The CRISPR-Cas9 RNA-guided DNA endonuclease has contributed to an explosion of advances in the life sciences that have grown from the ability to edit genomes within living cells. In this Review, we ...summarize CRISPR-based technologies that enable mammalian genome editing and their various applications. We describe recent developments that extend the generality, DNA specificity, product selectivity, and fundamental capabilities of natural CRISPR systems, and we highlight some of the remarkable advancements in basic research, biotechnology, and therapeutics science that these developments have facilitated.
CRISPR-based genome-editing technologies provide powerful tools to study basic biology and may lead to new treatments for human disease.
Due to the rapid emergence of antibiotic-resistant bacteria, there is a growing need to discover new antibiotics. To address this challenge, we trained a deep neural network capable of predicting ...molecules with antibacterial activity. We performed predictions on multiple chemical libraries and discovered a molecule from the Drug Repurposing Hub—halicin—that is structurally divergent from conventional antibiotics and displays bactericidal activity against a wide phylogenetic spectrum of pathogens including Mycobacterium tuberculosis and carbapenem-resistant Enterobacteriaceae. Halicin also effectively treated Clostridioides difficile and pan-resistant Acinetobacter baumannii infections in murine models. Additionally, from a discrete set of 23 empirically tested predictions from >107 million molecules curated from the ZINC15 database, our model identified eight antibacterial compounds that are structurally distant from known antibiotics. This work highlights the utility of deep learning approaches to expand our antibiotic arsenal through the discovery of structurally distinct antibacterial molecules.
Display omitted
•A deep learning model is trained to predict antibiotics based on structure•Halicin is predicted as an antibacterial molecule from the Drug Repurposing Hub•Halicin shows broad-spectrum antibiotic activities in mice•More antibiotics with distinct structures are predicted from the ZINC15 database
A trained deep neural network predicts antibiotic activity in molecules that are structurally different from known antibiotics, among which Halicin exhibits efficacy against broad-spectrum bacterial infections in mice.
In the present work the effect of concrete incorporation with two types of nano-lead compounds on its γ-ray shielding characteristics is investigated. The concrete samples were prepared according to ...the local standards of building materials and doped by different percentages of PbO and PbTiO3 nano powders which were prepared using co-precipitation and oxalate precursor techniques, respectively. In addition, commercial PbO2 powder additive was used to check the effect of particle size on concrete attenuation properties. The phase composition and particle size of all the lead-oxide additives were confirmed by XRD and TEM imaging. The γ-rays attenuation coefficients were measured as a function of the additive percentage of lead compounds for γ-ray energies of 662, 1173 and 1332keV using 137Cs and 60Co sources. The microstructure changes occurred in the concrete samples doped with Pb compounds additives were probed using the positron annihilation spectroscopy (PAS) and the results were compared with that for normal concrete. The obtained data revealed that the overall defect density of the investigated samples, as seen by the positrons, decreases with increasing the nano-PbO contents which is in agreement with the determined values of the samples apparent densities. It was found that the γ-ray attenuation coefficient of concrete doped by nano-PbO is improved. The results are explained in the view of the fine structure enhanced modification and its impact on the γ-ray interaction probability at different energies.
Abstract
Antibiotic biosynthetic gene clusters (BGCs) produce bioactive metabolites that impart a fitness advantage to their producer, providing a mechanism for natural selection. This selection ...drives antibiotic evolution and adapts BGCs for expression in different organisms, potentially providing clues to improve heterologous expression of antibiotics. Here, we use phage-assisted continuous evolution (PACE) to achieve bioactivity-dependent adaptation of the BGC for the antibiotic bicyclomycin (BCM), facilitating improved production in a heterologous host. This proof-of-principle study demonstrates that features of natural bioactivity-dependent evolution can be engineered to access unforeseen routes of improving metabolic pathways and product yields.
