Two-photon laser spectroscopy of antiprotonic helium and the antiproton-to-electron mass ratio

Multi-strain phage induced clearance of bacterial infections

Bacteriophage (or 'phage' - viruses that infect and kill bacteria) are increasingly considered as a therapeutic alternative to treat antibiotic-resistant bacterial infections. However, bacteria can evolve resistance to phage, presenting a significant challenge to the near- and long-term success of phage therapeutics. Application of mixtures of multiple phage (i.e., 'cocktails') have been proposed to limit the emergence of phage-resistant bacterial mutants that could lead to therapeutic failure. Here, we combine theory and computational models of in vivo phage therapy to study the efficacy of a phage cocktail, composed of two complementary phages motivated by the example of Pseudomonas aeruginosa facing two phages that exploit different surface receptors, LUZ19v and PAK_P1. As confirmed in a Luria-Delbrück fluctuation test, this motivating example serves as a model for instances where bacteria are extremely unlikely to develop simultaneous resistance mutations against both phages. We then quantify therapeutic outcomes given single- or double-phage treatment models, as a function of phage traits and host immune strength. Building upon prior work showing monophage therapy efficacy in immunocompetent hosts, here we show that phage cocktails comprised of phage targeting independent bacterial receptors can improve treatment outcome in immunocompromised hosts and reduce the chance that pathogens simultaneously evolve resistance against phage combinations. The finding of phage cocktail efficacy is qualitatively robust to differences in virus-bacteria interactions and host immune dynamics. Altogether, the combined use of theory and computational analysis highlights the influence of viral life history traits and receptor complementarity when designing and deploying phage cocktails in immunocompetent and immunocompromised hosts.

Bioenergetic stress potentiates antimicrobial resistance and persistence

Antimicrobial resistance (AMR) is a global health crisis and there is an urgent need to better understand AMR mechanisms. Antibiotic treatment alters several aspects of bacterial physiology, including increased ATP utilization, carbon metabolism, and reactive oxygen species (ROS) formation. However, how the "bioenergetic stress" induced by increased ATP utilization affects treatment outcomes is unknown. Here we utilized a synthetic biology approach to study the direct effects of bioenergetic stress on antibiotic efficacy. We engineered a genetic system that constitutively hydrolyzes ATP or NADH in Escherichia coli. We found that bioenergetic stress potentiates AMR evolution via enhanced ROS production, mutagenic break repair, and transcription-coupled repair. We also find that bioenergetic stress potentiates antimicrobial persistence via potentiated stringent response activation. We propose a unifying model that antibiotic-induced antimicrobial resistance and persistence is caused by antibiotic-induced. This has important implications for preventing or curbing the spread of AMR infections.

Gram-positive bacteria are primed for surviving lethal doses of antibiotics and chemical stress

Antibiotic resistance kills millions worldwide yearly. However, a major contributor to recurrent infections lies in a small fraction of bacterial cells, known as persisters. These cells are not inherently antibiotic-resistant, yet they lead to increased antibiotic usage, raising the risk of developing resistant progenies. In a bacterial population, individual cells exhibit considerable fluctuations in their gene expression levels despite being cultivated under identical, stable conditions. This variability in cell-to-cell characteristics (phenotypic diversity) within an isogenic population enables persister cells to withstand antibiotic exposure by entering a non-dividing state. We recently showed the existence of "primed cells" in E. coli. Primed cells are dividing cells prepared for antibiotic stress before encountering it and are more prone to form persisters. They also pass their "prepared state" down for several generations through epigenetic memory. Here, we show that primed cells are common among distant bacterial lineages, allowing for survival against antibiotics and other chemical stress, and form in different growth phases. They are also responsible for increased persister levels in transition and stationary phases compared to the log phase. We tested and showed that the Gram-positive bacterium Bacillus megaterium, evolutionarily very distant from E. coli, forms primed cells and has a transient epigenetic memory that is maintained for 7 generations or more. We showed this using ciprofloxacin and the non-antibiotic chemical stress fluoride. It is well established that persister levels are higher in the stationary phase than in the log phase, and B. megaterium persisters levels are nearly identical from the early to late-log phase but are ~2-fold and ~4-fold higher in the transition and stationary phase, respectively. It was previously proposed that there are two distinct types of persisters: Type II forms in the log phase, while Type I forms in the stationary phase. However, we show that primed cells lead to increased persisters in the transition and stationary phase and found no evidence of Type I or II persisters with distant phenotypes. Overall, we have provided substantial evidence of the importance of primed cells and their transitory epigenetic memories to surviving stress.

Mapping the dynamics of epigenetic adaptation during heterochromatin misregulation

A classical and well-established mechanism that enables cells to adapt to new and adverse conditions is the acquisition of beneficial genetic mutations. Much less is known about epigenetic mechanisms that allow cells to develop novel and adaptive phenotypes without altering their genetic blueprint. It has been recently proposed that histone modifications, such as heterochromatin-defining H3K9 methylation (H3K9me), normally reserved to maintain genome integrity, can be redistributed across the genome to establish new and potentially adaptive phenotypes. To uncover the dynamics of this process, we developed a precision engineered genetic approach to trigger H3K9me redistribution on-demand in fission yeast. This enabled us to trace genome-scale RNA and chromatin changes over time prior to and during adaptation in long-term continuous cultures. Establishing adaptive H3K9me occurs over remarkably slow time-scales relative to the initiating stress. During this time, we captured dynamic H3K9me redistribution events ultimately leading to cells converging on an optimal adaptive solution. Upon removal of stress, cells relax to new transcriptional and chromatin states rather than revert to their initial (ground) state, establishing a tunable memory for a future adaptive epigenetic response. Collectively, our tools uncover the slow kinetics of epigenetic adaptation that allow cells to search for and heritably encode adaptive solutions, with implications for drug resistance and response to infection.

