A facile method for detection of the genuine sapogenin from a saponin extract

We present a simple, efficient system for preparative polyacrylamide gel electrophoresis (PAGE) in sodium dodecyl sulfate. The instrument features a novel sample collection assembly which is fitted directly onto the bottom of the gel cylinder. Buffer pumped uniformly upward through a porous plastic disk from the lower tray sweeps the emerging sample into a collection system with high efficiency. Measures which prevent the destruction of tryptophan residues and the blockage of α-amino groups observed in electrophoresed polypeptides are described.     

A novel intact circular dsDNA supercoil

A novel intact circular dsDNA supercoil is proposed as an alternative to the conventional DNA supercoil, so that the two complementary strands of ssDNA circles are separable without any covalent bond breakage. This new structure can be visualized by using two tubings: one black and one clear. Twist the black tubing a number of times and connect its two ends. Do the same for the clear tubing. Then wrap the two tubings together. This forms the separable or novel supercoil. On the other hand, the conventional supercoil can be modeled by twisting the black and clear tubings together and then connect their respective ends, so that the two tubings are not separable unless one of them is cut. Experimentally, in the absence of any enzyme, many intact plasmid dsDNA circles give two bands on agarose gel electrophoresis under a certain given condition, while the same plasmid molecules after cutting once by a restriction enzyme give only one band under the same, condition. In the case of intact pUC19 plasmids, these two bands can then be, recovered and sequenced separately, using two primers in opposite directions. Each band gives mostly one sequence which is complementary to that of the other band. The combination of the above theoretical model and experimental results strongly suggests that there is an alternative structure of DNA which does not have the usual difficulty of unwinding, rewinding and requiring numerous covalent bond breakages and ligations during semiconservative replication.     

Hydrolysis of butteroil by immobilized lipase using a hollow-fiber reactor: IV. Effects of temperature

A lipase from Aspergillus niger, immobilized by adsorption on microporous polypropylene hollow fibers, was used to effect the hydrolysis of the glycerides of melted butterfat at pH. 7.0 at 40, 50, 55, and 60 degrees C. Mcllvane buffer was pumped upward through the lumen, and melted butterfat was pumped upward through the shell side of a hollow fiber reactor. Nonlinear regression methods were employed to determine the kinetic parameters of models based on combinations of three nested rate expressions for the hydrolysis reaction with three nested rate expressions for thermal deactivation of the enzyme. A rate expression containing four lumped parameters is sufficient to model the release of free fatty acids as a function of reactor space time and time elapsed after immobilization. Nonlinear regression methods were also employed in global fits of the data to rate expressions containing an explicit dependence on temperature. For the reaction conditions used in this research, a 14-parameter rate expression is necessary to accurately model the overall release of free fatty acids as a continuous function of the absolute temperature, initial substrate concentrations, reactor space time, and time elapsed after immobilization of the lipase.     

Gradients with depth in electrospun fibrous scaffolds for directed cell behavior

A major obstacle in creating viable tissue-engineered constructs using electrospinning is the lack of complete cellularization and vascularization due to the limited porosity in these densely packed fibrous scaffolds. One potential approach to circumvent this issue is the use of various gradients of chemical and biophysical cues to drive the infiltration of cells into these structures. Toward this goal, this study focused on creating durotactic (mechanical) and haptotactic (adhesive) gradients through the thickness of electrospun hyaluronic acid (HA) scaffolds using a unique, yet simple, modification of common electrospinning protocols. Specifically, both mechanical (via cross-linking: ranging from 27-100% modified methacrylated HA, MeHA) and adhesive (via inclusion of the adhesive peptide RGD: 0-3 mM RGD) gradients were each fabricated by mixing two solutions (one ramping up, one ramping down) prior to electrospinning and fiber collection. Gradient formation was verified by fluorescence microscopy, FTIR, atomic force microscopy, and cellular morphology assessment of scaffolds at different points of collection (i.e., with scaffold thickness). To test further the functionality of gradient scaffolds, chick aortic arch explants were cultured on adhesive gradient scaffolds for 7 days, and low RGD-high RGD gradient scaffolds showed significantly greater cell infiltration compared with high RGD-low RGD gradients and uniform high RGD or uniform low RGD control scaffolds. In addition to enhanced infiltration, this approach could be used to fabricate graded tissue structures, such as those that occur at interfaces.     

Simultation of gradient and band propagation in the centrifuge.

A technique is developed for simulating the behavior of both the gradient-forming solute and macromolecular bands in a centrifuge. The change with time of the density gradient due to diffusion and sedimentation of the gradient-forming solute is calculated by a finite difference method, making use of the results of earlier work on the theory of the equilibrium density gradient. Using a perturbation technique, the concentration profiles of dilute bands of macromolecules are then calculated as they sediment and diffuse through the varying supporting gradient. Results of the stimulaion techniques are compared with experiment.     

