Weakly useful sequences

An infinite binary sequence x is defined to be

(i) strongly useful if there is a computable time bound within which every decidable sequence is Turing reducible to x; and

(ii) weakly useful if there is a computable time bound within which all the sequences in a non-measure 0 subset of the set of decidable sequences are Turing reducible to x.

Juedes, Lathrop, and Lutz [Theorectical Computer Science 132 (1994) 37] proved that every weakly useful sequence is strongly deep in the sense of Bennett [The Universal Turing Machine: A Half-Century Survey, 1988, 227] and asked whether there are sequences that are weakly useful but not strongly useful. The present paper answers this question affirmatively. The proof is a direct construction that combines the martingale diagonalization technique of Lutz [SIAM Journal on Computing 24 (1995) 1170] with a new technique, namely, the construction of a sequence that is “computably deep” with respect to an arbitrary, given uniform reducibility. The abundance of such computably deep sequences is also proven and used to show that every weakly useful sequence is computably deep with respect to every uniform reducibility.

Effect of sterol alterations on conjugation in Saccharomyces cerevisiae.

Sterol auxotrophic strains of Saccharomyces cerevisiae were grown and allowed to conjugate on media supplemented with various sterols. The mating efficiency of the auxotrophs is perturbed by the replacement of the normal yeast sterol, ergosterol, with other sterols. After 4 h of mating, cells grown on ergosterol exhibited a 30-fold higher productive mating efficiency than those cells grown in stigmasterol. Aberrant budding by the conjugants was enhanced following incubation on stigmasterol and other non-ergosterol sterols. Using light and electron microscopy, we demonstrated that there is a reduced ability for stigmasterol-grown cells to undergo cytoplasmic fusion during conjugation. Many of the mated pairs remained adherent but prezygotic even after 12 h of incubation. The addition of ergosterol to cells previously grown on stigmasterol rescued the organisms, allowing for zygote formation and normal budding.     

Predicting methyl tert-butyl ether, tert-butyl formate, and tert-butyl alcohol levels in the environment using the fugacity approach

Through its extensive use as a fuel oxygenate, methyl tert-butyl ether (MTBE) is found nearly ubiquitouslythroughout the environment. To better understand the environmental fate of MTBE, fugacity models are commonly used. However, models developed by the scientific community and by governmental bodies differ in their predictions of relative MTBE concentrations for relevant environmental compartments and of seasonal concentration variations; further, to date they have not considered the formation of transformation products. In this study, the sensitivity of predicted environmental concentrations of MTBE and its two major degradation products, tert-butyl formate (TBF) and tert-butyl alcohol (TBA), to all types of model input parameters is analyzed in a probabilistic sensitivity analysis. This analysis allowed for an assessment of the most influential parameters for predicting soil, water, and air concentrations and thereby provided insight into why previous modeling studies on MTBE differed. Further, the information from the sensitivity analysis was used to parametrize a multispecies transformation model for predicting European concentration levels of MTBE and, for the first time, TBF and TBA. Water and air concentrations of MTBE predicted with the transformation model were in good agreement with measurements of environmental samples. No studies are available on environmental TBF and TBA levels to compare with model predictions; however, the modeling results indicate that, in the water phase, TBA concentrations may reach appreciable levels. One major uncertainty identified regarding the prediction of TBA levels was the fraction of TBA formed from atmospheric MTBE and TBF.     

Application of multimedia models for screening assessment of long-range transport potential and overall persistence

We propose a multimedia model-based methodology to evaluate whether a chemical substance qualifies as POP-like based on overall persistence (Pov) and potential for long-range transport (LRTP). It relies upon screening chemicals against the Pov and LRTP characteristics of selected reference chemicals with well-established environmental fates. Results indicate that chemicals of high and low concern in terms of persistence and long-range transport can be consistently identified by eight contemporary multimedia models using the proposed methodology. Model results for three hypothetical chemicals illustrate that the model-based classification of chemicals according to Pov and LRTP is not always consistent with the single-media half-life approach proposed by the UNEP Stockholm Convention and thatthe models provide additional insight into the likely long-term hazards associated with chemicals in the environment. We suggest this model-based classification method be adopted as a complement to screening against defined half-life criteria at the initial stages of tiered assessments designed to identify POP-like chemicals and to prioritize further environmental fate studies for new and existing chemicals.     

