Carbon System Measurements and Potential Climatic Drivers at a Site of Rapidly Declining Ocean pH

We explored changes in ocean pH in coastal Washington state, USA, by extending a decadal-scale pH data series, by reporting independent measures of dissolved inorganic carbon (DIC), spectrophotometric pH, and total alkalinity (TA), by exploring pH patterns over larger spatial scales, and by probing for long-term trends in environmental variables reflecting potentially important drivers of pH. We found that pH continued to decline in this area at a rapid rate, that pH exhibited high natural variability within years, that our measurements of pH corresponded well to spectrophotometric pH measures and expected pH calculated from DIC/TA, and that TA estimates based on salinity predicted well actual alkalinity. Multiple datasets reflecting upwelling, including water temperature, nutrient levels, phytoplankton abundance, the NOAA upwelling index, and data on local wind patterns showed no consistent trends over the period of our study. Multiple datasets reflecting precipitation change and freshwater runoff, including precipitation records, local and regional river discharge, salinity, nitrate and sulfate in rainwater, and dissolved organic carbon (DOC) in rivers also showed no consistent trends over time. Dissolved oxygen did not decline over time, indicating that long-term changes did not result from shifts in contributions of respiration to pH levels. These tests of multiple potential drivers of the observed rapid rate of pH decline indicate a primary role for inorganic carbon and suggest that geochemical models of coastal ocean carbon fluxes need increased investigation.     

Construction of validated, non-redundant composite protein sequence databases

A strategy has been developed for the construction of a validated, comprehensive composite protein sequence database. Entries are amalgamated from primary source data bases by a largely automated set of processes in which redundant and trivially different entries are eliminated. A modular approach has been adopted to allow scientific judgement to be used at each stage of database processing and amalgamation. Source databases are assigned a priority depending on the quality of sequence validation and commenting. Rejection of entries from the lower priority database, in each pairwise comparison of databases, is carried out according to optionally defined redundancy criteria based on sequence segment mismatches. Efficient algorithms for this methodology are embodied in the COMPO software system. COMPO has been applied for over 2 years in construction and regular updating of the OWL composite protein sequence database from the source databases NBRF-PIR, SWISS-PROT, a GenBank translation retrieved from the feature tables, NBRF-NEW, NEWAT86, PSD-KYOTO and the sequences contained in the Brookhaven protein structure databank. OWL is part of the ISIS integrated data resource of protein sequence and structure [Akrigg et al. (1988) Nature, 335, 745-746]. The modular nature of the integration process greatly facilitates the frequent updating of OWL following releases of the source databases. The extent of redundancy in these sources is revealed by the comparison process. The advantages of a robust composite database for sequence similarity searching and information retrieval are discussed.     

Expression of the Escherichia coli glutamate dehydrogenase gene in the cyanobacterium Synechococcus PCC6301 causes ammonium tolerance

The unicellular cyanobacterium Synechococcus PCC6301 lacks a hybridisable homologue of the strongly conserved gdhA gene of E. coli that encodes NADP-specific glutamate dehydrogenase. This is consistent with the failure to find this enzyme in extracts of the cyanobacterium. The E. coli gdhA gene was transferred to Synechococcus PCC6301 by transformation with an integrative vector. High levels of glutamate dehydrogenase activity, similar to those found in ammonium grown E. coli cells, were found in these transformants. These transformed cyanobacteria displayed an ammonium tolerant phenotype, consistent with the action of their acquired glutamate dehydrogenase activity as an ammonium detoxification mechanism. Minor differences in colony size and in growth at low light intensity were also observed.     

Bioenergetics of growth of a cyprinid, Phoxinus phoxinus: the effect of ration, temperature and body size on food consumption, faecal production and nitrogenous excretion

Food consumption, faecal production and nitrogen excretion by minnows, Phoxinus phoxinus , weighing 1–5.5 g were studied at five rations ranging from starvation to ad libitum and four temperatures ranging from 5 to 15°C.
The maximum rate of food consumption (C_max) was related to body weight ( W ) and temperature ( T ) by the relationship: C _max= aW^b1T^b2 . There were significant daily variations in C_max, which tended to decline over time. Absorption efficiency increased with increasing ration size and decreasing temperature. Body weight had no significant effect on the faecal production. The equation F = a C^b1e^b2 T described the relationship between faecal production ( F ), food consumption ( C ) and temperature. Ammonia-N predominated over urea-N in the excreta of most experimental fish. The proportion of urea-N in the total nitrogen excreted was generally higher at lower rations than at higher rations. Rates of nitrogen excretion increased with increased ration size and were, to a lesser extent, influenced by temperature. Body weight had no significant effect on the nitrogen excretion by feeding minnows. The equation N = a+b_lT+b₂C described the effects of food consumption and temperature on nitrogen excretion ( N ) other than urea-N excretion. The relationship between urea-N excretion ( N_u ), food consumption and temperature was described by the equation N_u= ae^b1T ((C+1) ^b 2.
On the average, 11 % of food energy was lost in faecal production and nitrogen excretion by minnows feeding on whiteworms, Enchytraeus spp.     

