HPC Cloud for Scientific and Business Applications: Taxonomy, Vision, and Research Challenges

High Performance Computing (HPC) clouds are becoming an alternative to on-premise clusters for executing scientific applications and business analytics services. Most research efforts in HPC cloud aim to understand the cost-benefit of moving resource-intensive applications from on-premise environments to public cloud platforms. Industry trends show hybrid environments are the natural path to get the best of the on-premise and cloud resources---steady (and sensitive) workloads can run on on-premise resources and peak demand can leverage remote resources in a pay-as-you-go manner. Nevertheless, there are plenty of questions to be answered in HPC cloud, which range from how to extract the best performance of an unknown underlying platform to what services are essential to make its usage easier. Moreover, the discussion on the right pricing and contractual models to fit small and large users is relevant for the sustainability of HPC clouds. This paper brings a survey and taxonomy of efforts in HPC cloud and a vision on what we believe is ahead of us, including a set of research challenges that, once tackled, can help advance businesses and scientific discoveries. This becomes particularly relevant due to the fast increasing wave of new HPC applications coming from big data and artificial intelligence.Comment: 29 pages, 5 figures, Published in ACM Computing Surveys (CSUR

Biosurfactants: production, applications and future potential

Book of Abstracts of CEB Annual Meeting 2017[Excerpt] Surfactants are one of the most important classes of industrial chemicals in terms of production volume. These compounds exhibit a wide variety of applications in several industries and are present in nearly every product and aspect of our daily life. They can be found in detergents, laundry formulations, household cleaning products, cosmetics, herbicides or pesticides, and are also used in bioremediation, agriculture, food, pharmaceutical, textile, paper or the petroleum industries, among others. Most conventional surfactants available nowadays are derived from non-renewable resources and their use may lead to significant ecological problems due to their toxicity and low biodegradability. In the recent years, an increase in environmental awareness has led to much more interest in the use of renewablebased, biodegradable and more environmentally friendly surfactants. Among them biosurfactants, surface-active compounds synthesized by microorganisms, are attracting a pronounced interest due to their potential advantages over their synthetic counterparts, and to the fact that they could replace some of the synthetics in many environmental and industrial applications. [...]info:eu-repo/semantics/publishedVersio

Development of low-cost culture media for effective biosurfactant production

In this work, biosurfactant production by Pseudomonas aeruginosa and Bacillus subtillis strains was optimized using low-cost substrates. The highest biosurfactant production (3.2 g/L) by the P. aeruginosa strain was obtained using a culture medium containing corn steep liquor (CSL) (10% (v/v)) and molasses (10% (w/v)), whereas the best biosurfactant production by the B. subtillis isolate (1.3 g/L) was obtained using a culture medium consisting of 10% (v/v) of CSL. Subsequently, for the B. subtillis strain, the effect of different metals (iron, manganese and magnesium) on biosurfactant production was evaluated. When the culture medium CSL 10% was supplemented with the optimum concentration of those metals simultaneously, the biosurfactant production was increased up to 4.8 g/L. The biosurfactant produced by the P. aeruginosa strain was characterized as a mixture of eight different rhamnolipid congeners, being the most abundant the mono-rhamnolipid Rha-C10-C10, and the biosurfactant produced by the B. subtillis isolate consisted of a mixture of C13-, C14- and C15-surfactin. Both biosurfactants exhibited a good performance in oil recovery assays when compared with chemical surfactants, suggesting their potential use as an alternative to traditional chemical surfactants in enhanced oil recovery or bioremediation

Sodium chloride effect on the aggregation behaviour of rhamnolipids and their antifungal activity

