Article
Biology
Anthony Santella, Irina Kolotuev, Caroline Kizilyaprak, Zhirong Bao
Summary: Analyzing brain development, structure, and function across imaging modalities can provide valuable information. This study combines electron microscopy and time-lapse fluorescence microscopy to study the emergence of the nervous system in Caenorhabditis elegans embryogenesis.
Article
Multidisciplinary Sciences
Chenfei Hu, Shenghua He, Young Jae Lee, Yuchen He, Edward M. Kong, Hua Li, Mark A. Anastasio, Gabriel Popescu
Summary: The study introduces a method for assessing cell viability without the need for labeling, utilizing deep learning techniques combined with quantitative phase imaging to accurately determine cell survival status without causing damage to the cells.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Andreas Boden, Francesca Pennacchietti, Giovanna Coceano, Martina Damenti, Michael Ratz, Ilaria Testa
Summary: A new 3D pRESOLFT microscope method with sub-80-nm resolution has been developed to visualize the volumetric architecture of organelles and molecules inside whole living cells, allowing for targeted 3D confinement of fluorescence and observation of dynamic structural alterations in cells.
NATURE BIOTECHNOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Yang Zhang, Hao Jiang, Taoyu Ye, Mario Juhas
Summary: Despite the significant interest in deep learning in microbiology, its full potential is yet to be realized. Deep-learning-based systems are believed to play a crucial role in monitoring and investigating microorganisms in the future.
TRENDS IN MICROBIOLOGY
(2021)
Article
Biology
Ina Lantzsch, Che-Hang Yu, Yu-Zen Chen, Vitaly Zimyanin, Hossein Yazdkhasti, Norbert Lindow, Erik Szentgyoergyi, Ariel M. Pani, Steffen Prohaska, Martin Srayko, Sebastian Furthauer, Stefanie Redemann
Summary: Female meiotic spindles undergo significant morphological changes from metaphase to anaphase, with an increase in microtubule numbers, decrease in average length, and significant changes in microtubule lengths near the chromosome surface. Microtubule turnover is the major driver of spindle rearrangements, with a minor fraction of microtubules being severed in metaphase, mainly those in close contact with chromosomes. The mechanisms of microtubule severing in this transition appear to be dependent on katanin.
Article
Optics
Zewei Luo, Ge Wu, Mengting Kong, Zhi Chen, Zhengfei Zhuang, Junchao Fan, Tongsheng Chen
Summary: Forster resonance energy transfer (FRET) microscopy is a valuable tool for studying biological systems, but super-resolution FRET imaging in living cells is challenging. In this study, we propose a SR FRET method called SIM-FRET that combines SR structured illumination microscopy (SIM) imaging and acceptor sensitized emission FRET imaging to achieve live-cell quantitative SR FRET imaging. Our method provides enhanced spatial resolution and maintains the advantages of quantitative FRET analysis. We validate the effectiveness of SIM-FRET through simulated models and live-cell samples, and demonstrate its ability to reveal the intricate structure of FRET signals.
PHOTONICS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Tom Baladi, Jesper R. Nilsson, Audrey Gallud, Emanuele Celauro, Cecile Gasse, Fabienne Levi-Acobas, Ivo Sarac, Marcel R. Hollenstein, Anders Dahlen, Elin K. Esbjorner, L. Marcus Wilhelmsson
Summary: The study introduces a stealth labeling strategy to efficiently generate RNA transcripts and translate them into correct proteins, providing an important tool for biological research and RNA delivery studies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Developmental Biology
Mostafa Aakhte, Hans-Arno J. Mueller
Summary: Light-sheet or selective plane illumination microscopy (SPIM) is suitable for in toto imaging of living specimens at high temporal-spatial resolution, but faces limitations due to light scattering in opaque specimens. The Multiview tiling SPIM (MT-SPIM) combines the strengths of Multi-view SPIM (M-SPIM) and a confined, multi-tiled light sheet, providing high-resolution, robust, and rotation-free imaging of living specimens. It improves axial resolution by a factor of two, enhancing automated segmentation of cellular structures.
