How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy steps.

MOTIVATION: The reconstruction of genetic networks is the holy grail of functional genomics. Its core task is to identify the causal structure of a gene network, that is, to distinguish direct from indirect regulatory interactions among gene products. In other words, to reconstruct a genetic network is to identify, for each network gene, which other genes and their activity the gene influences directly. Crucial to this task are perturbations of gene activity. Genomic technology permits large-scale experiments perturbing the activity of many genes and assessing the effect of each perturbation on all other genes in a genome. However, such experiments cannot distinguish between direct and indirect effects of a genetic perturbation. RESULTS: I present an algorithm to reconstruct direct regulatory interactions in gene networks from the results of gene perturbation experiments. The algorithm is based on a graph representation of genetic networks and applies to networks of arbitrary size and complexity. Algorithmic complexity in both storage and time is low, less than O(n(2)). In practice, the algorithm can reconstruct networks of several thousand genes in mere CPU seconds on a desktop workstation. AVAILABILITY: A perl implementation of the algorithm is given in the Appendix. CONTACT: wagnera@unm.edu     

Purified hybrid cells from dendritic cell and tumor cell fusions are superior activators of antitumor immunity

The use of fusions between dendritic cells (DCs) and tumor cells as vaccines has been proved very effective in stimulating antitumor immune responses, both in animal studies and in early human clinical trials. Because of the difficulty of purifying the hybrid cells from the fusion, fusion mixtures were used in these studies. Recently, we developed a technique using fluorescent-dye staining and fluorescence-activated cell sorting that enabled the hybrid cells to be instantly purified from the fusion mixture. In the present study, the hybrid cells were purified from a fusion between mouse DCs and B16F0 melanoma tumor cells using the new technique. The purified cells, named instant dendritomas (IDs) were then compared with fusion mixtures in stimulating antitumor immune responses. The results from cytotoxicity assays, interferon-gamma production and in vivo lung tumor metastasis demonstrated that IDs are more effective than fusion mixture in stimulating antitumor immunity. Meanwhile, there was no significant difference in the antitumor immunities activated by IDs from allogenic fusion or IDs from syngenic fusion.     

Sequence-selective peptide detection by small synthetic chemosensors selected from an encoded combinatorial chemosensor library.

Synthetic chemosensors hold great potential in many diagnostic applications. In this study, we describe the design and preparation of the first encoded combinatorial library of chemosensors for tripeptides. Subsequent screening of the library resulted in the discovery of novel chemosensors able to distinguish between random tripeptides.     

Synthesis of derivatives of the novel cyclophilin-binding immunosuppressant sanglifehrin A with reduced numbers of polar functions.

The syntheses and the biological activities of 53-deoxo sanglifehrin A (2) and 61-deoxy octahydrosanglifehrin A (3) are described. Compound 2 shows intracellular cyclophilin (CyP)-binding and immunosuppressive activity in the mixed-lymphocyte reaction (MLR) similar to that of sanglifehrin A (1). Compound 3 is much less active in the MLR despite unchanged intracellular CyP-binding. This indicates that the 53-keto group is not necessary for immunosuppressive activity, while the 61 hydroxy group is required.     

Physical and enzymatic properties of a class III isozyme of human liver alcohol dehydrogenase: chi-ADH

chi-Alcohol dehydrogenase (chi-ADH), a class III isozyme characterized by its anodic electrophoretic mobility and lack of inhibition by 4-methylpyrazole, has been isolated from human liver and purified to homogeneity in a reducing medium. chi-ADH resembles other human liver ADH isozymes of classes I and II with respect to its molecular weight, dimeric structure, stoichiometry of zinc and NADH binding, and pH optima for the oxidation of alcohols. This homodimer exhibits subtle differences in its absorption spectrum and amino acid composition relative to those of other human isozymes but differs markedly from their specificity toward alcohols and aldehydes. chi-ADH oxidizes ethanol very poorly. The reaction is bimolecular, and an apparent Km cannot be discerned up to 2.3 M ethanol. The enzyme is inactive toward methanol, ethylene glycol, digitoxigenin, digoxigenin, and gitoxigenin , but alcohols with carbon chain lengths greater than four are oxidized rapidly with Km values decreasing with increasing carbon chain length. Taken jointly, the composition, structure, and enzymatic properties of the ADH isozymes purified and studied so far strongly imply that their metabolic roles, yet to be discovered, will give a new perspective to ethanol metabolism and pathology.     

