Heavy-meromyosin-decorated actin filaments: a simple method to preserve actin filaments for rotary shadowing

It has become accepted that deep-freeze-drying at or below -90 degrees C is necessary to preserve the structure of supramolecular assemblies such as actin filaments (AFs) for metal shadowing. This has kept the metal shadowing technique from widespread use in the study of proteins complexed with AFs because of the limited availability of the apparatus for deep-freeze-drying. I report here that adsorption to freshly cleaved mica, treatment with buffered uranyl acetate in glycerol solution, rinsing, and removal of liquid eliminate the need of freeze-drying to preserve the structure of AFs. This technique, in combination with metal shadowing, was applied to the study of AFs decorated with heavy meromyosin (HMM). It was observed that (1) when HMM molecules are associated with single AFs in the majority of cases only one head of each HMM molecule makes contact at the point furthest from the neck region; (2) binding of HMM causes bundling of AFs, probably by the two heads of each molecule binding different filaments; and (3) the binding of HMM to the bundled AFs appears to be more stable than that to a single AF. This method of specimen preparation requires no freeze-drying and is therefore easily applicable to other large protein complexes.     

A simple and effective sample preparation method for atomic force microscopy visualization of individual DNA molecules in situ

A simple, controllable and effective sample preparation method was established for atomic force microscopy (AFM) imaging of individual DNA molecules in aqueous solution. Firstly, magnesium ion (Mg²⁺) at a concentration of 5.0–10.0 mM as a positively charged bridge was transferred onto mica to immobilize DNA molecules. Then Mg²⁺-modified mica was used to investigate DNA molecules in any buffer without magnesium ion by AFM. AFM images demonstrated that DNA molecules can be successfully observed in solution with good resolution, reproducibility, and stability. Further, this DNA sample preparation method makes AFM successful to investigate DNA molecular interaction in situ and DNA/chitosan complex in gene delivery.     

Response Surface Optimization of Lyoprotectant for Lactobacillus bulgaricus During Vacuum Freeze-Drying

The individual and interactive effects of skimmed milk powder, lactose, and sodium ascorbate on the number of viable cells and freeze-drying survival for vacuum freeze-dried powder formulation of Lactobacillus bulgaricus were studied by response surface methodology, and the optimal compound lyoprotectant formulations were gained. It is shown that skim milk powder, lactose, and sodium ascorbate had a significant impact on variables and survival of cultures after freeze-drying. Also, their protective abilities could be enhanced significantly when using them as a mixture of 28% w/v skim milk, 24% w/v lactose, and 4.8% w/v sodium ascorbate. The optimal freeze-drying survival rate and the number of viable cells of Lactobacillus bulgaricus were observed to be (64.41 ± 0.02)% and (3.22 ± 0.02) × 10¹¹ colony-forming units (CFU)/g using the optimal compound protectants, which were very close to the expected values 64.47% and 3.28 × 10¹¹ CFU/g.     

Atomic force microscopic study on topological structures of pBR322 DNA

Plasmid pBR322 DNA (0.5mg/mL) isolated from Escherichia coli HB101 was suspended in Tris-HCl-EDTA (1 mol/L - 0.1 mol/L, pH8.5); then a drop of the above solution was deposited on freshly cleaved mica substrate. After adsorption for about 1 min, the sample was stained with phosphotungstic acid. The residua] solution was removed with a piece of filter paper. Afterwards the sample was imaged with a home-made atomic force microscope (AFM) in air. The AFM images of pBR322 DNA with a molecular resolution have been obtained. These images show that pBR322 DNA exists in several different topological structures: (i) relaxed circular DNA with a different diameter; (ii) supercondensed DNA with different particle sizes; (iii) dimeric catenane connected by one relaxed circular molecule and another dose-compacted molecule which might be either supercoiled or intramolecular knotted form; (iv) oligomeric catenane with multiple irregular molecules in which DNA is interlocked into a complex oligomer; (v) possibly-existing     

正交法优化嗜酸氧化亚铁硫杆菌冷冻干燥保护剂

利用正交实验方法,以甘油、海藻糖、蔗糖和牛血清蛋白为因素,对嗜酸氧化亚铁硫杆菌（Acididfiobacillus ferrooxidans,A．ferrooxidans）冷冻干燥保护剂的最优化配比进行了研究。直观分析、因素指标分析和方差分析的结果表明：由甘油、海藻糖、蔗糖和牛血清蛋白组成的冷冻干燥保护剂中,对存活率影响的主次顺序依次为：甘油〉海藻糖〉牛血清蛋白〉蔗糖。保护剂的最优化组合为甘油5％、海藻糖15％、蔗糖18％、牛血清蛋白10％。经过验证,该组合的保护剂可使冷冻干燥嗜酸氧化亚铁硫杆菌的存活率达到94％。     

Atomic force microscopy of uncoated plasmid DNA: nanometer resolution with only nanogram amounts of sample.

