When the most potent combination of antibiotics selects for the greatest bacterial load: the Smile-Frown transition

Final published PDF version of article deposited in accordance with SHERPA RoMEO guidelinesConventional wisdom holds that the best way to treat infection with antibiotics is to ‘hit early and hit hard’. A favoured strategy is to deploy two antibiotics that produce a stronger effect in combination than if either drug were used alone. But are such synergistic combinations necessarily optimal? We combine mathematical modelling, evolution experiments, whole genome sequencing and genetic manipulation of a resistance mechanism to demonstrate that deploying synergistic antibiotics can, in practice, be the worst strategy if bacterial clearance is not achieved after the first treatment phase. As treatment proceeds, it is only to be expected that the strength of antibiotic synergy will diminish as the frequency of drug-resistant bacteria increases. Indeed, antibiotic efficacy decays exponentially in our five-day evolution experiments. However, as the theory of competitive release predicts, drug-resistant bacteria replicate fastest when their drug-susceptible competitors are eliminated by overly-aggressive treatment. Here, synergy exerts such strong selection for resistance that an antagonism consistently emerges by day 1 and the initially most aggressive treatment produces the greatest bacterial load, a fortiori greater than if just one drug were given. Whole genome sequencing reveals that such rapid evolution is the result of the amplification of a genomic region containing four drug-resistance mechanisms, including the acrAB efflux operon. When this operon is deleted in genetically manipulated mutants and the evolution experiment repeated, antagonism fails to emerge in five days and antibiotic synergy is maintained for longer. We therefore conclude that unless super-inhibitory doses are achieved and maintained until the pathogen is successfully cleared, synergistic antibiotics can have the opposite effect to that intended by helping to increase pathogen load where, and when, the drugs are found at sub-inhibitory concentrations

Crystal Phase Quantum Well Emission with Digital Control

One of the major challenges in the growth of quantum well and quantum dot heterostructures is the realization of atomically sharp interfaces. Nanowires provide a new opportunity to engineer the band structure as they facilitate the controlled switching of the crystal structure between the zinc-blende (ZB) and wurtzite (WZ) phases. Such a crystal phase switching results in the formation of crystal phase quantum wells (CPQWs) and quantum dots (CPQDs). For GaP CPQWs, the inherent electric fields due to the discontinuity of the spontaneous polarization at the WZ/ZB junctions lead to the confinement of both types of charge carriers at the opposite interfaces of the WZ/ZB/WZ structure. This confinement leads to a novel type of transition across a ZB flat plate barrier. Here, we show digital tuning of the visible emission of WZ/ZB/WZ CPQWs in a GaP nanowire by changing the thickness of the ZB barrier. The energy spacing between the sharp emission lines is uniform and is defined by the addition of single ZB monolayers. The controlled growth of identical quantum wells with atomically flat interfaces at predefined positions featuring digitally tunable discrete emission energies may provide a new route to further advance entangled photons in solid state quantum systems

Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis.

Arbuscular mycorrhizal (AM) fungi are symbionts of most plants, increasing plant growth and diversity. The model AM fungus Rhizophagus irregularis (isolate DAOM 197198) exhibits low within-fungus polymorphism. In contrast, another study reported high within-fungus variability. Experiments with other R. irregularis isolates suggest that within-fungus genetic variation can affect the fungal phenotype and plant growth, highlighting the biological importance of such variation. We investigated whether there is evidence of differing levels of within-fungus polymorphism in an R. irregularis population. We genotyped 20 isolates using restriction site-associated DNA sequencing and developed novel approaches for characterizing polymorphism among haploid nuclei. All isolates exhibited higher within-isolate poly-allelic single-nucleotide polymorphism (SNP) densities than DAOM 197198 in repeated and non-repeated sites mapped to the reference genome. Poly-allelic SNPs were independently confirmed. Allele frequencies within isolates deviated from diploids or tetraploids, or that expected for a strict dikaryote. Phylogeny based on poly-allelic sites was robust and mirrored the standard phylogeny. This indicates that within-fungus genetic variation is maintained in AM fungal populations. Our results predict a heterokaryotic state in the population, considerable differences in copy number variation among isolates and divergence among the copies, or aneuploidy in some isolates. The variation may be a combination of all of these hypotheses. Within-isolate genetic variation in R. irregularis leads to large differences in plant growth. Therefore, characterizing genomic variation within AM fungal populations is of major ecological importance

High‐throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations

High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: (a) to provide a comprehensive overview about the state-of-the-art high-throughput quantification and molecular identification methods used to address population dynamics, community ecology and host associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; (b) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and (c) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Finally, we evaluate the overall perspectives of the state-of-the-art and still evolving methods for diagnostics and population- and community-level ecological research of pathogens and pests

deeptools/deepTools: 3.5.4

error handling fix and cases for bigwigAverage for > 2 samples (@lldelisle) Tick.label deprecation to support matplotlib 3.8 matplotlib minimal supported version from 3.3 to 3.5 tag check changes in pypi upload actio

deeptools/deepTools: 3.5.4

error handling + cases for bwAverage with > 2 samples (@lldelisle ) Tick.label deprecated for matplotlib 3.8 (@lldelisle ) matplotlib minimal version is now 3.5 cicd update for pypi pus

deeptools/deepTools: 3.5.4

error handling + cases for bwAverage with > 2 samples (@lldelisle) tick.label deprecation for compatibility with matplotlib 3.8 (@lldelisle) matplotlib minimal version from 3.3 to 3.5 pypi upload cicd stricter check for tag creatio

Fine-scale genomics and functional analysis demonstrate importance of nematocidal toxins and other genetic elements during adaptation.

<p><b>A,</b> Workflow: Genomic variation of BT-679 populations was contrasted between treatments or correlated with phenotypic variation. <b>B,</b> mviN gene deletion and plasmid with cry toxins. <b>C,</b> Pathogen killing ability correlates negatively with mviN deletion frequency (left axis, filled circles) and positively with toxin plasmid copy number (right axis, open diamonds). The two most deviating values in all three considered traits were recorded for the same two populations (coevolved populations one and five, both from transfer 20, as indicated adjacent to the measured values), strongly indicating a link between reduced plasmid copy number, increased deletion frequency, and loss of virulence. <b>D,</b> Significant variation among the evolution treatments in population genomic statistics for the plasmid Bti_GWDALJX04I0LJH_51–405_fm319.5 (its structure is given in the outer circle). Using a sliding window-based analysis, approximately 65 kb of the plasmid yielded significant ANOVA FDR-corrected q-values, which are shown as-log₁₀(q) on the light grey inner circles as coloured areas for the three inferred population genomic statistics (Θ_W, Θ_π, and D_T; see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002169#sec008" target="_blank">Materials and Methods</a>). The 5% significance threshold is indicated by the dark grey line within each light grey circle. Thus, coloured areas above this line indicate significant variation among the evolution treatments. This region contains genes encoding for transposases, toxins with unknown effect, a membrane protein, a secreted acid phosphatase, and other proteins (outer circle and legend at the bottom). The total size of the plasmid is about 126 kb. The original data is given in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002169#pbio.1002169.s005" target="_blank">S5 Data</a>, <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002169#pbio.1002169.s033" target="_blank">S19 Table</a>, and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002169#pbio.1002169.s034" target="_blank">S20 Table</a>. The results for the statistical analysis is provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002169#pbio.1002169.s028" target="_blank">S14</a>–<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002169#pbio.1002169.s035" target="_blank">S21</a> Tables.</p