Continuous multiparametric monitoring of cell metabolism in response to transient overexpression of the sirtuin deacetylase SIRT3

The analysis and visualisation of research data in an environment which is most similar to living conditions belong to the most challenging claims of present scientific research endeavours. To date, the effect of protein function on cell metabolism is most commonly assessed from a series of end point analyses, which finally allows an approximate estimation on how a specific effect takes its course. In the study presented herein, we demonstrate how the combination of transient transfection and a biosensor chip system gives the opportunity to analyse the effect of a specific protein on cell metabolism in living cells through real-time monitoring of metabolically relevant parameters, such as oxygen consumption, acidification rate and cell adhesion. In addition, this method allows online monitoring of the time course of metabolic changes due to changes in expression levels of metabolic regulative proteins from the time of transfection to maximum overexpression. The methodology presented herein was assessed for the transient overexpression of the sirtuin deacetylase SIRT3, a mitochondrial key element in the regulation of energy metabolism, metabolic disease, cancer and ageing

Highly strained, radially π-conjugated porphyrinylene nanohoops

Small π-conjugated nanohoops are difficult to prepare, but offer an excellent platform for studying the interplay between strain and optoelectronic properties, and, increasingly, these shape-persistent macrocycles find uses in host-guest chemistry and self-assembly. We report the synthesis of a new family of radially π-conjugated porphyrinylene/phenylene nanohoops. The strain energy in the smallest nanohoop [2]CPT is approximately 54 kcal mol⁻¹, which results in a narrowed HOMO-LUMO gap and a red shift in the visible part of the absorption spectrum. Because of its high degree of preorganization and a diameter of ca. 13 Å, [2]CPT was found to accommodate C₆₀ with a binding affinity exceeding 10⁸ M⁻¹ despite the fullerene not fully entering the cavity of the host (X-ray crystallography). Moreover, the ?-extended nanohoops [2]CPTN, [3]CPTN, and [3]CPTA (N for 1,4-naphthyl; A for 9,10-anthracenyl) have been prepared using the same strategy, and [2]CPTN has been shown to bind C₇₀ 5 times more strongly than [2]CPT. Our failed synthesis of [2]CPTA highlights a limitation of the experimental approach most commonly used to prepare strained nanohoops, because in this particular case the sum of aromatization energies no longer outweighs the buildup of ring strain in the final reaction step (DFT calculations). These results indicate that forcing ring strain onto organic semiconductors is a viable strategy to fundamentally influence both optoelectronic and supramolecular properties

Calorie restriction alters mitochondrial protein acetylation

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72130/1/j.1474-9726.2009.00503.x.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/72130/2/ACEL_503_sm_FigS1.pd

The Context-Freeness Problem Is coNP-Complete for Flat Counter Systems

International audienceBounded languages have recently proved to be an important class of languages for the analysis of Turing-powerful models. For instance, bounded context-free languages are used to under-approximate the behav-iors of recursive programs. Ginsburg and Spanier have shown in 1966 that a bounded language L ⊆ a * 1 · · · a * d is context-free if, and only if, its Parikh image is a stratifiable semilinear set. However, the question whether a semilinear set is stratifiable, hereafter called the stratifiability problem, was left open, and remains so. In this paper, we give a partial answer to this problem. We focus on semilinear sets that are given as finite systems of linear inequalities, and we show that stratifiability is coNP-complete in this case. Then, we apply our techniques to the context-freeness problem for flat counter systems, that asks whether the trace language of a counter system intersected with a bounded regular language is context-free. As main result of the paper, we show that this problem is coNP-complete

Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53

Theresa Klett,1,* Martin Schwer,1,* Larissa N Ernst,1,* Marc U Engelhardt,1 Simon J Jaag,2 Benedikt Masberg,2 Cornelius Knappe,2 Michael Lämmerhofer,2 Matthias Gehringer,3,4 Frank M Boeckler1,5 1Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany; 2Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany; 3Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany; 4Medicinal Chemistry, Institute for Biomedical Engineering, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany; 5Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany*These authors contributed equally to this workCorrespondence: Frank M Boeckler, Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8 (Haus B), Tübingen, D – 72076, Germany, Tel +49 7071 29 74567, Email [email protected]: Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN).Methods: After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5’-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS).Results: In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53.Conclusion: The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and − 9.1 °C. Keywords: covalent fragment-based drug discovery, differential scanning fluorimetry, 5,5’-dithiobis-(2-nitrobenzoic acid), intact protein mass spectrometry, glutathion

Charge Imbalance Effects on Interlayer Hopping and Fermi Surfaces in Multilayered High-T_c Cuprates

We study doping dependence of interlayer hoppings, t_\perp, in multilayered cuprates with four or more CuO_2 planes in a unit cell. When the double occupancy is forbidden in the plane, an effective amplitude of t_\perp in the Gutzwiller approximation is shown to be proportional to the square root of the product of doping rates in adjacent two planes, i.e., t^eff_\perp \propto t_\perp \sqrt{\delta_1\delta_2}, where \delta_1 and \delta_2 represent the doping rates of the two planes. More than three-layered cuprates have two kinds of \cuo planes, i.e., inner- and outer planes (IP and OP), resulting in two different values of t^eff_{\perp}, i.e., t^eff_\perp 1 \propto t_\perp \sqrt{\delta_IP \delta_IP} between IP's, and t^eff_\perp 2 \propto t_\perp \sqrt{\delta_IP \delta_OP} between IP and OP. Fermi surfaces are calculated in the four-layered t-t'-t''-J model by the mean-field theory. The order parameters, the renormalization factor of t_\perp, and the site-potential making the charge imbalance between IP and OP are self-consistently determined for several doping rates. We show the interlayer splitting of the Fermi surfaces, which may be observed in the angle resolved photoemission spectroscopy measurement.Comment: Some typographical errors are revised. Journal of Physical Society of Japan, Vol.75, No.3, in pres

