"The European Union and Democratization ‘From Below’ in Turkey"

[From the Introduction]. This paper addresses this issue by examining the role of forces ‘from below’ within Turkey in the Turkish reform project and the role of the EU in encouraging such forces. As such, it seeks to understand the nexus between external and internal agents of democratization. As noted, if the reforms are more a European than a Turkish project and if they do not have diffuse support among the population or benefit from a sense of domestic ownership, one would expect both the accession process to be more difficult and the reforms to be poorly institutionalized. On the other hand, to the extent that the EU is able to work with Turks and foster acceptance of democratic norms and empower democratically-oriented forces within Turkey, one would be far more sanguine about democratic consolidation in Turkey

Delegative democracy in Russia and Ukraine

This paper applies the concept of delegative democracy to contemporary developments in Russia and Ukraine. They qualify as examples of this phenomenon insofar as leaders in these states are elected by the people but use their democratic legitimacy to justify authoritarian behavior. Factors which contribute to this trend are a deep socio-economic crisis, existent political culture, and a lack of institutions to safeguard democratic norms. While recognizing the various arguments endorsing this solution, this paper concludes that this form of rule is unlikely to live up to its promises and ultimately undermines the emergence of a representative, pluralist democracy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31158/1/0000057.pd

The effects of external Mn2+ concentration on hyphal morphology and citric acid production are mediated primarily by the NRAMP-family transporter DmtA in Aspergillus niger

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Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression

Gaining new knowledge through fungal monoculture responses to lignocellulose is a widely used approach that can lead to better cocktails for lignocellulose saccharification (the enzymatic release of sugars which are subsequently used to make biofuels). However, responses in lignocellulose mixed cultures are rarely studied in the same detail even though in nature fungi often degrade lignocellulose as mixed communities. Using a dual RNA-seq approach, we describe the first study of the transcriptional responses of wild-type strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw. Based on quantification of species-specific rRNA, a set of conditions was identified where mixed cultures could be sampled so as to obtain sufficient RNA-seq reads for analysis from each species. The number of differentially-expressed genes varied from a couple of thousand to fewer than one hundred. The proportion of carbohydrate active enzyme (CAZy) encoding transcripts was lower in the majority of the mixed cultures compared to the respective straw monocultures. A small subset of P. chrysogenum CAZy genes showed five to ten-fold significantly increased transcript abundance in a two-species mixed culture with T. reesei. However, a substantial number of T. reesei CAZy transcripts showed reduced abundance in mixed cultures. The highly induced genes in mixed cultures indicated that fungal antagonism was a major part of the mixed cultures. In line with this, secondary metabolite producing gene clusters showed increased transcript abundance in mixed cultures and also mixed cultures with T. reesei led to a decrease in the mycelial biomass of A. niger. Significantly higher monomeric sugar release from straw was only measured using a minority of the mixed culture filtrates and there was no overall improvement. This study demonstrates fungal interaction with changes in transcripts, enzyme activities and biomass in the mixed cultures and whilst there were minor beneficial effects for CAZy transcripts and activities, the competitive interaction between T. reesei and the other fungi was the most prominent feature of this study

Target 2035-update on the quest for a probe for every protein

Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome

Secondary Metabolites of Marine Microbes: From Natural Products Chemistry to Chemical Ecology

Marine natural products (MNPs) exhibit a wide range of pharmaceutically relevant bioactivities, including antibiotic, antiviral, anticancer, or anti-inflammatory properties. Besides marine macroorganisms such as sponges, algae, or corals, specifically marine bacteria and fungi have shown to produce novel secondary metabolites (SMs) with unique and diverse chemical structures that may hold the key for the development of novel drugs or drug leads. Apart from highlighting their potential benefit to humankind, this review is focusing on the manifold functions of SMs in the marine ecosystem. For example, potent MNPs have the ability to exile predators and competing organisms, act as attractants for mating purposes, or serve as dye for the expulsion or attraction of other organisms. A large compilation of literature on the role of MNPs in marine ecology is available, and several reviews evaluated the function of MNPs for the aforementioned topics. Therefore, we focused the second part of this review on the importance of bioactive compounds from crustose coralline algae (CCA) and their role during coral settlement, a topic that has received less attention. It has been shown that certain SMs derived from CCA and their associated bacteria are able to induce attachment and/or metamorphosis of many benthic invertebrate larvae, including globally threatened reef-building scleractinian corals. This review provides an overview on bioactivities of MNPs from marine microbes and their potential use in medicine as well as on the latest findings of the chemical ecology and settlement process of scleractinian corals and other invertebrate larvae

