also illustrate how the dynamical deficiencies of one feedback motif can be mitigated by an additional loop, while maintaining the original steady-state properties. CONCLUSIONS: Our analysis emphasizes the core of the regulation found in many motifs at the interface between the metabolic network and the environment of the cell. By simplifying the regulation into uptake and the first metabolic step, we provide a basis for elaborate studies of more realistic network structures. Particularly, this theoretical analysis predicts that FeS cluster formation plays an important role in the dynamics of iron homeostasis

Reconciling conflicting evidence for the cause of the observed early 21st century Eurasian cooling

It is now well established that the Arctic is warming at a faster rate than the global average. This warming, which has been accompanied by a dramatic decline in sea ice, has been linked to cooling over the Eurasian subcontinent over recent decades, most dramatically during the period 1998–2012. This is a counter-intuitive impact under global warming given that land regions should warm more than ocean (and the global average). Some studies have proposed a causal teleconnection from Arctic sea-ice retreat to Eurasian wintertime cooling; other studies argue that Eurasian cooling is mainly driven by internal variability. Overall, there is an impression of strong disagreement between those holding the “ice-driven” versus “internal variability” viewpoints. Here, we offer an alternative framing showing that the sea ice and internal variability views can be compatible. Key to this is viewing Eurasian cooling through the lens of dynamics (linked primarily to internal variability with some potential contribution from sea ice; cools Eurasia) and thermodynamics (linked to sea-ice retreat; warms Eurasia). This approach, combined with recognition that there is uncertainty in the hypothesized mechanisms themselves, allows both viewpoints (and others) to co-exist and contribute to our understanding of Eurasian cooling. A simple autoregressive model shows that Eurasian cooling of this magnitude is consistent with internal variability, with some periods exhibiting stronger cooling than others, either by chance or by forced changes. Rather than posit a “yes-or-no” causal relationship between sea ice and Eurasian cooling, a more constructive way forward is to consider whether the cooling trend was more likely given the observed sea-ice loss, as well as other sources of low-frequency variability. Taken in this way both sea ice and internal variability are factors that affect the likelihood of strong regional cooling in the presence of ongoing global warming.</p

In-cell NMR in E. coli to Monitor Maturation Steps of hSOD1

In-cell NMR allows characterizing the folding state of a protein as well as posttranslational events at molecular level, in the cellular context. Here, the initial maturation steps of human copper, zinc superoxide dismutase 1 are characterized in the E. coli cytoplasm by in-cell NMR: from the apo protein, which is partially unfolded, to the zinc binding which causes its final quaternary structure. The protein selectively binds only one zinc ion, whereas in vitro also the copper site binds a non-physiological zinc ion. However, no intramolecular disulfide bridge formation occurs, nor copper uptake, suggesting the need of a specific chaperone for those purposes

The Myxococcus xanthus Two-Component System CorSR Regulates Expression of a Gene Cluster Involved in Maintaining Copper Tolerance during Growth and Development

Myxococcus xanthus is a soil-dwelling member of the δ–Proteobacteria that exhibits a complex developmental cycle upon starvation. Development comprises aggregation and differentiation into environmentally resistant myxospores in an environment that includes fluctuations in metal ion concentrations. While copper is essential for M. xanthus cells because several housekeeping enzymes use it as a cofactor, high copper concentrations are toxic. These opposing effects force cells to maintain a tight copper homeostasis. A plethora of paralogous genes involved in copper detoxification, all of which are differentially regulated, have been reported in M. xanthus. The use of in-frame deletion mutants and fusions with the reporter gene lacZ has allowed the identification of a two-component system, CorSR, that modulates the expression of an operon termed curA consisting of nine genes whose expression slowly increases after metal addition, reaching a plateau. Transcriptional regulation of this operon is complex because transcription can be initiated at different promoters and by different types of regulators. These genes confer copper tolerance during growth and development. Copper induces carotenoid production in a ΔcorSR mutant at lower concentrations than with the wild-type strain due to lack of expression of a gene product resembling subunit III of cbb3-type cytochrome c oxidase. This data may explain why copper induces carotenoid biosynthesis at suboptimal rather than optimal growth conditions in wild-type strains.This work has been funded by the Spanish Government (grants CSD2009-00006 and BFU2012-33248, 70% funded by FEDER). This work was also supported by the National Institute of General Medical Science of the National Institutes of Health under award number R01GM095826 to LJS, and by the National Science Foundation under award number MCB0742976 to LJS. JMD and JP received a fellowship from Junta de Andalucía to do some work at University of Georgia

The apicomplexan plastid and its evolution

Protistan species belonging to the phylum Apicomplexa have a non-photosynthetic secondary plastid—the apicoplast. Although its tiny genome and even the entire nuclear genome has been sequenced for several organisms bearing the organelle, the reason for its existence remains largely obscure. Some of the functions of the apicoplast, including housekeeping ones, are significantly different from those of other plastids, possibly due to the organelle’s unique symbiotic origin

Biochemical Discrimination between Selenium and Sulfur 1: A Single Residue Provides Selenium Specificity to Human Selenocysteine Lyase

Selenium and sulfur are two closely related basic elements utilized in nature for a vast array of biochemical reactions. While toxic at higher concentrations, selenium is an essential trace element incorporated into selenoproteins as selenocysteine (Sec), the selenium analogue of cysteine (Cys). Sec lyases (SCLs) and Cys desulfurases (CDs) catalyze the removal of selenium or sulfur from Sec or Cys and generally act on both substrates. In contrast, human SCL (hSCL) is specific for Sec although the only difference between Sec and Cys is the identity of a single atom. The chemical basis of this selenium-over-sulfur discrimination is not understood. Here we describe the X-ray crystal structure of hSCL and identify Asp146 as the key residue that provides the Sec specificity. A D146K variant resulted in loss of Sec specificity and appearance of CD activity. A dynamic active site segment also provides the structural prerequisites for direct product delivery of selenide produced by Sec cleavage, thus avoiding release of reactive selenide species into the cell. We thus here define a molecular determinant for enzymatic specificity discrimination between a single selenium versus sulfur atom, elements with very similar chemical properties. Our findings thus provide molecular insights into a key level of control in human selenium and selenoprotein turnover and metabolism