Dissertationen zum Thema „CNOT3“

Gene expression is a process that is tightly regulated by many factors. Different genes are transcribed not only in a cell specific manner but are also differentially expressed at different stages of the cell cycle. Cnot3 is part of the CCR4-NOT deadenylation complex, which is involved in the turnover of mRNAs in the cytoplasm and has also been shown to have roles in regulating transcription and cell proliferation and in maintaining ES cell pluripotency. Previous work demonstrated that Cnot3 interacts directly with Aurora B kinase and is phosphorylated by Aurora B in an in vitro assay. Aurora B and Cnot3 co-localise at active gene promoters in resting B cells. Since Aurora B is a cell cycle kinase, I have developed a cell synchronization system to analyse the role of the Cnot3-Aurora B interaction at different stages of the cell cycle in primary B cells. Using this system, I have demonstrated that the interaction between Cnot3 and Aurora B varies during cell cycle progression. In vitro analysis showed that the interaction occurs through the NOT box domain of Cnot3. Mass spectrometry analysis of Cnot3 interactors, performed on nuclear extracts from B cells in the early G1 and G2 phases of the cell cycle, identified interactions with many factors that are known to have roles in transcription regulation and RNA processing. Interaction of Cnot3 with Histone H1 was confirmed using a peptide binding assay, suggesting a potential role in chromatin organization. Cnot3 was also shown to interact with Xrn2, a 5'-3' exoribonuclease that is involved in RNA turnover and termination of transcription. ChIP analysis demonstrated promoter binding of Cnot3 at a number of cell cycle stages. Cnot3 shows cell cycle dependent binding to promoters of a wide range of active genes, including promoters that are not directly involved in cell cycle regulation. Genome wide analysis using ChIP sequencing revealed changes in the binding profiles of Cnot3 at promoters and enhancers during cell cycle progression. A Cnot3 conditional knock out mouse has been generated, which will be used to test the functional importance of these observations.

The human BTG/TOB protein family comprises six members (BTG1, BTG2/PC3/Tis21, BTG3/Ana, BTG4/PC3B, TOB1/Tob, and TOB2) that display anti-proliferative activity in a number of cell types. They are characterised by a conserved N-terminal BTG domain that mediates interactions with the Caf1a (CNOT7) and Caf1b (CNOT8) deadenylases. It was unclear whether the anti-proliferative activity of the BTG/TOB proteins was mediated through interactions with Caf1a (CNOT7) and Caf1b (CNOT8). To address this we further characterised the amino acid residues located along the BTG2 and TOB1 interaction surface with Caf1a (CNOT7)/Caf1b (CNOT8) to identify residues required for the interaction. We then analysed the role of BTG2 and TOB1 in the regulation of cell proliferation, translation and mRNA abundance using a mutant that is no longer able to interact with Caf1a (CNOT7)/Caf1b (CNOT8). We conclude that the anti-proliferative activity of BTG/TOB proteins is mediated through interactions with the Caf1a (CNOT7) and Caf1b (CNOT8) deadenylase enzymes. We also demonstrate that recruitment of BTG2 and TOB1 to mRNA leads to reduced protein levels and mRNA degradation. Furthermore, we show that the regulation of mRNA abundance and protein levels is dependent on Caf1a (CNOT7)/Caf1b (CNOT8), but does not appear to require other Ccr4-Not components, including the Ccr4a (CNOT6)/Ccr4b (CNOT6L) deadenylases, or the non-catalytic subunits CNOT1 or CNOT3.

L’avènement des nouvelles techniques de séquençage a permis d’augmenter de façon considérable le taux diagnostique des troubles du développement intellectuel (TDI) et plus de 2000 gènes impliqués sont aujourd’hui connus. Malgré ces progrès considérables, l’interprétation des variants identifiés par les techniques de séquençage reste parfois difficile et l’histoire naturelle des TDI nouvellement décrits est souvent méconnue. Notre travail a consisté à étudier quatre formes de TDI rares de modes de transmissionvariés sur les plans clinique et génétique afin de mieux comprendre ces affections et les mécanismes qui les sous-tendent. Nous avons d’une part précisé les tableaux cliniques associés aux variations de BRAT1, CNOT3 et MTOR et avons recherché l’existence d’éventuelles corrélations phénotype-génotype pour les variations de ces gènes. D’autre part, nous avons participé à la mise en place d’un test fonctionnel permettant de reclasser les variants de signification incertaine de PQBP1
The advent of new sequencing techniques has dramatically increased the diagnostic rate of intellectual disability (ID), and more than 2,000 genes are currently known to be involved. Despite these considerable progresses, interpreting the variants identified by sequencing methods remains challenging, and the natural history of newly described ID is often poorly understood. To better understand these disorders and their underlying mechanisms, we have studied four rare forms of ID with various inheritance patterns from both clinical and genetic perspectives. On one hand, we defined the clinical pictures associated with variations in BRAT1, CNOT3 and MTOR, and we investigated the existence of any phenotype-genotype correlations. On the other hand, we contributed to the design of a functional test to reclassify PQBP1 variants of uncertain significance

