Microscopic Counting and Adenosine 5′-Triphosphate Measurement in Determining Microbial Growth in Soils

A microscopic technique utilizing dispersion of fungal hyphae in a Waring blender, filtration through membrane filters (Nucleopore Corp.), and counting on a fluorescence microscope was developed for counting fungal hyphal biomass. Nonfluorescent staining techniques of the soil-filter preparation did not give quantitative recoveries. Water-soluble aniline blue, which binds to the β-1,3-glucans of the fungal cell wall, made visualization of the hyphae by fluorescence possible. A range of fungi added to soil were quantitatively recovered. Adenosine 5′-triphosphate (ATP) was extracted from soil by lysis of the organisms with CHCl₃ in NaHCO₃, which prevented adsorption of the organic phosphorus to the soil colloids. Centrifugation and removal of CHCl₃ was followed by dilution with pH 7.8 tris(hydroxymethyl)aminomethane buffer. ATP concentrations were measured by using the luciferase-luciferin light reaction. Since NaHCO₃ interfered to some extent with this reaction, the standards were made up in equivalent mixtures of tris(hydroxymethyl)aminomethane buffer and NaHCO₃. Recovery of ATP was rapid and quantitative in a range of soils. Measurement of the ATP and bacterial and fungal numbers in an incubated soil showed that fungal and bacterial population increases were delayed by phosphorus deficiency. Microbial populations were not affected at a later date. The ATP content of the soil system was reduced by phosphorus deficiency throughout the incubation period. This indicated that ATP could be altered without major changes in the microbial populations.     

Efficient extraction of proteins from formalin-fixed paraffin-embedded tissues requires higher concentration of tris(hydroxymethyl)aminomethane

Background

Numerous formaldehyde-fixed and paraffin-embedded clinical tissues have been created in the past decades and stored in pathological depositories at hospitals as well as in clinical laboratories worldwide. In addition to the archived tissues, formaldehyde-fixation is also mandatory for preparing proteomics samples from diseased patients or animal models in order to inactivate contagious agents. Protein extraction from formaldehyde-fixed tissues is hampered by the Schiff base formation between the amino groups of proteins and formaldehyde. Although achievement of the highest extraction efficiency of proteins from the formaldehyde-fixed tissues is essential for obtaining maximum proteomics information, no attention has been paid to the concentration dependence of tris(hydroxymethyl)aminomethane on the extraction efficacy. We suspected that the concentration of tris(hydroxymethyl)aminomethane affects the protein extraction efficiency because of its property as a primary amine that reverses the Schiff base formation between the primary amines of proteins and formaldehyde. Thus we pursued optimization of the component and protocol of protein extraction buffer to achieve better extraction efficiency of proteins from formaldehyde-fixed and paraffin-embedded tissues.

Results

In order to simulate protein extraction from diseased tissues we made formaldehyde-fixed and paraffin-embedded samples from mouse liver slices and investigated the protein extraction efficiency and speed by changing the concentration of the protein extraction buffer component tris(hydroxymethyl)aminomethane under various extraction conditions. We find, as expected, that tris(hydroxymethyl)aminomethane significantly affects the performance of protein extraction from the formaldehyde-fixed and paraffin-embedded samples both in the extraction yield and in the extraction speed.

Conclusions

We recommend the concentration of tris(hydroxymethyl)aminomethane in protein extraction buffer to be higher than 300 mM when extraction is conducted for 90 min at 90°C to achieve the most efficient protein extraction in a shorter time. The information will be essential for performing the most efficient protein extraction from formaldehyde-fixed and paraffin-embedded tissue samples for proteomics analysis.     

Isolation and electron microscopic observations of intracytoplasmic inclusions containing Chlamydia psittaci.

