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Biomedical subjects

Eve Syrkin Wurtele

Publications and source records attributed to Eve Syrkin Wurtele.

13 recordsLinked to original sources

Year-and-a-half old, dried Echinacea roots retain cytokine-modulating capabilities in an in vitro human older adult model of influenza vaccination.

Alcohol tinctures prepared from aged Echinacea roots are typically taken for preventing or treating upper respiratory infections, as they are purported to stimulate immunity in this context. The effects of long-term (> 1 year) dry storage on the capabilities of Echinacea spp. roots from mature individuals to modulate cytokine production are unknown. Using an older human adult model of influenza vaccination, we collected peripheral blood mononuclear cells from subjects 6 months post-vaccination and stimulated them in vitro with the two Type A influenza viruses contained in the trivalent 2004-2005 vaccine with a 50 % alcohol tincture prepared from the roots of one of seven Echinacea species: E. angustifolia, E. pallida, E. paradoxa, E. purpurea, E. sanguinea, E. simulata, and E. tennesseensis. Before being processed into extracts, all roots had been stored under dry conditions for sixteen months. Cells were cultured for 48 hours; following incubation, supernatants were collected and assayed for interleukin-2, interleukin-10, and interferon-gamma production, cytokines important in the immune response to viral infection. Four species ( E. angustifolia, E. purpurea, E. simulata, E. tennesseensis) augmented IL-10 production, diminished IL-2 production, and had no effect on IFN-gamma production. Echinacea pallida suppressed production of all cytokines; E. paradoxa and E. sanguinea behaved similarly, although to a lesser extent. The results from these in vitro bioactivity assays indicate that dried Echinacea roots stored for sixteen months maintain cytokine-modulating capacities. Our data support and extend previous research and indicate that tinctures from different Echinacea species have different patterns of immune modulation; further, they indicate that certain species may be efficacious in the immune response to viral infection.

Aged↗

PubMed Assistant: a biologist-friendly interface for enhanced PubMed search.

MEDLINE is one of the most important bibliographical information sources for biologists and medical workers. Its PubMed interface supports Boolean queries, which are potentially expressive and exact. However, PubMed is also designed to support simplicity of use at the expense of query expressiveness and exactness. Many PubMed users have never tried explicit Boolean queries. We developed a Java program, PubMed Assistant, to make literature access easier in several ways. PubMed Assistant provides an interface that efficiently displays information about the citations and includes useful functions such as keyword highlighting, export to citation managers, clickable links to Google Scholar and others that are lacking in PubMed.

Artificial Intelligence↗

Integration of metabolic networks and gene expression in virtual reality.

MOTIVATION: Metabolic networks combine metabolism and regulation. These complex networks are difficult to understand and visualize due to the amount and diverse types of information that need to be represented. For example, pathway information gives indications of interactions. Experimental data, such as transcriptomics, proteomics and metabolomics data, give snapshots of the system state. Stereoscopic virtual environments provide a true three-dimensional representation of metabolic networks, which can be intuitively manipulated, and may help to manage the data complexity. RESULTS: MetNet3D, a 3D virtual reality system, allows a user to explore gene expression and metabolic pathway data simultaneously. Normalized gene expression data are processed in R and visualized as a 3D plot. Users can find a particular gene of interest or a cluster of genes that behave similarly and see how these genes function in metabolic networks from MetNetDB, a database of Arabidopsis metabolic networks, using animated network graphs. Interactive virtual reality, with its enhanced ability to display more information, makes such integration more effective by abstracting key relationships. AVAILABILITY: MetNet3D and some sample datasets are available at http://www.vrac.iastate.edu/research/sites/metnet/Download/Download.htm. SUPPLEMENTARY INFORMATION: Color snapshots and movies are available at http://www.vrac.iastate.edu/research/sites/metnet/Bioinformatics/SupplementaryInformation.htm.

Algorithms↗

Modeling gene expression networks using fuzzy logic.

Gene regulatory networks model regulation in living organisms. Fuzzy logic can effectively model gene regulation and interaction to accurately reflect the underlying biology. A new multiscale fuzzy clustering method allows genes to interact between regulatory pathways and across different conditions at different levels of detail. Fuzzy cluster centers can be used to quickly discover causal relationships between groups of coregulated genes. Fuzzy measures weight expert knowledge and help quantify uncertainty about the functions of genes using annotations and the gene ontology database to confirm some of the interactions. The method is illustrated using gene expression data from an experiment on carbohydrate metabolism in the model plant Arabidopsis thaliana. Key gene regulatory relationships were evaluated using information from the gene ontology database. A new regulatory relationship concerning trehalose regulation of carbohydrate metabolism was also discovered in the extracted network.

Animals↗

Reverse genetic characterization of cytosolic acetyl-CoA generation by ATP-citrate lyase in Arabidopsis.