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis

Nation, State, and Economy in Central Asia: Does Atatürk Provide a Model?

The Donald W. Treadgold Papers publication series was created to honor a great teacher and scholar. Donald W. Treadgold was professor of history and international studies at the University of Washington from 1949 to 1993. During that time he wrote seven books, on of which - Twentieth Century Russia - went into eight editions. He was twice editor of Slavic Review, the organ of the American Association for the Advancement of Slavic Studies, and received the AAASS Award for Distinguished Contributions to Slavic Studies, as well as the AAASS Award for Destinguished Service. Professor Treadgold molded several generations of Russian historians and contributed enormously to the field of Russian history. He was, in other ways as well, an inspiration to all who knew him. The Treadgold Papers series was created in 1993 on the occaision of Professor Treadgold's retirement, on the initiative of Professor Daniel Waugh. Professor Treadgold passed away in December 1994. The series is dedicated to the memory of a great man, publishing papers in those areas which were close to his heart

Dancing with the Devil: Explaining the European Union’s Engagement with Ukraine under Viktor Yanukovych

Introduction: In February 2014, Ukrainian President Viktor Yanukovych was forced from office, capping three months of protests against his rule. The epicenter of the anti-Yanukovych rallies was Kyiv’s Independence Square, which gained the moniker “Euromaidan” because the demonstrations were sparked by Yanukovych’s last minute rejection of an Association Agreement (AA) with the European Union (EU) and protesters demanded closer integration with the EU as well as a government committed to democracy and the rule of law. Yanukovych’s ouster was celebrated by the EU, and he was subsequently widely pilloried as a “thug” and head of a “gangster regime.” Those with short memories were reminded of his past transgressions, including the attempt to steal the 2004 presidential elections, which led to the so-called Orange Revolution and subsequent installation of a pro-Western government. The Orange Revolution, alas, failed to fulfill its promise, and, in light of the Russian annexation of Crimea in March 2014 and the on-going, bloody separatist conflict in parts of eastern Ukraine, it is clear that Ukraine faces immense difficulties after the more recent “Euro Revolution.” Furthermore, there is no doubt that managing relations with Kyiv and Moscow will be a long-term challenge for EU foreign policy. This paper, however, asks a different question, one that looks back rather than forward and focuses attention less on the Euromaidan and its aftermath and more on the decision by the EU to proffer an AA to Ukraine while it was ruled by Yanukovych. In short, the EU’s engagement with Yanukovych—now somewhat forgotten given his ouster and dramatic subsequent events—is a bit of a puzzle given its past policies and stated priorities. The EU, of course, has long pursued close ties with Ukraine, concluding a Partnership and Cooperation Agreement with Kyiv in 1994. It created numerous programs and supplied aid to promote security as well as economic and political reform. Membership, however, has never been on the table, and, particularly, under President Leonid Kuchma (1994-2005), Kyiv’s “declarative Europeanization” fit uneasily with its corrupt, semi-authoritarian political system (Wolczuk 2004). The calculus changed after the Orange Revolution, when a new government promised real change and expected rapid progress toward EU membership. This did not occur. While there were some initiatives from the EU, including new aid programs and an Action Plan, Ukraine was lumped together with countries that had no membership perspective in the 2004 European Neighborhood Policy (ENP). The later 2008-2009 Eastern Partnership (EaP) offered to six post-Soviet states was portrayed as an upgrade in ties but likewise had no statement about or roadmap for EU accession. Even concluding an AA with the EU long remained an elusive goal. A 2010 report from a Kyiv-based think tank concluded that Ukraine had mostly elicited “distrust, fatigue, disappointment, and irritation” from the EU (ICPS 2010: 42). Both the ENP and the EaP were outgrowths of the EU’s largely successful use of democratic conditionality in its expansion