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Holtz C, Smith TM, Winters FD. Childhood obesity. THE JOURNAL OF THE AMERICAN OSTEOPATHIC ASSOCIATION 1999; 99:366-71. [PMID: 10441935 DOI: 10.7556/jaoa.1999.99.7.366] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Childhood obesity has become one of the more alarming nutritional problems plaguing the American population, with estimates as high as 25% of all children being obese. Aside from obesity's associated risks, there are psychosocial and emotional burdens carried by obese children as well. Clinicians are encountering many of these children in their clinics everyday for other reasons and yet are failing to address the issue of obesity. The problem is not so much that physicians are not recognizing it, but rather that they are ignoring it, especially if the parent or child is unaware that there is a problem. Unfortunately, much controversy exists regarding the treatment of childhood obesity. This article attempts to sort through the myriad issues surrounding childhood obesity and to dispel some of the rumors and myths surrounding this subject.
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Kirley TL, Gerber LK, Smith TM. Expression and characterization of chicken muscle ecto-ATPase in mammalian COS cells. IUBMB Life 1999; 48:67-72. [PMID: 10791917 DOI: 10.1080/713803482] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Chicken muscle ecto-ATPase has unusual enzyme kinetics and properties not found in many other E-type ATPases. To determine whether the unique properties of the chicken ecto-ATPase are inherent in the protein sequence and not mediated by some unique property of the chicken system, we have spliced together two partial cDNAs encoding the ecto-ATPase. The enzymatic properties of the COS (green monkey kidney) cell-expressed protein are indistinguishable from the purified chicken gizzard ecto-ATPase, including a 2- to 3-fold stimulation of membrane-bound activity by crosslinking and lectins, properties not shared by most other E-type ATPases. The expressed enzyme is specific for nucleotide triphosphates (ATPase:ADPase hydrolysis ratio of 26:1) and is inhibited by Cibacron Blue (IC50 = 10 microM). The active, expressed enzyme can be affinity-purified with Cibacron Blue, is relatively resistant to deglycosylation, and is less stable than other E-type ATPases. Expression in the presence of tunicamycin resulted in an inactive, unfolded enzyme.
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Smith TM, Lewis Carl SA, Kirley TL. Mutagenesis of two conserved tryptophan residues of the E-type ATPases: inactivation and conversion of an ecto-apyrase to an ecto-NTPase. Biochemistry 1999; 38:5849-57. [PMID: 10231536 DOI: 10.1021/bi990171k] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A human brain E-type ATPase (HB6 ecto-apyrase) was subjected to site-directed mutagenesis to assess the functional significance of two highly conserved tryptophan residues (Trp 187 and Trp 459), the only two tryptophans conserved in nearly all E-type ATPases. Mutation of tryptophan 187 to alanine yielded a poorly expressed ecto-apyrase completely devoid of nucleotidase activity. Immunolocalization of the W187A mutant in mammalian COS cells showed a cellular distribution clearly different from that of the wild-type enzyme, with the majority of the immunoreactivity concentrated in the interior of the cell. Unlike the wild-type enzyme, this mutant did not bind the nucleotide analogue Cibacron Blue and was sensitive to proteolytic digestion by chymotrypsin. These results suggest alteration of the tertiary structure, causing the enzyme to be improperly folded and retained within the cell. In contrast, mutation of tryptophan 459 to alanine resulted in an ecto-apyrase with enhanced NTPase activity, but diminished NDPase activity. Immunolocalization of this active mutant ecto-apyrase revealed a cellular pattern similar to that of the wild-type enzyme, distributed along the cell periphery and in cell processes. Coupling this active W459A mutation to a previously described mutation (D219E) resulted in an enzyme which preferentially hydrolyzes nucleoside triphosphates over diphosphates. The D219E/W459A double mutant had an ATPase:ADPase ratio of 11:1 and a UTPase:UDPase ratio of 148:1. In addition, the double mutant is substantially less sensitive to inhibition by azide, a more potent inhibitor of ecto-apyrases than ecto-ATPases. Thus, mutation of only two amino acids of an E-type ATPase essentially converts an ecto-apyrase to an ecto-NTPase.
