Melanoma RBPome identification reveals PDIA6 as an unconventional RNA-binding protein involved in metastasis

RNA-binding proteins (RBPs) have been relatively overlooked in cancer research despite their contribution to virtually every cancer hallmark. Here, we use RNA interactome capture (RIC) to characterize the melanoma RBPome and uncover novel RBPs involved in melanoma progression. Comparison of RIC profiles of a non-tumoral versus a metastatic cell line revealed prevalent changes in RNA-binding capacities that were not associated with changes in RBP levels. Extensive functional validation of a selected group of 24 RBPs using five different in vitro assays unveiled unanticipated roles of RBPs in melanoma malignancy. As proof-of-principle we focused on PDIA6, an ER-lumen chaperone that displayed a novel RNA-binding activity. We show that PDIA6 is involved in metastatic progression, map its RNA-binding domain, and find that RNA binding is required for PDIA6 tumorigenic properties. These results exemplify how RIC technologies can be harnessed to uncover novel vulnerabilities of cancer cells.     

Orthogonal projections to latent structures as a strategy for microarray data normalization

Background  

During generation of microarray data, various forms of systematic biases are frequently introduced which limits accuracy and precision of the results. In order to properly estimate biological effects, these biases must be identified and discarded.     

Renewable resources in the chemical industry – Breaking away from oil?

Rising prices for fossil-based raw materials suggest that sooner or later renewable raw materials will, in principle, become economically viable. This paper examines this widespread paradigm. Price linkages like those seen for decades particularly in connection with petrochemical raw materials are now increasingly affecting renewable raw materials. The main driving force is the competing utilisation as an energy source because both fossil-based and renewable raw materials are used primarily for heat, electrical power and mobility. As a result, prices are determined by energy utilisation. Simple observations show how prices for renewable carbon sources are becoming linked to the crude oil price. Whether the application calls for sugar, starch, virgin oils or lignocellulose, the price for the raw material rises with the oil price. Consequently, expectations regarding price trends for fossil-based energy sources can also be utilised for the valuation of alternative processes. However, this seriously calls into question the assumption that a rising crude oil price will favour the economic viability of alternative products and processes based on renewable raw materials. Conversely, it follows that these products and processes must demonstrate economic viability today. Especially in connection with new approaches in white biotechnology, it is evident that, under realistic assumptions, particularly in terms of achievable yields and the optimisation potential of the underlying processes, the route to utilisation is economically viable. This makes the paradigm mentioned at the outset at least very questionable.     