Local translation of mRNAs in dendrites is vital for synaptic plasticity and learning and memory. Tight regulation of this translation is key to preventing neurological disorders resulting from aberrant local translation. Here we find that CNOT7, the major deadenylase in eukaryotic cells, takes on the distinct role of regulating local translation in the hippocampus. Depletion of CNOT7 from cultured neurons affects the poly(A) state, localization, and translation of dendritic mRNAs while having little effect on the global neuronal mRNA population. Following synaptic activity, CNOT7 is rapidly degraded resulting in polyadenylation and a change in the localization of its target mRNAs. We find that this degradation of CNOT7 is essential for synaptic plasticity to occur as keeping CNOT7 levels high prevents these changes. This regulation of dendritic mRNAs by CNOT7 is necessary for normal neuronal function in vivo, as depletion of CNOT7 also disrupts learning and memory in mice. We utilized deep sequencing to identify the neuronal mRNAs whose poly(A) state is governed by CNOT7. Interestingly these mRNAs can be separated into two distinct populations: ones that gain a poly(A) tail following CNOT7 depletion and ones that surprisingly lose their poly(A) tail following CNOT7 depletion. These two populations are also distinct based on the lengths of their 3’ UTRs and their codon usage, suggesting that these key features may dictate how CNOT7 acts on its target mRNAs. This work reveals a central role for CNOT7 in the hippocampus where it governs local translation and higher cognitive function.

OLIVEIRA. M. S. R. Contribuições para comunicação e computação quânticas: análise do PMD e PDL em um sistema de DQC, geração de um estado entrelaçado de quatro modos e uma porta CNOT para qubits de estados coerentes. 2013. 60 f. Dissertação (Mestrado em Engenharia de Teleinformática) - Centro de Tecnologia, Universidade Federal do Ceará, Fortaleza, 2013.
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This work presents contributions to the quantum communication and in computation fields. In the area of quantum communication, we analyzed the impacts of the effects of PMD and PDL on the performance of a quantum key distribution system based on BB84 protocol in a fiber optic network. It was presented an analytical expression for the average fidelity as a function of the PMD and PDL parameters which makes possible to analyze the behavior of bit error and secure bit generation rates for a quantum communication system. In the field of quantum computing, we proposed two optical systems based on linear optics for coherent state qubits. The first system is a probabilistic generator of a four-mode-type entangled state with a maximum efficiency of 25%. From this it state was possible to propose a second system that is able to perform a probabilistically CNOT gate. Both proposed systems may be implemented with existing photonics technology. They do not use single-qubit gate or quantum teleportation that are commonly used in quantum information processing using coherent states.
Este trabalho apresenta contribuições para a área quântica, no âmbito da comunicação e da computação. Na área de comunicação quântica, foram analisados os impactos dos efeitos do PMD e PDL no desempenho de sistemas de distribuição quântica de chaves baseados no protocolo BB84, sob uma rede óptica a fibra. É demonstrada uma expressão analítica da fidelidade média em função dos parâmetros de PMD e PDL, o qual torna possível a análise do comportamento das taxas de erro de bit e de geração de bit seguro de um sistema de comunicação quântica. No campo da computação quântica, são propostos dois sistemas ópticos baseados em óptica linear para qubits de estados coerentes. O primeiro consiste em um gerador probabilístico de um tipo de estado entrelaçado de quatro modos com uma eficiência máxima de 25%. A partir desse estado foi possível propor um segundo sistema que é capaz de realizar uma porta CNOT probabilisticamente. Ambos os sistemas propostos são de implementação factível com a tecnologia fotônica existente, não utilizam portas de um qubit nem teleportação quântica, que são recursos comumente empregados em processamento quântico da informação para estados coerentes.

Pour exécuter un algorithme abstrait sur un ordinateur quantique il faut compiler l'algorithme en une séquence d'instructions bas niveau exécutables par le processeur. L'étape de compilation est cruciale car elle détermine la quantité de ressources nécessaire pour l'exécution d'un algorithme ; par conséquent elle se doit d'être optimisée. Dans cette thèse nous nous intéressons à une brique de la compilation~: la synthèse de circuits quantiques à partir d'une spécification abstraite d'un opérateur. Dans un premier temps nous étudions le cas où la matrice unitaire d'un opérateur quantique nous est donnée et nous explorons la minimisation des ressources quantiques et la minimisation des ressources classiques. Même si l'optimisation simultanée de ces deux types de ressources semble difficile, nous proposons de meilleurs compromis améliorant la littérature.Dans un second temps nous nous intéressons à la classe des opérateurs dits linéaires réversibles. Nous nous intéressons cette fois-ci exclusivement à l'optimisation des ressources quantiques et nous améliorons l'état de l'art dans diverses cas de métriques (taille et profondeur du circuit) et de processeurs quantiques (processeurs NISQ, ou à connectivité complète)
To run an abstract algorithm on a quantum computer, the algorithm must be compiled into a sequence of low-level instructions that can be executed by the processor. The compilation step is crucial because it determines the quantity of resources necessary for the execution of an algorithm. Therefore, the compilation stage must be optimized. In this thesis, we are interested in a brick of compilation: the synthesis of quantum circuits from an abstract specification of an operator.First, we study the case where the unitary matrix of a quantum operator is given to us and we explore the minimization of both quantum resources and classical resources. Even if the simultaneous optimization of these two types of resources seems difficult, we propose better compromises improving the literature.Secondly, we are interested in the class of so-called reversible linear operators. This time we are exclusively interested in the optimization of quantum resources and we improve the state of the art in various cases of quantum metrics (circuit size, circuit depth) and processors (NISQ, fully-connected processors)

