doi: 10.1242/10.1242/dev.00167
The Schmidtea mediterranea database as a molecular resource for studying platyhelminthes, stem cells and regeneration
Alejandro Sánchez Alvarado*,
,
,
Phillip A. Newmark*,
,
Sofia M. C. Robb and
Réjeanne Juste
Carnegie Institution of Washington, Department of Embryology, Baltimore,
MD 21210, USA
Present address: University of Utah School of Medicine, Department of
Neurobiology and Anatomy, Salt Lake City, UT 84132-3401, USA
Present address: University of Illinois at Urbana-Champaign, Department of
Cell and Structural Biology, Urbana-Champaign, IL 61801, USA
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Fig. 1. Bioinformatics and categorization of S. mediterranea sequences.
(A) Organigram depicting the steps performed to produce a non-redundant
collection of S. mediterranea cDNA sequences (SmedDb). Bioinformatic
analyses compared the database against itself to identify and remove redundant
clones before sending sequences to the public databases. The GenBank protein
and nucleotide collections as well as the EST database (dbEST) were queried
using the BLAST algorithm. Sequences returning significant matches
(E 10-4) were subjected to annotation into functional categories
based on the identity/function of the GenBank match. (B) Distribution of
informative sequences by functional categories. For simplicity the cell
signaling category includes the cell/cell communication and internal signaling
categories. Metabolism is an amalgamation of the general metabolism,
mitochondria and protein metabolism categories. Visit
http://planaria.neuro.utah.edu
for a detailed categorization profile and access to sequences. (C)
Distribution by percentage of planarian genes displaying highest similarities
with members of either the vertebrates or invertebrates.
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Fig. 2. Representative results of high-throughput, whole-mount in situ
hybridization. (A-C) Probe identity corresponding to the images is given from
top to bottom with each clone ID in parentheses as follows. (A) Gene
expression patterns within the nervous system of S. mediterranea:
synaptotagmin (H.6.7h); quinoid dihydropteridine reductase (H.9.5b); pax6
(H.109.7h) and degenerin (H.112.3c). (B) Gene expression patterns in organ
systems: gastrovascular system (D.14; unknown function), dorsal epithelium
(H.7.1e; gp25L/p24 family), excretory system (H.14.9d; carbonic anhydrase);
and pharynx (H.14.11f; unknown function). (C) Gene expression in discrete cell
types: matrix metalloproteinase (A115) in central secretory cells; epithelial
cells (H.12.11a; intermediate filament); subepidermal marginal adhesive gland
cells (H.1.3b; zonadhesin); and free-mesenchymal cells (neoblasts) expressing
piwi (H.2.12c). (D) Ventral view (left) of clone H.8.1f (unknown function),
and lateral view of the same specimen (right) demonstrate a dorsoventral
segregation of differentiation. The red asterisk indicates the position of the
pigmented photoreceptor. Anterior is to the left in all panels.
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Fig. 3. Regulation of cell number in planarians of different lengths. (A) In situ
hybridization of clone H112.3c, showing distribution of putative
chemoreceptive neurons underlying anterior margin. Nomarski DIC view. Scale
bar: 100 µm. (B) Number of H112.3c-positive cells/side in organisms of
different lengths. Mean number of H112.3c-positive cells (±s.d.) is
indicated (for 1 mm, n=14; 2 mm, n=9; 6 mm, n=10; 8
mm, n=7).
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© The Company of Biologists Ltd 2002
