Search

High energy density materials (HEDMs) have emerged as a research focus due to their advantageous ultra-high detonation pressure and velocity. The key objective of this study is to design materials with the best performance. Density functional theory (DFT) was utilized to evaluate the geometric structure, energy properties, and sensitivities of 28 designed F-containing derivatives. The theoretical density (ρ) and heat of formation (HOF) were used to estimate the detonation velocity (D) and pressure (P) of the title compounds. Our study shows that the introduction of fluorine-containing substituents or fluorine-free substituents into the CHOFN backbone or the CHON backbone can significantly enhance the detonation performance of derivatives. Among them, derivative B1 exhibites the best overall performance, including superior density, detonation performance, and sensitivity (P = 58.89 GPa, D = 8.02 km/s, ρ = 1.93 g/cm³, and characteristic height H50 = 34.6 cm). Our molecular design strategy contributes to the development of more novel HEDMs with excellent detonation performance and stability. It also marks a significant step towards a material engineering era guided by theory-based rational design. Methods For an accurate analyze, we employed the B3LYP functional with the 6-31+G(d,p) basis set for geometry optimization and exploration of physicochemical properties of the materials. The minima with no imaginary frequencies were confirmed using harmonic vibrational frequency results at the same theory level. With the assistance of DFT calculation, the quantum properties of the materials were analyzed using the Chapman-Jouguet (C-J) thermodynamic detonation theory. Our broad analysis facilitated an extensive assessment of these properties.

Patients with Parkinson’s disease (PD) exhibit differences in their gut microbiomes compared to healthy individuals. Although differences have most commonly been described in the abundances of bacterial taxa, changes to viral and archaeal populations have also been observed. Mechanistic links between gut microbes and PD pathogenesis remain elusive but could involve molecules that promote α-synuclein aggregation. Here, we show that 2-hydroxypyridine (2-HP) represents a key molecule for the pathogenesis of PD. We observe significantly elevated 2-HP levels in faecal samples from patients with PD or its prodrome, idiopathic REM sleep behaviour disorder (iRBD), compared to healthy controls. 2-HP is correlated with the archaeal species Methanobrevibacter smithii and with genes involved in methane metabolism, and it is detectable in isolate cultures of M. smithii. We demonstrate that 2-HP is selectively toxic to transgenic α-synuclein overexpressing yeast and increases α-synuclein aggregation in a yeast model as well as in human induced pluripotent stem cell derived enteric neurons. It also exacerbates PD-related motor symptoms, α-synuclein aggregation, and striatal degeneration when injected intrastriatally in transgenic mice overexpressing human α-synuclein. Our results highlight the effect of an archaeal molecule in relation to the gut-brain axis, which is critical for the diagnosis, prognosis, and treatment of PD.

A disintegrin-like and metalloprotease domain with thrombospondin type 1 motifs (ADAMTS)8 is a secreted protease, which was recently implicated in pathogenesis of pulmonary arterial hypertension (PAH). However, the substrate repertoire of ADAMTS8 and regulation of its activity are incompletely understood. Although considered a proteoglycanase because of high sequence similarity and close phylogenetic relationship to the proteoglycan-degrading proteases ADAMTS1, 4, 5, and 15, as well as tight genetic linkage with ADAMTS15 on human chromosome 11, its aggrecanase activity was reportedly weak. Several post-translational factors are known to regulate ADAMTS proteases such as autolysis, inhibition by endogenous inhibitors, and receptor-mediated endocytosis, but their impacts on ADAMTS8 are unknown. Here, we show that ADAMTS8 undergoes autolysis at six different sites within its spacer domain. We also found that in contrast to ADAMTS4 and 5, ADAMTS8 levels were not regulated through low-density lipoprotein receptor-related protein 1 (LRP1)-mediated endocytosis. Additionally, ADAMTS8 lacked significant activity against the proteoglycans aggrecan, versican, and biglycan. Instead, we found that ADAMTS8 cleaved osteopontin, a phosphoprotein whose expression is upregulated in PAH. Multiple ADAMTS8 cleavage sites were identified using liquid chromatography-tandem mass spectrometry. Osteopontin cleavage by ADAMTS8 was efficiently inhibited by TIMP-3, an endogenous inhibitor of ADAMTS1, 4, and 5, as well as by TIMP-2, which has no previously reported inhibitory activity against other ADAMTS proteases. These differences in post-translational regulation and substrate repertoire differentiate ADAMTS8 from other family members and may help to elucidate its role in PAH.

