Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study

Background Diagnosing drug-resistance remains an obstacle to the elimination of tuberculosis. Phenotypic drug-susceptibility testing is slow and expensive, and commercial genotypic assays screen only common resistance-determining mutations. We used whole-genome sequencing to characterise common and rare mutations predicting drug resistance, or consistency with susceptibility, for all first-line and second-line drugs for tuberculosis. Methods Between Sept 1, 2010, and Dec 1, 2013, we sequenced a training set of 2099 Mycobacterium tuberculosis genomes. For 23 candidate genes identified from the drug-resistance scientific literature, we algorithmically characterised genetic mutations as not conferring resistance (benign), resistance determinants, or uncharacterised. We then assessed the ability of these characterisations to predict phenotypic drug-susceptibility testing for an independent validation set of 1552 genomes. We sought mutations under similar selection pressure to those characterised as resistance determinants outside candidate genes to account for residual phenotypic resistance. Findings We characterised 120 training-set mutations as resistance determining, and 772 as benign. With these mutations, we could predict 89·2% of the validation-set phenotypes with a mean 92·3% sensitivity (95% CI 90·7–93·7) and 98·4% specificity (98·1–98·7). 10·8% of validation-set phenotypes could not be predicted because uncharacterised mutations were present. With an in-silico comparison, characterised resistance determinants had higher sensitivity than the mutations from three line-probe assays (85·1% vs 81·6%). No additional resistance determinants were identified among mutations under selection pressure in non-candidate genes. Interpretation A broad catalogue of genetic mutations enable data from whole-genome sequencing to be used clinically to predict drug resistance, drug susceptibility, or to identify drug phenotypes that cannot yet be genetically predicted. This approach could be integrated into routine diagnostic workflows, phasing out phenotypic drug-susceptibility testing while reporting drug resistance early

Paving the Way to Eureka-Introducing "Dira" as an Experimental Paradigm to Observe the Process of Creative Problem Solving

“Dira” is a novel experimental paradigm to record combinations of behavioral and metacognitive measures for the creative process. This task allows assessing chronological and chronometric aspects of the creative process directly and without a detour through creative products or proxy phenomena. In a study with 124 participants we show that (a) people spend more time attending to selected vs. rejected potential solutions, (b) there is a clear connection between behavioral patterns and self-reported measures, (c) the reported intensity of Eureka experiences is a function of interaction time with potential solutions, and (d) experiences of emerging solutions can happen immediately after engaging with a problem, before participants explore all potential solutions. The conducted study exemplifies how “Dira” can be used as an instrument to narrow down the moment when solutions emerge. We conclude that the “Dira” experiment is paving the way to study the process, as opposed to the product, of creative problem solving

Movement of the human foot in 100 pain free individuals aged 18–45 : implications for understanding normal foot function

Background: Understanding motion in the normal healthy foot is a prerequisite for understanding the effects of pathology and thereafter setting targets for interventions. Quality foot kinematic data from healthy feet will also assist the development of high quality and research based clinical models of foot biomechanics. To address gaps in the current literature we aimed to describe 3D foot kinematics using a 5 segment foot model in a population of 100 pain free individuals. Methods: Kinematics of the leg, calcaneus, midfoot, medial and lateral forefoot and hallux were measured in 100 self reported healthy and pain free individuals during walking. Descriptive statistics were used to characterise foot movements. Contributions from different foot segments to the total motion in each plane were also derived to explore functional roles of different parts of the foot. Results: Foot segments demonstrated greatest motion in the sagittal plane, but large ranges of movement in all planes. All foot segments demonstrated movement throughout gait, though least motion was observed between the midfoot and calcaneus. There was inconsistent evidence of movement coupling between joints. There were clear differences in motion data compared to foot segment models reported in the literature. Conclusions: The data reveal the foot is a multiarticular structure, movements are complex, show incomplete evidence of coupling, and vary person to person. The data provide a useful reference data set against which future experimental data can be compared and may provide the basis for conceptual models of foot function based on data rather than anecdotal observations

Evaluation of the full set of habitat suitability models for vulnerable marine ecosystem indicator taxa in the South Pacific high seas

