Seawater carbonate chemistry and biological processes of coral Acropora muricata during experiments and observations in La Saline fringing reef, La Reunion Island, western Indian Ocean, 2011

The effect of decreasing aragonite saturation state (Omega Arag) of seawater (elevated pCO2) on calcification rates of Acropora muricata was studied using nubbins prepared from parent colonies located at two sites of La Saline reef (La Réunion Island, western Indian Ocean): a back-reef site (BR) affected by nutrient-enriched groundwater discharge (mainly nitrate), and a reef flat site (RF) with low terrigenous inputs. Protein and chlorophyll a content of the nubbins, as well as zooxanthellae abundance, were lower at RF than BR. Nubbins were incubated at ~27°C over 2 h under sunlight, in filtered seawater manipulated to get differing initial pCO2 (1,440-340 µatm), Omega Arag (1.4-4.0), and dissolved inorganic carbon (DIC) concentrations (2,100-1,850 µmol/kg). Increasing DIC concentrations at constant total alkalinity (AT) resulted in a decrease in Omega Arag and an increase in pCO2. AT at the beginning of the incubations was kept at a natural level of 2,193 ± 6 µmol/kg (mean ± SD). Net photosynthesis (NP) and calcification were calculated from changes in pH and AT during the incubations. Calcification decrease in response to doubling pCO2 relative to preindustrial level was 22% for RF nubbins. When normalized to surface area of the nubbins, (1) NP and calcification were higher at BR than RF, (2) NP increased in high pCO2 treatments at BR compared to low pCO2 treatments, and (3) calcification was not related to Omega Arag at BR. When normalized to NP, calcification was linearly related to Omega Arag at both sites, and the slopes of the relationships were not significantly different. The increase in NP at BR in the high pCO2 treatments may have increased calcification and thus masked the negative effect of low Omega Arag on calcification. Removing the effect of NP variations at BR showed that calcification declined in a similar manner with decreased Omega Arag (increased pCO2) whatever the nutrient loading.

Seawater carbonate chemistry and biological processes during experiments with temperate coral Cladocora caespitosa, 2010

Atmospheric CO2 partial pressure (pCO2) is expected to increase to 700 µatm or more by the end of the present century. Anthropogenic CO2 is absorbed by the oceans, leading to decreases in pH and the CaCO3 saturation state of the seawater. Elevated pCO2 was shown to drastically decrease calcification rates in tropical zooxanthellate corals. Here we show, using the Mediterranean zooxanthellate coral Cladocora caespitosa, that an increase in pCO2, in the range predicted for 2100, does not reduce its calcification rate. Therefore, the conventional belief that calcification rates will be affected by ocean acidification may not be widespread in temperate corals. Seasonal change in temperature is the predominant factor controlling photosynthesis, respiration, calcification and symbiont density. An increase in pCO2, alone or in combination with elevated temperature, had no significant effect on photosynthesis, photosynthetic efficiency and calcification. The lack of sensitivity C. caespitosa to elevated pCO2 might be due to its slow growth rates, which seem to be more dependent on temperature than on the saturation state of calcium carbonate in the range projected for the end of the century.

Seawater carbonate chemistry, growth rate and processes during experiments with Coccolithus pelagicus and Calcidiscus leptoporus, 2006

