AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions

Background  

Replication origins are considered important sites for understanding the molecular mechanisms involved in DNA replication. Many computational methods have been developed for predicting their locations in archaeal, bacterial and eukaryotic genomes. However, a prediction method designed for a particular kind of genomes might not work well for another. In this paper, we propose the AT excursion method, which is a score-based approach, to quantify local AT abundance in genomic sequences and use the identified high scoring segments for predicting replication origins. This method has the advantages of requiring no preset window size and having rigorous criteria to evaluate statistical significance of high scoring segments.     

DNA-binding properties and antitumour activity of monofunctional alkylating groups attached to the DNA-intercalating chromophore phenanthridine: n-bromoalkylphenanthridinium bromides

We have synthesised an homologous series of n-bromoalkylphenanthridinium bromides and studied their DNA-binding and antitumour properties. Each of these compounds has the capacity both to intercalate and alkylate DNA. Dialysis measurements reveal a relatively high affinity for calf thymus DNA, being about 10(5) M-1 at ionic strength 0.01. Incubating calf thymus DNA-ligand complexes having a ligand-to-basepair ratio of 0.4 at 37 degrees C for 18 h leads to maximum alkylation levels of about one ligand molecule bound irreversibly per 40 basepairs. The reactivity of these compounds towards DNA is chain-length dependent, the n-decyl compound, for example, requiring about 10-times the ligand-to-basepair input ratio of the n-hexyl derivative to reach the same level of alkylation. The limited degree of alkylation is a consequence of conversion of the alkylbromides to the less reactive alkylchlorides in the buffer medium. The results of DNA sequencing experiments indicate that the n-hexyl derivative alkylates at guanines occurring in 5'-GT-3' sequences and in runs of guanines [(Gp)n]. The corresponding n-decyl compound, on the other hand, is highly selective for guanines in 5'-GT-3' sequences only and also reacts weakly with some adenines. None of the phenanthridinium compounds showed significant antitumour activity in the P388 murine leukaemia test system.     

Interaction of paired homologous series of diacridines and triacridines with deoxyribonucleic acid

Viscometric measurements using covalently closed circular DNA and sonicated rod-like DNA fragments were performed to investigate unwinding and extension of the DNA helix associated with binding of paired homologous series of diacridines and triacridines. The maximum interchromophore distance for members of the diacridine series spans from 15.1 to 27.5 A, permitting the largest of these ligands to cover up to 4 or 5 base-pairs, allowing for helical twist and local unwinding in a bisintercalated complex lacking severe bending or kinking of the DNA backbone. Helix unwinding angles and increments in DNA contour length are characteristic of bifunctional reaction for all the diacridines studied, the DNA lattice appearing to saturate with one ligand molecule bound per 4 base-pairs. The triacridines, whose maximum end-to-end interchromophore distances are the same as those of their paired diacridines, have maximum central-to-terminal interchromophore distances covering the range 7.5-13.8 A and thus have the potential to form trisintercalated complexes with one or two base-pairs sandwiched between each chromophore. However, helix extension and unwinding parameters for the triacridines are similar to those of the diacridines, and we find no evidence of a transition from bifunctional to trifunctional reaction as the homologous series is ascended. In general, the binding site size appears to be 5 base-pairs for the triacridines. The stereochemical requirements for trisintercalation of triacridines are discussed with reference to the present findings and to the work of others.     

Phagocytosis of degenerating myelin in transected feline optic nerve: an immunohistochemical study

The phagocytic activity of neuroglial cells in adult feline degenerating optic nerve was investigated by immunocytochemistry at both light and electron microscopy levels. Degeneration was initiated by unilateral eye enucleation and the segment distal to the transection showing true Wallerian degeneration was examined. Following enucleation, twelve adult domestic cats were examined over a period of seven to 215 days. All cases showed slow clearance of myelin debris and absence of proliferating monocytes throughout the post-enucleation period. All phagocytic cells present were neuroglial cells, and many of these cells expressed oligodendroglial antigens. These findings demonstrate the persistence of an active population of oligodendrocytes that might play an additional functional role during Wallerian degeneration of feline optic nerve.     

