Genome analysis: A new approach for visualization of sequence organization in genomes

In this article we describe and demonstrate the versatility of a computer program, GENOME MAPPING, that uses interactive graphics and runs on an IRIS workstation. The program helps to visualize as well as analyse global and local patterns of genomic DNA sequences. It was developed keeping in mind the requirements of the human genome sequencing programme, which requires rapid analysis of the data. Using GENOME MAPPING one can discern signature patterns of different kinds of sequences and analyse such patterns for repetitive as well as rare sequence strings. Further, one can visualize the extent of global homology between different genomic sequences. An application of our method to the published yeast mitochondrial genome data shows similar sequence organizations in the entire sequence and in smaller subsequences     

Localisation of the gene for Norrie disease to between DXS7 and DXS426 on Xp

Summary A highly informative microsatellite marker, DXS426, which maps proximal to DXS7 in the interval Xp11.4–Xp11.23, has been used to refine further the localisation of the gene for Norrie disease (NDP). The results from a multiply informative crossover localize the NDP gene proximal to DXS7. In conjunction with information from 2 NDP patients who have a deletion for DXS7 but not for DSX426, our data indicate that the NDP gene lies between DXS7 and DXS426 on proximal Xp.     

Light-stable rhodopsin. II. An opsin mutant (TRP-265----Phe) and a retinal analog with a nonisomerizable 11-cis configuration form a photostable chromophore.

In order to prepare a completely light-stable rhodopsin, we have synthesized an analog, II, of 11-cis retinal in which isomerization at the C11-C12 cis-double bond is blocked by formation of a cyclohexene ring from the C10 to C13-methyl. We used this analog to generate a rhodopsin-like pigment from opsin expressed in COS-1 cells and opsin from rod outer segments (Bhattacharya, S., Ridge, K.D., Knox, B.E., and Khorana, H. G. (1992) J. Biol. Chem. 267, 6763-6769). The pigment (lambda max, 512 nm) formed from opsin and analog II (rhodospin-II) showed ground state properties very similar to those of rhodopsin, but was not entirely stable to light. In the present work, 12 opsin mutants (Ala-117----Phe, Glu-122----Gln(Ala, Asp), Trp-126----Phe(Leu, Ala), Trp-265----Ala(Tyr, Phe), Tyr-268----Phe, and Ala-292----Asp), where the mutations were presumed to be in the retinal binding pocket, were reconstituted with analog II. While all mutants formed rhodopsin-like pigments with II, blue-shifted (12-30 nm) chromophores were obtained with Ala-117----Phe, Glu-122----Gln(Ala), Trp-126----Leu(Ala), and Trp-265----Ala(Tyr, Phe) opsins. The extent of chromophore formation was markedly reduced in the mutants Ala-117----Phe and Trp-126----Ala. Upon illumination, the reconstituted pigments showed varying degrees of light sensitivity; the mutants Trp-126----Phe(Leu) showed light sensitivity similar to wild-type. Continuous illumination of the mutants Glu-122----Asp, Trp-265----Ala, Tyr-268----Phe, and Ala-292----Asp resulted in hydrolysis of the retinyl Schiff base. Markedly reduced light sensitivity was observed with the mutant Trp-265----Tyr, while the mutant Trp-265----Phe was light-insensitive. Consistent with this result, the mutant Trp-265----Phe showed no detectable light-dependent activation of transducin or phosphorylation by rhodopsin kinase.     

Central modulation of croton oil induced subacute inflammation in rats

Earlier studies from this laboratory have indicated that CNS exerts a modulatory influence over acute inflammation in rats. The present study examines the existence of a similar modulatory effect of CNS on a subacute inflammatory paradigm, the croton oil-induced granuloma pouch in rats. The inflammatory exudate, collected on 6th day after croton oil administration, was found to be substantially less in intracerebroventricular (icv) cannulated and artificial cerebrospinal fluid administered rats as compared to their uncannulated saline (ip) administered counterparts. This effect may be due to stress induced by cannulation. Centrally administered pharmacological agents which attenuate central monoaminergic, cholinergic or prostaglandin systems had insignificant effects on the inflammatory exudate. However, induced increase in central noradrenergic activity was found to attenuate the inflammation when the treatment was done before, but not 48 hr after, the induction of the inflammation. In contrast, induced increase in central serotonergic activity had no effect on the volume of the inflammatory exudate at either time period. Steady state levels of rat brain noradrenaline and serotonin, but not dopamine, were enhanced by the inflammatory procedure. However, these effects may be attributed to the stress induced by croton oil inflammation. The investigation indicates that the modulatory influence of CNS remains limited to the acute phase of inflammation, being exerted mainly by the central noradrenergic system. Once the inflammation has progressed, this modulatory influence of CNS is no longer apparent.     

Brain monoamines during footshock-induced aggression in paired rats

Regional brain monoamine concentrations were investigated following footshock induced fighting behaviour in paired rats, by a spectrophotofluorometric method. The dopamine (DA) levels of the diencephalon-midbrain (DM), and that of the caudate nucleus (CN), were significantly augmented as compared to unshocked but paired rats, the increase being substantially more in DM. Noradrenaline (NA) concentrations of both DM and pons-medulla (PM) increased to almost similar extents, though the data remained statistically insignificant in comparison to controls. The 5-hydroxytryptamine (5HT) of both DM and PM, however, recorded a decrease, which was statistically significant in the latter brain area. The biochemical data are consonant with the reported facilitatory effect of central DA, and the inhibitory role of central 5HT, in experimental aggression. The observed changes in NA levels, for which a role in experimental aggression remains equivocal, may be due to the stress of footshock kept minimal due to the coping factor of fighting in response to the shock.     

Permeability and Enterotoxic Factors of Nonagglutinable Vibrios Vibrio alcaligenes and Vibrio parahaemolyticus

Enterotoxic factor (EF) was present and could be developed in nonagglutinable vibrios, but not the permeability factor (PF). Presence of PF without EF in Vibrio parahaemolyticus is significant. Both EF and PF were absent in V. alcaligenes.