Lymphangitic Retroperitoneal Carcinomatosis Occurring From Metastatic Sarcomatoid Chromophobe Renal Cell Carcinoma

AbstractA 45-year-old man with left renal mass underwent nephrectomy to reveal a 20-cm tumor diagnosed as sarcomatoid chromophobe renal cell carcinoma. Lymph node metastasis of chromophobe and sarcomatoid components, disseminated tumor in retroperitoneal fat, lymphatic vessels, and perirenal adipose tissue in lymphangitic carcinomatosis pattern were identified. Chromophobe epithelial cells were positive for epithelial membrane antigen, c-Kit, and cytokeratin 7; sarcomatoid cells were positive for CD10 and smooth muscle antigen with high proliferation index. Chromophobe epithelial cells had loss of heterozygosity in chromosomes 1p and 1q, whereas sarcomatoid cells had loss of heterozygosity in 3p, 1p, and 1q. In conclusion, sarcomatoid chromophobe renal cell carcinoma has aggressive biologic behavior and potential to metastasize in unusual patterns

Hierarchical deep learning for predicting GO annotations by integrating protein knowledge

Motivation: Experimental testing and manual curation are the most precise ways for assigning Gene Ontology (GO) terms describing protein functions. However, they are expensive, time-consuming and cannot cope with the exponential growth of data generated by high-throughput sequencing methods. Hence, researchers need reliable computational systems to help fill the gap with automatic function prediction. The results of the last Critical Assessment of Function Annotation challenge revealed that GO-terms prediction remains a very challenging task. Recent developments on deep learning are significantly breaking out the frontiers leading to new knowledge in protein research thanks to the integration of data from multiple sources. However, deep models hitherto developed for functional prediction are mainly focused on sequence data and have not achieved breakthrough performances yet. Results: We propose DeeProtGO, a novel deep-learning model for predicting GO annotations by integrating protein knowledge. DeeProtGO was trained for solving 18 different prediction problems, defined by the three GO sub-ontologies, the type of proteins, and the taxonomic kingdom. Our experiments reported higher prediction quality when more protein knowledge is integrated. We also benchmarked DeeProtGO against state-of-the-art methods on public datasets, and showed it can effectively improve the prediction of GO annotations.Fil: Merino, Gabriela Alejandra. European Molecular Biology Laboratory. European Bioinformatics Institute.; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Saidi, Rabie. European Molecular Biology Laboratory. European Bioinformatics Institute.; Reino UnidoFil: Milone, Diego Humberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Stegmayer, Georgina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Martin, Maria J.. European Molecular Biology Laboratory. European Bioinformatics Institute.; Reino Unid

Computational mechanistic study of thionation of carbonyl compounds with Lawesson's reagent

The thionation reaction of carbonyl compounds with Lawesson's reagent (LR) has been studied using density functional theory methods and topological analyses. After dissociation of LR, the reaction takes place through a two-step mechanism involving (i) a concerted cycloaddition between one monomer and the carbonyl compound to form a four-membered intermediate and (ii) a cycloreversion leading to the thiocarbonyl derivative and phenyl(thioxo)phosphine oxide. Topological analyses confirmed the concertedness and asynchronicity of the process. The second step is the rate-limiting one, and the whole process resembles the currently accepted mechanism for the lithium salt-free Wittig reaction. No zwitterionic intermediates are formed during the reaction, although stabilizing electrostatic interactions are present in initial stages. Phenyl(thioxo)phosphine oxide formed in the thionation reaction is capable of performing a second thionation, although with energy barriers higher than the first one. The driving force of the thionation reactions is the formation of trimers from the resulting monomers. In agreement with experimental observations, the amides are the most reactive when compared with esters, aldehydes, and ketones and the reaction is slightly influenced by the polarity of the solvent. Whereas for amides and esters substituents have little effect, aldehydes and ketones are influenced by both steric and electronic effects.This work was supported by the Spanish Ministerio de Economia y Competitividad (MINECO) (Project CTQ2013-44367-C2-1-P), by the Fondos Europeos para el Desarrollo Regional (FEDER), and by the Gobierno de Aragon (Zaragoza, Spain, Bioorganic Chemistry Group, E-10). M.A.C. thanks the University of Catania for partial financial support.Peer Reviewe

Preparation of palladium-supported periodic mesoporous organosilicas and their use as catalysts in the Suzuki cross-coupling reaction

Three periodic mesoporous materials, i.e., two organosilicas with either ethylene or phenylene bridges and one silica, have been used as supports for Pd nanoparticles. All Pd-supported samples (1.0 wt%) were prepared by the incipient wetness method and subsequently reduced in an H2 stream at 200 °C. Both hydrogen chemisorption and temperature programmed reduction experiments revealed significant differences depending on the support. Pd2+ species were more reducible on the mesoporous organosilicas than on their silica counterpart. Also, remarkable differences on the particle morphology were observed by transmission electron microscopy. All Pd-supported samples were active in the Suzuki cross-coupling reaction between bromobenzene and phenylboronic acid

Gold compounds inhibit the Ca2+-ATPase activity of brain PMCA and human neuroblastoma SH-SY5Y cells and decrease cell viability

