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D K Dube

Publications and source records attributed to D K Dube.

At least 37 records · Page 2Linked to original sources
PubMed1996

Nucleotide sequence and expression of ribosomal protein S3 mRNA during embryogenesis in the Mexican axolotl (Ambystoma mexicanum).

We have isolated and sequenced a full-length (0.9 kb) cDNA clone of ribosomal protein S3 by subtraction hybridization using a single-stranded cDNA library from stage 25-27 (tracer) and the mRNA from stage 15-17 (driver) of embryonic Mexican axolotl (Ambystoma mexicanum). The axolotl is a unique animal model for studying heart development as well as myofibrillogenesis because it carries a mutation in gene c. The deduced amino acid sequence of axolotl S3 protein shows about 93.9% identity with human S3 protein over a 243 amino acid residue overlap. When compared with mouse and Xenopus laevis ribosomal S3 proteins, the axolotl sequenc shows 94.3 and 93.9% identity respectively. Interestingly, the axolotl S3 sequence shows higher identity at the nucleic acid level with human and/or other mammals than with Xenopus. The S3 transcript, as determined by RT-PCR, is present at stage 2-4 in a lower amount and the onset of transcription is most likely at the beginning of gastrulation (10-12). The expression level of S3 transcripts reaches a maximum by mid gastrulation (stages 13-14) and then follows a biphasic pattern being lower at stages 16-17 with subsequently steady increases until the mid tailbud stages (25-27).

Ambystoma mexicanum↗
PubMed1996

Expression of myosin heavy chain transcripts in normal and cardiac mutant Mexican axolotls.

In this study, we have cloned a 1.0 kb myosin heavy chain (MHC) cDNA by screening an axolotl heart cDNA library with the monoclonal antibody MF20 against a light meromyosin (LMM) region of MHC. The nucleotide sequence analysis shows 85-86% homology at the amino acid and 78-81% homology at the nucleic acid level with MHC from other vertebrates. Phylogenetic analyses suggest that axolotl beta-MHC forms a cluster with the myosin II group of vertebrate striated muscles. Within the myosin II cluster, axolotl beta-MHC forms a distinct subclade from avian MHC and is instead closer to mammalian MHC. RT-PCR analyses show that transcripts of beta-MHC are present at stage 2 and the onset of the MHC gene expression is at stage 8-10 (gastrulation). Expression increases with embryonic development and reaches a maximum at stage 20. Beyond stage 35, the heart-beat initiation stage, the expression level of beta-MHC is higher in cardiac muscle than in skeletal muscle. We could not detect significant differences in the levels of expression of MHC transcripts in normal and cardiac lethal mutant (c/c) axolotls (Ambystoma mexicanum).

Ambystoma mexicanum↗
PubMed1995

Identification and expression of a homologue of the murine HoxA5 gene in the Mexican axolotl (Ambystoma mexicanum).

An excellent model for studying heart development in vertebrates is the cardiac non-function lethal mutant (gene c) Mexican axolotl, Ambystoma mexicanum. In order to facilitate our analyses of the mutant system, we have undertaken a search for stage-specific molecular markers during embryonic development of the axolotl. We have concentrated on homeobox genes as suitable candidates for monitoring molecular changes during development. A 270-bp probe encoding a portion of the axolotl homeobox gene Ahox-1 was generated by PCR from a stage-18 axolotl embryonic cDNA library. 32P-labelled PCR-amplified Ahox-1 DNA was used as the probe for screening a lambda AM18 cDNA library using moderately stringent conditions. We isolated six clones and determined their partial nucleotide (nt) sequences. One of the clones, which has very high homology to human, mouse and rat Hox A5 (83 and 99% at the nt and amino-acid levels, respectively, in the homeodomain region), was analyzed further. RT-PCR analyses show that the level of expression of HoxA5 is very low at stage 11 of embryonic development (gastrula). The level of expression reaches maximum at stage 25 (tailbud) and then plateaus at stages 30 and 35 (heartbeat onset). Although the expression of Ahox-1 was also found to start at stage 11, it reaches a maximum level at stage 25 and declines at stage 35. We have also studied, using RT-PCR, the tissue-specific expression of HoxA5 and Ahox-1 in juvenile axolotl.

