Showing papers by "Andrew J. Watson published in 2013"

A uniform, quality controlled Surface Ocean CO2 Atlas (SOCAT)

Abstract: A well-documented, publicly available, global data set of surface ocean carbon dioxide (CO2) parameters has been called for by international groups for nearly two decades. The Surface Ocean CO2 Atlas (SOCAT) project was initiated by the international marine carbon science community in 2007 with the aim of providing a comprehensive, publicly available, regularly updated, global data set of marine surface CO2, which had been subject to quality control (QC). Many additional CO2 data, not yet made public via the Carbon Dioxide Information Analysis Center (CDIAC), were retrieved from data originators, public websites and other data centres. All data were put in a uniform format following a strict protocol. Quality control was carried out according to clearly defined criteria. Regional specialists performed the quality control, using state-of-the-art web-based tools, specially developed for accomplishing this global team effort. SOCAT version 1.5 was made public in September 2011 and holds 6.3 million quality controlled surface CO2 data points from the global oceans and coastal seas, spanning four decades (1968–2007). Three types of data products are available: individual cruise files, a merged complete data set and gridded products. With the rapid expansion of marine CO2 data collection and the importance of quantifying net global oceanic CO2 uptake and its changes, sustained data synthesis and data access are priorities.

An assessment of the Atlantic and Arctic sea–air CO2 fluxes, 1990–2009

Abstract: The Atlantic and Arctic Oceans are critical components of the global carbon cycle Here we quantify the net sea–air CO2 flux, for the first time, across different methodologies for consistent time and space scales for the Atlantic and Arctic basins We present the long-term mean, seasonal cycle, interannual variability and trends in sea–air CO2 flux for the period 1990 to 2009, and assign an uncertainty to each We use regional cuts from global observations and modeling products, specifically a pCO2-based CO2 flux climatology, flux estimates from the inversion of oceanic and atmospheric data, and results from six ocean biogeochemical models Additionally, we use basin-wide flux estimates from surface ocean pCO2 observations based on two distinct methodologies Our estimate of the contemporary sea–air flux of CO2 (sum of anthropogenic and natural components) by the Atlantic between 40° S and 79° N is −049 ± 005 Pg C yr−1, and by the Arctic it is −012 ± 006 Pg C yr−1, leading to a combined sea–air flux of −061 ± 006 Pg C yr−1 for the two decades (negative reflects ocean uptake) We do find broad agreement amongst methodologies with respect to the seasonal cycle in the subtropics of both hemispheres, but not elsewhere Agreement with respect to detailed signals of interannual variability is poor, and correlations to the North Atlantic Oscillation are weaker in the North Atlantic and Arctic than in the equatorial region and southern subtropics Linear trends for 1995 to 2009 indicate increased uptake and generally correspond between methodologies in the North Atlantic, but there is disagreement amongst methodologies in the equatorial region and southern subtropics

Rates and mechanisms of turbulent dissipation and mixing in the Southern Ocean: Results from the Diapycnal and Isopycnal Mixing Experiment in the Southern Ocean (DIMES)

Abstract: turbulent dissipation rates are found to increase from O 1 � 10 � 10 Wk g � 1 �� in the Southeast Pacific to O 1 � 10 � 9 Wk g � 1 �� in the Scotia Sea, typically reaching 3 � 10 � 9 Wk g � 1 within a kilometer of the seabed. Enhanced levels of turbulent mixing are associated with strong near-bottom flows, rough topography, and regions where the internal wavefield is found to have enhanced energy, a less-inertial frequency content and a dominance of upward propagating energy. These results strongly suggest that bottomgenerated internal waves play a major role in determining the spatial distribution of turbulent dissipation in the ACC. The energy flux associated with the bottom internal wave generation process is calculated using wave radiation theory, and found to vary between 0.8 mW m � 2 in the Southeast Pacific and 14 mW m � 2 in the Scotia Sea. Typically, 10%–30% of this energy is found to dissipate within 1 km of the seabed. Comparison between turbulent dissipation rates inferred from finestructure parameterizations and microstructurederived estimates suggests a significant departure from wave-wave interaction physics in the near-field of wave generation sites.

