A novel means to develop strain-specific DNA probes for detecting bacteria in the environment.

A simple means to develop strain-specific DNA probes for use in monitoring the movement and survival of bacteria in natural and laboratory ecosystems was developed. The method employed amplification of genomic DNA via repetitive sequence-based PCR (rep-PCR) using primers specific for repetitive extragenic palindromic (REP) elements, followed by cloning of the amplified fragments. The cloned fragments were screened to identify those which were strain specific, and these were used as probes for total genomic DNA isolated from microbial communities and subjected to rep-PCR. To evaluate the utility of the approach, we developed probes specific for Burkholderia cepacia G4 and used them to determine the persistence of the strain in aquifer sediment microcosms following bioaugmentation. Two of four probes tested were found to specifically hybridize to DNA fragments of the expected sizes in the rep-PCR fingerprint of B. cepacia G4 but not to 64 genetically distinct bacteria previously isolated from the aquifer. One of these probes, a 650-bp fragment, produced a hybridization signal when as few as 10 CFU of B. cepacia G4 were present in a mixture with 10(6) CFU nontarget strains, indicating that the sensitivity of these probes was comparable to those of other PCR-based detection methods. The probes were used to discriminate groundwater and microcosm samples that contained B. cepacia G4 from those which did not. False-positive results were obtained with a few samples, but these were readily identified by using hybridization to the second probe as a confirmation step. The general applicability of the method was demonstrated by constructing probes specific to three other environmental isolates.     

A Similar Dichotomy of Sugar Modulation and Developmental Expression Affects Both Paths of Sucrose Metabolism: Evidence from a Maize Invertase Gene Family

Invertase and sucrose synthase catalyze the two known paths for the first step in carbon use by sucrose-importing plant cells. The hypothesis that sugar-modulated expression of these genes could provide a means of import adjustment was initially suggested based on data from sucrose synthases alone; however, this hypothesis remained largely conjectural without critical evidence for invertases. Toward this end, a family of maize invertases was cloned and characterized. Here, we show that invertases are indeed sugar modulated and, surprisingly, like the sucrose synthase genes, fall into two classes with contrasting sugar responses. In both families, one class of genes is upregulated by increasing carbohydrate supply (Sucrose synthase1 [Sus1] and Invertase2 [Ivr2]), whereas a second class in the same family is repressed by sugars and upregulated by depletion of this resource (Shrunken1 [Sh1] and Invertase1 [Ivr1]). The two classes also display differential expression during development, with sugar-enhanced genes (Sus1 and Ivr2) expressed in many importing organs and sugar-repressed, starvation-tolerant genes (Sh1 and Ivr1) upregulated primarily during reproductive development. Both the Ivr1 and Ivr2 invertase mRNAs are abundant in root tips, very young kernels, silk, anthers, and pollen, where a close relationship is evident between changes in message abundance and soluble invertase activity. During development, patterns of expression shift as assimilate partitioning changes from elongating silks to newly fertilized kernels. Together, the data support a model for integrating expression of genes differentially responsive to carbohydrate availability (i.e., feast and famine conditions) with developmental signals. The demonstration that similar regulatory patterns occur in both paths of sucrose metabolism indicates a potential to influence profoundly the adjustment of carbon resource allocation.     

Reduced product formation following perturbation of ethanol- and propionate-fed methanogenic CSTRs

Energetic analysis was applied to reduced product formation following perturbation of ethanol- and propionate-fed methanogenic continuous stirred tank reactors (CSTRs). Formation and dissipation of longer-chained n-carboxylic acids corresponded with the variation in Gibbs free energy change associated with beta-oxidation reactions. Formation appeared to occur from acetate and propionate by reductive back-reactions, made energetically favorable by elevated hydrogen partial pressure (P(H(2) )), and possibly mediated by biosynthetic enzymes. The formed longer-chained acids dissipated when the P(H(2) ) fell and equilibrium shifted to favor beta-oxidations. n-Propanol was found to be produced from propionate in a coupled ethanol oxidation/propionate reduction reaction, mediated by ethanol-oxidizing organisms during high rates of ethanol utilization and elevated P(H(2) ). When P(H(2) ) declined, n-propanol was oxidized back to its precursor propionate. Both reaction energetics and intracellular diffusion of the electron carrier may effect transient mediation of this coupled reaction.     