The Tradeoffs Between Persistence and Mutation Rates at Sub-Inhibitory Antibiotic Concentrations in Staphylococcus aureus

The rational design of the antibiotic treatment of bacterial infections employs these drugs to reach concentrations that exceed the minimum needed to prevent the replication of the target bacteria. However, within a treated patient, spatial and physiological heterogeneity promotes antibiotic gradients such that the concentration of antibiotics at specific sites is below the minimum needed to inhibit bacterial growth. Here, we investigate the effects of sub-inhibitory antibiotic concentrations on three parameters central to bacterial infection and the success of antibiotic treatment, using in vitro experiments with Staphylococcus aureus and mathematical-computer simulation models. Our results, using drugs of six different classes, demonstrate that exposure to sub-inhibitory antibiotic concentrations not only alters the dynamics of bacterial growth but also increases the mutation rate to antibiotic resistance and decreases the rate of production of persister cells thereby reducing the persistence level. Understanding this trade-off between mutation rates and persistence levels resulting from sub-inhibitory antibiotic exposure is crucial for optimizing, and mitigating the failure of, antibiotic therapy.

Investigating low frequency somatic mutations in Arabidopsis with Duplex Sequencing

Mutations are the source of novel genetic diversity but can also lead to disease and maladaptation. The conventional view is that mutations occur randomly with respect to their environment-specific fitness consequences. However, intragenomic mutation rates can vary dramatically due to transcription coupled repair and based on local epigenomic modifications, which are non-uniformly distributed across genomes. One sequence feature associated with decreased mutation is higher expression level, which can vary depending on environmental cues. To understand whether the association between expression level and mutation rate creates a systematic relationship with environment-specific fitness effects, we perturbed expression through a heat treatment in Arabidopsis thaliana. We quantified gene expression to identify differentially expressed genes, which we then targeted for mutation detection using Duplex Sequencing. This approach provided a highly accurate measurement of the frequency of rare somatic mutations in vegetative plant tissues, which has been a recent source of uncertainty in plant mutation research. We included mutant lines lacking mismatch repair (MMR) and base excision repair (BER) capabilities to understand how repair mechanisms may drive biased mutation accumulation. We found wild type (WT) and BER mutant mutation frequencies to be very low (mean variant frequency 1.8×10-8 and 2.6×10-8, respectively), while MMR mutant frequencies were significantly elevated (1.13×10-6). These results show that somatic variant frequencies are extremely low in WT plants, indicating that larger datasets will be needed to address the fundamental evolutionary question as to whether environmental change leads to gene-specific changes in mutation rate.

Metapopulation model of phage therapy of an acute Pseudomonas aeruginosa lung infection

Infections caused by multi-drug resistant (MDR) pathogenic bacteria are a global health threat. Phage therapy, which uses phage to kill bacterial pathogens, is increasingly used to treat patients infected by MDR bacteria. However, the therapeutic outcome of phage therapy may be limited by the emergence of phage resistance during treatment and/or by physical constraints that impede phage-bacteria interactions in vivo. In this work, we evaluate the role of lung spatial structure on the efficacy of phage therapy for Pseudomonas aeruginosa infection. To do so, we developed a spatially structured metapopulation network model based on the geometry of the bronchial tree, and included the emergence of phage-resistant bacterial mutants and host innate immune responses. We model the ecological interactions between bacteria, phage, and the host innate immune system at the airway (node) level. The model predicts the synergistic elimination of a P. aeruginosa infection due to the combined effects of phage and neutrophils given sufficiently active immune states and suitable phage life history traits. Moreover, the metapopulation model simulations predict that local MDR pathogens are cleared faster at distal nodes of the bronchial tree. Notably, image analysis of lung tissue time series from wild-type and lymphocyte-depleted mice (n=13) revealed a concordant, statistically significant pattern: infection intensity cleared in the bottom before the top of the lungs. Overall, the combined use of simulations and image analysis of in vivo experiments further supports the use of phage therapy for treating acute lung infections caused by P. aeruginosa while highlighting potential limits to therapy given a spatially structured environment, such as impaired innate immune responses and low phage efficacy.

Light antiproton one-electron quasi-molecular ions within the relativistic A-DKB method

In the present work, two quasi-molecular compounds each involving one antiproton and one electron (p̄), He+-p̄ and H-p̄, are investigated. Using completely relativistic calculations within the finite-basis method adapted to systems with axial symmetry, the adiabatic potential curves are constructed by numerically solving the two-center Dirac equation. The binding energies of electron are obtained as a function of the inter-nuclear distance and compared with the corresponding nonrelativistic values and relativistic leading-order corrections calculated in the framework of other approaches. A semantic analysis of antiproton quasi-molecular ions with compounds containing a proton (p) instead of an antiproton is given. The advantages of the A-DKB method are demonstrated.

