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The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction.

La crisis energética, la escasez del agua y la mala calidad del aire son temas que deben ser atendidos urgentemente con el objetivo de garantizar el bienestar de la población. El uso de tecnologías alternativas como los humedales construidos (HC) permiten el tratamiento de aguas residuales de diversa índole; cuando estas tecnologías son acopladas a sistemas bioelectroquímicos (SBE) se optimiza la remoción de la carga orgánica y se puede generar energía eléctrica. Así, el objetivo de este trabajo fue realizar un análisis de los avances, entre los años 2010 a 2017, sobre el diseño de diversas configuraciones de sistemas de HC acoplados a SBE. Se logró identificar las variables más importantes que determinan la eficiencia de remoción de contaminantes y generación de corriente como son los materiales anódico y catódico, el área de los electrodos, el tipo de macrófitas y la carga orgánica. Así mismo, se presentan los valores de la carga orgánica removida y las máximas densidades de potencia obtenidas con las tres macrófitas más utilizadas.

En el presente reporte se describirá el trabajo realizado en un centro especializado para personas diagnosticadas con el Trastorno del Espectro Autista, el cual es un trastorno del desarrollo con disfunción neurológica, y se manifiesta desde la infancia. Se caracteriza debido a las dificultades que presentan en el área social y de la comunicación. Estas características se evidencian mediante sus conductas, por ejemplo, no realizan contacto visual, suelen aislarse de los demás, se fijan en los detalles y tienden a ser estructurados y repetitivos (Ruggieri y Arberas, 2007). El trabajo realizado en este centro con las personas autistas, está orientado en la Teoría de la Mente, esto es la comprensión y predicción que tiene la persona sobre el comportamiento de otro sujeto. Es así que el entrenamineto en esta teoría busca desarollar en la persona con autismo el “conectarse” con los demás, comprendiendo lo sentimientos, pensamientos y creencias y llegando a inferir los estados mentales de los otros, para así generar una mejor calidad de vida en un futuro, teniendo mejores relaciones y aceptación social (Baron-Cohen, 2008).

Background Hyaluronic acid (HA) is a polysaccharide present in almost all animal tissues, in which it carries out important biological functions, among them, the protection of the joints by lubricating them and dampening the tension in them. Objective This study compares the viscoelastic properties of several commercial preparations of HA, to determine their suitability for use as viscosupplementation therapy in joint pathology (osteoarthritis). Methods 4 HA hydrogels: Durolane®, Synocrom_Forte_One®, Synvisc_One® and Viscoplus_Matrix® and 4 HA solutions: Ostenil®, Ostenil_Plus®, Viscoplus_Gel® and Orthovisc® were analyzed to compare their viscoelatsic rheological parameters using an oscillatory-rotational rheometer. Results With respect to the 4 HA hydrogels, comparison of crossover frequencies allowed division into two main groups: Synvisc_One® and Viscoplus_Matrix®, with crossover frequencies in the order of magnitude of 10-2 Hz, while Synocrom_Forte_One® and Durolane® showed crossover frequencies on the order of 10-1 Hz. Only one of the 4 HA solutions, Viscoplus_Gel®, showed a crossover frequency on the order of 10-2, whereas Ostenil_Plus® and Orthovisc® showed crossover frequencies on the order of 10-1, and Ostenil® remained as a predominantly viscous fluid for frequencies as high as 4.8 Hz. Conclusions The viscoelastic properties of the HA preparations can be ordered according to the values of G∗ (the rigidity, or vector sum of the elastic modulus G' and the viscous modulus G'') at both transition points (0.5 and 2.5 Hz) as follows: Viscoplus_Matrix® > Viscoplus_Gel® > Durolane® > Synocrom_Forte_One® > Ostenil_Plus® > Synvisc_One® > Orthovisc® > Ostenil®.

