Isolation of neuronal nuclei from rat brain cortex

The use of targeted proteomics to determine the stoichiometry of large macromolecular assemblies

Accurate knowledge of the stoichiometry of protein complexes is a crucial prerequisite for understanding their structure and function. To purify or enrich large and intricate protein complexes such that their structure is preserved and to absolutely quantify all of their protein components is an enormous technical challenge. In this chapter, we describe how to purify nuclear envelopes from human tissue culture cells that are highly enriched for nuclear pore complexes. We use the nuclear pore as an example to discuss how the structural preservation of such preparations can be controlled. Furthermore, we give a practical guide how to develop and employ targeted proteomic assays for both, the absolute quantification of stoichiometries and the relative quantification of protein complex composition across multiple biological conditions. The concept discussed here is universally applicable to any protein complex.

Neuronal DNA content variation (DCV) with regional and individual differences in the human brain

It is widely assumed that the human brain contains genetically identical cells through which postgenomic mechanisms contribute to its enormous diversity and complexity. The relatively recent identification of neural cells throughout the neuraxis showing somatically generated mosaic aneuploidy indicates that the vertebrate brain can be genomically heterogeneous (Rehen et al. [2001] Proc. Natl. Acad. Sci. U. S. A. 98:13361-13366; Rehen et al. [2005] J. Neurosci. 25:2176-2180; Yurov et al. [2007] PLoS ONE:e558; Westra et al. [2008] J. Comp. Neurol. 507:1944-1951). The extent of human neural aneuploidy is currently unknown because of technically limited sample sizes, but is reported to be small (Iourov et al. [2006] Int. Rev. Cytol. 249:143-191). During efforts to interrogate larger cell populations by using DNA content analyses, a surprising result was obtained: human frontal cortex brain cells were found to display "DNA content variation (DCV)" characterized by an increased range of DNA content both in cell populations and within single cells. On average, DNA content increased by approximately 250 megabases, often representing a substantial fraction of cells within a given sample. DCV within individual human brains showed regional variation, with increased prevalence in the frontal cortex and less variation in the cerebellum. Further, DCV varied between individual brains. These results identify DCV as a new feature of the human brain, encompassing and further extending genomic alterations produced by aneuploidy, which may contribute to neural diversity in normal and pathophysiological states, altered functions of normal and disease-linked genes, and differences among individuals.

Methods using tissue preparations and isolated biomolecules

The possibility to use organs, organelle preparations and biologically active chemicals in toxicity tests and in toxicology will be reviewed. Examples are perfused liver preparations, tissue slices and homogenates, isolated nerve preparations, nerve-muscle preparations, membrane preparations, microsomes, mitochondria, synaptosomes, antibodies and isolated chemical compounds (receptors, enzymes).

Variations in DNA topoisomerase I activity after gamma irradiation of mature neurons

The activity of DNA topoisomerase I in nuclear extracts from rat cerebral cortex neurons increases about two-fold after gamma irradiation (700 rads) of rats or incubated cerebral cortex slices. Analysis of the salt dependence of the DNA topoisomerase I association with chromatin shows a change of the activity only for tight-bound pool of the enzyme. The change appears to reflect a modification of the enzyme which results from its repair function.

Alternate domains of neuron DNA topoisomerase I in developing rat brain

The DNA topoisomerase found in rat brain neurons relaxes supercoiled DNA in the absence of ATP or Mg2+. The estimated content of the active enzyme per nucleus of nerve cell is constant during development from a fetal proliferating neuroblast at the embryonic stage of 18 days to the terminally differentiated neuron (postnatal age of 60 days). The salt stability of DNA topoisomerase association with chromatin varies with the stage of development of nerve cells: at 300 mM NaCl most of the enzyme activity (greater than 90% of the removed activity) elutes from differentiated neuron chromatin, whereas only approx. 25% of the enzyme activity elutes from neuroblast chromatin.

The DNA content of cerebral cortex neurons. Determinations by cytophotometry and high performance liquid chromatography

Previous work from our laboratories has indicated that the DNA content of rat cerebral cortex neurons increases postnatally to a level of slightly above 3c, where 2c denotes the diploid DNA complement. We have re-evaluated this concept by using various cytophotometric assays and a novel high performance liquid chromatography (HPLC) technique. The latter consists of digesting the DNA in isolated neuronal nuclei by a mixture of DNA-degrading enzymes followed by analysis of the resulting deoxynucleosides by HPLC. We find that the various methods fall into two groups. The first gives evidence of a postnatal DNA (or histone) increase, while the second does not. The first group (DNA increase) comprises cytofluorometry for DNA following Schiff-type staining with fluorochromes 2,5-bis-(4-aminophenyl)-1,3,4-oxadiazole (BAO) and pararosaniline, ultraviolet absorption scanning for DNA and cytofluorometry for histones following staining with sulfaflavine at pH 8. The second group (no DNA increase) consists of cytofluorometry for DNA following staining with the DNA-complexing agents mithramycin, chromomycin A3, 4',6-diamidino-2-phenylindole (DAPI) and bisbenzimide (Hoechst 33258), as well as the newly developed HPLC technique. Since the HPLC technique measures DNA by a direct chemical approach without interference from other nuclear constituents or from higher order packaging in the chromatin, and detects at least 94-95% of the total DNA contained in neuronal nuclei independent of the developmental stage, we infer that the HPLC technique and, by consequence, the cytochemical assays of the second group reflect true DNA values. Therefore, we propose that cerebral cortex neurons retain a diploid DNA level throughout development.

