101 results on '"Tibbetts C"'
Search Results
2. Characterizing injury patterns and outcomes in hospitalized trauma patients with non-English Language Preferences
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Meyer, C.H., primary, Zeidan, A., additional, Beshara, G., additional, Cortes, J., additional, Tibbetts, C., additional, Tracy, Brett M., additional, Jayaraman Muralidharan, V., additional, Sola, R., additional, Hernandez Irizarry, R., additional, Williams, K., additional, Thompson, A., additional, Todd, S.R., additional, Sciarretta, J.D., additional, and Smith, R.N., additional
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- 2022
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3. Surveillance of transcriptomes in basic military trainees with normal, febrile respiratory illness, and convalescent phenotypes
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Thach, D C, Agan, B K, Olsen, C, Diao, J, Lin, B, Gomez, J, Jesse, M, Jenkins, M, Rowley, R, Hanson, E, Tibbetts, C, Stenger, D A, and Walter, E
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- 2005
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4. Neural Networks for Automated Base-calling of Gel-based DNA Sequencing Ladders
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TIBBETTS, C., primary, BOWLING, J.M., additional, and GOLDEN, J.B., additional
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- 1994
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5. RNA aptamer delivery through intact human skin
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Lenn, J. D., Neil, J., Donahue, C., Demock, K., Tibbetts, C. V., Cote-Sierra, J., Smith, S. H., Rubenstein, D., Therrien, J.-P., Pendergrast, P. S., Killough, J., Brown, M. B., and Williams, Adrian
- Abstract
It is generally recognised that only relatively small molecular weight (typically < ~500 Da) drugs can effectively permeate through intact stratum corneum. Here, we challenge this orthodoxy using a 62-nucleotide (MW=20,395) RNA-based aptamer, highly specific to the human IL-23 cytokine, with picomolar activity. Results demonstrate penetration of the aptamer into freshly excised human skin using two different fluorescent labels. A dual hybridisation assay quantified aptamer from the epidermis and dermis giving levels far exceeding the cellular IC50 values (> 100,000-fold) and aptamer integrity was confirmed using an oligonucleotide precipitation assay. A Th17 response was stimulated in freshly excised human skin resulting in significantly upregulated IL-17f, and 22; topical application of the IL-23 aptamer decreased both IL-17f and IL-22 by approximately 45% but did not result in significant changes to IL-23 mRNA levels, confirming that the aptamer did not globally suppress mRNA levels. This study demonstrates that very large molecular weight RNA aptamers can permeate across the intact human skin barrier to therapeutically relevant levels into both the epidermis and dermis and that the skin penetrating aptamer retains its biologically active conformational structure capable of binding to endogenous IL-23.
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- 2018
6. Using the Whole-Genome Sequence To Characterize and Name Human Adenoviruses
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Seto, D., Chodosh, J., Brister, J. R., Jones, M. S., Akusjärvi, G., Arnold, J.C., Blanchette, P., Boulanger, P., Branton, P.E., Casimiro, D.R., Chiu, C.Y., Chroboczek, J., Curiel, D.T., Dobner, T., Doerfler, W., Dyer, D.W., Fender, P., Ferreyra, L.R., Gooding, L.R., Grand, R.J., Greber, U.F., Heim, A., Hemmi, S., Henquell, C., Kremer, E.J., Leppard, K.N., Lieber, A., Lion, T., Lukashev, A.N., Madupu, R., Mathews, M.B., Mitraki, A., Nates, S.V., Nemerow, G.R., Ornelles, D.A., Qu, Z., Reddy, V.S., San Martin, C., Schoehn, G., Smith, J.G., Stewart, P.L., Szolajska, E., Tibbetts, C., Tollefson, A.E., Turnell, A.S., Raaij, M.J., Wan, C., Wang, Y., Wong, S., Weitzman, M.D., Wilson, J.M., Wold, W.S., Xu, Wei-Jiang, Yuan, X., Wei Zhang, Q., Zhou, R., Institut de Génétique Moléculaire de Montpellier (IGMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
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Human Adenoviruses ,Adenoviruses ,Human/*classification/*genetics Base Sequence DNA ,Immunology ,Viral Humans *Terminology as Topic ,Genome, Viral ,Computational biology ,Biology ,Microbiology ,Genome ,03 medical and health sciences ,Viral genetics ,Terminology as Topic ,Virology ,Humans ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Base sequence ,Dna viral ,Letters to the Editor ,030304 developmental biology ,Genetics ,Whole genome sequencing ,0303 health sciences ,Base Sequence ,030306 microbiology ,Adenoviruses, Human ,Viral/*chemistry/*genetics *Genome ,Human genetics ,Editorial ,Insect Science ,DNA, Viral ,Human taxonomy - Abstract
We propose that human adenoviruses (HAdVs) be identified, characterized, and typed on the basis of complete genome sequence analyses rather than serological approaches. This idea has recently percolated through the community of adenovirologists. As a result, an open-floor discussion took place at
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- 2011
7. Case Study: Care Coordination and Case Finding of Undetected Depression in a 72-Year-Old Man With Type 2 Diabetes
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Tibbetts, C., primary
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- 2003
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8. Functional diversity of E1A gene autoregulation among human adenoviruses
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Cogan, J D, primary, Jones, S N, additional, Hall, R K, additional, and Tibbetts, C, additional
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- 1992
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9. Mutation spectrum and sequence alkylation selectivity resulting from modification of bacteriophage M13mp18 DNA with S-(2-chloroethyl)glutathione. Evidence for a role of S-(2-N7-guanyl)ethyl)glutathione as a mutagenic lesion formed from ethylene dibromide.
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Cmarik, J.L., primary, Humphreys, W.G., additional, Bruner, K.L., additional, Lloyd, R.S., additional, Tibbetts, C, additional, and Guengerich, F.P., additional
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- 1992
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10. Rat angiotensin II receptor: cDNA sequence and regulation of the gene expression
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Iwai, N., primary, Yamano, Y., additional, Chaki, S., additional, Konishi, F., additional, Bardhan, S., additional, Tibbetts, C., additional, Sasaki, K., additional, Hasegawa, M., additional, Matsuda, Y., additional, and Inagami, T., additional
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- 1991
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11. Viral DNA sequences and gene products in hamster cells transformed by adenovirus type 2
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Johansson, K, Persson, H, Lewis, A M, Pettersson, U, Tibbetts, C, and Philipson, L
- Abstract
Complementary strand-specific adenovirus DNA of full length or from endonuclease BamHI fragments was used as a probe to estimate the fractional representation and abundance of viral sequences in five hamster cell lines (Ad2HE1-5) transformed with UV-inactivated adenovirus type 2. The fraction of the viral genome present in the five transformed cell lines varied from 44% in the Ad2HE5 cell line to 84% in the Ad2HE3 cell line. The number of viral DNA copies per diploid cell equivalent ranged from 1.8 in the Ad2HE1 line to 7.1 in the Ad2HE4 line. In vivo labeling with [35S]methionine followed by immunoprecipitation with an antiserum against adenovirus type 2 early proteins revealed virus-specific polypeptides with molecular weights of 42,000 to 58,000 in extracts from all five hamster cell lines. Several other early viral polypeptides were detected in some of the adenovirus type 2-transformed hamster cell lines.
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- 1978
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12. Targeted deletions of sequences from closed circular DNA.
