Isopycnic centrifugation of mammalian metaphase chromosomes in Nycodenz

Separation of chromosomes on the basis of buoyant density has proved difficult due to their high density and sensitivity to high ionic strength. Nycodenz is a new non-ionic gradient medium which offers significant advantages over previously described media for separation of chromosomes. The purpose of this study was to examine the banding characteristics of isolated mammalian metaphase chromosomes in Nycodenz gradients. The results indicate that chromosomes can be efficiently concentrated and separated from nuclei using Nycodenz gradients. Furthermore, chromosomes density-labeled with bromodeoxyuridine (BrdU) can be separated from unlabeled chromosomes in Nycodenz gradients. Nycodenz does not appear to alter chromosome morphology or protein complement. The introduction of Nycodenz represents a significant new tool for use in chromosome separation and purification.     

Buoyant densities of macromolecules, macromolecular complexes, and cell organelles in Nycodenz gradients

Nycodenz is a new nonionic iodinated density gradient medium which has several advantages over metrizamide. Although, overall, biological samples band at similar densities in Nycodenz and metrizamide gradients, a number of significant differences were found. As compared with metrizamide, not only does Nycodenz appear to interact less with proteins but also the buoyant density of chromatin is less affected by the amount loaded onto the gradient. A high degree of resolution is obtainable using Nycodenz gradients; thus, it is possible to separate density-labeled DNA and to subfractionate subcellular membrane fractions.     

Buoyant density of Escherichia coli is determined solely by the osmolarity of the culture medium

In previous studies, we had shown that the buoyant density ofEscherichia coli is determined by the osmolarity of the growth medium by varying the osmolarity of the medium with NaCl or sucrose. However, the buoyant density of the cells always exceeded that of the growth medium. Here we determined the effect of medium with a buoyant density greater than the expected buoyant density of cells by adding Nycodenz to Luria broth. Percoll gradients of cells were analyzed by laser light scattering. The buoyant density for 125- and 375-mOsM-grown cells was 0.002 g/ml and 0.003 g/ml more, respectively, for cells grown in the presence of Nycodenz than those grown without Nycodenz, while the buoyant density of 250-mOsM-grown cells was 0.005 g/ml less for cells grown in the presence of Nycodenz than those grown without Nycodenz. Cells grown in 500-mOsM medium with or without Nycodenz had the same buoyant density. the buoyant density of cultures grown in defined medium was the same as those grown in rich medium, with only the medium osmolarity correlating to buoyant density. We conclude from these experiments that neither buoyant density nor chemical make-up of the medium determines the buoyant density of cells grown in that medium. Only the medium osmolarity determines cell buoyant density, suggesting thatE. coli has no mechanisms to sense buoyant density.     

A rapid method for the preparation of the neutrophil fraction of granulocytes from human blood by centrifugation on isotonic Nycodenz gradients

A rapid method for the preparation of neutrophils of the granulocyte fraction of human blood is described. A leucocyte-rich fraction is loaded onto preformed isotonic Nycodenz gradients, formed by mixing a stock isotonic Nycodenz solution with a NaCl diluent solution. After low speed centrifugation a neutrophil fraction of high viability, yield and purity can be isolated from the gradients.     

Isolation of the major subcellular organelles from mouse liver using Nycodenz gradients without the use of an ultracentrifuge

Commonly, subcellular organelles such as nuclei, mitochondria, lysosomes, and Golgi membranes are isolated first by differential centrifugation in low-speed or high-speed centrifuges and then purified by gradient centrifugation in ultracentrifuges. We have prepared these organelles using a new high-speed centrifuge (28,000 rpm max) which allows the generation of higher radial centrifugal forces (rcfs) than are available in standard machines. We have shown that most subcellular organelles can be purified by using low-viscosity Nycodenz gradients at rcfs lower than those normally used in ultracentrifuges, without increasing the time of centrifugation. Use of Nycodenz also allows rapid harvesting of material from gradients and we have adapted a number of enzyme assays to facilitate gradient analysis.     

