Separation of cell organelles in density gradients based on their permeability characteristics

The buoyant density of intracellular organelles is dependent in part on the nature of the buffer composition of the density gradient and the permeability characteristics of the organelle membrane to the constituents of this buffer. Therefore, knowledge of the transport properties of different organelles allows the design of density gradients useful for their purification. We have used this approach to significantly decrease mitochondrial contamination of pancreatic zymogen granules in a one-step purification procedure on a 40% Percoll density gradient. These gradients, prepared with isoosmotic sucrose, yield a narrow band of zymogen granules and mitochondria. However, by substitution of sucrose with salts to which mitochondria but not zymogen granules are permeable, the densities of mitochondria are altered to give a significant separation. For example, the incorporation of 100 mM sodium succinate in the Percoll gradient can produce a 70% reduction in mitochondrial contamination. The increased ionic strength has an additional beneficial effect on zymogen granule yield by 5-10%. The recognition and utilization of transport pathways in organelle membranes is the principal feature of this technique and should prove to be widely applicable to other isolation procedures.     

A semiautomated system for the production and analysis of sucrose density gradients

A semiautomated system permitting considerable accuracy, speed and reproducibility in the making and fractionation of sucrose density gradients is described. The system consists of a modified Beckman gradient forming device which makes six gradients simultaneously and delivers them into six 12.5 ml polyallomer centrifuge tubes in such a manner that new material is continuously added to the meniscus of the gradient. The gradients are fractionated three at a time and up to 100 fractions per gradient can be collected automatically directly into scintillation vials with a choice of drop counting or time mode with rinse and automatic addition of scintillation fluid to each vial. The system can process up to six gradients per hour but centrifugation time is usually the limiting factor. With neutral sucrose gradients, sharp, reproducible, monodisperse peaks containing up to 100% of the gradient radioactivity are usually obtained but a smaller monodisperse peak containing as little as 3.5% of the gradient radioactivity can be detected under conditions where some pairs of molecules might tangle or dimerize. The resolution and reproducibility of this system when used with neutral sucrose gradients is at least the equal if not superior to that commonly claimed for alkaline sucrose gradients.     

Use of dextran-40 gradients for separation of pea cotyledon mitochondria into different fractions

A crude pea (Pisum sativum L. var. Homesteader) mitochrondrial preparation was divided into two equal parts. One part was layered on a Dextran-40 step gradient, and the other on a sucrose step gradient, and they were centrifuged to obtain different bands of particles. The densities at which the particles banded and the mitochondrial respiratory activities of the particles were determined. Dextran-40 density gradient centrifugation resulted in a better separation of mitochondrial populations than did sucrose density gradient centrifugation. Separation by sucrose density gradient centrifugation may not be according to the true densities of the particles. On the other hand, the use of gradients of Dextran-40, a solute of low osmotic potential, facilitated separation of particles acording to their true densities. Such mitochondria showed better respiratory control ratio and ADP:0 values, than those isolated by sucrose density gradient centrifugation.     

A method for predicting the location of particles sedimenting in sucrose gradients

A theory was developed for the calculation of the positions of zones of particles sedimenting through a sucrose gradient. Equations were derived for particles sedimenting through gradients in which the sucrose concentration is (a) a linear function of radius, or (b) a hyperbolic function of radius. Computations were made for both swing-out and zonal rotors. The theory, which is based on direct integration of the sedimentation equation, exploits equations relating (a) the density of sucrose solutions to sucrose concentration and (b) the viscosity of sucrose solutions to sucrose concentration, and also the concept of reduced time (T/2 = S20.w integral of t to w2dt) of Fujita. The required computations may be made using a scientific calculator. Experimental support for the theory was obtained.     

Production of Ficoll, Percoll, and albumin gradients by the freeze-thaw method.

Ficoll, sucrose, albumin, and Percoll, a modified colloidal silica centrifugation medium, all form density gradients upon freezing and thawing. The data suggest that any density gradient material will form gradients upon freezing and thawing, provided the material is stable to freezing.     