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Green, C and Tibbetts, C
- Abstract
Closed circular DNA interacts with complementary sequences of single-stranded DNA to form displacement loop (D loop) structures in vitro. The site of D-loop formation can be directed by using single-stranded DNA derived from a selected restriction fragment. Circular DNA containing a D loop can then be linearized by cleavage with endonuclease S1. This cleavage appears to remove a limited number of nucleotides from each strand of the circular DNA substrate. Incubation with polynucleotide ligase followed by propagation in vivo leads to circular DNA molecules that bear small, single deletions in the region of the single-stranded DNA sequence chosen for the formation of the D loops. We have utilized these manipulations of DNA to construct tetracycline-sensitive deletion mutants of plasmid pBR322. The level of mutagenesis obtained by the procedure is sufficiently high that selective growth and screening procedures are not necessary for the isolation or identification of mutants. The frequency, variety, and small size of the deletions obtained within the selected target regions present considerable advantage for genetic and biochemical analysis. The method is quite general in rationale and should be immediately applicable to phage and viruses having infectious circular DNA genomes or recombinant DNA species propagated in circular plasmid vectors.
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- 1980
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13. Polar encapsidation of adenovirus DNA: cloning and DNA sequence of the left end of adenovirus type 3
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Kosturko, L D, Sharnick, S V, and Tibbetts, C
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The left-end adenovirus type 3 DNA sequence is very similar to those of other subgroup B adenoviruses, especially in the area between the HinfI site (320 base pairs) and the early-region Ia gene. This segment of the genome has been implicated as necessary for the left-end polarity of adenovirus DNA encapsidation. This segment and the sequences flanking it are compared with the corresponding sequences of adenovirus type 5 and adenovirus type 12, and the extent and pattern of intersubgroup homologies are discussed.
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- 1982
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14. Upstream DNA sequences determine different autoregulatory responses of the adenovirus types 5 and 3 E1A promoters
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Jones, S N and Tibbetts, C
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Adenovirus types 5 and 3 (Ad5 and Ad3), two human adenovirus serotypes of evolutionarily divergent subgroups, show very different levels of E1A gene expression early after infection of permissive cells. Since adenovirus E1A gene expression is known to be transcriptionally autoregulated, we have investigated the difference between Ad3 and Ad5 by monitoring transient expression of a reporter gene under transcriptional control of the E1A promoter of Ad5 or Ad3. There was only a modest difference between the basal levels of transcription driven by these two E1A promoters. This difference was amplified from 10 to 100 times by the different net responses of the E1A promoters to concomitantly expressed E1A genes. Each promoter had a characteristic net response to positive and negative regulation by E1A gene products. The Ad5 E1A promoter was more strongly repressed, whereas the Ad3 E1A promoter was more strongly activated by E1A gene products. Experiments with a chimeric Ad5/3 E1A promoter indicated that these different autoregulatory responses are determined by DNA sequences which are more than 50 base pairs upstream from the E1A transcriptional start site. A plausible target DNA sequence for positive and negative autoregulation by E1A gene products is discussed.
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- 1989
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15. Autoregulation of adenovirus E1A gene expression
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Tibbetts, C, Larsen, P L, and Jones, S N
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We examined E1A gene expression by two evolutionarily divergent human adenoviruses, type 5 (subgroup C) and type 3 (subgroup B). Adenovirus type 3 (Ad3)-infected A549 cells contained much larger amounts of E1A-specific RNA than adenovirus type 5 (Ad5)-infected cells, from very early (3 h) through the late stages (20 h) after infection. The appearance of such abundant Ad3 E1A transcripts was delayed after infection of Ad5 E1A-expressing 293 cells, suggesting a down regulation of the Ad3 E1A gene by Ad5 E1A gene products. In a reciprocal manner, coinfection of A549 cells led to typically early and intense Ad3 E1A transcription and strongly inhibited transcription of the Ad5 E1A gene. Transient expression assays were developed so that the autoregulation of the E1A gene could be studied apart from the more complex background of infected cells. The DNA sequence surrounding the transcription start site of the Ad3 E1A gene was placed 5' to the sequence which encodes the bacterial chloramphenicol acetyltransferase gene. Cotransfection of HeLa cells with Ad3 or Ad5 E1A-expression plasmids increased the expression of the Ad3 E1A promoter-driven chloramphenicol acetyltransferase gene. Taken together, these results suggest dual autoregulatory features of adenovirus E1A gene expression. The positive and negative effects appear to be temporally distinguished under different conditions, both in viral infection and in transient assays with plasmid-cloned genes.
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- 1986
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16. In vitro association of empty adenovirus capsids with double-stranded DNA
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Tibbetts, C and Giam, C Z
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Several lines of evidence suggest that empty adenovirus capsids are preassembled intermediates in the pathway of virion assembly. We have observed that purified empty capsids of subgroup B adenoviruses have a remarkable affinity for DNA in vitro. The products of capsid-DNA association are sufficiently stable, once formed in low-salt solution, to permit purification and characterization in CsCl density gradients. Neither virions nor the DNA-containing incomplete particles of subgroup B adenoviruses can give rise to such in vitro reaction products. The average molecular weight of the empty adenovirus capsids is about 123 X 10(6), consistent with the absence of viral core peptides and a small deficiency of exterior shell polypeptides. Electron microscopy of negatively stained capsids and the capsids bound to DNA reveals a typical adenovirus size and architecture. The particles appear with a surface discontinuity that is presumed to expose the DNA binding site(s). The DNA molecules associated with the empty capsids are susceptible to the actions of DNase and restriction endonucleases. The dependence of rate of capsid-DNA association on DNA length suggests randomly distributed binding sites on the DNA molecules. Although the DNA molecules can successively acquire additional empty capsids, the empty particles themselves are restricted to interactionwith only one DNA molecule. Electron microscopy of the capsid-DNA complexes spread in cytochrome c films shows that the particles are bo-nd along the contour of extended duplex DNA. The amount of DNA within each bound particle appears to be less than 300 base pairs, as estimated by the length of the DNA molecules visible outside of the bound particle. The empty capsid-DNA association product described in this report provides an interesting substrate for further investigation of the DNA packaging process in a defined in vitro system, with extracts or purified components from infected cells.
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- 1979
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17. Physical organization of subgroup B human adenovirus genomes
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Tibbetts, C
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Cleavage sites of nine bacterial restriction endonucleases were mapped in the DNA of adenovirus type 3 (Ad3) and Ad7, representative serotypes of the "weakly oncogenic" subgroup B human adenoviruses. Of 94 sites mapped, 82 were common to both serotypes, in accord with the high overall sequence homology of DNA among members of the same subgroups. Of the sites in Ad3 and Ad7 DNA, fewer than 20% corresponded to mapped restriction sites in the DNA of Ad2 or Ad5. The latter serotypes represent the "nononcogenic" subgroup C, having only 10 to 20% overall sequence homology with the DNA of subgroup B adenoviruses. Hybridization mapping of viral mRNA from Ad7-infected cells resulted in a complex physical map that was nearly identical to the map of early and late gene clusters in Ad2 DNA. Thus the DNA sequences of human adenoviruses of subgroups B and C have significantly diverged in the course of viral evolution, but the complex organization of the adenovirus genome has been rigidly conserved.
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- 1977
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18. Reassociation of complementary strand-specific adenovirus type 2 DNA with viral DNA sequences of transformed cells
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Johansson, K, Pettersson, U, Philipson, L, and Tibbetts, C
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Complementary strand-specific adenovirus DNA, either full length or from restriction enzyme cleavage fragments, was used to estimate the fractional representation and abundance of viral sequences in two adenovirus type 2 (Ad2)-transformed rat cell lines, A2F19 and A2T2C4. The reassociation method introduced is based on the linear relationship, after exhaustive hybridization, between the inverted fraction of hybrid DNA and the molar ratio of probe to cellular DNA in the reaction mixture. The amount of viral DNA in A2F19 cells represents 12 to 14% of the viral genome at a level of around seven copies per diploid cell equivalent. For the cell line A2T2C4, the pattern of integrated viral DNA sequences is more complex. With full-length Ad2 DNA strands as a probe, about 56% of the probe was represented in cellular DNA. When each of the four BamHI fragment strands of Ad2 DNA was used as a probe, the fraction of the viral DNA present also amounted to around 56% with one to five copies from different regions of the viral genome. The results demonstrate the advantage of using strand-specific viral DNA as a probe in reassociation analysis with denatured cell DNA. The method should be useful in any system in which complementary strand separation of viral DNA sequences can be achieved.
