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S Adkins

Publications and source records attributed to S Adkins.

At least 19 recordsLinked to original sources
PubMed2004

Determination of complete nucleotide sequence of Hibiscus latent Singapore virus: evidence for the presence of an internal poly(A) tract.

We have sequenced the complete genome of a hibiscus-infecting tobamovirus, Hibiscus latent Singapore virus (HLSV). The experimental host range of HLSV is similar to that of another distinct species of hibiscus infecting tobamovirus, Hibiscus latent Fort Pierce virus (HLFPV). The genomic structure of HLSV is similar to other tobamoviruses in general. It consists of a 5' untranslated region (UTR), followed by ORFs encoding for a 128 kDa protein and a 186 kDa readthrough protein, a 30 kDa movement protein (MP), 18 kDa coat protein (CP) and a 3' UTR. The unique feature of HLSV is the presence of a poly(A) tract within its 3' UTR. In our previous work, we have reported MP and CP sequences of HLSV and its phylogenetic analysis. Here we report the complete nucleotide sequence of HLSV, phylogenetic analysis of the nucleotide and amino acid sequences of 128/186 kDa ORFs and the presence of a uniquely located poly(A) tract within the 3' UTR.

3' Untranslated Regions↗
PubMed2000

Melatonin suppression by light in euthymic bipolar and unipolar patients.

BACKGROUND: Previous studies have suggested that bipolar patients are supersensitive to light suppression of melatonin and that this may be a trait marker for genetic vulnerability. The present study was an attempt to replicate and extend this observation. Propranolol hydrochloride effects were compared with light effects because of the documented influence of beta-adrenergic receptors on melatonin production. Nighttime levels of corticotropin and cortisol were also examined as potential trait vulnerability markers. METHODS: Melatonin levels in euthymic bipolar patients (n= 29) were tested before and after 500-lux light was administered between 2 and 4 AM and on a separate night in the dark. Results were compared with those of a group of patients with unipolar depression (n= 24) and with those of a group of non-psychiatrically ill control subjects (n= 50). Lithium effects and propranolol effects were tested in subgroups. RESULTS: No group differences were seen in light suppression among bipolar patients, unipolar patients, and controls; an analysis of the whole group did not reveal differences in propranolol effect, differences in corticotropin or cortisol levels, or evidence for a lithium effect. However, patients with bipolar I affective disorder showed the following: (1) significantly lower melatonin levels on the light night, at baseline and following light exposure; and (2) a later peak time for melatonin on the dark night. CONCLUSIONS: The general hypothesis of increased light sensitivity in bipolar patients was not supported. However, melatonin secretion abnormalities were confirmed in the subgroup with bipolar I disorder. Further assessments of circadian rhythm disruption as a vulnerability marker in bipolar illness are indicated.

Adrenocorticotropic Hormone↗
PubMed1998

Subgenomic RNA promoters dictate the mode of recognition by bromoviral RNA-dependent RNA polymerases.

Both the brome mosaic virus (BMV) and cowpea chlorotic mottle virus (CCMV) RNA-dependent RNA polymerases (RdRps) were found to recognize the BMV core subgenomic promoter in the same manner, requiring specific functional groups at positions -17, -14, -13, and -11 relative to the subgenomic initiation site (+1). For CCMV subgenomic RNA synthesis, both RdRps required the same nucleotides and four additional nucleotides at positions -20, -16, -15, and -10. The -20 nucleotide is partially responsible for the differential mode of recognition of the two promoters. These data provide evidence that the RNA can induce RdRps to alter the mode of promoter recognition.

Bromovirus↗
PubMed1998

Fine genetic and comparative mapping of the deafness mutation Ames waltzer on mouse chromosome 10.

The Ames waltzer (av) mouse mutant is an autosomal recessive deafness mutation on mouse Chromosome 10. Previously, av had not been mapped relative to molecular markers. We have performed an intersubspecific backcross with Mus musculus castaneus and mapped microsatellite markers in this cross. Toothpick PCR on previously frozen tissue samples from offspring was used as an efficient strategy to screen a large number of animals quickly. In 1258 progeny tested we found three recombinants for each of the flanking markers D10Mit199 and D10Mit64. In addition, nine different genes (Ank3, Bcr, Gnaz, Tfam, Mif, Mmp11, Dcoh, Pyp, and Gstt2) were mapped and eliminated genetically as candidate genes for av. av had been discussed as a potential mouse model for the human deafness loci Usher syndrome type ID (USH1D) and DFNB12. Comparative mapping shows that av maps near an evolutionary break point and makes it unlikely that those loci are human homologues of av. A human homologue of av is predicted to lie either on 22q11.2 or on 10q21. The orientation of conserved linkage groups between these two human chromosomal regions relative to mouse Chromosome 10 was determined.

