Draft genome sequences of <i>Pantoea agglomerans</i> and <i>Pantoea vagans</i> isolates associated with termites

The genus Pantoea incorporates many economically and clinically important species. The plant-associated species, Pantoea agglomerans and Pantoea vagans, are closely related and are often isolated from similar environments. Plasmids conferring certain metabolic capabilities are also shared amongst these two species. The genomes of two isolates obtained from fungus-growing termites in South Africa were sequenced, assembled and annotated. A high number of orthologous genes are conserved within and between these species. The difference in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7 (4,598,703 bp) can largely be attributed to the differences in plasmid content. The genome sequences of these isolates may shed light on the common traits that enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated niches.The Danish Council for Independent Research, Natural Sciences (STENO grant: Michael Poulsen), the National Research Foundation (NRF) (RCA Fellowship: Pieter De Maayer) and the NRF/Dept. of Science and Technology Centre of Excellence in Tree Health Biotechnology (CTHB), South Africa.http://www.standardsingenomics.org/index.php/sigenam2016Forestry and Agricultural Biotechnology Institute (FABI)Microbiology and Plant Patholog

The enterobacterium <i>Trabulsiella odontotermitis</i> presents novel adaptations related to its association with fungus-growing termites

Fungus-growing termites rely on symbiotic microorganisms to help break down plant material and to obtain nutrients. Their fungal cultivar, Termitomyces, is the main plant degrader and food source for the termites, while gut bacteria complement Termitomyces in the degradation of foodstuffs, fixation of nitrogen, and metabolism of amino acids and sugars. Due to the community complexity and because these typically anaerobic bacteria can rarely be cultured, little is known about the physiological capabilities of individual bacterial members of the gut communities and their associations with the termite host. The bacterium Trabulsiella odontotermitis is associated with fungus-growing termites, but this genus is generally understudied, with only two described species. Taking diverse approaches, we obtained a solid phylogenetic placement of T. odontotermitis among the Enterobacteriaceae, investigated the physiology and enzymatic profiles of T. odontotermitis isolates, determined the localization of the bacterium in the termite gut, compared draft genomes of two T. odontotermitis isolates to those of their close relatives, and examined the expression of genes relevant to host colonization and putative symbiont functions. Our findings support the hypothesis that T. odontotermitis is a facultative symbiont mainly located in the paunch compartment of the gut, with possible roles in carbohydrate metabolism and aflatoxin degradation, while displaying adaptations to association with the termite host, such as expressing genes for a type VI secretion system which has been demonstrated to assist bacterial competition, colonization, and survival within hosts

JWST Directly Images Giant Planet Candidates Around Two Metal-Polluted White Dwarf Stars

We report the discovery of two directly imaged, giant planet candidates orbiting the metal-rich DAZ white dwarfs WD 1202-232 and WD 2105-82. JWST's Mid-Infrared Instrument (MIRI) data on these two stars show a nearby resolved source at a projected separation of 11.47 and 34.62 au, respectively. Assuming the planets formed at the same time as their host stars, with total ages of 5.3 and 1.6Gyr, the MIRI photometry is consistent with giant planets with masses about 1-7 Jupiter Masses. The probability of both candidates being false positives due to red background sources is approximately 1 in 3000. If confirmed, these would be the first directly imaged planets that are similar in both age and separation to the giant planets in our own solar system, and they would demonstrate that widely separated giant planets like Jupiter survive stellar evolution. Giant planet perturbers are widely used to explain the tidal disruption of asteroids around metal-polluted white dwarfs. Confirmation of these two planet candidates with future MIRI imaging would provide evidence that directly links giant planets to metal pollution in white dwarf stars.Comment: 9 Pages, 3 Figures, 2 Tables, Accepted for Publication in The Astrophysical Journal Letter

Interleukin-1 Stimulates β-Cell Necrosis and Release of the Immunological Adjuvant HMGB1

