Determination of the equilibrium constants of self-associating protein systems. X. Evaluation of the weight fraction of monomer from the diffusion coefficient as a function of concentration

A simplified procedure for determining the mode of association and weight fraction of monomer of a self-associating protein system based on the average diffusion coefficient as a function of concentration is described. This procedure is applicable to cases of monomer-n-mer, three species or indefinite association.     

De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides

Self-association is a common phenomenon in biology and one that can have positive and negative impacts, from the construction of the architectural cytoskeleton of cells to the formation of fibrils in amyloid diseases. Understanding the nature and mechanisms of self-association is important for modulating these systems and in creating biologically-inspired materials. Here, we present a two-stage de novo peptide design framework that can generate novel self-associating peptide systems. The first stage uses a simulated multimeric template structure as input into the optimization-based Sequence Selection to generate low potential energy sequences. The second stage is a computational validation procedure that calculates Fold Specificity and/or Approximate Association Affinity (K^*_association) based on metrics that we have devised for multimeric systems. This framework was applied to the design of self-associating tripeptides using the known self-associating tripeptide, Ac-IVD, as a structural template. Six computationally predicted tripeptides (Ac-LVE, Ac-YYD, Ac-LLE, Ac-YLD, Ac-MYD, Ac-VIE) were chosen for experimental validation in order to illustrate the self-association outcomes predicted by the three metrics. Self-association and electron microscopy studies revealed that Ac-LLE formed bead-like microstructures, Ac-LVE and Ac-YYD formed fibrillar aggregates, Ac-VIE and Ac-MYD formed hydrogels, and Ac-YLD crystallized under ambient conditions. An X-ray crystallographic study was carried out on a single crystal of Ac-YLD, which revealed that each molecule adopts a β-strand conformation that stack together to form parallel β-sheets. As an additional validation of the approach, the hydrogel-forming sequences of Ac-MYD and Ac-VIE were shuffled. The shuffled sequences were computationally predicted to have lower K^*_association values and were experimentally verified to not form hydrogels. This illustrates the robustness of the framework in predicting self-associating tripeptides. We expect that this enhanced multimeric de novo peptide design framework will find future application in creating novel self-associating peptides based on unnatural amino acids, and inhibitor peptides of detrimental self-aggregating biological proteins.     

Comparison of Selected Methods for the Enumeration of Fecal Coliforms and Escherichia coli in Shellfish

In a comparison of five selected methods for the enumeration of fecal coliforms and Escherichia coli in naturally contaminated and sewage-seeded mussels (Choromytilus spp.) and oysters (Ostrea spp.), a spread-plate procedure with mFC agar without rosolic acid and preincubation proved the method of choice for routine quality assessment.     

Specificity of Prodan for the Self-associating Domain of Spectrin: A Molecular Docking Study

Abstract

The hydrophobic fluorescent probe Prodan binds to the self-associating domain of spectrin with 1:1 stoichiometry. A model of the self-associating domain was generated based on its homology with other domains of spectrin. Prodan was then docked onto the model, and several sites with low interaction energy were identified. To verify whether the binding of Prodan is specific towards the self-associating domain of spectrin, it was docked on to several other domains of spectrin, having a known three-dimensional structure. Analysis of the docking results suggests that the binding of Prodan to the self-associating domain of spectrin will involve hydrophobic and hydrophilic groups of Prodan. The results clearly indicate the preference of Prodan for a particular binding site of the self-associating domain.     

Sedimentation coefficients of self-associating species: I. Basic theory

Under the same solution conditions, the apparent weight average sedimentation coefficient, s_wa, and some quantities obtained from it can be combined with the equilibrium constant or constants, K_i, and the monomer concentration, c_I, obtained from sedimentation equilibrium, light scattering or osmotic pressure experiments on the same self-associating solute, so that the individual sedimentation coefficients, s_i, of the self-associating species, and also the hydrodynamic concentration dependence parameter,g or $\text{g}$, can be evaluated. Using two different models for the hydrodynamic concentration parameter, four different methods are presented for the evaluation of the s_i's. Methods for evaluating g or $\text{g}$, once the s_i's are known, are presented. A method for obtaining the number average sedimentation coefficient, s_N, and its application to self-associations is presented. Methods are shown for the evaluation of Z average properties, x_zc, as well as number average properties,x_Nc, of a self-associating solute from its weight average properties, x_wc.     