Postnatal changes in the activity ratio of specific and nonspecific cholinesterases from neuronal perikarya

A soluble fraction from rat brain neuronal perikarya was shown to contain both the specific and nonspecific forms of the enzyme acetylcholinesterase (EC's 3.1.1.7. and 3.1.1.8., respectively). The ratio of the enzyme activities varied along the course of brain development: the nonspecific form being predominant from 1 to 15 days of age and the specific one showing the pattern of rising activity from day 15 onward. We suggest a possible relationship between this changing in cholinesterase activities and the establishment of synapses within the rat cerebral cortex.

Diazepam receptor: specific nuclear binding of [3H]flunitrazepam

Autoradiographic localization of [3H]flunitrazepam in nuclei of the rat cerebral cortex was further confirmed by biochemical analysis of specific nuclear binding. Highly purified rat cerebral cortex nuclei were shown to bind [3H]flunitrazepam specifically. The Kd(app) for nuclear binding was 28 nM for the nuclei compared with a Kd(app) of 1.1 nM for binding of [3H] flunitrazepam to synaptosomal membrane fractions of the same tissue. Inhibition of the nuclear binding with inosine and hypoxanthine was greater than inhibition of the synaptic membrane fractions. These results lead to to conclude that specific binding may occur at both the synaptic membrane and the nuclear levels and that different endogenous ligands may compete at each site for binding. Furthermore, the possibility exists for translocation and alteration of the bound ligand complex from membrane site to nuclear site.

Diadenosine 5',5'''-P1,P4-tetraphosphate, a ligand of the 57-kilodalton subunit of DNA polymerase alpha

By equilibrium dialysis a disadenosine 5',5'''-P1,P2-tetraphosphate (Ap4A) binding activity is shown to be present in mammalian cells. The Ap4A binding activity copurifies with DNA polymerase alpha during the isolation procedure, which includes chromatography on phospho-, DEAE-, and DNA-cellulose; gel filtration; sucrose gradient centrifugation; and electrophoresis in nondenaturing polyacrylamide gels. After these purification steps, DNA polymerase alpha appears to be homogeneous in nondenaturing polyacrylamide gels. Sodium dodecyl sulfate/polyacrylamide gel electrophoresis of such a purified DNA polymerase alpha preparation reveals seven distinct protein bands with apparent Mrs of 64,000, 63,000, 62,000, 60,000, 57,000, 55,000, and 52,000. By affinity labeling, the protein with Mr 57,000 has been shown to be the Ap4A-binding constituent of DNA polymerase alpha. The binding activity of DNA polymerase alpha for Ap4A is highly specific because neither structural analogs nor several other adenine nucleotides compete effectively with Ap4A for its binding site. The Ap4A binding site is lost in neuronal cells during maturation of rat brains concomitantly with the loss of DNA polymerase alpha and mitotic activity in those cells. From these results, DNA polymerase seems to be the intracellular target of Ap4A. This is discussed in respect to the recently reported of Ap4A to trigger DNA replication in quiescent mammalian cells [Grummt, F. (1978) Proc. Natl. Acad. Sci. USA 75, 371-375].

Morphological identification and biochemical characterization of isolated brain cell nuclei from the developing rat cerebellum

Cell nuclei from developing rat cerebellum were isolated and the various types of nuclei were characterized and quantified. Nuclear pellets appeared to be both quantitatively and qualitatively representative of the entire cerebellum, and of sufficient purity to perform biochemical studies as well as morphological comparison with histological sections. Isolated nuclei were classified into 6 groups based on nuclear size and shape, heterochromatin aggregations, and nucleoplasmic density. The total population of cerebellar cells primarily consisted of two types of nuclei after day 10. One group of nuclei, resembling those of internal granule neurons or external germinal cells, contributed at least 70% of the total isolated cell nuclei from day 1 to day 90, whereas another nuclear group that was identified as dark oligodendrocytes constituted 8-9% of the total population on days 45 and 90. Nuclear DNA, RNA, and protein content of the cerebellum also were determined throughout postnatal development. DNA concentration markedly declined after day 15, while the RNA/DNA ratio increased until day 3 and remained constant to day 90. The nuclear protein/DNA ratio increased from birth to day 3, decreased to its lowest value on day 10, and increased to day 90. Utilizing DNA values, the total cell population as well as contributions of different cell types were calculated. At birth the cerebellum was estimated to contain 5.9 million cells, increasing to 94 million by day 21. By day 90, 107 million cells were present, of which 8.6 million oligodendrocytes and 93.6 million internal granule cells were estimated.

Are all the neuronal nuclei polyploid?

The DNA analysis of rat brain nuclei by two independent cytochemical methods, namely microfluorometry and UV-absorption, brings completely different results to those published previously by many investigators. The neuronal nuclei possess twice as much DNA as the glial nuclei.