Article
Chemistry, Multidisciplinary
Sayantan Chatterjee, Yelena Kan, Mateusz Brzezinski, Kaloian Koynov, Roshan Mammen Regy, Anastasia C. Murthy, Kathleen A. Burke, Jasper J. Michels, Jeetain Mittal, Nicolas L. Fawzi, Sapun H. Parekh
Summary: The authors show that thermal trigger can lead to formation of at least two distinct liquid condensed phases of the FUS LC domain. Forming FUS LC condensates directly at low temperature leads to metastable, kinetically trapped condensates showing arrested coalescence, which can be escaped via thermal annealing to untrapped condensates. This study demonstrates two unique liquid FUS condensates with different molecular structures and dynamics.
Article
Chemistry, Physical
Hamidreza Mahdavi, Huacheng Zhang, Lauren K. Macreadie, C. M. Doherty, Durga Acharya, Stefan J. D. Smith, Xavier Mulet, Matthew R. Hill
Summary: The research on porous liquids (PLs) as a potential nanocomposite has revealed the combination of the ease of handling liquid absorbents with the high permanent porosity of metal organic frameworks. The study investigates the component materials systematically, elucidating the parameter space for stable photoluminescence, related to gas sorption capacities and other performance parameters. This research may have broader implications for future investigations in the field of nanocomposites.
Article
Chemistry, Multidisciplinary
Meng-Ying Sun, Mo Xie, Chuang-Wei Zhou, Xue-Zhi Wang, Zhao-Xia Lian, Zi-Ye Chen, Yong-Liang Huang, Xiao-Ping Zhou, Dan Li
Summary: In this work, we report the self-assembly of four cubic Zn8L12Br4 molecular containers, which can bind hydrocarbon gases including methane, ethane, and ethene at ambient temperature. Two gas binding sites are discovered in these containers, one in the cavity and the other at the window, as confirmed by NMR spectra and DFT calculations. The performance of gas encapsulation can be tuned by adjusting substituent groups, making these metal-organic cages promising for studying and mimicking the functions of biological systems in binding and transforming hydrocarbon gases.
SCIENCE CHINA-CHEMISTRY
(2023)
Article
Public, Environmental & Occupational Health
Jordana Muroff, Daniel Do, Cristina Araujo Brinkerhoff, Deborah Chassler, Myrna Alfaro Cortes, Michelle Baum, Genessis Guzman-Betancourt, Daniela Reyes, Luz M. Lopez, Maylid Roberts, Diliana De Jesus, Emily Stewart, Linda Sprague Martinez
Summary: Photovoice is a form of visual ethnography that aims to engage impacted communities in research and action to address injustices. It has been increasingly used with Latinx communities to address health inequities. The experiences and voices of the Latinx community are crucial in shaping policies, enhancing providers' understanding, and informing culturally appropriate services.
Article
Entomology
Ivan Drahun, Katherine A. Hunt, Willem G. van Herk, Bryan J. Cassone
Summary: This study evaluated the effect of bait trapping duration, seed formulation, and their relationship with CO2 production and soil temperature on wireworm catch. The results provided valuable guidelines to improve current wireworm sampling methods, and can be integrated into strategies aimed at managing these important pests to crop production.
JOURNAL OF ECONOMIC ENTOMOLOGY
(2022)
Article
Nanoscience & Nanotechnology
Hamidreza Mahdavi, Nathan T. Eden, Cara M. Doherty, Durga Acharya, Stefan J. D. Smith, Xavier Mulet, Matthew R. Hill
Summary: Porous liquids (PLs), with the combination of easy liquid handling and high adsorption capacity, have unique advantages in various applications. This study aims to create PLs using different metal-organic frameworks (MOFs) modification methods and investigate the influence of solvents on the overall stability of the nanocomposites. The results show that by combining zirconium-based MOFs with specific solvents, high CO2 sorption capacity can be achieved. These findings have significant implications for future research in the field of PLs.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Multidisciplinary
Abdulrab Abdulwahab Almashwali, Mazlin Idress, Bhajan Lal, Akram Salem, Quah Chong Jin
Summary: This experimental study investigates the inhibitory effects of sodium chloride (NaCl) on methane hydrate in an oil-dominated system, both kinetically and thermodynamically. The results show that NaCl has a weak inhibitory effect kinetically, but significantly shifts the equilibrium curve to higher pressures and lower temperatures thermodynamically.
