12 results on '"Gall, Alexander"'
Search Results
2. Rapid Detection of Bacillus anthracisBloodstream Infections by Use of a Novel Assay in the GeneXpert System
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Banada, Padmapriya P., Deshpande, Srinidhi, Russo, Riccardo, Singleton, Eric, Shah, Darshini, Patel, Bhavana, Burday, Michele, Koshy, Ranie, Wang, Qing, Jones, Martin, Gall, Alexander, Lokhov, Sergey, Kwiatkowski, Robert, Persing, David, Connell, Nancy, and Alland, David
- Abstract
ABSTRACTBacillus anthracisis a tier 1 select agent with the potential to quickly cause severe disease. Rapid identification of this pathogen may accelerate treatment and reduce mortality in the event of a bioterrorism attack. We developed a rapid and sensitive assay to detect B. anthracisbacteremia using a system that is suitable for point-of-care testing. A filter-based cartridge that included both sample processing and PCR amplification functions was loaded with all reagents needed for sample processing and multiplex nested PCR. The assay limit of detection (LOD) and dynamic range were determined by spiking B. anthracisDNA into individual PCR mixtures and B. anthracisCFU into human blood. One-milliliter blood samples were added to the filter-based detection cartridge and tested for B. anthracison a GeneXpert instrument. Assay specificity was determined by testing blood spiked with non-anthrax bacterial isolates or by testing blood samples drawn from patients with concurrent non-B. anthracisbacteremia or nonbacteremic controls. The assay LODs were 5 genome equivalents per reaction and 10 CFU/ml blood for both the B. anthracisSterne and V1B strains. There was a 6-log10dynamic range. Assay specificity was 100% for tests of non-B. anthracisbacterial isolates and patient blood samples. Assay time was less than 90 min. This automated system suitable for point-of-care detection rapidly identifies B. anthracisdirectly from blood with high sensitivity. This assay might lead to early detection and more rapid therapy in the event of a bioterrorism attack.
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- 2017
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3. Detection of Isoniazid-, Fluoroquinolone-, Amikacin-, and Kanamycin-Resistant Tuberculosis in an Automated, Multiplexed 10-Color Assay Suitable for Point-of-Care Use
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Chakravorty, Soumitesh, Roh, Sandy S., Glass, Jennifer, Smith, Laura E., Simmons, Ann Marie, Lund, Kevin, Lokhov, Sergey, Liu, Xin, Xu, Peng, Zhang, Guolong, Via, Laura E., Shen, Qingyu, Ruan, Xianglin, Yuan, Xing, Zhu, Hong Zhu, Viazovkina, Ekaterina, Shenai, Shubhada, Rowneki, Mazhgan, Lee, Jong Seok, Barry, Clifton E., Gao, Qian, Persing, David, Kwiatkawoski, Robert, Jones, Martin, Gall, Alexander, and Alland, David
- Abstract
ABSTRACTExtensively drug-resistant (XDR) tuberculosis (TB) cannot be easily or quickly diagnosed. We developed a rapid, automated assay for the detection of XDR-TB plus resistance to the drug isoniazid (INH) for point-of-care use. Using a simple filter-based cartridge with an integrated sample processing function, the assay identified a wide selection of wild-type and mutant sequences associated with XDR-TB directly from sputum. Four new large-Stokes-shift fluorophores were developed. When these four Stokes-shift fluorophores were combined with six conventional fluorophores, 10-color probe detection in a single PCR tube was enabled. A new three-phase, double-nested PCR approach allowed robust melting temperature analysis with enhanced limits of detection (LODs). Finally, newly designed sloppy molecular beacons identified many different mutations using a small number of probes. The assay correctly distinguished wild-type sequences from 32 commonly occurring mutant sequences tested in gyrA, gyrB, katG, and rrsgenes and the promoters of inhAand eisgenes responsible for resistance to INH, the fluoroquinolone (FQ) drugs, amikacin (AMK), and kanamycin (KAN). The LOD was 300 CFU of Mycobacterium tuberculosisin 1 ml sputum. The rate of detection of heteroresistance by the assay was equivalent to that by Sanger sequencing. In a blind study of 24 clinical sputum samples, resistance mutations were detected in all targets with 100% sensitivity, with the specificity being 93.7 to 100%. Compared to the results of phenotypic susceptibility testing, the sensitivity of the assay was 75% for FQs and 100% each for INH, AMK, and KAN and the specificity was 100% for INH and FQ and 94% for AMK and KAN. Our approach could enable testing for XDR-TB in point-of-care settings, potentially identifying highly drug-resistant TB more quickly and simply than currently available methods.
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- 2016
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4. Atomic Force Microscopy of DNA and Protein-DNA Complexes Using Functionalized Mica Substrates.
