Our monthly newsletter features a variety of information, highlighting
 current domestic and international issues concerning bioresources.

BioResource Newsletter  Vol.4 No.3

Introduction to
     Resource Center No.22F

ENBRP  "Cellular Slime Molds"




  Graduate School of  Life and Environmental
  Sciences,University of Tsukuba)

Ongoing Column  No.30F

EDevelopment of Desktop Applications by Flex



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Bioresources information is available at the following URLs

NBRP http://www.nbrp.jp/index.jsp
SHIGEN  http://www.shigen.nig.ac.jp/
WGR http://www.shigen.nig.ac.jp/wgr/
JGR http://www.shigen.nig.ac.jp/wgr/jgr/jgrUrlList.jsp

  Introduction to Resource Center No.22


 National BioResource Project
     "Cellular Slime Molds"

     Hideko URUSHIBARA, Professor,

     Graduate School of Life and Environmental
     Sciences, University of Tsukuba


    1. What are cellular slime molds ?        

logo [What are cellular slime molds?]
   Cellular slime molds are referred to as dictyostelid, a group of microorganism that inhabits relatively wet surfaces of soil, such as underneath fallen leaves. A feature of cellular slime molds is that under starvation stress, unicellular amoebas spread multicellularly, sporulate, and form carpophores that are composed of a cluster of spores and a supporting stalk (Fig. 1). At the mention of "slime molds", we often think of myxomycetes with colorful carpophores on a plasmodium, which grow in sizes in the order of square meters (these myxomycetes are well known from the research of Kumagusu Minakata). However, these myxomycetes are true slime molds consisting of multinuclear cytomegalic cells and are different from cellular slime molds.Carpophores of cellular slime molds are mononuclear and multicellular and grow to approximately 1-5 mm in height, which can be barely identified by naked eyes. The so-called pseudoplasmodium is a slug-like structure that is formed in the process of carpophore formation; it is motile in most species and is called "slug" in English and "mobile body" in Japanese (Fig. 2). Although carpophores develop asexually, sexual reproduction leading to the formation of macrocysts is also noted. Cellular slime molds are classified into 3 genera--Dictyostelium, which forms a typical carpophore in which a spore cluster is supported by a single steady stalk; Polysphondylium, which has a branched stalk; and Acytostelium, which develops a fragile noncellular stalk (Fig. 3).


} 1.
Fig. 1: Enlarged images of carpophores (left), spores
(top right), and a stalk
(bottom right) of cellular
slime molds.



} 2.
Fig. 2 : A scanning microscopic image that helps to understand the life cycle of Dictyostelium discoideum at a glance (reprinted from the image collection of dictyBase; a slug is shown on the bottom left).




Fig. 3

Fig. 3 : Carpophores of the 3 genera of cellular
slime molds. The images correspond to the names on the phylogenetic tree shown above.            

logo  [Position of Cellular Slime Molds on the Phylogenetic Tree]

   Although cellular slime molds exhibit amoeboid movement or possess a slug body at a certain stage of development, they form a stalk composed of cellulose and vacuolized stalk cells; this characteristic of stalk formation appears to be similar to that of plants. On the other hand, as symbolized by the Japanese name "Kiirotamahokorikabi" (yellow spherical dust fungus), carpophores remind us of fungi. However, recent molecular phylogenetic analysis and genome comparison have revealed that cellular slime molds diverged after the evolution of plants and before the evolution of fungi on the phylogenetic tree of eukaryotes (Fig. 4). I usually answer a frequently asked question, "Are cellular slime molds animals or plants?" by saying, "They are unique organisms that are neither animals nor plants."

