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Sascha Ott

Publications and source records attributed to Sascha Ott.

13 recordsLinked to original sources
PubMed2026

Exploratory single-nucleus multiomics analysis of myeloid cell states associated with neoadjuvant chemotherapy response in pancreatic ductal adenocarcinoma.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) continues to be one of the most lethal human malignancies, with the vast majority of patients ineligible for immunotherapy. Tumour-associated macrophages (TAMs) are key regulators of the PDAC tumour microenvironment (TME), yet their transcriptional and epigenomic heterogeneity in the context of chemotherapy response is poorly understood. Therefore, we performed an exploratory single nucleus multiomics analysis of PDAC tumors stratified by histopathologic response to neoadjuvant chemotherapy. METHODS: Surgical resection specimens from PDAC patients were classified as responders or non-responders using the American College of Pathologists (CAP) histopathologic criteria. Frozen tissue underwent simultaneous snRNA-seq and snATAC-seq on the 10x Genomics Chromium Single Cell Multiome platform, followed by downstream analyses such as differential gene expression, GO and hallmark pathway enrichment, pseudotime trajectory inference and ChromVAR transcription factor motif analysis. RESULTS: Multiomics profiling of 30 840 high-quality nuclei revealed a myeloid compartment that differed in composition and transcriptional state between CAP-defined responders and non-responders in this small cohort. We observed a trend toward higher LAM-like state proportions in the responders than non-responders (38.4% vs. 26.7%), although this disparity did not achieve statistical significance. The transcriptional programs of the responder myeloid cells are associated with phagocytosis and lipid handling. Chromatin accessibility analysis further suggested candidate response-associated transcription factor motif accessibility patterns. CONCLUSIONS: Neoadjuvant-treated PDAC tumours from CAP-defined responders in this cohort myeloid landscape with apparent enrichment of LAM-like states and immune-activating transcriptional/epigenetic programs. However, these findings are preliminary and hypothesis-generating because of the small cohort size, heterogeneous treatment regimens, absence of matched pre-treatment biopsies, and lack of knockout validation. Larger treatment cohorts and functional/mechanistic studies are needed to determine whether LAM-like myeloid programs contribute to chemotherapy response or reflect a consequence of chemotherapy treatment.

Humans↗
PubMed2006

Dynamic ligation at the first amine-coordinated iron hydrogenase active site mimic.

The first model of the iron hydrogenase active site has been prepared in which an amine ligand is loosely coordinated to an Fe(i) centre, and can be replaced by a solvent molecule; irrespective of the ligand set, the one electron reduction of both complexes is chemically reversible and is shown to proceed through the same species which features a bridging CO ligand.

Amines↗
PubMed2006

Bio-inspired, side-on attachment of a ruthenium photosensitizer to an iron hydrogenase active site model.

The first ruthenium-diiron complex [(mu-pdt)Fe2(CO)5{PPh2(C6H4CCbpy)}Ru(bpy)2]2+ 1 (pdt = propyldithiolate, bpy = 2,2'-bipyridine) is described in which the photoactive ruthenium trisbipyridyl unit is linked to a model of the iron hydrogenase active site by a ligand directly attached to one of the iron centers. Electrochemical and photophysical studies show that the light-induced MLCT excited state of the title complex is localized towards the potential diiron acceptor unit. However, the relatively mild potential required for the reduction of the acetylenic bipyridine together with the easily oxidized diiron portion leads to a reductive quenching of the excited state, instead. This process results in a transiently oxidized diiron unit which may explain the surprisingly high light sensitivity of complex 1.

Binding Sites↗
PubMed2006

Photoinduced energy transfer coupled to charge separation in a Ru(II)-Ru(II)-acceptor triad.

