Extracts from Chlorella vulgaris Protect Mesenchymal Stromal Cells from Oxidative Stress Induced by Hydrogen Peroxide

Microalgae as unicellular eukaryotic organisms demonstrate several advantages for biotechnological and biological applications. Natural derived microalgae products demand has increased in food, cosmetic and nutraceutical applications lately. The natural antioxidants have been used for attenuation of mitochondrial cell damage caused by oxidative stress. This study evaluates the in vitro protective effect of Chlorella vulgaris bioactive extracts against oxidative stress in human mesenchymal stromal/stem cells (MSCs). The classical solid-liquid and the supercritical extraction, using biomass of commercially available and laboratory cultivated C. vulgaris, are employed. Oxidative stress induced by 300 μM H₂O₂ reduces cell viability of MSCs. The addition of C. vulgaris extracts, with increased protein content compared to carbohydrates, to H₂O₂ treated MSCs counteracted the oxidative stress, reducing reactive oxygen species levels without affecting MSC proliferation. The supercritical extraction was the most efficient extraction method for carotenoids resulting in enhanced antioxidant activity. Pre-treatment of MSCs with C. vulgaris extracts mitigates the oxidative damage ensued by H₂O_2. Initial proteomic analysis of secretome from licensed (TNFα-activated) MSCs treated with algal extracts reveals a signature of differentially regulated proteins that fall into clinically relevant pathways such as inflammatory signaling. The enhanced antioxidative and possibly anti-inflammatory capacity could be explored in the context of future cell therapies.

Second-Generation Escherichia coli SuptoxR Strains for High-Level Recombinant Membrane Protein Production

Escherichia coli is one of the most widely utilized hosts for recombinant protein production, including that of membrane proteins (MPs). We have recently engineered a specialized E. coli strain for enhanced recombinant MP production, termed SuptoxR. By appropriately co-expressing the effector gene rraA, SuptoxR can suppress the high toxicity, which is frequently observed during the MP-overexpression process, and, at the same time, enhance significantly the cellular accumulation of membrane-incorporated and properly folded recombinant MP. The combination of these two beneficial effects results in dramatically enhanced volumetric yields for various prokaryotic and eukaryotic MPs. Here, we engineered second-generation SuptoxR strains with further improved properties, so that they can achieve even higher levels of recombinant MP production. We searched for naturally occurring RraA variants with similar or improved MP toxicity-suppressing and production-promoting effects to that of the native E. coli RraA of the original SuptoxR strain. We found that the RraA proteins from Proteus mirabilis and Providencia stuartii can be even more potent enhancers of MP productivity than the E. coli RraA. By exploiting these two newly identified RraAs, we constructed two second-generation SuptoxR strains, termed SuptoxR2.1 and SuptoxR2.2, whose MP-production capabilities often surpass those of the original SuptoxR significantly. SuptoxR2.1 and SuptoxR2.2 are expected to become widely useful expression hosts for recombinant MP production in bacteria.

Computational Analysis of Transcriptomic and Proteomic Data for Deciphering Molecular Heterogeneity and Drug Responsiveness in Model Human Hepatocellular Carcinoma Cell Lines

Hepatocellular carcinoma (HCC) is associated with high mortality due to its inherent heterogeneity, aggressiveness, and limited therapeutic regimes. Herein, we analyzed 21 human HCC cell lines (HCC lines) to explore intertumor molecular diversity and pertinent drug sensitivity. We used an integrative computational approach based on exploratory and single-sample gene-set enrichment analysis of transcriptome and proteome data from the Cancer Cell Line Encyclopedia, followed by correlation analysis of drug-screening data from the Cancer Therapeutics Response Portal with curated gene-set enrichment scores. Acquired results classified HCC lines into two groups, a poorly and a well-differentiated group, displaying lower/higher enrichment scores in a "Specifically Upregulated in Liver" gene-set, respectively. Hierarchical clustering based on a published epithelial-mesenchymal transition gene expression signature further supported this stratification. Between-group comparisons of gene and protein expression unveiled distinctive patterns, whereas downstream functional analysis significantly associated differentially expressed genes with crucial cancer-related biological processes/pathways and revealed concrete driver-gene signatures. Finally, correlation analysis highlighted a diverse effectiveness of specific drugs against poorly compared to well-differentiated HCC lines, possibly applicable in clinical research with patients with analogous characteristics. Overall, this study expanded the knowledge on the molecular profiles, differentiation status, and drug responsiveness of HCC lines, and proposes a cost-effective computational approach to precision anti-HCC therapies.

