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

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.publishersversionpublishe

Búsqueda de biomarcadores séricos de artrosis mediante depleción secuencias combinada con DIGE

Comunicaciones a congreso

Reducing high abundance proteins in human serum: depletion versus equalization

Comunicaciones a congreso

Development of Cyanine 813@Imidazole-Based Doped Supported Devices for Divalent Metal Ions Detection

PM003/2016 IF/00007/2015 CEECIND/00648/2017A 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.publishersversionpublishe

Validation of a Standard Luminescence Method for the Fast Determination of the Antimicrobial Activity of Nanoparticles in Escherichia coli

Publisher Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland.The use of nanoparticles in multiple industries has raised concerned voices about the assessment of their toxicity/antimicrobial activity and the development of standardized handling protocols. Issues emerge during the antimicrobial assaying of multiple cargo, colorimetric, colloidal nanoformulations, as standard protocols often rely on visual evaluations, or optical density (OD) measurements, leading to high variance inhibitory concentrations (MIC). Thus, a fast, luminescence-based assay for the effective assessment of the antimicrobial activity of nanoparticles is herein reported, using the bioluminescence of an in-house E. coli ATCC® 8739™ construct with the pMV306G13 + Lux plasmid (E. coli Lux). The new strain’s sensitivity to ofloxacin as a standard antibiotic was confirmed, and the methodology robustness verified against multiple nanoparticles and colorimetric drugs. The reduction of incubation from 24 to only 8 h, and the sole use of luminescence (LUX490) to accurately determine and distinguish MIC50 and MIC90, are two main advantages of the method. By discarding OD measurements, one can avoid turbidity and color interferences when calculating bacterial growth. This approach is an important tool that contributes to the standardization of methods, reducing samples’ background interference and focusing on luminescence as a direct probe for bacterial metabolic activity, growth and, most importantly, the correct assessment of nanomaterials’ antimicrobial activity.publishersversionpublishe

A Espectrometria de Massa de Alta Resolução na Medicina Personalizada: Proteína 4 de Ligação ao Retinol como Candidata a Biomarcador Preditor de Progressão no Carcinoma Urotelial da Bexiga

Introduction: Bladder cancer (BC) is the seventh most commonly diagnosed cancer in males. A large proportion of T1 cases and some Ta cases are under-staged and the significant risk of residual tumour after initial TURB of TaT1 lesions has been demonstrated. A second TURB is recommended in T1 tumours because it can increase recurrence-free survival (RFS) providing prognostic information. Non-invasive methods differentiating bladder cancer stages would be essential for diagnosis of under staged cases. Previously we demonstrated that a panel of urinary proteins measured by high resolution mass spectrometry could predict bladder cancer stages namely Ta, T1 and T2 cases. Our aim is to increase the accuracy of the biomarker panel for BC stage differentiation using a more patients, also intending to identify proteins that could be a signature to bladder cancer progression. Methods: Forty-eight urine samples were collected from volun- teers of these groups: 20 patients with bladder cancer stage Ta; 19 patients with BC stage T1 and 9 patients with BC stage T2+ (T2, T3 and T4). Urinary proteome was cleaned and digested using the Filter-Aided Sample Preparation methodology and analysed by liquid chromatography-mass spectrometry. For protein identification and label-free quantification we used MaxQuant, the data was further interrogated with the bioinformatics platform Perseus. Results: A biomarker panel was developed which consists of 87 proteins which were down-regulated between three different urothelial bladder carcinoma stages evaluated. Retinol-binding protein 4 (RBP4) consistently increases from Ta to T1, to T2+ (p <0.001) and in high grade tumours (p = 0.006). Conclusion: Our results showed a proteomic biomarker panel capable to differentiate bladder cancer stages. Besides, retinolbinding protein 4 can be a candidate signature of progression.Introdução: O carcinoma urotelial da bexiga é a sétima neoplasia mais comum dos homens. Uma proporção significativa de T1 e Ta são subestadiados e o risco de doença residual já foi demonstrado. Assim, a segunda RTU-V recomenda-se nos tumores T1 e está associada ao aumento da taxa livre de recidiva fornecendo informação prognóstica. Por isso, métodos não invasivos, capazes de diferenciar os estadios assim como diagnosticar os casos subestadiados são cada vez mais necessários. Num estudo prévio, desenvolvemos um painel de proteínas identificadas por espetrometria de massa de alta resolução capaz de diferencias os estadios Ta, T1 e T2+ (T2 a T4). O objetivo deste estudo consiste em aumentar a eficácia deste painel em diferenciar os estadios do carcinoma urotelial da bexiga e associadamente identificar candidatos promissores a biomarcadores de progressão. Métodos: Colheram-se 48 urinas de voluntários dos seguintes grupos: 20 doentes com carcinoma urotelial da bexiga Ta; 19 doentes com T1 e 9 doentes com T2 + (T2, T3 e T4). O proteoma urinário foi preparado usando a metodologia filter-aided sample e analisado através da cromotografia liquida e espetrometria de massa de alta resolução. Para a identificação e quantificação das proteínas utilizamos o MaxQuant e os resultados analisados pela plataforma bioinformática Perseus. Resultados: Um painel de biomarcadores proteicos com 87 proteinas sobre e sub expressas nos diferentes estadios foi conseguido. A proteína de ligação ao retinol 4 aumentou consistentemente de Ta para T1 e T2+ (p < 0,001) e nos tumores de alto grau comparativamente aos de baixo grau (p = 0,006). Conclusão: O estudo mostrou um painel de biomarcadores proteicos capaz de diferenciar os estadios do carcinoma da bexiga. Além disso, a proteína de ligação ao retinol 4 poderá ser um candidato promissor a biomarcador de progressão.