Article
Green & Sustainable Science & Technology
Jingchen Ding, Changhui Yan, Yongming He, Changcheng Wang
Summary: The study presents experimental investigations on supercritical carbon dioxide (SCCO2) sequestration and enhanced gas recovery (EGR) in tight gas reservoirs. Results show that SCCO2 has higher adsorption capacity in tight sandstone, leading to significant EGR effects, especially in tight gas reservoirs with lower permeability, higher water saturation, and greater dip angle.
INTERNATIONAL JOURNAL OF GREENHOUSE GAS CONTROL
(2021)
Review
Oncology
Shinsuke Ito, Nando Dulal Das, Takashi Umehara, Haruhiko Koseki
Summary: The review focuses on emerging views of chromatin conformations associated with enhancer-promoter interactions and the factors that establish or maintain such interactions, which may regulate gene expression. It also discusses various mechanisms that regulate eukaryotic gene expression, including the roles of histone acetylation and methylation, pioneer transcription factors, and architectural proteins.
Editorial Material
Microbiology
Elise Landais, Devin Sok
Summary: The development of broadly neutralizing antibodies to HIV-1 is influenced by complex viral and host interactions. Early interactions between B cells and the virus during acute infection are predictive of later bnAb responses.
CELL HOST & MICROBE
(2021)
Article
Engineering, Environmental
Xiaojian Yang, Yufeng Wei, Wei Shyy, Kun Xu
Summary: The gas-solid particle two-phase flow in a fluidized bed is studied using a multi-scale algorithm that combines the gas-kinetic scheme (GKS) for the gas phase and the unified gas-kinetic wave-particle method (UGKWP) for the solid particle phase. The UGKWP seamlessly transitions between wave and discrete particle formulations based on the particle cell's Knudsen number. The algorithm captures the particle phase in different regimes with high accuracy and efficiency.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Energy & Fuels
Namrata Gaikwad, Gaurav Bhattacharjee, Jitendra S. Sangwai, Rajnish Kumar, Praveen Linga
Summary: This study investigates the kinetics and morphology of hydrate crystal growth in gas-water and gas-liquid hydrocarbon-water systems using different additives. The addition of tryptophan significantly enhances gas uptake and hydrate formation rate. In the gas-liquid hydrocarbon-water system, the presence of water-insoluble Cyclo-O hinders mass transfer between gas and bulk water phase, resulting in cloudlike hydrate formation.
Article
Multidisciplinary Sciences
Hongyi Xiao, Ge Zhang, Entao Yang, Robert Ivancic, Sean Ridout, Robert Riggleman, Douglas J. Durian, Andrea J. Liu
Summary: This study introduces a new structuro-elastoplastic (StEP) model to tune the degree of strain localization in disordered solids, based on the stability of the disordered local structure represented by a machine learning-based descriptor called softness. The model exhibits semiquantitative agreement with experimental results for different disordered solids and provides a microscopic understanding of the interplay between structure, plasticity, and elasticity in strain localization.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Engineering, Environmental
Alberto Maria Gambelli
Summary: Replacement processes have the potential to recover methane from natural gas hydrate reservoirs, but their industrial application is limited. This study discusses the influencing factors of replacement, including heat and mass transfer limitations, expansion of the thermodynamic region, maximum efficiency achievable, and the role of gas phase composition. Experimental investigation shows that methane recovery and carbon dioxide storage are influenced by the composition of the replacing gas phase.
CHEMICAL ENGINEERING JOURNAL
(2023)
Review
Materials Science, Multidisciplinary
Zhi-Feng Zhang, Ye-Xin Yang, Song-Lin Zhu, Yan Shi, Jiang-Feng Song, Guang-Kun Ren, Shun-Jie Deng, Xiao-Feng Tian, Zhe Zheng
Summary: This study discusses the methods of using single-wall carbon nanotubes to fabricate hydrogen gas detectors and factors influencing the performance of detectors, including additives and structural parameters.
