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J Filipski

Publications and source records attributed to J Filipski.

At least 19 recordsLinked to original sources
PubMed1992

The distribution of 5-methylcytosine in the nuclear genome of plants.

We have determined the 5-methylcytosine (5mC) content in high molecular weight DNA, from two dicot (tobacco and pea) and two monocot (wheat and maize) plant species, fractionated according to base composition. The results show that the proportion of 5mC in the genomic fractions increases linearly with their guanine + cytosine (G + C) content while the proportion of non-methylated cytosine remains almost constant. This can be interpreted as a consequence of a difference in mutation pressure related to spontaneous deamination of 5mC to thymine between the different compartments of plant genomes.

5-Methylcytosine↗
PubMed1990

Periodicity of DNA folding in higher order chromatin structures.

Each level of DNA folding in cells corresponds to a distinct chromatin structure. The basic chromatin units, nucleosomes, are arranged into solenoids which form chromatin loops. To characterize better the loop organization of chromatin we have assumed that the accessibility of DNA inside these structures is lower than on the outside and examined the size distribution of high mol. wt DNA fragments obtained from cells and isolated nuclei after digestion with endogenous nuclease or topoisomerase II. The largest discrete fragments obtained contain 300 kbp of DNA. Their further degradation proceeds through another discrete size step of 50 kbp. This suggests that chromatin loops contain approximately 50 kbp of DNA and that they are grouped into hexameric rosettes at the next higher level of chromatin structure. Based upon these observations a model by which the 30 nm chromatin fibre can be folded up into compact metaphase chromosomes is also described.

Animals↗
PubMed1989

Chromosome localization-dependent compositional bias of point mutations in Alu repetitive sequences.

The Alu repetitive sequence family originated from a common ancestor. Its members, apparently free from functional constraints, are interspersed throughout primate genomes. We have found that base substitutions occurring during the evolution of primates caused a decrease in the average G + C content of those members of the family that are located in an A + T-rich region of the genome. The family members that are located in a G + C-rich genomic region have not changed their, already high, G + C content. This suggests that the regional differences in G + C content, which are responsible for chromosomal banding, are caused by an accumulation of mutations that, although selectively neutral in the majority, show different compositional bias in different regions of the vertebrate chromosome.

Animals↗
PubMed1988

Why the rate of silent codon substitutions is variable within a vertebrate's genome.

Different genes within the murine genome are diverging at different rates. The rate of synonymous codon substitutions in these genes is related to their base composition. It is proposed that the variabilities of rate of mutation accumulation, of codon choice and of average GC content within vertebrate genomes are caused by differences between DNA synthesis in repair and replication, as far as the frequency and compositional bias of mutations introduced by these systems are concerned. DNA repair contributes substantially to the evolution of the DNA domains, which are actively repaired in germline cells and which correspond to regions available for transcription in these cells and to Giemsa-negative bands in stained chromosomes.

Animals↗
PubMed1988

Development of a Salmonella-specific biotinylated DNA probe for rapid routine identification of Salmonella.

Classical microbiological techniques used in the detection and identification of Salmonella spp. in foods, drinking water and clinical samples are relatively lengthy. Immunoassays, on the other hand, have the major disadvantage of often generating false positives and false negatives. Recombinant DNA technology offers more efficient alternatives to the detection of a specific organism by employing cloned DNA sequences unique to the organism. Demonstration of a presence of complementary sequences among a heterogeneous population of molecules of DNA isolated from bacteria can be made by using a DNA-DNA hybridization technique. We have obtained a fragment of DNA from Salmonella typhimurium chromosomal DNA, cloned it in Escherichia coli plasmid and tested it in colony hybridization tests with 57 strains of Salmonella and other enterobacteriaceae. In all tests, the fragment was found to be Salmonella-specific in that it gave a positive reaction with all strains of Salmonella tested and was negative when tested against other Enterobacteriaceae.

Animals↗
PubMed1987

Correlation between molecular clock ticking, codon usage fidelity of DNA repair, chromosome banding and chromatin compactness in germline cells.

The vertebrate genome is built of long DNA regions, relatively homogeneous in GC content, which likely correspond to bands on stained chromosomes. Large differences in composition have been found among DNA regions belonging to the same genome. They are paralleled by differences in codon usage in genes differently localized. The hypothesis presented here asserts that these differences in composition are caused by different mutational bias of alpha and beta DNA polymerases, these polymerases being involved to different extents in the repair of DNA lesions in compact and relaxed chromatin, respectively, in germline cells.

