A family of lysozyme-like virulence factors in bacterial pathogens of plants and animals.

We describe a conserved family of bacterial gene products that includes the VirB1 virulence factor encoded by tumor-inducing plasmids of Agrobacterium spp., proteins involved in conjugative DNA transfer of broad-host-range bacterial plasmids, and gene products that may be involved in invasion by Shigella spp. and Salmonella enterica. Sequence analysis and structural modeling show that the proteins in this group are related to chicken egg white lysozyme and are likely to adopt a lysozyme-like structural fold. Based on their similarity to lysozyme, we predict that these proteins have glycosidase activity. Iterative data base searches with three conserved sequence motifs from this protein family detect a more distant relationship to bacterial and bacteriophage lytic transglycosylases, and goose egg white lysozyme. Two acidic residues in the VirB1 protein of Agrobacterium tumefaciens form a putative catalytic dyad, Each of these residues was changed into the corresponding amide by site-directed mutagenesis. Strains of A. tumefaciens that express mutated VirB1 proteins have a significantly reduced virulence. We hypothesize that many bacterial proteins involved in export of macromolecules belong to a widespread class of hydrolases and cleave beta-1,4-glycosidic bonds as part of their function.

Production of avian leukosis virus particles in mammalian cells can be mediated by the interaction of the human immunodeficiency virus protein Rev and the Rev-responsive element.

In human immunodeficiency virus type 1-infected cells, the efficient expression of viral proteins from unspliced and singly spliced RNAs is dependent on two factors: the presence in the cell of the viral protein Rev and the presence in the viral RNA of the Rev-responsive element (RRE). We show here that the HIV-1 Rev/RRE system can increase the expression of avian leukosis virus (ALV) structural proteins in mammalian cells (D-17 canine osteosarcoma) and promote the release of mature ALV virions from these cells. In this system, the Rev/RRE interaction appears to facilitate the export of full-length unspliced ALV RNA from the nucleus to the cytoplasm, allowing increased production of the ALV structural proteins. Gag protein is produced in the cytoplasm of the ALV-transfected cells even in the absence of a Rev/RRE interaction. However, a functional Rev/RRE interaction increases the amount of Gag present intracellularly and, more strikingly, results in the release of mature ALV particles into the supernatant. RCAS virus containing an RRE is replication-competent in chicken embryo fibroblasts; however, we have been unable to determine whether the particles produced in D-17 cells are as infectious as the particles produced in chicken embryo fibroblasts.

Adenoviral E1B-55kDa protein inhibits yeast mRNA export and perturbs nuclear structure.

The mechanisms of export of RNA from the nucleus are poorly understood; however, several viral proteins modulate nucleocytoplasmic transport of mRNA. Among these are the adenoviral proteins E1B-55kDa and E4-34kDa. Late in infection, these proteins inhibit export of host transcripts and promote export of viral mRNA. To investigate the mechanism by which these proteins act, we have expressed them in Saccharomyces cerevisiae. Overexpression of either or both proteins has no obvious effect on cell growth. By contrast, overexpression of E1B-55kDa bearing a nuclear localization signal (NLS) dramatically inhibits cell growth. In this situation, the NLS-E1B-55kDa protein is localized to the nuclear periphery, fibrous material is seen in the nucleoplasm, and poly(A)+ RNA accumulates in the nucleus. Simultaneous overexpression of E4-34kDa bearing or lacking an NLS does not modify these effects. We discuss the mechanisms of selective mRNA transport.

Protein export from the nucleus requires the GTPase Ran and GTP hydrolysis.

Nuclei of digitonin-permeabilized cells that had been preloaded with a model transport substrate in a cytosol-dependent import reaction were subsequently incubated to investigate which conditions would result in export of transport substrate. We found that up to 80% of the imported substrate was exported when recombinant human Ran and GTP were present in the export reaction. Ran-mediated export was inhibited by nonhydrolyzable GTP analogs and also by wheat germ agglutinin but was unaffected by a nonhydrolyzable ATP analog. Moreover, a recombinant human Ran mutant that was deficient in its GTPase activity inhibited export. These data indicate that export of proteins from the nucleus requires Ran and GTP hydrolysis but not ATP hydrolysis. We also found that digitonin-permeabilized cells were depleted of their endogenous nuclear Ran, thus allowing detection of Ran as a limiting factor for export. In contrast, most endogenous karyopherin alpha was retained in nuclei of digitonin-permeabilized cells. Unexpectedly, exogenously added, fluorescently labeled Ran, although it accessed the nuclear interior, was found to dock at the nuclear rim in a punctate pattern, suggesting the existence of Ran-binding sites at the nuclear pore complex.

