Extensive variation of human immunodeficiency virus type-1 in vivo

Genotypic variation among independent isolates of human immunodeficiency virus type-1 (HIV-1) is well known, but its molecular basis and biological consequences are poorly understood. We examined the genesis of molecular variation in HIV-1 by sequential virus isolations from two chronically infected individuals and analysis of recombinant HIV-1 genomic clones. In three different virus isolates full-length HIV-1 clones were identified and found to consist, respectively, of 17, 9 and 13 distinguishable, but highly-related, viral genotypes. Thirty-five viral clones derived from two HIV-1 isolates obtained from the same individual but 16 months apart showed progressive change, yet were clearly related. Similar changes in the HIV-1 genome did not occur in vitro during virus isolation and amplification. The results indicate that HIV-1 variation in vivo is rapid, that a remarkably large number of related but distinguishable genotypic variants evolve in parallel and coexist during chronic infection, and that 'isolates' of HIV-1, unless molecularly or biologically cloned, generally consist of complex mixtures of genotypically distinguishable viruses.

Optical parallel image skeletonization using contentaddressable memory-based symbolic substitution

In this paper, two optical image skeletonization algorithms are introduced. In both algorithms, the matching between an input and a set of precalculated parallel check patterns is performed. Based on the matching results, multistage symbolic substitution operations are incorporated. For an optical implementation, an optical hologram-based content-addressable memory technique is employed. The corresponding optical architecture as well as character skeletonization examples are presented.

Nucleotide sequence of the gene coding for a 130-kDa mosquitocidal protein of Bacillus thuringiensis israelensis

The nucleotide sequence of pVB131 containing the gene coding for a 130-kDa Bacillus thuringiensis israelensis (B.t.isr) mosquitocidal protein was determined. The pVB131 plasmid was constructed by Sekar and Carlton [Gene 33 (1985) 151-158]. Our sequencing revealed only one open reading frame large enough to code for a protein of 130 kDa. The translation start site was determined by sequencing the protein isolated from B.t.isr. The amino acid sequence of the protein was deduced from the nucleotide sequence, and its Mr was determined as 128,505. Immunological and biochemical analyses of B.t.isr mosquitocidal proteins indicated that the 130-kDa protein coded by pVB131 was indeed expressed in B.t.isr. Comparing the peptide sequence of the 130-kDa B.t.isr toxin with the sequences of other B.t. toxins having activities specific to lepidopteran species showed that several domains were highly homologous. This suggests that they are evolutionarily related to each other, and in the evolutionary process the sequences in the homologous domains that are important to the insecticidal activity have been conserved.

Characterization and design of bar code systems for accurate alignment

The main peak in the autocorrelation function of bar codes is here utilized as the signal of accurate alignment. Attention is therefore directed to the problem of how to increase the contrast of the main autocorrelation peak above the remaining part of the correlation signal and to the problem concerned with the upper limit that the contrast may attain. To meet different requirements of accurate alignment, a series of bar codes is designed. They are classified into several categories according to their performance characteristics. The internal relations between these categories are discussed in greater detail.

Parallel optical pyramidal image processing

Pyramidal processing is a form of multiresolution image processing in which the image is decomposed into a sequence of images at different resolutions. Pyramidal processing aims to extract and interpret significant features of an image at different resolutions. Digital pyramidal image processing, because of the large number of convolution- type operations, is time consuming. On the other hand, optical pyramidal processors, described here, are preferable in real-time image-understanding applications because of their ease in performing convolution operations. Preliminary experimental results for optical Gaussian and Laplacian pyramidal image processing are presented.

Parallel digital and symbolic optical computation via optical phase conjugation

The use of the optical phase conjugation (OPC) process for parallel digital and symbolic optical computing is described. Using spatially encoded logic and symbolic variables, various OPC-based parallel ultrafast optical logic, symbolic as well as interconnect processors are detailed. The proposed devices are experimentally verified using picosecond pulses from a mode-locked Nd(3+):YAG laser. Based on these processors, an OPC-based ultrafast optical computing architecture is proposed.