BACKGROUND: There are at least two phases of β-cell death during the development of autoimmune diabetes: an initiation event that results in the release of β-cell-specific antigens, and a second, antigen-driven event in which β-cell death is mediated by the actions of T lymphocytes. In this report, the mechanisms by which the macrophage-derived cytokine interleukin (IL)-1 induces β-cell death are examined. IL-1, known to inhibit glucose-induced insulin secretion by stimulating inducible nitric oxide synthase expression and increased production of nitric oxide by β-cells, also induces β-cell death. METHODS AND FINDINGS: To ascertain the mechanisms of cell death, the effects of IL-1 and known activators of apoptosis on β-cell viability were examined. While IL-1 stimulates β-cell DNA damage, this cytokine fails to activate caspase-3 or to induce phosphatidylserine (PS) externalization; however, apoptosis inducers activate caspase-3 and the externalization of PS on β-cells. In contrast, IL-1 stimulates the release of the immunological adjuvant high mobility group box 1 protein (HMGB1; a biochemical maker of necrosis) in a nitric oxide-dependent manner, while apoptosis inducers fail to stimulate HMGB1 release. The release of HMGB1 by β-cells treated with IL-1 is not sensitive to caspase-3 inhibition, while inhibition of this caspase attenuates β-cell death in response to known inducers of apoptosis. CONCLUSIONS: These findings indicate that IL-1 induces β-cell necrosis and support the hypothesis that macrophage-derived cytokines may participate in the initial stages of diabetes development by inducing β-cell death by a mechanism that promotes antigen release (necrosis) and islet inflammation (HMGB1 release)

An AeroCom–AeroSat study: intercomparison of satellite AOD datasets for aerosol model evaluation

To better understand and characterize current uncertainties in the important observational constraint of climate models of aerosol optical depth (AOD), we evaluate and intercompare 14 satellite products, representing nine different retrieval algorithm families using observations from five different sensors on six different platforms. The satellite products (super-observations consisting of 1 degrees x 1 degrees daily aggregated retrievals drawn from the years 2006, 2008 and 2010) are evaluated with AErosol RObotic NETwork (AERONET) and Maritime Aerosol Network (MAN) data. Results show that different products exhibit different regionally varying biases (both under- and overestimates) that may reach +/- 50 %, although a typical bias would be 15 %-25 % (depending on the product). In addition to these biases, the products exhibit random errors that can be 1.6 to 3 times as large. Most products show similar performance, although there are a few exceptions with either larger biases or larger random errors. The intercomparison of satellite products extends this analysis and provides spatial context to it. In particular, we show that aggregated satellite AOD agrees much better than the spatial coverage (often driven by cloud masks) within the 1 degrees x 1 degrees grid cells. Up to similar to 50 % of the difference between satellite AOD is attributed to cloud contamination. The diversity in AOD products shows clear spatial patterns and varies from 10 % (parts of the ocean) to 100 % (central Asia and Australia). More importantly, we show that the diversity may be used as an indication of AOD uncertainty, at least for the better performing products. This provides modellers with a global map of expected AOD uncertainty in satellite products, allows assessment of products away from AERONET sites, can provide guidance for future AERONET locations and offers suggestions for product improvements. We account for statistical and sampling noise in our analyses. Sampling noise, variations due to the evaluation of different subsets of the data, causes important changes in error metrics. The consequences of this noise term for product evaluation are discussed

Proinflammatory cytokines suppress nonsense-mediated RNA decay to impair regulated transcript isoform processing in pancreatic β cells