[Background]: Some marine bacteria, such as Moritella marina, produce the nutraceutical docosahexaenoic acid (DHA) thanks to a specifc enzymatic complex called Pfa synthase. Escherichia coli heterologously expressing the pfa gene cluster from M. marina also produces DHA. The aim of this study was to fnd genetic or metabolic conditions to increase DHA production in E. coli., [Results]: First, we analysed the efect of the antibiotic cerulenin, showing that DHA production increased twofold. Then, we tested a series of single gene knockout mutations afecting fatty acid biosynthesis, in order to optimize the synthesis of DHA. The most efective mutant, fabH, showed a threefold increase compared to wild type strain. The combination of cerulenin inhibition and fabH deletion rendered a 6.5-fold improvement compared to control strain. Both strategies seem to have the same mechanism of action, in which fatty acid synthesis via the canonical pathway (fab pathway) is afected in its frst catalytic step, which allows the substrates to be used by the heterologous pathway to synthesize DHA., [Conclusions]: DHA-producing E. coli strain that carries a fabH gene deletion boosts DHA production by tuning down the competing canonical biosynthesis pathway. Our approach can be used for optimization of DHA production in diferent organisms., The work in the FdlC and GM laboratories was fnanced by the Spanish Ministry of Economy, Industry and Competitiveness Grant BFU2014-55534-C2.

[Background]: Rhodococcus jostii RHA1 and other actinobacteria accumulate triglycerides (TAG) under nutrient starvation. This property has an important biotechnological potential in the production of sustainable oils. [Results]: To gain insight into the metabolic pathways involved in TAG accumulation, we analysed the transcriptome of R jostii RHA1 under nutrient-limiting conditions. We correlate these physiological conditions with significant changes in cell physiology. The main consequence was a global switch from catabolic to anabolic pathways. Interestingly, the Entner-Doudoroff (ED) pathway was upregulated in detriment of the glycolysis or pentose phosphate pathways. ED induction was independent of the carbon source (either gluconate or glucose). Some of the diacylglycerol acyltransferase genes involved in the last step of the Kennedy pathway were also upregulated. A common feature of the promoter region of most upregulated genes was the presence of a consensus binding sequence for the cAMP-dependent CRP regulator. [Conclusion]: This is the first experimental observation of an ED shift under nutrient starvation conditions. Knowledge of this switch could help in the design of metabolomic approaches to optimize carbon derivation for single cell oil production., This work was financed by Grants BIO2010-14809 from the Spanish Ministry of Science and Innovation and BFU2014-55534-C2-2-P from the Spanish Ministry of Economy and Competitiveness to GM. H.M. Alvarez is a career investigator of the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.

Triglycerides (TAGs), the major storage molecules of metabolic energy and source of fatty acids, are produced as single cell oil by some oleogenic microorganisms. However, these microorganisms require strict culture conditions, show low carbon source flexibilities, lack efficient genetic modification tools and in some cases pose safety concerns. TAGs have essential applications such as behaving as a source for added-value fatty acids or giving rise to the production of biodiesel. Hence, new alternative methods are urgently required for obtaining these oils. In this work we describe TAG accumulation in the industrially appropriate microorganism Escherichia coli expressing the heterologous enzyme tDGAT, a wax ester synthase/triacylglycerol:acylCoA acyltranferase (WS/DGAT). With this purpose, we introduce a codon-optimized gene from the thermophilic actinomycete Thermomonospora curvata coding for a WS/DGAT into different E. coli strains, describe the metabolic effects associated to the expression of this protein and evaluate neutral lipid accumulation. We observe a direct relation between the expression of this WS/DGAT and TAG production within a wide range of culture conditions. More than 30% TAGs were detected within the bacterial neutral lipids in 90 minutes after induction. TAGs were observed to be associated with the hydrophobic enzyme while forming round intracytoplasmic bodies, which could represent a bottleneck for lipid accumulation in E. coli. We detected an increase of almost 3- fold in the monounsaturated fatty acids (MUFA) occurring in the recombinant strains. These MUFA were predominant in the accumulated TAGs achieving 46% of the TAG fatty acids. These results set the basis for further research on the achievement of a suitable method towards the sustainable production of these neutral lipids., This work was financed by Grants BIO2010-14809 from the Spanish Ministry of Science and Innovation and BFU2014-55534-C2-2-P from the Spanish Ministry of Economy and Competitiveness to GM, São Paulo Research Foundation (FAPESP) to CM and IB14DM0176 from the European Commission to BL.

