Quasi-elastic light scattering from migrating chemotactic bands of Escherichia coli.

We report the observation of migrating chemotactic bands of Escherichia coli in a buffer solution. The temporal development of the bacterial density profile is observed by the scattered light intensity as the band migrates through a stationary laser beam. We have made a preliminary analysis of the observed band profile with help of the Keller-Segel theory. The model accounts for only some aspects of the observed time evolution of the density profile. The microscopic motility characteristics of the E. coli in the band are simultaneously studied by photon correlation. The measured correlation functions are analyzed to obtain the spatial dependence of the half-width within the band. A simple analytical model is proposed to account for the contribution of the twiddle motion to the correlation function. By analyzing the correlation function as a superposition of straight-line and twiddle motions, we obtain a satisfactory agreement between the theory and the measured angular dependence of the line shape. As a consequence we are able to extract a parameter beta, which measures the average fraction of twiddling bacteria in the center of the band at a given time.     

Quasi-elastic light scattering from migrating chemotactic bands of Escherichia coli. III. Studies of band formation propagation and motility in oxygen and serine substrates.

A series of light scattering experiments have been performed to study both macroscopic aspects of band formation and propagation and microscopic motility parameters of Escherichia coli in the combined substrate gradients of oxygen and serine. From the band formation experiment the conclusion is drawn that a minimum threshold gradient of the substrate is required for bacteria to form a band. From the band propagation experiment in the serine substrate the motility coefficient mu and chemotactic coefficient delta are determined. A separate quasi-elastic scattering experiment has been made with a propagating band to obtain three microscopic motility parameters: mean twiddle time tau 1, mean run time tau 2, and mean run speed V2. Finally, a scaling argument is made to connect the macroscopic parameters mu and delta with the microscopic parameters tau 1, tau 2, and V2, thus achieving a unified understanding of macroscopic and microscopic aspect of chemotaxis.     

Structure and dynamics of the dilauroylphosphatidylethanolamine lipid bilayer.

A 200-ps molecular dynamics (MD) simulation trajectory of a model dilauroylphosphatidylethanolamine (DLPE) bilayer in water at 315 K has been generated. Segmental order parameters, electron density profiles, and water pair distribution functions have been calculated. Comparison to experiment is made where possible. The dynamics of the system has been studied by analyzing the velocity autocorrelation functions (VAF) of both water and lipid atoms. Furthermore, the diffusive properties of water have been analyzed by computing the mean square displacement (MSD) and orientational correlation function (OCF) of water in two regions around the bilayer. The calculated order parameters show a behavior similar to the liquid crystalline phase of other bilayers, but the region around C1-C3 does not show the expected behavior. The electron density profile shows features that are characteristic of the liquid crystalline phase. The radial distribution functions suggest ordering of water near the charged head groups, which results in about 15 water molecules solvating each lipid molecule. We find from the VAF, MSD, and OCF calculation that the water molecules near the head groups of the lipid bilayer move more slowly than those further away. The VAF of the hydrocarbon chains have features of low-frequency motions that are probably cooperative nature in addition to the high-frequency motions associated with bond angle and torsional motions.     

Lipid mobility and order in bovine rod outer segment disk membranes. A spin-label study of lipid-protein interactions