The use of two populations of hepatocytes with different triacylglycerol contents as a model to study the accumulation of liver lipid in the laying hen.

(1) A method has been developed to separate hepatocytes, isolated from laying hens, according to their densities, using discontinuous density-gradient centrifugation on Nycodenz. (2) The hepatocytes recovered from the interface of the 5% and 10% Nycodenz layers were rich in triacylglycerol and were termed 'fatty' hepatocytes: 'non-fatty' hepatocytes were obtained from the interface of the 15% and 30% Nycodenz layers and contained less than one-quarter as much triacylglycerol. (3) 'Fatty' hepatocytes incorporated radiolabelled glucose and glycerol into total lipid at more than twice the rate of 'non-fatty' cells: the corresponding increases in the incorporation of radiolabelled choline and valine into phospholipid and protein respectively were smaller and not statistically significant. (4) A higher proportion of glycerol and glucose incorporated into total lipid was found to be phospholipid in the 'non-fatty' hepatocytes. (5) A higher proportion of radiolabelled lipid or protein formed from glycerol or valine respectively was secreted into the medium by the 'non-fatty' hepatocytes. (6) The use of these hepatocytes as a model to study fatty liver syndromes is discussed.     

Extraction of methane-oxidizing bacteria from soil particles

Abstract: We present a method for extraction of active methane (CH₄)-oxidizing bacteria from soil samples. The method is based on physical dispersion of bacteria from the soil particles followed by separation of bacteria and soil particles by floatation in the density media Nycodenz or Percoll. Separation on Nycodenz produced very pure bacterial suspensions while separation on Percoll produced rather impure suspensions. However, more than 60% of the methane-oxidizing activity was irreversibly inhibited in the procedure using Nycodenz compared to less than 10% irreversible inhibition when Percoll was employed. The bacterial suspensions extracted from soil can be used to study the physiology and ecology of soil bacteria that oxidize methane at atmospheric concentrations. Our data indicated that these bacteria are extremely difficult to dislodge from particles compared to the majority of bacteria in soil. Tentatively, we interpret the strong attachment to long residence time (i.e. slow turnover) of the methane-oxidizing bacteria. A slow turnover/growth rate would explain why soil disturbances, like cultivation, have a long lasting effect on the oxidation of atmospheric methane in soil.     

Routine fluorescence in situ hybridization in soil

The use of fluorescence in situ hybridization (FISH) to identify and enumerate soil bacteria has long been hampered by the autofluorescence of soil particles masking the bacterial signals and because the need of counting hundreds of bacteria in order to achieve statistically reliable data is time consuming. Recently, it was demonstrated that Nycodenz facilitates FISH in soil by concentrating bacteria on membrane filters and avoiding autofluorescent soil particles. We present a routine protocol for FISH in soil including the use of Nycodenz. The protocol allows fast and easy enumeration of hundreds of bacteria. We propose the use of silicon grease coated slides to treat in parallel seven samples per hybridization. Further, we developed a semi-automated approach for the enumeration of bacteria by implementing macros concatenating all steps of the image analyzes in the Image J software. Using Nycodenz, software-assisted bacterial counts statistically matched eye-counts of the same images and it was possible to count 880 DAPI stained bacteria per ten images. Fifty-five percent of these bacteria were co-labelled with the FISH probe specific for the Domain Bacteria, in accordance with recent FISH studies of bacterial populations in bulk soil. With a soil slurry protocol used for comparison, soil particles impaired automatic counts of the bacteria and FISH analysis, and only 88 DAPI stained bacteria per ten images could be counted by eye. With the Nycodenz protocol, 5 mM Na(2)EDTA used as an extractant increased the number of bacteria observed by 49%. In contrast, Tween 20 (1% or 5%) had no significant effect and increased the variability between the samples. Overall, the proposed procedure allows to process a high number of samples and to achieve a time efficient FISH characterization of soil bacterial communities.     

