Author: "Hugo M. Santos" - Searchworks@Jio Institute Digital Library Search Results

147 results on '"Hugo M. Santos"'

1. Exploring the Hypocholesterolemic Potential of a Fucus vesiculosus Extract: Omic Insights into Molecular Mechanisms at the Intestinal Level

Author: Rebeca André, Rita Pacheco, Hugo M. Santos, and Maria Luísa Serralheiro
Subjects: Fucus vesiculosus, proteomics, metabolomics, NPC1, Caco-2 cell line, Biology (General), QH301-705.5
Abstract: High blood cholesterol levels are a major risk factor for cardiovascular diseases. A purified aqueous extract of Fucus vesiculosus, rich in phlorotannins and peptides, has been described for its potential to inhibit cholesterol biosynthesis and intestinal absorption. In this work, the effect of this extract on intestinal cells’ metabolites and proteins was analysed to gain a deeper understanding of its mode of action on lipids’ metabolism, particularly concerning the absorption and transport of exogenous cholesterol. Caco-2 cells, differentiated into enterocytes, were exposed to the extract, and analysed by untargeted metabolomics and proteomics. The results of the metabolomic analysis showed statistically significant differences in glutathione content of cells exposed to the extract compared to control cells, along with an increased expression of fatty acid amides in exposed cells. A proteomic analysis showed an increased expression in cells exposed to the extract compared to control cells of FAB1 and NPC1, proteins known to be involved in lipid metabolism and transport. To the extent of our knowledge, this study is the first use of untargeted metabolomics and a proteomic analysis to investigate the effects of F. vesiculosus on differentiated Caco-2 cells, offering insights into the molecular mechanism of the extract’s compounds on intestinal cells.
Published: 2024
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2. The Hypocholesterolemic Potential of the Edible Algae Fucus vesiculosus: Proteomic and Quantitative PCR Analysis

Author: Rebeca André, Rita Pacheco, Ana Catarina Alves, Hugo M. Santos, Mafalda Bourbon, and Maria Luísa Serralheiro
Subjects: Fucus vesiculosus, cholesterol synthesis, cholesterol excretion, ezetimibe, NPC1L1, ABCG5, Chemical technology, TP1-1185
Abstract: A brown seaweed consumed worldwide, Fucus vesiculosus, has been used to prevent atherosclerosis and hypercholesterolemia, among other uses. However, the mechanisms of action that lead to these effects are not yet fully understood. This work aims to study the in vitro effect of an aqueous extract of F. vesiculosus, previously characterized as rich in phlorotannins and peptides, on the expression of different proteins involved in the synthesis and transport of cholesterol. A proteomic analysis, Western blot, and qRT-PCR analysis were performed to identify protein changes in HepG2 cells exposed to 0.25 mg/mL of the F. vesiculosus extract for 24 h. The proteomic results demonstrated that, in liver cells, the extract decreases the expression of four proteins involved in the cholesterol biosynthesis process (CYP51A1, DHCR24, HMGCS1 and HSD17B7). Additionally, a 12.76% and 18.40% decrease in the expression of two important transporters proteins of cholesterol, NPC1L1 and ABCG5, respectively, was also observed, as well as a 30% decrease in NPC1L1 mRNA levels in the cells exposed to the extract compared to control cells. Our study reveals some of the mechanisms underlying the actions of bioactive compounds from F. vesiculosus that may explain its previously reported hypocholesterolemic effect, future prospecting its use as a functional food.
Published: 2023
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3. Absolute quantitative proteomics using the total protein approach to identify novel clinical immunohistochemical markers in renal neoplasms

Author: Susana Jorge, José L. Capelo, William LaFramboise, Swati Satturwar, Dimitrios Korentzelos, Sheldon Bastacky, Gabriela Quiroga-Garza, Rajiv Dhir, Jacek R. Wiśniewski, Carlos Lodeiro, and Hugo M. Santos
Subjects: Renal neoplasms, Immunohistochemistry, Mass spectrometry-based proteomics, Total protein approach (TPA), Tissue micro-array (TMA), Medicine
Abstract: Abstract Background Renal neoplasms encompass a variety of malignant and benign tumors, including many with shared characteristics. The diagnosis of these renal neoplasms remains challenging with currently available tools. In this work, we demonstrate the total protein approach (TPA) based on high-resolution mass spectrometry (MS) as a tool to improve the accuracy of renal neoplasm diagnosis. Methods Frozen tissue biopsies of human renal tissues [clear cell renal cell carcinoma (n = 7), papillary renal cell carcinoma (n = 5), chromophobe renal cell carcinoma (n = 5), and renal oncocytoma (n = 5)] were collected for proteome analysis. Normal adjacent renal tissue (NAT, n = 5) was used as a control. Proteins were extracted and digested using trypsin, and the digested proteomes were analyzed by label-free high-resolution MS (nanoLC-ESI-HR-MS/MS). Quantitative analysis was performed by comparison between protein abundances of tumors and NAT specimens, and the label-free and standard-free TPA was used to obtain absolute protein concentrations. Results A total of 205 differentially expressed proteins with the potential to distinguish the renal neoplasms were found. Of these proteins, a TPA-based panel of 24, including known and new biomarkers, was selected as the best candidates to differentiate the neoplasms. As proof of concept, the diagnostic potential of PLIN2, TUBB3, LAMP1, and HK1 was validated using semi-quantitative immunohistochemistry with a total of 128 samples assessed on tissue micro-arrays. Conclusions We demonstrate the utility of combining high-resolution MS and the TPA as potential new diagnostic tool in the pathology of renal neoplasms. A similar TPA approach may be implemented in any cancer study with solid biopsies.
Published: 2021
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4. Exploring Coumarin-Based Boron Emissive Complexes as Temperature Thermometers in Polymer-Supported Materials

Author: Gonçalo Pedro, Frederico Duarte, Dmitrii A. Cheptsov, Nikita Yu. Volodin, Ivan V. Ivanov, Hugo M. Santos, Jose Luis Capelo-Martinez, Cristián Cuerva, Elisabete Oliveira, Valerii F. Traven, and Carlos Lodeiro
Subjects: coumarin derivatives, boron complexes, doped polymers, temperature sensors, Chemical technology, TP1-1185
Abstract: Three coumarin-based boron complexes (L1, L2 and L3) were designed and successfully incorporated into polymeric matrixes for evaluation as temperature probes. The photophysical properties of the complexes were carried out in different solvents and in the solid state. In solution, compound L1 exhibited the highest fluorescence quantum yield, 33%, with a positive solvatochromism also being observed on the absorption and emission when the polarity of the solvent increased. Additionally in the presence of anions, L1 showed a colour change from yellow to pink, followed by a quenching in the emission intensity, which is due to deprotonation with the formation of a quinone base. Absorption and fluorescence spectra of L1 were calculated at different temperatures by the DFT/B3LYP method. The decrease in fluorescence of compound L1 with an increase in temperature seems to be due to the presence of pronounced torsional vibrations of the donor and acceptor fragments relative to the single bond with C(carbonyl)-C (styrene fragment). L1, L2 and L3, through their incorporation into the polymeric matrixes, became highly emissive by aggregation. These dye@doped polymers were evaluated as temperature sensors, showing an excellent fluorescent response and reversibility after 15 cycles of heating and cooling.
Published: 2023
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5. Development of Cyanine 813@Imidazole-Based Doped Supported Devices for Divalent Metal Ions Detection

Author: Joana Galhano, Gonçalo A. Marcelo, Hugo M. Santos, José Luis Capelo-Martínez, Carlos Lodeiro, and Elisabete Oliveira
Subjects: cyanine@imidazole derivative, colourimetric, metal ions, PMMA nanoparticles, mesoporous silica nanoparticles, Biochemistry, QD415-436
Abstract: A NIR cyanine@imidazole derivative Cy1 was synthesized and evaluated as a metal ion sensor in solution. Cy1 was shown to be very sensitive to all metal ions tested, presenting a blue shift in the absorption from 668 nm to 633 nm, followed by a change in colour from pale green to blue with Zn2+, Cd2+, Co2+, Ni2+ and Hg2+ ions. Despite the blue shift in the absorption, a decrease at 633 nm (with a colour change from pale green to colourless), as well as a quenching in the emission intensity at 785 nm were observed for Cu2+ ions. The results show the formation of sandwich complexes of two ligands per metal ion with the highest association constant observed for Cu2+ (Log Kass.abs = 14.76 ± 0.09; Log Kass.emis. = 14.79 ± 0.06). The minimal detectable amounts were found to be 31 nM and 37 nM, with a naked eye detection of 2.9 ppm and 2.1 ppm for Hg2+ and Cu2+ ions, respectively. These results prompted us to explore the applicability of Cy1 by its combination with nanomaterials. Thus, Cy1@ doped MNs and Cy1@ doped PMMA nanoparticles were synthesized. Both nanosystems were shown to be very sensitive to Cu2+ ions in water, allowing a naked-eye detection of at least 1 ppm for Cy1@ doped MNs and 7 ppm for Cy1@ doped PMMA. This colourimetric response is an easy and inexpensive way to assess the presence of metals in aqueous media with no need for further instrumentation.
Published: 2022
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6. Unraveling the Organotellurium Chemistry Applied to the Synthesis of Gold Nanomaterials

Author: Javier Fernández-Lodeiro, Benito Rodríguez-González, Hugo M. Santos, Emilia Bertolo, José Luis Capelo, Alcindo A. Dos Santos, and Carlos Lodeiro
Subjects: Chemistry, QD1-999
Published: 2016
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7. Multiomics Assessment of Gene Expression in a Clinical Strain of CTX-M-15-Producing ST131 Escherichia coli

Author: Luís Pinto, Carmen Torres, Concha Gil, Júlio D. Nunes-Miranda, Hugo M. Santos, Vítor Borges, João P. Gomes, Catarina Silva, Luís Vieira, José E. Pereira, Patrícia Poeta, and Gilberto Igrejas
Subjects: bacteria, antimicrobial resistance, public health, genomics, transcriptomics, proteomics, Microbiology, QR1-502
Abstract: Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strain C999 was isolated of a Spanish patient with urinary tract infection. Previous genotyping indicated that this strain presented a multidrug-resistance phenotype and carried beta-lactamase genes encoding CTX-M-15, TEM-1, and OXA-1 enzymes. The whole-cell proteome, and the membrane, cytoplasmic, periplasmic and extracellular sub-proteomes of C999 were obtained in this work by two-dimensional gel electrophoresis (2DE) followed by fingerprint sequencing through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). A total of 602 proteins were identified in the different cell fractions, several of which are related to stress response systems, cellular responses, and antibiotic and drug responses, consistent with the multidrug-resistance phenotype. In parallel, whole genome sequencing (WGS) and RNA sequencing (RNA-Seq) was done to identify and quantify the genes present and expressing. The in silico prediction following WGS confirmed our strain as being serotype O25:H4 and sequence type ST131. The presence of proteins related to antibiotic resistance and virulence in an O25:H4-ST131 E. coli clone are serious indicators of the continued threat of antibiotic resistance spread amongst healthcare institutions. On a positive note, a multiomics approach can facilitate surveillance and more detailed characterization of virulent bacterial clones from hospital environments.
Published: 2019
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8. Editorial: Rational Design of Multi-Functional Nanomaterials

Author: Carlos Lodeiro, José Luis Capelo, and Hugo M. Santos
Subjects: nanomaterials, nanoparticles, structural control, rational functionalization, detection, delivery, Chemistry, QD1-999
Published: 2019
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9. Study and Preparation of Multifunctional Poly(L-Lysine)@Hyaluronic Acid Nanopolyplexes for the Effective Delivery of Tumor Suppressive MiR-34a into Triple-Negative Breast Cancer Cells

Author: Jamila Djafari, Javier Fernández-Lodeiro, Hugo M. Santos, Julia Lorenzo, Sergi Rodriguez-Calado, Emilia Bértolo, José Luis Capelo-Martínez, and Carlos Lodeiro
Subjects: polyplexes RNA, Poly-Lysine, triple negative breast cancer, Technology, Electrical engineering. Electronics. Nuclear engineering, TK1-9971, Engineering (General). Civil engineering (General), TA1-2040, Microscopy, QH201-278.5, Descriptive and experimental mechanics, QC120-168.85
Abstract: Non-viral gene delivery using exogenous microRNAs is a potential strategy for fighting cancers with poor prognosis and which lack specific therapies, such as triple-negative breast cancer (TNBC). Herein we report the synthesis of six nontoxic electrostatic polymeric nanocapsules (P1 to P6) for microRNA delivery in TNBC cells. 1H Nuclear Magnetic Resonance (NMR) spectroscopy and Scanning Electron Microscopy (SEM) were used to characterize the nanopolyplexes, synthesized with Poly(L-Lysine) and hyaluronic acid (Ha). Studies on the activity of the ternary HA/PLI/miRNA-34 nanopolyplexes towards TNBC cell line MDA-MB-231 were conducted. The nanopolyplexes mediated intracellular restoration of tumor suppressor miR34a was evaluated by using Western blotting to quantify the expression level of the Bcl-2 protein. The results suggest that the P5, with a ratio PLI/Ha of 0.05, was the most promising for the delivery of miR-34a into TNBC cells; the P5 nanocapsules were able to reduce Bcl-2 expression at a protein level, and had an effect in the overall cell viability after 24 h treatment.
Published: 2020
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10. Para uma visão complexa do bullying homofóbico: Desocultando o quotidiano da homofobia nas escolas

Author: Hugo M. Santos, Sofia Marques da Silva, and Isabel Menezes
Subjects: escola, bullying, homofobia, masculinidade, Women. Feminism, HQ1101-2030.7
Abstract: Apesar do crescente interesse pela investigação LGBTI, em Portugal são escassos os estudos sobre bullying homofóbico. Este artigo explora as representações e as experiências de estudantes do ensino secundário sobre bullying homofóbico, com recurso a 36 grupos de discussão focalizada com 232 raparigas e rapazes em 12 escolas públicas do Norte de Portugal. Constata-se a incapacidade do conceito de bullying homofóbico em abarcar todas as formas de violência homofóbica e heteronormativa da e na escola. A maior expressividade do fenómeno relaciona-se com os seus processos de construção da masculinidade no contexto das culturas juvenis, cuja incidência quotidiana nos desafa a questionar as oportunidades para a construção de uma cidadania inclusiva da diversidade sexual na escola.
Published: 2017
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11. Complete Proteome of a Quinolone-Resistant Salmonella Typhimurium Phage Type DT104B Clinical Strain