Intracytoplasmic inclusions containing Chlamydia psittaci were isolated by a newly established method. Infected L-cells at 20 h after infection were suspended in 0.25 M sucrose-tris(hydroxymethyl)aminomethane buffer containing ethylene-diaminetetraacetic acid, homogenized in a Dounce tissue grinder, and filtered through a 2,000-mesh screen. Isolated inclusions were stabilized in 5% bovine serum albumin in 10 mM tris(hydroxymethyl)aminomethane buffer. Electron microscopic observations revealed the presence of surface projections on the vegetative, reticulate bodies and a direct connection between the reticulate bodies and the inclusion membrane by means of projections.     

Purification and characterization of a molecular weight 100,000 coat protein from coated vesicles obtained from bovine brain

A protein designated as a 100-kDa protein on the basis of sodium dodecyl sulfate gel electrophoresis was purified from coated vesicles obtained from bovine brain, with uncoated vesicles as starting material. Two gel filtration steps, one involving 0.5 M tris(hydroxymethyl)aminomethane, pH 8.0, buffer, and the other 0.01 M tris(hydroxymethyl)aminomethane, pH 8.0, and 3 M urea buffer, were employed. The purified protein has a native molecular weight of 114,000 as determined by sedimentation equilibrium analysis. Circular dichroism data showed that the protein has 28% helical structure, 29% beta-structure, and 15% beta-turns, and the rest is random coil. Addition of the purified protein to clathrin results in the polymerization of clathrin to homogeneous size baskets of sedimentation velocity 150 S. A scan of the Coomassie Blue stained electrophoresis gels of the polymerized baskets shows that, for every clathrin trimer, there is approximately one 100-kDa protein molecule.     

Deoxyribonucleic acid replication in permeable and fully viable Escherichia coli cells.

Escherichia coli cells made permeable with a hypotonic tris(hydroxymethyl)aminomethane buffer utilized exogenous deoxyribonucleoside triphosphates to perform semiconservative replication. The rate of replication was the same as in cells made permeable with toluene or sucrose.     

A note on the synthesis of 5'-AMP ester of tris (hydroxymethyl)aminomethane by rat liver plasma membrane.

The alcohol-AMP synthesizine enzyme of rat liver plasma membrane also synthesizes the 5'-AMP ester of tris(hydroxymethyl)aminomethane as judged by the use of [alpha-32P] ATP and [U-14C] ATP. This synthetic process may decrease significantly the concentration of ATP during incubation.     

Production and Heat Stability of Staphylococcal Nuclease

No correlation existed between numbers of organisms and nuclease activity in laboratory-grown cultures of Staphylococcus aureus. Nuclease production was inhibited by anaerobic incubation and stimulated by aeration. Strains of S. aureus varied in the production of nuclease. The optimum pH for enzyme production was 8.3 and employment of a tris(hydroxymethyl)aminomethane buffer system resulted in increased production of the enzyme as compared with a phosphate buffer. The nuclease was extremely heat-stable and had a D value of 16.6 min at 130 C.     

The in vitro effects of EDTA-tris, EDTA-tris-lysozyme, and antimicrobial agents on equine genital isolants of Pseudomonas aeruginosa

Five isolants of Pseudomonas aeruginosa collected from clinical cases of equine genital infection and one standard strain of P. aeruginosa were exposed to various concentrations of ethylene-diaminetetraacetic acid (EDTA) and tris (hydroxymethyl) aminomethane (tris buffer pH 8) and EDTA-tris lysozyme. Colony forming units of the isolants and minimal inhibitory concentrations for 11 antimicrobial agents were determined with each isolant before and after exposure to the EDTA solutions. Decreased cellular viability was found with all six isolants after exposure to the EDTA-tris solutions. Reversal of antimicrobial resistance was variable and unpredictable. These effects were not enhanced by the addition of lysozyme. The results suggest that EDTA-tris could be a useful adjunct in treating equine genital infections caused by Pseudomonas aeruginosa .     

Method for the lysis of Gram-positive, asporogenous bacteria with lysozyme.