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Smith TM, Kirley TL. Glycosylation is essential for functional expression of a human brain ecto-apyrase. Biochemistry 1999; 38:1509-16. [PMID: 9931016 DOI: 10.1021/bi9821768] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of N-linked glycosylation for the function and oligomerization of an E-type ATPase was examined by using tunicamycin and peptide N-glycosidase F, two agents used to prevent and remove glycosylations, respectively. The cDNA encoding a human ecto-apyrase (HB6), predicted to have seven N-linked glycosylation sites, was transiently expressed in mammalian COS cells and the resulting membrane preparations were treated with peptide N-glycosidase F (PNGase-F). PNGase-F caused a decrease in the apparent molecular weight of the protein (consistent with glycan removal) and a decrease in enzymatic activity over time. The ecto-apyrase was also expressed in the presence of tunicamycin, which completely prevented N-linked glycosylation, resulting in a nonglycosylated core protein devoid of ATP and ADP hydrolyzing activity. However, control and tunicamycin-treated cells expressed the enzyme to similar levels and localization. Interestingly, the quaternary structure of this E-type ATPase appears to be dependent upon the presence of glycan chains. The glycosylated ecto-apyrase exists as a homodimer in situ as assessed by both size-exclusion chromatography of detergent-solubilized ecto-apyrase and cross-linking of membrane-bound ecto-apyrase, in contrast to the enzymatically deglycosylated ecto-apyrase and the tunicamycin-treated ecto-apyrase. These results suggest that glycosylation is necessary for homooligomerization and nucleotide hydrolyzing activity, but not for expression and plasma membrane localization of the E-type ATPase. Similar results were obtained with another human ecto-apyrase, CD39, suggesting that the importance of glycosylation may be generalized to all membrane-bound E-type ATPases.
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Smith TM, Kirley TL. Site-directed mutagenesis of a human brain ecto-apyrase: evidence that the E-type ATPases are related to the actin/heat shock 70/sugar kinase superfamily. Biochemistry 1999; 38:321-8. [PMID: 9890913 DOI: 10.1021/bi9820457] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
On the basis of sequence homologies observed between members of the E-type ATPases and the phosphate binding motifs of the actin/heat shock protein 70/sugar kinase superfamily, a human ecto-apyrase was analyzed by site-directed mutagenesis of conserved amino acids in apyrase conserved regions (ACR) I and IV. The expressed proteins were analyzed to assess the significance of these amino acids. A conserved aspartic acid residue in ACR IV was mutated to alanine, asparagine, and glutamic acid, and the relative activity and Km for ATP and ADP were determined. Mutation of this Asp 219 to Ala or Asn yielded an enzyme severely reduced in ATP hydrolyzing activity (>90%) and completely devoid of ADPase activity, along with a similar extent of inhibition of hydrolysis of other nucleoside di- and triphosphates. Interestingly, mutation of Asp 219 to Glu completely restored the ability of the enzyme to hydrolyze nucleoside triphosphates at levels above that of the wild-type enzyme, while the ability to hydrolyze nucleoside diphosphates was slightly reduced. Mutation of a second conserved aspartic acid in ACR I (Asp 62) and two invariant glycine residues in both ACR I (Gly 64) and ACR IV (Gly 221) also severely disrupted nucleotidase activity. These results demonstrate that the E-type ATPases contain the nucleoside phosphate binding domains present in the actin/heat shock protein/sugar kinase superfamily. Together with analysis of computer-predicted secondary structures, the results suggest that the ecto-ATPases and ecto-apyrases are part of, or closely related to, the actin superfamily of proteins.
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Ng WV, Ciufo SA, Smith TM, Bumgarner RE, Baskin D, Faust J, Hall B, Loretz C, Seto J, Slagel J, Hood L, DasSarma S. Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome? Genome Res 1998; 8:1131-41. [PMID: 9847077 DOI: 10.1101/gr.8.11.1131] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Extremely halophilic archaea, which flourish in hypersaline environments, are known to contain a variety of large dynamic replicons. Previously, the analysis of one such replicon, pNRC100, in Halobacterium sp. strain NRC-1, showed that it undergoes high-frequency insertion sequence (IS) element-mediated insertions and deletions, as well as inversions via recombination between 39-kb-long inverted repeats (IRs). Now, the complete sequencing of pNRC100, a 191,346-bp circle, has shown the presence of 27 IS elements representing eight families. A total of 176 ORFs or likely genes of 850-bp average size were found, 39 of which were repeated within the large IRs. More than one-half of the ORFs are likely to represent novel genes that have no known homologs in the databases. Among ORFs with previously characterized homologs, three different copies of putative plasmid replication and four copies of partitioning genes were found, suggesting that pNRC100 evolved from IS element-mediated fusions of several smaller plasmids. Consistent with this idea, putative genes typically found on plasmids, including those encoding a restriction-modification system and arsenic resistance, as well as buoyant gas-filled vesicles and a two-component regulatory system, were found on pNRC100. However, additional putative genes not expected on an extrachromosomal element, such as those encoding an electron transport chain cytochrome d oxidase, DNA nucleotide synthesis enzymes thioredoxin and thioredoxin reductase, and eukaryotic-like TATA-binding protein transcription factors and a chromosomal replication initiator protein were also found. A multi-step IS element-mediated process is proposed to account for the acquisition of these chromosomal genes. The finding of essential genes on pNRC100 and its property of resistance to curing suggest that this replicon may be evolving into a new chromosome.