Author: Susana Correia, Júlio D. Nunes-Miranda, Luís Pinto, Hugo M. Santos, María de Toro, Yolanda Sáenz, Carmen Torres, José Luis Capelo, Patrícia Poeta, and Gilberto Igrejas
Subjects: Salmonella enterica serovar Typhimurium, DT104B, SL1344, proteome, aminoglycoside 6'-N-acetyltransferase type Ib-cr4, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract: Salmonellosis is one of the most common and widely distributed foodborne diseases. The emergence of Salmonella strains that are resistant to a variety of antimicrobials is a serious global public health concern. Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) is one of these emerging epidemic multidrug resistant strains. Here we collate information from the diverse and comprehensive range of experiments on Salmonella proteomes that have been published. We then present a new study of the proteome of the quinolone-resistant Se20 strain (phage type DT104B), recovered after ciprofloxacin treatment and compared it to the proteome of reference strain SL1344. A total of 186 and 219 protein spots were recovered from Se20 and SL1344 protein extracts, respectively, after two-dimensional gel electrophoresis. The signatures of 94% of the protein spots were successfully identified through matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS). Three antimicrobial resistance related proteins, whose genes were previously detected by polymerase chain reaction (PCR), were identified in the clinical strain. The presence of these proteins, dihydropteroate synthase type-2 (sul2 gene), aminoglycoside resistance protein A (strA gene) and aminoglycoside 6'-N-acetyltransferase type Ib-cr4 (aac(6')-Ib-cr4 gene), was confirmed in the DT104B clinical strain. The aac(6')-Ib-cr4 gene is responsible for plasmid-mediated aminoglycoside and quinolone resistance. This is a preliminary analysis of the proteome of these two S. Typhimurium strains and further work is being developed to better understand how antimicrobial resistance is developing in this pathogen.
Published: 2014
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12. Synthesis of Gold Functionalised Nanoparticles with the Eranthis hyemalis Lectin and Preliminary Toxicological Studies on Caenorhabditis elegans

Author: Jamila Djafari, Marie T. McConnell, Hugo M. Santos, José Luis Capelo, Emilia Bertolo, Simon C. Harvey, Carlos Lodeiro, and Javier Fernández-Lodeiro
Subjects: Caenorhabditis elegans, toxicity, gold nanoparticles, nanocomposites, lectin protein, Reactive Oxygen Species (ROS), Technology, Electrical engineering. Electronics. Nuclear engineering, TK1-9971, Engineering (General). Civil engineering (General), TA1-2040, Microscopy, QH201-278.5, Descriptive and experimental mechanics, QC120-168.85
Abstract: The lectin found in the tubers of the Winter Aconite (Eranthis hyemalis) plant (EHL) is a Type II Ribosome Inactivating Protein (RIP). Type II RIPs have shown anti-cancer properties and have great potential as therapeutic agents. Similarly, colloidal gold nanoparticles are successfully used in biomedical applications as they can be functionalised with ligands with high affinity and specificity for target cells to create therapeutic and imaging agents. Here we present the synthesis and characterization of gold nanoparticles conjugated with EHL and the results of a set of initial assays to establish whether the biological effect of EHL is altered by the conjugation. Gold nanoparticles functionalised with EHL (AuNPs@EHL) were successfully synthesised by bioconjugation with citrate gold nanoparticles (AuNPs@Citrate). The conjugates were analysed by UV-Vis spectroscopy, Dynamic Light Scattering (DLS), Zeta Potential analysis, and Transmission Electron Microscopy (TEM). Results indicate that an optimal functionalisation was achieved with the addition of 100 µL of EHL (concentration 1090 ± 40 µg/mL) over 5 mL of AuNPs (concentration [Au0] = 0.8 mM). Biological assays on the effect of AuNPs@EHL were undertaken on Caenorhabditis elegans, a free-living nematode commonly used for toxicological studies, that has previously been shown to be strongly affected by EHL. Citrate gold nanoparticles did not have any obvious effect on the nematodes. For first larval stage (L1) nematodes, AuNPs@EHL showed a lower biological effect than EHL. For L4 stage, pre-adult nematodes, both EHL alone and AuNPs@EHL delayed the onset of reproduction and reduced fecundity. These assays indicate that EHL can be conjugated to gold nanoparticles and retain elements of biocidal activity.
Published: 2018
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13. Omic Studies on the Effect of Fucus vesiculosus on Differentiated Caco-2 Cells: A Potential Functional Food

Author: Rebeca André, Rita Pacheco, Hugo M. Santos, and Maria-Luísa Serralheiro
Abstract: High blood cholesterol levels are one of the main risks for atherosclerotic disease. A purified aqueous extract of Fucus vesiculosus, characterized as rich in phlorotannins and peptides, was described as having the capacity to inhibit cholesterol biosynthesis and intestinal absorption. In this work, the effect of this extract on intestinal cells metabolites and proteins was analysed, aiming to expand the knowledge about its mode of action targeting cholesterol metabolism, in particular exogenous cholesterol absorption and transport. Caco-2 cells differentiated into enterocytes were exposed to the purified aqueous extract of F. vesiculosus and analysed by undirected metabolomics and proteomics. The results of the metabolomic analysis showed only statistically significant differences in glutathione content of the cells exposed to the extract relatively to the control cells, with a decreased glutathione expression in exposed cells. The proteomic analysis showed an increased expression for cells exposed to the extract of NPC1, an important protein known to be involved in cholesterol transport. To extent of our knowledge this is the first study using untargeted metabolomics and proteomic analysis to study the effect of F. vesiculosus on differentiated Caco-2 cells, which aims to provide some insight about the molecular mechanism of extract compounds on intestinal cells.
Published: 2023

14. Development of fluorochromic polymer doped materials as platforms for temperature sensing using three dansyl derivatives bearing a sulfur bridge

Author: Frederico Duarte, Georgi Dobrikov, Atanas Kurutos, José Luis Capelo-Martínez, Hugo M. Santos, Elisabete Oliveira, and Carlos Lodeiro
Abstract: Three novel bis-dansyl derivatives bearing a sulfur bridge have been synthesized and fully characterized. Their photophysical characterization has been studied in solution as well as in the solid state. All compounds exhibit fluorescence emission with quantum yields up to 60%, which vary significantly depending on the solvent used, and the inherent molecular structure. Moreover, these compounds demonstrate positive solvatofluorochromic behaviour emitting from bluish-green to yellow. Kamlet-Taft studies were performed to understand the solute-solvent interactions better. Due to the intrinsic characteristics of the compounds, efforts were made to understand their potential usefulness for environmental remediation, and thus metal ion sensing studies were investigated. Compounds L1 and L2 showed high sensitivity to Cu2+ and Hg2+ ions and were found to modulate their emission extensively, with L2 capable of detecting and quantifying up to 4 µM of Hg2+. Considering the solid-state emission of these compounds, the application towards temperature sensing was put forth. L3 was found to quench its emission linearly with temperatures up to 170 ºC. Several doped polymer thin films were fabricated, which served as a platform to establish a linear relation with temperature beyond their melting point. Polymethylmethacrylate (PMMA) films emitted up to temperatures of 218 ºC, which could be fully restored at room temperature. These results suggest the potential application of these bis-chromophoric compounds as molecular thermometers.
Published: 2023

15. Biochemical network analysis of protein-protein interactions to follow-up T1 bladder cancer patients

Author: Luís B. Carvalho, José Luis Capelo Martínez, Carlos Lodeiro, Rafael Bento, Rajiv Dhir, Jeremiah J. Morrissey, Luis Campos Pinheiro, Mariana Medeiros, Hugo M. Santos, DQ - Departamento de Química, LAQV@REQUIMTE, and NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)
Subjects: Mass spectrometry, SDG 3 - Good Health and Well-being, Bladder cancer, Urine proteomics, Biophysics, Cubilin (CUBN), Biochemistry, Neutrophil extracellular traps, myeloperoxidase (MPO)
Abstract: PM003/2016). LBC, JLC, CL, RB, and HMS acknowledge the funding provided by the Associate Laboratory for Green Chemistry LAQV which is financed by national funds from FCT/MCTES, Fundação para a Ciência e Tecnologia and Ministério da Ciência, Tecnologia e Ensino Superior, through the projects UIDB/50006/2020 and UIDP/50006/2020. HMS acknowledges the Associate Laboratory for Green Chemistry-LAQV (LA/P/0008/2020) funded by FCT/MCTES for his research contract. LBC thanks the FCT/MCTES for his Ph.D. grant (SFRH/BD/144222/2019). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [30] partner repository with the data set number PXD026784. Publisher Copyright: © 2023 The Authors Bladder cancer (BCa) is a prevalent disease with a high risk of aggressive recurrence in T1-stage patients. Despite the efforts to anticipate recurrence, a reliable method has yet to be developed. In this work, we employed high-resolution mass spectrometry to compare the urinary proteome of T1-stage BCa patients with recurring versus non-recurring disease to uncover actionable clinical information predicting recurrence. All patients were diagnosed with T1-stage bladder cancer between the ages of 51 and 91, and urine samples were collected before medical intervention. Our results suggest that the urinary myeloperoxidase to cubilin ratio could be used as a new tool for predicting recurrence and that dysregulation of the inflammatory and immune systems may be a key driver of disease worsening. Furthermore, we identified neutrophil degranulation and neutrophil extracellular traps (NETs) as key pathways in the progression of T1-stage BCa. We propose that proteomics follow-up of the inflammatory and immune systems may be useful for monitoring the effectiveness of therapy. Significance: This article describes how proteomics can be used to characterize tumor aggressiveness in patients with the same diagnosis of bladder cancer (BCa). LC-MS/MS in combination with label free quantification (LFQ) were used to explore potential protein and pathway level changes related to the aggressiveness of the disease in 13 and 17 recurring and non-recurring T1 stage BCa patients. We have shown that the MPO/CUBN protein ratio is a candidate for a urine prognosis tool in BCa. Furthermore, we identify dysregulation of inflammation process as a driver for BCa recurrence and progression. Moreover, we propose using proteomics to track the effectiveness of therapy in the inflammatory and immune systems. publishersversion published
Published: 2023

16. Diphenyl ditelluride assisted synthesis of noble metal-based Silver-Telluride 2D organometallic Nanofibers with enhanced aggregation-induced emission (AIE) using oleylamine

Author: Jamila Djafari, Frederico Duarte, Javier Fernández-Lodeiro, Adrián Fernández-Lodeiro, Hugo M Santos, Eva Bladt, Sara Bals, Aikaterini Flessa-Savvidou, Luis Balicas, Benito Rodríguez-González, Alcindo Aparecido Dos Santos, José Luis Capelo-Martínez, and Carlos Lodeiro
Abstract: Silver-Telluride 2D organometallic nanofibers using diphenyl ditelluride (DPDT) as a precursor were synthesized. The synthesis was carried out by reacting DPDT with AgNO3 in acetonitrile at room temperature (RT) under an inert atmosphere. The resulting material was fully characterized using various techniques, including UV-VIS-NIR spectroscopy, steady-state and excited-state fluorescent spectroscopy, IR-FTIR-ATR spectroscopy, HR ESI MS spectrometry, high-resolution transmission electron microscopy (HRTEM), BF-STEM or HAADF-STEM, and confocal fluorescence microscopy images and conductivity measurements. Initially, the nanofibers were almost non-emissive. However, a remarkable modification was observed after treating the nanofibers with oleylamine under ultrasound treatment. This methodology induced an aggregation emission effect (AIE) in the solution and in the solid state, resulting in the formation of a highly red emissive fluorescent nanomaterial. This research provides valuable insights for developing new fluorescent materials with potential applications in various optical fields. Initially, the nanofibers were almost non-emissive. However, we observed a remarkable modification after treating the nanofibers with oleylamine under ultrasound treatment. This treatment induced an aggregation emissive effect (AIE) in the solution and solid state, resulting in the formation of a highly red emissive fluorescent material. Overall, our findings demonstrate the successful synthesis of 2D Silver-Telluride 2D organometallic nanofibers and the induction of AIE in the resulting material through oleylamine treatment. This research provides valuable insights for developing new fluorescent materials with potential applications in various fields.
Published: 2023

17. Enhancing water sensing via aggregation-induced emission (AIE) and solvatofluorochromic studies using two new dansyl derivatives containing a disulfide bound: Pollutant metal ions detection and preparation of water-soluble fluorescent polymeric particles

Author: Frederico Duarte, Georgi Dobrikov, Atanas Kurutos, Hugo M Santos, Javier Fernández-Lodeiro, Jose Luis Capelo-Martínez, Elisabete Oliveira, and Carlos Lodeiro
Abstract: Polarity-sensitive dansyl derivatives L1 and L2 were synthesized, and their ability to sense pollutant metal ions was investigated. All compounds were highly sensitive towards Cu2+ and Hg2+ metal ions, while L2 could detect and quantify Hg2+ concentrations as low as 2.5 µM. Both L1 and L2 exhibit positive solvatofluorochromic behaviour, modulated in the presence of water, which in turn results in fluorescence enhancement via aggregation-induced emission (AIE). Seeking stability and water solubility, luminescent L1-based polystyrene-block-polybutadiene-block-polystyrene (SBS) microparticles (size: 520 ± 76 nm) were successfully prepared while maintaining the fluorescence emission of fluorophore L1 (22%). This work shows the dansyl-derivative's multiple properties and promising applications in biomedicine and environmental fields.
Published: 2023

18. Prescriptomics: the next frontier in medicine

Author: José L. Capelo, Carlos Lodeiro, Rajiv Dhir, Nataly Kravchenko-Balasha, and Hugo M. Santos
Subjects: Genetics, Molecular Biology, Biochemistry
Published: 2022

19. Label-free quantitative mass spectrometry from formalin-fixed paraffin-embedded samples of nasopharyngeal carcinoma: Preliminary results from a non-endemic European cohort of patients

Author: Hugo M. Santos, Miguel Rito, José Cabeçadas, José Luis Capelo-Martínez, E. Netto, M. Roldão, and Luis B. Carvalho
Subjects: Oncology, medicine.medical_specialty, Formalin fixed paraffin embedded, Proteomic Profiling, business.industry, medicine.disease, Article, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Nasopharyngeal carcinoma, Median follow-up, 030220 oncology & carcinogenesis, Internal medicine, Cohort, medicine, Biomarker (medicine), Radiology, Nuclear Medicine and imaging, Biomarker discovery, business, Label free
Abstract: AIM: Report our results of biomarker discovery in formalin-fixed paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) via proteomic analysis. BACKGROUND: Nasopharyngeal carcinoma (NPC) is a rare cancer in Western countries. Proteomic analysis have already been reported as a useful tool to provide biomarkers. Formalin-fixed paraffin-embedded (FFPE) samples, despite largely underused, can provide invaluable information for biomarker research via proteomic analysis. METHODS: FFPE samples of NPC were submitted to protein extraction followed by FASP-digestion and label-free quantitative mass spectrometry (MS). Patients’ received concurrent chemoradiation with or without adjuvant chemotherapy as per Intergroup 0099 trial. IMRT was delivered following the RTOG0615 specifications. Toxicity was scored using the CTCAE 4.03 tables. Survival was estimated using Kaplan–Meier curves. Log-rank was used to detect differences. KEGG ontology graphics were generated. RESULTS: 28 FFPE samples from NPC patients were used. Patients were: 79% male, 97% Caucasians, 86% WHO type 3, 40% T1, 10% T2, 25% T3, and 25% T4. With a median follow up of 37 months, local control was 83 (T1, 100% T2, T3 and T4), overall survival was 84%, and six patients developed distant metastases. All five patients that died were due to metastatic disease. Tumor samples contained a median of 75% of tumor material. We found Epstein–Barr (EBV) and Herpes simplex (HSV) viruses’ related proteins significantly present in early-stage primary NPC (T1 and T2, p
Published: 2020

20. Preparation of tetrahydro-1H-xanthen-1-one and chromen-1-one derivatives via a Morita-Baylis-Hillman/oxa-Michael/elimination cascade

