Protein secretion in Lactococcus lactis : an efficient way to increase the overall heterologous protein production

Anderson MIYOSHI, Daniela FREITAS, Luciana RIBEIRO, Jane E. GABRIEL, Sophie LECLERCQ, Maricê N. OLIVEIRA, and Valeria D. GUIMARÃES were recipients of a CAPES fellowship (project CAPESCOFECUB #319II). Luis BERMUDEZ and Sébastien NOUAILLE were recipients of a fellowship from the French Ministry of Education and Research. INRA and Région IledeFrance also financed L. BERMUDEZ and V. GUIMARAES. Cathy CHARLIER is recipient of a fellowship from INRA and Région Bretagne.

Transient transfection of serum-free suspension HEK 293 cell culture for efficient production of human rFVIII

Abstract Background Hemophilia A is a bleeding disorder caused by deficiency in coagulation factor VIII. Recombinant factor VIII (rFVIII) is an alternative to plasma-derived FVIII for the treatment of hemophilia A. However, commercial manufacturing of rFVIII products is inefficient and costly and is associated to high prices and product shortage, even in economically privileged countries. This situation may be solved by adopting more efficient production methods. Here, we evaluated the potential of transient transfection in producing rFVIII in serum-free suspension HEK 293 cell cultures and investigated the effects of different DNA concentration (0.4, 0.6 and 0.8 μg/106 cells) and repeated transfections done at 34° and 37°C. Results We observed a decrease in cell growth when high DNA concentrations were used, but no significant differences in transfection efficiency and in the biological activity of the rFVIII were noticed. The best condition for rFVIII production was obtained with repeated transfections at 34°C using 0.4 μg DNA/106 cells through which almost 50 IU of active rFVIII was produced six days post-transfection. Conclusion Serum-free suspension transient transfection is thus a viable option for high-yield-rFVIII production. Work is in progress to further optimize the process and validate its scalability.

Physico-chemical, spectroscopical and thermal characterization of biodiesel obtained by enzymatic route as a tool to select the most efficient immobilized lipase

Two microbial lipases from Burkholderia cepacia and Pseudomonas fluorescens were evaluated as catalysts for the enzymatic transesterification of beef tallow with ethanol and the most efficient lipase source was selected by taking into account the properties of the product to be used as fuel. Both lipases were immobilized on an epoxy silica-polyvinyl alcohol composite by covalent immobilization and used to perform the reactions under the following operational conditions: beef tallow-to-ethanol molar ratio of 1:9, 45ºC and 400 units of enzymatic activity per gram of fat. Products, characterized using Fourier Transform Infrared spectroscopy (FTIR), viscosimetry, thermogravimetry and ¹H NMR spectroscopy, suggested that the biodiesel sample obtained in the reaction catalyzed by Burkholderia cepacia lipase has the best set of properties for fuel usage.

A contribution for developing more efficient dynamic modelling algorithms of parallel robots

Parallel kinematic structures are considered very adequate architectures for positioning and orienti ng the tools of robotic mechanisms. However, developing dynamic models for this kind of systems is sometimes a difficult task. In fact, the direct application of traditional methods of robotics, for modelling and analysing such systems, usually does not lead to efficient and systematic algorithms. This work addre sses this issue: to present a modular approach to generate the dynamic model and through some convenient modifications, how we can make these methods more applicable to parallel structures as well. Kane’s formulati on to obtain the dynamic equations is shown to be one of the easiest ways to deal with redundant coordinates and kinematic constraints, so that a suitable c hoice of a set of coordinates allows the remaining of the modelling procedure to be computer aided. The advantages of this approach are discussed in the modelling of a 3-dof parallel asymmetric mechanisms.

Applying many-body expansion aiming to make ab in initio molecular dynamics more efficient