Continuous evolution of user-defined genes at 1-million-times the genomic mutation rate

When nature maintains or evolves a gene's function over millions of years at scale, it produces a diversity of homologous sequences whose patterns of conservation and change contain rich structural, functional, and historical information about the gene. However, natural gene diversity likely excludes vast regions of functional sequence space and includes phylogenetic and evolutionary eccentricities, limiting what information we can extract. We introduce an accessible experimental approach for compressing long-term gene evolution to laboratory timescales, allowing for the direct observation of extensive adaptation and divergence followed by inference of structural, functional, and environmental constraints for any selectable gene. To enable this approach, we developed a new orthogonal DNA replication (OrthoRep) system that durably hypermutates chosen genes at a rate of >10 -4 substitutions per base in vivo . When OrthoRep was used to evolve a conditionally essential maladapted enzyme, we obtained thousands of unique multi-mutation sequences with many pairs >60 amino acids apart (>15% divergence), revealing known and new factors influencing enzyme adaptation. The fitness of evolved sequences was not predictable by advanced machine learning models trained on natural variation. We suggest that OrthoRep supports the prospective and systematic discovery of constraints shaping gene evolution, uncovering of new regions in fitness landscapes, and general applications in biomolecular engineering.

The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development

A suite of molecular sensory systems enables Caulobacter to control growth, development, and reproduction in response to levels of essential elements. The bacterial enhancer binding protein (bEBP) NtrC, and its cognate sensor histidine kinase NtrB, are key regulators of nitrogen assimilation in many bacteria, but their roles in Caulobacter metabolism and development are not well defined. Notably, Caulobacter NtrC is an unconventional bEBP that lacks the σ54-interacting loop commonly known as the GAFTGA motif. Here we show that deletion of C. crescentus ntrC slows cell growth in complex medium, and that ntrB and ntrC are essential when ammonium is the sole nitrogen source due to their requirement for glutamine synthetase (glnA) expression. Random transposition of a conserved IS3-family mobile genetic element frequently rescued the growth defect of ntrC mutant strains by restoring transcription of the glnBA operon, revealing a possible role for IS3 transposition in shaping the evolution of Caulobacter populations during nutrient limitation. We further identified dozens of direct NtrC binding sites on the C. crescentus chromosome, with a large fraction located near genes involved in polysaccharide biosynthesis. The majority of binding sites align with those of the essential nucleoid associated protein, GapR, or the cell cycle regulator, MucR1. NtrC is therefore predicted to directly impact the regulation of cell cycle and cell development. Indeed, loss of NtrC function led to elongated polar stalks and elevated synthesis of cell envelope polysaccharides. This study establishes regulatory connections between NtrC, nitrogen metabolism, polar morphogenesis, and envelope polysaccharide synthesis in Caulobacter .

Alternative end-joining results in smaller deletions in heterochromatin relative to euchromatin

Pericentromeric heterochromatin is highly enriched for repetitive sequences prone to aberrant recombination. Previous studies showed that homologous recombination (HR) repair is uniquely regulated in this domain to enable 'safe' repair while preventing aberrant recombination. In Drosophila cells, DNA double-strand breaks (DSBs) relocalize to the nuclear periphery through nuclear actin-driven directed motions before recruiting the strand invasion protein Rad51 and completing HR repair. End-joining (EJ) repair also occurs with high frequency in heterochromatin of fly tissues, but how alternative EJ (alt-EJ) pathways operate in heterochromatin remains largely uncharacterized. Here, we induce DSBs in single euchromatic and heterochromatic sites using a new system that combines the DR- white reporter and I-SceI expression in spermatogonia of flies. Using this approach, we detect higher frequency of HR repair in heterochromatin, relative to euchromatin. Further, sequencing of mutagenic repair junctions reveals the preferential use of different EJ pathways across distinct euchromatic and heterochromatic sites. Interestingly, synthesis-dependent microhomology-mediated end joining (SD-MMEJ) appears differentially regulated in the two domains, with a preferential use of motifs close to the cut site in heterochromatin relative to euchromatin, resulting in smaller deletions. Together, these studies establish a new approach to study repair outcomes in fly tissues, and support the conclusion that heterochromatin uses more HR and less mutagenic EJ repair relative to euchromatin.

Self-Consistent Extraction of Spectroscopic Bounds on Light New Physics

Fundamental physical constants are determined from a collection of precision measurements of elementary particles, atoms, and molecules. This is usually done under the assumption of the standard model (SM) of particle physics. Allowing for light new physics (NP) beyond the SM modifies the extraction of fundamental physical constants. Consequently, setting NP bounds using these data, and at the same time assuming the Committee on Data of the International Science Council recommended values for the fundamental physical constants, is not reliable. As we show in this Letter, both SM and NP parameters can be simultaneously determined in a consistent way from a global fit. For light vectors with QED-like couplings, such as the dark photon, we provide a prescription that recovers the degeneracy with the photon in the massless limit and requires calculations only at leading order in the small new physics couplings. At present, the data show tensions partially related to the proton charge radius determination. We show that these can be alleviated by including contributions from a light scalar with flavor nonuniversal couplings.

Optical Channeling of Low Energy Antiprotons in Thin Crystal Targets

A relevant aspect of the interactions between charged fermions and crystal targets is coherence, which can exist at both classical and quantum levels. In the case of antiprotons crossing crystal targets, there are theories and measurements of classical-level coherence effects, in particular, channeling effects. For the present study, we assume the existence of a low-energy regime where the electrostatic interactions between an antiproton and the crystal atoms lead to a local loss in the beam flux as their leading effect. We expect this assumption to be well-justified for antiproton (p¯) energies below 100 eV, with a progressive transition to a standard “Rutherford regime” in the energy range 100–1000 eV. Under these conditions, the target can be treated as an optical absorber with a periodical structure, which can be simplified by considering a multi-layer planar structure only. As in standard optics, wave absorption is accompanied by interference and diffraction. Assuming sub-nanometer ranges for the relevant parameters and a realistic angular spread for the antiproton beam, we find narrow-angle focusing effects that reproduce the classical channeling effect at a qualitative level. We also find that diffraction dominates over interference, although this may strongly depend on the target details.

