Separate jasmonate-dependent and salicylate-dependent defense-response pathways in Arabidopsis are essential for resistance to distinct microbial pathogens

The endogenous plant hormones salicylic acid (SA) and jasmonic acid (JA), whose levels increase on pathogen infection, activate separate sets of genes encoding antimicrobial proteins in Arabidopsis thaliana. The pathogen-inducible genes PR-1, PR-2, and PR-5 require SA signaling for activation, whereas the plant defensin gene PDF1.2, along with a PR-3 and PR-4 gene, are induced by pathogens via an SA-independent and JA-dependent pathway. An Arabidopsis mutant, coi1, that is affected in the JA-response pathway shows enhanced susceptibility to infection by the fungal pathogens Alternaria brassicicola and Botrytis cinerea but not to Peronospora parasitica, and vice versa for two Arabidopsis genotypes (npr1 and NahG) with a defect in their SA response. Resistance to P. parasitica was boosted by external application of the SA-mimicking compound 2,6-dichloroisonicotinic acid [Delaney, T., et al. (1994) Science 266, 1247–1250] but not by methyl jasmonate (MeJA), whereas treatment with MeJA but not 2,6-dichloroisonicotinic acid elevated resistance to Alternaria brassicicola. The protective effect of MeJA against A. brassicicola was the result of an endogenous defense response activated in planta and not a direct effect of MeJA on the pathogen, as no protection to A. brassicicola was observed in the coi1 mutant treated with MeJA. These data point to the existence of at least two separate hormone-dependent defense pathways in Arabidopsis that contribute to resistance against distinct microbial pathogens.

Defects in transforming growth factor-β signaling cooperate with a Ras oncogene to cause rapid aneuploidy and malignant transformation of mouse keratinocytes

Genetic inactivation of the transforming growth factor-β (TGF-β) signaling pathway can accelerate tumor progression in the mouse epidermal model of multistage carcinogenesis. By using an in vitro model of keratinocyte transformation that parallels in vivo malignant conversion to squamous cell carcinoma, we show that v-rasHa transduced primary TGF-β1−/− keratinocytes and keratinocytes expressing a TGF-β type II dominant-negative receptor transgene have significantly higher frequencies of spontaneous transformation than control genotypes. Malignant transformation in the TGF-β1−/− keratinocytes is preceded by aneuploidy and accumulation of chromosomal aberrations. Similarly, transient inactivation of TGF-β signaling with a type II dominant-negative receptor adenovirus causes rapid changes in ploidy. Exogenous TGF-β1 can suppress aneuploidy, chromosome breaks, and malignant transformation of the TGF-β1−/− keratinocytes at concentrations that do not significantly arrest cell proliferation. These results point to genomic instability as a mechanism by which defects in TGF-β signaling could accelerate tumor progression in mouse multistage carcinogenesis.

Coiled Bodies and U2 snRNA Genes Adjacent to Coiled Bodies Are Enriched in Factors Required for snRNA Transcription

A significant percentage of the gene clusters that contain the human genes for U1 small nuclear RNA (snRNA) or for U2 snRNA have been found associated with small nuclear domains, known as coiled bodies. We show here, by immunofluorescent labeling of human cells, that coiled bodies are enriched in factors required for the transcription of these snRNA genes. The 45-kDa γ-subunit of the transcription factor, proximal element sequence-binding transcription factor (PTF), which is specific for the snRNA genes, was found in high concentrations in coiled bodies, along with the general transcription factor TATA-box binding protein and a subset of RNA polymerase II. We show that the transcription factors and RNA polymerase II are concentrated in irregularly shaped domains that not only overlap with coiled bodies but also extend to their immediate surroundings. Fluorescent in situ hybridization showed that these domains can overlap with U2 snRNA genes adjacent to coiled bodies. In addition, we found the domains to contain newly synthesized RNA, visualized by 5-bromo-uridine triphosphate labeling. Our data suggest that coiled bodies are involved in the expression of snRNA genes, which leads us to propose the model that coiled bodies are associated with snRNA genes to facilitate and regulate their transcription. These findings point to a general principle of higher order organization of gene expression in the nucleus.

