Towards cloud-based parallel metaheuristics: A case study in computational biology with Differential Evolution and Spark

[Abstract] Many key problems in science and engineering can be formulated and solved using global optimization techniques. In the particular case of computational biology, the development of dynamic (kinetic) models is one of the current key issues. In this context, the problem of parameter estimation (model calibration) remains as a very challenging task. The complexity of the underlying models requires the use of efficient solvers to achieve adequate results in reasonable computation times. Metaheuristics have been the focus of great consideration as an efficient way of solving hard global optimization problems. Even so, in most realistic applications, metaheuristics require a very large computation time to obtain an acceptable result. Therefore, several parallel schemes have been proposed, most of them focused on traditional parallel programming interfaces and infrastructures. However, with the emergence of cloud computing, new programming models have been proposed to deal with large-scale data processing on clouds. In this paper we explore the applicability of these new models for global optimization problems using as a case study a set of challenging parameter estimation problems in systems biology. We have developed, using Spark, an island-based parallel version of Differential Evolution. Differential Evolution is a simple population-based metaheuristic that, at the same time, is very popular for being very efficient in real function global optimization. Several experiments were conducted both on a cluster and on the Microsoft Azure public cloud to evaluate the speedup and efficiency of the proposal, concluding that the Spark implementation achieves not only competitive speedup against the serial implementation, but also good scalability when the number of nodes grows. The results can be useful for those interested in using parallel metaheuristics for global optimization problems benefiting from the potential of new cloud programming models.Ministerio de Economía y Competitividad and FEDER; through the Project SYNBIOFACTORY; DPI2014-55276-C5-2-RMinisterio de Economía y Competitividad and FEDER; TIN2013-42148-PMinisterio de Economía y Competitividad and FEDER; TIN2016-75845-PXunta de Galicia; R2014/04

Using the Cloud for Parameter Estimation Problems: Comparing Spark vs MPI with a Case-Study

Date of Conference: 14-17 May 2017. Conference Location: Madrid[Abstract] Systems biology is an emerging approach focused in generating new knowledge about complex biological systems by combining experimental data with mathematical modeling and advanced computational techniques. Many problems in this field are extremely challenging and require substantial supercomputing resources to be solved. This is the case of parameter estimation in large-scale nonlinear dynamic systems biology models. Recently, Cloud Computing has emerged as a new paradigm for on-demand delivery of computing resources. However, scientific computing community has been quite hesitant in using the Cloud, simply because traditional programming models do not fit well with the new paradigm, and the earliest cloud programming models do not allow most scientific computations being efficiently run in the Cloud. In this paper we explore and compare two distributed computing models: the MPI (message-passing interface) model, that is high-performance oriented, and the Spark model, which is throughput oriented but outperforms other cloud programming solutions adding improved support for iterative algorithms through in-memory computing. The performance of a very well known metaheuristic, the Differential Evolution algorithm, has been thoroughly assessed using a challenging parameter estimation problem from the domain of computational systems biology. The experiments have been carried out both in a local cluster and in the Microsoft Azure public cloud, allowing performance and cost evaluation for both infrastructures.Gobierno de España; DPI2014-55276-C5-2-RFondos Feder; TIN2016-75845-PXunta de Galicia; R2016/045Xunta de Galicia; GRC2013/05

Microbial inoculum development for ameliorating crop drought stress:A case study of Variovorax paradoxus 5C-2

Drought affects plant hormonal homeostasis, including root to shoot signalling. The plant is intimately connected below-ground with soil-dwelling microbes, including plant growth promoting rhizobacteria (PGPR) that can modulate plant hormonal homeostasis. Incorporating PGPR into the rhizosphere often delivers favourable results in greenhouse experiments, while field applications are much less predictable. We review the natural processes that affect the formation and dynamics of the rhizosphere, establishing a model for successful field application of PGPR utilizing an example microbial inoculum, Variovorax paradoxus 5C-2

Aplicación de Proteómica a la búsqueda de nuevos mecanismos tumorales en cáncer de tiroides

Comunicaciones a congreso

Administration of chitosan-tripolyphosphate-DNA nanoparticles to knockdown glutamate dehydrogenase expression impairs transdeamination and gluconeogenesis in the liver

