Mechanisms of Cdc42 Polarization in Yeast

Polarization is important for the function and morphology of many different cell types. The keys regulators of polarity in eukaryotes are the Rho-family GTPases. In the budding yeast Saccharomyces cerevisiae, which must polarize in order to bud and to mate, the master regulator is the highly conserved Rho GTPase, Cdc42. During polarity establishment, active Cdc42 accumulates at a site on the plasma membrane characterizing the “front” of the cell where the bud will emerge. The orientation of polarization is guided by upstream cues that dictate the site of Cdc42 clustering. However, in the absence of upstream cues, yeast can still polarize in a random direction during symmetry breaking. Symmetry breaking suggests cells possess an autocatalytic polarization mechanism that can amplify stochastic fluctuations of polarity proteins through a positive feedback mechanism.

Two different positive feedback mechanisms have been proposed to polarize Cdc42 in budding yeast. One model posits that Cdc42 activation must be localized to a site at the plasma membrane. Another model posits that Cdc42 delivery must be localized to a particular site at the plasma membrane. Although both mechanisms could work in parallel to polarize Cdc42, it is unclear which mechanism is critical to polarity establishment. We directly tested the predictions of the two positive feedback models using genetics and live microscopy. We found that localized Cdc42 activation is necessary for polarity establishment.

While this explains how active Cdc42 localizes to a particular site at the plasma membrane, it does not address how Cdc42 concentrates at that site. Several different mechanisms have been proposed to concentrate Cdc42. The GDI can extract Cdc42 from membranes and selective mobilize GDP-Cdc42 in the cytoplasm. It was proposed that selectively mobilizing GDP-Cdc42 in combination with local activation could locally concentrate total Cdc42 at the polarity site. Although the GDI is important for rapid Cdc42 accumulation at the polarity site, it is not essential to Cdc42 concentration. It was proposed that delivery of Cdc42 by actin-mediated vesicle can act as a backup pathway to concentrate Cdc42. However, we found no evidence for an actin-dependent concentrating pathway. Live microscopy experiments reveal that prenylated proteins are not restricted to membranes, and can enter the cytoplasm. We found that the GDI-independent concentrating pathway still requires Cdc42 to exchange between the plasma membrane and the cytoplasm, which is supported by computational modeling. In the absence of the GDI, we found that Cdc42 GAP became essential for polarization. We propose that the GAP limits GTP-Cdc42 leak into the cytoplasm, which would be prohibitive to Cdc42 polarization.

Resonance Energy Transfer-Based Molecular Switch Designed Using a Systematic Design Process Based on Monte Carlo Methods and Markov Chains

A RET network consists of a network of photo-active molecules called chromophores that can participate in inter-molecular energy transfer called resonance energy transfer (RET). RET networks are used in a variety of applications including cryptographic devices, storage systems, light harvesting complexes, biological sensors, and molecular rulers. In this dissertation, we focus on creating a RET device called closed-diffusive exciton valve (C-DEV) in which the input to output transfer function is controlled by an external energy source, similar to a semiconductor transistor like the MOSFET. Due to their biocompatibility, molecular devices like the C-DEVs can be used to introduce computing power in biological, organic, and aqueous environments such as living cells. Furthermore, the underlying physics in RET devices are stochastic in nature, making them suitable for stochastic computing in which true random distribution generation is critical.

In order to determine a valid configuration of chromophores for the C-DEV, we developed a systematic process based on user-guided design space pruning techniques and built-in simulation tools. We show that our C-DEV is 15x better than C-DEVs designed using ad hoc methods that rely on limited data from prior experiments. We also show ways in which the C-DEV can be improved further and how different varieties of C-DEVs can be combined to form more complex logic circuits. Moreover, the systematic design process can be used to search for valid chromophore network configurations for a variety of RET applications.

