Review
Cell Biology
Sheng-Yi Wu, Yi Shen, Irene Shkolnikov, Robert E. Campbell
Summary: This review provides an overview of the current landscape of genetically encodable and synthetic indicators for visualizing and detecting monatomic ion concentration in biological systems, serving as a valuable guide for researchers and tool developers.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Physical
Jiake Wei, Bin Feng, Ryo Ishikawa, Tatsuya Yokoi, Katsuyuki Matsunaga, Naoya Shibata, Yuichi Ikuhara
Summary: Grain boundary migration in polycrystalline materials is crucial in modifying microstructures and properties, governed by the atomistic mechanism. Experimental findings show that the migration proceeds through cooperative shuffling of atoms along low-energy structures.
Article
Chemistry, Physical
Domagoj Belic, Oihane Fragueiro, Dina Salah, Alison Beckett, Martin Volk, Mathias Brust
Summary: This study demonstrates a method for direct imaging of engineered nanomaterials in biological cells using environmental scanning electron microscopy and wet-scanning transmission electron microscopy. The approach allows for high-throughput analysis of fully hydrated cells with nanometer resolution without the need for destructive processing steps.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Biochemistry & Molecular Biology
Kelly A. Parker, Stephanie Ribet, Blaise R. Kimmel, Roberto dos Reis, Milan Mrksich, Vinayak P. Dravid
Summary: Soft electron microscopy is essential for studying the characteristics of macromolecules, using low electron doses to enhance contrast. By performing scanning transmission electron microscopy in a scanning electron microscope, larger structures can be efficiently characterized with high contrast.
Review
Cell Biology
Xiaoyu Pu, Siyang Ma, Yan Gao, Tiankai Xu, Pengyu Chang, Lihua Dong
Summary: Radiation-induced damage is common in cancer patients undergoing radiotherapy, with mesenchymal stem cells and exosomes derived from them being ideal candidates for repair. Exosomes carry various bioactive substances that can affect immunomodulation, angiogenesis, cell survival, and proliferation, potentially providing new insights into the management of radiation damage.
Article
Engineering, Mechanical
Fatemeh Pourahmadian
Summary: The differential evolution indicators introduced in this study were examined in a laboratory setting for imaging mechanical evolution in highly scattering solids, with a focus on tracking the advancement of damage zones in elastic specimens. The results showed that the differential indicators successfully reconstructed the support of newborn fractures and the locations of discontinuities in the process zone, aiding in better understanding the damage mechanism.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2021)
Article
Chemistry, Multidisciplinary
Sytze de Graaf, Majid Ahmadi, Ivan Lazic, Eric G. T. Bosch, Bart J. Kooi
Summary: STEM is the most commonly used tool for atomic scale characterization of two-dimensional materials, but damage-free imaging remains a challenge, especially when observing combinations of light and heavy elements, particularly when recording fast dynamic phenomena.
Article
Chemistry, Physical
Ibrahim Eliah Dawod, Nicusor Timneanu, Adrian P. Mancuso, Carl Caleman, Oscar Granas
Summary: X-ray free-electrons lasers have revolutionized imaging biological macromolecules by allowing structural determination of single particles and crystals at room temperature with reduced radiation damage effects. Understanding how radiation damage affects atomic-scale structure is crucial for accurate reconstruction in the presence of damage.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Biology
Victoria T. Ly, Pierre Baudin, Pattawong Pansodtee, Erik A. Jung, Kateryna Voitiuk, Yohei M. Rosen, Helen Rankin Willsey, Gary L. Mantalas, Spencer T. Seiler, John A. Selberg, Sergio A. Cordero, Jayden M. Ross, Marco Rolandi, Alex A. Pollen, Tomasz J. Nowakowski, David Haussler, Mohammed A. Mostajo-Radji, Sofie R. Salama, Mircea Teodorescu
Summary: The study introduces a low-cost imaging system called Picroscope capable of simultaneous longitudinal bright-field z-stack imaging for 24 wells, highlighting its versatility and affordability for various biological imaging applications.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jiake Wei, Bin Feng, Eita Tochigi, Naoya Shibata, Yuichi Ikuhara
Summary: This study demonstrates that grain boundaries absorb point defects through the climb motion of disconnections under high energy electron beam irradiation, thereby improving the radiation resistance of materials.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Baokun Liang, Yingying Zhang, Christopher Leist, Zhaowei Ou, Miroslav Polozij, Zhiyong Wang, David Muecke, Renhao Dong, Zhikun Zheng, Thomas Heine, Xinliang Feng, Ute Kaiser, Haoyuan Qi
Summary: This paper presents the challenge of high-resolution imaging of organic 2D materials using transmission electron microscopes, and demonstrates the reduction of resolution gap between achievable resolution and instrumental limit by selecting the appropriate incident electron energy. The authors find that the highest resolution of 1.9 angstrom is achieved at 120 kV, and successfully detect interstitial defects and functional groups in 2D polymer thin films.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Elspeth F. Garman, Martin Weik
Summary: This review discusses recent research progress on radiation damage effects in macromolecular X-ray crystallography observed at synchrotrons and X-ray free electron lasers. It also briefly covers radiation damage in small molecule X-ray crystallography, small angle X-ray scattering experiments, microelectron diffraction, and single particle cryo-electron microscopy.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Joseph W. N. L. Reustle, Benjamin A. Belgrad, Amberle McKee, Delbert L. Smee
Summary: Hydrodynamic stress plays a significant role in shaping wave-swept environments and determining community structure. Barnacles, specifically ivory barnacles, have been found to exhibit phenotypic changes in response to flow and can serve as indicators of flow differences among sites. This study demonstrates the usefulness of barnacles as cheap, accessible, and biologically relevant flow indicators.
