A model roseobacter, ruegeria pomeroyi dss-3, employs a diffusible killing mechanism to eliminate competitors

The Roseobacter clade is a group of alphaproteobacteria that have diverse metabolic and regulatory capabilities. They are abundant in marine environments and have a substantial role in marine ecology and biogeochemistry. However, interactions between roseobacters and other bacterioplankton have not been extensively explored. In this study, we identify a killing mechanism in the model roseobacter Ruegeria pomeroyi DSS-3 by coculturing it with a group of phylogenetically diverse bacteria. The killing mechanism is diffusible and occurs when cells are grown both on surfaces and in suspension and is dependent on cell density. A screen of random transposon mutants revealed that the killing phenotype, as well as resistance to killing, require genes within an -8-kb putative gamma-butyrolactone synthesis gene cluster, which resembles similar pheromone-sensing systems in actinomycetes that regulate secondary metabolite production, including antimicrobials. Transcriptomics revealed the gene cluster is highly upregulated in wild-type DSS-3 compared to a nonkiller mutant when grown in liquid coculture with a roseobacter target. Our findings show that R. pomeroyi has the capability to eliminate closely and distantly related competitors, providing a mechanism to alter the community structure and function in its native habitats. IMPORTANCE Bacteria carry out critical ecological and biogeochemical processes and form the foundations of ecosystems. Identifying the factors that influence microbial community composition and the functional capabilities encoded within them is key to predicting how microbes impact an ecosystem. Because microorganisms must compete for limited space and nutrients to promote their own propagation, they have evolved diverse mechanisms to outcompete or kill competitors. However, the genes and regulatory strategies that promote such competitive abilities are largely underexplored, particularly in free-living marine bacteria. Here, genetics and omics techniques are used to investigate how a model marine bacterium is capable of quickly eliminating natural competitors in coculture. We determined that a previously uncharacterized horizontally acquired gene cluster is required for this bacterium to kill diverse competitors. This work represents an important step toward understanding the mechanisms bacterial populations can use to become dominant members in marine microbial communities

Baryon Decuplet to Octet Electromagnetic Transitions in Quenched and Partially Quenched Chiral Perturbation Theory

We calculate baryon decuplet to octet electromagnetic transition form factors in quenched and partially quenched chiral perturbation theory. We work in the isospin limit of SU(3) flavor, up to next-to-leading order in the chiral expansion, and to leading order in the heavy baryon expansion. Our results are necessary for proper extrapolation of lattice calculations of these transitions. We also derive expressions for the case of SU(2) flavor away from the isospin limit.Comment: 16 pages, 3 figures, revtex

Non-perturbative improvement of composite operators with Wilson fermions

We propose a method to improve lattice operators composed of Wilson fermions which allows the removal of all corrections of $O(a)$, including those proportional to the quark mass, leaving only errors of $O(a^2)$. The method exploits the fact that chiral symmetry is restored at short distances. By imposing this requirement on correlation functions of improved lattice operators at short distances, the coefficients which appear in these operators can be determined. The method is an extension of the improvement program of the ALPHA collaboration, which, up to now, has only been applicable in the chiral limit. The extension to quarks with non-zero masses is particularly important for applications in heavy quark physics.Comment: 15 pages, Late

Para-Aminobenzoic Acid, Calcium, and c-di-GMP Induce Formation of Cohesive, Syp-Polysaccharide-Dependent Biofilms in Vibrio fischeri

The marine bacterium Vibrio fischeri efficiently colonizes its symbiotic squid host, Euprymna scolopes, by producing a transient biofilm dependent on the symbiosis polysaccharide (SYP). In vitro, however, wild-type strain ES114 fails to form SYP-dependent biofilms. Instead, genetically engineered strains, such as those lacking the negative regulator BinK, have been developed to study this phenomenon. Historically, V. fischeri has been grown using LBS, a complex medium containing tryptone and yeast extract; supplementation with calcium is required to induce biofilm formation by a binK mutant. Here, through our discovery that yeast extract inhibits biofilm formation, we uncover signals and underlying mechanisms that control V. fischeri biofilm formation. In contrast to its inability to form a biofilm on unsupplemented LBS, a binK mutant formed cohesive, SYP-dependent colony biofilms on tTBS, modified LBS that lacks yeast extract. Moreover, wild-type strain ES114 became proficient to form cohesive, SYP-dependent biofilms when grown in tTBS supplemented with both calcium and the vitamin para-aminobenzoic acid (pABA); neither molecule alone was sufficient, indicating that this phenotype relies on coordinating two cues. pABA/calcium supplementation also inhibited bacterial motility. Consistent with these phenotypes, cells grown in tTBS with pABA/calcium were enriched in transcripts for biofilm-related genes and predicted diguanylate cyclases, which produce the second messenger cyclic-di-GMP (c-di-GMP). They also exhibited elevated levels of c-di-GMP, which was required for the observed phenotypes, as phosphodiesterase overproduction abrogated biofilm formation and partially rescued motility. This work thus provides insight into conditions, signals, and processes that promote biofilm formation by V. fischeri. IMPORTANCE Bacteria integrate environmental signals to regulate gene expression and protein production to adapt to their surroundings. One such behavioral adaptation is the formation of a biofilm, which can promote adherence and colonization and provide protection against antimicrobials. Identifying signals that trigger biofilm formation and the underlying mechanism(s) of action remain important and challenging areas of investigation. Here, we determined that yeast extract, commonly used for growth of bacteria in laboratory culture, inhibits biofilm formation by Vibrio fischeri, a model bacterium used for investigating host-relevant biofilm formation. Omitting yeast extract from the growth medium led to the identification of an unusual signal, the vitamin para-aminobenzoic acid (pABA), that when added together with calcium could induce biofilm formation. pABA increased the concentrations of the second messenger, c-di-GMP, which was necessary but not sufficient to induce biofilm formation. This work thus advances our understanding of signals and signal integration controlling bacterial biofilm formation

