I. Quantitative determination of the amount of DNA per nucleus by interference microscopy

Synchrotron Radiation Circular Dichroism Spectroscopy of Oligonucleotides at Millimolar Concentrations

Circular dichroism spectroscopy of nucleic acids has been traditionally performed at sample concentrations orders of magnitude lower than what occur in biological systems. While recent work from us demonstrated the flexibility of an adjustable sample cell that allowed for successful recording of CD spectra of an 18- and a 21-mer double stranded DNA sequences at around 1 mM, sample concentrations beyond 1 mM present a challenge for standard benchtop CD spectrometers. In the present work, the synchrotron radiation circular dichroism (SRCD) spectra were recorded for d(CG)₉ and a mixed 18-mer double stranded DNA at 1, 5, and 10 mM in 100 mM or 4 M NaCl. SRCD of low molecular weight salmon DNA was also measured at a 10 mg/ml concentration. These results represent the first report of CD spectra of DNA samples measured at concentrations comparable to those found in the nucleus. The results suggest that dsDNA maintain very similar structures at concentrations up to 10s of mg/ml, as evident by the very similar CD patterns in this concentration range. Furthermore, the SRCD allowed for the recording of CD patterns of DNA in the far UV region, which is not readily accessible by standard benchtop CD spectropolarimeters. These far UV signals appear to be quite characteristic of DNA structures and are sensitive to sample conditions.

Molecular and Morphological Characteristics of the De-Obstructed Rat Urinary Bladder—An Update

Many patients with outlet obstruction secondary to prostatic enlargement have lower urinary tract symptoms (LUTSs) and an increased frequency of micturition. The standard treatment is transurethral resection of the prostate (TURP), which alleviates obstruction and symptoms. However, after TURP, 20–40 percent of patients continue to experience LUTSs. The aim of the present study in rats was to identify the mechanisms that do not normalize after the removal of the obstruction and that could explain the persisting symptoms. We had microarray data from control, obstructed, and de-obstructed female rat bladders, which made it possible to study 14,553 mRNA expressions. We also had a bank of electron micrographs from similar detrusors. Microarrays: There were significant differences between the control and obstructed bladders for 1111 mRNAs. The obstructed and de-obstructed bladders differed significantly for 1059 mRNAs. The controls and the de-obstructed bladders differed significantly for 798 mRNAs. We observed many mRNAs that were increased in the obstructed bladder and then decreased to control levels after de-obstruction, and many mRNAs that were decreased in the obstructed bladder and then increased following de-obstruction. mRNAs that were significantly higher or lower in the de-obstructed bladder than in the control bladder were also found. Ultrastructure: The detrusor cells in the obstructed bladders had cross-sectional areas that were much larger than those in the controls. The control cells had smooth outlines and similar cross-sectional areas. The de-obstructed detrusor cells had larger cross-sectional areas than the controls, as well as corrugated surfaces. The cell areas varied, suggesting that the shrinkage of the de-obstructed cells was not even. We did not find any points of contact of the gap junction plaque type between the detrusor cells. There were abundant finger-like processes between the detrusor cells in the obstructed and in de-obstructed bladders, which were only occasionally found in the control detrusors. They are the only possible localization for gap junction channels. The de-obstructed rat bladder is not an organ with properties intermediate between those of the control and obstructed bladders. Instead, de-obstructed bladders have gene expressions, morphologies, and functional properties of the individual cells and their organization, which make them distinctly different from both control and obstructed bladders.

Circular dichroism spectroscopy of DNA duplexes at near-biological concentrations

Circular dichroism (CD) of nucleic acids has been typically carried out at sample concentrations below 10 μM, which is far lower than nucleic acid concentrations in biological systems. Attempts to study nucleic acid conformations by CD at higher concentrations using 10 and 1 mm pathlength cuvettes led to instrument artifacts. By shortening the light pathlength to around 0.1 mm, we herein report the first CD profiles of nucleic acids at sub-mM concentrations, which are relevant to nucleic acid concentrations in cellular cytoplasm and nucleus. These CD experimental conditions will allow future conformational studies of nucleic acids under biologically relevant conditions.

