Reducing the standard deviation in multiple-assay experiments where the variation matters but the absolute value does not

You measure the value of a quantity x for a number of systems (cells, molecules, people, chunks of metal, DNA vectors, etc.). You repeat the whole set of measures in different occasions or assays, which you try to design as equal to one another as possible. Despite the effort, you find that the results are too different from one assay to another. As a consequence, some systems' averages present standard deviations that are too large to render the results statistically significant. In this work, we present a novel correction method of very low mathematical and numerical complexity that can reduce the standard deviation in your results and increase their statistical significance as long as two conditions are met: inter-system variations of x matter to you but its absolute value does not, and the different assays display a similar tendency in the values of x; in other words, the results corresponding to different assays present high linear correlation. We demonstrate the improvement that this method brings about on a real cell biology experiment, but the method can be applied to any problem that conforms to the described structure and requirements, in any quantitative scientific field that has to deal with data subject to uncertainty.Comment: Supplementary material at http://bit.ly/14I718

Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts.

BACKGROUND: An in silico mechanism-of-action analysis protocol was developed, comprising molecule bioactivity profiling, annotation of predicted targets with pathways and calculation of enrichment factors to highlight targets and pathways more likely to be implicated in the studied phenotype. RESULTS: The method was applied to a cytotoxicity phenotypic endpoint, with enriched targets/pathways found to be statistically significant when compared with 100 random datasets. Application on a smaller apoptotic set (10 molecules) did not allowed to obtain statistically relevant results, suggesting that the protocol requires modification such as analysis of the most frequently predicted targets/annotated pathways. CONCLUSION: Pathway annotations improved the mechanism-of-action information gained by target prediction alone, allowing a better interpretation of the predictions and providing better mapping of targets onto pathways.This is the author's accepted manuscript. The final version is available from Future Science in Future Medicinal Chemistry (http://dx.doi.org/10.4155/fmc.14.137)

Pharmacology and preclinical validation of a novel anticancer compound targeting PEPCK-M

Background: Phosphoenolpyruvate carboxykinase (PEPCK) catalyzes the decarboxylation of oxaloacetate to phosphoenolpyruvate. The mitochondrial isozyme, PEPCK-M is highly expressed in cancer cells, where it plays a role in nutrient stress response. To date, pharmacological strategies to target this pathway have not been pursued. Methods: A compound embodying a 3-alkyl-1,8-dibenzylxanthine nucleus (iPEPCK-2), was synthesized and successfully probed in silico on a PEPCK-M structural model. Potency and target engagement in vitro and in vivo were evaluated by kinetic and cellular thermal shift assays (CETSA). The compound and its target were validated in tumor growth models in vitro and in murine xenografts. Results: Cross-inhibitory capacity and increased potency as compared to 3-MPA were confirmed in vitro and in vivo. Treatment with iPEPCK-2 inhibited cell growth and survival, especially in poor-nutrient environment, consistent with an impact on colony formation in soft agar. Finally, daily administration of the PEPCK-M inhibitor successfully inhibited tumor growth in two murine xenograft models as compared to vehicle, without weight loss, or any sign of apparent toxicity. Conclusion: We conclude that iPEPCK-2 is a compelling anticancer drug targeting PEPCK-M, a hallmark gene product involved in metabolic adaptations of the tumor

Self-acetylation at the active site of phosphoenolpyruvate carboxykinase (PCK1) controls enzyme activity

Acetylation is known to regulate the activity of cytosolic phosphoenolpyruvate carboxykinase (PCK1), a key enzyme in gluconeogenesis, by promoting the reverse reaction of the enzyme (converting phosphoenolpyruvate to oxaloacetate). It is also known that the histone acetyltransferase p300 can induce PCK1 acetylation in cells, but whether that is a direct or indirect function was not known. Here we initially set out to determine whether p300 can acetylate directly PCK1 in vitro. We report that p300 weakly acetylates PCK1, but surprisingly, using several techniques including protein crystallization, mass spectrometry, isothermal titration calorimetry, saturation-transfer difference nuclear magnetic resonance and molecular docking, we found that PCK1 is also able to acetylate itself using acetyl-CoA independently of p300. This reaction yielded an acetylated recombinant PCK1 with a 3-fold decrease in kcat without changes in Km for all substrates. Acetylation stoichiometry was determined for 14 residues, including residues lining the active site. Structural and kinetic analyses determined that site-directed acetylation of K244, located inside the active site, altered this site and rendered the enzyme inactive. In addition, we found that acetyl-CoA binding to the active site is specific and metal dependent. Our findings provide direct evidence for acetyl-CoA binding and chemical reaction with the active site of PCK1 and suggest a newly discovered regulatory mechanism of PCK1 during metabolic stress

