Global Self-Organization of the Cellular Metabolic Structure

Background: Over many years, it has been assumed that enzymes work either in an isolated way, or organized in small catalytic groups. Several studies performed using "metabolic networks models'' are helping to understand the degree of functional complexity that characterizes enzymatic dynamic systems. In a previous work, we used "dissipative metabolic networks'' (DMNs) to show that enzymes can present a self-organized global functional structure, in which several sets of enzymes are always in an active state, whereas the rest of molecular catalytic sets exhibit dynamics of on-off changing states. We suggested that this kind of global metabolic dynamics might be a genuine and universal functional configuration of the cellular metabolic structure, common to all living cells. Later, a different group has shown experimentally that this kind of functional structure does, indeed, exist in several microorganisms. Methodology/Principal Findings: Here we have analyzed around 2.500.000 different DMNs in order to investigate the underlying mechanism of this dynamic global configuration. The numerical analyses that we have performed show that this global configuration is an emergent property inherent to the cellular metabolic dynamics. Concretely, we have found that the existence of a high number of enzymatic subsystems belonging to the DMNs is the fundamental element for the spontaneous emergence of a functional reactive structure characterized by a metabolic core formed by several sets of enzymes always in an active state. Conclusions/Significance: This self-organized dynamic structure seems to be an intrinsic characteristic of metabolism, common to all living cellular organisms. To better understand cellular functionality, it will be crucial to structurally characterize these enzymatic self-organized global structures.

The biological sense of smell: olfactory search behavior and a metabolic view for olfactory perception

Part I of the thesis describes the olfactory searching and scanning behaviors of rats in a wind tunnel, and a detailed movement analysis of terrestrial arthropod olfactory scanning behavior. Olfactory scanning behaviors in rats may be a behavioral correlate to hippocampal place cell activity.

Part II focuses on the organization of olfactory perception, what it suggests about a natural order for chemicals in the environment, and what this in tum suggests about the organization of the olfactory system. A model of odor quality space (analogous to the "color wheel") is presented. This model defines relationships between odor qualities perceived by human subjects based on a quantitative similarity measure. Compounds containing Carbon, Nitrogen, or Sulfur elicit odors that are contiguous in this odor representation, which thus allows one to predict the broad class of odor qualities a compound is likely to elicit. Based on these findings, a natural organization for olfactory stimuli is hypothesized: the order provided by the metabolic process. This hypothesis is tested by comparing compounds that are structurally similar, perceptually similar, and metabolically similar in a psychophysical cross-adaptation paradigm. Metabolically similar compounds consistently evoked shifts in odor quality and intensity under cross-adaptation, while compounds that were structurally similar or perceptually similar did not. This suggests that the olfactory system may process metabolically similar compounds using the same neural pathways, and that metabolic similarity may be the fundamental metric about which olfactory processing is organized. In other words, the olfactory system may be organized around a biological basis.

The idea of a biological basis for olfactory perception represents a shift in how olfaction is understood. The biological view has predictive power while the current chemical view does not, and the biological view provides explanations for some of the most basic questions in olfaction, that are unanswered in the chemical view. Existing data do not disprove a biological view, and are consistent with basic hypotheses that arise from this viewpoint.

Oceanographic Profiling Observations MOCE-4 Cruise: 26 January to 12 February 1998

This report contains results from the fourth cruise of the MODIS Optical Characterization Experiment (MOCE). Also resented are oceanographic data from two MOBY maintenance cruises L-20 and L-25. The MOCE4 cruise was the first NOAAINESDIS-Ied SeaWiFS Initialization cruise during which a variety ofspectroradiometric observations ofthe upper water column and atmosphere were made by investigators from NOAA, the University of Miami, CHORS and MLML. Data presented in this report were obtained by oceanographic CTD profiler: salinity, temperature, dissolved oxygen, beam attenuation and chlorophyll-a fluorescence~ and by water samplers: total suspended matter and suspended organic carbon and nitrogen, salinity and dissolved oxygen. (PDF contains 142 pages).

Oceanographic Profiling and Spectroradiometer Observations from the MOCE-2 Cruise: 28 March to 14 April 1993

This report contains results from the second cruise of the Modis Optical Characterization Experiment (MOCE). Data presented here were obtained on the Mexican Research Vessel El Puma between 29 March and 13 April along the Pacific coast of Baja California and in the Gulf of California. Three types of data are reported: high spectral resolution radiometry at three depths for 13 stations; salinity, temperature beam attenuation and chlorophyll-a fluorescence, profiles at the same stations; and total suspended matter and suspended organic carbon and nitrogen.(PDF is 90 pages.)