Mutations in succinate dehydrogenase (SDH) are associated with tumor development and neurodegenerative diseases. Only in tumors, loss of SDH activity is accompanied with the loss of complex I activity. Yet, it remains unknown whether the metabolic phenotype of SDH mutant tumors is driven by loss of complex I function, and whether this contributes to the peculiarity of tumor development versus neurodegeneration. We addressed this question by decoupling loss of SDH and complex I activity in cancer cells and neurons. We found that sole loss of SDH activity was not sufficient to recapitulate the metabolic phenotype of SDH mutant tumors, because it failed to decrease mitochondrial respiration and to activate reductive glutamine metabolism. These metabolic phenotypes were only induced upon the additional loss of complex I activity. Thus, we show that complex I function defines the metabolic differences between SDH mutation associated tumors and neurodegenerative diseases, which could open novel therapeutic options against both diseases. ispartof: Metabolic Engineering vol:43 issue:Pt B pages:187-197 ispartof: location:Belgium status: published

Beside its genomic properties, DNA is also recognized as a novel material in the field of nanoengineering. The specific bonding of base pairs can be used to direct the assembly of highly structured materials with specific nanoscale features such as periodic 2D arrays, 3D nanostructures, assembly of nanomaterials, and DNA nanomachines. In recent years, a variety of DNA nanomachines are developed because of their many potential applications in biosensing, diagnostics, and therapeutic applications. In this review, the fuel-powered motors and secondary structure motors, whose working mechanisms are inspired or derived from natural phenomena and nanomachines, are discussed. The combination of DNA motors with other platforms is then discussed. In each section of these motors, their mechanisms and their usage in the biomedical field are described. Finally, it is believed that these DNA-based nanomachines and hybrid motifs will become an integral point-of-care diagnostics and smart, site-specific therapeutic delivery.

Metabolomic markers associated with incident central adiposity gain were investigated in young adults. In a 9-mo prospective study of university freshmen (n = 264). Blood samples and anthropometry measurements were collected in the first 3 d on campus and at the end of the year. Plasma from individuals was pooled by phenotype [incident central adiposity, stable adiposity, baseline hemoglobin A1c (HbA1c) > 5.05%, HbA1c < 4.92%] and assayed using GC-MS, chromatograms were analyzed using MetaboliteDetector software, and normalized metabolite levels were compared using Welch's t test. Assays were repeated using freshly prepared pools, and statistically significant metabolites were quantified in a targeted GC-MS approach. Isotope tracer studies were performed to determine if the potential marker was an endogenous human metabolite in men and in whole blood. Participants with incident central adiposity gain had statistically significantly higher blood erythritol [P < 0.001, false discovery rate (FDR) = 0.0435], and the targeted assay revealed 15-fold [95% confidence interval (CI): 13.27, 16.25] higher blood erythritol compared with participants with stable adiposity. Participants with baseline HbA1c > 5.05% had 21-fold (95% CI: 19.84, 21.41) higher blood erythritol compared with participants with lower HbA1c (P < 0.001, FDR = 0.00016). Erythritol was shown to be synthesized endogenously from glucose via the pentose-phosphate pathway (PPP) in stable isotope-assisted ex vivo blood incubation experiments and through in vivo conversion of erythritol to erythronate in stable isotope-assisted dried blood spot experiments. Therefore, endogenous production of erythritol from glucose may contribute to the association between erythritol and obesity observed in young adults.

Background Metabolism gained increasing interest for the understanding of diseases and to pinpoint therapeutic intervention points. However, classical metabolomics techniques only provide a very static view on metabolism. Metabolic flux analysis methods, on the other hand, are highly targeted and require detailed knowledge on metabolism beforehand. Results We present a novel workflow to analyze non-targeted metabolome-wide stable isotope labeling data to detect metabolic flux changes in a non-targeted manner. Furthermore, we show how similarity-analysis of isotopic enrichment patterns can be used for pathway contextualization of unidentified compounds. We illustrate our approach with the analysis of changes in cellular metabolism of human adenocarcinoma cells in response to decreased oxygen availability. Starting without a priori knowledge, we detect metabolic flux changes, leading to an increased glutamine contribution to acetyl-CoA production, reveal biosynthesis of N-acetylaspartate by N-acetyltransferase 8-like (NAT8L) in lung cancer cells and show that NAT8L silencing inhibits proliferation of A549, JHH-4, PH5CH8, and BEAS-2B cells. Conclusions Differential stable isotope labeling analysis provides qualitative metabolic flux information in a non-targeted manner. Furthermore, similarity analysis of enrichment patterns provides information on metabolically closely related compounds. N-acetylaspartate and NAT8L are important players in cancer cell metabolism, a context in which they have not received much attention yet. Electronic supplementary material The online version of this article (doi:10.1186/s40170-016-0150-z) contains supplementary material, which is available to authorized users.

