Article
Biochemical Research Methods
Valeria Garcia-Flores, Yi Xu, Errile Pusod, Roberto Romero, Roger Pique-Regi, Nardhy Gomez-Lopez
Summary: Single-cell RNA-sequencing (scRNA-seq) is a powerful tool to study cellular composition and interactions in complex tissues. This study presents a protocol for preparing high-quality single-cell suspensions from human placental tissues, including the basal plate, placental villi, and chorioamniotic membranes. The protocol includes tissue collection, tailored dissociation procedures, and cryopreservation of single-cell suspensions. The resulting suspensions are compatible with droplet-based scRNA-seq technology and exhibit high yield and viability. The entire process takes approximately 6 hours, with an additional 2 hours for thawing of cryopreserved single cells.
Review
Plant Sciences
Regina Geris, Matheus A. Pinho, Elisangela F. Boffo, Thomas J. Simpson
Summary: This review provides a critical analysis of the naturally occurring partially reduced perylenequinones from fungi. It covers their structures, biosynthesis, and biological activities. These perylenequinones are natural pigments with various biological activities, such as antimicrobial and anti-HIV effects.
JOURNAL OF NATURAL PRODUCTS
(2022)
Review
Biochemistry & Molecular Biology
Mai Nguyen, Clodia Osipo
Summary: Breast cancer therapies have improved survival rates, but recurrence and drug resistance remain challenging. Phytoestrogens have been found to target breast cancer stem cells and may complement conventional therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Yanna Shi, Bai-Jun Li, Donald Grierson, Kun-Song Chen
Summary: Insights into cell wall changes during fruit softening are gained from studies on transgenic and naturally occurring mutants. Excessive softening during fruit ripening can cause physical damage and infection, leading to quality reduction and supply chain losses. Changes in cell wall metabolism, including loosening and disassembly of macromolecules, are the main cause of softening.
Review
Environmental Sciences
Sara Shahba, Jalil Mehrzad, Amir Mohammad Malvandi
Summary: Exogenous toxins have the potential to disrupt neuroimmune homeostasis, with mycotoxins being a noticeable source leading to immune dysregulation, particularly affecting the central nervous system. Even low-level exposure to mycotoxins can induce inflammatory responses, disrupting homeostasis in the CNS.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Computer Science, Artificial Intelligence
Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie
Summary: TIGON is a dynamic and unbalanced optimal transport algorithm that can reconstruct dynamic trajectories, population growth, and gene regulatory networks. It uses a deep learning method to tackle the high-dimensional optimal transport problem and has demonstrated robustness and accuracy in predicting cell state transition and population growth.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Biochemical Research Methods
Micha Sam Brickman Raredon, Junchen Yang, Neeharika Kothapalli, Wesley Lewis, Naftali Kaminski, Laura E. Niklason, Yuval Kluger
Summary: NICHES is a tool that explores extracellular signaling at the truly single-cell level by embedding ligand-receptor signal proxies to visualize heterogeneous signaling archetypes within and between cell clusters as well as across experimental conditions. It can be applied to spatial transcriptomic data to reflect local cellular microenvironment, is compatible with existing single-cell packages, and allows rapid, flexible analysis of cell-cell signaling at single-cell resolution.
Review
Cell Biology
Maria A. Dimitriu, Irina Lazar-Contes, Martin Roszkowski, Isabelle M. Mansuy
Summary: Recent advances in single-cell analyses have led to comprehensive characterization of cellular and molecular states, with the development of multiplexed assays offering simultaneous analysis of multiple factors and processes. These technologies have rapidly evolved, providing better specificity, precision, and resolution. This review summarizes recent progress in single-cell multiomics approaches, focusing on innovative techniques that integrate genome, epigenome, and transcriptome profiling.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Genetics & Heredity
Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma
Summary: Spatial transcriptomics is a method to reveal spatially resolved gene expression of diverse cells in complex tissues. SpiceMix, an interpretable method based on probabilistic, latent variable modeling, improves on the inference of cell types and their spatial patterns. By analyzing spatial transcriptome data of brain regions in human and mouse, SpiceMix enhances the inference of complex cell identities, reveals interpretable spatial metagenes, and uncovers differentiation trajectories. SpiceMix is a generalizable analysis framework for spatial transcriptome data to investigate cell-type composition and spatial organization of cells in complex tissues.
