Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations.

Antibiotic-resistant pathogens are a major public health threat. A deeper understanding of how an antibiotic's mechanism of action influences the emergence of resistance would aid in the design of new drugs and help to preserve the effectiveness of existing ones. To this end, we developed a model that links bacterial population dynamics with antibiotic-target binding kinetics. Our approach allows us to derive mechanistic insights on drug activity from population-scale experimental data and to quantify the interplay between drug mechanism and resistance selection. We find that both bacteriostatic and bactericidal agents can be equally effective at suppressing the selection of resistant mutants, but that key determinants of resistance selection are the relationships between the number of drug-inactivated targets within a cell and the rates of cellular growth and death. We also show that heterogeneous drug-target binding within a population enables resistant bacteria to evolve fitness-improving secondary mutations even when drug doses remain above the resistant strain's minimum inhibitory concentration. Our work suggests that antibiotic doses beyond this "secondary mutation selection window" could safeguard against the emergence of high-fitness resistant strains during treatment.

Direct Patterning of Perovskite Nanocrystals on Nanophotonic Cavities with Electrohydrodynamic Inkjet Printing.

Overcoming the challenges of patterning luminescent materials will unlock additive and more sustainable paths for the manufacturing of next-generation on-chip photonic devices. Electrohydrodynamic (EHD) inkjet printing is a promising method for deterministically placing emitters on these photonic devices. However, the use of this technique to pattern luminescent lead halide perovskite nanocrystals (NCs), notable for their defect tolerance and impressive optical and spin coherence properties, for integration with optoelectronic devices remains unexplored. In this work, we additively deposit nanoscale CsPbBr3 NC features on photonic structures via EHD inkjet printing. We perform transmission electron microscopy of EHD inkjet printed NCs to demonstrate that the NCs' structural integrity is maintained throughout the printing process. Finally, NCs are deposited with sub-micrometer control on an array of parallel silicon nitride nanophotonic cavities and demonstrate cavity-emitter coupling via photoluminescence spectroscopy. These results demonstrate EHD inkjet printing as a scalable, precise method to pattern luminescent nanomaterials for photonic applications.

Organic building blocks at inorganic nanomaterial interfaces.

This tutorial review presents our perspective on designing organic molecules for the functionalization of inorganic nanomaterial surfaces, through the model of an "anchor-functionality" paradigm. This "anchor-functionality" paradigm is a streamlined design strategy developed from a comprehensive range of materials (e.g., lead halide perovskites, II-VI semiconductors, III-V semiconductors, metal oxides, diamonds, carbon dots, silicon, etc.) and applications (e.g., light-emitting diodes, photovoltaics, lasers, photonic cavities, photocatalysis, fluorescence imaging, photo dynamic therapy, drug delivery, etc.). The structure of this organic interface modifier comprises two key components: anchor groups binding to inorganic surfaces and functional groups that optimize their performance in specific applications. To help readers better understand and utilize this approach, the roles of different anchor groups and different functional groups are discussed and explained through their interactions with inorganic materials and external environments.

Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark.

BACKGROUND: Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS: For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS: 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION: The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.

Coherent Spin Precession and Lifetime-Limited Spin Dephasing in CsPbBr3 Perovskite Nanocrystals.

Carrier spins in semiconductor nanocrystals are promising candidates for quantum information processing. Using a combination of time-resolved Faraday rotation and photoluminescence spectroscopies, we demonstrate optical spin polarization and coherent spin precession in colloidal CsPbBr3 nanocrystals that persists up to room temperature. By suppressing the influence of inhomogeneous hyperfine fields with a small applied magnetic field, we demonstrate inhomogeneous hole transverse spin-dephasing times (T2*) that approach the nanocrystal photoluminescence lifetime, such that nearly all emitted photons derive from coherent hole spins. Thermally activated LO phonons drive additional spin dephasing at elevated temperatures, but coherent spin precession is still observed at room temperature. These data reveal several major distinctions between spins in nanocrystalline and bulk CsPbBr3 and open the door for using metal-halide perovskite nanocrystals in spin-based quantum technologies.

