SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Background The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. Results In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Conclusion Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net

Enhanced dietary formulation to mitigate winter thermal stress in gilthead sea bream (Sparus aurata): a 2D-DIGE plasma proteome study

Low water temperatures during winter are common in farming of gilthead sea bream in the Mediterranean. This causes metabolic disorders that in extreme cases can lead to a syndrome called "winter disease." An improved immunostimulatory nutritional status might mitigate the effects of this thermal metabolic stress. A trial was set up to assess the effects of two different diets on gilthead sea bream physiology and nutritional state through plasma proteome and metabolites. Four groups of 25 adult gilthead sea bream were reared during winter months, being fed either with a control diet (CTRL) or with a diet called "winter feed" (WF). Proteome results show a slightly higher number of proteins upregulated in plasma of fish fed the WF. These proteins are mostly involved in the immune system and cell protection mechanisms. Lipid metabolism was also affected, as shown both by plasma proteome and by the cholesterol plasma levels. Overall, the winter feed diet tested seems to have positive effects in terms of fish condition and nutritional status, reducing the metabolic effects of thermal stress

Volatiles of the Inflorescences of the Madeiran Orchids, Goodyera macrophylla Lowe and Gennaria diphylla (Link) Parl. and Their Role in Pollination

Goodyera macrophylla, considered a rare endemic, and Gennaria diphylla are two native terrestrial Orchidaceae species that can be found mainly in Madeiran Laurisilva. The volatile compounds contributing to the floral scent of these two Madeiran orchids were analysed and compared for the first time. The volatiles, isolated by distillation-extraction in a Likens-Nickersontype apparatus, and those extracted by headspace sorption, were analysed by GC and GC-MS. The main volatile components isolated by distillation-extraction were γ-terpinene (13%) and n-nonanal (11%) in G. macrophylla and n-octacosane (19%) and n-heptacosane (13%) in G. diphylla. The main volatile components isolated by headspace sorption were p-cymene (21%), α-pinene (15%) and linalool (14%) in G. macrophylla and cis-arbusculone (28%) and lilac alcohol (26%) in G. diphylla. The importance of the volatiles in the pollination of these orchids is discussed.Portuguese Foundation for the Science and Technology (FCT, Fundação para a Ciência e Tecnologia) has sponsored this work, through the Centre of Macaronesian Studies (CEM). The authors are also grateful to the Madeiran Centre of Science and Technology (CITMA) for financial support.info:eu-repo/semantics/publishedVersio

An approach to simulate autonomous vehicles in urban traffic scenarios

The most common cause of traffic accidents is arguably the driver error due to lack of attention. And it is very unlikely this is going to change soon thanks to increasingly cell-phone usage, in-car entertainment systems, and naturally the more frequent traffic jams in highly populated areas. Autonomous vehicles, such as driverless cars, are a promising approach to decrease traffic accidents, as well as congestions. To test this approach, simulations are a safer, more efficient, and cheaper way than live testing. This paper presents an approach to implement a simulator to test such vehicles. It includes a study of the state of the art in driverless car simulation and discusses on the specific objectives that this particular simulator aims to achieve in order to aid testing the interactions of multiple driverless cars in urban networks

Characterization and genomic analysis of a new phage infecting Helicobacter pylori

Helicobacter pylori, a significant human gastric pathogen, has been demonstrating increased antibiotic resistance, causing difficulties in infection treatment. It is therefore important to develop alternatives or complementary approaches to antibiotics to tackle H. pylori infections, and (bacterio)phages have proven to be effective antibacterial agents. In this work, prophage isolation was attempted using H. pylori strains and UV radiation. One phage was isolated and further characterized to assess potential phage-inspired therapeutic alternatives to H. pylori infections. HPy1R is a new podovirus prophage with a genome length of 31,162 bp, 37.1% GC, encoding 36 predicted proteins, of which 17 were identified as structural. Phage particles remained stable at 37 °C, from pH 3 to 11, for 24 h in standard assays. Moreover, when submitted to an in vitro gastric digestion model, only a small decrease was observed in the gastric phase, suggesting that it is adapted to the gastric tract environment. Together with its other characteristics, its capability to suppress H. pylori population levels for up to 24 h post-infection at multiplicities of infection of 0.01, 0.1, and 1 suggests that this newly isolated phage is a potential candidate for phage therapy in the absence of strictly lytic phages.This study was supported by the Portuguese Foundation for Science and Technology (FCT), under the scope of the strategic funding of the UIDB/04469/2020 unit, and Project Helicophage PTDC/SAU-PUB/29182/2017 (POCI-01-0145-FEDER-029182). R.F. and R.F.S.G. acknowledge the FCT grants SFRH/BD/146496/2019 and SFRH/BD/140182/2018, respectivelyinfo:eu-repo/semantics/publishedVersio

