Life history patterns shape energy allocation among fishes on coral reefs

Although critically important, the link between animal life histories and ecosystem energetics is seldom explored. In the pursuit of ecological simplification, ecosystem properties are typically described by models based on static counts, where organisms are aggregated into trophic- or size-based groups. Consequently, output is often based on an assumption that larger group biomass equals greater energetic contribution. Here, we modelled the individual growth of over 58,000 fishes from 74 genera within a coral reef ecosystem to investigate the role and importance of taxon-specific life histories to the division, spatial distribution and relative contribution of biomass production within 14 coral reef fish families. Rank changes among families in standing biomass to biomass production indicated that small cryptic families (e.g. Gobiidae and Blenniidae) exhibit collective growth potentials equal to or exceeding those of many other common families composed of individuals with body-sizes 1–3 orders of magnitude larger. Remaining at high risk of predation throughout their lives as a consequence of their small size, these cryptic fishes also provide a constant food resource and supply of reproductive energy to coral reefs throughout the year. Enhanced further by the strength and diversity of their trophic relationships within food webs, the highly productive nature of these small cryptic fishes suggests they make a substantial contribution to the flow of energy in coral reef ecosystems via predatory pathways. It appears that life histories leave a strong imprint on ecosystem energy fluxes and illustrate the importance of incorporating taxon-specific features when assigning values to key ecosystem processes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A structural alignment kernel for protein structures

MOTIVATION: This work aims to develop computational methods to annotate protein structures in an automated fashion. We employ a support vector machine (SVM) classifier to map from a given class of structures to their corresponding structural (SCOP) or functional (Gene Ontology) annotation. In particular, we build upon recent work describing various kernels for protein structures, where a kernel is a similarity function that the classifier uses to compare pairs of structures. RESULTS: We describe a kernel that is derived in a straightforward fashion from an existing structural alignment program, MAMMOTH. We find in our benchmark experiments that this kernel significantly out-performs a variety of other kernels, including several previously described kernels. Furthermore, in both benchmarks, classifying structures using MAMMOTH alone does not work as well as using an SVM with the MAMMOTH kernel. AVAILABILITY: http://noble.gs.washington.edu/proj/3dkernel     

Use of isotope ratio mass spectrometry to detect doping with oral testosterone undecanoate: inter-individual variability of 13C/12C ratio

The metabolic effect of multiple oral testosterone undecanoate (TU) doses over 4 weeks was assessed in seven voluntary men. The protocol was designed to detect accumulation of the substance by choosing the appropriate spot urines collections time and to study the urinary clearance of the substance after weeks of treatment. Urines were analysed by a new GC/C/isotope ratio mass spectrometry (IRMS) method to establish the delta(13)C-values of testosterone metabolites (androsterone and etiocholanolone) together with an endogenous reference compound (16(5alpha)-androsten-3alpha-ol). The significant differences in inter-individual metabolism following TU intake was illustrated by large variations in delta(13)C-values of both T metabolites (maximum Deltadelta(13)C-values = 5.5 per thousand), as well as by very stable longitudinal T/E profiles and carbon isotopic ratios in the first hours following administration. According to T/E ratios and delta(13)C-values, the washout period after 80 mg TU intake was less than 48 h for all subjects and no accumulation phenomenon was observed upon chronic oral administration.     

A peptide mimicking the C-terminal part of the reactive center loop induces the transition to the latent form of plasminogen activator inhibitor type-1

Plasminogen activator inhibitor-1 (PAI-1) is the primary inhibitor of plasminogen activators (uPA and tPA) and thus plays a central role in fibrinolysis. The spontaneous insertion of its reactive centre loop (RCL) into β-sheet A is responsible for its irreversible conversion into the inactive latent form. In this study, we used two peptides mimicking residues P14-P9 and P8-P3 of the RCL so as to understand this dynamic process. We show that both peptides inhibit the formation of PAI-1/uPA and PAI-1/tPA complexes via two different mechanisms. Targeting the N-terminal part of the loop induces the cleavage of PAI-1 by the proteases uPA/tPA while targeting its C-terminal part greatly favors the irreversible formation of latent PAI-1.     