A method developed for the lysis of oral streptococci that employed the action of lysozyme suspended in dilute tris(hydroxymethyl)aminomethane-hydrochloride buffer containing polyethylene glycol has been adapted for use with lactobacilli, actinomycetes, propionibacteria, and pediococci. Most of the cellular deoxyribonucleic acid was liberated from many strains of bacteria usually thought to be lysozyme resistant. The major observations were as follows: (i) supplementation of the growth medium with L-threonine, L-lysine, or both frequently produced cells that were more susceptible to lysis by lysozyme; (ii) glucose-containing media produced cells that were more easily lysed than those from cultures grown on other substrates; (iii) polyethylene glycol not only served as an osmotic stabilizer, it also enhanced the extent of lysis; and (iv) dilute tris(hydroxymethyl)aminomethane buffer was superior to the buffer systems most commonly employed in published muramidase-based lysis techniques. Stationary-phase cells of Lactobacillus casei and Streptococcus mutans were more easily lysed than those isolated from log-phase cultures. The method as detailed in this report should be generally applicable for the lysis of gram-positive, asporogenous bacteria.     

Quantification of single-stranded nucleic acid and oligonucleotide interactions with metal ions by affinity capillary electrophoresis: part I

The interactions between oligonucleotides and inorganic cations have been measured by capillary zone electrophoresis. With increasing concentrations of divalent cations (Ca²⁺, Mg²⁺, Mn²⁺ and Ni²⁺) in the running buffer, the migration behavior was evaluated by calculation of the binding constants. Besides these fundamental studies of binding equilibria, different buffer components, tris(hydroxymethyl)aminomethane and 3-(N-morpholino)propanesulfonic acid, have been investigated and their effects on metal ion binding quantified.     

Defective Deoxyribonucleic Acid Replication of T4rII Bacteriophage in Lambda-Lysogenic Host Cells

Sedimentation of the replicative deoxyribonucleic acid through alkaline sucrose gradients showed that rII single chains reached the half-mature size at a time when wild-type molecules formed long chains (dimers and trimers of genome size). Long rII single chains could be observed on substitution of tris(hydroxymethyl)aminomethane buffer for Na⁺K⁺ phosphate in the growth medium.     

Bleomycin-DNA interactions: fluorescence and proton magnetic resonance studies.

The interaction of bleomycin A2 with DNA has been examined by fluorescence spectroscopy and proton magnetic resonance techniques. Fluorescence bands observed at 353 and 405 nm in the spectrum of bleomycin were assigned to the bithiazole and 4-aminopyrimidine rings, respectively. Quenching of bithiazole fluorescence by DNA was used to determine apparent equilibrium constants for the complex which, in 2.5 mM tris(hydroxymethyl)aminomethane buffer, pH 8.4, are 1.2 X 10(5) M-1 for bleomycin and 1.4 X 10(5) M-1 for tripeptide S, a partial acid hydrolysis product of the antibiotic. Uner these conditions, one molecule of bleomycin binds for every five to six base pairs in DNA. In the proton magnetic resonance spectrum of bleomycin, resonances emanating from the bithiazole rings and dimethylsulfonium groups are preferentially broadened and reduced in intensity in the presence of DNA, suggesting that these moieties bind most tightly to the polymer.     

菌丝室接种解磷细菌Bacillus megaterium C4对土壤有机磷矿化和植物吸收的影响

通过30μm尼龙网将根盒分成根室和菌丝室,菌丝室中的低磷土壤施加75 mg P/kg土壤的植酸钙,研究了菌丝室土壤中丛枝菌根(AM)真菌Glomus intraradices和解磷细菌Bacillus megaterium C4对有机磷的矿化和吸收.结果表明,在试验条件下,植酸钙的溶解性很低,对土壤溶液有机磷的贡献不大.接种解磷细菌C4提高了土壤中磷酸酶的活性,减少了土壤中有机磷的含量.但是,由于存在解磷细菌与AM真菌对磷的竞争,解磷细菌矿化出的磷大部分被自身利用,AM真菌的生长受到抑制,解磷细菌对植物磷营养的改善没有表现出显著的贡献.     