Observations from Preliminary Experiments on Spatial and Temporal Pressure Measurements from Near-Field Free Air Explosions

It is self-evident that a crucial step in analysing the performance of protective structures is to be able to accurately quantify the blast load arising from a high explosive detonation. For structures located near to the source of a high explosive detonation, the resulting pressure is extremely high in magnitude and highly non-uniform over the face of the target. There exists very little direct measurement of blast parameters in the nearfield, mainly attributed to the lack of instrumentation sufficiently robust to survive extreme loading events yet sensitive enough to capture salient features of the blast. Instead literature guidance is informed largely by early numerical analyses and parametric studies. Furthermore, the lack of an accurate, reliable data set has prevented subsequent numerical analyses from being validated against experimental trials. This paper presents an experimental methodology that has been developed in part to enable such experimental data to be gathered. The experimental apparatus comprises an array of Hopkinson pressure bars, fitted through holes in a target, with the loaded faces of the bars flush with the target face. Thus, the bars are exposed to the normally or obliquely reflected shocks from the impingement of the blast wave with the target. Pressure-time recordings are presented along with associated Arbitary-Langrangian-Eulerian modelling using the LS-DYNA explicit numerical code. Experimental results are corrected for the effects of dispersion of the propagating waves in the pressure bars, enabling accurate characterisation of the peak pressures and impulses from these loadings. The combined results are used to make comments on the mechanism of the pressure load for very near-field blast events

Sirtuin 3, a New Target of PGC-1α, Plays an Important Role in the Suppression of ROS and Mitochondrial Biogenesis

Sirtuin 3 (SIRT3) is one of the seven mammalian sirtuins, which are homologs of the yeast Sir2 gene. SIRT3 is the only sirtuin with a reported association with the human life span. Peroxisome proliferator-activated receptor gamma coactivator-1alpha (PGC-1alpha) plays important roles in adaptive thermogenesis, gluconeogenesis, mitochondrial biogenesis and respiration. PGC-1alpha induces several key reactive oxygen species (ROS)-detoxifying enzymes, but the molecular mechanism underlying this is not well understood.Here we show that PGC-1alpha strongly stimulated mouse Sirt3 gene expression in muscle cells and hepatocytes. Knockdown of PGC-1alpha led to decreased Sirt3 gene expression. PGC-1alpha activated the mouse SIRT3 promoter, which was mediated by an estrogen-related receptor (ERR) binding element (ERRE) (-407/-399) mapped to the promoter region. Chromatin immunoprecipitation and electrophoretic mobility shift assays confirmed that ERRalpha bound to the identified ERRE and PGC-1alpha co-localized with ERRalpha in the mSirt3 promoter. Knockdown of ERRalpha reduced the induction of Sirt3 by PGC-1alpha in C(2)C(12) myotubes. Furthermore, Sirt3 was essential for PGC-1alpha-dependent induction of ROS-detoxifying enzymes and several components of the respiratory chain, including glutathione peroxidase-1, superoxide dismutase 2, ATP synthase 5c, and cytochrome c. Overexpression of SIRT3 or PGC-1alpha in C(2)C(12) myotubes decreased basal ROS level. In contrast, knockdown of mSIRT3 increased basal ROS level and blocked the inhibitory effect of PGC-1alpha on cellular ROS production. Finally, SIRT3 stimulated mitochondrial biogenesis, and SIRT3 knockdown decreased the stimulatory effect of PGC-1alpha on mitochondrial biogenesis in C(2)C(12) myotubes.Our results indicate that Sirt3 functions as a downstream target gene of PGC-1alpha and mediates the PGC-1alpha effects on cellular ROS production and mitochondrial biogenesis. Thus, SIRT3 integrates cellular energy metabolism and ROS generation. The elucidation of the molecular mechanisms of SIRT3 regulation and its physiological functions may provide a novel target for treating ROS-related disease

Transcript Specificity in Yeast Pre-mRNA Splicing Revealed by Mutations in Core Spliceosomal Components

Appropriate expression of most eukaryotic genes requires the removal of introns from their pre–messenger RNAs (pre-mRNAs), a process catalyzed by the spliceosome. In higher eukaryotes a large family of auxiliary factors known as SR proteins can improve the splicing efficiency of transcripts containing suboptimal splice sites by interacting with distinct sequences present in those pre-mRNAs. The yeast Saccharomyces cerevisiae lacks functional equivalents of most of these factors; thus, it has been unclear whether the spliceosome could effectively distinguish among transcripts. To address this question, we have used a microarray-based approach to examine the effects of mutations in 18 highly conserved core components of the spliceosomal machinery. The kinetic profiles reveal clear differences in the splicing defects of particular pre-mRNA substrates. Most notably, the behaviors of ribosomal protein gene transcripts are generally distinct from other intron-containing transcripts in response to several spliceosomal mutations. However, dramatically different behaviors can be seen for some pairs of transcripts encoding ribosomal protein gene paralogs, suggesting that the spliceosome can readily distinguish between otherwise highly similar pre-mRNAs. The ability of the spliceosome to distinguish among its different substrates may therefore offer an important opportunity for yeast to regulate gene expression in a transcript-dependent fashion. Given the high level of conservation of core spliceosomal components across eukaryotes, we expect that these results will significantly impact our understanding of how regulated splicing is controlled in higher eukaryotes as well