Myeloblastin is a granulocyte colony-stimulating factor-responsive gene conferring factor-independent growth to hematopoietic cells

Hematopoiesis depends on a pool of quiescent hematopoietic stem/progenitor cells. When exposed to specific cytokines, a portion of these cells enters the cell cycle to generate an amplified progeny. Myeloblastin (MBN) initially was described as involved in proliferation of human leukemia cells. The granulocyte colony-stimulating factor (G-CSF), which stimulates the proliferation of granulocytic precursors, up-regulates MBN expression. Here we show that constitutive overexpression of MBN confers factor-independent growth to murine bone marrow-derived Ba/F3/G-CSFR cells. Our results point to MBN as a G-CSF responsive gene critical to factor-independent growth and indicate that expression of the G-CSF receptor is a prerequisite to this process. A 91-bp MBN promoter region containing PU.1, C/EBP, and c-Myb binding sites is responsive to G-CSF treatment. Although PU.1, C/EBP, and c-Myb transcription factors all were critical for expression of MBN, its up-regulation by G-CSF was associated mainly with PU.1. These findings suggest that MBN is an important target of PU.1 and a key protease for factor-independent growth of hematopoietic cells.

Phosphatidylinositol 3-kinase binding to polyoma virus middle tumor antigen mediates elevation of glucose transport by increasing translocation of the GLUT1 transporter.

Elevation in the rate of glucose transport in polyoma virus-infected mouse fibroblasts was dependent upon phosphatidylinositol 3-kinase (PI 3-kinase; EC 2.7.1.137) binding to complexes of middle tumor antigen (middle T) and pp60c-src. Wild-type polyoma virus infection led to a 3-fold increase in the rate of 2-deoxyglucose (2DG) uptake, whereas a weakly transforming polyoma virus mutant that encodes a middle T capable of activating pp60c-src but unable to promote binding of PI 3-kinase induced little or no change in the rate of 2DG transport. Another transformation-defective mutant encoding a middle T that retains functional binding of both pp60c-src and PI 3-kinase but is incapable of binding Shc (a protein involved in activation of Ras) induced 2DG transport to wild-type levels. Wortmannin (< or = 100 nM), a known inhibitor of PI 3-kinase, blocked elevation of glucose transport in wild-type virus-infected cells. In contrast to serum stimulation, which led to increased levels of glucose transporter 1 (GLUT1) RNA and protein, wild-type virus infection induced no significant change in levels of either GLUT1 RNA or protein. Nevertheless, virus-infected cells did show increases in GLUT1 protein in plasma membranes. These results point to a posttranslational mechanism in the elevation of glucose transport by polyoma virus middle T involving activation of PI 3-kinase and translocation of GLUT1.

Computational approach to anaphora resolution in Spanish dialogues

This paper presents an algorithm for identifying noun-phrase antecedents of pronouns and adjectival anaphors in Spanish dialogues. We believe that anaphora resolution requires numerous sources of information in order to find the correct antecedent of the anaphor. These sources can be of different kinds, e.g., linguistic information, discourse/dialogue structure information, or topic information. For this reason, our algorithm uses various different kinds of information (hybrid information). The algorithm is based on linguistic constraints and preferences and uses an anaphoric accessibility space within which the algorithm finds the noun phrase. We present some experiments related to this algorithm and this space using a corpus of 204 dialogues. The algorithm is implemented in Prolog. According to this study, 95.9% of antecedents were located in the proposed space, a precision of 81.3% was obtained for pronominal anaphora resolution, and 81.5% for adjectival anaphora.