A Study on the Effect of Macro- and Micro- Nutrients on Nannochloropsis oceanica Growth, Fatty Acid Composition and Magnetic Harvesting Efficiency

The effect of iron, manganese, phosphorus and nitrogen on growth and lipid synthesis of the microalgae Nannochloropsis oceanica CCMP1779, as well as their impact on the magnetic harvesting efficiency, are examined under their depriving cell culture conditions. Herein, it is demonstrated that nitrogen and manganese depletion primarily reduced cell growth while phosphorus and iron restriction led to higher dry biomass. Subsequently, the role of those nutrients on fatty acids profile was examined. Phosphorus and nitrogen restriction resulted in lower and higher lipid content, respectively. High amounts of polyunsaturated fatty acids like eicosapentaenoic acid are produced under iron and manganese depletion. Phosphorus deprivation favors monounsaturated fatty acids such as C18:1 and C16:1, while nitrogen restriction favors saturated fatty acid production like C14:0, C16:0 and C18:0. Since the presence/absence of macro- and micro-elements may affect the overall electrostatic charges on the outmost microalgae surface, it was also analyzed how these elements affect the magnetic harvesting efficiency. Results showed that phosphorus deprivation led to the best magnetic harvesting efficiency of N. oceanica cells (93%) as compared to other nutrient starvation as well as standard medium.

XynDZ5: A New Thermostable GH10 Xylanase

Xylanolytic enzymes have a broad range of applications in industrial biotechnology as biocatalytic components of various processes and products, such as food additives, bakery products, coffee extraction, agricultural silage and functional foods. An increasing market demand has driven the growing interest for the discovery of xylanases with specific industrially relevant characteristics, such as stability at elevated temperatures and in the presence of other denaturing factors, which will facilitate their incorporation into industrial processes. In this work, we report the discovery and biochemical characterization of a new thermostable GH10 xylanase, termed XynDZ5, exhibiting only 26% amino acid sequence identity to the closest characterized xylanolytic enzyme. This new enzyme was discovered in an Icelandic hot spring enrichment culture of a Thermoanaerobacterium species using a recently developed bioinformatic analysis platform. XynDZ5 was produced recombinantly in Escherichia coli, purified and characterized biochemically. This analysis revealed that it acts as an endo-1,4-β-xylanase that performs optimally at 65–75°C and pH 7.5. The enzyme is capable of retaining high levels of catalytic efficiency after several hours of incubation at high temperatures, as well as in the presence of significant concentrations of a range of metal ions and denaturing agents. Interestingly, the XynDZ5 biochemical profile was found to be atypical, as it also exhibits significant exo-activity. Computational modeling of its three-dimensional structure predicted a (β/α)₈ TIM barrel fold, which is very frequently encountered among family GH10 enzymes. This modeled structure has provided clues about structural features that may explain aspects of its catalytic performance. Our results suggest that XynDZ5 represents a promising new candidate biocatalyst appropriate for several high-temperature biotechnological applications in the pulp, paper, baking, animal-feed and biofuel industries.

RNA-seq data analysis of stimulated hepatocellular carcinoma cells treated with epigallocatechin gallate and fisetin reveals target genes and action mechanisms

Hepatocellular carcinoma (HCC) is an essentially incurable inflammation-related cancer. We have previously shown by network analysis of proteomic data that the flavonoids epigallocatechin gallate (EGCG) and fisetin (FIS) efficiently downregulated pro-tumor cytokines released by HCC through inhibition of Akt/mTOR/RPS6 phospho-signaling. However, their mode of action at the global transcriptome level remains unclear. Herein, we endeavor to compare gene expression alterations mediated by these compounds through a comprehensive transcriptome analysis based on RNA-seq in HEP3B, a responsive HCC cell line, upon perturbation with a mixture of prototypical stimuli mimicking conditions of tumor microenvironment or under constitutive state.

Analysis of RNA-seq data revealed extended changes on HEP3B transcriptome imposed by test nutraceuticals. Under stimulated conditions, EGCG and FIS significantly modified, compared to the corresponding control, the expression of 922 and 973 genes, respectively, the large majority of which (695 genes), was affected by both compounds. Hierarchical clustering based on the expression data of shared genes demonstrated an almost identical profile in nutraceutical-treated stimulated cells which was virtually opposite in cells exposed to stimuli alone. Downstream enrichment analyses of the co-modified genes uncovered significant associations with cancer-related transcription factors as well as terms of Gene Ontology/Reactome Pathways and highlighted ECM dynamics as a nodal modulation point by nutraceuticals along with angiogenesis, inflammation, cell motility and growth. RNA-seq data for selected genes were independently confirmed by RT-qPCR.

Overall, the present systems approach provides novel evidence stepping up the mechanistic understanding of test nutraceuticals, thus rationalizing their clinical exploitation in new preventive/therapeutic modalities against HCC.

ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data

Metagenomic analysis of environmental samples provides deep insight into the enzymatic mixture of the corresponding niches, capable of revealing peptide sequences with novel functional properties exploiting the high performance of next-generation sequencing (NGS) technologies. At the same time due to their ever increasing complexity, there is a compelling need for ever larger computational configurations to ensure proper bioinformatic analysis, and fine annotation. With the aiming to address the challenges of such an endeavor, we have developed a novel web-based application named ANASTASIA (automated nucleotide aminoacid sequences translational plAtform for systemic interpretation and analysis). ANASTASIA provides a rich environment of bioinformatic tools, either publicly available or novel, proprietary algorithms, integrated within numerous automated algorithmic workflows, and which enables versatile data processing tasks for (meta)genomic sequence datasets. ANASTASIA was initially developed in the framework of the European FP7 project HotZyme, whose aim was to perform exhaustive analysis of metagenomes derived from thermal springs around the globe and to discover new enzymes of industrial interest. ANASTASIA has evolved to become a stable and extensible environment for diversified, metagenomic, functional analyses for a range of applications overarching industrial biotechnology to biomedicine, within the frames of the ELIXIR-GR project. As a showcase, we report the successful in silico mining of a novel thermostable esterase termed “EstDZ4” from a metagenomic sample collected from a hot spring located in Krisuvik, Iceland.