NEW CARBON MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Mirela Sarbu, Dragana Fabris, Zeljka Vukelic, David E. Clemmer, Alina D. Zamfir
Summary: Gangliosides play an important role in the central nervous system and can be used as diagnostic markers and potential therapeutic agents. Ion mobility separation mass spectrometry and IMS tandem mass spectrometry were used to study gangliosides in human central nervous system and cerebrospinal fluid. The results demonstrate the potential of IMS MS/MS in biomarker discovery and characterization, and its application in early diagnosis of CNS diseases through molecular fingerprints.
Article
Physics, Atomic, Molecular & Chemical
Syuan-Ting Kuo, Shuli Tang, David H. Russell, Xin Yan
Summary: This study reports a method for characterizing the positional and geometric isomers of phospholipids using copper (I) ion complexed with phospholipids. By applying multi-stage fragmentation and measuring collision cross sections, the method enables rapid and effective distinction of isomers in lipid samples.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Kai S. Yang, Lauren R. Blankenship, Syuan-Ting Alex Kuo, Yan J. Sheng, Pingwei Li, Carol A. Fierke, David H. Russell, Xin Yan, Shiqing Xu, Wenshe Ray Liu
Summary: As a novel covalent modification, a Y-shaped, S-O-N-O-S-bridged post-translational cross-link connecting three residues C22, C44, and K61 in the main protease (M-Pro) of SARS-CoV-2 was frequently observed during crystallographic analyses. This cross-link potentially serves as a redox switch to regulate the catalytic activity of M-Pro, a drug target of COVID-19. Targeting the open active site formed by this linkage could be a potential strategy for the development of SARS-CoV-2 antivirals, especially in combination with other active-site-targeting molecules such as paxlovid.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Analytical
Varun V. Gadkari, Brock R. Juliano, Christopher S. Mallis, Jody C. May, Ruwan T. Kurulugama, John C. Fjeldsted, John A. McLean, David H. Russell, Brandon T. Ruotolo
Summary: Through comparing three laboratories, the reproducibility of collision-induced unfolding (CIU) in protein studies was evaluated. The results showed that within the same laboratory, CIU fingerprints were repeatable with an RMSD value of less than 5%. The collision cross section (CCS) values of CIU intermediates were consistent across the laboratories, but the activation potentials required for protein CIU transitions varied between the three laboratories.
Article
Chemistry, Analytical
Liqi Fan, David H. Russell
Summary: Cu, a highly redox active metal, can damage DNA and other cellular components, but its adverse effects can be mitigated by metallothioneins (MT). This study used mass spectrometry techniques to investigate the structure and stability of Cu-MT complexes and compared them with Ag-MT complexes. The results showed that Cu+ ions first bind to the beta-domain and then to the alpha-domain to form different Cu-i-MT complexes.
Article
Chemistry, Analytical
Robert L. Schrader, Thomas E. Walker, Sumeet Chakravorty, Gordon A. Anderson, Peter T. A. Reilly, David H. Russell
Summary: Digital mass filters are useful for analyzing large molecules as they can isolate high-m/z ions without requiring high RF and DC voltages. The Mathieu stability diagrams show that capacitors introduce voltage offsets between quadrupole rod pairs, depending on the waveform voltage and duty cycle. This changes the ion's a value, allowing for isolation of single-charge states for protein complexes up to 800 kDa. An isolation resolving power of approximately 280 was achieved for an ion of m/z 12,315 (z = 65+) for the 800.5 kDa GroEL D398A complex, corresponding to an m/z window of 44.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Cheng-Wei Lin, Shelby D. Oney-Hawthorne, Syuan-Ting Kuo, David P. Barondeau, David H. Russell
Summary: Iron-sulfur (Fe-S) cluster (ISC) cofactors are essential for many cellular processes. IscU plays a key role in the ISC Fe-S cluster biosynthetic pathway and exists in multiple conformational states. Zn binding affects the conformation of IscU and its interaction with IscS. This study provides a structural rationale for the role of Zn in stabilizing IscU conformations and IscS in preparing for cluster synthesis.
Article
Biochemical Research Methods
Mirela Sarbu, Raluca Ica, Edie Sharon, David E. Clemmer, Alina D. Zamfir
Summary: In this study, an advanced glycomics method based on ion mobility separation mass spectrometry and tandem mass spectrometry was used to characterize the chondroitin sulfate disaccharide domains in BGN. Five distinct disaccharide motifs were identified in BGN, with four showing irregular sulfation patterns. Trisulfated unsaturated and bisulfated saturated disaccharides were found, the latter indicating the non-reducing end of the chains. Structural investigation revealed a rare bisulfated motif, 3-O-sulfated GlcA-4-O-sulfated GalNAc, at the non-reducing end of one or both CS/DS chains in BGN. The influence of these newly identified sequences on cancer cell spreading will be investigated in future studies.