Cell Population Growth Kinetics in the Presence of Stochastic Heterogeneity of Cell Phenotype

Recent studies at individual cell resolution have revealed phenotypic heterogeneity in nominally clonal tumor cell populations. The heterogeneity affects cell growth behaviors, which can result in departure from the idealized exponential growth. Here we measured the stochastic time courses of growth of an ensemble of populations of HL60 leukemia cells in cultures, starting with distinct initial cell numbers to capture the departure from the exponential growth model in the initial growth phase. Despite being derived from the same cell clone, we observed significant variations in the early growth patterns of individual cultures with statistically significant differences in growth kinetics and the presence of subpopulations with different growth rates that endured for many generations. Based on the hypothesis of existence of multiple inter-converting subpopulations, we developed a branching process model that captures the experimental observations.

Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells

Pluripotency can be induced in somatic cells by the expression of the four "Yamanaka" factors OCT4, KLF4, SOX2, and MYC. However, even in homogeneous conditions, usually only a rare subset of cells admit reprogramming, and the molecular characteristics of this subset remain unknown. Here, we apply retrospective clone tracing to identify and characterize the individual human fibroblast cells that are primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis led to increased reprogramming efficiency, identifying it as a barrier to reprogramming. Changing the frequency of reprogramming by inhibiting the activity of LSD1 led to an enlarging of the pool of cells that were primed for reprogramming. Our results show that even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.

Recent progress of laser spectroscopy measurements of pionic helium

We review the results of recent laser spectroscopy experiments on metastable pionic helium atoms at the Paul Scherrer Institute’s 590 MeV cyclotron facility that was carried out by the PiHe collaboration. Some future perspectives are briefly discussed.

High-resolution laser resonances of antiprotonic helium in superfluid 4He

When atoms are placed into liquids, their optical spectral lines corresponding to the electronic transitions are greatly broadened compared to those of single, isolated atoms. This linewidth increase can often reach a factor of more than a million, obscuring spectroscopic structures and preventing high-resolution spectroscopy, even when superfluid helium, which is the most transparent, cold and chemically inert liquid, is used as the host material^1–6. Here we show that when an exotic helium atom with a constituent antiproton^7–9 is embedded into superfluid helium, its visible-wavelength spectral line retains a sub-gigahertz linewidth. An abrupt reduction in the linewidth of the antiprotonic laser resonance was observed when the liquid surrounding the atom transitioned into the superfluid phase. This resolved the hyperfine structure arising from the spin–spin interaction between the electron and antiproton with a relative spectral resolution of two parts in 10⁶, even though the antiprotonic helium resided in a dense matrix of normal matter atoms. The electron shell of the antiprotonic atom retains a small radius of approximately 40 picometres during the laser excitation⁷. This implies that other helium atoms containing antinuclei, as well as negatively charged mesons and hyperons that include strange quarks formed in superfluid helium, may be studied by laser spectroscopy with a high spectral resolution, enabling the determination of the particle masses⁹. The sharp spectral lines may enable the detection of cosmic-ray antiprotons^10,11 or searches for antideuterons¹² that come to rest in liquid helium targets.

The spectral lines of antiprotonic helium atoms are shown to retain their sub-gigahertz linewidth upon submersion in a bath of superfluid helium, enabling the hyperfine structure to be resolved.

Low Energy Antimatter Physics

We will review the motivations and the general features of experiments devoted to testing fundamental laws with antimatter at low energies, namely the study of CPT invariance and the Weak Equivalence Principle. A summary of the recent experimental results will be presented.

De novo mutation rates at the single-mutation resolution in a human HBB gene-region associated with adaptation and genetic disease

Although it is known that the mutation rate varies across the genome, previous estimates were based on averaging across various numbers of positions. Here, we describe a method to measure the origination rates of target mutations at target base positions and apply it to a 6-bp region in the human hemoglobin subunit beta (HBB) gene and to the identical, paralogous hemoglobin subunit delta (HBD) region in sperm cells from both African and European donors. The HBB region of interest (ROI) includes the site of the hemoglobin S (HbS) mutation, which protects against malaria, is common in Africa, and has served as a classic example of adaptation by random mutation and natural selection. We found a significant correspondence between de novo mutation rates and past observations of alleles in carriers, showing that mutation rates vary substantially in a mutation-specific manner that contributes to the site frequency spectrum. We also found that the overall point mutation rate is significantly higher in Africans than in Europeans in the HBB region studied. Finally, the rate of the 20A→T mutation, called the “HbS mutation” when it appears in HBB, is significantly higher than expected from the genome-wide average for this mutation type. Nine instances were observed in the African HBB ROI, where it is of adaptive significance, representing at least three independent originations; no instances were observed elsewhere. Further studies will be needed to examine mutation rates at the single-mutation resolution across these and other loci and organisms and to uncover the molecular mechanisms responsible.