Studies on the catalytic behavior of a membrane-bound lipolytic enzyme from the microalgae Nannochloropsis oceanica CCMP1779

The catalytic behavior of a membrane-bound lipolytic enzyme (MBL-Enzyme) from the microalgae Nannochloropsis oceanica CCMP1779 was investigated. The biocatalyst showed maximum activity at 50 °C and pH 7.0, and was stable at pH 7.0 and temperatures from 40 to 60 °C. Half-lives at 60 °C, 70 °C and 80 °C were found 866.38, 150.67 and 85.57 min respectively. Thermal deactivation energy was 68.87 kJ mol^-1. The enzyme's enthalpy (ΔΗ*), entropy (ΔS*) and Gibb's free energy (ΔG*) were in the range of 65.86-66.27 kJ mol^-1, 132.38-140.64 J mol^-1 K^-1 and 107.80-115.81 kJ mol^-1, respectively. Among p-nitrophenyl esters of fatty acids tested, MBL-Enzyme exhibited the highest hydrolytic activity against p-nitrophenyl palmitate (pNPP). The K_m and V_max values were found 0.051 mM and of 0.054 mmole pNP mg protein^-1 min^-1, respectively with pNPP as substrate. The presence of Mn²⁺ increased lipolytic activity by 68.25%, while Fe³⁺ and Cu²⁺ ions had the strongest inhibitory effect. MBL-Enzyme was stable in the presence of water miscible (66% of the initial activity in ethanol) and water immiscible (71% of the initial activity in n-octane) solvents. Myristic acid was found to be the most efficient acyl donor in esterification reactions with ethanol. Methanol was the best acyl acceptor among the primary alcohols tested.

Publisher Correction: An integrated bacterial system for the discovery of chemical rescuers of disease-associated protein misfolding

In the version of this Article originally published, in Fig. 1c-e, on the x axes, the lines labelled 'Aβ₄₂' and 'Aβ₄₂(F19S;L34P)' grouped the data incorrectly; the line labelled Aβ₄₂ should have grouped the data for Random 1-2 and Clones 1-10, and the line labelled Aβ₄₂(F19S;L34P) should have only grouped the data for Random 1-2 on the right end of the plots and blots. These figures have now been corrected in all versions of the Article.

Development of Escherichia coli Strains That Withstand Membrane Protein-Induced Toxicity and Achieve High-Level Recombinant Membrane Protein Production

Membrane proteins perform critical cellular functions in all living organisms and constitute major targets for drug discovery. Escherichia coli has been the most popular overexpression host for membrane protein biochemical/structural studies. Bacterial production of recombinant membrane proteins, however, is typically hampered by poor cellular accumulation and severe toxicity for the host, which leads to low final biomass and minute volumetric yields. In this work, we aimed to rewire the E. coli protein-producing machinery to withstand the toxicity caused by membrane protein overexpression in order to generate engineered bacterial strains with the ability to achieve high-level membrane protein production. To achieve this, we searched for bacterial genes whose coexpression can suppress membrane protein-induced toxicity and identified two highly potent effectors: the membrane-bound DnaK cochaperone DjlA, and the inhibitor of the mRNA-degrading activity of the E. coli RNase E, RraA. E. coli strains coexpressing either djlA or rraA, termed SuptoxD and SuptoxR, respectively, accumulated markedly higher levels of final biomass and produced dramatically enhanced yields for a variety of prokaryotic and eukaryotic recombinant membrane proteins. In all tested cases, either SuptoxD, or SuptoxR, or both, outperformed the capabilities of commercial strains frequently utilized for recombinant membrane protein production purposes.

Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases

Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.

EstDZ3: A New Esterolytic Enzyme Exhibiting Remarkable Thermostability

Lipolytic enzymes that retain high levels of catalytic activity when exposed to a variety of denaturing conditions are of high importance for a number of biotechnological applications. In this study, we aimed to identify new lipolytic enzymes, which are highly resistant to prolonged exposure to elevated temperatures. To achieve this, we searched for genes encoding for such proteins in the genomes of a microbial consortium residing in a hot spring located in China. After performing functional genomic screening on a bacterium of the genus Dictyoglomus, which was isolated from this hot spring following in situ enrichment, we identified a new esterolytic enzyme, termed EstDZ3. Detailed biochemical characterization of the recombinant enzyme, revealed that it constitutes a slightly alkalophilic and highly active esterase against esters of fatty acids with short to medium chain lengths. Importantly, EstDZ3 exhibits remarkable thermostability, as it retains high levels of catalytic activity after exposure to temperatures as high as 95°C for several hours. Furthermore, it exhibits very good stability against exposure to high concentrations of a variety of organic solvents. Interestingly, EstDZ3 was found to have very little similarity to previously characterized esterolytic enzymes. Computational modeling of the three-dimensional structure of this new enzyme predicted that it exhibits a typical α/β hydrolase fold that seems to include a “subdomain insertion”, which is similar to the one present in its closest homolog of known function and structure, the cinnamoyl esterase Lj0536 from Lactobacillus johnsonii. As it was found in the case of Lj0536, this structural feature is expected to be an important determinant of the catalytic properties of EstDZ3. The high levels of esterolytic activity of EstDZ3, combined with its remarkable thermostability and good stability against a range of organic solvents and other denaturing agents, render this new enzyme a candidate biocatalyst for high-temperature biotechnological applications.

