Pathways database system: an integrated system for biological pathways

MOTIVATION: During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers. RESULTS: In this paper we present an integrated system, called Pathways Database System, with a set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (a) genomic information integrated with other biological data and presented from a pathway, rather than from the DNA sequence, perspective; (b) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (c) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels, and to pose predetermined queries; and (d) an implementation that allows for web(XML)-based dissemination of query outputs (i.e. pathways data) to researchers in the community, giving them control on the use of pathways data. AVAILABILITY: Available on request from the authors.     

Activation of extracellular-regulated kinase pathways in ovarian granulosa cells by the novel growth factor type 1 follicle-stimulating hormone receptor. Role in hormone signaling and cell proliferation

Follicle-stimulating hormone (FSH) regulated growth and function of the ovarian follicle was previously thought to be mediated solely through activation of G(s)-coupled receptors. In this study, we show for the first time that this function is predominantly mediated through the alternatively spliced and novel growth factor type 1 receptor (oFSH-R3) that is also present in the ovary. Immortalized granulosa cells lacking endogenous FSH receptors, when transfected with either oFSH-R3 cDNA (JC-R3) or the G(s)-coupled oFSH-R1 (JC-R1), expressed the corresponding glycosylated receptor. In JC-R3 or JC-R1 cells labeled with bromodeoxyuridine or [(3)H]thymidine, FSH stimulated the cells to progress through S-phase and divide. The growth promoting effect of recombinant FSH in JC-R3 cells was preceded by the rapid activation of ERK1 and ERK2. This effect was hormone-specific and transient. In JC-R3 cells inhibitors like calphostin C, PD98059, Ag 18, or calcium chelators EGTA or 1,2-bis(O-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid/AM inhibited both mitogen-activated protein kinase activation and bromodeoxyuridine incorporation. FSH induced phosphorylation of the FSH-R3 receptor was blocked by pretreating cells with calphostin C. There was no cAMP induction by FSH in JC-R3 cells. The cAMP independent growth promoting effect of FSH is mediated by activation of Ca(2+) and mitogen-activated protein kinase-dependent pathways. Thus, alternative splicing of a G-protein coupled receptor creates the expression of a novel receptor motif that can mediate a widely recognized function of the glycoprotein hormone.     

A cluster of genes for the biosynthesis of spinosyns, novel macrolide insect control agents produced by Saccharopolyspora spinosa

Spinosyns A and D are the active ingredients in a family of insect control agents produced by fermentation of Saccharopolyspora spinosa. Spinosyns are 21–carbon tetracyclic lactones to which are attached two deoxysugars. Most of the genes involved in spinosyn biosynthesis are clustered in an 74 kb region of the S. spinosa genome. This region has been characterized by DNA sequence analysis and by targeted gene disruptions. The spinosyn biosynthetic gene cluster contains five large genes encoding a type I polyketide synthase, and 14 genes involved in modification of the macrolactone, or in the synthesis, modification and attachment of the deoxysugars. Four genes required for rhamnose biosynthesis (two of which are also required for forosamine biosynthesis) are not present in the cluster. A pathway for the biosynthesis of spinosyns is proposed.     

Changes in Saccharide Metabolism Induced by Infection of Camellia Sinensis by Exobasidium Vexans

Changes in saccharide contents of tea leaves during infection with blister blight fungus Exobasidium vexans Masse was studied. Saccharose and glucose contents decreased in the blistered portions when compared to the normal regions until sporulation and remained constant during the entire period of sporulation. Fructose content increased abruptly during the initiation of sporulation and remained constant up to the end of sporulation in both blistered and non-blistered regions. Starch content continuously decreased in the blistered region. Peroxidase activity was highly enhanced during the final stages of leaf senescence. The activity of acid invertase was inversely proportional to the starch content and closely related to the changes in the saccharose and glucose contents. Protein and chlorophyll contents gradually decreased in the blistered regions. This revised version was published online in July 2006 with corrections to the Cover Date.     

Micropropagation of licorice (Glycyrrhiza glabra L.) through shoot tip and nodal cultures

Summary Apical and axillary buds ofGlycyrrhiza glabra commonly known as licorice, a plant of repute in the Indian system of medicine, were used for induction of adventitious shoots. For induction of multiple shoots, Murashige and Skoog’s (MS) medium with N⁶-benzyladenine (BA, 0.88–8.87 μM) was used. Reduction in major salts of MS medium enhanced the multiplication ratio up to 1∶10. Plants transferred to the greenhouse showed 90% survival. The present work describes a stepwise protocol for production ofGlycyrrhiza glabra plants on simple minimal media, where very high multiplication rates with healthy root systems were obtained. Roots being the organ of commercial importance, the protocol has tremendous potential.     

Crystallization of the NAD-dependent malic enzyme from the parasitic nematode Ascaris suum.

The malic enzyme from muscle mitochondria of the parasitic nematode Ascaris suum is a tetramer of 65 kDa monomers that catalyzes the oxidative decarboxylation of malate to pyruvate and CO2 with NAD cofactor as oxidant. This malic enzyme is critical to the nematode for muscle function under anaerobic conditions. Unlike mammalian versions of the enzyme such as that found in rat liver, which require NADP as cofactor, the nematode version is an NAD-dependent enzyme. We report the crystallization of samples of the nematode enzyme at room temperature from pH 7.5 solutions of polyethylene glycol 4000 containing magnesium sulfate, NAD and sodium tartronate. Immediately upon mixing of protein and precipitant solutions, a marked precipitation of the protein occurs. Out of this precipitate, crystals appear almost immediately, most commonly in a truncated cube form that can grow to 0.5 to 0.7 mm on a cube edge in two to three days. The crystals are trigonal, space group P3(1)21 or its enantiomer, with a = b = 131.2(7) A, c = 152.6(9) A, and two monomers per asymmetric unit. Fresh crystals diffract X-radiation from a synchrotron source (lambda = 0.95 A) to about 3.0 A resolution. Rotational analysis of Patterson functions indicates that the malic enzyme tetramer has 222 symmetry.     

Studies on phytoplankton pigments in Porto Novo waters (India). I. Mangrove

The annual variations of phytoplankton pigments were studied from January to December, 1971, at two stations of the local mangrove (Pichavaram) environment. At these two stations, chlorophyll a varied from 2.90 to 35.06; chlorophyll b from 0 to 10.02 and chlorophyll c from 0 to 18.12 μg/l. Plant carotenoids varied from 1.56 to 13.83 MSPU/m³ and phaeopigments from 0 to 12.28 μg/l. The main (primary) peak of chlorophyll a was recorded during March at Station 1, and during June at Station 2.Secondary maxima occurred during June and August at Station 1, and during September at Station 2. During the period studied chlorophyll a was the dominant pigment at both the stations, followed by chlorophyll c and chlorophyll b in that order. The increase in the concentration of pigments was mainly due to the presence of phytoplankton species belonging to the genera such as Coscinodiscus, Rhizosolenia, Thalassiothrix, Melosira, Chaetoceros and Biddulphia. During October, phytoplankton was less and the pigment concentration was also low.