Parasites of the reintroduced Iberian Lynx (Lynx pardinus) and Sympatric Mesocarnivores in Extremadura, Spain

Research Areas: MicrobiologyABSTRACT - The Iberian lynx (Lynx pardinus) is one of the most endangered felid species in the world. Conservation efforts have increased its population size and distribution and reinforced their genetic diversity through captive breeding and reintroduction programmes. Among several threats that the Iberian lynx faces, infectious and parasitic diseases have underlined effects on the health of their newly reintroduced populations, being essential to identify the primary sources of these agents and assess populations health status. To achieve this, 79 fresh faecal samples from Iberian lynx and sympatric mesocarnivores were collected in the reintroduction area of Extremadura, Spain. Samples were submitted to copromicroscopic analyses to assess parasite diversity, prevalence, and mean intensity of parasite burden. Overall, 19 (24.1%, ±15.1–35.0) samples were positive for at least one enteric parasite species. Parasite diversity and prevalence were higher in the Iberian lynx (43.8%) compared with the others mesocarnivores under study (e.g., the red fox Vulpes vulpes and the Egyptian mongoose Herpestes ichneumon). Ancylostomatidae and Toxocara cati were the most prevalent (15.6%) parasites. Obtained results revealed that Iberian lynx role as predator control might have reduced parasite cross-transmission between this felid and mesocarnivores due to their decreasing abundances. Surveillance programs must include regular monitoring of this endangered felid, comprising mesocarnivores, but also domestic/feral and wild cat communities.info:eu-repo/semantics/publishedVersio

Development of an edible coating for preservation of Serra da Estrela cheese : surface characterization and coating formulation

Serra da Estrela cheese is the most prestigious traditional Portuguese cheese, being recognized worldwide. In order to prolong the shelf life of this product, which occurs mostly by external spoilage and growth of fungi and moulds on its surface, the application of an edible coating has been considered. For this purpose, the external surface characterization was performed and the type of surface determined. For this, the sessile drop method was applied, i.e. the contact angle between the surface and the droplet of three pure liquids - bromonaphthalene, formamide and water - was calculated and the surface energy was determined. Polar and apolar components obtained were 7.09 mN/m and 35.53 mN/m, being the cheese surface tension 42.62 mN/m, which means that the cheese has a low surface energy (i.e. <100 mN/m). This value allows using Zisman’s method and calculating the critical surface tension (32.68 mN/m). In order to determine the coating formulation with the best composition for application on cheese, the wettability of 27 formulations (three different polymers were used - alginate, guar gum and chitosan - with different concentrations of glycerol and Tween 20, totaling 9 formulations for each polymer) was evaluated. Formulations with 1% (w/v) alginate with 0.1% (w/v) of glycerol and 0.15% (w/v) of Tween 20; 1% (w/v) guar gum with 0.3% (w/v) of glycerol and 0.15% (w/v) of Tween 20; 1% (w/v) chitosan with 0.3% (w/v) of glycerol and 0.15% (w/v) of Tween 20, were the solutions with better wetting capacity on cheese surface. The spreading coefficients were -15.20 mN/m, -21.83 mN/m and -15.07 mN/m for alginate, guar gum and chitosan solutions, respectively. Pareto charts analysis allowed concluding that for alginate-based coatings, the variation of the polymer formulation, together with glycerol and Tween 20 concentrations have significant influence on the values obtained. The same happened in guar gum films. Regarding the coatings containing chitosan, it is only the biopolymer concentration that has significant influence on the values of wettability. These three alternative compositions for edible coatings can now be tested aiming at valorizing this traditional cheese by improving its shelf-life and marketing potential

H. pylori phages: from genome release to hope for use as therapy

The increasing antibiotic-resistant Helicobacter pylori infections worldwide and the ineffectiveness of treatments led the World Health Organization to designate clarithromycin-resistant H. pylori as a high-priority bacterium for antibiotic research and development. (Bacterio)phages, viruses that infect bacteria, showing effectiveness in the treatment of pathogenic bacteria, could be a promising alternative strategy in the fight against H. pylori infections. Material and methods In this work, a collection of 74 Portuguese H. pylori-clinical strains was used to screen for the presence of phage genes, using a new PCR-based method. Selected strains were subsequently sequenced and prophage isolation was attempted using UV radiation. Three phages were isolated, one of which was further characterized genetically and biologically. Results PCR-based detection indicated the presence of target phage sequences in 14 strains, and the induction strategies resulted in the release of a new phage. It presents a genome length of 31,162 bp with a G+C content of 37.1 %. This podovirus showed capability to form phage plaques in five strains, was stable under an in vitro gastric digestion model, and was able to maintain a H. pylori population at low levels for up to 24h post-infection. Conclusion The new PCR screening method proved to be very effective in the selection of strains carrying prophages, resulting in the isolation of a new H. pylori phage. This phage presented very promising characteristics in terms of stability and efficacy, being therefore a small step towards the future use of phage therapy in the fight against H. pylori infections.info:eu-repo/semantics/publishedVersio