Acetyl-CoA provides organisms with the chemical flexibility to biosynthesize a plethora of natural products that constitute much of the structural and functional diversity in nature. Recent studies have characterized a novel ATP-citrate lyase (ACL) in the cytosol of Arabidopsis thaliana. In this study, we report the use of antisense RNA technology to generate a series of Arabidopsis lines with a range of ACL activity. Plants with even moderately reduced ACL activity have a complex, bonsai phenotype, with miniaturized organs, smaller cells, aberrant plastid morphology, reduced cuticular wax deposition, and hyperaccumulation of starch, anthocyanin, and stress-related mRNAs in vegetative tissue. The degree of this phenotype correlates with the level of reduction in ACL activity. These data indicate that ACL is required for normal growth and development and that no other source of acetyl-CoA can compensate for ACL-derived acetyl-CoA. Exogenous malonate, which feeds into the carboxylation pathway of acetyl-CoA metabolism, chemically complements the morphological and chemical alterations associated with reduced ACL expression, indicating that the observed metabolic alterations are related to the carboxylation pathway of cytosolic acetyl-CoA metabolism. The observations that limiting the expression of the cytosolic enzyme ACL reduces the accumulation of cytosolic acetyl-CoA-derived metabolites and that these deficiencies can be alleviated by exogenous malonate indicate that ACL is a nonredundant source of cytosolic acetyl-CoA.

ATP Citrate (pro-S)-Lyase↗

Diacetylenic isobutylamides of Echinacea: synthesis and natural distribution.

The syntheses of three diacetylenic isobutylamides of Echinacea angustifolia have been achieved by direct synthetic routes by way of a common intermediate. The key step is the alkylation of the anion of the silylated diacetylene. We report the presence of all three diacetylenic isobutylamides in six of the nine Echinacea species: E. angustifolia, E. sanguinea, E. simulata, E. tennesseensis, E. atrorubens and E. laevigata. The accumulation of these amides is sensitive to organ type and age.

Acetylene↗

A proposed framework for the description of plant metabolomics experiments and their results.

The study of the metabolite complement of biological samples, known as metabolomics, is creating large amounts of data, and support for handling these data sets is required to facilitate meaningful analyses that will answer biological questions. We present a data model for plant metabolomics known as ArMet (architecture for metabolomics). It encompasses the entire experimental time line from experiment definition and description of biological source material, through sample growth and preparation to the results of chemical analysis. Such formal data descriptions, which specify the full experimental context, enable principled comparison of data sets, allow proper interpretation of experimental results, permit the repetition of experiments and provide a basis for the design of systems for data storage and transmission. The current design and example implementations are freely available (http://www.armet.org/). We seek to advance discussion and community adoption of a standard for metabolomics, which would promote principled collection, storage and transmission of experiment data.

Database Management Systems↗

Plant biotin-containing carboxylases.

Biotin-containing proteins are found in all forms of life, and they catalyze carboxylation, decarboxylation, or transcarboxylation reactions that are central to metabolism. In plants, five biotin-containing proteins have been characterized. Of these, four are catalysts, namely the two structurally distinct acetyl-CoA carboxylases (heteromeric and homomeric), 3-methylcrotonyl-CoA carboxylase and geranoyl-CoA carboxylase. In addition, plants contain a noncatalytic biotin protein that accumulates in seeds and is thought to play a role in storing biotin. Acetyl-CoA carboxylases generate two pools of malonyl-CoA, one in plastids that is the precursor for de novo fatty acid biosynthesis and the other in the cytosol that is the precursor for fatty acid elongation and a large number of secondary metabolites. 3-Methylcrotonyl-CoA carboxylase catalyzes a reaction in the mitochondrial pathway for leucine catabolism. The exact metabolic function of geranoyl-CoA carboxylase is as yet unknown, but it may be involved in isoprenoid metabolism. This minireview summarizes the recent developments in our understanding of the structure, regulation, and metabolic functions of these proteins in plants.

Acetyl-CoA Carboxylase↗

The role of biotin in regulating 3-methylcrotonyl-coenzyme a carboxylase expression in Arabidopsis.

As a catalytic cofactor, biotin has a critical role in the enzymological mechanism of a number of enzymes that are essential in both catabolic and anabolic metabolic processes. In this study we demonstrate that biotin has additional non-catalytic functions in regulating gene expression in plants, which are biotin autotrophic organisms. Biotin controls expression of the biotin-containing enzyme, methylcrotonyl-coenzyme A (CoA) carboxylase by modulating the transcriptional, translational and/or posttranslational regulation of the expression of this enzyme. The bio1 mutant of Arabidopsis, which is blocked in the de novo biosynthesis of biotin, was used to experimentally alter the biotin status of this organism. In response to the bio1-associated depletion of biotin, the normally biotinylated A-subunit of methylcrotonyl-CoA carboxylase (MCCase) accumulates in its inactive apo-form, and both MCCase subunits hyperaccumulate. This hyperaccumulation occurs because the translation of each subunit mRNA is enhanced and/or because the each protein subunit becomes more stable. In addition, biotin affects the accumulation of distinct charge isoforms of MCCase. In contrast, in response to metabolic signals arising from the alteration in the carbon status of the organism, biotin modulates the transcription of the MCCase genes. These experiments reveal that in addition to its catalytic role as an enzyme cofactor, biotin has multiple roles in regulating gene expression.