Uptake of half of the fossil fuel CO2 into the ocean causes gradual seawater acidification. This has been shown to slow down calcification of major calcifying groups, such as corals, foraminifera, and coccolithophores. Here we show that two of the most productive marine calcifying species, the coccolithophores Coccolithus pelagicus and Calcidiscus leptoporus, do not follow the CO2-related calcification response previously found. In batch culture experiments, particulate inorganic carbon (PIC) of C. leptoporus changes with increasing CO2 concentration in a nonlinear relationship. A PIC optimum curve is obtained, with a maximum value at present-day surface ocean pCO2 levels (?360 ppm CO2). With particulate organic carbon (POC) remaining constant over the range of CO2 concentrations, the PIC/POC ratio also shows an optimum curve. In the C. pelagicus cultures, neither PIC nor POC changes significantly over the CO2 range tested, yielding a stable PIC/POC ratio. Since growth rate in both species did not change with pCO2, POC and PIC production show the same pattern as POC and PIC. The two investigated species respond differently to changes in the seawater carbonate chemistry, highlighting the need to consider species-specific effects when evaluating whole ecosystem responses. Changes of calcification rate (PIC production) were highly correlated to changes in coccolith morphology. Since our experimental results suggest altered coccolith morphology (at least in the case of C. leptoporus) in the geological past, coccoliths originating from sedimentary records of periods with different CO2 levels were analyzed. Analysis of sediment samples was performed on six cores obtained from locations well above the lysocline and covering a range of latitudes throughout the Atlantic Ocean. Scanning electron micrograph analysis of coccolith morphologies did not reveal any evidence for significant numbers of incomplete or malformed coccoliths of C. pelagicus and C. leptoporus in last glacial maximum and Holocene sediments. The discrepancy between experimental and geological results might be explained by adaptation to changing carbonate chemistry.

Seawater carbonate chemistry and biological processes of oysters Crassostrea virginica during experiments, 2010

Estuarine organisms are exposed to periodic strong fluctuations in seawater pH driven by biological carbon dioxide (CO2) production, which may in the future be further exacerbated by the ocean acidification associated with the global rise in CO2. Calcium carbonate-producing marine species such as mollusks are expected to be vulnerable to acidification of estuarine waters, since elevated CO2 concentration and lower pH lead to a decrease in the degree of saturation of water with respect to calcium carbonate, potentially affecting biomineralization. Our study demonstrates that the increase in CO2 partial pressure (pCO2) in seawater and associated decrease in pH within the environmentally relevant range for estuaries have negative effects on physiology, rates of shell deposition and mechanical properties of the shells of eastern oysters Crassostrea virginica (Gmelin). High CO2 levels (pH ~7.5, pCO2 ~3500 µatm) caused significant increases in juvenile mortality rates and inhibited both shell and soft-body growth compared to the control conditions (pH ~8.2, pCO2 ~380 µatm). Furthermore, elevated CO2 concentrations resulted in higher standard metabolic rates in oyster juveniles, likely due to the higher energy cost of homeostasis. The high CO2 conditions also led to changes in the ultrastructure and mechanical properties of shells, including increased thickness of the calcite laths within the hypostracum and reduced hardness and fracture toughness of the shells, indicating that elevated CO2 levels have negative effects on the biomineralization process. These data strongly suggest that the rise in CO2 can impact physiology and biomineralization in marine calcifiers such as eastern oysters, threatening their survival and potentially leading to profound ecological and economic impacts in estuarine ecosystems.

Seawater carbonate chemistry and processes during experiments with cyanobacterium Trichodesmium (IMS101), 2009

We investigated carbon acquisition by the N2-fixing cyanobacterium Trichodesmium IMS101 in response to CO2 levels of 15.1, 37.5, and 101.3 Pa (equivalent to 150, 370, and 1000 ppm). In these acclimations, growth rates as well as cellular C and N contents were measured. In vivo activities of carbonic anhydrase (CA), photosynthetic O2 evolution, and CO2 and HCO3- fluxes were measured using membrane inlet mass spectrometry and the 14C disequilibrium technique. While no differences in growth rates were observed, elevated CO2 levels caused higher C and N quotas and stimulated photosynthesis and N2 fixation. Minimal extracellular CA (eCA) activity was observed, indicating a minor role in carbon acquisition. Rates of CO2 uptake were small relative to total inorganic carbon (Ci) fixation, whereas HCO{3 contributed more than 90% and varied only slightly over the light period and between CO2 treatments. The low eCA activity and preference for HCO3- were verified by the 14C disequilibrium technique. Regarding apparent affinities, half-saturation concentrations (K1/2) for photosynthetic O2 evolution and HCO3- uptake changed markedly over the day and with CO2 concentration. Leakage (CO2 efflux : Ci uptake) showed pronounced diurnal changes. Our findings do not support a direct CO2 effect on the carboxylation efficiency of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) but point to a shift in resource allocation among photosynthesis, carbon acquisition, and N2 fixation under elevated CO2 levels. The observed increase in photosynthesis and N2fixation could have potential biogeochemical implications, as it may stimulate productivity in N-limited oligotrophic regions and thus provide a negative feedback in rising atmospheric CO2 levels.