Oceanographic Profiling Observations from the MOBY-L7 Cruise: 25 to 30 June 1994

This report contains CTD profiling results from the seventh cruise to the Marine Optics Buoy (MOBY) site near the Island of Lanai. Data presented here were obtained on the University of Hawaii Research Vessel Moana Wave between 26 and 30 June 1994. Two types of data are reported: vertical profile observations of salinity, temperature beam attenuation and chlorophyll-a fluorescence, profiles; and total suspended matter and suspended organic carbon and nitrogen taken from water samplers at those stations.

Oceanographic Profiling Observations from the MOCE-3 Cruise: 27 October to 15 November 1994

This report contains results from the third cruise of the Marine Optical Characterization Experiment (Fig. 1). A variety of spectroradiometric observations of the upper water column and atmosphere were made by investigators from the University of Miami, NOAA, CHORS and MLML. Data presented here were obtained by oceanographic CTD profiler: salinity, temperatllre, dissolved oxygen, beam attenuation and chlorophyll-a fluorescence; and by water samplers: total suspended matter and suspended organic carbon and nitrogen, salinity, and dissolved oxygen.

Physical, Metabolic, and Energetic Investigations of Methane-Metabolizing Microbial Communities

Understanding the roles of microorganisms in environmental settings by linking phylogenetic identity to metabolic function is a key challenge in delineating their broad-scale impact and functional diversity throughout the biosphere. This work addresses and extends such questions in the context of marine methane seeps, which represent globally relevant conduits for an important greenhouse gas. Through the application and development of a range of culture-independent tools, novel habitats for methanotrophic microbial communities were identified, established settings were characterized in new ways, and potential past conditions amenable to methane-based metabolism were proposed. Biomass abundance and metabolic activity measures – both catabolic and anabolic – demonstrated that authigenic carbonates associated with seep environments retain methanotrophic activity, not only within high-flow seep settings but also in adjacent locations exhibiting no visual evidence of chemosynthetic communities. Across this newly extended habitat, microbial diversity surveys revealed archaeal assemblages that were shaped primarily by seepage activity level and bacterial assemblages influenced more substantially by physical substrate type. In order to reliably measure methane consumption rates in these and other methanotrophic settings, a novel method was developed that traces deuterium atoms from the methane substrate into aqueous medium and uses empirically established scaling factors linked to radiotracer rate techniques to arrive at absolute methane consumption values. Stable isotope probing metaproteomic investigations exposed an array of functional diversity both within and beyond methane oxidation- and sulfate reduction-linked metabolisms, identifying components of each proposed enzyme in both pathways. A core set of commonly occurring unannotated protein products was identified as promising targets for future biochemical investigation. Physicochemical and energetic principles governing anaerobic methane oxidation were incorporated into a reaction transport model that was applied to putative settings on ancient Mars. Many conditions enabled exergonic model reactions, marking the metabolism and its attendant biomarkers as potentially promising targets for future astrobiological investigations. This set of inter-related investigations targeting methane metabolism extends the known and potential habitat of methanotrophic microbial communities and provides a more detailed understanding of their activity and functional diversity.

Physiological Determinants of Invasive Success Linking Distribution Patterns to Metabolic Physiology in Native and Invasive Blue Mussels (genus Mytilus)

In the early 20th century, a blue mussel species from the Mediterranean invaded the California coast and subsequently out-competed the native species south of Monterey Bay. Like other invasive species, Mytilus galloprovincialis has physiological traits that make it successful in habitats formerly occupied by the native M. trossulus, namely its adaptation to warm sea surface temperatures. This study looks at the current genotype distributions and enzymatic activities of field-acclimatized mussels within the hybrid zone where the species co-occur as well as mussels that have been acclimated for four weeks to different temperature and salinity conditions. In the field-acclimatized and laboratory-acclimated mussels, the native species exhibited significantly higher enzyme rates, which may reflect an evolutionary adaptation to compensate to low habitat temperatures. Indeed, the results of the laboratory acclimation indicate that these differences are genetically based. Whether an acclimation capacity exists may require even longer-term acclimation to different temperatures. Current findings suggest that the further spread of the invasive species is likely to be governed in large measure by the potentially counteracting effects of rising temperatures, which would favor the northerly spread of M. galloprovincialis, and increased winter precipitation, which would favor the persistence of M. trossulus. However, the success of M. galloprovincialis during acclimation to ‘dilute’ salinity (25 ppt) suggests that the invasive species can tolerate a greater salinity range than previously thought. Thus, further investigation is needed to build a comprehensive predictive model of the movement of M. galloprovincialis and the hybrid zone along the California coast.