Chlorophyll thermoluminescence of leaf discs: simple instruments and progress in signal interpretation open the way to new ecophysiological indicators

Luminescence from photosynthetic material observed in darkness following illumination is a delayed fluorescence produced by a recombination of charge pairs stored in photosystem II, i.e. the back-reaction of photosynthetic charge separation. Thermoluminescence (TL) is a technique consisting of a rapid cooling followed by the progressive warming of a preilluminated sample to reveal the different types of charge pairs as successive emission bands, which are resolved better than the corresponding decay phases recorded at constant temperatures. Progress in thermoelectric Peltier elements and in compact light detectors made the development of simple, affordable and transportable instruments possible. These instruments take advantage of multifurcated light guides for combined TL, fluorescence and absorbance/reflectance measurements. Meanwhile, experiments on unfrozen leaf discs, with excitation by single turn-over flashes or far red light and infiltration by specific inhibitors/uncouplers, have led to a better understanding of in vivo TL signals. Much like chlorophyll fluorescence and in a complementary way, TL in the 0-60 degrees C temperature range not only informs on the state of photosystem II in leaf tissues and its possible alterations, but also gives a broader insight into the energetic state inside the chloroplast by probing (1) the light-induced or dark-stable thylakoid proton gradient through the protonation of the Mn oxygen-evolving complex, (2) the induction of cyclic/chlororespiratory electron flow towards the plastoquinone pool, (3) the [NADPH+ATP] assimilatory potential. By a different mechanism, warming above 60 degrees C without preillumination reveals chemiluminescence high temperature thermoluminescence (HTL) bands due to the radiative thermolysis of peroxides, which are indicators of oxidative stress in leaves.     

The effect of endogenous proteases on the spectrin binding proteins of human erythrocytes

We have demonstrated that in human erythrocyte ghosts endogenous proteolytic activity is responsible for the digestion of the spectrin binding proteins (bands 2.1 to 2.6). The pH optimum, cofactor requirements and inhibitor sensitivity have been established. Our results indicate that proteolysis of bands 2.1 to 2.6 and the formation of 3′, a fragment containing an active spectrin binding site, can occur through two enzymatic pathways: a cascade of consecutive proteolytic cleavages of the spectrin binding proteins inhibited by phenylmethylsulfonyl fluoride or a Ca²⁺-stimulated, phenylmethylsulfonyl fluoride-insensitive, EDTA-inhibited cleavage of band 2.1 to band 2.3, followed by digestion to band 3′ by phenylmethylsulfonyl fluoride-inhibitable enzymes. These findings may provide the techniques necessary to prevent proteolysis of the spectrin binding proteins during purification and reconstitution experiments and provide insight into how they are formed in vivo.     

Blast shock wave mitigation using the hydraulic energy redirection and release technology

A hydraulic energy redirection and release technology has been developed for mitigating the effects of blast shock waves on protected objects. The technology employs a liquid-filled plastic tubing as a blast overpressure transformer to transfer kinetic energy of blast shock waves into hydraulic energy in the plastic tubings. The hydraulic energy is redirected through the plastic tubings to the openings at the lower ends, and then is quickly released with the liquid flowing out through the openings. The samples of the specifically designed body armor in which the liquid-filled plastic tubings were installed vertically as the outer layer of the body armor were tested. The blast test results demonstrated that blast overpressure behind the body armor samples was remarkably reduced by 97% in 0.2 msec after the liquid flowed out of its appropriate volume through the openings. The results also suggested that a volumetric liquid surge might be created when kinetic energy of blast shock wave was transferred into hydraulic energy to cause a rapid physical movement or displacement of the liquid. The volumetric liquid surge has a strong destructive power, and can cause a noncontact, remote injury in humans (such as blast-induced traumatic brain injury and post-traumatic stress disorder) if it is created in cardiovascular system. The hydraulic energy redirection and release technology can successfully mitigate blast shock waves from the outer surface of the body armor. It should be further explored as an innovative approach to effectively protect against blast threats to civilian and military personnel.     

