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20 results on '"Swaminathan, Jagannath"'

1. Robust and scalable single-molecule protein sequencing with fluorosequencing

Author

Mapes, James H, primary, Stover, Julia, additional, Stout, Heather D, additional, Folsom, Tucker M, additional, Babcock, Emily, additional, Loudwig, Sandra, additional, Martin, Christopher, additional, Austin, Mariah, additional, Howdieshell, Casey J, additional, Simpson, Zachary B, additional, Blom, Thomas, additional, Weaver, Daniel, additional, Winkler, Daniel, additional, Velden, Kent Vander, additional, Ossareh, Parham M, additional, Beierle, John M, additional, Somekh, Talli, additional, Bardo, Angela M, additional, Anslyn, Eric V, additional, Marcotte, Edward M, additional, and Swaminathan, Jagannath, additional

Published
2023
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3. Evaluating the Effect of Dye–Dye Interactions of Xanthene-Based Fluorophores in the Fluorosequencing of Peptides

Author

Bachman, James L., primary, Wight, Christopher D., additional, Bardo, Angela M., additional, Johnson, Amber M., additional, Pavlich, Cyprian I., additional, Boley, Alexander J., additional, Wagner, Holden R., additional, Swaminathan, Jagannath, additional, Iverson, Brent L., additional, Marcotte, Edward M., additional, and Anslyn, Eric V., additional

Published
2022
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5. Photoredox-catalyzed decarboxylative C-terminal differentiation for bulk and single molecule proteomics

Author

Swaminathan, Jagannath

Subjects
proteomics, single molecule image, fluorosequencing
Abstract

Raw image files generated by fluorosequencing experiment represented in figure 4. The files are * Angiotensin_Norb_Alkyne.zip - This contains subfolderESN_2021_04_09_00_mx070 with nd2 files for 1 Pre, 3 Mocks and 10 Edman cycles. Sample results are represented as "blue" bars with legend Angiotensin-Alkyne * Angiotensin_negative.zip- This contains subfolderEN_2021_04_10_00_mx071 with nd2 files for1 Pre, 3 Mocks and 10 Edman cycles. Sample results are represented as "orange" bars with legend Angiotensin-Norbornenone * NegativeControl.zip - This contains subfolderESN_2021_04_11_00_jsp122 with nd2 files1 Pre, 3 Mocks and 10 Edman cycles. Sample results are represented as "gray" bars with legend Negative control peptide &nbsp

Published
2021
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11. Influence of competing metabolic processes on the molecular weight of hyaluronic acid synthesized by Streptococcus zooepidemicus

Author

Swaminathan Jagannath and K.B. Ramachandran

Subjects
synthesis, Polymers, Dispersity, Biomass, Molecular weight, nitrogen, chemistry.chemical_compound, Metabolic flux analysis, pyruvic acid, Hyaluronic acid, Carbon fiber reinforced plastics, Streptococcus zooepidemicus, Hyaluronic acids, chemistry.chemical_classification, biology, Polymer, Streptococcus equi zooepidemicus, glycolysis, Polydispersity, Biochemistry, priority journal, uridine diphosphate n acetylglucosamine 2 epimerase, Synthesis (chemical), Rheology, Biotechnology, energy, Environmental Engineering, n acetylglucosamine, Biomedical Engineering, bacterium culture, Bioengineering, engineering.material, Hydroxylation, Organic acids, Weighing, Streptococcus equi subsp. zooepidemicus, Biomolecules, nonhuman, Stirred Tank, Biological materials, biology.organism_classification, Metabolism, Tanks (containers), chemistry, carbon source, engineering, Biopolymer, Flux (metabolism)
Abstract