IntroductionProinflammatory cytokines are implicated in pancreatic ß cell failure in type 1 and type 2 diabetes and are known to stimulate alternative RNA splicing and the expression of nonsense-mediated RNA decay (NMD) components. Here, we investigate whether cytokines regulate NMD activity and identify transcript isoforms targeted in ß cells.MethodsA luciferase-based NMD reporter transiently expressed in rat INS1(832/13), human-derived EndoC-ßH3, or dispersed human islet cells is used to examine the effect of proinflammatory cytokines (Cyt) on NMD activity. The gain- or loss-of-function of two key NMD components, UPF3B and UPF2, is used to reveal the effect of cytokines on cell viability and function. RNA-sequencing and siRNA-mediated silencing are deployed using standard techniques.ResultsCyt attenuate NMD activity in insulin-producing cell lines and primary human ß cells. These effects are found to involve ER stress and are associated with the downregulation of UPF3B. Increases or decreases in NMD activity achieved by UPF3B overexpression (OE) or UPF2 silencing raise or lower Cyt-induced cell death, respectively, in EndoC-ßH3 cells and are associated with decreased or increased insulin content, respectively. No effects of these manipulations are observed on glucose-stimulated insulin secretion. Transcriptomic analysis reveals that Cyt increases alternative splicing (AS)-induced exon skipping in the transcript isoforms, and this is potentiated by UPF2 silencing. Gene enrichment analysis identifies transcripts regulated by UPF2 silencing whose proteins are localized and/or functional in the extracellular matrix (ECM), including the serine protease inhibitor SERPINA1/α-1-antitrypsin, whose silencing sensitizes ß-cells to Cyt cytotoxicity. Cytokines suppress NMD activity via UPR signaling, potentially serving as a protective response against Cyt-induced NMD component expression.ConclusionOur findings highlight the central importance of RNA turnover in ß cell responses to inflammatory stress

Aerosol retrieval experiments in the ESA Aerosol_cci project

Within the ESA Climate Change Initiative (CCI) project Aerosol_cci (2010–2013), algorithms for the production of long-term total column aerosol optical depth (AOD) datasets from European Earth Observation sensors are developed. Starting with eight existing pre-cursor algorithms three analysis steps are conducted to improve and qualify the algorithms: (1) a series of experiments applied to one month of global data to understand several major sensitivities to assumptions needed due to the ill-posed nature of the underlying inversion problem, (2) a round robin exercise of "best" versions of each of these algorithms (defined using the step 1 outcome) applied to four months of global data to identify mature algorithms, and (3) a comprehensive validation exercise applied to one complete year of global data produced by the algorithms selected as mature based on the round robin exercise. The algorithms tested included four using AATSR, three using MERIS and one using PARASOL. This paper summarizes the first step. Three experiments were conducted to assess the potential impact of major assumptions in the various aerosol retrieval algorithms. In the first experiment a common set of four aerosol components was used to provide all algorithms with the same assumptions. The second experiment introduced an aerosol property climatology, derived from a combination of model and sun photometer observations, as a priori information in the retrievals on the occurrence of the common aerosol components. The third experiment assessed the impact of using a common nadir cloud mask for AATSR and MERIS algorithms in order to characterize the sensitivity to remaining cloud contamination in the retrievals against the baseline dataset versions. The impact of the algorithm changes was assessed for one month (September 2008) of data: qualitatively by inspection of monthly mean AOD maps and quantitatively by comparing daily gridded satellite data against daily averaged AERONET sun photometer observations for the different versions of each algorithm globally (land and coastal) and for three regions with different aerosol regimes. The analysis allowed for an assessment of sensitivities of all algorithms, which helped define the best algorithm versions for the subsequent round robin exercise; all algorithms (except for MERIS) showed some, in parts significant, improvement. In particular, using common aerosol components and partly also a priori aerosol-type climatology is beneficial. On the other hand the use of an AATSR-based common cloud mask meant a clear improvement (though with significant reduction of coverage) for the MERIS standard product, but not for the algorithms using AATSR. It is noted that all these observations are mostly consistent for all five analyses (global land, global coastal, three regional), which can be understood well, since the set of aerosol components defined in Sect. 3.1 was explicitly designed to cover different global aerosol regimes (with low and high absorption fine mode, sea salt and dust)