Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID)

Proximity-dependent trans-biotinylation by the Escherichia coli biotin ligase BirA mutant R118G (BirA*) allows stringent streptavidin affinity purification of proximal proteins. This so-called BioID method provides an alternative to the widely used co-immunoprecipitation (co-IP) to identify protein-protein interactions. Here, we used BioID, on its own and combined with co-IP, to identify proteins involved in nonsense-mediated mRNA decay (NMD), a post-transcriptional mRNA turnover pathway that targets mRNAs that fail to terminate translation properly. In particular, we expressed BirA* fused to the well characterized NMD factors UPF1, UPF2 and SMG5 and detected by liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) the streptavidin-purified biotinylated proteins. While the identified already known interactors confirmed the usefulness of BioID, we also found new potentially important interactors that have escaped previous detection by co-IP, presumably because they associate only weakly and/or very transiently with the NMD machinery. Our results suggest that SMG5 only transiently contacts the UPF1-UPF2-UPF3 complex and that it provides a physical link to the decapping complex. In addition, BioID revealed among others CRKL and EIF4A2 as putative novel transient interactors with NMD factors, but whether or not they have a function in NMD remains to be elucidated.

Hydrolytic behaviour of mono-and dithiolato-bridged dinuclear arene ruthenium complexes and their interactions with biological ligands

The hydrolysis and the reactivity of two dinuclear p-cymene ruthenium monothiolato complexes, [(η6-p-MeC6H4Pri)2Ru2Cl2(µ-Cl)(µ-S-m-9-B10C2H11)] (1) and [(η6-p-MeC6H4Pri)2¬Ru2Cl2(µ-Cl)¬(µ-S¬CH2-p-C6H4-NO2)] (2), and of two dinuclear p-cymene ruthenium dithiolato complexes, [(η6-p-MeC6H4Pri)2Ru2(µ-SCH2CH2Ph)2Cl2] (3) and [(η6-p-Me¬C6H4¬Pri)2¬Ru2(S¬CH2¬C6H4-p-O¬Me)2¬Cl2] (4) towards amino acids, nucleotides, and a single-stranded DNA dodecamer were studied using NMR and mass spectrometry. In aqueous solutions at 37 °C, the monothiolato com¬plexes 1 and 2 undergo rapid hydrolysis, irrespective of the pH value, the predominant species in D2O/acetone-d6 solution at equilibrium being the neutral hydroxo complexes [(η6-p-Me¬C6H4¬Pri)2Ru2(OD)2(µ-OD)(µ-SR)]. The dithiolato complexes 3 and 4 are stable in water under acidic conditions, but undergo slow hydrolysis under neutral and basic conditions. In both cases, the cationic hydroxo complexes [(η6-p-MeC6H4Pri)2Ru2(µ-SR)2¬(OD)¬(CD3CN)]+ are the only spe¬cies observed in D2O/CD3CN at equilibrium. Surprisingly, no adducts are observed upon addition of an excess of L-methionine or L-histidine to the aqueous solutions of the complexes. Upon addition of an excess of L-cysteine, on the other hand, 1 and 2 form the unusual cationic trithiolato complexes [(η6-p-MeC6H4Pri)2¬Ru2{µ-SCH2CH(NH2)COOH}2(µ-SR)]+ containing two bridging cysteinato li¬gands, while 3 and 4 yield cationic trithiolato complexes [(η6-p-MeC6H4Pri)2Ru2[µ-SCH2CH¬(NH2)COOH](µ-SR)2]+ containing one bridging cysteinato ligand. A representative of catio¬nic trithiolato complexes containing a cysteinato bridge of this type, [(η6-p-MeC6H4Pri)2¬Ru2[µ-S¬CH2CH(NH2)COOH](µ-SCH2-p-C6H4-But)2]+ (6) could be synthesised from the di¬thiolato complex [(η6-p-Me¬C6H4¬Pri)2-Ru2(S¬CH2¬C6H4-p-But)2Cl2] (5), isolated as the tetra¬fluo¬ro¬borate salt and fully characterised. Moreover, the mono- and dithiolato complexes 1 - 4 are inert toward nucleotides and DNA, suggesting that DNA is not a target of cytotoxic thiolato-bridged arene ruthenium complexes. In contrast to the trithiolato complexes, monothiolato and dithio¬lato complexes hydrolyse and react with L-cysteine. These results may have im¬portant implications for the mode of action of thiolato-bridged dinuclear arene ruthenium drug candidates, and suggest that their modes of action are different to those of other arene ruthenium complexes.