Differential expression of two somatostatin genes during zebrafish embryonic development

We have identified the cDNAs of two new zebrafish preprosomatostatins, PPSS1 and PPSS3, in addition to the previously cloned PPSS2 (Argenton et al., 1999). PPSS1 is the orthologue of mammalian PPSSs, with a conserved C-terminal SS-14 sequence, PPSS2 is a divergent SS precursor and PPSS3 is a cortistatin-like prohormone. Using whole-mount in situ hybridisation, we have analysed the expression of PPSS1 and PPSS2 in zebrafish embryos up to 5 days post fertilisation. PPSS1 was expressed in the developing pancreas and central nervous system (CNS), whereas PPSS2 expression was exclusively pancreatic. In the CNS, PPSS1 was detected in several areas, in particular in the vagal motor nucleus and in cells that pioneer the tract of the postoptic commissure. PPSS1 was also expressed transiently in the telencephalon and spinal motor neurons. In all areas but the telencephalon PPSS1 was coexpressed with islet-1.     

Rapid high-performance liquid chromatographic determination with fluorescence detection of furosemide in human body fluids and its confirmation by gas chromatography—mass spectrometry

Furosemide (FD; Lasix^®) is a loop diuretic which strongly increases both urine flow and electrolyte urinary excretion. Healthy volunteers were administered 40 mg orally (dissolved in water) and concentrations of FD were determined in serum and urine for up to 6 h for eight subjects, who absorbed water at a rate of 400 ml/h. Quantification was performed by HPLC with fluorescence detection (excitation at 233 nm, emission at 389 nm) with a limit of detection of 5 ng/ml for a 300-μl sample. The elution of FD was completed within 4 min using a gradient of acetonitrile concentration rising from 30 to 50% in 0.08 M phosphoric acid. The delay to the peak serum concentration ranged from 60 to 120 min. FD was still easily measurable in the sera from all subjects 6 h after administration. In urine, the excretion rates reached their maximum between 1 and 3 h. The total amount of FD excreted in the urine averaged 11.2 mg (range 7.6–14.0 mg), with a mean urine volume of 3024 ml (range 2620–3596 ml). Moreover, the urine density was lower than 1.010 (recommended as an upper limit in doping analyses to screen diuretics) only for 2 h. An additional volunteer was administered 40 mg of FD and his urine was collected over a longer period. FD was still detectable 48 h after intake. Gas chromatography—mass spectrometry with different types of ionization was used to confirm the occurrence of FD after permethylation of the extract. Negative-ion chemical ionization, with ammonia as reactant gas, was found to be the most sensitive method of detection.     

CO2 emission from mineral soils following land‐cover change in Brazil

This paper presents a first approximation of net CO₂ fluxes from mineral soil due to land use, land‐use changes and forestry (LULUCF) activities in Brazil for the periods 1970–90 and 1975–95. The methodology employed is an adaptation of the approach proposed by the IPCC in ‘Revised 1996 guidelines for national greenhouse gas inventories’, which is based on the variations in soil C stocks as a function of changes in land‐use activities. The calculation was done separately for each Brazilian state and subsequently summarized for all of Brazil. The annual fluxes for Brazil indicate a net emission of CO₂ to the atmosphere, which decreased from 93.3 Tg CO₂ for the period 1970–90 to 46.4 Tg CO₂ for the period 1975–95. This corresponded to yearly net emission rates of 11.0 g CO₂ m^?2 year^?1 for the 1970–90 period and 5.5 g CO₂ m^?2 year^?1 for the 1975–95 period. Within each administrative region, considerable differences in the yearly emission rates between the states could be observed. Several sources of uncertainties could be identified. The most important uncertainties were linked to the impact factor values, which represent changes in native C stock associated with conversion of the native vegetation to agricultural use.