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dictyNews Volume 25 Number 09
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.
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Abstracts
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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]
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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]
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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]
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[End Dicty News, volume 25, number 9] 