Animals↗
PubMed1987

Nonrandom distribution of MMTV proviral sequences in the mouse genome.

Integrated sequences of mouse mammary tumor virus (MMTV) have been localized in the genomes of five inbred mouse strains (Balb/c, C3H, DBA/2, A.TH, 129-SV) and one mammary tumor cell line (GR). Two major classes of MMTV sequences have been detected in mouse DNA fractions as obtained by Cs2SO4/BAMD (3,6-bis-(acetatomercurimethyl)dioxane) density gradient centrifugation. The first one corresponds to previously described endogenous sequences (Mtv loci), whereas the second one corresponds to endogenous sequences not previously known, and/or recently acquired; in the case of GR cells exogenous sequences may also be present in this class. The genome distribution is somewhat different for the two classes of sequences, the first one being practically only present in the lightest DNA segments of the mouse genome (GC congruent to 38%); the second one being also represented in heavier segments (GC congruent to 43%). This integration pattern suggests that "ancient" endogenous sequences are practically only localized in genome segments of roughly matching composition, whereas exogenous and recently acquired endogenous MMTV sequences may also be present in heavier fractions.

Animals↗
PubMed1987

Two distinct compositional classes of vertebrate gene-bearing DNA stretches, their structures and possible evolutionary origin.

Genomes of vertebrates are built of long, compositionally uniform DNA regions differing in guanine and cytidine (G + C) content. Examination of G + C distribution and CpG dinucleotide frequency in the longest stretches of vertebrate DNA base sequences available show that the long-range structural features are correlated with the structure of genes. Two classes of DNA stretches are conspicuous: (i) the stretches having low G + C content and low CpG doublet frequency and (ii) stretches rich in G + C containing CpG-rich islands. Both classes show other compositional islands containing exons. These structural features result from evolutionary pressures acting on the DNA or RNA level, as well as from mutations and repair differently biased in different genomic compartments. The analysis presented provides a rationale for a discussion of evolution of the long-range structural characteristics of DNA.

Animals↗
PubMed1986

Genomic localization of hepatitis B virus in a human hepatoma cell line.

The integration of hepatitis B viral sequences in the human hepatoma Alexander cell line has been investigated after fractionation of the cell line DNA by centrifugation in a Cs2SO4/BAMD (3,6-(bis-acetato mercurimethyl) dioxane) density gradient. Eight out of nine integrated viral sequences were localized in DNA component H3, which only represents 4% of the human genome and matches the base composition of HBV sequences. These results indicate a targeting and/or a higher stability of the latter in a specific, small compartment of the host genome.

Carcinoma, Hepatocellular↗
PubMed1986

Gene distribution and nucleotide sequence organization in the mouse genome.

Mouse DNA was fractionated by preparative centrifugation in density gradients of Cs2SO4 containing 3,6-bis(acetatomercurimethyl)dioxane (BAMD). The effects of temperature, BAMD/nucleotide molar ratio and solvent on the fractionation were explored. The fractions so obtained were investigated by analytical centrifugation in CsCl density gradient and by hybridization with a number of gene probes. These approaches led to the definition of satisfactory conditions for the rapid fractionation of mouse DNA; to the localization of a number of genes in mouse DNA fractions; and to a better understanding of the mosaic organization of the mouse genome and, more specifically, to a better estimate of both the intermolecular and intramolecular compositional heterogeneity of mouse DNA in the (75-150) X 10(3)-base size range.

Actins↗
PubMed1986

Gene distribution and nucleotide sequence organization in the human genome.

Human DNA was fractionated by centrifugation in Cs2SO4 density gradients containing 3,6-bis(acetatomercurimethyl)dioxane (BAMD). Fractions were investigated in their analytical CsCl profiles and a number of specific sequences were localized in them. The results so obtained led to an improved understanding of the organization of nucleotide sequences in the human genome, as well as to the discovery that a class of DNA having a very high G + C content and not represented in the mouse genome, is particularly rich in genes and interspersed repetitive sequences.

Base Sequence↗
PubMed1986

Isolation of intercalator-dependent protein-linked DNA strand cleavage activity from cell nuclei and identification as topoisomerase II.

