Steve Yannone - Academia.edu (original) (raw)

Papers by Steve Yannone

Research paper thumbnail of Nucleic acids useful for integrating into and gene expression in hyperthermophilic acidophilic Archaea

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information), May 25, 2021

Research paper thumbnail of Nucleic acids useful for integrating into and gene expression in hyperthermophilic acidophilic Archaea

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information), Sep 4, 2018

Research paper thumbnail of Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase

Biochemistry, 2018

Protein engineering to alter recognition underlying ligand binding and activity has enormous pote... more Protein engineering to alter recognition underlying ligand binding and activity has enormous potential. Here, ligand binding for Escherichia coli phosphoenolpyruvate carboxykinase (PEPCK), which converts oxaloacetate into CO 2 and phosphoenolpyruvate as the first committed step in gluconeogenesis, was engineered to accommodate alternative ligands as an exemplary system with structural information. From our identification of bicarbonate binding in the PEPCK active site at the supposed CO 2 binding site, we probed binding of nonnative ligands with three oxygen atoms arranged to resemble the bicarbonate geometry. Crystal structures of PEPCK and point mutants with bound nonnative ligands thiosulfate and methanesulfonate along with strained ATP and reoriented oxaloacetate intermediates and unexpected bicarbonate were determined and analyzed. The mutations successfully altered the bound ligand position and orientation and its specificity: mutated PEPCKs bound either thiosulfate or methanesulfonate but never both. Computational calculations predicted a methanesulfonate binding mutant and revealed that release of the active site ordered solvent exerts a strong influence on ligand binding. Besides nonnative ligand binding, one mutant altered the Mn 2+ coordination sphere: instead of the canonical octahedral ligand arrangement, the mutant in question had an only five-coordinate arrangement. From this work, *

Research paper thumbnail of Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database

Nature Protocols, Feb 7, 2013

Untargeted metabolomics provides a comprehensive platform to identify metabolites whose levels ar... more Untargeted metabolomics provides a comprehensive platform to identify metabolites whose levels are altered between two or more populations. By using liquid chromatography quadrupole time-offlight mass spectrometry (LC-Q-ToF-MS), hundreds to thousands of peaks with a unique m/z and retention time are routinely detected from most biological samples in an untargeted profiling experiment. Each peak, termed a metabolomic feature, can be characterized on the basis of its accurate mass, retention time, and tandem mass spectral fragmentation pattern. Here a 7-step protocol is suggested for such a characterization by using the METLIN metabolite database. The protocol starts from untargeted metabolomic LC-Q-ToF-MS data that has been analyzed with the bioinformatic program XCMS, and describes a strategy for selecting interesting features as well as performing subsequent targeted tandem mass spectrometry. The 7 steps described will require 2-4 hours to complete per feature, depending on the compound.

Research paper thumbnail of Novel hyperthermoacidic archaeal enzymes for removal of thermophilic biofilms from stainless steel

Journal of Applied Microbiology

Aims To test the efficacy of novel hot/acid hyperthermoacidic enzyme treatments on the removal of... more Aims To test the efficacy of novel hot/acid hyperthermoacidic enzyme treatments on the removal of thermophilic spore-forming biofilms from stainless steel surfaces. Methods and results The present study measured the efficacy of hyperthermoacidic enzymes (protease, amylase, and endoglucanase) that are optimally active at low pH (≈3.0) and high temperatures (≈80°C) at removing thermophilic bacilli biofilms from stainless steel (SS) surfaces. Plate counts, spore counts, impedance microbiology, as well as epifluorescence microscopy, and scanning electron microscopy (SEM) were used to evaluate the cleaning and sanitation of biofilms grown in a continuous flow biofilm reactor. Previously unavailable hyperthermoacidic amylase, protease, and the combination of amylase and protease were tested on Anoxybacillus flavithermus and Bacillus licheniformis, and endoglucanase was tested on Geobacillus stearothermophilus. In all cases, the heated acidic enzymatic treatments significantly reduced biof...

