An RNA interference phenotypic screen identifies a role for FGF signals in colon cancer progression

In tumor cells, stepwise oncogenic deregulation of signaling cascades induces alterations of cellular morphology and promotes the acquisition of malignant traits. Here, we identified a set of 21 genes, including FGF9, as determinants of tumor cell morphology by an RNA interference phenotypic screen in SW480 colon cancer cells. Using a panel of small molecular inhibitors, we subsequently established phenotypic effects, downstream signaling cascades, and associated gene expression signatures of FGF receptor signals. We found that inhibition of FGF signals induces epithelial cell adhesion and loss of motility in colon cancer cells. These effects are mediated via the mitogen-activated protein kinase (MAPK) and Rho GTPase cascades. In agreement with these findings, inhibition of the MEK1/2 or JNK cascades, but not of the PI3K-AKT signaling axis also induced epithelial cell morphology. Finally, we found that expression of FGF9 was strong in a subset of advanced colon cancers, and overexpression negatively correlated with patients' survival. Our functional and expression analyses suggest that FGF receptor signals can contribute to colon cancer progression.     

Qualitative and quantitative multiplexed proteomic analysis of complex yeast protein fractions that modulate the assembly of the yeast prion Sup35p

Background

The aggregation of the baker''s yeast prion Sup35p is at the origin of the transmissible [PSI⁺] trait. We and others have shown that molecular chaperones modulate Sup35p aggregation. However, other protein classes might be involved in [PSI⁺] formation.

Results

We designed a functional proteomic study that combines two techniques to identify modulators of Sup35p aggregation and describe the changes associated to [PSI⁺] formation. The first allows measuring the effect of fractionated Saccharomyces cerevisiae cytosolic extracts from [PSI⁺] and [psi⁻] yeast cells on Sup35p assembly. The second is a multiplex qualitative and quantitative comparison of protein composition of active and inactive fractions using a gel-free and label-free LC-MS approach. We identify changes in proteins involved in translation, folding, degradation, oxido-reduction and metabolic processes.

Conclusion

Our functional proteomic study provides the first inventory list of over 300 proteins that directly or indirectly affect Sup35p aggregation and [PSI⁺] formation. Our results highlight the complexity of the cellular changes accompanying [PSI⁺] formation and pave the way for in vitro studies aimed to document the effect of individual and/or combinations of proteins identified here, susceptible of affecting Sup35p assembly.     

Some secrets of fluorescent proteins: distinct bleaching in various mounting fluids and photoactivation of cyan fluorescent proteins at YFP-excitation

Background

The use of spectrally distinct variants of green fluorescent protein (GFP) such as cyan or yellow mutants (CFP and YFP, respectively) is very common in all different fields of life sciences, e.g. for marking specific proteins or cells or to determine protein interactions. In the latter case, the quantum physical phenomenon of fluorescence resonance energy transfer (FRET) is exploited by specific microscopy techniques to visualize proximity of proteins.

Methodology/Principal Findings

When we applied a commonly used FRET microscopy technique - the increase in donor (CFP)-fluorescence after bleaching of acceptor fluorophores (YFP), we obtained good signals in live cells, but very weak signals for the same samples after fixation and mounting in commercial microscopy mounting fluids. This observation could be traced back to much faster bleaching of CFP in these mounting media. Strikingly, the opposite effect of the mounting fluid was observed for YFP and also for other proteins such as Cerulean, TFP or Venus. The changes in photostability of CFP and YFP were not caused by the fixation but directly dependent on the mounting fluid. Furthermore we made the interesting observation that the CFP-fluorescence intensity increases by about 10 - 15% after illumination at the YFP-excitation wavelength – a phenomenon, which was also observed for Cerulean. This photoactivation of cyan fluorescent proteins at the YFP-excitation can cause false-positive signals in the FRET-microscopy technique that is based on bleaching of a yellow FRET acceptor.

Conclusions/Significance

Our results show that photostability of fluorescent proteins differs significantly for various media and that CFP bleaches significantly faster in commercial mounting fluids, while the opposite is observed for YFP and some other proteins. Moreover, we show that the FRET microscopy technique that is based on bleaching of the YFP is prone to artifacts due to photoactivation of cyan fluorescent proteins under these conditions.     

Low digit ratio 2D:4D in alcohol dependent patients

The ratio of the lengths of the second and fourth finger (2D∶4D) has been described as reflecting the degree of prenatal androgen exposure in humans. 2D∶4D is smaller for males than females and is associated with traits such as left-handedness, physical aggression, attention-deficit-hyperactivity disorder and a genetic polymorphism of the androgen receptor. All of these traits are known to be correlated to the vulnerability for alcohol dependency. We therefore hypothesized low 2D∶4D in patients with alcohol dependency. In the present study on 131 patients suffering from alcohol dependency and 185 healthy volunteers, we found that alcohol dependent patients had smaller 2D∶4D ratios compared to controls with preserved sexual dimorphism but with reduced right-left differences. The detection of alcohol dependency based on 2D∶4D ratios was most accurate using the right hand of males (ROC-analysis: AUC 0.725, sensitivity 0.667, specificity 0.723). These findings provide novel insights into the role of prenatal androgen exposure in the development of alcohol dependency and for the use of 2D∶4D as a possible trait marker in identifying patients with alcohol dependency.     