DNA intercalating agents such as 4'-(9-acridinylamino)methanesulfon-m-anisidide (m-AMSA) have previously been found to induce in mammalian cells the formation of protein-associated DNA single- and double-strand breaks. In the current work, an activity characterized by the production of DNA-protein links associated with DNA strand breaks and by stimulation by m-AMSA was isolated from L1210 cell nuclei and was shown to be due to topoisomerase II. Nuclei were extracted with 0.35 M NaCl, and the extract was fractionated by gel filtration, DNA-cellulose chromatography, and glycerol gradient centrifugation. A rapid filter binding assay was devised to monitor the fractionation procedure on the basis of DNA-protein linking activity. The active DNA-cellulose fraction contained both topoisomerase I and topoisomerase II whereas the glycerol gradient purified material contained only topoisomerase II activity. The properties of the active material were studied at both stages of purification. m-AMSA enhanced the formation of complexes between purified topoisomerase II and SV40 DNA in which the DNA sustained a single- or double-strand cut and the enzyme was covalently linked to the 5' terminus of the DNA. This action was further enhanced by ATP, as well as by nonhydrolyzable ATP analogues. m-AMSA inhibited the topoisomerization and catenation reactions of topoisomerase II, probably because of trapping of the enzyme-DNA complexes. The activity showed a dependence on the type of DNA intercalators used, analogous to what was previously observed in intact cells. m-AMSA had no effect on topoisomerase I.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1985

The mosaic genome of warm-blooded vertebrates.

Most of the nuclear genome of warm-blooded vertebrates is a mosaic of very long (much greater than 200 kilobases) DNA segments, the isochores; these isochores are fairly homogeneous in base composition and belong to a small number of major classes distinguished by differences in guanine-cytosine (GC) content. The families of DNA molecules derived from such classes can be separated and used to study the genome distribution of any sequence which can be probed. This approach has revealed (i) that the distribution of genes, integrated viral sequences, and interspersed repeats is highly nonuniform in the genome, and (ii) that the base composition and ratio of CpG to GpC in both coding and noncoding sequences, as well as codon usage, mainly depend on the GC content of the isochores harboring the sequences. The compositional compartmentalization of the genome of warm-blooded vertebrates is discussed with respect to its evolutionary origin, its causes, and its effects on chromosome structure and function.

Animals↗
PubMed1979

Thiourea reverses cross-links and restores biological activity in DNA treated with dichlorodiaminoplatinum (II).

Cis and trans dichlorodiaminoplatinum (II) compounds bind to DNA and form DNA cross-links, which are usually considered to be irreversible. Thiourea can reverse these cross-links without any apparent breakdown of the DNA. In addition, cis- and trans-Pt (II) treatment of lambda decreases its transfectivity. After suitable incubation with thiourea, full transfectivity of Pt(II)-treated lambda DNA can be restored.

Animals↗
PubMed1978

Complex of DNA with chromatin proteins investigated by isopycnic centrifugation in metrizamide.

Complexes of mouse main band DNA with a fraction of non-histone proteins (NHP), having a high affinity for DNA, in the absence or presence of histones have been investigated by gradient centrifugation in metrizamide. Two types of complexes were formed at an input ratio of NHP to DNA between 1 and 2.5. In metrizamide gradients a majority of DNA was found in the light complex (at the density of 1.14-1.16 g/cm3) even at the very high NHP to DNA ratio. When histones were present in the reaction mixture, most of the DNA was found in the heavy complex (1.19-1.21 g/cm3). The electrophoretic profiles of the proteins recovered from the heavy and light complexes were different; some fractions of nonhistone proteins were present only in the heavy component.

Animals↗
PubMed1977

Interactions of some nitro-derivatives of substituted 9-aminoacridine with DNA.

The mechanism of the biological activity of the 1-nitro and 2-nitro aminoacridine derivatives containing the dimethylaminopropyl side chain was studied. RNA synthesis in the isolated rat liver nuclei was only slightly influenced by both compounds. They do not differ in their ability to form an intercalative complex with DNA. Only the 1-nitro derivative exhibited strong inhibitory effect on RNA biosynthesis and caused distinct ultrastructural changes (nucleolar segregation, chromatine margination etc.) in a living cell. The 1-nitro derivative binds covalently to DNA in vivo resulting in crosslink formation. It is concluded that the biological activity of 1-nitro acridine derivatives depends more on their crosslinking activity than on their ability to intercalate into DNA.

Acridines↗