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Comparison of Illumina and Oxford Nanopore sequencing data quality for Clostridioides difficile genome analysis and their application for epidemiological surveillance.
BMC Genomics
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Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
Background: The burden of Clostridioides difficile as a nosocomial- and community-acquired pathogen has been increasing over the recent decades, including reports of severe outbreaks. Molecular and virulence genotyping are central for the epidemiological surveillance of this pathogen, but need to balance accuracy and rapid turnaround time of the results. While Illumina short-read sequencing has been adopted as the gold standard to investigate C.
View Article and Find Full Text PDFOptimized convolutional neural network using African vulture optimization algorithm for the detection of exons.
Sci Rep
January 2025
Department of Communication Engineering, School of Electronics Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
The detection of exons is an important area of research in genomic sequence analysis. Many signal-processing methods have been established successfully for detecting the exons based on their periodicity property. However, some improvement is still required to increase the identification accuracy of exons.
View Article and Find Full Text PDFThe TCP transcription factor TAC8 positively regulates the tiller angle in rice (Oryza sativa L.).
Theor Appl Genet
January 2025
College of Agronomy, Hunan Agricultural University, Changsha, 420128, China.
The tiller angle, one of the critical factors that determine the rice plant type, is closely related to rice yield. An appropriate rice tiller angle can improve rice photosynthetic efficiency and increase yields. In this study, we identified a transcription factor, TILLRE ANGLE CONTROL 8 (TAC8), that is highly expressed in the rice tiller base and positively regulates the tiller angle by regulating cell length and endogenous auxin content; TAC8 encodes a TEOSINTE BRANCHED1/CYCLOIDEA/PCF transcriptional activator that is highly expressed in the nucleus.
View Article and Find Full Text PDFEfficient secretory expression, purification, and characterization of lipase in Pseudomonas aeruginosa M18, with multifunctional applications in diagnostics.
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Zybio Inc, Chongqing, 400082, China.
Lipase (EC 3.1.1.
View Article and Find Full Text PDFRapid and Non-Targeted Qualitative and Quantitative Detection of miRNA in Complex Biological Samples Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry with a 3-Aminoquinoline and 2',4',6'-Trihydroxyacetophenone Ionic Liquid Matrix.
J Am Soc Mass Spectrom
January 2025
Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China.
A novel ionic liquid MALDI matrix, 3-aminoquinoline/2',4',6'-trihydroxyacetophenone monohydrate (3-AQ/THAP), was developed for the rapid qualitative and quantitative detection of miRNA from biological samples. Compared to the traditional matrix 2,5-dihydroxybenzoic acid (DHB) and previously reported oligonucleotide-specific matrices, such as 3-aminopicolinic acid (3-APA), 3-hydroxypicolinic acid (3-HPA), and 6-aza-2-thiothymine (ATT), the 3-AQ/THAP matrix offers several advantages. It produces fewer alkali metal adduct peaks, exhibits higher sensitivity, and ensures better spot-to-spot repeatability.
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