- Author
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Walker, John M., Moss, Tom, Lyubchenko, Yuri L., Gall, Alexander A., and Shlyakhtenko, Luda S.
- Abstract
Atomic force microscopy (AFM; also called scanning force microscopy [SFM]) is a rather novel technique that offers unique advantages in the potential for the very high resolution of DNA and small ligands in the absence of stains, shadows, and labels (1,2). Furthermore, the scanning can be performed in air or liquid. The latter is particularly important for resolving fully hydrated structures. The AFM is theoretically capable of resolving structural details at the level of atomic dimensions, provided that the specimen is not dynamic. [ABSTRACT FROM AUTHOR]
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- 2001
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5. Grenzen der Sicherheit: Unfälle, Medien und Politik im deutschen Kaiserreich.
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Gall, Alexander
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- 2023
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6. A Flexible Nanoarray Approach for the Assembly and Probing of Molecular Complexes
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Krasnoslobodtsev, Alexey V., Zhang, Yuliang, Viazovkina, Ekaterina, Gall, Alexander, Bertagni, Chad, and Lyubchenko, Yuri L.
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Immobilization is a key step involved in probing molecular interactions using single-molecule force spectroscopy methods, including atomic force microscopy (AFM). To our knowledge, we describe a novel approach termed flexible nanoarray (FNA) in which the interaction between the two internally immobilized amyloid βpeptides is measured by pulling of the tether. The FNA tether was synthesized with nonnucleotide phosphoramidite monomers using the DNA synthesis chemistry. The two anchoring points for immobilization of the peptides inside the tether were incorporated at defined distances between them and from the ends of the polymer. Decamers of amyloid βpeptide capable of dimer formation were selected as a test system. The formation of the peptide dimers was verified by AFM force spectroscopy by pulling the tether at the ends. In these experiments, the thiolated end of the FNA tether was covalently immobilized on the AFM substrate functionalized with maleimide. The other end of the FNA tether was functionalized with biotin to form a noncovalent link with the streptavidin functionalized AFM tip during the approach stage. The dimers’ rupture fingerprint was unambiguously identified on the force curves by its position and the force value. The FNA design allowed reversible experiments in which the monomers were allowed to associate after the rupture of the dimers by performing the approach stage before the rupture of the biotin-streptavidin link. This suggests that the FNA technique is capable of analyzing multiple intermolecular interactions in the same molecular complex. The computational analysis showed that the tethered peptides assemble into the same dimer structure as that formed by nontethered peptides, suggesting that the FNA tether has the necessary flexibility to enable assembly of the dimer even during the course of the force spectroscopy experiment.
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- 2015
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7. Atomic Force Microscopy Imaging of DNA Covalently Immobilized on a Functionalized Mica Substrate
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Shlyakhtenko, Luda S., Gall, Alexander A., Weimer, Jeffrey J., Hawn, David D., and Lyubchenko, Yuri L.
- Abstract
A procedure for covalent binding of DNA to a functionalized mica substrate is described. The approach is based on photochemical cross-linking of DNA to immobilized psoralen derivatives. A tetrafluorphenyl (TFP) ester of trimethyl psoralen (trioxalen) was synthesized, and the procedure to immobilize it onto a functionalized aminopropyl mica surface (AP-mica) was developed. DNA molecules were cross-linked to trioxalen moieties by UV irradiation of complexes. The steps of the sample preparation procedure were analyzed with x-ray photoelectron spectroscopy (XPS). Results from XPS show that an AP-mica surface can be formed by vapor phase deposition of silane and that this surface can be derivatized with trioxalen. The derivatized surface is capable of binding of DNA molecules such that, after UV cross-linking, they withstand a thorough rinsing with SDS. Observations with atomic force microscopy showed that derivatized surfaces remain smooth, so DNA molecules are easily visualized. Linear and circular DNA molecules were photochemically immobilized on the surface. The molecules are distributed over the surface uniformly, indicating rather even modification of AP-mica with trioxalen. Generally, the shapes of supercoiled molecules electrostatically immobilized on AP-mica and those photocross-linked on trioxalen-functionalized surfaces remain quite similar. This suggests that UV cross-linking does not induce formation of a noticeable number of single-stranded breaks in DNA molecules.