Plasma membrane calcium ATPases (PMCA) are key proteins in the maintenance of calcium (Ca2+) homeostasis. Dysregulation of PMCA function is associated with several human pathologies, including neurodegenerative diseases, and, therefore, these proteins are potential drug targets to counteract those diseases. Gold compounds, namely of Au(I), are well-known for their therapeutic use in rheumatoid arthritis and other diseases for centuries. Herein, we report the ability of dichloro(2-pyridinecarboxylate)gold(III) (1), chlorotrimethylphosphinegold(I) (2), 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidenegold(I) chloride (3), and chlorotriphenylphosphinegold(I) (4) compounds to interfere with the Ca2+-ATPase activity of pig brain purified PMCA and with membranes from SH-SY5Y neuroblastoma cell cultures. The Au(III) compound (1) inhibits PMCA activity with the IC50 value of 4.9 µM, while Au(I) compounds (2, 3, and 4) inhibit the protein activity with IC50 values of 2.8, 21, and 0.9 µM, respectively. Regarding the native substrate MgATP, gold compounds 1 and 4 showed a non-competitive type of inhibition, whereas compounds 2 and 3 showed a mixed type of inhibition. All gold complexes showed cytotoxic effects on human neuroblastoma SH-SY5Y cells, although compounds 1 and 3 were more cytotoxic than compounds 2 and 4. In summary, this work shows that both Au (I and III) compounds are high-affinity inhibitors of the Ca2+-ATPase activity in purified PMCA fractions and in membranes from SH-SY5Y human neuroblastoma cells. Additionally, they exert strong cytotoxic effects.Projects BFU2017-85723-P (to A.M.M. and C.G.-M.), and PID2020-115512GB-I00 (to A.M.M.) funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future”. We acknowledge Fundação para a Ciência e a Tecnologia (FCT) project UIDB/04326/2020, Associate Laboratory for Green Chemistry–LAQV, financed by national funds from FCT/MCTES (UIDB/50006/2020 and UIDP/50006/2020) and Scientific Employment Stimulus-Institutional Call (CEECINST/00102/2018).info:eu-repo/semantics/publishedVersio

Tailoring block copolymer nanoporous thin films with acetic acid as a small guest molecule

Block copolymers offer the fabrication of mesoporous thin films with distinct nanoscale structural features. In this contribution, we present the use of acetic acid (CH3COOH) as a low‐molecular‐weight guest molecule to tune the supramolecular assembly of poly[styrene‐block‐(4‐vinylpyridine)] (PS‐b‐P4VP), offering a versatile and straightforward method to obtain tailored nanostructured films with controlled topography and pore size. Spin‐coating toluene solutions of PS‐b‐P4VP, with a variable amount of CH3COOH, leads to micellar thin films, where the micelles contain the carboxylic acid as a guest molecule. The size can be conveniently modified in these films (from 48 to 75 nm) by varying the amount of organic acid in the starting solutions. Subsequent surface reconstruction of micellar films using ethanol leads to ring‐shaped copolymer nanoporous films with modulated diameter. Controlling the micelle reconstruction process, cylindrical porous films are also obtained. Interestingly, changing the type of aliphatic carboxylic acid leads to a modification of the observed film morphology from micelles to out‐of‐plane P4VP cylinders (or lamellae) in a PS matrix

Inhibition of SERCA and PMCA Ca2+-ATPase activities by polyoxotungstates

Plasma membrane calcium ATPases (PMCA) and sarco(endo) reticulum calcium ATPases (SERCA) are key proteins in the maintenance of calcium homeostasis. Herein, we compare for the first time the inhibition of SERCA and PMCA calcium pumps by several polyoxotungstates (POTs), namely by Wells-Dawson phospho-tungstate anions [P2W18O62]6-(intact, {P2W18}), [P2W17O61]10-(monolacunary, {P2W17}), [P2W15O56]12-(trilacunary, {P2W15}), [H2P2W12O48]12-(hexalacunary, {P2W12}), [H3P2W15V3O62]6- (trivanadium-substituted, {P2W15V3}) and by Preyssler-type anion [NaP5W30O110]14-({P5W30}). The speciation in the solu-tions of tested POTs was investigated by 31P and 51V NMR spectroscopy. The tested POTs inhibited SERCA Ca2+- ATPase activity, whereby the Preyssler POT showed the strongest effect, with an IC50 value of 0.37 mu M. For {P2W17} and {P2W15V3} higher IC50 values were determined: 0.72 and 0.95 mu M, respectively. The studied POTs showed to be more potent inhibitors of PMCA Ca2+-ATPase activity, with lower IC50 values for {P2W17}, {P5W30} and {P2W15V3}.info:eu-repo/semantics/publishedVersio

Perceived discrimination amongst the indigenous Mapuche people in Chile : some comparisons with Australia

With similar settler-colonial histories having left them occupying the position of marginalized minority groups, indigenous people in Chile and Australia are struggling to assert their rights and retain their cultures. Research in each location suggests that there is widespread prejudice and discrimination against them, even though the mainstream society sees itself as tolerant and harmonious. This paper reports on a study in which thirty Mapuche people in Chile were interviewed about their perceptions of discrimination against them. Their responses were systematically analysed using a taxonomy of racist experiences established in a study of Aborigines in Australia. Like indigenous Australians, the Mapuche people of Chile reported that they experience extensive discrimination in all areas of life. These findings are discussed with respect to the issues related to relationships between settlers and colonized communities.<br /