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DNA barcoding employs standard molecular techniques (e.g., DNA extraction, PCR, and Sanger sequencing) to taxonomically identify biological samples. While DNA barcoding is a useful experimental workflow for in-class active learning exercises, extracting DNA from diverse sample types in a time and cost-effective manner can be challenging in a classroom setting. Here, we provide two time and cost-effective methods that have been used by novice students to successfully extract DNA from a variety of animal, fungal, algal, and plant tissues for DNA barcoding.
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http://dx.doi.org/10.1007/978-1-0716-3581-0_7 | DOI Listing |
Ecol Evol
September 2025
MPG Ranch Florence Montana USA.
DNA fecal metabarcoding has revolutionized the field of herbivore diet analyses, offering deeper insight into plant-herbivore interactions and more reliable ecological inferences. However, due to PCR amplification bias, primer selection has a major impact on the validity of these inferences and insights. Using two pooling approaches on four mock communities and a case study examining diets of four large mammalian herbivores (LMH), we evaluated the efficacy of two primer pairs targeting the internal transcribed spacer 2 (ITS2) region: the widely used ITS-S2F/ITS4 pair and the UniPlant F/R pair, designed specifically for DNA metabarcoding.
View Article and Find Full Text PDFAnalyst
September 2025
School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
Microfluidics-assisted spatially barcoded microarray technology offers a high-throughput, low-cost approach towards spatial transcriptomic profiling. A uniform barcoded microarray is crucial for spatially unbiased mRNA analysis. However, non-specific adsorption of barcoding reagents in microchannels occurs during liquid transport, causing non-uniform barcoding in the chip's functional regions.
View Article and Find Full Text PDFBull Entomol Res
September 2025
Insect Biosystematics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
This study presents the first record of Kanturski & Lee, 2024 (Aphididae: Lachninae) in South Korea, thereby extending its known distribution beyond Japan and identifying a new host plant, (Rosaceae). We describe diagnostic morphological traits across multiple life stages and compare them with those of Japanese populations. Comparative analyses with Japanese populations demonstrated consistent morphological differentiation, notably elevated ratios of the ultimate rostral segment to antennal segments across multiple morphs in the Korean population, indicating potential ecological adaptation.
View Article and Find Full Text PDFNat Biotechnol
September 2025
Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA.
RNA-protein interactions critically regulate gene expression and cellular processes, yet their comprehensive mapping remains challenging due to their structural diversity. We introduce PRIM-seq (protein-RNA interaction mapping by sequencing), a method for concurrent de novo identification of RNA-binding proteins and their associated RNAs. PRIM-seq generates unique chimeric DNA sequences by proximity ligation of RNAs with protein-linked DNA barcodes, which are subsequently decoded through sequencing.
View Article and Find Full Text PDFACS Synth Biol
September 2025
Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States.
Microbes can be programmed to record participation in gene transfer by coding biological-recording devices into mobile DNA. Upon DNA uptake, these devices transcribe a catalytic RNA (cat-RNA) that binds to conserved sequences within ribosomal RNAs (rRNAs) and perform a trans-splicing reaction that adds a barcode to the rRNAs. Existing cat-RNA designs were generated to be broad-host range, providing no control over the organisms that were barcoded.
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