Article
Microscopy
Daniel Nicholls, Jack Wells, Andrew Stevens, Yalin Zheng, Jony Castagna, Nigel D. Browning
Summary: Sub-sampling during image acquisition in STEM can increase the acquisition speed and control the dose effectively. Optimizing control parameters can improve the resolution, precision, and sensitivity of inpainted images. When combined with hardware for rapidly sub-sampling images in STEM, this approach has significant implications for imaging beam-sensitive materials and dynamic processes.
Article
Chemistry, Multidisciplinary
Jana Vasiljevic, Bo Cederwall
Summary: An organic scintillator-based radiation portal monitor prototype system with imaging capabilities has been developed using neutron-gamma emission tomography technique. It enables rapid detection and precise location of small amounts of special nuclear materials and can efficiently address global security threats.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemical Research Methods
Luke K. Brewer, Jace W. Jones, Catherine B. Blackwood, Mariette Barbier, Amanda Oglesby-Sherrouse, Maureen A. Kane
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2020)
Article
Cell & Tissue Engineering
Manasa P. Srikanth, Jace W. Jones, Maureen Kane, Ola Awad, Tea Soon Park, Elias T. Zambidis, Ricardo A. Feldman
Summary: Gaucher disease is caused by mutations in the GBA1 gene, leading to the accumulation of GlcSph which activates an mTORC1-dependent pathogenic mechanism in neurons. Inhibition of acid ceramidase can prevent mTOR hyperactivity and lysosomal dysfunction, suggesting a potential therapeutic target for GBA1-associated neurodegeneration. Incubation with exogenous GlcSph in wild-type neurons can recapitulate the abnormalities observed in mutant neurons, highlighting the role of GlcSph in the pathogenesis of Gaucher disease.
STEM CELLS TRANSLATIONAL MEDICINE
(2021)
Article
Biochemical Research Methods
Anh Tran, I. Abrrey Monreal, Eugene Moskovets, Hector C. Aguilar, Jace W. Jones
Summary: An unmet need exists for analytical strategies that can characterize the lipid composition of viral envelopes and do so on a high-throughput scale. The use of atmospheric pressure MALDI with lithium adduct consolidation allows for rapid and confident profiling of total lipid extracts from enveloped viruses, specifically geared towards sphingolipid detection. This approach provides a robust and high-throughput lipid detection platform for structural characterization of lipid extracts from viruses.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Medicine, Research & Experimental
Ni Yang, Lauren E. Parker, Jianshi Yu, Jace W. Jones, Ting Liu, Kyriakos N. Papanicolaou, C. Conover Talbot, Kenneth B. Margulies, Brian O'Rourke, Maureen A. Kane, D. Brian Foster
Summary: The study showed that there is a decline in cardiac ATRA in heart failure, despite sufficient reserves of cardiac vitamin A. Strategies to normalize ATRA metabolism, such as CYP26 inhibition, may have therapeutic potential in preventing cardiac remodeling and functional decline. This suggests that low cardiac ATRA attenuates critical gene expression programs in heart failure.
Article
Chemistry, Analytical
Yulemni Morel, Nivedita Hegdekar, Chinmoy Sarkar, Marta M. Lipinski, Maureen A. Kane, Jace W. Jones
Summary: The study developed a targeted, quantitative method using HILIC separation and selective reaction monitoring mass spectrometry for specific and sensitive quantitation of 100 PE-P structures. Application of this assay to a TBI mouse model demonstrated distinct temporal profiles for plasma PE-P up to 28 days post injury, showing a significant increase 24 hours after induced TBI followed by a gradual reduction to sham concentrations by day 28.
ANALYTICA CHIMICA ACTA
(2021)
Article
Biochemistry & Molecular Biology
Sebastian Carballal, Victor Vitvitsky, Roshan Kumar, David A. Hanna, Marouane Libiad, Aditi Gupta, Jace W. Jones, Ruma Banerjee
Summary: This study demonstrates that H2S increases lipid synthesis in cells by affecting mitochondrial NAD(P)H pools and enabling reductive carboxylation of alpha-ketoglutarate. H2S also leads to time-dependent changes in various lipid classes, upregulating triglycerides while downregulating phosphatidylcholine.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Environmental Sciences
Ludovic Muller, Weiliang Huang, Jace W. Jones, Ann M. Farese, Thomas J. MacVittie, Maureen A. Kane
Summary: Radiation exposure leads to dysregulation of lipid and protein composition in the mesenteric lymph node (MLN), affecting pathways regulating lipids and acute phase response. The study demonstrates molecular alterations in MLN after acute radiation exposure, potentially informing on injury mechanism in a non-human primate model of acute radiation syndrome of the gastrointestinal tract.
