Interaction of the Ras-related protein associated with diabetes Rad and the putative tumor metastasis suppressor NM23 provides a novel mechanism of GTPase regulation

Rad is the prototypic member of a new class of Ras-related GTPases. Purification of the GTPase-activating protein (GAP) for Rad revealed nm23, a putative tumor metastasis suppressor and a development gene in Drosophila. Antibodies against nm23 depleted Rad-GAP activity from human skeletal muscle cytosol, and bacterially expressed nm23 reconstituted the activity. The GAP activity of nm23 was specific for Rad, was absent with the S105N putative dominant negative mutant of Rad, and was reduced with mutations of nm23. In the presence of ATP, GDP⋅Rad was also reconverted to GTP⋅Rad by the nucleoside diphosphate (NDP) kinase activity of nm23. Simultaneously, Rad regulated nm23 by enhancing its NDP kinase activity and decreasing its autophosphorylation. Melanoma cells transfected with wild-type Rad, but not the S105N-Rad, showed enhanced DNA synthesis in response to serum; this effect was lost with coexpression of nm23. Thus, the interaction of nm23 and Rad provides a potential novel mechanism for bidirectional, bimolecular regulation in which nm23 stimulates both GTP hydrolysis and GTP loading of Rad whereas Rad regulates activity of nm23. This interaction may play important roles in the effects of Rad on glucose metabolism and the effects of nm23 on tumor metastasis and developmental regulation.

Predominant VH genes expressed in innate antibodies are associated with distinctive antigen-binding sites

Antibodies to phosphatidylcholine (PtC), a common constituent of mammalian and bacterial cell membranes, represent a large proportion of the natural antibody repertoire in mice. Previous studies of several mouse strains (e.g., C57BL/6) have shown that anti-PtC antibodies are mainly encoded by the VH11 and VH12 immunoglobulin heavy chain variable region gene families. We show here, however, that VH11 and VH12 encode only a small proportion of the anti-PtC antibodies in BALB/c mice. Instead, VHQ52-encoded antibodies predominate in this strain. In addition, two-thirds of the cells expressing VHQ52 family genes use a single gene (which, interestingly, has been previously shown to predominate in the anti-oxazolone response). We also show here that in anti-PtC antibodies from all strains, the distinctive antigen-binding sites associated with VHQ52 differ substantially from those associated with VH11 and VH12. That is, VHQ52-containing transcripts preferentially use the joining region JH4 rather than JH1 and exhibit more diverse complementarity-determining region 3 (CDR3) junctions with more N-region nucleotide additions at the gene segment junctions. Thus, the VH gene family that predominates in the anti-PtC repertoire differs among mouse strains, whereas the distinctive VHDJH rearrangements (CDR3, JH) associated with each VH gene family are similar in all strains. We discuss these findings in the context of a recent hypothesis suggesting that CDR3 structure, independent of VH framework, is sufficient to define the specificity of an antibody.

Predicting the reactivity of proteins from their sequence alone: Kazal family of protein inhibitors of serine proteinases

An additivity-based sequence to reactivity algorithm for the interaction of members of the Kazal family of protein inhibitors with six selected serine proteinases is described. Ten consensus variable contact positions in the inhibitor were identified, and the 19 possible variants at each of these positions were expressed. The free energies of interaction of these variants and the wild type were measured. For an additive system, this data set allows for the calculation of all possible sequences, subject to some restrictions. The algorithm was extensively tested. It is exceptionally fast so that all possible sequences can be predicted. The strongest, the most specific possible, and the least specific inhibitors were designed, and an evolutionary problem was solved.

Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs

The HIV Reverse Transcriptase and Protease Sequence Database is an on-line relational database that catalogs evolutionary and drug-related sequence variation in the human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease enzymes, the molecular targets of anti-HIV therapy (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protease sequences, including submissions from International Collaboration databases and sequences published in journal articles. Sequences are linked to data about the source of the sequence sample and the antiretroviral drug treatment history of the individual from whom the isolate was obtained. During the past year 3500 sequences have been added and the data model has been expanded to include drug susceptibility data on sequenced isolates. Database content has also been integrated with didactic text and the output of two sequence analysis programs.

