Dicty News Electronic Edition Volume 25, number 9 October 21, 2005 Please submit abstracts of your papers as soon as they have been accepted for publication by sending them to dicty@northwestern.edu or by using the form at http://dictybase.org/db/cgi-bin/dictyBase/abstract_submit. Back issues of Dicty-News, the Dicty Reference database and other useful information is available at dictyBase - http://dictybase.org. ============= Abstracts ============= Protrusion force transmission of amoeboid cells crawling on soft biological tissue Guy Ladam, Laurent Vonna and Erich Sackmann Acta Biomaterialia, Volume 1, Issue 5, September 2005, Pages 485-497 We applied a colloidal force microscopy technique to measure the spreading and retraction forces generated by protrusions (pseudopodia) of vegetative amoeboid cells (Dictyostelium discoideum) adhering on soft tissue analogues composed of 2-mm thick hydrogels of hyaluronic acid exhibiting Young 92s moduli between 10 and 200 Pa. Local shear deformations of the polymer films evoked by magnetic tweezers and by cellular protrusions were determined by analyzing the deflections of colloidal beads randomly deposited on the surface of the polymer cushions, which enabled us to measure forces generated by advancing ( 93pushing 94 forces) and retracting ( 93pulling 94 forces) protrusions in a direct way. We found that the maximum amplitudes generated by the advancing protrusions (pushes) decrease with increasing stiffness of the HA substrate while the amplitudes of the retractions do not show such a dependence. The maximum forces transmitted by the advancing and retracting protrusions increase with increasing stiffness of the HA films (from 0.02 to 1 nN for the case of pushing). The protrusions spread or retract with constant velocities which are higher for retractions (100 nm s-1) than for spreadings (50 nm s-1) and are not significantly influenced by the substrate rigidity. We provide evidence that elastic equilibrium during protrusion formation and retraction is maintained by local elastic dipole fields generated at the rim of the protrusions. A model of protrusion force transmission by coupling of growing actin gel in the cytoplasm of the protrusions to cell surface receptors through talin clutches is proposed. Submitted by: Guy Ladam [Guy.Ladam@univ-rouen.fr] ----------------------------------------------------------------------------- Microarray Phenotyping in Dictyostelium Reveals a Regulon of Chemotaxis Genes Ezgi O. Booth, Nancy Van Driessche, Olga Zhuchenko, Adam Kuspa and Gad Shaulsky Graduate Program in Structural and Computational Biology and Molecular Biophysics; Department of Molecular and Human Genetics; Department of Biochemistry and Molecular Biology; Baylor College of Medicine, Houston, TX 77030 Bioinformatics, In Press Motivation: Coordinate regulation of gene expression can provide information on gene function. To begin a large-scale analysis of Dictyostelium gene function, we clustered genes based on their expression in wild-type and mutant strains and analyzed their functions. Results: We found 17 modes of wild-type gene expression and refined them into 57 sub-modes considering mutant data. Annotation analyses revealed correlations between co-expression and function and an unexpected correlation between expression and function of genes involved in various aspects of chemotaxis . Co-regulation of chemotaxis genes was also found in published data from neutrophils. To test the predictive power of the analysis, we examined the phenotypes of mutations in 7 co-regulated genes that had no published role in chemotaxis. Six mutants exhibited chemotaxis defects, supporting the idea that function can be inferred from co-expression. The clustering and annotation analyses provide a public resource for Dictyostelium functional genomics. Supplement: http://dictygenome.org/supplement/gadi/okyay_2005/ Submitted by: Gad Shaulsky [gadi@bcm.tmc.edu] ----------------------------------------------------------------------------- Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi Markus Kuhlmann1#, Branimira E. Borisova1#, Markus Kaller1, Pontus Larsson2, Dirk Stach3, Jianbo Na4,  Ludwig Eichinger4, Frank Lyko3, Victor Ambros5, Fredrik Söderbom6, Christian Hammann1 and Wolfgang Nellen1* Nucleic Acids Research, in press We have identified a DNA methyltransferase of the Dnmt2 family in Dictyostelium that was denominated DnmA. Expression of the dnmA gene is downregulated during the developmental cycle. Overall DNA methylation in Dictyostelium is approximately 0.2% of the cytosine residues, which indicates its restriction to a limited set of genomic loci. Bisulfite sequencing of specific sites revealed that DnmA is responsible for methylation of mostly asymmetric C residues in the retrotransposons DIRS-1 and Skipper. Disruption of the gene resulted in a loss of methylation and in increased transcription and mobilization of Skipper. Skipper transcription was also upregulated in strains that had genes encoding components of the RNA interference pathway disrupted. In contrast, DIRS-1 expression was not affected by a loss of DnmA but was strongly increased in strains that had the RNA directed RNA polymerase gene rrpC disrupted. A large number of siRNAs was found that corresponded to the DIRS-1 sequence, suggesting concerted regulation of DIRS-1 expression by RNAi and DNA modification. No siRNAs corresponding to t he standard Skipper element were found. The data show that DNA methylation plays a crucial role in epigenetic gene silencing in Dictyostelium but that different, partially overlapping mechanisms control transposon silencing. Submitted by: Wolfgang Nellen [nellen@uni-kassel.de] ============================================================================== [End Dicty News, volume 25, number 9]