The Role of Specific Tomato Volatiles in Tomato-Whitefly Interaction

Bemisia tabaci (whitefly) infestations and the subsequent transfer of viruses are the cause of severe losses in crop production and horticultural practice. To improve biological control of B. tabaci, we investigated repellent properties of plant-produced semiochemicals. The mix of headspace volatiles, collected from naturally repellent wild tomato accessions, influenced B. tabaci initial choice behavior, indicating a role for plant semiochemicals in locating host plants. A collection of wild tomato accessions and introgression lines (Solanum pennellii LA716 × Solanum lycopersicum ‘Moneyberg’) were extensively screened for attractiveness to B. tabaci, and their headspace profiles were determined by means of gas chromatography-mass spectrometry. Correlation analysis revealed that several terpenoids were putatively involved in tomato-whitefly interactions. Several of these candidate compounds conferred repellence to otherwise attractive tomato plants when applied to the plant''s branches on paper cards. The sesquiterpenes zingiberene and curcumene and the monoterpenes p-cymene, α-terpinene, and α-phellandrene had the strongest effects in free-choice bioassays. These terpenes also elicited a response of receptors on the insect''s antennae as determined by electroantennography. Conversely, the monoterpene β-myrcene showed no activity in both assays. B. tabaci apparently uses, besides visual cues, specific plant volatile cues for the initial selection of a host. Altering whitefly choice behavior by manipulation of the terpenoid composition of the host headspace may therefore be feasible.During the last decades, a worldwide spread of the pest insects Bemisia tabaci (Gennadius) and greenhouse whitefly (Trialeurodes vaporariorum) has led to local devastation of vegetable and ornamental crops, resulting in large economic losses. The damage whiteflies cause by their feeding behavior, such as affected biochemistry and development (for review, see Inbar and Gerling, 2008), is far exceeded by the secondary, indirect crop losses due to virus transmission. Specifically B. tabaci outbreaks are associated with the emergence of viruses for which they serve as vectors (Polston and Anderson, 1997). B. tabaci is capable of transmitting >100 different virus species of which the majority belong to the genus Begomovirus, such as Tomato yellow leaf curl virus, Tomato mottle virus (Jones, 2003), and African cassava mosaic virus (Maruthi et al., 2001). Damage caused by virus infection ranges from mild symptoms, such as leaf discolorations, to overall yield reduction, severe fruit necrosis, flower and fruit abortions, and plant death. Viral diseases are particularly severe since no chemical control is available and good sources of virus resistance for interspecific crossing are not always available (Maruthi et al., 2003). To date, only a limited number of virus resistance genes have been identified, and due to high mutation rates, viruses rapidly evolve (Drake and Holland, 1999; García-Andrés et al., 2006) and break monogenic resistances. Herbivores, such as whiteflies and thrips, can apparently benefit from transmitting viruses (Medeiros et al., 2004; Jiu et al., 2007; Belliure et al., 2008).B. tabaci was originally restricted to subtropical regions and greenhouses. However, the new and extremely invasive B and Q biotypes have the ability to rapidly adapt to more temperate zones and new host species (Jones, 2003; Wan et al., 2008). To date, the main control strategy for many crops is the application of insecticides, though effective spraying is complicated because of the insect''s preference for the abaxial side of the leaf (Simmons, 1994). Moreover, B. tabaci is difficult to control chemically due to emerging resistance to active ingredients (Horowitz et al., 2005). A new biological control agent, the phytoseiid predator Typhlodromips swirskii, has only been successful on plants without trichomes in closed greenhouses (Nomikou et al., 2002). The root-knot nematode resistance gene Mi1.2, which confers partial resistance to B. tabaci (Nombela et al., 2003), is widely used in modern tomato (Solanum spp.) varieties but is not sufficient to provide adequate protection against whitefly infestations.During insect host selection, orientation, and landing, both visual and olfactory cues play a predominant role (Visser, 1988). Color is an important factor in host-plant selection, and it was shown that B. tabaci reacts to blue-UV and yellow wavelengths (Van Lenteren and Noldus, 1990). The olfactory stimuli associated with the host plant initiate host targeting, whereas visual cues improve the accuracy of landing. In the initial phase of host targeting, olfaction may cause a positive chemotactic response, i.e. a flight up an odor gradient. Plant odor specificity might be achieved by a particular ratio of constituent volatiles (Bruce et al., 2005a). In the case of whiteflies, the role of olfaction in attraction or repellence has not received much prior attention. After host contact, B. tabaci evaluates host plant quality by labial dabbing and probing using piercing mouthparts. By probing, persistent viruses are transmitted via the insects'' salivary glands and mouthparts (Ghanim et al., 1998; Rosell et al., 1999). Therefore, to avoid virus transmission by B. tabaci, probing should be prevented.Volatile organic compounds released by plants can act as semiochemicals. They play an important role in enabling insects to recognize host plants from a distance (Schütz et al., 1997; Bruce et al., 2005a) or in attracting predators and parasitoids upon herbivory (De Moraes et al., 1998; Van Poecke and Dicke, 2002; Kappers et al., 2005). Moreover, they can play a role in the direct defense against herbivores and pathogens (Kessler and Baldwin, 2001; Shiojiri et al., 2006). A large number of different plant volatiles, with numerous ecological roles, have been identified so far (Sacchettini and Poulter, 1997; Pichersky et al., 2006). The largest class of plant volatiles is derived from the isoprenoid or terpenoid pathway. Solanaceous plants, like tomato, often make use of these terpenes for the defense against herbivores (Snyder et al., 1993; Kennedy, 2003). Some terpenes have been shown to exhibit repellent properties to insects (Peterson et al., 2002; Birkett et al., 2004; Terry et al., 2007). These plant-produced semiochemicals can potentially be used as insect repellents of natural origin, thus providing an alternative to the use of pesticides (Peterson and Coats, 2001). Engineering terpene emission to make crop plants more attractive to herbivore enemies has already been shown to be feasible (Degenhardt et al., 2003; Kappers et al., 2005; Schnee et al., 2006).The aim of this study is to identify the role of plant volatiles in the B. tabaci-tomato host interaction and to identify the terpenes that cause repellence of a selection of wild tomato accessions. The potential of several terpenes as repellent olfactory cues in B. tabaci host-preference behavior has been assessed in behavioral studies and through electroantennography (EAG).     

