Deciphering the RNA landscape by RNAome sequencing

Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from rRNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. RNAome sequencing quantitatively preserved all RNA classes, allowing cross-class comparisons that facilitates the identification of relationships between different RNA classes. We demonstrate the strength of RNAome sequencing in mouse embryonic stem cells treated with cisplatin. MicroRNA and mRNA expression in RNAome sequencing significantly correlated between replicates and was in concordance with both existing RNA sequencing methods and gene expression arrays generated from the same samples. Moreover, RNAome sequencing also detected additional RNA classes such as enhancer RNAs, anti-sense RNAs, novel RNA species and numerous differentially expressed RNAs undetectable by other methods. At the level of complete RNA classes, RNAome sequencing also identified a specific global repression of the microRNA and microRNA isoform classes after cisplatin treatment whereas all other classes such as mRNAs were unchanged. These characteristics of RNAome sequencing will significantly improve expression analysis as well as studies on RNA biology not covered by existing methods

Detection of chemically induced ecotoxicological effects in rivers of the Nidda catchment (Hessen, Germany) and development of an ecotoxicological, Water Framework Directive–compliant assessment system

Abstract Background Approximately 90% of German surface waters do not meet the objectives of the European Water Framework Directive (EU-WFD). This is primarily due to deficits in water body structure and biological quality components, which in turn are negatively affected by chemical pollution. In this context, hydromorphological restoration measures have often been conducted to improve habitat and species diversity and, therefore, the ecological status of water bodies. However, habitat improvement is not necessarily accompanied by biota enhancement and thus by the improvement of the ecological status of rivers. To prioritize water management measures, decision criteria for the water management practice are necessary, which enable the prognosis, whether chemical pollution and its resulting effects or other factors, such as structural deficits of the water bodies, are the main cause for the failure to meet the objective of a good ecological status. Results To address this need, we applied the freshwater mudsnail Potamopyrgus antipodarum and the amphipod Gammarus fossarum in active monitoring campaigns and in laboratory experiments with combined water/sediment samples and analyzed water and sediment samples with in vitro assays quarterly over the course of 1 year to provide evidence and guideline to assess if chemical contamination is a relevant stress factor for the aquatic biodiversity in rivers of the Nidda catchment (Hessen, Germany). On the basis of these results, an ecotoxicological, WFD–compliant assessment system was developed which, in comparison with the ecological status classes of the EU-WFD, permits the identification of the probable causes for the failure to meet the objectives of the EU-WFD. From these findings, recommendations for action were derived for the implementation of priority measures in water management practice. For the rivers Nidda, Usa, and Horloff, we identified a need for action to improve water and sediment quality at all investigated sampling sites except for the reference sites in the headwaters. The ecotoxicological assessment system also highlighted that hydromorphological restoration measures on their own will not lead to a good ecological status of rivers, as long as water and sediment quality are deficient. Conclusion Hydromorphological restoration measures should be performed in conjunction with measures to reduce chemical contamination to achieve a good ecological status of the rivers Nidda, Usa, and Horloff

ニューオーリーンズの都市構造と核心地区

Genome Instability and Cance

Deciphering the RNA landscape by RNAome sequencing

Genome Instability and Cance

Divergent Molecular and Cellular Responses to Low and High-Dose Ionizing Radiation

Cancer risk after ionizing radiation (IR) is assumed to be linear with the dose; however, for low doses, definite evidence is lacking. Here, using temporal multi-omic systems analyses after a low (LD; 0.1 Gy) or a high (HD; 1 Gy) dose of X-rays, we show that, although the DNA damage response (DDR) displayed dose proportionality, many other molecular and cellular responses did not. Phosphoproteomics uncovered a novel mode of phospho-signaling via S12-PPP1R7, and large-scale dephosphorylation events that regulate mitotic exit control in undamaged cells and the G2/M checkpoint upon IR in a dose-dependent manner. The phosphoproteomics of irradiated DNA double-strand breaks (DSBs) repair-deficient cells unveiled extended phospho-signaling duration in either a dose-dependent (DDR signaling) or independent (mTOR-ERK-MAPK signaling) manner without affecting signal magnitude. Nascent transcriptomics revealed the transcriptional activation of genes involved in NRF2-regulated antioxidant defense, redox-sensitive ERK-MAPK signaling, glycolysis and mitochondrial function after LD, suggesting a prominent role for reactive oxygen species (ROS) in molecular and cellular responses to LD exposure, whereas DDR genes were prominently activated after HD. However, how and to what extent the observed dose-dependent differences in molecular and cellular responses may impact cancer development remain unclear, as the induction of chromosomal damage was found to be dose-proportional (10-200 mGy).Cancer Signaling networks and Molecular Therapeutic