Optical on-the-fly conversion of a modified signed digit into two's complement binary number representation

An optical carry-free technique is introduced for conversion of a modified signed digit (MSD) into two's complement binary number. Using a combination of optical polarizing beam splitters and retardation waveplates, the proposed device performs this conversion on the fly. The availability of this converter will lead to a large speed increase for various proposed optical parallel MSD arithmetic processors.

Transient expression and sequence of the matrix (M1) gene of WSN influenza A virus in a vaccinia vector

A cDNA encoding the entire amino acid sequence of the matrix (M1) protein of influenza A/WSN/33 virus was cloned, sequenced, and expressed in a vaccinia virus system consisting of the T7 bacteriophage RNA polymerase and a plasmid carrying the M1 gene flanked by T7 polymerase promoter and terminator sequences. The transiently expressed M1 gene product comigrated on SDS-polyacrylamide gels with the endogenous WSN virus M1 protein and was recognized in Western blot analysis by three epitope-specific monoclonal antibodies directed to the M1 protein. The nucleotide sequence and the predicted amino acid sequence of the cloned WSN virus M1 coding region was found to be more than 97% homologous to that of the M1 gene of influenza virus A/PR/8/34 reported by G. Winter and S. Fields (Nucleic Acids Res. 8, 1965-1974, 1980).

Point mutations in glycoprotein gene of vesicular stomatitis virus (New Jersey serotype) selected by resistance to neutralization by epitope-specific monoclonal antibodies

Antigenic variants of the New Jersey serotype of vesicular stomatitis virus (VSV-NJ) were isolated and cloned by selecting virus plaques resistant to neutralization by high-titered monoclonal antibodies (MAbs) directed to glycoprotein (G) epitopes V, VI, VII, or VIII. The G proteins of each neutralization-resistant virus variant also exhibited markedly reduced antigenic reactivity with each corresponding epitope-specific MAb as determined by enzyme-linked immuno-absorbent assay and by Western blot analysis. Loss of antigenic reactivity of certain mutant G proteins to a MAb other than the one used to select the mutant virus suggested close antigenic proximity, particularly for epitopes VI and VII. The virion RNAs coding for the entire G gene of the wild-type virus and 10 MAb-induced mutants were sequenced by primer DNA extension using the dideoxy method. Each mutant G gene exhibited only a single nucleotide change, leading in each case to a single amino acid substitution, as follows: Glu210----Lys for all three mutants selected by MAb14 (epitope VII); Pro268----Thr for one mutant selected by MAb12 (epitope VI); Ser277----Lys for all three mutants selected by MAb15 (epitope VIII); and Glu364----Lys for all three mutants selected by MAb11 (epitope V). These neutralizing MAb-selected mutations are clustered in the middle third of the 517-amino acid VSV-NJ G protein, presumably resulting in conformational changes that alter recognition of one or more antigenic determinants by a specific monoclonal antibody.

A simple method for clinical assay of superoxide dismutase

This assay for superoxide dismutase (SOD, EC 1.15.1.1) activity involves inhibition of nitroblue tetrazolium reduction, with xanthine-xanthine oxidase used as a superoxide generator. By using a reaction terminator, we can determine 40 samples within 55 min. One unit of activity of pure bovine liver Cu,ZnSOD and chicken liver MnSOD was expressed by 30 ng and 500 ng of protein, respectively. The mean concentrations of Cu,ZnSOD as measured by this method in blood from normal adults were 242 (SEM 4) mg/L in erythrocytes, 548 (SEM 20) micrograms/L in serum, and 173 (SEM 11) micrograms/L in plasma. The Cu,ZnSOD concentrations in serum and plasma of patients with cancer of the large intestine tended to be less and greater than these values, respectively, but not statistically significantly so.