Animals↗
PubMed1998

Mechanistic analysis of RNA synthesis by RNA-dependent RNA polymerase from two promoters reveals similarities to DNA-dependent RNA polymerase.

The brome mosaic virus (BMV) RNA-dependent RNA polymerase (RdRp) directs template-specific synthesis of (-)-strand genomic and (+)-strand subgenomic RNAs in vitro. Although the requirements for (-)-strand RNA synthesis have been characterized previously, the mechanism of subgenomic RNA synthesis has not. Mutational analysis of the subgenomic promoter revealed that the +1 cytidylate and the +2 adenylate are important for RNA synthesis. Unlike (-)-strand RNA synthesis, which required only a high GTP concentration, subgenomic RNA synthesis required high concentrations of both GTP and UTP. Phylogenetic analysis of the sequences surrounding the initiation sites for subgenomic and genomic (+)-strand RNA synthesis in representative members of the alphavirus-like superfamily revealed that the +1 and +2 positions are highly conserved as a pyrimidine-adenylate. GDP and dinucleotide primers were able to more efficiently stimulate (-)-strand synthesis than subgenomic synthesis under conditions of limiting GTP. Oligonucleotide products of 6-, 7-, and 9-nt were synthesized and released by RdRp in 3-20-fold molar excess to full-length subgenomic RNA. Termination of RNA synthesis by RdRp was not induced by template sequence alone. Our characterization of the stepwise mechanism of subgenomic and (-)-strand RNA synthesis by RdRp permits comparisons to the mechanism of DNA-dependent RNA synthesis.

Alphavirus↗
PubMed1997

Sequence-specific recognition of a subgenomic RNA promoter by a viral RNA polymerase.

RNA templates of 33 nucleotides containing the brome mosaic virus (BMV) core subgenomic promoter were used to determine the promoter elements recognized by the BMV RNA-dependent RNA polymerase (RdRp) to initiate RNA synthesis. Nucleotides at positions -17, -14, -13, and -11 relative to the subgenomic initiation site must be maintained for interaction with the RdRp. Changes to every other nucleotide at these four positions allow predictions for the base-specific functional groups required for RdRp recognition. RdRp contact of the nucleotide at position -17 was suggested with a template competition assay. Comparison of the BMV subgenomic promoter to those from other plant and animal alphaviruses shows a remarkable degree of conservation of the nucleotides required for BMV subgenomic RNA synthesis. We show that the RdRp of the plant-infecting BMV is capable of accurately, albeit inefficiently, initiating RNA synthesis from the subgenomic promoter of the animal-infecting Semliki Forest virus. The sequence-specific recognition of RNA by the BMV RdRp is analogous to the recognition of DNA promoters by DNA-dependent RNA polymerases.

Animals↗
PubMed1997

Novel cystatin B mutation and diagnostic PCR assay in an Unverricht-Lundborg progressive myoclonus epilepsy patient.

Two mutations in the cystatin B gene, a 3' splice mutation and a stop codon mutation, were previously found in patients with progressive myoclonus epilepsy of Unverricht-Lundborg type [Pennacchio et al. (1996): Science 271:1731-1734]. We present here a new mutation 2404deltaTC: a 2-bp deletion within the third exon of the cystatin B gene in an Unverricht-Lundborg patient. This mutation results in a frameshift and consequently premature termination of protein synthesis. Complete sequencing of the coding region and splice junctions of the cystatin B gene showed that neither of the two previously known mutations was present in this patient. The level of cystatin B mRNA in an immortalized cell line was found to be decreased, as had been reported for other Unverricht-Lundborg patients. The new mutation further supports the argument that defects in the cystatin B gene cause the Unverricht-Lundborg form of progressive myoclonus epilepsy. We describe a simple PCR method which can detect the 2404deltaTC deletion. This assay, together with previously described PCR assays for the other two known mutations, should prove useful in confirming clinically difficult diagnoses of Unverricht-Lundborg disease.

Amino Acid Sequence↗
PubMed1997

Minimal templates directing accurate initiation of subgenomic RNA synthesis in vitro by the brome mosaic virus RNA-dependent RNA polymerase.