Author: Hugo M. Santos, Lucas A. Zeoly, Deborah de Alencar Simoni, Fernando Coelho, Albert Moyano, and Manoel T. Rodrigues
Subjects: Catàlisi, Stereochemistry, Cascade, Chemistry, Química de l'aigua, Organic Chemistry, Morita therapy, Imidazoles, Water chemistry, Catalysis
Abstract: The Morita-Baylis-Hillman (MBH) reaction is a carbon-carbon bond forming transformation between an electrophile, typically an aldehyde, and an activated olefin. MBH adducts obtained from 2-hydroxy- benzaldehydes and cyclic enones are potential substrates for the synthesis of xanthenone and chromenone derivatives. In this work, we investigated conditions to obtain tetrahydro-1H-xanthen-1-ones and chromen- 1-ones directly via a Morita-Baylis-Hillman/oxa-Michael/elimination cascade catalyzed by a bifunctional, bicyclic imidazolyl alcohol (BIA), which proved to be an effective catalyst for this transformation. The reactions were performed at room temperature in water to give the products in 10-74 % yield.
Published: 2020

21. Snap-heated freeze-free preservation and processing of the urine proteome using the combination of stabilizor-based technology and filter aided sample preparation

Author: Hugo M. Santos, José Luis Capelo-Martínez, Jacek R. Wiśniewski, Carlos Lodeiro, and Luis B. Carvalho
Subjects: Adult, Male, Proteome, Sample (material), Ultrafiltration, 02 engineering and technology, Urine, Proof of Concept Study, 01 natural sciences, Biochemistry, Specimen Handling, Analytical Chemistry, Heating, Young Adult, Cluster Analysis, Humans, Environmental Chemistry, Sample preparation, Spectroscopy, Preservation methods, Chromatography, Chemistry, 010401 analytical chemistry, Liquid Biopsy, Acute Kidney Injury, 021001 nanoscience & nanotechnology, Heat stabilization, 0104 chemical sciences, Filter (video), 0210 nano-technology, Biomarkers
Abstract: We present a method to preserve and process urine proteins for proteomic analysis in a filter aided sample preparation (FASP) format. The method combines concentration of urine proteins in ultrafiltration devices, their thermal stabilization, allowing long term storage of the samples, and filter aided sample preparation. Proteomes of four different urines were preserved during 48 h and 6 months using (i) the classic freeze preservation at −20 °C, (ii) snap-heated freeze-free preservation at laboratory temperature (20 °C) and (iii) snap-heated preservation at −60 °C. The three storage methods can effetely preserve the urine proteome for at least 6 months without significant alterations. Abundances of more than 500 proteins and specially 24 selected -cleared or -approved protein assayed in serum or plasma were found similar within the three preservation methods assessed. The new method here proposed dramatically simplifies the conditions for preserving the urine proteome for biobanks in terms of space and storage, including lowering the risks of sample degradation caused by misfunction of the freezer. Furthermore, the shipping of large number of samples can be made without the need of freezing. The application of the FASP format to isolate and preserve the proteins facilitates long-term storage and processing of proteome of urine samples.
Published: 2019

22. Proteomic changes driven by urban pollution suggest particulate matter as a deregulator of energy metabolism, mitochondrial activity, and oxidative pathways in the rat brain

Author: José Luis Capelo, Hugo M. Santos, Carlos Lodeiro, Mário Diniz, Julia Y. Ljubimova, Michael T. Kleinman, Antonella Chiechi, Anna Galstyan, J.E. Araújo, and Susana Jorge
Subjects: Male, Proteomics, Environmental Engineering, Proteome, 010504 meteorology & atmospheric sciences, Central nervous system, Respiratory chain, Oxidative phosphorylation, 010501 environmental sciences, medicine.disease_cause, 01 natural sciences, Air Pollution, medicine, Animals, Environmental Chemistry, Waste Management and Disposal, 0105 earth and related environmental sciences, Air Pollutants, Chemistry, Neurodegeneration, Brain, medicine.disease, Pollution, Rats, Cell biology, Oxidative Stress, Metabolic pathway, medicine.anatomical_structure, Particulate Matter, Energy Metabolism, Carcinogenesis, Astrocyte
Abstract: The adverse effects of air pollution have been long studied in the lung and respiratory systems, but the molecular changes that this causes at the central nervous system level have yet to be fully investigated and understood. To explore the evolution with time of protein expression levels in the brain of rats exposed to particulate matter of different sizes, we carried out two-dimensional gel electrophoresis followed by determination of dysregulated proteins through Coomassie blue staining-based densities (SameSpots software) and subsequent protein identification using MALDI-based mass spectrometry. Expression differences in dysregulated proteins were found to be statistically significant with p-value
Published: 2019

23. Absolute quantitative proteomics using the total protein approach to identify novel clinical immunohistochemical markers in renal neoplasms

Author: José Luis Capelo, Rajiv Dhir, Hugo M. Santos, Susana Jorge, Dimitrios Korentzelos, Swati Satturwar, William A. LaFramboise, Gabriela Quiroga-Garza, Carlos Lodeiro, Jacek R. Wiśniewski, Sheldon I. Bastacky, DQ - Departamento de Química, LAQV@REQUIMTE, and Faculdade de Ciências e Tecnologia (FCT)
Subjects: Oncology, Proteomics, medicine.medical_specialty, Quantitative proteomics, Diagnosis, Differential, Mass spectrometry-based proteomics, Total protein approach (TPA), SDG 3 - Good Health and Well-being, Tandem Mass Spectrometry, Health science, Internal medicine, Tissue micro-array (TMA), Biomarkers, Tumor, Medicine, Humans, Biomarker discovery, Carcinoma, Renal Cell, Total protein, Label free, Medicine(all), business.industry, Cancer, General Medicine, medicine.disease, Kidney Neoplasms, Renal neoplasms, Immunohistochemistry, Tissue bank, Immunohistochemistry, business, Research Article
Abstract: Background Renal neoplasms encompass a variety of malignant and benign tumors, including many with shared characteristics. The diagnosis of these renal neoplasms remains challenging with currently available tools. In this work, we demonstrate the total protein approach (TPA) based on high-resolution mass spectrometry (MS) as a tool to improve the accuracy of renal neoplasm diagnosis. Methods Frozen tissue biopsies of human renal tissues [clear cell renal cell carcinoma (n = 7), papillary renal cell carcinoma (n = 5), chromophobe renal cell carcinoma (n = 5), and renal oncocytoma (n = 5)] were collected for proteome analysis. Normal adjacent renal tissue (NAT, n = 5) was used as a control. Proteins were extracted and digested using trypsin, and the digested proteomes were analyzed by label-free high-resolution MS (nanoLC-ESI-HR-MS/MS). Quantitative analysis was performed by comparison between protein abundances of tumors and NAT specimens, and the label-free and standard-free TPA was used to obtain absolute protein concentrations. Results A total of 205 differentially expressed proteins with the potential to distinguish the renal neoplasms were found. Of these proteins, a TPA-based panel of 24, including known and new biomarkers, was selected as the best candidates to differentiate the neoplasms. As proof of concept, the diagnostic potential of PLIN2, TUBB3, LAMP1, and HK1 was validated using semi-quantitative immunohistochemistry with a total of 128 samples assessed on tissue micro-arrays. Conclusions We demonstrate the utility of combining high-resolution MS and the TPA as potential new diagnostic tool in the pathology of renal neoplasms. A similar TPA approach may be implemented in any cancer study with solid biopsies.
Published: 2021

24. The role of methyl jasmonate in enhancing biomass yields and bioactive metabolites in Stauroneis sp. (Bacillariophyceae) revealed by proteome and biochemical profiling

Author: Nicolas Touzet, Rachel Parkes, Lorraine Archer, Hugo M. Santos, Gerard T.A. Fleming, and Dónal Mc Gee
Subjects: 0106 biological sciences, Diatoms, 0303 health sciences, Methyl jasmonate, Proteome, Metabolite, Biophysics, Cyclopentanes, Acetates, Photosynthesis, 01 natural sciences, Biochemistry, Plastid terminal oxidase, Chloroplast, 03 medical and health sciences, chemistry.chemical_compound, chemistry, Lipid biosynthesis, Fucoxanthin, Trolox, Biomass, Oxylipins, 030304 developmental biology, 010606 plant biology & botany
Abstract: The diatom Stauroneis sp. was previously identified as a promising source of fucoxanthin and omega-3 oils. Methyl jasmonate (MJ) supplementation is known to enhance metabolite yields in this species without impacting on growth or photosynthesis. Therefore, a label-free proteomics approach was undertaken to further evaluate the functional role of MJ on the diatom's physiology. Of the twenty cultivation regimes were screened, Uf/2 medium with green+white LED's induced the greatest metabolic response when exposed to 10 μM MJ treatment. These conditions significantly enhanced the pigment and total cellular lipids contents. The increase in fucoxanthin correlating with a 20% increase in Trolox reducing equivalent in the total antioxidant assay, indicating a non-enzymatic antioxidant role of fucoxanthin to mitigate the detrimental effects of a redox imbalance within chloroplasts. The proteomics identified 197 proteins up-regulated 48 h after MJ exposure including cell signalling cascades, photosynthetic processes, carbohydrate metabolism, lipid biosynthesis and chloroplast biogenesis. MJ strengthened the dark reactions of photosynthesis to support growth and metabolite fluxes. The MJ-induced ER stress protein triggered lipid body production, facilitating metabolite turnover and trafficking between cellular organelles. Plastid terminal oxidase and glutamate 1-semialdehyde 2,1-aminomutase may act as MJ-induced ROS responsive regulatory switch to support chloroplast biosynthesis. Significance statement Phytohormones represents a promising tool to enhance the high-value metabolite yields in plants and algae, however little is known of the role of methyl jasmonate in diatoms at a molecular level. A shotgun proteomics approach was undertaken to determine the influence of MJ on the diatom's cellular physiology in the marine diatom Stauroneis sp., revealing a signal transduction cascade leading to increased lipid and pigment content and identified promising targets for genetic engineering.
Published: 2021

25. Pathway centered analysis to guide clinical decision-making in precision medicine

Author: José Luis Capelo, Medeiros M, Carlos Lodeiro, Rajiv Dhir, Lara Carvalho, Hugo M. Santos, and Pinheiro Lc
Subjects: Clinical decision making, business.industry, Proteome, Human proteome project, Medicine, Disease, business, Bioinformatics, Precision medicine, Medical care, Disease treatment
Abstract: Changes in the human proteome caused by disease before, during and after medical care is phenotype-dependent, so the proteome of each individual at any time point is a snapshot of the body’s response to disease and to disease treatment. Here, we introduce a new concept named differential Personal Pathway index (dPPi). This tool extracts and summates comprehensive disease-specific information contained within an individual’s proteome as a holistic way to follow the response to disease and medical care over time. We demonstrate the principle of the dPPi algorithm on proteins found in urine from patients suffering from neoplasia of the bladder. The relevance of the dPPi results to the individual clinical cases is described. The dPPi concept can be extended to other malignant and non-malignant diseases, and to other types of biopsies, such as plasma, serum or saliva. We envision the dPPi as a tool for clinical decision-making in precision medicine.
Published: 2021

26. Designing Eu-β-diketonate complexes as a support of ionic liquid crystals (ILCs) with additional luminescent properties

Author: Gonçalo Marcelo, Carlos Lodeiro, Elisabete Oliveira, José A. Campo, Hugo M. Santos, Ignacio González Sánchez, Cristián Cuerva, and Mercedes Cano
Subjects: chemistry.chemical_classification, Ligand, Process Chemistry and Technology, General Chemical Engineering, Ionic bonding, chemistry.chemical_element, Mesophase, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, 0104 chemical sciences, Crystallography, chemistry.chemical_compound, chemistry, Liquid crystal, Ionic liquid, 0210 nano-technology, Luminescence, Europium, Alkyl
Abstract: Here we describe the preparation, characterisation, liquid crystal properties and photophysical studies of new potassium salts of tetrakis(β-diketonate)europium(III) complexes based on long-chained symmetrical and unsymmetrically substituted 1,3-dialkyloxyphenyl-β-diketones ligands, K[Eu(OOR(n)R(m))4] (R(n) = OC6H4OCnH2n+1; R(m) = OC6H4OCmH2m+1; n = m = 8, 10, 12, 14, 16; n = 4, 8, m = 12, 16; n = 12, m = 16). All compounds exhibit mesomorphic and luminescence behaviour, regardless the presence of symmetrical or unsymmetrical ligands. It has been shown that the shortest molecular lengths, established by the summation of the two alkyl chains at the substituents of the β-diketonate ligand, give rise to more effective mesophase transition temperatures, while the asymmetry favours higher clearing temperatures. Related to the ionic salts based on long-chained pirazolium cations [H2pzR(n)]+ (R(n) = OC6H4OCnH2n+1; n = 4, 6, 8, 10, 12, 14, 16, 18) and tetrakis(1,3-bis(methoxyphenyl)propane-1,3-dionate)europium(III) as anion, they have also been studied and proved to be luminescent materials. By contrast, none of them was found to be mesomorphic. Therefore, the strategically increased chain length at the cation did not show to be effective for achieving liquid crystal properties. Integration of one of these luminescent europium complexes onto a polymeric PMMA matrix was positively evaluated towards its use as a temperature sensor and fluoride or cyanide ion sensor.
Published: 2018

27. Translational Urinomics

Author: Hugo M. Santos and Sofia De Azeredo Pereira
Published: 2021

28. Data Streams for Unsupervised Analysis of Company Data

Author: Hugo M. Santos, Nuno Marques, and Miguel Carrega
Subjects: Data stream, Exploratory data analysis, Computer science, Data stream mining, Process (engineering), media_common.quotation_subject, Financial analysis, Stock market, Quality (business), Function (engineering), Data science, media_common
Abstract: Financial data is increasingly made available in high quantities and in high quality for companies that trade in the stock market. However, such data is generally made available comprising many distinct financial indicators and most of these indicators are highly correlated and non-stationary. Computational tools for visualizing the huge diversity of available financial information, especially when it comes to financial indicators, are needed for micro and macro-economic financial analysis and forecasting. In this work we will present an automatic tool that can be a valuable assistant on this process: the Ubiquitous Self-Organizing Map (UbiSOM). The UbiSOM can be used for performing advance exploratory data analysis in company fundamental data and help to uncover new and emergent correlations in companies with similar company financial fundamentals that would remain undetected otherwise. Our results show that the generated SOM are stable enough to function as conceptual maps, that can accurately describe and adapt to the highly volatile financial data stream, even in the presence of financial shocks. Moreover, the SOM is presented as a valuable tool capable of describing different technological companies during the period of 2003–2018, based solely on four key fundamental indicators.
Published: 2021

29. Impacts of environmental issues on health and well-being: a global pollution challenge

Author: José Luis Capelo-Martínez, Elisabete Oliveira, Hugo M. Santos, and Carlos Lodeiro
Subjects: Pollution, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Environmental remediation, Health, Toxicology and Mutagenesis, media_common.quotation_subject, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Well-being, Caparica, 010501 environmental sciences, 01 natural sciences, Soil, PTIM2019, Environmental Chemistry, Soil Pollutants, Environmental planning, 0105 earth and related environmental sciences, media_common, Portugal, Environmental control, General Medicine, Editorial, Health, Business, Environmental Pollution, Environmental Monitoring
Abstract: Every 2 years, the environmental, chemical, and health research communities meet in Costa de Caparica, Portugal to showcase the latest technologies, methodologies and research advances in pollution detection, contamination control, remediation, and related health issues. Since its inception in 2015, the International Caparica Conference on Pollution Metal Ions and Molecules (PTIM) has become a biennial global forum to hear from those who protect the land, the water, and the air at all environmental scales. During past PTIM editions, we have learned about numerous efforts to develop new recovery and clean-up processes to restore the natural equilibria of our planet. Soil, land, water, and air are the key focus of efforts that will require deeper understanding and better control.
Published: 2020