\ua9 2024 The Authors. Fisheries Management and Ecology published by John Wiley & Sons Ltd. In the high seas, regional fishery management organisations are required to implement measures to prevent significant adverse impacts on vulnerable marine ecosystems (VMEs). Our objectives were to develop habitat suitability models for use in the spatial management of bottom fisheries in the South Pacific and to evaluate these and existing models using independent data from high-quality seafloor imagery. Presence-only models for seven VME indictor taxa were developed to complement previous modelling. Evaluation of habitat suitability models using withheld data indicated high mean True Skill Statistic scores of 0.44–0.64. Most habitat suitability models performed adequately when assessed with independent data on taxon presence and absence but were poor surrogates for abundance. We therefore advocate caution when using presence-only models for spatial management and call for more systematically collected data to develop abundance models

Early signs of recovery suggested by changes in the structure and function of deep-sea megabenthic communities on a seamount 19 years after fishing

\ua9 2025 The AuthorsBottom trawling is the most widespread and severe human disturbance affecting deep-seafloor environments. Seafloor communities inhabiting seamounts (undersea hills or mountains) are especially vulnerable to trawling impacts as they are often dominated by long-lived, sessile epifauna (e.g., cold-water corals) that are easily damaged and/or removed by fishing gear. Trawling on seamounts is spatially concentrated, compounding effects on the benthos. However, the extent to which communities on seamounts that are closed to fishing can recover from earlier trawling impacts is uncertain. Previous studies have hypothesised that any post-trawling recovery of benthic communities on seamounts will probably be initially patchy, recolonised by surviving remnant populations, and may take several decades or more to occur. A fine-scale approach is thus needed to understand and determine the spatio-temporal dynamics of recovery. To address this need, we studied a New Zealand seamount located on Chatham Rise, Morgue, that was heavily trawled in the 1990s before being closed to fishing in 2001. We analysed seafloor imagery collected with a towed camera during repeat surveys in 2001, 2005, 2009, 2015, and 2020 to examine potential changes in benthic community structure and function after trawling ceased. A temporal shift in community structure driven by changes in the abundances of several taxa (mainly bryozoans, stylasterid hydrocorals, and comatulid crinoids) was observed over the study timescale, indicating the communities may have been in the early stages of post-trawling recovery. However, structural variation between different seamount sides and the summit (i.e., spatial variation) was still more pronounced than temporal variation and reflected the trawl fishing footprint. Community function showed little sign of ongoing recovery overall, though some change (driven by colonisation by stylasterid hydrocorals and bryozoans) indicative of early recovery was observed for communities on the seamount summit. Juvenile colonies of the reef-forming stony coral Solenosmilia variabilis were also observed between 8 and 19 years after the closure, demonstrating that the fisheries closure may have facilitated the early recovery process of this species and its associates. Overall, this work has important implications for the spatial management of seamounts vulnerable to bottom-contact fishing operations

A Complete Pathway Model for Lipid A Biosynthesis in Escherichia coli.

Lipid A is a highly conserved component of lipopolysaccharide (LPS), itself a major component of the outer membrane of Gram-negative bacteria. Lipid A is essential to cells and elicits a strong immune response from humans and other animals. We developed a quantitative model of the nine enzyme-catalyzed steps of Escherichia coli lipid A biosynthesis, drawing parameters from the experimental literature. This model accounts for biosynthesis regulation, which occurs through regulated degradation of the LpxC and WaaA (also called KdtA) enzymes. The LpxC degradation signal appears to arise from the lipid A disaccharide concentration, which we deduced from prior results, model results, and new LpxK overexpression results. The model agrees reasonably well with many experimental findings, including the lipid A production rate, the behaviors of mutants with defective LpxA enzymes, correlations between LpxC half-lives and cell generation times, and the effects of LpxK overexpression on LpxC concentrations. Its predictions also differ from some experimental results, which suggest modifications to the current understanding of the lipid A pathway, such as the possibility that LpxD can replace LpxA and that there may be metabolic channeling between LpxH and LpxB. The model shows that WaaA regulation may serve to regulate the lipid A production rate when the 3-deoxy-D-manno-oct-2-ulosonic acid (KDO) concentration is low and/or to control the number of KDO residues that get attached to lipid A. Computation of flux control coefficients showed that LpxC is the rate-limiting enzyme if pathway regulation is ignored, but that LpxK is the rate-limiting enzyme if pathway regulation is present, as it is in real cells. Control also shifts to other enzymes if the pathway substrate concentrations are not in excess. Based on these results, we suggest that LpxK may be a much better drug target than LpxC, which has been pursued most often