L'obiettivo di questo elaborato è di dare una descrizione generale del funzionamento di un computer quantistico a ioni intrappolati, dal confinamento degli ioni in trappole unidimensionali fino all’implementazione delle porte logiche. Partendo dalla descrizione della trappola ionica di Paul che confina gli ioni tramite un potenziale di tipo armonico, si è poi descritto in che modo è possibile modificare lo stato interno degli ioni tramite l’interazione con il campo elettromagnetico generato da un laser esterno Si è esaminato nel dettaglio quali sono le principali tipologie di gate a singolo qubit e due tipologie di gate CNOT multi-qubit, quella di Cirac-Zoller e quella di Mølmer–Sørensen. Anche in questo caso, sono state descritte le implementazioni di tali gate nel caso specifico di un computer a ioni intrappolati. Nella parte finale viene presentata un’implementazione di un algoritmo quantistico su un processore reale a ioni intrappolati reso disponibile online dalla compagnia IonQ. In particolare sono stati preparati e misurati due tipi di stati quantistici: lo stato di Bell e il più generale stato GHZ.

碩士
國立臺灣大學
物理研究所
96
We investigate how pulse-sequences and operation times of elementary quantum gates can be optimized for silicon-based donor electron spin quantum computer architecture, complementary to the original Kane''s nuclear spin proposal. This gate-sequence-optimal or time-optimal quantum gate control in a quantum circuit is in addition to the more conventional concept of optimality in terms of the number of elementary gates needed in a quantum transformation. The optimal control method we use is the so-called gradient ascent pulse engineering (GRAPE) scheme. We focus on the high fidelity controlled-NOT (CNOT) gate and explicitly find the digitized control sequences by optimizing the effective, reduced donor electron spin Hamiltonian, with external controls over the hyperfine A and exchange J interactions. We first try different piecewise constant control steps and numerically calculate the fidelity (error) against the time needed to implement a CNOT gate with stopping criteria of error in the optimizer set to 〖10〗^(-9) in order to economize the simulation time. Here, the error is defined as 1-F, where F is fidelity. The error is less than 〖10〗^(-8) for times longer than 100ns, and it is found that 30 piecewise constant control steps for the CNOT gate operation will be sufficient to meet the required fidelity (error), and the performance would not be improved further with more steps. With operation time t=100ns and stopping criteria of error set to 〖10〗^(-16), we can find that the near time-optimal, high-fidelity CNOT gate control sequence has an error of 〖1.11×10〗^(-16). We then simulate the control sequences of the CNOT gate, obtained from reduced Hamiltonian simulations, with the full spin Hamiltonian. We find the error of about 〖10〗^(-6) which is below the error threshold required for fault-tolerant (〖10〗^(-4)) quantum computation. The CNOT gate operation time of 100ns is 3 times faster than the globally controlled electron spin scheme of 297ns. One of the great advantages of this near optimal-time high fidelity CNOT gate is that the exchange interaction is not required to be strong (the maximum value is J/h=20MHz compared to the typical value of 10.2GHz. This relaxes significantly the stringent distance constraint of two neighboring donor atoms of about 10nm as reported in the original Kane''s proposal to be about 30nm which is within the reach of the current fabrication technology.

碩士
國立陽明大學
生命科學系暨基因體科學研究所
102
Abstract Influenza A virus (IAV) is an enveloped RNA virus. Its genome consists of eight single-stranded negative-sense RNAs that encode 12 viral proteins. Each viral RNA segment is packaged with viral nucleoprotein (NP) and RNA-dependent RNA polymerase complex (PB1, PB2 and PA) to form viral ribonucleoprotein (vRNP) complexes. Our previous report showed that NP is a mono-ubiquitinated protein and can be specifically deubiquitinated by cellular deubiquitinase USP11. Ubiquitination of NP could alter the interaction of NP with viral RNA, and USP11 can cleave ubiquitin from NP, thereby reducing the RNA replication efficiency. Given these findings, we attempted to determine which E3 ligase(s) are responsible for NP ubiquitination; we used a small-scale RNAi screen based on candidates derived from RNAi pooled screening. An E3 ubiquitin ligase termed CNOT4 was picked from that screening for follow-up study. We found that expression of virus NP was decreased in a CNOT4 knockdown A549 cell line upon IAV infection. In addition, using CNOT4 knockdown 293T cells, we determined that viral RdRp activity was also inhibited as demonstrated by the minireplicon reporter assay. These findings suggest that CNOT4 may play a role in viral RNA transcription and replication. Interestingly, NP ubiquitination was decreased as evaluated by an in vitro ubiquitin assay in CNOT4 knockdown cells. When overexpressed wobble CNOT4, both NP ubiquitination and viral RdRp activity ware rescued in knockdown cells. Furthermore, when USP11 was co-expressed with CNOT4, the level of ubiquitination of NP was lower as compared with CNOT4 expressed alone. The results indicate that CNOT4 may increase ubiquitination of viral NP protein and enhance viral RdRp activity, and CNOT4 has opposite function with USP11 for IAV replication. Based on current findings, we hypothesize that CNOT4 is an E3 ligase of NP protein.