In this present work we present a methodology that aims to apply the many-body expansion to decrease the computational cost of ab initio molecular dynamics, keeping acceptable accuracy on the results. We implemented this methodology in a program which we called ManBo. In the many-body expansion approach, we partitioned the total energy E of the system in contributions of one body, two bodies, three bodies, etc., until the contribution of the Nth body [1-3]: E = E1 + E2 + E3 + …EN. The E1 term is the sum of the internal energy of the molecules; the term E2 is the energy due to interaction between all pairs of molecules; E3 is the energy due to interaction between all trios of molecules; and so on. In Manbo we chose to truncate the expansion in the contribution of two or three bodies, both for the calculation of the energy and for the calculation of the atomic forces. In order to partially include the many-body interactions neglected when we truncate the expansion, we can include an electrostatic embedding in the electronic structure calculations, instead of considering the monomers, pairs and trios as isolated molecules in space. In simulations we made we chose to simulate water molecules, and use the Gaussian 09 as external program to calculate the atomic forces and energy of the system, as well as reference program for analyzing the accuracy of the results obtained with the ManBo. The results show that the use of the many-body expansion seems to be an interesting approach for reducing the still prohibitive computational cost of ab initio molecular dynamics. The errors introduced on atomic forces in applying such methodology are very small. The inclusion of an embedding electrostatic seems to be a good solution for improving the results with only a small increase in simulation time. As we increase the level of calculation, the simulation time of ManBo tends to largely decrease in relation to a conventional BOMD simulation of Gaussian, due to better scalability of the methodology presented. References [1] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 3, 46 (2007). [2] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 4, 1 (2008). [3] R. Rivelino, P. Chaudhuri and S. Canuto; J. Chem. Phys., 118, 10593 (2003).

CID: an efficient complexity-invariant distance for time series

The ubiquity of time series data across almost all human endeavors has produced a great interest in time series data mining in the last decade. While dozens of classification algorithms have been applied to time series, recent empirical evidence strongly suggests that simple nearest neighbor classification is exceptionally difficult to beat. The choice of distance measure used by the nearest neighbor algorithm is important, and depends on the invariances required by the domain. For example, motion capture data typically requires invariance to warping, and cardiology data requires invariance to the baseline (the mean value). Similarly, recent work suggests that for time series clustering, the choice of clustering algorithm is much less important than the choice of distance measure used.In this work we make a somewhat surprising claim. There is an invariance that the community seems to have missed, complexity invariance. Intuitively, the problem is that in many domains the different classes may have different complexities, and pairs of complex objects, even those which subjectively may seem very similar to the human eye, tend to be further apart under current distance measures than pairs of simple objects. This fact introduces errors in nearest neighbor classification, where some complex objects may be incorrectly assigned to a simpler class. Similarly, for clustering this effect can introduce errors by “suggesting” to the clustering algorithm that subjectively similar, but complex objects belong in a sparser and larger diameter cluster than is truly warranted.We introduce the first complexity-invariant distance measure for time series, and show that it generally produces significant improvements in classification and clustering accuracy. We further show that this improvement does not compromise efficiency, since we can lower bound the measure and use a modification of triangular inequality, thus making use of most existing indexing and data mining algorithms. We evaluate our ideas with the largest and most comprehensive set of time series mining experiments ever attempted in a single work, and show that complexity-invariant distance measures can produce improvements in classification and clustering in the vast majority of cases.

Efficient 1535 nm light emission from an all-Si-based optical micro-cavity containing Er3+ and Yb3+ ions

This work reports on the construction and spectroscopic analyses of optical micro-cavities (OMCs) that efficiently emit at ~1535 nm. The emission wavelength matches the third transmission window of commercial optical fibers and the OMCs were entirely based on silicon. The sputtering deposition method was adopted in the preparation of the OMCs, which comprised two Bragg reflectors and one spacer layer made of either Er- or ErYb-doped amorphous silicon nitride. The luminescence signal extracted from the OMCs originated from the 4I13/2→4I15/2 transition (due to Er3+ ions) and its intensity showed to be highly dependent on the presence of Yb3+ ions.According to the results, the Er3+-related light emission was improved by a factor of 48 when combined with Yb3+ ions and inserted in the spacer layer of the OMC. The results also showed the effectiveness of the present experimental approach in producing Si-based light-emitting structures in which the main characteristics are: (a) compatibility with the actual microelectronics industry, (b) the deposition of optical quality layers with accurate composition control, and (c) no need of uncommon elements-compounds nor extensive thermal treatments. Along with the fundamental characteristics of the OMCs, this work also discusses the impact of the Er3+-Yb3+ ion interaction on the emission intensity as well as the potential of the present findings.