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Smith TM, Carl SA, Kirley TL. Immunological detection of ecto-ATPase in chicken and rat tissues: characterization, distribution, and a cautionary note. BIOCHEMISTRY AND MOLECULAR BIOLOGY INTERNATIONAL 1998; 45:1057-66. [PMID: 9739470 DOI: 10.1002/iub.7510450523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have generated a polyclonal antibody (CKG2) against native chicken gizzard ecto-ATPase for immunolocalization and immunoprecipitation. Active ecto-ATPase is immunoprecipitated from solubilized chicken and rat membranes and shown to be localized to the plasma membrane of the chicken smooth muscle cells. This antibody is specific for the ecto-ATPases, since the more abundant chicken stomach ecto-apyrase is not recognized in immunoprecipitation, western blot or immunolocalization analyses. The CKG2 antibody cross-reacts with mammalian (rat) ecto-ATPase in western blots, with testis being the most abundant source. Interestingly, when the same rat membranes are analyzed by western blot under non-reducing conditions, the 66 kDa ecto-ATPase is not recognized, instead a 200 kDa protein is detected, previously postulated to be an oligomer of ecto-ATPase. However, this 200 kDa cross-reacting protein is not related to the ecto-ATPases, but is instead an immunoglobulin binding protein, comprised of 50 kDa subunits.
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Smith TM, Kirley TL. Cloning, sequencing, and expression of a human brain ecto-apyrase related to both the ecto-ATPases and CD39 ecto-apyrases1. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1386:65-78. [PMID: 9675246 DOI: 10.1016/s0167-4838(98)00063-6] [Citation(s) in RCA: 149] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An extracellular ATPase (E-type ATPase) clone was isolated from a human brain cDNA library and sequenced. The transcript shows similarity to the previously published chicken smooth muscle and rat brain ecto-ATPase cDNAs, human CD39L1 cDNA (putative human ecto-ATPase), and mammalian CD39 (lymphoid cell activation antigen, ecto-apyrase, ATPDase, ATP-diphosphohydrolase) cDNAs. The full-length human brain cDNA encodes a 529 amino acid glycoprotein with a putative membrane spanning region near each terminus, with the majority of the protein found extracellularly. Expression of this clone in mammalian COS-1 cells yielded NaN3-sensitive ATPase and ADPase activity detectable both on intact cells and cell membrane preparations. The nucleotide hydrolysis ratio of the expressed protein is approx. 2.75:1 (ATPase:ADPase activity), classifying it as an ecto-apyrase. However, this hydrolysis ratio is intermediate between that observed for the ecto-ATPases and the CD39 ecto-apyrases (L. Plesner, Int. Rev. Cytol. 158 (1995) 141-214). Quantitative analyses of amino acid identities and similarities between this ecto-apyrase and other vertebrate E-type ATPases suggest that this human brain enzyme is nearly equally related to the ecto-ATPases and the CD39s, and phylogenetic analysis suggests that it could be an ancestral enzyme from which both ecto-ATPases and CD39 ecto-apyrases are derived.