Recent advances in environmental risk assessment of transformation products

When micropollutants degrade in the environment, they may form persistent and toxic transformation products, which should be accounted for in the environmental risk assessment of the parent compounds. Transformation products have become a topic of interest not only with regard to their formation in the environment, but also during advanced water treatment processes, where disinfection byproducts can form from benign precursors. In addition, environmental risk assessment of human and veterinary pharmaceuticals requires inclusion of human metabolites as most pharmaceuticals are not excreted into wastewater in their original form, but are extensively metabolized. All three areas have developed their independent approaches to assess the risk associated with transformation product formation including hazard identification, exposure assessment, hazard assessment including dose-response characterization, and risk characterization. This review provides an overview and defines a link among those areas, emphasizing commonalities and encouraging a common approach. We distinguish among approaches to assess transformation products of individual pollutants that are undergoing a particular transformation process, e.g., biotransformation or (photo)oxidation, and approaches with the goal of prioritizing transformation products in terms of their contribution to environmental risk. We classify existing approaches for transformation product assessment in degradation studies as exposure- or effect-driven. In the exposure-driven approach, transformation products are identified and quantified by chemical analysis followed by effect assessment. In the effect-driven approach, a reaction mixture undergoes toxicity testing. If the decrease in toxicity parallels the decrease of parent compound concentration, the transformation products are considered to be irrelevant, and only when toxicity increases or the decrease is not proportional to the parent compound concentration are the TPs identified. For prioritization of transformation products in terms of their contribution to overall environmental risk, we integrate existing research into a coherent model-based, risk-driven framework. In the proposed framework, read-across from data of the parent compound to the transformation products is emphasized, but limitations to this approach are also discussed. Most prominently, we demonstrate how effect data for parent compounds can be used in combination with analysis of toxicophore structures and bioconcentration potential to facilitate transformation product effect assessment.     

Effect of fungal damage on seed composition and quality of soybeans

Fungal damage caused by pathogens such asFusarium, Cercospora, andPhomopsis can have a devastating impact on physical quality and farm price of soybeans. In some price-discount schedules, soybeans may be rejected with as low as 5% fungal damage. Although the severity of this problem varies throughout the United States, millions of bushels of fungus-damaged soybeans may be destroyed annually due to a lack of markets. The effect of fungal damage on seed composition was evaluated to assess potential utility of highly damaged soybeans. Graded samples of the cv. Centennial soybean were dried to 10% moisture and blended on a proportional weight basis to derive a series of treatments from 0 to 80% fungal damage. A positive correlation was found between fungal damage and both protein and oil concentrations. This condition was attributed to loss of residual seed mass. As a result, the protein concentration of defatted meal increased from ca. 54 to 66% over the range of 0 to 80% fungal damage. Mycotoxin contamination appeared to be insignificant in these high-protein meals. Fixed colors in bleached, alkali refined oils were intensified by heat treatment prior to extraction. No significant differences, however, were noted in total polar lipid content, phospholipid, or tocopherol composition among treatments of up to 20% fungal damage. Oils from treatments of more than 40% fungal damage were more severely oxidized and could not be degummed effectively. These data suggest that fungus-damaged soybeans may be blended with high-quality soybeans to alleviate the chemical symptoms associated with unacceptable product quality. Thus, through various blend ratios, processors may consider using fungus-damaged soybeans to gain economic advantage, especially when high-quality soybeans have lower protein concentration.     

