Article
Nanoscience & Nanotechnology
Yuanyuan Zhang, Jinwen Zhao, Guomin Yang, Ying He, Shihong Chen, Ruo Yuan
Summary: A quadrivalent cruciform DNA nanostructure (qCDN)-mediated cascaded catalyzed hairpin assembly (CHA) amplifier was developed for the fluorescence detection of amyloid beta oligomer species (A beta Os), achieving high FRET efficiency and fast reaction rate, with a detection limit as low as 0.69 pM. The combination of DD-A FRET binary probes and qCDN-mediated cascaded amplifier shows great promise for detecting biomarkers at trace levels.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Review
Biochemistry & Molecular Biology
Richard P. Bowater, Natalia Bohalova, Vaclav Brazda
Summary: This article reviews the processes that influence the formation and stability of cruciforms in genomes and highlights the significance of inverted repeat sequences in DNA metabolism, genome evolution, and human diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biophysics
Wan Huang, Danyan Zhan, Yiming Xie, Xin Li, Guosong Lai
Summary: The researchers successfully formed a tripedal DNAzyme-DNA walker using a dual-catalytic hairpin assembly strategy, and developed a novel proteinase-free dual-mode biosensing method for kanamycin antibiotic detection.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Chemistry, Analytical
Rong Zou, Shuang Wang, Chunyan Chen, Xiaoming Chen, Hang Gong, Changqun Cai
Summary: A fluorescence strategy based on MoS2 nanosheets and catalytic hairpin assembly was proposed for highly sensitive and selective detection of H5N1 DNA. The platform reduced background signal in the absence of target, but significantly enhanced fluorescence signal upon addition of target DNA.
Article
Microbiology
Hailan Meng, Qi Wang, Meiling Liu, Ziwei Li, Xiaojing Hao, Di Zhao, Yaqin Dong, Shuang Liu, Feng Zhang, Jin Cui, Bo Ni, Hu Shan, Fuxiao Liu
Summary: This study investigated the structure and function of the 5' end of the SVA genome, as well as the impact of genetic modifications on SVA replication. The results showed that the UUU-HPH structure played an important role in SVA replication, while certain mutated sequences had a lethal effect on SVA replication.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Analytical
Guo-Xi Liang, Shu-Ying Ye, Hao-Ming Yu, Kai-Ren Zhao, Peng-Fei Liu, Zhi-Jun Liu, Li Wang
Summary: This study proposes a new Zika virus diagnostic platform that combines a DNA walker structure and a localized catalytic hairpin assembly (LCHA) cascade amplification strategy for fast, low-cost, and accurate diagnosis. The method allows for Zika virus sequence detection down to 20 pM without enzymatic DNA amplification, and can detect the virus directly from serum samples.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Spectroscopy
Yan Zhou, Zefeng Wang, Shengnan Zhang, Le Deng
Summary: By integrating the advantages of catalytic hairpin components and multi-foot DNA walker, a high-sensitivity detection method for pathogen bacteria has been designed. This method does not rely on enzymes or sophisticated instrumentation, making it a promising technique for pathogenic bacteria detection.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
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
Mechanics
W. M. Scherzinger
Summary: This study focuses on the quantification and application of yield surface curvature in the instability analysis of a cruciform column under compression. The results demonstrate that the curvature of the yield surface has a strong impact on the stability of the column.
INTERNATIONAL JOURNAL OF SOLIDS AND STRUCTURES
(2022)
Article
Engineering, Electrical & Electronic
Anjan Kumar, Mustafa K. A. Mohammed, Mayeen Uddin Khandaker, H. I. Elsaeedy, T. Ch. Anil Kumar, Gurumurthy B. Ramaiah, M. Khalid Hossain
Summary: This study focuses on improving the photovoltaic performance and stability of perovskite solar cells (PSCs) without a hole transport layer (HTL) by modifying the interface of the tin (IV) oxide (SnO2) electron transport layer (ETL). Results showed that the use of hydrofluoric acid (HF) as a modifier increased charge transfer at the ETL/perovskite interface and improved the wettability of SnO2, resulting in higher efficiency (14.65%) and enhanced stability in the treated PSCs compared to control PSCs (12.92%).
JOURNAL OF MATERIALS SCIENCE-MATERIALS IN ELECTRONICS
(2023)
Article
Chemistry, Analytical
Xiaojia Zhao, Zicheng Zhu, Rong Zou, Lingyun Wang, Hang Gong, Changqun Cai
Summary: A 3D DNA walker was developed for the reliable and quantitative detection of H5N1 DNA, demonstrating excellent analytical sensitivity and specificity with a detection limit of 60 pM. The method showed potential for clinical applications by selectively detecting H5N1 DNA in clinical blood serum samples.