The sulfonic acid resin Dowex ® 50W × 8 can be used to replace mineral acids in the reaction between p -hydroxymandelic acid and urea in water or NaCl solutions. The synthesis of p -hydroxymandelic acid is efficiently carried out using NaOH to promote the reaction between phenol and glyoxylic acid. Alternatively, KF/alumina can be used to obtain methyl p -hydroxymandelate by reaction of phenol with methyl 2-hydroxy-2-methoxyacetate, although, this process is carried out in an organic solvent and gives a lower yield. A comparison between the three alternative methods for the synthesis of 5-(4-hydroxyphenyl)hydantoin shows that the direct route from glyoxylic acid, urea and phenol is the most efficient method, although the p -hydroxymandelic acid route would be an interesting alternative if its heterogeneous synthesis were optimized.

Clays, zeolites and organic polymers bearing sulfonic acid groups are used to promote the direct synthesis of dl-5-(4-hydroxyphenyl)hydantoin from urea, phenol and glyoxylic acid. Only organic polymers lead to good results, in particular a sulfonic polystyrene-divinylbenzene resin with a small particle size, whereas very poor results are obtained when clays or zeolites are used to promote this amidoalkylation reaction. A possible explanation for these rather surprising differences in behavior involves the different hydrophilic/hydrophobic character of the solids, particularly given the aqueous reaction medium. The pre-treatment of the resin and the particle size are important factors that influence the final result. Although the results are no better than those obtained with hydrochloric acid in the homogeneous phase, these resins do represent the only environmentally friendly alternative., We are indebted to DSM Deretil for financial support and providing some of the reagents and products.

Survival of Campylobacter jejuni at 4 and 20°C was investigated by using cellular integrity, respiratory activity, two-dimensional (2D) protein profile, and intact DNA content as indicators of potential viability of nonculturable cells. Intact DNA content after 116 days, along with cellular integrity and respiring cells, was detected for up to 7 months at 4°C by pulsed-field gel electrophoresis. Most changes in 2D protein profiles involved up- or down-regulation.

The combined effect of low pH (5.0), low salinity (0.5%) and temperature (5 and 20°C) on the survival ofVibrio vulnificuscells was studied. The effect of the combined stress was examined on the basis of the decrease in cell counts throughout 6 h of incubation in brain–heart infusion broth pH 5. Combined stress had an immediate effect that did not produce cellular lysis but a marked loss of culturability on thiosulphate citrate–bile salts–sucrose agar. However, a large number of cells remained viable, as determined both by direct viable counts and by colony forming units on non-selective medium. Cell injury affected a great number of cells but the survival fraction of non-injured cells remained above 20% of the initial number. The inactivation of a significant number of cells was examined in terms of theD8-values. They varied depending on the parameter examined but in generalD8values were obtained more rapidly at 20 than at 5°C. However, after 24 h of incubation, when no cells could be detected onto non-selective medium, viable cells were detected by direct viable counts, both at 5 and 20°C.

Escherichia coli O25:H-42 was selected to study the effect of pre-treatments on the enumeration of direct viable cells from milk samples. Before and after inducing cell elongation by cellular division inhibitors, three pre-treatments for milk-filtration were used. One involved a pre-treatment with trypsin (1.5 min at 50 degrees C), addition of hot Triton X-100 after heating and filter rinses with phosphate saline buffer. The other two involved pre-treatment with trypsin and Triton X-100 (10 min at 50 degrees C), filter rinses with hot Triton X-100 and organic solvents. Pre-treatments applied after inducing cell elongation had an effect on cell recovery from milk samples depending on the pre-treatment used. The most suitable, on the basis of the number and percentage of enlarged cells obtained was the first described. The others selectively affected recovery of elongated cells. Pre-treatments applied before inducing the cell elongation, negatively affected viability with enumeration in milk samples being significantly (P < 0.001) lower than those found in controls. However, the negative effects of first pre-treatment on viability was lower than that produced by the pre-treatments involving organic solvents.

A description is given of a pre-treatment for milk samples which allows it to be filtered through 0.2 μm pore-size membrane filters without reducing the initial number of bacteria. The efficiency of the method was demonstrated in milk samples inoculated with Escherichia coli O25:H-42, a food-borne pathogen, by comparison with a control in tryptone soya broth (TSB). No significant differences were found between direct microscopic counts in milk samples and controls in TSB.

