Strukturelle und funktionelle Charakterisierung zweier glycolytischer Enzyme des hyperthermophilen Archaeums Thermoproteus tenax

Hauptziel dieser Arbeit war es, die strukturellen und funktionellen Eigenschaften der Triosephosphat-Isomerase (TIM) und der Pyruvat-Kinase (PK) des hyperthermophilen Archaeums T. tenax zu charakterisieren und damit einen Beitrag zur Aufklärung der Regulation des Embden-Meyerhof-Parnas-Weges (EMP-Weg) in diesem Organismus zu leisten. Auf der Basis der Struktur- und Funktionsdaten sollte auch eine Analyse thermoadaptiver Merkmale sowie phylogenetischer Studien durchgeführt werden. Im ersten Teil der Arbeit wurde das TIM-kodierende tpi-Gen aus T. tenax kloniert und sequenziert. Zu vergleichende Untersuchungen wurde die TIM von T. tenax ebenso wie die TIMs des mesophilen Methanogenen M. bryantii und des hyperthermophilen Methanogenen M. fervidus in E. coli experimentiert. Das tpi-Gen von T. tenax ist mit dem Aconitase-Gen assoziiert und wird nach preliminären Untersuchungen möglicherweise mit diesem kotranskribiert. Dabei liegt die Kopienzahl der Transkripte unter heterotrophen Wachstumsbedingungen deutlich höher als unter autotrophen und spricht für die Regulation auf Transkriptebene. Die TIM von T. tenax liegt nach den vorliegenden Untersuchungen ebenso wie die TIMs der hyperthermophilen Euryarchaeota M. fervidus und p. woesei als Tetramer vor. Im Gegensatz dazu sind alle bekannten TIMs aus Eucarya und Bacteria sowie die TIM von M. bryantii Dimere. Dies bestätigt einen Trend zur Bildung höherer Aggredationsformen, der inzwischen auch bei anderen Enzymen aus hyperthermophilen Organismen vorgefunden wurde und unter dem Aspekt der Thermoadaption interpretiert wird. Der zweite Teil der Arbeit setzt sich mit der strukturellen und funktionellen Charakterisierung der PK auseinander. Das PK-kodierende pyk-Gen liegt isoliert im Genom von T.tenax und wird als monocistronische mRNS abgelesen. Die pyk-Transkriptmenge liegt in heterotrophen Zellen höher als in autotrophen Zellen und korreliert mit der PK-Aktivität in Zellen, die unter den entsprechenden trophischen Bedingungen angezogen wurden. Neben dieser Regulation auf Transkriptebene liegt eine Regulationsmöglichkeit auf Proteinebene vor: Das Enzym weist eine positive Bindungskooperativität für das Substrat Phosphoenolpyruvat sowie Mg 2+- bzw. Mn 2+-Ionen auf. Die Ergebnisse deuten daraufhin, dass die PK neben der nicht-phosphorylierenden GAPDH einen wichtigen Kontrollpunkt im EMP-Weg von T. tenax darstellt, über den der Organismus in die Lage versetzt wird, den Kohlenstofflux durch den Abbauweg kurzfristig (auf Proteinebene) und langfristig (durch genetische Regulation) zu ändern. Die phylogenetische Analyse zeigt, dass sich im Verlauf der Evolution zwei Großgruppen von PKs (PK I und PK II) gebildet haben. Die PKs der Eucarya, einige Enzyme von gram-positiven und gram-negativen Bacteria gehören zu der Großgruppe PK I, während die andere Gruppe (PK II) einen Großteil der gram-negativen Bacteria, Myco- und Corynebacteria, plastidäre Enzyme sowie die Archaea als monophyletische Gruppe umfaßt. Die Topologie des Baums legt nahe, dass die eucaryalen PKs von einem proteobacterialen Vorläuferenzym abstammen

Computational Barriers to Estimation from Low-Degree Polynomials

One fundamental goal of high-dimensional statistics is to detect or recover structure from noisy data. In many cases, the data can be faithfully modeled by a planted structure (such as a low-rank matrix) perturbed by random noise. But even for these simple models, the computational complexity of estimation is sometimes poorly understood. A growing body of work studies low-degree polynomials as a proxy for computational complexity: it has been demonstrated in various settings that low-degree polynomials of the data can match the statistical performance of the best known polynomial-time algorithms for detection. While prior work has studied the power of low-degree polynomials for the task of detecting the presence of hidden structures, it has failed to address the estimation problem in settings where detection is qualitatively easier than estimation. In this work, we extend the method of low-degree polynomials to address problems of estimation and recovery. For a large class of "signal plus noise" problems, we give a user-friendly lower bound for the best possible mean squared error achievable by any degree-D polynomial. To our knowledge, this is the first instance in which the low-degree polynomial method can establish low-degree hardness of recovery problems where the associated detection problem is easy. As applications, we give a tight characterization of the low-degree minimum mean squared error for the planted submatrix and planted dense subgraph problems, resolving (in the low-degree framework) open problems about the computational complexity of recovery in both cases.Comment: 38 page

