Spatial Structure of Pelagic Ecosystem Processes in the Global Ocean

We propose an operational definition of spatial structure in the oceanic ecosystem; it is equivalent to the large-scale, horizontal distribution of the dominant ecophysiological rate parameters for the questions of interest. In an important, particular case, the relevant rate parameters are those that characterize autotrophic production. In the ocean, these parameters are believed to be distributed in a manner that is not smoothly continuous. Rather, they seem to have a piecewise continuous distribution. This leads to a requirement to partition the ocean into a suite of provinces where the boundaries between the provinces mark the locations of abrupt changes in the magnitudes of the rate parameters. The area covered by a particular province represents an area of common physical forcing, insofar as the forcing is relevant to autotrophic production. The boundaries are taken to be elastic rather than fixed, such that they can respond to variations in forcing. At any given time, the boundaries can be located with the aid of remotely sensed imagery, especially ocean-color imagery. Received 7 January 1999; accepted 2 June 1999.     

A Toolkit for Ecosystem Ecologists in the Time of Big Science

Ecosystem ecologists are being challenged to address the increasingly complex problems that comprise Big Science. These problems include multiple levels of biological organization that cross multiple interacting temporal and spatial scales, from individual plants, animals, and microbes to landscapes, continents, and the globe. As technology improves, the availability of data, derived data products, and information to address these complex problems are increasing at finer and coarser scales of resolution, and legacy, dark data are brought to light. Data analytics are improving as big data increase in importance in other fields that are improving access to these data. New data sources (crowdsourcing, social media) and ease of communication and collaboration among ecosystem ecologists and other disciplines are increasingly possible via the internet. It is increasingly important that ecosystem ecologists be able to communicate their findings, and to translate their concepts and findings into concrete bits of information that a general public can understand. Traditional approaches that portray ecosystem sciences as a dichotomy between empirical research and theoretical research will keep the field from fully contributing to the complexity of global change questions, and will keep ecosystem ecologists from taking full advantage of the data and technology available. Building on previous research, we describe a more forward-looking, integrated empirical–theoretical modeling approach that is iterative with learning to take advantage of the elements of Big Science. We suggest that training ecosystem ecologists in this integrated approach will be critical to addressing complex Earth system science questions, now and in the future.     

The Role of Sharks and Longline Fisheries in a Pelagic Ecosystem of the Central Pacific

The increased exploitation of pelagic sharks by longline fisheries raised questions about changes in the food webs that include sharks as apex predators. We used a version of Ecopath/Ecosim models to evaluate changes in trophic interactions due to shark exploitation in the Central North Pacific. Fisheries targeted on blue sharks tend to produce compensatory responses that favor other shark species and billfishes, but they have only modest effects on the majority of food web components. Modest levels of intraguild predation (adult sharks that eat juvenile sharks) produce strong, nonlinear responses in shark populations. In general, analysis of the Central North Pacific model reveals that sharks are not keystone predators, but that increases in longline fisheries can have profound effects on the food webs that support sharks. Received 19 April 2001; accepted 2 October 2001.     

CAPRI: a Critical Assessment of PRedicted Interactions

CAPRI is a communitywide experiment to assess the capacity of protein-docking methods to predict protein-protein interactions. Nineteen groups participated in rounds 1 and 2 of CAPRI and submitted blind structure predictions for seven protein-protein complexes based on the known structure of the component proteins. The predictions were compared to the unpublished X-ray structures of the complexes. We describe here the motivations for launching CAPRI, the rules that we applied to select targets and run the experiment, and some conclusions that can already be drawn. The results stress the need for new scoring functions and for methods handling the conformation changes that were observed in some of the target systems. CAPRI has already been a powerful drive for the community of computational biologists who development docking algorithms. We hope that this issue of Proteins will also be of interest to the community of structural biologists, which we call upon to provide new targets for future rounds of CAPRI, and to all molecular biologists who view protein-protein recognition as an essential process.     