In this work, the antifungal activity of rhamnolipids produced by Pseudomonas aeruginosa #112 was evaluated against Aspergillus niger MUM 92.13 and Aspergillus carbonarius MUM 05.18. It was demonstrated that the di-rhamnolipid congeners were responsible for the antifungal activity exhibited by the crude rhamnolipid mixture, whereas mono-rhamnolipids showed a weak inhibitory activity. Furthermore, in the presence of NaCl (from 375 mM to 875 mM), the antifungal activity of the crude rhamnolipid mixture and the purified di-rhamnolipids was considerably increased. Dynamic Light Scattering studies showed that the size of the structures formed by the rhamnolipids increased as the NaCl concentration increased, being this effect more pronounced in the case of di-rhamnolipids. These results were confirmed by Confocal Scanning Laser Microscopy, which revealed the formation of giant vesicle-like structures (in the µm range) by self-assembling of the crude rhamnolipid mixture in the presence of 875 mM NaCl. In the case of the purified mono- and di-rhamnolipids, spherical structures (also in the µm range) were observed at the same conditions. The results herein obtained demonstrated a direct relationship between the rhamnolipids antifungal activity and their aggregation behaviour, opening the possibility to improve their biological activities for application in different fields.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit, COMPETE 2020 (POCI-01–0145-FEDER-006684) and the project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462). The authors also acknowledge financial support from BioTecNorte operation (NORTE-01-0145-FEDER-000004) and the project MultiBiorefinery (POCI-01-0145-FEDER-016403) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte. A. I. Rodrigues was supported by the doctoral Grant SFRH/111600/2015 provided by FCT. E. J. Gudiña was supported by the Post-Doctoral grant CEBBPD/01/2015/07 from the project UID/BIO/04469/2013, funded by FCT.info:eu-repo/semantics/publishedVersio

Improved biosurfactant production by a Pseudomonas aeruginosa strain using agro-industrial wastes

Microbial surfactants are amphipathic molecules produced by a variety of microorganisms that exhibit pronounced surface and emulsifying activities. Biosurfactants can replace synthetic surfactants in environmental and industrial applications, such as bioremediation and microbial enhanced oil recovery. Furthermore, some biosurfactants have been reported as suitable alternatives to synthetic medicines and antimicrobial agents and may be used as effective therapeutic agents, due to their antibacterial, antifungal, antiviral and anti-adhesive activities. The main advantages of biosurfactants when compared with synthetic surfactants include their diversity, specificity, environmentally friendly nature, non-toxicity and high biodegradability, effectiveness at extreme temperatures or pH values, as well as their suitability for scale-up production. Many of the potential applications that have been considered for biosurfactants depend on whether they can be produced economically at large-scale. Several efforts have been conducted to reduce production costs, including the use of agro-industrial wastes as substrates, optimization of medium and culture conditions and efficient recovery processes. In this work, biosurfactant production by a Pseudomonas aeruginosa strain isolated from a crude oil sample was optimized using agro-industrial wastes. A culture medium containing corn step liquor (10% v/v) and molasses (10% w/v) led to the production of 5 g biosurfactant/l, which is about ten times the amount of biosurfactant produced when using LB medium. The crude biosurfactant reduced the surface tension of water to 31 mN/m and exhibited high emulsifying activity (60%), with a critical micelle concentration of 200 mg/l. Moreover, it showed antimicrobial activity against a broad range of Gram-positive and Gram-negative bacteria, as well as a high efficiency in removing oil from contaminated sand, when compared with chemical surfactants. The results obtained suggest the possibility of using this biosurfactant as an alternative to traditional chemical surfactants

New microbial surface-active compounds: the ultimate alternative to chemical surfactants?

Surface active compounds (SACs) produced by microorganisms are attracting a pronounced interest due to their potential advantages over synthetic counterparts, and to the fact that they could replace some of the synthetics in many environmental and industrial applications. Bioemulsifier production by a Paenibacillus strain isolated from crude oil was studied. The bioemulsifier was produced using sucrose with and without adding hydrocarbons (paraffin or crude oil) under aerobic and anaerobic conditions at 40ºC. It formed stable emulsions with several hydrocarbons, exhibiting similar or better emulsifying activity when compared with chemical SACs, and its emulsifying ability was not affected by exposure to high salinities (up to 300 g/l), high temperatures (100-121ºC) or a wide range of pH values (2-13). In addition, it presented low toxicity and high biodegradability when compared with chemical surfactants, implying a greater environmental compatibility. A preliminary chemical characterization by Fourier Transform Infrared Spectroscopy (FT-IR), proton and carbon nuclear magnetic resonance (1H NMR and 13C CP-MAS NMR) and size exclusion chromatography indicated that the bioemulsifier is a low molecular weight oligosaccharide-lipid complex. To the best of our knowledge, bioemulsifier production by a Paenibacillus strain has not been previously reported. This is also the first description of a low molecular weight bioemulsifier. The features of this novel bioemulsifier make it an interesting biotechnological product for many environmental and industrial applications.Financial support from the projects BIOCLEAN-Desenvolvimento de produtos contendo surfactantes microbianos para limpeza e desinfeção de superfícies industriais e domésticas. QREN-n.º 2013/030215, and NCMICROBIOS -Desenvolvimento de bioprocessos usando microrganismos não convencionais para a produção de biosurfactantes - Convénio FCT-CNPq Nº 17/2013 – Ref.: Projecto nº 6818

