Article
Biochemistry & Molecular Biology
Krystian Galecki, Agnieszka Kowalska-Baron, Katarzyna E. Nowak, Anna Gajda, Beata Kolesinska
Summary: This study demonstrates the utility of time-resolved fluorescence spectroscopy in detecting subtle changes in the microenvironment of tryptophan chromophore in AOT reverse micelles. The results show evident changes in spectral characteristics and fluorescence decay kinetics when tryptophan and its peptides are inserted into micelles.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Bingjie Zhang, Ting Lei, Nanrong Zhao
Summary: Research shows that in active environments, factors such as active crowder size, activity, and crowding have significant effects on the looping kinetics of polymer chains. Specifically, the size of active particles plays a crucial role in either facilitating or inhibiting looping, and the underlying looping mechanisms vary in different active crowder size regimes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Aarat P. Kalra, Alfy Benny, Sophie M. Travis, Eric A. . Zizzi, Austin Morales-Sanchez, Daniel G. Oblinsky, Travis J. A. . Craddock, Stuart R. Hameroff, M. Bruce MacIver, Jack A. . Tuszynski, Sabine Petry, Roger Penrose, Gregory D. Scholes
Summary: The repeating arrangement of tubulin dimers in microtubules provides great mechanical strength and allows for energy transfer. By studying tryptophan autofluorescence lifetimes, it was discovered that energy can diffuse over 6.6 nm in microtubules, and this diffusion is influenced by tubulin polymerization state but not by the average number of protofilaments. The presence of anesthetics also affects exciton diffusion.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Physical
Bingjie Zhang, Fei Tan, Nanrong Zhao
Summary: This study systematically investigates polymer looping kinetics in active heterogeneous media crowded with a mixture of mobile active particles and immobile obstacles using Langevin dynamics simulations. The results reveal the novel phenomena of inhibition-facilitation transition of the looping rate induced by heterogeneity, crowdedness, and activity, as well as a very non-trivial crowder size effect on the looping kinetics. The underlying mechanism is rationalized by the interplay of polymer diffusion, conformational change, and looping free-energy barrier.
Article
Chemistry, Applied
Emma Alexander, Jose Chavez, Luca Ceresa, Michael Seung, Danh Pham, Zygmunt Gryczynski, Ignacy Gryczynski
Summary: We observe efficient room temperature phosphorescence from coumarin 106 embedded in a poly (vinyl alcohol) film. This phosphorescence occurs at 465 nm, which is outside the absorption band, when directly excited to the triplet state. The phosphorescence properties, such as spectra, lifetimes, and temperature dependence, are similar for UV and blue excitations but the emission anisotropy differs significantly.
Article
Materials Science, Multidisciplinary
Yong-Yi Huang
Summary: This paper explains that the canonical transformations in matrix mechanics are actually just transformations of different representations in standard quantum mechanics. It also demonstrates the non-degenerate, degenerate, and time-dependent perturbation theory in matrix mechanics, solving the mystery of time-dependent perturbation theory in this context. Additionally, the Kramers' dispersion formula from time-dependent perturbation theory in matrix mechanics is derived from wave mechanics.
RESULTS IN PHYSICS
(2022)
Article
Engineering, Environmental
N. L. Dilani Perera, Jaroslava Miksovska, Kevin E. O'Shea
Summary: This study investigates the structural alterations of human serum albumin (HSA) upon the addition of Gen X and the specific binding sites and equilibrium association constant of Gen X with HSA. The results demonstrate the potential application of beta-CD for the remediation of PFAS from biological systems by effectively extracting Gen X from the HSA:Gen X complex.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Chemistry, Analytical
Arul Pundi, Chi-Jung Chang, Jemkun Chen, Shih-Rong Hsieh, Ming-Ching Lee
Summary: The chiral carbazole based sensor (CCS) was prepared and shown to effectively detect Fe3+, L-tryptophan (Trp), and L-histidine (His) with low limits of detection in a high water-content environment. The CCS Fe3+ complex based chemosensor was successfully used to quantify the L-tryptophan content in commercial capsules with accurate results.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Biochemistry & Molecular Biology
Christine Stephen, Tatiana V. Mishanina
Summary: This article introduces a newly discovered pH-responsive element (PRE) riboswitch, which is different from the traditional ligand-based model. The study found that pH regulates riboswitch folding in two possible ways, but not by regulating the transcription rate of RNA polymerase as previously proposed. Alkaline pH either decreases or has no effect on RNAP pause longevity, suggesting that RNA itself may actively participate in pH sensing.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Nanoscience & Nanotechnology
Imen Boumar, Muhammedin Deliorman, Pavithra Sukumar, Mohammad A. Qasaimeh
Summary: This paper introduces a novel hybrid flow assay for the detection and screening of IgM and IgG antibodies in SARS-CoV-2 infections. The assay utilizes gold nanoparticles conjugated with SARS-CoV-2 S and N proteins to capture antibodies from a small amount of blood in just one step and provides quick results. The adhesive bandage-like design allows for rapid, low-cost, and easy-to-use tests for large-scale detection and screening in households.