Supplemental information. List of isotopically enriched compounds and their mass isotopomer distributions; selected mass spectra. (PDF 308 kb)

Figure S3. Response of PH5CH1 and PH5CH7 non-neoplastic hepatocytes to OSM, hypoxia, and a combination of both stimuli. PH5CH1 and PH5CH7 cells were treated with OSM (50 ng/ml), hypoxia (1 % O2), or a combinatorial treatment for the indicated periods of time. (A, D) Quantitative RT-PCR of PDP2, PDK1, and HIF-1 α mRNA. Fold changes were calculated relative to the untreated control. (B, E) Western blot analysis for HIF-1 α, HIF-2 α, PDK1, and all three PDH phosphorylation sites (S232, S293, S300). Vinculin and α-tubulin were used as loading controls, and one representative blot is shown. (C, F) Quantification of PDK1 protein levels. (PDF 428 kb)

Table S2. Mass isotopomer distributions (MIDs) from [13C6]glucose in PH5CH8 immortalized human hepatocytes treated for 36 h with 50 ng/mL OSM or left untreated. MIDs were corrected for natural isotope abundance. (PDF 94.2 kb)

Table S3. Mass isotopomer distributions (MIDs) from [13C5]glutamine in PH5CH8 immortalized human hepatocytes treated for 36 h with 50 ng/mL OSM or left untreated. MIDs were corrected for natural isotope abundance. (PDF 94.2 kb)

Table S1. For GC/MS measurements, the detector was operated in single ion mode (SIM). Metabolite specific parameters (selected ions, dwell time, retention time) are described. (PDF 66.8 kb)

Figure S2. (A) Glucose uptake and lactate secretion rates in PH5CH8 immortalized hepatocytes in response to a 36 h treatment with 50 ng/mL OSM. Uptake and secretion rates were determined by GC/MS. (B) Îą-ketoglutarate to citrate ratios in PH5CH8 cells treated with 50ng/mL of OSM for 36 h in comparison to the respective untreated control. (PDF 42.2 kb)

Figure S1. Effects of OSM and hypoxia on HIF-1 α and HIF-2 α protein expression in hepatoma cells and hepatocytes. Eleven hepatoma cell lines and two immortalized hepatocyte cell lines (PH5CH8 and THLE-2) were treated with 20 ng/ml OSM (O) or grown at 1 % O2 (H) over 8 and 36 h. (A) HIF-1 α protein expression after OSM treatment represented in comparison to untreated cells (Ut). (B) HIF-1 α protein expression after OSM treatment represented in comparison to cells grown under hypoxia. (C) HIF-2 α protein expression after OSM treatment represented in comparison to untreated cells. (D) HIF-2 α protein expression after OSM treatment represented in comparison to cells grown under hypoxia. (E) HIF-1 α and HIF-2 α protein induction in non-neoplastic THLE-2 hepatocytes after OSM or hypoxia or a combinatorial treatment. (PDF 655 kb)

The accurate determination of mass isotopomer distributions (MID) is of great significance for stable isotope-labeling experiments. Most commonly, MIDs are derived from gas chromatography/electron ionization mass spectrometry (GC/EI-MS) measurements. The analysis of fragment ions formed during EI, which contain only specific parts of the original molecule can provide valuable information on the positional distribution of the label. The chemical formula of a fragment ion is usually applied to derive the correction matrix for accurate MID calculation. Hence, the correct assignment of chemical formulas to fragment ions is of crucial importance for correct MIDs. Moreover, the positional distribution of stable isotopes within a fragment ion is of high interest for stable isotope-assisted metabolomics techniques. For example, (13)C-metabolic flux analyses ((13)C-MFA) are dependent on the exact knowledge of the number and position of retained carbon atoms of the unfragmented molecule. Fragment ions containing different carbon atoms are of special interest, since they can carry different flux information. However, the process of mass spectral fragmentation is complex, and identifying the substructures and chemical formulas for these fragment ions is nontrivial. For that reason, we developed an algorithm, based on a systematic bond cleavage, to determine chemical formulas and retained atoms for EI derived fragment ions. Here, we present the fragment formula calculator (FFC) algorithm that can calculate chemical formulas for fragment ions where the chemical bonding (e.g., Lewis structures) of the intact molecule is known. The proposed algorithm is able to cope with general molecular rearrangement reactions occurring during EI in GC/MS measurements. The FFC algorithm is able to integrate stable isotope labeling experiments into the analysis and can automatically exclude candidate formulas that do not fit the observed labeling patterns.1 We applied the FFC algorithm to create a fragment ion repository that contains the chemical formulas and retained carbon atoms of a wide range of trimethylsilyl and tert-butyldimethylsilyl derivatized compounds. In total, we report the chemical formulas and backbone carbon compositions for 160 fragment ions of 43 alkylsilyl-derivatives of primary metabolites. Finally, we implemented the FFC algorithm in an easy-to-use graphical user interface and made it publicly available at http://www.ffc.lu .