碩士
國立臺灣大學
應用物理所
101
When building a quantum computer, high precision gate operations are needed. In particular, the controlled-not (CNOT) operation regarded as a crucial universal two-qubit gate is a very important quantum gate to implement. However, real world contains a lot of problems and causes the difference between experimental results and theoretical simulations. In this thesis, we investigate CNOT gate operation using quantum optimal control theory for superconducting charge qubit system taking into account the effects of leakage states and a non-Markovian environment. First, we give a brief introduction to superconducting qubits and decide the Hamiltonian of a simple one-qubit model. Then we describe the noise power spectrum of environments, which gives the relation between the relaxation rate and the bath correlation function through the Fermi golden rule . After that, we describe the non-Markovian master equation approach and apply it to our model together with the quantum optimal control theory. The Krotov optimal control method that we used in this thesis can minimize the error of gate operations and find the corresponding optimal control pulses to realize the gate operations. Considering the non-local memory effect in non-Markovian open quantum systems. We also discuss the effect of different shapes and behaviors in the bath correlation function on the optimal control gate fidelity. We find that it is possible to implement high-fidelity CNOT gates with error about 1e-4~1e-5 in superconducting charge qubit system with environment parameters extracted from the realistic noise power spectrum of experiments.

To understand the mechanisms of transcriptional regulation of PXR, we performed yeast two-hybrid screenings to search for PXR-interacting proteins in a human liver cDNA library using the PXR ligand binding domain as the bait. More than one million independent clones were screened. One positive clone was a partial cDNA of CNOT2 (amino acid 183-540). CNOT2 is a component of CCR4-NOT that is a multi-subunit protein complex highly conserved from yeast to humans. Using a mammalian two-hybrid system in CV-1 cells and GST-pull down assays, we confirmed the direct interaction between PXR and CNOT2 and mapped the specific domains of association. In HepG2 cells, over expression of CNOT2 suppressed the PXR-regulated luciferase reporter gene activity. siRNA knockdown of CNOT2 potentiated PXR-transcriptional activity. These results strongly suggest that the CCR4-NOT complex is significantly involved in transcriptional regulation of PXR. The immuno-precipitated CNOT2 complex contained deadenylase activity as determined by an in vitro RNA decay assay. The presence of transfected PXR inhibited the cNOT2-associated deadenylase activity, as demonstrated by poly(A) tail PCR. Cellular localization of PXR and cNOT2 by immuno-fluorescence microscopy indicates that the interaction might occur within Cajal Bodies. Taken together, these results suggest that PXR regulates the mRNA turnover through direct interaction with the NOT2 component of the CCR4-NOT complex. PXR is also involved in colon cancer progression. Our results indicate that the evolutionarily conserved PXR protects organisms from carcinogenesis by inhibiting tumor growth as well as eliminating carcinogenic substances. Our laboratory proposes that pregnane X receptor has an important role in maintaining the balance of cells progressing through the cell cycle. In vitro and in vivo experiments demonstrate expression of PXR in colon cancer cells slows the progression of tumor formation. Colony growth of the PXR-transfected HT29 cells was suppressed in soft agar assay. In the xenograft assay, the tumor size formed in nude mice was significantly suppressed in HT29 cells stably transfected with PXR (310 mg /- 6.2 vs. 120 mg±6, p<0.01). The number of Ki-67 positive cells were significantly decreased in PXR-transfected HT29 xenograft tumor tissue compared vector-transfected HT29 controls (p<0.01) as determined by immuno-histochemistry suggesting that PXR inhibits proliferation of colon cancer cells. Results of flow cytometry analysis indicated that PXR-transfection in HT29 cells caused G0/G1 arrest. The growth inhibitory effects of PXR are likely mediated through the E2F/Rb-regulated check point since E2F1 nuclear expression was significantly inhibited by PXR over expression.

No
We present a demonstrative application of the nonholonomic control method to a real physical system composed of two cold Cesium atoms. In particular, we show how to implement a CNOT quantum gate in this system by means of a controlled Stark field.

碩士
國立臺灣大學
物理學研究所
107
Every realistic quantum computer inevitably suffers from decoherence and noise, resulting in errors. Hence, for quantum computing to be viable, delving into the errors for quantum systems and looking for a method, such as the optimal control method for error suppression, has become a critical task. This thesis investigates quantum gate operations for quantum computing based on the electron spins of donors in silicon, which is one of the most promising candidates for spin-based quantum computation as the electron spin qubits have relatively long $T_{1}^{*}$ and $T^*_{2}$ times. However, this system faces a stiff challenge on implementing two-qubit gates owing to the strength of the interaction between qubits depending sensitively on the exact positioning of qubits, which is not precisely known. Therefore, in this thesis, we focus on the discussion of the errors coming from this system parameter uncertainty and use an optimal control method to try to find error-suppression pulses for two-qubit gates. The thesis is organized as follows: First, we introduce the electron spins of an exchange-coupled pair of donors in silicon and use the ability to set the donor nuclear spins in arbitrary states to enlarge the effective magnetic detuning. Then, we present an optimal control method, which combines the sampling-based learning control and the gradient-free Nelder-Mead algorithm, to search for error-suppression pulses. Lastly, we present our result of a smooth pulse set for a two-qubit CNOT gate that can tolerate the parameter uncertainty error of about 10% of exchange interaction, while achieving a gate fidelity of 99%.