Lipid-protein interactions in bovine rod outer segment disk membranes have been studied by using a series of eight stearic acid spin-label probes which were labeled at different carbon atom positions in the chain. In randomly oriented membrane dispersions, the electron spin resonance (ESR) spectra of the C-8, C-9, C-10, C-11, C-12, C-13, and C-14 atom positional isomers all apparently consist of two components. One of the components corresponds closely to the spectra obtained from dispersions of the extracted membrane lipids, and the other, which is characterized by a considerably greater degree of motional restriction of the lipid chains, is induced by the presence of the protein. Digital subtraction has been used to separate the two components. The proportion of the motionally restricted lipid component is approximately constant, independent of the position of the spin-label group, and corresponds to 30-40% of the total spin-label spectral intensity. The hyperfine splitting of the outer maxima in the difference spectra of the motionally restricted component decreases, and concomitantly, the line widths increase with increasing temperature but change relatively little with increasing distance of the spin-label group from the polar head-group region. This indicates that the corresponding chain motions of the protein-interacting lipids lie in the slow-motion regime of spin-label ESR spectroscopy (tau R approximately 10(-8) S) and that the mobility of these lipids increases with increasing temperature but does not vary greatly along the length of the chain. The data from the hyperfine splittings also suggest the existence of a polarity gradient immediately adjacent to the protein surface, as observed in the fluid lipid regions of the membrane. The more fluid lipid component is only slightly perturbed relative to the lipids alone (for label positions 5-14, inclusive), indicating the presence of chain motions on the nanosecond time scale, and the spectra also reveal a similar polarity profile in both lipid and membrane environments. ESR spectra have also been obtained as a function of magnetic field orientation with oriented membrane samples. For the C-14 atom positional isomer, the motionally restricted component is observed to have a large hyperfine splitting, with the magnetic field oriented both parallel and perpendicular to the membrane normal. This indicates that the motionally restricted lipid chains have a broad distribution of orientations at this label position.(ABSTRACT TRUNCATED AT 400 WORDS)     

The altitudinal gradient of vascular plant richness in Aurland, western Norway

Differences in vascular plant species richness; along the altitudinal gradient in the Aurland area of western Norway have been investigated. Based on field surveys, as complete lists as possible of all vascular plants have been compiled for each 100 m altitudinal band, from sea level to the highest mountain (1764 m). For each of the 18 altitudinal bands, climatic data have been estimated. A total of 444 vascular plant species were recorded. Highest species richness (263 species) occurred in the 600–700 in band, whereas the uppermost band had only 10 species. There are minor differences in species number between the altitudinal bands < 1000 m. Partial least squares regression shows that species richness for the overall altitudinal gradient is well predicted by mean July and January temperatures and mean annual precipitation. Species turnover is highest in the 100–200 m. 600–700 m. and 1400–1500 m altitudinal bands. In terms of the gradient in summer temperature, the study supports the generally assumed linear relationship between July temperature and the number of vascular plant species between 700 and 1500 m corresponding with a mean July temperature range of 7–11°C. The study shows a decrease of ca 30 vascular plant species with a 1°C decrease in mean July temperature, and that the “climatic vascular plant limit” is here estimated to occur at a mean July temperature of 2.4°C. Above 1500 and below 700 m. species number is lower than expected based on summer iemperature conditions alone. The 700–800 m band represents the highest floristic difference compared to the other bands. Ordination and classification analyses of the floristic compositional data of all the bands highlight the 600–800 and 1500–1600 m altitudinal bands as the major biotic boundaries along the gradient. No major discontinuity in species richness, composition, or turnover was consistently found, however, at the 1100–1200 m band representing the forest-limit ecotone in Aurland.     

Spatio-temporal structure of migrating chemotactic band of Escherichia coli. I. Traveling band profile.

We developed a rapid-scanning, light-scattering densitometer by which extensive measurements of band migration speeds and band profiles of chemotactic bands of Escherichia coli in motility buffer both with and without serine have been made. The purpose is to test the applicability of the phenomenological model proposed by Keller and Segel (J. Theor. Biol. 1971. 30:235) and to determine the motility (mu) and chemotactic (delta) coefficients of the bacteria. We extend the previous analytical solution of the simplified Keller-Segel model by taking into account the substrate diffusion which turns out to be significant in the case of oxygen. We demonstrate that unique sets of values of mu and delta can be obtained for various samples at different stages of migration by comparing the numerical solution of the model equation and the experimental data. The rapid-scanning technique also reveals a hitherto unobserved time-dependent fine structure in the bacterial band. We give a qualitative argument to show that the fine structure is an example of the dissipative structure that arises from a nonlinear coupling between the bacterial density and the oxygen concentration gradient. Implications for a further study of the dissipative structure in testing the Keller-Segel model of chemotaxis are briefly discussed.     

