Biochemical differences between subsarcolemmal and interfibrillar mitochondria from rat cardiac muscle: effects of procedural manipulations

Differences in oxidative metabolism between subsarcolemmal and interfibrillar heart mitochondria were investigated. Interfibrillar mitochondria oxidized substrates donating reducing equivalents at Complex I (NADH-CoQ reductase), Complex II (succinate-CoQ reductase), and Complex III (CoQH2-cytochrome c reductase) more rapidly than did subsarcolemmal mitochondria. There was no difference in oxidation of substrates entering the electron transport chain at Complex IV (cytochrome c oxidase). Differences expressed in normal-ionic-strength medium at Complexes II and III but not I were eliminated in low-ionic-strength medium. The concentrations of cytochromes and activities of NADH and cytochrome c oxidase were virtually the same in the two populations. In permeabilized mitochondria, activities of succinate-duroquinone and TMPD plus ascorbate oxidase were significantly lower in the subsarcolemmal mitochondria. Differences in membrane permeability between the populations were suggested by the greater permeability of subsarcolemmal mitochondria to exogenous NADH. The influence of isolation buffers and preparative procedures on the two classes of mitochondria were also examined. Characteristic biochemical and morphological properties of the two populations were unchanged by exposing each to the preparative procedure used to isolate the alternate population; the oxidative performance of the two populations cannot be equalized by experimental manipulation.     

In vitro 14C-leucine incorporation into nonsynaptic and synaptic rat brain mitochondria isolated by Ficoll gradients

The in vitro incorporation of 14C-leucine by nonsynaptic and synaptic rat brain mitochondria purified by means of discontinuous Ficoll gradients has been characterised. The incorporation was linear for the first 45 min for both populations. Synaptic mitochondria showed a higher rate of incorporation than the nonsynaptic mitochondria at high concentrations of leucine. The incorporation was more effective in the presence of Mg2+ and inhibited by dinitrophenol. The incorporation was sensitive to chloramphenicol and insensitive to cycloheximide. Bacterial contamination was in any case lower than 1,000 colonies per ml after the incubation period. The incorporation was carried out in the presence of either an external ATP-generating system consisting of ATP, phosphoenolpyruvate and pyruvate kinase or with mitochondria respiring with oxidisable substrates plus ADP (state III). The rates obtained for incorporation in this state III were higher for all the substrates assayed (succinate, pyruvate and glutamate) than in the presence of exogenous ATP. The highest rate obtained was found when glutamate was the respiratory substrate. No significant metabolic oxidation of leucine occurs in either synaptic or nonsynaptic mitochondria in the presence of exogenous ATP. Glutamate did not increase leucine uptake in any mitochondrial populations.     

Improved method for isolation of mitochondria from chick breast muscle using Nagarse.

An improved procedure to isolate mitochondria from chick pectoralis muscle is described. The muscle is digested with the proteinase Nagarse and homogenized using a Teflon pestle. Mitochondria are isolated by differential centrifugation. These organelles are able to utilize a variety of substrates with a higher degree of respiratory control than mitochondria isolated without Nagarse. Contrary to previous reports, mitochondria isolated by this method from chick pectoralis muscle (αW fibers) are able to oxidize the substrate β-hydroxybutyrate with good respiratory control.     

Biochemical studies of taste sensation. III. Preparation of a suspension of bovine taste bud cells and their labeling with a fluorescent probe.

A method to prepare suspensions of taste bud cells is described. Bovine circumvallate papillae, which contain most of the taste buds in this animal, are incubated in collagenase-containing medium and the epidermal sidewall tissue is then dissected from the inner gelatinous dermis. The sidewall tissue, which contains the taste buds, is gently homogenized by manual operation of an all-glass homogenizer with a loose-fitting pestle. The suspended material is separated on a discontinous Ficoll gradient (2%, 8%, 10%, 12% w/w). The material banding at the 8-2% interface is greatly enriched in spindle-shaped cells that are morphologically similar to taste bud cells as they appear in situ. These cells are not seen when the procedure is done with tissues devoid of taste buds, namely the upper surface of the circumvallate papilla or epithelium from the intermolar eminence. Fluorescence analysis indicates that the hydrophobic probe, 8-anilino-1-naphthalenesulfonate (ANS), binds to relatively nonpolar sites in the suspension. It is postulated that the probe is adsorbing onto the surface membrane of the cell. These preparations may be useful in studying specificity and transduction in taste sensation.     

