Automated input structure generation for single-ended reaction path optimizations.

The exploration of a reaction network requires highly automated workflows to avoid error-prone and time-consuming manual steps. In this respect, a major bottleneck is the search for transition-state (TS) structures, which frequently fails and, therefore, makes (manual) revision necessary. In this work, we present a technique for obtaining suitable input structures for automated TS searches based on single-ended reaction path optimization algorithms, which makes subsequent TS searches via this method significantly more robust. First, possible input structures are generated based on the spatial alignment of the reactants. The appropriate orientation of reacting groups is achieved via stepwise rotations along selected torsional degrees of freedom. Second, a ranking of the obtained structures is performed according to selected geometric criteria. The main goals are to properly align the reactive atoms, to avoid hindrance within the reaction channel and to resolve steric clashes between the reactants. The developed procedure has been carefully tested on a variety of examples and provides suitable input structures for TS searches within seconds. The method is in daily use in an industrial setting.

Highly Stable and Reactive Platinum Single Atoms on Oxygen Plasma-Functionalized CeO2 Surfaces: Nanostructuring and Peroxo Effects.

Atomically dispersed precious metals on oxide supports have recently become increasingly interesting catalytic materials. Nonetheless, their non-trivial preparation and limited thermal and environmental stability constitutes an issue for their potential applications. Here we demonstrate that an oxygen plasma pre-treatment of the ceria (CeO2 ) surface serves to anchor Pt single atoms, making them active and resistant towards sintering in the CO oxidation reaction. Through a combination of experimental results obtained on well-defined CeO2 films and theory, we show that the O2 plasma causes surface nanostructuring and the formation of surface peroxo (O2 2- ) species, favoring the uniform and dense distribution of isolated strongly bonded Pt2+ atoms. The promotional effect of the plasma treatment was further demonstrated on powder Pt/CeO2 catalysts. We believe that plasma functionalization can be applied to other metal/oxide systems to achieve tunable and stable catalysts with a high density of active sites.

Band positions of anatase (001) and (101) surfaces in contact with water from density functional theory.

Titanium dioxide in the anatase configuration plays an increasingly important role in photo(electro)catalytic applications due to its superior electronic properties when compared to rutile. In aqueous environments, the surface chemistry and energetic band positions upon contact with water determine charge-transfer processes over solid-solid or solid-electrolyte interfaces. Here, we study the interaction of anatase (001) and (101) surfaces with water and the resulting energetic alignment by means of hybrid density functional theory. While the alignment of band positions favors charge-transfer processes between the two facets for the pristine surfaces, we find the magnitude of this underlying driving force to crucially depend on the water coverage and the degree of dissociation. It can be largely alleviated for intermediate water coverages. Surface states and their passivation by dissociatively adsorbed water play an important role here. Our results suggest that anatase band positions can be controlled over a range of almost 1 eV via its surface chemistry.

The BCR-ABL inhibitor nilotinib influences phenotype and function of monocyte-derived human dendritic cells.

In chronic myeloid leukemia (CML), the translocation t(9;22) results in the fusion protein BCR-ABL (breakpoint cluster region-abelson murine leukemia), a tyrosine kinase mediating oncogenic signaling which is successfully targeted by treatment with BCR-ABL inhibitors like imatinib. However, BCR-ABL inhibitors may also affect antitumor immunity. For instance, it was reported that imatinib impairs the function of dendritic cells (DCs) that play a central role in initiating and sustaining T cell responses. Meanwhile, second generation BCR-ABL inhibitors like nilotinib, which inhibits BCR-ABL with enhanced potency have become standard of treatment, at least in patients with BCR-ABL kinase domain mutations. In this study we analyzed the influence of therapeutic concentrations of nilotinib on human monocyte-derived DCs and compared its effects to imatinib. We found that both tyrosine kinase inhibitors (TKI) comparably and significantly impaired differentiation of monocytes to DCs as revealed by curtated downregulation of CD14 and reduced upregulation of CD1a and CD83. This was only partially restored after withdrawal of the TKI. Moreover, both TKI significantly reduced activation-induced IL-12p70 and C-C motif chemokine ligand (CCL) 3 secretion, while divergent TKI effects for CCL2 and CCL5 were observed. In contrast, only nilotinib significantly impaired the migratory capacity of DCs and their capacity to induce T-cell immune responses in MLRs. Our results indicate that imatinib and nilotinib may differ significantly with regard to their influence on antitumor immunity. Thus, for future combinatory approaches and particularly stop studies in CML treatment, choice of the most suitable BCR-ABL inhibitor requires careful consideration.

Interplay of mitochondrial metabolism and microRNAs.

