Browsing by Issue Date, starting with "2014-07"
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- Maternal thyroid hormones are essential for neural development in ZebrafishPublication . Campinho, Marco António; Saraiva, João; Florindo, Claudia; Power, Deborah M.Teleost eggs contain an abundant store of maternal thyroid hormones (THs), and early in zebrafish embryonic development, all the genes necessary for TH signaling are expressed. Nonetheless the function of THs in embryonic development remains elusive. To test the hypothesis that THs are fundamental for zebrafish embryonic development, an monocarboxilic transporter 8 (Mct8) knockdown strategy was deployed to prevent maternal TH uptake. Absence of maternal THs did not affect early specification of the neural epithelia but profoundly modified later dorsal specification of the brain and spinal cord as well as specific neuron differentiation. Maternal THs acted upstream of pax2a, pax7, and pax8 genes but downstream of shha and fgf8a signaling. The lack of inhibitory spinal cord interneurons and increased motoneurons in the mct8 morphants is consistent with their stiff axial body and impaired mobility. The mct8 mutations are associated with X-linked mental retardation in humans, and the cellular and molecular consequences of MCT8 knockdown during embryonic development in zebrafish provides new insight into the potential role of THs in this condition.
- FEBS 50th Anniversary Virtual Issue: PortugalPublication . Aureliano, M.; Antunes, Fernando; Castanho, Miguel; Marcos, João Carlos; Soveral, GraçaThis celebratory Virtual Issue for the 50th anniversary of FEBS (2014) highlights the high quality and diversity of biochemistry research carried out in Portugal. Up to 2013, 303 articles were published in FEBS Letters and The FEBS Journal / European Journal of Biochemistry with at least one author having Portugal as an address.
- Live-cell FRET imaging reveals clustering of the prion protein at the cell surface induced by infectious prionsPublication . Tavares, Evandro; Macedo, J.A.; Paulo, Pedro M. R.; Sousa, Catarina; Lopes, Carlos; Melo, EduardoPrion diseases are associated to the conversion of the prion protein into a misfolded pathological isoform. The mechanism of propagation of protein misfolding by protein templating remains largely unknown. Neuroblastoma cells were transfected with constructs of the prion protein fused to both CFP-GPI-anchored and to YFP-GPI-anchored and directed to its cell membrane location. Live-cell FRET imaging between the prion protein fused to CFP or YFP was measured giving consistent values of 10 +/- 2%. This result was confirmed by fluorescence lifetime imaging microscopy and indicates intermolecular interactions between neighbor prion proteins. In particular, considering that a maximum FRET efficiency of 17 +/- 2% was determined from a positive control consisting of a fusion CFP-YFP-GPI-anchored. A stable cell clone expressing the two fusions containing the prion protein was also selected to minimize cell-to-cell variability. In both, stable and transiently transfected cells, the FRET efficiency consistently increased in the presence of infectious prions - from 4 +/- 1% to 7 +/- 1% in the stable clone and from 10 +/- 2% to 16 +/- 1% in transiently transfected cells. These results clearly reflect an increased clustering of the prion protein on the membrane in the presence of infectious prions, which was not observed in negative control using constructs without the prion protein and upon addition of non-infected brain. Our data corroborates the recent view that the primary site for prion conversion is the cell membrane. Since our fluorescent cell clone is not susceptible to propagate infectivity, we hypothesize that the initial event of prion infectivity might be the clustering of the GPI-anchored prion protein. (C) 2014 Elsevier B.V. All rights reserved.
- Use of vibration measurements to determine the most suitable locations to improve sound insulation in buildingsPublication . Rosão, Vitor; Carreira, A. S.In the present work in situ sound insulation measurements were performed, according to the applicable standards of ISO 140 series, and vibration measurements of the separator elements in question (floor, ceiling, side walls). We intend to compare the results of direct measure-ments of sound insulation with the results of the predictions of sound insulation, based on the vibration measurements, to verify the feasibility of using vibration measurements to determine the most suitable locations of sound propagation (floor, ceiling, side walls) to act in order to improve, where it is needed, sound insulation in buildings. The principles of sound propaga-tion considered in EN 12354 series standards are used, e.g., 5 major structural paths, depend-ing on the sound radiating element in the receiver compartment [1) partition wall, 2) ceiling, 3) floor, 4) wall left side, 5) wall right side] and 2 major airborne path [1) openings in the par-tition element, 2) openings in other elements]. Different Radiation Factors, to convert vibra-tion of elements in sound are also considered, depending on the radiation element type and on the frequency in question.
- Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteriaPublication . Hernandez-Prieto, Miguel A.; Semeniuk, Trudi A.; Futschik, Matthias E.Cyanobacteria are essential primary producers in marine ecosystems, playing an important role in both carbon and nitrogen cycles. In the last decade, various genome sequencing and metagenomic projects have generated large amounts of genetic data for cyanobacteria. This wealth of data provides researchers with a new basis for the study of molecular adaptation, ecology and evolution of cyanobacteria, as well as for developing biotechnological applications. It also facilitates the use of multiplex techniques, i.e., expression profiling by high-throughput technologies such as microarrays, RNA-seq, and proteomics. However, exploration and analysis of these data is challenging, and often requires advanced computational methods. Also, they need to be integrated into our existing framework of knowledge to use them to draw reliable biological conclusions. Here, systems biology provides important tools. Especially, the construction and analysis of molecular networks has emerged as a powerful systems-level framework, with which to integrate such data, and to better understand biological relevant processes in these organisms. In this review, we provide an overview of the advances and experimental approaches undertaken using multiplex data from genomic, transcriptomic, proteomic, and metabolomic studies in cyanobacteria. Furthermore, we summarize currently available web-based tools dedicated to cyanobacteria, i.e., CyanoBase, CyanoEXpress, ProPortal, Cyanorak, CyanoBIKE, and CINPER. Finally, we present a case study for the freshwater model cyanobacteria, Synechocystis sp. PCC6803, to show the power of meta-analysis, and the potential to extrapolate acquired knowledge to the ecologically important marine cyanobacteria genus, Prochlorococcus.
- StemCellNet: an interactive platform for network-oriented investigations in stem cell biologyPublication . Pinto, Jose P.; Kalathur, Ravi Kiran Reddy; Machado, Rui; JM Xavier; Bragança, José; Futschik, Matthias E.Stem cells are characterized by their potential for self-renewal and their capacity to differentiate into mature cells. These two key features emerge through the interplay of various factors within complex molecular networks. To provide researchers with a dedicated tool to investigate these networks, we have developed StemCellNet, a versatile web server for interactive network analysis and visualization. It rapidly generates focused networks based on a large collection of physical and regulatory interactions identified in human and murine stem cells. The StemCellNet web-interface has various easy-to-use tools for selection and prioritization of network components, as well as for integration of expression data provided by the user. As a unique feature, the networks generated can be screened against a compendium of stemness-associated genes. StemCellNet can also indicate novel candidate genes by evaluating their connectivity patterns. Finally, an optional dataset of generic interactions, which provides large coverage of the human and mouse proteome, extends the versatility of StemCellNet to other biomedical research areas in which stem cells play important roles, such as in degenerative diseases or cancer. The StemCellNet web server is freely accessible at http://stemcellnet.sysbiolab.eu.
- The future of the northeast Atlantic benthic flora in a high CO2 worldPublication . Brodie, Juliet; Williamson, Christopher J.; Smale, Dan A.; Kamenos, Nicholas A.; Mieszkowska, Nova; Santos, Rui; Cunliffe, Michael; Steinke, Michael; Yesson, Christopher; Anderson, Kathryn M.; Asnaghi, Valentina; Brownlee, Colin; Burdett, Heidi L.; Burrows, Michael T.; Collins, Sinead; Donohue, Penelope J. C.; Harvey, Ben; Foggo, Andrew; Noisette, Fanny; Nunes, Joana; Ragazzola, Federica; Raven, John A.; Schmidt, Daniela N.; Suggett, David; Teichberg, Mirta; Hall-Spencer, JasonSeaweed and seagrass communities in the northeast Atlantic have been profoundly impacted by humans, and the rate of change is accelerating rapidly due to runaway CO2 emissions and mounting pressures on coastlines associated with human population growth and increased consumption of finite resources. Here, we predict how rapid warming and acidification are likely to affect benthic flora and coastal ecosystems of the northeast Atlantic in this century, based on global evidence from the literature as interpreted by the collective knowledge of the authorship. We predict that warming will kill off kelp forests in the south and that ocean acidification will remove maerl habitat in the north. Seagrasses will proliferate, and associated epiphytes switch from calcified algae to diatoms and filamentous species. Invasive species will thrive in niches liberated by loss of native species and spread via exponential development of artificial marine structures. Combined impacts of seawater warming, ocean acidification, and increased storminess may replace structurally diverse seaweed canopies, with associated calcified and noncalcified flora, with simple habitats dominated by noncalcified, turf-forming seaweeds.