to East Central Europe, and these programs sought to employ conditionality as well (Kelley 2006; Sasse 2008; Stewart 2015). In the language of the ENP, the “pace of development of the European Union’s engagement [with targeted countries] will depend upon commitment to common values,” including, inter alia, democracy, human rights, and the rule of law (Commission 2004). The EaP stated that the same principle applied: “how far we [the EU] go in relations with each country will continue to depend on the progress made by the partners in their reform and modernization efforts” (Commission 2009). In short, there would be more [aid, engagement, integration] for more [reform], and the EU stipulated that AAs were possible only if there was a “sufficient level of progress in terms of democracy, the rule of law, and human rights” (Commission 2008: 4). Although this conditionality was not as strong as that tied to membership, prior to 2010 Ukraine did make some reforms in these areas, although, to be sure, they were limited (Kubicek 2007; Solonenko 2009; Gawrich et al 2010; Freyburg and Richter 2013; Tolstrup 2014). This did not lead, however, to a major breakthrough or new dynamic in Ukraine-EU ties or a re-categorization of Ukraine in relation to other, less democratic post-Soviet states (Pridham 2011: 22). This ultimately did occur, however, with the AA that offered, inter alia, a Deep and Comprehensive Free Trade Area, more sectoral cooperation and financial assistance, and prospects for visa-free travel for Ukrainians to the EU. This was, in the EU’s terms, “ambitious” and “innovative,” the “first of a new generation of Association Agreements” with post-Soviet states, putting EU-Ukrainian relations on a higher level than those with other EaP states. What is notable, however, is that while negotiations for this agreement were launched in 2007, they continued even after Yanukovych assumed the presidency in 2010 and began taking Ukraine in a more authoritarian direction. It was initialed by the two sides in 2012 and remained on the table throughout 2013, even as Kyiv failed to meet key, public EU demands for political reform and liberalization and some Ukrainian opposition parties called for EU sanctions, not engagement. The question, then, is why the EU, pace its pledges in the ENP, EaP, and other documents, ended up offering, in effect, “more for less”? This question, which concerns the (non)application of conditionality, has relevance well beyond the Ukrainian case. The EU has committed itself to use of conditionality in numerous agreements with non-member states. Conditionality works on the logic of employing blandishments to reward good behavior and punishments or withholding of benefits to rebuke bad behavior. Of course, there can be problems employing conditionality (e.g. are the “carrots” and “sticks” enough to produce the desired effect?; are there countervailing domestic political calculations?; do targeted states have other options besides the EU? how much “reform” or “progress” is enough?). With respect to conditionality on issues of democratization, there is little doubt that the EU frequently engages with “reluctant democratizers” (Kubicek 2003) or is left trying to promote “democracy without democrats” (Youngs 2010: 72-77), and other goals (e.g. security, maintaining trade or energy ties) might make it difficult to manage relations with non-democratic regimes and affect the level and type of EU democracy promotion (Wetzel and Orbie 2015). However, the rewards offered to Ukraine under Yanukovych—which went far beyond other cases such as the “functional cooperation” offered under the EaP to dictatorial Belarus (Bosse 2012)—are rather jarring, particularly given how quickly the EU embraced his ouster. Understanding EU engagement with Ukraine is thus an interesting and important case of its application of democratic conditionality and can shed light on EU policy elsewhere, including, perhaps most significantly, with an increasingly autocratic and militant Russia. This paper is made up of three additional sections. First, it will briefly suggest hypotheses that could explain EU behavior. Secondly, it will examine, based upon evidence both during and prior to Yanukovych’s 2010-2014 presidency, each hypothesis in turn to determine which one(s) best match with available evidence. Lastly, it will conclude reflecting upon what lessons can be derived from examination of this case