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Lewis Carl SA, Smith TM, Kirley TL. Cross-linking induces homodimer formation and inhibits enzymatic activity of chicken stomach ecto-apyrase. BIOCHEMISTRY AND MOLECULAR BIOLOGY INTERNATIONAL 1998; 44:463-70. [PMID: 9556206 DOI: 10.1080/15216549800201482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have investigated the effect of cross-linking on the enzymatic activity and oligomer formation of the chicken stomach ecto-apyrase. Cross-linking with the hydrophobic, lysine-specific dithiobis(succinimidylpropionate) (DSP) caused equal inhibition of ATPase and ADPase activity in both the membrane-bound and detergent-solubilized ecto-apyrase. The inhibitory effect of cross-linking was reversed upon the addition of the reductant dithiothreitol. Western blots of aliquots of the cross-linked samples show decreased amounts of the monomeric 80 kDa ecto-apyrase and the appearance of a 160 kDa dimer under conditions inducing enzyme inhibition. Therefore, the chicken stomach ecto-apyrase, like the chicken gizzard ecto-ATPase, is likely a homodimer in vivo. Unlike the related gizzard ecto-ATPase, however, the native stomach ecto-apyrase is not stimulated, but rather inhibited by cross-linking, presumably due to different quaternary structural stability of the two enzymes.
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Abstract
Fetal rat kidney contains renin in renal microvasculature, whereas adult rat kidney contains renin predominantly in juxtaglomerular cells. It is hypothesized that renin isoforms stored within these renal tissues may differ chemically and functionally. To test this hypothesis, stored renin isoforms in fetal and adult rat kidney were compared by isolating renin from adult and fetal kidney homogenate with pepstatin agarose. Pepstatin-eluted renin isoforms were separated by relative molecular size using one-dimensional polyacrylamide gel electrophoresis (SDS-PAGE), or by isoelectric point (pI) and size using two-dimensional (2D) gel electrophoresis. Isoforms were identified either by silver staining or immunoblotting. One-dimensional polyacrylamide gel electrophoresis of pepstatin-treated kidney homogenates showed a silver-stained band in the range of approximately 45 kDa, which corresponded to a silver-stained spot consistently seen on 2D gels. In fetal kidney homogenate, the approximately 45 kDa band had a pI of 5.3 +/- 0.1, whereas the corresponding band in adult samples had a basic pI of 6.0 +/- 0.05. Angiotensin I generation was measured to assess renin enzymatic activity. There was significantly more inactive renin in fetal kidney homogenate than in adult kidney homogenate (60.2 +/- 22.4 v 9.6 +/- 4.0 ng AI/mg protein/h, P < .05). There was significantly less active renin in fetal kidney homogenate than in adult kidney homogenate (5.4 +/- 0.4 v 36.5 +/- 14.2 ng AI/mg protein/h, P < .05). The average total renin activity in fetal kidney homogenate was significantly higher than in adult kidney homogenate (65.6 +/- 22.3 v 46.0 +/- 15.2, P < .05). These results demonstrate major differences in the physical and enzymatic forms of stored renin found in fetal and adult kidney. It is speculated that these variations in stored renin isoforms play a role in the developmental differential regulation of the intrarenal renin angiotensin system.
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Abstract
Segmented filamentous bacteria (SFB) were observed in a 28-day-old calf, attached to the absorptive villi. Morphologically, they were similar to SFB described in other animal species. Because these organisms cannot be cultured, further characterization was not possible. The organisms were confined to the upper third of the absorptive villi and were not seen attached to the follicle-associated epithelium of the Peyer's patch, or observed in the caecum or colon. Although they were often associated with minor lesions, their pathological significance was doubtful. With this report, segmented filamentous bacteria have now been described in virtually all the commercially important livestock and poultry species, in other domestic animals, and in man.
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Smith TM, Abajian C, Hood L. Hopper: software for automating data tracking and flow in DNA sequencing. COMPUTER APPLICATIONS IN THE BIOSCIENCES : CABIOS 1997; 13:175-82. [PMID: 9146965 DOI: 10.1093/bioinformatics/13.2.175] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
MOTIVATION Genome-scale DNA sequencing is a multistep process in which large numbers of small template clones are propagated, purified, sequenced and analyzed on acrylamide gels. A significant challenge to these projects is the scale at which the data handling must be done. Hence, large-scale sequencing facilities will benefit from tracking template DNA information (purification methods, reaction and electrophoresis conditions) in a systematic fashion. A lack of software tools that support automated sample entry, and automatic data storage, retrieval and analysis are a major hindrance to recording and using laboratory workflow information to monitor the overall quality of data production. RESULTS The UNIX file system has been used to prototype automation of the flow of data from the ABI sequencer to a data repository. Data are automatically processed by a central Perl program, Hopper, which runs a series of programs that analyze data quality (read length estimate, fraction of indeterminate bases, and number of contaminating and repetitive sequences), assemble shotgun sequence data, and generates simple reports describing the results.