Hyaluronic acid (HA) is a linear high molecular weight glycosaminoglycan polymer with its molecular weight determining its physiological role, rheological properties and applications. The commercially used microbial source-Streptococcus zooepidemicus is incapable of synthesizing very high molecular weight polymer with low polydispersity, an essential niche in the HA market. In this organism, three important metabolic processes-glycolysis, hyaluronic acid synthesis and biomass formation compete for carbon source, nitrogen source, energy and precursors to determine the molecular weight of the synthesized polymer. After studying the role of culture conditions on these competing processes, it was found that the best strategy for enhancing molecular weight was to weaken the glycolytic process, strengthen HA synthesis process and maintain nitrogen under limiting condition to reduce the rate of biomass formation. Based on this newly developed strategy-temperature switches, addition of precursor N-acetylglucosamine and addition of pyruvate experiments enhanced the molecular weight of the polymer by 23%, 74% and 64%, respectively. Improving precursor levels, particularly UDP-N-acetylglucosamine and thereby strengthening the HA flux plays a direct role in improving molecular weight of hyaluronic acid. � 2009 Elsevier B.V. All rights reserved.

Published
2010

12. Peptide Fragment Ion Analyser (PFIA): A simple and versatile tool for the interpretation of tandem mass spectrometric data and de novo sequencing of peptides

Author

Swaminathan Jagannath and Varatharajan Sabareesh

Subjects
Spectrometry, Mass, Electrospray Ionization, sequence analysis, Sequence analysis, peptide mapping, Molecular Sequence Data, computer interface, Mass spectrometry, chemistry, electrospray mass spectrometry, Sensitivity and Specificity, Analytical Chemistry, Adduct, User-Computer Interface, Protein methods, Sequence Analysis, Protein, computer program, Computer Graphics, Amino Acid Sequence, Peptide sequence, reproducibility, Spectroscopy, chemistry.chemical_classification, Ions, algorithm, Tandem, Organic Chemistry, Reproducibility of Results, methodology, Combinatorial chemistry, Cyclic peptide, Peptide Fragments, Amino acid, peptide fragment, molecular genetics, ion, Algorithms, Software
Abstract

The software Peptide Fragment Ion Analyser (PFIA) aids in the analysis and interpretation of tandem mass spectrometric data of peptides. The software package has been designed to facilitate the analysis of product ions derived from acyclic and cyclic peptide natural products that possess unusual amino acid residues and are heavily post-translationally modified. The software consists of two programmes: (a) PFIA-I lists the amino acid compositions and their corresponding product ion types for 'a queried m/z value' (z = +1) and (b) PFIA-II displays fragmentation pattern diagram(s) and lists all sequence-specific product ion types for the protonated adduct of 'a queried sequence'. The unique feature of PFIA-II is its ability to handle cyclic peptides. The two programmes used in combination can prove helpful for deriving peak assignments in the de novo sequencing of novel peptides. Copyright � 2007 John Wiley & Sons, Ltd.

Published
2007
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14. A self-assembling lanthanide molecular nanoparticle for optical imaging

Author

Brown, Katherine A., primary, Yang, Xiaoping, additional, Schipper, Desmond, additional, Hall, Justin W., additional, DePue, Lauren J., additional, Gnanam, Annie J., additional, Arambula, Jonathan F., additional, Jones, Jessica N., additional, Swaminathan, Jagannath, additional, Dieye, Yakhya, additional, Vadivelu, Jamuna, additional, Chandler, Don J., additional, Marcotte, Edward M., additional, Sessler, Jonathan L., additional, Ehrlich, Lauren I. R., additional, and Jones, Richard A., additional

Published
2015
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17. Lanthanide nano-drums: a new class of molecular nanoparticles for potential biomedical applications

Author

Jones, Richard A., primary, Gnanam, Annie J., additional, Arambula, Jonathan F., additional, Jones, Jessica N., additional, Swaminathan, Jagannath, additional, Yang, Xiaoping, additional, Schipper, Desmond, additional, Hall, Justin W., additional, DePue, Lauren J., additional, Dieye, Yakhya, additional, Vadivelu, Jamuna, additional, Chandler, Don J., additional, Marcotte, Edward M., additional, Sessler, Jonathan L., additional, Ehrlich, Lauren I. R., additional, and Brown, Katherine A., additional