A rat liver cell-free system for the synthesis of proteins and their transport into mitochondria

A rat liver cytosol was used to study protein synthesis per se and also to study import of proteins into mitochondria since rat liver cytosol represents an environment closer to that of liver mitochondria than the generally used reticulocytes lysates. Two ATP-regenerating systems were compared. The creatine phosphate/creatine kinase yields higher protein synthesis than the phosphoenol pyruvate/pyruvate kinase system. Hemin, necessary to maintain synthesis by reticulocyte lysates, does not affect the rat liver cytosol. The level of protein synthesis obtained with this cell-free system is comparable to other eukaryotic systems described recently and to the expected value for "in vivo" conditions. Isolated mitochondria incorporated, under our standard conditions, newly synthesized proteins linearly up to 30 min, it ceases when a component(s) in the cytosol had been depleted; addition of freshly translated cytosol restores the import. The bulk of imported proteins are retained in mitoplasts or in mitochondria after treatment with trypsin. The cytosol system will be useful to study questions such as regulation of liver mRNA translation and mitochondrial protein turnover.     

Oxidation of acetoacetate and palmitylcarnitine by brain and liver mitochondria from suckling and adult rats

Experiments in which we investigated the possible oxidative utilization of lipoid substrates by brain and liver mitochondria were carried out with rats aged 5 and 90 days, kept under completely standardized conditions. Brain mitochondria were isolated on a Ficoll gradient after Clark and Nicklas (1970). Respiratory activity (or the respiratory control index-R.C.) was determined in the manner described in an earlier paper (Dobesová and Mourek 1980). Na succinate or Na malate was used as the testing substrate; palmityl carnitine, acetyl carnitine and acetoacetate were used as lipoid substrates. Oxygen consumption was measured with a Clark's oxygen electrode and respiration was expressed in nAt oxygen per min per mg protein, which was measured by the method of Lowry et al. (1951). When using succinate or malate, in agreement with our previous results we did not find any development changes in the respiratory activity of the brain mitochondria. The oxidation of acetoacetate by the brain mitochondria of 5-day-old rats was about five times greater, and of acetyl carnitine over two times greater, compared with the CNS mitochondria of adult rats. The oxidative utilization of lipoid substrates by the liver mitochondria of 5-day-old rats was significantly greater than their utilization by CNS mitochondria (in the case of palmityl carnitine three times greater, for example) and was always significantly greater than in the liver mitochondria of adult rats. We demonstrated that mitochondria isolated from the brain of 5-day-old rats are equipped with an enzymatic apparatus which allows them to utilize lipoid substrates on a significantly greater scale than in adulthood.     

A simple and inexpensive "cell dissociation sieve-tissue grinder" apparatus

A simple and inexpensive cell dissociation sieve-tissue grinder apparatus consisting essentially of stainless steel sieve (the one popularly used for sieving tea leaves) and a glass syringe plunger acting as pestle, is described for making single cell suspension.     

Isolation of centrolobular and perilobular hepatocytes after phenobarbital treatment

Daily phenobarbital (PB) injections, on 3-7 consecutive days, induce an intense proliferation of smooth endoplasmic reticulum (ER) associated with a decrease of the glucose-6-phosphatase activity. This situation first affects the centrolobular hepatocytes, enhancing the degree of liver lobule heterogeneity. This experimental model was used for isolation and further subfractionation of hepatocytes on Ficoll density gradients, as described in the preceding paper. Profiles of protein, DNA, RNA, glycogen, phosphorylase, and glucose-6-phosphatase were determined all along the gradient. Two liver cell populations were distinguished: (a) light hepatocytes (mean density 1.10) present the same morphological characteristics as centrolobular cells, i.e., an abundant smooth ER composed of tubular elements, numerous small mitochondria, and few glycogen particles; (b) heavy hepatocytes (mean density 1.14) are characterized by large and compact glycogen areas and prominent rough endoplasmic cisternae, as are the perilobular cells. After incubation in the Wachstein-Meisel medium, Centrolobular hepatocytes exhibit dispersed reaction sites of glucose-6-phosphatase activity, whereas perilobular cells present a continuous and intense reaction. Morphometric determinations were carried out for both cell populations. Centrolobular PB hepatocytes are considerably enlarged (mean diameter: 23.7 mum); perilobular hepatocytes have a significantly smaller mean diameter of 19.2 mum, which is close to the values of control liver cells.     