Glutamate dehydrogenase (GDH) plays a major role in amino acid catabolism. To increase the current knowledge of GDH function, we analysed the effect of GDH silencing on liver intermediary metabolism from gilthead sea bream (Sparus aurata). Sequencing of GDH cDNA from S. aurata revealed high homology with its vertebrate orthologues and allowed us to design short hairpin RNAs (shRNAs) to knockdown GDH expression. Following validation of shRNA-dependent downregulation of S. aurata GDH in vitro, chitosan-tripolyphosphate (TPP) nanoparticles complexed with a plasmid encoding a selected shRNA (pCpG-sh2GDH) were produced to address the effect of GDH silencing on S. aurata liver metabolism. Seventy-two hours following intraperitoneal administration of chitosan-TPP-pCpG-sh2GDH, GDH mRNA levels and immunodetectable protein decreased in the liver, leading to reduced GDH activity in both oxidative and reductive reactions to about 53-55 % of control values. GDH silencing decreased glutamate, glutamine and aspartate aminotransferase activity, while increased 2-oxoglutarate content, 2-oxoglutarate dehydrogenase activity and 6-phosphofructo-1-kinase/fructose-1,6-bisphosphatase activity ratio. Our findings show for the first time that GDH silencing reduces transdeamination and gluconeogenesis in the liver, hindering the use of amino acids as gluconeogenic substrates and enabling protein sparing and metabolisation of dietary carbohydrates, which would reduce environmental impact and production costs of aquaculture

Are Farm-Reared Quails for Game Restocking Really Common Quails (Coturnix coturnix)?: A Genetic Approach

The common quail (Coturnix coturnix) is a popular game species for which restocking with farm-reared individuals is a common practice. In some areas, the number of released quails greatly surpasses the number of wild breeding common quail. However, common quail are difficult to raise in captivity and this casts suspicion about a possible hybrid origin of the farmed individuals from crosses with domestic Japanese quail (C. japonica). In this study we used a panel of autosomal microsatellite markers to characterize the genetic origin of quails reared for hunting purposes in game farms in Spain and of quails from an experimental game farm which was founded with hybrids that have been systematically backcrossed with wild common quails. The genotypes of these quail were compared to those of wild common quail and domestic strains of Japanese quail. Our results show that more than 85% of the game farm birds were not common quail but had domestic Japanese quail ancestry. In the experimental farm a larger proportion of individuals could not be clearly separated from pure common quails. We conclude that the majority of quail sold for restocking purposes were not common quail. Genetic monitoring of individuals raised for restocking is indispensable as the massive release of farm-reared hybrids could represent a severe threat for the long term survival of the native species

LAT-1 and GLUT-1 Carrier Expression and Its Prognostic Value in Gastroenteropancreatic Neuroendocrine Tumors

Cancer cells develop mechanisms that increase nutrient uptake, including key nutrient carriers, such as amino acid transporter 1 (LAT-1) and glucose transporter 1 (GLUT-1), regulated by the oxygen-sensing Von Hippel Lindau-hypoxia-inducible factor (VHL-HIF) transcriptional pathway. We aimed to analyze these metabolic players in gastroenteropancreatic neuroendocrine tumors (GEP-NET) and correlate them with tumor malignancy and progression. LAT-1, GLUT-1, and pVHL expression was analyzed in 116 GEP-NETs and 48 peritumoral tissue samples by immunohistochemistry. LAT-1 was stably silenced using specific shRNA in the human NET BON cell line. LAT-1 expression was significantly increased in tumor tissue compared to non-tumor tissue in both gastrointestinal (67% vs. 44%) and pancreatic NETs (54% vs. 31%). Similarly, GLUT-1 was substantially elevated in gastrointestinal (74% vs. 19%) and pancreatic (58% vs. 4%) NETs. In contrast, pVHL expression was decreased (85% vs. 58%) in pancreatic NETs. Tumors with metastases at diagnosis displayed increased LAT-1 and GLUT-1 and decreased pVHL expression (p < 0.001). In accordance with these data, silencing LAT-1 curtailed cell proliferation in BON cells. These findings suggest that specific mechanisms that increase nutrient uptake, such as LAT-1 and GLUT-1, are increased in GEP-NETs, whereas pVHL is decreased. These markers might be related to the proliferation and metastatic capacity of these tumors