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- 1977
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19. Adenovirus E1A gene autorepression: revertants of an E1A promoter mutation encode altered E1A proteins.
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Larsen, P L and Tibbetts, C
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Revertants have been isolated from Ad3hr15, a mutant of human adenovirus type 3 that carries a defective E1A promoter. Transcription of these revertant E1A genes is restored--from nil for Ad3hr15 mutant to levels exceeding that of the wild-type virus. The mutant Ad3hr15 virus and the revertants all have an aberrant E1A promoter that contains two short tandem duplications of viral DNA sequence. The E1A gene-coding region of the mutant is the same as that for wild-type adenovirus type 3, whereas the revertants are characterized by short in-frame deletions within the 5' exon region of their E1A genes. Location of these reverting, second-site deletions is discussed in relation to E1A gene autoregulation and the evolved diversity of E1A-related oncogenic potential among different human adenoviruses.
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- 1987
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20. RNA Synthesis and Processing in Adenovirus-infected Cells
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Philipson, L., primary, Pettersson, U., additional, Lindberg, U., additional, Tibbetts, C., additional, Vennstrom, B., additional, and Persson, T., additional
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- 1974
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21. "Business English" in the American High School: Some Recent Observations
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Tibbetts, A. M., primary and Tibbetts, C., additional
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- 1977
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22. Development of X-screw: a load-sensitive actuator incorporating a variable transmission
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Hirose, S., primary, Tibbetts, C., additional, and Hagiwara, T., additional
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23. Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses
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Blaney Kate M, Long Nina C, Kidd Carolyn, Lin Baochuan, Malanoski Anthony P, Wang Zheng, Thach Dzung C, Tibbetts Clark, and Stenger David A
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Febrile respiratory illness (FRI) has a high impact on public health and global economics and poses a difficult challenge for differential diagnosis. A particular issue is the detection of genetically diverse pathogens, i.e. human rhinoviruses (HRV) and enteroviruses (HEV) which are frequent causes of FRI. Resequencing Pathogen Microarray technology has demonstrated potential for differential diagnosis of several respiratory pathogens simultaneously, but a high confidence design method to select probes for genetically diverse viruses is lacking. Results Using HRV and HEV as test cases, we assess a general design strategy for detecting and serotyping genetically diverse viruses. A minimal number of probe sequences (26 for HRV and 13 for HEV), which were potentially capable of detecting all serotypes of HRV and HEV, were determined and implemented on the Resequencing Pathogen Microarray RPM-Flu v.30/31 (Tessarae RPM-Flu). The specificities of designed probes were validated using 34 HRV and 28 HEV strains. All strains were successfully detected and identified at least to species level. 33 HRV strains and 16 HEV strains could be further differentiated to serotype level. Conclusion This study provides a fundamental evaluation of simultaneous detection and differential identification of genetically diverse RNA viruses with a minimal number of prototype sequences. The results demonstrated that the newly designed RPM-Flu v.30/31 can provide comprehensive and specific analysis of HRV and HEV samples which implicates that this design strategy will be applicable for other genetically diverse viruses.
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- 2008
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24. Development of X-screw: a load-sensitive actuator incorporating a variable transmission.
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Hirose, S., Tibbetts, C., and Hagiwara, T.
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- 1999
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25. Complementary strand-specific sequences from unique fragments of adenovirus type 2 DNA for hybridization-mapping experiments*1
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TIBBETTS, C
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- 1974
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26. Viral DNA sequences from incomplete particles of human adenovirus type 7
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Tibbetts, C
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- 1977
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27. Adenovirus E1A gene autorepression: revertants of an E1A promoter mutation encode altered E1A proteins
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Tibbetts, C
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- 1987
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28. Representation of patients with non-English language preferences in motor vehicle collision trauma and emergency medicine research.
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Smith M, Tibbetts C, Agrawal P, Cordone A, Leff R, Smith RN, Moran TP, Brackett A, and Zeidan A
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- Humans, Accidents, Traffic, Motor Vehicles, Accidental Injuries, Biomedical Research
- Abstract
Background: Individuals with non-English language preferences (NELP) represent a growing proportion of the USA population. Prior studies demonstrate disparate health outcomes related to NELP status; however, this patient population is often excluded from medical research. There is a paucity of literature describing the impact of NELP status on trauma, specifically injury and outcomes related to vehicle occupants injured during motor vehicle collisions (MVCs). The goal of this study was to evaluate the representation of patients with NELP in both emergency medicine and trauma literature., Methods: We conducted a systematic search of US-based publications from 2010 to 2021. Titles, abstracts and full texts of eligible articles were evaluated. Data were extracted using an a priori determined standardised reporting tool to evaluate language as study inclusion/exclusion criteria, manuscript reporting of language, assessment of language as a primary variable and consideration of language in study methodology., Results: A total of 82 studies met inclusion criteria. Twenty-three studies (28%) excluded NELP populations and only one study explicitly included the NELP population. None of the studies evaluated language as a primary outcome of the study or included language as a variable in the analysis. Over half of the studies (53.6%) used a public data set or registry., Conclusion: NELP populations are routinely excluded from and are difficult to identify in MVC trauma research. Without appropriate inclusion and identification, it will be difficult to understand the prevalence and outcomes of traumatic injury in NELP patients and to develop culturally and linguistically appropriate interventions., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. No commercial re-use. See rights and permissions. Published by BMJ.)
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- 2023
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29. Characterizing injury patterns and outcomes in hospitalized trauma patients with non-English Language Preferences.
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Meyer CH, Zeidan A, Beshara G, Cortes J, Tibbetts C, Tracy BM, Jayaraman Muralidharan V, Sola R Jr, Hernandez Irizarry R, Williams K, Thompson A, Todd SR, Sciarretta JD, and Smith RN
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- Humans, Emergency Service, Hospital, Retrospective Studies, Hospital Mortality, Injury Severity Score, Length of Stay, Language, Trauma Centers
- Abstract
Introduction: Patients with Non-English Language Preferences (NELP) experience challenges navigating the US healthcare system which can lead to disparate outcomes. This study sought to investigate injury patterns and outcomes in hospitalized trauma patients with NELP., Methods: A retrospective review was performed at a trauma center from January 2019-December 2020. An institutional database of all emergency department video consultations for interpreter services was cross-referenced with the trauma registry and comparisons were made between NELP and English-preferred (EP) speaking patients., Results: During the study, 257 NELP patients were hospitalized after traumatic injury. Twenty-two percent had work related injuries compared to only 3.0% in the EP cohort (p < 0.001). When propensity score matched, there were no significant differences in ICU and hospital length of stay or mortality between NELP and EP patients., Discussion: Trauma patients are linguistically diverse and understanding their injury patterns and outcomes is crucial for guiding culturally and linguistically appropriate injury prevention., Competing Interests: Declaration of competing interest The authors of this manuscript do not have any conflicts of interest., (Copyright © 2022 Elsevier Inc. All rights reserved.)
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- 2023
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30. Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using a high-density resequencing pathogen microarray platform.