Multidrug-resistant tuberculosis treatment failure detection depends on monitoring interval and microbiological method.

Debate persists about monitoring method (culture or smear) and interval (monthly or less frequently) during treatment for multidrug-resistant tuberculosis (MDR-TB). We analysed existing data and estimated the effect of monitoring strategies on timing of failure detection.We identified studies reporting microbiological response to MDR-TB treatment and solicited individual patient data from authors. Frailty survival models were used to estimate pooled relative risk of failure detection in the last 12 months of treatment; hazard of failure using monthly culture was the reference.Data were obtained for 5410 patients across 12 observational studies. During the last 12 months of treatment, failure detection occurred in a median of 3 months by monthly culture; failure detection was delayed by 2, 7, and 9 months relying on bimonthly culture, monthly smear and bimonthly smear, respectively. Risk (95% CI) of failure detection delay resulting from monthly smear relative to culture is 0.38 (0.34-0.42) for all patients and 0.33 (0.25-0.42) for HIV-co-infected patients.Failure detection is delayed by reducing the sensitivity and frequency of the monitoring method. Monthly monitoring of sputum cultures from patients receiving MDR-TB treatment is recommended. Expanded laboratory capacity is needed for high-quality culture, and for smear microscopy and rapid molecular tests.

Fundamental Difference in Reductive Lithiations with Preformed Radical Anions versus Catalytic Aromatic Electron-Transfer Agents: N,N-Dimethylaniline as an Advantageous Catalyst.

The reductive lithiation of phenyl thioethers, or alkyl chlorides, by either preformed aromatic radical anions or by lithium metal and an aromatic electron-transfer catalyst, is commonly used to prepare organolithiums. Revealed herein is that these two methods are fundamentally different. Reductions with radical anions occur in solution, whereas the catalytic reaction occurs on the surface of lithium, which is constantly reactivated by the catalyst, an unconventional catalyst function. The order of relative reactivity is reversed in the two methods as the dominating factor switches from electronic to steric effects of the alkyl substituent. A catalytic amount of N,N-dimethylaniline (DMA) and Li ribbon can achieve reductive lithiation. DMA is significantly cheaper than alternative catalysts, and conveniently, the Li ribbon does not require the removal of the oxide coating when DMA is used as the catalyst.

Reductive Lithiation in the Absence of Aromatic Electron Carriers. A Steric Effect Manifested on the Surface of Lithium Metal Leads to a Difference in Relative Reactivity Depending on Whether the Aromatic Electron Carrier Is Present or Absent.

One of the most widely used methods of preparation of organolithium compounds is by the reductive lithiation of alkyl phenyl thioethers or, usually less conveniently, alkyl halides with either aromatic radical-anions of lithium or lithium metal in the presence of an aromatic electron-transfer catalyst. Here we present results showing that lithium dispersion can achieve reductive lithiation in the absence of the electron-transfer agent. This procedure is more efficient, and surprisingly, the order of reactivity of substrates is reversed depending on whether the electron-transfer agent is present or absent. For example, in the presence of a preformed radical-anion, tert-butyl phenyl sulfide cleaves significantly faster than methyl phenyl sulfide, whereas in the absence of the radical-anion, it is just the opposite. Density functional theory calculations reveal that the exothermicity of the cleavage of the C-S bond in alkyl phenyl thioethers on the lithium surface is dependent on the size of the alkyl group, the smaller the alkyl group the greater the exothermicity. The increased reactivity is attributed to the smaller steric repulsion between the alkyl group and the lithium surface. The methodology includes, but may not be limited to, the lithium dispersion reductive lithiation of phenyl thioethers, alkyl chlorides, acrolein diethyl acetal, and isochroman.

The Stereoselective Reductions of Ketones to the Most Thermodynamically Stable Alcohols Using Lithium and Hydrated Salts of Common Transition Metals.