Pitfalls in the Evaluation of the Thermodynamic Consistency of Experimental VLE Data Sets

The thermodynamic consistency of almost 90 VLE data series, including isothermal and isobaric conditions for systems of both total and partial miscibility in the liquid phase, has been examined by means of the area and point-to-point tests. In addition, the Gibbs energy of mixing function calculated from these experimental data has been inspected, with some rather surprising results: certain data sets exhibiting high dispersion or leading to Gibbs energy of mixing curves inconsistent with the total or partial miscibility of the liquid phase, surprisingly, pass the tests. Several possible inconsistencies in the tests themselves or in their application are discussed. Related to this is a very interesting and ambitious initiative that arose within the NIST organization: the development of an algorithm to assess the quality of experimental VLE data. The present paper questions the applicability of two of the five tests that are combined in the algorithm. It further shows that the deviation of the experimental VLE data from the correlation obtained by a given model, the basis of some point-to-point tests, should not be used to evaluate the quality of these data.

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.

Automatic Abdominal Aortic Aneurysm segmentation in MR images

Abdominal Aortic Aneurism is a disease related to a weakening in the aortic wall that can cause a break in the aorta and the death. The detection of an unusual dilatation of a section of the aorta is an indicative of this disease. However, it is difficult to diagnose because it is necessary image diagnosis using computed tomography or magnetic resonance. An automatic diagnosis system would allow to analyze abdominal magnetic resonance images and to warn doctors if any anomaly is detected. We focus our research in magnetic resonance images because of the absence of ionizing radiation. Although there are proposals to identify this disease in magnetic resonance images, they need an intervention from clinicians to be precise and some of them are computationally hard. In this paper we develop a novel approach to analyze magnetic resonance abdominal images and detect the lumen and the aortic wall. The method combines different algorithms in two stages to improve the detection and the segmentation so it can be applied to similar problems with other type of images or structures. In a first stage, we use a spatial fuzzy C-means algorithm with morphological image analysis to detect and segment the lumen; and subsequently, in a second stage, we apply a graph cut algorithm to segment the aortic wall. The obtained results in the analyzed images are pretty successful obtaining an average of 79% of overlapping between the automatic segmentation provided by our method and the aortic wall identified by a medical specialist. The main impact of the proposed method is that it works in a completely automatic way with a low computational cost, which is of great significance for any expert and intelligent system.

Time to move north? CEPS Commentary, 27 May 2013

A staggering one out of every four young people is presently unemployed in Spain. And comparable numbers in Greece, Portugal and Italy are hardly more encouraging. Germany, on the other hand, enjoys a historically low youth unemployment rate of 8% and is experiencing skill shortages in some occupations. Against this background, this Commentary calls upon the European Commission to use its considerable strength and know-how in bringing partners and stakeholders together in order to facilitate the necessary infrastructure to allow better matching across borders of workers and employers. The authors point to the June European Council meeting as offering a good occasion to launch initiatives to this effect.

Whole rock analytical techniques and glas analytical techniques of silicic magmas from the South East Rift, Manus Basin

There has been much recent interest in the origin of silicic magmas at spreading centres away from any possible influence of continental crust. Here we present major and trace element data for 29 glasses (and 55 whole-rocks) sampled from a 40 km segment of the South East Rift in the Manus Basin that span the full compositional continuum from basalt to rhyolite (50-75 wt % SiO2). The glass data are accompanied by Sr-Nd-Pb, O and U-Th-Ra isotope data for selected samples. These overlap the ranges for published data from this part of the Manus Basin. Limited increases in Cl/K ratios with increasing SiO2, La-SiO2 and Yb-SiO2 relationships, and the oxygen isotope data rule out models in which the more silicic lavas result from partial melting of altered oceanic crust or altered oceanic gabbros. Rather, the data form a coherent array that is suggestive of closed-system fractional crystallization and this is well simulated by MELTS models run at 0.2 GPa and QFM (quartz-fayalite-magnetite buffer) with 1 wt % H2O, using a parental magma chosen from the basaltic glasses. Although some assimilation of altered oceanic crust or gabbro cannot be completely ruled out, there is no evidence that this plays an important role in the origin of the silicic lavas. The U-series disequilibria are dominated by 238U and 226Ra excesses that limit the timescale of differentiation to less than a few millennia. Overall, the data point to rapid evolution in relatively small magma lenses located near the base of thick oceanic crust; we speculate that this was coupled with relatively low rates of basaltic recharge. A similar model may be applicable to the generation of silicic magmas elsewhere in the ocean basins.

