Bio-Isobutene production: When the key enzymes are nowhere to be found

As of today, most industrial bio production processes are based on naturally occurring metabolic pathways or biochemical reactions, preventing the access to many of the chemistry’s largest market. For example, the development of bio-processes for the efficient production of light olefins such as propylene, linear butylene, butadiene and isobutene, remains a technological challenge: since these molecules are not synthesized by natural microorganisms, the design of a complete metabolic pathway for their production is hampered by the lack of identified enzymes able to perform the final biochemical step. In order to bridge this gap, Global Bioenergies has engineered artificial biocatalysts, and combined them with natural enzymes into metabolic pathways leading to the production of isobutene. Thus, in contrast with most former approaches, the new metabolic routes leading to isobutene involve non-naturally occurring reactions. The same type of approach was also used for butadiene and other molecules. The scale-up of this innovative bio-based production process is currently ongoing. Whereas a pilot plant with a capacity of 10 tons/year of oxidation-grade isobutene is running since 2014 in Pomacle (France) a demo plant with a capacity of 100 tons/year of polymer-grade isobutene has recently started operations on the refinery site of Leuna (Germany). It will cover the whole of isobutene’s wide product tree, including rubber applications. The company prepares now the first full-scale plant through a Joint-Venture with Cristal Union, named IBN-One. In the same time, Global Bioenergies is developing a strategy of diversification, in order to propose a pipeline of processes covering all possible feedstocks, from first to third generation

Raskaudenaikaiseen tupakointiin puuttuminen

Tämän tutkimuksen tarkoituksena on kuvata raskauden aikana tupakoivien naisten näkemyksiä muiden ihmisten oikeudesta puuttua heidän tupakointiinsa. Tutkimuksen tavoitteena on saada tietoa, jonka avulla voidaan jatkossa paremmin kuunnella raskauden aikana tupakoivia naisia. Tutkimuskysymykset ovat 1) Kenellä on oikeus puuttua raskaudenaikaiseen tupakointiin ja miksi? 2) Missä tilanteissa raskaudenaikaiseen tupakointiin saa puuttua? ja 3) Miten naiset kokevat raskaudenaikaiseen tupakointiin puuttumisen? Aineisto kerättiin sähköisellä Webropol-kirjoituspyynnöllä huhtikuun lopusta kesäkuun loppuun 2015. Kirjoituspyyntö julkaistiin stumppi.fi sivustolla, keskustelupalstoilla (suomi24.fi ja kaksplus.fi) sekä joissakin imetykseen tai lapsiin liittyvissä keskusteluryhmissä Facebookissa. Aineisto koostuu 53 raskauden aikana tupakoivasta tai tupakoineesta naisesta. Kirjoitukset analysoitiin induktiivisella sisällönanalyysilla. Tutkimukseen on saatu eettinen ennakkoarviointi Turun yliopistolta ja tutkimusluvat on haettu asiaankuuluvasti. Tulosten perusteella naiset kokivat tarvitsevansa tukea ja kannustusta tupakoinnin lopettamiseen sekä neuvolasta että läheisiltään. Naiset kokivat usein, että terveydenhuollolla oli oikeus tai velvollisuus puuttua heidän tupakointiinsa, mutta muuten näkemykset vaihtelivat siitä, että kaikki saavat puuttua tupakointiin siihen, että kukaan ei saa puuttua. Tilanteina, joissa tupakointiin sai puuttua mainittiin äidin hyväksyntä puuttumiselle, jokin erityistilanne tai se, jos äiti jatkaa tupakointia. Naiset kertoivat olevansa tietoisia riskeistä, mutta tupakoinnin olevan heidän oma valintansa. Jotkut kokivat puuttumisen positiivisena, jotkut negatiivisena ja jotkut ajattelivat sen jopa lisäävän tupakointia. Puuttuminen herätti monia, lähinnä negatiivisia, tunteita. Puuttumisen pelossa tupakointia saatettiin myös salailla ja tupakointia oikeutettiin eri tavoin. Jatkossa tupakoinninlopettamispalveluita tulisi kehittää paremmin äitien tarpeita vastaaviksi ja helposti lähestyttäviksi. Olisi hyödyllistä tutkia sitä mitä mieltä terveydenhuollon ammattilaiset ja puolisot ovat oikeudestaan puuttua raskauden aikaiseen tupakointiin. Kummillakin on merkittävä rooli äidin tupakoinnin lopettamisessa, joten olisi tärkeää saada heidän näkökulmansa asiasta esiin

Polissage mécano-chimique pour la fabrication de films minces de silicium poly-cristallin dopé in-situ en bore et leur assemblage par collage direct

L’industrie de la microélectronique met en œuvre des procédés de fabrication innovants afin d’assurer l’amélioration des performances et l’augmentation de la durée de vie des technologies à base de matériaux semi-conducteurs. L’assemblage par collage direct est un procédé permettant de lier des tranches de silicium entre elles. Ainsi, il est possible de connecter différentes technologies, de réaliser des assemblages 3D ou encore de fermer des cavités, notamment pour les applications de type MEMS. Comme le collage direct se fait par interaction chimique directement entre les surfaces à assembler, il est impératif de contrôler la rugosité de ces surfaces. L’étude et l’optimisation du polissage mécano-chimique (CMP) sur des surfaces d’ISDP ont été réalisées afin de minimiser la rugosité de surface (<0,2nm RMS) et d’assurer la réussite des collages directs. L’utilisation de ce procédé a rendu possible le collage direct ISDP/ISDP et a permis d’améliorer le collage direct ISDP/SiO2. Ces résultats sont appuyés par des analyses mécaniques, optiques ou encore par la mesure de taux de fuite sur des cavités sous vide