Mitogenic activity of hydroxyapatite: requirement for somatomedin C

Synovial hyperplasia is a feature of the chronic synovitis associated with basic calcium phosphate crystals [hydroxyapatite (HA), octacalcium phosphate, tricalcium phosphate] and calcium pyrophosphate. Each of these crystals stimulated mitosis of cultured human skin fibroblasts or canine synovial fibroblasts in a concentration-dependent fashion. We examined the effect of pure somatomedin C (Sm-C) on HA crystal induced mitogenesis. Confluent cultures of human fibroblasts were rendered quiescent by incubation in the presence of 1% platelet-poor-Sm-C free plasma (PPSCFP) for 24 hours. HA crystals stimulated thymidine incorporation 2.3-fold over control value. Addition of Sm-C significantly augmented the effect of HA crystals (P less than 0.01). Nearly identical effects were observed in the presence of 100 micrograms/ml HA crystals or 15 ng/ml PDGF. Monoclonal antibodies against Sm-C had little effect on the basal 3H thymidine uptake by control cells incubated in 1% PPSCFP but blocked over 50% of the HA crystal or PDGF-induced 3H thymidine incorporation both in the presence or absence of Sm-C. The incomplete blocking suggested either the presence of other "progression" factors, such as insulin-like growth factor II in the conditioned media or the possibility that HA or PDGF in high enough dosage enabled cells to escape their dependence on Sm-C for DNA synthesis.     

Spherical Lactic Acid-producing Bacteria of Southern-grown Raw and Processed Vegetables

The frequency and levels of population of the spherical lactic acid-producing bacteria were determined on raw and processed yellow summer and zucchini squash, a variety of greens, green beans, okra, southern peas, and butter and lima beans, and on fresh cucumbers and corn flowers. Six taxa occurred consistently: Leuconostoc mesenteroides, yellow-pigmented streptococci, Streptococcus faecium, Aerococcus viridans, and S. faecalis and S. faecalis var. liquefaciens. The same taxa occurred with the same order of frequency on processed, frozen vegetables, but with a marked decrease in the occurrence of S. faecalis var. liquefaciens. S. lactis, S. cremoris, S. equinus, S. bovis, and pediococci were isolated infrequently. No other member of the viridans group of the streptococci and no member of the pyogenic group was isolated. Approximately 88% of the cultures were identified. Total counts of the lactic-acid-producing bacteria rarely exceeded 10⁵ per gram of sample, and there was a reduction by 90% during the second year of study, probably because of drought. Only one bacterial species was found on 40% of the raw and 34% of the processed vegetable samples. Two or more species or taxa were present on the remainder of 153 raw and 56 processed vegetable samples. A. viridans was present on squash, greens, okra, and southern peas, and its frequency of occurrence on vegetables suggests that plants are its natural habitat.     

Calcium-dependent control of volume regulation in renal proximal tubule cells: II. Roles of dihydropyridine-sensitive and-insensitive Ca2+ entry pathways

