Multi-frequency multimode modulated technology as a clean, fast, and sustainable process to recover antioxidants from a coffee by-product

Coffee chaff is a major coffee roasting by-product that could be valued as a source of antioxidants. In the present work, we compared classic, but optimized, solid-liquid extraction conditions with a new concept, namely, the Multi-frequency Multimode Modulated (MMM) vibration technique. The extracts obtained by both methods were analysed and compared in relation to several parameters, namely, phenolics profile (by HPLC/DAD), 5-caffeoylquinic acid content, total phenolics content, and Ferric Reducing Antioxidant Power. Compared to an optimized solid-liquid extraction (using a hydroethanolic solvent (1:1) at 40 °C for 60 min), the acoustic probe allowed a higher recovery of antioxidants in only 10 min and using only water as extraction solvent. Moreover, the effects that arise from the acoustic cavitation in the medium allowed the suppression of the sample preparation step (grinding). These results show that this type of technology can be of high interest to recover antioxidants from natural matrices, in a green, fast and very efficient way.info:eu-repo/semantics/publishedVersio

With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast

The Gastropoda is one of the best studied classes of marine invertebrates. Yet, most species have been delimited based on morphology only. The application of DNA barcodes has shown to be greatly useful to help delimiting species. Therefore, sequences of the cytochrome c oxidase I gene from 108 specimens of 34 morpho-species were used to investigate the molecular diversity within the gastropods from the Portuguese coast. To the above dataset, we added available COI-5P sequences of taxonomically close species, in a total of 58 morpho-species examined. There was a good match between ours and sequences from independent studies, in public repositories. We found 32 concordant (91.4%) out of the 35 Barcode Index Numbers (BINs) generated from our sequences. The application of a ranking system to the barcodes yield over 70% with top taxonomic congruence, while 14.2% of the species barcodes had insufficient data. In the majority of the cases, there was a good concordance between morphological identification and DNA barcodes. Nonetheless, the discordance between morphological and molecular data is a reminder that even the comparatively well-known European marine gastropods can benefit from being probed using the DNA barcode approach. Discordant cases should be reviewed with more integrative studies.The present study was financed by FEDER through POFC-COMPETE, in the scope the project FCOMP-01-0124-FEDER-015429 funded by "Fundacao para a Ciencia e a Tecnologia" (FCT), Portugal. Work at CBMA was supported by FCT I.P. through the strategic funding UID/BIA/04050/2013. Sequencing at the Biodiversity Institute of Ontario was funded by the International Barcode of Life (iBOL), through the Canadian Centre for DNA Barcoding, from the Ontario Genomics Institute, Genome Canada, the Ontario Ministry of Research and Innovation, and the Natural Sciences and Engineering Research Council of Canada. Claudia Hollatz was supported by a CAPES Post-doctoral fellowship (Ministry of Education, Brazil), while Jorge Lobo was supported by a PhD fellowship (SFRH/BD/69750/2010) from FCT.info:eu-repo/semantics/publishedVersio

With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast

The Gastropoda is one of the best studied classes of marine invertebrates. Yet, most species have been delimited based on morphology only. The application of DNA barcodes has shown to be greatly useful to help delimiting species. Therefore, sequences of the cytochrome c oxidase I gene from 108 specimens of 34 morpho-species were used to investigate the molecular diversity within the gastropods from the Portuguese coast. To the above dataset, we added available COI-5P sequences of taxonomically close species, in a total of 58 morpho-species examined. There was a good match between ours and sequences from independent studies, in public repositories. We found 32 concordant (91.4%) out of the 35 Barcode Index Numbers (BINs) generated from our sequences. The application of a ranking system to the barcodes yield over 70% with top taxonomic congruence, while 14.2% of the species barcodes had insufficient data. In the majority of the cases, there was a good concordance between morphological identification and DNA barcodes. Nonetheless, the discordance between morphological and molecular data is a reminder that even the comparatively well-known European marine gastropods can benefit from being probed using the DNA barcode approach. Discordant cases should be reviewed with more integrative studies.The present study was financed by FEDER through POFC-COMPETE, in the scope the project FCOMP-01-0124-FEDER-015429 funded by "Fundacao para a Ciencia e a Tecnologia" (FCT), Portugal. Work at CBMA was supported by FCT I.P. through the strategic funding UID/BIA/04050/2013. Sequencing at the Biodiversity Institute of Ontario was funded by the International Barcode of Life (iBOL), through the Canadian Centre for DNA Barcoding, from the Ontario Genomics Institute, Genome Canada, the Ontario Ministry of Research and Innovation, and the Natural Sciences and Engineering Research Council of Canada. Claudia Hollatz was supported by a CAPES Post-doctoral fellowship (Ministry of Education, Brazil), while Jorge Lobo was supported by a PhD fellowship (SFRH/BD/69750/2010) from FCT.info:eu-repo/semantics/publishedVersio

