[1] We investigate the functioning of the ocean's biological pump by analyzing the vertical transfer efficiency of particulate organic carbon (POC). Data evaluated include globally distributed time series of sediment trap POC flux, and remotely sensed estimates of net primary production (NPP) and sea surface temperature (SST). Mathematical techniques are developed to compare these temporally discordant time series using NPP and POC flux climatologies. The seasonal variation of NPP is mapped and shows regional-and basin-scale biogeographic patterns reflecting solar, climatic, and oceanographic controls. Patterns of flux are similar, with more high-frequency variability and a subtropical-subpolar pattern of maximum flux delayed by about 5 days per degree latitude increase, coherent across multiple sediment trap time series. Seasonal production-to-flux analyses indicate during intervals of bloom production, the sinking fraction of NPP is typically half that of other seasons. This globally synchronous pattern may result from seasonally varying biodegradability or multiseasonal retention of POC. The relationship between NPP variability and flux variability reverses with latitude, and may reflect dominance by the large-amplitude seasonal NPP signal at higher latitudes. We construct algorithms describing labile and refractory flux components as a function of remotely sensed NPP rates, NPP variability, and SST, which predict POC flux with accuracies greater than equations typically employed by global climate models. Globally mapped predictions of POC export, flux to depth, and sedimentation are supplied. Results indicate improved ocean carbon cycle forecasts may be obtained by combining satellite-based observations and more mechanistic representations taking into account factors such as mineral ballasting and ecosystem structure.Citation: Lutz, M. J., K. Caldeira, R. B. Dunbar, and M. J. Behrenfeld (2007), Seasonal rhythms of net primary production and particulate organic carbon flux to depth describe the efficiency of biological pump in the global ocean,

[1] Carbon transport within sinking biogenic matter in the ocean contributes to the uptake of CO 2 from the atmosphere. Here we assess the extent to which particulate organic carbon (POC) transport to the ocean's interior can be predicted from primary production or export flux. Relationships between POC flux and depth are generally described by a uniform power law or rational decrease with depth, scaled to new or total primary production of POC. While these parameterizations of flux are used in most quantitative biogeochemical models, they are based on data sets from a limited geographic and depth range. We examine these relationships through a review of parameters derived from 14 C uptake experiments, regional remote sensing, 234 Th studies, nitrogen balances, and sediment trap records. Ocean regions considered include sites studied by the Joint Global Ocean Flux Study, Hawaii Ocean Time-series, and Bermuda Atlantic Time-series Study programs and involve observed and radiochemically corrected flux to depth. We demonstrate regional variability in the efficiency of the biological pump to transport organic carbon from surface waters to the ocean's interior. Commonly applied flux relationships, while representative of some areas of the ocean, generally overestimate flux to depth. We estimate that the fraction of carbon transported as POC to depths greater than 1.5 km ranges between 0.10 and 8.8% (1.1% average) of primary production and between 0.28 and 30% (5.7% average) of export from the base of the euphotic zone. We develop empirical parameterizations of flux to depth using region-specific constants. Using a one-dimensional ocean model, we predict that the residence time of biogenic carbon may vary by up to 2 orders of magnitude depending on the regional efficiency of export and vertical transport.

As the next step towards generating a synthetic biology from artificial genetic information systems, we have examined variants of HIV reverse transcriptase (RT) for their ability to synthesize duplex DNA incorporating the non-standard base pair between 2,4-diaminopyrimidine (pyDAD), a pyrimidine presenting a hydrogen bond 'donor-acceptor-donor' pattern to the complementary base, and xanthine (puADA), a purine presenting a hydrogen bond 'acceptor-donor-acceptor' pattern. This base pair fits the Watson-Crick geometry, but is joined by a pattern of hydrogen bond donor and acceptor groups different from those joining the GC and AT pairs. A variant of HIV-RT where Tyr 188 is replaced by Leu, has emerged from experiments where HIV was challenged to grow in the presence of drugs targeted against the RT, such as L-697639, TIBO and nevirapine. These drugs bind at a site near, but not in, the active site. This variant accepts the pyDAD-puADA base pair significantly better than wild type HIV-RT, and we used this as a starting point. A second mutation, E478Q, was introduced into the Y188L variant, in the event that the residual nuclease activity observed is due to the RT, and not a contaminant. The doubly mutated RT incorporated the non-standard pair with sufficient fidelity that the variant could be used to amplify oligonucleotides containing pyDAD and puADA through several rounds of a polymerase chain reaction (PCR) without losing the non-standard base pair. This is the first time where DNA containing non-standard base pairs with alternative hydrogen bonding patterns has been amplified by a full PCR. This work also illustrates a research strategy that combines in clinico pre-evolution of proteins followed by rational design to obtain an enzyme that meets a particular technological specification.

Mammalian DNA polymerases alpha and epsilon, the Klenow fragment of Escherichia coli DNA polymerase I and HIV-1 reverse transcriptase (RT) were examined for their ability to incorporate components of an expanded genetic alphabet in different forms. Experiments were performed with templates containing 2'-deoxyxanthosine (dX) or 2'-deoxy-7-deazaxanthosine (c7dX), both able to adopt a hydrogen bonding acceptor-donor-acceptor pattern on a purine nucleus (puADA). Thus these heterocycles are able to form a non-standard nucleobase pair with 2,4-diaminopyrimidine (pyDAD) that fits the Watson-Crick geometry, but is joined by a non-standard hydrogen bonding pattern. HIV-1 RT incorporated d(pyDAD)TP opposite dX with a high efficiency that was largely independent of pH. Specific incorporation opposite c7dX was significantly lower and also independent of pH. Mammalian DNA polymerases alpha and epsilon from calf thymus and the Klenow fragment from E. coli DNA polymerase I failed to incorporate d(pyDAD)TP opposite c7dX.