Główna teza dysertacji zatytułowanej In cammino verso la totalità. Esperienza personale come problema filosofico nel pensiero di Nietzsche, Benn, Warburg e Biral, zakłada, że myśl Nietzschego, Benna, Warburga i Birala skierowana jest wobec całości. Nietzsche, Benn, Warburg i Biral deklinują całość na własny sposób: według Nietzschego całość zakłada nobilitację i udoskonalenie człowieka pojmowanego jako ciało i duch, a to uszlachetnienie wymaga totalnego przewartościowania kultury, nowożytnych moralnych, politycznych i religijnych wartości – człowiek musi stać się silniejszy; zdaniem Benna całość zakłada stworzenie doskonałej i skończonej formy poetyckiej, według Warburga całość każe myśleć o mapie całej kolektywnej pamięci ludzkości, która pozwala „dobrym Europejczykom” zdiagnozować, a w konsekwencji również wyleczyć, wewnętrzne napięcia; według Birala wreszcie, poszukiwanie całości to synonim poszukiwania szczęścia, czyli doskonałej mądrości, ponieważ, jak to zrozumiał już Platon, mędrzec to człowiek skończenie szczęśliwy, niczego mu bowiem nie brak. Pryncypium metodologiczne wykorzystane w dysertacji opiera się na adherencji aplikacyjnej do metody użytej przez każdego myśliciela w jego własnych badaniach. Tak oto, kiedy poddawano analizie myśl Nietzschego, Warburga, Benna i Birala, założeniem pracy było ustanowienie dialogu z tekstami autorów. Praca starała się odpowiedzieć na pytania, które Nietzsche postawił w swoich aforyzmach i fragmentach wydanych pośmiertnie, posługując się badaniem genealogicznym użytych przez niego pojęć. Tą właśnie drogą przywiedziono doktrynę Nietzschego do jego woli mocy, przystosowując zatem do jego myśli metodę genealogiczną, której Nietzsche używał do analizy prawd innych filozofów i legislatorów wartości. Taki punkt wyjścia umożliwił wyjaśnienie filozofii Nietzschego „od wewnątrz”, bez konieczności mierzenia się z nią w sposób obiektywny (w znaczeniu przedmiotu badania oddzielonego od elementu osobowego filozofa, od jego doświadczeń, jak również od doświadczeń samego badacza). Również dialog z innymi badanymi myślicielami prowadzony był przy użyciu metody adherencji aplikacyjnej do metod przez nich wypracowanych i używanych. Tak oto konfrontacja z Aby Warburgiem zakładała korzystanie z filologii metamorfozy symboli. Dzięki tej metodzie poddany analizie został symbol węża i rola, jaką spełniał on w myśli Warburga i Nietzschego. W dialogu z Alessandro Biralem posłużyłiśmy się metodą historii pojęć (Begriffsgeschichte), którą Biral przejął od historyka Otto Brunnera. Zdaniem Birala nasze pojęcia, poprzez które orientujemy się w świecie praktycznym i w sferze myśli, kształtowały się historycznie, dlatego też pełne ich zrozumienie wymaga historycznego badania semantycznych stratyfikacji, z których każde pojęcie jest złożone. Metoda ta jest szczególnie przydatna w zrozumieniu tych starożytnych pojęć, których sens przewartościowała nowożytność, jak na przykład „cnota”, „polityka”, „głosowanie”. Podsumowując, można powiedzieć, że ogólna metoda badawcza to dialog genealogiczny. Składa się ona z interrogacji tekstów oraz pojęć w nich zawartych, poprzez genealogiczne badanie psycho-historycznych powodów, na których opierają się pojęcie użyte przez Nietzschego, Benna, Warburga i Birala. Praca odsyła do pytania o to, jak można poszukiwać różnie deklinowanej całości oraz, w jaki sposób można ją ewentualnie osiągnąć. Nowożytna nauka i nowożytna filozofia zakładają, że poszukiwanie prawdy równa się wzięciu w nawias osobistych doświadczeń: prawda, począwszy od Kartezjusza, jest zawsze obiektywna i powszechna, a zatem wszystko to, co odsyła do sfery osobistej (namiętności, pasje, doświadczenia życiowe) jest przeszkodą w odnalezieniu prawdy powszechnej. Inaczej mówiąc, to czysty rozum odnajduje prawdę. Rozum, który jest zanieczyszczony tym, co osobiste, jako że każda jednostka jest różna od innych, a jej prawda jest zawsze częściowa, jest opinią. Prawda nowożytna jest bezosobowa. Zdaniem czterech myślicieli , których refleksje zostały poddane analizie w niniejszej pracy, powszechna prawda nie istnieje. Jest tylko projekcją szczegółowych prawd. Prawda bezosobowa jest dla Nietzschego nie tylko nieistniejąca, ale również szkodliwa, ponieważ, zakładając własną absolutność, uniemożliwia poszukiwanie prawd, które uszlachetniają konkretny typ ludzki. Jedyną prawdą, do której człowiek może mieć dostęp, jest prawda osobista, a więc perspektywiczna. Nie wszyscy ludzie, żeby żyć lepiej, potrzebują tej samej prawdy. Ludzie bowiem nie są tacy sami. Co więcej, człowiek nie może się nigdy odseparować od tego, co mu przynależy, co go konstytuuje jako istotę żyjącą. Człowiek nie może się oddzielić od swoich doświadczeń osobistych. Tak więc prawda, jaką wyraża filozof, jest częścią jego osobistych doświadczeń i na nich się opiera: prawda nie jest celem, ale środkiem, warunkiem, narzędziem, które służy myślicielowi do uszlachetnienia własnego „ja” i do życia w sposób pełniejszy. Z jednej strony zatem prawda filozoficzna jest ugruntowana w całości osobistych doświadczeń i powinna być z nimi połączona. Z drugiej zaś, całości sensu, radości i prawdy nie można osiągnąć dzięki nowożytnej metodzie brania w nawias, usuwania osobistego składnika. Prawda jest „stronnicza”, ma swoje podziemne powody, a ich ujawnienie pozwala nam zrozumieć sens prawdy, czyli powody psycho-historyczne, dla których dany typ ludzki musiał i chciał widzieć świat w sposób, który odpowiadał strukturze jego duszy i sile jego instynktów. W celu udowodnienia głównej tezy dysertacji, analizie poddane zostały następujące zagadnienia: Nietzscheańska genealogia, Nietzscheańska krytyka moralności, przewartościowanie pojęcia cnoty, Nietzscheański makiawelizm, krytyka Benna względem propozycji pedagogicznych wypracowanych przez Nietzschego oraz relacji z nihilizmem, wiedza o kulturze Warburga jako nowa, interdyscyplinarna droga do zrozumienia i leczenia napięć obecnych w europejskiej duszy, Biraliańskie wyjaśnienie nowożytnej polityki i jego powrót do starożytnych pojęć cnoty i władzy, jak również Nietzscheańskie pojęcie odkupienia pojmowane jako tragiczny, nieskończony proces kroczenia w stronę całości.
