ABSTRACT
BACKGROUND & OBJECTIVES: Different routes for the transmission of HIV-1 in India have been reported and the majority of infections occurred through heterosexual route of transmission. In order to understand the dynamics of HIV-1 transmission, a systematic study was undertaken to determine the viral subtypes circulating among the female sex workers in Calcutta, India. METHODS: Peptide enzyme immunoassay (PEIA), heteroduplex mobility assay (HMA) and DNA sequence analysis were used to ascertain the HIV-1 subtypes. RESULTS: V3 serotyping of 52 HIV-1 seropositive samples identified 33 (60%) to be subtype C. A DNA fragment within C2-V3/C2-V5 regions of HIV-1 gp120 was amplified directly from the lymphocyte DNA to avoid any bias in selecting viral variants and used in HMA. Of the 40 samples analyzed, 38 (95%) belonged to subtype C and 2 were found to be non-typable. Further analysis of these 38 samples revealed that 26 (68%) had maximum homology to the C3-Indian reference strain (IND868), 11 (29%) were most homologous to C2-Zambian strain (ZM18) and 1 (3%) showed close resemblance to C1-Malawi strain (MA959). Nucleotide sequence of 11 subsamples encompassing about 325 base pairs was aligned for the Indian and other geographically distinct isolates. On distance and parsimony trees, most of the samples (8/11) clustered together as subtype C. INTERPRETATION & CONCLUSIONS: Subtype C was the major circulating HIV-1 strain in this geographical region, although variation within this subtype was also noticed. DNA sequence analysis was found to be the best method in determining the nature of the HIV-1 subtype followed by HMA and peptide enzyme immunoassay. These findings may have important implications for the design of effective vaccines in India and emphasizes the need for constant monitoring of the HIV-1 subtypes in different parts of India.
Subject(s)
Amino Acid Sequence , Base Sequence , DNA Primers , DNA, Viral/genetics , Female , HIV Envelope Protein gp120/chemistry , HIV Infections/epidemiology , HIV-1/classification , Humans , Immunoenzyme Techniques , India/epidemiology , Molecular Sequence Data , Peptide Fragments/chemistry , Sex Work , Sequence Analysis, DNA , Sequence Homology, Amino AcidABSTRACT
Existence of long range correlations within the DNA sequences of living organism has immense importance in understanding the language of DNA sequences. Recently it has been reported that long range correlations occur in DNA sequences. Some investigators claimed that these type of correlations occur only on intron containing DNA sequences. Some observers, however, have the opinion that long range correlations do not distinguish between the intron containing DNA sequences and intronless DNA sequences. The biological origin of long range correlations in the DNA sequences is not clearly known. In this paper we have demonstrated that long range correlations also occur on intronless mitochondrial DNA sequences, indicating that these special type of correlations are not the unique features for intron containing DNA sequences. We have also demonstrated that long range correlations simply originate in the region around which there is a large variation of pyrimidine and purine ratios. The similarities among the mitochondrial DNA sequences can be inferred by computing the fractal exponents in the region where there is a large variation of pyrimidine and purine ratio, as well as in the region where the ratio of pyrimidine and purine fluctuates in a nearly constant manner. In other words the similarities among the mitochondrial DNA sequences cannot be inferred by calculating the fractral exponents for the whole sequence.
Subject(s)
Animals , DNA, Mitochondrial/chemistry , Evolution, Molecular , Fractals , Humans , Introns/genetics , Models, Biological , Purines/chemistry , Pyrimidines/chemistry , Schizosaccharomyces/genetics , Sequence Homology, Nucleic AcidABSTRACT
This paper describes the program "GENOLYTE" which has been developed for the visualisation and identification of the global and local patterns of long genomic DNA sequences quickly in a few minutes, with the aid of a microcomputer. Apart from global and local identification, GENOLYTE comparatively depicts the similarity of two or more than two genomic DNA sequences. The utility of the program has been demonstrated by analysing the complete mitochondrial DNA sequences (taken from EMBL databank) as an example and the results are discussed from therein. The program written in TURBO C++ has the following minimum requirements: (i) PC 386 AT, (ii) SVGA colour monitor, (iii) the [BGI] directory of TURBO C++ version 3.0.
Subject(s)
Animals , Base Sequence , Genome , Genome, Human , Humans , Microcomputers , Molecular Sequence Data , SoftwareABSTRACT
Teichoic acid (TA) isolated from the Gram-positive bacteria Staphylococcus aureus induces blue shifted metachromasia in the dye 1,9-dimethyl methyleneblue (DMMB). Results of conductometric titrations show that DMMB binds to TA with 1:1 stoichiometry. Unlike DNA, this TA does not induce a definite metachromatic band in the dye acridine orange. S. aureus TA also induces strong circular dichroism (CD) in this dye with molar ellipticity value of the order of 10(4). This induction of CD in DMMB supports our earlier inference that TA in dilute solution at neutral pH has a helical conformation, and is not a random coil polymer.