Summary Chromosomes in proliferating metazoan cells undergo dramatic structural metamorphoses every cell cycle, alternating between highly condensed mitotic structures facilitating chromosome segregation, and decondensed interphase structures accommodating transcription, gene silencing and DNA replication. Here we use single-cell Hi-C to study chromosome conformations in thousands of individual cells, and discover a continuum of cis-interaction profiles that finely position individual cells along the cell cycle. We show that chromosomal compartments, topological associated domains (TADs), contact insulation and long-range loops, all defined by bulk Hi-C maps, are governed by distinct cell-cycle dynamics. In particular, DNA replication correlates with build-up of compartments and reduction in TAD insulation, while loops are generally stable from G1 through S and G2. Whole-genome 3D structural models reveal a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data thereby allow for re-interpretation of chromosome conformation maps through the prism of the cell cycle.

Bacterial antibiotic resistance is typically quantified by the minimum inhibitory concentration (MIC), which is defined as the minimal concentration of antibiotic that inhibits bacterial growth starting from a standard cell density. However, when antibiotic resistance is mediated by degradation, the collective inactivation of antibiotic by the bacterial population can cause the measured MIC to depend strongly on the initial cell density. In cases where this inoculum effect is strong, the relationship between MIC and bacterial fitness in the antibiotic is not well defined. Here, we demonstrate that the resistance of a single, isolated cell—which we call the single-cell MIC (scMIC)—provides a superior metric for quantifying antibiotic resistance. Unlike the MIC, we find that the scMIC predicts the direction of selection and also specifies the antibiotic concentration at which selection begins to favor new mutants. Understanding the cooperative nature of bacterial growth in antibiotics is therefore essential in predicting the evolution of antibiotic resistance.

Natural populations throughout the tree of life undergo range expansions in response to changes in the environment. Recent theoretical work suggests that range expansions can have a strong effect on evolution, even leading to the fixation of deleterious alleles that would normally be outcompeted in the absence of migration. However, little is known about how range expansions might influence alleles under frequency-or density-dependent selection. Moreover, there is very little experimental evidence to complement existing theory, since expanding populations are difficult to study in the natural environment. In this study, we have used a yeast experimental system to explore the effect of range expansions on the maintenance of cooperative behaviors, which commonly display frequency-and density-dependent selection and are widespread in nature. We found that range expansions favor the maintenance of cooperation in two ways: (i) through the enrichment of cooperators at the front of the expanding population and (ii) by allowing cooperators to "outrun" an invading wave of defectors. In this system, cooperation is enhanced through the coupling of population ecology and evolutionary dynamics in expanding populations, thus providing experimental evidence for a unique mechanism through which cooperative behaviors could be maintained in nature.microbes | Allee effect | eco-evolutionary feedback N atural populations often increase the geographical area that they occupy through population growth and dispersal into new territory (1-4). Such events, termed range expansions, occur repeatedly during the life history of a species in response to changes in the environment (for instance, forest fires or seasonal changes in climate) as well as changes in phenotype that allow the species to colonize regions that were previously inaccessible to them (1, 5). Despite their widespread occurrence, the effect of range expansions on genetic diversity has only begun to be explored. Recent theoretical analyses suggest that genetic drift on the low-density front of an expanding population can lead to the fixation of neutral (or even deleterious) alleles in a way that mimics positive selection (6, 7). This effect, known as "allele surfing," is a stochastic effect that has been demonstrated experimentally for neutral alleles in expanding bacterial colonies (8) and was recently suggested to underlie the global patterns of human phenotypic variation observed today (9-11).Here, we chose to study the maintenance of cooperative alleles in the context of populations undergoing range expansions. By definition, a "cooperator" provides a benefit to other members of the population at a cost to itself (12). Examples of cooperation are ubiquitous in the wild, ranging from siderophore production in bacteria to the formation of communities in human populations (12-15). However, given the appearance of "defectors" that exploit the benefit provided by the cooperators without incurring the cost, explaining the origin and maintenance of cooperation in nature remains...

Forty-three accessions of Phaseolus vulgaris and four of P. coccineus were classified on the basis of the reaction of their primary leaves and pods to inoculation with races 1 and 2 of the pathogen Pseudomonas phaseolicola. Four groups were recognised, (I) highly resistant to race 1 only, (2) resistant to both races, (3) slightly resistant to both races or (4) susceptible to both races. Race 1 resistance was present in a number of accessions (e.g. Red Mexican U13, Rona, Cornell 42-242). Resistance to race 1 and 2 was present in PI 150414, GN Nebraska No. 1 sel. 27, OSU 10183 and other accessions with PI 150414 in their parentage.Studies on the inheritance of resistance in Red Mexican UT3 and PI 150414 were made in crosses with various susceptible bean cultivars. A single dominant factor was responsible for race 1 resistance in Red Mexican UI3. The resistance factor in PI 150414 to races 1 and 2 behaved as a recessive in crosses with Cascade and Seafarer but was partially dominant in crosses with Gallatin 50. These findings suggest that genetic background can influence the expression of the resistance factor from PI 150414 and largely reconcile the conflicting evidence of previous investigators.

SummaryChromosomes in proliferating metazoan cells undergo dramatic structural metamorphoses every cell cycle, alternating between highly condensed mitotic structures facilitating chromosome segregation, and decondensed interphase structures accommodating transcription, gene silencing and DNA replication. Here we use single-cell Hi-C to study chromosome conformations in thousands of individual cells, and discover a continuum of cis-interaction profiles that finely position individual cells along the cell cycle. We show that chromosomal compartments, topological associated domains (TADs), contact insulation and long-range loops, all defined by bulk Hi-C maps, are governed by distinct cell-cycle dynamics. In particular, DNA replication correlates with build-up of compartments and reduction in TAD insulation, while loops are generally stable from G1 through S and G2. Whole-genome 3D structural models reveal a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data thereby allow for re-interpretation of chromosome conformation maps through the prism of the cell cycle.As cells progress from mitosis to interphase and back again, their chromosomes undergo dramatic structural alterations that have intrigued microscopists for over a century1. In preparation for mitosis and cell division, chromosomes are packaged into rod-like structures