Superhelix density heterogeneity of intracellular simian virus 40 deoxyribonucleic acid

Ferrets as Models for Viral Respiratory Disease

Domestic ferrets (Mustela putorius furo) have been used in biomedical research to study influenza viruses since the early 20th century. Ferrets have continued to gain importance for the study of viral respiratory disease due to their disease susceptibility and anatomic similarities to humans. Here we review features of ferret biology and management that should be considered when planning to work with this species, particularly in models of respiratory disease. We specifically discuss biosafety and husbandry, clinical and pathologic assessments, and anesthetic considerations for ferrets with respiratory disease and systemic illness. These considerations are important for animal welfare, fidelity of the model to human disease, and ensuring accuracy and reproducibility of acquired data. Finally, we briefly review the use of ferrets to study respiratory diseases by discussing their respiratory anatomy and 2 frequently studied viral respiratory diseases, influenza and coronavirus disease 2019 (COVID-19).

Dispersive segregation of nucleosomes during replication of simian virus 40 chromosomes

The distribution of preformed ("old") histone octamers between the two arms of DNA replication forks was analyzed in simian virus 40(SV40)-infected cells following treatment with cycloheximide to prevent nucleosome assembly from nascent histones. Viral chromatin synthesized in the presence of cycloheximide was shown to be deficient in nucleosomes. Replicating SV40 DNA (wild-type 800 and capsid assembly mutant, tsB11) was radiolabeled in either intact cells or nuclear extracts supplemented with cytosol. Nascent nucleosomal monomers were then released by extensive digestion of isolated nuclei, nuclear extracts or isolated viral chromosomes with micrococcal nuclease. The labeled nucleosomal DNA was purified and found to hybridize to both strands of SV40 DNA restriction fragments taken from each side of the origin of DNA replication, whereas Okazaki fragments hybridized only to the strand representing the retrograde DNA template. In addition, isolated, replicating SV40 chromosomes were digested with two strand-specific exonucleases that excised nascent DNA from either the forward or the retrograde side of replication forks. Pretreatment of cells with cycloheximide did not result in an excess of prenucleosomal DNA on either side of replication forks, but did increase the amount of internucleosomal DNA. These data are consistent with a dispersive model for nucleosome segregation in which "old" histone octamers are distributed to both arms of DNA replication forks.

Simian virus 40 DNA extracted from infected cells with sodium deoxycholate no longer reflects its in vivo superhelix density

When simian virus 40 DNA is extracted from infected cells with low concentrations of sodium deoxycholate, which selectively extract non-encapsidated simian virus 40 DNA, the DNA has a lower average number of superhelical turns than the DNA extracted from purified viral particles. During extraction, a partial deproteinization of the DNA by a concentration of detergent that did not inactivate a nicking-closing activity led to the removal of some superhelical turns. The DNA extracted in this way no longer reflected its in vivo number of superhelical turns.

Superhelix densities of circular DNA's: a generalized equation for their determination by the bouyant method

Equations for the measurement of the supertwisting of circular DNA's from banding positions in buoyant density gradients containing intercalating dyes have required the use of SV40 DNA isolated from virions as a reference DNA. These equations are modified to allow the use of any closed circular DNA of known superhelix density as a reference DNA.

The effect of H1 histone on the action of DNA-relaxing enzyme

The action of DNA-relaxing enzyme on H1-DNA complexes was investigated. Complexes of superhelical and relaxed closed circular duplex DNA with H1 were treated with mammalian relaxing enzyme, deproteinized, and electrophoresed on agarose gels. At relatively low ratios of H1 to superhelical DNA, molecules of superhelical density intermediate between those of the starting material and relaxed DNA, the normal product, were generated. At relatively high H1 histone concentrations (H1:DNA greater than 0.4 w/w), the superhelical DNA was not relaxed. Further, no superhelical turns were introduced into relaxed closed duplex DNA at any concentration of H1 tested. Thus, the binding of H1 histone to DNA prevents the action of the relaxing enzyme. Moreover, H1 histone does not appear to unwind the DNA duplex upon binding. The implications of these observations and the previously demonstrated specificity of H1 histone for superhelical DNA are discussed in relation to the structure of chromatin.