Surface Ocean CO2 Atlas (SOCAT) gridded data products

Abstract: As a response to public demand for a well-documented, quality controlled, publically available, global surface ocean carbon dioxide (CO2) data set, the international marine carbon science community developed the Surface Ocean CO2 Atlas (SOCAT). The first SOCAT product is a collection of 6.3 million quality controlled surface CO2 data from the global oceans and coastal seas, spanning four decades (1968–2007). The SOCAT gridded data presented here is the second data product to come from the SOCAT project. Recognizing that some groups may have trouble working with millions of measurements, the SOCAT gridded product was generated to provide a robust, regularly spaced CO2 fugacity (fCO2) product with minimal spatial and temporal interpolation, which should be easier to work with for many applications. Gridded SOCAT is rich with information that has not been fully explored yet (e.g., regional differences in the seasonal cycles), but also contains biases and limitations that the user needs to recognize and address (e.g., local influences on values in some coastal regions).

Habitable Zone Lifetimes of Exoplanets around Main Sequence Stars

Abstract: The potential habitability of newly discovered exoplanets is initially assessed by determining whether their orbits fall within the circumstellar habitable zone of their star. However, the habitable zone (HZ) is not static in time or space, and its boundaries migrate outward at a rate proportional to the increase in luminosity of a star undergoing stellar evolution, possibly including or excluding planets over the course of the star's main sequence lifetime. We describe the time that a planet spends within the HZ as its “habitable zone lifetime.” The HZ lifetime of a planet has strong astrobiological implications and is especially important when considering the evolution of complex life, which is likely to require a longer residence time within the HZ. Here, we present results from a simple model built to investigate the evolution of the “classic” HZ over time, while also providing estimates for the evolution of stellar luminosity over time in order to develop a “hybrid” HZ model. These models re...

Stress-inducible phosphoprotein 1 has unique cochaperone activity during development and regulates cellular response to ischemia via the prion protein

Abstract: Stress-inducible phosphoprotein 1 (STI1) is part of the chaperone machinery, but it also functions as an extracellular ligand for the prion protein. However, the physiological relevance of these STI1 activities in vivo is unknown. Here, we show that in the absence of embryonic STI1, several Hsp90 client proteins are decreased by 50%, although Hsp90 levels are unaffected. Mutant STI1 mice showed increased caspase-3 activation and 50% impairment in cellular proliferation. Moreover, placental disruption and lack of cellular viability were linked to embryonic death by E10.5 in STI1-mutant mice. Rescue of embryonic lethality in these mutants, by transgenic expression of the STI1 gene, supported a unique role for STI1 during embryonic development. The response of STI1 haploinsufficient mice to cellular stress seemed compromised, and mutant mice showed increased vulnerability to ischemic insult. At the cellular level, ischemia increased the secretion of STI1 from wild-type astrocytes by 3-fold, whereas STI1 haploinsufficient mice secreted half as much STI1. Interesting, extracellular STI1 prevented ischemia-mediated neuronal death in a prion protein-dependent way. Our study reveals essential roles for intracellular and extracellular STI1 in cellular resilience.

Rapid cross-density ocean mixing at mid-depths in the Drake Passage measured by tracer release