Reproducible, high-contrast, nanometer-resolution AFM images of uncoated plasmid DNA can be obtained with nanogram quantities of DNA with the help of two advances in sample preparation: (1) Heating a DNA solution at 35 degrees C for 10 to 20 minutes before deposition on mica helps separate and spread the DNA, and (2) Using 5 microliter drops of the heated DNA solution in the concentration range of 2 to 10 nanogram/microliter in contact with a specially prepared mica surface for 5 to 10 minutes gives optimal coverage with only nanograms of DNA.     

Effect of culture age, protectants, and initial cell concentration on viability of freeze-dried cells of Metschnikowia pulcherrima

The effect of freeze-drying using different lyoprotectants at different concentrations on the viability and biocontrol efficacy of Metschnikowia pulcherrima was evaluated. The effects of initial yeast cell concentration and culture age on viability were also considered. Yeast cells grown for 36 h were more resistant to freeze-drying than were 48 h cells. An initial concentration of 10? cells·mL?1 favoured the highest survival after freeze-drying. When maltose (25%, m/v) was used as protectant, a high cell viability was obtained (64.2%). Cells maintained a high viability after 6 months of storage at 4 °C. The biocontrol efficacy of freeze-dried cells was similar to the activity of fresh cells on 'Gala' apples and was slightly lower on 'Golden Delicious' apples. After optimizing freeze-drying conditions, the viability of M. pulcherrima cells was similar to that obtained in other studies. The results constitute a first step towards the commercial development of M. pulcherrima as a biocontrol agent.     

A simple method for freeze-drying of macromolecules and macromolecular complexes

We present a simple approach for effective freeze-drying and rotary shadowing of large molecules, molecular assemblies, and cell organelles. Simply, a suspension of specimen is adsorped to a glass coverslip, stabilized, and rinsed with 30% methanol. A second coverslip is "sandwiched" on top, and excess methanol is withdrawn from the edges then frozen by plunging into liquid nitrogen and split. Following either rotary or unidirectional shadowing and replication, the coverslip is dissolved in hydrofluoric acid. In addition to avoiding the problems encountered with air-drying specimens for rotary shadowing, the technique also reproducibly provides the thin layer of solution necessary for proper freeze-drying, regardless of how hydrophobic the sample is. The "glass sandwich" technique allows modification of the glass substrate (making it hydrophobic with carbon or hydrophilic by soaking it in alcian blue) which clearly alters the shape of macromolecular assemblies such as myosin filaments and decorated thin filaments.     

Tapping mode atomic force microscopy of scleroglucan networks

Tapping mode Atomic Force Microscopy (TmAFM) has been used to study the fungal polysaccharide scleroglucan deposited from aqueous solution and dimethyl sulfoxide (DMSO) onto a mica surface. The solutions from which the microscope samples were produced were prepared by first dissolving the solid scleroglucan in 0.1M NaOH, then neutralizing the solution with HCl, followed by dilution to the required concentration in either water or DMSO. It was found that from the aqueous solution described above, scleroglucan forms networks. Based on a comparison of the denatured-renatured and aqueous solution samples, network formation is due to the imperfect registration between the chains forming the triple helices. The relatively large stiffness of the scleroglucan triple helix is also assumed to contribute to the formation of the extended networks. The triple helix diameter was measured to be 0.92 ± 0.27 nm, which is in the same range as that obtained by other researchers using similar techniques. Denatured scleroglucan, deposited from DMSO onto mica, forms a web-like layer on top of which there are sphere-like structures. These morphologies are believed to be due to triple helix denaturation yielding highly flexible single chains in DMSO, which results in coiling and web-like dense packing of scleroglucan upon deposition onto mica. Most interestingly after addition of water to the samples deposited from DMSO, some of the chains can be renatured into short, stiff rod-like structures which are similar to the structures observed by other researchers. The imaging data for aqueous solution deposition can be analyzed by plotting maximum end-to-end distance versus the perimeter of the networks deposited onto mica. This yields a Flory-like exponent of 0.67, which is almost similar in value to that obtained by other researchers for linear structures of scleroglucan but less than that expected for a polymer chain following a self-avoiding walk (v = 0.75) model on a two-dimensional surface. The fractal dimension that can be used to characterize the networks was determined graphically to be 1.22 ± 0.06. © 1997 John Wiley & Sons, Inc. Biopoly 42: 89–100, 1997     

