Aflatoxin — induced alteration in the levels of membrane chemicals of subcellular organelles isolated from excised,incubated Glycine max,cv. ‘Essex’ roots

Isolates of aflatoxin-producing strains of Aspergillus grow on autoclaved and field-grown (lesser extent) Glycine max beans. Both mixed and aflatoxin B₁ inhibit G. max, cv. Essex bean germination and elongation of either attached or excised cultured roots. Because B₁ impairs the latter roots' ability to intracellularize [¹⁴C]-leucine, it may alter plasmalemma structure and/or function. To determine whether incubation of excised roots for 18 hours in toxin-containing medium could affect cellular membrane chemical content, organelles were isolated by differential centrifugation (1 000, 40 000, and 80 000 xg) of homogenates and characterized chemically. Statistically significant differences between treated and untreated roots in acid insoluble protein but not either sterol or lipid phosphorus levels were observed for both 40,000 and 80,000 xg pellets. Protein and sterol recoveries were 81 (treated) and 84 (untreated) % for the former and 77 (treated) and 79 (untreated) % for the latter. Lipid phosphorus recoveries were 87.3 (treated) and 136 (untreated) % with and 96 (treated) and 83 (untreated) without membrane stabilization. Protein:sterol:lipid phosphorus were 35.74.51 (1 000 xg), 18.93.61 (40000 xg), 26.34.61 (80 000 xg) and 1,010291 (80 000 xg supernatant) for untreated and 36.93.31 (1,000 xg), 23.13.81 (40 000 xg), 36.24.81 (80 000 xg) and 1,05321.71 (80 000 xg supernatant) for treated roots. Significant differences in RNA content between treated and untreated roots were found for both 1 000 and 40 000 xg pellets but not for the 80 000 xg pellet and its supernatant. Whereas a significant increase in the 1 000 xg pellet occurred upon treatment, a decrease was noted for the 40 000 xg pellet but not for the 80 000 xg pellet and its supernatant. Similar pH 6 (plasmalemma marker enzyme) and 9 (mitochondrial marker enzyme) K⁺-stimulated ATPase activities were demonstrated for 40 000 and 80 000 xg pellets. The 1 000 xg pellet contained greater than 50% of the NADH-cytochrome c-reductase activity (endoplasmic reticulum marker enzyme) recovered from fractions examined for this activity which was absent from the 40 000 xg pellet. Both the 80 000 xg pellet and its supernatant possessed equivalent reductase activities. Inosine diphosphatase activity (dictyosome marker enzyme) was not present in 1 000 xg pellets obtained from either treated or untreated roots but was in both 40 000 and 80 000 xg pellets. Based on these results, a tentative assignment of organelles to each fraction (xg force) is reported.Abbreviations used AFB₁ aflatoxin B₁ - AFB₂ aflatoxin, B₂ - AFG₁ aflatoxin G₁ - AFG₂ aflatoxin G₂ - ATPase adenosine triphosphatase - IDPase inosine diphosphatase - NADH reduced nicotinamide-adenine dinucleotide - PCA perchloric acid - TCA trichloroacetic acid - 2, 4-D 2,4-dichlorophenoxyacetic acid Aided by grant IN-127 from the American Cancer Society to WVD and funds from the Departments of Biology, West Virginia University and Virginia Commonwealth University as well as a Sigma Xi award to JMD.     

Gibberellic-acid-induced synthesis and release of cell-wall-degrading endoxylanase by isolated aleurone layers of barley

When aleurone layers of barley (Hordeum vulgare L.) are incubated with gibberellic acid (GA₃) xylose and arabinose—both as free sugars and bound to larger molecules—are released into the medium. Release begins 10–12h after the start of incubation and continues for at least 60h. At the same time there is a GA₃-induced breakdown of the cell wall resulting in a loss of 2/3 of the cell-wall pentose during 60h of incubation. GA₃ causes the appearance in the medium of an enzyme (or enzymes) which hydrolyze larchwood xylan and aleurone-layer arabinoxylan. Release of the enzyme(s) into the medium begins 28–32h after the start of incubation. Enzyme activity does not accumulate to any large extent in the tissue prior to release into the medium, and is present in very low levels only in the absence of GA₃. Xylanase activity is associated with a protein (or proteins) with a molecular weight of 29,000. The hydrolysis of the xylans is largely caused by endoxylanase activity, indicating the importance of endoglycosidases in the GA₃-induced breakdown of the aleurone cell wall.     

