Implications of a scalar dark force for terrestrial experiments

A long-range intergalactic force between dark matter (DM) particles, mediated by an ultralight scalar, is tightly constrained by galactic dynamics and large scale structure formation. We examine the implications of such a ‘‘dark force” for several terrestrial experiments, including Eötvös tests of the Weak Equivalence Principle (WEP), direct-detection DM searches, and collider studies. The presence of a dark force implies a nonvanishing effect in Eötvös tests that could be probed by current and future experiments depending on the DM model. For scalar DM that is a singlet under the standard model gauge groups, a dark force of astrophysically relevant magnitude is ruled out in large regions of parameter space by the DM relic density and WEP constraints. WEP tests also imply constraints on the Higgs-exchange contributions to the spin-independent (SI) DM-nucleus direct-detection cross section. For WIMP scenarios, these considerations constrain Higgs-exchange contributions to the SI cross section to be subleading compared to gauge-boson mediated contributions. In multicomponent DM scenarios, a dark force would preclude large shifts in the rate for Higgs decay to two photons associated with DM-multiplet loops that might otherwise lead to measurable deviations at the LHC or a future linear collider. The combination of observations from galactic dynamics, large scale structure formation, Eötvös experiments, DM-direct-detection experiments, and colliders can further constrain the size of new long-range forces in the dark sector

Implementing User Rights for Research in the Field of Artificial Intelligence: A Call for International Action

Last year, before the onset of a global pandemic highlighted the critical and urgent need for technology-enabled scientific research, the World Intellectual Property Organization (WIPO) launched an inquiry into issues at the intersection of intellectual property (IP) and artificial intelligence (AI). We contributed comments to that inquiry, with a focus on the application of copyright to the use of text and data mining (TDM) technology. This article describes some of the most salient points of our submission and concludes by stressing the need for international leadership on this important topic. WIPO could help fill the current gap on international leadership, including by providing guidance on the diverse mechanisms that countries may use to authorize TDM research and serving as a forum for the adoption of rules permitting cross-border TDM projects

Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance

Background: A common assumption of microorganisms is that laboratory stocks will remain genetically and phenotypically constant over time, and across laboratories. It is becoming increasingly clear, however, that mutations can ruin strain integrity and drive the divergence or “domestication” of stocks. Since its discovery in 1960, a stock of Methylobacterium extorquens AM1 (“AM1”) has remained in the lab, propagated across numerous growth and storage conditions, researchers, and facilities. To explore the extent to which this lineage has diverged, we compared our own “Modern” stock of AM1 to a sample archived at a culture stock center shortly after the strain’s discovery. Stored as a lyophilized sample, we hypothesized that this Archival strain would better reflect the first-ever isolate of AM1 and reveal ways in which our Modern stock has changed through laboratory domestication or other means. Results: Using whole-genome re-sequencing, we identified some 29 mutations – including single nucleotide polymorphisms, small indels, the insertion of mobile elements, and the loss of roughly 36 kb of DNA - that arose in the laboratory-maintained Modern lineage. Contrary to our expectations, Modern was both slower and less fit than Archival across a variety of growth substrates, and showed no improvement during long-term growth and storage. Modern did, however, outperform Archival during growth on nutrient broth, and in resistance to rifamycin, which was selected for by researchers in the 1980s. Recapitulating selection for rifamycin resistance in replicate Archival populations showed that mutations to RNA polymerase B (rpoB) substantially decrease growth in the absence of antibiotic, offering an explanation for slower growth in Modern stocks. Given the large number of genomic changes arising from domestication (28), it is somewhat surprising that the single other mutation attributed to purposeful laboratory selection accounts for much of the phenotypic divergence between strains. Conclusions: These results highlight the surprising degree to which AM1 has diverged through a combination of unintended laboratory domestication and purposeful selection for rifamycin resistance. Instances of strain divergence are important, not only to ensure consistency of experimental results, but also to explore how microbes in the lab diverge from one another and from their wild counterparts

A novel pair of inducible expression vectors for use in Methylobacterium extorquens