The bichromophoric system Ru-Ru(C)-PI ([(bpy)3Ru-Ph-Ru(dpb)(Metpy-PI)][PF6]3, where bpy is 2,2'-bipyridine, Hdpb is 1,3-di(2-pyridyl)-benzene, Metpy is 4'-methyl-2,2':6',2' '-terpyridine and PI is pyromellitimide) containing two Ru(II) polypyridyl chromophores with a N6 and a N5C ligand set, respectively, was synthesized and characterized. Its photophysical properties were investigated and compared to those of the monochromophoric cyclometalated complexes Ru(C)-PI ([Ru(dpb)(Metpy-PI)][PF6]), Ru(C)-phi-PI ([Ru(dpb)(ttpy-PI)][PF6], ttpy is 4'-p-tolyl-2,2':6',2' '-terpyridine), Ru(C)-phi ([Ru(dpb)(ttpy)][PF6]), and Ru(C) ([Ru(dpb)(Metpy)][PF6]). Excitation of the Ru(C) unit in the dyads leads to oxidative quenching, forming the Ru(C)(III)-phi-PI*- and Ru(C)(III)-Pl.- charge-separated (CS) states with k(f)(ET) = 7.7 x 10(7) s(-1) (CH3CN, 298 K) in the tolyl-linked Ru(C)-phi-PI and k(f)(ET) = 4.4 x 10(9) s(-1) (CH2Cl2, 298 K) in the methylene-linked Ru(C)-PI. In the Ru-Ru(C)-PI triad, excitation of the Ru(C) chromophore leads to dynamics similar to those in the Ru(C)-PI dyad, generating the Ru(II)-Ru(C)(III)-PI*- CS state, whereas excitation of the Ru unit results in an initial energy transfer (k(EnT) = 4.7 x 10(11) s(-1)) to the cyclometalated Ru(C) unit. Subsequent electron transfer to the PI acceptor results in the formation of the same Ru(II)-Ru(C)(III)-PI*- CS state with k(f)(ET) = 5.6 x 10(9) s(-1) that undergoes rapid recombination with k(b)(ET) = 1 x 10(10) s(-1) (CH2Cl2, 298 K). The fate of the Ru(II)-Ru(C)(III)-PI*- CS state upon a second photoexcitation was studied by pump-pump-probe experiments in an attempt to detect the fully charge-separated Ru(III)-Ru(C)(II)-PI*- state.

Chromatography, High Pressure Liquid↗
PubMed2005

Iron hydrogenase active site mimic holding a proton and a hydride.

The first model of the iron hydrogenase active site has been prepared which concomitantly carries a proton and a hydride; the title species was characterized by IR and NMR spectroscopy and is reduced at more positive potential than any other mimic of this kind.

Binding Sites↗
PubMed2005

Rapid energy transfer in bichromophoric tris-bipyridyl/cyclometallated ruthenium(II) complexes.

The synthesis, characterization, and photophysical properties of the N6-N5C bichromophoric [(bpy)2Ru(I)Ru(ttpy)][PF6]3 (bpy is 2,2'-bipyridine and ttpy is 4'-p-tolyl-2,2':6',2''-terpyridine) and [(bpy)2Ru(II)Ru(ttpy)][PF6]3 (I and II are bpy-dipyridylbenzene ditopic ligands bridged by an ethynyl and phenyl unit, respectively) complexes are reported together with the model mononuclear complexes [(bpy)2Ru(I)][PF6]2, [(bpy)2Ru(II)][PF6]2, [Ru(VI)(ttpy)][PF6] (VI is 3,5-di(2-pyridyl)-biphenyl) and [Ru(dpb)(ttpy)][PF(6)] (Hdpb is 1,3-di(2-pyridyl)-benzene). The electrochemical data show that there is little ground state electronic communication between the metal centers in the bimetallic complexes. Selective excitation of the N(5)C unit in the bichromophoric systems leads to luminescence typical for a bis-tridentate cyclometallated ruthenium complex and is similar to the [Ru(VI)(ttpy)][PF6] model complex. In contrast, the luminescence from the tris-bidentate N6 unit is efficiently quenched by energy transfer to the N5C unit. The energy transfer rate has been determined by femtosecond pump-probe measurements to 0.7 ps in the ethynyl-linked [(bpy)2Ru(I)Ru(ttpy)][PF6]3 and to 1.5 ps in the phenyl-linked [(bpy)2Ru(II)Ru(ttpy)][PF6]3 (in acetonitrile solution at 298 K), and is inferred to occur via a Dexter mechanism.

