Additional file 2 of Genome-wide mapping of GlnR-binding sites reveals the global regulatory role of GlnR in controlling the metabolism of nitrogen and carbon in Paenibacillus polymyxa WLY78

Additional file 2. The GlnR putative binding sets in Paenibacillus polymyxa WLY78 identified by the MEME-MAST tool

Additional file 3 of Genome-wide mapping of GlnR-binding sites reveals the global regulatory role of GlnR in controlling the metabolism of nitrogen and carbon in Paenibacillus polymyxa WLY78

Additional file 3. The expression of genes in Paenibacillus polymyxa WLY78 in WT and delta glnR mutant under nitrogen excess and limited conditions. Table S1. Primers used in this study. Table S2. Transcription of genes involved in nitrogen fixation and metabolism. Table S3. Transcription of genes involved in carbon metabolism. Fig. S1. The original blots of EMSA results in Fig. 1B. Each lane contained 0.3 nM labeled probe. For the 5 lanes of the EMSA of each gene promoter, lanes 1 to 5 contained 0, 0.5, 1, 1, and 1 μM His6-GlnR respectively. A 200-fold excess of unlabelled specific probe (lanes 4) or nonspecific competitor DNA (Probe 1) (lanes 5) was used in competition assays. Fig. S2. The SDS-PAGE result of the purified His6-GlnR protein. The lanes from left to right are marker, solution eluted by lysis buffer containing 20 mM imidazole, solution eluted by 1 mL lysis buffer containing 250 mM imidazole from the first to the fourth time. Fig. S3. The titer of GlnR polyclonal antibody determined by ELISA

Additional file 1 of Genome-wide mapping of GlnR-binding sites reveals the global regulatory role of GlnR in controlling the metabolism of nitrogen and carbon in Paenibacillus polymyxa WLY78

Additional file 1. The promoter sequence set of Paenibacillus polymyxa WLY78

Quantitative Validation and Application of the Photo-Cross-Linking Selection for Double-Stranded DNA-Encoded Libraries

The DNA-encoded compound library (DEL) technology has accelerated the target hits discovery in new drug development. While affinity-based DEL selection can distinguish high-affinity ligands, moderate-affinity ligands are also potential drug candidates with further modifications. Herein, we designed a photo-cross-linking selection method for DELs with double-stranded DNA (dsDELs) to screen moderate-affinity ligands. We constructed two photo-cross-linking libraries with linkers of different lengths that connect a diazirine group to the DNA encoded compound. The diazirine group can be activated by UV irradiation and thus bond with the target protein in a reachable distance. In the model selection, the feasibility of the photo-cross-linking screening system was verified by qPCR and NGS technology. Both high-affinity and moderate-affinity ligands were successfully selected from the libraries

Reaction Kinetic Model Considering the Solvation Effect Based on the FMO Theory and Deep Learning

Reaction solvents are capable of significantly enhancing the kinetic rate and selectivity of chemical reactions through the solvation effects. However, the commonly used reaction kinetic models considering the solvation effects are based on the transition state theory, which is generally limited to the demanding exploration of transition states. In this paper, a reaction solvent screen framework is established for screening potential reaction solvents, where a novel reaction kinetic model is proposed based on the frontier molecular orbital theory correlating the reaction rate constants with the numbers of hydrogen bond donors/acceptors of solvents and the solvation HOMO/LUMO energies of reactants, which quantify the solvation effects on reaction systems independent of transition states and are calculated through the implicit solvation model using the solvent dielectric constants. To facilitate high-throughput screening of reaction solvents in a wide search space, a tailor-made text-based deep learning model is then developed for fast and accurate predictions of dielectric constants. Finally, two case studies, namely, SNAr and Menschutkin reactions, are presented to demonstrate the feasibility and effectiveness of the proposed reaction solvent screen framework

Quantitative Validation and Application of the Photo-Cross-Linking Selection for Double-Stranded DNA-Encoded Libraries

The DNA-encoded compound library (DEL) technology has accelerated the target hits discovery in new drug development. While affinity-based DEL selection can distinguish high-affinity ligands, moderate-affinity ligands are also potential drug candidates with further modifications. Herein, we designed a photo-cross-linking selection method for DELs with double-stranded DNA (dsDELs) to screen moderate-affinity ligands. We constructed two photo-cross-linking libraries with linkers of different lengths that connect a diazirine group to the DNA encoded compound. The diazirine group can be activated by UV irradiation and thus bond with the target protein in a reachable distance. In the model selection, the feasibility of the photo-cross-linking screening system was verified by qPCR and NGS technology. Both high-affinity and moderate-affinity ligands were successfully selected from the libraries