New lattice approaches to the ΔI=1/2\Delta I=1/2 rule

Lattice QCD should allow a derivation of the $\Delta I=1/2$ rule from first principles, but numerical calculations to date have been plagued by a variety of problems. After a brief review of these problems, we present several new methods for calculating $K\to\pi\pi$ amplitudes. These are designed for Wilson fermions, though they can be used also with staggered fermions. They all involve a non-perturbative determination of matching coefficients. We show how problems of operator mixing can be greatly reduced by using point-split hadronic currents, and how CP violating parts of the $K\to\pi\pi$ amplitudes can be calculated by introducing a fake top quark. Many of the methods can also be applied to the calculation of two body non-leptonic B-meson decays.Comment: 22 pages, 1 figure, uses epsfi

Chirally improving Wilson fermions - I. O(a) improvement

We show that it is possible to improve the chiral behaviour and the approach to the continuum limit of correlation functions in lattice QCD with Wilson fermions by taking arithmetic averages of correlators computed in theories regularized with Wilson terms of opposite sign. Improved hadronic masses and matrix elements can be obtained by similarly averaging the corresponding physical quantities separately computed within the two regularizations. To deal with the problems related to the spectrum of the Wilson--Dirac operator, which are particularly worrisome when Wilson and mass terms are such as to give contributions of opposite sign to the real part of the eigenvalues, we propose to use twisted-mass lattice QCD for the actual computation of the quantities taking part to the averages. The choice $\pm \pi/2$ for the twisting angle is particularly interesting, as O($a$) improved estimates of physical quantities can be obtained even without averaging data from lattice formulations with opposite Wilson terms. In all cases little or no extra computing power is necessary, compared to simulations with standard Wilson fermions or twisted-mass lattice QCD.Comment: 71 pages, Latex, Keywords: Lattice, Improvement, Chirality. Version v2: mistake corrected in transformation properties under \omega -> -\omega, sect. 5.3.1 (see also sect. 6.1). Minor corrections in App. D and argument clarified in App. F. Version v3: minor modifications in sect. 2 (pag. 8-10: on the odd r-parity of M_crit(r)), in sect. 3.1.3 and 5.4.1 (few sentences about cutoff effects at small quark mass) and in sect. 3.2 (details of discussion below eq. 3.17); updated/added some reference

Up, down, strange and charm quark masses with N-f=2+1+1 twisted mass lattice QCD

We present a lattice QCD calculation of the up, down, strange and charm quark masses performed using the gauge configurations produced by the European Twisted Mass Collaboration with N-f = 2 + 1 + 1 dynamical quarks, which include in the sea, besides two light mass degenerate quarks, also the strange and charm quarks with masses close to their physical values. The simulations are based on a unitary setup for the two light quarks and on a mixed action approach for the strange and charm quarks. The analysis uses data at three values of the lattice spacing and pion masses in the range 210-450 MeV, allowing for accurate continuum limit and controlled chiral extrapolation. The quark mass renormalization is carried out non-perturbatively using the RI'-MOM method. The results for the quark masses converted to the (MS) over bar scheme are: m(ud) (2 GeV) = 3.70(17) MeV, m(s)(2 GeV) = 99.6(4.3) MeV and m(c)(m(c)) = 1.348(46) GeV. We obtain also the quark mass ratios m(s)/m(ud) = 26.66(32) and m(c)/m(s) = 11.62(16). By studying the mass splitting between the neutral and charged kaons and using available lattice results for the electromagnetic contributions, we evaluate m(u)/m(d) = 0.470(56), leading to m(u) = 2.36(24) MeV and m(d) = 5.03(26) MeV

Models for Type Ia supernovae and related astrophysical transients

We give an overview of recent efforts to model Type Ia supernovae and related astrophysical transients resulting from thermonuclear explosions in white dwarfs. In particular we point out the challenges resulting from the multi-physics multi-scale nature of the problem and discuss possible numerical approaches to meet them in hydrodynamical explosion simulations and radiative transfer modeling. We give examples of how these methods are applied to several explosion scenarios that have been proposed to explain distinct subsets or, in some cases, the majority of the observed events. In case we comment on some of the successes and shortcoming of these scenarios and highlight important outstanding issues.Comment: 20 pages, 2 figures, review published in Space Science Reviews as part of the topical collection on supernovae, replacement corrects typos in the conclusions sectio

TRY plant trait database – enhanced coverage and open access

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives