Composition of the folded chromosome from Anabaena variabilis

A "heavy" nucleoid (folded chromosome) from A. variabilis has been isolated in preparative amounts. The composition of the folded chromosome and that of a more simple DNA--protein complex isolated from the "heavy" nucleoid of A. variabilis by chromatography on a column with methylated albumin (MAK) were studied. It was shown that the "heavy" nucleoids contain total cell DNA in a complex with the definite membrane fragment, which can be discovered by a large number of membrane proteins, phospholipids, lipopolysaccharides and amino sugars. After MAK chromatography the DNA--protein complex also contains total cellular DNA, a negligible amount of membrane polypeptides and noticeable amounts of phospholipids and lipopolysaccharides.     

Structural properties of leukemic and normal lymphoid cells

DNA synthesis intensity and spectral and fluorescent properties of leucemic, PHA-induced and intact normal mouse spleen cells and of nuclei isolated from these cells were investigated. The cell electrophoretic mobility and DNA-protein interaction in the nuclei were studied. Similarity in cell and nuclei fluorescence, fluorescence of the probe ANS conjugated with the cells, the electrophoretic mobility and tightness of DNA--protein interaction for leucemic and PHA--induced cells and also the similarity of the tightness of DNA--protein interaction for leucemic and normal intact cells were found inspite of the differences in DNA synthesis intensity and cell functional peculiarities.     

Use of DNA-protein interaction to isolate specific genomic DNA sequences.

We describe a simple and rapid method for the isolation of specific genomic DNA sequences recognized by DNA-binding proteins. This procedure consists of four steps: (1) restriction enzyme digestion and size fractionation of genomic DNA; (2) DNA--protein binding using the gel mobility-shift assay; (3) ligation of isolated DNA fragments followed by transformation of Escherichia coli; and (4) screening of recombinant clones for inserts containing specific DNA--protein binding sequences. We have used this protocol to isolate human DNA sequences, 100-200 bp in size, that are recognized by both partially purified and affinity purified proteins. Unlike other procedures designed to identify genomic target sequences, the method described does not require polymerase chain reaction or successive immunoprecipitations.     

Structure of nucleosomes. Localization of the H2A and H2B histone segments interacting with DNA using DNA-protein crosslinking]

Histones' H2A and H2B peptidic points which interact with nucleosomal DNA have been identified by using the methods of DNA--protein covalent cross-linking. H2B can be linked to DNA via its N-terminal tail and via several lysines contained within residues 24-34. The most prominent site of histone H2A covalent linking to DNA is His-123, the less prominent being Lys-119 and Lys-124.     

Probing DNA-protein interactions in vitro with the CpG DNA methyltransferase.

A sensitive method was devised to monitor the in vitro binding of nuclear proteins from HeLa cells presumably to the major groove of DNA. Upon the incubation of DNA with nuclear extracts, the complexed DNA was incubated with the CpG DNA methyltransferase from Spiroplasma species. Subsequently, the DNA was repurified, and the location of the methylated cytidine residues was determined by the hydrazine reaction of the DNA sequencing method. By using as DNA substrate the VAI (virus associated) region of human adenovirus type 2 (Ad2) DNA or specific Alu sequences associated with a number of human genes, it was documented that those segments of DNA that were protected by bound proteins against the reaction with DNasel also escaped in vitro methylation by the CpG DNA methyltransferase. This new footprinting method provides a sensitive indicator for in vitro DNA--protein interactions which are specific for the major groove of DNA.     

Complex of single-stranded phage DNA and protein--a product of bacteriophage fl gene 3. Distribution of gene 3 protein in the DNA molecule

Upon a 50% isopropanol treatment of phage fl in a 1 M NaCl solution protein A (gene 3 product)--DNA complex is precipitated while protein B (gene 8 product) was still solubilized. After such a treatment the DNA--protein complex containing 10--40% of protein A and less than 0.0025% of protein B was obtained. Evidence was obtained that there was no non-specific rearrangement of protein A during the isolation procedure. The complex was treated with endonuclease R.HAC III, followed by electrophoresis of the resulted fragments and estimation of the [14C] protein A (labeled with [14C]histidine) throughout the gel. The maximal radioactivity coincided with the DNA bands, being proportional to the DNA content in the respective bands. The data obtained indicate that protein A is iniformly arranged along the DNA molecule.     