Leishmania tarentolae: proline anabolism in promastigotes.

Using ¹⁴C-labeled substrates in conjunction with thin-layer Chromatographic radioautography, studies were done to determine the precursors for proline synthesis utilized by promastigotes of Leishmania tarentolae. The only substances in Trager's Defined Medium capable of acting as proline precursors under the conditions studied were l-arginine and l-ornithine. None of the other substrates tested (16 amino acids, five purines and pyrimidines, and glucose) were converted to proline. l-glutamate, l-aspartate, and d-glucose did not act as precursors for the imino acid although they stimulated oxygen uptake better than did l-arginine and l-ornithine. Proline synthesis was unaffected by the presence of preformed proline indicating the absence of end product feedback inhibition.     

Über die Mitosenverteilung im Meristem der Wurzelspitzen

Ohne ZusammenfassungMit 11 Textabbildungen.     

Mechanism of activation of the protein kinase I from rabbit skeletal muscle. The high-affinity ATP site of the holoenzyme.

The high-affinity binding site for ATP of the holoenzyme of cAMP-dependent protein kinase (type I) from rabbit skeletal muscle has been investigated. Binding affinity of a series of ATP derivatives substituted at different sites in the molecule was determined by competition with tritiated ATP. The results were compared with data available from cAMP derivatives with the same substituents, in order to analyse the electronic and steric features of these two sites on the protein kinase. The comparison revealed significant differences of the effect of substituents towards the two sites. In particular the N6-derivatives of ATP and substituents affecting the gamma-phosphate indicate that the high-affinity ATP site of the protein kinase has similar properties as those found for phosphotransferase sites. The present results are consistent with the supposition that the high-affinity site for ATP on the holoenzyme is congruent with the phosphotransferase site of the catalytic subunit. Upon combination of catalytic and regulatory subunits this site would be transformed into a high-affinity site for ATP with simultaneous blocking of the phosphotransferase activity.     

Highly Invasive Listeria monocytogenes Strains Have Growth and Invasion Advantages in Strain Competition

Multiple Listeria monocytogenes strains can be present in the same food sample; moreover, infection with more than one L. monocytogenes strain can also occur. In this study we investigated the impact of strain competition on the growth and in vitro virulence potential of L. monocytogenes. We identified two strong competitor strains, whose growth was not (or only slightly) influenced by the presence of other strains and two weak competitor strains, which were outcompeted by other strains. Cell contact was essential for growth inhibition. In vitro virulence assays using human intestinal epithelial Caco2 cells showed a correlation between the invasion efficiency and growth inhibition: the strong growth competitor strains showed high invasiveness. Moreover, invasion efficiency of the highly invasive strain was further increased in certain combinations by the presence of a low invasive strain. In all tested combinations, the less invasive strain was outcompeted by the higher invasive strain. Studying the effect of cell contact on in vitro virulence competition revealed a complex pattern in which the observed effects depended only partially on cell-contact suggesting that competition occurs at two different levels: i) during co-cultivation prior to infection, which might influence the expression of virulence factors, and ii) during infection, when bacterial cells compete for the host cell. In conclusion, we show that growth of L. monocytogenes can be inhibited by strains of the same species leading potentially to biased recovery during enrichment procedures. Furthermore, the presence of more than one L. monocytogenes strain in food can lead to increased infection rates due to synergistic effects on the virulence potential.