CHCHD4 regulates tumour proliferation and EMT-related phenotypes, through respiratory chain-mediated metabolism

Abstract: Background: Mitochondrial oxidative phosphorylation (OXPHOS) via the respiratory chain is required for the maintenance of tumour cell proliferation and regulation of epithelial to mesenchymal transition (EMT)-related phenotypes through mechanisms that are not fully understood. The essential mitochondrial import protein coiled-coil helix coiled-coil helix domain-containing protein 4 (CHCHD4) controls respiratory chain complex activity and oxygen consumption, and regulates the growth of tumours in vivo. In this study, we interrogate the importance of CHCHD4-regulated mitochondrial metabolism for tumour cell proliferation and EMT-related phenotypes, and elucidate key pathways involved. Results: Using in silico analyses of 967 tumour cell lines, and tumours from different cancer patient cohorts, we show that CHCHD4 expression positively correlates with OXPHOS and proliferative pathways including the mTORC1 signalling pathway. We show that CHCHD4 expression significantly correlates with the doubling time of a range of tumour cell lines, and that CHCHD4-mediated tumour cell growth and mTORC1 signalling is coupled to respiratory chain complex I (CI) activity. Using global metabolomics analysis, we show that CHCHD4 regulates amino acid metabolism, and that CHCHD4-mediated tumour cell growth is dependent on glutamine. We show that CHCHD4-mediated tumour cell growth is linked to CI-regulated mTORC1 signalling and amino acid metabolism. Finally, we show that CHCHD4 expression in tumours is inversely correlated with EMT-related gene expression, and that increased CHCHD4 expression in tumour cells modulates EMT-related phenotypes. Conclusions: CHCHD4 drives tumour cell growth and activates mTORC1 signalling through its control of respiratory chain mediated metabolism and complex I biology, and also regulates EMT-related phenotypes of tumour cells

Lipidomic signature of the green macroalgae Ulva rigida farmed in a sustainable integrated multi-trophic aquaculture

Ulva species, green macroalgae, are widely distributed across the globe, being one of the most heavily traded edible seaweeds. Nonetheless, although this genus has been largely used in scientific studies, its lipidome remains rather unexplored. The present study sheds light over the lipid profile of Ulva rigida produced in a land-based integrated multi-trophic aquaculture (IMTA) system using liquid chromatography coupled to high-resolution mass spectrometry for molecular lipid species identification. The lipidome of U. rigida revealed the presence of distinct beneficial n-3 fatty acids for human health, namely alpha-linoleic acid (ALA) and docosapentaenoic acid (DPA). A total of 87 molecular species of glycolipids, 58 molecular species of betaine lipids, and 57 molecular species of phospholipids were identified in the lipidome of U. rigida including some species bearing PUFA and with described bioactive properties. Overall, the present study contributes to the valorization and quality validation of sustainably farmed U. rigida.publishe

BCAT1 affects mitochondrial metabolism independently of leucine transamination in activated human macrophages

In response to environmental stimuli, macrophages change their nutrient consumption and undergo an early metabolic adaptation that progressively shapes their polarization state. During the transient, early phase of pro-inflammatory macrophage activation, an increase in tricarboxylic acid (TCA) cycle activity has been reported, but the relative contribution of branched-chain amino acid (BCAA) leucine remains to be determined. Here, we show that glucose but not glutamine is a major contributor of the increase in TCA cycle metabolites during early macrophage activation in humans. We then show that, although uptake of BCAAs is not altered, their transamination by BCAT1 is increased following 8 h lipopolysaccharide (LPS) stimulation. Of note, leucine is not metabolized to integrate into the TCA cycle in basal or stimulated human macrophages. Surprisingly, the pharmacological inhibition of BCAT1 reduced glucose-derived itaconate, α-ketoglutarate and 2-hydroxyglutarate levels without affecting succinate and citrate levels, indicating a partial inhibition of the TCA cycle. This indirect effect is associated with NRF2 (also known as NFE2L2) activation and anti-oxidant responses. These results suggest a moonlighting role of BCAT1 through redox-mediated control of mitochondrial function during early macrophage activation