Article
Biochemistry & Molecular Biology
Owen B. Becette, Anh Tran, Jace W. Jones, John P. Marino, Robert G. Brinson
Summary: Nucleic acids are a popular platform for developing biotherapeutics. There are currently 14 short oligonucleotide therapeutics and 2 mRNA vaccines approved by the FDA. However, there is a lack of high-resolution structural techniques for characterizing these molecules. In this study, nuclear magnetic resonance (NMR) methods were used to structurally fingerprint short oligonucleotide therapeutics, demonstrating their utility and broad applicability.
NUCLEIC ACID THERAPEUTICS
(2022)
Article
Cell Biology
Jianshi Yu, Mariarita Perri, Jace W. Jones, Keely Pierzchalski, Natalia Ceaicovscaia, Erika Cione, Maureen A. Kane
Summary: The study investigated the relationship between RBP1 expression and atRA, finding that RBP1 and atRA are reduced in mammary tumor tissue and tumorigenic epithelial cell lines. Increasing atRA levels could activate direct atRA targets, inhibit proliferation, and collagen deposition. Conditions in tumor microenvironments reduced RBP1 expression and atRA, while treatments with specific agonists or agents could restore RBP1 expression and atRA levels. This work highlights the potential therapeutic benefit of restoring RBP1 expression and endogenous atRA in diseases with reduced RBP1.
Article
Substance Abuse
Bryan Mackowiak, Mingjiang Xu, Yuhong Lin, Yukun Guan, Wonhyo Seo, Ruixue Ren, Dechun Feng, Jace W. Jones, Hongbing Wang, Bin Gao
Summary: The study found that mice chronically fed with ethanol responded less severely to multiple binge ethanol consumption compared to a single binge. The upregulation of the Cyp2b10 gene after binge ethanol intake can indirectly modify ethanol metabolism and reduce acute-on-chronic ethanol-induced liver injury.
ALCOHOL-CLINICAL AND EXPERIMENTAL RESEARCH
(2022)
Article
Physics, Atomic, Molecular & Chemical
Owen B. Becette, Anh Tran, John P. Marino, Jace W. Jones, Robert G. Brinson
Summary: In this study, a simplified and quick method for identification and assessment of a known impurity in nucleic acid drugs was developed using lithium adduct consolidation combined with mass spectrometry and nuclear magnetic resonance spectroscopy. The method is believed to have broad applicability in academic and industrial laboratories.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2022)
Article
Genetics & Heredity
Clorissa L. Washington-Hughes, Shubhrajit Roy, Herana Kamal Seneviratne, Senthilkumar S. Karuppagounder, Yulemni Morel, Jace W. Jones, Alex Zak, Tong Xiao, Tatiana N. Boronina, Robert N. Cole, Namandje N. Bumpus, Christopher J. Chang, Ted M. Dawson, Svetlana Lutsenko
Summary: This study reveals the importance of Cu transporter Atp7b in maintaining Cu homeostasis in the brain during postnatal development. Loss of Atp7b function leads to morphological changes in choroid plexus and affects Cu transporters Atp7a and Slc31a, resulting in Cu deficit and associated imbalance of catecholamines and lipids. These findings contribute to our understanding of the neuropathology of Wilson disease.
Article
Biochemical Research Methods
Yulemni Morel, Jace W. Jones
Summary: Lipid peroxidation is crucial in the development of various diseases, as it causes oxidative damage to lipids, leading to dysfunction and death of cells. This study presents an analytical approach for characterizing the structure of oxidized products of specific types of phospholipids, providing insights into the initial impact of lipid peroxidation on cellular membranes and their role in redox biology.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Stephanie Zalesak-Kravec, Weiliang Huang, Jace W. Jones, Jianshi Yu, Jenna Alloush, Amy E. Defnet, Alexander R. Moise, Maureen A. Kane
Summary: This study investigated the impact of CRBP1 loss on the adult mouse heart using a multi-omics approach. The results showed that RA levels were decreased in Rbp1(-/-) mouse heart tissue, and metabolomics and proteomics analyses revealed disrupted pathways related to cellular metabolism and cardiac metabolism. These findings characterize the effect of CRBP1 loss and reduced RA in the adult heart.
Article
Biochemical Research Methods
Anh Tran, Liting Wan, Zhenbo Xu, Janette M. Haro, Bing Li, Jace W. Jones
Summary: The research team utilized lithium adduct consolidation to enhance mass-spectrometry-based sphingolipid analysis and implemented an optimized MALDI matrix system for high-throughput detection. They successfully applied the technology to detect differentially expressed sphingolipids in liver, brain, and plasma matrices, validating the method's efficacy.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)