Spatial and Temporal Variability in the Ecosystem Metabolism of a High-elevation Lake: Integrating Benthic and Pelagic Habitats

We characterized spatial and temporal variability in net ecosystem production (NEP), community respiration (CR), and gross primary production (GPP) over an ice-free season in an oligotrophic high-elevation lake using high-frequency measurements of dissolved oxygen. We combined the use of free-water and incubation chamber measurements to compare pelagic and benthic habitats and estimate their relative contributions to whole-lake metabolism. Despite a brief period of predominant heterotrophy after snowmelt, both free-water and incubation chamber measurements confirmed autotrophy of the epilimnion in all habitats throughout the ice-free season. In contrast, benthic incubation chambers showed the benthos to be consistently heterotrophic. Although temperature was the strongest seasonal driver of benthic metabolism, bacterioplankton density and indexes of organic matter quality explained the most variability in pelagic metabolism. Driven largely by benthic metabolism, free-water measurements of GPP and CR were twice as high in littoral than pelagic habitats. However, rates of water column primary production overlying the littoral benthos were high enough to overcome net benthic heterotrophy, and seasonal mean NEP in littoral habitats remained positive and not significantly different from pelagic habitats. Benthic rates averaged about 25% of whole-lake metabolism. Pelagic metabolism measurements were affected by littoral rates about half the time, with the degree of isolation between the two a function of advection and water column stability. These results emphasize the importance of characterizing spatial and temporal variability in metabolism within the context of physical dynamics and challenge the notion that benthic metabolism will necessarily be larger than pelagic metabolism in oligotrophic lakes.     

Fishery-Induced Changes in the Subtropical Pacific Pelagic Ecosystem Size Structure: Observations and Theory

We analyzed a 16-year (1996–2011) time series of catch and effort data for 23 species with mean weights ranging from 0.8 kg to 224 kg, recorded by observers in the Hawaii-based deep-set longline fishery. Over this time period, domestic fishing effort, as numbers of hooks set in the core Hawaii-based fishing ground, has increased fourfold. The standardized aggregated annual catch rate for 9 small (<15 kg) species increased about 25% while for 14 large species (>15 kg) it decreased about 50% over the 16-year period. A size-based ecosystem model for the subtropical Pacific captures this pattern well as a response to increased fishing effort. Further, the model projects a decline in the abundance of fishes larger than 15 kg results in an increase in abundance of animals from 0.1 to 15 kg but with minimal subsequent cascade to sizes smaller than 0.1 kg. These results suggest that size-based predation plays a key role in structuring the subtropical ecosystem. These changes in ecosystem size structure show up in the fishery in various ways. The non-commercial species lancetfish (mean weight 7 kg) has now surpassed the target species, bigeye tuna, as the species with the highest annual catch rate. Based on the increase in snake mackerel (mean weight 0.8 kg) and lancetfish catches, the discards in the fishery are estimated to have increased from 30 to 40% of the total catch.     

Interactions Between Physical Template and Self-organization Shape Plant Dynamics in a Stream Ecosystem

Ecosystems - Both internal feedbacks and preexisting heterogeneity of a physical template can produce biological patchiness in ecosystems. The relative importance of the two drivers might change...     

Photosynthesis and Calcification at Cellular, Organismal and Community Levels in Coral Reefs: A Review on Interactions and Control by Carbonate Chemistry

SYNOPSIS. Photosynthesis and calcification in zooxanthellatescleractinian corals and coral reefs are reviewed at severalscales: cellular (pathways and transport mechanisms of inorganiccarbon and calcium), organismal (interaction between photosynthesisand calcification, effect of light) and ecosystemic (communityprimary production and calcification, and air-sea CO₂ exchanges). The coral host plays a major role in supplying carbon for thephotosynthesis by the algal symbionts through a system similarto the carbon-concentrating mechanism described in free livingalgal cells. The details of carbon supply to the calcificationprocess are almost unknown, but metabolic CO₂ seems to be asignificant source. Calcium supply for calcification is diffusionalthrough oral layers, and active membrane transport only occursbetween the calicoblastic cells and the site of calcification.Photosynthesis and calcification are tightly coupled in zooxanthellatescleractinian corals and coral reef communities. Calcificationis, on average, three times higher in light than in darkness.The recent suggestion that calcification is dark-repressed ratherthan light-enhanced is not supported by the literature. Thereis a very strong correlation between photosynthesis and calcificationat both the organism and community levels, but the ratios ofcalcification to gross photosynthesis (0.6 in corals and 0.2in reef communities) differ from unity, and from each otheras a function of level. The potential effect of global climatic changes (pCO₂ and temperature)on the rate of calcification is also reviewed. In various calcifyingphotosynthetic organisms and communities, the rate of calcificationdecreases as a function of increasing pCO₂ and decreasing calciumcarbonate saturation state. The calculated decrease in CaCO₃,production, estimated using the scenarios considered by theInternational Panel on Climate Change (IPCC), is 10% between1880 and 1990, and 9–30% (mid estimate: 22%) from 1990to 2100. Inadequate understanding of the mechanism of calcificationand its interaction with photosynthesis severely limits theability to provide an accurate prediction of future changesin the rate of calcification.     