"Water users must be efficient producers". Women's access to and use of land in Chókwè irrigation scheme, Mozambique

The irrigation scheme Eduardo Mondlane, situated in Chókwè District - in the Southern part of the Gaza province and within the Limpopo River Basin - is the largest in the country, covering approximately 30,000 hectares of land. Built by the Portuguese colonial administration in the 1950s to exploit the agricultural potential of the area through cash-cropping, after Independence it became one of Frelimo’s flagship projects aiming at the “socialization of the countryside” and at agricultural economic development through the creation of a state farm and of several cooperatives. The failure of Frelimo’s economic reforms, several infrastructural constraints and local farmers resistance to collective forms of production led to scheme to a state of severe degradation aggravated by the floods of the year 2000. A project of technical rehabilitation initiated after the floods is currently accompanied by a strong “efficiency” discourse from the managing institution that strongly opposes the use of irrigated land for subsistence agriculture, historically a major livelihood strategy for smallfarmers, particularly for women. In fact, the area has been characterized, since the end of the XIX century, by a stable pattern of male migration towards South African mines, that has resulted in an a steady increase of women-headed households (both de jure and de facto). The relationship between land reform, agricultural development, poverty alleviation and gender equality in Southern Africa is long debated in academic literature. Within this debate, the role of agricultural activities in irrigation schemes is particularly interesting considering that, in a drought-prone area, having access to water for irrigation means increased possibilities of improving food and livelihood security, and income levels. In the case of Chókwè, local governments institutions are endorsing the development of commercial agriculture through initiatives such as partnerships with international cooperation agencies or joint-ventures with private investors. While these business models can sometimes lead to positive outcomes in terms of poverty alleviation, it is important to recognize that decentralization and neoliberal reforms occur in the context of financial and political crisis of the State that lacks the resources to efficiently manage infrastructures such as irrigation systems. This kind of institutional and economic reforms risk accelerating processes of social and economic marginalisation, including landlessness, in particular for poor rural women that mainly use irrigated land for subsistence production. The study combines an analysis of the historical and geographical context with the study of relevant literature and original fieldwork. Fieldwork was conducted between February and June 2007 (where I mainly collected secondary data, maps and statistics and conducted preliminary visit to Chókwè) and from October 2007 to March 2008. Fieldwork methodology was qualitative and used semi-structured interviews with central and local Government officials, technical experts of the irrigation scheme, civil society organisations, international NGOs, rural extensionists, and water users from the irrigation scheme, in particular those women smallfarmers members of local farmers’ associations. Thanks to the collaboration with the Union of Farmers’ Associations of Chókwè, she has been able to participate to members’ meeting, to education and training activities addressed to women farmers members of the Union and to organize a group discussion. In Chókwè irrigation scheme, women account for the 32% of water users of the familiar sector (comprising plot-holders with less than 5 hectares of land) and for just 5% of the private sector. If one considers farmers’ associations of the familiar sector (a legacy of Frelimo’s cooperatives), women are 84% of total members. However, the security given to them by the land title that they have acquired through occupation is severely endangered by the use that they make of land, that is considered as “non efficient” by the irrigation scheme authority. Due to a reduced access to marketing possibilities and to inputs, training, information and credit women, in actual fact, risk to see their right to access land and water revoked because they are not able to sustain the increasing cost of the water fee. The myth of the “efficient producer” does not take into consideration the characteristics of inequality and gender discrimination of the neo-liberal market. Expecting small-farmers, and in particular women, to be able to compete in the globalized agricultural market seems unrealistic, and can perpetuate unequal gendered access to resources such as land and water.

Efficient ultrasonic signal processing techniques for aided medical diagnostics

Ultrasound imaging is widely used in medical diagnostics as it is the fastest, least invasive, and least expensive imaging modality. However, ultrasound images are intrinsically difficult to be interpreted. In this scenario, Computer Aided Detection (CAD) systems can be used to support physicians during diagnosis providing them a second opinion. This thesis discusses efficient ultrasound processing techniques for computer aided medical diagnostics, focusing on two major topics: (i) Ultrasound Tissue Characterization (UTC), aimed at characterizing and differentiating between healthy and diseased tissue; (ii) Ultrasound Image Segmentation (UIS), aimed at detecting the boundaries of anatomical structures to automatically measure organ dimensions and compute clinically relevant functional indices. Research on UTC produced a CAD tool for Prostate Cancer detection to improve the biopsy protocol. In particular, this thesis contributes with: (i) the development of a robust classification system; (ii) the exploitation of parallel computing on GPU for real-time performance; (iii) the introduction of both an innovative Semi-Supervised Learning algorithm and a novel supervised/semi-supervised learning scheme for CAD system training that improve system performance reducing data collection effort and avoiding collected data wasting. The tool provides physicians a risk map highlighting suspect tissue areas, allowing them to perform a lesion-directed biopsy. Clinical validation demonstrated the system validity as a diagnostic support tool and its effectiveness at reducing the number of biopsy cores requested for an accurate diagnosis. For UIS the research developed a heart disease diagnostic tool based on Real-Time 3D Echocardiography. Thesis contributions to this application are: (i) the development of an automated GPU based level-set segmentation framework for 3D images; (ii) the application of this framework to the myocardium segmentation. Experimental results showed the high efficiency and flexibility of the proposed framework. Its effectiveness as a tool for quantitative analysis of 3D cardiac morphology and function was demonstrated through clinical validation.