Produção de lipase a partir de leveduras não convencionais isoladas do bagaço de caju

As lipases (E.C. 3.1.1.3) são uma classe de enzimas que catalisam a hidrólise dos triglicerídeos de ácidos gordos livres e glicerol. Essas enzimas encontram uma grande aplicação nas indústrias de alimentos, detergentes, cosméticos, síntese orgânica e farmacêutica. Neste trabalho, as leveduras Candida tropicalis e Meyerozyma caribbica isoladas do bagaço de caju foram testadas quanto à sua capacidade de produção de lipase. As fermentações foram conduzidas em agitador rotatório a 30 °C e 170 rpm. A medida da atividade foi feita através da hidrólise com o pNFL (p-nitrofenil laurato). Para a produção da enzima foi utilizado um meio de cultura contendo resíduos agroindustriais, nomeadamente melaço 10 g/L, milhocina 4 g/L, águas russas 1,0 % (v/v). A atividade do sobrenadante da C. tropicalis foi 233 ± 10 U/L e da M. caribbica foi 146 ± 7,30 U/L em 24 h de fermentação. Esses resultados mostram o potencial dessas estirpes para a produção da enzima lipase a partir de resíduos agroalimentares

Isolation of microorganisms from oil samples for application in microbial enhanced oil recovery

Este resumo faz parte de: Book of abstracts of the Meeting of the Institute for Biotechnology and Bioengineering, 2, Braga, Portugal, 2010. A versão completa do livro de atas está disponível em: http://hdl.handle.net/1822/1096

Biosurfactant-producing Bacillus subtilis strains isolated from crude oil samples enhance oil recovery at lab scale

Biosurfactant-producing Bacillus subtilis strains isolated from crude oil samples enhance oil recovery at lab scale Eduardo J Gudiña, Lígia R. Rodrigues, José A. Teixeira IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal Microbial Enhanced Oil Recovery (MEOR) is potentially useful to increment oil recovery from reservoirs beyond primary and secondary recovery operations using microorganisms and their metabolites. Stimulation of bacterial growth and biosurfactant production by indigenous microorganisms can reduce the capillary forces that retain the oil into the reservoir. MEOR offers major advantages over conventional EOR, namely low amounts of energy consumption and independence of the price of crude oil [1]. In this work, a sand pack column model was designed to simulate the oil recovery operations in oil reservoirs and evaluate the mobilization of residual oil. Three Bacillus subtilis strains, previously isolated from crude oil samples [2], were used. Those strains grow and produce extracellular biosurfactants at 40ºC under anaerobic conditions in medium supplemented with hydrocarbons. Biosurfactants produced reduce the surface tension of water from 72 to 30 mN/m, exhibit emulsifying activity and are not affected by exposure to high temperatures (121ºC) which makes them good candidates for application in biosurfactant mediated MEOR. Sand pack column assays were performed using paraffin and crude oil. Additional oil recovery using paraffin ranged from 19 to 35% with the different isolates. When crude oil was used as hydrocarbon, the isolates recovered between 19 and 21% of the entrapped oil. The results obtained suggest that stimulation of biosurfactant production by these strains in situ can contribute to mobilize entrapped oil and improve the oil fluidity. [1] Sen R, “Biotechnology in petroleum recovery: The microbial EOR”, Progress in Energy and Combustion Science (2008) 34: 714-724. [2] Gudiña EJ, Pereira JFB, Rodrigues LR, Coutinho JAP, Teixeira JA, “Isolation and study of microorganisms from oil samples for application in Microbial Enhanced Oil Recovery”, International Biodeterioration and Biodegradation (2012) 68: 56-64