Parameterization and classification of the protein universe via geometric techniques

We present a scheme for the classification of 3487 non-redundant protein structures into 1207 non-hierarchical clusters by using recurring structural patterns of three to six amino acids as keys of classification. This results in several signature patterns, which seem to decide membership of a protein in a functional category. The patterns provide clues to the key residues involved in functional sites as well as in protein-protein interaction. The discovered patterns include a "glutamate double bridge" of superoxide dismutase, the functional interface of the serine protease and inhibitor, interface of homo/hetero dimers, and functional sites of several enzyme families. We use geometric invariants to decide superimposability of structural patterns. This allows the parameterization of patterns and discovery of recurring patterns via clustering. The geometric invariant-based approach eliminates the computationally explosive step of pair-wise comparison of structures. The results provide a vast resource for the biologists for experimental validation of the proposed functional sites, and for the design of synthetic enzymes, inhibitors and drugs.     

A cybernetic model to predict the effect of freely available nitrogen substrate on rifamycin B production in complex media

It is well-known that secondary metabolite production is repressed by excess nitrogen substrate available in the fermentation media. Although the nitrogen catabolite repression has been known, quantitative process models have not been reported to represent this phenomenon in complex medium. In this paper, we present a cybernetic model for rifamycin B production via Amycolatopsis mediterranei S699 in complex medium, which is typically used in industry. Nitrogen substrate is assumed to be present in two forms in the medium; available nitrogen (S _ANS) such as free amino acids and unavailable nitrogen (S _UNS) such as peptides and proteins. The model assumes that an inducible enzyme catalyzes the conversion of S _UNS to S _ANS. Although S _ANS is required for growth and product formation, high concentrations were found to inhibit rifamycin production. To experimentally validate the model, five different organic nitrogen sources were used that differ in the ratio of S _ANS/S _UNS. The model successfully predicts higher rifamycin B productivity for nitrogen sources that contain lower initial S _ANS. The higher productivity is attributed to the sustained availability of S _ANS at low concentration via conversion of S _UNS to S _ANS, thereby minimizing the effects of nitrogen catabolite repression on rifamycin production. The model can have applications in model-based optimization of substrate feeding recipe and in monitoring and control of fed batch processes.     

Hierarchical amino acid utilization and its influence on fermentation dynamics: rifamycin B fermentation using Amycolatopsis mediterranei S699, a case study

Background  

Industrial fermentation typically uses complex nitrogen substrates which consist of mixture of amino acids. The uptake of amino acids is known to be mediated by several amino acid transporters with certain preferences. However, models to predict this preferential uptake are not available. We present the stoichiometry for the utilization of amino acids as a sole carbon and nitrogen substrate or along with glucose as an additional carbon source. In the former case, the excess nitrogen provided by the amino acids is excreted by the organism in the form of ammonia. We have developed a cybernetic model to predict the sequence and kinetics of uptake of amino acids. The model is based on the assumption that the growth on a specific substrate is dependent on key enzyme(s) responsible for the uptake and assimilation of the substrates. These enzymes may be regulated by mechanisms of nitrogen catabolite repression. The model hypothesizes that the organism is an optimal strategist and invests resources for the uptake of a substrate that are proportional to the returns.     

A germacranolide from cyathocline lutea

While Cyathocline lyrata only afforded known compounds, the aerial parts of C. lutea gave a new sesquiterpene lactone, 5β-hydroxy-4,9-oxidogermacr-11-en-6,12-olide.     

Robust,small-scale cultivation platform for <Emphasis Type="Italic">Streptomyces coelicolor</Emphasis>

Background  

For fermentation process and strain improvement, where one wants to screen a large number of conditions and strains, robust and scalable high-throughput cultivation systems are crucial. Often, the time lag between bench-scale cultivations to production largely depends on approximate estimation of scalable physiological traits. Microtiter plate (MTP) based screening platforms have lately become an attractive alternative to shake flasks mainly because of the ease of automation. However, there are very few reports on applications for filamentous organisms; as well as efforts towards systematic validation of physiological behavior compared to larger scale are sparse. Moreover, available small-scale screening approaches are typically constrained by evaluating only an end point snapshot of phenotypes.     

A Eudesmanolide and a guaianolide from Cyathocline purpurea

Two new sesquiterpene lactones, the eudesmanolide, isoivangustin, and the guaianolide, 6α-hydroxy-4(14),10(15)-guaianadien-8α,12-olide, have been isolated from Cyathocline purpurea.     

Defining immigrant newcomers in new destinations: symbolic boundaries in Williamsburg,Virginia

Abstract

This article examines media representations of immigration in Williamsburg, Virginia, a ‘new immigrant destination’ in the USA. Through a content analysis of coverage in Williamsburg's local newspaper, we explore how reporters, columnists and readers draw on nationally and internationally circulating discourses to produce public interpretations of immigration issues and construct symbolic boundaries between and among in-groups and ‘others’ in the community. ‘National boundaries drawn locally’ captures how media actors use nationally recognizable frames to interpret local issues and define the parameters of community and national belonging. ‘Localized symbolic boundaries’ take their meanings from place-based, cultural understandings, specific economic conditions and demographics in the local setting. Newspaper discussions in Williamsburg distinguish between ‘deserving’ foreign student workers (primarily from Eastern Europe and Asia) and ‘undeserving’, racialized, Latino ‘others’. Our analysis advances theories of boundary construction and holds implications for the politics of belonging more generally in other immigrant-receiving contexts.     

Effect of high CO<Subscript>2</Subscript> concentrations on the growth and macromolecular composition of a heat- and high-light-tolerant microalga

A green microalga, Acutodesmus sp., a close relative of Acutodesmus deserticola, was isolated from the wastewater discharges of an oil refinery in India. This study examined the effects of light intensity, temperature, pH, and high-CO₂ treatments (up to 20 %) on the growth of the alga and investigated the effects of different CO₂ treatments on its macromolecular composition (protein, carbohydrate, and lipids). Under controlled laboratory conditions, the alga showed high growth rates over a wide range of light (up to 700 μmol photons m^?2 s^?1), temperature (up to 40 °C), and pH (5–10) conditions. In the stationary phase, the highest protein and carbohydrate content was found to be 71.52 and 40.72 % of dry weight at 5 and 15 % CO₂, respectively. After 5 days of cultivation, the maximum dry weight biomass attained in these cultures was 1.149, 1.99, 1.75, and 1.65 g L^?1 at 5, 10, 15, and 20 % CO₂, respectively, indicating that this strain has significant tolerance to CO₂. These results indicate that this strain is a promising candidate for use in biofixation of CO₂ from the flue gases emitted by industries, and it also has a strong potential as a feedstock for value-added substances.