Review
Cell Biology
Elizabeth J. Apsley, Esther B. E. Becker
Summary: Despite their similar appearance, Purkinje cells exhibit remarkable diversity in terms of their molecular phenotypes, physiological properties, connectivity, and vulnerability. This diversity arises early in development with distinct embryonic cell clusters identified soon after Purkinje cell specification. Traditional methods of characterizing cerebellar development and cell types have been based on selected markers, but recent single-cell RNA sequencing studies have provided greater resolution and understanding of Purkinje cell development and function.
Article
Multidisciplinary Sciences
Xiao Liu, Ivy Aneas, Noboru Sakabe, Rebecca L. Anderson, Christine Billstrand, Cristina Paz, Harjot Kaur, Brian Furner, Seong Choi, Adriana Y. Prichina, Elizabeth Ann L. Enninga, Haidong Dong, Amy Murtha, Gregory E. Crawford, John A. Kessler, William Grobman, Marcelo A. Nobrega, Sarosh Rana, Carole Ober
Summary: The mechanisms underlying the timing of labor in humans are largely unknown. This study aimed to characterize the cells at the maternal-fetal interface (MFI) in term and preterm pregnancies in Black women. High-dimensional single-cell resolution analysis revealed distinct cell populations at the MFI, including immune and non-immune cells. Perturbations in the PD1/PD-L1 pathway at the MFI may play a role in the onset of spontaneous preterm labor.
SCIENTIFIC REPORTS
(2023)
Article
Pharmacology & Pharmacy
Jianlin Du, Xin Yuan, Haijun Deng, Rongzhong Huang, Bin Liu, Tianhua Xiong, Xianglin Long, Ling Zhang, Yingrui Li, Qiang She
Summary: This study identified gene markers and functions of mature epicardial cells using single-cell transcriptomic and spatial transcriptomic analyses, and found that extracellular matrix signaling plays a critical role in the mature epicardium.
JOURNAL OF PHARMACEUTICAL ANALYSIS
(2023)
Article
Biotechnology & Applied Microbiology
Thomas Walle, Dana Peer
Summary: Most cell features are determined by gene programs, and the Spectra factor analysis method enhances our ability to decode single-cell transcriptomic data by incorporating knowledge about gene programs and cell types, offering insights into challenging tumor immune contexts.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Yan Yan, Bridget Truitt, Junyi Tao, Sean Michael Boyles, Danielle Antoine, William Hulme, Sabita Roy
Summary: The cycle of substance use disorder leading to dependence is a complex process involving multiple neurocircuitries and brain regions. This study focused on the amygdala, a core brain region involved in withdrawal, anxiety, and depressive-like behaviors, to examine the transcriptional changes in different cell types during substance use disorder. Using single-cell RNA sequencing, the researchers classified all cell types in the mouse amygdala and identified distinct gene expression changes in glial cells during dependence compared to naive or withdrawal state. The findings provide unique insights into the biological processes involved in substance use disorder and the alterations in the brain.
Article
Veterinary Sciences
J. Blake Everett, Bruno C. Menarim, Sarah H. Barrett, Sophie H. Bogers, Christopher R. Byron, R. Scott Pleasant, Stephen R. Werre, Linda A. Dahlgren
Summary: This study evaluated the ability of intra-articular bone marrow mononuclear cell (BMNC) therapy to improve clinical signs of naturally occurring equine osteoarthritis (OA). The results showed significant improvements in joint circumference and objective lameness in the BMNC-treated group, with no adverse effects observed.
FRONTIERS IN VETERINARY SCIENCE
(2023)