Abstract: Diapycnal mixing (across density surfaces) is an important process in the global ocean overturning circulation1, 2, 3. Mixing in the interior of most of the ocean, however, is thought to have a magnitude just one-tenth of that required to close the global circulation by the downward mixing of less dense waters4. Some of this deficit is made up by intense near-bottom mixing occurring in restricted ‘hot-spots’ associated with rough ocean-floor topography5, 6, but it is not clear whether the waters at mid-depth, 1,000 to 3,000 metres, are returned to the surface by cross-density mixing or by along-density flows7. Here we show that diapycnal mixing of mid-depth (~1,500 metres) waters undergoes a sustained 20-fold increase as the Antarctic Circumpolar Current flows through the Drake Passage, between the southern tip of South America and Antarctica. Our results are based on an open-ocean tracer release of trifluoromethyl sulphur pentafluoride. We ascribe the increased mixing to turbulence generated by the deep-reaching Antarctic Circumpolar Current as it flows over rough bottom topography in the Drake Passage. Scaled to the entire circumpolar current, the mixing we observe is compatible with there being a southern component to the global overturning in which about 20 sverdrups (1 Sv = 106 m3 s−1) upwell in the Southern Ocean, with cross-density mixing contributing a significant fraction (20 to 30 per cent) of this total, and the remainder upwelling along constant-density surfaces. The great majority of the diapycnal flux is the result of interaction with restricted regions of rough ocean-floor topography.

p38 MAPK regulates cavitation and tight junction function in the mouse blastocyst.

Abstract: Blastocyst formation is essential for implantation and maintenance of pregnancy and is dependent on the expression and coordinated function of a series of proteins involved in establishing and maintaining the trans-trophectoderm ion gradient that enables blastocyst expansion. These consist of Na/K-ATPase, adherens junctions, tight junctions (TJ) and aquaporins (AQP). While their role in supporting blastocyst formation is established, the intracellular signaling pathways that coordinate their function is unclear. The p38 MAPK pathway plays a role in regulating these proteins in other cell types and is required for embryo development at the 8–16 cell stage, but its role has not been investigated in the blastocyst. Hypothesis p38 MAPK regulates blastocyst formation by regulating blastocyst formation gene expression and function. Methods Embryos were cultured from the early blastocyst stage for 12 h or 24 h in the presence of a potent and specific p38 MAPK inhibitor, SB 220025. Blastocyst expansion, hatching, gene family expression and localization, TJ function and apoptosis levels were analyzed. Results Inhibition of the p38 MAPK pathway reduced blastocyst expansion and hatching, increased tight junction permeability, affected TJP1 localization, reduced Aqp3 expression, and induced a significant increase in apoptosis. Conclusion The p38 MAPK pathway coordinates the overall events that regulate blastocyst formation.

Post-translational modification in the archaea: structural characterization of multi-enzyme complex lipoylation.

Abstract: Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multi-enzyme complexes, is essential for metabolism in aerobic bacteria and eukarya. In Escherichia coli, lipoylation is catalysed by LplA (lipoate protein ligase) or by LipA (lipoic acid synthetase) and LipB [lipoyl(octanoyl) transferase] combined. Whereas bacterial and eukaryotic LplAs comprise a single two-domain protein, archaeal LplA function typically involves two proteins, LplA-N and LplA-C. In the thermophilic archaeon Thermoplasma acidophilum, LplA-N and LplA-C are encoded by overlapping genes in inverted orientation (lpla-c is upstream of lpla-n). The T. acidophilum LplA-N structure is known, but the LplA-C structure is unknown and LplA-C's role in lipoylation is unclear. In the present study, we have determined the structures of the substrate-free LplA-N-LplA-C complex and E2lipD (dihydrolipoyl acyltransferase lipoyl domain) that is lipoylated by LplA-N-LplA-C, and carried out biochemical analyses of this archaeal lipoylation system. Our data reveal the following: (i) LplA-C is disordered but folds upon association with LplA-N; (ii) LplA-C induces a conformational change in LplA-N involving substantial shortening of a loop that could repress catalytic activity of isolated LplA-N; (iii) the adenylate-binding region of LplA-N-LplA-C includes two helices rather than the purely loop structure of varying order observed in other LplA structures; (iv) LplAN-LplA-C and E2lipD do not interact in the absence of substrate; (v) LplA-N-LplA-C undergoes a conformational change (the details of which are currently undetermined) during lipoylation; and (vi) LplA-N-LplA-C can utilize octanoic acid as well as lipoic acid as substrate. The elucidated functional inter-dependence of LplA-N and LplA-C is consistent with their evolutionary co-retention in archaeal genomes.