Cosmic-ray exposure ages of pallasites

We analyzed cosmogenic nuclides in metal and/or silicate (primarily olivine) separated from the main-group pallasites Admire, Ahumada, Albin, Brahin, Brenham, Esquel, Finmarken, Glorieta Mountain, Huckitta, Imilac, Krasnojarsk, Marjalahti, Molong, Seymchan, South Bend, Springwater, and Thiel Mountains and from Eagle Station. The metal separates contained an olivine fraction which although small, <1 wt% in most cases, nonetheless contributes significantly to the budgets of some nuclides (e.g., up to 35% for Ne-21 and Al-26). A correction for olivine is therefore essential and was made using model calculations and/or empirical relations for the production rates of cosmogenic nuclides in iron meteoroids and/or measured elemental concentrations. Cosmic-ray exposure (CRE) ages for the metal phases of the main-group pallasites range from 7 to 180 Ma, but many of the ages cluster around a central peak near 100 Ma. These CRE ages suggest that the parent body of the main-group pallasites underwent a major break-up that produced most of the meteorites analyzed. The CRE age distribution for the pallasites overlaps only a small fraction of the distribution for the IIIAB iron meteorites. Most pallasites and IIIAB irons originated in different collisions, probably on different parent bodies; a few IIIABs and pallasites may have come out of the same collision but a firm conclusion requires further study. CRE ages calculated from noble gas and radionuclide data of the metal fraction are higher on average than the Ne-21 exposure ages obtained for the olivine samples. As the metal and olivine fractions were taken in most cases from different specimens, the depth-dependency of the production rate ratio Be-10/Ne-21 in metal, not accounted for in our calculations, may explain the difference.

Loss of activator protein-2alpha results in overexpression of the thrombin receptor and correlates with the malignant phenotype of human melanoma

Increasing evidence demonstrates that the thrombin receptor (protease activated receptor-1, PAR-1) plays a major role in tumor invasion and contributes to the metastatic phenotype of human melanoma. We demonstrate that the metastatic potential of human melanoma cells correlates with overexpression of PAR-1. The promoter of the PAR-1 gene contains multiple putative AP-2 and Sp1 consensus elements. We provide evidence that an inverse correlation exists between the expression of AP-2 and the expression of PAR-1 in human melanoma cells. Re-expression of AP-2 in WM266-4 melanoma cells (AP-2 negative) resulted in decreased mRNA and protein expression of PAR-1 and significantly reduced the tumor potential in nude mice. ChIP analysis of the PAR-1 promoter regions bp −365 to −329 (complex 1) and bp −206 to −180 (complex 2) demonstrates that in metastatic cells Sp1 is predominantly binding to the PAR-1 promoter, while in nonmetastatic cells AP-2 is bound. In vitro analysis of complex 1 demonstrates that AP-2 and Sp1 bind to this region in a mutually exclusive manner. Transfection experiments with full-length and progressive deletions of the PAR-1 promoter luciferase constructs demonstrated that metastatic cells had increased promoter activity compared to low and nonmetastatic melanoma cells. Our data shows that exogenous AP-2 expression decreased promoter activity, while transient expression of Sp1 further activated expression of the reporter gene. Mutational analysis of complex 1 within PAR-1 luciferase constructs further demonstrates that the regulation of PAR-1 is mediated through interactions with AP-2 and Sp1. Moreover, loss of AP-2 in metastatic cells alters the AP-2 to Sp1 ratio and DNA-binding activity resulting in overexpression of PAR-1. In addition, we evaluated the expression of AP-2 and PAR-1 utilizing a tissue microarray of 93 melanocytic lesions spanning from benign nevi to melanoma metastasis. We report loss of AP-2 expression in malignant tumors compared to benign tissue while PAR-1 was expressed more often in metastatic melanoma cells than in benign melanocytes. We propose that loss of AP-2 results in increased expression of PAR-1, which in turn results in upregulation of gene products that contribute to the metastatic phenotype of melanoma. ^

Dynamic Stock Market Interactions between the Canadian, Mexican, and the United States Markets: The NAFTA Experience

This paper explores the dynamic linkages that portray different facets of the joint probability distribution of stock market returns in NAFTA (i.e., Canada, Mexico, and the US). Our examination of interactions of the NAFTA stock markets considers three issues. First, we examine the long-run relationship between the three markets, using cointegration techniques. Second, we evaluate the dynamic relationships between the three markets, using impulse-response analysis. Finally, we explore the volatility transmission process between the three markets, using a variety of multivariate GARCH models. Our results also exhibit significant volatility transmission between the second moments of the NAFTA stock markets, albeit not homogenous. The magnitude and trend of the conditional correlations indicate that in the last few years, the Mexican stock market exhibited a tendency toward increased integration with the US market. Finally, we do note that evidence exists that the Peso and Asian financial crises as well as the stock-market crash in the US affect the return and volatility time-series relationships.

