Article
Biotechnology & Applied Microbiology
Derek H. Janssens, Dominik J. Otto, Michael P. Meers, Manu Setty, Kami Ahmad, Steven Henikoff
Summary: CUT&Tag is a method for chromatin profiling in small samples and single cells, which allows high-resolution mapping of both active and repressive regulomes. It provides a complete profiling strategy suitable for high-throughput single-cell platforms.
Article
Multidisciplinary Sciences
Moshe Giladi, Michal Lisnyansky Bar-El, Pavla Vankova, Alisa Ferofontov, Emelia Melvin, Suha Alkaderi, Daniel Kavan, Boris Redko, Elvira Haimov, Reuven Wiener, Petr Man, Yoni Haitin
Summary: Isoprenoids are synthesized by the prenyltransferase superfamily, and the correlation between active site volume and product length is not observed in long-chain products and rubber synthases. In the human cis-prenyltransferase complex, elongating products exit through an outlet, and product elongation is closely correlated with membrane association.
Review
Physiology
Kunal R. Shah, Xin Guan, Jiusheng Yan
Summary: Ion channels can form macromolecular signaling complexes to ensure accurate signal transduction. The BK channel limits increases in [Ca2+]i levels through K+ efflux and rapid membrane repolarization, serving as a negative feedback regulator.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Robert J. Hall, Jonathan O'Loughlin, Charlotte K. Billington, Dhruma Thakker, Ian P. Hall, Ian Sayers
Summary: GPR126 is an adhesion G protein-coupled receptor associated with lung function and COPD, with identified SNPs affecting its function/expression. Activation of GPR126 in airway cells leads to downstream gene/pathway alterations, suggesting a role in airway remodeling. Further research is warranted to elucidate the exact mechanisms involved.
Article
Neurosciences
Xiaoting Huang, Yangsa Du, Danni Guo, Fangfang Xie, Chunyao Zhou
Summary: This study aimed to evaluate the coupling of structural connectivity (SC) and functional connectivity (FC) in the entire brain of healthy controls (HCs) and individuals with temporal lobe epilepsy (TLE). The results showed that TLE patients had lower SC-FC coupling strength in specific brain regions compared to HCs, indicating higher susceptibility to pathological disruption.
FRONTIERS IN NEUROSCIENCE
(2023)
Article
Biology
Akihito Otsuki, Yasunobu Okamura, Noriko Ishida, Shu Tadaka, Jun Takayama, Kazuki Kumada, Junko Kawashima, Keiko Taguchi, Naoko Minegishi, Shinichi Kuriyama, Gen Tamiya, Kengo Kinoshita, Fumiki Katsuoka, Masayuki Yamamoto
Summary: Long-read sequencing on activated T-cells from a sample of 333 Japanese individuals (representing 111 parent-offspring trios) provides a useful reference dataset of structural variation in the Japanese population.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Andrea Cipriano, Martina Macino, Giulia Buonaiuto, Tiziana Santini, Beatrice Biferali, Giovanna Peruzzi, Alessio Colantoni, Chiara Mozzetta, Monica Ballarino
Summary: This study identified a novel lncRNA, Lnc-Rewind, which regulates MuSC proliferation and expansion by influencing the expression of skeletal muscle genes and components of the WNT signaling pathway in mouse. The interaction of Lnc-Rewind with the G9a histone lysine methyltransferase mediates the repression of the Wnt7b gene, providing insights into the epigenetic regulation of adult muscle stem cells fate by lncRNAs.
Article
Immunology
Jhonatan Antonio alvarez Gomez, Diana Celeste Salazar-Camarena, Ilce Valeria Roman-Fernandez, Pablo Cesar Ortiz-Lazareno, Alvaro Cruz, Jose Francisco Munoz-Valle, Miguel Marin-Rosales, Noemi Espinoza-Garcia, Nefertari Sagrero-Fabela, Claudia Azucena Palafox-Sanchez
Summary: This study aims to analyze the expression of the BAFF system in CXCR5- CD11c+ atypical B cell subsets in SLE patients and found increased expression in these subsets. Additionally, decreased TACI expression on atypical B cells DN2 was associated with higher disease activity.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Eshan Bundhoo, Anisah W. Ghoorah, Yasmina Jaufeerally-Fakim
Summary: TAGOPSIN is a command line program written in Java that allows rapid and systematic retrieval of select data from seven popular public biological databases relevant to comparative genomics and protein structure studies. It efficiently integrates data for various organisms and facilitates interspecific comparative analyses of protein-coding genes or identification of taxa-specific protein domains and three-dimensional structures. TAGOPSIN is available for download as a JAR file under the GNU General Public License.