We also describe a feasibility study for a technique used to control the orientation of chromophores attached to DNA. Being able to control the orientation can expand the design space for RET networks because it provides another parameter to tune their collective behavior. While results showed limited control over orientation, the analysis required the development of a mathematical model that can be used to determine the distribution of dipoles in a given sample of chromophore constructs. The model can be used to evaluate the feasibility of other potential orientation control techniques.

Non-Consumptive Effects of Predators in Coral Reef Communities and the Indirect Consequences of Marine Protected Areas

Predators exert strong direct and indirect effects on ecological communities by intimidating their prey. Non-consumptive effects (NCEs) of predators are important features of many ecosystems and have changed the way we understand predator-prey interactions, but are not well understood in some systems. For my dissertation research I combined a variety of approaches to examine the effect of predation risk on herbivore foraging and reproductive behaviors in a coral reef ecosystem. In the first part of my dissertation, I investigated how diet and territoriality of herbivorous fish varied across multiple reefs with different levels of predator biomass in the Florida Keys National Marine Sanctuary. I show that both predator and damselfish abundance impacted diet diversity within populations for two herbivores in different ways. Additionally, reef protection and the associated recovery of large predators appeared to shape the trade-off reef herbivores made between territory size and quality. In the second part of my dissertation, I investigated context-dependent causal linkages between predation risk, herbivore foraging behavior and resource consumption in multiple field experiments. I found that reef complexity, predator hunting mode, light availability and prey hunger influenced prey perception of threat and their willingness to feed. This research argues for more emphasis on the role of predation risk in affecting individual herbivore foraging behavior in order to understand the implications of human-mediated predator removal and recovery in coral reef ecosystems.

Carbon and Nitrogen Stable Isotopic Patterns in South Florida Coastal Ecosystems: Modern and Paleoceanographic Perspectives

Long term management plans for restoration of natural flow conditions through the Everglades increase the importance of understanding potential nutrient impacts of increased freshwater delivery on coastal biogeochemistry. The present study sought to increase understanding of the coastal marine system of South Florida under modern conditions and through the anthropogenic changes in the last century, on scales ranging from individual nutrient cycle processes to seasonal patterns in organic material (OM) under varying hydrodynamic regime, to century scale analysis of sedimentary records. In all applications, carbon and nitrogen stable isotopic compositions of OM were examined as natural recorders of change and nutrient cycling in the coastal system. High spatial and temporal variability in stable isotopic compositions were observed on all time scales. During a transient phytoplankton bloom, ä15N values suggested nitrogen fixation as a nutrient source supporting enhanced productivity. Seasonally, particulate organic material (POM) from ten sites along the Florida Reef Tract and in Florida Bay demonstrated variable fluctuations dependent on hydrodynamic setting. Three separate intra-annual patterns were observed, yet statistical differences were observed between groupings of Florida Bay and Atlantic Ocean sites. The POM ä15N values ranged on a quarterly basis by 7‰, while ä13C varied by 22‰. From a sediment history perspective, four cores collected from Florida Bay further demonstrated the spatial and temporal variability of the system in isotopic composition of bulk OM over time. Source inputs of OM varied with location, with terrestrial inputs dominating proximal to Everglades freshwater discharge, seagrasses dominating in open estuary cores, and a marine mixture of phytoplankton and seagrass in a core from the boundary zone between Florida Bay and the Gulf of Mexico. Significant shifts in OM geochemistry were observed coincident with anthropogenic events of the 20th century, including railroad and road construction in the Florida Keys and Everglades, and also the extensive drainage changes in Everglades hydrology. The sediment record also preserved evidence of the major hurricanes of the last century, with excursions in geochemical composition coincident with Category 4-5 storms.