Rapid Technique for the Enumeration of Clostridium perfringens

A new medium, Tryptone-sulfite-neomycin (TSN) agar, and an incubation procedure for the enumeration of Clostridium perfringens are described. Tolerance to neomycin, optimal growth at 46 C, and sulfite-reducing properties of C. perfringens were used as a basis for development of the medium. Comparisons were made between sulfite-polymyxin-sulfadiazine (SPS) agar and TSN agar at 37 and 46 C with C. perfringens and other organisms. These studies indicate the quantitative and selective superiority of TSN agar, incubated at 46 C, over SPS agar.     

Immobilization and Detection of Listeria monocytogenes

A procedure was developed for immobilization of Listeria monocytogenes cells on metal hydroxides coupled with detection and enumeration using an automated optical system. The results of the immobilization procedure (<1 h) and detection during overnight incubation agreed with calculated plate counts, and this technique is simple and rapid and provides samples that are ready for confirmation of the presence of the pathogen by rapid methods.     

Membrane Filter Technique for Enumeration of Pseudomonas aeruginosa

A membrane filter procedure for the quantitation of Pseudomonas aeruginosa (mPA procedure) has been developed. Through the use of inhibitors and an elevated incubation temperature, the level of background microbial flora was decreased approximately 10,000-fold. Using P. aeruginosa cells suspended in sea water and held for 24 hr, between 70 and 100% of the „viable” cells could be recovered by the mPA procedure. Assay variability was found to be insignificant. The recoveries of P. aeruginosa from surface (fresh and salt) waters, potable waters, and sewage by the mPA procedure exceeded those obtainable by current methods. Subsequent to its development and evaluation, the mPA procedure was used at three other laboratories for the enumeration of P. aeruginosa in potable and recreational waters and in sewage samples. It was found amenable to routine use, and confirmation of typical colonies approached 100%.     

Comparison and Recovery of Escherichia coli and Thermotolerant Coliforms in Water with a Chromogenic Medium Incubated at 41 and 44.5°C

This study compared the performance of a commercial chromogenic medium, CHROMagarECC (CECC), and CECC supplemented with sodium pyruvate (CECCP) with the membrane filtration lauryl sulfate-based medium (mLSA) for enumeration of Escherichia coli and non-E. coli thermotolerant coliforms (KEC). To establish that we could recover the maximum KEC and E. coli population, we compared two incubation temperature regimens, 41 and 44.5°C. Statistical analysis by the Fisher test of data did not demonstrate any statistically significant differences (P = 0.05) in the enumeration of E. coli for the different media (CECC and CECCP) and incubation temperatures. Variance analysis of data performed on KEC counts showed significant differences (P = 0.01) between KEC counts at 41 and 44.5°C on both CECC and CECCP. Analysis of variance demonstrated statistically significant differences (P = 0.05) in the enumeration of total thermotolerant coliforms (TTCs) on CECC and CECCP compared with mLSA. Target colonies were confirmed to be E. coli at a rate of 91.5% and KEC of likely fecal origin at a rate of 77.4% when using CECCP incubated at 41°C. The results of this study showed that CECCP agar incubated at 41°C is efficient for the simultaneous enumeration of E. coli and KEC from river and marine waters.     

Membrane Filter Technique for Enumeration of Enterococci in Marine Waters

A membrane filter procedure is described for the enumeration of enterococci in marine waters. The procedure utilizes a highly selective and somewhat differential primary isolation medium followed by an in situ substrate test for identifying colonies of those organisms capable of hydrolyzing esculin. The procedure (mE) was evaluated with known streptococci strains and field samples with regard to its accuracy, sensitivity, selectivity, specificity, precision, and comparability to existing methods. Essentially quantitative recovery was obtained with seawater-stressed cells of Streptococcus faecalis and S. faccium. Neither S. bovis, S. equinus, S. mitis, nor S. salivarius grew on the medium. The selectivity of the medium was such that a 10,000-fold reduction in background organisms was obtained relative to a medium which contained no inhibitors and was incubated at 35 C. About 90% of those typical colonies designated as enterococci confirmed as such and about 12% of the colonies not so designated were, in fact, identified as enterococci. Plate to plate variability across samples approximated that expected by chance alone. Verified recoveries of enterococci from natural samples by the mE procedure, on the average, exceeded those by the KF method by one order of magnitude.     

Fluorescent antibody staining method for enumeration of viable environmental Vibrio cholerae 01

A membrane filtration method has been developed which is useful for enumeration of viable Vibriocholerae 01 in environmental water samples by immunofluorescent staining. The samples are incubated with yeast extract and nalidixic acid. Substrate responsive cells, i.e., viable cells, elongate and after staining with specific antiserum and fluorescein conjugate, viable V. cholera cells appear as long, peripheral fluorescent green banded bacilli when viewed under the microscope. Using an ocular reticule, the number of viable cells per ml can be calculated. The procedure has been adapted for use with other bacterial species if specific antisera are employed.     