Ruthenium-Catalyzed Remote Electronic Activation of Aromatic CF Bonds

Abstract: The tandem isomerization and nucleophilic aromatic substitution of allylic fluoro-substituted benzylic alcohols is described for the first time. In the presence of the ruthenium complex Ru(PPh3)3(CO)(H) 2, 1-(4-fluorophenyl)prop-2-en-1-ol is converted into the corresponding para-amino ketone or para-phenolic substituted ketone.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus.

Abstract: The enzyme N-acetylneuraminate lyase (EC 4.1.3.3) is involved in the metabolism of sialic acids. Specifically, the enzyme catalyzes the retro-aldol cleavage of N-acetylneuraminic acid to form N-acetyl-d-mannosamine and pyruvate. Sialic acids comprise a large family of nine-carbon amino sugars, all of which are derived from the parent compound N-acetylneuraminic acid. In recent years, N-acetylneuraminate lyase has received considerable attention from both mechanistic and structural viewpoints and has been recognized as a potential antimicrobial drug target. The N-acetylneuraminate lyase gene was cloned from methicillin-resistant Staphylococcus aureus genomic DNA, and recombinant protein was expressed and purified from Escherichia coli BL21 (DE3). The enzyme crystallized in a number of crystal forms, predominantly from PEG precipitants, with the best crystal diffracting to beyond 1.70 A resolution in space group P21. Molecular replacement indicates the presence of eight monomers per asymmetric unit. Understanding the structural biology of N-acetylneuraminate lyase in pathogenic bacteria, such as methicillin-resistant S. aureus, will provide insights for the development of future antimicrobials.

Endogenous Folate Accumulation in Oocytes and Preimplantation Embryos and Its Epigenetic Implications