The synthesis of allantoin from glyoxylic acid and urea has been studied using several heterogeneous catalysts. Organic resins and nanocomposites, particularly sulfonic resins, lead to higher yields than zeolites. Polymer morphology has a significant influence on the performance of the catalyst. The possibility of using the same type of solid acid in the reaction of allantoin with phenol has also been explored. However, this route requires a larger amount of acid and leads to lower para/ortho selectivity than the direct route from glyoxylic acid and urea., We are indebted to Dr. Mark A. Harmer, from DuPont Research and Development, for the generous gift of SAC-13. The financial support of DSM Deretil and the Spanish M.C.Y.T. (project PPQ2000-0322-P4) are acknowledged.

Mestrado em Biotecnologia A transferência horizontal de genes permite a adaptação microbiana a nichos especiais, dos quais dois bons exemplos são a camada superficial do mar e a coluna de água. Os plasmídeos com gama alargada de hospedeiros (BHR), responsáveis pelo fluxo de material genético entre cromossomas bacterianos (inclusivamente entre microorganismos muito afastados filogeneticamente) têm um papel essencial na evolução das comunidades microbianas. Entre eles, os plasmídeos pertencendo ao grupo de incompatibilidade IncP-1 têm um interesse especial por causa da sua extraordinária flexibilidade na iniciação da replicação e da estabilidade na sua manutenção numa ampla gama de hospedeiros. Estes elementos genéticos móveis, além de constituírem ferramentas úteis na engenharia genética, representam uma grande fonte de genes que codificam para características tão significativas como a resistência a antibióticos e a degradação de xenobióticos. No entanto, a diversidade nesta família de plasmídeos BHR tem sido subestimada até agora: actualmente sabe-se da existência de cinco subgrupos divergentes, mas embora alguns plamídeos modelo tenham sido estudados ao detalhe, ainda há muito para investigar. Em trabalhos anteriores na Ria de Aveiro (costa NW de Portugal), foi feita a captura exógena de plasmídeos bem como o isolamento de bactérias potencialmente hospedeiras de plasmídeos endógenos. Neste trabalho, sequências de nucleótidos específicas foram amplificadas mediante reacções em cadeia da polimerase para determinar a presença de plasmídeos BHR. Os sete plasmídeos IncP-1 detectados, foram em primeiro lugarfilogeneticamente estudados. O alinhamento das sequências de nucleótidos de 281 pb que foram amplificadas e que correspondem a um fragmento do gene trfA (que codifica para uma proteína do início da replicaçao) sugeriu o estabelecimento de dois novos clusters situados filogeneticamente em dois subgrupos diferentes de IncP-1: IncP-1β e o recentemente descrito IncP-1ε. Estes constituem os primeiros replicões IncP-1 provenientes de ambientes estuarinos a serem detectados e isolados. De seguida, uma comparação e caracterização preliminar genética e fenotípica foi realizada com os plasmídeos purificados, considerando a descrição já conhecida dos dois plasmídeos arquétipos evolutivamente mais próximos, pB10 e pKJK5. Assim, as análises de fragmentos de restrição, determinação da inibição do crescimento do hospedeiro na presença de mercúrio e ensaios de resistência a diferentes antibióticos ajudaram a compreender o elevado interesse que recai nestes plasmídeos revelando a diversidade fenotípica e genotípica. Uma completa descrição de qualquer destes novos plasmídeos pode ter una enorme importância ecológica, evolutiva e biotecnológica, incrementada pela sua procedência dum ambiente não clínico. Portanto este trabalho justifica um estudo em maior profundidade destes replicões promíscuos. The horizontal gene transfer allows microbial adaptation to special niches, from which the sea-surface microlayer or the subsurface waters in estuarine environments might be good examples. Broad host range plasmids, responsible for the reshuffling of genetic material between bacterial chromosomes (even amongst distantly related microorganims), play an essential role on the evolution and diversity of microbial communities. Among them, the incompatibility group IncP-1 plasmids have a special interest due to their extraordinary flexibility in the replication initiation and stable maintenance in such a wide spectrum of hosts. These mobile genetic elements, in addition to the helpful genetic engineering tools they mean, represent a great source of potentially useful genes encoding for traits as significant as antibiotic resistance or xenobiotic degradation. Nevertheless, the diversity of this family of BHR plasmids has been underestimated until recently: it is currently known to have five divergent sub-groups, but although some prototype plasmids have been studied in great detail, there is still much left to research. In previous investigations exogenous plasmid capture was carried out as well as putative endogenous plasmid bacterial hosts isolated in the Ria de Aveiro lagoon (NW coast of Portugal). In this work, polymerase chain reactions were developed to amplify specific nucleotide sequences and determine BHR plasmids presence. From a bioinformatical approach, the seven IncP-1 plasmids detected were firstly phylogenetically studied. The alignment of the amplified 281 bp nucleotide sequences corresponding to a fragment of the replication initiation protein encoding gene trfA suggested the formation of two novel clusters belonging to two different IncP-1 plasmid subgroups: IncP-1β and the lately described IncP-1ε. Additionally, these represent the first estuarine IncP-1 replicons to be detected and isolated. Then a preliminary genetic and phenotypic comparison was performed with the purified plasmids, by taking into account the known description of the evolutionary closest models, pB10 and pKJK5. That way, restriction fragment analysis as well as antibiotic and mercury resistance determination assays helped to comprehend the high significance falling on the captured plasmids by revealing the genetic and phenotypic diversity. A whole description of any of these novel plasmids may have a huge ecological, evolutionary and biotechnological importance, even more due to its precedence from a non-clinical environment. Therefore this work justifies further studies on these promiscuous replicons.