Consolidation of Democracy in Central and Eastern Europe 1990-2001: Cumulation PCP I und II

Current state of the democratic consolidation in the newly implemented democracies. Topics: Political activities: discussions, convince friends, work in community, political meeting, contact politicians, work for party; meaning of democracy; democracy best form of government; democracy in (country) best; respect for individual human rights; importance of freedom and equality; Left-Right self placement; meaning of "Left" and "Right; membership in organisations and political parties; satisfaction with democracy; tolerance against: minority opinion, extremist demonstrations, free speech, too much freedom, critics on the way of life, right to own opinion, foreign critics; free market economy: right/wrong for country; satisfaction with free market; economic situation during present government, next year and compared to the socialist/communist regime; country´s economic situation during present government, next year and compared to the socialist/communist regime; conditions of workers, peasants, middle class, entrepreneurs during present government and compared to the socialist/communist regime; corruption during present government; public safety during present government, next year and compared to the socialist/communist regime; income differences right/wrong; one´s own financial situation compared to that of parents and neighbours; speed of change; satisfaction with present government and with the socialist/communist regime; communism good idea; better performance in: education, economy, poverty, black market, inflation, unemployment, public security, participation, corruption, public health, representation of interests, crime; pride in citizenship; pride to live in country; citizenship; women care of house; accept homosexuals; abortion; trust in institutions; medical care: self/governmental; income limits; government protects citizens; ecology vs. economy; conflicts: rich/poor, law-abiding/-breaker, speak language/not; (in Germany: conflicts between East/West), left/right, young/old, church moral/not, nationalists/others; police force against demonstrators; sentence against protestors, law against demonstrators, troops against strikes; big interests vs. all the people; trust in government; election best way to choose government; need for parliament; vote in last parliamentary election; vote intention; government responsible for providing job, health care, living standard for old and unemployed people, reduce income differences; governmental priorities; actions against bad governmental and local decisions; living conditions in western country; democracy in country: needs western development, never consolidated, same as in western countries, consolidation difficult process, notyet accomplished; Russia: country has own, difficult way; democracy problem will be solved; national political situation; change in political situation; state of democracy; parties: need of parties, no difference between parties, provide participation, for leaders´ interests; development since the end of the socialist/communist regime; characteristics of capitalist and socialist economy: strike, freedom, inequality, technical progress, wealth, selfishness, power, profit, justice, scarcity, humane, progress, planning, efficacy, repress, corruption; capitalist economy best; capitalist economy solves problems; management of industrial enterprises; close to party; political protest; one-person vs. multi-person system; interest in government; politicians against peoples´ interference; everybody can have say; better not get involved in politics; no trust in politicians; politicians seek views of people; people excl from power; make fortune get in politics; politicians only interested when trouble; participation is duty; satisfaction with changes: workers, engineers, artists, scientists, clerks, peasants, miners, entrepreneurs, politicians, army officers, policemen, leaders communist party; country where the living is better, better equality, people greater influence; importance in life: everybody voice in public matters, work for all, equality, everybody well-off, no arbitrary will, no big income differences, no state interference, live without worries, rest/entertain, free organisations, free speech, learn/access to culture; partner work outside; partner work full-/part-time; religion at birth; degree of