Laser Spectroscopy Measurements of Metastable Pionic Helium Atoms at Paul Scherrer Institute

We review recent experiments carried out by the PiHe collaboration of the Paul Scherrer Institute (PSI) that observed an infrared transition of three-body pionic helium atoms by laser spectroscopy. These measurements may lead to a precise determination of the charged pion mass, and complement experiments of antiprotonic helium atoms carried out at the new ELENA facility of CERN.

An Interferometric Method for Particle Mass Measurements

We present an interferometric method suitable to measure particle masses and, where applicable to the particle and its corresponding antiparticle, their mass ratio in order to detect possible symmetry violations between matter and antimatter. The method is based on interferometric techniques tunable to the specific mass range of the particle under consideration. The case study of electron and positron is presented, following the recent observation of positron interferometry.

Chirp-compensated pulsed titanium-sapphire laser system for precision spectroscopy

Active frequency-chirp control for a narrowband pulsed titanium-sapphire laser oscillator-amplifier laser system is demonstrated using an intra-cavity electro-optic modulator, resulting in improved spectral resolution and stability. Beat-note measurements of its output to a continuous-wave laser locked to an optical frequency comb yields an Allan deviation of 5×10^-11 (at 10 s). Correction of residual chirp from a comparison with the fourth-harmonic upconverted pulsed output to a molecular H₂ two-photon resonance delivers a value for the uncertainty contribution due to frequency chirp below the 1.5×10^-10 level.

Effect of tolerance on the evolution of antibiotic resistance under drug combinations

Drug combinations are widely used in clinical practice to prevent the evolution of resistance. However, little is known about the effect of tolerance, a different mode of survival, on the efficacy of drug combinations for preventing the evolution of resistance. In this work, we monitored Staphylococcus aureus strains evolving in patients under treatment. We detected the rapid emergence of tolerance mutations, followed by the emergence of resistance, despite the combination treatment. Evolution experiments on the clinical strains in vitro revealed a new way by which tolerance promotes the evolution of resistance under combination treatments. Further experiments under different antibiotic classes reveal the generality of the effect. We conclude that tolerance is an important factor to consider in designing combination treatments that prevent the evolution of resistance.

Laser spectroscopy of pionic helium atoms

Charged pions¹ are the lightest and longest-lived mesons. Mesonic atoms are formed when an orbital electron in an atom is replaced by a negatively charged meson. Laser spectroscopy of these atoms should permit the mass and other properties of the meson to be determined with high precision and could place upper limits on exotic forces involving mesons (as has been done in other experiments on antiprotons^2-9). Determining the mass of the π^- meson in particular could help to place direct experimental constraints on the mass of the muon antineutrino^10-13. However, laser excitations of mesonic atoms have not been previously achieved because of the small number of atoms that can be synthesized and their typically short (less than one picosecond) lifetimes against absorption of the mesons into the nuclei¹. Metastable pionic helium (π⁴He⁺) is a hypothetical^14-16 three-body atom composed of a helium-4 nucleus, an electron and a π^- occupying a Rydberg state of large principal (n ≈ 16) and orbital angular momentum (l ≈ n - 1) quantum numbers. The π⁴He⁺ atom is predicted to have an anomalously long nanosecond-scale lifetime, which could allow laser spectroscopy to be carried out¹⁷. Its atomic structure is unique owing to the absence of hyperfine interactions^18,19 between the spin-0 π^- and the ⁴He nucleus. Here we synthesize π⁴He⁺ in a superfluid-helium target and excite the transition (n, l) = (17, 16) → (17, 15) of the π^--occupied π⁴He⁺ orbital at a near-infrared resonance frequency of 183,760 gigahertz. The laser initiates electromagnetic cascade processes that end with the nucleus absorbing the π^- and undergoing fission^20,21. The detection of emerging neutron, proton and deuteron fragments signals the laser-induced resonance in the atom, thereby confirming the presence of π⁴He⁺. This work enables the use of the experimental techniques of quantum optics to study a meson.

The evolutionary dynamics and fitness landscape of clonal hematopoiesis

Somatic mutations acquired in healthy tissues as we age are major determinants of cancer risk. Whether variants confer a fitness advantage or rise to detectable frequencies by chance remains largely unknown. Blood sequencing data from ~50,000 individuals reveal how mutation, genetic drift, and fitness shape the genetic diversity of healthy blood (clonal hematopoiesis). We show that positive selection, not drift, is the major force shaping clonal hematopoiesis, provide bounds on the number of hematopoietic stem cells, and quantify the fitness advantages of key pathogenic variants, at single-nucleotide resolution, as well as the distribution of fitness effects (fitness landscape) within commonly mutated driver genes. These data are consistent with clonal hematopoiesis being driven by a continuing risk of mutations and clonal expansions that become increasingly detectable with age.

Cold and stable antimatter for fundamental physics

The field of cold antimatter physics has rapidly developed in the last 20 years, overlapping with the period of the Antiproton Decelerator (AD) at CERN. The central subjects are CPT symmetry tests and Weak Equivalence Principle (WEP) tests. Various groundbreaking techniques have been developed and are still in progress such as to cool antiprotons and positrons down to extremely low temperature, to manipulate antihydrogen atoms, to construct extremely high-precision Penning traps, etc. The precisions of the antiproton and proton magnetic moments have improved by six orders of magnitude, and also laser spectroscopy of antihydrogen has been realized and reached a relative precision of 2 × 10-12 during the AD time. Antiprotonic helium laser spectroscopy, which started during the Low Energy Antiproton Ring (LEAR) time, has reached a relative precision of 8 × 10-10. Three collaborations joined the WEP tests inventing various unique approaches. An additional new post-decelerator, Extra Low ENergy Antiproton ring (ELENA), has been constructed and will be ready in 2021, which will provide 10-100 times more cold antiprotons to each experiment. A new era of the cold antimatter physics will emerge soon including the transport of antiprotons to other facilities.