Characterization of Adult and Neonatal Articular Cartilage From the Equine Stifle

A significant portion of equine lameness is localized to the stifle joint. Effective cartilage repair strategies are largely lacking, however, recent advances in surgical techniques, biomaterials, and cellular therapeutics have broadened the clinical strategies of cartilage repair. To date, no studies have been performed directly comparing neonatal and adult articular cartilage from the stifle across multiple sites. An understanding of the differences in properties between the therapeutic target cartilage (i.e., adult cartilage) as well as potential donor cartilage (i.e., neonatal cartilage) could aid in selection of optimal harvest sites within a donor joint as well as evaluation of the success of the grafted cells or tissues within the host. Given the dearth of characterization studies of the equine stifle joint, and in particular neonatal stifle cartilage, the goal of this study was to measure properties of both potential source tissue and host tissue. Articular cartilage of the distal femur and patella (P) was assessed in regards to two specific factors, age of the animal and specific site within the joint. Two age groups were considered: neonatal (<1 week) and adult (4-14 years). Cartilage samples were harvested from 17 sites across the distal femur and patella. It was hypothesized that properties would vary significantly between neonatal and adult horses as well as within age groups on a site-by-site basis. Adult thickness varied by site. With the exception of water content, there were no significant biochemical differences among sites within regions of the distal femur (condyles and trochlea) and the patella in either the adult or neonate. Neonatal cartilage had a significantly higher water content than adult. Surprisingly, biochemical measurements of cellularity did not differ significantly between neonatal and adult, however, adult cartilage had greater variance in cellularity than neonatal. Overall, there were no significant differences between neonatal and adult glycosaminoglycan content. Collagen per wet weight was found to be significantly higher in adult cartilage than neonatal when averaged across all levels. In terms of biomechanical properties, aggregate modulus varied significantly across the condyles of adult cartilage but not the neonate. Neonatal cartilage was significantly less permeable, and the Young's modulus of neonatal cartilage was significantly higher than the adult. The tensile strength did not vary in a statistically significant manner between age groups. An understanding of morphological, histological, biochemical, and biomechanical properties enhances the understanding of cartilage tissue physiology and structure-function relationships. This study revealed important differences in biomechanical and biochemical properties among the 17 sites and among the six joint regions, as well as age-related differences between neonatal and adult cartilage. These location and age-related variations are informative toward determining the donor tissue harvest site.

High-Affinity Low-Capacity and Low-Affinity High-Capacity N-Acetyl-2-Aminofluorene (AAF) Macromolecular Binding Sites Are Revealed During the Growth Cycle of Adult Rat Hepatocytes in Primary Culture

Long-term cultures of primary adult rat hepatocytes were used to study the effects of N-acetyl-2-aminofluorene (AAF) on hepatocyte proliferation during the growth cycle; on the initiation of hepatocyte DNA synthesis in quiescent cultures; and, on hepatocyte DNA replication following the initiation of DNA synthesis. Scatchard analyses were used to identify the pharmacologic properties of radiolabeled AAF metabolite binding to hepatocyte macromolecules. Two classes of growth cycle-dependent AAF metabolite binding sites-a high-affinity low-capacity site (designated Site I) and a low-affinity high-capacity site (designated Site II)-associated with two spatially distinct classes of macromolecular targets, were revealed. Based upon radiolabeled AAF metabolite binding to purified hepatocyte genomic DNA or to DNA, RNA, proteins, and lipids from isolated nuclei, Site IDAY 4 targets (KD[APPARENT] ≈ 2-4×10-6 M and BMAX[APPARENT] ≈ 6 pmol/106 cells/24 h) were consistent with genomic DNA; and with AAF metabolized by a nuclear cytochrome P450. Based upon radiolabeled AAF binding to total cellular lysates, Site IIDAY 4 targets (KD[APPARENT] ≈ 1.5×10-3 M and BMAX[APPARENT] ≈ 350 pmol/106 cells/24 h) were consistent with cytoplasmic proteins; and with AAF metabolized by cytoplasmic cytochrome P450s. DNA synthesis was not inhibited by concentrations of AAF that saturated DNA binding in the neighborhood of the Site I KD. Instead, hepatocyte DNA synthesis inhibition required higher concentrations of AAF approaching the Site II KD. These observations raise the possibility that carcinogenic DNA adducts derived from AAF metabolites form below concentrations of AAF that inhibit replicative and repair DNA synthesis.

Transduction of fetal mice with a feline lentiviral vector induces liver tumors which exhibit an E2F activation signature

Lentiviral vectors are widely used in basic research and clinical applications for gene transfer and long-term expression; however, safety issues have not yet been completely resolved. In this study, we characterized hepatocarcinomas that developed in mice 1 year after in utero administration of a feline-derived lentiviral vector. Mapped viral integration sites differed among tumors and did not coincide with the regions of chromosomal aberrations. Furthermore, gene expression profiling revealed that no known cancer-associated genes were deregulated in the vicinity of viral integrations. Nevertheless, five of the six tumors exhibited highly significant upregulation of E2F target genes, of which a majority are associated with oncogenesis, DNA damage response, and chromosomal instability. We further show in vivo and in vitro that E2F activation occurs early on following transduction of both fetal mice and cultured human hepatocytes. On the basis of the similarities in E2F target gene expression patterns among tumors and the lack of evidence implicating insertional mutagenesis, we propose that transduction of fetal mice with a feline lentiviral vector induces E2F-mediated major cellular processes that drive hepatocytes toward uncontrolled proliferation culminating in tumorigenesis.