Predicted Effects of Missense Mutations on Native-State Stability Account for Phenotypic Outcome in Phenylketonuria, a Paradigm of Misfolding Diseases

Phenylketonuria (PKU) is a genetic disease caused by mutations in human phenylalanine hydroxylase (PAH). Most missense mutations result in misfolding of PAH, increased protein turnover, and a loss of enzymatic function. We studied the prediction of the energetic impact on PAH native-state stability of 318 PKU-associated missense mutations, using the protein-design algorithm FoldX. For the 80 mutations for which expression analyses have been performed in eukaryote systems, in most cases we found substantial overall correlations between the mutational energetic impact and both in vitro residual activities and patient metabolic phenotype. This finding confirmed that the decrease in protein stability is the main molecular pathogenic mechanism in PKU and the determinant for phenotypic outcome. Metabolic phenotypes have been shown to be better predicted than in vitro residual activities, probably because of greater stringency in the phenotyping process. Finally, all the remaining 238 PKU missense mutations compiled at the PAH locus knowledgebase (PAHdb) were analyzed, and their phenotypic outcomes were predicted on the basis of the energetic impact provided by FoldX. Residues in exons 7–9 and in interdomain regions within the subunit appear to play an important structural role and constitute hotspots for destabilization. FoldX analysis will be useful for predicting the phenotype associated with rare or new mutations detected in patients with PKU. However, additional factors must be considered that may contribute to the patient phenotype, such as possible effects on catalysis and interindividual differences in physiological and metabolic processes

The FoldX web server: an online force field

FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at . The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed

SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs

Single nucleotide polymorphisms (SNPs) are an increasingly important tool for genetic and biomedical research. However, the accumulated sequence information on allelic variation is not matched by an understanding of the effect of SNPs on the functional attributes or ‘molecular phenotype’ of a protein. Towards this aim we developed SNPeffect, an online resource of human non-synonymous coding SNPs (nsSNPs) mapping phenotypic effects of allelic variation in human genes. SNPeffect contains 31 659 nsSNPs from 12 480 human proteins. The current release of SNPeffect incorporates data on protein stability, integrity of functional sites, protein phosphorylation and glycosylation, subcellular localization, protein turnover rates, protein aggregation, amyloidosis and chaperone interaction. The SNP entries are accessible through both a search and browse interface and are linked to most major biological databases. The data can be displayed as detailed descriptions of individual SNPs or as an overview of all SNPs for a given protein. SNPeffect will be regularly updated and can be accessed at http://snpeffect.vib.be/

Développement et caractérisation mécanique de membranes silicone architecturées

International audienceDes applications médicales nécessitent l'élaboration de membranes à anisotropie de comportement mécanique. La présente étude vise à proposer une solution à partir d'un seul matériau constitutif. Le principe repose sur la création de membranes architecturées en créant localement au niveau du Volume Elémentaire Représentatif des hétérogénéités de réticulation aux motifs contrôlés. Un matériau silicone est choisi pour la réalisation de ces membranes, à la fois pour sa facilité à le modifier chimiquement et ses propriétés élastomériques intrinsèques. Le degré de réticulation du silicone est maitrisé localement par irradiation UV d'un photo-inhibiteur avant vulcanisation : les zones irradiées réagissent moins en hydrosilylation, générant une phase plus élastique. Cette manipulation permet la création de membranes aux propriétés architecturées de par le contrôle local du degré de réticulation du réseau polymère

Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

info:eu-repo/semantics/publishe

Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production

From Springer Nature via Jisc Publications RouterHistory: received 2021-03-02, accepted 2021-07-29, registration 2021-08-20, pub-electronic 2021-09-06, online 2021-09-06, collection 2021-12Publication status: PublishedFunder: EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council); doi: https://doi.org/10.13039/100010663; Grant(s): pre-FAB 695013Abstract: Isobutene is a high value gaseous alkene used as fuel additive and a chemical building block. As an alternative to fossil fuel derived isobutene, we here develop a modified mevalonate pathway for the production of isobutene from glucose in vivo. The final step in the pathway consists of the decarboxylation of 3-methylcrotonic acid, catalysed by an evolved ferulic acid decarboxylase (Fdc) enzyme. Fdc belongs to the prFMN-dependent UbiD enzyme family that catalyses reversible decarboxylation of (hetero)aromatic acids or acrylic acids with extended conjugation. Following a screen of an Fdc library for inherent 3-methylcrotonic acid decarboxylase activity, directed evolution yields variants with up to an 80-fold increase in activity. Crystal structures of the evolved variants reveal that changes in the substrate binding pocket are responsible for increased selectivity. Solution and computational studies suggest that isobutene cycloelimination is rate limiting and strictly dependent on presence of the 3-methyl group

BriX: a database of protein building blocks for structural analysis, modeling and design

High-resolution structures of proteins remain the most valuable source for understanding their function in the cell and provide leads for drug design. Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches using small, recurrent protein fragments have been employed. Here we present two databases that provide a vast resource for implementing such fragment-based strategies. The BriX database contains fragments from over 7000 non-homologous proteins from the Astral collection, segmented in lengths from 4 to 14 residues and clustered according to structural similarity, summing up to a content of 2 million fragments per length. To overcome the lack of loops classified in BriX, we constructed the Loop BriX database of non-regular structure elements, clustered according to end-to-end distance between the regular residues flanking the loop. Both databases are available online (http://brix.crg.es) and can be accessed through a user-friendly web-interface. For high-throughput queries a web-based API is provided, as well as full database downloads. In addition, two exciting applications are provided as online services: (i) user-submitted structures can be covered on the fly with BriX classes, representing putative structural variation throughout the protein and (ii) gaps or low-confidence regions in these structures can be bridged with matching fragments