The Influence of Drag on Nonlinear Oscillatory Flow through Concentric Annulus

A mathematical model has been developed to study the effect of particle drag parameter and frequency parameter on velocity and pressure gradient in nonlinear oscillatory two phase flow. The main purpose is to apply the model to study the combined effect of introduction of the catheter and elastic properties of the arterial wall on the pulsatile nature of the blood flow. We model the artery as an isotropic thin walled elastic tube and the catheter as a coaxial flexible tube. Blood is modeled as an incompressible particulate viscous Newtonian fluid. Perturbation technique has been applied to find the approximations for velocity and pressure gradient up to second order. Numerical solutions are investigated with graphical presentations to understand the effects of drag parameter, frequency parameter and phase angle on velocity along radial direction and pressure gradient along axial directions. As the drag parameter increases, mean pressure gradient and mean velocity will be decreased. As frequency parameter increases mean velocity profile bends near the outer wall. Due to elastic nature of artery wall, a thin catheter experience small oscillations and a thick catheter remains stationary inside the artery. Finally, the effect of catheterization on various physiologically important flow rate characteristics—mean velocity, mean pressure gradient are studied for a range of different catheter sizes, particle drag parameter and frequency parameters.     

Soil Microbial Community Response to Drought and Precipitation Variability in the Chihuahuan Desert

Increases in the magnitude and variability of precipitation events have been predicted for the Chihuahuan Desert region of West Texas. As patterns of moisture inputs and amounts change, soil microbial communities will respond to these alterations in soil moisture windows. In this study, we examined the soil microbial community structure within three vegetation zones along the Pine Canyon Watershed, an elevation and vegetation gradient in Big Bend National Park, Chihuahuan Desert. Soil samples at each site were obtained in mid-winter (January) and in mid-summer (August) for 2 years to capture a component of the variability in soil temperature and moisture that can occur seasonally and between years along this watershed. Precipitation patterns and amounts differed substantially between years with a drought characterizing most of the second year. Soils were collected during the drought period and following a large rainfall event and compared to soil samples collected during a relatively average season. Structural changes within microbial community in response to site, season, and precipitation patterns were evaluated using fatty acid methyl ester (FAME) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses. Fungal FAME amounts differed significantly across seasons and sites and greatly outweighed the quantity of bacterial and actinomycete FAME levels for all sites and seasons. The highest fungal FAME levels were obtained in the low desert scrub site and not from the high elevation oak–pine forests. Total bacterial and actinomycete FAME levels did not differ significantly across season and year within any of the three locations along the watershed. Total bacterial and actinomycete FAME levels in the low elevation desert-shrub and grassland sites were slightly higher in the winter than in the summer. Microbial community structure at the high elevation oak–pine forest site was strongly correlated with levels of NH₄ ⁺–N, % soil moisture, and amounts of soil organic matter irrespective of season. Microbial community structure at the low elevation desert scrub and sotol grasslands sites was most strongly related to soil pH with bacterial and actinobacterial FAME levels accounting for site differences along the gradient. DGGE band counts of amplified soil bacterial DNA were found to differ significantly across sites and season with the highest band counts found in the mid-elevation grassland site. The least number of bands was observed in the high elevation oak–pine forest following the large summer-rain event that occurred after a prolonged drought. Microbial responses to changes in precipitation frequency and amount due to climate change will differ among vegetation zones along this Chihuahuan Desert watershed gradient. Soil bacterial communities at the mid-elevation grasslands site are the most vulnerable to changes in precipitation frequency and timing, while fungal community structure is most vulnerable in the low desert scrub site. The differential susceptibility of the microbial communities to changes in precipitation amounts along the elevation gradient reflects the interactive effects of the soil moisture window duration following a precipitation event and differences in soil heat loads. Amounts and types of carbon inputs may not be as important in regulating microbial structure among vegetation zones within in an arid environment as is the seasonal pattern of soil moisture and the soil heat load profile that characterizes the location.     