Growth ofCururbita maxima L. plants in the presence of the cycloartenol synthase inhibitor U18666A1

Squash, like other Cucurbitaceae, have unique sterol profiles that offer an excellent opportunity to examine the relationship between sterol biosynthesis and plant growth. To determine the effect of sterol biosynthesis inhibition on squash growth, Cucurbita maxima seedlings with and without cotyledons were subjected to increasing concentrations of the cycloartenol synthase (EC 5.4.99.8) inhibitor 3β-(2-diethylaminoethoxy) androstenone (U18666A). Inhibition of shoot growth was concentration-dependent (from 0, 2, 5, 10, and 20 μM); plants with intact cotyledons grew to 26.4, 23.7, 21.6, 20.0, and 15.6 cm, respectively, at the above inhibitor concentrations, compared to 25.5, 19.4, 17.0, 12.0, and 11 cm for plants with severed cotyledons. In plants with severed cotyledons, 10 and 20 μM U18666A caused rapid necrosis of the first two, newly emerged, primary leaves, and halted new leaf formation. Secondary root formation was initially affected at all inhibitor concentrations regardless of whether cotyledons were present or not. Vegetative tissue showed a decrease in the accumulation of the major squash sterol, 7, 22-stigmastadienol, accompanied by increased accumulation of minor sterol components. Sterol profiles in cotyledons were unaltered. The data show that sterols are crucial for maintaining plant growth and viability, but do not address the cotyledonary effect on growth with respect to sterol biosynthesis. Based on a paper presented at the Symposium on the “Regulation of Biosynthesis and Function of Isopentenoids”, Atlanta, Georgia, May 1994.     

Pesticide nonextractable residue formation in soil: insights from inverse modeling of degradation time series

Formation of soil nonextractable residues (NER) is central to the fate and persistence of pesticides. To investigate pools and extent of NER formation, an established inverse modeling approach for pesticide soil degradation time series was evaluated with a Monte Carlo Markov Chain (MCMC) sampling procedure. It was found that only half of 73 pesticide degradation time series from a homogeneous soil source allowed for well-behaved identification of kinetic parameters with a four-pool model containing a parent compound, a metabolite, a volatile, and a NER pool. A subsequent simulation indeed confirmed distinct parameter combinations of low identifiability. Taking the resulting uncertainties into account, several conclusions regarding NER formation and its impact on persistence assessment could nonetheless be drawn. First, rate constants for transformation of parent compounds to metabolites were correlated to those for transformation of parent compounds to NER, leading to degradation half-lives (DegT50) typically not being larger than disappearance half-lives (DT50) by more than a factor of 2. Second, estimated rate constants were used to evaluate NER formation over time. This showed that NER formation, particularly through the metabolite pool, may be grossly underestimated when using standard incubation periods. It further showed that amounts and uncertainties in (i) total NER, (ii) NER formed from the parent pool, and (iii) NER formed from the metabolite pool vary considerably among data sets at t→∞, with no clear dominance between (ii) and (iii). However, compounds containing aromatic amine moieties were found to form significantly more total NER when extrapolating to t→∞ than the other compounds studied. Overall, our study stresses the general need for assessing uncertainties, identifiability issues, and resulting biases when using inverse modeling of degradation time series for evaluating persistence and NER formation.     

Pleiotropic mutations in Saccharomyces cerevisiae affecting sterol uptake and metabolism

Sterol uptake control mutants (upc-) have been isolated via ethylmethanesulfonate mutagenesis from wild-type Saccharomyces cerevisiae. These mutants are heme and sterol competent but possess the ability to accumulate exogenous sterol(s) under aerobic conditions. Previous studies demonstrate sterol uptake only in a hem-, erg- background; however, the Upc- strains described here are Hem+ and do not require exogenous sterol for growth. We were unable to obtain viable hem+, erg-, upc+ recombinants; such combinations appear to be lethal. Isolates of Upc mutants demonstrated different levels of sterol uptake, and sterol analysis revealed a broad phenotypic range with regard to amounts and accumulation of ergosterol and non-ergosterol sterols. Assays of acyl CoA: ergosterol acyltransferase and sterol ester hydrolase showed no apparent difference in activity between Upc mutants and the wild type.