The virtosome-a novel cytosolic informative entity and intercellular messenger

Studies on a range of prokaryote and eukaryote cells and tissues have shown that a newly synthesized DNA/RNA-lipoprotein complex is released in a regulated manner. This complex, termed a virtosome, is a novel cytosolic component of eukaryote cells. The released virtosomes can readily enter other cells where they can modify the biology of the recipient cells. Such modifications include immunological changes and transformation from normal to cancer cells. The virtosomes form a normal component of the circulating nucleic acids in plasma and serum currently used for clinical diagnostic purposes. Given the transformative powers of virtosomes released from tumour cells, the presence of such a complex in human plasma could readily offer the basis of an alternative mechanism for the initiation of metastases.

Neonatal gene therapy of glycogen storage disease type Ia using a feline immunodeficiency virus-based vector

Glycogen storage disease type Ia (GSD-Ia), also known as von Gierke disease, is caused by a deficiency of glucose-6-phosphatase-alpha (G6Pase), a key enzyme in glucose homeostasis. From birth, affected individuals cannot maintain normal blood glucose levels and suffer from a variety of metabolic disorders, leading to life-threatening complications. Gene therapy has been proposed as a possible option for treatment of this illness. Vectors have been constructed from feline immunodeficiency virus (FIV), a nonprimate lentivirus, because the wild-type virus does not cause disease in humans. Previously, we have shown that these vectors are capable of integrating stably into hepatocyte cell lines and adult murine livers and lead to long-term transgene expression. In the current work, we have assessed the ability to attenuate disease symptoms in a murine model of GSD-Ia. Single administration of FIV vectors containing the human G6Pase gene to G6Pase-alpha(-/-) mice did not change the biochemical and pathological phenotype. However, a double neonatal administration protocol led to normalized blood glucose levels, significantly extended survival, improved body weight, and decreased accumulation of liver glycogen associated with the disease. This approach shows a promising paradigm for treating GSD-Ia patients early in life thereby avoiding long-term consequences.

Identification of a second DNA binding site in human DNA methyltransferase 3A by substrate inhibition and domain deletion

The human DNA methyltransferase 3A (DNMT3A) is essential for establishing DNA methylation patterns. Knowing the key factors involved in the regulation of mammalian DNA methylation is critical to furthering understanding of embryonic development and designing therapeutic approaches targeting epigenetic mechanisms. We observe substrate inhibition for the full length DNMT3A but not for its isolated catalytic domain, demonstrating that DNMT3A has a second binding site for DNA. Deletion of recognized domains of DNMT3A reveals that the conserved PWWP domain is necessary for substrate inhibition and forms at least part of the allosteric DNA binding site. The PWWP domain is demonstrated here to bind DNA in a cooperative manner with muM affinity. No clear sequence preference was observed, similar to previous observations with the isolated PWWP domain of Dnmt3b but with one order of magnitude weaker affinity. Potential roles for a low affinity, low specificity second DNA binding site are discussed.

Metabolic DNA as the origin of spontaneously released DNA?

A DNA fraction is spontaneously released from living, but not dead or dying, human, other mammalian, avian, amphibian, plant, and prokaryote cells. The spontaneously released DNA fraction has been shown to be (a) present in both actively dividing and nondividing, differentiated cell populations; (b) labile; (c) associated with DNA-dependent RNA or DNA polymerase; (d) associated with an RNA fraction; and to have (e) a lower molecular weight than the typical genetic DNA fraction; and (f) Alu repeat sequences in increased proportions compared to a unique gene in plasma/serum. On the other hand, early autoradiographic and biochemical and quantitative cytochemical and cytophysical studies on DNA permitted the identification of a DNA fraction which was (1) present in both actively dividing and nondividing, differentiated cell populations; (2) labile; and (3) had a lower molecular weight than the typical genetic DNA fraction. This DNA fraction was termed metabolic DNA (m-DNA) and was proposed as possibly forming extra gene copies for the rapid production of m-RNA, to be destroyed subsequently. Therefore, we suggest that the metabolic DNA fraction might represent the precursor to the formation of the spontaneously released DNA fraction.