Mapping backbone dynamics in solution with site-directed spin labeling: GCN4-58 bZip free and bound to DNA

In site-directed spin labeling, a nitroxide-containing side chain is introduced at selected sites in a protein. The EPR spectrum of the labeled protein encodes information about the motion of the nitroxide on the nanosecond time scale, which has contributions from the rotary diffusion of the protein, from internal motions in the side chain, and from backbone fluctuations. In the simplest model for the motion of noninteracting (surface) side chains, the contribution from the internal motion is sequence independent, as is that from protein rotary diffusion. Hence, differences in backbone motions should be revealed by comparing the sequence-dependent motions of nitroxides at structurally homologous sites. To examine this model, nitroxide side chains were introduced, one at a time, along the GCN4-58 bZip sequence, for which NMR (15)N relaxation experiments have identified a striking gradient of backbone mobility along the DNA-binding region [Bracken et al. (1999) J. Mol. Biol. 285, 2133]. Spectral simulation techniques and a simple line width measure were used to extract dynamical parameters from the EPR spectra, and the results reveal a mobility gradient similar to that observed in NMR relaxation, indicating that side chain motions mirror backbone motions. In addition, the sequence-dependent side chain dynamics were analyzed in the DNA/protein complex, which has not been previously investigated by NMR relaxation methods. As anticipated, the backbone motions are damped in the DNA-bound state, although a gradient of motion persists with residues at the DNA-binding site being the most highly ordered, similar to those of helices on globular proteins.     

Enzyme dynamics and activity: time-scale dependence of dynamical transitions in glutamate dehydrogenase solution.

We have examined the temperature dependence of motions in a cryosolution of the enzyme glutamate dehydrogenase (GDH) and compared these with activity. Dynamic neutron scattering was performed with two instruments of different energy resolution, permitting the separate determination of the average dynamical mean square displacements on the sub-approximately 100 ps and sub-approximately 5 ns time scales. The results demonstrate a marked dependence on the time scale of the temperature profile of the mean square displacement. The lowest temperature at which anharmonic motion is observed is heavily dependent on the time window of the instrument used to observe the dynamics. Several dynamical transitions (inflexions of the mean squared displacement) are observed in the slower dynamics. Comparison with the temperature profile of the activity of the enzyme in the same solvent reveals dynamical transitions that have no effect on GDH function.     

Two-dimensional motion of DNA bands during 120° pulsed-field gel electrophoresis. I. Effect of molecular weight

The instantaneous position and velocity of bands of linear, double-stranded DNA were measured during 120° pulsed-field electrophoresis in 1% agarose gels, using a video micrometer capable of simultaneous measurements in two dimensions. When the direction of the field was switched, the band initially retraced the last portion of its path during the preceding pulse. The distance the band moved backward increased with DNA length: 48.5 kb (kilobase pair) DNA moved backward only 0.2 μm, but 1110 kb DNA moved backward 24 μm, before setting off in a positive direction. The velocity of the DNA band was particularly rapid during the backward movement: the magnitude of the velocity spike increased with M, reaching 2.4 μm/s for 1110 kb DNN, which was about 5 times the steady-state velocity. The velocity in the y direction, perpendicular to the mean drift direction, allowed an even larger transient spike, which also increased with M. Simulation of the dynamics of long DNA chins undergoing gel electrophoresis by a dynamic Monte Carlo method gave instantaneous xy position and velocity in excellent agreement with experiment. The simulation included extensional motions of the DNA within the tube of interconnected agarose pores as well as the possibility of loops (hernias) that escape laterally from the tube. © 1995 John Wiley & Sons, Inc.     

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers

The structures of three bacterial outer membrane proteins (OmpA, OmpX and PagP) have been determined by both X-ray diffraction and NMR. We have used multiple (7 × 15 ns) MD simulations to compare the conformational dynamics resulting from the X-ray versus the NMR structures, each protein being simulated in a lipid (DMPC) bilayer. Conformational drift was assessed via calculation of the root mean square deviation as a function of time. On this basis the ‘quality’ of the starting structure seems mainly to influence the simulation stability of the transmembrane β-barrel domain. Root mean square fluctuations were used to compare simulation mobility as a function of residue number. The resultant residue mobility profiles were qualitatively similar for the corresponding X-ray and NMR structure-based simulations. However, all three proteins were generally more mobile in the NMR-based than in the X-ray simulations. Principal components analysis was used to identify the dominant motions within each simulation. The first two eigenvectors (which account for >50% of the protein motion) reveal that such motions are concentrated in the extracellular loops and, in the case of PagP, in the N-terminal α-helix. Residue profiles of the magnitude of motions corresponding to the first two eigenvectors are similar for the corresponding X-ray and NMR simulations, but the directions of these motions correlate poorly reflecting incomplete sampling on a ∼10 ns timescale.     