Computer programs for the analysis of nucleotide sequences (MALK)

A system for the computer analysis of nucleic acid and protein sequences ("Helix") is described. Format of the DNA sequences is EMBL--compatible and may be easily commented with the help of convenient menus. "Helix" has also following possibilities: an effective alignment of gele reading data and formation of the final sequence; simple making of recombined molecules "in calcular"; calculations of nucleotide and dinucleotide distribution along the sequence; looking for coding frames; calculations percentage of codons and amino acids in coding frames; searching for direct and inverted repeats; sequences alignment; protein secondary structure prediction; restriction mapping; DNA--protein translation. "Helix" also contain programs for RNA-structure prediction, looking for homologies throughover the EMAL bank, choosing optimal sequence for probes and searching promoters. All the programs are written at FORTRAN-77 and automatically translated into FORTRAN-4. "Helix" require only 64 kbite.     

Dependence on androgens of the specific DNA-binding activity of rat ventral-prostate non-histone chromosomal proteins.

Interactions between rat prostate non-histone chromosomal proteins and DNA were studied by using a nitrocellulose-filter-binding technique to monitor the formation of DNA--protein complexes. The total binding activity of the non-histones, as measured by binding of proteins to a trace quantity of labelled DNA, displays no preference for rat DNA relative to Escherichia coli DNA. Sequestration of non-specific binding proteins by preincubation with unlabelled bacterial DNA enables detection of a fraction of rat prostate non-histones that binds preferentially to labelled rat DNA relative to labelled E. coli DNA. After castration of adult male rats, both total and specific binding activities decrease. Administration of 5 alpha-dihydrotestosterone to castrated rats stimulates both total and specific DNA-binding activities of prostate non-histones; specific binding is stimulated to a greater extent than total DNA, indicating that the specific binding proteins constitute a larger fraction of the non-histone proteins in the presence of androgens. The specific DNa-binding activity is dependent on the dose of steroid administered.     

Mutagenicity, cytotoxicity and DNA crosslinking in V79 Chinese hamster cells treated with cis- and trans-Pt(II) diamminedichloride.

The mutagenicity and cytotoxicity of cis- and trans-Pt(II) diamminedichloride (PDD) were examined in V79 Chinese hamster lung cells and compared with effects on DNA measured by alkaline elution. DNA--protein crosslinks and DNA interstrand crosslinks were detected following doses of cis-PDD which reduced cell survival 80--90% and which produced a mutant frequency of 3 X 10(-4) at the HGPRT locus. Equitoxic doses of trans-PDD were much less mutagenic than cis-PDD. At equitoxic doses, trans-PDD produced more DNA-protein crosslinking than did cis-PDD, but interstrand crosslinking for the two isomers was comparable. Hence, the interstrand crosslink could be the cytotoxic lesion produced by these Pt compounds whereas neither of these DNA lesions are necessarily mutagenic. The mutagenesis produced by cis-PDD could be due to crosslinks of a different type than those produced by trans-PDD or it may be due to monofunctional damage.     

The reactions of the EcoRi and other restriction endonucleases.

The reaction of the EcoRI restriction endonuclease was studied with both the plasmid pMB9 and DNA from bacteriophage lambda as the substrates. With both circular and linear DNA molecules, the only reaction catalysed by the EcoRI restriction endonuclease was the hydrolysis of the phosphodiester bond within one strand of the recognition site on the DNA duplex. The cleavage of both strands of the duplex was achieved only after two independent reactions, each involving a single-strand scission. The reactivity of the enzyme for single-strand scissions was the same for both the first and the second cleavage within its recognition site. No differences were observed between the mechanism of action on supercoiled and linear DNA substrates. Other restriction endonucleases were tested against plasmid pMB9. The HindIII restriction endonuclease cleaved DNA in the same manner as the EcoRI enzyme. However, in contrast with EcoRI, the Sa/I and the BamHI restriction endonucleases appeared to cleave both strands of the DNA duplex almost simultaneously. The function of symmetrical DNA sequences and the conformation of the DNA involved in these DNA--protein interactions are discussed in the light of these observations. The fact that the same reactions were observed on both supercoiled and linear DNA substrates implies that these interactions do not involve the unwinding of the duplex before catalysis.     

Ataxia-telangiectasia cells are not uniformly deficient in poly(ADP-ribose) synthesis following X-irradiation

Inducibility of 6-thioguanine-resistant (6TGr) mutants and single-strand scission of DNA by cadmium chloride (CdCl2) was investigated in cultured Chinese hamster V79 cells. Frequency of 6TGr mutants increased concentration dependently by 24-h treatment with CdCl2 up to 3 X 10(-6) M but decreased beyond 3 X 10(-6) M. Mutagenic potency of cadmium in the absence of S9 was about half that of benzo[a]pyrene in the presence of S9 at equitoxic concentrations. Treatment of the cultured cells with cadmium after benzo[a]pyrene treatment was not synergistic but additive to the mutagenicity of benzo[a]pyrene. Single-strand scission of DNA by alkaline elution techniques was observed in the cells treated with CdCl2 for 2 h in a concentration-dependent manner. The single-strand scission by cadmium was detected only in combination with proteinase K digestion of the cell lysates, indicating formation of DNA--protein cross-linking by the metal. These biological and biochemical findings indicate that cadmium is mutagenic in mammalian cells, and its mutagenic effect seems to be accompanied by single-strand scission of DNA.     