Adaptive mutability of colorectal cancers in response to targeted therapies

The emergence of drug resistance limits the efficacy of targeted therapies in human tumors. The prevalent view is that resistance is a fait accompli: when treatment is initiated, cancers already contain drug-resistant mutant cells. Bacteria exposed to antibiotics transiently increase their mutation rates (adaptive mutability), thus improving the likelihood of survival. We investigated whether human colorectal cancer (CRC) cells likewise exploit adaptive mutability to evade therapeutic pressure. We found that epidermal growth factor receptor (EGFR)/BRAF inhibition down-regulates mismatch repair (MMR) and homologous recombination DNA-repair genes and concomitantly up-regulates error-prone polymerases in drug-tolerant (persister) cells. MMR proteins were also down-regulated in patient-derived xenografts and tumor specimens during therapy. EGFR/BRAF inhibition induced DNA damage, increased mutability, and triggered microsatellite instability. Thus, like unicellular organisms, tumor cells evade therapeutic pressures by enhancing mutability.

The Genetic Basis of Mutation Rate Variation in Yeast

Mutations are the root source of genetic variation and underlie the process of evolution. Although the rates at which mutations occur vary considerably between species, little is known about differences within species, or the genetic and molecular basis of these differences. Here, we leveraged the power of the yeast Saccharomyces cerevisiae as a model system to uncover natural genetic variants that underlie variation in mutation rate. We developed a high-throughput fluctuation assay and used it to quantify mutation rates in seven natural yeast isolates and in 1040 segregant progeny from a cross between BY, a laboratory strain, and RM, a wine strain. We observed that mutation rate varies among yeast strains and is heritable (H² = 0.49). We performed linkage mapping in the segregants and identified four quantitative trait loci underlying mutation rate variation in the cross. We fine-mapped two quantitative trait loci to the underlying causal genes, RAD5 and MKT1, that contribute to mutation rate variation. These genes also underlie sensitivity to the DNA-damaging agents 4NQO and MMS, suggesting a connection between spontaneous mutation rate and mutagen sensitivity.

Quantum Forces from Dark Matter and Where to Find Them

We observe that sub-GeV dark matter (DM) induces Casimir-Polder forces between nucleons that can be accessed by experiments from nuclear to molecular scales. We calculate the nucleon-nucleon potentials arising in the DM effective theory and note that their main features are fixed by dimensional analysis and the optical theorem. Molecular spectroscopy and neutron scattering turn out be DM search experiments and are found to be complementary to nucleon-based DM direct detection. Existing data set limits on DM with mass up to ∼3-50  MeV and with effective interaction up to the O(10-100)  MeV scale, constraining a region typically difficult to reach for other experiments.

Recent progress of laser spectroscopy experiments on antiprotonic helium

The Atomic Spectroscopy and Collisions Using Slow Antiprotons (ASACUSA) collaboration is currently carrying out laser spectroscopy experiments on antiprotonic helium [Formula: see text] atoms at CERN's Antiproton Decelerator facility. Two-photon spectroscopic techniques have been employed to reduce the Doppler width of the measured [Formula: see text] resonance lines, and determine the atomic transition frequencies to a fractional precision of 2.3-5 parts in 109 More recently, single-photon spectroscopy of buffer-gas cooled [Formula: see text] has reached a similar precision. By comparing the results with three-body quantum electrodynamics calculations, the antiproton-to-electron mass ratio was determined as [Formula: see text], which agrees with the known proton-to-electron mass ratio with a precision of 8×10-10 The high-quality antiproton beam provided by the future Extra Low Energy Antiproton Ring (ELENA) facility should enable further improvements in the experimental precision.This article is part of the Theo Murphy meeting issue 'Antiproton physics in the ELENA era'.

Experimental technique for antiproton-nucleus annihilation cross section measurements at low energy

The interaction of very low energy antiprotons (ps) and antineutrons (ns) with nuclei is interesting for its influence on both fundamental cosmology and nuclear physics. Measuring the annihilation cross section of antimatter on matter can help in solving the universe matter-antimatter puzzle and could give relevant hints in the definition of strong interaction model parameters as well. The ASACUSA collaboration recently measured the antiproton-carbon annihilation cross section at 5.3 MeV of kinetic energy of the incoming antiproton. The experimental apparatus consisted in a vacuum chamber containing thin foils (~0.7-1 μm) of carbon crossed by a bunched beam of antiprotons from the CERN Antiproton Decelerator (AD). The fraction of antiprotons annihilating on the target nucleons gives origin to charged pions which can be detected and counted by segmented scintillators placed outside the chamber. This work describes the experimental details of the apparatus and the technique to perform the cross section measurements.

Models & Searches of CPT Violation: a personal, very partial, list

In this talk, first I motivate theoretically, and then I review the phenomenology of, some models entailing CPT Violation (CPTV). The latter is argued to be responsible for the observed matter-antimatter asymmetry in the Cosmos, and may owe its origin to either Lorentz-violating background geometries, whose effects are strong in early epochs of the Universe but very weak today, being temperature dependent in general, or to an ill-defined CPT generator in some quantum gravity models entailing decoherence of quantum matter as a result of quantum degrees of freedom in the gravity sector that are inaccessible to the low-energy observers. In particular, for the latter category of CPTV, I argue that entangled states of neutral mesons (Kaons or B-systems), of central relevance to KLOE-2 experiment, can provide smoking-gun sensitive tests or even falsify some of these models. If CPT is ill-defined one may also encounter violations of the spin-statistics theorem, with possible consequences for the Pauli Exclusion Principle, which I only briefly touch upon.

