SOS response promotes horizontal dissemination of antibiotic resistance genes

Mobile genetic elements have a crucial role in spreading antibiotic resistance genes among bacterial populations. Environmental and genetic factors that regulate conjugative transfer of antibiotic resistance genes in bacterial populations are largely unknown. Integrating conjugative elements (ICEs) are a diverse group of mobile elements that are transferred by means of cell-cell contact and integrate into the chromosome of the new host. SXT is a approximately 100-kilobase ICE derived from Vibrio cholerae that encodes genes that confer resistance to chloramphenicol, sulphamethoxazole, trimethoprim and streptomycin. SXT-related elements were not detected in V. cholerae before 1993 but are now present in almost all clinical V. cholerae isolates from Asia. ICEs related to SXT are also present in several other bacterial species and encode a variety of antibiotic and heavy metal resistance genes. Here we show that SetR, an SXT encoded repressor, represses the expression of activators of SXT transfer. The 'SOS response' to DNA damage alleviates this repression, increasing the expression of genes necessary for SXT transfer and hence the frequency of transfer. SOS is induced by a variety of environmental factors and antibiotics, for example ciprofloxacin, and we show that ciprofloxacin induces SXT transfer as well. Thus, we present a mechanism by which therapeutic agents can promote the spread of antibiotic resistance genes.     

A second generation human haplotype map of over 3.1 million SNPs

We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.     

The CRAC channel consists of a tetramer formed by Stim-induced dimerization of Orai dimers

Ca(2+)-release-activated Ca(2+) (CRAC) channels underlie sustained Ca(2+) signalling in lymphocytes and numerous other cells after Ca(2+) liberation from the endoplasmic reticulum (ER). RNA interference screening approaches identified two proteins, Stim and Orai, that together form the molecular basis for CRAC channel activity. Stim senses depletion of the ER Ca(2+) store and physically relays this information by translocating from the ER to junctions adjacent to the plasma membrane, and Orai embodies the pore of the plasma membrane calcium channel. A close interaction between Stim and Orai, identified by co-immunoprecipitation and by F?rster resonance energy transfer, is involved in the opening of the Ca(2+) channel formed by Orai subunits. Most ion channels are multimers of pore-forming subunits surrounding a central channel, which are preassembled in the ER and transported in their final stoichiometry to the plasma membrane. Here we show, by biochemical analysis after cross-linking in cell lysates and intact cells and by using non-denaturing gel electrophoresis without cross-linking, that Orai is predominantly a dimer in the plasma membrane under resting conditions. Moreover, single-molecule imaging of green fluorescent protein (GFP)-tagged Orai expressed in Xenopus oocytes showed predominantly two-step photobleaching, again consistent with a dimeric basal state. In contrast, co-expression of GFP-tagged Orai with the carboxy terminus of Stim as a cytosolic protein to activate the Orai channel without inducing Ca(2+) store depletion or clustering of Orai into punctae yielded mostly four-step photobleaching, consistent with a tetrameric stoichiometry of the active Orai channel. Interaction with the C terminus of Stim thus induces Orai dimers to dimerize, forming tetramers that constitute the Ca(2+)-selective pore. This represents a new mechanism in which assembly and activation of the functional ion channel are mediated by the same triggering molecule.     

Early life history of the sheepnose (Plethobasus cyphyus) (Mollusca: Bivalvia: Unionoida)