Effect of high sucrose concentrations on mitochondria: Analysis of mitochondrial populations by density-gradient centrifugation after fixation with glutaraldehyde

It has been shown previously that intact rat liver mitochondria can be separated into two populations (designated B2 and B3) with mean buoyant densities of 1·184 and 1·216 respectively, by isopycnic sucrose density gradient centrifugation. A comparison has been made of some properties of these mitochondrial fractions from density gradients with non-fractionated mitochondria. Use was made of density gradient centrifugation for analysis of preparations fixed with appropriate concentrations of glutaraldehyde. The permeability of the membranes of non-fractionated mitochondria to sucrose was increased by exposure to hypoosmotic sucrose solutions. The B3 mitochondria differed from the non-fractionated mitochondria in their response to changes in osmotic pressure of the suspending medium while the B2 mitochondria showed essentially identical behaviour with the controls. However, under conditions of energized swelling the B2 mitochondria were markedly different to the controls. This difference, which is attributed to reduced permeability of the mitochondrial membranes to metabolites brought about by exposure to the high concentrations of sucrose encountered in the density gradient, was reversed by incubation in hypo-osmotic sucrose solutions in the presence of oxidizable substrate and permeant ions.Died December, 1969.     

Precision of sensing cell length via concentration gradients

Unicellular organisms are typically found to have a characteristic cell size. To achieve a homeostatic distribution of cell sizes over many generations requires that cell length is actively sensed and regulated. However, the mechanisms by which cell size is controlled remain poorly understood. Recent experiments in fission yeast have shown that cell length is controlled in part by polar gradients of the protein Pom1 together with localized measurement of concentration at midcell. Dilution as the cell grows leads to a reduction in the midcell protein concentration, which lifts a block on mitosis. Here we analyze the precision of this mechanism for length sensing in the presence of inevitable intrinsic noise in the processes leading to formation and measurement of this gradient. We find that the use of concentration gradients allows for more robust length sensing than a comparable spatially uniform system, and allows for reliable length determination even if the average protein concentration throughout the cell remains constant as the cell grows. Optimal values for the gradient decay length and receptor dissociation constant emerge from maximizing sensitivity while minimizing the impact of density fluctuations.     

The isolation of purified neurosecretory vesicles from bovine neurohypophysis using isoosmolar density gradients

Two different density gradients are described for the isolation of highly purified fractions of neurosecretory vesicles in isoosmotic solutions (300 mosm/kg) from bovine neurohypophyses. The techniques involve differential centrifugation of neural lobe homogenates followed by density gradient centrifugation on metrizamide-sucrose or Percoll-sucrose gradients. The purified fraction contained 44 and 65 μg vasopressin/mg protein, respectively. Neurosecretory vesicles thus isolated were only slightly contaminated with other subcellular organelles, e.g., mitochondria and lysosomes. These vesicles were highly stable in isotonic sucrose solutions (pH 7.5 and 5.5) even at 37°C for at least 2 h, retaining more than 90% of their hormonal content.     

In situ studies of subcellular particles immobilized in sucrose-acrylamide density gradients.

In order to study subcellular particles. I have applied a method to immobilize the content of a sucrose density gradient with acrylamide after centrifugation. The different zones in the gels were localized and analyzed by specific stains and enzymatic, histochemical tests. This method allows the demonstration of several specific zones which could not be determined by traditional procedures. Moreover, the method requires only a few milligrams of material and can also be applied to other purposes such as autoradiography of gels containing minute amounts of radioactive products which could not be detected in a scintillation counter.     

Separation of biological macromolecules in vertical rotors using sucrose gradients shaped by a microprocessor-controlled gradient former

The separation of macromolecules in vertical rotors using linear or isokinetic sucrose gradients permits shorter centrifugation times and a higher sample capacity compared to swing-out rotors. In vertical rotors appropriate gradients give a resolution almost identical to that in swinging bucket rotors. This could be demonstrated for the isolation of polysomes and oligonucleosomes from rat liver. A microprocessor-controlled gradient former is presented which produces gradients of any desired shape. This device has been applied to prepare gradients with the desired linear or isokinetic shape after reorientation in the vertical tube during centrifugation.     

Isolation of transverse tubules by fractionation of sarcoplasmic reticulum preparations in ion-free sucrose density gradients

A new method for the preparation of transverse tubules (T-tubules) from rabbit skeletal muscles is reported. When crude sarcoplasmic reticulum (SR) preparations were centrifuged on sucrose density gradients containing buffering ions (buffered gradients) 70-80% of the material sedimented as a single heavy band in the region of 43% sucrose. When this fraction (or crude SR) was recentrifuged on sucrose gradients prepared free of buffer or other ions (ion-free gradients) the heavy band dissociated into three fractions of different densities. The lightest fraction sedimented at 28% sucrose and was identified as T-tubules on the basis of its nitrendipine and ouabain binding properties. The enzymatic properties, cholesterol contents, and protein compositions of the fractions obtained when SR is centrifuged on buffered and ion-free sucrose density gradients were measured. The T-tubules were enriched in cholesterol and in marker enzymes for surface membranes while the other fractions were shown to be terminal cisternae and longitudinal cisternae on the basis of their (Ca2+,Mg2+)-ATPase activities and characteristic protein profiles.     