Effects of Consumer Interactions on Benthic Resources and Ecosystem Processes in a Neotropical Stream

The effect of consumers on their resources has been demonstrated in many systems but is often confounded by trophic interactions with other consumers. Consumers may also have behavioral and life history adaptations to each other and to co-occurring predators that may additionally modulate their particular roles in ecosystems. We experimentally excluded large consumers from tile periphyton, leaves and natural benthic substrata using submerged electrified frames in three stream reaches with overlapping consumer assemblages in Trinidad, West Indies. Concurrently, we assessed visits to (non-electrified) control frames by the three most common large consumers–primarily insectivorous killifish (Rivulus hartii), omnivorous guppies (Poecilia reticulata) and omnivorous crabs (Eudaniela garmani). Consumers caused the greatest decrease in final chlorophyll a biomass and accrual rates the most in the downstream reach containing all three focal consumers in the presence of fish predators. Consumers also caused the greatest increase in leaf decay rates in the upstream reach containing only killifish and crabs. In the downstream reach where guppies co-occur with predators, we found significantly lower benthic invertebrate biomass in control relative to exclosure treatments than the midstream reach where guppies occur in the absence of predators. These data suggest that differences in guppy foraging, potentially driven by differences in their life history phenotype, may affect ecosystem structure and processes as much as their presence or absence and that interactions among consumers may further mediate their effects in these stream ecosystems.     

A Critical Assessment of Putative Gatekeeper Interactions in the Villin Headpiece Helical Subdomain

The helical subdomain of the villin headpiece (HP36) is one of the smallest naturally occurring proteins that folds cooperatively. Its small size, rapid folding, and simple three-helix topology have made it an extraordinary popular model system for computational, theoretical, and experimental studies of protein folding. Aromatic-proline interactions involving Trp64 and Pro62 have been proposed to play a critical role in specifying the subdomain fold by acting as gatekeeper residues. Note that the numbering corresponds to full-length headpiece. Mutation of Pro62 has been shown to lead to a protein that does not fold, but this may arise for two different reasons: The residue may make interactions that are critical for the specificity of the fold or the mutation may simply destabilize the domain. In the first case, the protein cannot fold, while in the second, the small fraction of molecules that do fold adopt the correct structure. The modest stability of the wild type prevents a critical analysis of these interactions because even moderately destabilizing mutations lead to a very small folded state population. Using a hyperstable variant of HP36, denoted DM HP36, as our new wild type, we characterized a set of mutants designed to assess the role of the putative gatekeeper interactions. Four single mutants, DM Pro62Ala, DM Trp64Leu, DM Trp64Lys, and DM Trp64Ala, and a double mutant, DM Pro62Ala Trp64Leu, were prepared. All mutants are less stable than DM HP36, but all are well folded as judged by CD and ¹H NMR. All of the mutants display sigmoidal thermal unfolding and urea-induced unfolding curves. Double-mutant cycle analysis shows that the interactions between Pro62 and Trp64 are weak but favorable. Interactions involving Pro62 and proline-aromatic interactions are, thus, not required for specifying the subdomain fold. The implications for the design and thermodynamics of miniature proteins are discussed.     