BMC BIOINFORMATICS
(2021)
Article
Oncology
Nobuhiko Imahashi, Rafet Basar, Yuefan Huang, Fang Wang, Natalia Baran, Pinaki Prosad Banerjee, Junjun Lu, Ana Karen Nunez Cortes, Nadima Uprety, Emily Ensley, Luis Muniz-Feliciano, Tamara J. Laskowski, Judy S. Moyes, May Daher, Mayela Mendt, Lucila N. Kerbauy, Mayra Shanley, Li Li, Francesca Lorraine Wei Inng Lim, Hila Shaim, Ye Li, Marina Konopleva, Michael Green, Jennifer Wargo, Elizabeth J. Shpall, Ken Chen, Katayoun Rezvani
Summary: This study shows that activated B cells suppress T-cell responses through metabolic competition, including increased oxygen consumption and glucose deprivation. These findings provide new insights into immunometabolism and its potential implications for cancer immunotherapy.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Biochemistry & Molecular Biology
Barbara Cisterna, Manuela Costanzo, Maria Assunta Lacavalla, Mirco Galie, Osvaldo Angelini, Gabriele Tabaracci, Manuela Malatesta
Summary: Oxygen-ozone therapy at low concentrations can induce different effects on fibroblasts depending on their activation state, stimulating proliferation and cytokine secretion in non-activated fibroblasts, while enhancing antioxidant response in already activated fibroblasts. This study provides insights into the potential activation-like responses induced by low O-3 concentrations in fibroblasts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Haiqin Jiang, Chuang-Wei Wang, Zhaoxi Wang, Yufei Dai, Yanping Zhu, Yun-Shien Lee, Yang Cao, Wen-Hung Chung, Songying Ouyang, Hongsheng Wang
Summary: This study investigates the molecular mechanisms of HLA-B*13:01 in the pathogenesis of Dapsone-induced drug hypersensitivity. The crystal structure of HLA-B*13:01-beta-2-microglobulin complex is determined, and key residues mediating the binding of DDS are identified. Single-cell TCR and RNA sequencing indicate that clonotype-specific TCRs can recognize HLA-B*13:01-DDS complex to trigger inflammatory cytokines associated with DDS-DIHS.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
P. N. Vinodh Kumar, Mallana Gowdra Mallikarjuna, Shailendra Kumar Jha, Anima Mahato, K. R. Yathish, Shambhu Krishan Lal, Hirenallur Chandappa Lohithaswa, Viswanathan Chinnusamy
Summary: SWEETs are sugar transporters that play a crucial role in various biological processes, such as plant development, nectar secretion, and stress regulation. A comprehensive study on maize SWEET transporters has been conducted to understand their structural, evolutionary, and functional characteristics for maize improvement.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Cell Biology
Shelby D. Ma, Marion Mussbacher, Elena V. Galkina
Summary: This review highlights the dual role of B cells in atherosclerosis, with different B cell subsets exerting either pro-atherogenic or atheroprotective functions based on their characteristics. Furthermore, the article focuses on the three major B cell functions: antibody production, antigen presentation/T cell interaction, and cytokine release.
Article
Chemistry, Multidisciplinary
Jin-Qiu You, Yi-Nan Liu, Jun-Su Zhou, Xin-Yu Sun, Chun Lei, Qing Mu, Jing-Ya Li, Ai-Jun Hou
Summary: Twelve new cis-clerodane diterpenoids, named crispinoids A-L (1-12), along with three known analogues (13-15), were isolated from Tinospora crispa. Their structures were fully determined using comprehensive spectroscopic techniques, single-crystal X-ray diffraction experiments, and electronic circular dichroism (ECD) analyses. The isolated compounds exhibited diverse heterocyclic frameworks and demonstrated inhibition of key pathways and inflammatory responses.
CHINESE JOURNAL OF CHEMISTRY
(2022)
Article
Cell Biology
Konstantina Antoniou, Fanny Ender, Tillman Vollbrandt, Yves Laumonnier, Franziska Rathmann, Chandrashekhar Pasare, Harinder Singh, Joerg Koehl
Article
Cell Biology
Margaret M. McDaniel, Leah C. Kottyan, Harinder Singh, Chandrashekhar Pasare
Article
Urology & Nephrology
Kevin Louis, Camila Macedo, Elodie Bailly, Louis Lau, Bala Ramaswami, Marilyn Marrari, Douglas Landsittel, Alexander Chang, Uma Chandran, Paul Fadakar, Masaki Yamada, Geetha Chalasani, Parmjeet Randhawa, Adriana Zeevi, Harinder Singh, Carmen Lefaucheur, Diana Metes
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2020)
Editorial Material
Multidisciplinary Sciences
Harinder Singh
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Shiqun Zhang, Tara N. Edwards, Virendra K. Chaudhri, Jianing Wu, Jonathan A. Cohen, Toshiro Hirai, Natalie Rittenhouse, Elizabeth G. Schmitz, Paul Yifan Zhou, Benjamin D. McNeil, Yi Yang, H. Richard Koerber, Tina L. Sumpter, Amanda C. Poholek, Brian M. Davis, Kathryn M. Albers, Harinder Singh, Daniel H. Kaplan
Summary: A subset of sensory nonpeptidergic neurons expressing MrgprD play a crucial role in regulating skin inflammation, suppressing mast cell hyperresponsiveness and cutaneous immune homeostasis via glutamate release.