Discovery and Characterization of a Thermostable and Highly Halotolerant GH5 Cellulase from an Icelandic Hot Spring Isolate

With the ultimate goal of identifying robust cellulases for industrial biocatalytic conversions, we have isolated and characterized a new thermostable and very halotolerant GH5 cellulase. This new enzyme, termed CelDZ1, was identified by bioinformatic analysis from the genome of a polysaccharide-enrichment culture isolate, initiated from material collected from an Icelandic hot spring. Biochemical characterization of CelDZ1 revealed that it is a glycoside hydrolase with optimal activity at 70°C and pH 5.0 that exhibits good thermostability, high halotolerance at near-saturating salt concentrations, and resistance towards metal ions and other denaturing agents. X-ray crystallography of the new enzyme showed that CelDZ1 is the first reported cellulase structure that lacks the defined sugar-binding 2 subsite and revealed structural features which provide potential explanations of its biochemical characteristics.

Network-Based Analysis of Nutraceuticals in Human Hepatocellular Carcinomas Reveals Mechanisms of Chemopreventive Action

Chronic inflammation is associated with the development of human hepatocellular carcinoma (HCC), an essentially incurable cancer. Anti-inflammatory nutraceuticals have emerged as promising candidates against HCC, yet the mechanisms through which they influence the cell signaling machinery to impose phenotypic changes remain unresolved. Herein we implemented a systems biology approach in HCC cells, based on the integration of cytokine release and phospoproteomic data from high-throughput xMAP Luminex assays to elucidate the action mode of prominent nutraceuticals in terms of topology alterations of HCC-specific signaling networks. An optimization algorithm based on SigNetTrainer, an Integer Linear Programming formulation, was applied to construct networks linking signal transduction to cytokine secretion by combining prior knowledge of protein connectivity with proteomic data. Our analysis identified the most probable target phosphoproteins of interrogated compounds and predicted translational control as a new mechanism underlying their anticytokine action. Induced alterations corroborated with inhibition of HCC-driven angiogenesis and metastasis.

Integrative workflows for metagenomic analysis

The rapid evolution of all sequencing technologies, described by the term Next Generation Sequencing (NGS), have revolutionized metagenomic analysis. They constitute a combination of high-throughput analytical protocols, coupled to delicate measuring techniques, in order to potentially discover, properly assemble and map allelic sequences to the correct genomes, achieving particularly high yields for only a fraction of the cost of traditional processes (i.e., Sanger). From a bioinformatic perspective, this boils down to many GB of data being generated from each single sequencing experiment, rendering the management or even the storage, critical bottlenecks with respect to the overall analytical endeavor. The enormous complexity is even more aggravated by the versatility of the processing steps available, represented by the numerous bioinformatic tools that are essential, for each analytical task, in order to fully unveil the genetic content of a metagenomic dataset. These disparate tasks range from simple, nonetheless non-trivial, quality control of raw data to exceptionally complex protein annotation procedures, requesting a high level of expertise for their proper application or the neat implementation of the whole workflow. Furthermore, a bioinformatic analysis of such scale, requires grand computational resources, imposing as the sole realistic solution, the utilization of cloud computing infrastructures. In this review article we discuss different, integrative, bioinformatic solutions available, which address the aforementioned issues, by performing a critical assessment of the available automated pipelines for data management, quality control, and annotation of metagenomic data, embracing various, major sequencing technologies and applications.

HuR-regulated mRNAs associated with nuclear hnRNP A1-RNP complexes

Post-transcriptional regulatory networks are dependent on the interplay of many RNA-binding proteins having a major role in mRNA processing events in mammals. We have been interested in the concerted action of the two RNA-binding proteins hnRNP A1 and HuR, both stable components of immunoselected hnRNP complexes and having a major nuclear localization. Specifically, we present here the application of the RNA-immunoprecipitation (RIP)-Chip technology to identify a population of nuclear transcripts associated with hnRNP A1-RNPs as isolated from the nuclear extract of either HuR WT or HuR-depleted (KO) mouse embryonic fibroblast (MEF) cells. The outcome of this analysis was a list of target genes regulated via HuR for their association (either increased or reduced) with the nuclear hnRNP A1-RNP complexes. Real time PCR analysis was applied to validate a selected number of nuclear mRNA transcripts, as well as to identify pre-spliced transcripts (in addition to their mature mRNA counterpart) within the isolated nuclear hnRNP A1-RNPs. The differentially enriched mRNAs were found to belong to GO categories relevant to biological processes anticipated for hnRNP A1 and HuR (such as transport, transcription, translation, apoptosis and cell cycle) indicating their concerted function in mRNA metabolism.