Caratteristiche micromeccaniche di giunzioni friction welding

Studio della caratterizzazione micromeccanica di provini in alluminio 6082 T6 saldati con la tecnica della rotary friction welding, tecnica innovativa nell’ambito delle tecnologie di giunzione solida, che sfrutta il principio della saldatura per attrito. Dopo un'introduzione teorica sulle principali tematiche affrontate e sui principali sistemi di misura usati, verranno effettuate micrografie dei giunti e prove di microdurezza sugli stessi. Si termina riportando i grafici delle microdurezze trovate, in modo da poter confrontare i risultati ottenuti con le caratteristiche del materiale base. Da questi si osserva che: nonostante la qualità accettabile dei giunti, le elevate temperature raggiunte durante la saldatura hanno alterato il trattamento termico del materiale base, che da T6 assume caratteristiche più simili a un T4. In altre parole il materiale saldato presenta caratteristiche micromeccaniche inferiori a quelle nominalmente assegnabili al materiale base.

Analisi di microdurezza su giunti friction welding

Il presente lavoro di tesi si pone come obiettivo la caratterizzazione microstrutturale di una serie di giunti realizzati tramite un innovativo processo di saldatura allo stato solido denominato Rotary Friction Welding. In tale ricerca si descrive il percorso seguito per arrivare a tale caratterizzazione partendo da una discussione delle principali tecniche di saldatura, in particolare quelle per attrito, per passare poi ad un’analisi dettagliata della fase di creazione dei giunti saldati e della successiva fase dedicata alla verifica microstrutturale. I risultati ottenuti, ci forniranno indici di confronto sulla qualità del materiale, sui processi tecnologici, sui trattamenti e su alcune fondamentali proprietà meccaniche

Efficient calculation of gluon amplitudes with n legs and an implementation of parton showers using the dipole formalism

The conventional way to calculate hard scattering processes in perturbation theory using Feynman diagrams is not efficient enough to calculate all necessary processes - for example for the Large Hadron Collider - to a sufficient precision. Two alternatives to order-by-order calculations are studied in this thesis.rnrnIn the first part we compare the numerical implementations of four different recursive methods for the efficient computation of Born gluon amplitudes: Berends-Giele recurrence relations and recursive calculations with scalar diagrams, with maximal helicity violating vertices and with shifted momenta. From the four methods considered, the Berends-Giele method performs best, if the number of external partons is eight or bigger. However, for less than eight external partons, the recursion relation with shifted momenta offers the best performance. When investigating the numerical stability and accuracy, we found that all methods give satisfactory results.rnrnIn the second part of this thesis we present an implementation of a parton shower algorithm based on the dipole formalism. The formalism treats initial- and final-state partons on the same footing. The shower algorithm can be used for hadron colliders and electron-positron colliders. Also massive partons in the final state were included in the shower algorithm. Finally, we studied numerical results for an electron-positron collider, the Tevatron and the Large Hadron Collider.

Simulazione FEM e validazione sperimentale del processo di friction welding

Nel seguente elaborato si propone lo sviluppo di un modello agli elementi finiti (FEM) del processo di friction welding del quale, attraverso i dati rilevati da prove sperimentali di validazione termica, vengono valutati i parametri ottimali di simulazione. Ai risultati così ottenuti vengono applicati anche algoritmi per la valutazione della microstruttura e della qualità della saldatura, sviluppati originariamente per l'analisi dell'estrusione: in entrambi i casi a seguito del confronto con le analisi metallografiche dei provini è stato possibile validare ulteriormente il modello creato.