NBLAST: a cluster variant of BLAST for NxN comparisons

Background  

The BLAST algorithm compares biological sequences to one another in order to determine shared motifs and common ancestry. However, the comparison of all non-redundant (NR) sequences against all other NR sequences is a computationally intensive task. We developed NBLAST as a cluster computer implementation of the BLAST family of sequence comparison programs for the purpose of generating pre-computed BLAST alignments and neighbour lists of NR sequences.     

Hormonal regulation of genetic tumor induction: Cytokinin and abscisic acid

Young seedlings of the tumor-prone amphiploid Nicotiana suaveolens? N. langsdorjfii were grown aseptically on nutrient mediumin a controlled environment chamber. At regular intervals theincidence of tumor formation was scored and plants were harvested.Total cytokinin activity was determined by means of the cucumbercotyledon bioassay, while ABA activity was measured by radioimmunoassay.A close correlation between onset of tumor formation and elevationin endogenous cytokinin activity was demonstrated, but no correlationwas observed between onset of tumorigenesis and change in thelevel of ABA. In addition, exposure of plants to exogenous ABAdid not alter therate of tumor formation. These results arediscussed in relation to the trigger mechanism for tumor inductionin the Nicotiana system. ¹A preliminary report of some of this work was presented atthe American Society of Plant Physiologists meeting in June1978. ³Present address: Department of Biology, West Virginia University,Morgantown, West Virginia 26506, U.S.A. (Received March 10, 1979; )     

Mycotoxigenic isolates and toxin production on buckwheat and rice hulls used as bedding materials

Summary A pre-evaluation of the samples of both buckwheat and rice hulls, planned for use as pillow fill-materials, showed the presence ofAspergillus flavus, A glaucus, andPenicillium spp. Buckwheat- and rice-hull media (BHM and RHM) inoculated withA. flavus both supported the production of aflatoxins (AFB₁ and AFG₁) in the parts per million (ppm) range; BHM yielded approximately twice the quantity of both AFB₁ and AFG₁ than did RHM. Both BHM and RHM inoculated withFusarium tricinctum yielded trichothecenes (T-2 toxins) in the ppm range, with the BHM producing approximately three times more T-2 toxins than the RHM. Also,F. tricinctum grown on both media produced several metabolites which included HT-2, 3-OH T-2, neosolariol, T-2 triol, and T-2 tetraol. The BHM yielded all of the above, while the RHM failed to support the production of the 3-OH T-2 toxin. In addition, neither medium inoculated withMyrothecium roridum yielded any detectable levels of macrocyclic trichothecenes. The results indicated that these materials have the potential to become contaminated with mycotoxins.     

SECRETORY CELLS OF LILY PISTILS. II. ELECTRON MICROSCOPE CYTOCHEMISTRY OF CANAL CELLS

The secretory cells which line the canal of Lilium longiflorum pistils possess, on the side facing the canal, an elaborate wall which, with associated structures, Rosen and Thomas (1970) termed the “secretion zone.” We examined the secretion zone in the electron microscope following treatment of excised pistil slices with extraction procedures which remove pectin, hemicellulose, cellulose, lipid, or protein. The outer, fibrillar wall (layer 1) of the secretion zone contains protein, pectin, and cellulose. Internal to layer 1 is a granular-fibrillar wall (layer 2) several microns thick. It consists of outer and inner regions which can be distinguished from each other cytochemically. The granular component is composed of pectin which is not esterified with methyl groups and which may be complexed with protein. The short, randomly dispersed microfibrils of layer 2 were sensitive to procedures which dissolve cellulose. The extraction procedures did not reveal the chemical nature of the “osmiophilic islands” of layer 2. Paramural body membranes appear to be composed of glycoprotein and may function in secretion by serving as sites of pinocytic interchange at the plasmalemma. The origin of stigmatic exudate and the release of canal cell secretion product are discussed.     