Pathways to quiescence: SHARDS view on the star formation histories of massive quiescent galaxies at 1.0 < z < 1.5

We present star formation histories (SFHs) for a sample of 104 massive (stellar mass M > 10^10 M_⊙) quiescent galaxies (MQGs) at z = 1.0–1.5 from the analysis of spectrophotometric data from the Survey for High-z Absorption Red and Dead Sources (SHARDS) and HST/WFC3 G102 and G141 surveys of the GOODS-North field, jointly with broad-band observations from ultraviolet (UV) to far-infrared (far-IR). The sample is constructed on the basis of rest-frame UVJ colours and specific star formation rates (sSFRs = SFR/Mass). The spectral energy distributions (SEDs) of each galaxy are compared to models assuming a delayed exponentially declining SFH. A Monte Carlo algorithm characterizes the degeneracies, which we are able to break taking advantage of the SHARDS data resolution, by measuring indices such as MgUV and D4000. The population of MQGs shows a duality in their properties. The sample is dominated (85 per cent) by galaxies with young mass-weighted ages, t_M t_M < 2 Gyr, short star formation time-scales, 〈τ〉 ∼ 60–200 Myr, and masses log(M/M_⊙) ∼ 10.5. There is an older population (15 per cent) with t_M t_M = 2–4 Gyr, longer star formation time-scales, 〈τ〉∼ 400 Myr, and larger masses, log(M/M_⊙) ∼ 10.7. The SFHs of our MQGs are consistent with the slope and the location of the main sequence of star-forming galaxies at z > 1.0, when our galaxies were 0.5–1.0 Gyr old. According to these SFHs, all the MQGs experienced a luminous infrared galaxy phase that lasts for ∼500 Myr, and half of them an ultraluminous infrared galaxy phase for ∼100 Myr. We find that the MQG population is almost assembled at z ∼ 1, and continues evolving passively with few additions to the population.

Convergence analysis and validation of low cost distance metrics for computational cost reduction of the Iterative Closest Point algorithm

The Iterative Closest Point algorithm (ICP) is commonly used in engineering applications to solve the rigid registration problem of partially overlapped point sets which are pre-aligned with a coarse estimate of their relative positions. This iterative algorithm is applied in many areas such as the medicine for volumetric reconstruction of tomography data, in robotics to reconstruct surfaces or scenes using range sensor information, in industrial systems for quality control of manufactured objects or even in biology to study the structure and folding of proteins. One of the algorithm’s main problems is its high computational complexity (quadratic in the number of points with the non-optimized original variant) in a context where high density point sets, acquired by high resolution scanners, are processed. Many variants have been proposed in the literature whose goal is the performance improvement either by reducing the number of points or the required iterations or even enhancing the complexity of the most expensive phase: the closest neighbor search. In spite of decreasing its complexity, some of the variants tend to have a negative impact on the final registration precision or the convergence domain thus limiting the possible application scenarios. The goal of this work is the improvement of the algorithm’s computational cost so that a wider range of computationally demanding problems from among the ones described before can be addressed. For that purpose, an experimental and mathematical convergence analysis and validation of point-to-point distance metrics has been performed taking into account those distances with lower computational cost than the Euclidean one, which is used as the de facto standard for the algorithm’s implementations in the literature. In that analysis, the functioning of the algorithm in diverse topological spaces, characterized by different metrics, has been studied to check the convergence, efficacy and cost of the method in order to determine the one which offers the best results. Given that the distance calculation represents a significant part of the whole set of computations performed by the algorithm, it is expected that any reduction of that operation affects significantly and positively the overall performance of the method. As a result, a performance improvement has been achieved by the application of those reduced cost metrics whose quality in terms of convergence and error has been analyzed and validated experimentally as comparable with respect to the Euclidean distance using a heterogeneous set of objects, scenarios and initial situations.

The concept of 'economic activity' in the EU treaty: from ideological dead-ends to workable judicial concepts. Research Paper in Law 06/2011

[From the Introduction]. The economic rules, or put more ambitiously, the economic constitution of the Treaty,1 only apply to economic activities. This general principle remains valid, even if some authors strive to demonstrate that certain Treaty rules also apply in the absence of an economic activity,2 and despite the fact that non-economic (horizontal) Treaty provisions (e.g. principle of nondiscrimination, rules on citizenship) are also applicable in the absence of any economic activity.3 Indeed, the exercise of some economic activity transcends the concepts of ‘goods’ (having positive or negative market value),4 workers (even if admitted in an extensive manner),5 and services (offered for remuneration).6 It is also economic activity or ‘the activity of offering goods and services into the market’7 that characterises an ‘undertaking’ thus making the competition rules applicable. Further, it is for regulating economic activity that Article 115 TFEU, Article 106(3) TFEU and most other legal bases in the TFEU provide harmonisation powers in favour of the EU. Last but not least, Article 14 TFEU on the distinction between services of general economic interest (SGEIs) and non-economic services of general interest (NESGIs), as well as Protocol n. 26 on Services of General Interest (SGIs) confirm the constitutional significance of the distinction between economic and non-economic: a means of dividing competences between the EU and the member states. The distinction between economic and non-economic activities is fraught with legal and technical intricacies – the latter being generated by dynamic technological advances and regulatory experimentation. More importantly, however, the distinction is overcharged with political and ideological significations and misunderstandings and, even, terminological confusions.8

Economic Incentives for Indirect TTIP Spillovers. CEPS Special Report No. 94/October 2014 [TTIP Series No. 2]

A deep, comprehensive and ambitious TTIP should not undermine or otherwise negatively affect the WTO and its signatories. Among other things, this means that trade diversion ought to be minimised and positive spillovers stimulated. The present CEPS Special Report provides some elementary quantification, which helps to understand the economic incentives for third countries to seek regulatory alignment with TTIP results, where relevant, and for which TTIP should be ‘open’. It focuses on ‘indirect’ spillovers and employs a rather aggregate economic approach. We find that, of three groups of countries that are important for trade with the EU and the US, the ‘closest’ neighbours (NAFTA, EEA, Switzerland and Turkey) exhibit powerful incentives to align so as to benefit from positive spillovers. This is less clear for two other groups. Of the (seven) ‘biggest traders’ (in manufactured goods, for which spillovers matter most), China turns out to have the greatest interest in alignment in selected sectors, followed by Israel, Japan and South Korea. Whereas the latter three either have or are negotiating FTAs with the US and the EU, precisely China has none and remains outside TPP as well. In terms of sectors, the chemical sector followed by electronic equipment are by far the most important, with agro-products and fish as a good third (SPS issues). However, in chemicals and electrical equipment, the TTIP negotiations so far, and recent US/EU regulatory cooperation, do not indicate an ambitious approach, which could reduce regulatory barriers to market access drastically.

An economy with unrealistic indicators: an evaluation of the economic situation in Belarus and a forecast for 2013. OSW Commentary No. 103, 2013-02-20

The macroeconomic results achieved by Belarus in 2012 laid bare the weakness and the inefficiency of its economy. Belarus’s GDP and positive trade balance were growing in the first half of last year. However, this trend was reversed when Russia blocked the scheme of extremely lucrative manipulations in the re-export of Russian petroleum products by Belarus and when the demand for potassium fertilisers fell on the global market. It became clear once again that the outdated Belarusian model of a centrally planned economy is unable to generate sustainable growth, and the Belarusian economy needs thorough structural reforms. Nevertheless, President Alyaksandr Lukashenka consistently continues to block any changes in the system and at the same time expects that the economic indicators this year will reach levels far beyond the possibilities of the Belarusian economy. Therefore, there is a risk that the Belarusian government may employ – as they used to do – instruments aimed at artificially stimulating domestic demand, including money creation. This may upset the relative stability of state finances, which the regime managed to achieve last year. The worst case scenario would see a repeat of what happened in 2011, when a serious financial crisis occurred, forcing Minsk to make concessions (including selling the national network of gas pipelines) to Moscow, its only real source of loans. It thus cannot be ruled out that also this time the only way to recover from the slump will be to receive additional loan support and energy subsidies from Russia at the expense of selling further strategic companies to Russian investors.

Manufactured Exports and FDI in Southern Mediterranean Countries: Evolution, determinants and prospects. MEDPRO Technical Report No. 14/April 2012

This paper investigates the evolution and determinants of manufactured exports and foreign direct investment (FDI) in 11 southern Mediterranean countries over the period 1985–2009, as well as their prospects under different scenarios pertaining to the development of the determinants. The econometric analysis confirms the role of exchange rate depreciation, the openness of the economy and the quality of institutions and infrastructure in fostering manufactured exports and FDI inflows in the region. The assessment of the prospects suggests that a scenario of deeper integration with the EU entails superior performance for manufactured exports and FDI compared with either the status quo or less integration with the EU but greater integration within the region.

A partial success of trade cooperation within the ‘16+1’ formula: the case of food exports to China. OSW COMMENTARY #189, 2015-10-29

