Article
Chemistry, Analytical
Brock R. Juliano, Joseph W. Keating, Brandon T. Ruotolo
Summary: Membrane proteins are challenging targets for mass spectrometry due to the need for membrane mimetics. Infrared photoactivation has emerged as an alternative to liberate membrane proteins from surfactant micelles, but its mechanism and application in native proteomics are still unknown. This study evaluates and probes infrared photoactivation for membrane protein sequencing, proteoform identification, and native proteomics applications, and reveals its ability to dissociate detergent micelles and other membrane mimetics, as well as improve sequence coverage.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Luis A. A. Macias, Sara P. P. Garcia, Kayla M. M. Back, Yue Wu, G. Hall Johnson, Sekar Kathiresan, Andrew M. M. Bellinger, Ellen Rohde, Michael A. A. Freitas, James A. A. Madsen
Summary: The development of CRISPR-based gene editing tools has the potential to cure genetic disorders and revolutionize treatment for common diseases. This study focuses on the importance of guide RNA, which plays a crucial role in the success of CRISPR-based medicine. Using top-down mass spectrometry, the researchers were able to accurately assess and quantify highly modified guide RNAs, as well as identify impurities and sequence variations.
ACS CENTRAL SCIENCE
(2023)
Article
Engineering, Aerospace
Jean-Charles Mare
Summary: A top-down process for position control of electromechanical actuators (EMA) is proposed and virtually validated. It facilitates early design phases by providing a simple means for algebraic calculations based on specified performance and top-level EMA design parameters. The process includes position, speed, and current controllers, and uses charts to define optimal gain, damping factor, and natural frequency. Virtual tests validate the process using a flight control actuator example, confirming its soundness.
Article
Chemistry, Analytical
Brock R. Juliano, Joseph W. Keating, Brandon T. Ruotolo
Summary: Membrane proteins are difficult to study using native top-down mass spectrometry due to the need for membrane mimetics. In this study, infrared photoactivation was explored as an alternative method for liberating membrane proteins from surfactant micelles. The results showed that infrared photoactivation can dissociate micelles composed of different detergent classes and can be extended to other membrane mimetics such as nanodiscs, liposomes, and bicelles. This technique significantly improves membrane protein sequence coverage, typically ranging from 40% to 60%.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Abanoub Mikhael, Travis D. Fridgen, Michel Delmas, Joseph Banoub
Summary: The top-down lignomic analysis of VRL extracted from French oak wood using APPI-QqTOF-MS and ESI-QqTOF-MS technologies identified various lignin oligomers. Kendrick mass defect analysis was used to simplify the data and low-energy CID-MS/MS analyses helped tentatively assign structures. Different ambient ionization techniques enhanced the ionization of various lignin oligomers.
JOURNAL OF MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Zach Rolfs, Lloyd M. Smith
Summary: A significant portion of unidentified fragment ion intensity in top-down proteomics is believed to come from internal fragment ions, which contain neither protein terminus. The computational complexity of internal fragment ions has historically limited their application to low-complexity samples, but the implementation of internal fragment ion functionality in MetaMorpheus allows for proteome-wide annotation of these ions, leading to disambiguation of proteoforms and increased identification accuracy. MetaMorpheus demonstrated success in disambiguating previously unclear proteoforms and improving proteoform-spectrum matches in mammalian cell lysates.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Ecology
Franz W. Simon, David A. Vasseur
Summary: The study delves into top-down and bottom-up theories of trophic control and predicts community responses in fluctuating environments. It reveals that primary producers and secondary consumers have the highest temporal variability at low frequencies, and variation cascades amplify temporal variation up the food chain at intermediate frequencies.
Article
Computer Science, Information Systems
Vitor de Castro Silva, Bruno Bogaz Zarpelao, Eric Medvet, Sylvio Barbon Jr
Summary: A wide range of Machine Learning algorithms can model time series, but they often struggle with characteristics such as repeating patterns and seasonal variations. Current approaches to time series segmentation need improvement and tend to neglect explainability. In this study, we proposed the eXplainable Time Series Tree (XTSTree), which divides a time series into a binary tree based on change detectors. The XTSTree provides a more comprehensive pattern explanation while automatically identifying different time series patterns.