Ambystoma↗
PubMed1995

Cloning, sequencing and expression of an isoform of cardiac C-protein from the Mexican axolotl (Ambystoma mexicanum).

C-protein, a myosin binding protein, is thought to regulate and stabilize thick filaments during assembly of sarcomeric A-bands. Multiple isoforms of C-protein have been characterized in avian and mammalian systems. We now report the isolation and the nucleic acid sequence of a partial C-protein cDNA clone from an axolotl heart cDNA expression library in lambda gt11. The clone was isolated by screening the library with a heterologous monoclonal anti-C-protein antibody (MF1). Sequence comparison revealed that CPROAxocard1 has an average sequence identity of 62-68% at the nuclei acid and 72-78% at the amino acid levels respectively to human and chicken sequences. We could not detect any significant differences at the levels of expression of the cardiac isoform of C-protein (CPROAxocard1) in normal and non-beating heart tissues of the double-recessive cardiac lethal mutant (c/c) axolotl, Ambystoma mexicanum. This is the first report of a C-protein sequence from an amphibian species.

Ambystoma mexicanum↗
PubMed1995

Immunohistochemical analysis of C-protein isoforms in cardiac and skeletal muscle of the axolotl, Ambystoma mexicanum.

Of the several proteins located within sarcomeric A-bands, C-protein, a myosin binding protein (MyBP) is thought to regulate and stabilize thick filaments during assembly. This paper reports the characterization of C-protein isoforms in juvenile and adult axolotls, Ambystoma mexicanum, by means of immunofluorescent microscopy and Western blot analyses. C-protein and myosin are found specifically within the A-bands, whereas tropomyosin and alpha-actin are detected in the I-bands of axolotl myofibrils. The MF1 antibody prepared against the fast skeletal muscle isoform of chicken C-protein specifically recognizes a cardiac isoform (Axcard1) in juvenile and adult axolotls but does not label axolotl skeletal muscle. The ALD66 antibody, which reacts with the C-protein slow isoform in chicken, local- izes only in skeletal muscle of the axolotl. This slow axolotl isoform (Axslow) displays a heterogeneous distribution in fibers of dorsalis trunci skeletal muscle. The C315 antibody against the chicken C-protein cardiac isoform identifies a second axolotl cardiac isoform (Axcard2), which is present also in axolotl skeletal muscle. No C-protein was detected in smooth muscle of the juvenile and adult axolotl with these antibodies.

Actins↗
PubMed1995

Confocal microscopy of a newly identified protein associated with heart development in the Mexican axolotl.

Recessive mutant gene c for "'cardiac nonfunction" in the mexican axolotl, Ambystoma mexicanum, results in a failure of affected embryos to develop contracting hearts. Mutant embryos survive approximately 4 weeks after fertilization, but eventually die from a lack of circulation. Morphological studies show that mutant hearts lack organized sarcomeric myofibrils. This abnormality can be corrected by co-culturing early mutant hearts with normal anterior endoderm/mesoderm tissues, by culturing them in a medium "conditioned" by this normal tissue, or by RNA isolated from normal endoderm/mesoderm. Additionally, RNA isolated from normal anterior endoderm/mesoderm conditioned medium corrects the mutant hearts in a dose-dependent manner. A cDNA library is constructed using this RNA. On the basis of sequence analyses on this cDNA library, it was estimated that 56% of the total RNA present in the conditioned medium is rRNA, while 44% is nonribosomal RNA. One of the nonribosomal RNAs that showed no significant homology with other known sequences in the Genebank was examined further. An RT-PCR analysis showed that this RNA (designated "N1") is expressed in juvenile skeletal muscle, brain, and heart in significant amounts, less in the lung and not at all in the liver tissue. Affinity-purified polyclonal antipeptide antibodies were produced against the most antigenic portion of the polypeptide which was deduced from this RNA. Western blot analyses of adult heart homogenates, using these antibodies, showed a specific doublet staining at 67 kDa and 65 kDa. These doublets were purified and analyzed for their amino acid composition which showed that both bands most likely belong to the same protein. The N1-protein was further investigated to determine its localization in normal isolated hearts at embryonic stages 35, 38, and 41 and on cross-sections through the heart regions of whole normal embryos at stages 16, 33-34, 37-38, and 41-42 using immunohistochemical techniques and confocal microscopy. In addition, mutant embryos at stage 37-38 were studied for the presence and distribution of the N1-protein on cross-sections through their heart regions. The N1-protein staining was significantly reduced in mutant hearts when compared to normal.