Appetite and growth compensation in the European minnow,Phoxinus phoxinus (Cyprinidae), following short periods of food restriction

Synopsis Changes in the daily appetite and weekly growth rates of individual adult minnows,Phoxinus phoxinus, on ad libitum rations were recorded before and after they had experienced 4 or 16 days of food restriction. Feeding levels during the restriction periods were either starvation or a maintenance ration. The latter was estimated from a previously determined regression model. Water temperature was 15°C and the photoperiod 9L15D in all experiments. The mean weight of fish used ranged from 1.06 to 2.15 g. The 4 day restriction had no detectable effects on appetite or growth. After the 16 day restriction, the minnows showed hyperphagia and had increased specific growth rates and growth efficiencies compared with control fish. The compensatory increases in appetite and growth were not sustained and within three weeks had declined to levels not significantly different from those of the control fish. At the end of the experiments, there were no significant differences between the mean weights or cumulative food consumption of the restricted and control groups. The results suggest that adult minnows regulate their appetite and growth rate in relation to their previous nutritional history.     

Characterization of the binding of the anti-sickling compound, BW12C, to haemoglobin.

The anti-sickling agent BW12C [Beddell, Goodford, Kneen, White, Wilkinson & Wootton (1984) Br. J. Pharmacol. 82, 397-407] was designed to left-shift the oxygen saturation curve of haemoglobin (HbA) by preferential binding to the oxy conformation at a single site between the terminal amino groups of the alpha-chains through Schiff's base formation, ionic and hydrophobic interactions. In the present work, Schiff's base linkages formed with [14C]BW12C were reduced with NaBH4 and the alpha- and beta-globin chains separated. Under oxy conditions at a molar ratio of 2:1, the covalently bound BW12C is localized almost exclusively on a single alpha-chain; tryptic digestion confirms the terminal amino group (alpha 1-valine) as the reaction site, in accord with the design hypothesis. However, about half the labelled BW12C is released on tetramer disruption, suggesting the presence of additional non-covalent binding. Under deoxy conditions, alpha- and beta-chains are labelled approximately equally, and at higher molar ratios additional binding in both oxy and deoxy conditions is seen. Isoelectric-focusing studies under oxy conditions show a complex pattern of modified bands for both HbA and HbA1c (blocked beta-terminal amino groups) but no modification for HbA carbamylated at both alpha- and beta-terminal amino groups or at the alpha-chains only, again confirming the alpha-terminal amino region as the main interaction site. Equilibrium dialysis measurements under oxy conditions indicate two strong binding sites with a binding constant of less than 10(-6) M and a number of weaker binding sites. The present data thus confirm that BW12C binds at the intended locus but reveal additional non-covalent binding at an undefined site, and weaker binding through Schiff's base formation with other amino groups.     

Feeding and growth of juvenile sea bass: the effect of ration and temperature on growth rate and efficiency

The effect of ration on the growth of pairs of juvenile sea bass Dicentrarchus labrax fed squid mantle was recorded at four temperatures: 6, 10, 14 and 18) C, covering the range typical of Welsh coastal waters. Initial weight of the fish ranged from 2.8 to 15.9 g. A predictive model for the maximum meal size (M_max) at temperatures between 10 and 18) C, accounted for 95% of the variance in lnM_max. Even when offered excess food, bass at 6) C had a low rate of food consumption [0.19% body weight (BW) day^?1] and lost weight (G=?0.04% day^?1). Predictive regression models for specific growth rate (G) accounted for 86% of the variance at reduced rations and 70% at maximum meals. The relationship between G (calculated for total biomass per tank) and ration was a decelerating curve. G at maximum meals increased with temperature, at lower rations G decreased with temperature. For a pair of bass with a combined weight of 15 g, predicted maintenance ration ranged between 0.7 and 2.3% BW day^?1 and increased with temperature. Maximum meal size was more sensitive to temperature than maintenance ration. At 18) C optimum ration was 7.4% BW day^?1. At lower temperatures, the optimum ration was the maximum meal. The maximum gross growth efficiency was 17.4% at 18) C. Mean absorption efficiency was 94.8%. Ration level had no significant effect on absorption efficiency, which was lowest at 6) C. Condition indices (Fulton condition factor, wet and dry liver—somatic indices and body depth index) increased with meal size at all temperatures except 6) C. An increase in temperature between 10 and 18) C generally resulted in a decrease in condition indices at a given ration. When comparisons were made at a given standard length, gut and carcass weight increased with ration. Visceral fat and gut weight decreased with increased temperature.