- Intact protein folding in the glutathione-depleted endoplasmic reticulum implicates alternative protein thiol reductantsPublication . Tsunoda, Satoshi; Avezov, Edward; Zyryanova, Alisa; Konno, Tasuku; Leonardo Mendes-Silva; Melo, Eduardo; Harding, Heather P.; Ron, DavidProtein folding homeostasis in the endoplasmic reticulum (ER) requires efficient protein thiol oxidation, but also relies on a parallel reductive process to edit disulfides during the maturation or degradation of secreted proteins. To critically examine the widely held assumption that reduced ER glutathione fuels disulfide reduction, we expressed a modified form of a cytosolic glutathione-degrading enzyme, ChaC1, in the ER lumen. ChaC1(CtoS) purged the ER of glutathione eliciting the expected kinetic defect in oxidation of an ER-localized glutathione-coupled Grx1-roGFP2 optical probe, but had no effect on the disulfide editing-dependent maturation of the LDL receptor or the reduction-dependent degradation of misfolded alpha-1 antitrypsin. Furthermore, glutathione depletion had no measurable effect on induction of the unfolded protein response (UPR); a sensitive measure of ER protein folding homeostasis. These findings challenge the importance of reduced ER glutathione and suggest the existence of alternative electron donor(s) that maintain the reductive capacity of the ER.
- Reconstructed catches and trends for mainland Portugal fisheries between 1938 and 2009: implications for sustainability, domestic fish supply and importsPublication . Miguel de Sousa Leitão, Francisco; Baptista, V.; Zeller, D.; Erzini, KarimIllegal, Unreported and Unregulated catches (IUU) are an important topic in fisheries, both from an economic and environmental perspective. Here, we estimated the likely total Portuguese mainland catches between 1938 and 2009 by estimating unreported catches (i.e., missing from official statistics) using a fishery-by-fishery approach. Landings increased from 1938, peaking between 1964 and 1972 (period when landings reached highest values across the time series), and declined thereafter, reaching values below the mean after 1993. Higher misreporting (unreported values above the mean) were recorded between 1956 and 1988. Overall, we estimated that over 25,013,000 t were caught between 1938 and 2009, which is 36% (range 28.2-41.5%) higher than the 16,121,510 t officially reported for the same time period, based on annual catches of around 123,000 t-year(-1). Trawl fisheries accounted for the largest part of unreported catches, with 54% of total unreported catches, while accounting for 21% of total reported landings. The multi-gear fisheries accounted for the second largest percentage of estimated catches (25% of total unreported catches, 30% of reported landings). Purse seine fisheries accounted for 49% of total reported landings, but had the smallest proportion of unreported catches (19%). Unreported catches from the recreational/subsistence sector were lower, accounting for 1.5% of total unreported catches. Finfish accounted for 94% (115,000 t.year(-1)) of unreported catches, followed by cephalopods (2,400 t year(-1)) and crustaceans (1,800 t.year(-1)). (C) 2014 Elsevier B.V. All rights reserved.
- Prediction of low frequency vibration and sound propagation through reinforced concrete structuresPublication . Carreira, A. S.; Neves e Sousa, AlbanoPrediction of low frequency sound fields generated in buildings by internal sources as machines or external sources such as road or rail traffic is a difficult task. Assuming that the source is well known, predictions are generally based on the Finite Element Method (FEM), which is used to model building structures and vibration and sound fields, but other hybrid or coupling methods also can be used. In general, these methods are too much time consuming and provide results which are reliable only below 100-150 Hz. Reliability at higher frequencies requires much larger models. It is, thus, important to develop simpler methods to be used with confidence by acousticians and other consultants. In the present paper a method for prediction of vibration propagation to building slabs based on the use of simplified transfer functions between fundamental joints of the structure is presented. The method was developed numerically for traditional multi-storey building with reinforced concrete slabs supported by reinforced concrete beams and columns and also was experimentally validated. The method can be used together with theoretical modal analysis to predict sound fields in dwellings.