A5076350453- RNA and protein synthesis mechanisms
- nanoparticles nucleation surface interactions
- Advanced biosensing and bioanalysis techniques
- Computational Drug Discovery Methods
- Material Dynamics and Properties
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Biosensors and Analytical Detection
- Gene Regulatory Network Analysis
- Advanced Chemical Physics Studies
- Animal testing and alternatives
- Advanced Biosensing Techniques and Applications
- Monoclonal and Polyclonal Antibodies Research
- Advanced Thermodynamics and Statistical Mechanics
- Cholinesterase and Neurodegenerative Diseases
- RNA modifications and cancer
- CRISPR and Genetic Engineering
- Bacterial Genetics and Biotechnology
- EEG and Brain-Computer Interfaces
- Viral Infections and Immunology Research
- Chemical Thermodynamics and Molecular Structure
- Chemical Synthesis and Analysis
- Theoretical and Computational Physics
- Effects and risks of endocrine disrupting chemicals
- Phase Equilibria and Thermodynamics
Henry M. Jackson Foundation
2016-2025
United States Air Force Research Laboratory
2008-2025
Wright-Patterson Air Force Base
2009-2024
Jackson Foundation
2014-2023
United States Army Medical Research and Development Command
2007-2009
Telemedicine & Advanced Technology Research Center
2009
United States Department of the Army
2009
United States Army Medical Command
2008
University of Michigan–Ann Arbor
1999-2004
Institute for Condensed Matter Physics of the National Academy of Sciences of Ukraine
1999
In vitro selection of RNA aptamers that bind to a specific ligand usually begins with random pool sequences. We propose computational approach for designing starting sequences the analyte binding. Our consists three steps: (i) based on their secondary structure, (ii) generating library three-dimensional (3D) structures molecules and (iii) high-throughput virtual screening this select binding affinity desired small molecule. developed set criteria allows one sequence potential from protocol...
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The utilization of structure-switching aptamers (SSAs) has enabled the development novel sensing platforms for sensitive and continuous detection molecules. De novo SSAs, however, is complex laborious. Here we describe a rational approach to SSA optimization that simultaneously improves aptamer binding affinity introduces target-dependent conformation-switching compatibility with real-world biosensor applications. Key structural features identified from NMR computational modeling were used...
Molecular dynamics simulations were performed on series of gold nanoclusters comprised 459, 1157, and 3943 atoms, to study their structures properties during heating cooling. The increased depression melting point as particle size decreases has been interpreted in terms Pawlow's triple theory, the liquid shell model, extensions two. solid−liquid interfacial free energy σsl ∼0.15 J/m2 inferred from model was close values predicted by several empirical relations. When molten particles a given...
Inhalation of toxic substances and contaminants can have adverse effects on the respiratory tract, leading to a range health problems, such as irritation inflammation, allergic reaction asthma, lung damage, or even death. It is not possible experimentally evaluate toxicity for all thousands chemicals in use. Here, we generated structural alerts developed machine learning (ML) classification models predict sensitization hazards using experimental data from publicly available databases...
Riboswitches are RNA sequences that regulate expression of associated downstream genes in response to the presence or absence specific small molecules. A novel riboswitch activates protein translation E. coli cells 2,4-dinitrotoluene (DNT) has been engineered. plasmid library was constructed by incorporation 30 degenerate bases between a previously described trinitrotoluene aptamer and ribosome binding site. Screening performed placing upstream Tobacco Etch Virus (TEV) protease coding...
The detection of chemicals using natural allosteric transcription factors is a powerful strategy for point-of-use molecular sensing, particularly fieldable cell-free gene expression (CFE) systems. However, the reliance schemes on characterized protein-based sensors limits number measurable analytes. One alternative solution to this issue develop new by generating RNA aptamers against target analyte and then incorporating them directly into riboswitch scaffold ligand-inducible genetic control...
Bimetallic particles have two features not observed in one-component systems: surface segregation and compositional ordering. Molecular dynamics simulations been performed to study the freezing of Ni−Al nanoclusters at different compositions. It was found that for Al-rich equiatomic compositions Al atoms inhibits nucleation, causing supercooled clusters solidify an amorphous aggregate. In case Ni3Al particles, where there are enough complete layer, froze multiply twinned structures with...
An account of a computer simulation the nucleation kinetics and crystal growth during freezing series SeF6 clusters is presented. Although has stable monoclinic phase at temperatures studied, froze initially to body-centered cubic then transformed low-energy structure. The temperature dependence rate obtained in simulations approximate agreement with that predicted by classical theory. A theoretical model cluster crystallization includes time-dependent finite-size effects proposed, applied,...