The Preparation of Subcellular Organelles from Mouse Liver in Self-Generated Gradients of Iodixanol

This paper reports the use of a new density gradient compound, Iodixanol, for the resolution of the major organelles from mouse liver. A major advantage of Iodixanol over other iodinated density gradient media is its ready ability to form self-generated gradients. Gradient-forming conditions have been modulated to provide optimal recoveries of Golgi membranes, lysosomes, mitochondria, and peroxisomes. The organelles were isolated in high yield (80-90% of gradient input) and high purity. Nycodenz and Iodixanol were compared using preformed gradients. Iodixanol provided resolution superior to that of Nycodenz, notably of peroxisomes and mitochondria and the separation of lysosomes from endoplasmic reticulum. Because Iodixanol does not interfere significantly with marker enzyme activities, gradient fractions can be analyzed without removal of the gradient medium.     

Subfractionation of hepatic endosomes in Nycodenz gradients and by free-flow electrophoresis. Separation of ligand-transporting and receptor-enriched membranes.

The complexity of rat liver endosome fractions containing internalized radioiodinated asialotransferrin, asialo-(alkaline phosphatase), insulin and prolactin was investigated by using free-flow electrophoresis and isopycnic centrifugation in Nycodenz gradients. Two subfractions were separated by free-flow electrophoresis. Both subfractions contained receptors for asialoglycoprotein and insulin. Glycosyltransferase activities were associated with the more electronegative vesicles, whereas 5'-nucleotidase and alkaline phosphodiesterase activities were associated with the less electronegative vesicles. Three subfractions were separated on Nycodenz gradients. Two subfractions, previously shown to become acidified in vitro, contained the ligands. At short intervals after uptake (1-2 min), ligands were mainly in subfraction DN-2 (density 1.115 g/cm3), but movement into subfraction DN-1 (density 1.090 g/cm3) had occurred 10-15 min after internalization. Low amounts of glycosyltransferase activities were associated with subfraction DN-2, and 5'-nucleotidase and alkaline phosphodiesterase activities were mainly located in subfraction DN-1. The binding sites for asialoglycoproteins and insulin were distributed towards the higher density range in the Nycodenz gradients, thus indicating a segregation of receptor-enriched vesicles and those vesicles containing the various ligands 10-15 min after internalization. Electron microscopy of the subfractions separated on Nycodenz gradients indicated that whereas the ligand-transporting fractions consisted mainly of empty vesicles (average diameter 100-150 nm), the receptor-enriched component was more granular and smaller (average diameter 70-95 nm). The properties of the endosome subfraction are used to assign their origin to the regions of the endocytic compartment where ligand-receptor dissociation and separation occur.     

Effect of ligand binding on the buoyant density of DNA in Nycodenz gradients.

The effect of ligand binding upon the buoyant density of DNA in Nycodenz gradients has been studied using DNAs of differing base compositions. The effect of both intercalating ligands (ethidium bromide and proflavin) and non-intercalating ligands (distamycin A, DAPI and netropsin) has been studied. The binding of intercalating ligands to DNA has essentially no effect on the buoyant density of DNA in Nycodenz gradients. The non-intercalating ligands were found to increase the buoyant density of DNA in a base specific manner. The increase in buoyant density can be interpreted in terms of disruption of the hydration shell of the DNA molecule caused by the binding of the ligand along the minor groove of the DNA helix.     

Evaluation of methods for extraction of bacteria from soil

Abstract Several methods for dispersion of soil were tested for possible use in procedures for extraction of bacteria. Physical cell damage on cells and efficiency in extraction of indigenous cells from soil, were investigated. Cell damage by the dispersion methods was investigated by measuring the physical cell integrity and viability of pure cultures of Escherichia coli and Bacillus subtilis , as well as soil bacteria extracted from soil, when dispersed in slurries of γ-sterilized soil. Separation of bacteria and soil particles on the basis of buoyant density was conducted with the nonionic density gradient medium Nycodenz. When slurries of γ-sterilized soil with added pure cultured cells were centrifuged (10000 × g ) over cushions of Nycodenz (1.3 g ml⁻¹), practically all the added cells were recovered in a layer on top of the cushion. This proves that a reversible attachment and cosedimentation is not an important phenomenon in this procedure. The efficiency of the different dispersion methods for the extraction of indigenous soil bacteria, was assessed after separation of dislodged and attached soil bacteria. This separation was done either on the basis of sedimentation rate by low speed centrifugation, or buoyant density by Nycodenz density gradient centrifugation. The physical dispersion by ultrasonic treatment and chemical dispersion by the use of a chelating agent together with a detergent, were inferior to physical dispersion either by Waring blender (for large volumes) or a rotating rubber pestle treatment (for smaller volumes). The physical dispersion did not appear to be destructive to the cells tested.     