Re-structuring of marine communities exposed to environmental change: a global study on the interactive effects of species and functional richness

Species richness is the most commonly used but controversial biodiversity metric in studies on aspects of community stability such as structural composition or productivity. The apparent ambiguity of theoretical and experimental findings may in part be due to experimental shortcomings and/or heterogeneity of scales and methods in earlier studies. This has led to an urgent call for improved and more realistic experiments. In a series of experiments replicated at a global scale we translocated several hundred marine hard bottom communities to new environments simulating a rapid but moderate environmental change. Subsequently, we measured their rate of compositional change (re-structuring) which in the great majority of cases represented a compositional convergence towards local communities. Re-structuring is driven by mortality of community components (original species) and establishment of new species in the changed environmental context. The rate of this re-structuring was then related to various system properties. We show that availability of free substratum relates negatively while taxon richness relates positively to structural persistence (i.e., no or slow re-structuring). Thus, when faced with environmental change, taxon-rich communities retain their original composition longer than taxon-poor communities. The effect of taxon richness, however, interacts with another aspect of diversity, functional richness. Indeed, taxon richness relates positively to persistence in functionally depauperate communities, but not in functionally diverse communities. The interaction between taxonomic and functional diversity with regard to the behaviour of communities exposed to environmental stress may help understand some of the seemingly contrasting findings of past research.     

Basidial development, spindle pole body, septal pore, and host-parasite-interaction in Ustilago esculenta

Smut spore-germination, spindle pole bodies, septal pores, and host-parasite interactions have been investigated in Ustilago esculenta . The species is compared with other Ustilago species parasitizing on grasses. The taxonomy of U. esculenta and the Yeniaceae is discussed.     

Termite (Insecta: Isoptera) Species Composition in a Primary Rain Forest and Agroforests in Central Amazonia

Termites play important roles in organic matter decomposition, nutrient cycling, and soil structure in tropical rain forests. When forests are replaced by agriculture, termite species richness, abundance, and function often decline. We compared the termite assemblage of a primary forest site with that of a low plant diversity, palm-based agroforest (five plant species) and a high plant diversity, home-garden agroforest (10 plant species) using a rapid biodiversity assessment protocol. In comparing the primary forest termite species composition to previously published studies, we found soil feeders and the Apicotermitinae to be more dominant than previously reported in Amazonia. Thirty percent of the species belonged to the Apicotermitinae, and an unusually high percentage (57%) of species were soil feeders. Unexpectedly, the palm-based agroforest, despite its lower plant diversity, was closer to primary forest in termite species composition, rate of species accumulation, and proportions of species in taxonomic and functional classes than was the home-garden agroforest. This suggests that particular plant attributes may better determine the termite assemblage than plant diversity alone in these agroecosystems. Unlike other agroecosystems reported in the literature, Apicotermitinae and soil feeders were proportionally more abundant in these agroforests than in primary forest. The ability of agroforests to support populations of soil feeders has a potentially positive effect on soil fertility in these agroecosystems; insomuch as feeding guild is a proxy for function, these closed-canopy agroforests may be able to sustain the same termite-mediated functions as primary forest.     

Die wirkung von Aphidenstichen auf pflanzliche Zellen

Zusammenfassung Die Aphiden rufen durch den Einstich bei ihren Wirtspflanzen Reaktionen mannigfaltiger Art hervor. So sind uns Auswirkungen auf den Wasserhaushalt und den Stoffwechsel pflanzlicher Gewebe bekannt, die auf die Einwirkung pflanzensaugender Insekten zurückzuführen sind. Diese Reaktionen werden durch das Zusammenwirken der mechanischen und chemischen Komponente des Stiches ausgelöst.

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Summary The result of puncturing plant-cells by aphids was demonstrated as follows: The aphids, Myzus ascalonicus Donc., were allowed to pierce detached bulb scales of Allium cepa, in green light, and were then anaesthetized with CO₂. The stylets were then severed using iridectomy scissors (Fig. 1). The epidermis was dissected off, mounted on a slide and observed under a phase-contrast microscope. The point of injection remained marked by the stylets which stuck in the epidermis. Intercellular and extracellular puncturing could be distinguished.It was possible to demonstrate a shortening of the time deplasmolysis in the cells lying close to the injection, and also an increase of streaming in the cell plasma. In cells which had been pierced directly, a saliva-sheath was formed (Fig. 2 and 3). The extent of the effect of the saliva was studied using radioactive aphids. After these radioactive aphids had pierced the epidermis the part containing the stylets was mounted on a slide. This preparation was kept in the dark for 14 days, with a special film (Kodak, Scientific Plates, Auto radiographic) covering it. The film was developed and fixed, and a preparation was thus obtained with the developed film covering the epidermis. Darkened spots on the film showed the parts of the cells which had been made radioactive by the saliva.Very fine needles made by galvanic etching were also stuck into the cells, to demonstrate the mechanical effects of aphid punctures. This mechanical stimulus by needles only a few in diameter caused streaming in the cell plasma and a shortening of deplasmolysis time. It is clear that the importance of these mechanical effects must not be underestimated. The increased plasma-streaming was apparently caused by amino-acids in aphid's saliva, and also by the amino-acids produced from proteins when the cells were injured. Kloft (1956) found 4 amino-acids in the saliva of M. ascalonicus. The effect of these amino-acids on deplasmolysis-time is being examined, but as yet no effect has been detected.Finally, when fine glass-capillaries are used to imitate piercing by plantsucking insects and when the glass-capillaries contain amino-acids, deplasmolysis-time is reduced.