Set of instruments for innovative, safe and sterile sigmoid access for natural-orifice transluminal endoscopic surgery / Ein Instrumentenset für den innovativen, sicheren und sterilen sigmoidalen Zugang für die transluminale endoskopische Chirurgie über natürliche K?rper?ffnungen

Abstract One of the current main challenges in transluminal surgery is in obtaining sterile and secure access to the peritoneal cavity. Since the transgastric approach has not fulfilled these requirements up to now, a new transcolonic surgical approach was developed to achieve these objectives and enhance the potential of transluminal surgery. A new set of instruments comprising an endoscopic trocar, a flexible obturator and a modified transanal endoscopic microsurgery device was designed to permit sterile sigmoid access for transcolonic surgery. The set of instruments has already been successfully tested in an experimental in vivo survival study that confirmed safety and sterility as objectives during surgical intervention. The suitability of the instruments for use in the human anatomy was confirmed by a cadaveric study.     

Regulation of nuclear–cytoplasmic shuttling and function of Family with sequence similarity 13, member A (Fam13a), by B56-containing PP2As and Akt

Recent genome-wide association studies reveal that the FAM13A gene is associated with human lung function and a variety of lung diseases, including chronic obstructive pulmonary disease, asthma, lung cancer, and pulmonary fibrosis. The biological functions of Fam13a, however, have not been studied. In an effort to identify novel substrates of B56-containing PP2As, we found that B56-containing PP2As and Akt act antagonistically to control reversible phosphorylation of Fam13a on Ser-322. We show that Ser-322 phosphorylation acts as a molecular switch to control the subcellular distribution of Fam13a. Fam13a shuttles between the nucleus and cytoplasm. When Ser-322 is phosphorylated by Akt, the binding between Fam13a and 14-3-3 is enhanced, leading to cytoplasmic sequestration of Fam13a. B56-containing PP2As dephosphorylate phospho–Ser-322 and promote nuclear localization of Fam13a. We generated Fam13a-knockout mice. Fam13a-mutant mice are viable and healthy, indicating that Fam13a is dispensable for embryonic development and physiological functions in adult animals. Intriguingly, Fam13a has the ability to activate the Wnt pathway. Although Wnt signaling remains largely normal in Fam13a-knockout lungs, depletion of Fam13a in human lung cancer cells causes an obvious reduction in Wnt signaling activity. Our work provides important clues to elucidating the mechanism by which Fam13a may contribute to human lung diseases.     

The recent impact of solid-phase synthesis on medicinally relevant benzoannelated nitrogen heterocycles

Benzoannelated heterocycles such as benzodiazepines and indoles can be prepared efficiently through cyclization on solid supports, although no single approach is currently universal for the preparation of all benzoannelated N-heterocycle chemistries. In this review, a number of synthetic strategies for the generation of benzoannelated nitrogen heterocycles using resin-bound substrates have been described. Classical heterocycle forming reactions such as the Fischer indole, the Bischler-Napieralski tetrahydroisoquinoline, the Pictet-Spengler tetrahydro-beta-carboline, the Tsuge, the Nenitzescu and the Richter cinnoline reaction are presented. In addition, the Heck, Sonogashira, Wittig, Diels-Alder, and olefin metathesis reactions have been also used. Multicomponent reactions such as the Grieco three-component assembly have been exploited for the synthesis of heterocycles. Cyclative cleavage from the solid support is particularly suitable for the synthesis of heterocycles while particular emphasis has been focused on the synthesis of libraries and the use of combinatorial chemistry techniques. In addition, the most relevant pharmacological properties of benzoannelated nitrogen heterocycles are included.     

Parameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc

ObjectivesWe analysed the impact of different parameters on genotypic tropism testing related to clinical outcome prediction in 108 patients on maraviroc (MVC) treatment.Methods87 RNA and 60 DNA samples were used. The viral tropism was predicted using the geno2pheno_[coreceptor] and T-CUP tools with FPR cut-offs ranging from 1%-20%. Additionally, 27 RNA and 28 DNA samples were analysed in triplicate, 43 samples with the ESTA assay and 45 with next-generation sequencing. The influence of the genotypic susceptibility score (GSS) and 16 MVC-resistance mutations on clinical outcome was also studied.ResultsConcordance between single-amplification testing compared to ESTA and to NGS was in the order of 80%. Concordance with NGS was higher at lower FPR cut-offs. Detection of baseline R5 viruses in RNA and DNA samples by all methods significantly correlated with treatment success, even with FPR cut-offs of 3.75%-7.5%. Triple amplification did not improve the prediction value but reduced the number of patients eligible for MVC. No influence of the GSS or MVC-resistance mutations but adherence to treatment, on the clinical outcome was detected.ConclusionsProviral DNA is valid to select candidates for MVC treatment. FPR cut-offs of 5%-7.5% and single amplification from RNA or DNA would assure a safe administration of MVC without excluding many patients who could benefit from this drug. In addition, the new prediction system T-CUP produced reliable results.