Research paper thumbnail of Novel hyperthermoacidic archaeal enzymes for removal of thermophilic biofilms from stainless steel

Journal of Applied Microbiology, May 22, 2023

Aims: To test the efficacy of novel hot/acid hyperthermoacidic enzyme treatments on the removal o... more Aims: To test the efficacy of novel hot/acid hyperthermoacidic enzyme treatments on the removal of thermophilic spore-forming biofilms from stainless steel surfaces. Methods and results: The present study measured the efficacy of hyperthermoacidic enzymes (protease, amylase, and endoglucanase) that are optimally active at low pH (≈3.0) and high temperatures (≈80 • C) at removing thermophilic bacilli biofilms from stainless steel (SS) surfaces. Plate counts, spore counts, impedance microbiology, as well as epifluorescence microscopy, and scanning electron microscopy (SEM) were used to evaluate the cleaning and sanitation of biofilms grown in a continuous flow biofilm reactor. Previously unavailable hyperthermoacidic amylase, protease, and the combination of amylase and protease were tested on Anoxybacillus flavithermus and Bacillus licheniformis, and endoglucanase was tested on Geobacillus stearothermophilus. In all cases, the heated acidic enzymatic treatments significantly reduced biofilm cells and their sheltering extracellular polymeric substances (EPS). Conclusions: Hyperthermoacidic enzymes and the associated heated acid conditions are effective at removing biofilms of thermophilic bacteria from SS surfaces that contaminate dairy plants. Significance and impact of study Hyperthermoacidic archaeal enzymes (HTA-enzymes) function optimally in conditions that are toxic to most microbes and are tested here for cleaning and removal of biofilms. Anoxybacillus flavithermus, B. licheniformis, and G. stearothermophilus are abundant thermophilic biofilmformers in the dairy industry. Due to the inadequate hygienic performance of conventional cleaning approaches on biofilms, enzymes have been studied as an alternative, predominately on non-spore-forming mesophilic or psychrophilic biofilms at a basic or neutral pH at ≈60 • C. This study showed the potential for HTA-enzymes as natural and effective cleaning and sanitation products for the removal of biofilms. Additionally, the use of enzymatic cleaning formulations will reduce the environmental impacts caused by the disposal of traditional cleaners such as NaOH and quaternary ammonium compounds (QACs).

Research paper thumbnail of High throughput DNA damage quantification of human tissue with home-based collection device

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information), Apr 3, 2018

Research paper thumbnail of Biochemical analysis of a physical interaction between DNA repair proteins, DNA-PK and XRCC4/ligase IV

Research paper thumbnail of Functional interaction of WRN with NBS1 in DNA damage response

Research paper thumbnail of Formation of WRN foci in response to DNA damage

Research paper thumbnail of Targetable mechanisms driving immunoevasion of persistent senescent cells link chemotherapy-resistant cancer to aging

Research paper thumbnail of Biochemical analysis of a physical interaction between DNA repair proteins, DNA-PK and XRCC4/ligase IV

Research paper thumbnail of Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase

Biochemistry, Oct 30, 2018

Protein engineering to alter recognition underlying ligand binding and activity has enormous pote... more Protein engineering to alter recognition underlying ligand binding and activity has enormous potential. Here, ligand binding for Escherichia coli phosphoenolpyruvate carboxykinase (PEPCK), which converts oxaloacetate into CO 2 and phosphoenolpyruvate as the first committed step in gluconeogenesis, was engineered to accommodate alternative ligands as an exemplary system with structural information. From our identification of bicarbonate binding in the PEPCK active site at the supposed CO 2 binding site, we probed binding of nonnative ligands with three oxygen atoms arranged to resemble the bicarbonate geometry. Crystal structures of PEPCK and point mutants with bound nonnative ligands thiosulfate and methanesulfonate along with strained ATP and reoriented oxaloacetate intermediates and unexpected bicarbonate were determined and analyzed. The mutations successfully altered the bound ligand position and orientation and its specificity: mutated PEPCKs bound either thiosulfate or methanesulfonate but never both. Computational calculations predicted a methanesulfonate binding mutant and revealed that release of the active site ordered solvent exerts a strong influence on ligand binding. Besides nonnative ligand binding, one mutant altered the Mn 2+ coordination sphere: instead of the canonical octahedral ligand arrangement, the mutant in question had an only five-coordinate arrangement. From this work, *