Studies on the interaction of H1 histone with superhelical DNA: characterization of the recognition and binding regions of H1 histones

The very lysine rich histone, H1, isolated from a variety of sources interacts preferentially with superhelical DNA compared to relaxed DNA duplexes. The nature of this specific interaction has been investigated by studying the ability of various purified fragments of H1 histone from calf thymus to recognize and bind superhelical DNA. The data suggest that the globular region of the H1 histone molecule (amino acid residues 72-106) is involved in the recognition of superhelical DNA. Thus, the H1 histone carboxy-terminal fragment, 72-212, resembles native H1 histone both quantitatively and qualitatively in its ability to discriminate between and bind to superhelical and relaxed DNA while the H1 histone carboxy-terminal fragment, residues 106-212, has lost this specificity, binding superhelical and relaxed DNA equally well. Furthermore, under conditions in which the globular region of the intact H1 histone has been unfolded, the molecule loses its ability to discriminate between superhelical and relaxed DNA, and binds both forms of DNA equally.

Process of infection with bacteriophage phi X 174 XXXVIII. Replication of phi chi 174 replicative form in vivo

The replication of bacteriophage phi X 174 replicative-form DNA has been studied by structural analysis of pulse-labeled replicative-intermediate molecules. Such intermediates were identified by pulse-labeling with [13H]thymidine and separated into four major fractions (A, B, C, and D) in a propidium diiodide-cesium chloride buoyand density gradient. Sedimentation analysis of each of these fractions suggests the following features of phi X replicative-form DNA replication in vivo. (i) At the end of one cycle of replication, one daughter replicative form (RFII) contains a nascent plus (+) strand of the unit viral length, and the other daughter RFII contains small fragments of nascent minus (-) strand. (ii) Asymmetry is also associated with production of the first supercoiled RFI after addition of pulse label in that only the minus strand becomes radioactive. (iii) A supercoiled DNA (RFI') seems to occur in vivo. This DNA is observed at a position of greater density in a propidium diiodide-cesium chloride buoyant density gradient than normal RFI. (iv) A novel DNA component is observed, at a density greater than RFI, which releases, in alkali, a plus strand longer (1.5 to 1.7 times) than the unit viral length. These results are discussed in terms of the possible sequence of events in phi X 174 replicative-form replication in vivo.

DNA synthesis in polyoma virus infection. IV. Mechanism of formation of closed-circular viral DNA deficient in superhelical turns

A marked reduction in the rate of viral DNA synthesis is accompanied by an alteration to the superhelicity of progeny DNA in polyoma virus-infected cells in which protein synthesis has been inhibited by cycloheximide. Viral DNA molecules formed in the presence of cycloheximide consist predominantly of closed-circular monometric species (referred to as form Ic) characterized by a decreased superhelix density, corresponding to deltasigmao = 0.0195, as compared to form I DNA by propidium diiodide-cesium chloride isopycnic analysis. Form Ic is synthesized on pre-existing form I templates without the intervention of progeny form I as an intermediate. It is concluded that inhibition of protein synthesis results in the alteration of some process in the closure of daughter DNA that leads to a marked reduction of superhelical turns of progeny molecules. About two-thirds of form Ic molecules return to the form I conformation upon reversal of cycloheximide inhibition by a mechanism independent of DNA replication.

Nucleoprotein complexes containing replicating Simian virus 40 DNA: comparison with polyoma nucleoprotein complexes

Procedures for isolating nucleoprotein complexes containing replicating polyoma DNA from infected mouse cells were used to prepare short-lived nucleoprotein complexes (r-SV40 complexes) containing replicating simian virus 40 (SV40) DNA from infected monkey cells. Like the polyoma complexes, r-SV40 complexes were only partially released from nuclei by cell lysis but could be extracted from nuclei by prolonged treatment with solutions containing Triton X-100. r-SV40 complexes sedimented faster than complexes containing SV40 supercoiled DNA (SV40 complex) in sucrose gradients, and both types of SV40 nucleoprotein complexes sedimented ahead of polyoma complexes containing supercoiled polyoma DNA (py complex). The sedimentation rates of py complex and SV40 complex were 56 and 61S, respectively, based on the sedimentation rate of the mouse large ribosomal subunit as a marker. r-SV40 complexes sedimented as multiple peaks between 56 and 75S. Sedimentation and buoyant density measurements indicated that protein is bound to all forms of SV40 DNA at about the same ratio of protein to DNA (1-2/1) as was reported for polyoma nucleoproteins.