The main thesis of the dissertation titled In cammino verso la totalità. Esperienza personale come problema filosofico nel pensiero di Nietzsche, Benn, Warburg e Biral, is that Nietzsche, Benn, Warburg and Biral's thought is directed towards totality. Nietzsche, Benn, Warburg and Biral decline totality each in their own way. According to Nietzsche, the totality implies man's ennoblement and perfection; man is here intended as the unity of body and spirit and his ennoblement requires a complete cultural transvaluation, as well as a transvaluation of modern moral, political and religious values – that is to say, man has to become stronger. According to Benn, the totality implies the creation of the perfect and accomplished poetical form. According to Warburg, the totality requires the elaboration of mankind's collective memory map, which shall allow „the good European” to diagnose and therefore to take care of his inner tensions. According to Biral, finally, the research of totality is synonymous with the research of happiness, thus of perfect wisdom, because, as already Plato meant it, the wise man, having nothing to desire, is the only one who is perfectly happy. The methodological principle of the dissertation is based on the applicative adherence to the method used by each thinker in his own investigations. Therefore, when we have studied Nietzsche, Warburg, Benn and Biral's thought, we have tried to create a dialogue with their texts. The work answers to questions left by Nietzsche in aphorisms and fragments by the genealogical research of concepts he made use of. Thus we have traced back Nietzsche's doctrines to his will to power and we applied to his thinking the genealogical method, which Nietzsche developed in order to analyze others philosophers and value-legislators truths. The method allows to explain Nietzsche's philosophy “from the inside” and permits to exclude an objective confrontation with it (that is to say, a confrontation with an object separated from philosopher's personal element, from his experiences, as well as from the researcher's ones). The dialogue with other thinkers was also based on the adherent application of methods they elaborated and applied. The confrontation with Aby Warburg implied the use of the philology of symbol-metamorphoses. Thanks to this method we analyzed the serpent symbol and the role it fulfilled within Nietzsche and Warburg's thought. While interacting with Alessandro Biral we used the history of concepts (Begriffsgeschichte) method. Biral learned this method from the historian Otto Brunner. According to Biral, our concepts, by which we orientate ourselves in both practical and theoretical world, have historically become. In order to comprehend them, a historical research of semantic stratification each concept is built of is needed. This method is particularly useful in order to understand the ancient concepts which meaning the modernity has transvaluated, as for instance “virtue”, “politics”, “voting”. To sum up, we can say that the general method is a genealogical dialogue. This method is composed of textual and conceptual interrogation which is made through psycho-historical research of motives from which Nietzsche, Benn, Warburg and Biral's concepts originated. The dissertation answers the question concerning the possibility of searching for and eventually achieving the totality. According to modern science and to modern philosophy, the searching for truth implies a suspension of personal experiences: from Descrates onwards, the truth is always objective and universal and all that refers to individual sphere (instincts, passions, life experiences) hinders the finding of the universal truth. In other words, only the pure reason finds out the truth. This means that each individual differs from other and that each individual truth is always partial, that is to say it is an opinion. The modern truth is impersonal. According to four thinkers whose reflection is here analyzed, an universal truth does not exist. According to Nietzsche, the impersonal truth non only does not exist, but it is dangerous because, being thought as absolute, makes impossible the research of the individual truth which ennobles a specific type of man. The only truth we have access to is an individual one, that is to say a perspective one. Not everybody, in order to live better, needs the same truth. Men are not equal. Furthermore, man can never separate himself from what belongs to him and constitutes him as a living person. Man cannot separate himself from his own personal experiences. For that reason the truth expressed by a philosopher is part of his personal experiences and is built on them: the truth is not a goal, but rather a mean, a condition, an instrument that helps the thinker to ennoble his self and to live more fully. On the one hand the philosophical truth is rooted in the totality of personal experiences of the philosopher and has to be linked to them. On the other hand, the totality of sense, happiness and truth, is not to be obtained thanks to the modern method of suspension of the personal element. Truth is “sided”, it has its own underground motives. To reveal them is to understand the sense of a truth, that is to say the psycho-historical motives that forced a certain type of man to see the world correspondingly to the structure of his soul and to the power of his instincts. In order to prove the main theses of the dissertation, we have analyzed the following topics: Nietzsche's genealogy, Nietzsche' criticism of morality and the transvaluation of the concept of virtue, Nietzsche's politics as Machiavellianism, Benn's criticism of Nietzsche's pedagogical argumentation and the relationship with nihilism, Warburg's science of culture as a new, interdisciplinary way of understanding and healing the tensions present in European soul, Biral's explanation of modern politics and the urgency of the return to the ancient concepts of virtue and government and, finally, Nietzsche's concept of redemption seen as a tragical, incomplete process of stepping towards totality.