The epoxidation of cyclohexene with aqueous hydrogen peroxide over mesostructured Ti(Cp)2Cl2-grafted silica catalysts is described for the first time. Three kinds of Ti-containing systems with different textural properties have been employed: Ti/SiO2, Ti/MCM-41 and Ti/MCM-48. A minimal local H2O2 concentration in the surroundings of Ti sites, obtained by a controlled dropwise addition of aqueous H2O2 (4.17 mmol H2O2 h-1 gcat -1), is crucial for an effective and highly selective epoxidation. Excellent selectivity (>98%) in cyclohexene epoxide is obtained at the end of the slow H2O2 addition in acetonitrile. Higher yields in epoxide are found over Ti/MCM-48 than over Ti/MCM-41 or Ti/SiO2 thanks to better isolation, dispersion and stability of Ti(IV) sites.

XII Expedição Científica do Departamento de Biologia - Pico 2005. Submitted by Duarte Furtado (dfurtado@uac.pt) on 2010-11-19T15:38:36Z No. of bitstreams: 1 Actividades realizadas pelo CCPA no decorrer da XII Expedição Científica do Departamento de Biologia - Pico 2005.pdf: 80936 bytes, checksum: 948dc29903f1d843e289c58ba6af4ef1 (MD5) Made available in DSpace on 2010-11-29T12:23:01Z (GMT). No. of bitstreams: 1 Actividades realizadas pelo CCPA no decorrer da XII Expedição Científica do Departamento de Biologia - Pico 2005.pdf: 80936 bytes, checksum: 948dc29903f1d843e289c58ba6af4ef1 (MD5) Previous issue date: 2006-06

The routine technique for detecting antibodies specific to infectious bursal disease virus (IBDV) is a serological evaluation by enzyme-linked immunosorbent assay (ELISA) with preparations of whole virions as the antigens. To avoid using complete virus in the standard technique, we have developed two new antigens through the expression of the VPX and VP3 genes in insect cells. VPX and especially VP3 were expressed at high levels in insect cells and simple to purify. The immunogenicity of both proteins was similar to that of the native virus. VPX was able to elicit neutralizing antibodies but VP3 was not. Purified VPX and VP3 were tested in an indirect ELISA with more than 300 chicken sera. There was an excellent correlation between the results of the ELISA using VPX and those of the two commercial kits. VP3 did not perform as well as VPX, and the linear correlation was significantly lower. A comparison with the standard reference technique, seroneutralization, showed that the indirect ELISA was more sensitive. Therefore, VPX-based ELISA is a good alternative to conventional ELISAs that use whole virions.

Several titanium derivatives supported on silica have been investigated as catalysts in the sulfide→sulfoxide oxidation; the supported titanium/tartaric acid catalyst is highly suited to reactions carried out with H2O2, leading to high yields and high sulfoxide/sulfone selectivities, while small asymmetric inductions (up to 13%) are observed., This work was made possible by the generous financial support of the C.I.C.Y.T. (Project MAT96-1053).