religiosity; main language; in Russia: nationality; since when in neighbourhood; relations with neighbours; paid for work; reasons for not being paid; work full-/part-time; monthly income compared to average; percent of savings; one´s own social class and that of the parents; entrepreneur in family; family produce agricultural goods; easy replacement for job; work overtime/extra work; income of extra work; region; Germany: size of household and persons over 18 years, East-West socialization; weighting.Gegenwärtiger Stand der Konsolidierung der neu entstandenen Demokratien in den Ländern Mittel- und Osteuropas. Themen: Politische Aktivitäten: Diskussionen, eigene Meinungsführerschaft, in einer Gemeinschaft arbeiten; Bedeutung von Demokratie; Demokratie als beste Regierungsform; die Demokratie im eigenen Land ist die beste; Respektieren der Menschenrechte im eigenen Land; Wichtigkeit von Freiheit und Gleichheit; Selbsteinstufung auf einem Links-Rechts-Kontinuum; Bedeutung von Links und Rechts; Mitgliedschaft in Organisationen und politischen Parteien; Demokratiezufriedenheit im eigenen Land; Toleranz gegenüber: Meinungen von Minderheiten, extremistischen Demonstrationen, freier Meinungsäußerung, zu viel Freiheit, Kritik an bestimmten Lebensweisen; Recht auf eigene Meinung; ausländische Kritik; freie Marktwirtschaft; Zufriedenheit mit Marktwirtschaft im eigenen Land; gegenwärtige und erwartete eigene ökonomische Situation und Vergleich mit der Situation zur Zeit des sozialistischen Regimes; gegenwärtige und erwartete ökonomische Situation des Landes und Vergleich mit der Situation zur Zeit des sozialistischen Regimes; gegenwärtige Bedingungen für Arbeiter, Bauern, Mittelschicht und Unternehmer sowie im Vergleich zur Situation während der Zeit des sozialistischen Regimes; gegenwärtige Korruption; gegenwärtiger Zustand und erwartete Entwicklung der öffentlichen Sicherheit sowie Vergleich mit der Situation während der Zeit des sozialistischen Regimes; Einkommensdifferenzen; finanzielle Situation verglichen mit der von Eltern und Nachbarn; Geschwindigkeit der Veränderungen; Zufriedenheit mit der gegenwärtigen Regierung und mit dem sozialistischen Regime; Kommunismus als Idee; bessere Leistungen hinsichtlich Bildung, Wirtschaft, Armut, Schwarzmarkt, Inflation, Arbeitslosigkeit, öffentliche Sicherheit, Mitbestimmung, Korruption, Gesundheitswesen, Interessenvertretung und Kriminalität; Nationalstolz; Staatsbürgerschaft; Rolle der Frau; Abtreibung; Akzeptanz Homosexueller; Vertrauen in Institutionen; medizinische Versorgung; Einkommensgrenzen; Schutz des Bürgers durch den Staat; Ökologie versus Ökonomie; gesellschaftliche Konflikte (Ostdeutschland: Ost- West); Polizeikräfte gegen Demonstranten; Verurteilung von Protestanten; Gesetze gegen Demonstranten; militärische Kräfte gegen Streikende; Interessen einzelner gegen die aller; Vertrauen in die Regierung; Wahlen als beste Möglichkeit die Regierung zu bestimmen; Notwendigkeit eines Parlaments; Wahlverhalten bei der letzten Parlamentswahl; Wahlabsicht; Verantwortung der Regierung; Prioritäten des Staates; Aktionen gegen schlechte Regierungsentscheidungen; besseres Leben in westlichen Ländern; Demokratieentwicklung verglichen mit der in westlichen Ländern; eigene Demokratieform in Russland; Lösung der Demokratieprobleme möglich; Änderung der politischen Situation im Land; nationale politische Situation; Zustand der Demokratie; Rolle der Parteien; Entwicklung seit dem Ende des kommunistischen Regimes; Merkmale der kapitalistischen and sozialistischen Wirtschaft; Führung der Industrieunternehmen; Parteipräferenz; politischer Protest; Einpersonen- versus Mehrpersonensystem; Vertrauen in Politiker und Regierung; Politikbeteiligung ist Bürgerpflicht; Zufriedenheit mit den Veränderungen in verschiedenen gesellschaftlichen Gruppen; Wichtigkeit von Lebensbereichen. Demographie: Auswärtsbeschäftigung des Partners; Teilzeitbeschäftigung; Religionszugehörigkeit bei Geburt; Sprache; Russland: Nationalität; seit wann in Nachbarschaft und Beziehung zu den Nachbarn; Lohnerhalt; monatliches Einkommen verglichen mit dem Durchschnitt; Erspartes; eigene Schichtzugehörigkeit und die der Eltern; Unternehmer in der Familie; Herstellung von landwirtschaftlichen Produkten; schnell einen neuen Job; Einkommen aus zusätzlicher Arbeit; Region; Gewichtung; Deutschland: Größe des Haushaltes und Anzahl der Personen über 18 Jahre; aufgewachsen in Ost oder West