A simple method is presented for the highly stereoselective reductions of ketones to the most thermodynamically stable alcohols. In this procedure, the ketone is treated with lithium dispersion and either FeCl2·4H2O or CuCl2·2H2O in THF at room temperature. This protocol is applied to a large number and variety of ketones and is both more convenient and efficient than those commonly reported for the diastereoselective reduction of five- and six-membered cyclic ketones.

Effect of study design and setting on tuberculosis clustering estimates using Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR): a systematic review.

OBJECTIVES: To systematically review the evidence for the impact of study design and setting on the interpretation of tuberculosis (TB) transmission using clustering derived from Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) strain typing. DATA SOURCES: MEDLINE, EMBASE, CINHAL, Web of Science and Scopus were searched for articles published before 21st October 2014. REVIEW METHODS: Studies in humans that reported the proportion of clustering of TB isolates by MIRU-VNTR were included in the analysis. Univariable meta-regression analyses were conducted to assess the influence of study design and setting on the proportion of clustering. RESULTS: The search identified 27 eligible articles reporting clustering between 0% and 63%. The number of MIRU-VNTR loci typed, requiring consent to type patient isolates (as a proxy for sampling fraction), the TB incidence and the maximum cluster size explained 14%, 14%, 27% and 48% of between-study variation, respectively, and had a significant association with the proportion of clustering. CONCLUSIONS: Although MIRU-VNTR typing is being adopted worldwide there is a paucity of data on how study design and setting may influence estimates of clustering. We have highlighted study design variables for consideration in the design and interpretation of future studies.

The impact of antiretroviral therapy on mortality in HIV positive people during tuberculosis treatment: a systematic review and meta-analysis.

OBJECTIVE: To quantify the impact of antiretroviral therapy (ART) on mortality in HIV-positive people during tuberculosis (TB) treatment. DESIGN: We conducted a systematic literature review and meta-analysis. Studies published from 1996 through February 15, 2013, were identified by searching electronic resources (Pubmed and Embase) and conference books, manual searches of references, and expert consultation. Pooled estimates for the outcome of interest were acquired using random effects meta-analysis. SUBJECTS: The study population included individuals receiving ART before or during TB treatment. MAIN OUTCOME MEASURES: Main outcome measures were: (i) TB-case fatality ratio (CFR), defined as the proportion of individuals dying during TB treatment and, if mortality in HIV-positive people not on ART was also reported, (ii) the relative risk of death during TB treatment by ART status. RESULTS: Twenty-one studies were included in the systematic review. Random effects pooled meta-analysis estimated the CFR between 8% and 14% (pooled estimate 11%). Among HIV-positive TB cases, those receiving ART had a reduction in mortality during TB treatment of between 44% and 71% (RR = 0.42, 95%CI: 0.29-0.56). CONCLUSION: Starting ART before or during TB therapy reduces the risk of death during TB treatment by around three-fifths in clinical settings. National programmes should continue to expand coverage of ART for HIV positive in order to control the dual epidemic.

Synthesis of (-)-α-kainic acid via TMSCl-promoted Pd-catalyzed zinc-ene cyclization of an allyl acetate.

A highly practical synthesis of enantiopure (-)-α-kainic acid is accomplished in 37% overall yield, using 13 linear steps and a minimum of chromatographic separations via an unprecedented TMSCl-promoted palladium-catalyzed zinc-ene cyclization of an allyl acetate.

Site-specific methylation in Bacillus subtilis chemotaxis: effect of covalent modifications to the chemotaxis receptor McpB.