JOURNAL OF MASS SPECTROMETRY
(2023)
Article
Multidisciplinary Sciences
Jixing Lyu, Chang Liu, Tianqi Zhang, Samantha Schrecke, Nicklaus P. Elam, Charles Packianathan, Georg K. A. Hochberg, David Russell, Minglei Zhao, Arthur Laganowsky
Summary: In this study, the authors characterized the structural basis and functional roles of the bacterial ABC transporter MsbA binding to copper and specific lipids using native mass spectrometry, X-ray crystallography, cryo-EM, and biochemical approaches.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Dallas P. Freitas, Xi Chen, Erin A. Hirtzel, Madison E. Edwards, Joohan Kim, Hongying Wang, Yuxiang Sun, Klaudia I. Kocurek, David Russell, Xin Yan
Summary: In this study, we developed an in situ droplet-based derivatization method for rapid analysis of tissue lipids at multiple isomer levels. The method involves on-tissue derivatization using the TriVersa NanoMate LESA pipette, followed by extraction and analysis of the derivatized lipids using chip-based LESA mass spectrometry (MS) and tandem MS. This approach enables characterization of lipid isomers at the carbon-carbon double-bond positional and sn-positional levels, as well as relative quantitation based on diagnostic ion intensities. The method allows for multiple derivatizations at different spots in the same functional region of an organ, facilitating orthogonal lipid isomer analysis using a single tissue slide. Lipid isomers in different regions of the mouse brain were profiled, demonstrating the potential of this droplet-based derivatization method in tissue lipid studies requiring fast sample-to-result turnovers.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Lucas W. Henderson, Edie M. Sharon, Amit K. S. Gautam, Adam J. Anthony, Martin F. Jarrold, David H. Russell, Andreas Matouschek, David E. Clemmer
Summary: Mass spectrometry studies show that the stability of S. cerevisiae 20S proteasome undergoes related configurations and transitions during temperature changes, possibly linked to the opening of the proteolytic core. The study indicates that the proteasome remains intact and all transitions are reversible. Three types of structures are identified based on thermodynamic analysis: energetically stabilized closed configurations, high-entropy precursor states, and open pore structures. Opening of the 20S pore in the absence of the regulatory unit involves a charge-priming process. However, only a small fraction of precursor configurations actually open to expose the catalytic cavity.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemical Research Methods
Robert L. Schrader, Thomas E. Walker, David H. Russell
Summary: The use of mild collisional activation has been found to remove salts and adducts from large molecules, enhancing measurement accuracy and mass resolution. Adding a short square quadrupole between the ion funnel and transmission quadrupole effectively removes adducts and improves ejection efficiency for ions with low size-to-charge ratio.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Multidisciplinary
Thomas Walker, He Mirabel Sun, Tiffany Gunnels, Vicki Wysocki, Arthur Laganowsky, Hays Rye, David Russell
Summary: Variable-temperature electrospray ionization (vT-ESI) native mass spectrometry (nMS) is used to investigate the thermodynamics of ATP binding to the GroEL tetradecamer chaperonin complex. The study reveals strong enthalpy-entropy compensation (EEC) and variations in stepwise free energy changes, which are consistent with the established nested cooperativity model of GroEL-ATP interactions. The entropy-driven ATP binding is attributed to ligand-induced conformational changes and reorganization of water molecules within the GroEL complex.
ACS CENTRAL SCIENCE
(2023)
Meeting Abstract
Biochemical Research Methods
Jonathan C. Trinidad, Xuyao Zeng, David E. Clemmer
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Xuyao Zeng, Milos Novotny, David E. Clemmer, Jonathan C. Trinidad
Summary: A substantial shortcoming of large-scale datasets is the difficulty in representing and visualizing key features, particularly in the study of glycopeptides and glycans. This paper presents a simple and concise graphical representation method to capture the microheterogeneity of glycan modification at specific sites, and provides visual illustrations of glycans and glycopeptides from various species.