A Shift to Organismal Stress Resistance in Programmed Cell Death Mutants

Animals have many ways of protecting themselves against stress; for example, they can induce animal-wide, stress-protective pathways and they can kill damaged cells via apoptosis. We have discovered an unexpected regulatory relationship between these two types of stress responses. We find that C. elegans mutations blocking the normal course of programmed cell death and clearance confer animal-wide resistance to a specific set of environmental stressors; namely, ER, heat and osmotic stress. Remarkably, this pattern of stress resistance is induced by mutations that affect cell death in different ways, including ced-3 (cell death defective) mutations, which block programmed cell death, ced-1 and ced-2 mutations, which prevent the engulfment of dying cells, and progranulin (pgrn-1) mutations, which accelerate the clearance of apoptotic cells. Stress resistance conferred by ced and pgrn-1 mutations is not additive and these mutants share altered patterns of gene expression, suggesting that they may act within the same pathway to achieve stress resistance. Together, our findings demonstrate that programmed cell death effectors influence the degree to which C. elegans tolerates environmental stress. While the mechanism is not entirely clear, it is intriguing that animals lacking the ability to efficiently and correctly remove dying cells should switch to a more global animal-wide system of stress resistance.     

Interaction between Workers during a Short Time Window Is Required for Bacterial Symbiont Transmission in Acromyrmex Leaf-Cutting Ants

Stable associations between partners over time are critical for the evolution of mutualism. Hosts employ a variety of mechanisms to maintain specificity with bacterial associates. Acromyrmex leaf-cutting ants farm a fungal cultivar as their primary nutrient source. These ants also carry a Pseudonocardia Actinobacteria exosymbiont on their bodies that produces antifungal compounds that help inhibit specialized parasites of the ants'' fungal garden. Major workers emerge from their pupal cases (eclose) symbiont-free, but exhibit visible Actinobacterial coverage within 14 days post-eclosion. Using subcolony experiments, we investigate exosymbiont transmission within Acromyrmex colonies. We found successful transmission to newly eclosed major workers fostered by major workers with visible Actinobacteria in all cases (100% acquiring, n = 19). In contrast, newly eclosed major workers reared without exosymbiont-carrying major workers did not acquire visible Actinobacteria (0% acquiring, n = 73). We further show that the majority of ants exposed to major workers with exosymbionts within 2 hours of eclosion acquired bacteria (60.7% acquiring, n = 28), while normal acquisition did not occur when exposure occurred later than 2 hours post-eclosion (0% acquiring, n = 18). Our findings show that transmission of exosymbionts to newly eclosed major workers occurs through interactions with exosymbiont-covered workers within a narrow time window after eclosion. This mode of transmission likely helps ensure the defensive function within colonies, as well as specificity and partner fidelity in the ant-bacterium association.     

A Developmental Window for Salt-Adaptation in Sorghum bicolor

Following exposure to specific NaCl treatments, certain Sorghumbicolor genotypes developed increased salinity tolerance, ‘adaptation’,which was accompanied by a morphological modification in thedevelopment of one or several leaves. Adaptation differed fromthe more common response of the plant to salinity, ‘pre–existingresistance’, which rested on the prevalent tolerance mechanismsexisting prior to the salinization treatment. Induction of adaptationwas possible only during a specific time period of plant development.This time-limited capacity for adjustment to a changing environmentalparameter, developmental window, resembled similar processesoccurring in animal development. Key words: Sorghum, adaptation, resistance, salinity, developmental window     

内皮抑素抗黑色素瘤血管新生时间窗及最佳剂量的研究

目的:获取不同黑色素瘤发展阶段的荷瘤鼠的最佳治疗时间以及最佳用药量。方法:将肿瘤大小不等的雄性黑色素瘤荷瘤鼠进行内皮抑素分组对比治疗,在用药3、5、7天后处死荷瘤鼠,剥离瘤体,称瘤重,分析生长趋势,做病理切片并进行HE染色和免疫组化。在与对照组进行对照后,根据肿瘤的大小、恶性化的程度以及CD31和VEGF的表达情况,找出内皮抑素的用药最有效的治疗时间窗。然后通过进一步实验,在已经检测出的不同肿瘤大小的荷瘤鼠的恩度作用时间窗内,给荷瘤鼠使用用不同浓度梯度的药物,在不同肿瘤发展大小之后剥离瘤体,做与上述类似的操作并分析,确定在治疗时间窗时的恩度使用的最佳剂量。结论:5天为内皮抑素抗黑色素瘤血管新生时间窗,两个实验组中,中等剂量即15 mg/kg和20 mg/kg为恩度作用最佳剂量。