The Bacillus subtilis chemotaxis pathway employs a receptor methylation system that functions differently from the one in the canonical Escherichia coli pathway. Previously, we hypothesized that B. subtilis employs a site-specific methylation system for adaptation where methyl groups are added and removed at different sites. This study investigated how covalent modifications to the adaptation region of the chemotaxis receptor McpB altered its apparent affinity for its cognate ligand, asparagine, and also its ability to activate the CheA kinase. This receptor has three closely spaced adaptation sites located at residues Gln371, Glu630 and Glu637. We found that amidation, a putative methylation mimic, of site 371 increased the receptor's apparent affinity for asparagine and its ability to activate the CheA kinase. Conversely, amidation of sites 630 and 637 reduced the receptor's ability to activate the kinase but did not affect the apparent affinity for asparagine, suggesting that activity and sensitivity are independently controlled in B. subtilis. We also examined how electrostatic interactions may underlie this behaviour, using homology models. These findings further our understanding of the site-specific methylation system in B. subtilis by demonstrating how the modification of specific sites can have varying effects on receptor function.

Regio- and enantioselective iridium-catalyzed allylation of thiophenol: synthesis of enantiopure allyl phenyl sulfides.

A highly regio- and enantioselective allylic alkylation of sodium thiophenoxide has been realized by [Ir(COD)Cl](2)/phosphoramidite along with CsF as an additive, producing highly enantioenriched allyl phenyl sulfide compounds with up to 99% ee.

Readily prepared 3-chloro-1-(phenylthio)propene, a versatile three-carbon annulating agent.

3-Chloro-1-(phenylthio)propene, simply generated by chlorination of commercial allyl phenyl sulfide, is a versatile 3-carbon annulating agent for ketones and phenols.

Enantio- and diastereoselective tandem zn-promoted brook rearrangement/ene-allene carbocyclization reaction.

The zinc-catalyzed addition of various alkynes to acylsilanes followed by a Zn-Brook rearrangement and either the Zn-ene-allene or Zn-yne-allene cyclization led to the enantio- and diastereoselective formation of carbocycles in a single-pot operation.

A laboratory demonstration illustrating bioseparations using colorful proteins.

A simple in class laboratory illustrating the principles of ion exchange chromatography as a bioseparation technique is described. A protein's isoelectric point as a driving force for ion exchange chromatography is easily demonstrated by using combinations of proteins with natural color or fluorescence, such as DsRed2, enhanced green fluorescent protein (EGFP), and flavodoxin. Simple equipment is required for this separation which can be performed on a desk top. The experiment can stimulate a range of discussion about process parameters that would create a more efficient separation of the proteins, other types of chromatography, and bioseparations in general.

Intramolecular carbozincation of unactivated alkenes occurs through a zinc radical transfer mechanism.

The cyclizations of a number of terminally unsaturated alkenyl zinc iodides to cyclopentylmethylzinc iodides, formerly believed to be nonradical in nature, have been revealed as radical chain cyclizations initiated by adventitious oxygen. Five cases are presented in which the published carbozincation cis/trans selectivities are essentially the same as those found for the cyclizations of the unsaturated alkyl iodide precursors of the alkylzinc iodides by the iodine atom transfer method at approximately the same temperatures. In addition, it has been found that one of the organozinc cyclizations does not occur in a system in which oxygen has been rigorously excluded. The combined findings strongly suggest that these organozinc cyclizations occur by a zinc radical transfer mechanism rather than by a conventional carbometallation that is thought to occur with the analogous organolithium and organomagnesium cyclizations.

Two syntheses of (-)-kainic acid via highly stereoselective zinc-ene cyclizations.

Two concise, high-yielding syntheses of enantioenriched (-)-kainic acid are presented. Both routes feature a Pd-catalyzed Zn-ene cyclization that proceeds with complete diastereoselectivity. The key step can be carried out on a multigram scale, and the overall yields are among the highest to date for this marine alkaloid.

Computational study of the stereochemistry of intramolecular carbolithiation of an alkene by a secondary alkyllithium: stereochemistry change caused by a single THF molecule of solvation.

Theoretical calculations reveal that the 40:1 ratio of trans- to cis-2-methylcyclopentylmethyllithium formed in the cyclization of 6-lithio-1-heptene by intramolecular carbolithiation is due to steric crowding in the transition state for the cis-cyclization pathway when a single THF molecule complexes the lithium cation. In the absence of this specific solvation, the cis-cyclization pathway is predicted to be slightly favored.