When in 2012 China approached the countries of Central and Eastern Europe (CEE) with a proposal of cooperation in the ‘16+1’ formula, it declared it was willing to meet the needs of CEE countries. Beijing had been aware of the political importance of the problem of trade deficit (which has been ongoing for years) and launched cooperation with the governments of 16 CEE countries to boost imports from these states. The years 2011–2014 brought an improvement in the balance of trade between China and: Hungary, Latvia, the Czech Republic, Romania, Bulgaria and Croatia. The remaining ten CEE countries recorded an increase in their trade deficits. Changes in CEE countries’ balance of trade with China resulted only slightly from political actions. Instead, they were due to the macroeconomic situation and to a deterioration of the debt crisis in the EU which, for example, caused a decline in the import of Chinese goods in some of these countries. Multilateral trade cooperation was successfully developed in the entire region only in the agricultural and food production sector – the area of greatest interest to China. The pace of bilateral cooperation with specific countries varied, with the fastest being Poland, Latvia, Romania, Hungary and Bulgaria. Actions by governments of CEE countries resulted in Chinese market opening up to hundreds of local companies which, in turn, translated into an increase in the volume of foodstuffs sold by ‘the 16’ to China from US$ 137 million in 2011 to US$ 400 million in 2014. The success achieved in the agricultural and food production sector has demonstrated the effectiveness of trade cooperation in the ‘16+1’ formula. It is, however, insufficient to generate a significant improvement of the trade balance. At present, the sector’s share in the total volume of goods sold to China by CEE states is a mere 3.7%, and any reduction of the trade deficit would require long-term and more comprehensive solutions still to be implemented by the governments of individual CEE states.

The twilight of the oil Eldorado. How the activity of Russian oil companies on the EU market has evolved. OSW Studies 55, April 2016

The European Union has traditionally been the most important outlet for Russian oil exports. At the same time, during the period 2011-2014 a systematic decline was observed in crude oil supplies to the EU, while at the same time the export of petroleum products increased. It is now difficult to say that Russia is following a coherent oil strategy vis-a-vis the EU. The current shape of Russian activity is more the result of the business interests of individual companies, rather than the result of activities coordinated by the state. Although in the short term (up to 2020), the negative trend in crude oil exports to the EU could be halted (as confirmed by the figures for 2015), the long-term prospects for Russia's position on the EU market are pessimistic. This is because the importance of factors unfavourable to Russia is rising, such as the decrease in consumption of oil in the EU, the increased competition among exporters to the EU market, and the deterioration of the climate of Russian/EU cooperation in the context of the anti-Russian sanctions, as well as unclear prospects for the development of the upstream sector in Russia.

Innovation and Development in the Age of Climate Change Adaptation: Open or Closed?

Change Adaptation: Open or Closed? Paper read at the Second African International Economic Law Network Conference, 7-8 March 2013, Wits School of Law, Johannesburg, South Africa. In a time of rapid convergence of technologies, goods, services, hardware, software, the traditional classifications that informed past treaties fail to remove legal uncertainty, or advance welfare and innovation. As a result, we turn our attention to the role and needs of the public domain at the interface of existing intellectual property rights and new modes of creation, production and distribution of goods and services. The concept of open culture would have it that knowledge should be spread freely and its growth should come from further developing existing works on the basis of sharing and collaboration without the shackles of intellectual property. Intellectual property clauses find their way into regional, multilateral, bilateral and free trade agreements more often than not, and can cause public discontent and incite unrest. Many of these intellectual property clauses raise the bar on protection beyond the clauses found in the WTO Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS). In this paper we address the question of the protection and development of the public domain in service of open innovation in accord with Article 15 of the International Covenant on Economic, Social and Cultural Rights (ICESCR) in light of the Objectives (Article 7) and Principles (Article 8) set forth in TRIPS. Once areas of divergence and reinforcement between the intellectual property regime and human rights have been discussed, we will enter into options that allow for innovation and prosperity in the global south. We then conclude by discussing possible policy developments.

Sampling intervals, fluxes, percentages of total flux, organic carbon and lithogen for sediment trap CB9

We combined the analysis of sediment trap data and satellite-derived sea surface chlorophyll to quantify the amount of organic carbon export to the deep sea in the upwelling induced high production area off northwest Africa. In contrast to the generally global or basin-wide adoption of export models, we used a regionally fitted empirical model. Furthermore, the application of our model was restricted to a dynamically defined region of high chlorophyll concentration in order to restrict the model application to an environment of more homogeneous export processes. We developed a correlation-based approximation to estimate the surface source area for a sediment trap deployed from 11 June 1998 to 7 November 1999 at 21.25°N latitude and 20.64°W longitude off Cape Blanc. We also developed a regression model of chlorophyll and export of organic carbon to the 1000 m depth level. Carbon export was calculated for an area of high chlorophyll concentration (>1 mg/m**3) adjacent to the coast on a daily basis. The resulting zone of high chlorophyll concentration was 20,000-800,000 km**2 large and yielded a yearly export of 1.123 to 2.620 Tg organic carbon. The average organic carbon export within the area of high chlorophyll concentration was 20.6 mg/m**2d comparable to 13.3 mg/m**2d as found in the sediment trap results if normalized to the 1000 m level. We found strong interannual variability in export. The period autumn 1998 to summer 1999 was exceeding the mean of the other three comparable periods by a factor of 2.25. We believe that this approach of using more regionally fitted models can be successfully transferred even to different oceanographic regions by selecting appropriate definition criteria like chlorophyll concentration for the definition of an area to which it is applicable.