30. Copper Complexes with 1,10-Phenanthroline Derivatives: Underlying Factors Affecting Their Cytotoxicity

Author: Isabel Correia, Cristina G. de Azevedo, Isabel Cavaco, Sofia Gama, Fernanda Marques, A. P. Alves de Matos, Teresa Pinheiro, João Costa Pessoa, Margarida M. Correia dos Santos, Patrique Nunes, José-Luis Capelo, and Hugo M. Santos
Subjects: Phenanthroline, Serum albumin, Antineoplastic Agents, 010402 general chemistry, Electrochemistry, Ligands, 01 natural sciences, Medicinal chemistry, Inorganic Chemistry, chemistry.chemical_compound, Coordination Complexes, Cell Line, Tumor, Molecule, Animals, Humans, Physical and Theoretical Chemistry, Bovine serum albumin, Cytotoxicity, Incubation, biology, 010405 organic chemistry, Serum Albumin, Bovine, 0104 chemical sciences, Chemistry, chemistry, Cell culture, biology.protein, Cattle, Drug Screening Assays, Antitumor, Copper, Phenanthrolines, Protein Binding
Abstract: The interpretation of in vitro cytotoxicity data of Cu(II)-1,10-phenanthroline (phen) complexes normally does not take into account the speciation that complexes undergo in cell incubation media and its implications in cellular uptake and mechanisms of action. We synthesize and test the activity of several distinct Cu(II)-phen compounds; up to 24 h of incubation, the cytotoxic activity differs for the Cu complexes and the corresponding free ligands, but for longer incubation times (e.g., 72 h), all compounds display similar activity. Combining the use of several spectroscopic, spectrometric, and electrochemical techniques, the speciation of Cu-phen compounds in cell incubation media is evaluated, indicating that the originally added complex almost totally decomposed and that Cu(II) and phen are mainly bound to bovine serum albumin. Several methods are used to disclose relationships between structure, activity, speciation in incubation media, cellular uptake, distribution of Cu in cells, and cytotoxicity. Contrary to what is reported in most studies, we conclude that interaction with cell components and cell death involves the separate action of Cu ions and phen molecules, not [Cu(phen)(n)] species. This conclusion should similarly apply to many other Cu-ligand systems reported to date. Fundacao para a Ciencia e Tecnologia (FCT)Portuguese Foundation for Science and TechnologyEuropean Commission [UID/Multi/04349/2019, UIDB/00100/2020, UID/QUI/50006/2019, UID/BIO/04565/2020] FCTPortuguese Foundation for Science and TechnologyEuropean Commission [IF/00841/2012, IF/00007/2015, SFRH/BD/108743/2015] Programa Operacional Regional de Lisboa 2020 [007317] PROTEOMASS Scientific Society COST Action, NECTAR (Network for Equilibria and Chemical Thermodynamics Advanced Research) - COST (European Cooperation in Science and Technology) [CA18202] info:eu-repo/semantics/publishedVersion
Published: 2020

31. Ultrasonic-Based Filter Aided Sample Preparation as the General Method to Sample Preparation in Proteomics

Author: José Luis Capelo-Martínez, Hugo M. Santos, Jacek R. Wiśniewski, Carlos Lodeiro, and Luis B. Carvalho
Subjects: Proteomics, Proteome, Protein digestion, Sample (material), Sonication, 010402 general chemistry, 01 natural sciences, Analytical Chemistry, Mice, Protein alkylation, Escherichia coli, Animals, Sample preparation, Peptide-mass fingerprint, Protocol (science), Chromatography, Chemistry, Escherichia coli Proteins, 010401 analytical chemistry, Brain, Caseins, 0104 chemical sciences, Liver, Filter (video), Oxidation-Reduction, Filtration
Abstract: We propose a new high-throughput ultrafast method for large-scale proteomics approaches by speeding up the classic filter aided sample preparation protocol, FASP, from overnight to 2.5 h. Thirty-six samples can be treated in 2.5 h, and the method is scalable to 96-well plate-based pipelines. After a modification of the FASP-tube, the steps of protein reduction, protein alkylation, and protein digestion of complex proteomes are done in just 5.25 min, each one under the effects of an ultrasonic field (7 cycles: 30 s on and 15 s off). The new method was compared to the standard overnight digestion FASP protocol, and no statistical differences were found for more than 92.4%, 92%, and 93.3% of the proteins identified by studying the proteome of E. coli, mouse brain, and mouse liver tissue samples, respectively. Furthermore, the successful relative label-free quantification of four spiked proteins in E. coli samples, BSA, β-lactoglobulin, α-casein, and α-lactalbumin, was achieved, using either the ultrasonic-based FASP protocol or the classic overnight one. The new US-FASP method matches the analytical minimalism rules as time, cost, sample requirement, reagent consumption, energy requirements, and production of waste products are reduced to a minimum while maintaining high sample throughput in a robust manner as all of the advantages of the filter aided sample preparation protocol are maintained.
Published: 2020

32. Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant

Author: Luís, Pinto, Carmen, Torres, Concha, Gil, Hugo M, Santos, José Luís, Capelo, Vítor, Borges, João Paulo, Gomes, Catarina, Silva, Luís, Vieira, Patrícia, Poeta, and Gilberto, Igrejas
Subjects: Genotype, Proteome, Computational Biology, Drug Resistance, Microbial, Molecular Sequence Annotation, Microbial Sensitivity Tests, Anti-Bacterial Agents, Vancomycin-Resistant Enterococci, Bacterial Proteins, Stress, Physiological, Vancomycin, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Enterococcus faecalis, Humans, Transcriptome, Genome, Bacterial, Gram-Positive Bacterial Infections, Phylogeny
Abstract: Antibiotic resistance and hospital acquired infections are on the rise worldwide. Vancomycin-resistant enterococci have been reported in clinical settings in recent decades. In this multiomics study, we provide comprehensive proteomic and transcriptomic analyses of a vancomycin-resistant
Published: 2020

33. Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain

Author: José Luis Capelo, Catarina Silva, Hugo M. Santos, Luís Vieira, Concha Gil, Luís Pinto, Vítor Borges, Patrícia Poeta, Gilberto Igrejas, Carmen Torres, and João Paulo Gomes
Subjects: Proteomics, Genotype, Proteome, Microbial Sensitivity Tests, medicine.disease_cause, Biochemistry, Enterococcus faecalis, Microbiology, Vancomycin-Resistant Enterococci, Transcriptome, Antibiotic resistance, Bacterial Proteins, Stress, Physiological, Vancomycin, Translational Research, Genetics, medicine, Humans, Transcriptomics, Molecular Biology, Gram-Positive Bacterial Infections, Phylogeny, Whole genome sequencing, biology, Resistência aos Antimicrobianos, Computational Biology, Pathogenic bacteria, Drug Resistance, Microbial, Molecular Sequence Annotation, biology.organism_classification, Multiomics, Anti-Bacterial Agents, Genómica Funcional e Estrutural, Enterococcus, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Antibiotic Resistance, Molecular Medicine, Genome, Bacterial, Biomarkers, Biotechnology
Abstract: Antibiotic resistance and hospital acquired infections are on the rise worldwide. Vancomycin-resistant enterococci have been reported in clinical settings in recent decades. In this multiomics study, we provide comprehensive proteomic and transcriptomic analyses of a vancomycin-resistant Enterococcus faecalis clinical isolate from a patient with a urinary tract infection. The previous genotypic profile of the strain C2620 indicated the presence of antibiotic resistance genes characteristic of the vanB cluster. To further investigate the transcriptome of this pathogenic strain, we used whole genome sequencing and RNA-sequencing to detect and quantify the genes expressed. In parallel, we used two-dimensional gel electrophoresis followed by MALDI-TOF/MS (Matrix-assisted laser desorption/ionization-Time-of-flight/Mass spectrometry) to identify the proteins in the proteome. We studied the membrane and cytoplasm subproteomes separately. From a total of 207 analysis spots, we identified 118 proteins. The protein list was compared to the results obtained from the full transcriptome assay. Several genes and proteins related to stress and cellular response were identified, as well as some linked to antibiotic and drug responses, which is consistent with the known state of multiresistance. Even though the correlation between transcriptome and proteome data is not yet fully understood, the use of multiomics approaches has proven to be increasingly relevant to achieve deeper insights into the survival ability of pathogenic bacteria found in health care facilities. L.P. was granted a PhD fellowship by Fundação para a Ciência e a Tecnologia and European Social Fund (SFRH/BD/81307/2011). This work was supported by the Associate Laboratory for Green Chemistry-LAQV, which is financed by national funds from Fundação para a Ciência e a Tecnologia/ MCTES (UID/QUI/50006/2019). This research is also a result of the GenomePT project (POCI-01-0145-FEDER- 022184), supported by COMPETE 2020—Operational Programme for Competitiveness and Internationalisation, Lisboa Portugal Regional Operational Programme (Lisboa, 2020), Algarve Portugal Regional Operational Programme (CRESC Algarve, 2020), under the PORTUGAL 2020 Partnership Agreement, through the EuropeanRegionalDevelopment Fund, andbyFundação para a Ciência e a Tecnologia.Work performed in University of La Rioja was supported by project SAF2016- 76571-R of Agencia Estatal de Investigatio´n and FEDER. info:eu-repo/semantics/publishedVersion
Published: 2020

34. Study and Preparation of Multifunctional Poly(L-Lysine)@Hyaluronic Acid Nanopolyplexes for the Effective Delivery of Tumor Suppressive MiR-34a into Triple-Negative Breast Cancer Cells

Author: Julia Lorenzo, Jamila Djafari, Carlos Lodeiro, Javier Fernández-Lodeiro, José Luis Capelo-Martínez, Hugo M. Santos, Emilia Bértolo, Sergi Rodríguez-Calado, LAQV@REQUIMTE, and DQ - Departamento de Química
Subjects: Poly-Lysine, Gene delivery, Polyplexes RNA, lcsh:Technology, Nanocapsules, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Materials Science(all), SDG 3 - Good Health and Well-being, Hyaluronic acid, microRNA, General Materials Science, Triple negative breast cancer, Viability assay, lcsh:Microscopy, Triple-negative breast cancer, lcsh:QC120-168.85, 030304 developmental biology, 0303 health sciences, polyplexes RNA, lcsh:QH201-278.5, lcsh:T, Communication, 3. Good health, Blot, chemistry, lcsh:TA1-2040, triple negative breast cancer, 030220 oncology & carcinogenesis, Cancer research, lcsh:Descriptive and experimental mechanics, lcsh:Electrical engineering. Electronics. Nuclear engineering, lcsh:Engineering (General). Civil engineering (General), lcsh:TK1-9971, Intracellular
Abstract: POCI-01-0145-FEDER-007265 UIDB/04077/2020 PTDC/QEQ-MED/2118/2014 2015 (IF/00007/2015) RTI2018-098027-B-C22 Non-viral gene delivery using exogenous microRNAs is a potential strategy for fighting cancers with poor prognosis and which lack specific therapies, such as triple-negative breast cancer (TNBC). Herein we report the synthesis of six nontoxic electrostatic polymeric nanocapsules (P1 to P6) for microRNA delivery in TNBC cells. 1H Nuclear Magnetic Resonance (NMR) spectroscopy and Scanning Electron Microscopy (SEM) were used to characterize the nanopolyplexes, synthesized with Poly(L-Lysine) and hyaluronic acid (Ha). Studies on the activity of the ternary HA/PLI/miRNA-34 nanopolyplexes towards TNBC cell line MDA-MB-231 were conducted. The nanopolyplexes mediated intracellular restoration of tumor suppressor miR34a was evaluated by using Western blotting to quantify the expression level of the Bcl-2 protein. The results suggest that the P5, with a ratio PLI/Ha of 0.05, was the most promising for the delivery of miR-34a into TNBC cells; the P5 nanocapsules were able to reduce Bcl-2 expression at a protein level, and had an effect in the overall cell viability after 24 h treatment. publishersversion published
Published: 2020

35. S2P: A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data

Author: Hugo M. Santos, Daniel Glez-Peña, Miguel Reboiro-Jato, Florentino Fdez-Riverola, José Luis Capelo, Susana Jorge, Hugo López-Fernández, and J.E. Araújo
Subjects: Adult, Male, 0301 basic medicine, Biomedical Research, Proteome, Java, Computer science, Software tool, Datasets as Topic, Health Informatics, Mass spectrometry, computer.software_genre, 01 natural sciences, User-Computer Interface, 03 medical and health sciences, Tandem Mass Spectrometry, Computer Graphics, Humans, Electrophoresis, Gel, Two-Dimensional, Aged, computer.programming_language, Reproducibility, 010401 analytical chemistry, Computational Biology, Reproducibility of Results, Blood Proteins, Middle Aged, 0104 chemical sciences, Computer Science Applications, Matrix-assisted laser desorption/ionization, Electrophoresis, 030104 developmental biology, Urinary Bladder Neoplasms, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Potential biomarkers, Female, Programming Languages, Protein identification, Data mining, Peritoneal Dialysis, computer, Biomarkers, Software, Chromatography, Liquid
Abstract: Background and objective 2D-gel electrophoresis is widely used in combination with MALDI-TOF mass spectrometry in order to analyze the proteome of biological samples. For instance, it can be used to discover proteins that are differentially expressed between two groups (e.g. two disease conditions, case vs. control, etc.) thus obtaining a set of potential biomarkers. This procedure requires a great deal of data processing in order to prepare data for analysis or to merge and integrate data from different sources. This kind of work is usually done manually (e.g. copying and pasting data into spreadsheet files), which is highly time consuming and distracts the researcher from other important, core tasks. Moreover, engaging in a repetitive process in a non-automated, handling-based manner is prone to error, thus threatening reliability and reproducibility. The objective of this paper is to present S2P, an open source software to overcome these drawbacks. Methods S2P is implemented in Java on top of the AIBench framework, and relies on well-established open source libraries to accomplish different tasks. Results S2P is an AIBench based desktop multiplatform application, specifically aimed to process 2D-gel and MALDI-mass spectrometry protein identification-based data in a computer-aided, reproducible manner. Different case studies are presented in order to show the usefulness of S2P. Conclusions S2P is open source and free to all users at http://www.sing-group.org/s2p . Through its user-friendly GUI interface, S2P dramatically reduces the time that researchers need to invest in order to prepare data for analysis.
Published: 2018

36. An overview on sensing materials depending on the electromagnetic spectra region applied

Author: Hugo M. Santos and Elisabete Oliveira
Subjects: 010405 organic chemistry, Infrared, business.industry, Chemistry, Electromagnetic spectrum, Process Chemistry and Technology, General Chemical Engineering, Chromophore, 010402 general chemistry, medicine.disease_cause, Photochemistry, 01 natural sciences, 0104 chemical sciences, Rhodamine, chemistry.chemical_compound, Ultraviolet light, medicine, Optoelectronics, Corrole, business, Ultraviolet, Visible spectrum
Abstract: The electromagnetic spectrum covers a wide long range of light that surrounds us every day. However, our eyes are sensitive to a minor part of the light. From all regions of the electromagnetic spectrum such as microwaves, infrared light, visible light, ultraviolet light, x-rays and gamma-rays, the ultraviolet and visible ones are the most appealing to us, since here are located the optical chemosensors (fluorimetric and colorimetric) which can be sensitive and selective to several relevant analytes. Herein, we will focus in distinguishing optical probes containing invisible and visible excitable chromophores and in their chemoresponsive towards several targets in solution and also in the solid state. Probes containing chromophores as coumarin, anthracene, benzoxazole, pyrene, crown ethers (benzo)imidazole-based, anthraquinones, indolylmethanes, fluorescein, cresyl violet, rhodamine, corrole, porphyrin, as well as, boron, palladium and platinum complexes are addressed. Concerning this area, the latest advances in our group will be emphasized, such as the way to the construction of more robust and efficient systems (76 references).
Published: 2016