Simultaneous Separation of Antioxidants and Carbohydrates From Food Wastes Using Aqueous Biphasic Systems Formed by Cholinium-Derived Ionic Liquids

project CICECO-Aveiro Institute of Materials, UID/CTM/50011/2019. Associate Laboratory for Green Chemistry-LAQV, FCT Ref. UID/QUI/50006/2019. POCI-01-0145-FEDER-016403. Investigator FCT project IF/00621/2015. Programa Mais Centro under project CENTRO-07-ST24-FEDER-002008. COMPETE: PEst-C/SAU/UI0709/2011.The food industry produces significant amounts of waste, many of them rich in valuable compounds that could be recovered and reused in the framework of circular economy. The development of sustainable and cost-effective technologies to recover these value added compounds will contribute to a significant decrease of the environmental footprint and economic burden of this industry sector. Accordingly, in this work, aqueous biphasic systems (ABS) composed of cholinium-derived bistriflimide ionic liquids (ILs) and carbohydrates were investigated as an alternative process to simultaneously separate and recover antioxidants and carbohydrates from food waste. Aiming at improving the biocompatible character of the studied ILs and proposed process, cholinium-derived bistriflimide ILs were chosen, which were properly designed by playing with the cation alkyl side chain and the number of functional groups attached to the cation to be able to create ABS with carbohydrates. These ILs were characterized by cytotoxicity assays toward human intestinal epithelial cells (Caco-2 cell line), demonstrating to have a significantly lower toxicity than other well-known and commonly used fluorinated ILs. The capability of these ILs to form ABS with a series of carbohydrates, namely monosaccharides, disaccharides and polyols, was then appraised by the determination of the respective ternary liquid-liquid phase diagrams at 25 degrees C. The studied ABS were finally used to separate carbohydrates and antioxidants from real food waste samples, using an expired vanilla pudding as an example. With the studied systems, the separation of the two products occurs in one-step, where carbohydrates are enriched in the carbohydrate-rich phase and antioxidants are mainly present in the IL-rich phase. Extraction efficiencies of carbohydrates ranging between 89 and 92% to the carbohydrate-rich phase, and antioxidant relative activities ranging between 65 and 75% in the IL-rich phase were obtained. Furthermore, antioxidants from the IL-rich phase were recovered by solid-phase extraction, and the IL was recycled for two more times with no losses on the ABS separation performance. Overall, the obtained results show that the investigated ABS are promising platforms to simultaneously separate carbohydrates and antioxidants from real food waste samples, and could be used in further related applications foreseeing industrial food waste valorization.publishersversionpublishe

Phosphoprotein Phosphatase 1 isoforms alpha and gamma respond differently to prodigiosin treatment and present alternative kinase targets in melanoma cells

Reversible protein phosphorylation is a central regulatory mechanism of cell function. Deregulation of the balanced actions of protein kinases and phosphatases has been frequently associated with several pathological conditions, including cancer. Many studies have already addressed the role of protein kinases misregulation in cancer. However, much less is known about protein phosphatases influence. Phosphoprotein Phosphatase 1 (PPP1) is one of the major serine/threonine protein phosphatases who has three catalytic isoforms: PPP1CA, PPP1CB, and PPP1CC. Its function is achieved by binding to regulatory subunits, known as PPP1-interacting proteins (PIPs), which may prefer a catalytic isoform. Also, some inhibitors/enhancers may exhibit isoform specificity. Here we show that, prodigiosin (PG), a molecule with anticancer properties, promotes the formation of PPP1CA-AKT complex and not of PPP1CC-MAPK complex. Both, AKT and MAPK, are wellknown PIPs from two pathways that crosstalk and regulate melanoma cells survival. In addition, the analysis performed using surface plasmon resonance (SPR) technology indicates that PPP1 interacts with obatoclax (OBX), a drug that belongs to the same family of PG. Overall, these results suggest that PG might, at least in part, act through PPP1C/PIPs. Also, this study is pioneer in demonstrating PPP1 isoform-specific modulation by small molecules.publishe