Claves de la ciudadanía política femenina en la primera mitad del siglo XX en Argentina

En este artículo, se exploran algunos hechos que jalonaron la edificación de la Argentina y configuraron dispositivos centrales para la construcción de los sexos en la primera mitad del siglo XX. En ese camino, se examinan cambios y continuidades en la construcción de la ciudadanía política femenina. Desde una perspectiva de género, se subraya las diferentes imposiciones legales e institucionales asociadas a la masculinidad y a la feminidad de las prácticas sociales. El problema central, en ese sentido, se vincula con la definición de las mujeres como sujeto e individuo

El enfoque biográfico en el análisis social : Claves para un estudio de los aspectos teórico-metodológicos de las trayectorias laborales

Este trabajo desarrolla los supuestos que se esconden tras los estudios biográficos, centrándose en los enfoques europeo y norteamericano. Intenta vislumbrar los distintos ámbitos de producción en donde surgieron los fundamentos epistemológicos, teóricos y metodológicos, los cuales enmarcan el análisis de las trayectorias: la centralidad del sujeto, la relación individuo-sociedad, la integración de perspectivas metodológicas y la importancia de la dimensión espacio-temporal. La relevancia de esta tarea radica en que el enfoque biográfico se constituye como telón de fondo en el estudio de las trayectorias laborales. En el primer apartado se indagan los orígenes del uso de biografías en la investigación social; en el segundo y el tercero, se examinan los supuestos centrales del enfoque biográfico y del curso de vida, al encontrar en ellos las raíces que encuadran y dan sentido al estudio de las trayectorias. Por último, se desarrollan los aportes y potencialidades de los estudios con trayectorias laborales a través del análisis de un corpus de investigaciones empíricas producidas en América Latina

Claves de la ciudadanía política femenina en la primera mitad del siglo XX en Argentina

En este artículo, se exploran algunos hechos que jalonaron la edificación de la Argentina y configuraron dispositivos centrales para la construcción de los sexos en la primera mitad del siglo XX. En ese camino, se examinan cambios y continuidades en la construcción de la ciudadanía política femenina. Desde una perspectiva de género, se subraya las diferentes imposiciones legales e institucionales asociadas a la masculinidad y a la feminidad de las prácticas sociales. El problema central, en ese sentido, se vincula con la definición de las mujeres como sujeto e individuo

El enfoque biográfico en el análisis social : Claves para un estudio de los aspectos teórico-metodológicos de las trayectorias laborales

Este trabajo desarrolla los supuestos que se esconden tras los estudios biográficos, centrándose en los enfoques europeo y norteamericano. Intenta vislumbrar los distintos ámbitos de producción en donde surgieron los fundamentos epistemológicos, teóricos y metodológicos, los cuales enmarcan el análisis de las trayectorias: la centralidad del sujeto, la relación individuo-sociedad, la integración de perspectivas metodológicas y la importancia de la dimensión espacio-temporal. La relevancia de esta tarea radica en que el enfoque biográfico se constituye como telón de fondo en el estudio de las trayectorias laborales. En el primer apartado se indagan los orígenes del uso de biografías en la investigación social; en el segundo y el tercero, se examinan los supuestos centrales del enfoque biográfico y del curso de vida, al encontrar en ellos las raíces que encuadran y dan sentido al estudio de las trayectorias. Por último, se desarrollan los aportes y potencialidades de los estudios con trayectorias laborales a través del análisis de un corpus de investigaciones empíricas producidas en América Latina

Claves de la ciudadanía política femenina en la primera mitad del siglo XX en Argentina

En este artículo, se exploran algunos hechos que jalonaron la edificación de la Argentina y configuraron dispositivos centrales para la construcción de los sexos en la primera mitad del siglo XX. En ese camino, se examinan cambios y continuidades en la construcción de la ciudadanía política femenina. Desde una perspectiva de género, se subraya las diferentes imposiciones legales e institucionales asociadas a la masculinidad y a la feminidad de las prácticas sociales. El problema central, en ese sentido, se vincula con la definición de las mujeres como sujeto e individuo

El enfoque biográfico en el análisis social : Claves para un estudio de los aspectos teórico-metodológicos de las trayectorias laborales