Seawater carbonate chemistry and biological processes of Mytilus edulis during experiments, 2011

Progressive ocean acidification due to anthropogenic CO2 emissions will alter marine ecosytem processes. Calcifying organisms might be particularly vulnerable to these alterations in the speciation of the marine carbonate system. While previous research efforts have mainly focused on external dissolution of shells in seawater under saturated with respect to calcium carbonate, the internal shell interface might be more vulnerable to acidification. In the case of the blue mussel Mytilus edulis, high body fluid pCO2 causes low pH and low carbonate concentrations in the extrapallial fluid, which is in direct contact with the inner shell surface. In order to test whether elevated seawater pCO2 impacts calcification and inner shell surface integrity we exposed Baltic M. edulis to four different seawater pCO2 (39, 142, 240, 405 Pa) and two food algae (310-350 cells mL-1 vs. 1600-2000 cells mL-1) concentrations for a period of seven weeks during winter (5°C). We found that low food algae concentrations and high pCO2 values each significantly decreased shell length growth. Internal shell surface corrosion of nacreous ( = aragonite) layers was documented via stereomicroscopy and SEM at the two highest pCO2 treatments in the high food group, while it was found in all treatments in the low food group. Both factors, food and pCO2, significantly influenced the magnitude of inner shell surface dissolution. Our findings illustrate for the first time that integrity of inner shell surfaces is tightly coupled to the animals' energy budget under conditions of CO2 stress. It is likely that under food limited conditions, energy is allocated to more vital processes (e.g. somatic mass maintenance) instead of shell conservation. It is evident from our results that mussels exert significant biological control over the structural integrity of their inner shell surfaces.

Seawater carbonate chemistry and biological processes during experiments with four strains of Emiliania huxleyi

Four strains of the coccolithophore E. huxleyi (RCC1212, RCC1216, RCC1238, RCC1256) were grown in dilute batch culture at four CO2 levels ranging from ~200 µatm to ~1200 µatm. Growth rate, particulate organic carbon content, and particulate inorganic carbon content were measured, and organic and inorganic carbon production calculated. The four strains did not show a uniform response to carbonate chemistry changes in any of the analysed parameters and none of the four strains displayed a response pattern previously described for this species. We conclude that the sensitivity of different strains of E. huxleyi to acidification differs substantially and that this likely has a genetic basis. We propose that this can explain apparently contradictory results reported in the literature.

Seawater carbonate chemistry and biological processes during experiments with spider crab Hyas araneus, 2011

The combined effects of ocean warming and acidification were compared in larvae from two populations of the cold-eurythermal spider crab Hyas araneus, from one of its southernmost populations (around Helgoland, southern North Sea, 54°N, habitat temperature 3-18°C; collection: January 2008, hatch: January-February 2008) and from one of its northernmost populations (Svalbard, North Atlantic, 79°N, habitat temperature 0-6°C; collection: July 2008, hatch: February-April 2009). Larvae were exposed to temperatures of 3, 9 and 15°C combined with present-day normocapnic (380 ppm CO2) and projected future CO2 concentrations (710 and 3,000 ppm CO2). Calcium content of whole larvae was measured in freshly hatched Zoea I and after 3, 7 and 14 days during the Megalopa stage. Significant differences between Helgoland and Svalbard Megalopae were observed at all investigated temperatures and CO2 conditions. Under 380 ppm CO2, the calcium content increased with rising temperature and age of the larvae. At 3 and 9°C, Helgoland Megalopae accumulated more calcium than Svalbard Megalopae. Elevated CO2 levels, especially 3,000 ppm, caused a reduction in larval calcium contents at 3 and 9°C in both populations. This effect set in early, at 710 ppm CO2 only in Svalbard Megalopae at 9°C. Furthermore, at 3 and 9°C Megalopae from Helgoland replenished their calcium content to normocapnic levels and more rapidly than Svalbard Megalopae. However, Svalbard Megalopae displayed higher calcium contents under 3,000 ppm CO2 at 15°C. The findings of a lower capacity for calcium incorporation in crab larvae living at the cold end of their distribution range suggests that they might be more sensitive to ocean acidification than those in temperate regions.