Interferometric studies of endothelial cells in primary culture

A population of endothelial cells grown from Xenopus laevis tadpole hearts was investigated by microinterferometry. The resulting interferograms were evaluated by an automatic image analyzer. The mean values of dry mass were 778 +/- 340 pg (10(-15) g) for whole cells, 648 +/- 309 pg for cytoplasm, 116 +/- 45 pg for nuclei, and 19 +/- 10 pg for nucleoli. Two subpopulations of cells were identified, an actively growing one and a less active one. The density (dry mass per microm2) of the nuclei and nucleoli of less active cells was greater than that of the nuclei and nucleoli of actively growing cells. In addition, the inactive cells were always large and possessed a considerable amount of cytoplasm. The entrance of cells into S-phase could not be detected by microinterferometry; and no differences were apparent between cells possessing one nucleolus and those containing two nucleoli. The values obtained in these amphibian cells were compared with those derived from mammalian cells.

Base composition changes in hepatocyte nuclei DNA of rats at different ages

DNA extracted from isolated hepatic nuclei of rats at different aged (1 h, 6 and 30 days of life) has been characterized by (i) melting temperature, (ii) buoyant density, (iii) thermal denaturation on hydroxyapatite and (iv) nucleoside composition. The melting midpoint (Tm) determined spectrophotometrically in 0.1 X SSC (0.15 M NaCl/0.0015 M sodium citrate) is 71.9 +/- 0.4 for 1-h-old rats and decreases to 70.7 +/- 0.3 in 6-day-old animals. The buoyant densities of DNAs determined by CsCl on both native and alkaline-denaturated and reneutralized DNA were also found to decrease with age. Hydroxyapatite thermal denaturation of sonicated DNA confirmed the significant difference between the Tm values of 1-h-old and 6-day-old rats (86.5 +/- 0.5 and 85.2 +/- 0.1, respectively). The possibility that these differences in Tm values could be due to an increase in methyl bases, has been ruled out by the finding that the amount of [3H]methyl incorporated in relation to the DNA synthesis is constant at these two ages. The alternative possibility of a change in base composition has been tested by the chromatographic analysis of nucleosides. The dG + dC content is 0.433 +/- 0.003 in 1-h-old rats and decreases to 0.411 +/- 0.002 and to 0.403 +/- 0.005 in 6-day- and 30-day-old rats, respectively. The physiological significance of the different base composition is discussed in relation to the possibility that specific DNA sequences are synthesized during the non-premitotic synthesis which has been found to take place during the first 6 days of life.

Feulgen-Naphthol Yellow S cytophotometry of liver cells. The effect of formaldehyde induced shrinkage on nuclear Naphthol Yellow S binding

1. In isolated liver cells, fixed in 4 per cent formaldehyde (NFS) for Feulgen-Naphthol Yellow S (F-NYS) staining of DNA and protein, nuclear shrinkage increases the nuclear concentration of solids to 46 per cent (w/v) before the start of the NYS staining. 2. When a fixative mixture of methanol:acetic acid:formalin (85:5:10 by volume; MAF) is used, the concentration of nuclear solids during NYS staining remain at a physiological level of 19 per cent. 3. By exposing liver cells to NFS for 10 to 120 seconds before fixation in MAF, increasing nuclear shrinkage can be induced with increasing pretreatment in NFS. Nuclear NYS binding decreases in parallel with the decreasing nuclear volume in cells thus treated. As the shrinkage induced reduction in NYS binding may vary with the net charge of nuclear non-histone proteins, MAF fixation must be preferred for quantitative determinations of nuclear non-histone protein in F-NYS stained, isolated cells. 4. Fixation in MAF offers the same advantages as NFS fixation as regards the small loss of proteins during the Feulgen staining procedure and the excellent reproducibility of the F-NYS staining. Storage of MAF fixed cells in the fixative for a few days does not alter their F-NYS staining properties. 5. In MAF fixed, F-NYS stained cells there is no NYS binding to histone basic amino acid residues.

II. Differences in adrenal medulla nuclear DNA content among rats of different strains following intermittent exposure to cold

The amount of DNA per nucleus in the adrenal medulla cells of four different strains of rats (Wistar, Sprague-Dawley, Long-Evans, and Italico) is determined both under control conditions and after 300 hr of intermittent exposure to cold. The adrenal medulla nuclei of the four strains of rats contain the same amount of DNA; however, the loss of DNA observed after the same experimental treatment differs markedly in the different strains. The loss is small in Wistar and Sprague-Dawley rats (8-13%), larger in Long-Evans rats (20%) and still larger in Italico rats (45%). The DNA loss in Wistar rats increases if the animals are fed the same diet as the Italico rats, and the DNA loss in Italico rats is reduced if the animals are fed the same diet as the Wistar rats. The different behavior of the four strains is discussed in terms of turnover of DNA.