TIGER: the universal biosensor

Hofstadler, Steven A.; Sampath, Rangarajan; Blyn, Lawrence B.; Eshoo, Mark W.; Hall, Thomas A.; Jiang, Yun; Drader, Jared J.; Hannis, James C.; Sannes‐Lowery, Kristin A.; Cummins, Lendell L.; Libby, Brian; Walcott, Demetrius J.; Schink, Amy; Massire, Christian; Ranken, Raymond; Gutierrez, Jose R.; Manalili, Sheri; Ivy, Cristina; Melton, Rachael; Levene, Harold B.; Barrett-Wilt, Greg; Li, Feng; Zapp, Vanessa; White, Neill; Samant, Vivek; McNeil, John A.; Knize, Duane J.; Robbins, David W.; Rudnick, Karl; Desai, Anjali; Moradi, Emily; Ecker, David J.

doi:10.1016/j.ijms.2004.09.014

Cited by 145 publications

(179 citation statements)

References 24 publications

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“…Analysis was performed using the software version 2.6.052 (Ibis Biosciences; Ecker et al, 2008). The PLEX-ID BAC Detection assay has a DNA calibrant in each reaction, which allows for semiquantitative analysis (Hofstadler et al, 2005). By comparing the relative intensity of the target DNA to that of the calibrant, the relative concentration of target DNA initially present is determined (Ecker et al, 2008).…”

Section: Pcr/esi-msmentioning

confidence: 99%

Evaluation of PCR electrospray-ionization mass spectrometry for rapid molecular diagnosis of bovine mastitis

Perreten

Endimiani

Thomann

et al. 2013

Journal of Dairy Science

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Bovine mastitis, an inflammatory disease of the mammary gland, is one of the most costly diseases affecting the dairy industry. The treatment and prevention of this disease is linked heavily to the use of antibiotics in agriculture and early detection of the primary pathogen is essential to control the disease. Milk samples (n = 67) from cows suffering from mastitis were analyzed for the presence of pathogens using PCR electrosprayionization mass spectrometry (PCR/ESI-MS) and were compared with standard culture diagnostic methods. Concurrent identification of the primary mastitis pathogens was obtained for 64% of the tested milk samples, whereas divergent results were obtained for 27% of the samples. The PCR/ESI-MS failed to identify some of the primary pathogens in 18% of the samples, but identified other pathogens as well as microorganisms in samples that were negative by culture. The PCR/ ESI-MS identified bacteria to the species level as well as yeasts and molds in samples that contained a mixed bacterial culture (9%). The sensitivity of the PCR/ESI-MS for the most common pathogens ranged from 57.1 to 100% and the specificity ranged from 69.8 to 100% using culture as gold standard. The PCR/ESI-MS also revealed the presence of the methicillin-resistant gene mecA in 16.2% of the milk samples, which correlated with the simultaneous detection of staphylococci including Staphylococcus aureus. We demonstrated that PCR/ESI-MS, a more rapid diagnostic platform compared with bacterial culture, has the significant potential to serve as an important screening method in the diagnosis of bovine clinical mastitis and has the capacity to be used in infection control programs for both subclinical and clinical disease.

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Section: Pcr/esi-msmentioning

confidence: 99%

Evaluation of PCR electrospray-ionization mass spectrometry for rapid molecular diagnosis of bovine mastitis

Perreten

Endimiani

Thomann

et al. 2013

Journal of Dairy Science

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“…The capability for performing all of these processes in high-throughput mode enables screening of large numbers of samples for both expected and unexpected variants and facilitates searches for associations between mtDNA variants and diseases. The ESI-MS method can be used as a rapid, low-cost tool to screen samples before the time-consuming and costly G8 C14 T18 A18 G8 C14 T18 A18 G8 C15 T17 T3271C 6 (44%) 8344 A24 G8 C10 T17 A24 G8 C10 T17 1-24 8356 A26 G7 C13 T14 A26 G7 C13 T14 1-24 A12 G7 C18 T9 1, 3-7, 9, 10 (8%), [11][12][13][14][16][17][18]19 process of direct DNA sequencing. In most cases, knowing that a mutation or SNP is present in a region of interest (even when the exact coordinates of the mutation are not known), and knowing the type of nucleotide substitution (e.g., A3 T) are the key data for discriminating a typical patient sample from a sample with 1 or more abnormalities requiring additional investigation.…”