The public health applications of law enforcement medical direction: A practical experience with the Dallas Police Department

In 2008, 132 law enforcement officers were killed in the line of duty in The United States. Additionally, some have explored both the public health implications of interactions with law enforcement as well as the potential benefits of the use of law enforcement officers as public health and emergency healthcare providers. By virtue of these novel analyses and techniques, professional medical direction of the emerging specialty of law enforcement medicine is needed. This paper, an analysis of law enforcement medical direction through a look at the Dallas Police Medical Direction Program, seeks to examine origins of law enforcement medicine through a comprehensive literature review, as well as begin to define to core competencies of law enforcement medical direction. ^ The unique intersection of public health, medicine and law enforcement, and the subsequent specialty that is developing to manage this interface, is in its relative infancy. An analysis of this nature is in order to begin to lay down the foundations necessary for future study and improvements in the field. ^

Molecular interactions of the central conserved domain of p53

p53 mutations are the most commonly observed genetic alterations in human cancers to date. A majority of these point mutations cluster in four evolutionarily conserved domains spanning amino acids 100-300. This region of p53 has been called its central conserved, or conformational domain. This domain of p53 is also targeted by the SV40 T antigen. Mutation, as well as interaction with SV40 T antigen results in inactivation of p53. We hypothesized that mutations and SV40 T antigen disrupt p53 function by interfering with the molecular interactions of the central conserved domain. Using a chimeric protein consisting of the central conserved domain of wild-type p53 (amino acids 115-295) and a protein A affinity tail, we isolated several cellular proteins that interact specifically with this domain of p53. These proteins range in size from 30K to 90K M$\rm\sb{r}.$ We also employed the p53 fusion protein to demonstrate that the central conserved domain of p53 possesses sequence-specific DNA-binding activity. Interestingly, the cellular proteins binding to the central conserved domain of p53 enhance the sequence-specific DNA-binding activity of full length p53. Partial purification of the individual proteins binding to the conformational domain of p53 by utilizing a sodium chloride step-gradient enabled further characterization of two proteins: (1) a 42K M$\rm\sb{r}$ protein that eluted at 0.5M NaCl, and bound DNA nonspecifically, and (2) a 35K M$\rm\sb{r}$ protein eluting into the 1.0M NaCl fraction, capable of enhancing the sequence-specific DNA-binding activity of p53. In order to determine the physiologic relevance of the molecular interactions of the conformational domain of p53, we examined the biochemical processes underlying the TNF-$\alpha$ mediated growth suppression of the NSCLC cell line H460. While growth suppression was accompanied by enhanced sequence-specific p53-DNA binding activity in TNF-$\alpha$ treated H460 nuclei, there was no increase in p53 protein levels. Furthermore, p35 was upregulated in TNF-$\alpha$ treated H460 cells, suggesting that the enhanced p53-DNA binding seen in these cells may be mediated by p35. Our studies define two novel interactions involving the central conserved domain of p53 that appear to be functionally relevant: (1) sequence-specific DNA-binding, and (2) interaction with other cellular proteins. ^

Antagonistic interactions between the african weaver ant Oecophylla longinoda and the parasitoid Anagyrus pseudococci potentially limits suppression of the invasive mealybug Rastrococcus iceryoides

The ant Oecophylla longinoda Latreille forms a trophobiotic relationship with the invasive mealybug Rastrococus iceryoides Green and promotes the latter's infestations to unacceptable levels in the presence of their natural enemies. In this regard, the antagonistic interactions between the ant and the parasitoid Anagyrus pseudococci Girault were assessed under laboratory conditions. The percentage of parasitism of R. iceryoides by A. pseudococci was significantly higher on "ant-excluded" treatments (86.6% ± 1.27%) compared to "ant-tended" treatments (51.4% ± 4.13%). The low female-biased sex-ratio observed in the "ant-tended" treatment can be attributed to ants' interference during the oviposition phase, which disrupted parasitoids' ability to fertilize eggs. The mean foraging time, host handling time and number of successful oviposition in "ant-excluded" treatment were significantly higher compared to "ant-tended" treatments. When ant workers were allowed access to sterilized sand grains, mummified and unmummified R. iceryoides, they selectively removed the mummified mealybugs, indicating that they recognized the mummies as potential foods (1.2 ± 0.46 to 7.8 ± 1.17 mummies at 10 min intervals for 2 h). Percentage emergence from mummified R. iceryoides removed by the ants was significantly lower compared to emergence from mummies not exposed to ants. Although, host seeking parasitoids frequently evaded attacks, some were killed by the foraging ant workers (2.0 ± 0.38 to 6.0 ± 0.88 at 10 min intervals for 2 h). These results suggest for the first time that the presence of O. longinoda has a detrimental effect on the abundance, reproductive success and possibly oviposition strategy of female parasitoids, which might be a delimiting factor in field conditions if both natural enemies are to be recommended for use within the same agro-ecosystem.

