Disruption of Mycobacterium avium subsp. paratuberculosis-specific genes impairs in vivo fitness

Background: Mycobacterium avium subsp. paratuberculosis (MAP) is an obligate intracellular pathogen that infects many ruminant species. The acquisition of foreign genes via horizontal gene transfer has been postulated to contribute to its pathogenesis, as these genetic elements are absent from its putative ancestor, M. avium subsp. hominissuis (MAH), an environmental organism with lesser pathogenicity. In this study, high-throughput sequencing of MAP transposon libraries were analyzed to qualitatively and quantitatively determine the contribution of individual genes to bacterial survival during infection. Results: Out of 52384 TA dinucleotides present in the MAP K-10 genome, 12607 had a MycoMarT7 transposon in the input pool, interrupting 2443 of the 4350 genes in the MAP genome (56%). Of 96 genes situated in MAP-specific genomic islands, 82 were disrupted in the input pool, indicating that MAP-specific genomic regions are dispensable for in vitro growth (odds ratio = 0.21). Following 5 independent in vivo infections with this pool of mutants, the correlation between output pools was high for 4 of 5 (R = 0.49 to 0.61) enabling us to define genes whose disruption reproducibly reduced bacterial fitness in vivo. At three different thresholds for reduced fitness in vivo, MAP-specific genes were over-represented in the list of predicted essential genes. We also identified additional genes that were severely depleted after infection, and several of them have orthologues that are essential genes in M. tuberculosis. Conclusions: This work indicates that the genetic elements required for the in vivo survival of MAP represent a combination of conserved mycobacterial virulence genes and MAP-specific genes acquired via horizontal gene transfer. In addition, the in vitro and in vivo essential genes identified in this study may be further characterized to offer a better understanding of MAP pathogenesis, and potentially contribute to the discovery of novel therapeutic and vaccine targets. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-415) contains supplementary material, which is available to authorized users

High-pressure behavior of polyiodides confined into single-walled carbon nanotubes: A Raman study

International audienceThe high-pressure behavior of polyiodides confined into the hollow core of single-walled carbon nanotubes organized into bundles has been studied by means of Raman spectroscopy. Several regimes of the structural properties are observed for the nanotubes and the polyiodides under pressure. Raman responses of both compounds exhibit correlations over the whole pressure range (0–17 GPa). Modifications, in particular, take place, respectively, between 1 and 2.3 GPa for polyiodides and between 7 and 9 GPa for nanotubes, depending on the experiment. Differences between one experiment to another are discussed in terms of nanotube filling homogeneity. These transitions can be presumably assigned to the tube ovalization pressure and to the tube collapse pressure. A nonreversibility of several polyiodide mode modifications is evidenced and interpreted in terms of a progressive linearization of the iodine polyanions and a reduction in the charged species on pressure release. Furthermore, the significant change in the mode intensities could be associated to an enhancement of lattice modes, suggesting the formation of a new structure inside the nanotube. Changes in the nanotube mode positions after pressure release point out a decrease in the charge transfer in the hybrid system consistent with the observed evolution of the charged species

High-pressure behavior of polyiodides confined into single-walled carbon nanotubes: A Raman study

International audienceThe high-pressure behavior of polyiodides confined into the hollow core of single-walled carbon nanotubes organized into bundles has been studied by means of Raman spectroscopy. Several regimes of the structural properties are observed for the nanotubes and the polyiodides under pressure. Raman responses of both compounds exhibit correlations over the whole pressure range (0–17 GPa). Modifications, in particular, take place, respectively, between 1 and 2.3 GPa for polyiodides and between 7 and 9 GPa for nanotubes, depending on the experiment. Differences between one experiment to another are discussed in terms of nanotube filling homogeneity. These transitions can be presumably assigned to the tube ovalization pressure and to the tube collapse pressure. A nonreversibility of several polyiodide mode modifications is evidenced and interpreted in terms of a progressive linearization of the iodine polyanions and a reduction in the charged species on pressure release. Furthermore, the significant change in the mode intensities could be associated to an enhancement of lattice modes, suggesting the formation of a new structure inside the nanotube. Changes in the nanotube mode positions after pressure release point out a decrease in the charge transfer in the hybrid system consistent with the observed evolution of the charged species

Phenotypic differentiation in love song traits among sibling species of the lutzomyia longipalpis complex in Brazil

Brazilian populations of Lutzomyia longipalpis may constitute a complex of cryptic species, and this report investigates the distribution and number of potential sibling species. One of the main differences observed among Brazilian populations is the type of acoustic signal produced by males during copulation. These copulation song differences seem to be evolving faster than neutral molecular markers and have been suggested to contribute to insemination failure observed in crosses between these sibling species. In previous studies, two main types of copulation songs were found, burst-type and pulse-type. The latter type can, in turn, be further subdivided into five different patterns. Methods We recorded male song from 13 new populations of the L. longipalpis complex from Brazil and compared the songs with 12 already available. Results Out of these 25 populations, 16 produce burst-type and 9 produce pulse-type songs. We performed a principal component analysis in these two main groups separately and an additional discriminant analysis in the pulse-type group. The pulse-type populations showed a clear separation between the five known patterns with a high correspondence of individuals to their correct group, confirming the differentiation between them. The distinctiveness of the burst-type subgroups was much lower than that observed among the pulse-type groups and no clear population structure was observed. This suggests that the burst-type populations represent a single species. Conclusion Overall, our results are consistent with the existence in Brazil of at least six species of the L. longipalpis complex, one with a wide distribution comprising all the populations with burst-type songs, and five more closely related allopatric siblings with different pulse-type song patterns and more restricted distribution ranges8CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPSem informaçãoSem informaçãoSem informaçã