MICROSYSTEMS & NANOENGINEERING
(2023)
Article
Spectroscopy
Vladislav Victorovich Khrustalev, Tatyana Aleksandrovna Khrustaleva, Victor Vitoldovich Poboinev, Aleksander Nicolaevich Stojarov, Larisa Valentinovna Kordyukova, Anastasia Aleksandrovna Akunevich
Summary: The study demonstrates the presence of three peak values in the fluorescence spectra of tryptophan, which vary depending on the polarity of the solvent. Smoothed spectra of Trp-containing proteins show a single fluorescence peak that can range between 330nm and 360nm, depending on different states within the protein.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Spectroscopy
Arul Pundi, Chi-Jung Chang, Jemkun Chen, Shih-Rong Hsieh, Ming-Ching Lee
Summary: The development of fluorescence molecules for the detection of L-tryptophan has attracted attention, and a chiral sensor SDPA was synthesized. It showed fluorescence quenching by Fe3+ and Cu2+ and could detect L-tryptophan and L-cysteine at trace levels by turn-on fluorescence.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Multidisciplinary Sciences
Annmaree K. Warrender, Jolyn Pan, Chris Pudney, Vickery L. Arcus, William Kelton
Summary: Red edge excitation shift (REES) spectroscopy is used to analyze the interaction between fluorophores and solvents, profiling protein molecular dynamics. This study shows that REES is highly sensitive to minor variations in protein structure and tryptophan composition.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Chemistry, Analytical
Samane Naeeminejad, Khalil Abnous, Seyed Mohammad Taghdisi
Summary: The fluorescent aptasensor introduced in this study utilizes the hairpin structure of TOB aptamer to quantitatively monitor tobramycin antibiotic with high sensitivity and a wide linear relationship. It can detect TOB in human serum and milk samples with low detection limits. This sensor has the potential to be used for human diagnostics, food control, and environmental monitoring with its key features of feasibility, simplicity, and high sensitivity.
MICROCHEMICAL JOURNAL
(2021)
Article
Nanoscience & Nanotechnology
Mehdi Ouahmane, Lahcen Arfa, Lahcen El Arroum
Summary: The diffusion mechanism of homogeneous Brownian particles through an imperfect substrate potential is studied using the Fokker-Planck equation (FPE) and the Matrix Continued Fractions Method (MCFM). The numerical results show that low frictions favor diffusion, while strong frictions reduce it. They also demonstrate that the potential structure has a significant effect on the particle dynamics, with oscillations at the bottom of wells blocking diffusion and sliding on trays accelerating it.
PHYSICA E-LOW-DIMENSIONAL SYSTEMS & NANOSTRUCTURES
(2023)
Article
Biotechnology & Applied Microbiology
Minjun Son, Delaram Ghoreishi, Sang-Joon Ahn, Robert A. Burne, Stephen J. Hagen
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2015)
Article
Biotechnology & Applied Microbiology
Zachary D. Moye, Minjun Son, Ariana E. Rosa-Alberty, Lin Zeng, Sang-Joon Ahn, Stephen J. Hagen, Robert A. Burne
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2016)
Article
Cell & Tissue Engineering
Dillon T. Seroski, Antonietta Restuccia, Anthony D. Sorrentino, Kevin R. Knox, Stephen J. Hagen, Gregory A. Hudalla
CELLULAR AND MOLECULAR BIOENGINEERING
(2016)
Article
Microbiology
Justin Kaspar, Simon A. M. Underhill, Robert C. Shields, Adrian Reyes, Suzanne Rosenzweig, Stephen J. Hagen, Robert A. Burne
JOURNAL OF BACTERIOLOGY
(2017)
Article
Microbiology
Robert C. Shields, Greg O'Brien, Natalie Maricic, Alexandria Kesterson, Megan Grace, Stephen J. Hagen, Robert A. Burne
JOURNAL OF BACTERIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
M. Son, J. Kaspar, S. J. Ahn, R. A. Burne, S. J. Hagen
MOLECULAR MICROBIOLOGY
(2018)
Article
Multidisciplinary Sciences
Edward D. Ramirez, Stephen J. Hagen
Article
Microbiology
Simon A. M. Underhill, Robert C. Shields, Justin R. Kaspar, Momin Haider, Robert A. Burne, Stephen J. Hagen
Correction
Microbiology
Simon A. M. Underhill, Robert C. Shields, Justin R. Kaspar, Momin Haider, Robert A. Burne, Stephen J. Hagen
Article
Biochemistry & Molecular Biology
Simon A. M. Underhill, Robert C. Shields, Robert A. Burne, Stephen J. Hagen
MOLECULAR MICROBIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Keval Patel, Coralis Rodriguez, Eric Stabb, Stephen J. Hagen
Summary: Many bacteria communicate using diffusible pheromone signals called autoinducers. When the concentration of autoinducer reaches a threshold, the bacteria activate specific gene regulatory pathways, spreading rapidly through the population as a self-sustaining front. This phenomenon can enhance intercellular communication over macroscopic distances in populations of bacteria under natural regulation.
Article
Microbiology
Elena Yarmola, Ivan P. Ishkov, Nicholas M. di Cologna, Megan Menashe, Robert L. Whitener, Joanna R. Long, Jacqueline Abranches, Stephen J. Hagen, L. Jeannine Brady
Summary: The number of bacterial species utilizing amyloid aggregation in biofilms is increasing. This study shows that amyloid formation reduces the activity of the Streptococcus mutans adhesin and is mainly found in the nonadherent fraction of biofilms. Understanding when and where S. mutans produces amyloid will help in developing therapeutic strategies for controlling tooth decay and other biofilm-related diseases.
MICROBIOLOGY SPECTRUM
(2022)
Article
Physics, Fluids & Plasmas
Keval Patel, Coralis Rodriguez, Eric V. Stabb, Stephen J. Hagen
Article
Biotechnology & Applied Microbiology
Matthew De Furio, Sang Joon Ahn, Robert A. Burne, Stephen J. Hagen
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Stephen J. Hagen, Minjun Son
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)