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Kourout M, Fisher C, Purkayastha A, Tibbetts C, Winkelman V, Williamson P, Nakhasi HL, and Duncan R
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- Bacterial Infections diagnosis, Blood Safety, DNA, Bacterial analysis, DNA, Viral analysis, Databases, Genetic, Humans, Molecular Diagnostic Techniques methods, Multiplex Polymerase Chain Reaction instrumentation, Multiplex Polymerase Chain Reaction methods, Oligonucleotide Array Sequence Analysis standards, Protozoan Infections diagnosis, Virus Diseases diagnosis, Blood Donors, Blood-Borne Pathogens isolation & purification, Oligonucleotide Array Sequence Analysis methods, Plasma microbiology, Plasma parasitology, Plasma virology
- Abstract
Background: The implementation of nucleic acid-based tests for blood donor screening has improved the safety of the blood supply; however, the increasing number of emerging pathogen tests is burdensome. Development of multiplex testing platforms that allow simultaneous screening for different pathogens is a potential solution., Study Design and Methods: The TessArray resequencing microarray is a platform that allows multiplex detection and identification of 97 different blood-borne pathogens in one single test. The objective was to evaluate the lowest concentration detected in blood or plasma, species discrimination, and applicability of the TessArray microarray platform for testing blood donors. Human blood or plasma spiked with selected pathogens (10,000, 1000, or 100 cells or copies/mL), including three viral, four bacterial, and four protozoan pathogens were each tested on this platform. The nucleic acids were extracted, amplified using multiplexed sets of pooled specific primers, fragmented, labeled, and hybridized to a microarray. Finally, the detected sequences were identified using an automated genomic database alignment algorithm., Results: The performance of this platform demonstrated detection for spiked bacterial and protozoan pathogens of 100 cells/mL and viral pathogens as low as 100 copies/mL. Coded specimens, including spiked and negative controls, were identified correctly for blood specimens (31/32, 97%) and for plasma specimens (20/22, 91%) demonstrating the effectiveness of the platform., Conclusion: These results indicated that the TessArray microarray platform could be employed for multiplex detection and identification, with a high level of discriminatory power for numerous blood-borne pathogen targets with potential for use in blood safety., (© 2016 AABB.)
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- 2016
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31. Development and performance of a comprehensive targeted sequencing assay for pan-ethnic screening of carrier status.
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Tanner AK, Valencia CA, Rhodenizer D, Espirages M, Da Silva C, Borsuk L, Caldwell S, Gregg E, Grimes E, Lichanska AM, Morris L, Purkayastha A, Weslowski B, Tibbetts C, Lorence MC, and Hegde M
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- Adult, DNA Mutational Analysis methods, Female, Heterozygote, High-Throughput Nucleotide Sequencing, Humans, Polymerase Chain Reaction, Pregnancy, Prenatal Diagnosis methods, Sensitivity and Specificity, Ethnicity genetics, Genetic Testing methods, Mutation, Oligonucleotide Array Sequence Analysis methods, Sequence Analysis, DNA methods
- Abstract
Identifying individuals as carriers of severe disease traits enables informed decision making about reproductive options. Although carrier screening has traditionally been based on ethnicity, the increasing ethnic admixture in the general population argues for the need for pan-ethnic carrier screening assays. Highly multiplexed mutation panels allow for rapid and efficient testing of hundreds of mutations concurrently. We report the development of the Pan-Ethnic Carrier Screening assay, a targeted sequencing assay for routine screening that simultaneously detects 461 common mutations in 91 different genes underlying severe, early-onset monogenic disorders. Mutation selection was aided by the use of an extensive mutation database from a clinical laboratory with expertise in newborn screening and lysosomal storage disease testing. The assay is based on the Affymetrix GeneChip microarray platform but generates genomic DNA sequence as the output. Analytical sensitivity and specificity, using genomic DNA from archived control cultures and from clinical specimens, was found to be >99% for all mutation types. This targeted sequencing assay has advantages over multiplex PCR and next-generation sequencing assays, including accuracy of mutation detection over a range of mutation types and ease of analysis and reporting of results., (Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)
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- 2014
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32. FDA workshop on emerging infectious diseases: evaluating emerging infectious diseases (EIDs) for transfusion safety.
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Atreya C, Nakhasi H, Mied P, Epstein J, Hughes J, Gwinn M, Kleinman S, Dodd R, Stramer S, Walderhaug M, Ganz P, Goodrich R, Tibbetts C, and Asher D
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- Communicable Diseases, Emerging blood, Communicable Diseases, Emerging diagnosis, Education, Health Priorities, Humans, Risk Assessment, United States, United States Food and Drug Administration, Blood Safety methods, Blood Safety trends, Blood Transfusion standards, Communicable Diseases, Emerging transmission
- Published
- 2011
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33. Broad spectrum respiratory pathogen analysis of throat swabs from military recruits reveals interference between rhinoviruses and adenoviruses.
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Wang Z, Malanoski AP, Lin B, Long NC, Leski TA, Blaney KM, Hansen CJ, Brown J, Broderick M, Stenger DA, Tibbetts C, Russell KL, and Metzgar D
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- Adolescent, Bacteria isolation & purification, Base Sequence, DNA, Viral analysis, Female, Fever etiology, Fever virology, Humans, Male, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Pharynx virology, Respiratory Tract Diseases etiology, Respiratory Tract Diseases virology, Young Adult, Adenoviridae isolation & purification, Adenovirus Infections, Human epidemiology, Military Personnel, Picornaviridae Infections epidemiology, Rhinovirus isolation & purification
- Abstract
Military recruits experience a high incidence of febrile respiratory illness (FRI), leading to significant morbidity and lost training time. Adenoviruses, group A Streptococcus pyogenes, and influenza virus are implicated in over half of the FRI cases reported at recruit training center clinics, while the etiology of the remaining cases is unclear. In this study, we explore the carriage rates and disease associations of adenovirus, enterovirus, rhinovirus, Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis in military recruits using high-density resequencing microarrays. The results showed that rhinoviruses, adenoviruses, S. pneumoniae, H. influenzae, and N. meningitidis were widely distributed in recruits. Of these five agents, only adenovirus showed significant correlation with illness. Among the samples tested, only pathogens associated with FRI, such as adenovirus 4 and enterovirus 68, revealed strong temporal and spatial clustering of specific strains, indicating that they are transmitted primarily within sites. The results showed a strong negative association between adenoviral FRI and the presence of rhinoviruses in recruits, suggesting some form of viral interference.
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- 2010
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34. Natural variants of human adenovirus type 3 provide evidence for relative genome stability across time and geographic space.
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Mahadevan P, Seto J, Tibbetts C, and Seto D
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- Adenoviridae Infections virology, Adenoviruses, Human chemistry, Adenoviruses, Human isolation & purification, Amino Acid Sequence, China, Cluster Analysis, Geography, Humans, Molecular Sequence Data, Phylogeny, Proteome analysis, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Time Factors, United States, Viral Proteins analysis, Adenoviruses, Human genetics, DNA, Viral genetics, Genetic Variation, Genomic Instability
- Abstract
Human adenovirus type 3 (HAdV-B3) has an apparently stable genome yet remains a major circulating and problematic respiratory pathogen. Comparisons of the prototype genome to genomes from three current field strains, including two isolated from epidemics, and a laboratory strain, yielded small-scale nucleotide variations across 50 years of time and space (U.S. and China). This is in contrast to the recombination events that have been reported recently for HAdV genomes. Recombinant genomes have been identified in emergent HAdV pathogens and is a pathway for the molecular evolution of types. These two contrasting views of HAdV genome stability have repercussions in the development and use of vaccines for countering HAdV-B3, as well as in the continued effectiveness of vaccines developed against earlier and current circulating types of HAdV., (Copyright 2009 Elsevier Inc. All rights reserved.)
- Published
- 2010
- Full Text
- View/download PDF
35. Single assay for simultaneous detection and differential identification of human and avian influenza virus types, subtypes, and emergent variants.