This thesis provides biophysical bases of the interactions between two proteins involved in microRNA (miRNA)-mediated silencing: CNOT1 and the silencing domain of GW182. The regulation of gene expression at the post-transcriptional level involves the crucial CCR4-NOT deadenylase complex, which deadenylates mRNA, and can also inhibit translation in an independent fashion. In miRNA-mediated silencing, the CCR4-NOT complex is brought into the vicinity of the target mRNA by the successive actions of the miRNA, the Argonaute protein and finally, the GW182 protein, which interacts directly with CCR4-NOT. In the case of silencing of mRNAs containing AU-rich elements, the same action is performed by the protein called tristetraprolin involved in the regulation of inflammatory processes. The interactions and interplay between all of these high molecular weight proteins are relatively poorly understood. In particular, the interaction sites between GW182 and the CCR4-NOT complex were previously unknown. Molecular biology experiments allowed the identification of CCR4-NOT interaction motifs on GW182. One of them is crucial for deadenylation, while the other is vital in mediating the interaction with CCR4-NOT via CNOT1, the scaffolding subunit of the CCR4-NOT complex. Biophysical experiments based on hydrogen-deuterium exchange mass spectrometry allowed the identification of the corresponding binding site on CNOT1(800-999). Surprisingly, the binding site of the GW182 silencing domain was found to be at the same CNOT1(800-999) surface region as the binding site of tristetraprolin. Biochemical experiments excluded their simultaneous binding to CNOT1. The GW182 and tristetraprolin proteins share a common motif, RLPXφ, that interacts with CNOT1 in a very similar, but not identical, manner. This sequence has been proposed to act as a short linear motif. Thus, the two different gene silencing pathways: miRNA-mediated silencing and ARE-mediated silencing intersect at CNOT1, which serves as a molecular hub. The structural dynamics of the GW182 silencing domain and the CNOT1(800-999) fragments were also studied. The GW182 silencing domain was experimentally proved to be natively unstructured except for an RNA-recognition motif (RRM) domain. The GW182 RRM domain was found to be a loose structure, contrary to the CNOT1(800-999) structure that was found to be very rigid. Experiments performed in this thesis have led to the discovery of the interaction sites between the natively disordered GW182 silencing domain and the helical CNOT1(800-999) protein fragment, contributing to the understanding of the molecular mechanisms of recognition within protein complexes involved in gene silencing in different physiological processes.
Niniejsza praca doktorska dotyczy biofizycznych podstaw oddziaływania między białkami zaangażowanymi w wyciszanie ekspresji genów przez mikro-RNA (miRNA), a mianowicie pomiędzy białkiem CNOT1 a domeną wyciszającą białka GW182. W procesie wyciszania ekspresji genów przez miRNA, cząsteczki te wiążą się z białkiem Argonaute i naprowadzają je na cząsteczkę mRNA, która ma ulec wyciszeniu. Z białkiem Argonaute oddziałuje białko GW182, które z kolei wiąże się z kompleksem deadenylaz CCR4-NOT. Kompleks ten deadenyluje mRNA oraz może także blokować jego translację, co łącznie prowadzi do wyciszenia ekspresji danego genu. Z kolei w wyciszaniu mRNA zawierających sekwencje bogate w adeninę i urydynę, rolę miRNA wraz z Argonaute i GW182 pełni białko o nazwie tristetraprolina, które odgrywa kluczową rolę w procesach odpowiedzi na stany zapalne. Oddziaływania pomiędzy składnikami tego skomplikowanego układu białek o wielkich masach cząsteczkowych są jeszcze stosunkowo słabo poznane. W szczególności, nieznane były miejsca odpowiedzialne za tworzenie kompleksu pomiędzy GW182 a CCR4-NOT. Doświadczenia z zakresu biologii molekularnej pozwoliły na identyfikację miejsc wiążących CCR4-NOT w sekwencji domeny wyciszającej białka GW182. Jedno z nich ma kluczowy wpływ na deadenylację, a drugie - kluczowy wpływ na oddziaływanie z kompleksem CCR4-NOT za pośrednictwem jego centralnej podjednostki CNOT1. Badania biofizyczne metodą wymiany wodór-deuter sprzężoną ze spektrometrią mas pozwoliły z kolei na identyfikację miejsca oddziaływania GW182 na białku CNOT1 (we fragmencie 800-999), które, niespodziewanie, okazało się bardzo dobrze pokrywać z miejscem oddziaływania CNOT1(800-999) z tristetraproliną. Eksperymenty biochemiczne wykazały, że białka te konkurują o miejsce oddziaływania na CNOT1(800-999). Białka GW182 i tristetraprolina oddziałują z CNOT1 wykorzystując ten sam motyw sekwencji, RLPXφ, w bardzo podobny, jednak nie identyczny sposób. Sekwencja ta prawdopodobnie działa jako tzw. krótki motyw liniowy (z ang. short linear motif, SLiM). Zatem te dwa szlaki kontroli nad ekspresją genów krzyżują się. W pracy zbadano także dynamikę strukturalną białka CNOT1(800-999) oraz domeny wyciszającej białka GW182. Wykazano eksperymentalnie, że białko GW182 ma nieustrukturyzowany charakter, oprócz domeny wiążącej RNA (RRM), która ma strukturę bardzo dynamiczną. Natomiast białko CNOT1(800-999) charakteryzuje się stabilną, ściśle upakowaną strukturą. Przeprowadzone badania doprowadziły do odkrycia miejsc oddziaływania pomiędzy natywnie nieustrukturyzowaną domeną wyciszającą GW182, a helikalnym fragmentem białka CNOT1(800 999), przyczyniając się do zrozumienia molekularnych mechanizmów rozpoznawania w kompleksach białkowych odpowiedzialnych za regulację ekspresji genów w różnych procesach komórkowych.