Modelled spatial and seasonal distribution of Blue Whiting (Micromesistius poutassou) larvae in the North-East Atlantic (1951 to 2005)

Blue whiting (Micromesistius poutassou, http://www.marinespecies.org/aphia.php?p=taxdetails&id=126439) is a small mesopelagic planktivorous gadoid found throughout the North-East Atlantic. This data contains the results of a model-based analysis of larvae captured by the Continuous Plankton Recorder (CPR) during the period 1951-2005. The observations are analysed using Generalised Additive Models (GAMs) of the the spatial, seasonal and interannual variation in the occurrence of larvae. The best fitting model is chosen using the Aikaike Information Criteria (AIC). The probability of occurrence in the continous plankton recorder is then normalised and converted to a probability distribution function in space (UTM projection Zone 28) and season (day of year). The best fitting model splits the distribution into two separate spawning grounds north and south of a dividing line at 53 N. The probability distribution is therefore normalised in these two regions (ie the space-time integral over each of the two regions is 1). The modelled outputs are on a UTM Zone 28 grid: however, for convenience, the latitude ("lat") and longitude ("lon") of each of these grid points are also included as a variable in the NetCDF file. The assignment of each grid point to either the Northern or Southern component (defined here as north/south of 53 N), is also included as a further variable ("component"). Finally, the day of year ("doy") is stored as the number of days elapsed from and included January 1 (ie doy=1 on January 1) - the year is thereafter divided into 180 grid points.

Channel Migration and Avulsion Hazards at Sunshine Point Campground, Mount Rainier National Park, Washington

In November 2006, the flood of record on the upper Nisqually River destroyed part of Sunshine Point Campground in Mount Rainier National Park, Washington. The Nisqually River migrated north and reoccupied five acres of its floodplain; Tahoma Creek partially avulsed into the west floodplain, topping banks of an undersized channel and flooding the campground. I assessed hazards to infrastructure at the old campground location, where the Park proposes to rebuild the remaining campground roads and sites. This assessment focuses on two major hazards: northward Nisqually River migration, which may reincorporate the floodplain into the river destroying infrastructure; and Tahoma Creek avulsions, which may flood the campgroud and deposit sediment burying campground infrastructure. I quantify northward migration by: estimating migration rates and changes to channel width; evaluating river occupation of the pre- and post-2006 campground; and estimating scour depths at revetments protecting the campground. I digitized the Nisqually River channels and channel centerlines from maps and images between 1955 and 2013 into a GIS, which I used to estimate migration rate and river width changes. Centerline migration rates average 9 ft/yr along the length of the Nisqually River study reach; at Sunshine Point lateral migration rates average 11 ft/yr. Maximum migration along the study reach was 19 ft/yr between 2006 and 2009. Greater than average migration rates and channel widths correspond to river confluences and include the Tahoma Creek confluence at Sunshine Point. To determine historical channel locations and the frequency that the river occupied different parts of its floodplain, I digitized the river from maps and images between 1903 and 2013. The Nisqually River flows through Sunshine Point Campground in eight out of 15 historical images. I assess scour at revetments protecting infrastructure from the Nisqually River during a 100-year recurrence interval flood using measured cross-sections. During a 100-year flood, the Nisqually River may scour up to 10 feet below the bed elevation. These scour depths can destabilize critical revetments leaving loose unconsolidated riverbanks exposed to Nisqually River flows. To determine the causes, locations, and frequency of flood hazards from Tahoma Creek avulsions, I field map avulsion channels and compare the results with imagery and channel width changes between 1955 and 2013. Mapped avulsion channels occur with swaths of dead vegetation or nascent vegetation; both dead and recent vegetation are visibly distinct from surrounding vegetation in aerial images. Times of changes to these vegetation anomalies correspond to increases in Tahoma Creek channel width. Avulsions have occurred at least three times in the study period: pre-1955, between 1979 and 1984, and in 2006. The 1984 and 2006 avulsions both occur after increases in Tahoma Creek reach averaged width. The NPS is considering two options to rebuild Sunshine Point Campground, both at the same location. The hazards posed by the Nisqually River and Tahoma Creek at Sunshine Point will affect both construction options equally. Migration hazards to the campground may be reduced by limiting the proposed campground infrastructure to an elevated ridge that has not been occupied by the Nisqually River since 1903. The hazards of damage from migration may be reduced by revetments, which were effective in preventing northward Nisqually River migration in 1959 and 1965. Tahoma Creek avulsions are related increased of Tahoma Creek reach averaged widths, which are near a 58- year maximum, and occurred during a 10-year flood in 1984. The campground may be as susceptible to flooding from avulsions during as little as a 10-year flood. A large avulsion may occur with the next significant Tahoma Creek width increase. Glacial retreat has been shown to increase debris flow activity and increase sediment delivery to Mount Rainier rivers. Increased sediment discharge has been correlated with aggradation, which will further encourage Tahoma Creek avulsions.

