Perturbing Pentalene: Aromaticity and Antiaromaticity in a Non-alternant Polycyclic Aromatic Hydrocarbon and BN-heteroanalogues.

Pentalene (C8H6) and NN- and BB-bridged heterocyclic analogues (BN)4H6, derived by replacement of CC pairs with BN, are taken as  paradigms for tuning of ring-current (anti)aromaticity by variation of π charge, electronegativity and substitution pattern.  Ab initio calculation of maps for the π current density induced in these model systems by a perpendicular external magnetic field exhibits the full range of tropicity, from diatropic aromatic to nonaromatic to paratropic antiaromatic, with a ready rationalisation in terms of an orbital model.  Further calculations on systems of varying charge in which these motifs are embedded in extended PAH systems with naphthalene and phenanthrene 'clamps' show promise for switching between current patterns and related  opto-electronic properties.

Ring Currents in the Clar Goblet Calculated Using Configurational State Averaging.

The closed-shell Hückel-London-Pople-McWeeny formalism for ring currents is extended to Aufbau configurations with open shells calculated as configurational averages. The method is applied to the non-Kekulean benzenoid known as the Clar goblet, recently synthesized on the Au(111) surface. Multiplicity of the ground state is a complication: for the Clar goblet, Hund's rule of maximum multiplicity implies a triplet whereas Ovchinnikov's rule implies a singlet.

Infection Inspection: using the power of citizen science for image-based prediction of antibiotic resistance in Escherichia coli treated with ciprofloxacin.

Antibiotic resistance is an urgent global health challenge, necessitating rapid diagnostic tools to combat its threat. This study uses citizen science and image feature analysis to profile the cellular features associated with antibiotic resistance in Escherichia coli. Between February and April 2023, we conducted the Infection Inspection project, in which 5273 volunteers made 1,045,199 classifications of single-cell images from five E.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites.

Prediction of pyrazinamide resistance in using structure-based machine-learning approaches.

Background: Pyrazinamide is one of four first-line antibiotics used to treat tuberculosis; however, antibiotic susceptibility testing for pyrazinamide is challenging. Resistance to pyrazinamide is primarily driven by genetic variation in , encoding an enzyme that converts pyrazinamide into its active form.

Methods: We curated a dataset of 664 non-redundant, missense amino acid mutations in PncA with associated high-confidence phenotypes from published studies and then trained three different machine-learning models to predict pyrazinamide resistance.

Compensatory mutations are associated with increased growth in resistant clinical samples of .

Mutations in associated with resistance to antibiotics often come with a fitness cost for the bacteria. Resistance to the first-line drug rifampicin leads to lower competitive fitness of populations when compared to susceptible populations. This fitness cost, introduced by resistance mutations in the RNA polymerase, can be alleviated by compensatory mutations (CMs) in other regions of the affected protein.

Tuning (Anti)Aromaticity: Variations on the [8]-Circulene Framework.

Optoelectronic properties of organic molecules are underpinned by delocalisation and delocalisability of π-electrons. These properties are sensitive to small changes in electron count, whether achieved by heteroatom substitution or redox chemistry. One measure of the delocalisability of π-electrons is the current induced by an external magnetic field, which is diagnostic of (anti)aromaticity.

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on .

Several bioinformatics genotyping algorithms are now commonly used to characterize antimicrobial resistance (AMR) gene profiles in whole-genome sequencing (WGS) data, with a view to understanding AMR epidemiology and developing resistance prediction workflows using WGS in clinical settings. Accurately evaluating AMR in Enterobacterales, particularly , is of major importance, because this is a common pathogen. However, robust comparisons of different genotyping approaches on relevant simulated and large real-life WGS datasets are lacking.

Inclusion of minor alleles improves catalogue-based prediction of fluoroquinolone resistance in .

Objectives: Fluoroquinolone resistance poses a threat to the successful treatment of tuberculosis. WGS, and the subsequent detection of catalogued resistance-associated mutations, offers an attractive solution to fluoroquinolone susceptibility testing but sensitivities are often less than 90%. We hypothesize that this is partly because the bioinformatic pipelines used usually mask the recognition of minor alleles that have been implicated in fluoroquinolone resistance.

Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis.

Background: Bedaquiline is a core drug for the treatment of multidrug-resistant tuberculosis; however, the understanding of resistance mechanisms is poor, which is hampering rapid molecular diagnostics. Some bedaquiline-resistant mutants are also cross-resistant to clofazimine. To decipher bedaquiline and clofazimine resistance determinants, we combined experimental evolution, protein modelling, genome sequencing, and phenotypic data.

Predicting antibiotic resistance in complex protein targets using alchemical free energy methods.

Drug resistant Mycobacterium tuberculosis, which mostly results from single nucleotide polymorphisms in antibiotic target genes, poses a major threat to tuberculosis treatment outcomes. Relative binding free energy (RBFE) calculations can rapidly predict the effects of mutations, but this approach has not been tested on large, complex proteins. We use RBFE calculations to predict the effects of M.

A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates.

Tuberculosis is a respiratory disease that is treatable with antibiotics. An increasing prevalence of resistance means that to ensure a good treatment outcome it is desirable to test the susceptibility of each infection to different antibiotics. Conventionally, this is done by culturing a clinical sample and then exposing aliquots to a panel of antibiotics, each being present at a pre-determined concentration, thereby determining if the sample isresistant or susceptible to each sample.

ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads.