Precision laser spectroscopy experiments on antiprotonic helium

At CERN‘s Antiproton Decelerator (AD) facility, the Atomic Spectroscopyand Collisions Using Slow Antiprotons (ASACUSA) collaboration is carrying out precise laser spectroscopy experiments on antiprotonic helium (p̅He+ ≡ p̅+He2++e−) atoms. By employing buffer-gas cooling techniquesin a cryogenic gas target, samples of atoms were cooled to temperatureT = 1.5–1.7 K, thereby reducing the Doppler width in the single-photon resonance lines. By comparing the results with three-body quantum electrodynamics calculations, the antiproton-to-electron mass ratio was determined as Mp̅/me = 1836.1526734(15). This agreed with the known proton-to-electron mass ratio with a precision of 8 . 1010. Further improvements in the experimental precision are currently being attempted. The high-quality antiproton beam provided by the future Extra Low Energy Antiproton Ring (ELENA) facility should further increase the experimental precision.

Buffer-gas cooling of antiprotonic helium to 1.5 to 1.7 K, and antiproton-to-electron mass ratio

Charge, parity, and time reversal (CPT) symmetry implies that a particle and its antiparticle have the same mass. The antiproton-to-electron mass ratio [Formula: see text] can be precisely determined from the single-photon transition frequencies of antiprotonic helium. We measured 13 such frequencies with laser spectroscopy to a fractional precision of 2.5 × 10^-9 to 16 × 10^-9 About 2 × 10⁹ antiprotonic helium atoms were cooled to temperatures between 1.5 and 1.7 kelvin by using buffer-gas cooling in cryogenic low-pressure helium gas; the narrow thermal distribution led to the observation of sharp spectral lines of small thermal Doppler width. The deviation between the experimental frequencies and the results of three-body quantum electrodynamics calculations was reduced by a factor of 1.4 to 10 compared with previous single-photon experiments. From this, [Formula: see text] was determined as 1836.1526734(15), which agrees with a recent proton-to-electron experimental value within 8 × 10^-10.

Sixfold improved single particle measurement of the magnetic moment of the antiproton

Our current understanding of the Universe comes, among others, from particle physics and cosmology. In particle physics an almost perfect symmetry between matter and antimatter exists. On cosmological scales, however, a striking matter/antimatter imbalance is observed. This contradiction inspires comparisons of the fundamental properties of particles and antiparticles with high precision. Here we report on a measurement of the g-factor of the antiproton with a fractional precision of 0.8 parts per million at 95% confidence level. Our value /2=2.7928465(23) outperforms the previous best measurement by a factor of 6. The result is consistent with our proton g-factor measurement gp/2=2.792847350(9), and therefore agrees with the fundamental charge, parity, time (CPT) invariance of the Standard Model of particle physics. Additionally, our result improves coefficients of the standard model extension which discusses the sensitivity of experiments with respect to CPT violation by up to a factor of 20.

Establishing nonlinearity thresholds with ultraintense X-ray pulses

X-ray techniques have evolved over decades to become highly refined tools for a broad range of investigations. Importantly, these approaches rely on X-ray measurements that depend linearly on the number of incident X-ray photons. The advent of X-ray free electron lasers (XFELs) is opening the ability to reach extremely high photon numbers within ultrashort X-ray pulse durations and is leading to a paradigm shift in our ability to explore nonlinear X-ray signals. However, the enormous increase in X-ray peak power is a double-edged sword with new and exciting methods being developed but at the same time well-established techniques proving unreliable. Consequently, accurate knowledge about the threshold for nonlinear X-ray signals is essential. Herein we report an X-ray spectroscopic study that reveals important details on the thresholds for nonlinear X-ray interactions. By varying both the incident X-ray intensity and photon energy, we establish the regimes at which the simplest nonlinear process, two-photon X-ray absorption (TPA), can be observed. From these measurements we can extract the probability of this process as a function of photon energy and confirm both the nature and sub-femtosecond lifetime of the virtual intermediate electronic state.

An improved limit on the charge of antihydrogen from stochastic acceleration

Antimatter continues to intrigue physicists because of its apparent absence in the observable Universe. Current theory requires that matter and antimatter appeared in equal quantities after the Big Bang, but the Standard Model of particle physics offers no quantitative explanation for the apparent disappearance of half the Universe. It has recently become possible to study trapped atoms of antihydrogen to search for possible, as yet unobserved, differences in the physical behaviour of matter and antimatter. Here we consider the charge neutrality of the antihydrogen atom. By applying stochastic acceleration to trapped antihydrogen atoms, we determine an experimental bound on the antihydrogen charge, Qe, of |Q| < 0.71 parts per billion (one standard deviation), in which e is the elementary charge. This bound is a factor of 20 less than that determined from the best previous measurement of the antihydrogen charge. The electrical charge of atoms and molecules of normal matter is known to be no greater than about 10(-21)e for a diverse range of species including H2, He and SF6. Charge-parity-time symmetry and quantum anomaly cancellation demand that the charge of antihydrogen be similarly small. Thus, our measurement constitutes an improved limit and a test of fundamental aspects of the Standard Model. If we assume charge superposition and use the best measured value of the antiproton charge, then we can place a new limit on the positron charge anomaly (the relative difference between the positron and elementary charge) of about one part per billion (one standard deviation), a 25-fold reduction compared to the current best measurement.