Properties of nucleoprotein complexes containing replicating polyoma DNA

Short-lived nucleoprotein complexes (r-py complex) containing replicating polyoma DNA were isolated from infected cells after lysis with Triton X-100. The Triton lysing procedure of Green, Miller, and Hendler (1971) releases most complexes containing supercoiled viral DNA (py complex) from nuclei, but liberates only a portion of r-py complexes. r-py Complexes are associated more strongly with nuclear sites but can be extracted by prolonged incubation of nuclei in lysing solution. Complexes containing replicating polyoma DNA appear to be precursors to stable complexes containing supercoiled DNA. Sedimentation and buoyant density studies indicate that protein is bound to both r-py complexes and py complexes at a ratio of protein to DNA of about 1 to 2/1. Both types of complexes sediment as if the viral DNA is more compact than free DNA and both undergo major reversible configurational changes with increased salt concentration. Changes resulting from enzymatic and chemical treatment indicate that there may be two or more protein components in both r-py complex and py complex. One component is digested by Pronase and trypsin while another is resistant to the enzymes but released by deoxycholate. The abundance and similarity in chemical and physical properties of protein bound to all forms of polyoma DNA suggest that part of the protein molecules may serve in a structural capacity.

Establishment and characterization of ethidium bromide resistance in simian virus 40-transformed hamster cells. Effects on mitochondria in vivo

This study describes the isolation and subsequent characterization of four mammalian cell lines resistant to ethidium bromide (EB). Treatment of the simian virus 40- (SV40) transformed hamster cell line F5-1 first led to the establishment of the F2 cell line, which is resistant to 2 microg EB/ml. At this concentration cytochromes c and b are present in almost normal or only slightly diminished amounts, whereas cytochromes a + a(3) show an obvious decrease. The mitochondria of the F2 cell show a normal ultrastructure, not distinct from the parental cell line F5-1, and contain closed circular DNA. The sensitive parental F5-1 cells, however, when exposed to the same dye concentration exhibit the typical EB-induced ultrastructural changes in the mitochondria, and no more component I mitochondrial DNA can be demonstrated. 1 yr after establishment we derived from the F2 cell three more cell lines, resistant against 4, 8, and 16 microg of EB/ml. These cell lines, termed F4, F8, and F16, respectively, also revealed relatively intact-appearing mitochondria, although distinguishable from F5-1 and F2 mitochondria by a more condensed or unorthodox cristae conformation. F4, F8, and F16 cell lines contained closed circular mitochondrial DNA in the same position as that of the parental F5-1 cells, when analyzed in an isopycnic CsCl-EB gradient. A small shoulder at the lower density side of the DNA I peaks was observed. The newly acquired drug resistance of the F cells is hereditarily transmitted to the progeny cells and retained even after a period of growth in EB-free medium.

An activity from mammalian cells that untwists superhelical DNA--a possible swivel for DNA replication (polyoma-ethidium bromide-mouse-embryo cells-dye binding assay)

Nuclei from secondary mouse-embryo cells contain an activity capable of untwisting closed-circular DNAs containing either negative or positive superhelical turns. The activity has no apparent effect on a closed-circular DNA containing no superhelical turns, and is not due to the combined action of an endonuclease and polynucleotide ligase. The enzyme apparently acts by introducing a single-strand nick into the DNA, forming a DNA-enzyme complex that allows the strands to rotate relative to the helix axis before reversing the reaction and sealing the break. The enzyme might possibly serve as a swivel during DNA replication.

Nucleoprotein complexes in simian virus 40-infected cells

When African green monkey kidney cells (BSC-1) were infected with simian virus 40 (SV40) and extracted with 0.25% Triton X-100 after exposure to (3)H-thymidine, the (3)H-SV40 deoxyribonucleic acid (DNA) was present in a form which had a sedimentation coefficient in sucrose gradients of 44S. The change from the sedimentation coefficient of purified SV40 DNA (21S) was shown to result from the association of the SV40 DNA in the Triton extracts with protein by means of sensitivity to Pronase digestion and labeling with (14)C-amino acids. Short-term labeling experiments with (3)H-thymidine demonstrated that SV40 DNA molecules in the course of replication (25S) were also present as nucleoprotein complexes in Triton-extracted material. Labeled DNA extracted with Triton in the form of nucleoprotein complexes was obtained in amounts which were quantitatively equivalent to the amounts extracted with deoxycholate in parallel experiments. This indicated that the newly synthesized pools of SV40 DNA may not occur as free DNA in the infected cell.

A novel closed-circular mitochondrial DNA with properties of a replicating intermediate

A fraction of the covalently closed mitochondrial DNA in mouse L cells contains a replicated heavy-strand segment that is hydrogen bonded to the circular light strand. The inserted single strand is dissociable from the circular duplex at an elevated temperature.