Article
Nanoscience & Nanotechnology
Andrew C. Lang, D. Scott Katzer, Neeraj Nepal, David J. Meyer, Rhonda M. Stroud
Summary: Epitaxial transition metal nitrides (TMNs) are a new class of crystalline thin film metals that can be integrated with common group III-nitride semiconductors. This study used high-resolution transmission electron microscopy to identify different phases of tantalum nitrides with N-sublattice ordering, revealing Ta-deficient films with specific planar defects. These findings lay the foundation for the application of this epitaxial TMN material in new electronic and superconducting device structures.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Biology
Jeremy Copperman, Sean M. Gross, Young Hwan Chang, Laura M. Heiser, Daniel M. Zuckerman
Summary: Time-lapse imaging is a powerful tool to study cell dynamics, but analyzing morphological changes over time is challenging. In this study, we use trajectory embedding to analyze cellular behavior based on multiple time points simultaneously. We apply this method to study the effects of microenvironmental perturbagens on MCF10A mammary epithelial cells. Our analysis reveals ligand-specific regulation of cell state transitions and provides descriptive models of single-cell trajectories. Incorporating trajectories improves the characterization of cell states and enables better identification of phenotypes compared to snapshot-based analysis. This approach has broad applications in live-cell imaging for studying cell responses.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Analytical
Olivier De Castro, Jean-Nicolas Audinot, Hung Quang Hoang, Cherif Coulbary, Olivier Bouton, Rachid Barrahma, Alexander Ost, Charlotte Stoffels, Chengge Jiao, Mikhail Dutka, Michal Geryk, Tom Wirtz
Summary: The article introduces the use of magnetic sector secondary ion mass spectrometry (SIMS) on a widely used instrument, focused ion beam (FIB)-scanning electron microscopy (SEM), for nanoscale investigations. It provides a detailed description of the instrument's layout and performance, as well as the research results obtained in various fields. The system demonstrates versatile capability for high-performance correlative studies in materials science and life sciences.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Allan S. Johnson, Jordi Valls Conesa, Luciana Vidas, Daniel Perez-Salinas, Christian M. Gunther, Bastian Pfau, Kent A. Hallman, Richard F. Haglund, Stefan Eisebitt, Simon Wall
Summary: Solid-state systems can host a variety of thermodynamic phases that are challenging to study on the nanoscale due to the coexistence of multiple phases. Coherent diffractive imaging spectroscopy (CDIS) enables nanometer-scale resolution hyperspectral imaging of vanadium oxide, extracting refractive indices of different phases from a single sample without evidence of correlation-driven phase transitions. CDIS allows quantitative full-field x-ray spectromicroscopy for studying phase separation in extreme sample environments.
Editorial Material
Endocrinology & Metabolism
Gary Siuzdak
Summary: Recent advances in mass spectrometry imaging, specifically the development of nano secondary ion mass spectrometry, have made subcellular quantitative analysis a reality, allowing for absolute quantification at the organelle level.
Article
Biochemistry & Molecular Biology
Anayat Bhat, Shuang Li, Daniel Hammler, Martin J. Winterhalder, Andreas Marx, Andreas Zumbusch
Summary: The hydrolysis of nucleotides is important for cellular energy, and the transfer of phosphates to proteins is crucial for post-translational modification. A novel fluorogenic adenosine 5'-tetraphosphate (Ap4) analog has been developed for real-time monitoring of ATP hydrolysis within live cells, with potential applications in studying cellular processes involving Ap4 hydrolysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Tatiana Latychevskaia, Alice Kohli
Summary: A low-dose imaging technique is proposed, where recognition is used instead of recording high-resolution images to verify structural hypotheses. By detecting only a few scattered particles, a structural hypothesis can be confirmed with a probability exceeding 95%. This technique can be applied to optical character recognition and minimizing radiation damage in sensitive materials.