Short regions of (-)-strand brome mosaic virus (BMV) RNA3, proscripts, were shown to direct accurate in vitro synthesis of (+)-strand subgenomic RNA by the BMV RNA-dependent RNA polymerase (RdRp), facilitating characterization of the sequences and/or structures directing subgenomic RNA synthesis. Proscripts retaining fewer than 8-nt of an 18-nt polyuridylate tract located just upstream of the core promoter sequence (French R, Ahlquist P, 1988, J Virol 62:2411-2420; Marsh LE, Dreher TW, Hall TC, 1988, Nucleic Acids Res 16:981-995) directed dramatically less synthesis of 26-nt or longer products. Original levels of RNA synthesis were not restored by replacement of the 3' polyuridylate tract with polyadenylate, polycytidylate, or polyguanylate tracts, or by movement of the polyuridylate tract to the 5' end of the proscript. The polyuridylate tract presumably binds some component(s) required for RdRp activity because the addition of poly(U) [but not poly(C)] RNA to RdRp reactions decreased RNA synthesis significantly. Quite surprisingly, deletions of the polyuridylate tract in proscripts directing synthesis of 24-nt or shorter products had little or no detrimental effect on subgenomic RNA synthesis, correlated with their inability to form a computer-predicted stem-loop present in longer proscripts requiring the polyuridylate tract. Successive 3' and 5' deletions demonstrated that the minimal elements required for accurate initiation of subgenomic RNA synthesis are within a proscript of 22-nt.

Bromovirus↗
PubMed1996

Initiation of (-)-strand RNA synthesis catalyzed by the BMV RNA-dependent RNA polymerase: synthesis of oligonucleotides.

RNA replication, a process of fundamental importance for pathogenesis by many viruses, remains poorly understood at the mechanistic level because relatively few of the responsible enzymes have been purified and characterized biochemically. Partially purified RNA-dependent RNA polymerase (RdRp) from brome mosaic virus (BMV)-infected barley leaves is able to synthesize (-)-strand RNAs from input (+)-strand templates. In resolving RdRp products generated during (-)-strand BMV RNA synthesis, we found that an RNA of eight nucleotides was generated at approximately 10-fold molar excess to the full-length (-)-strand RNA. Production of the 8-mer was dependent upon and specific to BMV RNA templates. Furthermore, inhibitors of full-length (-)-strand RNA synthesis by RdRp also affected the production of the 8-mer. Analysis of the sequence of the 8-mer suggests that it is initiated at the authentic initiation site on the BMV RNA template, consistent with the possibility that the 8-mer is an abortive initiation product of RNA synthesis by RdRp in vitro. Addition of heparin or Mn2+ differentially affected production of the 8-mer and full-length (-)-strand RNA, as did some nucleotide changes near the site of RNA initiation. These studies further define the initiation process of (-)-strand RNA synthesis.

Bromovirus↗
PubMed1996

Visualization of DNA in agarose gels as migrating colored bands: applications for preparative gels and educational demonstrations.

Visualization of DNA in electrophoretic gels typically requires UV radiation and the fluorescent dye ethidium bromide. Alternatively, we report here that by inclusion of visible dyes in standard agarose gels, DNA bands are observable in ambient light as they are separating. Such bands can be directly recovered from gels (approximately 50% yield) and used in standard enzymatic reactions (ligation, endonucleolytic cleavage, random labeling, PCR, and cycle-sequencing) without purification. Of 14 common commercially available stains that could visualize fractionating DNA, Nile blue was chosen for more extensive analysis as it gave the sharpest and most persistent bands and is not known to be toxic. Bands containing greater than 40 ng DNA could be detected by direct visual inspection of gels during electrophoresis. Drying the gels increased sensitivity to 4 ng. We describe relevant molecular features of these dyes and detail simple assays that may be employed to find other useful, and perhaps superior, dyes. This method also lends itself to situations in which easy visualization and convenience of DNA electrophoresis are important, such as classroom demonstrations.

Blotting, Southern↗
PubMed1995

Reconsideration of the catalytic center and mechanism of mammalian paraoxonase/arylesterase.

For three decades, mammalian paraoxonase (A-esterase, aromatic esterase, arylesterase; PON, EC 3.1.8.1) has been thought to be a cysteine esterase demonstrating structural and mechanistic homologies with the serine esterases (cholinesterases and carboxyesterases). Human, mouse, and rabbit PONs each contain only three cysteine residues, and their positions within PON have been conserved. In purified human PON, residues Cys-41 and Cys-352 form an intramolecular disulfide bond and neither could function as an active-center cysteine. Highly purified, enzymatically active PON contains a single titratable sulfhydryl group. Thus, Cys-283 is the only probable candidate for an active-center cysteine. Through site-directed mutagenesis of the human cDNA, Cys-283 was replaced with either serine (C283S) or alanine (C283A). The expressed C283 (wild-type) enzyme was inactivated by para-hydroxymercuribenzoate, but the C283S and C283A mutant enzymes were not inactivated. C283A and C283S mutant enzymes retained both paraoxonase and arylesterase activities, and the Km values for paraoxon and phenyl acetate were similar to those of the wild type. Clearly, residue Cys-283 is free in active PON, but a free sulfhydryl group is not required for either paraoxonase or arylesterase activities. Consequently, it is necessary to examine other models for the active-site structure and catalytic mechanism of PON.