What do the Maidan protests tell us about Ukraine? Diagnosis and prospects for Ukrainian politics. OSW Commentary No. 125, 22.01.2014

The outbreak of the protests in the Maidan in Kyiv, and also periodically in other Ukrainian cities, has come as a surprise to both the government and the opposition. These rallies have now been ongoing for several weeks and their most striking feature is their focus on citizenship and their apolitical nature and, by extension, a clear attempt to dissociate the protests from Ukraine’s political opposition. Neither Batkivshchyna, UDAR nor Svoboda have managed to take over full control of the demonstrations. On the one hand, this has been linked to the fact that the protesters have little confidence in opposition politicians and, on the other hand, to disputes over a joint strategy and to rivalry between the three parties. As a result, the citizen-led movement has managed to retain its independence from any political actors. As a consequence of the radicalisation and escalation of the protests following 19 January, the political opposition has lost a significant proportion of the control it had been in possession of until then. Maidan should also be seen as the first clear manifestation of a new generation of Ukrainians – raised in an independent Ukraine, well-educated and familiar with new social media, but nonetheless seeking to ground themselves in national tradition. After the initial shock and a series of failed attempts to quell the protests, the government has seemingly opted to wait out the unrest. At the same time, however, it has been creating administrative obstacles for both the political and the civil opposition, restricting their access to the media and severely limiting the legal possibility to organise demonstrations.

Ukraine: sovereign decentralisation or federalism without sovereignty? OSW Commentary No. 133, 18.04.2014

A key element of Russia’s policy towards the new government of Ukraine concerns demands for a constitutional reform that would transform the country from a unitary into a federal state in a way that would considerably privilege the eastern and southern regions. Such a change to Ukraine’s administrative system would enable Moscow to put pressure on Ukraine’s central government via the regions. In order to achieve its objectives, Russia has been pressuring Kyiv to establish a constitutional assembly in a form that would guarantee the endorsement of solutions dictated by Russia. In other words, Russia has been demanding, in what is practically an ultimatum, that Ukraine give up one of the fundamental sovereign rights of a state, the right to freely determine its system of government. Transforming Ukraine into a federal state is an unacceptable idea, primarily because the intention behind Russia’s demands is to undermine Ukraine’s sovereignty, both through the content of the proposed changes and the way in which they are to be implemented. However, keeping in place the current, centralist model of state governance is not a feasible alternative. Ukraine will have to grant its regions broad self-governance powers, including the power to hold local referendums, and to transfer a considerable portion of the prerogatives currently held by the state to the local self-governments, along with adequate financial resources. That is because decentralisation along these lines is the only way forward towards a modern democracy in Ukraine. Russia’s policy has forced Kyiv to undertake legislative work on constitutional reform as a matter of urgency, rather than waiting until a new parliament is elected in which the new, post-Maidan balance of political power will be reflected, as political logic would require. The first draft of the constitutional amendments (of which no details are known at this stage) is to be presented in mid-May, and is expected to come into force in early autumn. However, whether these plans can be put into practice depends on further developments in the eastern part of Ukraine, because (among other reasons) if a state of emergency is introduced, the constitutional amendment process will have to be suspended.

Crimean Tatars after Russia's annexation of the Crimean Peninsula. OSW Commentary No. 141, 30.06.2014

After Russia’s annexation of Crimea, Crimean Tatars face the necessity of working out a modus vivendi to cope with the difficult situation which now confronts them. On the one hand, the desire to remain in their homeland, which they regained after exile in Soviet times, is an imperative encouraging them to accept the status quo, while on the other, the fear of Russia and the strong relations of Crimean Tatar elites with Kyiv would favour opposing the present state of affairs. Another fact pointing in favour of an agreement with Moscow is that Kyiv has not attempted to defend Crimea and has not been active in demanding its return to Ukraine, which has undermined Kyiv’s authority in the eyes of the Tatars. Therefore, the leaders of the Mejlis of Crimean Tatars (the national self-government) act carefully, trying to avoid actions which could be seen as provocative and thus liable to incite retribution. It could be expected that this course of action will continue, although it faces ever greater difficulties in the context of the Russian authorities’ adoption of a strongly anti-Tatar policy, which is likely to evoke more radical attitudes among the Crimean Tatars.

