Population dynamics of cross-protection against β-lactam antibiotics in droplet microreactors.

Introduction: Bacterial strains that are resistant to antibiotics may protect not only themselves, but also sensitive bacteria nearby if resistance involves antibiotic degradation. Such cross-protection poses a challenge to effective antibiotic therapy by enhancing the long-term survival of bacterial infections, however, the current understanding is limited.

Methods: In this study, we utilize an automated nanoliter droplet analyzer to study the interactions between strains expressing a β-lactamase (resistant) and those not expressing it (sensitive) when exposed to the β-lactam antibiotic cefotaxime (CTX), with the aim to define criteria contributing to cross-protection.

Environmental, mechanistic and evolutionary landscape of antibiotic persistence.

Recalcitrant infections pose a serious challenge by prolonging antibiotic therapies and contributing to the spread of antibiotic resistance, thereby threatening the successful treatment of bacterial infections. One potential contributing factor in persistent infections is antibiotic persistence, which involves the survival of transiently tolerant subpopulations of bacteria. This review summarizes the current understanding of antibiotic persistence, including its clinical significance and the environmental and evolutionary factors at play.

Minimal Surviving Inoculum in Collective Antibiotic Resistance.

A common strategy used by bacteria to resist antibiotics is enzymatic degradation or modification. This reduces the antibiotic threat in the environment and is therefore potentially a collective mechanism that also enhances the survival of nearby cells. Collective resistance is of clinical significance, yet a quantitative understanding at the population level is still incomplete.

Interaction between mutation type and gene pleiotropy drives parallel evolution in the laboratory.

What causes evolution to be repeatable is a fundamental question in evolutionary biology. Pleiotropy, i.e.

Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution.

Mutations with large fitness benefits and mutations occurring at high rates may both cause parallel evolution, but their contribution is predicted to depend on population size. Moreover, high-rate and large-benefit mutations may have different long-term adaptive consequences. We show that small and 100-fold larger bacterial populations evolve resistance to a β-lactam antibiotic by using similar numbers, but different types of mutations.

Choice of β-Lactam Resistance Pathway Depends Critically on Initial Antibiotic Concentration.

Antibiotic resistance trajectories with different final resistance may critically depend on the first mutation, due to epistatic interactions. Here, we study the effect of mutation bias and the concentration-dependent effects on fitness of two clinically important mutations in TEM-1 β-lactamase in initiating alternative trajectories to cefotaxime resistance. We show that at low cefotaxime concentrations, the R164S mutation (a mutation of arginine to serine at position 164), which confers relatively low resistance, is competitively superior to the G238S mutation, conferring higher resistance, thus highlighting a critical influence of antibiotic concentration on long-term resistance evolution.

Coexistence of fluorescent strains in millifluidic droplet reactors.

Understanding competition and cooperation within microbiota is of high fundamental and clinical importance, helping to comprehend species' evolution and biodiversity. We co-encapsulated and cultured two isogenic Escherichia coli strains expressing blue (BFP) and yellow (YFP) fluorescent proteins into numerous emulsion droplets and quantified their growth by employing fluorescence measurements. To characterize and compare the bacterial growth kinetics and behavior in mono and co-culture, we compared the experimental observations with predictions from a simple growth model.

Clonal Interference and Mutation Bias in Small Bacterial Populations in Droplets.

Experimental evolution studies have provided key insights into the fundamental mechanisms of evolution. One striking observation is that parallel and convergent evolution during laboratory evolution can be surprisingly common. However, these experiments are typically performed with well-mixed cultures and large effective population sizes, while pathogenic microbes typically experience strong bottlenecks during infection or drug treatment.

Resurrected Protein Interaction Networks Reveal the Innovation Potential of Ancient Whole-Genome Duplication.

The evolution of plants is characterized by whole-genome duplications, sometimes closely associated with the origin of large groups of species. The gamma (γ) genome triplication occurred at the origin of the core eudicots, which comprise ∼75% of flowering plants. To better understand the impact of whole-genome duplication, we studied the protein interaction network of MADS domain transcription factors, which are key regulators of reproductive development.

Exploiting DELLA Signaling in Cereals.

The spectacular yield increases in rice and wheat during the green revolution were partly realized by reduced gibberellin (GA) synthesis or sensitivity, both causing the accumulation of DELLA proteins. Although insights into the regulation of plant growth and development by DELLA proteins advanced rapidly in arabidopsis (Arabidopsis thaliana), DELLA-mediated regulation of downstream responses in cereals has received little attention to date. Furthermore, translating this research from arabidopsis to cereals is challenging given their different growth patterns and our phylogenetic analysis which reveals that DELLA-related DGLLA proteins exist in cereals but not in arabidopsis.

The Origin of Floral Organ Identity Quartets.

The origin of flowers has puzzled plant biologists ever since Darwin referred to their sudden appearance in the fossil record as an abominable mystery. Flowers are considered to be an assembly of protective, attractive, and reproductive male and female leaf-like organs. Their origin cannot be understood by a morphological comparison to gymnosperms, their closest relatives, which develop separate male or female cones.

A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat.

Winter cereals require prolonged cold to transition from vegetative to reproductive development. This process, referred to as vernalization, has been extensively studied in Arabidopsis (Arabidopsis thaliana). In Arabidopsis, a key flowering repressor called FLOWERING LOCUS C (FLC) quantitatively controls the vernalization requirement.

FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes.

MADS-domain transcription factors have been shown to act as key repressors or activators of the transition to flowering and as master regulators of reproductive organ identities. Despite their important roles in plant development, the origin of several MADS-box subfamilies has remained enigmatic so far. Here we demonstrate, through a combination of genome synteny and phylogenetic reconstructions, the origin of three major, apparently angiosperm-specific MADS-box gene clades: FLOWERING LOCUS C- (FLC-), SQUAMOSA- (SQUA-) and SEPALLATA- (SEP-)-like genes.

The hybrid four-CBS-domain KINβγ subunit functions as the canonical γ subunit of the plant energy sensor SnRK1.

The AMPK/SNF1/SnRK1 protein kinases are a family of ancient and highly conserved eukaryotic energy sensors that function as heterotrimeric complexes. These typically comprise catalytic α subunits and regulatory β and γ subunits, the latter function as the energy-sensing modules of animal AMPK through adenosine nucleotide binding. The ability to monitor accurately and adapt to changing environmental conditions and energy supply is essential for optimal plant growth and survival, but mechanistic insight in the plant SnRK1 function is still limited.

Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification.

Comparative genome biology has unveiled the polyploid origin of all angiosperms and the role of recurrent polyploidization in the amplification of gene families and the structuring of genomes. Which species share certain ancient polyploidy events, and which do not, is ill defined because of the limited number of sequenced genomes and transcriptomes and their uneven phylogenetic distribution. Previously, it has been suggested that most, but probably not all, of the eudicots have shared an ancient hexaploidy event, referred to as the gamma triplication.