Mitochondria are important organelles in cellular metabolism. Several crucial metabolic pathways such as the energy producing electron transport chain or the tricarboxylic acid cycle are hosted inside the mitochondria. The proper function of mitochondria depends on the import of proteins, which are encoded in the nucleus and synthesized in the cytosol. Micro-ribonucleic acids (miRNAs) are short non-coding ribonucleic acid (RNA) molecules with the ability to prevent messenger RNA (mRNA)-translation or to induce the degradation of mRNA-transcripts. Although miRNAs are mainly located in the cytosol or the nucleus, a subset of ~150 different miRNAs, called mitomiRs, has also been found localized to mitochondrial fractions of cells and tissues together with the subunits of the RNA-induced silencing complex (RISC); the protein complex through which miRNAs normally act to prevent translation of their mRNA-targets. The focus of this review is on miRNAs and mitomiRs with influence on mitochondrial metabolism and their possible pathophysiological impact.

The transcription factor MITF is a critical regulator of GPNMB expression in dendritic cells.

BACKGROUND: Dendritic cells (DC) are the most potent antigen-presenting cells (APC) with the unique ability to activate naïve T cells and to initiate and maintain primary immune responses. Immunosuppressive and anti-inflammatory stimuli on DC such as the cytokine IL-10 suppress the activity of the transcription factor NF-κB what results in downregulation of costimulatory molecules, MHC and cytokine production. Glycoprotein NMB (GPNMB) is a transmembrane protein, which acts as a coinhibitory molecule strongly inhibiting T cell responses if present on APC. Interestingly, its expression on human monocyte-derived dendritic cells (moDC) is dramatically upregulated upon treatment with IL-10 but also by the BCR-ABL tyrosine kinase inhibitors (TKI) imatinib, nilotinib or dasatinib used for the treatment of chronic myeloid leukemia (CML). However, the molecular mechanisms responsible for GPNMB overexpression are yet unknown. RESULTS: The immunosuppressive cytokine IL-10 and the BCR-ABL TKI imatinib or nilotinib, that were examined here, concordantly inhibit the PI3K/Akt signaling pathway, thereby activating the downstream serine/threonine protein kinase GSK3ß, and subsequently the microphthalmia-associated transcription factor (MITF) that is phosphorylated and translocated into the nucleus. Treatment of moDC with a small molecule inhibitor of MITF activity reduced the expression of GPNMB at the level of mRNA and protein, indicating that GPNMB expression is in fact facilitated by MITF activation. In line with these findings, PI3K/Akt inhibition was found to result in GPNMB overexpression accompanied by reduced stimulatory capacity of moDC in mixed lymphocyte reactions (MLR) with allogeneic T cells that could be restored by addition of the GPNMB T cell ligand syndecan-4 (SD-4). CONCLUSIONS: In summary, imatinib, nilotinib or IL-10 congruently inhibit the PI3K/Akt signaling pathway thereby activating MITF in moDC, resulting in a tolerogenic phenotype. These findings extend current knowledge on the molecular mechanisms balancing activating and inhibitory signals in human DC and may facilitate the targeted manipulation of T cell responses in the context of DC-based immunotherapeutic interventions.

Low-Valent Manganese Atoms Stabilized on Ceria for Nitrous Oxide Synthesis.

Nitrous oxide, N2 O, exhibits unique reactivity in oxidation catalysis, but the high manufacturing costs limit its prospective uses. Direct oxidation of ammonia, NH3 , to N2 O can ameliorate this issue but its implementation is thwarted by suboptimal catalyst selectivity and stability, and the lack of established structure-performance relationships. Systematic and controlled material nanostructuring offers an innovative approach for advancement in catalyst design. Herein low-valent manganese atoms stabilized on ceria, CeO2 , are discovered as the first stable catalyst for NH3 oxidation to N2 O, exhibiting two-fold higher productivity than the state-of-the-art. Detailed mechanistic, computational and kinetic studies reveal CeO2 as the mediator of oxygen supply, while undercoordinated manganese species activate O2 and facilitate N2 O evolution via NN bond formation between nitroxyl, HNO, intermediates. Synthesis via simple impregnation of a small metal quantity (1 wt%) predominantly generates isolated manganese sites, while full atomic dispersion is achieved upon redispersion of sporadic oxide nanoparticles during reaction, as confirmed by advanced microscopic analysis and electron paramagnetic resonance spectroscopy. Subsequently, manganese speciation is maintained, and no deactivation is observed over 70 h on stream. CeO2 -supported isolated transition metals emerge as a novel class of materials for N2 O production, encouraging future studies to evaluate their potential in selective catalytic oxidations at large.

Lattice-Stabilized Chromium Atoms on Ceria for N2O Synthesis.

