Murine model for Fusarium oxysporum invasive fusariosis reveals organ-specific structures for dissemination and long-term persistence

Peer reviewedPublisher PD

Analysis of opo cis-regulatory landscape uncovers Vsx2 requirement in early eye morphogenesis

The self-organized morphogenesis of the vertebrate optic cup entails coupling the activation of the retinal gene regulatory network to the constriction-driven infolding of the retinal epithelium. Yet the genetic mechanisms underlying this coordination remain largely unexplored. Through phylogenetic footprinting and transgenesis in zebrafish, here we examine the cis-regulatory landscape of opo, an endocytosis regulator essential for eye morphogenesis. Among the different conserved enhancers identified, we isolate a single retina-specific element (H6_10137) and show that its activity depends on binding sites for the retinal determinant Vsx2. Gain- and loss-of-function experiments and ChIP analyses reveal that Vsx2 regulates opo expression through direct binding to this retinal enhancer. Furthermore, we show that vsx2 knockdown impairs the primary optic cup folding. These data support a model by which vsx2, operating through the effector gene opo, acts as a central transcriptional node that coordinates neural retina patterning and optic cup invagination in zebrafish.info:eu-repo/semantics/publishedVersio

What traits are carried on mobile genetic elements, and why?

Although similar to any other organism, prokaryotes can transfer genes vertically from mother cell to daughter cell, they can also exchange certain genes horizontally. Genes can move within and between genomes at fast rates because of mobile genetic elements (MGEs). Although mobile elements are fundamentally self-interested entities, and thus replicate for their own gain, they frequently carry genes beneficial for their hosts and/or the neighbours of their hosts. Many genes that are carried by mobile elements code for traits that are expressed outside of the cell. Such traits are involved in bacterial sociality, such as the production of public goods, which benefit a cell's neighbours, or the production of bacteriocins, which harm a cell's neighbours. In this study we review the patterns that are emerging in the types of genes carried by mobile elements, and discuss the evolutionary and ecological conditions under which mobile elements evolve to carry their peculiar mix of parasitic, beneficial and cooperative genes

Small but crucial : the novel small heat shock protein Hsp21 mediates stress adaptation and virulence in Candida albicans

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An HR-MAS MR Metabolomics Study on Breast Tissues Obtained with Core Needle Biopsy

BACKGROUND: Much research has been devoted to the development of new breast cancer diagnostic measures, including those involving high-resolution magic angle spinning (HR-MAS) magnetic resonance (MR) spectroscopic techniques. Previous HR-MAS MR results have been obtained from post-surgery samples, which limits their direct clinical applicability. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we performed HR-MAS MR spectroscopic studies on 31 breast tissue samples (13 cancer and 18 non-cancer) obtained by percutaneous core needle biopsy. We showed that cancer and non-cancer samples can be discriminated very well with Orthogonal Projections to Latent Structure-Discriminant Analysis (OPLS-DA) multivariate model on the MR spectra. A subsequent blind test showed 69% sensitivity and 94% specificity in the prediction of the cancer status. A spectral analysis showed that in cancer cells, taurine- and choline-containing compounds are elevated. Our approach, additionally, could predict the progesterone receptor statuses of the cancer patients. CONCLUSIONS/SIGNIFICANCE: HR-MAS MR metabolomics on intact breast tissues obtained by core needle biopsy may have a potential to be used as a complement to the current diagnostic and prognostic measures for breast cancers

Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD

Although culture-independent techniques have shown that the lungs are not sterile, little is known about the lung microbiome in chronic obstructive pulmonary disease (COPD). We used pyrosequencing of 16S amplicons to analyze the lung microbiome in two ways: first, using bronchoalveolar lavage (BAL) to sample the distal bronchi and air-spaces; and second, by examining multiple discrete tissue sites in the lungs of six subjects removed at the time of transplantation. We performed BAL on three never-smokers (NS) with normal spirometry, seven smokers with normal spirometry (“heathy smokers”, HS), and four subjects with COPD (CS). Bacterial 16 s sequences were found in all subjects, without significant quantitative differences between groups. Both taxonomy-based and taxonomy-independent approaches disclosed heterogeneity in the bacterial communities between HS subjects that was similar to that seen in healthy NS and two mild COPD patients. The moderate and severe COPD patients had very limited community diversity, which was also noted in 28% of the healthy subjects. Both approaches revealed extensive membership overlap between the bacterial communities of the three study groups. No genera were common within a group but unique across groups. Our data suggests the existence of a core pulmonary bacterial microbiome that includes Pseudomonas, Streptococcus, Prevotella, Fusobacterium, Haemophilus, Veillonella, and Porphyromonas. Most strikingly, there were significant micro-anatomic differences in bacterial communities within the same lung of subjects with advanced COPD. These studies are further demonstration of the pulmonary microbiome and highlight global and micro-anatomic changes in these bacterial communities in severe COPD patients

Improved THETA-1 for light olefins oligomerization to diesel: Influence of textural and acidic properties

The increase in diesel demand, especially in Europe, and the need for high fuel quality requirements are forcing refiners to move into additional processes for production of high cetane diesel in order to meet the present market trends. Oligomerization of light olefins into middle distillate range products is a viable option. The fuel produced through this technology is environmentally friendly, free of sulfur and aromatics, and the adequate choice of the heterogeneous catalyst will direct the selectivity towards low branched oligomers, which will result in a high quality product. In this work we show the benefits of combining basic desilication treatments for generation of additional mesoporosity in mono-directional Theta-1 zeolite, with selective acid dealumination steps that restore not only the microporosity to values close to those of the parent samples, but also the total and strong Bronsted acidity. These modified Theta-1 zeolites present an outstanding catalytic behavior for oligomerization of propene, with a largely increased initial activity, a much higher resistance to deactivation with time on stream, and an improved selectivity to products in the diesel fraction, as compared to the original microporous Theta-1.The authors thank BP Products of North America for their financial support and permission to publish this work, and Consolider Ingenio 2010-Multicat, the "Severo Ochoa Program", and MAT2012-31657 for financial support. R. Sanchis is acknowledged for technical support.Martínez, C.; Doskocil, EJ.; Corma Canós, A. (2014). Improved THETA-1 for light olefins oligomerization to diesel: Influence of textural and acidic properties. Topics in Catalysis. 57(6-9):668-682. https://doi.org/10.1007/s11244-013-0224-xS668682576-9Bellussi G, Mizia F, Calemma V, Pollesel P, Millini R (2012) Microporous Mesoporous Mater 164:127–134Bellussi G, Carati A, Millini R (2010) In: Cejka J, Corma A, Zones S (eds) Zeolites and Catalysis. Wiley-VCH Verlag GmbH & Co., Weinheim, pp 449–491Martinez C, Corma A (2011) Coord Chem Rev 255:1558–1580de Klerk A (2005) Ind Eng Chem Res 44:3887–3893de Klerk A (2006) Energy Fuels 20:439–445de Klerk A (2006) Energy Fuels 20:1799–1805Egloff G (1936) Ind Eng Chem Res 28:1461–1467Degnan TF Jr, Smith CM, Venkat CR (2001) Appl Catal A Gen 221:283–294Apelian MR, Boulton JR, Fung AS (1994) US5284989, to Mobil OilQuann RJ, Green LA, Tabak SA, Krambeck FJ (1988) Ind Eng Chem Res 27:565–570Tabak SA, Krambeck FJ, Garwood WE (1986) AIChE J 32:1526–1531Corma A, Martínez C, Doskocil EJ (2013) J Catal 300:183–196Martens JA, Ravishankar R, Mishin IE, Jacobs PE (2000) Angew Chem Int Ed Engl 39:4376–4379Martens JA, Verrelst WH, Mathys GM, Brown SH, Jacobs PA (2005) Angew Chem Int Ed Engl 117(5833–583):6Pater JPG, Jacobs PA, Martens JA (1998) J Catal 179:477–482Tabak SA (1981) US4254295, to Mobil OilOccelli ML, Hsu JT, Galya LG (1985) J Mol Catal A: Chem 32:377–390Tabak SA (1984) US4504693, to Mobil Oil CorpKholer E, Schmidt F, Wernicke HJ, Pontes MD, Roberts HL (1995, Summer) Hydrocarbon Technology InternationalMartens JA, Verduijn JP (1995) WO95/19945, to Exxon Chemical Patents Inc.Verrelst WH (1995) Martens LRM, WO95/22516, to Exxon Chemical Patents Inc.Verrelst WH, Martens LRM (2000) US6143942, to Exxon Chemical Patents Inc.Verrelst WH, Martens LRM, Verduijn JP (2006) US6013851, to Exxon Chemical Patents Inc.Dakka JM, Mathys GMK, Puttemans MPH (2003) WO03/035583 to Exxon-Mobil Chemical LimitedMatias P, Sa CC, Graca I, Lopes JM, Carvalho AP, Ramoa RF, Guisnet M (2011) Appl Catal A 399:100–109Chal R, Gérardin C, Bulut M, van Donk S (2011) ChemCatChem 3:67–81Perez-Ramirez J, Christensen CH, Egeblad K, Groen JC (2008) Chem Soc Rev 37:2530–2542Verboekend D, Perez-Ramirez J (2011) Catal Sci Technol 1:879–890Serrano DP, Escola JM, Pizarro P (2013) Chem Soc Rev 42:4004–4035Verboekend D, Chabaneix AM, Thomas K, Gilson JP, Perez-Ramirez J (2011) Cryst Eng Comm 13:3408–3416Emeis CA (1993) J Catal 141:347–354Perego C, Peratello S (1999) Catal Today 52:133–145Abello S, Bonilla A, Perez-Ramirez J (2009) Appl Catal A Gen 364:191–198Corma A, Martinez C, Doskocil EJ, Yaluris G (2011) WO2011002631A2, to BP Oil International Limited. BP Corporation North America Inc., UKCorma A, Martinez C, Doskocil EJ, Yaluris G (2011) WO2011002630A2, to BP Oil International Limited. BP Corporation North America Inc, UKHan S, Heck RH, DiGuiseppi FT (1993) US5234875, to Mobil Oil CorporationPeratello S, Molinari M, Bellussi G, Perego C (1999) Catal Today 52:271–27