MICROCHEMICAL JOURNAL
(2021)
Article
Multidisciplinary Sciences
Feng Li, Wenting Yu, Jiaojiao Zhang, Yuhang Dong, Xiaohui Ding, Xinhua Ruan, Zi Gu, Dayong Yang
Summary: DNA nanostructures have been used as carriers for gene delivery, but spatiotemporally programmable assembly of DNA under nanoconfinement is challenging due to DNA complexity. A strategy using cascade hybridization chain reaction of DNA hairpins in polymeric nanoframework enables precise siRNA delivery. The nanoframework provides stability and ease of functionalization, addressing DNA complexity issues. Phenylboronate installation on nanoframework enhances cellular uptake and lysosomal escape.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Jianmei Wang, Hong Zhou, Jing Liu, Wenrong Yang
Summary: By controlling surface nanoarchitectures of DNA modified electrode, a new biosensing interface for the detection of p53 gene was designed, showing high performance with potential applications in clinical diagnosis and biomedical research.
JOURNAL OF ELECTROANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Sajjad Ahmad, Ming Guan, Jinwook Kim, Xinjun He, Zhilin Ren, Hong Zhang, Haibin Su, Wallace C. H. Choy
Summary: This study presents a novel quasi-DJ-2D perovskite with improved efficiency and stability through enhanced rigidity and controlled phase purity.
ADVANCED ENERGY MATERIALS
(2023)
Article
Chemistry, Analytical
Hongkun Li, Yuqi Zhang, Guifen Jie
Summary: A DNA reticular nanostructure was assembled using hairpin DNA probes via a target-induced circular amplification strategy for the fluorescence biosensing of miRNA-21. This method allows sensitive detection of miRNA-21 and holds great application potential in biosensors and functional nanomaterials.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Biochemical Research Methods
Karen E. Butler, Jaclyn Gowen Kalmar, David C. Muddiman, Erin S. Baker
Summary: Glycosylation is a common protein modification associated with various diseases, causing challenges in understanding the relationship between glycans and biological functions. The combination of IMS and MS technologies with the INLIGHT(TM) strategy enhances glycan identification confidence and accelerates the identification process in complex biological samples.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Aivett Bilbao, Bryson C. Gibbons, Sarah M. Stow, Jennifer E. Kyle, Kent J. Bloodsworth, Samuel H. Payne, Richard D. Smith, Yehia M. Ibrahim, Erin S. Baker, John C. Fjeldsted
Summary: This article introduces a method and software that can improve the data quality of ion mobility-mass spectrometry measurements. The software generates new MS files with enhanced signal quality and in the same instrument format using various algorithmic implementations. The advantages of the tool include increased accuracy in lipid annotations and improved processing speed.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Noor A. Aly, James N. Dodds, Yu-Syuan Luo, Fabian A. Grimm, MaKayla Foster, Ivan Rusyn, Erin S. Baker
Summary: Persistent organic pollutants (POPs) pose risks to human health and the environment, requiring effective assessment methods. Chromatography coupled with mass spectrometry (MS) is commonly used, but challenges arise from the diverse range of chemical classes, necessitating multiple time-consuming analyses for different types of POPs. Ion mobility spectrometry coupled with MS (IMS-MS) shows potential as a rapid screening technique for assessing a variety of POP compounds and their metabolites.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Editorial Material
Biochemical Research Methods
Erin S. Baker, Detlef R. U. Knappe
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
James N. Dodds, Lingjue Wang, Gary J. Patti, Erin S. Baker
Summary: The combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS) is commonly used for feature annotation in untargeted omics experiments. However, ensuring that these features originate from endogenous metabolism remains challenging. In this paper, the authors evaluate the analytical utility of incorporating ion mobility spectrometry (IMS) into LC-MS/MS isotopologue workflows and demonstrate the enhanced separation space and increased annotation confidence provided by IMS.
ANALYTICAL CHEMISTRY
(2022)
Article
Engineering, Environmental
Kaylie Kirkwood, Jonathon Fleming, Helen Nguyen, David M. Reif, Erin S. Baker, Scott M. Belcher
Summary: As concerns over exposure to PFAS continue to rise, novel monitoring methods are needed. This study used pine needles as passive samplers and a multidimensional analytical method to detect over 70 PFAS in the needles. The results provide critical insights into PFAS transport, contamination, and reduction efforts over the past six decades.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Evelyn Rampler, Erin S. Baker, Kaylie Kirkwood, Michaela Schwaiger-Haber, Maggie Tam, Marissa A. Jones, Melissa Sherman
EXPERT REVIEW OF PROTEOMICS
(2022)
Article
Biochemical Research Methods
Karen E. Butler, Erin S. Baker
Summary: In this study, a rapid screening method for opioids and opioid urinary metabolites was developed using drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS). This approach allowed for the clear differentiation of most opioids without prior chromatographic separation, and when coupled with an automated solid phase extraction platform, enabled fast sample-to-sample analyses. Compared to traditional chromatographic analyses, this method significantly reduced analysis time and improved sample throughput.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Endocrinology & Metabolism
S. K. Witchey, M. G. Doyle, J. D. Fredenburg, G. St Armour, B. Horman, M. T. Odenkirk, D. L. Aylor, E. S. Baker, H. B. Patisaul
Summary: This study reveals multiple mechanisms by which the components of a common FR mixture are developmentally neurotoxic and that the OPFRs may be the compounds of greatest concern.