Quantitative Validation and Application of the Photo-Cross-Linking Selection for Double-Stranded DNA-Encoded Libraries

The DNA-encoded compound library (DEL) technology has accelerated the target hits discovery in new drug development. While affinity-based DEL selection can distinguish high-affinity ligands, moderate-affinity ligands are also potential drug candidates with further modifications. Herein, we designed a photo-cross-linking selection method for DELs with double-stranded DNA (dsDELs) to screen moderate-affinity ligands. We constructed two photo-cross-linking libraries with linkers of different lengths that connect a diazirine group to the DNA encoded compound. The diazirine group can be activated by UV irradiation and thus bond with the target protein in a reachable distance. In the model selection, the feasibility of the photo-cross-linking screening system was verified by qPCR and NGS technology. Both high-affinity and moderate-affinity ligands were successfully selected from the libraries

Mo Doping to Modify Lattice and Morphology of the LiNi_0.9Co_0.05Mn_0.05O₂ Cathode toward High-Efficient Lithium-Ion Storage

The Ni-rich Co-poor layered cathode (LiNixCoyMn1–x–yO2, x ≥ 0.9) is a candidate for the next-generation lithium-ion batteries due to its high specific capacity and low cost. However, the inherent structural instability and slow kinetics of Li+ migration hinder their large-scale application. Mo doping is proposed to enhance the crystal structure stability of LiNi0.9Co0.05Mn0.05O2 and to ensure the preservation of the spherical secondary particles after the cycle. The characterization results indicate that Mo doping not only significantly relieves the lattice strain accompanied by H2 → H3 phase transition but also alleviates particle stress accumulation to avoid pulverization. The Mo-modification allows the generation of uniform fine primary particulates and further agglomeration into the smooth secondary particles to inhibit electrolyte penetration. Hence, the Mo-modified sample NCM90-1%Mo displays an excellent capacity retention of 85.9% after 200 cycles at 0.5 C current density, which is 23.8% higher than that of the pristine NCM90. In addition, with the expansion of the Li slab to accelerate Li+ diffusion and the fine primary particles to shorten the Li+ pathway, the NCM90-1%Mo sample exhibits a high discharge capacity of 150 mAh g–1 at 5 C current density. This work provides a new thought for the design and construction of high-capacity cathode materials for the next-generation lithium-ion batteries

Synthesis of Unsupported d¹–d^<i>x</i> Oxido-Bridged Heterobimetallic Complexes Containing V^IV: A New Direction for Metal-to-Metal Charge Transfer

Heterobimetallic complexes composed only of first-row transition metals [(TMTAA)­V^IVO→M^IIPy₅Me₂]­(OTf)₂ (TMTAA = 7,16-dihydro-6,8,15,17-tetramethyldibenzo­[<i>b</i>,<i>i</i>]­[1,4,8,11]­tetraaza­cyclotetradecine; Py₅Me₂ = 2,6-bis­(1,1-bis­(2-pyridyl)­ethyl)­pyridine; M = Mn^II, Fe^II, Co^II, Ni^II, Cu^II; OTf = trifluoromethanesulfonate) have been synthesized through a dative interaction between a terminal oxido and M^II metal centers. This is the first series of V^IVO→M^II heterobimetallic complexes containing an unsupported oxido bridge. Among these five complexes, only V^IVO→Fe^II (<b>3b</b>) has a clear new absorption band upon formation of the dinuclear species (502 nm, ε = 1700 M^–1 cm^–1). This feature is assigned to a metal-to-metal charge transfer (MMCT) transition from V^IV to Fe^II, which forms a V^VOFe^I excited state. This assignment is supported by electrochemical data, electronic absorption profiles, and resonance Raman spectroscopy and represents the first report of visible-light induced MMCT in a heterobimetallic oxido-bridged molecule where the electron originates on a d¹ metal center

Additional file 1 of Effect of perioperative acupoint electrical stimulation on macrophages in mice under operative stress

Additional file 1