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Abstract
This paper provides an overview of the responsibilities and jurisdictional boundaries of Health Canada (HC) and Agriculture and Agri-Food Canada (AAFC) with regard to food regulation in Canada. It examines their interagency coordination within the federal structure and with other levels of government, industry, and the consumer. The international developments are considered with the North American Free Trade Agreement (NAFTA) and the Canada, United States Trade Agreement (CUSTA) being regarded as likely to have a significant future impact. The federal food safety and quality system is complex and fragmented. Federal food regulation comes under the jurisdiction of four federal departments: HC, AAFC, Industry Canada (IC), and Fisheries and Oceans Canada (FOC). All four departments are involved with inspection, surveillance, and the analysis of food sold in Canada. In addition, Canada's ten provincial and two territorial governments have provincial-, regional-, municipal-, and local-level governments that also have jurisdiction over food safety and quality. Consideration is first given to the main legislative provision covering food--the Federal Food and Drugs Act. This Act is administered by several of the Federal Government departments. The role of these departments is examined individually along with additional, more specific legal provisions for which responsibility is not divided (in particular, the Canada Agricultural Products [CAP] Act administered by AAFC, and the Consumer Packaging and Labeling Act [CPLA] administered by IC). The various reviews that have taken place in the recent past and those still in progress are considered, and the final part of this paper looks at the international developments that are likely to have a major impact on the future development of the Canadian food control system.
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Smith TM, Kirley TL, Hennessey TM. A soluble ecto-ATPase from Tetrahymena thermophila: purification and similarity to the membrane-bound ecto-ATPase of smooth muscle. Arch Biochem Biophys 1997; 337:351-9. [PMID: 9016833 DOI: 10.1006/abbi.1996.9779] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
For the first time, a soluble, dedicated E-type ecto-ATPase has been identified and purified. This fully soluble ecto-ATPase is released into the growth media of the single-celled eukaryote, Tetrahymena, at a constant rate over time (independent of the growth phase of the cells) and it has characteristics similar to those previously described for the membrane-bound ecto-enzyme in Tetrahymena. It was purified by a combination of ion-exchange, size exclusion, and affinity chromatography and nondenaturing gel electrophoresis. Its molecular weight was determined to be approximately 66,000 Da by denaturing gel electrophoresis and approximately 69,000 Da by size exclusion chromatography of the native form. The purified soluble enzyme displays the general characteristics of a dedicated E-type ecto-ATPase such as Ca2+ or Mg2+ dependence, hydrolysis of ATP and other nucleoside triphosphates (but not nucleoside diphosphates) and insensitivity to common ATPase inhibitors (vanadate, azide, ouabain, N-ethylmaleimide and p-chloromercuriphenyl sulfonate). It was further shown to be immunologically similar (by polyclonal antibodies) to both the membrane-bound ecto-ATPase of chicken gizzard smooth muscle (66 kDa) and a 66-kDa protein in Tetrahymena plasma membranes. The ecto-ATPase enzyme activity was also shown to be present in both the body plasma membrane and ciliary plasma membrane fractions but the body membrane had slightly higher specific activities. We propose that this ecto-ATPase of Tetrahymena may play a role in inactivating purinergic signals, such as in their chemorepulsion responses to external GTP and ATP. It may also play a minor role in extracellular nucleotide scavenging.