NEUROENDOCRINOLOGY
(2022)
Article
Environmental Sciences
Alan Valdiviezo, Yuki Kato, Erin S. Baker, Weihsueh A. Chiu, Ivan Rusyn
Summary: The evaluation of exposure to multiple contaminants in a mixture poses challenges, including the characterization of chemical metabolism and the development of suitable models. This study used various in vitro models to assess the metabolism of a mixture of 20 pesticides. The results showed that iHep-based suspension assays exhibit higher metabolic activity and ion mobility spectrometry-mass spectrometry can characterize the formation of metabolites, providing a comprehensive evaluation of in vitro chemical metabolism.
Article
Chemistry, Analytical
Markace A. Rainey, Chandler A. Watson, Carter K. Asef, Makayla R. Foster, Erin S. Baker, Facundo M. Fernandez
Summary: Metabolite annotation is a bottleneck in nontargeted metabolomics workflows. High-resolution mass spectrometry, isotope cluster evaluation, Kendrick mass defect analysis, chromatographic retention time matching, and gas-phase collision cross-section measurements are commonly used methods for metabolite annotation. In this study, a machine learning algorithm called CCSP 2.0 is developed to predict CCS values, which improves the accuracy of metabolite annotation.
ANALYTICAL CHEMISTRY
(2022)
Article
Environmental Sciences
Alina T. Roman-Hubers, Christoph Aeppli, James N. Dodds, Erin S. Baker, Kelly M. McFarlin, Daniel J. Letinski, Lin Zhao, Douglas A. Mitchell, Thomas F. Parkerton, Roger C. Prince, Tim Nedwed, Ivan Rusyn
Summary: This study investigates the impact of photooxidation on the environmental fate and effects of spilled oil. Through a simulated experiment, involving the generation of oil slicks and exposure to sunlight for 8 days, the researchers characterized the molecular composition of seawater underneath irradiated and non-irradiated oil slicks. The results show that photooxidation leads to the production of hydrocarbons with oxygen-and sulfur-containing by-products, but the overall ecotoxicity potential remains limited.
MARINE POLLUTION BULLETIN
(2022)
Article
Microbiology
Matthew H. Foley, Morgan E. Walker, Allison K. Stewart, Sarah O'Flaherty, Emily C. Gentry, Shakshi Patel, Violet V. Beaty, Garrison Allen, Meichen Pan, Joshua B. Simpson, Caroline Perkins, Molly E. Vanhoy, Michael K. Dougherty, Sarah K. McGill, Ajay S. Gulati, Pieter C. Dorrestein, Erin S. Baker, Matthew R. Redinbo, Rodolphe Barrangou, Casey M. Theriot
Summary: Bile acids play a role in the interaction between human and microbial cells and affect diseases, including Clostridioides difficile infection (CDI). Bile salt hydrolases (BSHs) shape the bile acid pool by deconjugating conjugated BAs, but their selectivity and impact on C. difficile remain unclear. This study investigates the diversity of BSHs in gut commensals and other members of the human gut microbiome. The results show that BSHs with different specificities can restrict C. difficile growth in vitro and colonization in vivo models. Furthermore, BSHs can reshape the pool of microbial conjugated bile acids (MCBAs) in the gut and restrict C. difficile virulence in vitro.
NATURE MICROBIOLOGY
(2023)
Article
Chemistry, Analytical
Jessie R. Chappel, Mary E. King, Jonathon Fleming, Livia S. Eberlin, David M. Reif, Erin S. Baker
Summary: Mass spectrometry imaging (MSI) is popular for tissue-based diagnostics, but current statistical approaches often fail to visualize subtle molecular changes. To address this, researchers developed aggregated molecular phenotype (AMP) scores using ensemble machine learning. AMP scores can evaluate multiple features simultaneously and accurately distinguish phenotypes. When combined with spatial coordinates, AMP scores allow for visualization of tissue sections, highlighting their diagnostic utility.
ANALYTICAL CHEMISTRY
(2023)
Article
Environmental Sciences
Alexandra C. Cordova, William D. Klaren, Lucie C. Ford, Fabian A. Grimm, Erin S. Baker, Yi-Hui Zhou, Fred A. Wright, Ivan Rusyn
Summary: This study used representative high production volume categories of petroleum UVCBs to compare the chemical composition and bioactivity data, finding that existing categories are not accurate enough and identifying specific constituents that influence these associations. This suggests that combining chemical composition and bioactivity data is a promising approach to better characterize the variability within manufacturing categories of petroleum UVCBs.
