Article
Hematology
Shannon R. McCurdy, Vedran Radojcic, Hua-Ling Tsai, Ante Vulic, Elizabeth Thompson, Sanja Ivcevic, Christopher G. Kanakry, Jonathan D. Powell, Brian Lohman, Djamilatou Adom, Sophie Paczesny, Kenneth R. Cooke, Richard J. Jones, Ravi Varadhan, Heather J. Symons, Leo Luznik
Summary: This study used machine learning to analyze the immunologic signatures associated with posttransplant outcomes in bone marrow transplantation using PTCy. The results identified specific lymphocyte subsets that predict clinical outcomes and offered new insights into the influence of PTCy on alloimmune responses. The study highlights the importance of NK cell counts and CD4(+) regulatory T cells in patient survival and acute graft-versus-host disease. The findings contribute to the discovery of biomarkers in bone marrow transplantation and provide directions for future therapeutic interventions.
Article
Biochemistry & Molecular Biology
Xiao-Ru Yan, Tao Shi, Jia-Ying Xiao, Ya-Fang Liu, Hui-Ling Zheng
Summary: This study investigated the transdifferentiation of GM-preadipocytes into MECs induced by conditioned media, revealing genes and transcription factors associated with the process. By integrating transcriptome, DNA methylome, and proteome data, regulatory axes related to cell cycle, cell polarity establishment, cell adhesion, cell reprogramming, and adipocyte plasticity were identified.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Genetics & Heredity
Meghana Manjunath, Snehal Nirgude, Anisha Mhatre, Sai G. Vemuri, Mallika Nataraj, Jayanti Thumsi, Bibha Choudhary
Summary: Breast cancer is one of the leading causes of cancer-associated death in women. Despite progress in treatment, drug resistance and recurrence still impact patient survival. This study aimed to identify lncRNA and mRNA signatures in Indian breast cancer patients using RNA-seq. The analysis revealed a gene set that could segregate the different molecular subtypes of breast cancer. Survival analysis showed that menopausal status, tumor grade, and hormone status significantly affected the risk of mortality due to breast cancer.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Sunil S. Adav, Ching Yung Leung, Kee Woei Ng
Summary: This study utilized proteomic analysis to profile hair characteristics of individuals from different ethnic groups, genders, and ages, and found that hair proteins can be used for individual identification and differentiation.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Multidisciplinary Sciences
Caralyn E. Flack, John S. Parkinson
Summary: Our study provides important insights into the molecular signaling mechanisms of transmembrane chemoreceptors in Escherichia coli, offering valuable clues for further research in this area.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Suji Lee, Sujung Yoon, Eun Namgung, Tammy D. Kim, Haejin Hong, Eunji Ha, Rye Young Kim, Yumi Song, Hyangwon Lee, Chaewon Suh, In Kyoon Lyoo
Summary: This study aims to dissect the heterogeneity of posttraumatic conditions to identify clinically meaningful subtypes in recently traumatized individuals and evaluate their neurobiological correlates and long-term prognosis. A data-driven classification approach was implemented to identify four distinct and replicable subtypes for trauma-exposed individuals based on posttraumatic stress symptoms.
MOLECULAR PSYCHIATRY
(2023)
Article
Cell Biology
Conner Kummerlowe, Simutanyi Mwakamui, Travis K. Hughes, Nolawit Mulugeta, Victor Mudenda, Ellen Besa, Kanekwa Zyambo, Jessica E. S. Shay, Ira Fleming, Marko Vukovic, Ben A. Doran, Toby P. Aicher, Marc H. Wadsworth, Juliet Tongue Bramante, Amiko M. Uchida, Rabiah Fardoos, Osaretin E. Asowata, Nicholas Herbert, Omer H. Yilmaz, Henrik N. Kloverpris, John J. Garber, Jose Ordovas-Montanes, Zev J. Gartner, Thomas Wallach, Alex K. Shalek, Paul Kelly
Summary: Environmental enteropathy (EE) is a subclinical condition of the small intestine that is highly prevalent in low- and middle-income countries. This study used single-cell RNA sequencing to analyze the cellular and molecular correlates of EE. The results showed that the transcriptional signatures of EE may be driven by an increased abundance of surface mucosal cells and identified dysregulated signaling pathways and increased proinflammatory cytokine gene expression in EE epithelium.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Oncology
Nikita Kotlov, Alexander Bagaev, Maria Revuelta, Jude M. Phillip, Maria Teresa Cacciapuoti, Zoya Antysheva, Viktor Svekolkin, Ekaterina Tikhonova, Natalia Miheecheva, Natalia Kuzkina, Grigorii Nos, Fabrizio Tabbo, Felix Frenkel, Paola Ghione, Maria Tsiper, Nava Almog, Nathan Fowler, Ari M. Melnick, John P. Leonard, Giorgio Inghirami, Leandro Cerchietti
Summary: In this study, a transcriptomic analysis of the microenvironment of DLBCL was conducted, revealing four major lymphoma microenvironment categories associated with distinct biological aberrations and clinical behavior. This research also identified genetic and epigenetic mechanisms used by cancer cells to evade microenvironmental constraints and suggested the use of DNA hypomethylating agents in selected DLBCL patients. Additionally, new therapeutic vulnerabilities in the extracellular matrix composition were uncovered, providing potential targets for decreasing DLBCL proliferation in preclinical models.