Journal Article↗
PubMed2004

Preparation and redox properties of N,N,N-1,3,5-trialkylated flavin derivatives and their activity as redox catalysts.

Eight different flavin derivatives have been synthesized and the electronic effects of substituents in various positions on the flavin redox chemistry were investigated. The redox potentials of the flavins, determined by cyclic voltammetry, correlated with their efficiency as catalysts in the H2O2 oxidation of methyl p-tolyl sulfide. Introduction of electron-withdrawing groups increased the stability of the reduced catalyst precursor.

Alkylation↗
PubMed2004

Model of the iron hydrogenase active site covalently linked to a ruthenium photosensitizer: synthesis and photophysical properties.

A model of the iron hydrogenase active site with the structure [(mu-ADT)Fe2(CO)6] (ADT = azadithiolate (S-CH2-NR-CH2-S), (2: R = 4-bromophenyl, 3: R = 4-iodophenyl)) has been assembled and covalently linked to a [Ru(terpy)2]2+ photosensitizer. This trinuclear complex 1 represents one synthetic step toward the realization of our concept of light-driven proton reduction. A rigid phenylacetylene tether has been incorporated as the linking unit in 1 in order to prolong the lifetime of the otherwise short-lived [Ru(terpy)2]2+ excited state. The success of this strategy is demonstrated by comparison of the photophysical properties of 1 and of two related ruthenium complexes bearing acetylenic terpyridine ligands, with those of [Ru(terpy)2]2+. IR and electrochemical studies reveal that the nitrogen heteroatom of the ADT bridge has a marked influence on the electronic properties of the [Fe2(CO)6] core. Using the Rehm-Weller equation, the driving force for an electron transfer from the photoexcited *[Ru(terpy)2]2+ to the diiron site in 1 was calculated to be uphill by 0.59 eV. During the construction of the trinuclear complex 1, n-propylamine has been identified as a decarbonylation agent on the [(mu-ADT)Fe2(CO)6] portion of the supermolecule. Following this procedure, the first azadithiolate-bridged dinuclear iron complex coordinated by a phosphine ligand [(mu-ADT)Fe2(CO)5PPh3] (4, R = 4-bromophenyl) was synthesized.

Binding Sites↗
PubMed2004

Increasing feasibility of optimal gene network estimation.

Disentangling networks of regulation of gene expression is a major challenge in the field of computational biology. Harvesting the information contained in microarray data sets is a promising approach towards this challenge. We propose an algorithm for the optimal estimation of Bayesian networks from microarray data, which reduces the CPU time and memory consumption of previous algorithms. We prove that the space complexity can be reduced from O(n(2) x 2(n)) to O(2(n)), and that the expected calculation time can be reduced from O(n(2) x 2(n)) to O(n x 2(n)), where n is the number of genes. We make intrinsic use of a limitation of the maximal number of regulators of each gene, which has biological as well as statistical justifications. The improvements are significant for some applications in research.

Algorithms↗
PubMed2003

Finding optimal gene networks using biological constraints.

The accurate estimation of gene networks from gene expression measurements is a major challenge in the field of Bioinformatics. Since the problem of estimating gene networks is NP-hard and exhibits a search space of super-exponential size, researchers are using heuristic algorithms for this task. However, little can be said about the accuracy of heuristic estimations. In order to overcome this problem, we present a general approach to reduce the search space to a biologically meaningful subspace and to find optimal solutions within the subspace in linear time. We show the effectiveness of this approach in application to yeast and Bacillus subtilis data.

Algorithms↗