A simple method for clinical assay of superoxide dismutase

This assay for superoxide dismutase (SOD, EC 1.15.1.1) activity involves inhibition of nitroblue tetrazolium reduction, with xanthine-xanthine oxidase used as a superoxide generator. By using a reaction terminator, we can determine 40 samples within 55 min. One unit of activity of pure bovine liver Cu,ZnSOD and chicken liver MnSOD was expressed by 30 ng and 500 ng of protein, respectively. The mean concentrations of Cu,ZnSOD as measured by this method in blood from normal adults were 242 (SEM 4) mg/L in erythrocytes, 548 (SEM 20) micrograms/L in serum, and 173 (SEM 11) micrograms/L in plasma. The Cu,ZnSOD concentrations in serum and plasma of patients with cancer of the large intestine tended to be less and greater than these values, respectively, but not statistically significantly so.

Expression of the M gene of vesicular stomatitis virus cloned in various vaccinia virus vectors

Initial attempts to clone the matrix (M) gene of vesicular stomatitis virus (VSV) in a vaccinia virus expression vector failed, apparently because the expressed M protein, and particularly a carboxy-terminus-distal two-thirds fragment, was lethal for the virus recombinant. Therefore, a transient eucaryotic expression system was used in which a cDNA clone of the VSV M protein mRNA was inserted into a region of plasmid pTF7 flanked by the promoter and terminator sequences for the T7 bacteriophage RNA polymerase. When CV-1 cells infected with recombinant vaccinia virus vTF1-6,2 expressing the T7 RNA polymerase were transfected with pTF7-M3, the cells produced considerable amounts of M protein reactive by Western blot (immunoblot) analysis with monoclonal antibodies directed to VSV M protein. Evidence for biological activity of the plasmid-expressed wild-type M protein was provided by marker rescue of the M gene temperature-sensitive mutant tsO23(III) at the restrictive temperature. Somewhat higher levels of M protein expression were obtained in CV-1 cells coinfected with a vaccinia virus-M gene recombinant under control of the T7 polymerase promoter along with T7 polymerase-expressing vaccinia virus vTF1-6,2.

Comparison of simian immunodeficiency virus isolates

Information on the extent of genetic variability among non-human primate lentiviruses related to human immunodeficiency virus (HIV) is sorely lacking. Here we describe the isolation of two molecular clones from the simian immunodeficiency virus (SIV) and their use to derive restriction endonuclease maps of five SIV isolates from rhesus macaques and one from a cynomolgus macaque. Although similar, all six viral isolates are readily distinguishable; the single isolate from a cynomolgus macaque is the most different. The restriction endonuclease map of one macaque isolate (SIVMAC-251) is identical to that published by others for STLV-IIIAGM of African green monkeys and for HTLV-IV of humans. Nucleotide sequences from the envelope region of cloned SIVMAC-251 have more than 99% identify to previously published sequences for STLV-IIIAGM (refs 2, 4) and HTLV-IV (ref. 4). These results and other observations provide strong evidence that isolates previously referred to as STLV-IIIAGM and HTLV-IV by others are not authentic, but were derived from cell cultures infected with SIVMAC-251.

Molecular genotypes of the human T cell receptor gamma-chain

New RFLP of the human TCR gamma-chain defined by a single restriction enzyme (PvuII) are described. They define three alleles and allow haplotype assignments within families. They occur at a high frequency within the population studied and are useful for studies on disease associations with the gamma-chain genes. The PvuII sites flank the C gamma 2 gene. A polymorphic site maps to an area 0.5 kb downstream of C gamma 2-exon III. The second RFLP appears to be the result of a 3-kb insertion giving rise to differences in the number of copies of exon II in the C gamma 2 gene.

Molecular genotypes of the human T cell receptor gamma-chain

New RFLP of the human TCR gamma-chain defined by a single restriction enzyme (PvuII) are described. They define three alleles and allow haplotype assignments within families. They occur at a high frequency within the population studied and are useful for studies on disease associations with the gamma-chain genes. The PvuII sites flank the C gamma 2 gene. A polymorphic site maps to an area 0.5 kb downstream of C gamma 2-exon III. The second RFLP appears to be the result of a 3-kb insertion giving rise to differences in the number of copies of exon II in the C gamma 2 gene.