Article
Biotechnology & Applied Microbiology
Amanda Marchi Maiorano, Diercles Francisco Cardoso, Roberto Carvalheiro, Gerardo Alves Fernandes Junior, Lucia Galvao de Albuquerque, Henrique Nunes de Oliveira
Summary: In this study, whole-genome sequencing was used to identify selection signature regions in Nelore cattle. Several genes and variants associated with adaptation, growth, and meat traits were discovered. These findings provide valuable insights into the genetic basis of economically important traits in this breed.
Article
Geochemistry & Geophysics
Shuwen Dong, Jianhua Li, Rui Gao, Peter A. Cawood, Hans Thybo, Stephen T. Johnston, Liqing Jiao, Yueqiao Zhang, Jinming Wang
Summary: In the Cretaceous extensional system of South China, lithospheric extension is mainly accommodated by localized normal faulting and distributed ductile stretching in the lower crust, followed by localized crustal necking and Moho uplift. These crustal and mantle features are kinematically linked, with lower-crustal stretching compensating for upper-crustal thinning and mantle shear zones affecting localized Moho uplift and crustal necking. The extension mechanism varies laterally from magma-poor to magma-rich conditions, resulting in changes in crustal melting, decoupling, and lithospheric mantle configuration.
EARTH AND PLANETARY SCIENCE LETTERS
(2023)
Article
Chemistry, Analytical
Katrin H. P. Vu, Ming-Che Lee, Gerhard H. Blankenburg, Yu-Jen Chang, Ming-Lee Chu, Andreas Erbe, Leonardo Lesser-Rojas, Yun-Ru Chen, Chia-Fu Chou
Summary: The study introduces a versatile platform using sub-10 nm nanogap electrodes for manipulating and sensing biomolecules in physiological conditions at a low copy number. This platform traps molecules via dielectrophoresis (DEP) across the nanogap, serving as a surface-enhanced Raman spectroscopy hotspot. The platform is demonstrated to be useful in studying the structural differences between A beta 40 and ZnA beta 40 peptides at different aggregation stages in physiologically relevant concentrations and in a solution phase.
ANALYTICAL CHEMISTRY
(2021)
Article
Plant Sciences
Ho-Wen Yang, Jae-Hoon Lee, Youfu Zhao
Summary: Erwinia amylovora, the causal agent of fire blight disease, activates the RpoN-HrpL sigma factor cascade to regulate the hypersensitive response (HR) and pathogenicity (hrp)-type III secretion system (T3SS). This study identified the RpoN regulon in E. amylovora using RNA-seq transcriptomic analysis and in silico binding site analysis. RpoN directly regulates genes associated with virulence, nitrogen assimilation, the PspF system, motility, and the YfhA/YfhK two-component regulatory system.
Article
Medicine, General & Internal
Kyoko Oshina, Keiji Kuroda, Kazuhiko Nakabayashi, Junko Tomikawa, Mari Kitade, Rikikazu Sugiyama, Kenichiro Hata, Atsuo Itakura
Summary: Chronic endometritis (CE) is characterized by persistent inflammation of the endometrium with the presence of plasma cell infiltration. CD138 immunohistochemistry is an effective diagnostic tool for CE. This study identified gene expression signatures associated with CE and potential new biomarkers using RNA-sequencing analysis.