Background: Due to the ever increasing use of diverse microbial taxa in basic research and industrial settings, there is a growing need for genetic tools to alter the physiology of these organisms. In particular, there is a dearth of inducible expression systems available for bacteria outside commonly used γ-proteobacteria, such as Escherichia coli or Pseudomonas species. To this end, we have sought to develop a pair of inducible expression vectors for use in the α-proteobacterium Methylobacterium extorquens, a model methylotroph. Findings: We found that the P R promoter from rhizobial phage 16-3 was active in M. extorquens and engineered the promoter to be inducible by either p-isopropyl benzoate (cumate) or anhydrotetracycline. These hybrid promoters, P R/cmtO and P R/tetO, were found to have high levels of expression in M. extorquens with a regulatory range of 10-fold and 30-fold, respectively. Compared to an existing cumate-inducible (10-fold range), high-level expression system for M. extorquens, P R/cmtO and P R/tetO have 33% of the maximal activity but were able to repress gene expression 3 and 8-fold greater, respectively. Both promoters were observed to exhibit homogeneous, titratable activation dynamics rather than on-off, switch-like behavior. The utility of these promoters was further demonstrated by complementing loss of function of ftfL - essential for growth on methanol - where we show P R/tetO is capable of not only fully complementing function but also producing a conditional null phenotype. These promoters have been incorporated into a broad-host-range backbone allowing for potential use in a variety of bacterial hosts. Conclusions: We have developed two novel expression systems for use in M. extorquens. The expression range of these vectors should allow for increased ability to explore cellular physiology in M. extorquens. Further, the P R/tetO promoter is capable of producing conditional null phenotypes, previously unattainable in M. extorquens. As both expression systems rely on the use of membrane permeable inducers, we suspect these expression vectors will be useful for ectopic gene expression in numerous proteobacteria

Dark-Matter-Induced Weak Equivalence Principle Violation

A long-range fifth force coupled to dark matter can induce a coupling to ordinary matter if the dark matter interacts with Standard Model fields. We consider constraints on such a scenario from both astrophysical observations and laboratory experiments. We also examine the case where the dark matter is a weakly interacting massive particle, and derive relations between the coupling to dark matter and the coupling to ordinary matter for different models. Currently, this scenario is most tightly constrained by galactic dynamics, but improvements in Eotvos experiments can probe unconstrained regions of parameter space.Comment: 4 page

Implementing User Rights for Research in the Field of Artificial Intelligence: A Call for International Action

Last year, before the onset of a global pandemic highlighted the critical and urgent need for technology-enabled scientific research, the World Intellectual Property Organization (WIPO) launched an inquiry into issues at the intersection of intellectual property (IP) and artificial intelligence (AI). We contributed comments to that inquiry, with a focus on the application of copyright to the use of text and data mining (TDM) technology. This article describes some of the most salient points of our submission and concludes by stressing the need for international leadership on this important topic. WIPO could help fill the current gap on international leadership, including by providing guidance on the diverse mechanisms that countries may use to authorize TDM research and serving as a forum for the adoption of rules permitting cross-border TDM projects

Composition and Biophysical Properties of the Sorting Platform Pods in the Shigella Type III Secretion System

Shigella flexneri, causative agent of bacillary dysentery (shigellosis), uses a type III secretion system (T3SS) as its primary virulence factor. The T3SS injectisome delivers effector proteins into host cells to promote entry and create an important intracellular niche. The injectisome’s cytoplasmic sorting platform (SP) is a critical assembly that contributes to substrate selection and energizing secretion. The SP consists of oligomeric Spa33 “pods” that associate with the basal body via MxiK and connect to the Spa47 ATPase via MxiN. The pods contain heterotrimers of Spa33 with one full-length copy associated with two copies of a C-terminal domain (Spa33C). The structure of Spa33C is known, but the precise makeup and structure of the pods in situ remains elusive. We show here that recombinant wild-type Spa33 can be prepared as a heterotrimer that forms distinct stable complexes with MxiK and MxiN. In two-hybrid analyses, association of the Spa33 complex with these proteins occurs via the full-length Spa33 component. Furthermore, these complexes each have distinct biophysical properties. Based on these properties, new high-resolution cryo-electron tomography data and architectural similarities between the Spa33 and flagellar FliM-FliN complexes, we provide a preliminary model of the Spa33 heterotrimers within the SP pods. From these findings and evolving models of SP interfaces and dynamics in the Yersinia and Salmonella T3SS, we suggest a model for SP function in which two distinct complexes come together within the context of the SP to contribute to form the complete pod structures during the recruitment of T3SS secretion substrates