Probing QED and fundamental constants through laser spectroscopy of vibrational transitions in HD(.)

The simplest molecules in nature, molecular hydrogen ions in the form of H2(+) and HD(+), provide an important benchmark system for tests of quantum electrodynamics in complex forms of matter. Here, we report on such a test based on a frequency measurement of a vibrational overtone transition in HD(+) by laser spectroscopy. We find that the theoretical and experimental frequencies are equal to within 0.6(1.1) parts per billion, which represents the most stringent test of molecular theory so far. Our measurement not only confirms the validity of high-order quantum electrodynamics in molecules, but also enables the long predicted determination of the proton-to-electron mass ratio from a molecular system, as well as improved constraints on hypothetical fifth forces and compactified higher dimensions at the molecular scale. With the perspective of comparisons between theory and experiment at the 0.01 part-per-billion level, our work demonstrates the potential of molecular hydrogen ions as a probe of fundamental physical constants and laws.

Use of a Continuous Wave Laser and Pockels Cell for Sensitive High-Resolution Collinear Resonance Ionization Spectroscopy

New technical developments have led to a 2 orders of magnitude improvement of the resolution of the collinear resonance ionization spectroscopy (CRIS) experiment at ISOLDE, CERN, without sacrificing the high efficiency of the CRIS technique. Experimental linewidths of 20(1) MHz were obtained on radioactive beams of francium, allowing us for the first time to determine the electric quadrupole moment of the short lived [t_{1/2}=22.0(5) ms] ^{219}Fr Q_{s}=-1.21(2) eb, which would not have been possible without the advantages offered by the new method. This method relies on a continuous-wave laser and an external Pockels cell to produce narrow-band light pulses, required to reach the high resolution in two-step resonance ionization. Exotic nuclei produced at rates of a few hundred ions/s can now be studied with high resolution, allowing detailed studies of the anchor points for nuclear theories.

High-precision comparison of the antiproton-to-proton charge-to-mass ratio

Invariance under the charge, parity, time-reversal (CPT) transformation is one of the fundamental symmetries of the standard model of particle physics. This CPT invariance implies that the fundamental properties of antiparticles and their matter-conjugates are identical, apart from signs. There is a deep link between CPT invariance and Lorentz symmetry--that is, the laws of nature seem to be invariant under the symmetry transformation of spacetime--although it is model dependent. A number of high-precision CPT and Lorentz invariance tests--using a co-magnetometer, a torsion pendulum and a maser, among others--have been performed, but only a few direct high-precision CPT tests that compare the fundamental properties of matter and antimatter are available. Here we report high-precision cyclotron frequency comparisons of a single antiproton and a negatively charged hydrogen ion (H(-)) carried out in a Penning trap system. From 13,000 frequency measurements we compare the charge-to-mass ratio for the antiproton (q/m)p- to that for the proton (q/m)p and obtain (q/m)p-/(q/m)p − 1 =1(69) × 10(-12). The measurements were performed at cyclotron frequencies of 29.6 megahertz, so our result shows that the CPT theorem holds at the atto-electronvolt scale. Our precision of 69 parts per trillion exceeds the energy resolution of previous antiproton-to-proton mass comparisons as well as the respective figure of merit of the standard model extension by a factor of four. In addition, we give a limit on sidereal variations in the measured ratio of <720 parts per trillion. By following the arguments of ref. 11, our result can be interpreted as a stringent test of the weak equivalence principle of general relativity using baryonic antimatter, and it sets a new limit on the gravitational anomaly parameter of |α − 1| < 8.7 × 10(-7).

An experimental limit on the charge of antihydrogen

The properties of antihydrogen are expected to be identical to those of hydrogen, and any differences would constitute a profound challenge to the fundamental theories of physics. The most commonly discussed antiatom-based tests of these theories are searches for antihydrogen-hydrogen spectral differences (tests of CPT (charge-parity-time) invariance) or gravitational differences (tests of the weak equivalence principle). Here we, the ALPHA Collaboration, report a different and somewhat unusual test of CPT and of quantum anomaly cancellation. A retrospective analysis of the influence of electric fields on antihydrogen atoms released from the ALPHA trap finds a mean axial deflection of 4.1 ± 3.4 mm for an average axial electric field of 0.51 V mm(-1). Combined with extensive numerical modelling, this measurement leads to a bound on the charge Qe of antihydrogen of Q=(-1.3 ± 1.1 ± 0.4) × 10(-8). Here, e is the unit charge, and the errors are from statistics and systematic effects.

mα(7)-order corrections in the hydrogen molecular ions and antiprotonic helium

We present a calculation of the complete set of QED corrections of order mα7 for one-electron two-center systems. Leading corrections of order mα8 are also considered, which allows us to estimate the magnitude of yet uncalculated contributions. The theoretical uncertainty on the frequencies of rovibrational transitions in the hydrogen molecular ions H2+ and HD+, and of two-photon transition in antiprotonic helium is reduced by about 1 order of magnitude, down to (3-4)×10-11 and 10-10, respectively. These results open new perspectives for improved determination of the proton- and antiproton-to-electron mass ratios by precision spectroscopy experiments.