yApoptosis: yeast apoptosis database

In the past few years, programmed cell death (PCD) has become a popular research area due to its fundamental aspects and its links to human diseases. Yeast has been used as a model for studying PCD, since the discovery of morphological markers of apoptotic cell death in yeast in 1997. Increasing knowledge in identification of components and molecular pathways created a need for organization of information. To meet the demands from the research community, we have developed a curated yeast apoptosis database, yApoptosis. The database structurally collects an extensively curated set of apoptosis, PCD and related genes, their genomic information, supporting literature and relevant external links. A web interface including necessary functions is provided to access and download the data. In addition, we included several networks where the apoptosis genes or proteins are involved, and present them graphically and interactively to facilitate rapid visualization. We also promote continuous inputs and curation by experts. yApoptosis is a highly specific resource for sharing information online, which supports researches and studies in the field of yeast apoptosis and cell death

Production and characterization of rhamnolipids from Pseudomonas aeruginosa san ai

Production and characterization of rhamnolipid biosurfactant obtained by strain Pseudomonas aeruginosa san ai was investigated. With regard to carbon and nitrogen source several media were tested to enhance production of rhamnolipids. Phosphate-limited proteose peptone-ammonium salt (PPAS) medium supplemented with sun flower oil as a source of carbon and mineral ammonium chloride and peptone as a nitrogen source greatly improved rhamnolipid production, from 0.15 on basic PPAS (C/N ratio 4.0), to 3 g L-1, on optimized PPAS medium (C/N ratio 7.7). Response surface methodology analysis was used for testing effect of three factors: temperature, concentration of carbon and nitrogen source (w/w), in optimized PPAS medium on rhamnolipid production. Isolated rhamnolipids were characterized by IR and ESI-MS. IR spectra confirmed that isolated compound corresponds to rhamnolipid structure, whereas MS indicated that isolated preparation is a mixture of mono-rhamno-mono-lipidic, mono-rhamno-di-lipidic- and dirhamno- di-lipidic congeners

Renormalization Group Analysis of the 2000-2002 anti-bubble in the US S&P 500 index: Explanation of the hierarchy of 5 crashes and Prediction

We propose a straightforward extension of our previously proposed log-periodic power law model of the ``anti-bubble'' regime of the USA market since the summer of 2000, in terms of the renormalization group framework to model critical points. Using a previous work by Gluzman and Sornette (2002) on the classification of the class of Weierstrass-like functions, we show that the five crashes that occurred since August 2000 can be accurately modelled by this approach, in a fully consistent way with no additional parameters. Our theory suggests an overall consistent organization of the investors forming a collective network which interact to form the pessimistic bearish ``anti-bubble'' regime with intermittent acceleration of the positive feedbacks of pessimistic sentiment leading to these crashes. We develop retrospective predictions, that confirm the existence of significant arbitrage opportunities for a trader using our model. Finally, we offer a prediction for the unknown future of the US S&P500 index extending over 2003 and 2004, that refines the previous prediction of Sornette and Zhou (2002).Comment: Latex document, 11 eps figures and 1 tabl

Kinetic models in industrial biotechnology - Improving cell factory performance

An increasing number of industrial bioprocesses capitalize on living cells by using them as cell factories that convert sugars into chemicals. These processes range from the production of bulk chemicals in yeasts and bacteria to the synthesis of therapeutic proteins in mammalian cell lines. One of the tools in the continuous search for improved performance of such production systems is the development and application of mathematical models. To be of value for industrial biotechnology, mathematical models should be able to assist in the rational design of cell factory properties or in the production processes in which they are utilized. Kinetic models are particularly suitable towards this end because they are capable of representing the complex biochemistry of cells in a more complete way compared to most other types of models. They can, at least in principle, be used to in detail understand, predict, and evaluate the effects of adding, removing, or modifying molecular components of a cell factory and for supporting the design of the bioreactor or fermentation process. However, several challenges still remain before kinetic modeling will reach the degree of maturity required for routine application in industry. Here we review the current status of kinetic cell factory modeling. Emphasis is on modeling methodology concepts, including model network structure, kinetic rate expressions, parameter estimation, optimization methods, identifiability analysis, model reduction, and model validation, but several applications of kinetic models for the improvement of cell factories are also discussed

The potential of discs from a "mean Green function"

By using various properties of the complete elliptic integrals, we have derived an alternative expression for the gravitational potential of axially symmetric bodies, which is free of singular kernel in contrast with the classical form. This is mainly a radial integral of the local surface density weighted by a regular "mean Green function" which depends explicitly on the body's vertical thickness. Rigorously, this result stands for a wide variety of configurations, as soon as the density structure is vertically homogeneous. Nevertheless, the sensitivity to vertical stratification | the Gaussian profile has been considered | appears weak provided that the surface density is conserved. For bodies with small aspect ratio (i.e. geometrically thin discs), a first-order Taylor expansion furnishes an excellent approximation for this mean Green function, the absolute error being of the fourth order in the aspect ratio. This formula is therefore well suited to studying the structure of self-gravitating discs and rings in the spirit of the "standard model of thin discs" where the vertical structure is often ignored, but it remains accurate for discs and tori of finite thickness. This approximation which perfectly saves the properties of Newton's law everywhere (in particular at large separations), is also very useful for dynamical studies where the body is just a source of gravity acting on external test particles.Comment: Accepted for publication in MNRAS, 11 page

Essential Genetic Interactors of SIR2 Required for Spatial Sequestration and Asymmetrical Inheritance of Protein Aggregates

Sir2 is a central regulator of yeast aging and its deficiency increases daughter cell inheritance of stress-and aging-induced misfolded proteins deposited in aggregates and inclusion bodies. Here, by quantifying traits predicted to affect aggregate inheritance in a passive manner, we found that a passive diffusion model cannot explain Sir2-dependent failures in mother-biased segregation of either the small aggregates formed by the misfolded Huntingtin, Htt103Q, disease protein or heat-induced Hsp104-associated aggregates. Instead, we found that the genetic interaction network of SIR2 comprises specific essential genes required for mother-biased segregation including those encoding components of the actin cytoskeleton, the actin-associated myosin V motor protein Myo2, and the actin organization protein calmodulin, Cmd1. Co-staining with Hsp104-GFP demonstrated that misfolded Htt103Q is sequestered into small aggregates, akin to stress foci formed upon heat stress, that fail to coalesce into inclusion bodies. Importantly, these Htt103Q foci, as well as the ATPase-defective Hsp104(Y662A)-associated structures previously shown to be stable stress foci, co-localized with Cmd1 and Myo2-enriched structures and super-resolution 3-D microscopy demonstrated that they are associated with actin cables. Moreover, we found that Hsp42 is required for formation of heat-induced Hsp104(Y662A) foci but not Htt103Q foci suggesting that the routes employed for foci formation are not identical. In addition to genes involved in actin-dependent processes, SIR2-interactors required for asymmetrical inheritance of Htt103Q and heat-induced aggregates encode essential sec genes involved in ER-to-Golgi trafficking/ER homeostasis