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Taloumis LJ, Smith TM, Hondrum SO, Lorton L. Force decay and deformation of orthodontic elastomeric ligatures. Am J Orthod Dentofacial Orthop 1997; 111:1-11. [PMID: 9009917 DOI: 10.1016/s0889-5406(97)70295-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This study evaluated commercially available molded gray elastomeric ligatures from seven companies for force decay, dimensional change, and the relationship between ligature dimension and force. The initial wall thickness, inside diameter, outside diameter, and force levels of each ligature were measured. Three of four test groups of ligatures were stretched over stainless steel dowels with a circumference approximating that of a large orthodontic twin bracket. Test group 1 was kept at room temperature and humidity for 28 days and test group 2 in a synthetic saliva bath at 37 degrees C, pH 6.84 for 28 days. The residual forces and dimensional changes were measured. The third test group was placed in a synthetic saliva bath at 37 degrees C, pH 6.84, and force levels recorded at initial, 24 hours, 7 days, 14 days, and 28 days. The fourth test group of unstretched samples was placed in a synthetic saliva bath at 37 degrees C, pH 6.84 for 28 days to evaluate dimensional changes due solely to moisture sorption. The results for stretched samples in a simulated oral environment revealed the following: (1) Moisture and heat had a pronounced effect on force decay and permanent deformation, (2) a positive correlation existed between the wall thickness and force, (3) a negative correlation existed between the inside diameter and force, (4) a weak correlation existed between outside diameter and force, (5) the greatest force loss occurred in the first 24 hours and the decay pattern was similar for all ligatures tested, and (6) unstretched ligatures absorbed moisture in the range of 0.060% to 3.15%. The ligatures tested appear to be suitable for use during initial aligning and leveling. However, the rapid force loss and permanent deformation of these products may preclude their use for rotational and torque corrections.
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Smith TM, Lee MK, Szabo CI, Jerome N, McEuen M, Taylor M, Hood L, King MC. Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1. Genome Res 1996; 6:1029-49. [PMID: 8938427 DOI: 10.1101/gr.6.11.1029] [Citation(s) in RCA: 199] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Over 100 distinct disease-associated mutations have been identified in the breast-ovarian cancer susceptibility gene BRCA1. Loss of the wild-type allele in > 90% of tumors from patients with inherited BRCA1 mutations indicates tumor suppressive function. The low incidence of somatic mutations suggests that BRCA1 inactivation in sporadic tumors occurs by alternative mechanisms, such as interstitial chromosomal deletion or reduced transcription. To identify possible features of the BRCA1 genomic region that may contribute to chromosomal instability as well as potential transcriptional regulatory elements, a 117,143-bp DNA sequence encompassing BRCA1 was obtained by random sequencing of four cosmids identified from a human chromosome 17 specific library. The 24 exons of BRCA1 span an 81-kb region that has an unusually high density of Alu repetitive DNA (41.5%), but relatively low density (4.8%) of other repetitive sequences. BRCA1 intron lengths range in size from 403 bp to 9.2 kb and contain the intragenic microsatellite markers D17S1323, D17S1322, and D17S855, which localize to introns 12, 19, and 20, respectively. In addition to BRCA1, the contig contains two complete genes: Rho7, a member of the rho family of GTP binding proteins, and VAT1, an abundant membrane protein of cholinergic synaptic vesicles. Partial sequences of the 1A1-3B B-box protein pseudogene and IFP 35, an interferon induced leucine zipper protein, reside within the contig. An L21 ribosomal protein pseudogene is embedded in BRCA1 intron 13. The order of genes on the chromosome is: centromere-1FP 35-VAT1-Rho7-BRCA1-1A1-3B-telomere.
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Priestley ND, Smith TM, Shipley PR, Floss HG. Studies on the biosynthesis of thiostrepton: 4-(1-hydroxyethyl)quinoline-2-carboxylate as a free intermediate on the pathway to the quinaldic acid moiety. Bioorg Med Chem 1996; 4:1135-47. [PMID: 8831986 DOI: 10.1016/0968-0896(96)00126-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Specifically 13C-labeled quinoline-2-carboxylate derivatives were synthesized from quinoline and used to study the biosynthesis of thiostrepton in a strain of Streptomyces laurentii. 13C NMR analysis of thiostrepton recovered after feeding methyl (RS)-[11-13C]-4-(1-hydroxyethyl)quinoline-2-carboxylate or methyl [11-13C]-4-acetylquinoline-2-carboxylate showed conclusively that these compounds are specifically and efficiently incorporated into thiostrepton. Both compounds were also detected in cultures of the producing organism by isotope dilution analysis. The significance of the relative endogenous concentrations of the two compounds and of the relative extent of the incorporation of exogenously added labeled material into thiostrepton are discussed in terms of the biosynthetic pathway linking tryptophan and 4-(1-hydroxyethyl)quinoline-2-carboxylate in S. laurentii. A highly specific enzyme activity was detected in cell-free extracts of S. laurentii that was capable of adenylating (12S)-4-(1-hydroxyethyl)quinoline-2-carboxylic acid. Partial purification of the enzyme was achieved. The enzyme was found to be specific for the enantiomer of the substrate which has the same absolute configuration as found in the natural antibiotic structure. The presence of one specific enzyme catalysing the adenylation process in S. laurentii was shown by photoaffinity labeling with [alpha-32P]-8-azido-ATP and subsequent SDS PAGE analysis of the labeled products. The native molecular weight of the active enzyme, determined by gel permeation chromatography, was found to be approximately 47 kDa, compared with a denatured weight of 50 kDa estimated for the photoaffinity-labeled protein. The enzyme is thus probably monomeric.