Eclipse kinetics as a probe of quaternary structure in bacteriophage phi X174

The extracellular form of bacteriophage phi X174 consists of single-stranded DNA within an icosahedral capsid, which has short spikes at each of its vertices. Each spike is composed of gene G and H proteins, while the capsid itself consists of gene F protein. Since several molecules of gene H protein are injected into the cell along with the DNA, specific protein--protein and DNA--protein interactions must be broken when the genome exits and leaves an intact capsid structure at the receptor site. To demonstrate this we examined the eclipse (DNA ejection) reaction with two types of phi X174 mutants. The first contains missense mutations in a capsid or spike protein gene, and the second involves insertions or deletions in non-coding regions of the DNA. Using an improved procedure, the eclipse rate in vivo of the eclipse mutants Fcs70 has been redetermined over a larger temperature range than in previous studies. The three- to fivefold decrease in rate between 37 degrees C and 25 degrees C is due to an increase in both the enthalpy and entropy of activation when compared to the wild-type values of these kinetic parameters. This missence mutation also confers an increase in virus stability in 2 to 3 M-urea. In contrast to this, inserting 163 bases into the length of DNA packaged within the phi X174 capsid does not lead to a detectable change in eclipse rate over the same temperature range. yet this insertion into the J--F intercistronic region imparts a significant decrease in virus stability in urea. These results suggest that a specific set of non-covalent interactions is involved in phi X174 DNA ejection. This is supported by the small (50%), but significant, increase in eclipse rate that occurs when 27 bases are deleted from the J--F intercistronic region. The latter effect must be base-sequence-specific since no change in rate is observed when only seven of the 27 bases are deleted. Thus, the kinetics of the phi X174 eclipse reaction can be used as a sensitive probe of quaternary structure by correlating the change in reaction rate with alterations in amino acid and base sequences in the structural components of the virus.     

The effect of the genotype on the expressiveness of the vestigial trait and polyteny of chromosomes in Drosophila melanogaster Meig

The effects of the Bar (B) and white (w) mutations on the expressiveness of the character vestigial (vg) and the degree of polyteny of salivary gland giant chromosomes were studied in Drosophila melanogaster. Either mutation changed both the expressiveness of vestigial and the degree of chromsome polyteny. A negative association between the vg expressiveness and the degree of chromosome polyteny was revealed and proved to be stronger in females than in males. The parameters under study were shown to differ between females and males.     

Characterization of the amino acid contribution to the folding degree of proteins

The folding degree index (Estrada, Bioinformatics 2002;18:697-704) is extended to account for the contribution of amino acids to folding. First, the mathematical formalism for extending the folding degree index is presented. Then, the amino acid contributions to folding degree of several proteins are used to analyze its relation to secondary structure. The possibilities of using these contributions in helping or checking the assignation of secondary structure to amino acids are also introduced. The influence of external factors to the amino acids contribution to folding degree is studied through the temperature effect on ribonuclease A. Finally, the analysis of 3D protein similarity through the use of amino acid contributions to folding degree is studied by selecting a series of lysozymes. These results are compared to that obtained by sequence alignment (2D similarity) and 3D superposition of the structures, showing the uniqueness of the current approach.     

Influence of the size of soil structural aggregates on the degree of nitrification

It was found that the degree of nitrification and the nitrate level in soils with a water stable structure was correlated to the size of the aggregates. The degree of nitrification and the nitrate level was in inverse proportion to the size of the aggregates. The correlation of the degree of nitrification to the specific surface area (the total outer area of one gramme of aggregates of a given fraction) has the form of a curve, similar in appearance to a hyperbola. Analysis of the conditions of nitrification in isolated fractions and in natural soil led to the conclusion that the factor controlling the degree of nitrification is the difference in aeration of aggregates of different sizes.     