- Author
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Metzgar D, Myers CA, Russell KL, Faix D, Blair PJ, Brown J, Vo S, Swayne DE, Thomas C, Stenger DA, Lin B, Malanoski AP, Wang Z, Blaney KM, Long NC, Schnur JM, Saad MD, Borsuk LA, Lichanska AM, Lorence MC, Weslowski B, Schafer KO, and Tibbetts C
- Subjects
- Animals, Base Sequence, Birds, Cell Line, Chick Embryo, Gene Expression Profiling methods, Gene Expression Regulation, Viral, Humans, Influenza A virus classification, Influenza in Birds virology, Influenza, Human virology, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Reproducibility of Results, Reverse Transcriptase Polymerase Chain Reaction, Sensitivity and Specificity, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Influenza A virus genetics, Influenza in Birds diagnosis, Influenza, Human diagnosis, Pathology, Molecular methods
- Abstract
For more than four decades the cause of most type A influenza virus infections of humans has been attributed to only two viral subtypes, A/H1N1 or A/H3N2. In contrast, avian and other vertebrate species are a reservoir of type A influenza virus genome diversity, hosting strains representing at least 120 of 144 combinations of 16 viral hemagglutinin and 9 viral neuraminidase subtypes. Viral genome segment reassortments and mutations emerging within this reservoir may spawn new influenza virus strains as imminent epidemic or pandemic threats to human health and poultry production. Traditional methods to detect and differentiate influenza virus subtypes are either time-consuming and labor-intensive (culture-based) or remarkably insensitive (antibody-based). Molecular diagnostic assays based upon reverse transcriptase-polymerase chain reaction (RT-PCR) have short assay cycle time, and high analytical sensitivity and specificity. However, none of these diagnostic tests determine viral gene nucleotide sequences to distinguish strains and variants of a detected pathogen from one specimen to the next. Decision-quality, strain- and variant-specific pathogen gene sequence information may be critical for public health, infection control, surveillance, epidemiology, or medical/veterinary treatment planning. The Resequencing Pathogen Microarray (RPM-Flu) is a robust, highly multiplexed and target gene sequencing-based alternative to both traditional culture- or biomarker-based diagnostic tests. RPM-Flu is a single, simultaneous differential diagnostic assay for all subtype combinations of type A influenza viruses and for 30 other viral and bacterial pathogens that may cause influenza-like illness. These other pathogen targets of RPM-Flu may co-infect and compound the morbidity and/or mortality of patients with influenza. The informative specificity of a single RPM-Flu test represents specimen-specific viral gene sequences as determinants of virus type, A/HN subtype, virulence, host-range, and resistance to antiviral agents.
- Published
- 2010
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36. Testing and validation of high density resequencing microarray for broad range biothreat agents detection.
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Leski TA, Lin B, Malanoski AP, Wang Z, Long NC, Meador CE, Barrows B, Ibrahim S, Hardick JP, Aitichou M, Schnur JM, Tibbetts C, and Stenger DA
- Subjects
- Limit of Detection, Polymerase Chain Reaction, Biological Warfare, Oligonucleotide Array Sequence Analysis methods
- Abstract
Rapid and effective detection and identification of emerging microbiological threats and potential biowarfare agents is very challenging when using traditional culture-based methods. Contemporary molecular techniques, relying upon reverse transcription and/or polymerase chain reaction (RT-PCR/PCR) provide a rapid and effective alternative, however, such assays are generally designed and optimized to detect only a limited number of targets, and seldom are capable of differentiation among variants of detected targets. To meet these challenges, we have designed a broad-range resequencing pathogen microarray (RPM) for detection of tropical and emerging infectious agents (TEI) including biothreat agents: RPM-TEI v 1.0 (RPM-TEI). The scope of the RPM-TEI assay enables detection and differential identification of 84 types of pathogens and 13 toxin genes, including most of the class A, B and C select agents as defined by the Centers for Disease Control and Prevention (CDC, Atlanta, GA). Due to the high risks associated with handling these particular target pathogens, the sensitivity validation of the RPM-TEI has been performed using an innovative approach, in which synthetic DNA fragments are used as templates for testing the assay's limit of detection (LOD). Assay specificity and sensitivity was subsequently confirmed by testing with full-length genomic nucleic acids of selected agents. The LOD for a majority of the agents detected by RPM-TEI was determined to be at least 10(4) copies per test. Our results also show that the RPM-TEI assay not only detects and identifies agents, but is also able to differentiate near neighbors of the same agent types, such as closely related strains of filoviruses of the Ebola Zaire group, or the Machupo and Lassa arenaviruses. Furthermore, each RPM-TEI assay results in specimen-specific agent gene sequence information that can be used to assess pathogenicity, mutations, and virulence markers, results that are not generally available from multiplexed RT-PCR/PCR-based detection assays.
- Published
- 2009
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37. Genomic and bioinformatics analyses of HAdV-14p, reference strain of a re-emerging respiratory pathogen and analysis of B1/B2.
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Seto J, Walsh MP, Mahadevan P, Purkayastha A, Clark JM, Tibbetts C, and Seto D
- Subjects
- Adenoviruses, Human pathogenicity, Base Sequence, Capsid Proteins analysis, Capsid Proteins genetics, DNA, Viral analysis, DNA, Viral genetics, Genome, Viral, Humans, Inverted Repeat Sequences, Molecular Sequence Data, Phylogeny, Proteome analysis, Sequence Alignment, Sequence Homology, Nucleic Acid, Virulence, Adenovirus Infections, Human virology, Adenoviruses, Human genetics, Computational Biology, Genomics
- Abstract
Unlike other human adenovirus (HAdV) species, B is divided into subspecies B1 and B2. Originally this was partly based on restriction enzyme (RE) analysis. B1 members, except HAdV-50, are commonly associated with respiratory diseases while B2 members are rarely associated with reported respiratory diseases. Recently two members of B2 have been identified in outbreaks of acute respiratory disease (ARD). One, HAdV-14, has re-emerged after an apparent 52-year absence. Genomic analysis and bioinformatics data are reported for HAdV-14 prototype for use as a reference and to understand and counter its re-emergence. The data complement and extend the original criteria for subspecies designation, unique amongst the adenoviruses, and highlight differences between B1 and B2, representing the first comprehensive analysis of this division. These data also provide finer granularity into the pathoepidemiology of the HAdVs. Whole genome analysis uncovers heterogeneous identity structures of the hexon and fiber genes amongst the HAdV-14 and the B1/B2 subspecies, which may be important in prescient vaccine development. Analysis of cell surface proteins provides insight into HAdV-14 tropism, accounting for its role as a respiratory pathogen. This HAdV-14 prototype genome is also a reference for applications of B2 adenoviruses as vectors for vaccine development and gene therapy.
- Published
- 2009
- Full Text
- View/download PDF
38. Universal detection and identification of avian influenza virus by use of resequencing microarrays.
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Lin B, Malanoski AP, Wang Z, Blaney KM, Long NC, Meador CE, Metzgar D, Myers CA, Yingst SL, Monteville MR, Saad MD, Schnur JM, Tibbetts C, and Stenger DA
- Subjects
- Animals, Birds, Molecular Sequence Data, Sensitivity and Specificity, Influenza A virus classification, Influenza A virus isolation & purification, Influenza in Birds diagnosis, Influenza in Birds virology, Oligonucleotide Array Sequence Analysis methods, RNA, Viral genetics, Sequence Analysis, DNA methods
- Abstract
Zoonotic microbes have historically been, and continue to emerge as, threats to human health. The recent outbreaks of highly pathogenic avian influenza virus in bird populations and the appearance of some human infections have increased the concern of a possible new influenza pandemic, which highlights the need for broad-spectrum detection methods for rapidly identifying the spread or outbreak of all variants of avian influenza virus. In this study, we demonstrate that high-density resequencing pathogen microarrays (RPM) can be such a tool. The results from 37 influenza virus isolates show that the RPM platform is an effective means for detecting and subtyping influenza virus, while simultaneously providing sequence information for strain resolution, pathogenicity, and drug resistance without additional analysis. This study establishes that the RPM platform is a broad-spectrum pathogen detection and surveillance tool for monitoring the circulation of prevalent influenza viruses in the poultry industry and in wild birds or incidental exposures and infections in humans.