Arabidopsis↗

Functional genomics: high-throughput mRNA, protein, and metabolite analyses.

A tremendous amount of DNA sequence information is now available to scientists and engineers. These DNA sequences provide the foundation for studying how the genome of an organism is functioning and they are particularly useful for metabolic engineers interested in manipulating plants for the production of chemicals and enzymes. Functional genomics relies on high-throughput techniques for measuring the mRNA (the transcriptome), protein (the proteome), and metabolite (the metabolome) components of plants as well as their organs and tissues. Microarray technologies, recent advances in protein mass spectrometry, and high-throughput metabolite analyses are beginning to provide detailed information on the total mRNA, protein, and metabolite components of plants. This knowledge will allow scientists to monitor changes in proteins and metabolites in plants. Ultimately, it may allow them to discover new metabolic pathways and to model metabolic and regulatory networks in plants.

Base Sequence↗

Metabolic and environmental regulation of 3-methylcrotonyl-coenzyme A carboxylase expression in Arabidopsis.

3-Methylcrotonyl-coenzyme A carboxylase (MCCase) is a nuclear-encoded, mitochondrial biotin-containing enzyme composed of two types of subunits: the biotinylated MCC-A subunit (encoded by the gene At1g03090) and the non-biotinylated MCC-B subunit (encoded by the gene At4g34030). The major metabolic role of MCCase is in the mitochondrial catabolism of leucine, and it also might function in the catabolism of isoprenoids and the mevalonate shunt. In the work presented herein, the single-copy gene encoding the Arabidopsis MCC-A subunit was isolated and characterized. It contains 15 exons separated by 14 introns. We examined the expression of the single-copy MCC-A and MCC-B genes in Arabidopsis by monitoring the accumulation of the two protein and mRNA products. In addition, the expression of these two genes was studied in transgenic plants containing the 1.1- and 1.0-kb 5' upstream sequences of the two MCCase subunit genes, respectively, fused to the beta-glucuronidase gene. Light deprivation induces MCCase expression, which is suppressed by exogenous carbohydrates, especially sucrose. Several lines of evidence indicate that the suppressor of MCCase expression is synthesized in illuminated photosynthetic organs, and can be translocated to other organs to regulate MCCase expression. These results are consistent with the hypothesis that the suppressor of MCCase expression is a carbohydrate, perhaps sucrose or a carbohydrate metabolite. We conclude that MCCase expression is primarily controlled at the level of gene transcription and regulated by a complex interplay between environmental and metabolic signals. The observed expression patterns may indicate that one of the physiological roles of MCCase is to maintain the carbon status of the organism, possibly via the catabolism of leucine.

Arabidopsis↗

Molecular characterization of a heteromeric ATP-citrate lyase that generates cytosolic acetyl-coenzyme A in Arabidopsis.

Acetyl-coenzyme A (CoA) is used in the cytosol of plant cells for the synthesis of a diverse set of phytochemicals including waxes, isoprenoids, stilbenes, and flavonoids. The source of cytosolic acetyl-CoA is unclear. We identified two Arabidopsis cDNAs that encode proteins similar to the amino and carboxy portions of human ATP-citrate lyase (ACL). Coexpression of these cDNAs in yeast (Saccharomyces cerevisiae) confers ACL activity, indicating that both the Arabidopsis genes are required for ACL activity. Arabidopsis ACL is a heteromeric enzyme composed of two distinct subunits, ACLA (45 kD) and ACLB (65 kD). The holoprotein has a molecular mass of 500 kD, which corresponds to a heterooctomer with an A(4)B(4) configuration. ACL activity and the ACLA and ACLB polypeptides are located in the cytosol, consistent with the lack of targeting peptides in the ACLA and ACLB sequences. In the Arabidopsis genome, three genes encode for the ACLA subunit (ACLA-1, At1g10670; ACLA-2, At1g60810; and ACLA-3, At1g09430), and two genes encode the ACLB subunit (ACLB-1, At3g06650 and ACLB-2, At5g49460). The ACLA and ACLB mRNAs accumulate in coordinated spatial and temporal patterns during plant development. This complex accumulation pattern is consistent with the predicted physiological needs for cytosolic acetyl-CoA, and is closely coordinated with the accumulation pattern of cytosolic acetyl-CoA carboxylase, an enzyme using cytosolic acetyl-CoA as a substrate. Taken together, these results indicate that ACL, encoded by the ACLA and ACLB genes of Arabidopsis, generates cytosolic acetyl-CoA. The heteromeric organization of this enzyme is common to green plants (including Chlorophyceae, Marchantimorpha, Bryopsida, Pinaceae, monocotyledons, and eudicots), species of fungi, Glaucophytes, Chlamydomonas, and prokaryotes. In contrast, all known animal ACL enzymes have a homomeric structure, indicating that a evolutionary fusion of the ACLA and ACLB genes probably occurred early in the evolutionary history of this kingdom.

ATP Citrate (pro-S)-Lyase↗