Influence of sulfate and phosphate on the deposition of plasmid DNA on silica and alumina-coated surfaces

Revealing the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation

It has been recently demonstrated that free DNA tracers have the potential in tracing water flow and contaminant transport through the vadose zone. However, whether the free DNA tracer can be used in flood irrigation area to track water flow and solute/contaminant transport is still unclear. To reveal the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation, we tested the fate and transport behavior of surface applied free DNA tracers through packed saturated sandy soil columns with a 10 cm water head mimicking flood irrigation. From the experimental breakthrough curves and by fitting a two-site kinetic sorption model (R2 = 0.83-0.91 and NSE = 0.79-0.89), adsorption/desorption rates could be obtained and tracer retention profiles could be simulated. Together these results revealed that 1) the adsorption of free DNA was dominantly to clay particles in the soil, which took up 1.96 % by volume, but took up >97.5 % by surface area and densely cover the surface of sand particles; and 2) at a pore water pH of 8.0, excluding the 4.9 % passing through and 3.1 % degradation amount, the main retention mechanisms in the experimental soil were ligand exchange (42.0 %), Van der Waals interactions (mainly hydrogen bonds), electrostatic forces and straining (together 44.7 %), and cation bridge (5.3 %). To our knowledge, this study is the first to quantify the contribution of each of the main retention mechanisms of free synthetic DNA tracers passing through soil. Our findings could facilitate the application of free DNA tracer to trace vadose zone water flow and solute/contaminant transport under flood irrigation and other infiltration conditions.

Deoxyribonucleic Acid Extraction from Mars Analog Soils and Their Characterization with Solid-State Nanopores

Life detection on Mars is an important topic that includes a direct search for biomarkers. This requires instruments for in situ biomarker detection that are compact, lightweight, and able to withstand operations in space. Solid-state nanopores are excellent candidates that allow fast single-molecule detection. They can withstand high temperatures and be sterilized to minimize planetary contamination. The instruments are portable with low-power requirements. We demonstrate a few key results in advancing the use of nanopores for in-space applications. First, we developed modified deoxyribonucleic acid (DNA) extraction protocols to extract DNA from Mars analog soils. Second, we used silicon nitride nanopores to demonstrate the detection of extracted DNA and corresponding current characteristics. The yields and properties of extracted DNA (e.g., estimated diameters) varied somewhat by soil types, extraction methods, and nanopores used. The yields varied from a minimum of 0.9 ng DNA/g soil for a magnesium carbonate sample from Lake Salda to a maximum of 210 ng DNA/g soil for a calcium carbonate sample from Trona Pinnacles. For a given soil type, yields from different methods varied by a factor of up to 50. These observations motivate future studies with a broader range of Mars-like soils and improved instruments to increase signal-to-noise-ratio at higher measurement bandwidths.

Effects of myo-inositol hexakisphosphate, ferrihydrite coating, ionic strength and pH on the transport of TiO2 nanoparticles in quartz sand

Evaluating the fate and transport of nanoparticles (NPs) in the subsurface environment is critical for predicting the potential risks to both of the human health and environmental safety. It is believed that numerous environmental factors conspire to control the transport dynamics of nanoparticles, yet the effects of organic phosphates on nanoparticles transport remain largely unknown. In this work, we quantified the transport process of TiO₂ nanoparticle (nTiO₂) and their retention patterns in water-saturated sand columns under various myo-inositol hexakisphosphate (IHP) or phosphate (Pi) concentrations (0-180 μM P), ferrihydrite coating fractions (λ, 0-30%), ionic strengths (1-50 mM KCl), and pH values (4-8). The transport of nTiO₂ was enhanced at increased P concentration due to the enhanced colloidal stability. As compared with Pi at the equivalent P level, IHP showed stronger effect on the electrokinetic properties of nTiO₂ particles due to its relatively more negative charge and higher adsorption affinity, thereby facilitating the nTiO₂ transport (and thus reduced retention) in porous media. At the IHP concentration of 5 μM, the retention of nTiO₂ increased with increasing λ and ionic strength, while decreased with pH. In addition, the retention profiles of nTiO₂ showed a typical hyperexponential pattern for most scenarios mainly due to the unfavorable attachment, and can be well described by a hybrid mathematical model that coupled convection dispersion equations with a two-site kinetic model and DLVO theory. These quantitative estimations revealed the importance of IHP on affecting the transport of nTiO₂ typically in phosphorus-enriched environments. It provides new insights into advanced understanding of the co-transport of nanoparticles and phosphorus in natural systems, essential for both nanoparticle exposure and water eutrophication.

Peptide Sequence-Dependent Gene Expression of PEGylated Peptide/DNA Complexes

Oligolysine-based PEG-peptides with 15 or 20 amino acid residues including two cysteines were synthesized to formulate cross-linked polyplex micelles (PMs) incorporating luciferase-coding plasmid DNA (pDNA). Two cysteine residues were separately allocated at the C-terminal, center, or N-terminal of peptide moieties. Although TEM observation showed that all PEG-peptides condensed pDNA into rod-like or toroidal morphologies, the rod length distribution of PMs was affected by both the amino acid sequence and the peptide length of PEG-peptides. In comparison to the cysteine-uninstalled PEG-peptides, the cysteine-installed PEG-peptides exhibited a reductive environment-responsive pDNA release, which was observed in a gel retardation assay. From physicochemical characterizations, a relationship between the amino acid sequence and the in vitro gene expression efficacy of PMs in a cell-free protein synthesis system has been clearly demonstrated. Finally, the cell-based assay using HeLa cells has been tested, and the differences between both results of cell-free and cell-based systems are discussed.