Ambystoma mexicanum↗
PubMed1995

In vivo protein synthesis in developing hearts of normal and cardiac mutant axolotls (Ambystoma mexicanum).

Recessive mutant gene c in axolotls causes a failure of the hearts of affected embryos to function. The mutant hearts (c/c) lack organized sarcomeric myofibrils. The present study was undertaken to determine the overall pattern of in vivo protein synthesis and subsequent accumulation of the newly synthesized proteins for a 24-h period in normal (+/+ or +/c) and cardiac mutant (c/c) axolotl hearts at various stages of development. Additionally, selected cytoskeletal/myofibrillar proteins were analyzed in detail for their synthesis during heart development. For such analyses, the hearts were radiolabeled with 35S-methionine for 24 h and subjected to SDS-PAGE and autoradiography. Quantitative densitometric analyses of the bands show that, even though the overall protein pattern is similar in normal and mutant heart tissues, a general reduction in the synthesis of the proteins in mutant hearts is observed even at the earlier stages of development (stages 35-36 and 37-38). Synthesis and accumulation of most of the proteins is significantly inhibited in mutant hearts at later stages (stages 41-42). Tropomyosin synthesis in mutant hearts is at a level of only 72.6% of that in normal embryonic hearts at stage 35. The synthesis and the accumulation of the tropomyosin in mutant hearts decreases further with increasing age until the protein essentially stops being synthesized by stage 41.

Ambystoma↗
PubMed1994

Molecular cloning, sequencing and expression of an isoform of cardiac alpha-tropomyosin from the Mexican axolotl (Ambystoma mexicanum).

The cDNA for alpha-tropomyosin (TM) was cloned by the polymerase chain reaction (PCR) from a lambda gt11 library constructed with mRNA from juvenile axolotl heart tissues. Subsequently, the nucleotide sequence of the cDNA was determined. This is the first reported cDNA for axolotl alpha-tropomyosin. Comparative analyses of the deduced amino acid sequence of this cDNA with Xenopus skeletal muscle alpha-tropomyosin sequences indicate that the axolotl heart cDNA has 93% and 96% homology in the regions of amino acids 39-80 (exon 2b) and 258-284 (exon 9a), respectively. However, there is about 86.55% homology at the nucleic acid level (coding region) and 97.5% homology at the amino acid level with that of Xenopus skeletal muscle alpha-tropomyosin cDNA. Northern blot analyses with polyA+ RNA from juvenile heart suggest the presence of at least two different transcripts for alpha-tropomyosin in axolotl heart. The results of 3'-RACE concur with those of northern blot analyses.

Ambystoma mexicanum↗
PubMed1994

Serological and nucleic acid analyses for HIV and HTLV infection on archival human plasma samples from Zaire.

In order to better understand the genomic diversity and molecular phylogeny of the human retroviruses, the plasmas from 250 Zairean patients collected in 1969 were tested for antibodies to human T-cell lymphoma and human immunodeficiency viruses (HTLV or HIV) using ELISA and confirmatory Western blots and for viral nucleic acids by reverse transcriptase-directed PCR (RT-PCR). Interestingly, none of the patients was confirmed positive for HIV, even though this region is now endemic for HIV-1. However, 74 (30%) and 3 (1%) of the samples were positive for antibodies to HTLV-I and II, respectively. Forty-four of 74 (59%) Western blot-positive Zairean samples were RT-PCR positive for HTLV-I, while 1 of 3 (33%) of HTLV-II-seropositive samples was RT-PCR positive. On the contrary, none of the Western blot-negative or indeterminate samples were RT-PCR positive for either HTLV-I or HTLV-II. We have cloned and sequenced 140 bp of the pol gene flanked by SK110/SK111 from 8 HTLV-I- and 1 HTLV-II-positive archival samples from Zaire. The HTLV-I isolates from Zaire cluster together as a phylogenetic group, diverging from the prototype Japanese HTLV-I (ATK) by a range of 1.4 to 3.6%. Their close homology to some African STLV-I isolates suggests relatively recent interspecies transmission. The Zairean HTLV-II isolate is closely grouped with the HTLV-II substrain of isolates found in Paleo-Amerindians of the New World, making it unlikely that it represents an endemic African strain.