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- 1999
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8. Single Molecule Studies of Early Stages of Amyloid Aggregation an Effect of pH
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Maity, Sibaprasad, Viazovkina, Ekaterina, Gall, Alexander, and Lyubchenko, Yuri
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- 2017
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9. The New Xpert MTB/RIF Ultra: Improving Detection of Mycobacterium tuberculosisand Resistance to Rifampin in an Assay Suitable for Point-of-Care Testing
- Author
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Chakravorty, Soumitesh, Simmons, Ann Marie, Rowneki, Mazhgan, Parmar, Heta, Cao, Yuan, Ryan, Jamie, Banada, Padmapriya P., Deshpande, Srinidhi, Shenai, Shubhada, Gall, Alexander, Glass, Jennifer, Krieswirth, Barry, Schumacher, Samuel G., Nabeta, Pamela, Tukvadze, Nestani, Rodrigues, Camilla, Skrahina, Alena, Tagliani, Elisa, Cirillo, Daniela M., Davidow, Amy, Denkinger, Claudia M., Persing, David, Kwiatkowski, Robert, Jones, Martin, and Alland, David
- Abstract
ABSTRACTThe Xpert MTB/RIF assay (Xpert) is a rapid test for tuberculosis (TB) and rifampin resistance (RIF-R) suitable for point-of-care testing. However, it has decreased sensitivity in smear-negative sputum, and false identification of RIF-R occasionally occurs. We developed the Xpert MTB/RIF Ultra assay (Ultra) to improve performance. Ultra and Xpert limits of detection (LOD), dynamic ranges, and RIF-R rpoBmutation detection were tested on Mycobacterium tuberculosisDNA or sputum samples spiked with known numbers of M. tuberculosisH37Rv or Mycobacterium bovisBCG CFU. Frozen and prospectively collected clinical samples from patients suspected of having TB, with and without culture-confirmed TB, were also tested. For M. tuberculosisH37Rv, the LOD was 15.6 CFU/ml of sputum for Ultra versus 112.6 CFU/ml of sputum for Xpert, and for M. bovisBCG, it was 143.4 CFU/ml of sputum for Ultra versus 344 CFU/ml of sputum for Xpert. Ultra resulted in no false-positive RIF-R specimens, while Xpert resulted in two false-positive RIF-R specimens. All RIF-R-associated M. tuberculosis rpoBmutations tested were identified by Ultra. Testing on clinical sputum samples, Ultra versus Xpert, resulted in an overall sensitivity of 87.5% (95% confidence interval [CI], 82.1, 91.7) versus 81.0% (95% CI, 74.9, 86.2) and a sensitivity on sputum smear-negative samples of 78.9% (95% CI, 70.0, 86.1) versus 66.1% (95% CI, 56.4, 74.9). Both tests had a specificity of 98.7% (95% CI, 93.0, 100), and both had comparable accuracies for detection of RIF-R in these samples. Ultra should significantly improve TB detection, especially in patients with paucibacillary disease, and may provide more-reliable RIF-R detection.IMPORTANCEThe Xpert MTB/RIF assay (Xpert), the first point-of-care assay for tuberculosis (TB), was endorsed by the World Health Organization in December 2010. Since then, 23 million Xpert tests have been procured in 130 countries. Although Xpert showed high overall sensitivity and specificity with pulmonary samples, its sensitivity has been lower with smear-negative pulmonary samples and extrapulmonary samples. In addition, the prediction of rifampin resistance (RIF-R) in paucibacillary samples and for a few rpoBmutations has resulted in both false-positive and false-negative results. The present study is the first demonstration of the design features and operational characteristics of an improved Xpert Ultra assay. This study also shows that the Ultra format overcomes many of the known shortcomings of Xpert. The new assay should significantly improve TB detection, especially in patients with paucibacillary disease, and provide more-reliable detection of RIF-R.
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- 2017
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10. All the small things
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Gall, Alexander
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- 2012
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11. Facile preparation of nuclease resistant 3' modified oligodeoxynucleotides
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Gamper, Howard B., Reed, Michael W., Cox, Thomas, Virosco, Jeanne S., Adams, A. David, Gall, Alexander A., Scholler, John K., and Meyer, Rich B.
- Abstract
An efficient chemical procedure for the immobilization of carboxylate containing conjugate groups onto controlled pore glass (CPG) is described. The derivatized supports were used in the automated synthesis of an oligodeoxynucleotide (20-mer ODN) containing a 3′ phosphodiester linked hexanol, aminohexyl, acridine, or cholesterol group. The stability of the oligomer in a hepatoma cell culture was found to be prolonged two to three fold by the presence of any one of the 3′ tails. By contrast, an aminohexyl group appended to the 5′ terminus of the ODN only marginally improved its nuclease resistance. These data support the notion that antlsense ODNs are primarily degraded by 3′ exonucleases. Introduction of simple 3′ tails which incorporate a normal phosphodiester linkage can increase ODN stability by interfering with these enzymes.
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- 1993
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12. The Corporate Eye.
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Gall, Alexander
- Abstract
The article contains a review of the book "The Corporate Eye. Photography and the Rationalization of American Commercial Culture 1884-1929" by Elspeth H. Brown.
- Published
- 2008
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