Stable Tagging of Rhizobium meliloti with the Firefly Luciferase Gene for Environmental Monitoring

A system for stable tagging of gram-negative bacteria with the firefly luciferase gene, luc, is described. A previously constructed fusion constitutively expressing luc from the λp_R promoter was used. Stable integration into the bacterial genome was achieved by use of mini-Tn5 delivery vectors. The procedure developed was applied for tagging of representative gram-negative bacteria, such as Escherichia coli, Rhizobium meliloti, Pseudomonas putida, and Agrobacterium tumefaciens. The system permitted the detection of tagged R. meliloti in the presence of more than 10⁵ CFU per plate without the use of any selective markers (such as antibiotic resistance genes). No significant differences in growth rates or soil survival were found between the marked strain and the wild-type strain. Studies of bioluminescent R. meliloti also revealed a good correlation between cell biomass and bioluminescence. The firefly luciferase tagging system is an easy, safe, and sensitive method for the detection and enumeration of bacteria in the environment.     

Comparison of Fecal Coliform Agar and Violet Red Bile Lactose Agar for Fecal Coliform Enumeration in Foods

A 24-h direct plating method for fecal coliform enumeration with a resuscitation step (preincubation for 2 h at 37 ± 1°C and transfer to 44 ± 1°C for 22 h) using fecal coliform agar (FCA) was compared with the 24-h standardized violet red bile lactose agar (VRBL) method. FCA and VRBL have equivalent specificities and sensitivities, except for lactose-positive non-fecal coliforms such as Hafnia alvei, which could form typical colonies on FCA and VRBL. Recovery of cold-stressed Escherichia coli in mashed potatoes on FCA was about 1 log unit lower than that with VRBL. When the FCA method was compared with standard VRBL for enumeration of fecal coliforms, based on counting carried out on 170 different food samples, results were not significantly different (P > 0.05). Based on 203 typical identified colonies selected as found on VRBL and FCA, the latter medium appears to allow the enumeration of more true fecal coliforms and has higher performance in certain ways (specificity, sensitivity, and negative and positive predictive values) than VRBL. Most colonies clearly identified on both media were E. coli and H. alvei, a non-fecal coliform. Therefore, the replacement of fecal coliform enumeration by E. coli enumeration to estimate food sanitary quality should be recommended.     

Semienclosed Tube Cultures of Bean Plants (Phaseolus vulgaris L.) for Enumeration of Rhizobium phaseoli by the Most-Probable-Number Technique

The semienclosed tube culture technique of Gibson was modified to permit growth of common bean (Phaseolus vulgaris L.) roots in humid air, enabling enumeration of the homologous (nodule forming) symbiont, Rhizobium phaseoli, by the most-probable-number plant infection method. A bean genotype with improved nodulation characteristics was used as the plant host. This method of enumeration was accurate when tubes were scored 3 weeks after inoculation with several R. phaseoli strains diluted from aqueous suspensions, peat-based inoculants, or soil. A comparison of population sizes obtained by most-probable-number tube cultures and plate counts indicated that 1 to 3 viable cells of R. phaseoli were a sufficient inoculant to induce nodule formation.     

A Simple, Rapid Method for Enumerating Total Viable and Metabolically Active Bacteria in Groundwater

We report here a new staining procedure which uses both the enzymatic dehydrogenation of 2-(p-iodophenyl)-3-p-(nitrophenyl)-5 phenyltetrazolium chloride to a pink intracellular formazan and the DNA-specific fluorochrome 4′,6′-diamidino-2-phenylindole. Application of this staining procedure to cells concentrated on filters and then transferred to microscope slides by the filter-transfer-freeze technique has proven valuable for statistically accurate enumeration of the total viable and metabolically active cells in groundwaters.     

Evaluation of Fusarium head blight in barley infected by Fusarium graminearum

Fusarium head blight, which is primarily caused by Fusarium graminearum, is a devastating disease in the barley field. A real-time PCR protocol was developed to evaluate the growth of this pathogen in the host plant tissues. All four strains harbored the gene encoding ATP-BINDING CASSETTE TRANSPORTER (FgABC; FGSG_00541) as a single copy within their genomes. Our Southern blot result was identical with the genomic data for F. graminearum strain PH-1. Based on the crossing point (CP) values obtained in our TaqMan real-time PCR analysis, two standard curves describing the relationship among the CP value, FgABC copy number, and amount of fungal DNA were constructed. Chronological enumeration of fungal growth was coincided with the symptom development.     

