Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
The copy number of a plasmid is linked to its functionality, yet there have been few attempts to optimize higher-copy-number mutants for use across diverse origins of replication in different hosts. We use a high-throughput growth-coupled selection assay and a directed evolution approach to rapidly identify origin of replication mutations that influence copy number and screen for mutants that improve Agrobacterium-mediated transformation (AMT) efficiency. By introducing these mutations into binary vectors within the plasmid backbone used for AMT, we observe improved transient transformation of Nicotiana benthamiana in four diverse tested origins (pVS1, RK2, pSa and BBR1). For the best-performing origin, pVS1, we isolate higher-copy-number variants that increase stable transformation efficiencies by 60-100% in Arabidopsis thaliana and 390% in the oleaginous yeast Rhodosporidium toruloides. Our work provides an easily deployable framework to generate plasmid copy number variants that will enable greater precision in prokaryotic genetic engineering, in addition to improving AMT efficiency.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC12147919 | PMC |
| http://dx.doi.org/10.1038/s41587-024-02462-2 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Recursive splice sites are rare motifs postulated to facilitate splicing across massive introns and shape isoform diversity, especially for long, brain-expressed genes. The necessity of this unique mechanism remains unsubstantiated, as does the role of recursive splicing (RS) in human disease. From analyses of rare copy number variants (CNVs) from almost one million individuals, we previously identified large, heterozygous deletions eliminating an RS site (RS1) in the first intron of that conferred substantial risk for attention deficit hyperactivity disorder (ADHD) and other neurobehavioral traits.
View Article and Find Full Text PDFApplication of low-coverage whole-genome sequencing technology in risk stratification of colorectal adenomas.
Front Oncol
August 2025
Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing University, Jiaxing, Zhejiang, China.
Objective: The diagnosis of precancerous lesions of colorectal cancer (CRC) presents significant challenges in clinical practice. In this study, we conducted a clinical investigation using the UCAD technique after analyzing chromosomal copy number variations (CNVs) in formalin-fixed, paraffin-embedded (FFPE) samples from various pathological stages, aiming to evaluate the value of detecting chromosomal instability (CIN) in CRC diagnosis.
Methods: Based on colonoscopic pathological findings, we selected 39 FFPE specimens of tubular adenomas, 8 FFPE specimens of villous adenomas, 16 cases diagnosed as tubular-villous adenomas, and 14 cases without defined pathological subtype classification.
Assembly theory and its relationship with computational complexity.
Npj Complex
September 2025
The Santa Fe Institute, Santa Fe, NM USA.
Assembly theory (AT) quantifies selection using the assembly equation, identifying complex objects through the assembly index, the minimal steps required to build an object from basic parts, and copy number, the observed instances of the object. These measure a quantity called Assembly, capturing causation necessary to produce abundant objects, distinguishing selection-driven complexity from random generation. Unlike computational complexity theory, which often emphasizes minimal description length via compressibility, AT explicitly focuses on the causation captured by selection as the mechanism behind complexity.
View Article and Find Full Text PDFIncreased Ribosome Biogenesis and Increased Oxidative Stress in Blood Leukocytes of Patients With Catatonic Schizophrenia Compared With Paranoid Schizophrenia.
Front Biosci (Landmark Ed)
August 2025
Laboratory of Molecular Biology, Research Centre for Medical Genetics (RCMG), 115522 Moscow, Russia.
Background: Schizophrenia (SZ) is associated with chronic oxidative stress in the patient's body. Previous studies revealed an increased copy number of genes for 47S pre-ribosomal RNA (pre-rRNA) in SZ patients. In this study, levels of oxidative stress and factors involved in the adaptive response to chronic stress (rDNA transcription) were, for the first time, compared in blood cells of patients with catatonic SZ(C) and paranoid SZ(P), chronic forms of schizophrenia, as well as healthy controls (HC).
View Article and Find Full Text PDFDriver Genes and Genomic Instability Predict the Incidence and Outcome of Brain Metastases.
Curr Cancer Drug Targets
September 2025
Department of Critical Care Medicine, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, 358 Datong Road, Pudong New District, Shanghai 200137, China.
Introduction: The incidence of brain metastases in patients diagnosed with ad-vanced lung cancer is high, drawing significant attention to the risk factors associated with this progression.
Methods: A total of 252 advanced non-small cell lung cancer (NSCLC) patients with brain metastases were enrolled in this study between July 2018 and December 2023 from our hos-pital. Additionally, driver genes, including EGFR, ALK, ROS1, KRAS, and RET, were doc-umented.