Este trabajo desarrolla los supuestos que se esconden tras los estudios biográficos, centrándose en los enfoques europeo y norteamericano. Intenta vislumbrar los distintos ámbitos de producción en donde surgieron los fundamentos epistemológicos, teóricos y metodológicos, los cuales enmarcan el análisis de las trayectorias: la centralidad del sujeto, la relación individuo-sociedad, la integración de perspectivas metodológicas y la importancia de la dimensión espacio-temporal. La relevancia de esta tarea radica en que el enfoque biográfico se constituye como telón de fondo en el estudio de las trayectorias laborales. En el primer apartado se indagan los orígenes del uso de biografías en la investigación social; en el segundo y el tercero, se examinan los supuestos centrales del enfoque biográfico y del curso de vida, al encontrar en ellos las raíces que encuadran y dan sentido al estudio de las trayectorias. Por último, se desarrollan los aportes y potencialidades de los estudios con trayectorias laborales a través del análisis de un corpus de investigaciones empíricas producidas en América Latina

Distribution of desmoscolecida (Nematoda) in surface sediments of the Iberian Deep-Sea, North Atlantic (Table 1)

1. Desmoscolecida from the continental slope and the deep-sea bottom (59-4354 m) off the Portuguese and Moroccan coasts are described. 18 species were identified: Desmoscolex bathyalis sp. nov., D. chaetalatus sp. nov., D. eftus sp. nov., D. galeatus sp. nov., D. lapilliferus sp. nov., D. longisetosus Timm, 1970, D. lorenzeni sp. nov., D. perspicuus sp. nov., D. pustulatus sp. nov., Quadricoma angulocephala sp. nov., Q. brevichaeta sp. nov., Q. iberica sp. nov., Q. loricatoides sp. nov., Tricoma atlantica sp. nov., T. bathycola sp. nov., T. beata sp. nov., T. incomposita sp. nov., T. meteora sp. nov., T. mauretania sp. nov. 2. The following new terms are proposed: "Desmos" (ring-shaped concretions consisting of secretion and concretion particles), "desmoscolecoid" and "tricomoid" arrangement of the somatic setae, "regelmaessige" (regular), "unregelmaessige" (irregular), "vollstaendige" (complete) and "unvollstaendige" (incomplete) arrangement of somatic seta (variations in the desmoscolecoid arrangement of the somatic setae). The length of the somatic setae is given in the setal pattern. 3. Desmoscolecida identical as to genus and species exhibit no morphological differences even if forthcoming from different bathymetrical zones (deep sea, sublitoral, litoral) or different environments (marin, freshwater, coastal subsoil water, terrestrial environment). 4. Lorenzen's (1969) contention that thearrangement of the somatic setae is more significant for the natural relationships between the different genera of Desmoscolecida than other characteristics is further confirmed. Species with tricomoid arrangement of somatic setae are regarded as primitive, species with desmoscolecoid arrangement of somatic setae are regarded as more advanced. 5. Three new genus are established: Desmogerlachia gen. nov., Desmolorenzenia gen. nov. and Desmofimmia gen. nov. - Protricoma Timm, 1970 is synonymized with Paratricoma Gerlach, 1964 and Protodesmoscolex Timm, 1970 is synonymized with Desmoscolex Claparede,1863. 6. Checklists of all species of the order Desmoscolecida and keys to species of the subfamilies Tricominae and Desmoscolecinae are provided. 7. The following nomenclatorial changes are suggested: Desmogerlachia papillifer (Gerlach, 1956) comb. nov., D .pratensis (Lorenz, 1969) comb. nov., Desmotimmia mirabilis (Timm, 1970) comb. nov., Paratricoma squamosa (Timm, 1970) comb. nov., Desmolorenzenia crassicauda (Timm, 1970) comb. nov., D. desmoscolecoides (Timm, 1970) comb. nov., D. eurycricus (Filipjev, 1922) comb. nov., D. frontalis (Gerlach, 1952) comb. nov., D. hupferi (Steiner, 1916) comb. nov., D. longicauda (Timm, 1970) comb. nov., D. parva (Timm, 1970) comb. nov., D. platycricus (Steiner, 1916) comb. nov., D. viffata (Lorenzen, 1969) comb. nov., Desmoscolex anfarcficos (Timm, 1970) comb. nov.