Separation of steroidal estrogens and their major unconjugated metabolites by high performance liquid chromatography

A high performance liquid chromatographic method is described for the rapid, non-destructive separation of a number of physiologically important steroidal estrogens, including the labile catechol estrogens. This procedures uses a "Diol" column and gradient elution to separate in a single run, estrogens ranging from 2-methoxy estrone, one of the least polar C18 steroids, to estriol, one of the most polar. Simpler, isocratic conditions, are provided for the separation of estrogens of similar polarity. A semi-preparative column of similar composition was used for the purification of samples containing 25 to 50 mg of individual steroids.     

Biochemical studies of taste sensation. III. Preparation of a suspension of bovine taste bud cells and their labeling with a fluorescent probe

A method to prepare suspensions of taste bud cells is described. Bovine circumvallate papillae, which contain most of the taste buds in this animal, are incubated in collagenase-containing medium and the epidermal sidewall tissue is then dissected from the inner gelatinous dermis. The sidewall tissue, which contains the taste buds, is gently homogenized by manual operation of an all-glass homogenizer with a loose-fitting pestle. The suspended material is separated on a discontinuous Ficoll gradient (2%, 8%, 10%, 12% w/w). The material banding at the 8–2% interface is greatly enriched in spindle-shaped cells that are morphologically similar to taste bud cells as they appear in situ. These cells are not seen when the procedure is done with tissues devoid of taste buds, namely the upper surface of the circumvallate papilla or epithelium from the intermolar eminence. Fluorescence analysis indicates that the hydrophobic probe, 8-anilino-1-naphthalenesulfonate (ANS), binds to relatively nonpolar sites in the suspension. It is postulated that the probe is adsorbing onto the surface membrane of the cell. These preparations may be useful in studying specificity and transduction in taste sensation.     

An analysis of the contribution of the preparatory technique to the appearance of condensed and orthodox conformations of liver mitochondria

The structure and volume of isolated mitochondria embedded for electron microscopy during different respiratory states were analyzed in thin sections. Three different embedding methods were compared; osmium tetroxide fixation/acetone dehydration, glutaraldehyde fixation/acetone dehydration, and glutaraldehyde fixation-osmium tetroxide postfixation/acetone dehydration. Analysis of fresh mitochondria, isolated in a sucrose medium, revealed the presence of a homogeneous population with respect to structure when any of the three methods were applied. After fixation with osmium alone, or in combination with glutaraldehyde, nearly 100% of the mitochondria were in a "condensed" conformation. Mitochondria fixed with glutaraldehyde alone resulted in a population of mitochondria that had large spaces separating the two membranes of the cristae which corresponds to the condensed conformation as observed after osmium fixation. Transfer of the mitochondria to the incubation medium led to the appearance of two classes of mitochondria with respect to size. One class had a volume close to that observed when suspended in sucrose, and another class was present that was 30-45% larger. In osmium fixed or in double-fixed preparations, these small and large classes corresponded to "condensed" and "orthodox" forms of mitochondria respectively. When glutaraldehyde was used alone as the fixative, the two size classes were also present. However, the mitochondria were homogeneous with respect to structure. In these mitochondria, the width of the space that separated the cristae membranes had become reduced when compared to mitochondria suspended in sucrose. The two size classes were also present in samples of mitochondria prepared during both states 3 and 4. State 4 conditions did not lead to any significant increase of the number of condensed mitochondria. In state 3 preparations, 65-70% of the population were condensed. The condensed and orthodox forms could be related to normal and swollen forms of mitochondria. Conditions that led to a swelling also led to an increase in the number of orthodox mitochondria in osmium-fixed material. The different appearance of the mitochondria is explained by the different conditions for fixation of the mitochondria that exist when nonswollen and swollen mitochondria are fixed. This difference is particularly crucial in the case of osmium tetroxide due to the unique way this fixative, among generally used fixatives, denatures proteins.     

Isolation of mitochondria from ascites tumor cells permeabilized with digitonin

A new, improved procedure for isolating mitochondria from ascites tumor cells is described. The unique feature of this technique is the use of digitonin to make the cells susceptible to disruption by Teflon pestle/glass vessel homogenization. The yield and respiratory control ratios of mitochondria isolated by this method from murine Ehrlich ascites tumor cells and rat AS30-D ascites hepatoma cells are significantly better than those obtained for mitochondria isolated by the commonly employed Nagarse method, which involves the use of proteolytic enzymes. Moreover, mitochondria isolated by this new procedure from three different lines of tumors exhibit respiratory control ratios with both adenosine diphosphate and a respiratory uncoupler comparable to those obtained with mitochondria present in situ within digitonin-permeabilized tumor cells.     