Electrophoresis time impacts the denaturing gradient gel electrophoresis-based assessment of bacterial community structure

We investigated the impact of denaturing gradient gel electrophoresis (DGGE) run time on the assessment of bacterial community structure. Results indicated that increased electrophoresis run time (while maintaining 1000 volt-hours) resulted in dissimilar profiles, likely due to instability of the denaturing gradient. We recommend that DGGE run times be minimized to provide optimal band resolution, as extended electrophoresis times can greatly impact subsequent band-based analyses.     

Characterization of Bacterial Magnetotactic Behaviors by Using a Magnetospectrophotometry Assay

Magnetotactic bacteria have the unique capacity of synthesizing intracellular single-domain magnetic particles called magnetosomes. The magnetosomes are usually organized in a chain that allows the bacteria to align and swim along geomagnetic field lines, a behavior called magnetotaxis. Two mechanisms of magnetotaxis have been described. Axial magnetotactic cells swim in both directions along magnetic field lines. In contrast, polar magnetotactic cells swim either parallel to the geomagnetic field lines toward the North Pole (north seeking) or antiparallel toward the South Pole (south seeking). In this study, we used a magnetospectrophotometry (MSP) assay to characterize both the axial magnetotaxis of “Magnetospirillum magneticum” strain AMB-1 and the polar magnetotaxis of magneto-ovoid strain MO-1. Two pairs of Helmholtz coils were mounted onto the cuvette holder of a common laboratory spectrophotometer to generate two mutually perpendicular homogeneous magnetic fields parallel or perpendicular to the light beam. The application of magnetic fields allowed measurements of the change in light scattering resulting from cell alignment in a magnetic field or in absorbance due to bacteria swimming across the light beam. Our results showed that MSP is a powerful tool for the determination of bacterial magnetism and the analysis of alignment and swimming of magnetotactic bacteria in magnetic fields. Moreover, this assay allowed us to characterize south-seeking derivatives and non-magnetosome-bearing strains obtained from north-seeking MO-1 cultures. Our results suggest that oxygen is a determinant factor that controls magnetotactic behavior.Magnetotactic bacteria are morphologically, metabolically, and phylogenetically diverse prokaryotes (1, 11). They synthesize unique intracellular organelles, the magnetosomes, which are single-domain magnetic crystals of the mineral magnetite or greigite enveloped by membranes. Magnetosomes are usually organized in a chain(s) within the cell and cause the cell to align along geomagnetic field lines while it swims. The highest numbers of magnetotactic bacteria are generally found at, or just below, the oxic-anoxic transition zone (OATZ) or redoxocline in aquatic habitats (1). Early studies showed that Northern Hemisphere magnetotactic bacteria swim preferentially northward in parallel with the geomagnetic field lines (north seeking [NS]) (2) and that those from the Southern Hemisphere swim preferentially antiparallel to the geomagnetic field lines to the magnetic South Pole (south seeking [SS]) (4). The geomagnetic field is inclined downward from horizontal in the Northern Hemisphere and upward in the Southern Hemisphere, with the inclination magnitude increasing from the equator to the poles. Therefore, magnetotaxis might guide cells in each hemisphere downward to less-oxygenated regions of aquatic habitats, where they would presumably stop swimming until conditions change (1). A recent study reported the coexistence of both NS and SS magnetotactic bacteria in the Northern Hemisphere, which conflicts with the prevalent model of the adaptive value of magnetotaxis (14).Under laboratory conditions, magnetotactic bacteria form microaerophilic bands of cells in oxygen-gradient medium. In fact, magnetotaxis and aerotaxis work together in these bacteria, and the behavior observed has been referred to as “magnetoaerotaxis.” Two different magnetoaerotactic mechanisms, termed polar and axial, are found in different bacterial species (6). The magnetotactic bacteria, principally the magnetotactic cocci, that swim persistently in one direction along the magnetic field (NS or SS) are polar magnetoaerotactic. Magnetotactic bacteria, especially the freshwater spirilla, that swim in either direction along the magnetic field lines with frequent, spontaneous reversals of swimming direction without turning around are axial magnetoaerotactic. For polar magnetotactic bacteria, the magnetic field provides an axis and a direction for motility, whereas for axial magnetotactic bacteria, the magnetic field provides only an axis of motility. The two mechanisms can best be seen in flattened capillary tubes containing suspensions of cells in reduced medium in a magnetic field oriented parallel to the capillary. An oxygen gradient forms along the tube, beginning at the ends of the capillary, with one oriented parallel and the other antiparallel to the magnetic field (1). Band formation by axial magnetoaerotactic cells, such as Magnetospirillum magnetotacticum cells, occurs at both ends of the capillary. Rotation of the magnetic field by 180° after the formation of the bands causes the cells in both bands to rotate 180°, but the bands remain intact. In contrast, band formation by polar magnetoaerotactic cells, such as the marine cocci, occurs only at the end of the capillary for which the magnetic field and the oxygen concentration gradient are oriented opposite to each other. Rotation of the magnetic field by 180° after the formation of the band causes the cells in the band to rotate 180° and swim away, resulting in the dispersal of the band (1). In this study, we developed a magnetospectrophotometry (MSP) assay that provides an alternative method for the quantitative and versatile characterization of the two magnetotactic mechanisms. Using this assay, we demonstrated the effect of artificial magnetic fields on the generation of homogeneous NS or SS magnetotactic bacterial populations.     