Toxic responses of germinating pollen and soybeans to aflatoxins

Aflatoxin producing strains of Aspergillus grow on soybeans thereby contaminating the latter through secretion of the toxin. Investigations dealing with either soybean seed germination or intact seedling growth responses to aflatoxin (B₁) are lacking. Similarly, a possible interaction of aflatoxins with phosphate in the germination and elongation of both soybeans and pollen as well as roots of the former and tubes of the latter has not been examined. Imbibition of Glycine max, cv. Essex seeds for 18 hours in solutions containing 0.38, 2.90, 5.80 or 11.60 g/ml (AFB₁) yielded% germination inhibitions of 5, 20, 40 and 80, respectively. By 36 hours these were 6, 4, 13 and 19 % for the same toxin concentration series. At 140 hours attached root elongation was inhibited 26, 35 and 50 % for 2.90, 5.80 and 11.60 g/ml AFB₁. No effect was noted at 0.38 g/ml AFB₁. Incubation of excised roots in medium containing 3.0 mM KH₂PO₄ stimulated their elongation 3.2 fold. Addition of 33.28 g/ml mixed aflatoxins together with KH₂PO₄ resulted in only a 1.5 fold stimulation. When KH₂PO₄ was added to a culture medium lacking AFB₁, Lilium longiflorum, cv. Ace pollen germination was enhanced 50%. Withholding KH₂PO₂ but supplying AFB₁ did not markedly affect germination. However, supplementing the medium with KH₂PO₄ while simultaneously adding AFB₁ did not inhibit germination at 5 and 10 g/ml but caused 27.3 and 45.1 % declines at 25 and 30 g/ml. In the absence of KH₂PO₄ AFB₁ stimulated pollen tube elongation 7.5, 14.3, 16.5 and 13.2 % at 5, 10, 15 and 20 g/ml but 30 g/ml inhibited it 11.1%. In contrast, tube elongation was suppressed at all AFB₁ concentrations (maximum 36.1% at 30 g/ml) tested upon KH₂PO₄ addition. Results derived from germinating pollen in medium supplemented with KH₂PO₄ or NaH₂PO₄ indicate that the phosphate anion does not preferentially promote aflatoxin-induced inhibition of tube elongation.Aided by grant IN-127 from the American Cancer Society to W.V. Dashek and funds from the Departments of Biology, West Virginia University and Virginia Commonwealth University and the West Virginia University Foundation.     

PreBIND and Textomy – mining the biomedical literature for protein-protein interactions using a support vector machine

Background

The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-readable format. We hypothesized that the formidable task-size of backfilling the database could be reduced by using Support Vector Machine technology to first locate interaction information in the literature. We present an information extraction system that was designed to locate protein-protein interaction data in the literature and present these data to curators and the public for review and entry into BIND.

Results

Cross-validation estimated the support vector machine's test-set precision, accuracy and recall for classifying abstracts describing interaction information was 92%, 90% and 92% respectively. We estimated that the system would be able to recall up to 60% of all non-high throughput interactions present in another yeast-protein interaction database. Finally, this system was applied to a real-world curation problem and its use was found to reduce the task duration by 70% thus saving 176 days.

Conclusions

Machine learning methods are useful as tools to direct interaction and pathway database back-filling; however, this potential can only be realized if these techniques are coupled with human review and entry into a factual database such as BIND. The PreBIND system described here is available to the public at http://bind.ca. Current capabilities allow searching for human, mouse and yeast protein-interaction information.     

An automated method for finding molecular complexes in large protein interaction networks

Background  

Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks. Initial mapping efforts have already produced a wealth of data. As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery.     

Domain-based small molecule binding site annotation

Background  

Accurate small molecule binding site information for a protein can facilitate studies in drug docking, drug discovery and function prediction, but small molecule binding site protein sequence annotation is sparse. The Small Molecule Interaction Database (SMID), a database of protein domain-small molecule interactions, was created using structural data from the Protein Data Bank (PDB). More importantly it provides a means to predict small molecule binding sites on proteins with a known or unknown structure and unlike prior approaches, removes large numbers of false positive hits arising from transitive alignment errors, non-biologically significant small molecules and crystallographic conditions that overpredict ion binding sites.