- Published
- 2009
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39. Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses.
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Wang Z, Malanoski AP, Lin B, Kidd C, Long NC, Blaney KM, Thach DC, Tibbetts C, and Stenger DA
- Subjects
- Base Sequence, Diagnosis, Differential, Enterovirus genetics, Humans, RNA Probes, RNA Viruses, Respiratory Tract Infections virology, Rhinovirus genetics, Enterovirus isolation & purification, Respiratory Tract Infections diagnosis, Rhinovirus isolation & purification
- Abstract
Background: Febrile respiratory illness (FRI) has a high impact on public health and global economics and poses a difficult challenge for differential diagnosis. A particular issue is the detection of genetically diverse pathogens, i.e. human rhinoviruses (HRV) and enteroviruses (HEV) which are frequent causes of FRI. Resequencing Pathogen Microarray technology has demonstrated potential for differential diagnosis of several respiratory pathogens simultaneously, but a high confidence design method to select probes for genetically diverse viruses is lacking., Results: Using HRV and HEV as test cases, we assess a general design strategy for detecting and serotyping genetically diverse viruses. A minimal number of probe sequences (26 for HRV and 13 for HEV), which were potentially capable of detecting all serotypes of HRV and HEV, were determined and implemented on the Resequencing Pathogen Microarray RPM-Flu v.30/31 (Tessarae RPM-Flu). The specificities of designed probes were validated using 34 HRV and 28 HEV strains. All strains were successfully detected and identified at least to species level. 33 HRV strains and 16 HEV strains could be further differentiated to serotype level., Conclusion: This study provides a fundamental evaluation of simultaneous detection and differential identification of genetically diverse RNA viruses with a minimal number of prototype sequences. The results demonstrated that the newly designed RPM-Flu v.30/31 can provide comprehensive and specific analysis of HRV and HEV samples which implicates that this design strategy will be applicable for other genetically diverse viruses.
- Published
- 2008
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40. Application of broad-spectrum, sequence-based pathogen identification in an urban population.
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Lin B, Malanoski AP, Wang Z, Blaney KM, Ligler AG, Rowley RK, Hanson EH, von Rosenvinge E, Ligler FS, Kusterbeck AW, Metzgar D, Barrozo CP, Russell KL, Tibbetts C, Schnur JM, and Stenger DA
- Subjects
- Bacteria genetics, Bacteria immunology, Bacteria isolation & purification, Humans, Orthomyxoviridae genetics, Orthomyxoviridae immunology, Orthomyxoviridae isolation & purification, Phylogeny, Respiratory Tract Diseases virology, Reverse Transcriptase Polymerase Chain Reaction, Respiratory Tract Diseases microbiology, Urban Population
- Abstract
A broad spectrum detection platform that provides sequence level resolution of target regions would have a significant impact in public health, case management, and means of expanding our understanding of the etiology of diseases. A previously developed respiratory pathogen microarray (RPM v.1) demonstrated the capability of this platform for this purpose. This newly developed RPM v.1 was used to analyze 424 well-characterized nasal wash specimens from patients presenting with febrile respiratory illness in the Washington, D. C. metropolitan region. For each specimen, the RPM v.1 results were compared against composite reference assay (viral and bacterial culture and, where appropriate, RT-PCR/PCR) results. Across this panel, the RPM assay showed >or=98% overall agreement for all the organisms detected compared with reference methods. Additionally, the RPM v.1 results provide sequence information which allowed phylogenetic classification of circulating influenza A viruses in approximately 250 clinical specimens, and allowed monitoring the genetic variation as well as antigenic variability prediction. Multiple pathogens (2-4) were detected in 58 specimens (13.7%) with notably increased abundances of respiratory colonizers (esp. S. pneumoniae) during viral infection. This first-ever comparison of a broad-spectrum viral and bacterial identification technology of this type against a large battery of conventional "gold standard" assays confirms the utility of the approach for both medical surveillance and investigations of complex etiologies of illness caused by respiratory co-infections.
- Published
- 2007
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41. Co-infections of adenovirus species in previously vaccinated patients.
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Vora GJ, Lin B, Gratwick K, Meador C, Hansen C, Tibbetts C, Stenger DA, Irvine M, Seto D, Purkayastha A, Freed NE, Gibson MG, Russell K, and Metzgar D
- Subjects
- Adenovirus Infections, Human epidemiology, Adenovirus Infections, Human prevention & control, Adenoviruses, Human genetics, DNA, Viral chemistry, DNA, Viral genetics, Enzyme-Linked Immunosorbent Assay, Humans, Military Personnel, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Respiratory Tract Infections epidemiology, Respiratory Tract Infections prevention & control, Serotyping methods, United States epidemiology, Adenovirus Infections, Human virology, Adenoviruses, Human growth & development, Disease Outbreaks, Respiratory Tract Infections virology, Viral Vaccines administration & dosage
- Abstract
Despite the success of the adenovirus vaccine administered to US military trainees, acute respiratory disease (ARD) surveillance still detected breakthrough infections (respiratory illnesses associated with the adenovirus serotypes specifically targeted by the vaccine). To explore the role of adenoviral co-infection (simultaneous infection by multiple pathogenic adenovirus species) in breakthrough disease, we examined specimens from patients with ARD by using 3 methods to detect multiple adenoviral species: a DNA microarray, a polymerase chain reaction (PCR)-enzyme-linked immunosorbent assay, and a multiplex PCR assay. Analysis of 52 samples (21 vaccinated, 31 unvaccinated) collected from 1996 to 2000 showed that all vaccinated samples had co-infections. Most of these co-infections were community-acquired serotypes of species B1 and E. Unvaccinated samples primarily contained only 1 species (species E) associated with adult respiratory illness. This study highlights the rarely reported phenomenon of adenoviral co-infections in a clinically relevant environment suitable for the generation of new recombinational variants.
- Published
- 2006
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- View/download PDF
42. Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays.
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Lin B, Wang Z, Vora GJ, Thornton JA, Schnur JM, Thach DC, Blaney KM, Ligler AG, Malanoski AP, Santiago J, Walter EA, Agan BK, Metzgar D, Seto D, Daum LT, Kruzelock R, Rowley RK, Hanson EH, Tibbetts C, and Stenger DA
- Subjects
- Bacterial Typing Techniques methods, Humans, Mycological Typing Techniques methods, Polymerase Chain Reaction, Predictive Value of Tests, Respiratory Tract Infections diagnosis, Sensitivity and Specificity, Oligonucleotide Array Sequence Analysis methods, Respiratory Tract Infections genetics, Sequence Analysis, DNA methods
- Abstract
The exponential growth of pathogen nucleic acid sequences available in public domain databases has invited their direct use in pathogen detection, identification, and surveillance strategies. DNA microarray technology has offered the potential for the direct DNA sequence analysis of a broad spectrum of pathogens of interest. However, to achieve the practical attainment of this potential, numerous technical issues, especially nucleic acid amplification, probe specificity, and interpretation strategies of sequence detection, need to be addressed. In this report, we demonstrate an approach that combines the use of a custom-designed Affymetrix resequencing Respiratory Pathogen Microarray (RPM v.1) with methods for microbial nucleic acid enrichment, random nucleic acid amplification, and automated sequence similarity searching for broad-spectrum respiratory pathogen surveillance. Successful proof-of-concept experiments, utilizing clinical samples obtained from patients presenting adenovirus or influenza virus-induced febrile respiratory illness (FRI), demonstrate the ability of this approach for correct species- and strain-level identification with unambiguous statistical interpretation at clinically relevant sensitivity levels. Our results underscore the feasibility of using this approach to expedite the early surveillance of diseases, and provide new information on the incidence of multiple pathogens.