Amino Acid Sequence↗
PubMed1995

An RNA-dependent RNA polymerase activity associated with virions of tomato spotted wilt virus, a plant- and insect-infecting bunyavirus.

An RNA-dependent RNA polymerase activity was found associated with virions of tomato spotted wilt virus (TSWV), a plant- and insect-infecting member of the family Bunyaviridae. Radiolabeled nucleoside triphosphates were incorporated into trichloroacetic acid-precipitable products by detergent-disrupted, purified TSWV virions. Incorporation was reduced to near-background levels when RNase was present in the reaction mixture. The predominantly double-stranded RNA products were RNase-resistant at high but not low salt concentrations. The activity required manganese and was independent of a DNA template. Discrete products of approximately 3.0 kb and heterogeneous smaller products were synthesized that hybridized to purified TSWV RNA and transcripts of cDNA clones encompassing parts of each of the three genomic RNAs. The predominant products were viral sense although significant amounts of viral complementary sense S RNA products were also synthesized.

Datura stramonium↗
PubMed1993

Recombinant human butyrylcholinesterase G390V, the fluoride-2 variant, expressed in Chinese hamster ovary cells, is a low affinity variant.

Kinetics of recombinant fluoride-2 variant of human butyrylcholinesterase (Gly390 Val) secreted by Chinese hamster ovary cells were compared to recombinant usual and to usual butyrylcholinesterase purified from human plasma. The usual and fluoride-2 variant were indistinguishable with regard to hydrolysis of benzoylcholine (Km = 5 microM), neutral esters, and at high concentrations of acetylthiocholine, propionylthiocholine, and butyrylthiocholine. However, at low substrate concentrations Km values for acetylthiocholine and succinyldithiocholine were 2-6-fold higher for the fluoride-2 variant. pH rate profiles revealed small differences in pKa that could be attributed to changes in the active site histidine environment. On the other hand, Arrhenius plot analysis of o-nitrophenylbutyrate hydrolysis at pH 7.5 showed no difference in activation energy between fluoride-2 and usual butyrylcholinesterases. Both exhibited an anomalous temperature dependence with a wavelike change in activation energy around 18 degrees C. Affinity of the fluoride-2 variant for sodium fluoride, tacrine, dibucaine, amodiaquin, and succinyldicholine was lower than for usual enzyme. Apparent Ki for succinyldicholine was 125 microM for the fluoride-2 variant and 20 microM for the usual enzyme. Organophosphate inhibition showed equivalent reactivity, indicating that the point mutation altered only the binding properties of the variant. Thus, Km and Ki changes explain the succinyldicholine sensitivity of people carrying the fluoride-2 variant.

Amino Acid Sequence↗
PubMed1993

Studies on human serum paraoxonase/arylesterase.

The complete amino acid sequence of human serum paraoxonase/arylesterase and the DNA sequence coding for that protein have recently been determined in two independent laboratories. There is now considerable evidence that the esterase exists in two genetically determined allozymic forms, and these A and B allozymes possess both paraoxonase and arylesterase activities. The B-type esterase has relatively higher paraoxonase activity and is stimulated to a greater degree by 1 M NaCl than the A allozyme. The structural basis for the distinctive isozymic properties is a single nucleotide base at position 572. Codon 191 is CAA (for glutamine) in the A-type esterase, and CGA (for arginine) in the B-type enzyme. There is a second polymorphic site which affects amino acid 54; this can be either methionine or leucine, but these alternatives have not been found to affect either the level or the quality of the allozymes. Purified A or B-type esterases are stimulated by the addition of phosphatidylcholine. The latter addition increases the maximum velocity rate, but does not alter the Km of the reaction with either paraoxon or phenylacetate. In serum, the esterase is tightly bound to the high density lipoproteins, particularly apo A-1, but the importance of this association as far as the stability and catalytic properties of the esterase is not clear, and still under study. No physiological role of the esterase has been established, but its ability to hydrolyze several potent organophosphates may be of some significance in protecting against organophosphate toxicity.

Amino Acid Sequence↗