Aging increases cell-to-cell transcriptional variability upon immune stimulation

Aging is characterized by progressive loss of physiological and cellular functions, but the molecular basis of this decline remains unclear. We explored how aging affects transcriptional dynamics using single-cell RNA sequencing of unstimulated and stimulated naïve and effector memory CD4(+) T cells from young and old mice from two divergent species. In young animals, immunological activation drives a conserved transcriptomic switch, resulting in tightly controlled gene expression characterized by a strong up-regulation of a core activation program, coupled with a decrease in cell-to-cell variability. Aging perturbed the activation of this core program and increased expression heterogeneity across populations of cells in both species. These discoveries suggest that increased cell-to-cell transcriptional variability will be a hallmark feature of aging across most, if not all, mammalian tissues.Funded by the European Research Council (F.C., T.F.R., D.T.O., S.A.T., and M.J.T.S.), EMBO Young Investigators Programme (D.T.O.), Cancer Research UK (H.-C.C., M.d.l.R., D.T.O., and J.C.M.), Janet Thornton Fellowship (WT098051 to C.P.M.-J.), Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (107609/Z/15/Z to M.d.l.R.), European Molecular Biology Laboratory (N.E., A.A.K., M.J.T.S., S.A.T., and J.C.M.), Medical Research Council Biostatistics Unit (MRC_MC_UP_0801/1 to C.A.V.), WTSI (C.P.M.-J., S.A.T., J.C.M., and D.T.O.), and Biotechnology and Biological Sciences Research Council–Collaborative Awards in Science and Engineering Studentship with Abcam plc (A.A.K.)

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