- Published
- 2006
- Full Text
- View/download PDF
43. Genomic and bioinformatics analyses of HAdV-4vac and HAdV-7vac, two human adenovirus (HAdV) strains that constituted original prophylaxis against HAdV-related acute respiratory disease, a reemerging epidemic disease.
- Author
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Purkayastha A, Su J, McGraw J, Ditty SE, Hadfield TL, Seto J, Russell KL, Tibbetts C, and Seto D
- Subjects
- Acute Disease, Adenovirus Infections, Human epidemiology, Adenovirus Infections, Human prevention & control, Adenoviruses, Human immunology, Amino Acid Sequence, Base Sequence, Capsid Proteins chemistry, Capsid Proteins genetics, Communicable Diseases, Emerging epidemiology, Genome, Viral, Humans, Molecular Sequence Data, Respiratory Tract Infections epidemiology, Sequence Analysis, DNA, Adenoviruses, Human genetics, Communicable Diseases, Emerging prevention & control, Computational Biology, Genomics, Respiratory Tract Infections prevention & control, Viral Vaccines administration & dosage
- Abstract
Vaccine strains of human adenovirus serotypes 4 and 7 (HAdV-4vac and HAdV-7vac) have been used successfully to prevent adenovirus-related acute respiratory disease outbreaks. The genomes of these two vaccine strains have been sequenced, annotated, and compared with their prototype equivalents with the goals of understanding their genomes for molecular diagnostics applications, vaccine redevelopment, and HAdV pathoepidemiology. These reference genomes are archived in GenBank as HAdV-4vac (35,994 bp; AY594254) and HAdV-7vac (35,240 bp; AY594256). Bioinformatics and comparative whole-genome analyses with their recently reported and archived prototype genomes reveal six mismatches and four insertions-deletions (indels) between the HAdV-4 prototype and vaccine strains, in contrast to the 611 mismatches and 130 indels between the HAdV-7 prototype and vaccine strains. Annotation reveals that the HAdV-4vac and HAdV-7vac genomes contain 51 and 50 coding units, respectively. Neither vaccine strain appears to be attenuated for virulence based on bioinformatics analyses. There is evidence of genome recombination, as the inverted terminal repeat of HAdV-4vac is initially identical to that of species C whereas the prototype is identical to species B1. These vaccine reference sequences yield unique genome signatures for molecular diagnostics. As a molecular forensics application, these references identify the circulating and problematic 1950s era field strains as the original HAdV-4 prototype and the Greider prototype, from which the vaccines are derived. Thus, they are useful for genomic comparisons to current epidemic and reemerging field strains, as well as leading to an understanding of pathoepidemiology among the human adenoviruses.
- Published
- 2005
- Full Text
- View/download PDF
44. Genomic and bioinformatics analysis of HAdV-7, a human adenovirus of species B1 that causes acute respiratory disease: implications for vector development in human gene therapy.
- Author
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Purkayastha A, Su J, Carlisle S, Tibbetts C, and Seto D
- Subjects
- Adenovirus Infections, Human virology, Adenoviruses, Human classification, Adenoviruses, Human pathogenicity, Amino Acid Sequence, Base Sequence, Computational Biology, Genetic Therapy, Humans, Molecular Sequence Data, Respiratory Tract Infections transmission, Respiratory Tract Infections virology, Sequence Homology, Amino Acid, Viral Proteins genetics, Adenoviruses, Human genetics, Genetic Vectors genetics, Genome, Viral, Respiratory Tract Infections epidemiology, Viral Proteins chemistry
- Abstract
Human adenovirus serotype 7 (HAdV-7) is a reemerging pathogen identified in acute respiratory disease (ARD), particularly in epidemics affecting basic military trainee populations of otherwise healthy young adults. The genome has been sequenced and annotated (GenBank accession no. ). Comparative genomics and bioinformatics analyses of the HAdV-7 genome sequence provide insight into its natural history and phylogenetic relationships. A putative origin of HAdV-7 from a chimpanzee host is observed. This has implications within the current biotechnological interest of using chimpanzee adenoviruses as vectors for human gene therapy and DNA vaccine delivery. Rapid genome sequencing and analyses of this species B1 member provide an example of exploiting accurate low-pass DNA sequencing technology in pathogen characterization and epidemic outbreak surveillance through the identification, validation, and application of unique pathogen genome signatures.
- Published
- 2005
- Full Text
- View/download PDF
45. Genomic and bioinformatics analysis of HAdV-4, a human adenovirus causing acute respiratory disease: implications for gene therapy and vaccine vector development.
- Author
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Purkayastha A, Ditty SE, Su J, McGraw J, Hadfield TL, Tibbetts C, and Seto D
- Subjects
- Adenovirus Infections, Human epidemiology, Adenovirus Infections, Human prevention & control, Adenoviruses, Human classification, Adenoviruses, Human pathogenicity, Cell Line, Tumor, Computational Biology, DNA, Viral chemistry, DNA, Viral genetics, Genetic Therapy, Humans, Molecular Sequence Data, Phylogeny, Respiratory Tract Infections prevention & control, Respiratory Tract Infections transmission, Respiratory Tract Infections virology, Viral Vaccines administration & dosage, Adenovirus Infections, Human therapy, Adenoviruses, Human genetics, Genome, Viral, Respiratory Tract Infections epidemiology, Viral Vaccines genetics
- Abstract
Human adenovirus serotype 4 (HAdV-4) is a reemerging viral pathogenic agent implicated in epidemic outbreaks of acute respiratory disease (ARD). This report presents a genomic and bioinformatics analysis of the prototype 35,990-nucleotide genome (GenBank accession no. AY594253). Intriguingly, the genome analysis suggests a closer phylogenetic relationship with the chimpanzee adenoviruses (simian adenoviruses) rather than with other human adenoviruses, suggesting a recent origin of HAdV-4, and therefore species E, through a zoonotic event from chimpanzees to humans. Bioinformatics analysis also suggests a pre-zoonotic recombination event, as well, between species B-like and species C-like simian adenoviruses. These observations may have implications for the current interest in using chimpanzee adenoviruses in the development of vectors for human gene therapy and for DNA-based vaccines. Also, the reemergence, surveillance, and treatment of HAdV-4 as an ARD pathogen is an opportunity to demonstrate the use of genome determination as a tool for viral infectious disease characterization and epidemic outbreak surveillance: for example, rapid and accurate low-pass sequencing and analysis of the genome. In particular, this approach allows the rapid identification and development of unique probes for the differentiation of family, species, serotype, and strain (e.g., pathogen genome signatures) for monitoring epidemic outbreaks of ARD.