Managing a rare species can be improved with knowledge of its natural history. The sheepnose (Plethobasus cyphyus) is a freshwater mussel recently listed by the US as federally endangered. We used standard methods to study P. cyphyus brooding behaviour, host fishes in the laboratory and under natural conditions, and glochidial morphology. We monitored a population of P. cyphyus in the Chippewa River, WI during spring and summer 2007–2009 and 2011 and found brooding animals between mid-May and early August. Gravid individuals ranged between 5 and 27 yr (mean age ± 1 s.d. = 13 ± 4 yr). Plethobasus cyphyus brooded glochidia in outer gills, which varied in colour from red, orange, pink, cream, or white. We observed mature glochidia more commonly in individuals with cream or white gills and these glochidia were released in a clear, adhesive, mucus matrix. In laboratory trials we found several minnow and topminnow species (29 spp.) served as productive suitable native hosts. The mean number of juvenile mussels released per cyprinid per day was significantly higher for trials conducted at 22–25°C compared with those at 18–20°C, and 83% of trials conducted at 18–20°C using suitable host species produced no juveniles. Glochidia had a unique outline and shell morphometrics that distinguished P. cyphyus from seven other Chippewa River mussel species that produce similar sized glochidia. Using morphometrics we determined that mimic shiners (Notropis volucellus) were natural hosts for P. cyphyus, round pigtoe (Pleurobema sintoxia), and Wabash pigtoe (Fusconaia flava). Releasing mucus-bound glochidia has evolved in a variety of mussel species and may be more common than is currently realized. Our data show that P. cyphyus is a cyprinid host specialist, and propagation efforts for this species can be strengthened through improved access to mature glochidia by using females with cream-coloured gills and increased juvenile production through warmer fish holding temperatures.     

γ-Aminobutyric acid (GABA) signalling in plants

The role of γ-aminobutyric acid (GABA) as a signal in animals has been documented for over 60 years. In contrast, evidence that GABA is a signal in plants has only emerged in the last 15 years, and it was not until last year that a mechanism by which this could occur was identified—a plant ‘GABA receptor’ that inhibits anion passage through the aluminium-activated malate transporter family of proteins (ALMTs). ALMTs are multigenic, expressed in different organs and present on different membranes. We propose GABA regulation of ALMT activity could function as a signal that modulates plant growth, development, and stress response. In this review, we compare and contrast the plant ‘GABA receptor’ with mammalian GABA_A receptors in terms of their molecular identity, predicted topology, mode of action, and signalling roles. We also explore the implications of the discovery that GABA modulates anion flux in plants, its role in signal transduction for the regulation of plant physiology, and predict the possibility that there are other GABA interaction sites in the N termini of ALMT proteins through in silico evolutionary coupling analysis; we also explore the potential interactions between GABA and other signalling molecules.     

Silent performances: Are “repertoires” really post-Kuhnian?

Ankeny and Leonelli (2016) propose “repertoires” as a new way to understand the stability of certain research programs as well as scientific change in general. By bringing a more complete range of social, material, and epistemic elements into one framework, they position their work as a correction to the Kuhnian impulse in philosophy of science and other areas of science studies. I argue that this “post-Kuhnian” move is not complete, and that repertoires maintain an internalist perspective. Comparison with an alternative framework, the “sociotechnical imaginaries” of Jasanoff and Kim (2015), illustrates precisely which elements of practice are externalized by Ankeny and Leonelli. Specifically, repertoires discount the role of audience, without whom the repertoires of science are unintelligible, and lack an explicit place for ethical and political imagination, which provide meaning for otherwise mechanical promotion of particular research programs. This comparison reveals, I suggest, two distinct modes of scholarship, one internalist and the other critical. While repertoires can be modified to meet the needs of critical STS scholars and to completely reject Kuhn's internalism, whether or not we do so depends on what we want our scholarship to achieve.     

John Dewey's pragmatist alternative to the belief-acceptance dichotomy

Defenders of value-free science appeal to cognitive attitudes as part of a wedge strategy, to mark a distinction between science proper and the uses of science for decision-making, policy, etc. Distinctions between attitudes like belief and acceptance have played an important role in defending the value-free ideal. In this paper, I will explore John Dewey's pragmatist philosophy of science as an alternative to the philosophical framework the wedge strategy rests on. Dewey does draw significant and useful distinctions between different sorts of cognitive attitudes taken by inquirers, but none can be used to support the wedge strategy.