37. Unraveling the Organotellurium Chemistry Applied to the Synthesis of Gold Nanomaterials

Author: Benito Rodríguez-González, Javier Fernández-Lodeiro, Carlos Lodeiro, Alcindo A. Dos Santos, José Luis Capelo, Hugo M. Santos, and Emilia Bértolo
Subjects: 010405 organic chemistry, Reducing agent, Chemistry, General Chemical Engineering, Diphenyl ditelluride, Nanoparticle, Nanotechnology, General Chemistry, 010402 general chemistry, Resonance (chemistry), 01 natural sciences, Environmentally friendly, Article, 0104 chemical sciences, Nanomaterials, lcsh:Chemistry, chemistry.chemical_compound, lcsh:QD1-999, Colloidal gold, Organotellurium chemistry
Abstract: Long-term preservation of the properties of gold nanoparticles in both solution and the dry powder form can be difficult. We have overcome this challenge by using organotellurium derivatives as both reducing agents and stabilizers in the synthesis of gold nanoparticles. This new synthetic protocol takes advantage of the photochemical and oxidative properties of diphenyl ditelluride (Ph2Te2), which, so far, have never been exploited in the synthesis of gold nanoparticles. The Au/Te core/shell (inorganic/organic) hybrid nanomaterial can be obtained in a one-step reaction, using only Ph2Te2 and HAuCl4. By modifying the reaction conditions, different resonance conditions of the gold core are achieved due to the formation of external shells with different thicknesses. The organotellurium shell can be easily removed by resuspension of the nanoparticles in environmentally friendly solvents, such as water or ethanol, making the Au core available for subsequent applications. A mechanism for the formation of core/shell nanoparticles has also been discussed.
Published: 2016

38. Development of a Robust Ultrasonic-Based Sample Treatment To Unravel the Proteome of OCT-Embedded Solid Tumor Biopsies

Author: Susana Jorge, Carlos Lodeiro, Hugo M. Santos, Rajiv Dhir, William A. LaFramboise, and José Luis Capelo
Subjects: 0301 basic medicine, Materials science, Proteome, Biopsy, Biochemistry, Proof of Concept Study, Specimen Handling, 03 medical and health sciences, Tandem Mass Spectrometry, Neoplasms, Adenoma, Oxyphilic, Humans, Ultrasonics, Solid tumor, Ultrasound energy, Carcinoma, Renal Cell, 030102 biochemistry & molecular biology, Tissue Embedding, business.industry, Ultrasound, General Chemistry, Kidney Neoplasms, 030104 developmental biology, Ultrasonic sensor, business, Biomedical engineering
Abstract: An effective three-step proteomics workflow is proposed to overcome the pitfalls caused by polymers present in optimum cutting temperature (OCT)-embedded tissue during its preparation for mass spectrometry analysis. First, the OCT-embedded tissue biopsies are cleaned using ethanol and water in a sequential series of ultrasonic washes in an ultrasound bath (35 kHz ultrasonic frequency, 100% ultrasonic amplitude, 2 min of ultrasonic duty time). Second, a fast ultrasonic-assisted extraction of proteins is done using an ultrasonic probe (30 kHz ultrasonic frequency, 50% ultrasonic amplitude, 2 min of ultrasonic duty time, 1 mm diameter tip). Third, a rapid ultrasonic digestion of complex proteomes is performed using a microplate horn assembly device (20 kHz ultrasonic frequency, 25% ultrasonic amplitude, 4 min of ultrasonic duty time). As a proof of concept, the new workflow was applied to human normal and tumor kidney biopsies including chromophobe renal cell carcinomas (chRCCs) and renal oncocytomas (ROs). A successful cluster of proteomics profiles was obtained comprising 511 and 172 unique proteins found in chRCC and RO samples, respectively. The new method provides high sample throughput and comprehensive protein recovery from OCT samples.
Published: 2019

39. Sustainable synthesis of luminescent CdTe quantum dots coated with modified silica mesoporous nanoparticles: Towards new protein scavengers and smart drug delivery carriers

Author: José Luis Capelo, Hugo M. Santos, Benito Rodríguez-González, Daniel Ruiz-Molina, Elisabete Oliveira, Fernando Novio, Carlos Lodeiro, Julia Lorenzo, Susana Jorge, Fundação para a Ciência e a Tecnologia (Portugal), Ministerio de Economía y Competitividad (España), European Commission, L'Oréal, Ministério da Educação e Ciência (Portugal), and L'Oréal-UNESCO For Women in Science
Subjects: Luminescence, General Chemical Engineering, Mesoporous silica nanoparticles, Nanoparticle, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, chemistry.chemical_compound, Rhodamine B, Bovine serum albumin, biology, Chemistry, Quantum dots, Process Chemistry and Technology, Proteins, Mesoporous silica, 021001 nanoscience & nanotechnology, Small molecule, Controlled release, 0104 chemical sciences, Chemical engineering, Targeted drug delivery, Doxorubicin, biology.protein, Nanoproteomics, 0210 nano-technology, Mesoporous material
Abstract: The synthesis and full characterization of a family of sustainable luminescent nanoparticles, CdTeQDs@MNs, made of quantum dots coated by modified mesoporous silica nanoparticles is reported. The presence of the luminescent QDs allows the imaging of the nanoparticles during cell internalization, as well as the visualization of selective release of doxorubicin inside the cell (via pH stimuli). The modified mesoporous silica nanoparticles lead to pore size improvement allowing better encapsulation and controlled release, of different active principles studied such as, small molecules (rhodamine B), drugs (doxorubicin), and isolated proteins such as bovine serum albumin, lysozyme, carbonic anhydrase, ovalbumin, α-lactalbumin, hemoglobin, myoglobin and cytochrome C. Finally, and as a proof-of-concept the efficacy of these novel platforms was demonstrated through the successful extraction and recognition of proteins in raw serum of osteoarthritis and prosthesis patients, without any previous protein depletion., This work was supported by PROTEOMASS Scientific Society (Portugal) and LAQV/REQUIMTE (UID/QUI/50006/2013). D.R-M and F.N. want to thanks project MAT2015-70615-R from the Spanish Government and by FEDER funds. ICN2 acknowledges support from the Severo Ochoa Program (MINECO, Grant SEV-2013-0295). J. L acknowledges support from project BIO2016-08057-R from MINECO-Spain. EO and SJ acknowledge the Post-Doctoral and Doctoral grants SFRH/BPD/108660/2015 and SFRH/BD/120537/2016, respectively, from Fundação para a Ciência e a Tecnologia (FCT-MEC) Portugal. EO thanks to Foundation L'Oreal (UNESCO and FCT) for the Prize Women in Science 2015, “Medalhas de Honra L’Oréal Portugal para as Mulheres na Ciência”. We also thank to Ms. Jessica Ariana-Machado for her help in the physical characterization (IR studies). H.M.S. is funded by the FCT 2015 Investigator Program (IF/00007/2015).
Published: 2019

40. Multiomics Assessment of Gene Expression in a Clinical Strain of CTX-M-15-Producing ST131

Author: Luís, Pinto, Carmen, Torres, Concha, Gil, Júlio D, Nunes-Miranda, Hugo M, Santos, Vítor, Borges, João P, Gomes, Catarina, Silva, Luís, Vieira, José E, Pereira, Patrícia, Poeta, and Gilberto, Igrejas
Subjects: transcriptomics, proteomics, public health, genomics, antimicrobial resistance, bacteria, Microbiology, Original Research
Abstract: Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strain C999 was isolated of a Spanish patient with urinary tract infection. Previous genotyping indicated that this strain presented a multidrug-resistance phenotype and carried beta-lactamase genes encoding CTX-M-15, TEM-1, and OXA-1 enzymes. The whole-cell proteome, and the membrane, cytoplasmic, periplasmic and extracellular sub-proteomes of C999 were obtained in this work by two-dimensional gel electrophoresis (2DE) followed by fingerprint sequencing through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). A total of 602 proteins were identified in the different cell fractions, several of which are related to stress response systems, cellular responses, and antibiotic and drug responses, consistent with the multidrug-resistance phenotype. In parallel, whole genome sequencing (WGS) and RNA sequencing (RNA-Seq) was done to identify and quantify the genes present and expressing. The in silico prediction following WGS confirmed our strain as being serotype O25:H4 and sequence type ST131. The presence of proteins related to antibiotic resistance and virulence in an O25:H4-ST131 E. coli clone are serious indicators of the continued threat of antibiotic resistance spread amongst healthcare institutions. On a positive note, a multiomics approach can facilitate surveillance and more detailed characterization of virulent bacterial clones from hospital environments.
Published: 2018

41. Proteogenomics: V international Caparica conference on analytical proteomics. V ICAP-2017

Author: Gilberto Igrejas, Hugo M. Santos, Carlos Lodeiro, and José Luis Capelo
Subjects: Proteomics, Chemistry, Biophysics, Humans, Computational biology, Congresses as Topic, Proteogenomics, Biochemistry
Published: 2018

42. Label-free quantification and post-translational modifications

Author: Carlos Lodeiro, José Luis Capelo, and Hugo M. Santos
Subjects: Label-free quantification, Chemistry, Biophysics, Posttranslational modification, Protein Processing, Post-Translational, Biochemistry, Mass Spectrometry
Published: 2020

43. Study of Multiporphyrin Compounds as Colorimetric Sitting-Atop Metal Complexes: Synthesis and Photophysical Studies

Author: Joana I. T. Costa, Carlos Lodeiro, Augusto C. Tomé, Hugo M. Santos, Maria G. P. M. S. Neves, and Elisabete Oliveira
Subjects: 010405 organic chemistry, Metal ions in aqueous solution, General Chemistry, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, Photochemistry, 01 natural sciences, Porphyrin, Fluorescence, 0104 chemical sciences, Metal, Crystallography, chemistry.chemical_compound, chemistry, visual_art, visual_art.visual_art_medium, Proton NMR, Colorimetry, Spectroscopy
Abstract: Mono-, di-, tri-, and hexaporphyrin derivatives were synthesized and their sensorial ability toward Na+ , Li+ , Ca2+ , Cu2+ , Ni2+ , Co2+ , Fe3+ , Zn2+ , Cd2+ , Hg2+ , Ag+ , Cr3+ , Pb2+ , and Al3+ was explored by absorption and emission spectroscopy and 1 H NMR spectroscopy. For all of the studied porphyrin derivatives the most significant spectral changes were observed upon addition of Zn2+ , Cd2+ , Cu2+ , Co2+ , Pb2+ , Hg2+ , and Fe3+ , which resulted in a color change from red to green. When the remaining metal ions were tested, no significant changes were observed. The results reveal, as expected, the formation of mononuclear complexes for porphyrin 4, dinuclear complexes for diporphyrin 7, and trinuclear complexes for triporphyrins 9 and 10. In addition, complexes of type M6 L were determined for hexaporphyrin 8. The NMR spectroscopy studies suggest that the interaction with the metals occurs with the formation of sitting-atop complexes. This study also shows that the sensitivity increases with increasing number of coordination sites, with the most pronounced case observed for Hg2+ . The lowest value of detectable concentration of 0.05 μm for Hg2+ was achieved for hexaporphyrin 8.
Published: 2015

44. Ultrasonic-assisted extraction and digestion of proteins from solid biopsies followed by peptide sequential extraction hyphenated to MALDI-based profiling holds the promise of distinguishing renal oncocytoma from chromophobe renal cell carcinoma

Author: Carlos Lodeiro, Hugo López-Fernández, Rajiv Dhir, William A. LaFramboise, Javier Fernández-Lodeiro, Kevin Pereira, Susana Jorge, José L. Capelo-Martínez, and Hugo M. Santos
Subjects: Adult, Male, Proteomics, Acetonitriles, Biopsy, Chromophobe Renal Cell Carcinoma, Peptide, 02 engineering and technology, Chromophobe cell, Kidney, urologic and male genital diseases, 01 natural sciences, Analytical Chemistry, Diagnosis, Differential, Mice, Biomarkers, Tumor, Ultrasonic assisted, medicine, Adenoma, Oxyphilic, Animals, Humans, Trypsin, Magnetite Nanoparticles, Renal oncocytoma, Carcinoma, Renal Cell, Aged, Aged, 80 and over, chemistry.chemical_classification, Chemistry, Solid Phase Extraction, 010401 analytical chemistry, Proteins, Middle Aged, Enzymes, Immobilized, 021001 nanoscience & nanotechnology, medicine.disease, Kidney Neoplasms, Peptide Fragments, 0104 chemical sciences, Ultrasonic Waves, Biochemistry, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Female, 0210 nano-technology, Protein depletion, medicine.drug
Abstract: A novel analytical approach is proposed to discriminate between solid biopsies of chromophobe renal cell carcinoma (chRCC) and renal oncocytoma (RO). The method comprises the following steps: (i) ultrasonic extraction of proteins from solid biopsies, (ii) protein depletion with acetonitrile, (iii) ultrasonic assisted in-solution digestion using magnetic nanoparticle with immobilized trypsin, (iv) C18 tip-based preconcentration of peptides, (v) sequential extraction of the peptides with ACN, (vi) MALDI-snapshot of the extracts and (vii) investigation of the extract containing the most discriminating features using high resolution mass spectrometry. With this approach we have been able to differentially cluster renal oncocytoma and chromophobe renal cell carcinoma and identified 18 proteins specific to chromophobe and seven unique to renal oncocytoma. Chromophobes express proteins associated with ATP function (ATP5I & 5E; VATE1 & G2; ADT2), glycolysis (PGK1) and neuromedin whilst oncocytomas express ATP5H, ATPA, DEPD7 and TRIPB thyroid receptor interacting protein.
Published: 2020

45. Label-free protein quantification after ultrafast digestion of complex proteomes using ultrasonic energy and immobilized-trypsin magnetic nanoparticles

Author: Carlos Lodeiro, Hugo M. Santos, José Luis Capelo, Javier Fernández-Lodeiro, Jamila Djafari, and Gonçalo Martins
Subjects: Spectrometry, Mass, Electrospray Ionization, Proteome, Quantitative proteomics, 02 engineering and technology, Mass spectrometry, Proteomics, 01 natural sciences, Analytical Chemistry, medicine, Sample preparation, Trypsin, Shotgun proteomics, Magnetite Nanoparticles, Chromatography, Chemistry, Escherichia coli Proteins, 010401 analytical chemistry, 021001 nanoscience & nanotechnology, Enzymes, Immobilized, 0104 chemical sciences, Label-free quantification, Ultrasonic Waves, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, 0210 nano-technology, medicine.drug, Chromatography, Liquid
Abstract: The ultimate high-throughput, high robustness and easy-to-handling sample treatment method for label-free shotgun proteomics is presented in this work. It is based on joining the effectiveness of immobilized trypsin at the nanoscale level with the latest technology to deliver ultrasonic energy. The new method can be used to reduce sample preparation time comprising the steps of reduction, alkylation and digestion time to just 15 min without compromising shotgun label-free protein quantification. It is demonstrated that trypsin immobilized at the nano-scale performs better than the commercially available counterpart macroparticles. Considering the current advances in (i) ultrasonic energy delivery that allows 96 samples to be treated at once in 30 min, and (ii) chromatography and mass spectrometry for shotgun proteomics, that allow to analyze complex proteomes in 5 min, we envision this methodology as the universal one to digest complex proteomes as it allows to profile quantitatively more than 200 samples per day.
Published: 2018