Combinatorial approaches for inverse metabolic engineering applications

Traditional metabolic engineering analyzes biosynthetic and physiological pathways, identifies bottlenecks, and makes targeted genetic modifications with the ultimate goal of increasing the production of high-value products in living cells. Such efforts have led to the development of a variety of organisms with industrially relevant properties. However, there are a number of cellular phenotypes important for research and the industry for which the rational selection of cellular targets for modification is not easy or possible. In these cases, strain engineering can be alternatively carried out using “inverse metabolic engineering”, an approach that first generates genetic diversity by subjecting a population of cells to a particular mutagenic process, and then utilizes genetic screens or selections to identify the clones exhibiting the desired phenotype. Given the availability of an appropriate screen for a particular property, the success of inverse metabolic engineering efforts usually depends on the level and quality of genetic diversity which can be generated. Here, we review classic and recently developed combinatorial approaches for creating such genetic diversity and discuss the use of these methodologies in inverse metabolic engineering applications.

Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes

Glucocorticoid receptor (GR) exerts anti-inflammatory action in part by antagonizing proinflammatory transcription factors such as the nuclear factor kappa-b (NFKB). Here, we assess the crosstalk of activated GR and RELA (p65, major NFKB component) by global identification of their binding sites and target genes. We show that coactivation of GR and p65 alters the repertoire of regulated genes and results in their association with novel sites in a mutually dependent manner. These novel sites predominantly cluster with p65 target genes that are antagonized by activated GR and vice versa. Our data show that coactivation of GR and NFKB alters signaling pathways that are regulated by each factor separately and provide insight into the networks underlying the GR and NFKB crosstalk.

Escherichia coli genome-wide promoter analysis: identification of additional AtoC binding target elements

Background

Studies on bacterial signal transduction systems have revealed complex networks of functional interactions, where the response regulators play a pivotal role. The AtoSC system of E. coli activates the expression of atoDAEB operon genes, and the subsequent catabolism of short-chain fatty acids, upon acetoacetate induction. Transcriptome and phenotypic analyses suggested that atoSC is also involved in several other cellular activities, although we have recently reported a palindromic repeat within the atoDAEB promoter as the single, cis-regulatory binding site of the AtoC response regulator. In this work, we used a computational approach to explore the presence of yet unidentified AtoC binding sites within other parts of the E. coli genome.

Results

Through the implementation of a computational de novo motif detection workflow, a set of candidate motifs was generated, representing putative AtoC binding targets within the E. coli genome. In order to assess the biological relevance of the motifs and to select for experimental validation of those sequences related robustly with distinct cellular functions, we implemented a novel approach that applies Gene Ontology Term Analysis to the motif hits and selected those that were qualified through this procedure. The computational results were validated using Chromatin Immunoprecipitation assays to assess the in vivo binding of AtoC to the predicted sites. This process verified twenty-two additional AtoC binding sites, located not only within intergenic regions, but also within gene-encoding sequences.

Conclusions

This study, by tracing a number of putative AtoC binding sites, has indicated an AtoC-related cross-regulatory function. This highlights the significance of computational genome-wide approaches in elucidating complex patterns of bacterial cell regulation.

GRISSOM platform: enabling distributed processing and management of biological data through fusion of grid and web technologies

Transcriptomic technologies have a critical impact in the revolutionary changes that reshape biological research. Through the recruitment of novel high-throughput instrumentation and advanced computational methodologies, an unprecedented wealth of quantitative data is produced. Microarray experiments are considered high-throughput, both in terms of data volumes (data intensive) and processing complexity (computationally intensive). In this paper, we present grids for in silico systems biology and medicine (GRISSOM), a web-based application that exploits GRID infrastructures for distributed data processing and management, of DNA microarrays (cDNA, Affymetrix, Illumina) through a generic, consistent, computational analysis framework. GRISSOM performs versatile annotation and integrative analysis tasks, through the use of third-party application programming interfaces, delivered as web services. In parallel, by conforming to service-oriented architectures, it can be encapsulated in other biomedical processing workflows, with the help of workflow enacting software, like Taverna Workbench, thus rendering access to its algorithms, transparent and generic. GRISSOM aims to set a generic paradigm of efficient metamining that promotes translational research in biomedicine, through the fusion of grid and semantic web computing technologies.

