Synthetic biology: advancing biological frontiers by building synthetic systems

Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field

Timed Quorum System for Large-Scale and Dynamic Environments

This paper presents Timed Quorum System (TQS), a new quorum system especially suited for large-scale and dynamic systems. TQS requires that two quorums intersect with high probability if they are used in the same small period of time. It proposed an algorithm that implements TQS and that verifies probabilistic atomicity: a consistency criterion that requires each operation to respect atomicity with high probability. This TQS implementation has quorum of size O(\sqrt{nD}) and expected access time of O(log \sqrt{nD}) message delays, where n measures the size of the system and D is a required parameter to handle dynamism

Review on bibliography related to antimicrobials

In this report, a bibliographic research has been done in the field of antimicrobials.In this report, a bibliographic research has been done in the field of antimicrobials. Not all antimicrobials have been included, but those that are being subject of matter in the group GBMI in Terrassa, and others of interest. It includes chitosan and other biopolymers. The effect of nanoparticles is of great interest, and in this sense, the effect of Ag nanoparticles and antibiotic nanoparticles (nanobiotics) has been revised. The report focuses on new publications and the antimicrobial effect of peptides has been considered. In particular, the influence of antimicrobials on membranes has deserved much attention and its study using the Langmuir technique, which is of great utility on biomimetic studies. The building up of antimicrobials systems with new techniques (bottom-up approach), as the Layer-by-Layer technique, can also be found in between the bibliography. It has also been considered the antibiofilm effect, and the new ideas on quorem sensing and quorum quenching.Preprin

Ageing as a price of cooperation and complexity: Self-organization of complex systems causes the ageing of constituent networks

The analysis of network topology and dynamics is increasingly used for the description of the structure, function and evolution of complex systems. Here we summarize key aspects of the evolvability and robustness of the hierarchical network-set of macromolecules, cells, organisms, and ecosystems. Listing the costs and benefits of cooperation as a necessary behaviour to build this network hierarchy, we outline the major hypothesis of the paper: the emergence of hierarchical complexity needs cooperation leading to the ageing of the constituent networks. Local cooperation in a stable environment may lead to over-optimization developing an ‘always-old’ network, which ages slowly, and dies in an apoptosis-like process. Global cooperation by exploring a rapidly changing environment may cause an occasional over-perturbation exhausting system-resources, causing rapid degradation, ageing and death of an otherwise ‘forever-young’ network in a necrosis-like process. Giving a number of examples we explain how local and global cooperation can both evoke and help successful ageing. Finally, we show how various forms of cooperation and consequent ageing emerge as key elements in all major steps of evolution from the formation of protocells to the establishment of the globalized, modern human society. Thus, ageing emerges as a price of complexity, which is going hand-in-hand with cooperation enhancing each other in a successful community

Oral Biofilms: Development, Control, and Analysis

The oral cavity harbors hundreds of microbial species that are present either as planktonic cells or incorporated into biofilms. The majority of the oral microbes are commensal organisms. Those that are pathogenic microbes can result in oral infections, and at times can initiate systemic diseases. Biofilms that contain pathogens are challenging to control. Many conventional antimicrobials have proven to be ineffective. Recent advances in science and technology are providing new approaches for pathogen control and containment and methods to characterize biofilms. This perspective provides (1) a general understanding of biofilm development; (2) a description of emerging chemical and biological methods to control oral biofilms; and (3) an overview of high-throughput analytical approaches to analyze biofilms

Investigation of the regulation mechanisms for bioplastics production from industrial residues

Dissertação para obtenção do Grau de Mestre em BiotecnologiaThe current high demand for plastics has become unsustainable. Polyhydroxyalkanoates are biopolymers stored by bacteria that can potentially replace modern plastics due to: wide range of applications; biodegradability; use of renewable resources as feedstock. High costs of current Polyhydroxyalkanoates production can be reduced using mixed cultures of organisms. Activated sludge from wastewater treatment plants is selected for Polyhydroxyalkanoates production through the imposition of cycles of intermittent feeding. In this study, the acclimation of activated sludge using synthetic volatile fatty acids (VFAs) as substrate resulted in a culture rich in Paracoccus spp. and unidentified filamentous bacteria. Low cost substrates such as sugarcane molasses (SM) or cheese whey (CW) can be employed as feedstock for further cost reduction. This requires an additional step before the microbial selection to ferment the feedstock into VFAs. In this work, the feedstock was changed from SM to CW. The population fed with SM was rich in Actinomycetaceae, while the population fed with CW was rich in Streptococcaceae, affecting the VFA composition. Consequently, the PHA-storing population and the polymer were affected. In the fermented SM (fSM) phase, the population was rich in Azoarcus (41.5 - 64.6%) and in the fCW phase the population was more diverse. Changing the pH in the fermentation reactor also affected the selection stage with an increase in Thauera and Azoarcus and a decrease in Paracoccus. A significant unidentified population of one layer sheet- forming bacteria was observed. Lastly, the occurrence of cell-to-cell communication (QS) in the selection stage was investigated. Possibly, QS molecules were detected when the carbon source was depleted. All steps of polyhydroxyalkanoate production are interconnected and for optimization, all stages must be studied and improved. Moreover, if QS proves to be involved in polyhydroxyalkanoate storage, the addition of QS molecules to the process may be explored for further optimization

Aeration and hydrodynamics in submerged membrane bioreactors

Membrane bioreactor (MBR) is already a well-developed wastewater treatment process for both municipal and industrial applications. Nonetheless, membrane fouling remains a significant problem for its wider development. In the case of submerged membrane bioreactors (SMBRs), one of the most efficient strategies to limit fouling is the use of a gas/liquid two-phase flow to enhance the mass transfer. However, the effect of aeration still remains incompletely understood. The complexity of flows and of the nature of activated sludge makes a theoretical approach difficult. Aeration is the source of a large part of the operating costs in most industrial scale plants and its optimization is a necessity to make the process really efficient. This paper first deals with hydrodynamics in MBRs, then it reviews the parameters of aeration and their impact on filtration performance. Finally, the effects of aeration mechanisms on biological media are described