Ukrainian economy overshadowed by war. OSW Commentary No. 148, 08.10.2014

Ukraine’s financial results over the past few months prove that the economic crisis which has been ongoing since mid 2012 has exacerbated. According to data from the Ukrainian Ministry of Economy, Gross Domestic Product for the first six months of 2014 shrank by 3%. In the second quarter, it fell by 4.6%1 and may further be reduced by as much as 8–10% over the year as a whole. After the first six months of this year, the balance of payments deficit reached US$4.3 billion. After deflation last year, prices grew by 12%, and the hryvnia dropped to a historic low. Although a surplus was seen in Ukrainian foreign trade in goods and services, reaching over US$3 billion at the end of June, its trade volume is shrinking. The main reason behind this deteriorating situation is the actions taken by Russia. Moscow has been fomenting the conflict in Donbas since April, has consistently imposed embargoes on imports of more and more Ukrainian goods and cut gas supplies to Ukraine in June. This has forced the government to focus on the current management of state finances and to carry out budget sequestration twice this year. The government has also used this as an excuse not to implement necessary systemic reforms. The increasing share of military expenditure, the shrinking exports (-5% in the first six months), including in particular to Russia, which until recently was Ukraine’s key trade partner, and the rapid fall in industrial production and investments have all made the situation even worse. All that saves Ukraine from an economic collapse is the loan from the International Monetary Fund and higher taxes, which allows the government to maintain budget liquidity. However, if the conflict in Donbas lasts longer and if Russia continues its economic blackmail, including withholding gas supplies, the economic crisis may prove to be long-lasting.

Before the parliamentary elections in Ukraine. OSW Commentary No. 149, 15.10.2014

The parliamentary elections to be held in Ukraine on 26 October will bring about deep changes in the political composition of the Verkhovna Rada, Ukraine’s parliament. It is very probable that after the elections only one or two of the five parties which are represented in the parliament today will remain, and the leading positions will be taken by groupings who were still considered marginal a year ago. The Petro Poroshenko Bloc, a party which according to polls can count on victory, did not exist a year ago and today still remains in the construction phase. It is likely that around two-thirds of the newly elected deputies will be people with no parliamentary or even no political experience. On the one hand, this may be a strong impetus to revival; but on the other the lack of experience of most of the parliamentarians may be a problem. Another source of potential problems may be the process of consolidating the internally unstable political parties which have emerged during the electoral campaign. All of the parties which will count in the upcoming elections have a pro-European programme. It is probable that the numerous supporters of an anti-Western orientation (although not necessarily a pro-Russian orientation, as recent events have shown) will be represented by very few deputies elected in single-mandate constituencies. On the one hand, this homogeneity within the Rada will facilitate the country’s reforms, including work on the new constitution, while on the other it might be a subject of permanent criticism by Moscow and its Ukrainian representatives. The elections will take place in the conditions of a growing wave of social disappointment and ongoing military actions in the eastern part of the country. Nevertheless, it can be expected that the vote will be held without any major disturbances, and its course will be transparent and fair.

The Ukrainian Orthodox Church's stance on the revolution and war. OSW Commentary No. 151, 27.10.2014

Volodymyr (secular name Viktor Sabodan), the Metropolitan of Kyiv and All-Ukraine, the head of the Ukrainian Orthodox Church (UOC), which recognises the honorary primacy of the Moscow Patriarchate, died on 5 July 2014 at the age of 79. He was replaced by Metropolitan Onufry (secular name Orest Berezovsky), aged 70. The fact that this representative of the moderate trend, far from politics, was elected signifies that the UOC’s previous policy will be continued in the coming years: strengthening the Church’s independence without questioning its canonical bonds with Moscow. Metropolitan Onufry’s task is to wait out the hard times, rather than to embark upon an active policy. The political developments this year have significantly weakened pro-Russian views and sentiments among the Ukrainian public, including members of the UOC. On the other hand, they have also contributed to the radicalisation of views within firmly pro-Russian circles. The hierarchs of the Ukrainian Orthodox Church have distanced themselves from these developments. The reasons for this included a lack of unity among them as regards this issue, as well as the leadership crisis linked to Metropolitan Volodymyr’sillness. The main problems the Ukrainian Orthodox Church is facing today are as follows: meeting the expectations of those of its members who hold patriotic views (mainly the younger generation) without at the same time antagonising its numerous members who are pro-Russian; and also continuing to disregard the Kyiv Patriarchate and maintaining bonds with the Russian Orthodox Church. Therefore, we may expect the UOC to continue avoiding taking a clear stance on the present conflict, instead focusing on charity.