Adaptive thermoregulatory reactions of the rabbit fetus at the end of the intrauterine development

The data of permanent simultaneous registration of electrocardiogram, rectal & brown adipose tissue temperatures of the rabbit foetus have been obtained in chronic experiments. The haemodynamic shift in intensity of maternal-placental and foeto-placental blood flow (by female trental injection) led to a decrease in the foetus rectal temperature (0.33 +/- 0.09 degree C in intact foetus and 0.58 +/- 0.27 degree C in retarded foetus, p < 0.05). Both foetuses reacted by rectal temperature decrease (0.65 +/- 0.28 & 0.68 +/- 0.31 degree C, respectively) during immobilisation (by foetus arduan injection). Thus in both series of experimental cooling of foetus, brown fat activation was similar in intact foetus (approximately 53%), but did not change in growth retardation foetus--as a result of its tissue functional immaturity, probably.     

Compartmentation of the inulin space in mouse brain slices

(1) Mouse cerebrum slices swell in tris-buffered Krebs-Ringer medium. Swelling is rapid at first, then slows to a more or less constant rate. Even after 3 hr incubation, water content/g of tissue dry wt. shows no sign of an asymptotic limit. Swelling is the same at 37 degrees and at 0 degree. (2) Tissue water measured by incubation with tritiated water is equal to total tissue water measured by drying slices. Equilibration between tritiated water and tissue water is complete within 2 min. (3) Tissue liquid can be divided into three phenomenologically distinguishable compartments: first inulin space, which is the compartment permeable to inulin at both 0 degree and 37 degrees; second inulin space, which is the compartment permeable to inulin at 37 degrees but not at 0 degree; and 37 degrees non-inulin space, which is the compartment impermeable to inulin at both 0 degree and 37 degrees. The evidence for this is: (a) Penetration of inulin into tissue is greater at 37 degrees than at 0 degree. After the first 20 min the rate of penetration at 0 degree is approximately equal to the rate of penetration at 37 degrees, and only slightly less than the rate of increase of total tissue water. Therefore the smaller inulin space observed at 0 degree cannot be due to slower entry of inulin. (b) The inulin content of slices incubated in inulin-containing medium at 37 degrees and cooled to 0 degree in the same medium is the same as the inulin content of tissue incubated at 37 degrees without subsequent cooling. In contrast, the inulin content of tissues preincubated in inulin-free medium at 37 degrees and then incubated in inulin-containing medium at 0 degree is the same as the inulin content of tissues incubated in inulin-containing medium at 0 degree without preincubation at 37 degrees. Therefore the smaller inulin space at 0 degree than at 37 degrees can be due neither to a reversible temperature-dependent change in the size of one single inulin space nor to an irreversible, greater swelling of a single inulin space at the higher temperature, but is due to some portion of the 37 degrees inulin space becoming impermeable to inulin at 0 degree. (c) Some inulin is retained by tissue incubated with inulin at 37 degrees, then transferred to inulin-free medium at 0 degree; the amount of retained inulin is equal to the difference between inulin content of tissue incubated with inulin at 37 degrees and tissue incubated with inulin at 0 degree This confirms 3b above and in addition shows that inulin which has entered the second inulin space at 37 degrees is trapped there when this space becomes impermeable to inulin at 0 degree. (4) The penetration of the amino acids, L-lysine and D-glutamate at 0 degree is equal to the penetration of inulin at 37 degrees. This confirms the real existence of the 37 degrees inulin space at 0 degree, and shows that the barrier at 0 degree between the first and second inulin spaces does not exist for these substances. (5) The amino acids L-leucine and glycine penetrate total tissue water at 0 degree. L-leucine is actively transported at this temperature. (6) The amino acids alpha-aminoisobutyric acid, L-leucine, and L-lysine at 2 mM have no effect at 37 degrees on either the inulin space or the non-inulin space. (7) The inulin space is insensitive at 37 degrees to physiologically significant changes in the medium. In contrast, the non-inulin space is quite sensitive to these changes. Addition of D-glutamate greatly increases the non-inulin space; addition of ouabain or cyanide, or omission of glucose, increases the non-inulin space slightly; and replacement of Na+ ion by choline+ ion greatly decreases this space. These changes are independent and roughly additive.     

Thermodynamic functions of lysozyme, myoglobin, beta-lactoglobulin, albumin, and poly-L-tryptophane in the temperature range 0-330 K

The temperature dependence of heat capacity for lysozyme, myoglobin, beta-lactoglobulin, albumin, and poly-L-tryptophan was studied in the temperature range 5-330 K using an adiabatic vacuum calorimeter. The accuracy of measurements was approximately 0.2%. From the data obtained, the thermodynamic functions of these proteins and the polyamino acid Cp degree (T), H degree (T)-H degree (0), S degree (T)-S degree (0), G degree (T)-H degree (0) in the temperature range 0-330 K, and the values of fractal dimension D and intrinsic temperature theta max were calculated.