Esterification reactions catalyzed by lipases in microemulsions: the role of enzyme localization in relation to its selectivity

The activity of lipases from Rhizopus delemar, Rhizopus arrhizus, and Penicillium simplicissimum entrapped in microemulsions formulated by bis-(2-ethylhexyl)sulfo-succinate sodium salt (AOT) in isooctane has been studied in esterification reactions of various aliphatic alcohols with fatty acids. The effect of the nature of the fatty acids (chain length) and of the alcohols (primary, secondary, or tertiary; chain length; cyclic structures) on the lipase activities was investigated in relation to the reverse micellar structure. The lipases tested showed a selectivity regarding the structure of the substrates used when hosted in the AOT/isooctane microemulsion systems. Penicillium simplicissimum lipase showed higher reaction rates in the esterification of long chain alcohols as well as secondary alcohols. Primary alcohols had a low reaction rate and tertiary a very slow rate of esterification. Long chain fatty acids were better catalyzed as compared to the shorter ones. Rhizopus delemar and R. arrhizus lipases showed a preference for the esterification of short chain primary alcohols, while the secondary alcohols had a low rate of esterification and the tertiary ones could not be converted. The reaction of medium chain length fatty acids was also better catalyzed than in the case of the long ones. The observed lipase selectivity appeared to be related to the localization of the enzyme molecule within the micellar microstructure due to the hydrophobic/hydrophilic character of the protein. The reverse micellar structural characteristics, as well as the localization of the enzyme, were examined by fluorescence quenching measurements and spectroscopical studies.

A transcriptomic computational analysis of mastic oil-treated Lewis lung carcinomas reveals molecular mechanisms targeting tumor cell growth and survival

Background

Mastic oil from Pistacia lentiscus variation chia, a blend of bioactive terpenes with recognized medicinal properties, has been recently shown to exert anti-tumor growth activity through inhibition of cancer cell proliferation, survival, angiogenesis and inflammatory response. However, no studies have addressed its mechanisms of action at genome-wide gene expression level.

Methods

To investigate molecular mechanisms triggered by mastic oil, Lewis Lung Carcinoma cells were treated with mastic oil or DMSO and RNA was collected at five distinct time points (3-48 h). Microarray expression profiling was performed using Illumina mouse-6 v1 beadchips, followed by computational analysis. For a number of selected genes, RT-PCR validation was performed in LLC cells as well as in three human cancer cell lines of different origin (A549, HCT116, K562). PTEN specific inhibition by a bisperovanadium compound was applied to validate its contribution to mastic oil-mediated anti-tumor growth effects.

Results

In this work we demonstrated that exposure of Lewis lung carcinomas to mastic oil caused a time-dependent alteration in the expression of 925 genes. GO analysis associated expression profiles with several biological processes and functions. Among them, modifications on cell cycle/proliferation, survival and NF-κB cascade in conjunction with concomitant regulation of genes encoding for PTEN, E2F7, HMOX1 (up-regulation) and NOD1 (down-regulation) indicated some important mechanistic links underlying the anti-proliferative, pro-apoptotic and anti-inflammatory effects of mastic oil. The expression profiles of Hmox1, Pten and E2f7 genes were similarly altered by mastic oil in the majority of test cancer cell lines. Inhibition of PTEN partially reversed mastic oil effects on tumor cell growth, indicating a multi-target mechanism of action. Finally, k-means clustering, organized the significant gene list in eight clusters demonstrating a similar expression profile. Promoter analysis in a representative cluster revealed shared putative cis-elements suggesting a common regulatory transcription mechanism.

Conclusions

Present results provide novel evidence on the molecular basis of tumor growth inhibition mediated by mastic oil and set a rational basis for application of genomics and bioinformatic methodologies in the screening of natural compounds with potential cancer chemopreventive activities.

Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB

Background

The microarray data analysis realm is ever growing through the development of various tools, open source and commercial. However there is absence of predefined rational algorithmic analysis workflows or batch standardized processing to incorporate all steps, from raw data import up to the derivation of significantly differentially expressed gene lists. This absence obfuscates the analytical procedure and obstructs the massive comparative processing of genomic microarray datasets. Moreover, the solutions provided, heavily depend on the programming skills of the user, whereas in the case of GUI embedded solutions, they do not provide direct support of various raw image analysis formats or a versatile and simultaneously flexible combination of signal processing methods.

Results

We describe here Gene ARMADA (Automated Robust MicroArray Data Analysis), a MATLAB implemented platform with a Graphical User Interface. This suite integrates all steps of microarray data analysis including automated data import, noise correction and filtering, normalization, statistical selection of differentially expressed genes, clustering, classification and annotation. In its current version, Gene ARMADA fully supports 2 coloured cDNA and Affymetrix oligonucleotide arrays, plus custom arrays for which experimental details are given in tabular form (Excel spreadsheet, comma separated values, tab-delimited text formats). It also supports the analysis of already processed results through its versatile import editor. Besides being fully automated, Gene ARMADA incorporates numerous functionalities of the Statistics and Bioinformatics Toolboxes of MATLAB. In addition, it provides numerous visualization and exploration tools plus customizable export data formats for seamless integration by other analysis tools or MATLAB, for further processing. Gene ARMADA requires MATLAB 7.4 (R2007a) or higher and is also distributed as a stand-alone application with MATLAB Component Runtime.

Conclusion

Gene ARMADA provides a highly adaptable, integrative, yet flexible tool which can be used for automated quality control, analysis, annotation and visualization of microarray data, constituting a starting point for further data interpretation and integration with numerous other tools.

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database

BACKGROUND

The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope. Originally used for illustration purposes, KEGG Pathways through KGML (KEGG Markup Language) files, can provide complete reaction sets and introduce species versioning, which offers advantages for the scope of cellular metabolism simulation modelling. In this project, KEGGconverter is described, implemented also as a web-based application, which uses as source KGML files, in order to construct integrated pathway SBML models fully functional for simulation purposes.