Impact of Mount St. Helens Eruption on Bacteriology of Lakes in the Blast Zone

Lakes lying within the blast zone of Mount St. Helens showed dramatic increases in heterotrophic bacterial numbers after the eruption of 18 May 1980. The total microscopic counts of bacteria in some of the most severely affected lakes were more than 10⁷ cells per ml, an order of magnitude above the counts in outlying control lakes. Likewise, the numbers of viable bacteria reached levels of more than 10⁶ cells per ml, compated with fewer than 10⁴ cells per ml in control lakes. The CPS medium used for enumeration provided growth of up to 81.5% of the bacteria during sampling of one of the blast zone lakes. The high numbers of bacteria and the efficacy of the viable enumeration procedure are evidence that the lakes have been transformed rapidly from oligotrophy to eutrophy due to the eruption and its aftermath. Organic material leached from the devastated forest vegetation is thought to be responsible for the enrichment of heterotrophs. Total coliform bacteria were found in all of the blast zone lakes, and some lakes contained fecal coliform bacteria. Klebsiella pneumoniae was the predominant total coliform and was also identified as one of the fecal coliform bacteria, although Escherichia coli was the predominant species in that category. Our data indicate that bacterial populations peaked in the outer blast zone lakes in the summer of 1980 and in most of the inner lakes during the summer of 1981.     

Enumeration of Anaerobic Chytridiomycetes as Thallus-Forming Units: Novel Method for Quantification of Fibrolytic Fungal Populations from the Digestive Tract Ecosystem

An endpoint dilution procedure, based on the technique of most probable numbers, was developed to enumerate anaerobic chytridiomycetes as thallus-forming units. The method does not distinguish between zoospores and thalli, but does permit enumeration of fungal populations with respect to their ability to digest plant cell walls. Fibrolytic populations in batch culture, ruminal contents, and feces were compared by relating viable counts to the dry matter content of enumerated samples (i.e., thallus-forming units per gram of dry matter). Batch cultures of Neocallimastix sp. strain R1 grown on wheat straw were used to assess the enumeration procedure and to demonstrate the potential of the technique for quantification of anaerobic fungi in vivo. Determination of total ruminal contents from steers enabled the quantification of the entire population of fiber-degrading anaerobic fungi in the reticulorumen. The enumeration procedure revealed substantial populations of fibrolytic anaerobic fungi in fresh and air-dried feces. Populations in fresh feces were equivalent to those in ruminal contents, but declined exponentially with time in dry feces. Minimum values were obtained from dry feces 90 days after drying, and anaerobic fungi were detectable for up to 210 days thereafter.     

Cytofluorometric detection of wine lactic acid bacteria: application of malolactic fermentation to the monitoring

In this study we report for the first time a rapid, efficient and cost-effective method for the enumeration of lactic acid bacteria (LAB) in wine. Indeed, up to now, detection of LAB in wine, especially red wine, was not possible. Wines contain debris that cannot be separated from bacteria using flow cytometry (FCM). Furthermore, the dyes tested in previous reports did not allow an efficient staining of bacteria. Using FCM and a combination of BOX/PI dyes, we were able to count bacteria in wines. The study was performed in wine inoculated with Oenococcus oeni (10⁶ CFU ml^?1) stained with either FDA or BOX/PI and analyzed by FCM during the malolactic fermentation (MLF). The analysis show a strong correlation between the numbers of BOX/PI-stained cells determined by FCM and the cell numbers determined by plate counts (red wine: R ² ≥ 0.97, white wine R ² ≥ 0.965). On the other hand, we found that the enumeration of O. oeni labeled with FDA was only possible in white wine (R ² ≥ 0.97). Viable yeast and LAB populations can be rapidly discriminated and quantified in simultaneous malolactic-alcoholic wine fermentations using BOX/PI and scatter parameters in a one single measurement. This rapid procedure is therefore a suitable method for monitoring O. oeni populations during winemaking, offers a detection limit of <10⁴ CFU ml^?1 and can be considered a useful method for investigating the dynamics of microbial growth in wine and applied for microbiological quality control in wineries.     

Transformation Frequency of a mariner-Based Transposon in Rickettsia rickettsii

Transformation frequencies of a mariner-based transposon system in Rickettsia rickettsii were determined using a plaque assay system for enumeration and isolation of mutants. Sequence analysis of insertion sites in both R. rickettsii and R. prowazekii indicated that insertions were random. Transposon mutagenesis provides a useful tool for rickettsial research.