Summary The Ca^2– entry pathways in the basolateral plasma membrane of the isolated, nonperfused proximal straight tubule (PST) of rabbit kidney were investigated using fura-2 fluorescence microscopy. Under isotonic conditions, reduction of bath [Ca^2–] from 1 mM to 1 M caused intracellular free calcium concentration ([Ca²⁺]_i) to fall close to zero. Treatment with 10 M verapamil, a calcium channel blocker, had a similar effect. Treatment with verapamil or low Ca²⁺ also induced fluctuations in cell volume. However, isotonic treatment with 10 M nifedipine, a dihydropyridine (DHP)-type calcium channel blocker, did not affect [Ca²⁺]_i or cell volume, indicating that the endogenous Ca²⁺ entry pathway is verapamil-sensitive but DHP-insensitive. When cells were exposed to hypotonic solutions in the presence of 1 mM Ca²⁺, they swelled and underwent normal RVD while [Ca²⁺]_i increased transiently to a peak before decreasing to a late phase plateau level above the baseline level (see McCarty, N.A., O'Neil, R.G. 1991.J. Membrane Biol. 123:149–160). When cells were swollen in the presence of verapamil or low bath [Ca²⁺], RVD was abolished and [Ca²⁺]_i fell well below the baseline during the late phase response. In contrast, when cells were swollen in the presence of nifedipine, RVD and the late phase rise in [Ca²⁺]_i were abolished, but [Ca²⁺]_i did not fall below the baseline level in the late phase, indicating that nifedipine inhibited the swelling-induced Ca²⁺ entry but that Ca²⁺ entry by another pathway was undisturbed. It was concluded that PST cells are characterized by two Ca²⁺ permeability pathways in the basolateral membrane. Under both isotonic and hypotonic conditions, Ca²⁺ entry occurs at a slow rate via a verapamil-sensitive, DHP-insensitive baseline Ca²⁺ entry pathway. Cell swelling activates a separate DHP-sensitive, verapamil-sensitive Ca²⁺ entry pathway, which is responsible for the supply of Ca ions to the Ca²⁺-dependent mechanism by which cell volume regulation is achieved.     

Characterization of the cysteinyl-containing peptides of the gamma subunit of coupling factor 1

The cysteinyl peptides of the gamma subunit of chloroplast coupling factor 1 (CF1) have been analyzed by high performance liquid chromatography. Analysis of the reduced enzyme alkylated with 4-vinylpyridine showed that the gamma subunit contains four cysteinyl residues. Two of these residues are involved in a disulfide linkage in CF1 either in solution or bound to washed thylakoid membranes. Two free sulfhydryls, one that is readily attacked by alkylating reagents and another that is less reactive, were also detected. Each of these four cysteinyl residues is present in a separate tryptic peptide derived from the gamma subunit. These results show that 4-vinylpyridine is an excellent reagent for the analysis of cysteinyl-containing peptides and support our analyses of the roles of cysteinyl residues in the gamma subunit in ATP synthesis and hydrolysis.     

Characterization and localization of the ATPase associated with pea chloroplast envelope membranes

Chloroplast envelope membranes isolated from Pisum sativum seedlings have been found to contain a Mg-ATPase activity (specific activity 50-175 nanomoles per minute per milligram protein). The ATPase had a broad pH optimum between 7.0 and 9.5. The activity was not inhibited by oligomycin, N,N′-dicyclohexylcarbodiimide, ouabain, or antibodies directed against chloroplast coupling factor 1; nor was the activity stimulated by monovalent cations. However, the ATPase was inhibited by vanadate, molybdate, and adenylyl imidodiphosphate.

The ATPase hydrolyzed a broad range of nucleoside triphosphates, but did not hydrolyze ADP, AMP, or pyrophosphate. The K_m for Mg-ATP was determined to be 0.2 millimolar. The ATPase was found to be distinct from ADPase and pyrophosphatase activities also present in pea envelope membranes.

The ATPase was determined to be located on the inner membrane of the envelope after resolution of inner and outer membranes by sucrose density gradient centrifugation.

     

Hypothesis formulation and testing in aquatic bioassays: a deterministic model approach

The paper examines the significance of toxicant kinetics information obtained from aquatic toxicity bioassays and bioconcentration tests. The data, bioconcentration kinetics and acute mortality versus exposure-duration information for juvenile American flagfish (Jordanella foridae) exposed to 1,4-dichlorobenzene, are interpreted in terms of a one-compartment, first-order kinetics model. The output of the model is used to formulate a testable hypothesis regarding the comparison of toxicant kinetics derived from both bioconcentration test exposures and toxicity bioassays. The model's estimates of the toxicant body burden attained at mortality are compared with theoretical and observed body burdens from literature sources. The use of a simple, deterministic residue-based, one-compartment, first-order kinetics model to evaluate existing data, as well as to formulate hypotheses to direct experimental designs, is examined.