Seawater carbonate chemistry and processes during an experiment with coral reef, 2000

The concentration of CO2 in the atmosphere is projected to reach twice the preindustrial level by the middle of the 21st century. This increase will reduce the concentration of [CO3]2- of the surface ocean by 30% relative to the preindustrial level and will reduce the calcium carbonate saturation state of the surface ocean by an equal percentage. Using the large 2650 m3 coral reef mesocosm at the BIOSPHERE-2 facility near Tucson, Arizona, we investigated the effect of the projected changes in seawater carbonate chemistry on the calcification of coral reef organisms at the community scale. Our experimental design was to obtain a long (3.8 years) time series of the net calcification of the complete system and all relevant physical and chemical variables (temperature, salinity, light, nutrients, Ca2+,pCO2, TCO2, and total alkalinity). Periodic additions of NaHCO3, Na2CO3, and/or CaCl2 were made to change the calcium carbonate saturation state of the water. We found that there were consistent and reproducible changes in the rate of calcification in response to our manipulations of the saturation state. We show that the net community calcification rate responds to manipulations in the concentrations of both Ca2+ and [CO3]2- and that the rate is well described as a linear function of the ion concentration product, [Ca2+]0.69[[CO3]2-]. This suggests that saturation state or a closely related quantity is a primary environmental factor that influences calcification on coral reefs at the ecosystem level. We compare the sensitivity of calcification to short-term (days) and long-term (months to years) changes in saturation state and found that the response was not significantly different. This indicates that coral reef organisms do not seem to be able to acclimate to changing saturation state. The predicted decrease in coral reef calcification between the years 1880 and 2065 A.D. based on our long-term results is 40%. Previous small-scale, short-term organismal studies predicted a calcification reduction of 14-30%. This much longer, community-scale study suggests that the impact on coral reefs may be greater than previously suspected. In the next century coral reefs will be less able to cope with rising sea level and other anthropogenic stresses.

Chemistry and biological processes during experiments with spider crab Hyas araneus

The combined effects of ocean warming and acidification were compared in larvae from two popula- tions of the cold-eurythermal spider crab Hyas araneus, from one of its southernmost populations (around Helgo- land, southern North Sea, 54°N, habitat temperature 3-18°C; collection: January 2008, hatch: January-February 2008) and from one of its northernmost populations (Svalbard, North Atlantic, 79°N, habitat temperature 0-6°C; collection: July 2008, hatch: February-April 2009). Larvae were exposed to temperatures of 3, 9 and 15°C combined with present-day normocapnic (380 ppm CO2) and projected future CO2 concentrations (710 and 3,000 ppm CO2). Calcium content of whole larvae was measured in freshly hatched Zoea I and after 3, 7 and 14 days during the Megalopa stage. Significant differences between Helgoland and Svalbard Megalopae were observed at all investigated temperatures and CO2 condi- tions. Under 380 ppm CO2, the calcium content increased with rising temperature and age of the larvae. At 3 and 9°C, Helgoland Megalopae accumulated more calcium than Svalbard Megalopae. Elevated CO2 levels, especially 3,000 ppm, caused a reduction in larval calcium contents at 3 and 9°C in both populations. This effect set in early, at 710 ppm CO2 only in Svalbard Megalopae at 9°C. Fur- thermore, at 3 and 9°C Megalopae from Helgoland replenished their calcium content to normocapnic levels and more rapidly than Svalbard Megalopae. However, Svalbard Megalopae displayed higher calcium contents under 3,000 ppm CO2 at 15°C. The findings of a lower capacity for calcium incorporation in crab larvae living at the cold end of their distribution range suggests that they might be more sensitive to ocean acidification than those in temperate regions.

