NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems

Understanding of genotype-phenotype associations is important not only for furthering our knowledge on internal cellular processes, but also essential for providing the foundation necessary for genetic engineering of microorganisms for industrial use (e.g., production of bioenergy or biofuels). However, genotype-phenotype associations alone do not provide enough information to alter an organism's genome to either suppress or exhibit a phenotype. It is important to look at the phenotype-related genes in the context of the genome-scale network to understand how the genes interact with other genes in the organism. Identification of metabolic subsystems involved in the expression of the phenotype is one way of placing the phenotype-related genes in the context of the entire network. A metabolic system refers to a metabolic network subgraph; nodes are compounds and edges labels are the enzymes that catalyze the reaction. The metabolic subsystem could be part of a single metabolic pathway or span parts of multiple pathways. Arguably, comparative genome-scale metabolic network analysis is a promising strategy to identify these phenotype-related metabolic subsystems. Network Instance-Based Biased Subgraph Search (NIBBS) is a graph-theoretic method for genome-scale metabolic network comparative analysis that can identify metabolic systems that are statistically biased toward phenotype-expressing organismal networks. We set up experiments with target phenotypes like hydrogen production, TCA expression, and acid-tolerance. We show via extensive literature search that some of the resulting metabolic subsystems are indeed phenotype-related and formulate hypotheses for other systems in terms of their role in phenotype expression. NIBBS is also orders of magnitude faster than MULE, one of the most efficient maximal frequent subgraph mining algorithms that could be adjusted for this problem. Also, the set of phenotype-biased metabolic systems output by NIBBS comes very close to the set of phenotype-biased subgraphs output by an exact maximally-biased subgraph enumeration algorithm ( MBS-Enum ). The code (NIBBS and the module to visualize the identified subsystems) is available at http://freescience.org/cs/NIBBS

Stigmatized work and stigmatized workers

Stigmas pervade organizational life. A stigma is a discrediting social evaluation that devalues an individual or group. We review research on stigmatized work and stigmatized workers, with a particular emphasis on how people become stigmatized and what they (and others) do about it. To do so, we connect stigma to other concepts in its nomological net and compare multiple models of stigma dynamics. We consider the intertwining nature of stigma and identity/image, how context affects stigma, and how stigma is managed by both the stigmatized and the nonstigmatized. We also offer critiques of key blind spots in workplace stigma research and point toward future research in this area that is more interconnected with other literatures and more inclusive of overlooked populations. Our vantage point is that workplace stigma continues to be an exciting domain of research with a high potential for theoretical discoveries and practical applications

Microbial degradation of acenapthene and napthalene under denitrification conditions in soil--water systems: Annual report, October 1987

This study examined the microbial degradation of acenaphthene and naphthalene under denitrification conditions at soil-to-water ratios of 1:25 and 1:50 with soil containing approximately 10/sup 5/ denitrifying organisms per gram of soil. Under nitrate-excess conditions, both acenaphthene and naphthalene were degraded microbially from initial aqueous-phase concentrations of about one and several mg/l, respectively, to nondetectable levels (<0.01 mg/l) in time periods less than 9 weeks. Acclimation periods of 12 to 36 days were observed prior to the onset of microbial degradation in tests with soil not previously exposed to PAH, while acclimation periods were absent in tests with soil reserved from prior PAH degradation tests. It was judged that the apparent acclimation period resulted from the time for a small population of organisms capable of PAH degradation to attain sufficient densities to exhibit detectable PAH reduction. About 0.9 percent of the naturally occurring soil organic carbon could be mineralized under denitrification conditions, and this accounted for the greater proportion of the nitrate depletion. The mineralization of the labile fraction of the soil organic carbon via microbial denitrification occurred without an observed acclimation period, and was rapid compared to PAH degradation. Under nitrate-limiting conditions the PAH compounds were stable owing to the depletion of nitrate via the more rapid process of soil organic carbon mineralization. The microbial degradation of the PAH compound depends on the interrelationships between: the desorption kinetics and the reversibility of desorption of sorbed compound from the soil, the concentration of PAH-degrading microorganisms, and the competing reaction for nitrate utilization via mineralization of the labile fraction of naturally occurring soil organic carbon. 44 refs., 10 figs

Sorption and Microbial Degradation of Naphthalene in Soil-Water Suspensions under Denitrification Conditions

The microbial degradation of naphthalene under den-itrification conditions in soil-water suspensions was de-pendent on solute partitioning between soil and water. Soil-associated naphthalene was in equilibrium with aqueous-phase solute, with the rate of naphthalene deg¬radation being mixed order with respect to aqueous con¬centration. The rate of degradation was modeled by coupling Michaelis-Menten kinetics for aqueous-phase solute with an intraaggregate radial diffusion model for naphthalene sorption and desorption with soil. It was shown by modeling and confirmed by experiment, for the soil suspension particle sizes employed in these tests, that the naphthalene sorption-desorption process was reversible and rapid compared to the rate of microbial degradation. The maximum rate of microbial degradation was propor¬tional to the soil-to-water ratio and independent of nitrate concentration for initial nitrate concentrations greater than several hundred micrograms per gram of soil. Nitrate reduction was described by utilizing the total mass removal of naphthalene and a stoichiometric conversion factor. A coupled solute desorption-degradation model is presented for microbial degradation of hydrophobic organic com-pounds that are desorbed from porous soil aggregates, assuming sorbed solute is inaccessible to microorganisms and that the rate of solute release from the solid is rapid compared to the rate of retarded intraaggregate diffusion. © 1991, American Chemical Society. All rights reserved