Research paper thumbnail of Nucleic acids useful for integrating into and gene expression in hyperthermophilic acidophilic Archaea

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information), May 25, 2021

Research paper thumbnail of Nucleic acids useful for integrating into and gene expression in hyperthermophilic acidophilic Archaea

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information), Sep 4, 2018

Research paper thumbnail of Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase

Biochemistry, 2018

Protein engineering to alter recognition underlying ligand binding and activity has enormous pote... more Protein engineering to alter recognition underlying ligand binding and activity has enormous potential. Here, ligand binding for Escherichia coli phosphoenolpyruvate carboxykinase (PEPCK), which converts oxaloacetate into CO 2 and phosphoenolpyruvate as the first committed step in gluconeogenesis, was engineered to accommodate alternative ligands as an exemplary system with structural information. From our identification of bicarbonate binding in the PEPCK active site at the supposed CO 2 binding site, we probed binding of nonnative ligands with three oxygen atoms arranged to resemble the bicarbonate geometry. Crystal structures of PEPCK and point mutants with bound nonnative ligands thiosulfate and methanesulfonate along with strained ATP and reoriented oxaloacetate intermediates and unexpected bicarbonate were determined and analyzed. The mutations successfully altered the bound ligand position and orientation and its specificity: mutated PEPCKs bound either thiosulfate or methanesulfonate but never both. Computational calculations predicted a methanesulfonate binding mutant and revealed that release of the active site ordered solvent exerts a strong influence on ligand binding. Besides nonnative ligand binding, one mutant altered the Mn 2+ coordination sphere: instead of the canonical octahedral ligand arrangement, the mutant in question had an only five-coordinate arrangement. From this work, *

Research paper thumbnail of Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database

Nature Protocols, Feb 7, 2013

Untargeted metabolomics provides a comprehensive platform to identify metabolites whose levels ar... more Untargeted metabolomics provides a comprehensive platform to identify metabolites whose levels are altered between two or more populations. By using liquid chromatography quadrupole time-offlight mass spectrometry (LC-Q-ToF-MS), hundreds to thousands of peaks with a unique m/z and retention time are routinely detected from most biological samples in an untargeted profiling experiment. Each peak, termed a metabolomic feature, can be characterized on the basis of its accurate mass, retention time, and tandem mass spectral fragmentation pattern. Here a 7-step protocol is suggested for such a characterization by using the METLIN metabolite database. The protocol starts from untargeted metabolomic LC-Q-ToF-MS data that has been analyzed with the bioinformatic program XCMS, and describes a strategy for selecting interesting features as well as performing subsequent targeted tandem mass spectrometry. The 7 steps described will require 2-4 hours to complete per feature, depending on the compound.

Research paper thumbnail of Novel hyperthermoacidic archaeal enzymes for removal of thermophilic biofilms from stainless steel

Journal of Applied Microbiology

Aims To test the efficacy of novel hot/acid hyperthermoacidic enzyme treatments on the removal of... more Aims To test the efficacy of novel hot/acid hyperthermoacidic enzyme treatments on the removal of thermophilic spore-forming biofilms from stainless steel surfaces. Methods and results The present study measured the efficacy of hyperthermoacidic enzymes (protease, amylase, and endoglucanase) that are optimally active at low pH (≈3.0) and high temperatures (≈80°C) at removing thermophilic bacilli biofilms from stainless steel (SS) surfaces. Plate counts, spore counts, impedance microbiology, as well as epifluorescence microscopy, and scanning electron microscopy (SEM) were used to evaluate the cleaning and sanitation of biofilms grown in a continuous flow biofilm reactor. Previously unavailable hyperthermoacidic amylase, protease, and the combination of amylase and protease were tested on Anoxybacillus flavithermus and Bacillus licheniformis, and endoglucanase was tested on Geobacillus stearothermophilus. In all cases, the heated acidic enzymatic treatments significantly reduced biof...

