Integration of biological networks and gene expression data using Cytoscape

Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.     

In vivo observations of timecourse and distribution of morphological dynamics in Xenopus retinotectal axon arbors

Changes in neuronal structure can contribute to the plasticity of neuronal connections in the developing and mature nervous system. However, the expectation that they would occur slowly precluded many from considering structural changes as a mechanism underlying synaptic plasticity that occurs over a period of minutes to hours. We took time-lapse confocal images of retinotectal axon arbors to determine the timecourse, magnitude, and distribution of changes in axon arbor structure within living Xenopus tadpoles. Images of axons were collected at intervals of 3 min, 30 min, and 2 h over total observation periods up to 8 h. Branch additions and retractions in arbors imaged at 3- or 30-min intervals were confined to shorter branches. Sites of additions and retractions were distributed throughout the arbor. The average lifetime of branches was about 10 min. Branches of up to 10 μm could be added to the arbor within a single 3-min observation interval. Observations of arbors at 3-min intervals showed rapid changes in the structure of branchtips, including transitions from lamellar growth cones to more streamlined tips, growth cone collapse, and re-extension. Simple branchtips were motile and appeared capable of exploratory behavior when viewed in time-lapse movies. In arbors imaged at 2-h intervals over a total of 8 h, morphological changes included longer branches, tens of microns in length. An average of 50% of the total branch length in the arbor was remodeled within 8 h. The data indicate that the elaboration of the arbor occurs by the random addition of branches throughout the arbor, followed by the selective stabilization of a small fraction of the new branches and the retraction of the majority of branches. Stabilized branches can then elongate and support the addition of more branches. These data show that structural changes in presynaptic axons can occur very rapidly even in complex arbors and can therefore play a role in forms of neuronal plasticity that operate on a timescale of minutes. © 1996 John Wiley & Sons, Inc.     

Safety evaluation of DT388IL3, a diphtheria toxin/interleukin 3 fusion protein, in the cynomolgus monkey

We developed a fusion toxin, DT₃₈₈IL3, consisting of the catalytic and translocation domains of diphtheria toxin (DT₃₈₈) linked to interleukin 3 (IL3) for the treatment of patients with acute myeloid leukemia (AML). Our goal in this study was to estimate a range for the maximum tolerated dose (MTD) and to evaluate the dose-limiting toxicity (DLT) of DT₃₈₈IL3 in cynomolgus monkeys (Macaca fasicularis), which possess cross-reactive IL3 receptors. In our previous study, we administered up to six infusions of DT₃₈₈IL3 at 40, 60, or 100 g/kg every other day to three pairs (one male monkey and one female monkey) of young adult monkeys. In five of six monkeys, results showed a dose-dependent increase in malaise and anorexia but no consistent abnormalities in serum chemistries or blood counts. There was no evidence of organ damage by blood tests or histopathology. However, the female treated at 100 g/kg, died of moderate to severe vasculitis of multiple tissues. Based on these findings, this study repeated the 100 g/kg group and added a group that received 150 g/kg in an effort to confirm a dose response. Two female monkeys were treated with up to six infusions of DT₃₈₈IL3 at 100 g/kg or 150 g/kg every other day. One additional female monkey was treated as a negative control. Monkeys in the 100 g/kg group showed moderate malaise and anorexia, but no consistent abnormalities in blood counts or serum chemistries. Moderate elevations of liver enzymes were noted in the 150 g/kg group in addition to severe malaise and anorexia. No significant findings were revealed at gross necropsy. The histopathological findings revealed regenerative myeloid hyperplasia and hepatic degeneration and regeneration in the 150 g/kg group. Similar lesions of less severity were detected in the 100 g/kg group. DT₃₈₈IL3 plasma half-life was approximately 20 min with a peak concentration of approximately 2 g/ml (30,000 pM). The IC₅₀ for AML blasts in vitro was 6 pM. Collectively, our results suggest that DT₃₈₈IL3 can be tolerated at doses up to 100 g/kg in a nonhuman primate, which is higher than previously reported for other AML directed diphtheria toxin fusion proteins, and should in principle allow for dose escalation with reduced toxic side effects. Based on these findings a phase I clinical trial has recently been initiated with DT₃₈₈IL3 for the treatment of AML.     

HUMAN MONOCYTES AND MACROPHAGES : Interaction with Antigen and Lymphocytes

PPD-sensitized monocytes and macrophages from tuberculin-positive subjects are both capable of inducing blastogenic transformation of autologous lymphocytes. Incorporation of thymidine-³H and morphological transformation were always greater in lymphocyte cultures containing macrophages than in those containing monocytes. More lymphocytes entered the first detectable S phase in cultures containing macrophages. Lymphocyte DNA synthesis occurred as early as 40 hr of culture and always in cells in contact with mononuclear phagocytes. By 120–144 hr, many transformed lymphocytes were free in suspension; at the same time, the "immunological cluster" had increased greatly in size and contained transformed and untransformed lymphocytes. The greater effectiveness of macrophages at induction of lymphocyte transformation may be related to the efficiency of this cell type at trapping antigen and its effectiveness at making contact with and binding lymphocytes.     

Alterations of class I HLA genes in human colon cancers

Summary Alterations of HLA class I genes were found in 3 of 12 human colon cancers. Rearrangements in HLA class I genes were observed in 2 cancers and amplification of HLA-coding genes was observed in 1 cancer. All 3 cancers were at an advanced stage. No examples of amplification or rearrangement in the HLA genes were found in 10 other tumours of diverse types. No alterations in the ₂-microgubulin gene were observed in 22 human solid tumours included in this study. The association between alterations in HLA genes and proto-oncogenes in these tumours is discussed.     

Functional Changes Associated with Structural Alterations Induced by Mobilization of a P Element Inserted in the Sex-lethal Gene of Drosophila

Genetic analysis of rearrangements within the multifunctional sex determining gene Sex-lethal has allowed correlation of changes in specific functions with DNA alterations. Rearrangements were isolated by mobilization of a P element which is on the 5' side of the gene, at coordinate 0. Previous work has shown that rearrangements associated with alterations in Sxl gene function are found within an 11-kb region between coordinates-11 and 0. Here it is shown that insertion of foreign DNA, per se, at coordinate 0 is compatible with wild-type gene function. However, deletion of sequences on either side of this point generates a mutant phenotype. Deletions extending distally beyond coordinate -6.5 kb result in a null phenotype, whereas smaller distal deletions or proximal deletions eliminate only some Sxl functions.     

Trilobites Calmoniidae de l'Ordovicien supérieur du Maroc et les origines de la Province Malvino-Cafre

A re-examination of the trilobite Baniaspis globosa Destombes (Phacopina) from the Ashgill of the Anti-Atlas (Morocco) shows that it has several derived characters which allow us to classify it in the family Calmoniidae. Calmoniids were characteristic members of the Malvino-Kaffric province during the Lower Devonian. Hence we regard the origins of this palaeogeographic province as located on the northern Gondwanan margin as early as Ashgill, or even Caradoc, times. We agree with those authors who have suggested that the trilobite associations present in the Anti-Atlas, the Montagne Noire (France) and Bohemia during the earlier Ordovician argue against the existence of a 'proto-Tethys' ocean.