DNA threading bis(9-aminoacridine-4-carboxamides): effects of piperidine sidechains on DNA binding, cytotoxicity and cell cycle arrest

We describe the synthesis of a series of DNA-threading bis(9-aminoacridine-4-carboxamides) comprising ethylpiperidino and N-methylpiperidin-4-yl sidechains, joined via neutral flexible alkyl chains, charged flexible polyamine chains and a semi-rigid charged piperazine linker. Their cytotoxicity towards human leukaemic cells gives IC(50) values ranging from 99 to 1100 nM, with the ethylpiperidino series generally being more cytotoxic than the N-methylpiperidin-4-yl series. Measurements with supercoiled DNA indicate that they bisintercalate.     

Tyvelose and protective responses to the intestinal stages of Trichinella spiralis

The unusual sugar tyvelose is the immunodominant portion of the major larval glycoprotein antigens of Trichinella spiralis, which play an important role in generating immunity against the intestinal stages of infection. The possibility that the tyvelose component itself may have a host- or parasite-protective role in the intestine was tested by following the outcome of challenge infections in mice primed and boosted with tyvelose-BSA, or in mice primed with tyvelose-BSA before boosting with larval antigen. Although antibody responses were raised against tyvelose there was no evidence of protective immunity against the intestinal stages, as assessed by total adult worm recovery or by size and fecundity of female worms in immunized mice. Equally, priming with tyvelose-BSA before boosting with larval antigen had no effect on the expression of immunity against a challenge infection. The predominant antibody isotype recorded in all immunized mice was IgG1, suggesting the induction of type 2 T cell responses, and this was confirmed by cytokine analysis, mesenteric node lymphocytes of all mice showing production of IL-5 but not IFN-gamma. Clearly immunization with tyvelose had no significant effect on T cell polarization. The data show that, with the experimental design employed, there was no evidence for a functional role of tyvelose in either host- or parasite-protection during the intestinal phase of infection.     

Genetic control of eosinophilia in parasitic infections: Responses of mouse strains to treatment with cyclophosphamide and parasite antigen

, and 1988. Genetic control of eosinophilia in parasitic infections: responses of mouse strains to treatment with cyclophosphamide and parasite antigen. International Journal for Parasitology18:1077–1085. Strain-dependent variation in the capacity of inbred and congenic mice to mount an eosinophilia in response to inoculation with the antigens of Mesocestoides corti, Trichinella spiralis or with Limulus haemocyanin (LCH), following pretreatment with cyclophosphamide (CY), is described. SWR, NIH, BALB/c, C3H and SJL mice were eosinophil high responder strains whereas C57 BL/10 and CBA mice were eosinophil low responder strains. Congenic strains with the B10 background (B10.S, B10.G and B10.BR) were all low eosinophil responders, although B10.G mice showed a level of response consistently above the other B10 congenic strains. Some of the gene(s) for high responsiveness appeared to be dominant, because F(In1)hybrids between high and low eosinophil response parental strains were intermediate to high responders. The strain-dependent pattern of eosinophil responsiveness to LHC or to M. corti and T. spiralis antigens, following CY pretreatment, was similar to that obtained previously following infection with either M. corti or T. spiralis, suggesting that heterogeneity in capacity to produce eosinophils operates independently of the nature of the eliciting stimulus.     

Transfer of immunity against Trichuris muris in the mouse by serum and cells

Transfer of immunity against Trichuris muris in the mouse by serum and cells. Internationaljournal for Parasitology 3: 717–722. A protective immunity against the nematode Trichuris muris was transferred with antiserum and cells taken from immunized mice. Immunity was transferred most reliably by cells, especially mesenteric lymph node cells, but most effectively by serum. The protective capacity of serum and cells taken from the same mice was not always related. Multiple immunization of the donors did not markedly increase protection in the recipients.