Mouse zygotes injected with mitochondria develop normally but the exogenous mitochondria are not detectable in the progeny

A microinjection procedure to introduce "paternal" mitochondria from a source other than spermatozoa into fertilized mouse eggs is described. When a mitochondrial suspension isolated from the testes or liver of Mus molossinus mice was microinjected into fertilized eggs of CD1 mice, the microinjected zygotes survived, developed normally, and offspring were produced. Mus molossinus mitochondrial DNA can be distinguished from CD1 mitochondrial DNA by Southern blot analyses using restriction enzymes such as Eco R1, Xba 1, or Spe 1. Although up to 120 viable mitochondria were injected, no exogenous mitochondrial DNA was detected in fetal samples or in the brain, liver, heart, testis, or ovary of the mature progeny. Under the experimental conditions used, similar results were obtained when mitochondria from the testes of New Zealand black mice or from testes of Syrian hamsters were microinjected into fertilized CD1 mouse eggs. Failure to detect the exogenous mitochondrial DNA under our assay conditions suggests that microinjected mitochondria from testis or liver did not selectively replicate during embryonic development. The "foreign" mitochondria appear to have the same fate during early embryogenesis as the mitochondria of the spermatozoon.     

Model for comparative analysis of antigen receptor repertoires

In modern molecular biology one of the standard ways of analyzing a vertebrate immune system is to sequence and compare the counts of specific antigen receptor clones (either immunoglobulins or T-cell receptors) derived from various tissues under different experimental or clinical conditions. The resulting statistical challenges are difficult and do not fit readily into the standard statistical framework of contingency tables primarily due to the serious under-sampling of the receptor populations. This under-sampling is caused, on one hand, by the extreme diversity of antigen receptor repertoires maintained by the immune system and, on the other, by the high cost and labor intensity of the receptor data collection process. In most of the recent immunological literature the differences across antigen receptor populations are examined via non-parametric statistical measures of the species overlap and diversity borrowed from ecological studies. While this approach is robust in a wide range of situations, it seems to provide little insight into the underlying clonal size distribution and the overall mechanism differentiating the receptor populations. As a possible alternative, the current paper presents a parametric method that adjusts for the data under-sampling as well as provides a unifying approach to a simultaneous comparison of multiple receptor groups by means of the modern statistical tools of unsupervised learning. The parametric model is based on a flexible multivariate Poisson-lognormal distribution and is seen to be a natural generalization of the univariate Poisson-lognormal models used in the ecological studies of biodiversity patterns. The procedure for evaluating a model's fit is described along with the public domain software developed to perform the necessary diagnostics. The model-driven analysis is seen to compare favorably vis a vis traditional methods when applied to the data from T-cell receptors in transgenic mice populations.     

Purification of synaptic vesicles from elasmobranch electric organ and the use of biophysical criteria to demonstrate purity.

We have purified cholinergic synaptic vesicles from the electric organs of two related marine elasmobranchs, Torpedo californica and Narcine brasiliensis, to a specific activity higher than had previously been obtained. We have demonstrated the homogeneity of the vesicles by biophysical criteria. The purification scheme consisted of differential centrifugation, flotation equilibrium in sucrose density gradients, and permeation chromatography on glass bead columns of average pore size 3000 A. Our criteria for purity were that bound acetylcholine, bound nucleotide triphosphate, protein, and lipid--phosphorus behave identically when vesicles were analyzed by procedures which depend on vesicle size, density, and charge. Contaminants were not detected when vesicles were fractionated by preparative and analytical sedimentation, by preparative equilibrium sedimentation using glycerol density gradients, or by electrophoresis in Ficoll density gradients. Pure synaptic vesicles, which have been purified 290-fold from the initial homogenate, contain per mg of protein: 8 mumol of acetylcholine, 3 mumol of ATP, and 7 mumol of lipid phosphorus. These procedures may be of general value in the purification of membrane vesicles.     

Fine mapping and replication of QTL in outbred chicken advanced intercross lines

Background

Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F₂ populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F₂ animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature.

Methods

We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F₂ population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight.

Results

Five of the nine QTL detected with the original F₂ population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL.

Conclusions

Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.     

Mixed-bed chromatography as a way to resolve peculiar protein fractionation situations

Mixed-bed chromatography is based on the use of multiple sorbents mixed together and packed in a single column. Solid-phase combinatorial libraries are a current example of mixed-bed chromatography with a large number of immobilized affinity ligands each of them attached to a different bead. They have been repeatedly reported to reduce the dynamic protein concentration range from biological extracts when used in large overloading conditions. By that way trace proteins can easily be enhanced and analyzed. When mixed libraries of ligands are used in under-saturation conditions they constitute a generic way to remove minor impurity traces still present in even highly purified biological product. Whereas ligand libraries are generally used in a neutral environment for the capturing phase, they can also be used in acidic or alkaline conditions with specific advantages due to the modulation of affinity constants. Mixed-bed cascades involving affinity libraries or ion exchangers are also approaches allowing protein fractionation. This review reports various applications of mixed-bed chromatography related to protein fractionation not only for proteomics investigations, but also for preparative purposes.     