RESULTS

A case study of the integration of six human metabolic pathways from KEGG depicts the ability of KEGGconverter to automatically produce merged and converted to SBML fully functional pathway models, enhanced with default kinetics. The suitability of the developed tool is demonstrated through a comparison with other state-of-the art relevant software tools for the same data fusion and conversion tasks, thus illustrating the problems and the relevant workflows. Moreover, KEGGconverter permits the inclusion of additional reactions in the resulting model which represent flux cross-talk with neighbouring pathways, providing in this way improved simulative accuracy. These additional reactions are introduced by exploiting relevant semantic information for the elements of the KEGG Pathways database. The architecture and functionalities of the web-based application are presented.

CONCLUSION

KEGGconverter is capable of producing integrated analogues of metabolic pathways appropriate for simulation tasks, by inputting only KGML files. The web application acts as a user friendly shell which transparently enables the automated biochemically correct pathway merging, conversion to SBML format, proper renaming of the species, and insertion of default kinetic properties for the pertaining reactions. The tool is available at: http://www.grissom.gr/keggconverter.

Mastic Oil from Pistacia lentiscus var. chia Inhibits Growth and Survival of Human K562 Leukemia Cells and Attenuates Angiogenesis

Mastic oil from Pistacia lentiscus var. chia, a natural plant extract traditionally used as a food additive, has been extensively studied for its antimicrobial activity attributed to the combination of its bioactive components. One of them, perillyl alcohol (POH), displays tumor chemopreventive, chemotherapeutic, and antiangiogenic properties. We investigated whether mastic oil would also suppress tumor cell growth and angiogenesis. We observed that mastic oil concentration and time dependently exerted an antiproliferative and proapoptotic effect on K562 human leukemia cells and inhibited the release of vascular endothelial growth factor (VEGF) from K562 and B16 mouse melanoma cells. Moreover, mastic oil caused a concentration-dependent inhibition of endothelial cell (EC) proliferation without affecting cell survival and a significant decrease of microvessel formation both in vitro and in vivo. Investigation of underlying mechanism(s) demonstrated that mastic oil reduced 1) in K562 cells the activation of extracellular signal-regulated kinases 1/2 (Erk1/2) known to control leukemia cell proliferation, survival, and VEGF secretion and 2) in EC the activation of RhoA, an essential regulator of neovessel organization. Overall, our results underscore that mastic oil, through its multiple effects on malignant cells and ECs, may be a useful natural dietary supplement for cancer prevention.

A novel lipolytic activity of Rhodotorula glutinis cells: production, partial characterization and application in the synthesis of esters

Cell-bound lipase activity (10 pNPL units/g dry cell weight) was released when the yeast Rhodotorula glutinis was cultured in a 7-l stirred tank fermentor using palm-oil as the sole carbon source. The enzyme showed relative specificity towards medium chain organic acids since the apparent K(m) values for pNPB (p-NitroPhenyl-Butyrate) and pNPL (p-NitroPhenyl-Laurate) were equal to 2.7 and 0.7 mM, respectively. In addition, 80% of this activity could be detected on the surface of the cells. The cell-bound nature of the enzyme increased its thermal stability showing half-life times of 200 and 60 min at 50 and 60 degrees C, respectively, as well as good stability in organic solvents. Freeze-dried cell preparations were successfully used to catalyze the synthesis of fatty acid esters of butanol and heptanol in nearly anhydrous organic solvents. A conversion of 60-62% was obtained upon esterification of palmitic or oleic acid with butanol, within 96 h. The enzyme preparation was used in four consecutive batch reactions with only 10% loss of activity.

Crystallographic studies on two bioisosteric analogues, N-acetyl-beta-D-glucopyranosylamine and N-trifluoroacetyl-beta-D-glucopyranosylamine, potent inhibitors of muscle glycogen phosphorylase

Structure-based inhibitor design has led to the discovery of a number of potent inhibitors of glycogen phosphorylase b (GPb), N-acyl derivatives of beta-D-glucopyranosylamine, that bind at the catalytic site of the enzyme. The first good inhibitor in this class of compounds, N-acetyl-beta-D-glucopyranosylamine (NAG) (K(i) = 32 microM), has been previously characterized by biochemical, biological and crystallographic experiments at 2.3 angstroms resolution. Bioisosteric replacement of the acetyl group by trifluoroacetyl group resulted in an inhibitor, N-trifluoroacetyl-beta-D-glucopyranosylamine (NFAG), with a K(i) = 75 microM. To elucidate the structural basis of its reduced potency, we determined the ligand structure in complex with GPb at 1.8 angstroms resolution. To compare the binding mode of N-trifluoroacetyl derivative with that of the lead molecule, we also determined the structure of GPb-NAG complex at a higher resolution (1.9 angstroms). NFAG can be accommodated in the catalytic site of T-state GPb at approximately the same position as that of NAG and stabilize the T-state conformation of the 280 s loop by making several favourable contacts to Asn284 of this loop. The difference observed in the K(i) values of the two analogues can be interpreted in terms of subtle conformational changes of protein residues and shifts of water molecules in the vicinity of the catalytic site, variations in van der Waals interaction, and desolvation effects.