Antibodies, Viral↗
PubMed1994

Herpes thymidine kinase mutants with altered catalytic efficiencies obtained by random sequence selection.

We have obtained 190 active Herpes simplex virus type 1 thymidine kinase mutants by substituting a 33 nucleotide sequence with 20% degeneracy for a portion of the nucleotide sequence that encodes the putative thymidine binding site [K.M. Munir, D.C. French, D.K. Dube and L.A. Loeb (1992) J. Biol. Chem., 167, 6584-6589]. In order to classify these mutants with respect to thymidine kinase activity we determined the ability of Escherichia coli harboring these mutants to form colonies in the presence of varying concentrations of thymidine. Escherichia coli harboring one of the mutant enzymes was able to form colonies at a concentration of thymidine lower than did the wild type. It was able to phosphorylate thymidine more rapidly than the wild type both in vivo and in vitro. The increased thymidine kinase activity was manifested by (i) a 42% enhanced uptake of [methyl-3H]thymidine into E. coli, (ii) a 2.4 times higher rate of [methyl-3H]thymidine incorporation into acid-insoluble material and (iii) a 5-fold increase in the kcat of the purified enzyme compared to the wild type. Herpes thymidine kinase purified from other mutants that formed colonies at higher thymidine concentrations than that of the wild type exhibited a decrease in kcat. The kcat of one of these mutant thymidine kinases was 10(-4) of that of the wild type enzyme. This study demonstrates that a spectrum of mutant enzymes with different catalytic properties can be obtained by selection from a plasmid with random sequence substitutions and this can be done in the absence of rational protein design.

Amino Acid Sequence↗
PubMed1993

Selection of new biologically active molecules from random nucleotide sequences.

Genetic diversity can be achieved in vitro by inserting random nucleotide (nt) sequences into cloned genes. In the case of enzymes, subsequent genetic complementation can be used to select for new mutants that exhibit different substrate specificities, altered catalytic activities, or altered temperature sensitivities. Using this technique, one can also analyze the contribution of different amino acid residues to the structure and function of enzyme. Selecting biologically active DNA sequences from large random populations provides a new method for identifying nt sequences with unique functions. Analogous random sequence selection techniques have been applied to determine the consensus sequence of the Escherichia coli promoters, DNA and RNA sequences that bind specific protein(s), DNA regulatory sequences, ribozyme(s) and ligand-specific RNA(s). In this manuscript, we will consider recent data obtained in our laboratory as a result of inserting random sequences into the putative nucleoside-binding site of herpes simplex virus type 1 (HSV-1) thymidine kinase (TK). We have obtained over 2000 new mutant HSV-1 TKs, some of which are stable at higher temperatures or have altered substrate specificity and/or catalytic rates when compared to those of the wild-type enzyme.

Base Sequence↗
PubMed1993

Sequence analysis of an immunogenic and neutralizing domain of the human T-cell lymphoma/leukemia virus type I gp46 surface membrane protein among various primate T-cell lymphoma/leukemia virus isolates including those from a patient with both HTLV-I-associated myelopathy and adult T-cell leukemia.