A simple technique for the preparation and storage of sucrose gradients

A method for preparing multiple sucrose gradients by quickly freezing layers of sucrose has been developed. These gradients may be stored in the freezer indefinitely, and thawed from 8 to 24 h at 4 degrees C before use. The middle region of the resulting sucrose gradients was linear. Thawing time and centrifugation had little effect on the shape of the gradient. The method is applicable for both small- and large-volume centrifuge tubes. Gradients prepared in the same batch were nearly identical.     

Detecting immunocomplex formation in sucrose gradients by enzyme immunoassay: application in determining epitope accessibility on ribosomes.

A sensitive method using enzyme immunoassay and sucrose gradient to analyze immunocomplexes of biological particles has been developed. The sensitivity and application of this method were demonstrated by that the in situ accessibility of ribosomal protein epitopes could be easily determined. We used sucrose gradients to separate the ribosome-bound and the free antibodies and traced the antibodies in the gradients by an enzyme-linked immunosorbent assay. Epitopes exposed in situ are bound by specific antibodies, which in turn are detected in sucrose gradients migrating with ribosomes. This method of detecting antibody migration is more sensitive than the conventional means of using A260nm to monitor the antibody-mediated dimerization of ribosomes. Furthermore, an epitope defined by a biotin-labeled monoclonal antibody can be analyzed in the presence of other unlabeled antibodies. Thus, the relationship of different accessible epitopes in situ can be readily examined. Versatility and sensitivity of this method should make it useful in analyzing a variety of immunocomplex systems.     

Calculation of s20,w values using ultracentrifuge sedimentation data from linear sucrose gradients, an improved, simplified method.

A mathematical method is described for calculating the sedimentation coefficient (S20,W) with ultracentrifuge data from linear sucrose gradients. Gradient density and viscosity functions are precisely described by regression equations, which permit continuous evaluation (by integration) of the effects of gradient geometry on particle sedimentation. The results agree with previously used and more complex methods.     

Isolation of Cryptosporidium oocysts and sporozoites using discontinuous sucrose and isopycnic Percoll gradients

Techniques for the large-scale isolation of Cryptosporidium oocysts and sporozoites, obtained from the feces of experimentally infected Holstein calves, were developed employing discontinuous sucrose gradients and isopycnic Percoll gradients. The oocyst recovery method utilized 2 sequential discontinuous sucrose gradients followed by 1 Percoll gradient. Recovered oocysts were essentially free of debris and bacteria and represented 34% of the original oocyst suspension. Sporozoites were recovered from excystation mixtures on a single Percoll gradient. Sixty-three percent of the original sporozoites were recovered with 2.2% contamination by intact oocysts and virtually no oocyst walls.     

The construction and analysis of sucrose gradients for use with zonal rotors.

The rate of sedimentation of a particle in a sucrose solution depends on the viscosity and density of the medium. These two variables are related to the sucrose concentration and the temperature of the medium by new simple equations. These equations were used in a rapid iterative procedure that relates the distance moved by a zone in a continuous sucrose gradient to its sedimentation coefficient. It is shown by comparison with experiment that this iterative method allows the distance moved by a zone to be calculated rapidly. The method may therefore be used to optimize the separation of particles in a sucrose-gradient-centrifugation experiment. The method also allows the unknown sedimentation coefficients of several zones to be measured from a single sucrose-gradient-centrifugation experiment.     

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry

The introduced protocol provides a tool for the analysis of multiprotein complexes in the thylakoid membrane, by revealing insights into complex composition under different conditions. In this protocol the approach is demonstrated by comparing the composition of the protein complex responsible for cyclic electron flow (CEF) in Chlamydomonas reinhardtii, isolated from genetically different strains. The procedure comprises the isolation of thylakoid membranes, followed by their separation into multiprotein complexes by sucrose density gradient centrifugation, SDS-PAGE, immunodetection and comparative, quantitative mass spectrometry (MS) based on differential metabolic labeling (¹⁴N/¹⁵N) of the analyzed strains. Detergent solubilized thylakoid membranes are loaded on sucrose density gradients at equal chlorophyll concentration. After ultracentrifugation, the gradients are separated into fractions, which are analyzed by mass-spectrometry based on equal volume. This approach allows the investigation of the composition within the gradient fractions and moreover to analyze the migration behavior of different proteins, especially focusing on ANR1, CAS, and PGRL1. Furthermore, this method is demonstrated by confirming the results with immunoblotting and additionally by supporting the findings from previous studies (the identification and PSI-dependent migration of proteins that were previously described to be part of the CEF-supercomplex such as PGRL1, FNR, and cyt f). Notably, this approach is applicable to address a broad range of questions for which this protocol can be adopted and e.g. used for comparative analyses of multiprotein complex composition isolated from distinct environmental conditions.     