Article
Biochemical Research Methods
Derek Reiman, Godhev Kumar Manakkat Vijay, Heping Xu, Andrew Sonin, Dianyu Chen, Nathan Salomonis, Harinder Singh, Aly A. Khan
Summary: This paper introduces a framework called Pseudocell Tracer, which utilizes validated biological knowledge to guide the inference of single cell trajectories. The framework has potential applications in analyzing dynamic immune cell responses and has been validated in the process of immunoglobulin class switch recombination.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Review
Immunology
Godhev K. Manakkat Vijay, Harinder Singh
Summary: This review focuses on the cellular dynamics and genetic programming of plasma cell precursors in secondary lymphoid organs and bone marrow. Progress has been made in understanding the circulating and bone marrow precursors of plasma cells, as well as their differentiation into short-lived and long-lived counterparts. However, the nature and genomic states of these precursors at the site of generation in secondary lymphoid organs remain to be elucidated.
IMMUNOLOGICAL REVIEWS
(2021)
Article
Immunology
Dianyu Chen, Yan Wang, Godhev K. Manakkat Vijay, Shujie Fu, Colt W. Nash, Di Xu, Danyang He, Nathan Salomonis, Harinder Singh, Heping Xu
Summary: Through single-cell transcriptomic analyses, researchers found that GC B cells with higher-affinity mutations had increased expression of OXPHOS genes. Deletion of mitochondrial genes in GC B cells resulted in reduced cell division and impaired positive selection. Enhancement of OXPHOS activity promoted affinity maturation in GC B cells.
Article
Biochemistry & Molecular Biology
Xiaojun Ma, Ashwin Somasundaram, Zengbiao Qi, Douglas J. Hartman, Harinder Singh, Hatice Ulku Osmanbeyoglu
Summary: The study introduces a computational method called SPaRTAN that can link cell-surface receptors with transcription factors to predict the relationships between signaling and transcriptional regulators. Applied to immune cells and tumor infiltrating CD8(+) T cells, the method offers a new approach to developing cell-context-specific maps of the interface between signaling and transcriptional regulators.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Karsen E. Shoger, Neha Cheemalavagu, Yuqi M. Cao, Brandon A. Michalides, Virendra K. Chaudhri, Jonathan A. Cohen, Harinder Singh, Rachel A. Gottschalk
Summary: The study demonstrates that CISH is constitutively expressed in alveolar macrophages in response to GM-CSF signaling, and its deficiency leads to the generation of foamy AMs and accumulation of pulmonary surfactant. These changes are associated with enhanced activation of signaling pathways, increased expression of transcription factor GATA2, and dysregulated immune and lipid-process modules. CISH acts as part of a feedback loop to constrain homeostatic cytokine signaling and Gata2 expression to maintain AM identity and function.
Article
Medicine, Research & Experimental
Kevin Louis, Elodie Bailly, Camila Macedo, Louis Lau, Bala Ramaswami, Alexander Chang, Uma Chandran, Douglas Landsittel, Xinyan Gu, Geetha Chalasani, Adriana Zeevi, Parmjeet Randhawa, Harinder Singh, Carmen Lefaucheur, Diana Metes
Summary: Alloimmune responses driven by donor-specific antibodies can lead to antibody-mediated rejection in organ transplantation. This study identified expanded numbers of activated memory B cells expressing T-bet in patients who developed DSAs and progressed to ABMR. These AM cells were found to be poised for plasma cell differentiation and played a pivotal role in promoting humoral responses and ABMR.
Article
Computer Science, Artificial Intelligence
Xin Bing, Tyler Lovelace, Florentina Bunea, Marten Wegkamp, Sudhir Pai Kasturi, Harinder Singh, Panayiotis Benos, Jishnu Das
Summary: High-dimensional cellular and molecular profiling of biological samples highlights the need for analytical approaches that can integrate multi-omic datasets to generate prioritized causal inferences. Here, we present Essential Regression (ER), a novel interpretable machine-learning approach that addresses these problems by identifying latent factors and their likely cause-effect relationships with system-wide outcomes/properties of interest. ER outperforms other methods in terms of prediction and can be coupled with probabilistic graphical modeling to strengthen causal inferences. The utility of ER is demonstrated using multi-omic system immunology datasets to generate and validate novel cellular and molecular inferences in various contexts.