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Abstract
The Drug Safety Research Unit's current methods of investigating adverse drug reactions using prescription event monitoring are discussed. The statistical properties of estimators of rates of occurrence of events in post-marketing surveillance using prescription event monitoring are considered, and a simple model is proposed based on an exponential distribution of time to first occurrence of the event. It is shown that current methodology closely relates to the use of maximum likelihood estimation under this assumption and the distributions of the estimators are shown to be approximately normal, which allows simple confidence intervals and tests to be developed. Two recent applications are considered and corresponding simulations are presented to verify the approximate properties of the test statistics, based on ratios of rates over time and between drugs. Sources of bias in the rates and rate ratios are considered, including under-reporting in later months. A rule-of-thumb, developed from many years experience, is shown to be generally conservative, except when these under-reporting biases are large.
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Lubiniecki AS, McAllister PR, Smith TM, Shadle PJ. Process evaluation for biopharmaceuticals: what is appropriate in process evaluation? DEVELOPMENTS IN BIOLOGICAL STANDARDIZATION 1996; 88:309-15. [PMID: 9119154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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McAllister PR, Shadle PJ, Smith TM, Scott RG, Lubiniecki AS. Use of a statistical strategy to evaluate sources of variability in viral safety experiments for a recombinant biopharmaceutical. DEVELOPMENTS IN BIOLOGICAL STANDARDIZATION 1996; 88:111-21. [PMID: 9119122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Smith TM, Winters FD. Smoking cessation: a clinical study of the transdermal nicotine patch. THE JOURNAL OF THE AMERICAN OSTEOPATHIC ASSOCIATION 1995; 95:655-6, 661-2. [PMID: 8575948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Although cigarette smoking is a declining trend in the United States, the amount of cigarettes consumed by the American public is the same today as in 1964. The role of cigarette smoking in many disease processes is publicly well known, and smoking cessation has been proved to reduce risk for some diseases, but the various methods of cessation are often met with a high rate of treatment failure or relapse. In this study, the short-term efficacy of nicotine-replacement therapy by way of the transdermal patch system was evaluated in 110 patients in a family practice setting. Patches were tapered from 21 mg of nicotine to 14 mg to 7 mg, each for 30 days. Subjects wore one patch for every 24 hours and were instructed not to smoke. Telephone follow-up was used at 2 to 3 weeks to check smoking status and inquire for side effects, and further follow-up of those who had completed the 3-month program was initiated 6 months after the program began. Nineteen patients never filled the prescription, and six were lost to follow-up. Of the 85 who finished the program, 35% were still not smoking at 6 months after the study began. The other 65% had relapsed. Side effects were mild and were mainly related to skin irritation at the patch site and abnormal dreams. Combinations of this cessation method with physician counseling and other behavioral methods should improve the success rate of this encouraging treatment.
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Smith TM, Jiang YF, Shipley P, Floss HG. The thiostrepton-resistance-encoding gene in Streptomyces laurentii is located within a cluster of ribosomal protein operons. Gene 1995; 164:137-42. [PMID: 7590303 DOI: 10.1016/0378-1119(95)00442-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A common approach to identify and clone biosynthetic gene from an antibiotic-producing streptomycete is to clone the resistance gene for the antibiotic of interest and then use that gene to clone DNA that is linked to it. As a first step toward cloning the genes responsible for the biosynthesis of thiostrepton (Th) in Streptomyces laurentii (Sl), the Th resistance-encoding gene (tsnR) was cloned as a 1.5-kb BamHI-PvuII fragment in Escherichia coli (Ec), and shown to confer Th resistance when introduced into S. lividans TK24. The tsnR-containing DNA fragment was used as a probe to isolate clones from cosmid libraries of DNA in the Ec cosmid vector SuperCos, and pOJ446 (an Ec/streptomycete) cosmid vector. Sequence and genetic analysis of the DNA flanking the tsnR indicates that the Sl tsnR is not closely linked to biosynthetic genes. Instead it is located within a cluster of ribosomal protein operons.