Biocatalytic preparation of acylated derivatives of flavonoid glycosides enhances their antioxidant and antimicrobial activity

Enzymatic synthesis of acylated derivatives of a monosaccharidic flavonoid chrysoeriol-7-O-beta-D-(3''-E-p-coumaroyl)-glucopyranoside as well as of a disaccharidic flavonoid chrysoeriol-7-[6'''-O-acetyl-beta-D-allosyl-(1-->2)-beta-D-glucopyranoside], isolated from Greek endemic plants, was performed using an immobilized Candida antarctica lipase in non-toxic organic solvents. The influence of the reaction parameters such as the molar ratio of acyl donor to flavonoid, as well as the nature of the acyl donor, on the performance of the biocatalytic process was pointed out using the acylation of naringin as a model reaction. With vinyl laurate as acyl donor, the highest conversion was observed at relatively high molar ratio (>or=10), using acetone as solvent. Lipase exhibits specificity towards primary alcohol of the glucose moiety of both flavonoid glycosides. The introduction of an acyl group into glucosylated flavonoids significantly improved their antioxidant activity towards both LDL and serum model in vitro. Furthermore, the acylated derivative of disaccharidic flavonoid increased its antimicrobial activity against two Gram-positive bacteria.

Perillyl alcohol is an angiogenesis inhibitor

Aberrant angiogenesis is essential for the progression of solid tumors and hematological malignancies. Thus, antiangiogenic therapy is one of the most promising approaches to control cancer. In the present work, we examined the ability of perillyl alcohol (POH), a dietary monoterpene with well-established tumor chemopreventive and chemotherapeutic activity, to interfere with the process of angiogenesis. POH remarkably prevented new blood vessel growth in the in vivo chicken embryo chorioallantoic membrane assay and proved to be effective in inhibiting the morphogenic differentiation of cultured endothelial cells into capillary-like networks both in collagen gel and Matrigel models. In addition, POH reduced the cell number in a proliferation assay and induced apoptosis of endothelial cells as indicated by the POH-mediated increase of caspase-3 activity and DNA fragmentation. Consistent with the observed antisurvival effect, POH treatment resulted in a significant inhibition of Akt phosphorylation in endothelial cells. Finally, POH was able to differentially modulate the release of two important angiogenic regulators: vascular endothelial growth factor (VEGF) and angiopoietin 2 (Ang2). POH decreased the release of VEGF from cancer cells but stimulated the expression of Ang2 by endothelial cells, indicating that it might suppress neovascularization and induce vessel regression. Overall, these data underscore the antiangiogenic potential of POH and suggest that POH, in addition to its anticancer activity, may be an effective agent in the treatment of angiogenesis-dependent diseases.

Impact of biological factors on binding media identification in art objects: Identification of animal glue in the presence ofAspergillus niger

The materials and especially organic materials used for creation of art objects can be utilized by various microorganisms for their growth and facilitate the microbial colonization of the object. An understanding of the chemical alterations in artefacts caused by the presence of microorganisms can be crucial for correct identification of the materials initially used for the artefact creation--nowadays an important step in restoration and/or art-historical investigation of the art object. The present article describes a model experiment in which we investigated the possible chemical alterations in animal glue films used as substrate for growth of the fungus Aspergillus niger. The sterilized animal glue solution was poured into Petri dishes, inoculated with Aspergillus niger, and subsequently incubated at 15 degrees C for 0, 7, 9, 14, and 28 days. After interruption of incubation, the content of the Petri dish was analyzed for amino acid composition by the GC-MS based method. It was found that the growth of Aspergillus niger on animal glue films did not cause significant changes in the amino acid composition of the film and had no impact on animal glue identification.

Metabolic flux analysis as a tool for the elucidation of the metabolism of neurotransmitter glutamate

A flux analysis model for the metabolism of neurotransmitter glutamate is constructed, in order to study functional aspects of its metabolism. This work is based on the potassium [K(+)] evoked neurotransmitter glutamate released, as measured in a series of experiments of superfused rat or mouse brain preparations. These measurements are combined with data reported, concerning the metabolism of glutamate and its precursors, glutamine and glucose in rat cerebral cells in vivo. The proposed stoichiometry of the specific reaction network renders the model solvable. The classification procedure establishes that the measured fluxes are all balanceable and all non-measured fluxes can be calculated. The system is well posed with a condition number of 7.8536. The results emphasize the importance of phosphate activated glutaminase and aspartate aminotransferase in the metabolism of neurotransmitter glutamate. Reported data on the rate of the malate-aspartate shuttle, as well as the anaplerotic flux of the glial pyruvate carboxylase reaction are in agreement with the estimations calculated from the proposed model.

Bioorganic reactions in microemulsions

Water-in-oil microemulsions, or reverse micelles, are being evaluated as a reaction medium for a variety of enzymatic reactions. These systems have many potential biotechnological applications. Important examples are the use of various lipase microemulsion systems for hydrolytic or synthetic reactions. This review illustrates the biotechnological applications of microemulsions as media for bioorganic reactions. The principal focus is on lipase catalyzed processes.