A method for eluting DNA in a wide range of molecular weights from agarose gels

We have developed a simple and rapid method for recovering DNAs of a wide range of molecular weights from agarose gels. A DNA-containing gel slice is placed on a Parafilm sheet in the center of a circular (positive) electrode and covered with a drop of buffer, while a linear (negative) electrode is placed on the top of the gel and driven about 1 mm into the gel itself. When a continuous current is applied, the DNA migrates into the buffer toward the circular electrode. We have obtained almost total recovery of DNAs up to 10 kb in size. Our method may also be used, under appropriate conditions, for higher molecular weight DNAs. The yield and all the biological assays performed on the DNAs obtained by our method recommend it for routine laboratory use.     

A method of sodium and potassium determination in red cells with a simple cell separation technique

Heparinized blood was centrifuged repeatedly in Eppendorf's test tubes at 7,500 g in the Unipan microcentrifuge type 320. Packed red cells were hemolysed, then sodium and potassium were determined by means of the flame photometer. The percentage of trapped plasma determined with indocyanine green amounted to on average 1 per cent. There was a good precision of the method controlled on 20 aliquots of the same blood sample. Results of red cell sodium and potassium in 80 healthy volunteers were 10.42 +/- 1.56 mmol/l and 87.8 +/- 4.03 mmol/l respectively. No significant changes in the red cell sodium and potassium concentration were observed in heparinized blood during 5 hours storage at room temperature. The method cannot be used interchangeably with the method of Helbock and Brown, since the correlation coefficients were too low in parallel examinations.     

Assessing potential bias in the determination of rotational correlation times of proteins by NMR relaxation

The various factors that influence the reliable and efficient determination of the correlation time describing molecular reorientation of proteins by NMR relaxation methods are examined. Nuclear Overhauser effects, spin-lattice, and spin-spin relaxation parameters of 15N NMR relaxation in ubiquitin have been determined at 17.6, 14.1, 11.7 and 9.4 Tesla. This unusually broad set of relaxation parameters has allowed the examination of the influence of chemical shift anisotropy, the functional form of the model-free spectral density, and the reliability of determined spin- spin relaxation parameters on the characterization of global tumbling of the protein. Treating the 15N chemical shift anisotropy (CSA) as an adjustable parameter, a consensus value of –170 ± 15ppm for the breadth of the chemical shift tensor and a global isotropic correlation time of 4.1ns are found when using the model-free spectral density to fit T1 and NOE data from all fields. The inclusion of T2 relaxation parameters in the determination of the global correlation time results in its increase to 4.6ns. This apparent inconsistency may explain a large portion of the discrepancy often found between NMR- and fluorescence-derived m values for proteins. The near identity of observed T2 and T1 values suggests that contributions from slow motions are not the origin of the apparent inconsistency with obtained T1 and NOE data. Various considerations suggest that the origin of this apparent discrepancy may reside in a contribution to the spectral density at zero frequency that is not represented by the simple model-free formalism in addition to the usual experimental difficulties associated with the measurement of these relaxation parameters. Finally, an axially symmetric diffusion tensor for ubiquitin is obtained using exclusively T1 and NOE data. A recommendation is reached on the types and combinations of relaxation data that can be used to reliably determine m values. It is also noted that the reliable determination of m values from 15N T1 and NOE relaxation parameters will become increasingly difficult as m increases.     

Method for the determination of myosin head orientation from EPR spectra.

The determination of the iodoacetamide spin label orientation in myosin heads (Fajer, 1994) allows us for the first time to determine directly protein orientation from EPR spectra. Computational simulations have been used to determine the sensitivity of EPR to both torsional and tilting motions of myosin heads. For rigor heads (no nucleotide), we can detect 0.2 degree changes in the tilt angle and 4 degrees in the torsion of the head. Sensitivity decreases with increasing head disorder, but even in the presence of +/- 30 degrees disorder as expected for detached heads, 10 degree changes in the center of the orientational distribution can be detected. We have combined these numerical simulations with a Simplex optimization to compare the orientation of intrinsic heads, with the orientation of labeled extrinsic heads that have been infused into unlabeled muscle fibers. The near identity (within 2 degrees) of the orientational distribution in the two instances can be attributed to myosin elasticity taking up the mechanical strain induced by the mismatch of myosin and actin filament periodicity. A similar analysis of the spectra of fibers with ADP bound to myosin revealed a small (approximately 5 degrees-10 degrees) torsional reorientation, without a substantial change of the tilt angle (< 2 degrees).     

A method for separation and determination of cytokinin nucleotides from plant tissues

Recent progress in the study of cytokinin metabolism in plants indicates that quantitative analysis of cytokinin nucleotides is essential for elucidation of early steps of the biosynthetic pathway. However, traditional procedures for purification and quantification of cytokinin cannot discriminate the various nucleotides. We describe here a method for separation and determination of cytokinin nucleotides through a series of anion-exchange column chromatography steps followed by liquid chromatography-mass spectrometry. This method enabled us to analyze the amount of each species of cytokinin nucleotide in plant tissues.     

Fluorescence correlation spectroscopy in the nanosecond time range: rotational diffusion of bovine carbonic anhydrase B

A fluorescence correlation experiment for measurement of rotational diffusion in the nanosecond time scale is described. Using this method, the rotational diffusion coefficient of bovine carbonic anhydrase B labelled with tetramethylrhodamine isothiocyanate was estimated to be D _r=(1.14±0.15)×10⁷ s^-1 at 22°C. The experiment is based on a cw argon ion laser, a microfluorimeter with local solution flow inside the sample cell, and two photon detectors. The fluorescence intensity autocorrelation function in the nanosecond time range is computed with the help of a time-to-amplitude converter and a multichannel pulse-amplitude analyser.     

