Analysis of 140 published GSMs and identification of the most common representation problems

The number of publications related to GSMs is increasing exponentially, but as most of these models are scattered across the Internet there is a need to centralize these data in a way that users can easily access and load them into stoichiometric modelling tools. This work presents a web platform to collect scientific work related with the reconstruction of GSMs, providing links to the original publications and the available models (www.optflux.org/models). The platform also indicates which models are compatible with OptFlux, an open-source reference computational platform for the optimization of cellular factories by the application of in silico ME methods, designed for non-computational experts by providing a user-friendly interface. The compatible models can be automatically loaded into OptFlux via a repository manager. This work also presents a thorough analysis on more than 140 published GSMs available in the platform. This analysis highlights some common problems in published models, such as the lack of standards to represent them. The SBML format has been adopted as the main standard by the community, despite some limitations in representing all the information required for modelling purposes. As consequence, this format has been extended ad-hoc by several authors, thus making its automatic interpretation a non-trivial problem. This analysis provides some insight into the limitations of formats used and the recurrent problems in the representation of GSMs

Development of novel genome-scale reconstruction strategies for production of terpenoids in Saccharomyces cerevisiae

info:eu-repo/semantics/publishedVersio

OptFlux3: an improved platform for in silico design of cellular factories

The rational design of cellular factories for industrial biotechnology aims to create optimized organisms for the production of bulk chemicals, pharmaceuticals, food ingredients and enzymes, among others. Metabolic engineering (ME) plays a key role in this process, supported by the latest advances in genetic engineering in combination with computational tools to define targets for strain improvement. OptFlux is an open-source reference computational platform for the optimization of cellular factories by the application of in silico ME methods, designed for non-computational experts by providing a user-friendly interface. It allows to load genome-scale models from several sources to be used in the prediction of cellular behavior and identification of metabolic targets for genetic engineering. Its latest version, OptFlux3, allows to perform the simulation of wild type and mutant strains (allowing the simulation of gene/ reaction deletion and over/under expression). Regarding strain optimization, the new architecture opts for a multi-objective framework, allowing users to easily add different goals as optimization targets in a flexible way. Specialized multi-objective algorithms, co-exist with traditional single objectives algorithms to be applied for each case. Also, OptFlux3 includes a new visualization framework for metabolic models and phenotype simulations and a new plug-in management interface that allows to install and remove plug-ins in execution time. Currently available plug-ins include the calculation and visualization of elementary modes, topological analysis and the ability to add reactions/ pathways to existing models. OptFlux is made freely available for all major operating systems, together with suitable documentation in www.optflux.org

Laparoscopic colorectal resection for a giant colonic diverticulum - video vignette

A giant colonic diverticulum (GCD) is a rare disease with less than 200 cases reported in the literature. By definition, a GCD is larger than 4cm in diameter with close sigmoid colon relationship in more than 90% of the cases. En bloc resection of the diverticulum with anterior sigmoid-rectal segment with primary anastomosis is the best treatment approach. The authors present a case of laparoscopic colorectal resection with partial cystectomy for a giant colonic diverticulum. A 62-years-old man with sigmoid colon diverticulosis and several episodes of diverticulitis presented at the office with a painless hypogastric/left iliac abdominal mass. CT scan showed a round 11 cm smooth walled structure filled with gas, adjacent to the sigmoid anti-mesenteric border and the urinary bladder. Four trocars were used for the laparoscopic approach. Step-by-step as follows: i. complete mobilization of colon splenic flexure. ii. Giant diverticulum dissection with partial bladder resection. iii. Bladder closure. iv. Sigmoid colon and intra-peritoneal rectum resection with primary anastomosis. The post-operative course was uneventful and the patient was discharged home on post-operative day 4. Vesical catheter was removed on post-operative day 10. Pathological specimen analysis confirmed the pre-operative diagnosis of a GCD. There is a consensus that this extremely rare diverticular disease complication should be approached with prompt standard resection due to high risk of diverticulum rupture. Laparoscopic approach seems to be feasible and safe despite of dissection higher complexity owing to the mega diverticulum. This article is protected by copyright. All rights reserved.info:eu-repo/semantics/publishedVersio

MIYeastK: The Metabolic Integrated Yeast Knowledgebase

The yeast Saccharomyces cerevisiae is one of the most widely used cell factories in industrial biotechnology. However, the development of optimized yeast strains for the production of novel compounds is a time-consuming process and represents a significant cost/time burden. Currently, genome-scale metabolic models play an important role to reduce cost and time in order to develop improved strains. Nevertheless, the existence of various genome-scale metabolic models for S. cerevisiae, with different metabolic information and predictability capabilities, increases the complexity of metabolic engineering studies. The MIYeastK is a web-accessible metabolic integrated knowledgebase (http://193.137.11.210/yeast/) that integrates the metabolic information of 10 genome-scale metabolic models of S. cerevisiae, not only between each other but also with external databases, such as KEGG and MetaCyc. An enhancement of the annotation of individual metabolites, reactions, genes and gene rules included in the models was also performed. Moreover, the gene information in the models is integrated with the myriad of information contained in SGD (Saccharomyces Genome Database) simplifying phenotype analysis. Hence, MIYeastK is valuable tool for users to compare and implement metabolic engineering strategies using yeast metabolic models

Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate

Background One of the European Union directives indicates that 10% of all fuels must be bio-synthesized by 2020. In this regard, biobutanolnatively produced by clostridial strainsposes as a promising alternative biofuel. One possible approach to overcome the difficulties of the industrial exploration of the native producers is the expression of more suitable pathways in robust microorganisms such as Escherichia coli. The enumeration of novel pathways is a powerful tool, allowing to identify non-obvious combinations of enzymes to produce a target compound. Results This work describes the in silico driven design of E. coli strains able to produce butanol via 2-oxoglutarate by a novel pathway. This butanol pathway was generated by a hypergraph algorithm and selected from an initial set of 105,954 different routes by successively applying different filters, such as stoichiometric feasibility, size and novelty. The implementation of this pathway involved seven catalytic steps and required the insertion of nine heterologous genes from various sources in E. coli distributed in three plasmids. Expressing butanol genes in E. coli K12 and cultivation in High-Density Medium formulation seem to favor butanol accumulation via the 2-oxoglutarate pathway. The maximum butanol titer obtained was 85±1 mg L1 by cultivating the cells in bioreactors. Conclusions In this work, we were able to successfully translate the computational analysis into in vivo applications, designing novel strains of E. coli able to produce n-butanol via an innovative pathway. Our results demonstrate that enumeration algorithms can broad the spectrum of butanol producing pathways. This validation encourages further research to other target compounds.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of a Ph.D. Grant (PD/BD/52366/2013) from MIT Portugal Program and the strategic funding of UID/BIO/04469 unit. Additional support was received by COMPETE 2020 (POCI-01-0145-FEDER-006684) and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020-Programa Operacional Regional do Norte. The authors also thank the Times New Roman project “Dynamics”, Ref. ERA-IB-2/0002/2014, funded by national funds through FCT/MCTES. The genes thl, hbd, crt and adhE1 were kindly provided by Kristala L. Jones Prather from MIT. The authors thank the project DDDeCaF - Bioinformatics Services for Data-Driven Design of Cell Factories and Communities, Ref. H2020-LEIT-BIO-2015-1 686070–1, funded by the European Commission and the Project LISBOA010145 FEDER007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020 Programa Operacional Competitividade e Internacionalização (POCI) and by national funds through FCT Fundacao para a Ciencia e a Tecnologiainfo:eu-repo/semantics/publishedVersio

Development of Automatic Systems for NDT Inspection of Wheels and Propeller Blades of Airplanes

Many maintenance operations in Aeronautic industry are based on the application of NDT techniques. Along with the demands for higher capability in accurately detect, localize and size the imperfections one key challenge for NDT technology is to cope with the high productivity demands.One solution to assure high reliability level and increase productivity is to automate many procedures which are still performed manually with validation of results typically pending on a certified NDT technician. The present paper addresses the design, implementation, calibration and validation of new automatized procedures for the quality inspection of aeronautic wheels, and aeronautic propeller blades

Novel manufacturing of multi-material component by hybrid friction stir channeling

The hybrid friction stir channeling (HC) is a recent manufacturing technique, reinforcing the broad range of solutions provided by the technological domain of solid-state friction stir-based welding and processing. HC enables the simultaneous welding of multiple components and the sub-surface channeling within the desired region at the stir zone. HC provides new demanding solutions having free path sub-surface channeling and welding for multi-material components with optimized physical and chemical performances. In the present investigation, a multi-material system consisting of 8 mm thick Al-Mg alloy (AA5083) and 3 mm thick oxygen free copper (Cu-OF) was processed by HC. A specially designed tool consists of the probe’s body features that steer materials extraction and the probe’s tip features that generate materials mixing was applied to produce sub-surface channel at AA5083, along with its simultaneous welding to Cu-OF material. Visual examination of the AA5083′s surface processed by the shoulder, cross-sectional dimensioning, optical 3D scanning of the internal surfaces of the channel, optical and scanning electron microscopy, energy dispersive X-ray spectroscopy, electron backscatter diffraction and micro-hardness measurements were applied to investigate the results. The successful application of HC to manufacture multi-material Al-Cu component is demonstrated. A large sub-surface quasi rectangular channel with 9.6 mm in width per 3.3 mm in height was produced in the AA5083 rib along with defect free welding to thin Cu-OF plate at just below the channel region multi-material. The resulted sub-surface channel was consisted of unique wall surface features, with non-uniform and non-oriented surface roughness, suitable to activate turbulent fluid flow. The microhardness field depicts a higher-strength domain of the stirred material, at the ceiling of the sub-surface channel in comparison with the base materials. The welding zone comprises a metal matrix composite structure with Al-Cu inter-mixing and a mechanical hooking from Cu into the Al matrix. The metallurgical features of the weld stirred zone were analyzed, with an interpretation of Al-Cu phases, and solid solution of Al and Cu in each other. In this zone, Cu-rich lamellae regions are dispersed within the Al-matrix, presenting thin layers of discontinuous intermetallic compounds. The effective potential of manufacturing multi-material component for applicability in thermal management system is demonstrated