Published
2014
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19. Single molecule peptide sequencing

Author

Swaminathan, Jagannath

Subjects
Peptide sequencing, Single molecule, Proteomics, Proteomes, Proteome changes, Fluorosequencing
Abstract

The proteome is a highly dynamic and complex set of proteins, specific not only to a particular organism, but to cell types and environmental conditions. Understanding proteome changes as they occur is especially important for molecular diagnostics and developing biomarkers. Currently, the primary technology for proteome wide identification and quantification is shotgun mass spectrometry; while powerful, it lacks high sensitivity and coverage. In this dissertation, I discuss my work in the development of a new technology, termed “fluorosequencing”, for sequencing peptides from a complex protein sample at the level of single molecules. The concept is to generate a positional information pattern of an amino acid(s) (such as xKxxK, where K is lysine and x can be any of the other amino acid residues). In order to obtain such a pattern, we proposed a scheme of (i) selectively labeling one or more amino acid(s) in the peptides, (ii) immobilizing millions of these individual fluorescently labeled peptides on a glass surface, (iii) monitoring their changing fluorescent pattern by TIRF microscopy as the (iv) N-terminal amino acid is sequentially cleaved by Edman chemistry and (v) using the resulting fluorescent signature (fluorosequences) to uniquely identify individual single molecule peptides in the mixture. We began by developing a computational framework to justify the feasibility of the concept. By modeling different sources of anticipated errors, we showed that the errors do not greatly affect the identification of proteins in the human proteome. Secondly, after screening fluorophores for their solvent stability, we used fluorescently labeled synthetic peptides covalently immobilized on beads to experimentally demonstrate the ability of the technique to determine the position of the fluorescently labeled residue in peptides. Finally, we translated the bead optimized chemistry procedures to a single molecule setup. We implemented the fluorosequencing method to sequence synthetic peptide molecules and provided evidence for the technique’s utility to discriminate peptides in a peptide mixture with single molecule sensitivity. By establishing the foundational work towards the proof-of-principle for fluorosequencing, we can now scale the method in order to realize the idea of single molecule proteome wide sequencing.

Published
2015

20. Robust and scalable single-molecule protein sequencing with fluorosequencing.

Author

Mapes JH, Stover J, Stout HD, Folsom TM, Babcock E, Loudwig S, Martin C, Austin MJ, Tu F, Howdieshell CJ, Simpson ZB, Blom T, Weaver D, Winkler D, Vander Velden K, Ossareh PM, Beierle JM, Somekh T, Bardo AM, Anslyn EV, Marcotte EM, and Swaminathan J

Abstract

The need to accurately survey proteins and their modifications with ever higher sensitivities, particularly in clinical settings with limited samples, is spurring development of new single molecule proteomics technologies. Fluorosequencing is one such highly parallelized single molecule peptide sequencing platform, based on determining the sequence positions of select amino acid types within peptides to enable their identification and quantification from a reference database. Here, we describe substantial improvements to fluorosequencing, including identifying fluorophores compatible with the sequencing chemistry, mitigating dye-dye interactions through the use of extended polyproline linkers, and developing an end-to-end workflow for sample preparation and sequencing. We demonstrate by fluorosequencing peptides in mixtures and identifying a target neoantigen from a database of decoy MHC peptides, highlighting the potential of the technology for high sensitivity clinical applications., Competing Interests: COMPETING INTERESTS E.M.M. and E.V.A. are co-founders and shareholders of Erisyon, Inc., and serve on the scientific advisory board. All other authors are affiliated with Erisyon, Inc., as employees or shareholders, and JS, AMB, HS, and CM additionally hold affiliation with UT Austin.

Published
2023
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