Induced optical activity of acridine orange bound to poly-S-carboxymethyl-L-cysteine

The absorption and rotatory properties of acridine orange-poly-S-carboxymethyl-L -cysteine system in water and in 0.2 M NaCl have been measured at different pH and polymer-to-dye mixing ratios. The absorption spectra indicate that the dyes are bound to the polymer in dimeric or highly aggregated forms. At neutral pH where the polymer is randomly coiled, no optical activity is induced on the absorption bands of bound acridine orange. At acid pH where the polymer has the β-conformation, a pair of positive and negative circular dichroic bands occur at each of the absorption bands, centered around 458 and 261 mμ. The signs of those bands are opposite to those found for α-helical poly-L -glutamic acid. A model for the binding of dye to the β-form polymer is presented, in which dimeric dyes are attached to ionized carboxyl groups and slack one another to form linear arrays on both sides of an extended polypeptide chain. The observed circular dichroism spectra can be explained by the Tinoco's exciton mechanism, based on this model. Low molecular weight poly-S-carboxymethyl-L -cysteine induces quite a different circular dichroism on bound acridine orange.     

Improved 2D nano-LC/MS for proteomics applications: a comparative analysis using yeast proteome.

The most commonly used method for protein identification with two-dimensional (2D) online liquid chromatography-mass spectrometry (LC/MS) involves the elution of digest peptides from a strong cation exchange column by an injected salt step gradient of increasing salt concentration followed by reversed phase separation. However, in this approach ion exchange chromatography does not perform to its fullest extent, primarily because the injected volume of salt solution is not optimized to the SCX column. To improve the performance of strong cation exchange chromatography, we developed a new method for 2D online nano-LC/MS that replaces the injected salt step gradient with an optimized semicontinuous pumped salt gradient. The viability of this method is demonstrated in the results of a comparative analysis of a complex tryptic digest of the yeast proteome using the injected salt solution method and the semicontinuous pump salt method. The semicontinuous pump salt method compares favorably with the commonly used injection method and also with an offline 2D-LC method.     

Diversity of microbial communities correlated to physiochemical parameters in a digestion basin of a zero-discharge mariculture system

Bacterial community structure and physiochemical parameters were examined in a sedimentation basin of a zero-discharge mariculture system. The system consisted of an intensively stocked fish basin from which water was recirculated through two separate treatment loops. Surface water from the basin was pumped over a trickling filter in one loop while bottom-water was recirculated through a sedimentation basin followed by a fluidized bed reactor in the other. Ammonia oxidation to nitrate in the trickling filter and organic matter digestion together with nitrate reduction in the sedimentation basin and fluidized bed reactor, allowed zero-discharge operation of the system. Relatively high concentrations of oxygen, nitrate, sulphate and organic matter detected simultaneously in the digestion basin suggested the potential for a wide range of microbially-mediated transformation processes. In this study, physiochemical parameters were correlated to bacterial diversity and distribution in horizontal and vertical profiles within this basin in an effort to obtain a basic understanding of the chemical and microbial processes in this system. Chemical activity and microbial diversity, the latter measured by denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR) amplified 16S rDNA fragments, were higher in the sludge layer than in the overlying aqueous layer of the basin. Chemical parameters in sludge samples close to the basin inlet suggested enhanced microbial activity relative to other sampling areas with evidence of both nitrate and sulphate reduction. Four of the nine DGGE bands identified in this zone were affiliated with the Bacteroidetes phylum. Detected sequences closely related to sequences of organisms involved in the sulphur cycle included Desulfovibrio, Dethiosulfovibrio and apparent sulphur oxidizers from the gamma-proteobacteria. In addition, a number of sequences from the beta and alpha-proteobacteria were identified.     

Studies on ethylene binding by cell-free preparations from cotyledons of Phaseolus vulgaris L.: subcellular localization

Abstract. Studies on the subcellular location of ethylene binding activity from developing cotyledons of Phaseolus vulgaris L. are described. Binding activity has been shown to be predominantly membrane bound. When separated by rate-zonal centrifugation more than 70% of this activity was of low sedimentation rate. The slowly sedimenting band of activity was further fractionated into three bands by isopycnic density gradient centrifugation. The three bands occur at sucrose densities of 1.125 g cm⁻³, 1.155 g cm⁻³ and 1.175 g cm⁻³, corresponding to the distribution of putative marker enzymes for the cell endomembrane system and to protein body membranes. Further circumstantial evidence was obtained by electron microscopy and sucrose step gradient centrifugation.     

Fusion between rat brain synaptosomes and phosphatidylserine liposomes

Synaptosomal fractions isolated from rat cerebral cortex were incubated in the absence and presence of phosphatidylserine (PS) liposomes. The PS treated synaptosomes yielded ligher bouyant bands when centrifugated on discontinuous sucrose gradients. In these bands an increase in the lipidic phosphorus/protein ratio together with a massive incorporation of PS and a relative decrease of phosphatidylcholine was observed. Besides, in the synaptosomes treated with PS (0.5–0.7 μg/mg protein). Na⁺, K⁺-ATPase activity was 30–50% higher than in the controls.