Effect of pH value of freeze-drying solution on the chromosome integrity and developmental ability of mouse spermatozoa

The nuclei of freeze-dried mouse spermatozoa are able to retain their chromosome integrity and developmental potential. To optimize the conditions of freeze-drying, we examined whether pH values of the freeze-drying solution affect the chromosome integrity and developmental potential of sperm nuclei. The sperm freeze-drying solution we used contained a high concentration (50 mM) of calcium-chelating EGTA. Sperm chromosomes were examined at the metaphase of the first mitosis after injection of freeze-dried spermatozoa into matured oocytes. The developmental potential of sperm nuclei was assessed by examining the development of fetuses in midgestation. The results showed that both sperm chromosomes and sperm developmental potential are maintained better when the freeze-drying solution was slightly alkaline (pH 8.0) rather than near neutral or acidic (pH 7.4-6.0). The data indicated that the chromosome integrity and developmental ability of mouse spermatozoa are affected by the pH value of freeze-drying solution.     

Comparison of two direct methods for the determination of fatty acids in infant feces

We have validated and compared two direct methods for the determination of fatty acids in feces by capillary gas chromatography. Method I consisted of esterification of fatty acids using acetyl chloride. Method II used boron trifluoride-methanol as esterification reagent. The two methods were assayed with and without previous freeze-drying of the fecal sample. We found that the two methods could be carried out without sample freeze-drying. Precision and recovery rates were determined and the results were satisfactory. Both methods gave similar results, but Method II has certain advantages over Method I, such as speed, safety, and better recovery rates.     

A Blaze-Dry Spreading Procedure for the Electron Microscopy of Chromosomes from Acid Alcohol-Fixed Human Lymphocytes

A procedure is described for the blaze-drying of human lymphocyte chromosomes on carbonized Parlodion film. Films are prepared by applying Parlodion solution to sheets of freshly cleaved mica. Damage to the film during blaze-drying is prevented by chilling the mica sheets on dry ice before flaming. After spreading, the film and metaphases are floated free from the mica and transferred to a slide of Formvar-coated electron microscope grids. The resulting preparations yield complete metaphase spreads and banded chromosomes morphologically similar to those observed with the light microscope.     

Effect of protective agents and previous acclimation on ethanol resistance of frozen and freeze-dried Lactobacillus plantarum strains

The aim of this work was to study the protective effect of sucrose, trehalose and glutamate during freezing and freeze-drying of three oenological Lactobacillus plantarum strains previously acclimated in the presence of ethanol. The efficiency of protective agents was assessed by analyses of membrane integrity and bacterial cultivability in a synthetic wine after the preservation processes. No significant differences in the cultivability, with respect to the controls cells, were observed after freezing at −80 °C and −20 °C, and pre-acclimated cells were more resistant to freeze-drying than non-acclimated ones. The results of multiparametric flow cytometry showed a significant level of membrane damage after freeze-drying in two of the three strains. The cultivability was determined after incubation in wine-like medium containing 13 or 14% v/v ethanol at 21 °C for 24 h and the results were interpreted using principal component analysis (PCA). Acclimation was the most important factor for preservation, increasing the bacterial resistance to ethanol after freezing and freeze-drying. Freeze-drying was the most drastic method of preservation, followed by freezing at −20 °C. The increase of ethanol concentration from 6 to 10% v/v in the acclimation medium improved the recovery of two of the three strains. In turn, the increase of ethanol content in the synthetic wine led to a dramatic decrease of viable cells in the three strains investigated. The results of this study indicate that a successful inoculation of dehydrated L. plantarum in wine depends not only on the use of protective agents, but also on the cell acclimation process prior to preservation, and on the ethanol content of wine.     

AFM analysis of DNA-protamine complexes bound to mica.

A novel method for reconstituting sperm chromatin was used to investigate how protamine 1 condenses DNA. Complexes formed in vitro using linearized plasmid DNA were imaged and measured by atomic force microscopy (AFM). The structures formed were found to be highly dependent on the sample preparation method used for reconstitution. Interstrand, side-by-side fasiculation of DNA and toroidal-like structures only 1-2 DNA diameters thick were observed for complexes formed in solution following direct mixing of the DNA and protamine. Large chromatin aggregates were also observed on the mica. However, if the DNA was first allowed to attach to the mica prior to addition of the protamine, well-defined toroidal complexes were formed without any observed DNA fasiculation or aggregate formation. The diameter of the toroids measured 30.6-50.2 nm (mean 39.4 nm). The dimensions of these structures indicate that the condensed DNA is stacked vertically by four to five turns, with each coil containing as little as 360-370 bp of 'B'-form DNA. This approach for preparing and imaging DNA-protamine complexes permits the analysis of intermediate structures 'trapped' on the mica as partially formed toruses of nucleoprotamine.     