A view of dynamics changes in the molten globule-native folding step by quasielastic neutron scattering

In order to understand the changes in protein dynamics that occur in the final stages of protein folding, we have used neutron scattering to probe the differences between a protein in its folded state and the molten globule states. The internal dynamics of bovine alpha-lactalbumin (BLA) and its molten globules (MBLA) have been examined using incoherent, quasielastic neutron scattering (IQNS). The IQNS results show length scale dependent, pico-second dynamics changes on length scales from 3.3 to 60 A studied. On shorter-length scales, the non-exchangeable protons undergo jump motions over potential barriers, as those involved in side-chain rotamer changes. The mean potential barrier to local jump motions is higher in BLA than in MBLA, as might be expected. On longer length scales, the protons undergo spatially restricted diffusive motions with the diffusive motions being more restricted in BLA than in MBLA. Both BLA and MBLA have similar mean square amplitudes of high frequency motions comparable to the chemical bond vibrational motions. Bond vibrational motions thus do not change significantly upon folding. Interestingly, the quasielastic scattering intensities show pronounced maxima for both BLA and MBLA, suggesting that "clusters" of atoms are moving collectively within the proteins on picosecond time scales. The correlation length, or "the cluster size", of such atom clusters moving collectively is dramatically reduced in the molten globules with the correlation length being 6.9 A in MBLA shorter than that of 18 A in BLA. Such collective motions may be important for the stability of the folded state, and may influence the protein folding pathways from the molten globules.     

The X-ray absorption spectroscopy Debye-Waller factors of an iron compound and of met-myoglobin as a function of temperature

Protein dynamics can be characterized by the mean square displacements of the individual atoms of a molecule. This concept is extended to X-ray absorption spectroscopy (XAS) of proteins where the physical information in the Debye-Waller factor is in general neglected. In a first step, a procedure for the investigation of the temperature dependence of XAS spectra has been developed for a small iron compound. Subsequently, experiments have been performed on met-myoglobin. It is shown that the mean square displacements of XAS are smaller than those obtained by M?ssbauer spectroscopy and far smaller than crystallographic mean square displacements. This behavior is explained by the different sensitivity of the methods. XAS measures a relative mean square displacement between the absorbing and backscattering atoms only. A comparison with mean square displacements calculated from normal modes shows that static displacements contribute significantly. It becomes obvious that the atoms of the active center show a high correlation of their motions.     

Correlations of atomic movements in lysozyme crystals.