Section: Discussionmentioning

confidence: 99%

“…We used a 600-MHz Pentium II data station running XMASS software (version 7.0.4; Bruker Daltonics) under a Windows NT 4.0 operating system (Microsoft) to control all aspects of pulse sequence and data collection. The FTICR data station triggered a CTC HTS PAL autosampler (LEAP Technologies) to extract a 15-L sample directly from the 96-well microtiter plate and inject it into a 10-L sample loop integrated with a fluid-handling system that supplies sample to the ESI source at a flow rate of 100 L/h (12 ). Application of an ESI source potential of Ϫ6000V generated a stable electrospray plume, and a countercurrent flow of dry nitrogen gas assisted in the desolvation process.…”

Section: Esi-fticr Ms Analysis Of Pcr Productsmentioning

confidence: 99%

“…To improve the signal-to-noise ratio, we coadded 32 scans for a total data-acquisition time of 74 s. We used custom processing software developed in-house to analyze the raw mass spectra. First, ICR2LS software (9,12,20 ) was used to deconvolute the FTICR spectra into monoisotopic neutral masses for all of the observed signals. From these high-precision monoisotopic mass measurements, we calculated base compositions for each amplicon pair (9,12,20 ).…”

Section: Esi-fticr Ms Analysis Of Pcr Productsmentioning

confidence: 99%

“…By taking into account the base complementarity of double-stranded DNA, investigators can further constrain the list of possible base compositions (11 ). The "softness" of the ionization processes of both matrix-assisted laser desorption/ionization and electrospray ionization (ESI) has enabled the ionization of PCR products for detection by MS. ESI Fourier transform ion cyclotron resonance MS (ESI-FTICR MS) and ESI time-of-flight MS (ESI-TOF MS) have routinely been used in our laboratory for PCR product analysis, a regular component of a biosensor funded by the Defense Advanced Research Projects Agency (12 ). For example, we recently applied this approach to rapidly genotype 217 isolates of Acinetobacter to determine the epidemiology and clonality of outbreaks in soldiers and civilians in Iraq and Kuwait (13 ).…”

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Mitochondrial DNA Mutation Detection by Electrospray Mass Spectrometry

et al. 2007

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Pyoderma Gangrenosum–Like Ulcer in a Patient With X-Linked Agammaglobulinemia

Murray¹,

Jain²,

Uzel³

et al. 2010

Arch Dermatol

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Background-Pyoderma gangrenosum-like ulcers and cellulitis of the lower extremities associated with recurrent fevers in patients with X-linked (Bruton) agammaglobulinemia have been reported to be caused by Helicobacter bilis (formerly classified as Flexispira rappini and then Helicobacter strain flexispira taxon 8). Consistent themes in these reports are the difficulty in recovering this organism in blood and wound cultures and in maintaining isolates in vitro. We confirmed the presence of this organism in a patient's culture by using a novel application of gene amplification polymerase chain reaction and electrospray ionization time-of-flight mass spectrometry.Observation-An adolescent boy with X-linked agammaglobulinemia presented with indurated plaques and a chronic leg ulcer whose origin was strongly suspected to be an H bilis organism. Histologic analysis demonstrated positive Warthin-Starry staining of curvilinear rods, which grew in culture but failed to grow when sub-cultured. They could not be identified by conventional techniques. A combination of gene amplification by polymerase chain reaction and electrospray ionization time-of-flight mass spectrometry confirmed the identity of this organism.Conclusions-This novel technology was useful in the identification of a difficult-to-grow Helicobacter organism, the cause of pyoderma gangrenosum-like leg ulcers in patients with Xlinked agammaglobulinemia. Correct identification of this organism as the cause of pyoderma gangrenosum-like ulcers in patients with X-linked agammaglobulinemia is of great importance for the early initiation of appropriate and curative antibiotic therapy.

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TIGER: the universal biosensor

Cited by 145 publications

References 24 publications

Evaluation of PCR electrospray-ionization mass spectrometry for rapid molecular diagnosis of bovine mastitis

Evaluation of PCR electrospray-ionization mass spectrometry for rapid molecular diagnosis of bovine mastitis

Mitochondrial DNA Mutation Detection by Electrospray Mass Spectrometry

Pyoderma Gangrenosum–Like Ulcer in a Patient With X-Linked Agammaglobulinemia

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