Population dynamics of mitochondria II. Turnover and ageing of rat liver mitochondria

Membrane-bound multi-protein complexes in mitochondria are provisionally classified into four categories based on possible mechanism of their assembly and degradation. These mechanisms may be investigated by the use of pulse-labeled radioactive markers which are not re-utilizable. Age dependent assembly is defined as that mechanism by which one or more of the pulse-labeled subunits are assembled into a complex, only while this complex is assembled. If the labeled sub-units can be taken up by the complex randomly during its life-span, then the mechanism is called age-independent assembly. Age-dependent degradation was defined as that mechanism by which the labeled subunits are decomposed, only when the complex is being degraded as an entity. If the labeled subunits are decomposed randomly, the mechanism is called age-independent degradation. Four categories are made by combining each of the assembly and degradation mechanisms. A differential equation was obtained to describe the fate of labeled sub-units that follow the age-dependent assembly and age-dependent degradation. Also derived was an equation for the age-independent assembly and age-dependent degradation. The other two categories which involve the age-independent degradation after age-dependent or age-independent assembly are described by single exponential kinetics. Practical application of the equations is illustrated with the use of experimental data on mitochondrial turnover found in the literature which suggests that the pulse-labeled proteins in rat liver mitochondria may follow the age-dependent assembly and degradation. The present attempts to introduce the concept of ageing into multi-protein complexes in mitochondria are the extensions of the steady state theory of mutation by Eyring & Stover (1970).     

Oxidative phosphorylation in rat liver mitochondria isolated by rate zonal centrifugation: Examination of Ficoll gradients and subpopulations of mitochondria

In order to measure the parameters of oxidative phosphorylation it is necessary to isolate physiologically intact mitochondria. The isolation of rat liver mitochondria by rate zonal centrifugation utilizing isoosmotic Ficoll gradients resulted in the uncoupling of oxidative phosphorylation in these organelles. Analysis of the Ficoll solutions used to construct the gradients indicated that the Ca²⁺ content (200–400 nmole Ca²⁺/mg protein) was sufficiently high to cause an uncoupling of oxidative phosphorylation. Treatment of the Ficoll solutions with Amberlite MB-3 resin reduced the Ca²⁺ content to levels below the limit of determination of the assay procedure. This resulted in the retention of respiratory control (1.42) in rate-zonally centrifuged mitochondria. The addition of bovine serum albumin (100 mg%) to the Ficoll gradients increased the respiratory control index to 2.10. The increase is due to an elevation in state 3 respiration rather than any change in state 4 respiration. The addition of 200 mg% bovine serum albumin to the Ficoll gradient did not further enhance the respiratory control index.Examination of subpopulations of rat liver mitochondria revealed that they are heterogeneous with regard to states 3 and 4 respiration, respiratory control indices, and ADP:O ratios. In mitochondrial subpopulations respiratory control indices ranged from 1.00 to 4.13 and ADP:O ratios ranged from 1.22 to 1.83. This investigation defined a procedure for the isolation of physiologically intact mitochondria from rat liver homogenates.     

Preparative electrophoresis on agarose submerged gels of two aggregating proteoglycan monomers from articular cartilage

Analytical electrophoresis on polyacrylamide-agarose gels of aggregating proteoglycan monomers from baboon articular cartilage produces two distinct bands, corresponding to two different aggregating monomer populations. A preparative electrophoresis procedure is described for isolating the two monomers. Proteoglycans were extracted from young baboon articular cartilage in 4 M guanidinium chloride containing proteolysis inhibitors and aggregated after hyaluronic acid addition. The aggregates were separated from non-aggregated proteoglycans by isopycnic centrifugation, followed by gel chromatography on Sepharose CL-2B. The monomers of the aggregates were obtained by isopycnic centrifugation under dissociative conditions. Two monomers were separated by preparative electrophoresis on 0.8 % agarose submerged gels. Approximately 60 % of the proteoglycans were recovered from the gel using a freeze-squeeze procedure. Aliquots of the separated monomers gave single bands when submitted to analytical polyacrylamide-agarose gel electrophoresis. Their migration and appearance were similar to that of the two bands present in the non separated preparation of monomers.