Existential witness extraction in classical realizability and via a negative translation

We show how to extract existential witnesses from classical proofs using Krivine's classical realizability---where classical proofs are interpreted as lambda-terms with the call/cc control operator. We first recall the basic framework of classical realizability (in classical second-order arithmetic) and show how to extend it with primitive numerals for faster computations. Then we show how to perform witness extraction in this framework, by discussing several techniques depending on the shape of the existential formula. In particular, we show that in the Sigma01-case, Krivine's witness extraction method reduces to Friedman's through a well-suited negative translation to intuitionistic second-order arithmetic. Finally we discuss the advantages of using call/cc rather than a negative translation, especially from the point of view of an implementation.Comment: 52 pages. Accepted in Logical Methods for Computer Science (LMCS), 201

Consensus on circulatory shock and hemodynamic monitoring. Task force of the European Society of Intensive Care Medicine.

OBJECTIVE: Circulatory shock is a life-threatening syndrome resulting in multiorgan failure and a high mortality rate. The aim of this consensus is to provide support to the bedside clinician regarding the diagnosis, management and monitoring of shock. METHODS: The European Society of Intensive Care Medicine invited 12 experts to form a Task Force to update a previous consensus (Antonelli et al.: Intensive Care Med 33:575-590, 2007). The same five questions addressed in the earlier consensus were used as the outline for the literature search and review, with the aim of the Task Force to produce statements based on the available literature and evidence. These questions were: (1) What are the epidemiologic and pathophysiologic features of shock in the intensive care unit ? (2) Should we monitor preload and fluid responsiveness in shock ? (3) How and when should we monitor stroke volume or cardiac output in shock ? (4) What markers of the regional and microcirculation can be monitored, and how can cellular function be assessed in shock ? (5) What is the evidence for using hemodynamic monitoring to direct therapy in shock ? Four types of statements were used: definition, recommendation, best practice and statement of fact. RESULTS: Forty-four statements were made. The main new statements include: (1) statements on individualizing blood pressure targets; (2) statements on the assessment and prediction of fluid responsiveness; (3) statements on the use of echocardiography and hemodynamic monitoring. CONCLUSIONS: This consensus provides 44 statements that can be used at the bedside to diagnose, treat and monitor patients with shock

UV Spectropolarimetry with Polstar: Massive Star Binary Colliding Winds

The winds of massive stars are important for their direct impact on the interstellar medium, and for their influence on the final state of a star prior to it exploding as a supernova. However, the dynamics of these winds is understood primarily via their illumination from a single central source. The Doppler shift seen in resonance lines is a useful tool for inferring these dynamics, but the mapping from that Doppler shift to the radial distance from the source is ambiguous. Binary systems can reduce this ambiguity by providing a second light source at a known radius in the wind, seen from orbitally modulated directions. From the nature of the collision between the winds, a massive companion also provides unique additional information about wind momentum fluxes. Since massive stars are strong ultraviolet (UV) sources, and UV resonance line opacity in the wind is strong, UV instruments with a high resolution spectroscopic capability are essential for extracting this dynamical information. Polarimetric capability also helps to further resolve ambiguities in aspects of the wind geometry that are not axisymmetric about the line of sight, because of its unique access to scattering direction information. We review how the proposed MIDEX-scale mission Polstar can use UV spectropolarimetric observations to critically constrain the physics of colliding winds, and hence radiatively-driven winds in general. We propose a sample of 20 binary targets, capitalizing on this unique combination of illumination by companion starlight, and collision with a companion wind, to probe wind attributes over a range in wind strengths. Of particular interest is the hypothesis that the radial distribution of the wind acceleration is altered significantly, when the radiative transfer within the winds becomes optically thick to resonance scattering in multiple overlapping UV lines.Comment: 26 pages, 12 figures, Review in a topical collection series of Astrophysics and Space Sciences on the proposed Polstar satellite. arXiv admin note: substantial text overlap with arXiv:2111.1155

Promoting the clearance of neurotoxic proteins in neurodegenerative disorders of ageing.

Neurodegenerative disorders of ageing (NDAs) such as Alzheimer disease, Parkinson disease, frontotemporal dementia, Huntington disease and amyotrophic lateral sclerosis represent a major socio-economic challenge in view of their high prevalence yet poor treatment. They are often called 'proteinopathies' owing to the presence of misfolded and aggregated proteins that lose their physiological roles and acquire neurotoxic properties. One reason underlying the accumulation and spread of oligomeric forms of neurotoxic proteins is insufficient clearance by the autophagic-lysosomal network. Several other clearance pathways are also compromised in NDAs: chaperone-mediated autophagy, the ubiquitin-proteasome system, extracellular clearance by proteases and extrusion into the circulation via the blood-brain barrier and glymphatic system. This article focuses on emerging mechanisms for promoting the clearance of neurotoxic proteins, a strategy that may curtail the onset and slow the progression of NDAs