Assortative and modular networks are shaped by adaptive synchronization processes

Modular organization and degree-degree correlations are ubiquitous in the connectivity structure of biological, technological, and social interacting systems. So far most studies have concentrated on unveiling both features in real world networks, but a model that succeeds in generating them simultaneously is needed. We consider a network of interacting phase oscillators, and an adaptation mechanism for the coupling that promotes the connection strengths between those elements that are dynamically correlated. We show that, under these circumstances, the dynamical organization of the oscillators shapes the topology of the graph in such a way that modularity and assortativity features emerge spontaneously and simultaneously. In turn, we prove that such an emergent structure is associated with an asymptotic arrangement of the collective dynamical state of the network into cluster synchronization.

Dreams: A tool for the design of dynamically reconfigurable embedded and modular systems

Dynamically Reconfigurable Systems are attracting a growing interest, mainly due to the emergence of novel applications based on this technology. However, commercial tools do not provide enough flexibility to design solutions, while keeping an acceptable design productivity. In this paper, a novel design flow is proposed, targeting dynamically reconfigurable systems. It is fully supported by a tool called Dreams, which is able to implement flexible systems, starting from a set of netlists corresponding to the modules, as well as a system description provided by the user. The tool automatically post-processes the nets, implementing a solution for the communications between reconfigurable regions, as well as the handling of routing conflicts, by means of a custom router. Since the design process of every module and the static system are independent, the proposed flow is compatible with system upgrade at run-time. In this paper, a use case corresponding to the design of a highly regular and parallel mesh-type architecture is described, in order to show the architectural flexibility offered by the tool.

Utilizing the Internet of Things to promote energy awareness and efficiency at discrete production processes: Practices and methodology