The development of selective catalysts for direct conversion of ammonia into nitrous oxide, N2O, will circumvent the conventional five-step manufacturing process and enable its wider utilization in oxidation catalysis. Deviating from commonly accepted catalyst design principles for this reaction, reliant on manganese oxide, we herein report an efficient system comprised of isolated chromium atoms (1 wt %) stabilized in the ceria lattice by coprecipitation. The latter, in contrast to a simple impregnation approach, ensures firm metal anchoring and results in stable and selective N2O production over 100 h on stream up to 79% N2O selectivity at full NH3 conversion. Raman, electron paramagnetic resonance, and in situ UV-vis spectroscopies reveal that chromium incorporation enhances the density of oxygen vacancies and the rate of their generation and healing. Accordingly, temporal analysis of products, kinetic studies, and atomistic simulations show lattice oxygen of ceria to directly participate in the reaction, establishing the cocatalytic role of the carrier. Coupled with the dynamic restructuring of chromium sites to stabilize intermediates of N2O formation, these factors enable catalytic performance on par with or exceeding benchmark systems. These findings demonstrate how nanoscale engineering can elevate a previously overlooked metal into a highly competitive catalyst for selective ammonia oxidation to N2O, paving the way toward industrial implementation.

Physiological phenotyping of mammalian cell lines by enzymatic activity fingerprinting of key carbohydrate metabolic enzymes: a pilot and feasibility study.

OBJECTIVE: Enzymatic fingerprinting of key enzymes of glucose metabolism is a valuable analysis tool in cell physiological phenotyping of plant samples. Yet, a similar approach for mammalian cell line samples is missing. In this study, we applied semi-high throughput enzyme activity assays that were originally designed for plant samples and tested their feasibility in extracts of six frequently used mammalian cell lines (Caco2, HaCaT, C2C12, HEK293, HepG2 and INS-1E). RESULTS: Enzyme activities for aldolase, hexokinase, glucose-6-phosphate dehydrogenase, phosphoglucoisomerase, phosphoglucomutase, phosphofructokinase could be detected in samples of one or more mammalian cell lines. We characterized effects of sample dilution, assay temperature and repeated freeze-thaw cycles causing potential biases. After careful selection of experimental parameters, the presented semi-high throughput methods could be established as useful tool for physiological phenotyping of cultured mammalian cells.

Hyperandrogenism and Metabolic Syndrome Are Associated With Changes in Serum-Derived microRNAs in Women With Polycystic Ovary Syndrome.

Polycystic ovary syndrome (PCOS) remains one of the most common endocrine disorder in premenopausal women with an unfavorable metabolic risk profile. Here, we investigate whether biochemical hyperandrogenism, represented by elevated serum free testosterone, resulted in an aberrant circulating microRNA (miRNAs) expression profile and whether miRNAs can identify those PCOS women with metabolic syndrome (MetS). Accordingly, we measured serum levels of miRNAs as well as biochemical markers related to MetS in a case-control study of 42 PCOS patients and 20 Controls. Patients were diagnosed based on the Rotterdam consensus criteria and stratified based on serum free testosterone levels (≥0.034 nmol/l) into either a normoandrogenic (n = 23) or hyperandrogenic (n = 19) PCOS group. Overall, hyperandrogenic PCOS women were more insulin resistant compared to normoandrogenic PCOS women and had a higher prevalence of MetS. A total of 750 different miRNAs were analyzed using TaqMan Low-Density Arrays. Altered levels of seven miRNAs (miR-485-3p, -1290, -21-3p, -139-3p, -361-5p, -572, and -143-3p) were observed in PCOS patients when compared with healthy Controls. Stratification of PCOS women revealed that 20 miRNAs were differentially expressed between the three groups. Elevated serum free testosterone levels, adjusted for age and BMI, were significantly associated with five miRNAs (miR-1290, -20a-5p, -139-3p, -433-3p, and -361-5p). Using binary logistic regression and receiver operating characteristic curves (ROC), a combination panel of three miRNAs (miR-361-5p, -1225-3p, and -34-3p) could correctly identify all of the MetS cases within the PCOS group. This study is the first to report comprehensive miRNA profiling in different subgroups of PCOS women with respect to MetS and suggests that circulating miRNAs might be useful as diagnostic biomarkers of MetS for a different subset of PCOS.

Isolation and Analysis of Mitochondrial Small RNAs from Rat Liver Tissue and HepG2 Cells.

The presence of noncoding RNAs, such as microRNAs (miRNAs), in mitochondria has been reported by several studies. The biological roles and functions of these mitochondrial miRNAs ("mitomiRs") have not been sufficiently characterized, but the mitochondrial localization of miRNAs has recently gained significance due to modified mitomiR-populations in certain states of diseases. Here, we describe the isolation and analysis of mitochondrial RNAs from rat liver tissue and HepG2 cells. The principle of the analysis is to prepare mitochondria by differential centrifugation. Cytosolic RNA contamination is eliminated by RNase A treatment followed by Percoll gradient purification and RNA extraction. Small RNA content is verified by capillary electrophoresis. Mitochondrial miRNAs are detected by qPCR following synthesis of cDNA. After qPCR-based mitomiR-profiling, the Normfinder algorithm is applied to identify the suitable reference miRNAs to use as normalizers for mitochondrial input and data analysis. The described procedure depicts a simple way of isolating and quantifying mitomiRs in tissue and cell culture samples.