Unity stronger than divisions. Ukraine's internal diversity. OSW Point of View Number 40, March 2014

Ukraine is deeply divided internally, although as a result of the changes that have taken place since its independence, the country’s internal divisions now have less and less to do with territorial divides, and the split into historical ‘sub-Ukraines’ has become less pronounced, especially for the younger generation. Ukraine is not a country of two competing regional identities, one in the west, the other in the east. The western identity, in which the unity of Ukraine is a key value, coexists with the multiple and diverse local patriotisms of the different regions in the east and the south of the country. The present protest movement has consolidated the country’s sense of unity. Its opponents have also been championing the indivisibility of Ukraine, even while they demanded a thorough decentralisation of the country, which was often mistaken for separatism. Russia has been stirring up separatist tendencies in Ukraine, but with little success. Crimea is an exception here, because in most respects it has remained unaffected by the dynamics of the social processes transforming mainland Ukraine – separatist tendencies are indeed deeply rooted in the peninsula.

Under the veneer of decentralisation. Ukraine's modernisation efforts stall due to lack of local government reform. OSW Commentary No. 102, 2013-02-12

President Viktor Yanukovych and his Party of Regions have been repeating the pledge to decentralise power in Ukraine and to give local government a greater decision-making role ever since the party appeared on the Ukrainian political scene. The implementation of this reform is crucial both for the economic recovery of Ukraine’s regions and the overall modernisation efforts of the Ukrainian state. At present relations between central government and the regions are regulated by Soviet-era legislation that fails to address the modern-day challenges facing Ukraine. The political elite in the country, including the opposition, appear to have reached consensus on the importance of the decentralisation reform. The first attempts to implement changes in this area were made in the late 1990s, followed by a comprehensive reform programme developed between 2007 and 2009 by Yulia Tymoshenko’s government. In 2012, the Constitutional Assembly under the President of Ukraine appointed a team of experts who drafted a document detailing the reform of local government and the territorial organisation of power1. The document envisages the implementation of what effectively are two major reforms: (1) an administrative-territorial reform, which would help consolidate the fragmented administrative structure, creating larger and more economically self-sufficient administrative units, and (2) local government reform, focusing on creating clearly defined powers for local authorities with a view to securing government funding for specific tasks delegated from central government. Nonetheless, despite these measures, and in spite of the rhetoric coming from President Yanukovych and other members of the Party of Regions, it seems unlikely that the reform will be implemented in the foreseeable future. A series of concrete political decisions taken by the president over the past three years indicate that Yanukovych has not abandoned his plan to build a highly centralised political system. This in turn limits the capacity to govern of local authorities and further restricts the sources of funding for Ukraine’s regions. This apparent resistance to change stems from the fact that by implementing the proposed reforms, the president and his political allies would be forced to relinquish much of their control over the political processes taking place in the country and would have to free up the distribution of budgetary resources between Kyiv and the regions. The implementation of the reform within the specified timeframe (i.e. by 2015) is also unlikely due to the upcoming presidential election and the deteriorating economic situation in Ukraine. Without a comprehensive reform of local government, however, Ukraine will be unable to undertake effective modernisation measures, which are key for the socio-economic development of the country’s regions.

The Party of Regions monopolises power in Ukraine. OSW Commentary No. 40, 2010-09-29

Since the Party of Regions took power in Ukraine, the process of strengthening the executive branch of government at the expense of the others, together with the instrumental use of the law, has been progressing steadily. By seeking to restrict criticism of the government, the ruling party is aiming at marginalisation of opposition groups and establishing informal control over the main media (largely by exerting pressure on their owners). The role of the Security Service of Ukraine (SBU) is growing, as it is used increasingly frequently to put pressure on Western-oriented NGOs. The government’s control over the judiciary is expanding. These trends had existed before the Party of Regions’ ascension to power, but they were much weaker, as the previous governments did not enjoy such a strong position or the ability to achieve their ends so efficiently. The Party of Regions is planning to take another step towards total power during the local elections scheduled for October 2010. The party is determined to establish control over the local self-governments; to this end, it has amended the legislation in a way which now undermines local civil initiatives. These changes not only illustrate the interests and political standpoint of the ruling elite; they also result from systemic reasons, and these are deeply rooted in the Soviet past. The present Ukrainian state has evolved through the evolutionary transformation of the Ukrainian Soviet Socialist Republic. As a result, the main features of the previous system have been sustained, including the weakness of the representative bodies and the instrumental use of the law. Twenty years into its independent development, Ukraine has developed a merely formal democracy, which is distant from EU standards.