In the present study, the acute and developmental toxicities of imidazolium ionic liquids (ILs) with different alkyl chain lengths, as well as the antioxidant response and lipid peroxidation levels were evaluated in the snail, Physa acuta. Longer alkyl chains corresponded to increased IL toxicity in snails. Long-term IL exposure at lower concentrations inhibited snail growth and reproduction. We also found that IL inhibited the activities of superoxide dismutase (SOD) and glutathione S-transferase (GST), promoted the activity of catalase (CAT), and increased the glutathione content. However, SOD, GST, and CAT activities returned to control levels after 96 h of recovery. In addition, malondialdehyde levels were increased in treatment groups compared with the control and did not return to control levels even after a recovery period, indicating that ILs induced lipid peroxidation in snail viscera. These results suggest that oxidative stress and lipid peroxidation may be involved in the mechanism of toxicity for ILs.

The oncogene DJ-1 has been originally identified as a suppressor of PTEN. Further on, loss-of-function mutations have been described as a causative factor in Parkinson's disease (PD). DJ-1 has an important function in cellular antioxidant responses, but its role in central metabolism of neurons is still elusive. We applied stable isotope assisted metabolic profiling to investigate the effect of a functional loss of DJ-1 and show that DJ-1 deficient neuronal cells exhibit decreased glutamine influx and reduced serine biosynthesis. By providing precursors for GSH synthesis, these two metabolic pathways are important contributors to cellular antioxidant response. Down-regulation of these pathways, as a result of loss of DJ-1 leads to an impaired antioxidant response. Furthermore, DJ-1 deficient mouse microglia showed a weak but constitutive pro-inflammatory activation. The combined effects of altered central metabolism and constitutive activation of glia cells raise the susceptibility of dopaminergic neurons towards degeneration in patients harboring mutated DJ-1. Our work reveals metabolic alterations leading to increased cellular instability and identifies potential new intervention points that can further be studied in the light of novel translational medicine approaches. published

Background Hypoxia and inflammation have been identified as hallmarks of cancer. A majority of hepatocellular carcinomas are preceded by hepatitis B- or C-related chronic infections suggesting that liver cancer development is promoted by an inflammatory microenvironment. The inflammatory cytokine oncostatin M (OSM) was shown to induce the expression of hypoxia-inducible factor-1 α (HIF-1 α) under normoxic conditions in hepatocytes and hepatoma cells. HIF-1 α is known to orchestrate the expression of numerous genes, many of which code for metabolic enzymes that play key roles in the adaptation of cellular metabolism to low oxygen tension. Results Here, we show that OSM-induced upregulation of HIF-1 α reprograms cellular metabolism in three clones of the human hepatocyte cell line PH5CH (PH5CH1, PH5CH7, and PH5CH8) towards a hypoxia-like metabolic phenotype but has no significant effect on cellular metabolism of HepG2 and JHH-4 hepatoma cells. Although we observed only minor changes in glucose uptake and lactate secretion in PH5CH8 upon OSM treatment, we identified more pronounced changes in intracellular fluxes based on stable isotope labeling experiments. In particular, glucose oxidation in the tricarboxylic acid (TCA) cycle is reduced through pyruvate dehydrogenase kinase 1 (PDK1)-mediated inhibition of the pyruvate dehydrogenase complex, thereby reducing the oxidative TCA cycle flux. As a result of the impaired mitochondrial glucose and glutamine oxidation, the reductive isocitrate dehydrogenase flux was increased. Conclusions We provide evidence that connects the inflammatory mediator OSM to a hypoxia-like metabolic phenotype. In the human hepatocyte cell line PH5CH, OSM-mediated upregulation of HIF-1 α and PDK1 can induce hypoxia-like metabolic changes, although to a lesser extent than hypoxia itself. Since PDK1 is overexpressed in several cancers, it might provide a causal link between chronic inflammation and malignant cellular transformation. Electronic supplementary material The online version of this article (doi:10.1186/s40170-016-0141-0) contains supplementary material, which is available to authorized users.