Demographic expansion and contraction in a neotropical fish during the Late Pleistocene-Holocene

Demographic changes during the late Pleistocene-Holocene left signatures in the DNA of contemporary populations. These signatures reveal demographic phenomena like the increase or decrease in effective population size. In this paper we searched for signatures of demographic change in the DNA of the Neotropical freshwater fish Poecilia vivipara . Also, we investigated whether demographic changes are correlated with palaeoclimatic events of the late Pleistocene-Holocene, in particular, if changes in effective population size are correlated with expansion and contraction of available habitats, induced by global ice-volume changes and sea-level fluctuations. We used Bayesian Skyline Plot (BSP) analysis with sequences from the mitochondrial gene cytochrome b to estimate the ancestral demography of the Neotropical freshwater fish P. vivipara . To test the assumptions of neutrality and absence of population structure we used Tajima?s D and Spatial Analysis of Molecular Variance (SAMOVA), respectively. Effective population size of P. vivipara remained stable until 75,000 years ago, increased by 10-fold reaching a maximum at approximately 25,000 years ago, then suddenly declined at the Pleistocene-Holocene boundary. Variation in effective population size in P. vivipara correlates with expansion and contraction of habitats induced by sea-level fluctuations, caused by the advance and retreat of ice sheets during the Last Glacial Maximum (LGM).Fil: Costa, Carolina L. N.. Universidade Estadual de Campinas; BrasilFil: Perez, Sergio Ivan. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Departamento Científico de Antropología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Louvise, José. Faculdade Do Vale Do Jaguaribe; BrasilFil: Tonhatti, Carlos H.. Universidade Estadual de Campinas; BrasilFil: Clemente Carvalho, Rute B. G.. Queens University. Department Of Biology; CanadáFil: Petryna, Ana Mabel. Universidade Federal do Rio de Janeiro; BrasilFil: dos Reis, S. F.. Universidade Estadual de Campinas; Brasi

SETDB2 and RIOX2 are differentially expressed among renal cell tumor subtypes, associating with prognosis and metastization

Increasing detection of small renal masses by imaging techniques entails the need for accurate discrimination between benign and malignant renal cell tumors (RCTs) as well as among malignant RCTs, owing to differential risk of progression through metastization. Although histone methylation has been implicated in renal tumorigenesis, its potential as biomarker for renal cell carcinoma (RCC) progression remains largely unexplored. Thus, we aimed to characterize the differential expression of histone methyltransferases (HMTs) and histone demethylases (HDMs) in RCTs to assess their potential as metastasis biomarkers. We found that SETDB2 and RIOX2 (encoding for an HMT and an HDM, respectively) expression levels was significantly altered in RCTs; these genes were further selected for validation by quantitative RT-PCR in 160 RCTs. Moreover, SETDB2, RIOX2, and three genes encoding for enzymes involved in histone methylation (NO66, SETD3, and SMYD2), previously reported by our group, were quantified (RT-PCR) in an independent series of 62 clear cell renal cell carcinoma (ccRCC) to assess its potential role in ccRCC metastasis development. Additional validation was performed using TCGA dataset. SETDB2 and RIOX2 transcripts were overexpressed in RCTs compared to renal normal tissues (RNTs) and in oncocytomas vs. RCCs, with ccRCC and papillary renal cell carcinoma (pRCC) displaying the lowest levels. Low SETDB2 expression levels and higher stage independently predicted shorter disease-free survival. In our 62 ccRCC cohort, significantly higher RIOX2, but not SETDB2, expression levels were depicted in cases that developed metastasis during follow-up. These findings were not apparent in TCGA dataset. We concluded that SETDB2 and RIOX2 might be involved in renal tumorigenesis and RCC progression, especially in metastatic spread. Moreover, SETDB2 expression levels might independently discriminate among RCC subgroups with distinct outcome, whereas higher RIOX2 transcript levels might identify ccRCC cases with more propensity to endure metastatic dissemination.This study was funded by research grants from Research Center of Portuguese Oncology Institute - Porto (CI-IPOP 4-2012 and CI-IPOP 27) and from Associacao Portuguesa de Urologia (APU-2010). ASP-L was supported by FCT-Fundacao para a Ciencia e a Tecnologia fellowship (SFRH/SINTD/94217/2013). CSG is supported by FCT- Fundacao para a Ciencia e Tecnologia PhD fellowships (SFRH/BD/92786/2013) and BMC is funded by FCT-Fundacao para a Ciencia e a Tecnologia (IF/00601/2012).info:eu-repo/semantics/publishedVersio