SCIENTIFIC REPORTS
(2022)
Article
Medical Laboratory Technology
Chad Fibke, Sylvie Giroux, Andre Caron, Elizabeth Starks, Jeremy D. K. Parker, Lucas Swanson, Loubna Jouan, Sylvie Langlois, Guy Rouleau, Francois Rousseau, Aly Karsan
Summary: The study found a positive association between cfDNA quantity and blood shipment time in EDTA tubes, which is significantly reduced with the use of Streck tubes. Plasma storage at -80 degrees Celsius is associated with a 4.4% annual relative decrease in cfDNA levels. FF was not associated with collection tube type, but was associated with factors such as gestational age, chromosomal abnormalities, BMI, and fetal sex.
CLINICAL CHEMISTRY AND LABORATORY MEDICINE
(2022)
Article
Immunology
Aparna Gopal, Rawa Ibrahim, Megan Fuller, Patricia Umlandt, Jeremy Parker, Jessica Tran, Linda Chang, Joanna Wegrzyn-Woltosz, Jeffrey Lam, Jenny Li, Melody Lu, Aly Karsan
Summary: This study uncovers a novel role for TIRAP in driving bone marrow failure, which is mediated by the up-regulation of Ifn γ and the subsequent disruption of the bone marrow endothelial niche. Additionally, this study reveals the inhibitory role of Ifn γ in the transformation of MDS to acute leukemia.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Article
Hematology
Nicole Thomas, Kostiantyn Dreval, Daniela S. Gerhard, Laura K. Hilton, Jeremy S. Abramson, Richard F. Ambinder, Stefan Barta, Nancy L. Bartlett, Jeffrey Bethony, Kishor Bhatia, Jay Bowen, Anthony C. Bryan, Ethel Cesarman, Corey Casper, Amy Chadburn, Manuela Cruz, Dirk P. Dittmer, Maureen A. Dyer, Pedro Farinha, Julie M. Gastier-Foster, Alina S. Gerrie, Bruno M. Grande, Timothy Greiner, Nicholas B. Griner, Thomas G. Gross, Nancy L. Harris, John D. Irvin, Elaine S. Jaffe, David Henry, Rebecca Huppi, Fabio E. Leal, Michael S. Lee, Jean Paul Martin, Marie-Reine Martin, Sam M. Mbulaiteye, Ronald Mitsuyasu, Vivian Morris, Charles G. Mullighan, Andrew J. Mungall, Karen Mungall, Innocent Mutyaba, Mostafa Nokta, Constance Namirembe, Ariela Noy, Martin D. Ogwang, Abraham Omoding, Jackson Orem, German Ott, Hilary Petrello, Stefania Pittaluga, James D. Phelan, Juan Carlos Ramos, Lee Ratner, Steven J. Reynolds, Paul G. Rubinstein, Gerhard Sissolak, Graham Slack, Shaghayegh Soudi, Steven H. Swerdlow, Alexandra Traverse-Glehen, Wyndham H. Wilson, Jasper Wong, Robert Yarchoan, Jean C. ZenKlusen, Marco A. Marra, Louis M. Staudt, David W. Scott, Ryan D. Merin
Summary: By sequencing the whole genome of 230 Burkitt lymphoma (BL) and 295 diffuse large B-cell lymphoma (DLBCL) tumors, additional significantly mutated genes were identified, new subtypes of BL and DLBCL were discovered, and genetic features associated with patient outcomes were determined. These findings highlight the shared pathogenesis between adult BL and pediatric BL, and provide a new framework for epidemiology, diagnosis, and therapeutic strategies.
Article
Hematology
Waleed Alduaij, Brett Collinge, Susana Ben-Neriah, Aixiang Jiang, Laura K. Hilton, Merrill Boyle, Barbara Meissner, Lauren Chong, Tomoko Miyata-Takata, Graham W. Slack, Pedro Farinha, Jeffrey W. Craig, Andrew Lytle, Kerry J. Savage, Diego Villa, Alina S. Gerrie, Ciara L. Freeman, Randy D. Gascoyne, Joseph M. Connors, Ryan D. Morin, Laurie H. Sehn, Andrew J. Mungall, Christian Steidl, David W. Scott
Summary: This study found that the molecular heterogeneity of DLBCL leads to variable outcomes with immunochemotherapy. DZsig expression extends beyond HGBCL-DH-BCL2 and captures a poor-prognosis DLBCL subgroup with short DTI, including patients unidentifiable by routine FISH testing, that should be considered for treatment intensification or novel therapies in prospective trials.