Human T-cell lymphoma/leukemia virus type I (HTLV-I) causes adult T-cell leukemia/lymphoma and HTLV-I-associated myelopathy. Specific regions within the outer envelope proteins of other retroviruses, e.g., human immunodeficiency virus type 1, are highly immunogenic and, because of the selective pressure of the host immune system, quite variable. Mutations in the external envelope protein gene of murine retroviruses and human immunodeficiency virus type 1 influence cellular tropism and disease pathogenesis. By contrast, no disease-specific viral mutations have been identified in HTLV-I-infected patients. However, all isolates studied thus far have originated from leukemic cell lines, peripheral blood mononuclear cells, or cerebrospinal fluid lymphocytes from patients with HTLV-I-associated myelopathy and adult T-cell leukemia/lymphoma and, therefore, may not truly reflect tissue-associated variation. The midregion of the HTLV-I gp46 external envelope glycoprotein (amino acids 190-209) induces an antibody response in 90% of infected individuals, and a hexapeptide in this region (amino acids 191-196) elicits antibodies in rabbits which inhibit syncytia formation and infection of target lymphocytes. Because of the above, we expected the neutralizing domain of the gp46 env gene of HTLV-I to possess disease or organ-associated mutations selected by the infected host's immune system. Hence, we amplified, cloned, and sequenced HTLV-I DNA directly from in vivo central nervous system, spleen, and kidney specimens, and a leukemic cell line from a patient (M. J.) with both HTLV-I-associated myelopathy and adult T-cell leukemia/lymphoma to discern the possibility of tissue- and/or disease-specific variants. In addition, we sequenced several HTLV-I isolates from different regions of the world, including Papua New Guinea, Bellona, and Liberia, and compared them to other previously published HTLV-I and related retroviral sequences. The 239-base pair sequence corresponding to amino acids 178 to 256 in gp46 displayed minor tissue-specific variation in clones derived from central nervous system tissues from patient M. J., but overall was highly conserved at both the DNA and amino acid levels. Variation was observed in this region among the other HTLV-I, simian T-cell lymphoma virus type I, and HTLV-II isolates in a pattern that was consistent with their known phylogenetic relationship. No consistent disease-related changes were observed.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1993

Spastic ataxia associated with human T-cell lymphotropic virus type II infection.

Human T-cell lymphotropic virus type one (HTLV-1) is associated with tropical spastic paraparesis or HTLV-I--associated myelopathy. We report 2 women with a spastic ataxic illness similar to HTLV-I--associated myelopathy infected solely with HTLV-II. Identification of HTLV-II infection was made serologically, by polymerase chain reaction, and by viral culture (in 1 woman). One woman, treated with 200 mg of danazol orally, three times daily, had pronounced improvement in ambulation, nocturnal spasticity, and nighttime urinary frequency. It appears that infection with HTLV-II may cause an illness similar to HTLV-I--associated myelopathy, but distinguished by the presence of ataxia.

Antibodies, Monoclonal↗
PubMed1993

Sequence and phylogenetic analyses of a new STLV-I from a naturally infected tantalus monkey from Central Africa.

Simian T-cell leukemia virus (STLV-I) is an oncovirus highly related to human T-cell leukemia virus type I (HTLV-I). To further examine the extent of variability, dissemination patterns, phylogeny, and evolution of these viruses, we analyzed a new STLV-I variant from a naturally infected Cercopithecus aethiops var. tantalus from the Central African Republic. Sequence analyses of its LTR, gag, pol, env, and pX (OrfII) genes indicated that this isolate, STLV-I (Tan 90), is 6% divergent from the prototype HTLV-I (ATK) and is the most divergent African STLV-I characterized to date. Our phylogenetic data indicate that southeast Asian and African STLV-I and HTLV-I strains segregated from each other thousands of years ago and that Japanese HTLV-I strains represent a relatively recent introduction of African or New World isolates. The data also indicate that interspecies transmission occurred several times on different continents over prolonged periods of time.

Africa, Central↗
PubMed1993

High rate of infection with the human T-cell leukemia retrovirus type II in four Indian populations of Argentina.