Quantitatively consistent computation of coherent and incoherent radiation in particle-in-cell codes - a general form factor formalism for macro-particles

Quantitative predictions from synthetic radiation diagnostics often have to consider all accelerated particles. For particle-in-cell (PIC) codes, this not only means including all macro-particles but also taking into account the discrete electron distribution associated with them. This paper presents a general form factor formalism that allows to determine the radiation from this discrete electron distribution in order to compute the coherent and incoherent radiation self-consistently. Furthermore, we discuss a memory-efficient implementation that allows PIC simulations with billions of macro-particles. The impact on the radiation spectra is demonstrated on a large scale LWFA simulation.Comment: Proceedings of the EAAC 2017, This manuscript version is made available under the CC-BY-NC-ND 4.0 licens

Configurations with few crossings in topological graphs

AbstractIn this paper we study the problem of computing subgraphs of a certain configuration in a given topological graph G such that the number of crossings in the subgraph is minimum. The configurations that we consider are spanning trees, s–t paths, cycles, matchings, and κ-factors for κ∈{1,2}. We show that it is NP-hard to approximate the minimum number of crossings for these configurations within a factor of k1−ε for any ε>0, where k is the number of crossings in G.We then give a simple fixed-parameter algorithm that tests in O⋆(2k) time whether G has a crossing-free configuration for any of the above, where the O⋆-notation neglects polynomial terms. For some configurations we have faster algorithms. The respective running times are O⋆(1.9999992k) for spanning trees and O⋆((3)k) for s-t paths and cycles. For spanning trees we also have an O⋆(1.968k)-time Monte-Carlo algorithm. Each O⋆(βk)-time decision algorithm can be turned into an O⋆((β+1)k)-time optimization algorithm that computes a configuration with the minimum number of crossings

Finitary Coloring

Suppose that the vertices of ${\mathbb Z}^d$ are assigned random colors via a finitary factor of independent identically distributed (iid) vertex-labels. That is, the color of vertex $v$ is determined by a rule that examines the labels within a finite (but random and perhaps unbounded) distance $R$ of $v$, and the same rule applies at all vertices. We investigate the tail behavior of $R$ if the coloring is required to be proper (that is, if adjacent vertices must receive different colors). When $d\geq 2$, the optimal tail is given by a power law for 3 colors, and a tower (iterated exponential) function for 4 or more colors (and also for 3 or more colors when $d=1$). If proper coloring is replaced with any shift of finite type in dimension 1, then, apart from trivial cases, tower function behavior also applies.Comment: 35 pages, 3 figure

Sensitivity to cdk1-inhibition is modulated by p53 status in preclinical models of embryonal tumors

Dysregulation of the cell cycle and cyclin-dependent kinases (cdks) is a hallmark of cancer cells. Intervention with cdk function is currently evaluated as a therapeutic option in many cancer types including neuroblastoma (NB), a common solid tumor of childhood. Re-analyses of mRNA profiling data from primary NB revealed that high level mRNA expression of both cdk1 and its corresponding cyclin, CCNB1, were significantly associated with worse patient outcome independent of MYCN amplification, a strong indicator of adverse NB prognosis. Cdk1 as well as CCNB1 expression were readily detectable in all embryonal tumor cell lines investigated. Pharmacological inhibition or siRNA-mediated knockdown of cdk1/CCNB1 induced proliferation arrest independent of MYCN status in NB cells. Sensitivity to cdk1 inhibition was modulated by TP53, which was demonstrated using isogenic cells with wild-type TP53 expressing either dominant-negative p53 or a short hairpin RNA directed against TP53. Apoptosis induced by cdk1 inhibition was dependent on caspase activation and was concomitant with upregulation of transcriptional targets of TP53. Our results confirm an essential role for the cdk1/CCNB1 complex in tumor cell survival. As relapsing embryonal tumors often present with p53 pathway alterations, these findings have potential implications for therapy approaches targeting cdks