Standard and routine metabolic rates of juvenile sandbar sharks (Carcharhinus plumbeus), including the effects of body mass and acute temperature change*

Standard and routine metabolic rates (SMRs and RMRs, respectively) of juvenile sandbar sharks (Carcharhinus plumbeus) were measured over a range of body sizes (n=34) and temperatures normally associated with western Atlantic coastal nursery areas. The mean SMR Q10 (increase in metabolic rate with temperature) was 2.9 ±0.2. Heart rate decreased with increasing body mass but increased with temperature at a Q10 of 1.8−2.2. Self-paired measures of SMR and RMR were obtained for 15 individuals. Routine metabolic rate averaged 1.8 ±0.1 times the SMR and was not correlated with body mass. Assuming the maximum metabolic rate of sandbar sharks is 1.8−2.75 times the SMR (as is observed in other elasmobranch species), sandbar sharks are using between 34% and 100% of their metabolic scope just to sustain their routine continuous activity. This limitation may help to explain their slow individual and population growth rates, as well as the slow recoveries from overfishing of many shark stocks worl

Dietary animal and plant protein intakes and their associations with obesity and cardio-metabolic indicators in European adolescents: the HELENA cross-sectional study

Background: Previous studies suggest that dietary protein might play a beneficial role in combating obesity and its related chronic diseases. Total, animal and plant protein intakes and their associations with anthropometry and serum biomarkers in European adolescents using one standardised methodology across European countries are not well documented. Objectives: To evaluate total, animal and plant protein intakes in European adolescents stratified by gender and age, and to investigate their associations with cardio-metabolic indicators (anthropometry and biomarkers). Methods: The current analysis included 1804 randomly selected adolescents participating in the HELENA study (conducted in 2006-2007) aged 12.5-17.5 y (47% males) who completed two non-consecutive computerised 24-h dietary recalls. Associations between animal and plant protein intakes, and anthropometry and serum biomarkers were examined with General linear Model multivariate analysis. Results: Average total protein intake exceeded the recommendations of World Health Organization and European Food Safety Authority. Mean total protein intake was 96 g/d (59% derived from animal protein). Total, animal and plant protein intakes (g/d) were significantly lower in females than in males and total and plant protein intakes were lower in younger participants (12.5-14.9 y). Protein intake was significantly lower in underweight subjects and higher in obese ones; the direction of the relationship was reversed after adjustments for body weight (g/(kg.d)). The inverse association of plant protein intakes was stronger with BMI z-score and body fat percentage (BF%) compared to animal protein intakes. Additionally, BMI and BF% were positively associated with energy percentage of animal protein. Conclusions: This sample of European adolescents appeared to have adequate total protein intake. Our findings suggest that plant protein intakes may play a role in preventing obesity among European adolescents. Further longitudinal studies are needed to investigate the potential beneficial effects observed in this study in the prevention of obesity and related chronic diseases.

Quantification of drag and lift imposed by pop-up satellite archival tags and estimation of the metabolic cost to cownose rays (Rhinoptera bonasus)

The recent development of the pop-up satellite archival tag (PSAT) has allowed the collection of information on a tagged animal, such as geolocation, pressure (depth), and ambient water temperature. The success of early studies, where PSATs were used on pelagic fishes, has spurred increasing interest in the use of these tags on a large variety of species and age groups. However, some species and age groups may not be suitable candidates for carrying a PSAT because of the relatively large size of the tag and the consequent energy cost to the study animal. We examined potential energetic costs to carrying a tag for the cownose ray (Rhinoptera bonasus). Two forces act on an animal tagged with a PSAT: lift from the PSATs buoyancy and drag as the tag is moved through the water column. In a freshwater flume, a spring scale measured the total force exerted by a PSAT at flume velocities from 0.00 to 0.60 m/s. By measuring the angle of deflection of the PSAT at each velocity, we separated total force into its constituent forces — lift and drag. The power required to carry a PSAT horizontally through the water was then calculated from the drag force and velocity. Using published metabolic rates, we calculated the power for a ray of a given size to swim at a specified velocity (i.e., its swimming power). For each velocity, the power required to carry a PSAT was compared to the swimming power expressed as a percentage, %TAX (Tag Altered eXertion). A %TAX greater than 5% was felt to be energetically significant. Our analysis indicated that a ray larger than 14.8 kg can carry a PSAT without exceeding this criterion. This method of estimating swimming power can be applied to other species and would allow a researcher to decide the suitability of a given study animal for tagging with a PSAT.