Effect of calcium and anaerobiosis on the thermostability of Bacillus stearothermophilus.

Bacillus stearothermophilus NCA 2184 lost viability and subsequently released cytoplasmic components when suspended in 0.1 M tris(hydroxymethyl)aminomethane (Tris) buffer (pH 7.2) and incubated at 60 degrees C. Cell lysis was prevented by the addition of 10 mM CaCl2 to the Tris-buffer suspension. Cells which were incubated under anaerobic conditions for 20 min in the growth medium before they were collected were stable in the Tris-buffer suspension without added calcium. Anaerobic incubation effected an increase in membrane cardiolipin which appeared to be related to the increase in the thermostability of the cells.     

A high pH discontinuous buffer system for resolution of isozymes in starch gel electrophoresis

A Tris-citrate pH 9.5 gel/borate pH 8.2 electrode discontinuous buffer system for starch gel electrophoresis of proteins was developed to resolve iso- and allozymes of aspartate aminotransferase in frogs (Hyla crucifer). This buffer system also enhanced resolution of NADP-dependent malate dehydrogenase and the L-lactate dehydrogenase-A locus in this species. It provided good resolution of NAD-dependent malate dehydrogenase in esocid fishes, and esterases, glycerol-3-phosphate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, alcohol dehydrogenase, and S-aconitate hydratase in ambystomatid salamanders. Variation suppressed by other buffers was revealed by this buffer for some enzyme encoding loci, while at other loci, this buffer suppressed electromorph variability. The concentration of tris(hydroxymethyl)aminomethane in gels made with this buffer was much higher than in pH 8.7 "Poulik" gels, but running characteristics of the two gel types were similar. Gels made with this new buffer were less prone to splitting and "warping" than Poulik gels, and were easier to handle. When screening a given taxon for enzyme variability, tests using multiple buffers are essential to maximize the amount of electrophoretically detectable variation.     

Increased outer membrane resistance to ethylenediaminetetraacetate and cations in novel lipid A mutants.

Polymyxin-resistant pmrA mutants of Salmonella typhimurium differed from their parents in that they were resistant to tris(hydroxymethyl)aminomethane-ethylenediaminetetraacetate-lysozyme, tris(hydroxymethyl)aminomethane-ethylenediaminetetraacetate-deoxycholate, and tris(hydroxymethyl)aminomethane-ethylenediaminetetraacetate-bacitracin. Tris(hydroxymethyl)aminomethane-ethylenediaminetetraacetate released about 50% less lipopolysaccharide from the pmrA strains than from the parental strains when the bacteria were grown in L-broth containing 2 mM Ca2+. Protamine, polylysine, octapeptin, benzalkonium chloride, cold NaCl, cold MgCl2, or cold tris(hydroxymethyl)aminomethane hydrochloride (pH 7.2) caused no leakage or markedly less leakage of periplasmic beta-lactamase from a pmrA mutant than from its parent strain. pmrA mutants were more resistant than their parent strains to protamine and polylysine but not to octapeptin or benzalkonium chloride, as measured by the ability of these agents to kill the bacteria or to sensitize them to deoxycholate-induced lysis. The pmrA strains did not differ from their parent strains in sensitivity to several antibiotics, in porin function (as measured by cephaloridine diffusion across the outer membrane), or in outer membrane-associated phospholipase A activity.     

Dissociation and reassembly of Escherichia coli type 1 pili.