Localization of a mitochondrial type of NADP-dependent isocitrate dehydrogenase in kidney and heart of rat: an immunocytochemical and biochemical study.

We studied the subcellular localization of the mitochondrial type of NADP-dependent isocitrate dehydrogenase (ICD1) in rat was immunofluorescence and immunoelectron microscopy and by biochemical methods, including immunoblotting and Nycodenz gradient centrifugation. Antibodies against a 14-amino-acid peptide at the C-terminus of mouse ICD1 was prepared. Immunoblotting analysis of the Triton X-100 extract of heart and kidney showed that the antibodies developed a single band with molecular mass of 45 kD. ICD1 was highly expressed in heart, kidney, and brown fat but only a low level of ICD1 was expressed in other tissues, including liver. Immunofluorescence staining showed that ICD1 was present mainly in mitochondria and, to a much lesser extent, in nuclei. Low but significant levels of activity and antigen of ICD1 were found in nuclei isolated by equilibrium sedimentation. Immunoblotting analysis of subcellular fractions isolated by Nycodenz gradient centrifugation from rat liver revealed that ICD1 signals were exclusively distributed in mitochondrial fractions in which acyl-CoA dehydrogenase was present. Immunofluorescence staining and postembedding electron microscopy demonstrated that ICD1 was confined almost exclusively to mitochondria and nuclei of rat kidney and heart muscle. The results show that ICD1 is expressed in the nuclei in addition to the mitochondria of rat heart and kidney. In the nuclei, the enzyme is associated with heterochromatin. In kidney, ICD1 distributes differentially in the tubule segments.     

Rates of beta-oxidation of fatty acids of various chain lengths and degrees of unsaturation in highly purified peroxisomes isolated from rat liver

Highly purified peroxisomes were obtained from the liver of untreated rats, and rates of peroxisomal beta-oxidation were measured using fatty acyl-CoAs differing in chain length and degree of unsaturation. A 20–24-fold purification of peroxisomes, indicated by the specific activities of the marker enzymes catalase and urate oxidase, respectively, was obtained from crude liver homogenate using differential centrifugation techniques followed by a 30% Nycodenz gradient separation. The use of a 30% Nycodenz gradient in the final step of purification was extremely effective (e.g. 5.5-fold reduction) in removing lysosomal contamination. The rate of peroxisomal beta-oxidation with lauroyl-CoA (C12:0) as substrate was the highest of all fatty acyl-CoAs tested. Butyryl-CoA (C4:0) was not oxidized by purified peroxisomes. In general, as chain length of the fatty acyl-CoAs increased above 12 carbons, the rates of beta-oxidation decreased.     

A physical method for separating Saccharomyces cerevisiae cells according to their ploidy

A centrifugation technique, using genetically marked Saccharomyces cerevisiae strains, has been developed to separate Saccharomyces cerevisiae cells of different ploidy levels from exponential phase cultures. The method involves the conversion of yeast cells to protoplasts, the separation of the protoplasts on an osmotically stabilized Nycodenz gradient, and their regeneration. This type of selection may be of importance where selectable markers are not available.     

Sexual development in Plasmodium berghei: the use of mitomycin C to separate infective gametocytes in vivo and ookinetes in vitro

Plasmodium berghei parasites were treated in vivo with mitomycin C. Giemsa stained smears of infected mouse blood showed that the asexual parasitaemia was immediately reduced while the immediate numbers of gametocytes remained unaffected. Mitomycin C treated gametocytes went on to produce ookinetes in culture. These ookinetes, which were shown to be infective to mosquitoes were readily purified by centrifugation onto 12% Nycodenz cushions at 1600 g for 10 min. The mechanism by which mitomycin C acts and the implications for Plasmodium are discussed.     

