Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes

If we tried to list every known chemical reaction within an organismhuman, plant or even bacteriawe would get quite a long and confusing read. But when this information is represented in so-called genome-scale metabolic networks, we have the means to access computationally each of those reactions and their interconnections. Some parts of the network have alternatives, while others are unique and therefore can be essential for growth. Here, we simulate growth and compare essential reactions and genes for the simplest type of unicellular speciesprokaryotesto understand which parts of their metabolism are universally essential and potentially ancestral. We show that similar patterns of essential reactions echo phylogenetic relationships (this makes sense, as the genome provides the building plan for the enzymes that perform those reactions). Our computational predictions correlate strongly with experimental essentiality data. Finally, we show that a crucial step of protein synthesis (tRNA charging) and the synthesis and transformation of small molecules that enzymes require (cofactors) are the most essential and conserved parts of metabolism in prokaryotes. Our results are a step further in understanding the biology and evolution of prokaryotes but can also be relevant in applied studies including metabolic engineering and antibiotic design.:This work was supported by grants from: the Fundac ¸ão para a Ciência e a Tecnologia (http:// www.fct.pt) with award number UID/BIO/04469/2013, the European Regional Development Fund (http://www.norte2020.pt) with award number NORTE-01-0145-FEDER-000004 (https://www. ceb.uminho.pt/Projects/Details/6040), Horizon 2020 (https://ec.europa.eu/programmes/ horizon2020) with award number 686070 (http:// dd-decaf.eu/) and COMPETE2020 with award number POCI-01-0145-FEDER-006684 to JCX and IR and the Fundação para a Ciência e a Tecnologia (http://www.fct.pt) with award number SFRH/BD/81626/2011 to JCX. The funders had no role in study design, data collectionand analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Biodiversity and characterization of Staphylococcus species isolated from a small manufacturing dairy plant in Portugal

The level and the diversity of the staphylococcal community occurring in the environment and dairy products of a small manufacturing dairy plant were investigated. Species identification was performed using different molecular methods, viz. Multiplex-PCR, amplified ribosomal DNA restriction analysis (ARDRA), and sodA gene sequencing. The main species encountered corresponded to Staphylococcus equorum (41 isolates, 39.0%), S. saprophyticus (28 isolates, 26.7%) and S. epidermidis (15 isolates, 14.3%). Additionally, low incidence of enterotoxin genes was obtained, with only 9 strains (8.6%) being positive for one or more toxin genes. With regard to antimicrobial resistance, 57.1% of the isolates showed at least resistance against one antibiotic, and 28.6% were multi-resistant, which might accomplish resistance for up to 6 antibiotics simultaneously. These results provided evidence that the presence of Staphylococcus species in dairy environment are mostly represented by S. equorum and S. saprophyticus, and illustrate that carrying antimicrobial resistance genes has become reasonably widespread in cheese and dairy environment.info:eu-repo/semantics/acceptedVersio

Apoptosis-associated microRNAs are modulated in mouse, rat and human neural differentiation

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRs or miRNAs) regulate several biological processes in the cell. However, evidence for miRNAs that control the differentiation program of specific neural cell types has been elusive. Recently, we have shown that apoptosis-associated factors, such as p53 and caspases participate in the differentiation process of mouse neural stem (NS) cells. To identify apoptosis-associated miRNAs that might play a role in neuronal development, we performed global miRNA expression profiling experiments in NS cells. Next, we characterized the expression of proapoptotic miRNAs, including miR-16, let-7a and miR-34a in distinct models of neural differentiation, including mouse embryonic stem cells, PC12 and NT2N cells. In addition, the expression of antiapoptotic miR-19a and 20a was also evaluated.</p> <p>Results</p> <p>The expression of miR-16, let-7a and miR-34a was consistently upregulated in neural differentiation models. In contrast, expression of miR-19a and miR-20a was downregulated in mouse NS cell differentiation. Importantly, differential expression of specific apoptosis-related miRNAs was not associated with increased cell death. Overexpression of miR-34a increased the proportion of postmitotic neurons of mouse NS cells.</p> <p>Conclusions</p> <p>In conclusion, the identification of miR-16, let-7a and miR-34a, whose expression patterns are conserved in mouse, rat and human neural differentiation, implicates these specific miRNAs in mammalian neuronal development. The results provide new insights into the regulation of neuronal differentiation by apoptosis-associated miRNAs.</p

Enzymatic Potential of Filamentous Fungi as a Biological Pretreatment for Acidogenic Fermentation of Coffee Waste