FRONTIERS IN MEDICINE
(2023)
Article
Multidisciplinary Sciences
Lauren Wegman-Points, Khaled Alganem, Ali Sajid Imami, Victoria Mathis, Justin Fortune Creeden, Robert McCullumsmith, Li-Lian Yuan
Summary: Protein kinases and their substrates form signaling networks across subcellular compartments, and assessing their activity in different fractions can provide insights into their functional roles. In this study, we used peptide arrays to evaluate the activity of serine/threonine protein kinases in synaptosomal, nuclear, and cytosolic fractions from rat frontal cortex. Our results showed differences in protein kinase activity among these fractions, and we identified enriched kinases in the synaptosomal fraction compared to the nuclear fraction. This study demonstrates the feasibility of using peptide arrays to assess subcellular fractions and reveals compartment-specific activity profiles associated with established and novel kinases.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Francesca Sansico, Mattia Miroballo, Daniele Salvatore Bianco, Francesco Tamiro, Mattia Colucci, Elisabetta De Santis, Giovanni Rossi, Jessica Rosati, Lazzaro Di Mauro, Giuseppe Miscio, Tommaso Mazza, Angelo Luigi Vescovi, Gianluigi Mazzoccoli, Vincenzo Giambra
Summary: The research conducted single-cell RNA sequencing analysis revealed that patients with COVID-19 exhibited an increase in COVID-specific surface markers in different subsets of immune cells, while the expression of cell receptors was reduced in response to the viral infection. These results highlight the presence of novel immunoreceptors in COVID-19 patients affecting immune functionality.
Article
Neurosciences
Paolo Follesa, Gabriele Floris, Gino P. Asuni, Antonio Ibba, Maria G. Tocco, Luca Zicca, Beniamina Mercante, Franca Deriu, Giorgio Gorini
FRONTIERS IN CELLULAR NEUROSCIENCE
(2015)
Article
Neurosciences
Mandy L. McCracken, Giorgio Gorini, Lindsay M. McCracken, R. Dayne Mayfield, R. Adron Harris, James R. Trudell
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2016)
Article
Biotechnology & Applied Microbiology
Yury O. Nunez, Jay M. Truitt, Giorgio Gorini, Olga N. Ponomareva, Yuri A. Blednov, R. Adron Harris, R. Dayne Mayfield
Review
Neurosciences
Giorgio Gorini, R. Adron Harris, R. Dayne Mayfield
NEUROPSYCHOPHARMACOLOGY
(2014)
Article
Multidisciplinary Sciences
Giorgio Gorini, Yury O. Nunez, R. Dayne Mayfield
Meeting Abstract
Substance Abuse
K. Marballi, G. Gorini, J. C. Crabbe, R. A. Harris, I. Ponomarev
ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH
(2014)
Meeting Abstract
Substance Abuse
G. Gorini, Y. O. Nunez, A. J. Roberts, R. D. Mayfield
Meeting Abstract
Substance Abuse
G. Gorini, Y. O. Nunez, A. J. Roberts, R. D. Mayfield
ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH
(2013)
Meeting Abstract
Substance Abuse
R. D. Mayfield, Y. O. Nunez, G. Gorini, J. M. Truitt, O. Ponomareva, G. R. Tiwari, A. J. Roberts, Y. A. Blednov, R. A. Harris
ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH
(2013)
Meeting Abstract
Substance Abuse
M. L. McCracken, G. Gorini, R. D. Mayfield, J. R. Trudell, R. A. Harris
ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH
(2013)
Meeting Abstract
Substance Abuse
G. Gorini, Y. O. Nunez, A. J. Roberts, R. D. Mayfield
ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH
(2012)
Meeting Abstract
Substance Abuse
Y. O. Nunez, G. Gorini, J. M. Truitt, O. Ponomareva, G. R. Tiwari, A. J. Roberts, Y. A. Blednov, R. A. Harris, R. D. Mayfield
ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH
(2012)
Meeting Abstract
Substance Abuse
Y. O. Nunez, J. M. Truitt, G. Gorini, O. Ponomareva, G. R. Tiwari, Y. A. Blednov, R. A. Harris, R. D. Mayfield
ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH
(2012)
Meeting Abstract
Substance Abuse
Y. O. Nunez, J. M. Truitt, O. Ponomareva, G. Gorini, G. R. Tiwari, Y. A. Blednov, R. A. Harris, R. D. Mayfield
ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH
(2012)