- Published
- 2005
- Full Text
- View/download PDF
46. Natural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1.
- Author
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Lauer KP, Llorente I, Blair E, Seto J, Krasnov V, Purkayastha A, Ditty SE, Hadfield TL, Buck C, Tibbetts C, and Seto D
- Subjects
- Adenovirus Infections, Human virology, Adenoviruses, Human classification, Adenoviruses, Human pathogenicity, Amino Acid Sequence, Capsid Proteins genetics, DNA Primers, Humans, Military Personnel, Molecular Sequence Data, Polymerase Chain Reaction, Sequence Alignment, Serotyping, Species Specificity, Adenoviruses, Human genetics, Genetic Variation, Genome, Viral
- Abstract
The 36,001 base pair DNA sequence of human adenovirus serotype 1 (HAdV-1) has been determined, using a 'leveraged primer sequencing strategy' to generate high quality sequences economically. This annotated genome (GenBank AF534906) confirms anticipated similarity to closely related species C (formerly subgroup), human adenoviruses HAdV-2 and -5, and near identity with earlier reports of sequences representing parts of the HAdV-1 genome. A first round of HAdV-1 sequence data acquisition used PCR amplification and sequencing primers from sequences common to the genomes of HAdV-2 and -5. The subsequent rounds of sequencing used primers derived from the newly generated data. Corroborative re-sequencing with primers selected from this HAdV-1 dataset generated sparsely tiled arrays of high quality sequencing ladders spanning both complementary strands of the HAdV-1 genome. These strategies allow for rapid and accurate low-pass sequencing of genomes. Such rapid genome determinations facilitate the development of specific probes for differentiation of family, serotype, subtype and strain (e.g. pathogen genome signatures). These will be used to monitor epidemic outbreaks of acute respiratory disease in a defined test bed by the Epidemic Outbreak Surveillance (EOS) project.
- Published
- 2004
- Full Text
- View/download PDF
47. Use of oligonucleotide microarrays for rapid detection and serotyping of acute respiratory disease-associated adenoviruses.
- Author
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Lin B, Vora GJ, Thach D, Walter E, Metzgar D, Tibbetts C, and Stenger DA
- Subjects
- Acute Disease, Adenoviridae classification, Humans, Polymerase Chain Reaction, Sensitivity and Specificity, Serotyping, Adenoviridae isolation & purification, Oligonucleotide Array Sequence Analysis, Respiration Disorders virology
- Abstract
The cessation of the adenovirus vaccination program for military trainees has resulted in several recent acute respiratory disease (ARD) outbreaks. In the absence of vaccination, rapid detection methods are necessary for the timely implementation of measures to prevent adenovirus transmission within military training facilities. To this end, we have combined a fluorogenic real-time multiplex PCR assay with four sets of degenerate PCR primers that target the E1A, fiber, and hexon genes with a long oligonucleotide microarray capable of identifying the most common adenovirus serotypes associated with adult respiratory tract infections (serotypes 3, 4, 7, 16, and 21) and a representative member of adenovirus subgroup C (serotype 6) that is a common cause of childhood ARD and that often persists into adulthood. Analyses with prototype strains demonstrated unique hybridization patterns for representative members of adenovirus subgroups B(1), B(2), C, and E, thus allowing serotype determination. Microarray-based sensitivity assessments revealed lower detection limits (between 1 and 100 genomic copies) for adenovirus serotype 4 (Ad4) and Ad7 cell culture lysates, clinical nasal washes, and throat swabs and purified DNA from clinical samples. When adenovirus was detected from coded clinical samples, the results obtained by this approach demonstrated an excellent concordance with those obtained by the more established method of adenovirus identification as well as by cell culture with fluorescent-antibody staining. Finally, the utility of this method was further supported by its ability to detect adenoviral coinfections, contamination, and, potentially, recombination events. Taken together, the results demonstrate the usefulness of the simple and rapid diagnostic method developed for the unequivocal identification of ARD-associated adenoviral serotypes from laboratory or clinical samples that can be completed in 1.5 to 4.0 h.
- Published
- 2004
- Full Text
- View/download PDF
48. Assessment of two methods for handling blood in collection tubes with RNA stabilizing agent for surveillance of gene expression profiles with high density microarrays.
- Author
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Thach DC, Lin B, Walter E, Kruzelock R, Rowley RK, Tibbetts C, and Stenger DA
- Subjects
- Humans, Blood Specimen Collection methods, Gene Expression Profiling, Oligonucleotide Array Sequence Analysis methods, RNA blood
- Abstract
Genome-wide expression studies of human blood samples in the context of epidemiologic surveillance are confronted by numerous challenges-one of the foremost being the capability to produce reliable detection of transcript levels. This led us to consider the Paxgene Blood RNA System, which consists of a stabilizing additive in an evacuated blood collection tube (PAX tube) and a sample processing kit (PAX kit). The PAX tube contains a solution that inhibits RNA degradation and gene induction as blood is drawn into the tube. The stability of RNA in PAX tubes under conditions for practical clinical applications has been determined by RT-PCR, but has not been assessed at the transcriptome level on Affymetrix microarrays. Here, we report a quality assured and controlled protocol that is capable of producing reliable gene expression profiles using the GeneChip system with RNA isolated from PAX tubes. Using this protocol, we compared quality metrics and gene-expression profiles of RNA, extracted from blood in PAX tubes that sat at room temperature for 2 h, with that of blood in PAX tubes incubated at room temperature for 9 h followed by storage at -20 degrees C for 6 days. Of numerous metrics, differences between the two handling methods were detected for the level of DNA contamination, RNA yield, and double stranded cDNA yield. Analysis of variance of gene-expression revealed small but significant differences between the handling methods. These results contribute to the determination of protocols for clinical studies and progress us towards the goal of using the transcriptome in diagnosis and surveillance.
- Published
- 2003
- Full Text
- View/download PDF
49. Modification of a commercially available DNA sequencer to increase sample throughput.
- Author
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Stuebe ET, Steward JQ, Chinwalla A, Cook LL, Cook M, Fronick B, Miller K, Mullen MK, O'Brien D, Panussis DA, Pohl C, Snider JE, Strong J, Williams D, Wilson RK, Tibbetts C, and Mardis ER
- Subjects
- Computer Systems, Data Collection standards, Electrophoresis instrumentation, Equipment Design, Software Design, Data Display standards, Electrophoresis methods, Sequence Analysis, DNA methods
- Published
- 2000
- Full Text
- View/download PDF
50. Phenotypic determinants of adenovirus E1A gene autoregulation: variable region between conserved coding domains 2 and 3.
- Author
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Hamid R, Cogan JD, Jones SN, and Tibbetts C
- Subjects
- Amino Acid Sequence, Base Sequence, Conserved Sequence, DNA, Viral genetics, Gene Expression Regulation, Viral, HeLa Cells, Humans, Molecular Sequence Data, Phenotype, Adenovirus E1A Proteins genetics, Adenoviruses, Human genetics, Genes, Viral, Promoter Regions, Genetic, Transcriptional Activation
- Abstract
Different serotypes and evolutionary variants of human adenoviruses exhibit distinctive patterns of positive and negative autoregulation of the viral E1A gene. An autoregulatory E1A promoter mutation of the adenovirus type 3 (Ad3) E1A gene renders Ad3hr15 incapable of growth in normally permissive cells. The promoter mutation is complemented in trans by E1A products of the heterologous helper adenovirus type 5 (Ad5). Second-site revertants of Ad3hr15 restore viability with high levels of E1A gene expression. The revertant E1A genotypes retain the mutant E1A promoter and have small in-frame deletions in the nonconserved region between the repression- and activation-associated conserved domains CR2 and CR3. Plasmid expression vectors were constructed as 12S and 13S cDNA forms of revertant E1A genes. These were used in cotransfection experiments with a reporter gene plasmid under transcriptional control of the mutant Ad3hr15 E1A promoter. The repression of the Ad3hr15 E1A promoter by helper Ad5 or revertant 12S E1A cDNA was consistently greater than that effected wild-type Ad3 12S cDNAs expression. Significantly greater levels of positive transactivation were observed in cotransfections with 13S cDNAs of Ad5 or with the 13S E1A cDNA of Ad3hr15 revertants, compared to the transactivation observed with the mutant-encoded wild-type Ad3 13S E1A cDNA. The Ad5 helper and dI-revertant phenotype of Ad3hr15 appear to be related to transactivation activities of coexpressed E1A genes. The nonconserved region which separates the conserved coding regions CR2 and CR3 of the type 3 E1A gene acts to attenuate E1A-mediated repression and transactivation of transcription.
- Published
- 1995
- Full Text
- View/download PDF
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