Escherichia coli type 1 pili, which mediate the mannose-sensitive adherence of the bacterium to eucaryotic cells, are comprised of very stable arrays of pilin protein subunits (molecular weight, approximately 17,000). Previous methods for the dissociation of pili caused their irreversible denaturation. We have found that incubation of pili in saturated guanidine hydrochloride at 37 degrees C led to their complete dissociation, as evidenced by nephelometry and electron microscopy. Gel chromatography of the dissociated pili on a Sepharose CL-6B column in the presence of saturated guanidine hydrochloride yielded a single protein peak with a molecular weight corresponding to that of pilin. Dialysis of this peak against 5 mM tris(hydroxymethyl)aminomethane hydrochloride (pH 8.0) and rechromatography in the same buffer afforded a major protein peak, probably consisting of pilin dimers. About 25% of the protein in this peak bound to a mannan-sepharose column and could be eluted with methyl alpha-D-mannoside. The pilin dimer gave a single protein band upon polyacrylamide gel electrophoresis in the presence of 0.1% sodium dodecyl sulfate (molecular weight, 16,600) or 10 M urea and penetrated completely into 7% gels in the absence of denaturants. Reassembly of the pilin dimers into pili was achieved upon dialysis against the tris(hydroxymethyl)aminomethane buffer containing 5 mM MgCl2, as observed by electron microscopy. Thus, the conditions used allow renaturation of the dissociated subunits and may aid in further studies of the structure-function relationship of pili.     

A turbidimetric and electron microscopic study of the effects of several parameters on the lysis of Streptococcus faecalis by lysozyme

The lytic effect of lysozyme on Streptococcus faecalis ATCC 9790 was studied by spectrophotometry and electron microscopy and it was found to be highly dependent on the ionic strength of the suspending media and on the ratio lysozyme to bacterial cell mass. When 7.2 X 10(8) bacteria/mL are exposed to 0.4 mg/mL of lysozyme in media with low ionic strength, the enzyme is bound in great amounts, as deduced from protein determinations and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS--PAGE); the binding prevents bacteriolysis in spite of the removal of the cell wall. Extensive lysis of S. faecalis could be obtained by reducing the ratio of lysozyme to bacterial cell mass. Stabilization of S. faecalis by lysozyme was also observed when exponential phase cells incubated under conditions that promote spontaneous autolysis (incubation in 0.05 M tris(hydroxymethyl)aminomethane buffer, pH 8.0, ionic strength = 0.01675) do not lyse and do not leak material which absorbs at 260 nm when lysozyme was present at the highest concentration.     

New Medium for Blood Cultures

A new medium suitable for blood cultures is described. It contains dextrose, cysteine, iron, and magnesium, in a tris(hydroxymethyl)aminomethane buffer, and a mixture of peptones derived from animal tissues, casein, and yeast. In comparison with Trypticase Soy Broth, the growth rate constants of Staphylococcus aureus, Streptococcus (Viridans group), enterococcus, and Escherichia coli were higher in this medium, and growth appeared earlier in a significant number of clinical blood cultures.     

A High Ph Discontinuous Buffer System for Resolution of Isozymes in Starch Gel Electrophoresis

A Tris-citrate pH 9.5 gel/borate pH 8.2 electrode discontinuous buffer system for starch gel electrophoresis of proteins was developed to resolve iso- and allozymes of aspartate aminotransferase in frogs (Hyla crucifer).- This buffer system also enhanced resolution of NADP-dependent malate dehydrogenase and the L-lactate dehydrogenase-A locus in this species. It provided good resolution of NAD-dependent malate dehydrogenase in esocid fishes, and esterases, glycerol-3-phosphate dehydrogenase, glyceraldehyde-3-phospbate dehydrogenase, alcohol dehydrogenase, and S-aconitate hydratase in ambystomatid salamanders. Variation suppressed by other buffers was revealed by this buffer for some enzyme encoding loci, while at other loci, this buffer suppressed electromorph variability. The concentration of tris(hydroxymethyl)aminomethane in gels made with this buffer was much higher than in pH 8.7 “Poulik” gels, but running characteristics of the two gel types were similar. Gels made with this new buffer were less prone to splitting and “warping” than Poulik gels, and were easier to handle. When screening a given taxon for enzyme variability, tests using multiple buffers are essential to maximize the amount of electrophoretically detectable variation.