Chemical treatment of mica for atomic force microscopy can affect biological sample conformation

An important aspect in the preparation of substrate materials to use in atomic force microscopy lies in the question of interactions introduced by treatments designed to immobilize the sample over the substrate. Here we used a mica substrate that was chemically modified with cationic nickel to immobilize actin filaments (F-actin). Chemical modification could be followed quantitatively by measuring the interaction force between the scanning tip and the mica surface. This approach allowed us to observe polymeric F-actin in a structure that resembles an actin gel. It also improved sample throughput and conferred sample stability as well as repeatability from run to run.     

THE INACTIVATION OF BACILLUS SUBTILIS SPORES IN PENICILLIN BY GAMMA RADIATION

SUMMARY: Sodium benzylpenicillin, contaminated with Bacillus subtilis spores by freeze-drying a suspension of spores in an aqueous penicillin solution ( c . 50% w/v), was exposed to gamma radiation and a 70-tube dilution method was used to determine the surviving spores after various doses. The correlation coefficient between log₁₀ percentage survival and dose was −0.9523. The regression of the former on the latter was calculated and the decimal reduction dose found to be 20.2 × 10⁴ rads. The regression and the decimal reduction dose were similar to those obtained when suspensions of spores in distilled water were irradiated.     

Imaging the RecA-DNA complex by atomic force microscopy.

Atomic force microscopy (AFM) was applied to study the RecA protein and its complexes with DNA in air and in aqueous solution. RecA and DNA were reacted under several conditions, and deposited onto a mica substrate pre-treated in various ways. We found that the structure of the RecA and RecA-DNA complexes, especially the height of the molecules, was affected by the sample preparation method such as gel filtration, and environment during imaging.     

A new freeze-drying method for the preservation of nitrogen-fixing and other fragile bacteria

A simple effective and compact freeze-drying method involving skim milk 20% (w/v) and glutamate 5% or meso-inositol 5% or honey 10% or raffinose 5% for the long-term preservation of bacteria is described. As a case example more than 160 strains representing 36 species of nitrogen-fixing bacteria, 11 species of chemolithorutotrophic bacteria and five species of Aquaspirillum were successfully preserved. All tested strains proved viable and showed about 10–100% survival after freeze-drying and during 2–3 years of storage at +9°C. In such lyophilized cultures no loss in plasmids or other desirable characters was observed. The method is also suitable for the preservation of other fragile and difficult microorganisms as several other strains including bacteria with introduced plasmids could equally survive well and retained plasmids after lyophilization with this method.     

Diatom Cells Grown and Baked on a Functionalized Mica Surface

We demonstrate the cultivation of diatom cells on a functionalized mica surface and the preparation of frustules on a mica surface by baking. Diatom cells were successfully grown on a mica surface treated with 3-aminopropyltriethoxysilane. After baking at 400?C for 2 h, frustule structures without the organic components of the diatom cells were successfully observed by scanning electron microscopy and atomic force microscopy. Furthermore, the frustules deformed and became slender when a sample was baked at 800?C for 2 h. Our method is effective for the direct characterization of frustule structures and physical properties without changing the configuration of the diatom cells grown on the mica surface.     

Improved Solvents for Paper Chromatography of Thiazine Stains

Paper chromatography with new solvents applied to some commercial samples of thiazine stains, especially azures, resulted in improved resolution which gave more spots than had been obtained with previously reported solvents. To a Whatman No. 1 filter paper strip, 50 cm in length, 0.08 ml of a 0.1% solution in water was spotted 18 cm from the edge of the strip. The solvent used in most cases was a mixture of t-butylalcohol, methylcellosolve and a 1% NH₄Cl solution in distilled water (60:20:20, v/v) with the ascending technique. Several batches of thionin were found to have a high degree of purity (concerning their content of coloured components). One sample of thionin (Chroma) contained only one component (violet). The thionin-SO₂ reagent showed a chromatogram with more spots than the thionin sample from which the reagent was prepared. Qualitatively a sample of azure A appeared to have practically the same composition as a sample of azure C. At least six spots were visible in the chromatogram of these azures, which contain thionin in addition to the other components.