This work was developed within the scope of the project CICECO-Aveiro Institute of Materials (UIDB/50011/2020, UIDP/50011/2020, and LA/P/0006/2020), and the Associate Laboratory for Green Chemistry-LAQV (UIDB/50006/2020 and UIDP/50006/2020). It was financed by national funds through the FCT/MCTES (PIDDAC) and, when appropriate, co-financed by FEDER under the PT2020 Partnership Agreement. Paulo C. Lemos acknowledges the support of FCT/MCTES for contract IF/01054/2014/CP1224/CT0005 and Joana Pereira thanks FCT/MCTES for her Ph.D. grant SFRH/BD/130003/2017.Spent coffee grounds (SCGs) are a promising substrate that can be valorized by biotechnological processes, such as for short-chain organic acid (SCOA) production, but their complex structure implies the application of a pretreatment step to increase their biodegradability. Physicochemical pretreatments are widely studied but have multiple drawbacks. An alternative is the application of biological pretreatments that include using fungi Trametes versicolor and Paecilomyces variotii that naturally can degrade complex substrates such as SCGs. This study intended to compare acidic and basic hydrolysis and supercritical CO 2 extraction with the application of these fungi. The highest concentration of SCOAs, 2.52 gCOD/L, was achieved after the acidification of SCGs pretreated with acid hydrolysis, but a very similar result, 2.44 gCOD/L, was obtained after submerged fermentation of SCGs by T. versicolor. This pretreatment also resulted in the best acidification degree, 48%, a very promising result compared to the 13% obtained with the control, untreated SCGs, highlighting the potential of biological pretreatments.publishersversionpublishe

From species detection to population size indexing : the use of sign surveys for monitoring a rare and otherwise elusive small mammal

Funding Information: Open access funding provided by FCT|FCCN (b-on). This study was funded by Fundo Europeu de Desenvolvimento Regional (FEDER) through the Programa Operacional Factores de Competitividade (COMPETE) and national funds through the Portuguese Foundation for Science and Technology (FCT) within the scope of the projects ‘MateFrag’ (PTDC/BIA-BIC/6582/2014) and ‘Agrivole’ (PTDC/BIA-ECO/31728/2017). DP was supported by the FCT grant SFRH/BD/133375/2017. TM was supported by the FCT grant SFRH/BD/145156/2019. PB was supported by EDP Biodiversity Chair. JP was supported by the European Union’s Horizon 2020 research and innovation programme under project EnvMetaGen (grant agreement no 668981). RP was supported by FCT, through a research contract under the Portuguese Decree-Law nr 57/2016.Peer reviewedPublisher PD

Community composition and habitat characterization of a rock sponge aggregation (Porifera, Corallistidae) in the Cantabrian Sea.

Deep-sea sponge-dominated communities are complex habitats considered hotspots of biodiversity and ecosystem functioning. They are classified as Vulnerable Marine Ecosystem and are listed as threatened or declining as a result of anthropogenic activities. Yet, studies into the distribution, community structure and composition of these habitats are scarce, hampering the development of appropriate management measures to ensure their conservation. In this study we describe a diverse benthic community, dominated by a lithistid sponge, found in two geomorphological features of important conservation status —Le Danois Bank and El Corbiro Canyon— of the Cantabrian Sea. Based on the analyses of visual transects using a photogrammetric towed vehicle and samples collected by rock dredge, we characterize the habitat and the associated community in detail. This deep-sea sponge aggregation was found on bedrock. It is dominated by one lithistid sponge, Neoschrammeniella aff. bowerbankii (0.2 ind./m2) and further composed of various sponge species as well as of other benthic invertebrates such as cnidarians, bryozoans and crustaceans. Using a non-invasive methodology (SfM – Structure from Motion) and empirical relationships of individuals size and biomass/volume obtained in laboratory for N. aff. bowerbankii, we were able to estimate a total biomass of 41 kg and volume of 39 l of this species in the surveyed area. This approach allows a fine tune methodology for estimating biomass and volume by image-based-observed area avoiding destructive techniques for this species.Postprin

Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA)