Rapid design, screening, and characterization of biorecognition elements (BREs) is essential for the development diagnostic tests antiviral therapeutics needed to combat spread viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To address this need, we developed a high-throughput pipeline combining in silico design peptide library specific SARS-CoV-2 spike (S) protein microarray screening identify binding sequences. Our optimized platform allowed simultaneous ~ 2.5...
Biomarkers which are indicative of acute physiological and emotional states studied in a number different areas cognitive neuroscience. Currently, many studies conducted based on programmed tasks followed by timed biofluid sampling, central laboratory processing, data analysis. In this work, we present sensor platform capable rapid biomarker detection specific for detecting neuropeptide orexin A, found blood saliva known as an indicator fatigue performance. A peptide recognition element that...
Riboswitches are regulatory RNAs located in the 5′-untranslated region of mRNA sequences that recognize and bind to small molecules regulate expression downstream genes. Creation synthetic riboswitches novel ligands depends on ability monitor riboswitch activation presence analyte. In our work, we have coupled a an optical reporter assay based fluorescence resonance energy transfer (FRET) between two genetically encoded fluorescent proteins. The theophylline-sensitive was placed upstream...
In recent years, several stochastic simulation algorithms have been developed to generate Monte Carlo trajectories that describe the time evolution of behavior biomolecular reaction networks. However, effects various and data analysis conditions on observed dynamics complex networks not recieved much attention. order investigate these issues, we employed a software package in out group, called Biomolecular Network Simulator (BNS), simulate analyze such systems. The hypothetical two gene...
Immobilization of nucleic acid aptamer recognition elements selected free in solution onto the surface biosensor platforms has proven challenging. This study investigated binding multiple aptamer/target pairs immobilized on a commercially available microarray as model system mimicking applications. The results indicate minimum distance (linker length) from and thymine nucleobase linker provides reproducible across varying conditions. An indirect labeling method, where target was labeled with...
The crystallization and subsequent solid-state transitions in a series of large clusters SeF6 two sizes have been studied by molecular dynamics simulations at constant temperature. Several diagnostic methods were applied to monitor details the clusters' structures their evolution with time. behavior 12 liquid 725 molecules 10 1722 was examined 140 130 K. During nanosecond runs all these froze, initially bcc or related but distorted structure. At higher temperature one larger underwent...
Riboswitches are RNA-based regulatory elements that utilize ligand-induced structural changes in the 5'-untranslated region of mRNA to regulate expression associated genes. The majority synthetic riboswitches have been selected and tested cell-based systems. Cell-free protein systems (CFPS) several advantages for development testing riboswitches, including eliminating interactions with complex cellular networks, decoupling transcription translation processes. To gain a better understanding...
A variety of environmental and physiological conditions can cause oxidative stress that damage cellular components such as DNA, proteins lipids. Oxidative is implicated in many human diseases including cancer, cardiovascular diseases, neurological inflammatory aging. The nuclear factor erythroid 2–related 2 (NRF2) a transcriptional plays key role the antioxidant defense system it regulates transcription detoxifying enzymes. There an urgent need to identify novel compounds activate NRF2...
Experimental studies have demonstrated that botulinum neurotoxin serotype A (BoNT/A) causes flaccid paralysis by a multi-step mechanism. Following its binding to specific receptors at peripheral cholinergic nerve endings, BoNT/A is internalized receptor-mediated endocytosis. Subsequently zinc-dependent catalytic domain translocates into the neuroplasm where it cleaves vesicle-docking protein, SNAP-25, block neurally evoked neurotransmission. We tested hypothesis mathematical models having...
A method for identifying an aptamer in a single round was developed using custom DNA microarrays containing computationally derived patterned libraries incorporating no information on the sequences of previously reported thrombin binding aptamers. The library specifically designed to increase probability by enhancing structural complexity sequence-space confined environment, much like generating lead compounds combinatorial drug screening library. sequence demonstrating highest fluorescence...
There are many mechanisms of neurotoxicity that initiated by the interaction chemicals with different neurological targets. Under U.S. Environmental Protection Agency's ToxCast program, biological activity thousands was screened in biochemical and cell-based assays a high-throughput manner. Two hundred sixteen screening database were identified as targeting total 123 proteins having functions according to Gene Ontology database. Data from these imported into Organization for Economic...
Wearable sensors for human health, performance, and state monitoring, which have a linear response to the binding of biomarkers found in sweat, saliva, or urine, are current interest many applications. A critical part any device is biological recognition element (BRE) that able bind biomarker at surface sensor with high affinity selectivity produce measurable signal response. In this study, we discover compare 12-mer peptides neuropeptide Y (NPY), stress health biomarker, using independent...