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Porifera OneZoom

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OneZoom (TM) web version 1.1 (2012)
Copyright (c) 2012 owned by James Rosindell and Imperial College, London
Citation: "OneZoom: A Fractal Explorer for the Tree of Life" PLoS Biology (2012) Rosindell, J. and Harmon, L. J.
All rights reserved.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

SICB 2013: PorToL Symposium Presentations

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The PorToL team hosted a symposium at the 2013 Annual Meeting of the Society for Integrative and Comparative Biology (SICB), titled Assembling the Poriferan Tree of Life. The symposium was co-sponsored by the the American Microscopical Society, the SICB Division of Phylogenetics and Comparative Biology, and the SICB Division of Invertebrate Zoology

Papers from the symposium were published in the September 2013 issue of Integrative and Comparative Biology.

The following presentations from the symposium are available to view. Please contact the authors of these presentations with your comments and suggestions.


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PorToL team members have participated in numerous meetings and workshops.

Here many of us are meeting with some of our international collaborators at Harbor Branch Oceanographic Institute, August 2011.

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Some PorToL Resources are available to authenticated users only.

Sponge Morphology

Boury-Esnault N and Ruetzler K (editors). 2007. Thesaurus of Sponge Morphology. Smithsonian Contributions to Zoology Number 596. 55 pages, 306 figures.
Download from the Smithsonian Institution

Electronic Version of the Thesaurus of Sponge Morphology

Sponge Courses

Preservation with RNAlater

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Preservation for RNA/DNA (using RNAlater)

This commercially available fixative is often used with success; other labs find it problematic. It is apparently not a good means for preserving microRNAs. Best practices are as follows:

A) Maintain a fixative:tissue ratio of 5:1 at least. More fixative is better.

B) Cut the tissue into very small pieces, e.g., 1-2 mm cubes.

C) Incubate overnight at room temperature.

D) Store at -20°C or -80°C.

Preservation for RNA (including microRNAs)

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Preservation for RNA (including microRNAs -- 75% ethanol series at -20°C)

To adequately preserve RNA, and particularly ensuring the preservation of microRNAs, multiple changes of ice-cold 75% ethanol can be used.

A) Keep materials on ice or ice-cold at all times.

B) It is best to preserve 2 “thumb-end size” pieces (or 4 1-cubic-cm pieces) in a 50 ml tube of ethanol. The larger volume ratio of ethanol:sponge, the better.

C) Put fresh tissue in 75% ethanol.

D) Change to fresh 75% ethanol after 15 minutes.

E) Change to fresh 75% ethanol after 1 hour.

Preservation for Histology

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Preservation for Histology: 4% paraformaldehyde (PFA) and 70% ethanol

For many morphological features, especially those observed with histological techniques, it is useful to fix specimens in 4% PFA, followed by storage in 70% ethanol. However, specimens processed in this manner yield little to no successful DNA extraction, PCR, and sequencing.

The following procedure works well to prepare specimens for histological sections used in confocal microscopy and FISH staining.

Basic Preservation

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Basic Preservation for DNA Extractions and Limited Morphological Work

A) Each individual specimen should be placed into a separate container. We find that 50 ml tubes or WhirlPaks work well.

B) Be sure to label the outside of the container with your specimen ID number. If you do not already have a system in place, you could use your initials followed by a number (e.g., RT53; or in conjunction with a collection event, e.g., Bali2010-RT53).

C) Appropriately label a small piece of solvent-resistant paper with pencil and place inside each specimen container.

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