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At least 1,567 records · Page 87

Environmental DNA Detection in Marine Macrophyte Ecosystems as a Potential Blue Carbon Source in Sediments

“Blue carbon” refers to the carbon sequestered by the world’s oceanic and coastal ecosystems, particularly through coastal vegetation such as mangroves, salt marshes, seagrasses, and marine macroalgae. These ecosystems play a crucial role in the global carbon cycle by serving as significant carbon sinks, absorbing carbon dioxide from the atmosphere and storing it in biomass and sediments over long periods. This study explores the use of environmental DNA (eDNA) to detect marine macrophytes and microalgae assemblages contributing to blue carbon in sediments across various coastal ecosystems. The research addresses the challenges of traditional monitoring methods by utilizing high-throughput sequencing of the 18S-V9 region amplified using eDNA from sediment samples collected at eight locations in the United States and South Korea. The results reveal a diverse array of taxa, underscoring the variability in community composition across different conditions. Notably, sites with seagrass beds and Ulva blooms showed distinct patterns in microalgal community structure. This study underscores the potential of eDNA analysis in providing comprehensive insights into the biodiversity of marine macrophyte ecosystems, thus informing conservation efforts and enhancing the understanding of marine ecological dynamics.

Xing, Qikun (ORCID:0000000206179027)↗

Selection of chromosomal DNA libraries using a multiplex CRISPR system

The directed evolution of biomolecules to improve or change their activity is central to many engineering and synthetic biology efforts. However, selecting improved variants from gene libraries in living cells requires plasmid expression systems that suffer from variable copy number effects, or the use of complex marker-dependent chromosomal integration strategies. We developed quantitative gene assembly and DNA library insertion into the Saccharomyces cerevisiae genome by optimizing an efficient single-step and marker-free genome editing system using CRISPR-Cas9. With this Multiplex CRISPR (CRISPRm) system, we selected an improved cellobiose utilization pathway in diploid yeast in a single round of mutagenesis and selection, which increased cellobiose fermentation rates by over 10-fold. Mutations recovered in the best cellodextrin transporters reveal synergy between substrate binding and transporter dynamics, and demonstrate the power of CRISPRm to accelerate selection experiments and discoveries of the molecular determinants that enhance biomolecule function.

59 BASIC BIOLOGICAL SCIENCES↗

Using DNA Affinity Purification sequencing (DAP-seq) to identify in vitro binding sites of transcription factors potentially involved in aromatic degradation

The genome-wide binding sites of 44 transcription factors from the aromatic metabolizing Alphaproteobacterium Novosphingobium aromaticivorans were identified using DNA Affinity Purification sequencing (DAP-seq). We report 32 of these transcription factors have at least one area of enrichment. These data will be valuable for better understanding of aromatic metabolism.

aromatic metabolism↗

GLC analysis of base composition of RNA and DNA hydrolysates

Various methods used for the analysis of the base composition of RNA and DNA hydrolysates are presented. The methods discussed are: (1) ion-exchange chromatography, (2) paper chromatography, (3) paper electrophoresis, (4) thin layer chromatography, (5) paper chromatography and time of flight mass spectrometry, and (6) gas-liquid chromatography. The equipment required and the conditions for obtaining the best results with each method are described.

Lakings, D. B.↗

Research progress in radiation detectors, pattern recognition programs, and radiation damage determination in DNA

The radiological implications of statistical variations in energy deposition by ionizing radiation were investigated in the conduct of the following experiments: (1) study of the production of secondary particles generated by the passage of the primary radiation through bone and muscle; (2) the study of the ratio of nonreparable to reparable damage in DNA as a function of different energy deposition patterns generated by X rays versus heavy fast charged particles; (3) the use of electronic radiography systems for direct fluoroscopic tomography and for the synthesis of multiple planes and; (4) the determination of the characteristics of systems response to split fields having different contrast levels, and of minimum detectable contrast levels between the halves under realistic clinical situations.

Baily, N. A.↗

In vitro selection of optimal DNA substrates for T4 RNA ligase

We have used in vitro selection techniques to characterize DNA sequences that are ligated efficiently by T4 RNA ligase. We find that the ensemble of selected sequences ligated about 10 times as efficiently as the random mixture of sequences used as the input for selection. Surprisingly, the majority of the selected sequences approximated a well-defined consensus sequence.

Harada, Kazuo↗

Capillary electrophoresis: Biotechnology for separation of DNA and chromosomes

Electrophoresis has been used for the separation of particles, ions, and molecules for a number of years. The technology for separation and detection of the results has many applications in the life sciences. One of the major goals of the scientific community is to separate DNA molecules and intact chromosomes based upon their different lengths or number of base pairs. This may be achieved by using some of the commercially available and widely used methods, but these processes require a considerable amount of time. The challenge is to achieve separation of intact chromosomes in a short time, preferably in a matter of minutes.

Williams, George O., Jr.↗