Seawater carbonate chemistry, structural and chemical characteristics of the seagrass Thalassia testudinum in an situ CO2 enrichment experiment

Seagrasses commonly display carbon-limited photosynthetic rates. Thus, increases in atmospheric pCO2, and consequentially oceanic CO2(aq) concentrations, may prove beneficial. While addressed in mesocosms, these hypotheses have not been tested in the field with manipulative experimentation. This study examines the effects of in situ CO2(aq) enrichment on the structural and chemical characteristics of the tropical seagrass, Thalassia testudinum. CO2(aq) availability was manipulated for 6 months in clear, open-top chambers within a shallow seagrass meadow in the Florida Keys (USA), reproducing forecasts for the year 2100. Structural characteristics (leaf area, leaf growth, shoot mass, and shoot density) were unresponsive to CO2(aq) enrichment. However, leaf nitrogen and phosphorus content declined on average by 11 and 21 %, respectively. Belowground, non-structural carbohydrates increased by 29 %. These results indicate that increased CO2(aq) availability may primarily alter the chemical composition of seagrasses, influencing both the nutrient status and resilience of these systems.

Mitigate DoS and DDoS Attack in Ad Hoc Networks

This paper proposes a technique to defeat Denial of Service (DoS) and Distributed Denial of Service (DDoS) attacks in Ad Hoc Networks. The technique is divided into two main parts and with game theory and cryptographic puzzles. Introduced first is a new client puzzle to prevent DoS attacks in such networks. The second part presents a multiplayer game that takes place between the nodes of an ad hoc network and based on fundamental principles of game theory. By combining computational problems with puzzles, improvement occurs in the efficiency and latency of the communicating nodes and resistance in DoS and DDoS attacks. Experimental results show the effectiveness of the approach for devices with limited resources and for environments like ad hoc networks where nodes must exchange information quickly.

Auditoría integrada de Información + Conocimiento: aplicación en un caso de estudio

Se presentan los resultados de la aplicación de una metodología integradora de auditoría de información y conocimiento, llevada a cabo en un Centro de Investigación del Ministerio de Ciencia, Tecnología y Medio Ambiente de la provincia de Holguín, Cuba, conformada por siete etapas con un enfoque híbrido dirigida a revisar la estrategia y la política de gestión de información y conocimiento, identificar e inventariar y mapear los recursos de I+C y sus flujos, y valorar los procesos asociados a su gestión. La alta dirección de este centro, sus especialistas e investigadores manifestaron la efectividad de la metodología aplicada cuyos resultados propiciaron reajustar la proyección estratégica en relación con la gestión de la I+C, rediseñar los flujos informativos de los procesos claves, disponer de un directorio de sus expertos por áreas y planificar el futuro aprendizaje y desarrollo profesional.

Opinion: Can coalescent models explain deep divergences in the diatoms and argue for the acceptance of paraphyletic taxa at all taxonomic hierarchies?

Although ancestral polymorphisms and incomplete lineage sorting are commonly used at the population level, increasing reports of these models have been invoked and tested to explain deep radiations. Hypotheses are put forward for ancestral polymorphisms being the likely reason for paraphyletic taxa at the class level in the diatoms based on an ancient rapid radiation of the entire groups. Models for ancestral deep coalescence are invoked to explain paraphyly and molecular evolution at the class level in the diatoms. Other examples at more recent divergences are also documented. Discussion as to whether or not paraphyletic groups seen in the diatoms at all taxonomic levels should be recognized is provided. The continued use of the terms centric and pennate diatoms is substantiated with additional evidence produced to support their use in diatoms both as descriptive terms for both groups and as taxonomic groups for the latter because new morphological evidence from the auxospores justifies the formal classification of the basal and core araphids as new subclasses of pennate diatoms in the Class Bacillariophyceae. Keys for higher levels of the diatoms showing how the terms centrics and araphid diatoms can be defined are provided.