Synthesis of mesoporous silica coated gold nanorods loaded with methylene blue and its potentials in antibacterial applications

Funding Information: Funding: We thank the financial support by the PROTEOMASS Scientific Society (Portugal) (General Funding Grant 2019–2020), as well as the Associate Laboratory Research Unit for Green Chemistry— Clean Processes and Technologies—LAQV-REQUIMTE financed by national funds from FCT/MEC (UIDB/04077/2020) and co-financed by the ERDF under the PT2020 Partnership Agreement (POCI-01-0145-FEDER—007265). J.D.; A.F.-L.; C.L.; J.F.-L. and J.L.C.-M. thanks to the FCT-MEC the research grant SiSi4Bacter (PTDC/QUI-COL/1517/2020). J.F.-L. thank FCT/MEC (Portugal) the junior researcher contract under DL57 pro-gramme. J.D. thanks the Project PTDC/QEQ-MED/2118/2014 for her researcher contract. A.F.-L. thanks the FCT-MEC Portugal for his doctoral grant associated with the Green Chemistry PhD. Program (SFRH/BD/52528/2014) and the PROTEOMASS Scientific Society Postdoctoral grant during August 2019–March 2021. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.In this work, the successful preparation and characterization of gold nanorods (AuNRs) coated with a mesoporous silica shell (AuNRs@Simes) was achieved. Conjugation with methylene blue (MB) as a model drug using ultrasound-stimulated loading has been explored for further application in light-mediated antibacterial studies. Lyophilization of this conjugated nanosystem was analyzed using trehalose (TRH) as a cryogenic protector. The obtained stable dry formulation shows potent antimicrobial activity against Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria after a simple post-treatment irradiation method with a red laser during a short time period.publishersversionpublishe

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

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.Ministerio de Economía y Competitividad | Ref. TIN2013-47153-C3-3-RXunta de GaliciaFundação para a Ciência e a Tecnologia | Ref. SFRH/BD/109201/2015Fundação para a Ciência e a Tecnologia | Ref. SFRH/BD/120537/201

Magneto-Fluorescent Mesoporous Nanocarriers for the Dual-Delivery of Ofloxacin and Doxorubicin to Tackle Opportunistic Bacterial Infections in Colorectal Cancer

Funding Information: This work was funded by the Associate Laboratory for Green Chemistry—LAQV which is financed by national funds from FCT/MCTES (UIDB/50006/2020 and UIDP/50006/2020) as well as the Scientific Society PROTEOMASS (Portugal) for funding support (General Funding Grant 2021). G.M thanks to FCT/MEC (Portugal) for his doctoral grant PD/BD/142865/2018. E.O thanks FCT/MEC (Portugal) for the individual contract, CEECIND/00648/2017. This work was also funded by FCT—Foundation for Science and Technology, I.P., through projects UIDB/04077/2020, UIDP/04077/2020, OrMagNa—PTDC/NAN-MAT/28785/2017, BioISI—UID/Multi/04046/2019, UIDB/04046/2020 and UIDP/04046/2020 Centre grants (BioISI) and NECL infrastructure. Publisher Copyright: © 2022 by the authors.Cancer-related opportunistic bacterial infections are one major barrier for successful clinical therapies, often correlated to the production of genotoxic factors and higher cancer incidence. Although dual anticancer and antimicrobial therapies are a growing therapeutic fashion, they still fall short when it comes to specific delivery and local action in in vivo systems. Nanoparticles are seen as potential therapeutic vectors, be it by means of their intrinsic antibacterial properties and effective delivery capacity, or by means of their repeatedly reported modulation and maneuverability. Herein we report on the production of a biocompatible, antimicrobial magneto-fluorescent nanosystem (NANO3) for the delivery of a dual doxorubicin–ofloxacin formulation against cancer-related bacterial infections. The drug delivery capacity, rendered by its mesoporous silica matrix, is confirmed by the high loading capacity and stimuli-driven release of both drugs, with preference for tumor-like acidic media. The pH-dependent emission of its surface fluorescent SiQDs, provides an insight into NANO3 surface behavior and pore availability, with the SiQDs working as pore gates. Hyperthermia induces heat generation to febrile temperatures, doubling drug release. NANO3-loaded systems demonstrate significant antimicrobial activity, specifically after the application of hyperthermia conditions. NANO3 structure and antimicrobial properties confirm their potential use in a future dual anticancer and antimicrobial therapeutical vector, due to their drug loading capacity and their surface availability for further modification with bioactive, targeting species.publishersversionpublishe

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

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 AuthorsBladder 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.publishersversionpublishe