Three time-slice simulations of the Eemian (eem), the mid-Holocene (hol), and a pre-industrial (pri) control run with the coupled atmosphere-ocean-model ECHAM5/MPI-OM

Orbital forcing does not only exert direct insolation effects, but also alters climate indirectly through feedback mechanisms that modify atmosphere and ocean dynamics and meridional heat and moisture transfers. We investigate the regional effects of these changes by detailed analysis of atmosphere and ocean circulation and heat transports in a coupled atmosphere-ocean-sea ice-biosphere general circulation model (ECHAM5/JSBACH/MPI-OM). We perform long term quasi equilibrium simulations under pre-industrial, mid-Holocene (6000 years before present - yBP), and Eemian (125 000 yBP) orbital boundary conditions. Compared to pre-industrial climate, Eemian and Holocene temperatures show generally warmer conditions at higher and cooler conditions at lower latitudes. Changes in sea-ice cover, ocean heat transports, and atmospheric circulation patterns lead to pronounced regional heterogeneity. Over Europe, the warming is most pronounced over the north-eastern part in accordance with recent reconstructions for the Holocene. We attribute this warming to enhanced ocean circulation in the Nordic Seas and enhanced ocean-atmosphere heat flux over the Barents Shelf in conduction with retreat of sea ice and intensified winter storm tracks over northern Europe.

Discovery of τ Neutrino Appearance in the CNGS Neutrino Beam with the OPERA Experiment

The OPERA experiment was designed to search for νµ → ντ oscillations in appearance mode, i.e. by detecting the τ leptons produced in charged current ντ interactions. The experiment took data from 2008 to 2012 in the CERN Neutrinos to Gran Sasso beam. The observation of the νµ → ντ appearance, achieved with four candidate events in a subsample of the data, was previously reported. In this Letter, a fifth ντ candidate event, found in an enlarged data sample, is described. Together with a further reduction of the expected background, the candidate events detected so far allow us to assess the discovery of νµ → ντ oscillations in appearance mode with a significance larger than 5 σ.

Measurement of the electron neutrino charged-current interaction rate on water with the T2K ND280 π0 detector

This paper presents a measurement of the charged current interaction rate of the electron neutrino beam component of the beam above 1.5 GeV using the large fiducial mass of the T2K π0 detector. The predominant portion of the νe flux (∼85%) at these energies comes from kaon decays. The measured ratio of the observed beam interaction rate to the predicted rate in the detector with water targets filled is 0.89 ± 0.08 (stat.) ± 0.11 (sys.), and with the water targets emptied is 0.90 ± 0.09 (stat.) ± 0.13 (sys.). The ratio obtained for the interactions on water only from an event subtraction method is 0.87 ± 0.33 (stat.) ± 0.21 (sys.). This is the first measurement of the interaction rate of electron neutrinos on water, which is particularly of interest to experiments with water Cherenkov detectors.

Las normativas de construcción con tierra en el mundo/The earth building normative documents in the world

La tierra ha sido utilizada como material de construcción desde hace siglos. No obstante, la normativa al respecto está muy dispersa, y en la mayoría de países desarrollados surgen numerosos problemas técnicos y legales para llevar a cabo una construcción con este material. Este artículo estudia el panorama normativo para las construcciones con tierra cruda a nivel internacional, analizando cincuenta y cinco normas y reglamentos de países repartidos por los cinco continentes, que representan el estado del arte de la normalización de la tierra cruda como material de construcción. Es un estudio referenciado sobre las normas y reglamentos vigentes desarrollados por los organismos nacionales de normalización o autoridades correspondientes. Se presentan las normativas y los organismos que las emiten, analizando la estructura y contenido de cada una. Se estudian y analizan los aspectos más relevantes, como la estabilización, selección de los suelos, requisitos de los productos y ensayos existentes, comparando las diferentes normativas. Este trabajo puede ser de gran utilidad para el desarrollo de futuras normas y como referencia para arquitectos e ingenieros que trabajen con tierra. For centuries, earth has been used as a construction material. Nevertheless, the normative in this matter is very scattered, and in the most developed countries, carrying out a construction with this material implies a variety of technical and legal problems. This article analyzes, in an international level, the normative panorama about constructions with earth, analyzing fifty five standards and regulations of countries all around the five continents; these represent the state of art that normalizes the earth as a construction material. It is a study indexed on the actual procedures and regulations developed by the national organisms of normalization or correspondent authorities. The standards and the organisms that produce them appear, analyzing the structure and the content of each one. We have studied and analyzed the most relevant aspects, such as stabilization, soil selections, the requisites of the products and the existent test, comparing the diverse normative. The knowledge from this study could be very useful for the development of future standards and as a reference for architects and engineers that work with earth.