We have employed an assay for lipid mixing based on the self-quenching relief of octadecylrhodamine B fluorescence. The decrease in the self-quenching of the probe in the gradient bands of liposomes treated synaptosomes, besides the chemical analysis data, indicated that a fusion process between synaptosomes and liposomes has taken place. It is the first time that a fusion process is proved between native synaptosomes and an artificial lipidic membrane.     

DENSITY GRADIENT ISOLATION OF RAT LIVER NUCLEI WITH HIGH DNA CONTENT

Rat liver nuclei, after preliminary isolation in 2.2 molar sucrose solution, were separated into density classes by centrifugation at 95,000 g for 45 to 85 minutes in a sucrose density gradient (density range, 1.28 to 1.33). Nuclei from normal liver separated into three bands with average DNA phosphorus content per nucleus of 0.67, 0.84, and 0.93 picogram for top, middle, and bottom bands, respectively. Nuclei from regenerating liver (26 hours after one-third hepatectomy) yielded three bands and a pellet fraction with average DNA phosphorus content per nucleus of 0.76, 1.02, 1.38, and 1.51 picograms (top to bottom of tube). This method appears capable of yielding nuclei which have increased their DNA content prior to mitosis, and this procedure should be valuable in studies of biochemical changes which occur in nuclei preparing for mitosis.     

A method for easily customizable gradient gel electrophoresis

Gradient polyacrylamide gel electrophoresis is a powerful tool for the resolution of polypeptides by relative mobility. Here, we present a simplified method for generating polyacrylamide gradient gels for routine analysis without the need for specialized mixing equipment. The method allows for easily customizable gradients which can be optimized for specific polypeptide resolution requirements. Moreover, the method eliminates the possibility of buffer cross contamination in mixing equipment, and the time and resources saved with this method in place of traditional gradient mixing, or the purchase of pre-cast gels, are noteworthy given the frequency with which many labs use gradient gel SDS-PAGE.     

Pollen foraging by bumblebees: Foraging patterns and efficiency on Lupinus polyphyllus

Summary Bumblebees foraging on vertical inflorescences start near the bottom and work upward, behavior commonly interpreted as a response to the greater amounts of nectar available in lower flowers. Lupinus polyphyllus, which produces no nectar, has more pollen available in upper flowers. Although bees are probably unable to detect this gradient, since pollen is hidden from their view, they still start low and forage upward. Therefore, we concluded that the bees' tendency to forage upward on vertical inflorescences is not tied to a reward gradient. In addition, bees use only about 15% of the flowers per inflorescence, although they could be much more efficient by visiting and revisiting every flower systematically. In general, revisits would not be penalized because most flowers contain enough pollen for several visits. Optimal foraging theory may not offer an adequate explanation for such gross inefficiency.     

Elevational gradients, area and tropical island diversity: an example from the palms of New Guinea

The factors causing spatial variation in species richness remain poorly known. In this study, factors affecting species richness of palms (Palmae/Arecaceae) were studied along the elevational gradient of New Guinea. Interpolated elevational ranges were calculated from a database of all known collections for 145 species in 32 genera. The amount of land area at different elevations greatly affects the species richness gradient. If assessed in equal-elevation bands species richness appears to decline monotonically, but when assessed in equal-area bands species richness shows a pronounced mid-elevation peak, due to the large proportion of lowlands in New Guinea. By randomising species ranges within the total elevational gradient for palms and accounting for area, we found the mid-elevation peak to be consistent with a mid-domain effect caused by the upper and lower limits to palm distribution. Our study illustrates the importance of accounting for area in macroecological studies of richness gradients and introduces a novel yet simple method for doing this through the use of equal-area bands. Together, the effect of area and the mid-domain effect explain the majority of variation in species richness of New Guinea palms. We support calls for the multivariate assessment of the mid-domain effect on an equal footing with other potential explanations of species richness.     

The Giardia lamblia trophozoite contains sets of closely related chromosomes.

Size variations in homologous chromosomes from six Giardia lamblia isolates have been demonstrated. Four or five intensely stained (major) bands as well as a variable number of lightly stained (minor) bands are present in pulsed field gradient separations. Southern blot analysis with total chromosomal DNA as well as chromosome specific probes indicates that each minor band cross-hybridizes with a major band. Minor bands of doubly cloned organisms appear identical to those of parent clones, indicating that the minor bands do not reflect the presence of variant members within the total population of trophozoites. Densitometric comparisons of chromosome bands from known numbers of Plasmodium falciparum ring stage forms and known numbers of Giardia trophozoites suggest that minor bands MBa and MBb are present in each Giardia trophozoite. Comparison of Not I restriction fragments from the major and minor bands reveals common restriction fragments. Taken together, the data imply that sets of closely related chromosomes occur in the Giardia trophozoite.