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Bechthold A, Sohng JK, Smith TM, Chu X, Floss HG. Identification of Streptomyces violaceoruber Tü22 genes involved in the biosynthesis of granaticin. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:610-20. [PMID: 7476861 DOI: 10.1007/bf02423457] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A 50 kb region of DNA from Streptomyces violaceoruber Tü22, containing genes encoding proteins involved in the biosynthesis of granaticin, was isolated. The DNA sequence of a 7.3 kb fragment from this region, located approximately 10 kb from the genes that encode the polyketide synthetase responsible for formation of the benzoisochromane quinone skeleton, revealed five open reading frames (ORF1-ORF5). The deduced amino acid sequence of GraE, encoded by ORF2, shows 60.8% identity (75.2% similarity) to a dTDP-glucose dehydratase (StrE) from Streptomyces griseus. Cultures of Escherichia coli containing plasmids with ORF2, on a 2.1 kb BamHI fragment, were able to catalyze the formation of dTDP-4-keto-6-deoxy-D-glucose from dTDP-glucose at 5 times the rate of control cultures, confirming that ORF2 encodes a dTDP-glucose dehydratase. The amino acid sequence encoded by ORF3 (GraD) is 51.4% identical (69.9% similar) to that of StrD, a dTDP-glucose synthase from Streptomyces griseus. The amino acid sequence encoded by ORF4 shares similarities with proteins that confer resistance to tetracycline and methylenomycin, and is suggested to be involved in transporting granaticin out of the cells by an active efflux mechanism.
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Smith TM, Steinhorn DM, Thusu K, Fuhrman BP, Dandona P. A liquid perfluorochemical decreases the in vitro production of reactive oxygen species by alveolar macrophages. Crit Care Med 1995; 23:1533-9. [PMID: 7664556 DOI: 10.1097/00003246-199509000-00014] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE To determine whether reactive oxygen metabolite production by alveolar macrophages is affected by liquid perfluorochemical exposure. DESIGN Controlled, animal laboratory investigation of alveolar macrophage function in vitro. SETTING Animal research facility of a health sciences university. SUBJECTS Six adult male New Zealand white rabbits and six young piglets. INTERVENTIONS Alveolar macrophages were obtained after sacrifice from both species by total lung lavage. Macrophages were divided into control and experimental groups. Macrophages in the experimental groups were exposed to perfluorooctylbromide. To determine production of reactive oxygen metabolites, hydrogen peroxide production and chemiluminescence were measured in both experimental and control groups after chemical stimulation. MEASUREMENTS AND MAIN RESULTS Perfluorooctylbromide-exposed alveolar macrophages produced significantly less hydrogen peroxide (1.4 +/- 1.5 vs. 2.4 +/- 1.6 nmol/10(6) cells; p = .002). Perfluorooctylbromide-exposed alveolar macrophages demonstrated significantly less chemiluminescence activity compared with nonexposed cells (0.70 +/- 0.2 vs. 1.5 +/- 0.2 mV of relative activity per 3.5 x 10(5) cells; p = .005). CONCLUSIONS Exposure of alveolar macrophages to perfluorooctylbromide in vitro decreases the responsiveness of macrophages to potent stimuli. This finding may partially explain the decrease in pulmonary inflammation seen in animals treated with partial liquid ventilation during experimentally induced lung injury.
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Gertner E, Marshall PS, Filandrinos D, Potek AS, Smith TM. Complications resulting from the use of Chinese herbal medications containing undeclared prescription drugs. ARTHRITIS AND RHEUMATISM 1995; 38:614-7. [PMID: 7748216 DOI: 10.1002/art.1780380506] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE Many patients with chronic disease use alternative therapies. Our objective was to investigate complications resulting from the use of Chinese herbal medications containing undeclared prescription drugs, and to analyze these pills. METHODS Medical records of 5 patients with complications were reviewed. Pills from symptomatic and asymptomatic individuals were analyzed for possible content of undeclared prescription drugs. RESULTS All pills analyzed contained mefenamic acid and diazepam. Complications related to the presence of these substances included, among others, massive gastrointestinal bleeding. CONCLUSION Chinese herbal medications may contain undeclared prescription drugs including nonsteroidal antiinflammatory drugs and benzodiazepines.
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