Letter
Cardiac & Cardiovascular Systems
Matthew Cheung, Ali Husain, Darson Du, Christopher O. Y. Li, Jeremy Parker, Adaya Weissler-Snir, Jeffrey B. Geske, Kevin Ong, Zachary Laksman
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2022)
Meeting Abstract
Hematology
Jasper Wong, Brett Collinge, Laura K. Hilton, Susana Ben-Neriah, Merrill Boyle, Barbara Meissner, Kelly Mekwunye, Graham W. Slack, Pedro Farinha, Jeffrey W. Craig, Laurie H. Sehn, Diego Villa, Alina S. Gerrie, Andrew J. Mungall, Christian Steidl, James R. Cook, Andrew L. Feldman, Lisa M. Rimsza, Kerry J. Savage, Ryan D. Morin, David W. Scott
Meeting Abstract
Hematology
Krysta M. Coyle, Qurat Ul Ain Qureshi, Balwinder Ruprai, Tejdeep Kang, Laura K. Hilton, Kostiantyn Dreval, Prasath Pararajalingam, Christopher K. Rushton, Nicole Thomas, Timothy E. Audas, Ryan D. Morin
Article
Cardiac & Cardiovascular Systems
Brianna Davies, Jacqueline Forman, Cheryl McIlroy, Heather Joe, Sina Safabakhsh, Janet Liew, Jeremy Parker, Darson Du, Jason G. Andrade, Matthew T. Bennett, Nathaniel M. Hawkins, Santabhanu Chakrabarti, John Yeung, Marc W. Deyell, Andrew D. Krahn, Robert Moss, Kevin Ong, Zachary Laksman
Summary: This study aimed to explore the psychological impact of using a smartphone-enabled insertable cardiac monitor (ICM) for arrhythmia monitoring in patients with hypertrophic cardiomyopathy (HCM). The study found that the feedback from ICM transmissions improved symptom clarity, provided reassurance, and helped with decision-making for implantable cardioverter defibrillators. However, participants had expectations for more data availability in the app interface.
EUROPEAN JOURNAL OF CARDIOVASCULAR NURSING
(2023)
Article
Multidisciplinary Sciences
Xuehai Wang, Michael Nissen, Deanne Gracias, Manabu Kusakabe, Guillermo Simkin, Aixiang Jiang, Gerben Duns, Clementine Sarkozy, Laura Hilton, Elizabeth A. Chavez, Gabriela C. Segat, Rachel Wong, Jubin Kim, Tomohiro Aoki, Rashedul Islam, Christina May, Stacy Hung, Kate Tyshchenko, Ryan R. Brinkman, Martin Hirst, Aly Karsan, Ciara Freeman, Laurie H. Sehn, Ryan D. Morin, Andrew J. Roth, Kerry J. Savage, Jeffrey W. Craig, Sohrab P. Shah, Christian Steidl, David W. Scott, Andrew P. Weng
Summary: In this study, the authors conducted comprehensive phenotypic profiling of 155 diagnostic follicular lymphoma (FL) biopsies using mass cytometry. They identified two recurrent patterns associated with transformation risk and found that increased follicular helper T cells and intratumoral phenotypic diversity were independently associated with increased risk of transformation. They also developed a reduced 26-marker panel which could be used for phenotypic profiling of future FL cohorts using conventional flow cytometry.
NATURE COMMUNICATIONS
(2022)
Article
Hematology
Kostiantyn Dreval, Laura K. Hilton, Manuela Cruz, Haya Shaalan, Susana Ben-Neriah, Merrill Boyle, Brett Collinge, Krysta M. Coyle, Gerben Duns, Pedro Farinha, Bruno M. Grande, Barbara Meissner, Prasath Pararajalingam, Christopher K. Rushton, Graham W. Slack, Jasper Wong, Andrew J. Mungall, Marco A. Marra, Joseph M. Connors, Christian Steidl, David W. Scott, Ryan D. Morin
Summary: Follicular lymphoma (FL) accounts for approximately 20% of new lymphoma cases. In this study, two genetically distinct subgroups of FL, called DLBCL-like (dFL) and constrained FL (cFL), were identified and characterized based on whole-genome sequencing data. Using a machine learning approach, patients with FL could be stratified into cFL and dFL subgroups, and it was found that cFL status is associated with a reduced risk of lymphoma transformation.