Sera from 215 non-drug-injecting Toba and Mataco-Mataguayo pure Indians belonging to four communities in northern Argentina were examined using assays that allow differentiation between reactivities due to type-specific antigens of the human T-cell leukemia/lymphoma virus (HTLV). Three of these populations have very little contact with non-Indian groups and reside in remote, isolated areas. HTLV-II type-specific seroreactivity was present in 24 (13.7%) of the 175 Indians older than 13 years of age and in none of the 40 who were of younger ages. None of the Indians had antibodies reacting with HTLV-I type-specific antigen. Seroreactivity was more prevalent and appeared at younger ages in females than in males. The majority of the HTLV-II-seropositive Indians belonged to the more isolated communities. The seroprevalences among the Tobas and Mataco-Mataguayo Indians were comparable. With the exception of a Toba who was positive in a test for Treponema pallidum, no serological evidence of sexually transmitted infections with this spirochete, hepatitis B virus, hepatitis C virus, and human immunodeficiency virus was found among the Indians tested. None of the 55 non-Indian people tested in the region showed HTLV-II type-specific seroreactivity. PCR analysis of DNA isolated from peripheral blood lymphocytes of seropositive Indians confirmed that the virus present in these populations is HTLV-II. Sequence analysis of PCR-amplified genomic segments showed that the virus belongs to the HTLV-II subtype which has been found to be endemic in other Paleo-American Indians.

Adolescent↗
PubMed1993

Genetic heterogeneity in human T-cell leukemia/lymphoma virus type II.

DNA from the peripheral blood mononuclear cells of 17 different individuals infected with human T-cell lymphoma/leukemia virus type II (HTLV-II) was successfully amplified by the polymerase chain reaction (PCR) with the primer pair SK110/SK111. This primer pair is conserved among the pol genes of all primate T-cell lymphoma viruses (PTLV) and flanks a 140-bp fragment of DNA which, when used in comparative analyses, reflects the relative degree of diversity among PTLV genomes. Cloning, sequencing, and phylogenetic comparisons of these amplified 140-bp pol fragments indicated that there are at least two distinct genetic substrains of HTLV-II in the Western Hemisphere. These data were confirmed for selected isolates by performing PCR, cloning, and sequencing with to 10 additional primer pair-probe sets specific for different regions throughout the PTLV genome. HTLV-II isolates from Seminole, Guaymi, and Tobas Indians belong in the new substrain of HTLV-II, while the prototype MoT isolate defines the original substrain. There was greater diversity among HTLV-II New World strains than among HTLV-I New World strains. In fact, the heterogeneity among HTLV-II strains from the Western Hemisphere was similar to that observed in HTLV-I and simian T-cell lymphoma/leukemia virus type I isolates from around the world, including Japan, Africa, and Papua New Guinea. Given these geographic and anthropological considerations and assuming similar mutation rates and selective forces among the PTLV, these data suggest either that HTLV-II has existed for a long time in the indigenous Amerindian population or that HTLV-II isolates introduced into the New World were more heterogeneous than the HTLV-I strains introduced into the New World.

Amino Acid Sequence↗
PubMed1993

RNA from normal anterior endoderm/mesoderm-conditioned medium stimulates myofibrillogenesis in developing mutant axolotl hearts.

In the axolotl, Ambystoma mexicanum, a recessive cardiac lethal mutation causes an incomplete differentiation of the myocardium. Mutant hearts do not contain sarcomeric myofibrils nor do they beat. We have previously shown that normal anterior endoderm, medium conditioned by endoderm, or total RNA extracted from endoderm stimulates differentiation of mutant hearts in culture as indicated by the presence of organized myofibrils and rhythmic contractions of the "rescued" mutant heart tube. In this study, to get a more highly purified sample of the "active" molecule, RNA extracted from endoderm-conditioned medium and was assayed for its ability to promote myofibrillogenesis in mutant hearts. Mutant heart mesoderm responded to conditioned-medium RNA in a dose-dependent manner. Proteinase K treatment of the RNA did not affect inductive activity, while digestion with RNase A completely abolished the ability to rescue mutant hearts. Confocal laser scanning microscopy of immunostained, organ-cultured hearts revealed that mutant hearts contain reduced amounts of the sarcomeric protein tropomyosin in an amorphous distribution, whereas normal and corrected mutant hearts contain tropomyosin primarily in organized myofibrils.

Ambystoma↗