46. Identification of genomic loci associated with genotypic and phenotypic variation among Pseudomonas aeruginosa clinical isolates from pneumonia

Author: José Luis Capelo, Pedro Soares-Castro, Hugo M. Santos, Pedro M. Santos, Cristina Mesquita, Alberta Faustino, and Universidade do Minho
Subjects: Male, 0301 basic medicine, epidemiological study, Ciências Biológicas [Ciências Naturais], Antimicrobial resistance, medicine.disease_cause, Genome, Genotype, Cluster Analysis, Child, Aged, 80 and over, Genetics, Middle Aged, Genotype profiling, Hospitals, Random Amplified Polymorphic DNA Technique, 3. Good health, Infectious Diseases, Child, Preschool, Pseudomonas aeruginosa, Female, Adult, Adolescent, Virulence Factors, 030106 microbiology, Virulence, Biology, Microbiology, Young Adult, 03 medical and health sciences, Pathogenomics, Antibiotic resistance, Pneumonia, Bacterial, medicine, Humans, Pseudomonas Infections, Gene, Aged, Comparative genomics, Ciências Naturais::Ciências Biológicas, Science & Technology, Portugal, Infant, Newborn, Infant, Molecular Typing, 030104 developmental biology, Biological Variation, Population, Genetic Loci
Abstract: In this work, a genotype-phenotype survey of a highly diversified Pseudomonas aeruginosa collection was conducted, aiming to detail pathogen-associated scenarios that clinicians face nowadays. Genetic relation based on RAPD-PCR of 705 isolates, retrieved from 424 patients and several clinical contexts, reported an almost isolate-specific molecular-pattern. Pneumonia-associated isolates HB13 and HB15, clustered in the same RAPD-PCR group, were selected to evaluate the genomic background underlying their contrasting antibiotic resistance and virulence. The HB13 genome harbors antibiotic-inactivating enzymes-coding genes (e.g. aac(3)-Ia, arr, blaVIM-2) and single-nucleotide variations (SNVs) in antibiotic targets, likely accounting for its pan-resistance, whereas HB15 susceptibility correlated to predicted dysfunctional alleles. Isolate HB13 showed the unprecedented rhl-cluster absence and variations in other pathogen competitiveness contributors. Conversely, HB15 genome comprises exoenzyme-coding genes and SNVs linked to increased virulence. Secretome analysis identified signatures features with unknown function as potential novel pathogenic (e.g. a MATE-protein in HB13, a protease in HB15) and antibiotic resistance (a HlyD-like secretion protein in HB13) determinants. Detection of active prophages, proteases (including protease IV and alkaline metalloproteinase), a porin and a peptidase in HB15 highlights the secreted arsenal likely essential for its virulent behavior. The presented phenotype-genome association will contribute to the current knowledge on Pseudomonas aeruginosa pathogenomics., This work was supported by the strategic programme UID/BIA/0050/2013 (POCI-01-0145-FEDER-007569) funded by national funds through FCT I.P., by ERDF through the COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI) and through a PhD grant (SFRH/BD/98558/2013) attributed to C.S.M. The facility for Biological Mass Spectrometry Isabel Moura was funded by Proteomass Scientific Society. H.M.S. is funded by the FCT 2015 Investigator Program (IF/00007/2015).
Published: 2019

47. Synthesis of Gold Functionalised Nanoparticles with the Eranthis hyemalis Lectin and Preliminary Toxicological Studies on Caenorhabditis elegans

Author: Hugo M. Santos, Carlos Lodeiro, Javier Fernández-Lodeiro, José Luis Capelo, Emilia Bértolo, Marie T. McConnell, Simon C. Harvey, and Jamila Djafari
Subjects: Bioconjugation, biology, Dynamic light scattering, 13. Climate action, Colloidal gold, Chemistry, Ribosome-inactivating protein, Biophysics, biology.protein, Lectin, Nanoparticle, Conjugated system, Conjugate
Abstract: The lectin found in the tubers of the Winter Aconite (Eranthis hyemalis) plant (EHL) is a Type II Ribosome Inactivating Protein (RIP); type II RIPs have shown anti-cancer properties, and have great potential as therapeutic agents. Similarly, colloidal gold nanoparticles are successfully used in biomedical applications as gold nanoparticles can be functionalised with ligands with high affinity and specificity for target cells to create therapeutic and imaging agents. Herein we present the synthesis and characterization of gold nanoparticles conjugated with EHL. The aim was to establish the viability of the conjugate and perform a set of initial assays to establish whether the biological effect of EHL is altered by the conjugation. The biological assays were performed in Caenorhabditis elegans, a free living nematode commonly used for toxicological studies; previous work from some of the authors using first life stage (L1) nematodes has shown that EHL has a strong biocidal effect on C. elegans. Gold nanoparticles functionalised with EHL (AuNPs@EHL) were successfully synthesised by bioconjugation with citrate gold nanoparticles (AuNPs@Citrate); the conjugates were analysed by UV-Vis spectroscopy, Dynamic Light Scattering (DLS), Zeta Potential analysis and Transmission Electron Microscopy (TEM). Results indicate that an optimal functionalisation was achieved with the addition of 100 µL of EHL (concentration 1090 ± 40 µg/mL) over 5 mL of AuNPs (concentration [Au0] = 0.8 mM). Biological assays on the effect of AuNPs@EHL on C. elegans were performed, using first life stage (L1) and pre-adult stage (L4) nematodes. Citrate gold nanoparticles did not have any obvious effect on the nematodes. For L1 stage nematodes, the assays show that conjugation with gold nanoparticles reduced the biological effect of EHL on C. elegans. As lectin binding activity is essential for the natural protein to bind and allow entry to cells, conformational changes due to conjugation may have affected this binding affinity. For L4 stage nematodes, both EHL alone and AuNPs@EHL showed biological activity, and reproductive delays and reduced fecundity were observed in both cases. These assays indicate that EHL can be conjugated to gold nanoparticles and retain elements of biocidal activity.
Published: 2018

48. Dithiothreitol-based protein equalization technology to unravel biomarkers for bladder cancer

Author: Paula A. Videira, Pedro Baltazar, Fernando Calais da Silva, Mário Diniz, José Luis Capelo, J.E. Araújo, Hugo M. Santos, Mylène A. Carrascal, Luís Campos Pinheiro, Hugo López-Fernández, DQ - Departamento de Química, UCIBIO - Applied Molecular Biosciences Unit, NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM), and DCV - Departamento de Ciências da Vida
Subjects: Proteomics, 0301 basic medicine, Fibrinogen-gamma chain, Proteome, Chemistry(all), Serum albumin, Dithiothreitol, Analytical Chemistry, 03 medical and health sciences, chemistry.chemical_compound, SDG 3 - Good Health and Well-being, Biomarkers, Tumor, medicine, Humans, Electrophoresis, Gel, Two-Dimensional, 2D-SDS-PAGE, Gel electrophoresis, Bladder cancer, biology, LUTS, Protein equalization, Haptoglobin, Blood Proteins, medicine.disease, S2P, Molecular biology, MALDI-TOF-MS, 3. Good health, 030104 developmental biology, Urinary Bladder Neoplasms, chemistry, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, biology.protein, Electrophoresis, Polyacrylamide Gel, Gelsolin
Abstract: The PROTEOMASS Scientific Society is acknowledged by the funding provided to the Biological Mass Spectrometry Isabel Moura. Authors acknowledge the funding provided by UCIBIO, Unidade de Ciencias Biomoleculares Aplicadas, which is financed by national funds from FCT/MEC (UID/Multi/04378/2013) and co-financed by the ERDF under the PT2020 Partnership Agreement (POCI-01-0145-FEDER-007728) and to the Associate Laboratory for Green Chemistry LAQV which is financed by national funds from FCT/MEC (UID/QUI/50006/2013) and co-financed by the ERDF under the PT2020 Partnership Agreement (POCI-01-0145-FEDER-007265). J. E. Araujo acknowledges the financial support given by the Portuguese Foundation for Science and Technology under doctoral grant number SFRH/BD/109201/2015. H. Lopez-Fernandez is supported by a post-doctoral fellowship from Xunta de Galicia. H.M.S. is funded by the FCT Investigator Programme 2015 (IF/00007/2015). The Nova Medical School is also acknowledged for financial support under project "Discovery of biomarkers for bladder carcinoma diagnosis" - NOVA health programme 2015. This study aimed to assess the benefits of dithiothreitol (DTT)-based sample treatment for protein equalization to assess potential biomarkers for bladder cancer. The proteome of plasma samples of patients with bladder carcinoma, patients with lower urinary tract symptoms (LUTS) and healthy volunteers, was equalized with dithiothreitol (DTT) and compared. The equalized proteomes were interrogated using two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry. Six proteins, namely serum albumin, gelsolin, fibrinogen gamma chain, Ig alpha-1 chain C region, Ig alpha-2 chain C region and haptoglobin, were found dysregulated in at least 70% of bladder cancer patients when compared with a pool of healthy individuals. One protein, serum albumin, was found overexpressed in 70% of the patients when the equalized proteome of the healthy pool was compared with the equalized proteome of the LUTS patients. The pathways modified by the proteins differentially expressed were analyzed using Cytoscape. The method here presented is fast, cheap, of easy application and it matches the analytical minimalism rules as outlined by Halls. Orthogonal validation was done using western-blot. Overall, DTT-based protein equalization is a promising methodology in bladder cancer research. authorsversion published
Published: 2018

49. Measurements of differential cross sections of top quark pair production in association with jets in pp collisions at √s=13 TeV using the ATLAS detector