Abstract: During mammalian development, chromatin is dynamically reprogrammed first in developing gametes and then after fertilization in the preimplantation embryo [1, 2]. In gametes, following an erasure phase that removes somatic DNA methylation, sex-specific DNA methylation is acquired. For female germ cells, this acquisition of methylation occurs in the growing oocyte, with an increasing progression of DNA methylation coincident with increasing oocyte size [1]. By the time the oocyte is fully grown, acquisition of DNA methylation is complete. During preimplantation development, DNA methylation is maintained primarily at imprinted genes and repetitive elements during global methylation erasure. This is followed by initiation of de novo DNA methylation late in preimplantation development [1]. During these chromatin remodeling periods, dynamic changes in histone methylation are also occurring. Importantly, these methylation patterns are critical to the overall health of gametes and embryos [1–4]. Both DNA and histone methylation are catalyzed by methyltransferases, which transfer a methyl group from the universal donor, S-adenosylmethionine (SAM), to CpG dinucleotides or histone tails [3–5]. Production of SAM is dependent on the 1-carbon folate pathway [3–5]. Thus, folates play a fundamental role in regulating DNA and histone methylation [3, 4]. In keeping with the critical reprogramming events described above, folate accumulation during oocyte and preimplantation development likely is essential to foster correct DNA and histone methylation patterns during gametogenesis and early development. Folates are essential nutrients that are acquired from our diet [3, 4]. Thus, a key question is how the oocyte and early embryo acquire and take up their folate pools. This question was address by Kooistra et al. [5] in their paper ‘‘Folate Transport in Mouse Cumulus-Oocyte Complexes and Preimplantation Embryos’’ published in this issue of Biology of Reproduction. Using gene expression studies, Kooistra et al. [5] show that mouse cumulus-oocyte complexes and oocytes harbor transcripts for the reduced folate carrier SLC19A1, an anion exchanger. In preimplantation embryos, Slc19a1 transcript abundance is very low due to the lack of embryonic gene activation. By comparison, folate receptor FOLR1 mRNA was present in preimplantation embryos beginning at the 2-cell stage but was lacking in oocytes and zygotes. This ying-yang expression pattern indicates that two distinct mechanisms may be operating in cumulus-oocyte complexes and preimplantation embryos [5]. To functionally characterize SLC19A1 and FOLR1 activity in cumulus-oocyte complexes, germinal vesicle oocytes, and mouse preimplantation embryos, transport experiments were employed to measure uptake of folates and the antifolate methotrexate, whereas biochemical inhibitors were used to distill the uptake mechanisms. The results indicate that folate transport occurs predominately through SLC19A1 in cumulusoocyte complexes but that FOLR1 is the principal uptake mechanism in embryos from the 2-cell through blastocyst stages. However, most interesting are the final experiments showing that SLC19A1 regulates cumulus cell folate uptake, with little to no uptake in fully grown oocytes. Thus, we are left with an intriguing question: What is the origin of endogenous folates in oocytes and zygotes? A careful look at the methods shows that fully grown oocytes were analyzed by Kooistra et al. Thus, it is reasonable to conclude that oocyte folate accumulation must occur during the early stages of folliculogenesis. Experiments now need to examine growing oocytes to determine when and through what mechanism folate uptake occurs. We are also left with the intriguing paradox that in vitro embryo development often occurs in non-folate supplemented culture medium. Does this mean that the early embryo relies on oocyte folate stores? And if so, why do early embryos have functional FOLR1 folate uptake? Future studies will also need to address whether variation in folate store accumulation is an important determinant of oocyte maturation and eventual embryonic developmental competence. We must also consider the implication of the Kooistra et al. study on DNA and histone methylation. With regard to DNA methylation in fully grown oocytes, acquisition would be complete. Thus, there may be no further need for folate uptake in fully grown oocytes. However, what would be the ramifications if oocytes failed to store sufficient levels of folates? One repercussion of reduced folate stores during the methylation acquisition phase in growing oocytes may be aberrant establishment of imprinted methylation. Interestingly, we have observed that initiation of methylation acquisition is impaired at the imprinted Peg1 gene in connexin 37-null oocytes [6]. We postulated that this may be due to reduced stores of a critical metabolite normally transported from granulosa cells to the oocyte via gap junctions. Another Correspondence: E-mail: mmann22@uwo.ca

Ruthenium‐Catalyzed Remote Electronic Activation of Aromatic C—F Bonds.

Abstract: For the first time the tandem isomerization and nucleophilic aromatic substitution of allylic fluoro-substituted benzylic alcohols is described.

Exact natural frequencies of multi-level elastically connected taut strings and related problems

Abstract: The dynamics of a family of simple, but extremely useful structural elements is governed by a second order Sturm-Liouville equation. This equation allows for the uniform distribution of mass and stiffness and enables the motion of strings and shear beams, together with the axial and torsional motion of bars to be described exactly. As a result, each member type in this family has been treated exhaustively when considered as a single member or when joined contiguously to others. However, when such members are linked in parallel by uniformly distributed elastic interfaces, their complexity becomes significantly more intractable and it is this class of structures that has led to renewed interest and which forms the basis of the work that follows. Initially, differential equations governing the coupled motion of the system are developed from first principles. These are organised into the form of a generalised linear symmetric eigenvalue problem, from which a family of uncoupled differential operators can be established. These operators define a series of exact substitute systems that together describe the complete motion of the original structure. These equations can then be used in either of two ways. In their most powerful form they can be developed into exact dynamic stiffness matrices that enable all the powerful features of the finite element method to be utilised. This subsequently enables sets of members carrying point masses and subject to point spring supports to be analysed easily. Alternatively, the equations are able to yield an exact relational model that links any uncoupled frequency of an original member to the corresponding set of coupled system frequencies. This approach enables ‘back of the envelope calculations’ to be undertaken quickly and efficiently. The exact mode shapes of the original structure can be recovered in either case. Due to space limitations, only aspects of the first technique are described briefly herein, but both are covered exhaustively elsewhere [1].