Though all theories for the origin of life require a source of energy to promote primordial chemical reactions, the nature of energy that drove the emergence of metabolism at origins is still debated. We reasoned that evidence for the nature of energy at origins should be preserved in the biochemical reactions of life itself, whereby changes in free energy, ΔG, which determine whether a reaction can go forward or not, should help specify the source. By calculating values of ΔG across the conserved and universal core of 402 individual reactions that synthesize amino acids, nucleotides and cofactors from H2, CO2, NH3, H2S and phosphate in modern cells, we find that 95-97% of these reactions are exergonic (ΔG ≤ 0 kJ⋅mol-1) at pH 7-10 and 80-100°C under nonequilibrium conditions with H2 replacing biochemical reductants. While 23% of the core's reactions involve ATP hydrolysis, 77% are ATP-independent, thermodynamically driven by ΔG of reactions involving carbon bonds. We identified 174 reactions that are exergonic by -20 to -300 kJ⋅mol-1 at pH 9 and 80°C and that fall into ten reaction types: six pterin dependent alkyl or acyl transfers, ten S-adenosylmethionine dependent alkyl transfers, four acyl phosphate hydrolyses, 14 thioester hydrolyses, 30 decarboxylations, 35 ring closure reactions, 31 aromatic ring formations, and 44 carbon reductions by reduced nicotinamide, flavins, ferredoxin, or formate. The 402 reactions of the biosynthetic core trace to the last universal common ancestor (LUCA), and reveal that synthesis of LUCA's chemical constituents required no external energy inputs such as electric discharge, UV-light or phosphide minerals. The biosynthetic reactions of LUCA uncover a natural thermodynamic tendency of metabolism to unfold from energy released by reactions of H2, CO2, NH3, H2S, and phosphate

Peripheral axonal ensheathment is regulated by RalA GTPase and the exocyst complex

Funding This work was supported by H2020 Marie Skłodowska-Curie Actions [H2020- GA661543-Neuronal Trafficking to R.O.T.], Fundo Regional para a Ciência e Tecnologia [IF/00392/2013/CP1192/CT0002 to R.O.T.] and iNOVA4Health (UID/Multi/04462/2013) (co-funded by FCT-FEDER-PT2020).Axon ensheathment is fundamental for fast impulse conduction and the normal physiological functioning of the nervous system. Defects in axonal insulation lead to debilitating conditions, but, despite its importance, the molecular players responsible are poorly defined. Here, we identify RalA GTPase as a key player in axon ensheathment in Drosophila larval peripheral nerves. We demonstrate through genetic analysis that RalA action through the exocyst complex is required in wrapping glial cells to regulate their growth and development. We suggest that the RalA-exocyst pathway controls the targeting of secretory vesicles for membrane growth or for the secretion of a wrapping glia-derived factor that itself regulates growth. In summary, our findings provide a new molecular understanding of the process by which axons are ensheathed in vivo, a process that is crucial for normal neuronal function.publishersversionpublishe

Extraction and characterization of collagen from Antarctic and Sub-Antarctic squid and its potential application in hybrid scaffolds for tissue engineering

Collagen is the most abundant protein found in mammals and it exhibits a low immunogenicity, high biocompatibility and biodegradability when compared with others natural polymers. For this reason, it has been explored for the development of biologically instructive biomaterials with applications for tissue substitution and regeneration. Marine origin collagen has been pursued as an alternative to the more common bovine and porcine origins. This study focused on squid (Teuthoidea: Cephalopoda), particularly the Antarctic squid Kondakovia longimana and the Sub-Antarctic squid Illex argentinus as potential collagen sources. In this study, collagen has been isolated fromthe skins of the squids using acid-based and pepsin-based protocols, with the higher yield being obtained from I. argentinus in the presence of pepsin. The produced collagen has been characterized in terms of physicochemical properties, evidencing an amino acid profile similar to the one of calf collagen, but exhibiting a less preserved structure, with hydrolyzed portions and a lower melting temperature. Pepsin-soluble collagen isolated fromI. argentinus was selected for further evaluation of biomedical potential, exploring its incorporation on poly-ε-caprolactone (PCL) 3D printed scaffolds for the development of hybrid scaffolds for tissue engineering, exhibiting hierarchical features.This work was partially funded by ERDF through POCTEP Project 0687_NOVOMAR_1_P and by the European Union Seventh Framework Programme for research, technological development and demonstration under grant agreement on ERC-2012-ADG 20120216-321266 (ComplexiTE). The Portuguese Foundation for Science and Technology (FCT) is also acknowledged for post-doctoral fellowships of JMS (SFRH/BPD/70230/2010) and RPP (SFRH/BPD/101886/2014), financed by POPH/FSE, and FCT Investigator grant of JX (IF/00616/2013). The authors also want to thank Dr. Julio Maroto (Fundación CETMAR, Spain) for the kind offer of the samples of skins of I. argentinus, to Dr. Dario Fassini for the assistance in SDS-PAGE and to Raphael Canadas for assistance in micro-CT data processing.info:eu-repo/semantics/publishedVersio