Theoretical calculations based on the Density Functional Theory (DFT) have been performed to investigate the interaction of H2S as well SO2 gaseous molecules at the surfaces of Be12O12 and Mg12O12 ...nano-cages. The results show that a Mg12O12 nano-cage is a better sorbent than a Be12O12 nano-cage for the considered gases. Moreover, the ability of SO2 gas to be adsorbed is higher than that of H2S gas. The HOMO–LUMO gap (Eg) of Be12O12 nano-cage is more sensitive to SO2 than H2S adsorption, while the Eg value of Mg12O12 nano-cage reveals higher sensitivity to H2S than SO2 adsorption. The molecular dynamic calculations show that the H2S molecule cannot be retained at the surface of a Be12O12 nano-cage within 300–700 K and cannot be retained on a Mg12O12 nano-cage at 700 K, while the SO2 molecule can be retained at the surfaces of Be12O12 and Mg12O12 nano-cages up to 700 K. Moreover, the thermodynamic calculations indicate that the reactions between H2S as well SO2 with Be12O12 and Mg12O12 nano-cages are exothermic. Our results suggest that we can use Be12O12 and Mg12O12 nano-cages as sorbents as well as sensors for H2S and SO2 gases.
The ribosome represents a promising avenue for synthetic biology, but its complexity and essentiality have hindered significant engineering efforts. Heterologous ribosomes, comprising rRNAs and ...r-proteins derived from different microorganisms, may offer opportunities for novel translational functions. Such heterologous ribosomes have previously been evaluated in E. coli via complementation of a genomic ribosome deficiency, but this method fails to guide the engineering of refractory ribosomes. Here, we implement orthogonal ribosome binding site (RBS):antiRBS pairs, in which engineered ribosomes are directed to researcher-defined transcripts, to inform requirements for heterologous ribosome functionality. We discover that optimized rRNA processing and supplementation with cognate r-proteins enhances heterologous ribosome function for rRNAs derived from organisms with ≥76.1% 16S rRNA identity to E. coli. Additionally, some heterologous ribosomes undergo reduced subunit exchange with E. coli-derived subunits. Cumulatively, this work provides a general framework for heterologous ribosome engineering in living cells.
Genetic code expansion technologies supplement the natural codon repertoire with assignable variants in vivo, but are often limited by heterologous translational components and low suppression ...efficiencies. Here, we explore engineered Escherichia coli tRNAs supporting quadruplet codon translation by first developing a library-cross-library selection to nominate quadruplet codon-anticodon pairs. We extend our findings using a phage-assisted continuous evolution strategy for quadruplet-decoding tRNA evolution (qtRNA-PACE) that improved quadruplet codon translation efficiencies up to 80-fold. Evolved qtRNAs appear to maintain codon-anticodon base pairing, are typically aminoacylated by their cognate tRNA synthetases, and enable processive translation of adjacent quadruplet codons. Using these components, we showcase the multiplexed decoding of up to four unique quadruplet codons by their corresponding qtRNAs in a single reporter. Cumulatively, our findings highlight how E. coli tRNAs can be engineered, evolved, and combined to decode quadruplet codons, portending future developments towards an exclusively quadruplet codon translation system.
The structural, electronic and optical properties of transition metal doped porphyrin (TM@P; TM = Mn, Co, Fe, Cu, Ni, Zn) as well as the effect of CO adsorption on TM@P properties have been ...investigated using the density functional theory (DFT). The presented results include adsorption energies, bond lengths, electronic configurations, magnetic moments, density of states, frontier molecular orbitals, and UV-Vis. spectra. Our calculation results show that, the CO molecule favors to be adsorbed on TM-doped Porphyrin with its carbon head. The most energetically stable adsorption of CO is reported for Fe doped Porphyrin. The interaction between CO molecules with TM@P is attributed to donation-back donation as well as charge transfer mechanisms. Mn, Co and Fe-doped porphyrins have visible active nature which may be affected by CO adsorption, whereas, Ni, Cu and Zn-doped porphyrins have UV active nature which not affected by CO adsorption. These results may be meaningful for CO removal and detection.
PDF