Research paper thumbnail of Novel hyperthermoacidic archaeal enzymes for removal of thermophilic biofilms from stainless steel

Journal of Applied Microbiology, May 22, 2023

Aims: To test the efficacy of novel hot/acid hyperthermoacidic enzyme treatments on the removal o... more Aims: To test the efficacy of novel hot/acid hyperthermoacidic enzyme treatments on the removal of thermophilic spore-forming biofilms from stainless steel surfaces. Methods and results: The present study measured the efficacy of hyperthermoacidic enzymes (protease, amylase, and endoglucanase) that are optimally active at low pH (≈3.0) and high temperatures (≈80 • C) at removing thermophilic bacilli biofilms from stainless steel (SS) surfaces. Plate counts, spore counts, impedance microbiology, as well as epifluorescence microscopy, and scanning electron microscopy (SEM) were used to evaluate the cleaning and sanitation of biofilms grown in a continuous flow biofilm reactor. Previously unavailable hyperthermoacidic amylase, protease, and the combination of amylase and protease were tested on Anoxybacillus flavithermus and Bacillus licheniformis, and endoglucanase was tested on Geobacillus stearothermophilus. In all cases, the heated acidic enzymatic treatments significantly reduced biofilm cells and their sheltering extracellular polymeric substances (EPS). Conclusions: Hyperthermoacidic enzymes and the associated heated acid conditions are effective at removing biofilms of thermophilic bacteria from SS surfaces that contaminate dairy plants. Significance and impact of study Hyperthermoacidic archaeal enzymes (HTA-enzymes) function optimally in conditions that are toxic to most microbes and are tested here for cleaning and removal of biofilms. Anoxybacillus flavithermus, B. licheniformis, and G. stearothermophilus are abundant thermophilic biofilmformers in the dairy industry. Due to the inadequate hygienic performance of conventional cleaning approaches on biofilms, enzymes have been studied as an alternative, predominately on non-spore-forming mesophilic or psychrophilic biofilms at a basic or neutral pH at ≈60 • C. This study showed the potential for HTA-enzymes as natural and effective cleaning and sanitation products for the removal of biofilms. Additionally, the use of enzymatic cleaning formulations will reduce the environmental impacts caused by the disposal of traditional cleaners such as NaOH and quaternary ammonium compounds (QACs).

Research paper thumbnail of High throughput DNA damage quantification of human tissue with home-based collection device

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information), Apr 3, 2018

Research paper thumbnail of Biochemical analysis of a physical interaction between DNA repair proteins, DNA-PK and XRCC4/ligase IV

Research paper thumbnail of Functional interaction of WRN with NBS1 in DNA damage response

Research paper thumbnail of Formation of WRN foci in response to DNA damage

Research paper thumbnail of Targetable mechanisms driving immunoevasion of persistent senescent cells link chemotherapy-resistant cancer to aging

Research paper thumbnail of Biochemical analysis of a physical interaction between DNA repair proteins, DNA-PK and XRCC4/ligase IV

Research paper thumbnail of Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase

Biochemistry, Oct 30, 2018

Protein engineering to alter recognition underlying ligand binding and activity has enormous pote... more Protein engineering to alter recognition underlying ligand binding and activity has enormous potential. Here, ligand binding for Escherichia coli phosphoenolpyruvate carboxykinase (PEPCK), which converts oxaloacetate into CO 2 and phosphoenolpyruvate as the first committed step in gluconeogenesis, was engineered to accommodate alternative ligands as an exemplary system with structural information. From our identification of bicarbonate binding in the PEPCK active site at the supposed CO 2 binding site, we probed binding of nonnative ligands with three oxygen atoms arranged to resemble the bicarbonate geometry. Crystal structures of PEPCK and point mutants with bound nonnative ligands thiosulfate and methanesulfonate along with strained ATP and reoriented oxaloacetate intermediates and unexpected bicarbonate were determined and analyzed. The mutations successfully altered the bound ligand position and orientation and its specificity: mutated PEPCKs bound either thiosulfate or methanesulfonate but never both. Computational calculations predicted a methanesulfonate binding mutant and revealed that release of the active site ordered solvent exerts a strong influence on ligand binding. Besides nonnative ligand binding, one mutant altered the Mn 2+ coordination sphere: instead of the canonical octahedral ligand arrangement, the mutant in question had an only five-coordinate arrangement. From this work, *