Rapid subcellular fractionation of the rat liver endocytic compartments involved in transcytosis of polymeric immunoglobulin A and endocytosis of asialofetuin.

The distributions of two endocytosed radiolabelled ligands (polymeric immunoglobulin A and asialofetuin) in rat liver endocytic compartments were investigated by using rapid subcellular fractionation of post-mitochondrial supernatants on vertical density gradients of Ficoll or Nycodenz. Two endocytic compartments were identified, both ligands being initially associated with a light endocytic-vesicle fraction on Ficoll gradients, asialofetuin then accumulating in denser endosomes before transfer to lysosomes for degradation.     

Generation of phosphatidylinositol 4,5-bisphosphate proceeds through an intracellular route in rat hepatocytes

The subcellular distribution in rat hepatocytes of enzymes participating in the entire generation cycle of phosphatidylinositol 4,5-bisphosphate, and phosphorylated intermediates of this pathway, has been examined by Nycodenz gradient centrifugation. Our results indicate that the synthesis of phosphatidylinositol takes place in the endoplasmic reticulum, and that its phosphorylation to phosphatidylinositol 4-phosphate occurs intracellularly in low-density membranes before translocation to the plasma membrane, where it is further phosphorylated to phosphatidylinositol 4,5-bisphosphate. The intracellular formation of PIP implies a vesicular transport to the plasma membrane.     

Preparation of a plasma membrane-rich fraction from rat spermatozoa

Monoclonal antibodies to antigens located on surface and intracellular membranes of spermatozoa from the rat cauda epididymidis have been used as probes to assess the purity of putative plasma membrane fractions. Spermatozoa were demembranated by shearing forces generated on a vortex-mixer. Immunofluorescence and ultrastructural analysis of vortex-mixed spermatozoa showed that they were denuded of approximately 90% of surface membrane. Areas of acrosomal membranes were also removed. Crude plasma membranes were recovered in low-speed wash fluids and fractionated on a 13-23% Nycodenz density gradient. Three bands containing membrane vesicles were resolved. Absorption curves and direct binding assays using monoclonal antibodies specific for acrosomal membranes, mitochondrial membranes and fibrous sheath showed relatively strong binding to bands 1 and 2 but weak binding to band 3. Conversely a monoclonal antibody specific for a surface membrane antigen bound strongly to band 3 and weakly to bands 1 and 2. Identification on immunoblots of the antigens recognized by the monoclonal antibodies revealed that band 3 was positive for surface membrane antigens but gave no reaction for intracellular antigens. However, bands 1 and 2 were strongly positive for intracellular components. The results suggest that vortex-mixing is a simple and efficient means of removing the plasma membrane from spermatozoa and that a membrane fraction can be recovered from a Nycodenz density gradient that is enriched 40- to 50-fold in surface antigens.     

Recovery and quantification of bacterial cells associated with streambed sediments

Efficient detachment and purification of bacterial cells associated with streambed sediments are required in order to quantify cell abundance and to assess community composition through the application of epifluorescence microscopy techniques. We applied chemical (i.e., sodium pyrophosphate and polysorbate) and physical treatments (i.e., shaking and sonication), followed by Nycodenz density gradient centrifugation to efficiently recover benthic bacteria. This procedure resulted in a highly purified cell suspension allowing for a precise cell quantification through the application of fluorescent dyes. About 93% of total cells were recovered from the original sediment, with higher recovery from the finer grain-size class (90%) in comparison to the coarse fraction (69%). The potential damaging effects of the applied procedures on cell integrity were assessed on planktonic bacteria in a pre-filtered water control. As a consequence of the high purity of the extracted bacteria, flow cytometry was successfully applied as counting method for sediment cell suspension. However, a significant decrease of protein synthesis in purified samples was measured by estimating the (3)H-Leucine incorporation rates, rising uncertainties on the possibility to apply potential metabolic assays after Nycodenz purification.