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Due to the ongoing crises of fossil fuel depletion, climate change, and environmental pollution, microbial processes are increasingly considered as a potential alternative for cleaner and more efficient production of the diverse chemicals required for modern civilization. However, many issues, including low efficiency of raw material conversion and unintended release of genetically modified microorganisms into the environment, have limited the use of bioprocesses that rely on recombinant microorganisms. Cell-free metabolic engineering is emerging as a new approach that overcomes the limitations of existing cell-based systems. Instead of relying on metabolic processes carried out by living cells, cell-free metabolic engineering harnesses the metabolic activities of cell lysates in vitro. Such approaches offer several potential benefits, including operational simplicity, high conversion yield and productivity, and prevention of environmental release of microorganisms. In this article, we review the recent progress in this field and discuss the prospects of this technique as a next-generation bioconversion platform for the chemical industry.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6632161 | PMC |
http://dx.doi.org/10.3390/mps2020033 | DOI Listing |
Nucleic Acids Res
September 2025
Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan.
Methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin, is catalyzed by Clr4/Suv39. Clr4/Suv39 contains two conserved domains-an N-terminal chromodomain and a C-terminal catalytic domain-connected by an intrinsically disordered region (IDR). Several mechanisms have been proposed to regulate Clr4/Suv39 activity, but how it is regulated under physiological conditions remains largely unknown.
View Article and Find Full Text PDFCell Rep Methods
July 2025
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China; Key Laboratory of Smart Farming for Agricultural Animals, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China; College of Informatics, Huazhong Agricult
We introduce a cell-free DNA (cfDNA) fragmentation pattern: the fragment dispersity index (FDI), which integrates information on the distribution of cfDNA fragment ends with the variation in fragment coverage, enabling precise characterization of chromatin accessibility in specific regions. The FDI shows a strong correlation with chromatin accessibility and gene expression, and regions with high FDI are enriched in active regulatory elements. Using whole-genome cfDNA data from five datasets, we developed and validated the FDI-oncology model, which demonstrates robust performance in early cancer diagnosis, subtyping, and prognosis.
View Article and Find Full Text PDFJ Vis Exp
August 2025
Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh;
Recent advances have enabled the Protein synthesis Using Recombinant Elements (PURE) cell-free system to be produced in individual laboratories economically and with reduced labor burden. However, the preparation of the 36 protein components and ribosome, which make up PURE, is still a complex undertaking, with much scope for variation and error. We present a detailed and updated procedure to manufacture PURE based on the recently published OnePot protocol, which involves regulating a number of key steps, in particular, the inoculation of cultures using optical density (OD)-normalized glycerol stocks, careful monitoring of cell growth, and controlling final glycerol concentrations.
View Article and Find Full Text PDFCell Mol Biol (Noisy-le-grand)
September 2025
Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud. Universidad de Guadalajara, Jalisco, México.
The objective of this study was to evaluate the concentration and integrity index of circulating cell-free DNA (ccf-DNA) as biomarkers for the detection and monitoring of minimal residual disease (MRD) in pediatric patients with B-cell acute lymphoblastic leukemia (B-ALL). Comparison with a validated methodology for the quantification of monoclonal rearrangements of the IGH gene was made. Peripheral blood and bone marrow samples were collected from 10 pediatric patients with B-ALL at diagnosis, remission, and maintenance phases.
View Article and Find Full Text PDFFront Immunol
September 2025
Department of Dermatology and Venereology, Medical University of Bialystok, Bialystok, Poland.
Adipose-derived mesenchymal stem cells (ADMSCs) offer a multifaceted approach to treating immune-mediated skin diseases by modulating the immune system and promoting tissue regeneration. Specifically, their ability to differentiate into multiple cell types such as keratinocytes and fibroblasts, modulate immune responses, and release growth factors and cytokines underscores their potential in treating a wide range of immune-related skin conditions. ADMSCs significantly reduced various aspects of psoriasis, including scaling, thickness, and erythema.
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