Pathogen-responsive expression of a putative ATP-binding cassette transporter gene conferring resistance to the diterpenoid sclareol is regulated by multiple defense signaling pathways in arabidopsis

The ATP-binding cassette (ABC) transporters are encoded by large gene families in plants. Although these proteins are potentially involved in a number of diverse plant processes, currently, very little is known about their actual functions. In this paper, through a cDNA microarray screening of anonymous cDNA clones from a subtractive library, we identified an Arabidopsis gene (AtPDR12) putatively encoding a member of the pleiotropic drug resistance (PDR) subfamily of ABC transporters. AtPDR12 displayed distinct induction profiles after inoculation of plants with compatible and incompatible fungal pathogens and treatments with salicylic acid, ethylene, or methyl jasmonate. Analysis of AtPDR12 expression in a number of Arabidopsis defense signaling mutants further revealed that salicylic acid accumulation, NPR1. function, and sensitivity to jasmonates and ethylene were all required for pathogen-responsive expression of AtPDR12. Germination assays using seeds from an AtPDR12 insertion line in the presence of sclareol resulted in lower germination rates and much stronger inhibition of root elongation in the AtPDR12 insertion line than in wild-type plants. These results suggest that AtPDR12 may be functionally related to the previously identified ABC transporters SpTUR2 and NpABC1, which transport sclareol. Our data also point to a potential role for terpenoids in the Arabidopsis defensive armory.

A composite DOP approach to excluding bottom reflectance in mapping water parameters of shallow coastal zones from TM imagery

In this paper we proposed a composite depth of penetration (DOP) approach to excluding bottom reflectance in mapping water quality parameters from Landsat thematic mapper (TM) data in the shallow coastal zone of Moreton Bay, Queensland, Australia. Three DOPs were calculated from TM1, TM2 and TM3, in conjunction with bathymetric data, at an accuracy ranging from +/-5% to +/-23%. These depths were used to segment the image into four DOP zones. Sixteen in situ water samples were collected concurrently with the recording of the satellite image. These samples were used to establish regression models for total suspended sediment (TSS) concentration and Secchi depth with respect to a particular DOP zone. Containing identical bands and their transformations for both parameters, the models are linear for TSS concentration, logarithmic for Secchi depth. Based on these models, TSS concentration and Secchi depth were mapped from the satellite image in respective DOP zones. Their mapped patterns are consistent with the in situ observed ones. Spatially, overestimation and underestimation of the parameters are restricted to localised areas but related to the absolute value of the parameters. The mapping was accomplished more accurately using multiple DOP zones than using a single zone in shallower areas. The composite DOP approach enables the mapping to be extended to areas as shallow as <3 m. (C) 2004 Elsevier Inc. All rights reserved.