BR-BCSC Signature: The Cancer Stem Cell Profile Enriched in Brain Metastases that Predicts a Worse Prognosis in Lymph Node-Positive Breast Cancer

Brain metastases remain an unmet clinical need in breast oncology, being frequently found in HER2-overexpressing and triple-negative carcinomas. These tumors were reported to be highly cancer stem-like cell-enriched, suggesting that brain metastases probably arise by the seeding of cancer cells with stem features. Accordingly, we found that brain-tropic breast cancer cells show increased stem cell activity and tumorigenic capacity in the chick embryo choriallantoic membrane when compared to the parental cell line. These observations were supported by a significant increase in their stem cell frequency and by the enrichment for the breast cancer stem cell (BCSC) phenotype CD44+CD24-/low. Based on this data, the expression of BCSC markers (CD44, CD49f, P-cadherin, EpCAM, and ALDH1) was determined and found to be significantly enriched in breast cancer brain metastases when compared to primary tumors. Therefore, a brain (BR)-BCSC signature was defined (3-5 BCSC markers), which showed to be associated with decreased brain metastases-free and overall survival. Interestingly, this signature significantly predicted a worse prognosis in lymph node-positive patients, acting as an independent prognostic factor. Thus, an enrichment of a BCSC signature was found in brain metastases, which can be used as a new prognostic factor in clinically challenging breast cancer patients.This work was funded by FEDER (Fundo Europeu de Desenvolvimento Regional) funds through the COMPETE 2020 Operacional Programme for Competitiveness and Internationalisation (POCI), Portugal 2020, and by FCT (Fundação para a Ciência e a Tecnologia) Ministério da Ciência, Tecnologia e Ensino Superior under the projects Pest-C/SAU/LA0003/2013, NORTE-01-0145-FEDER-000029, SAICTPAC/0022/2015 POCI—01-0145-FEDER-016390, and FCT/02/SAICT/2017/030625. A Novartis Oncology grant also funded part of the work, namely, the characterization of the Portuguese series of human brain metastases. FCT funded the research grant of R.C. (SFRH/BD/135831/2018). IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT in the framework of the project “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274)

Chitosan-mediated shRNA knockdown of cytosolic alanine aminotransferase improves hepatic carbohydrate metabolism

Alanine aminotransferase (ALT) catalyses a transamination reaction that links carbohydrate and amino acid metabolism. In this study, we examined the effect of silencing cytosolic ALT (cALT) expression on the hepatic metabolism in Sparus aurata. A number of siRNA and shRNA designed to down-regulate cALT expression were validated in HEK-293 cells transfected with plasmids expressing S. aurata cALT or mitochondrial ALT (mALT) isoforms: ALT silencing significantly decreased the expression levels of S. aurata mRNA cALT1 to 62 % (siRNA) and 48 % (shRNA) of the values observed in control cells. The effect of cALT silencing was analysed in the liver of S. aurata 72 h after intraperitoneal injection of chitosan-tripolyphosphate (TPP) nanoparticles complexed with a plasmid encoding a shRNA to down-regulate cALT expression (pCpG-si1sh1). In fish fed diets with different ratio of protein to carbohydrate and treated with chitosan-TPP-pCpG-si1sh1, cALT1 and cALT2 mRNA levels significantly decreased irrespective of the diet. Consistently, ALT activity decreased in liver of treated animals. In the liver of S. aurata treated with chitosan-TPP-pCpG-si1sh1 nanoparticles, down-regulation of cALT expression increased the activity of key enzymes in glycolysis (6-phosphofructo-1-kinase and pyruvate kinase) and protein metabolism (glutamate dehydrogenase). Besides showing for the first time that administration of chitosan-TPP-pCpG-si1sh1 nanoparticles silences hepatic cALT expression in vivo, our data support that down-regulation of cALT could improve the use of dietary carbohydrates to obtain energy and spare protein catabolis