El actual contexto de fabricación, con incrementos en los precios de la energía, una creciente preocupación medioambiental y cambios continuos en los comportamientos de los consumidores, fomenta que los responsables prioricen la fabricación respetuosa con el medioambiente. El paradigma del Internet de las Cosas (IoT) promete incrementar la visibilidad y la atención prestada al consumo de energía gracias tanto a sensores como a medidores inteligentes en los niveles de máquina y de línea de producción. En consecuencia es posible y sencillo obtener datos de consumo de energía en tiempo real proveniente de los procesos de fabricación, pero además es posible analizarlos para incrementar su importancia en la toma de decisiones. Esta tesis pretende investigar cómo utilizar la adopción del Internet de las Cosas en el nivel de planta de producción, en procesos discretos, para incrementar la capacidad de uso de la información proveniente tanto de la energía como de la eficiencia energética. Para alcanzar este objetivo general, la investigación se ha dividido en cuatro sub-objetivos y la misma se ha desarrollado a lo largo de cuatro fases principales (en adelante estudios). El primer estudio de esta tesis, que se apoya sobre una revisión bibliográfica comprehensiva y sobre las aportaciones de expertos, define prácticas de gestión de la producción que son energéticamente eficientes y que se apoyan de un modo preeminente en la tecnología IoT. Este primer estudio también detalla los beneficios esperables al adoptar estas prácticas de gestión. Además, propugna un marco de referencia para permitir la integración de los datos que sobre el consumo energético se obtienen en el marco de las plataformas y sistemas de información de la compañía. Esto se lleva a cabo con el objetivo último de remarcar cómo estos datos pueden ser utilizados para apalancar decisiones en los niveles de procesos tanto tácticos como operativos. Segundo, considerando los precios de la energía como variables en el mercado intradiario y la disponibilidad de información detallada sobre el estado de las máquinas desde el punto de vista de consumo energético, el segundo estudio propone un modelo matemático para minimizar los costes del consumo de energía para la programación de asignaciones de una única máquina que deba atender a varios procesos de producción. Este modelo permite la toma de decisiones en el nivel de máquina para determinar los instantes de lanzamiento de cada trabajo de producción, los tiempos muertos, cuándo la máquina debe ser puesta en un estado de apagada, el momento adecuado para rearrancar, y para pararse, etc. Así, este modelo habilita al responsable de producción de implementar el esquema de producción menos costoso para cada turno de producción. En el tercer estudio esta investigación proporciona una metodología para ayudar a los responsables a implementar IoT en el nivel de los sistemas productivos. Se incluye un análisis del estado en que se encuentran los sistemas de gestión de energía y de producción en la factoría, así como también se proporcionan recomendaciones sobre procedimientos para implementar IoT para capturar y analizar los datos de consumo. Esta metodología ha sido validada en un estudio piloto, donde algunos indicadores clave de rendimiento (KPIs) han sido empleados para determinar la eficiencia energética. En el cuarto estudio el objetivo es introducir una vía para obtener visibilidad y relevancia a diferentes niveles de la energía consumida en los procesos de producción. El método propuesto permite que las factorías con procesos de producción discretos puedan determinar la energía consumida, el CO2 emitido o el coste de la energía consumida ya sea en cualquiera de los niveles: operación, producto o la orden de fabricación completa, siempre considerando las diferentes fuentes de energía y las fluctuaciones en los precios de la misma. Los resultados muestran que decisiones y prácticas de gestión para conseguir sistemas de producción energéticamente eficientes son posibles en virtud del Internet de las Cosas. También, con los resultados de esta tesis los responsables de la gestión energética en las compañías pueden plantearse una aproximación a la utilización del IoT desde un punto de vista de la obtención de beneficios, abordando aquellas prácticas de gestión energética que se encuentran más próximas al nivel de madurez de la factoría, a sus objetivos, al tipo de producción que desarrolla, etc. Así mismo esta tesis muestra que es posible obtener reducciones significativas de coste simplemente evitando los períodos de pico diario en el precio de la misma. Además la tesis permite identificar cómo el nivel de monitorización del consumo energético (es decir al nivel de máquina), el intervalo temporal, y el nivel del análisis de los datos son factores determinantes a la hora de localizar oportunidades para mejorar la eficiencia energética. Adicionalmente, la integración de datos de consumo energético en tiempo real con datos de producción (cuando existen altos niveles de estandarización en los procesos productivos y sus datos) es esencial para permitir que las factorías detallen la energía efectivamente consumida, su coste y CO2 emitido durante la producción de un producto o componente. Esto permite obtener una valiosa información a los gestores en el nivel decisor de la factoría así como a los consumidores y reguladores. ABSTRACT In today‘s manufacturing scenario, rising energy prices, increasing ecological awareness, and changing consumer behaviors are driving decision makers to prioritize green manufacturing. The Internet of Things (IoT) paradigm promises to increase the visibility and awareness of energy consumption, thanks to smart sensors and smart meters at the machine and production line level. Consequently, real-time energy consumption data from the manufacturing processes can be easily collected and then analyzed, to improve energy-aware decision-making. This thesis aims to investigate how to utilize the adoption of the Internet of Things at shop floor level to increase energy–awareness and the energy efficiency of discrete production processes. In order to achieve the main research goal, the research is divided into four sub-objectives, and is accomplished during four main phases (i.e., studies). In the first study, by relying on a comprehensive literature review and on experts‘ insights, the thesis defines energy-efficient production management practices that are enhanced and enabled by IoT technology. The first study also explains the benefits that can be obtained by adopting such management practices. Furthermore, it presents a framework to support the integration of gathered energy data into a company‘s information technology tools and platforms, which is done with the ultimate goal of highlighting how operational and tactical decision-making processes could leverage such data in order to improve energy efficiency. Considering the variable energy prices in one day, along with the availability of detailed machine status energy data, the second study proposes a mathematical model to minimize energy consumption costs for single machine production scheduling during production processes. This model works by making decisions at the machine level to determine the launch times for job processing, idle time, when the machine must be shut down, ―turning on‖ time, and ―turning off‖ time. This model enables the operations manager to implement the least expensive production schedule during a production shift. In the third study, the research provides a methodology to help managers implement the IoT at the production system level; it includes an analysis of current energy management and production systems at the factory, and recommends procedures for implementing the IoT to collect and analyze energy data. The methodology has been validated by a pilot study, where energy KPIs have been used to evaluate energy efficiency. In the fourth study, the goal is to introduce a way to achieve multi-level awareness of the energy consumed during production processes. The proposed method enables discrete factories to specify energy consumption, CO2 emissions, and the cost of the energy consumed at operation, production and order levels, while considering energy sources and fluctuations in energy prices. The results show that energy-efficient production management practices and decisions can be enhanced and enabled by the IoT. With the outcomes of the thesis, energy managers can approach the IoT adoption in a benefit-driven way, by addressing energy management practices that are close to the maturity level of the factory, target, production type, etc. The thesis also shows that significant reductions in energy costs can be achieved by avoiding high-energy price periods in a day. Furthermore, the thesis determines the level of monitoring energy consumption (i.e., machine level), the interval time, and the level of energy data analysis, which are all important factors involved in finding opportunities to improve energy efficiency. Eventually, integrating real-time energy data with production data (when there are high levels of production process standardization data) is essential to enable factories to specify the amount and cost of energy consumed, as well as the CO2 emitted while producing a product, providing valuable information to decision makers at the factory level as well as to consumers and regulators.

PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the finite parts list of folds from an expanding number of perspectives. We have developed a new resource, called PartsList, that lets one dynamically perform these comparative fold surveys. It is available on the web at http://bioinfo.mbb.yale.edu/partslist and http://www.partslist.org. The system is based on the existing fold classifications and functions as a form of companion annotation for them, providing ‘global views’ of many already completed fold surveys. The central idea in the system is that of comparison through ranking; PartsList will rank the approximately 420 folds based on more than 180 attributes. These include: (i) occurrence in a number of completely sequenced genomes (e.g. it will show the most common folds in the worm versus yeast); (ii) occurrence in the structure databank (e.g. most common folds in the PDB); (iii) both absolute and relative gene expression information (e.g. most changing folds in expression over the cell cycle); (iv) protein–protein interactions, based on experimental data in yeast and comprehensive PDB surveys (e.g. most interacting fold); (v) sensitivity to inserted transposons; (vi) the number of functions associated with the fold (e.g. most multi-functional folds); (vii) amino acid composition (e.g. most Cys-rich folds); (viii) protein motions (e.g. most mobile folds); and (ix) the level of similarity based on a comprehensive set of structural alignments (e.g. most structurally variable folds). The integration of whole-genome expression and protein–protein interaction data with structural information is a particularly novel feature of our system. We provide three ways of visualizing the rankings: a profiler emphasizing the progression of high and low ranks across many pre-selected attributes, a dynamic comparer for custom comparisons and a numerical rankings correlator. These allow one to directly compare very different attributes of a fold (e.g. expression level, genome occurrence and maximum motion) in the uniform numerical format of ranks. This uniform framework, in turn, highlights the way that the frequency of many of the attributes falls off with approximate power-law behavior (i.e. according to V–b, for attribute value V and constant exponent b), with a few folds having large values and most having small values.

Diffusion and formation of microtubule asters: physical processes versus biochemical regulation.

Microtubule asters forming the mitotic spindle are assembled around two centrosomes through the process of dynamic instability in which microtubules alternate between growing and shrinking states. By modifying the dynamics of this assembly process, cell cycle enzymes, such as cdc2 cyclin kinases, regulate length distributions in the asters. It is believed that the same enzymes control the number of assembled microtubules by changing the "nucleating activity" of the centrosomes. Here we show that assembly of microtubule asters may be strongly altered by effects connected with diffusion of tubulin monomers. Theoretical analysis of a simple model describing assembly of microtubule asters clearly shows the existence of a region surrounding the centrosome depleted in GTP tubulin. The number of assembled microtubules may in some cases be limited by this depletion effect rather than by the number of available nucleation sites on the centrosome.