Author: S. Tapia Araya, Yasuyuki Okumura, Jemal Khubua, Silje Raddum, Stephen Watts, Tohru Takeshita, Katsuo Tokushuku, Remi Lafaye, Antonio Policicchio, Iskander Ibragimov, Wen Guan, Uwe Bratzler, Alexander Sydorenko, Giorgi Arabidze, Patrick Fassnacht, Radim Slovak, Nedaa Asbah, Janusz Chwastowski, Sharka Todorova-Nova, B. R. Mellado Garcia, Fumiya Yamane, Christian Grefe, Robert Johannes Langenberg, Johannes Erdmann, Markus Atkinson, Graham Richard Lee, Stephen Kam-wah Chan, Werner Spolidoro Freund, Louis Guillaume Gagnon, A. V. Akimov, K. J. R. Cormier, Jolanta Olszowska, Simon Feigl, Georges Azuelos, Davide Caforio, Yona Oren, L. Di Ciaccio, Mohammad Jawad Kareem, Stewart Patrick Swift, Justas Zalieckas, Rui Wang, Sara Ghasemi, Philippe Mermod, Michael Stoebe, Michel Vetterli, Richard Polifka, S.-C. Hsu, Marcin Wladyslaw Wolter, Aparajita Dattagupta, Alexander Grillo, Thomas James Neep, Nick Barlow, Barry King, S. C. Lee, Hannah Herde, C. M. Hawkes, Pavol Bartos, Marina Cobal, Michael Edward Nelson, Jiri Masik, Oleg Fedin, Christos Leonidopoulos, Yann Coadou, Karishma Sekhon, Heidi Sandaker, Sten Hellman, Steve Muanza, R. Cherkaoui El Moursli, Simon Berlendis, Evgeniy Khramov, Monica Dobre, R. Bartoldus, Chen Zhou, Felix Fidelio Klitzner, Arnaud Duperrin, Heather Gray, George Redlinger, M. Rescigno, Christian Johann Riegel, Anatoly Borisov, Steven Williams, Andrey Karyukhin, M. Reale, Tasneem Rashid, Eirik Gramstad, Nils Krumnack, Thu Pham, Robert McPherson, C. Petridou, Vivek Jain, Mahsana Haleem, Angel Campoverde, Hiroshi Sakamoto, T. S. Lau, Stamatios Gkaitatzis, Shuo Han, Isabel Marian Trigger, F. Lo Sterzo, Mauro Villa, Donnchadha Quilty, Amir Farbin, M. A. Nomura, L. Masetti, R. F. Y. Peters, Attilio Picazio, Thorsten Wengler, Konstantinos Ntekas, Matthias Klein, A. Lopez Solis, Alexey Talyshev, Vladimir Cindro, Pierre-Hugues Beauchemin, Aaron James Armbruster, K. H. Hiller, Dmitriy Maximov, I. Turk Cakir, Miroslav Hrabovsky, Kazunori Hanagaki, Benjamin Philip Nachman, Iurii Naryshkin, Krzysztof Wozniak, R. E. Blair, Riccardo Vari, Jong-Sung Yu, Maria Pilar Casado, Dennis Perepelitsa, Emma Tolley, Dimitrios Sampsonidis, Robert Clarke, Kouta Onogi, T. P. A. Åkesson, Jared Gregory Vasquez, Imma Riu, Rebecca Anne Linck, J. Manjarres Ramos, Denys Denysiuk, A. G. Clark, Dilip Jana, Anthony Keith Morley, Peter Wagner, V. W. S. Wong, Nigel Hessey, Marija Marjanovic, Ricardo Gonçalo, Fabrizio Fabbri, Mingliang Zhou, G. Marchiori, Alexander Khanov, Alexander Lincoln Read, J. C. Hill, Julien-christopher Beyer, R. Piegaia, Hyungsuk Son, B. A. Long, Giuseppe Iacobucci, Thomas Koffas, Christian Gumpert, Benjamin Trocmé, Barbara Wosiek, R. C. W. Henderson, F. De Lorenzi, M. J. Shochet, Aimilianos Koulouris, Alexandre Rozanov, T. Kobayashi, Claudio Santoni, M. G. D. Gilchriese, Giordon Stark, Jozsef Toth, Elena Korolkova, Carla Sbarra, Toshiaki Kaji, B. M. Waugh, Claire Antel, Charles Leggett, Fabian Huegging, Rute Pedro, Marc Geisen, T. M. H. Wolf, Katharina Maria Ecker, B. Alvarez Gonzalez, Pierfrancesco Butti, Paris Moschovakos, Markus Wobisch, Masahiro Ikeno, Stefano Zambito, Andrea Dell'Acqua, Kristof Kreutzfeldt, Alexander Naip Tuna, Alexey Myagkov, Luc Poggioli, Fabian Wilk, Kevin Hildebrand, Bostjan Macek, Elmar Ritsch, Verena Herget, Giuseppe Callea, Michael Begel, Minoru Hirose, Zara Jane Grout, P. Chang, Viktor Kramarenko, Antonio Sbrizzi, Pavel Shatalov, Mitsuaki Nozaki, Roland Jansky, Jochen Dingfelder, Alex Kastanas, Alaettin Serhan Mete, Osamu Sasaki, S. George, Chaowaroj Wanotayaroj, Yongsheng Gao, Dominik Duda, Nima Sherafati, Y. L. Liu, David Calvet, Lorenz Hauswald, Roger Jones, Aldo Saavedra, Atsuhiko Ochi, James Howarth, Manuel Patrice Geisler, Jiri Hejbal, Tim Jones, Giuseppe Mornacchi, Joao Saraiva, Otilia Anamaria Ducu, S. L. Lloyd, R. St. Denis, D. Vazquez Furelos, Mark Kruse, Alison Lister, G. Zhang, Ruo-yu Shang, Shunichi Akatsuka, Attila Krasznahorkay, Fabio Cardillo, Julius Hrivnac, T. Ženiš, Yosuke Yamazaki, Mohamad Kassem Ayoub, Arely Cortes-Gonzalez, Alexander Milov, Helge Christoph Beck, Oxana Smirnova, Konstantinos Bachas, O. Bessidskaia Bylund, Danijela Bogavac, Tadeusz Kowalski, Wainer Vandelli, R. D. Schamberger, Bing Zhou, Martin Kocian, R. Caminal Armadans, Didier Ferrere, Pascal Pralavorio, Marlon Barbero, Lamberto Luminari, Petter Nilsson, Andrew D. Hamilton, Arthur James Horton, T. Cuhadar Donszelmann, R. S. Orr, Vadim Bednyakov, Maciej Trzebinski, Fabian-Phillipp Tepel, Laurelle Maria Veloce, Ryuichi Takashima, Simon Schmitz, Ji Zhu, Gabriella Sciolla, Louis Fayard, Benoit Lefebvre, Thorwald Klapdor-kleingrothaus, Savanna Marie Shaw, A. Mirto, J. A. Wilson, C. A. Solans Sanchez, I. Ravinovich, Tatsumi Nitta, Tomas Slavicek, Oleksandr Viazlo, Christos Gentsos, Vasiliki Kouskoura, Emma Winkels, J. P. Thomas, Chiara Rizzi, Dusan Bruncko, Michael Dührssen, Tomo Lazovich, Guillaume Lefebvre, Troels Petersen, Eric Buschmann, J. C. Rivera Vergara, David Sosa, Odette Benary, Marcus Morgenstern, Mihai Caprini, S. Donati, Per Olov Joakim Gradin, Gregory David Hallewell, J. Jimenez Pena, Jiri Dolejsi, P. T. E. Taylor, Jean-Francois Laporte, Zinonas Zinonos, Alastair Dewhurst, Paul Tipton, Heinz Pernegger, Alexander Oh, Allen Mincer, Anatoly Kozhin, P. K. Teng, Gabija Zemaityte, Faig Ahmadov, Andrew Blue, Lidia Dell'Asta, M. E. Pozo Astigarraga, N. G. Gutierrez Ortiz, Lukas Plazak, Stephen Haywood, Sotirios Vlachos, Walter Lampl, F. Parodi, David Miller, Vladimir Vinogradov, Fabrice Hubaut, Ece Akilli, Nikiforos Nikiforou, Francesca Ungaro, Kyungeon Choi, C. J. E. Suster, Steven Goldfarb, Z. G. Zhao, Trisha Farooque, Alexander Paramonov, William Buttinger, David Francis, Pawel Klimek, Salvatore Bruno, Cheng-Chieh Peng, Paul Hanke, M. Franklin, Marcello Fanti, Igor Gavrilenko, Matteo Bauce, Adam Jinaru, Elvedin Tahirovic, Frank Ellinghaus, Marcello Bindi, Matteo Scornajenghi, Ryan Reece, Andreas Christian Dudder, Petr Tas, S. H. Oh, Laura Gonella, Stefano Veneziano, Elisa Guido, H. S. Chen, Antonio Limosani, J. A. Parsons, Daniel Mauricio Rauch, M. P. Giordani, Stefan Koperny, Julie Kirk, Craig Sawyer, Susanne Kersten, Chilufya Mwewa, Aidan Grummer, Sebastian Grinstein, Jason Veatch, Elena Plotnikova, A. J. Lankford, L. Han, Geoffrey Henry Herbert, Eda Yildirim, Marcella Bona, Nathalie Besson, Yu Him Justin Chiu, Laura Brittany Havener, Laurent Vacavant, Philippe Calfayan, P. van Gemmeren, Camilla Maiani, J. A. Valls Ferrer, Nikolaos Rompotis, Ruth Poettgen, Mark Andrew Pickering, Hisaya Kurashige, Snezana Nektarijevic, R. El Kosseifi, Ryo Tanioka, Cesare Bini, Zhen Yan, Michael Kagan, Rodney Walker, David Robert Wardrope, Christopher Potter, Gabriel Stoicea, Raymond Brock, G. 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Di Valentino, Yoichi Ninomiya, J. Del Peso, Chikara Fukunaga, Fares Djama, Stanley Lai, Xuanhong Lou, Kathryn Grimm, Nikolai Marcel Hartmann, M. Morii, V. Castillo Gimenez, Jonathan Shlomi, Andre Sopczak, Fabian Kuger, W. Fedorko, Sergey Kuleshov, Revital Kopeliansky, Harshna Jivan, Cristina Galea, Yang Gao, T. Saito, Elliott Cheu, F. Lasagni Manghi, R.-J. Wang, John Huth, Shuyang Hu, Stefan Simion, Alexander Melzer, Alan James Taylor, Philip Phillips, Samuel Silverstein, Chav Chhiv Chau, H. H. Williams, Giada Mancini, Michal Simon, Steinar Stapnes, Harish Potti, Yee Chinn Yap, Josh Moss, Enrique Kajomovitz, Evgenii Baldin, Louis Helary, Anna Mastroberardino, Bruno Lenzi, David Kirchmeier, Maximilian Hils, Alexey Buzykaev, Antonio Ereditato, Colleen Jennifer Treado, Harinder Singh Bawa, Oliver Kortner, Katharina Bierwagen, Brigitte Vachon, Arthur Eugen Bolz, H. Zhu, Felix Cormier, H. Kagan, Domizia Orestano, Semen Turchikhin, Ian Connelly, L. Pacheco Rodriguez, Richard Bates, Ossama AbouZeid, Birgit Sylvia Stapf, Carsten Bittrich, Phillip George Hamnett, Martin Rybar, Hans Peter Beck, Chao Wang, A. S. Thompson, Markus Nordberg, Vakhtang Tsiskaridze, Maria Curatolo, J. N. Butler, Anyes Taffard, You Zhou, Heather Lynn Russell, H. De la Torre, Simone Amoroso, John Morris, Manuel Silva, Nicolas Ellis, Kirill Grevtsov, Roman Lysak, Christoph Eckardt, Nicholas Adam Styles, Federico Meloni, V. Izzo, Carolyn Bertsche, A. Rodriguez Perez, Joe Taenzer, Andrea Catinaccio, Jason Lea Oliver, Robert Kehoe, Manfredi Ronzani, Renat Sadykov, Rudiger Voss, David Martin Bjergaard, Mutsuto Hagihara, Marco Vanadia, Koichi Nagai, M. J. Da Cunha Sargedas De Sousa, Marcin Pawel Guzik, Peter Loch, S. Argyropoulos, J. B. De Vivie De Regie, Jan Kretzschmar, Miriam Diamond, Miguel Arratia, Fengwangdong Zhang, Eleni Mountricha, Didier Lacour, Ondrej Penc, Ka Wa Tsang, J. Llorente Merino, Tingting Cao, Francesco Guescini, J. Barreiro Guimarães da Costa, Michela Paganini, Michael Bender, Sergey Burdin, Dmitry Emeliyanov, Yasuhiro Makida, Steve McMahon, Robert Gardner, Joaquin Hoya, Martin Spousta, Kentaro Kawade, Morad Aaboud, Christoph Falk Anders, Maike Christina Hansen, E. K. U. Gross, Göran Jarlskog, Emily Marie Duffield, Valerio Ippolito, Polina Nechaeva, Marco Valente, I. P. J. Shipsey, Marc Escalier, Victor Solovyev, Alyssa Montalbano, Jonathan Butterworth, Sergey Chekulaev, Kohei Yorita, Cristinel Diaconu, O. Cakir, Andree Robichaud-Veronneau, Catrin Bernius, Thomas Malte Spieker, Jan Thomas Kuechler, David William Casper, Yang Heng, Paul Miyagawa, A. C. König, M. Kuze, Laura Fabbri, Konstantin Zhukov, Natascha Savic, Jörgen Sjölin, Brian Thomas Amadio, Antonio Miucci, Tova Ray Holmes, Gunnar Jakel, Grzegorz Gach, Noemi Calace, Dean T. Yamaguchi, Wen Guo, Peter Vankov, Catalin Agheorghiesei, Yasuyuki Horii, Tristan Beau, J. Wotschack, X. T. Meng, Johanna Gramling, Howard Gordon, Marcel Weirich, P. Francavilla, Julian Glatzer, J. A. García Pascual, Nikita Smirnov, Leszek Adamczyk, Steven Schramm, Michela Biglietti, Emanuele Cavallaro, Julia Lynne Gonski, Miroslav Havranek, Pere Rados, S. Díez Cornell, Baojia Tong, Corrinne Mills, Centre de Physique des Particules de Marseille (CPPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Aix Marseille Université (AMU), Laboratoire de l'Accélérateur Linéaire (LAL), Université Paris-Sud - Paris 11 (UP11)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique de Clermont (LPC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Laboratoire de Physique Nucléaire et de Hautes Énergies (LPNHE (UMR_7585)), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Annecy de Physique des Particules (LAPP/Laboratoire d'Annecy-le-Vieux de Physique des Particules), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), Laboratoire de Physique Subatomique et de Cosmologie (LPSC), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Centre de Calcul de l'IN2P3 (CC-IN2P3), Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), ATLAS, TOBB ETU, Faculty of Engineering, Department of Material Science & Nanotechnology Engineering, TOBB ETÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü, Sultansoy, Saleh F., Akilli, Ece, Ancu, Lucian Stefan, Benoit, Mathieu, Calace, Noemi, Clark, Allan Geoffrey, Coccaro, Andrea, Della Volpe, Domenico, Di Bello, Francesco Armando, Dubreuil, Arnaud, Ferrere, Didier, Gadomski, Szymon, Golling, Tobias, Gonzalez Sevilla, Sergio, Iacobucci, Giuseppe, Jansky, Roland, Katre, Akshay, Khoo, Teng Jian, Kiehn, Moritz, Lanfermann, Marie Christine, Lionti, Anthony Eric, March Ruiz, Luis, Mermod, Philippe, Nessi, Marzio, Pandini, Carlo, Paolozzi, Lorenzo, Schramm, Steven, Sfyrla, Anna, Sultan, D M S, Valente, Marco, Wu, Xin, ATLAS (IHEF, IoP, FNWI), XENON (IHEF, IoP, FNWI), IHEF (IoP, FNWI), Aix Marseille Université (AMU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris-Sud - Paris 11 (UP11), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Laboratoire d'Annecy de Physique des Particules (LAPP), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Aaboud, M, Chiodini, G, Gorini, E, Longo, L, Mirto, A, Primavera, M, Reale, M, Spagnolo, S, Ventura, A, ATLAS Collaboration, And, Universidade do Minho, Współautorami artykułu są członkowie ATLAS Collaboration w liczbie 2883, Aaboud, M., Aad, G., Abbott, B., Abdinov, O., Abeloos, B., Abidi, S. H., Abouzeid, O. S., Abraham, N. L., Abramowicz, H., Abreu, H., Abulaiti, Y., Acharya, B. S., Adachi, S., Adamczyk, L., Adelman, J., Adersberger, M., Adye, T., Affolder, A. A., Afik, Y., Agheorghiesei, C., Aguilar-Saavedra, J. A., Ahmadov, F., Aielli, G., Akatsuka, S., Akerstedt, H., Åkesson, T. P. A., Akilli, E., Akimov, A. V., Alberghi, G. L., Albert, J., Albicocco, P., Alconada Verzini, M. J., Alderweireldt, S., Aleksa, M., Aleksandrov, I. N., Alexa, C., Alexander, G., Alexopoulos, T., Alhroob, M., Ali, B., Alimonti, G., Alison, J., Alkire, S. P., Allbrooke, B. M. M., Allen, B. W., Allport, P. P., Aloisio, A., Alonso, A., Alonso, F., Alpigiani, C., Alshehri, A. A., Alstaty, M. I., Alvarez Gonzalez, B., Álvarez Piqueras, D., Alviggi, M. G., Amadio, B. T., Amaral Coutinho, Y., Amelung, C., Amidei, D., Amor Dos Santos, S. P., Amoroso, S., Anastopoulos, C., Ancu, L. S., Andari, N., Andeen, T., Anders, C. F., Anders, J. K., Anderson, K. J., Andreazza, A., Andrei, V., Angelidakis, S., Angelozzi, I., Angerami, A., Anisenkov, A. V., Anjos, N., Annovi, A., Antel, C., Antonelli, M., Antonov, A., Antrim, D. J. A., Anulli, F., Aoki, M., Aperio Bella, L., Arabidze, G., Arai, Y., Araque, J. P., Araujo Ferraz, V., Arce, A. T. H., Ardell, R. E., Arduh, F. A., Arguin, J. -F., Argyropoulos, S., Arik, M., Armbruster, A. J., Armitage, L. J., Arnaez, O., Arnold, H., Arratia, M., Arslan, O., Artamonov, A., Artoni, G., Artz, S., Asai, S., Asbah, N., Ashkenazi, A., Asquith, L., Assamagan, K., Astalos, R., Atkinson, M., Atlay, N. B., Augsten, K., Avolio, G., Axen, B., Ayoub, M. K., Azuelos, G., Baas, A. E., Baca, M. J., Bachacou, H., Bachas, K., Backes, M., Bagnaia, P., Bahmani, M., Bahrasemani, H., Baines, J. T., Bajic, M., Baker, O. K., Bakker, P. J., Baldin, E. M., Balek, P., Balli, F., Balunas, W. K., Banas, E., Bandyopadhyay, A., Banerjee, S., Bannoura, A. A. E., Barak, L., Barberio, E. L., Barberis, D., Barbero, M., Barillari, T., Barisits, M. -S., Barkeloo, J., Barklow, T., Barlow, N., Barnes, S. L., Barnett, B. M., Barnett, R. M., Barnovska-Blenessy, Z., Baroncelli, A., Barone, G., Barr, A. J., Barranco Navarro, L., Barreiro, F., Barreiro Guimarães da Costa, J., Bartoldus, R., Barton, A. E., Bartos, P., Basalaev, A., Bassalat, A., Bates, R. L., Batista, S. J., Batley, J. R., Battaglia, M., Bauce, M., Bauer, F., Bauer, K. T., Bawa, H. S., Beacham, J. B., Beattie, M. D., Beau, T., Beauchemin, P. H., Bechtle, P., Beck, H. C., Beck, H. P., Becker, K., Becker, M., Becot, C., Beddall, A., Beddall, A. J., Bednyakov, V. A., Bedognetti, M., Bee, C. P., Beermann, T. A., Begalli, M., Begel, M., Behr, J. K., Bell, A. S., Bella, G., Bellagamba, L., Bellerive, A., Bellomo, M., Belotskiy, K., Beltramello, O., Belyaev, N. L., Benary, O., Benchekroun, D., Bender, M., Benekos, N., Benhammou, Y., Benhar Noccioli, E., Benitez, J., Benjamin, D. P., Benoit, M., Bensinger, J. R., Bentvelsen, S., Beresford, L., Beretta, M., Berge, D., Bergeaas Kuutmann, E., Berger, N., Bergsten, L. J., Beringer, J., Berlendis, S., Bernard, N. R., Bernardi, G., Bernius, C., Bernlochner, F. U., Berry, T., Berta, P., Bertella, C., Bertoli, G., Bertram, I. A., Bertsche, C., Besjes, G. J., Bessidskaia Bylund, O., Bessner, M., Besson, N., Bethani, A., Bethke, S., Betti, A., Bevan, A. J., Beyer, J., Bianchi, R. M., Biebel, O., Biedermann, D., Bielski, R., Bierwagen, K., Biesuz, N. V., Biglietti, M., Billoud, T. R. V., Bilokon, H., Bindi, M., Bingul, A., Bini, C., Biondi, S., Bisanz, T., Bittrich, C., Bjergaard, D. M., Black, J. E., Black, K. M., Blair, R. E., Blazek, T., Bloch, I., Blocker, C., Blue, A., Blumenschein, U., Blunier, Dr., Bobbink, G. J., Bobrovnikov, V. S., Bocchetta, S. S., Bocci, A., Bock, C., Boehler, M., Boerner, D., Bogavac, D., Bogdanchikov, A. G., Bohm, C., Boisvert, V., Bokan, P., Bold, T., Boldyrev, A. S., Bolz, A. E., Bomben, M., Bona, M., Bonilla, J. S., Boonekamp, M., Borisov, A., Borissov, G., Bortfeldt, J., Bortoletto, D., Bortolotto, V., Boscherini, D., Bosman, M., Bossio Sola, J. D., Boudreau, J., Bouhova-Thacker, E. V., Boumediene, D., Bourdarios, C., Boutle, S. K., Boveia, A., Boyd, J., Boyko, I. R., Bozson, A. J., Bracinik, J., Brandt, A., Brandt, G., Brandt, O., Braren, F., Bratzler, U., Brau, B., Brau, J. E., Breaden Madden, W. D., Brendlinger, K., Brennan, A. J., Brenner, L., Brenner, R., Bressler, S., Briglin, D. L., Bristow, T. M., Britton, D., Britzger, D., Brock, I., Brock, R., Brooijmans, G., Brooks, T., Brooks, W. K., Brost, E., Broughton, J. H., Bruckman de Renstrom, P. A., Bruncko, D., Bruni, A., Bruni, G., Bruni, L. S., Bruno, S., Brunt, B. H., Bruschi, M., Bruscino, N., Bryant, P., Bryngemark, L., Buanes, T., Buat, Q., Buchholz, P., Buckley, A. G., Budagov, I. A., Bugge, M. K., Bührer, F., Bulekov, O., Bullock, D., Burch, T. J., Burdin, S., Burgard, C. D., Burger, A. M., Burghgrave, B., Burka, K., Burke, S., Burmeister, I., Burr, J. T. P., Büscher, D., Büscher, V., Buschmann, E., Bussey, P., Butler, J. M., Buttar, C. M., Butterworth, J. M., Butti, P., Buttinger, W., Buzatu, A., Buzykaev, A. R., Cabrera Urbán, S., Caforio, D., Cai, H., Cairo, V. M. M., Cakir, O., Calace, N., Calafiura, P., Calandri, A., Calderini, G., Calfayan, P., Callea, G., Caloba, L. P., Calvente Lopez, S., Calvet, D., Calvet, S., Calvet, T. P., Camacho Toro, R., Camarda, S., Camarri, P., Cameron, D., Caminal Armadans, R., Camincher, C., Campana, S., Campanelli, M., Camplani, A., Campoverde, A., Canale, V., Cano Bret, M., Cantero, J., Cao, T., Capeans Garrido, M. D. M., Caprini, I., Caprini, M., Capua, M., Carbone, R. M., Cardarelli, R., Cardillo, F. C., Carli, I., Carli, T., Carlino, G., Carlson, B. T., Carminati, L., Carney, R. M. D., Caron, S., Carquin, E., Carrá, S., Carrillo-Montoya, G. D., Casadei, D., Casado, M. P., Casha, A. F., Casolino, M., Casper, D. W., Castelijn, R., Castillo Gimenez, V., Castro, N. F., Catinaccio, A., Catmore, J. R., Cattai, A., Caudron, J., Cavaliere, V., Cavallaro, E., Cavalli, D., Cavalli-Sforza, M., Cavasinni, V., Celebi, E., Ceradini, F., Cerda Alberich, L., Cerqueira, A. S., Cerri, A., Cerrito, L., Cerutti, F., Cervelli, A., Cetin, S. A., Chafaq, A., Chakraborty, D., Chan, S. K., Chan, W. S., Chan, Y. L., Chang, P., Chapman, J. D., Charlton, D. G., Chau, C. C., Chavez Barajas, C. A., Che, S., Cheatham, S., Chegwidden, A., Chekanov, S., Chekulaev, S. V., Chelkov, G. A., Chelstowska, M. A., Chen, C., Chen, C. H., Chen, H., Chen, J., Chen, S., Chen, S. J., Chen, X., Chen, Y., Cheng, H. C., Cheng, H. J., Cheplakov, A., Cheremushkina, E., Cherkaoui El Moursli, R., Cheu, E., Cheung, K., Chevalier, L., Chiarella, V., Chiarelli, G., Chiodini, G., Chisholm, A. S., Chitan, A., Chiu, Y. H., Chizhov, M. V., Choi, K., Chomont, A. R., Chouridou, S., Chow, Y. S., Christodoulou, V., Chu, M. C., Chudoba, J., Chuinard, A. J., Chwastowski, J. J., Chytka, L., Ciftci, A. K., Cinca, D., Cindro, V., Cioară, I. A., Ciocio, A., Cirotto, F., Citron, Z. H., Citterio, M., Ciubancan, M., Clark, A., Clark, M. R., Clark, P. J., Clarke, R. N., Clement, C., Coadou, Y., Cobal, M., Coccaro, A., Cochran, J., Colasurdo, L., Cole, B., Colijn, A. P., Collot, J., Colombo, T., Conde Muiño, P., Coniavitis, E., Connell, S. H., Connelly, I. A., Constantinescu, S., Conti, G., Conventi, F., Cooper-Sarkar, A. M., Cormier, F., Cormier, K. J. R., Corradi, M., Corrigan, E. E., Corriveau, F., Cortes-Gonzalez, A., Costa, G., Costa, M. J., Costanzo, D., Cottin, G., Cowan, G., Cox, B. E., Cranmer, K., Crawley, S. J., Creager, R. A., Cree, G., Crépé-Renaudin, S., Crescioli, F., Cribbs, W. A., Cristinziani, M., Croft, V., Crosetti, G., Cueto, A., Cuhadar Donszelmann, T., Cukierman, A. R., Cummings, J., Curatolo, M., Cúth, J., Czekierda, S., Czodrowski, P., Da Cunha Sargedas De Sousa, M. J., Da Via, C., Dabrowski, W., Dado, T., Dai, T., Dale, O., Dallaire, F., Dallapiccola, C., Dam, M., D’Amen, G., Dandoy, J. R., Daneri, M. F., Dang, N. P., Dann, N. D., Danninger, M., Dano Hoffmann, M., Dao, V., Darbo, G., Darmora, S., Dassoulas, J., Dattagupta, A., Daubney, T., D’Auria, S., Davey, W., David, C., Davidek, T., Davis, D. R., Davison, P., Dawe, E., Dawson, I., De, K., De Asmundis, R., De Benedetti, A., De Castro, S., De Cecco, S., De Groot, N., de Jong, P., De la Torre, H., De Lorenzi, F., De Maria, A., De Pedis, D., De Salvo, A., De Sanctis, U., De Santo, A., De Vasconcelos Corga, K., De Vivie De Regie, J. B., Debbe, R., Debenedetti, C., Dedovich, D. V., Dehghanian, N., Deigaard, I., Del Gaudio, M., Del Peso, J., Delgove, D., Deliot, F., Delitzsch, C. M., Della Pietra, M., Della Volpe, D., Dell’Acqua, A., Dell’Asta, L., Delmastro, M., Delporte, C., Delsart, P. A., Demarco, D. A., Demers, S., Demichev, M., Demilly, A., Denisov, S. P., Denysiuk, D., D’Eramo, L., Derendarz, D., Derkaoui, J. E., Derue, F., Dervan, P., Desch, K., Deterre, C., Dette, K., Devesa, M. R., Deviveiros, P. O., Dewhurst, A., Dhaliwal, S., Di Bello, F. A., Di Ciaccio, A., Di Ciaccio, L., Di Clemente, W. K., Di Donato, C., Di Girolamo, A., Di Girolamo, B., Di Micco, B., Di Nardo, R., Di Petrillo, K. F., Di Simone, A., Di Sipio, R., Di Valentino, D., Diaconu, C., Diamond, M., Dias, F. A., Diaz, M. A., Dickinson, J., Diehl, E. B., Dietrich, J., Díez Cornell, S., Dimitrievska, A., Dingfelder, J., Dita, P., Dita, S., Dittus, F., Djama, F., Djobava, T., Djuvsland, J. I., Do Vale, M. A. B., Dobre, M., Dodsworth, D., Doglioni, C., Dolejsi, J., Dolezal, Z., Donadelli, M., Donati, S., Donini, J., D’Onofrio, M., Dopke, J., Doria, A., Dova, M. T., Doyle, A. T., Drechsler, E., Dris, M., Du, Y., Duarte-Campderros, J., Dubinin, F., Dubreuil, A., Duchovni, E., Duckeck, G., Ducourthial, A., Ducu, O. A., Duda, D., Dudarev, A., Dudder, A. C., Duffield, E. 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I., Zimmermann, S., Zinonos, Z., Zinser, M., Ziolkowski, M., Zobernig, G., Zoccoli, A., Zou, R., Zur Nedden, M., Zwalinski, L., Aloisio, Alberto, Alviggi, Mariagrazia, Canale, Vincenzo, Della Pietra, Massimo, Merola, Leonardo, Conventi, Francesco, Rossi, Elvira, Carlino, Giampaolo, de Asmundis, Riccardo, Di Donato, Camilla, Doria, Alessandra, Iengo, Paolo, Izzo, Vincenzo, Perrella, Sabrina, Sekhniaidze, Givi, Cirotto, Francesco, Atlas, Collaboration, De Castro , S., Fabbri , L., Gabrielli , A., Rinaldi , L., Semprini Cesari , N., Sioli , M., Villa , M., Zoccoli , A., Bellagamba , L., Boscherini , D., Bruni , A., Bruni , G., D’Amen , G., Giacobbe , B., Polini , A., Sbarra , C., Sidoti , A., Spighi , R., Franchini , M., Mengarelli , A., Romano , M., Valentinetti , S., Alberghi , G. L., Biondi , S., Fabbri , F., Lasagni Manghi , F, Massa , L., Ucchielli , G., Vittori , C., ATLAS collaboration, and Fakülteler, Fen - Edebiyat Fakültesi, Fizik Bölümü
Subjects: Top quark, Большой адронный коллайдер, 13000 GeV-cms, Physics::Instrumentation and Detectors, Ciencias Físicas, High Energy Physics::Lattice, measured [channel cross section], Electron, pair production [top], transverse momentum dependence, 01 natural sciences, 7. Clean energy, High Energy Physics - Experiment, purl.org/becyt/ford/1 [https], Subatomär fysik, High Energy Physics - Experiment (hep-ex), Hadron-Hadron scattering (experiments), Subatomic Physics, Jets, scattering [p p], [PHYS.HEXP]Physics [physics]/High Energy Physics - Experiment [hep-ex], Collisions, Top physic, PLUS PLUS, протон-протонные столкновения, QC, Physics, proton–proton collisions, Large Hadron Collider, Settore FIS/01 - Fisica Sperimentale, ATLAS experiment, ATLAS, Computer Science::Computers and Society, Mathematics and natural scienses: 400::Physics: 430::Nuclear and elementary particle physics: 431 [VDP], CERN LHC Coll, Top physics, Nuclear and High Energy Physics, Computer Science::Mathematical Software, colliding beams [p p], top: pair production, channel cross section: measured, CIENCIAS NATURALES Y EXACTAS, Particle Physics - Experiment, ((n)jet lepton) [final state], Quark, p p: scattering, Particle physics, Ciências Naturais::Ciências Físicas, 530 Physics, PARTON DISTRIBUTIONS, Ciências Físicas [Ciências Naturais], jet: associated production, FOS: Physical sciences, final state: ((n)jet lepton), ddc:500.2, Física de Partículas y Campos, Computer Science::Digital Libraries, differential cross section: measured, transverse momentum [top], measured [differential cross section], 0103 physical sciences, Physics::Atomic and Molecular Clusters, ddc:530, High Energy Physics, associated production [jet], 010306 general physics, top quark, Ciencias Exactas, top: transverse momentum, Muon, Science & Technology, hep-ex, 010308 nuclear & particles physics, High Energy Physics::Phenomenology, Matematikk og naturvitenskap: 400::Fysikk: 430::Kjerne- og elementærpartikkelfysikk: 431 [VDP], Física, purl.org/becyt/ford/1.3 [https], Pair production, Jet, Experimental High Energy Physics, High Energy Physics::Experiment, ATLAS, детектор, Hadron-hadron collisions, p p: colliding beams, experimental results, Lepton
Abstract: Measurements of differential cross sections of top quark pair production in association with jets by the ATLAS experiment at the LHC are presented. The measurements are performed as functions of the top quark transverse momentum, the transverse momentum of the top quark-antitop quark system and the out-of-plane transverse momentum using data from pp collisions at √s =13 TeV collected by the ATLAS detector at the LHC in 2015 and corresponding to an integrated luminosity of 3.2 fb⁻¹. The top quark pair events are selected in the lepton (electron or muon) + jets channel. The measured cross sections, which are compared to several predictions, allow a detailed study of top quark production., La lista completa de autores que integran el documento puede consultarse en el archivo., Facultad de Ciencias Exactas, Instituto de Física La Plata
Published: 2018
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50. Modulating the protein content of complex proteomes using acetonitrile