Mitochondrial transcription initiation in the crustacean Artemia franciscana

Mitochondrial transcription has been studied in several vertebrate organisms, but so far no report on mitochondrial transcription initiation in invertebrates has been published. Here we present an analysis of transcription initiation sites using in vivo-synthesized transcripts in the crustacean Artemia franciscana. The mitochondrial genome of Artemia has the same coding capacity as most animal mitochondrial genomes, and its overall organization is almost identical to that of Drosophila. Using in vitro capping, RNA mapping techniques and northern hybridization, we have identified a main initiation site for heavy-strand transcription that matches the 5· end of 12S rRNA, on one end of the control region. This nascent RNA has an unusually small size and a highly heterogeneous 5· end. A second potential transcription-initiation site has been located 250 bp upstream of the former, giving rise to a larger, less abundant RNA which also has an heterogeneous 5· end. The two sites have sequence similarity from which a consensus could be derived. Using the same methods we failed to identify any clear initiation site for transcription of the light strand, nevertheless a candidate has been located on the opposite side of the control region, with respect to the heavy-strand initiation sites.This work was supported by research grants PB89-0005 and PB92-0059 from the Direccioón General de Investigación Científica y Técnica to C. G. V.. J. A. C. was a fellow of thePrograma de Formacio ́n de Personal Investigador,Ministerio de Educacio ́n y Ciencia

Optical absorption response of chemically modified single-walled carbon nanotubes upon ultracentrifugation in various dispersants

14 pages,8 figures, 6 tables; available on line 5 September 2013Arc discharge single-walled carbon nanotubes (SWCNTs) were modified through different oxidative treatments and functionalization reactions. The modified SWCNT powders were dispersed in four different aqueous media and purified by ultracentrifugation. Extinction coefficients of the modified SWCNTs depended on the SWCNT type but did not depend on the dispersion medium. According to visible/near infrared spectroscopy, the purity of all the modified SWCNT dispersions substantially improved after ultracentrifugation; however, the spectrum profile, the degree of purity and the centrifugation yield were influenced by the SWCNT type, the surface functional groups and the dispersion medium. Semi-quantitative purity indexes calculated from optical absorption spectra were supported by transmission electron microscopy observations. Contents in metal impurities were analyzed by energy dispersive X-ray spectroscopy. SWCNT samples processed by oxidative acid treatments and ultracentrifugation showed metal contents of lower than 0.5 wt%.This work was funded by the Spanish MINECO under the projects TEC2010-15736 and PRI-PIBAR-2011-1, and the Government of Aragon (DGA) and the European Social Fund (ESF) under Project DGA-ESF-T66 CNN.Peer Reviewe

Inhibition of pig phosphoenolpyruvate carboxykinase isoenzymes by 3-Mercaptopicolinic acid and novel inhibitors

There exist two isoforms of cytosolic phosphoenolpyruvate carboxykinase (PEPCK-C) in pig populations that differ in a single amino acid (Met139Leu). The isoenzymes have different kinetic properties, affecting more strongly the Km and Vmax of nucleotides. They are associated to different phenotypes modifying traits of considerable economic interest. In this work we use inhibitors of phosphoenolpyruvate carboxykinase activity to search for further differences between these isoenzymes. On the one hand we have used the wellknown inhibitor 3-mercaptopicolinic acid. Its inhibition patterns were the same for both isoenzymes: a three-fold decrease of the Ki values for GTP in 139Met and 139Leu (273 and 873 μM, respectively). On the other hand, through screening of a chemical library we have found two novel compounds with inhibitory effects of a similar magnitude to that of 3-mercaptopicolinic acid but with less solubility and specificity. One of these novel compounds, (N'1-({5-[1-methyl-5-(trifluoromethyl)-1H-pyrazol-3-yl]-2-thienyl}methylidene)-2,4-dichlorobenzene-1-carbohydrazide), exhibited significantly different inhibitory effects on either isoenzyme: it enhanced threefold the apparent Km value for GTP in 139Met, whereas in139Leu, it reduced it from 99 to 69 μM. The finding of those significant differences in the binding of GTP reinforces the hypothesis that the Met139Leu substitution affects strongly the nucleotide binding site of PEPCK-C.Supported by research grants AGL2008-01487ALI (www.mineco.gob.es), DGA-IAF FITE2012/2013 (www.aragob.es), and UZ2014-CIE-03 (www.unizar.es) to P.L.B., AGL2015-66177 to P.L.B. and J.A.C., and grants BFU2013-47064-P (www.micinn.es), BIO2014-57314-REDT (www.mineco.gob.es) and PI078/08 to J.S. P.L.Peer Reviewe