Transport and transformations of cadmium in water-biofilm-sediment phases as affected by hydrodynamic conditions.

Hydrodynamic conditions play a crucial role in governing the fate, transport, and risks of metal elements. However, the contribution of hydrodynamic conditions to the fate and transport of heavy metals among water, sediment, and biofilm phases is poorly understood. In our study, we conducted experiments in controlled hydrodynamic conditions using a total of 6 two-phase and 9 three-phase mesocosms consisting of water, biofilm, and sediment. We also measured Cd (cadmium) specification in different phases to assess how hydrodynamic forces control Cd bioavailability. We found that turbulent flow destroyed the surface morphology of the biofilm and significantly decreased the content of extracellular polymeric substances (p < 0.05). This led to a decrease in the biofilm's adsorption capacity for Cd, with the maximum adsorption capacity (0.124 mg/g) being one-tenth of that under static conditions (1.256 mg/g). The Cd chemical forms in the biofilm and sediment were significantly different, with the highest amount of Cd in the biofilm being acid-exchangeable, accounting for up to 95.1% of the total Cd content. Cd was more easily released in the biofilm due to its weak binding state, while Cd in the sediment existed in more stable chemical forms. Hydrodynamic conditions altered the migration behavior and distribution characteristics of Cd in the system by changing the adsorption capacity of the biofilm and sediment for Cd. Cd mobility increased in laminar flow but decreased in turbulent flow. These results enhance our understanding of the underlying mechanisms that control the mobility and bioavailability of metals in aquatic environments with varying hydrodynamic conditions.

Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing.

Targeted RNA sequencing (RNA-seq) aims to focus coverage on areas of interest that are inadequately sampled in standard RNA-seq experiments. Here we present multiplexed primer extension sequencing (MPE-seq), an approach for targeted RNA-seq that uses complex pools of reverse-transcription primers to enable sequencing enrichment at user-selected locations across the genome. We targeted hundreds to thousands of pre-mRNA splice junctions and obtained high-precision detection of splice isoforms, including rare pre-mRNA splicing intermediates.

DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency.

Synthetic scaffolds that permit spatial and temporal organization of enzymes in living cells are a promising post-translational strategy for controlling the flow of information in both metabolic and signaling pathways. Here, we describe the use of plasmid DNA as a stable, robust and configurable scaffold for arranging biosynthetic enzymes in the cytoplasm of Escherichia coli. This involved conversion of individual enzymes into custom DNA-binding proteins by genetic fusion to zinc-finger domains that specifically bind unique DNA sequences. When expressed in cells that carried a rationally designed DNA scaffold comprising corresponding zinc finger binding sites, the titers of diverse metabolic products, including resveratrol, 1,2-propanediol and mevalonate were increased as a function of the scaffold architecture. These results highlight the utility of DNA scaffolds for assembling biosynthetic enzymes into functional metabolic structures. Beyond metabolism, we anticipate that DNA scaffolds may be useful in sequestering different types of enzymes for specifying the output of biological signaling pathways or for coordinating other assembly-line processes such as protein folding, degradation and post-translational modifications.

Heavy metal fraction, pollution, and source-oriented risk assessment in biofilms on a river system polluted by mining activities.

The Lanping Pb-Zn mine is the largest source of Pb and Zn ores in China, thus posing a great threat to local ecosystems and human health. A total of seven heavy metals (Zn, Pb, Ni, Cu, Cr, Cd, and As) in the Bijiang River near the Pb-Zn mine were measured in winter and summer to assess their spatial-temporal enrichment, ecological risk, and source-oriented health risk in periphytic biofilms. Positive matrix factorization (PMF) receptor model and clustering analysis were used to quantitatively identify pollution sources. The results of PMF were then imported into the health risk assessment to further determine the carcinogenic and noncarcinogenic risks of various pollution sources. The results indicated distinct seasonal patterns in metal concentrations, with much higher concentrations in winter. Sites near the Pb-Zn mine tailing reservoir exhibited higher metal contamination levels than other sites. A strong correlation between the enrichment factor and the levels of nonresidual fraction suggested that anthropogenic inputs were the main source of these metals. Mining industries (Cd, Zn, and Pb), natural sources (As, Ni, and Cu), and agricultural activities (Cr) were the primary sources of heavy metal pollution in biofilms, accounting for 44.43%, 33.32%, and 22.26% of the total metal accumulation, respectively. Moreover, the carcinogenic and noncarcinogenic risks via dermal contact of the studied elements in biofilms were typically acceptable. Notably, as concentration was the main factor influencing these risks in children and adults. This study provides evidence that natural epilithic periphyton may be a potential metal biomonitor in aquatic systems and provide supporting information for effective source regulation.

Engineering antibody fitness and function using membrane-anchored display of correctly folded proteins.

A hallmark of the bacterial twin-arginine translocation (Tat) pathway is its ability to export folded proteins. Here, we discovered that overexpressed Tat substrate proteins form two distinct, long-lived translocation intermediates that are readily detected by immunolabeling methods. Formation of the early translocation intermediate Ti-1, which exposes the N- and C-termini to the cytoplasm, did not require an intact Tat translocase, a functional Tat signal peptide, or a correctly folded substrate. In contrast, formation of the later translocation intermediate, Ti-2, which exhibits a bitopic topology with the N-terminus in the cytoplasm and C-terminus in the periplasm, was much more particular, requiring an intact translocase, a functional signal peptide, and a correctly folded substrate protein. The ability to directly detect Ti-2 intermediates was subsequently exploited for a new protein engineering technology called MAD-TRAP (membrane-anchored display for Tat-based recognition of associating proteins). Through the use of just two rounds of mutagenesis and screening with MAD-TRAP, the intracellular folding and antigen-binding activity of a human single-chain antibody fragment were simultaneously improved. This approach has several advantages for library screening, including the unique involvement of the Tat folding quality control mechanism that ensures only native-like proteins are displayed, thus eliminating poorly folded sequences from the screening process.