Author: Hugo López-Fernández, Gonçalo Martins, José Luis Capelo, Carlos Lodeiro, Hugo M. Santos, and João Prates
Subjects: 0301 basic medicine, Male, Acetonitriles, Lymphoma, Proteome, Gene Expression, Proteomics, 01 natural sciences, Analytical Chemistry, Protein content, Diagnosis, Differential, 03 medical and health sciences, chemistry.chemical_compound, Cluster Analysis, Humans, Acetonitrile, Aged, 80 and over, Principal Component Analysis, Chromatography, Chemistry, 010401 analytical chemistry, Middle Aged, Serum samples, 0104 chemical sciences, Neoplasm Proteins, 030104 developmental biology, Case-Control Studies, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Electrophoresis, Polyacrylamide Gel, Female, Multiple Myeloma
Abstract: In this work we present acetonitrile as a tool to modulate the dynamic range of the proteome of complex samples. Different concentrations of acetonitrile ranging from 15% v/v to 65% v/v were used to modulate the protein content of serum samples from healthy people and patients with lymphoma and myeloma. We show that the proteome above 70 kDa is pelleted as a function of the concentration of acetonitrile and that profiling with PCA or Clustering is only possible using the supernatants obtained for concentrations of acetonitrile higher than 45% v/v or the pellets for concentrations of acetonitrile of 35% and 45%. The differentiation and classification of the three groups of sera samples (healthy, lymphoma and myeloma) were possible using acetonitrile at 55% v/v concentration. This work opens new avenues for the application of acetonitrile as a cost-effective tool in proteomics applications.
Published: 2017

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