Summary: Viral sequence data from clinical samples frequently contain contaminating human reads, which must be removed prior to sharing for legal and ethical reasons. To enable host read removal for SARS-CoV-2 sequencing data on low-specification laptops, we developed ReadItAndKeep, a fast lightweight tool for Illumina and nanopore data that only keeps reads matching the SARS-CoV-2 genome. Peak RAM usage is typically below 10 MB, and runtime less than 1 min.

iodoannulenes: A Generalized Annulene-within-an-Annulene Paradigm for Combined σ and π Ring Currents.

iodoannulene molecules and ions CI in planar geometry offer examples of systems with the potential for outer σ and inner π ring-current double aromaticity, given a sufficient overlap of tangential p-orbital manifolds on the large atoms of the outer cycle. Previous theoretical work indicated concentric diatropic currents in the dication CI. Ab initio ipsocentric calculations support an account in terms of frontier-orbital selection rules for current contributions in CI (and radical CI, implicated in recent experimental work on the oxidation of iodobenzene).

Cryo-EM structure and resistance landscape of M. tuberculosis MmpL3: An emergent therapeutic target.

Tuberculosis (TB) is the leading cause of death from a single infectious agent and in 2019 an estimated 10 million people worldwide contracted the disease. Although treatments for TB exist, continual emergence of drug-resistant variants necessitates urgent development of novel antituberculars. An important new target is the lipid transporter MmpL3, which is required for construction of the unique cell envelope that shields Mycobacterium tuberculosis (Mtb) from the immune system.

How quickly can we predict trimethoprim resistance using alchemical free energy methods?

The emergence of antimicrobial resistance threatens modern medicine and necessitates more personalized treatment of bacterial infections. Sequencing the whole genome of the pathogen(s) in a clinical sample offers one way to improve clinical microbiology diagnostic services, and has already been adopted for tuberculosis in some countries. A key weakness of a genetics clinical microbiology is it cannot return a result for rare or novel genetic variants and therefore predictive methods are required.

Differential occupational risks to healthcare workers from SARS-CoV-2 observed during a prospective observational study.

We conducted voluntary Covid-19 testing programmes for symptomatic and asymptomatic staff at a UK teaching hospital using naso-/oro-pharyngeal PCR testing and immunoassays for IgG antibodies. 1128/10,034 (11.2%) staff had evidence of Covid-19 at some time.

A Correlated Source-Sink-Potential Model Consistent with the Meir-Wingreen Formula.

We model a molecular device as a molecule attached to a set of leads treated at the tight-binding level, with the central molecule described to any desired level of electronic structure theory. Within this model, in the absence of electron-phonon interactions, the Landauer-Büttiker part of the Meir-Wingreen formula is shown to be sufficient to describe the transmission factor of the correlated device. The key to this demonstration is to ensure that the correlation self-energy has the same functional form as the exact correlation self-energy.

Modelling aromatisation of (BN)H azabora-annulenes.

Despite a long tradition of descriptions of borazine as an 'inorganic benzene', this molecule is a non-aromatic species according to the magnetic (ring-current) criterion. Borazine, borazocine, and the larger neutral (BN)nH2n azabora-annulene heterocycles in planar conformations, although π-isoelectronic with [2n]annulenes, support only localized induced currents in perpendicular magnetic fields. The π-current maps of these systems comprise superpositions of separate 'lone-pair' circulations on all nitrogen centres.

Ring-Current Maps for Benzenoids: Comparisons, Contradictions, and a Versatile Combinatorial Model.

As a key diagnostic property of benzenoids and other polycyclic hydrocarbons, induced ring current has inspired diverse approaches for calculation, modeling, and interpretation. Grid-based methods include the ipsocentric calculation of current maps, and its surrogate, the pseudo-π model. Graph-based models include a family of conjugated-circuit (CC) models and the molecular-orbital Hückel-London (HL) model.

Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex.

Background: A comprehensive understanding of the pre-existing genetic variation in genes associated with antibiotic resistance in the Mycobacterium tuberculosis complex (MTBC) is needed to accurately interpret whole-genome sequencing data for genotypic drug susceptibility testing (DST).

Methods: We investigated mutations in 92 genes implicated in resistance to 21 anti-tuberculosis drugs using the genomes of 405 phylogenetically diverse MTBC strains. The role of phylogenetically informative mutations was assessed by routine phenotypic DST data for the first-line drugs isoniazid, rifampicin, ethambutol, and pyrazinamide from a separate collection of over 7000 clinical strains.

Design of annulene-within-an-annulene systems by the altanisation approach. A study of altan-[n]annulenes.

The altanisation strategy, devised to design molecules with large and paratropic perimeter circulations, is applied to the family of [n]annulenes to give, altan-[n]annulenes, i.e. [n,5]coronenes.

Molecular graphs and molecular conduction: the d-omni-conductors.

Ernzerhof's source-and-sink-potential (SSP) model for ballistic conduction in conjugated π systems predicts transmission of electrons through a two-wire device in terms of characteristic polynomials of the molecular graph and subgraphs based on the pattern of connections. We present here a complete classification of conduction properties of all molecular graphs within the SSP model. An omni-conductor/omni-insulator is a molecular graph that conducts/insulates at the Fermi level (zero of energy) for all connection patterns.

In search of Coulson's lost theorem.

In Hückel theory, the bond number is the sum of the orders of the π bonds incident on a given carbon center. From the work of Coulson and his school, it has been believed for over 70 years that the bond number has a maximum of 3 and that this bound is realized by exactly one conjugated framework, that of the trimethylenemethane radical. Search of published literature and archived correspondence failed to find any formal proof of these two statements.