To elucidate the mechanism of transcription by cellular RNA polymerases (RNAPs), high resolution X-ray crystal structures together with structure-guided biochemical, biophysical and genetics studies are essential. The recently-solved X-ray crystal structures of archaeal RNA polymerase (RNAP) allow a structural comparison of the transcription machinery among all three domains of life. The archaea were once thought of closely related to bacteria, but they are now considered to be more closely related to the eukaryote at the molecular level than bacteria. According to these structures, the archaeal transcription apparatus, which includes RNAP and general transcription factors, is similar to the eukaryotic transcription machinery. Yet, the transcription regulators, activators and repressors, encoded by archaeal genomes are closely related to bacterial factors. Therefore, archaeal transcription appears to possess an intriguing hybrid of eukaryotic-type transcription apparatus and bacterial-like regulatory mechanisms. Elucidating the transcription mechanism in archaea, which possesses a combination of bacterial and eukaryotic transcription mechanisms that are commonly regarded as separate and mutually exclusive, can provide data that will bring basic transcription mechanisms across all three domains of life.

Summary All archaeal genomes encode RNA polymerase (RNAP) subunits E and F that share a common ancestry with the eukaryotic RNAP subunits A43 and A14 (Pol I), Rpb7 and Rpb4 (Pol II), and C25 and C17 (Pol III). By gene replacement, we have isolated archaeal mutants of Thermococcus kodakarensis with the subunit F-encoding gene (rpoF) deleted, but we were unable to isolate mutants lacking the subunit E-encoding gene (rpoE). Wild-type T. kodakarensis grows at temperatures ranging from 60 to 100 °C, optimally at 85°C, and the ΔrpoF cells grew at the same rate as wild-type at 70 °C, but much slower and to lower cell densities at 85 °C. The abundance of a chaperonin subunit, CpkB, was much reduced in the ΔrpoF strain growing at 85 °C and increased expression of cpkB, rpoF or rpoE integrated at a remote site in the genome, using a nutritionally-regulated promoter, improved the growth of ΔrpoF cells. RNAP preparations purified from ΔrpoF cells lacked subunit F and also subunit E and a transcription factor TFE that co-purifies with RNAP from wild-type cells, but in vitro, this mutant RNAP exhibited no discernible differences from wild-type RNAP in promoter-dependent transcription, abortive transcript synthesis, transcript elongation or termination.

Two ratiometric near-infrared fluorescent probes (A and B) have been developed to selectively and accurately detect mitochondrial pH changes based on highly efficient through-bond energy transfer (TBET) from cyanine donors to near-infrared-emissive hemicyanine acceptors.

Industry is increasingly turning to biobased and environmentally benign materials for use in high-value applications. Kraft lignin's low cost and inherent properties, such as its easily tunable amphiphilic nature, adsorption capacity, and natural cross-linking tendency, make it suitable for use as a raw material for high-value nanomaterials. To support that need, this paper describes the synthesis of innovative, double-shelled lignin nanocapsules from hardwood kraft lignin, their performance towards encapsulating a fungicide, and effectiveness at controlling its release. The recovered lignin was dissolved without further modification in tetrahydrofuran and inserted dropwise into a water/ethanol solution containing sacrificial surfactant templates. Monodispersed, hollow, double-shell nanocapsules were produced via a two-step self-assembly. The water/ethanol solution acted as a nonsolvent while simultaneously providing strategic sites for controlled-size production. The shells of the nanocapsules were cross-linked with biodegradable maleic anhydride to bolster the structural stability. The average hydrodynamic diameter of the particles was 241.8 ± 33.3 nm, and these structures were stable in water for a period of eight months. The specific surface area of kraft lignin increased by 4-fold in the double-shell nanocapsule form. The nanocapsules were loaded with propiconazole at an entrapment efficiency of 56.1%. This system could represent an effective method to enable biologically activated, controlled release of fungicides.

A near-infrared fluorescent probe (AH+) has been prepared by incorporating an oxazolidine switch into a near-infrared hemicyanine dye for pH detection in the mitochondria of HeLa cells.