Density gradient system. I. Formation and fractionation of density gradients

The instrumentation of a precise yet flexible system for the formation and fractionation of linear density gradients is described. The use of a special peristaltic pump and gradient-forming chambers permits the rapid formation of both dilute and concentrated solutions into ca. 5 to 300 ml of gradient. This gradient can be delivered to a single centrifuge tube or equally apportioned to as many as 24 tubes.The special peristaltic pump, which is described in the paper that follows, delivers the concentrated solution into the gradient-forming chamber as well as conveying the gradient from the chamber to the special centrifuge tube. A capillary in the wall of the tube conveys the gradient to the bottom, where it is dispersed into 18 equidistant orifices. This dispersion permits the rapid formation and fractionation of the gradient without disruption. A presettable counter coupled to the peristaltic pump permits the gradients to be apportioned into equal volume fractions.Results obtained with both dilute and concentrated gradients are presented.     

Tumor cell haptotaxis on covalently immobilized linear and exponential gradients of a cell adhesion peptide

The movement of cells up an adhesive substratum gradient has been proposed as a mechanism for directing cell migration during development and metastasis. Critical evaluation of this hypothesis (haptotaxis) benefits from the use of quantifiable, stable substratum gradients of biologically relevant adhesion molecules. We report covalent derivatization of polyacrylamide surfaces with quantifiable gradients of a nonapeptide containing the adhesive Arg-Gly-Asp sequence. Cell migration was studied by seeding derivatized surfaces evenly with B16F10 murine melanoma cells. Within 8 hr, cells on gradients redistributed markedly; higher cell densities were found at gel positions having higher immobilized peptide densities. In contrast, cells seeded on control gels with uniform concentrations of adhesive peptide did not redistribute. Redistribution occurred on gradients in both serum-free and serum-containing media. Experiments with uniform density peptide-derivatized gels demonstrated that redistribution on gradients was not due to preferential initial cell attachment or preferential growth on the higher density of immobilized peptide, but must have been due to cell translocation. Cells on exponential gradients of immobilized peptide migrated to a position on the gel surface corresponding to the highest immobilized peptide density, while cells on linear gradients of the same peptide migrated to a position of intermediate peptide density. These data suggest that the B16F10 cells respond to proportional changes in immobilized peptide density rather than to absolute changes, implying a sensing mechanism which utilizes adaptation. These results demonstrate that (1) a gradient of a small adhesive peptide is sufficient to generate redistribution of cell populations and (2) controlled quantifiable substratum gradients can be produced and used to probe the underlying cellular mechanisms of this behavior.     

Covalent surface chemistry gradients for presenting bioactive peptides

The activation of surfaces by covalent attachment of bioactive moieties is an important strategy for improving the performance of biomedical materials. Such techniques have also been used as tools to study cellular responses to particular chemistries of interest. The creation of gradients of covalently bound chemistries is a logical extension of this technique. Gradient surfaces may permit the rapid screening of a large range of concentrations in a single experiment. In addition, the biological response to the gradient itself may provide new information on receptor requirements and cell signaling. The current work describes a rapid and flexible technique for the covalent addition of bioactive peptide gradients to a surface or gel and a simple fluorescence technique for assaying the gradient. In this technique, bioactive peptides with a terminal cysteine are bound via a heterobifunctional coupling agent to primary amine-containing surfaces and gels. A gradient in the coupling agent is created on the surfaces or gels by varying the residence time of the coupling agent across the surface or gel, thereby controlling the extent of reaction. We demonstrate this technique using poly(l-lysine)-coated glass surfaces and fibrin gels. Once the surface or gel has been activated by the addition of the coupling agent gradient, the bioactive peptide is added. Quantitation of the gradient is achieved by measuring the reaction kinetics of the coupling agent with the surface or gel of interest. This can be done either by fluorescently labeling the coupling agent (in the case of surfaces) or by spectrophotometrically detecting the release of pyridine-2-thione, which is produced when the thiol-reactive portion of the coupling agent reacts. By these methods, we can obtain reasonably precise estimates for the peptide gradients without using expensive spectroscopic or radiolabeling techniques. Validation with changes in fibroblast cell migration behavior across a bioactive peptide gradient illustrates preservation of peptide function as well as the usefulness of this technique.