Finding complex oscillatory phenomena in biochemical systems. An empirical approach

Starting with a model for a product-activated enzymatic reaction proposed for glycolytic oscillations, we show how more complex oscillatory phenomena may develop when the basic model is modified by addition of product recycling into substrate or by coupling in parallel or in series two autocatalytic enzyme reactions. Among the new modes of behavior are the coexistence between two stable types of oscillations (birhythmicity), bursting, and aperiodic oscillations (chaos). On the basis of these results, we outline an empirical method for finding complex oscillatory phenomena in autonomous biochemical systems, not subjected to forcing by a periodic input. This procedure relies on finding in parameter space two domains of instability of the steady state and bringing them close to each other until they merge. Complex phenomena occur in or near the region where the two domains overlap. The method applies to the search for birhythmicity, bursting and chaos in a model for the cAMP signalling system of Dictyostelium discoideum amoebae.

Induction of ornithine decarboxylase and histidine decarboxylase activities in rat colon mucosa after application of 12-o-tetradecanoylphorbol-13-acetate (TPA), sodium deoxycholate and indole

Ornithine decarboxylase (ODC) and histidine decarboxylase (HDC) activities of rat colon mucosa were induced after intrarectal instillation of 12-o-tetradecanoylphorbol-13-acetate (TPA) and sodium deoxycholate. After instillation of sodium deoxycholate, ODC and HDC activities increased rapidly and reached a peak at 4 h, then decreased quickly towards control levels. Both enzymes activities also increased significantly 4 h after instillation in animals treated with TPA and sodium deoxycholate plus indole. However, there were no changes in ODC and HDC activities from 0-8 h after indole administration. These data are the first to show the induction of HDC activity in colon mucosa by TPA and sodium deoxycholate and suggest that the induction of activities in these two enzymes might be one mechanism of their action as cancer promoters.

Induction of beta-glucuronidase activity during dimethylhydrazine carcinogenesis and additive effects of cholic acid and indole

The kinetic change of beta-glucuronidase (beta-G) activity was measured in mouse large intestinal mucosa during dimethylhydrazine (DMH) carcinogenesis with addition of cholic acid and/or indole. The experiment lasted 21 weeks. The enzyme activity began to increase significantly at 5th week after treatment of DMH with cholic acid and/or indole, and at 7th week with DMH alone. Then, increased activity remained the rest of the time. Mouse intestinal cancer induced by DMH injection are also shown to have an increased beta-G activity. The induction of beta-G activity in the early stage of DMH colon carcinogenesis and additive effects of cholic acid and/or indole may imply one mechanism of action of DMH as a carcinogen and cholic acid as a promoter in large intestinal cancer.

Superoxide dismutase activity during dimethylhydrazine colon carcinogenesis and the effects of cholic acid and indole

Copper, zinc superoxide dismutase (Cu,ZnSOD) and manganese superoxide dismutase (MnSOD) activities were measured in mouse large intestinal mucosa during dimethylhydrazine (DMH) carcinogenesis. Mice were divided into five groups. Group A was subcutaneously injected with DMH (20 mg/kg) weekly and fed with a diet containing 0.2% cholic acid (C) and 0.8% indole (I). Group B was injected with DMH and given indole feeding. Group C was treated with DMH injection and cholic acid feeding. Group D was given DMH injection alone. Group E was an age-matched control group given 0.9% NaCl injection. The experiment last 21 weeks. The Cu, ZnSOD activity of intestinal mucosa in group A animals began to increase significantly at the 7th week of the experiment. In groups B, C and D, however, this enzyme was not elevated statistically until the 16th week, and then each of these groups kept an increased Cu,ZnSOD level the rest of the experimental period. MnSOD activity was elevated statistically in group C animals at the 7th week. The enzyme activity in group A and D animals increased at the 9th week, but the enzyme activity did not increase statistically until the 11th week in group B. After the 16th week of the experiment the increased activity of MnSOD in all experimental groups returned to the level of the control group. Large intestinal cancer tissues had increased Cu,ZnSOD activity and decreased MnSOD activity.