Niniejsza rozprawa dotyczy publicznych przedsięwzięć pomnikowych w Księstwie Warszawskim, Królestwie Polskim oraz Wolnym Mieście Krakowie w latach 1807-1830, a więc w tych politycznych bytach, które powszechnie uznawano wówczas za "wskrzeszoną" Polskę (po rozbiorach Rzeczypospolitej Obojga Narodów pod koniec XVIII wieku). Jest to interdyscyplinarne studium łączące metodologię historii kultury z metodami historycystycznego podejścia do sztuki i architektury, skupiające się na problemie ideologicznego i politycznego ugruntowania pomnikowych przedsięwzięć komemoracyjnych dotyczących wybitnych jednostek. Jestem przede wszystkim zainteresowany szeroko rozumianym społeczno-kulturowym kontekstem takich inicjatyw, których celem było promowanie w przestrzeni publicznej określonych wartości (uosabianych przez tych, których upamiętniano), na których ich inicjatorzy chcieli opierać "wskrzeszoną" wspólnotę narodową. Badania nad pomnikami są przeze mnie traktowane jako "case study" pozwalające na pogłębioną analizę tak kluczowych dla tej epoki problemów jak relacja pomiędzy państwem a społeczeństwem (opinią publiczną) w przestrzeni publicznej, hierarchia publicznego prestiżu obywatelskich zasług, prestiż władzy monarszej jak również współczesne polityki historyczne (praktyki odwoływania się do przeszłości jako narzędzia ideologicznego). Kluczowym elementem mojej rozprawy jest analiza artystycznej formy interesujących mnie obiektów pod kątem jej znaczenia dla ideologicznego komunikatu. W omawianym okresie podstawowym punktem odniesienia była pod tym względem tradycja grecko-rzymskiego antyku, łącząca wyobrażenie o ideale artystycznym z ideałem moralnym.
The dissertation deals with public memorial enterprises in the Duchy of Warsaw, Kingdom of Poland and Free City of Cracow (1807-1830), thus those early nineteenth-century political entities that aspired to the status of ‘resurrected’ Poland (after the collapse of the Polish-Lithuanian Commonwealth at the end of the previous century). It is an interdisciplinary study that links the methodology of cultural historiography with the methods of the historicist approach towards art and architecture and is focused on the problem of ideological and political framework of the cultural practice of monumental public commemoration of distinguished individuals. I am especially interested in the broadly understood socio-cultural context of such initiatives, which were intended to impose on the public (or more precisely, the politically conscious minority/elite) a given vision of the values (impersonated by those chosen to be monumentally commemorated) on which the initiators wanted to found the ‘resurrected’ national community. I am approaching the subject of monuments as a case study that enables me to tackle such crucial socio-cultural problems of the epoch in question as the character and ideological grounding of the relationship between the state and society (the public) in the public sphere, the hierarchy of public prestige of civic merits and virtues, the prestige of monarchical power as well as the contemporary historical policies (the practice of making use of history and historical imagination in current political activity). The crucial aspect of my study of monuments is the analysis of the artistic form and the investigation of its role as an agent of ideological meaning – I am interested in the relationship between what and how a given ideological message was expected to be conveyed. In the period in question it was the classical tradition of the Greco-Roman antiquity that served as the basic font of inspiration due to the fact that it presented the contemporary Polish culture with accepted paradigms of both artistic and heroic (moral) perfection – classicism was thus the normative idiom of monumental enterprises.