A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species

A silica sands-based method has been developed to isolate high quality genomic DNAs from cells of animals, plants and microorganisms, such as Hemisalanx prognathus, Spinacia oleracea, Pichia pastoris, Bacillus licheniformis and Escherichia coli. To the best of our knowledge, no DNA isolation method has so wide application until now. In addition, this method and a commercially available kit were compared in analysis of microbial communities using high-throughput 16s rDNA sequencing. As a result, the silica sands-based method was found to be even more efficient in isolating genomic DNA from gram-positive bacteria than the kit, indicating that it would become a very valuable choice to faithfully reflect the composition of microbial communities.     

Detection of three rotational correlation times for a rigid asymmetric molecule using frequency-domain fluorometry

We measured the frequency response of the polarized emission of Y_t-base in propylene glycol at 10 ° C. Data were obtained for excitation wavelengths of 290, 312 and 346 nm, for which the fundamental anisotropies are 0.05, 0.19 and 0.32, respectively. Additionally, data were obtained using CCl₄, to decrease the mean decay time from 9.1 to 4.2 ns. These nine sets of data were analyzed globally to recover the anisotropy decay law. Three correlation times were needed to fit the data, 0.8, 3.0 and 5.6 ns, a range of only 7-fold. We believe this is the first reported detection of three correlation times for a rigid molecule.     

A new method for wide frequency range dynamic olfactory stimulation and characterization

Sensory receptors often receive strongly dynamic, or time varying, inputs in their natural environments. Characterizing their dynamic properties requires control and measurement of the stimulus over a frequency range that equals or exceeds the receptor response. Techniques for dynamic stimulation of olfactory receptors have lagged behind other major sensory modalities because of difficulties in controlling and measuring the concentration of odorants at the receptor. We present a new method for delivering olfactory stimulation that gives linear, low-noise, wide frequency range control of odorant concentration. A servo-controlled moving bead of silicone elastomer occludes the tip of a Pasteur pipette that releases odorant plus tracer gas into a flow tube. Tracer gas serves as a surrogate indicator of odorant concentration and is measured by a photoionization detector. The system has well-defined time-dependent behavior (frequency response and impulse response functions) and gives predictable control of odorant over a significant volume surrounding the animal. The frequency range of the system is about 0-100 Hz. System characterization was based on random (white noise) stimulation, which allows more rapid and accurate estimation of dynamic behavior than deterministic signals such as sinusoids or step functions. Frequency response functions of Drosophila electroantennograms stimulated by fruit odors were used to demonstrate a typical application of the system.     

A simple method for correction of circular dichroism spectra obtained from membrane-containing samples

Circular dichroism (CD) spectroscopy is an important technique in structural biology for examining folding and conformational changes of proteins in solution. However, the use of CD spectroscopy in a membrane medium (and also in a nonhomogeneous medium) is limited by (i) high light scattering and (ii) differential scattering of incident left and right circularly polarized light, especially at shorter wavelengths (<200 nm). We report a novel methodology for estimating the distortion of CD spectra caused by light scattering for membrane-bound peptides and proteins. The method is applied to three proteins with very different secondary structures to illustrate the limits of its capabilities when calibrated with a simple soluble peptide ([Ac]ANLKALEAQKQKEQRQAAEELANAK[OH], standard peptide) with a balanced secondary structure. The method with this calibration standard was quite successful in estimating α-helix but more limited when it comes to proteins with very high β-sheet or β-turn content.     

A simple method for efficient separation and purification of c-phycocyanin and allophycocyanin from Spirulina platensis

c-Phycocyanin and allophycocyanin were separated and purified from Spirulina platensis by precipitation with ammonium sulphate, ion exchange chromatography and gel filtration chromatography. Pure c-phycocyanin and allophycocyanin were finally obtained with an A₆₂₀/A₂₈₀value of 5.06 and an A₆₅₅/A₂₈₀ value of 5.34, respectively.     

A simple method for the separation and assay of non-ionic detergents

A simple one-dimensional thin-layer chromatographic separation method is described that permits separation and estimation of the non-ionic detergents Lubrol WX, Triton X-100 and Brij 58 in the presence of the common natural lipids.     

A simple method for the separation of triacylglycerols from fatty acids released in lipase assays

A simple procedure for the partition of triacylglycerols from albumin-bound fatty acids is described. This procedure is based on the ability of fumed silicon dioxide to remove emulsified triacylglycerols from aqueous media. The method was developed for the assay of lipoprotein lipase activity but it may be used for the assay of other lipases.     

A method for the enumeration of myxomycetes in soils and its application to a wide range of soils

Abstract A standardised most-probable-number technique for estimating the number of myxomycete plasmodium-forming units (PFUs) in soils has been developed and tested experimentally. Application of the method to a local soil showed that the uppermost layers contained the most PFUs. Its application to 44 surface soils from various parts of the world detected myxomycetes in 36, of which 4 were desert soils. In general, highest numbers of PFUs (up to 9000·g⁻¹ soil) were recorded in grassland and agricultural soils. The nature of the PFUs has not been definitely resolved but they are probably myxamoebae, myxoflagellates and microcysts.