Article
Chemistry, Analytical
Simon Becher, Huixin Wang, Michael G. Leeming, William A. Donald, Sven Heiles
Summary: UVPD is a powerful method in top-down proteomics, with sequence coverages exceeding those obtained with other fragmentation methods. Factors influencing protein fragmentation and sequence coverage are actively debated. The study on UVPD experiments on model proteins revealed that sequence coverage increases with higher charge states, and the presence of charge remote and charge directed fragmentation types depending on protonation sites and protein charge states.
Article
Biochemical Research Methods
Xiaojing Shen, Tian Xu, Blake Hakkila, Mike Hare, Qianjie Wang, Qianyi Wang, Joseph S. Beckman, Liangliang Sun
Summary: This study introduced a novel approach by coupling capillary zone electrophoresis with electron-capture collision-induced dissociation for denaturing top-down proteomics, providing efficient separation and gas-phase fragmentation of small proteins.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Analytical
Benqian Wei, Muhammad A. Zenaidee, Carter Lantz, Rachel R. Ogorzalek Loo, Joseph A. Loo
Summary: This study compares the fragmentation patterns of internal and terminal fragments in mass spectrometry and finds that they share similar fragmentation propensities. The formation of internal fragments can be explained by the mobile proton model, and they can combine with terminal fragments to form complementary product ions that span the entire protein sequence.
ANALYTICA CHIMICA ACTA
(2022)
Article
Engineering, Environmental
Klon D. C. Hinneh, Koji Kosaka, Shinya Echigo, Sadahiko Itoh
Summary: This study investigated the LC-QTOF/MS fragmentation of potent ozone reactive NDMA precursors and identified TMDS and PCCID 141210417 as significant precursors. TMDS accounted for 20-24% of the total NDMA formation potential in sewage.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Chemistry, Physical
Mingyang Gao, Zhiyong Zhang, Wen Zhang, Qinzhe Cao, Zhifeng Tang, Wu Zhao
Summary: The Hansen solubility parameters theory, established in 1967, has been a significant guide in the synthesis of two-dimensional materials. In this study, MoS2 was used as a representative for a deep and practical exploration of the efficient exfoliation of 2D materials based on the Hansen solubility parameters theory in the co-solvent of acetonitrile/chloroform. The study found that the liquid condition of the co-solvent had a regulating effect on the fragmentation yield of nanoscale flakes from bulk MoS2. The optimal condition and related mechanism of the miscible liquid were discussed. Additionally, the purification capacity of the prepared few-layer samples was studied.
Article
Biochemical Research Methods
Kyle J. Juetten, Jennifer S. Brodbelt
Summary: The impact of supercharging on the fragmentation patterns of six proteins under denaturing conditions was investigated using five activation methods. Changes in sequence coverage, preferential cleavage sites, and fragment ion abundances were evaluated for each method. The results showed that supercharging had different effects on sequence coverage and preferential cleavage sites depending on the activation method and the protein.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Neurosciences
Adam Pines, Arielle S. Keller, Bart Larsen, Maxwell Bertolero, Arian Ashourvan, Dani S. Bassett, Matthew Cieslak, Sydney Covitz, Yong Fan, Eric Feczko, Audrey Houghton, Amanda R. Rueter, Manish Saggar, Golia Shafiei, Tinashe M. Tapera, Jacob Vogel, Sarah M. Weinstein, Russell T. Shinohara, Leanne M. Williams, Damien A. Fair, Theodore D. Satterthwaite
Summary: This study tracks cortical activity propagations using advanced neuroimaging and computer vision techniques in a large sample of youth (n = 388), showing that top-down cortical propagations become more prevalent with greater demands for cognitive control as well as with development in youth.
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)