Diffuse scattering data have been collected on two crystal forms of lysozyme, tetragonal and triclinic, using synchrotron radiation. The observed diffraction patterns were simulated using an exact theory for simple model crystals which relates the diffuse scattering intensity distribution to the amplitudes and correlations of atomic movements. Although the mean square displacements in the tetragonal form are twice that in the triclinic crystal, the predominant component of atomic movement in both crystals is accounted for by short-range coupled motions where displacement correlations decay exponentially as a function of atomic separation, with a relaxation distance of approximately 6 A. Lattice coupled movements with a correlation distance approximately 50 A account for only about 5-10% of the total atomic mean square displacements in the protein crystals. The results contradict various presumptions that the disorder in protein crystals can be modeled predominantly by elastic vibrations or rigid body movements.     

Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts

A temperature-gradient gel electrophoresis technique and its application to the study of structural transitions of nucleic acids and protein-nucleic acid complexes are described. The temperature gradient is established in a slab gel by means of a simple ancillary device for a commercial horizontal gel apparatus. The gradient may be freely selected between 10 and 80 degrees C, and is highly reproducible and linear. In a normal application the biopolymers migrate perpendicular to the temperature gradient so that every individual molecule is at constant temperature throughout electrophoresis. The structural transition of a biopolymer is seen as a continuous band which is retarded or speeded up in the temperature range of the transition. Dissociation processes are mostly irreversible under the conditions of electrophoresis and, therefore, show up as discontinuous transitions from a slow-moving to fast-moving band. As examples the conformational transitions of viroids, double-stranded RNA from reovirus, double-stranded satellite RNA from cucumber mosaic virus and repressor-operator complexes have been studied. It could be shown that by this method dsRNA molecules may be differentiated which differ only in one base-pair, or proteins differing in one amino acid only. As a particular advantage, temperature-gradient gel electrophoresis allows the study of conformational transitions of biopolymers which have not been purified. The biopolymer may either be identified by silver staining as a specific band among many others or, if the study is carried out on nucleic acids, these may be recorded by hybridization with a radioactive probe.     

Magneto-aerotaxis in marine coccoid bacteria.

Magnetotactic cocci swim persistently along local magnetic field lines in a preferred direction that corresponds to downward migration along geomagnetic field lines. Recently, high cell concentrations of magnetotactic cocci have been found in the water columns of chemically stratified, marine and brackish habitats, and not always in the sediments, as would be expected for persistent, downward-migrating bacteria. Here we report that cells of a pure culture of a marine magnetotactic coccus, designated strain MC-1, formed microaerophilic bands in capillary tubes and used aerotaxis to migrate to a preferred oxygen concentration in an oxygen gradient. Cells were able to swim in either direction along the local magnetic field and used magnetotaxis in conjunction with aerotaxis, i.e., magnetically assisted aerotaxis, or magneto-aerotaxis, to more efficiently migrate to and maintain position at their preferred oxygen concentration. Cells of strain MC-1 had a novel, aerotactic sensory mechanism that appeared to function as a two-way switch, rather than the temporal sensory mechanism used by other bacteria, including Magnetospirillum megnetotacticum, in aerotaxis. The cells also exhibited a response to short-wavelength light (< or = 500 nm), which caused them to swim persistently parallel to the magnetic field during illumination.     

Hydrodynamic calculations on the movements of cilia and flagella. II. Opalina.

Two different theoretical models are used to represent the propulsive mechanisms of Opalina. One model uses the concept of an envelope over all the cilia, while the other considers an array of elongated rods, similar to the model used in part 1. The envelope model shows a correlation between the motion of the cilium tip and the type of metachronism exhibited by the organism but under-predicts the velocities of propulsion. Calculations of the velocity profile, force and bending moment are carried out on the three-dimensional beat of a cilium of Opalina ranarum using the cilia sublayer model. The mean velocity profile is found to be twisted in form: in a clockwise direction at the top of the cilia sublayer relative to the effective stroke. Calculations of the force and rate of working emphasize the approximately equal duration of the effective and recovery strokes. Overall the sublayer model is found to be a more informative and useful approach than the envelope model which is limited to small amplitude motions.