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Integrating representation learning, permutation, and optimization to detect lineage-related gene expression patterns.
Nat Commun
January 2025
Laboratory for Information and Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA.
Recent barcoding technologies allow reconstructing lineage trees while capturing paired single-cell RNA-sequencing (scRNA-seq) data. Such datasets provide opportunities to compare gene expression memory maintenance through lineage branching and pinpoint critical genes in these processes. Here we develop Permutation, Optimization, and Representation learning based single Cell gene Expression and Lineage ANalysis (PORCELAN) to identify lineage-informative genes or subtrees where lineage and expression are tightly coupled.
View Article and Find Full Text PDFEarly retinoic acid signaling organizes the body axis and defines domains for the forelimb and eye.
Curr Top Dev Biol
January 2025
Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States. Electronic address:
All-trans RA (ATRA) is a small molecule derived from retinol (vitamin A) that directly controls gene expression at the transcriptional level by serving as a ligand for nuclear ATRA receptors. ATRA is produced by ATRA-generating enzymes that convert retinol to retinaldehyde (retinol dehydrogenase; RDH10) followed by conversion of retinaldehyde to ATRA (retinaldehyde dehydrogenase; ALDH1A1, ALDH1A2, or ALDH1A3). Determining what ATRA normally does during vertebrate development has been challenging as studies employing ATRA gain-of-function (RA treatment) often do not agree with genetic loss-of-function studies that remove ATRA via knockouts of ATRA-generating enzymes.
View Article and Find Full Text PDFNano-biopesticide formulation comprising of silver nanoparticles anchored to Ocimum sanctum: a sustainable approach to pest control in jute farming.
Sci Rep
January 2025
Ecology and Allergology Lab, Department of Zoology, Golapbag Campus, The University of Burdwan, Burdwan, 713104, West Bengal, India.
The jute hairy caterpillar, Spilosoma obliqua (Lepidoptera: Erebidae) is considered as one of the major threats to jute cultivation. The best eco-friendly methods to combat these jute pests involve administration of nano-biopesticides, as a successful alternative to the toxic chemicals. In this study, a nano-biopesticide formulation containing green synthesized silver nanoparticles (Ag NPs) using Ocimum sanctum leaf extract has been proposed.
View Article and Find Full Text PDFStrengthening biopolymer adhesives through ureolysis-induced calcium carbonate precipitation.
Sci Rep
January 2025
Department of Chemical & Biological Engineering, Montana State University, Bozeman, USA.
Common adhesives for nonstructural applications are manufactured using petrochemicals and synthetic solvents. These adhesives are associated with environmental and health concerns because of their release of volatile organic compounds (VOCs). Biopolymer adhesives are an attractive alternative because of lower VOC emissions, but their strength is often insufficient.
View Article and Find Full Text PDFMultiple roles for retinoid signaling in craniofacial development.
Curr Top Dev Biol
January 2025
Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States. Electronic address:
Retinoic acid (RA) signaling plays multiple essential roles in development of the head and face. Animal models with mutations in genes involved in RA signaling have enabled understanding of craniofacial morphogenic processes that are regulated by the retinoid pathway. During craniofacial morphogenesis RA signaling is active in spatially restricted domains defined by the expression of genes involved in RA production and RA breakdown.
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