Article
Oncology
Laura K. Hilton, Henry S. Ngu, Brett Collinge, Kostiantyn Dreval, Susana Ben-Neriah, Christopher K. Rushton, Jasper C. H. Wong, Manuela Cruz, Andrew Roth, Merrill Boyle, Barbara Meissner, Graham W. Slack, Pedro Farinha, Jeffrey W. Craig, Alina S. Gerrie, Ciara L. Freeman, Diego Villa, Judith A. Rodrigo, Kevin Song, Michael Crump, Lois Shepherd, Annette E. Hay, John Kuruvilla, Kerry J. Savage, Robert Kridel, Aly Karsan, Marco A. Marra, Laurie H. Sehn, Christian Steidl, Ryan D. Morin, David W. Scott
Summary: Diffuse large B-cell lymphoma (DLBCL) patients with early disease progression or relapse have poor outcomes. This study found that patients with late relapse had better outcomes after second-line therapy and autologous stem-cell transplantation compared to those with primary refractory or early relapse. Despite concordance in cell-of-origin classification and genetics-based subgroup between diagnostic and relapse biopsies, late relapses showed significant genetic differences and demonstrated branching evolution patterns. In highly divergent tumors, the same genes acquired new mutations independently, suggesting that shared precursor cells constrain tumor evolution towards the same genetics-based subgroups at both diagnosis and relapse.
JOURNAL OF CLINICAL ONCOLOGY
(2023)
Article
Oncology
Anuvrat Sircar, Satishkumar Singh, Zijun Y. Xu-Monette, Krysta Mila Coyle, Laura K. Hilton, Evangelia Chavdoula, Parvathi Ranganathan, Neeraj Jain, Walter Hanel, Philip Tsichlis, Lapo Alinari, Blake R. Peterson, Jianguo Tao, Natarajan Muthusamy, Robert Baiocchi, Narendranath Epperla, Ken H. Young, Ryan Morin, Lalit Sehgal
Summary: Mantle cell lymphoma (MCL) is a lethal hematological malignancy with a median survival of 4 years. The limited understanding of clinical tumor progression and resistance to current therapeutic regimes contributes to its lethality. Elucidating neoteric pharmacotherapeutic molecular targets involved in MCL progression is crucial for improved disease prevention.
Letter
Hematology
John R. Davies, Laura K. Hilton, Aixiang Jiang, Sharon Barrans, Catherine Burton, Peter W. M. Johnson, Andrew J. Davies, Ming-Qing Du, Reuben Tooze, Francesco Cucco, Matthew A. Care, Ryan D. Morin, Christian Steidl, Chulin Sha, David R. Westhead, David W. Scott
Meeting Abstract
Hematology
Laura K. Hilton, Henry S. Ngu, Brett Collinge, Kostiantyn Dreval, Susana Ben-Neriah, Christopher K. Rushton, Jasper Wong, Manuela Cruz, Andrew Roth, Merrill Boyle, Barbara Meissner, Graham W. Slack, Pedro Farinha, Jeffrey W. Craig, Alina S. Gerrie, Ciara L. Freeman, Diego Villa, Kerry J. Savage, Laurie H. Sehn, Marco A. Marra, Aly Karsan, Christian Steidl, Ryan D. Morin, David W. Scott
Meeting Abstract
Hematology
Waleed Alduaij, Aixiang Jiang, Diego Villa, Brett Collinge, Susana Ben-Neriah, Merrill Boyle, Barbara Meissner, Laura K. Hilton, Pedro Farinha, Graham W. Slack, Jeffrey W. Craig, Alina S. Gerrie, Ciara L. Freeman, Andrew J. Mungall, Christian Steidl, Laurie H. Sehn, David W. Scott, Kerry J. Savage