Fig. 4
Fig. 4: Phylogenetic tree showing the evolutionary position of cellular slime molds

logo [Usefulness of Cellular Slime Molds as a Model Organism]
   Cellular slime molds feed on bacteria in soil and agricultural environment. It is possible to isolate a standard strain of D. discoideum in a pure culture (Fig. 5) and to easily apply various biochemical and molecular biological approaches and genetic manipulation techniques. Cellular slime molds are frequently used as model organisms in various fields of basic science such as cell biology, developmental biology, biophysics, and mathematical biology because of their active proliferation and movement, adoption of a simple multicellular system in which cells differentiate into only 2 forms--spores and stalk cells--within a period of 24 hours, and flexible adjustment of the ratio between cell types. In contrast, it is known that cellular slime molds harbor numerous genes that are pathogenic for humans and can serve as hosts for pathogenic microorganisms (Fig. 6); hence, they are listed as important model organisms of medical science by NIH (http://www.nih.gov/science/models/). In addition, cellular slime molds are reported to secrete secondary metabolites that show antiproliferative effects on cancer cells; thus, cellular slime molds are considered to be promising microbiological resources for drug design. The genome and cDNA analyses of cellular slime molds were completed in 2005; thus, substantial genetic information is now available.


} 5.

Fig. 5: Culturing of cellular slime molds. The optimum temperature to culture cellular slime molds is 20oC -25oC. Although usually a simple incubator, as shown in the image (left) is used for culturing cellular slime molds, it is also possible to culture at room temperature, except in summer. Double culturing and development by using round and square dishes and shake-culturing in liquid media are illustrated. In addition, a microscope (top right) and a clean bench are shown.




} 6.

Fig. 6: Infection of Legionella bacterium (indicated by L), a causative microorganism of pneumonia (left). Although Legionella is incorporated into a food vacuole, it avoids fusion with lysosome and continues to proliferate, thereby completely filling the cell in a single day.
Farbrother et al.,Cell Microbiol. 8:438-456, 2006.



  2. Aim to Develop as a Core Facility of Cellular Slime Molds     

logo [Implementation Structure]
   The collection, preservation, and distribution of cellular slime mold resources are managed by the University of Tsukuba, the core facility dealing with gene clones of D. discoideum, and the National Institute of Advanced Industrial Science and Technology (AIST), a sub-institute that handles strains. These institutes cooperate with external administrative committee members who are selected from the workshop of cellular slime molds (Fig. 7).

Fig. 7
Fig. 7: Organizational chart for resource consolidation


logo [Genetic Resources]
   Non-redundant sets of cDNA clones preserved in the University of Tsukuba, which were primarily used for the EST analysis will be rearranged and preserved as genetic resources. Among 12,500 genes predicted, currently, approximately 3,000 full-length clones are arrayed on 96-well plates. All the non-redundant clones will be consolidated in the future. Since cellular slime molds are convenient to handle for post-genome analysis, research using gene sets as a whole has been initiated.

logo [Strain Resources]
   The Dicty Stock Center (DSC) established in Columbia University, US, is supported by NIH and preserves cellular slime molds. However, it is difficult to convey this information to Japanese researchers who have not used cellular slime molds as a research resource; furthermore, it is problematic to export cellular slime mold cultures from US to Japan, especially recombinant strains. Therefore, our project aimed to collect, preserve, and distribute resources with a focus on Japanese researchers. We closely cooperate with DSC and have established a framework to mutually complement each other so that the stock of resources at DSC and NBRP can serve as a global standard of cellular slime mold resources. Moreover, we hope to receive feedback from local and international gene clone users as we strive to consolidate both genes and recombinant strains as high quality resources. We also offer consultations to inexperienced researchers regarding which strain to use and culturing methods. We hope that all the researchers would feel free to use our resources as secondary materials.



logo A Request to Researchers
   We have a request to researchers who uses our bioresources for their research. Please include information of the resources in Materials & Methods or Acknowledgements when you publish your research journals. In addition, please contact the source of your resources.
   NBRP has opened a registration website for research journals. You can easily submit your information at the address provided below.






Database users


  Ongoing Column  No.30

 Development of Desktop Applications by Flex

   A web application developed by Flex and Flex Builder was introduced in the previous issue ihttp://www.shigen.nig.ac.jp/shigen/news/n_letter/2008/2/sample.swf).
In Flex, not only web applications but also desktop applications can be developed.
   Desktop applications can be developed in the same manner as web applications by Flex Builder using simple manipulations such as drag-and-drop.
   As an example, I have developed "sample.air", a simple desktop application which opens a website when you click on an image.

sample. air

   This application has an ".air" extension and you can run it on an environment where Adobe Integrated Runtime (AIR) is installed. The air files will run on the environments stated below.


   Developers can provide users with an installation option called seamless installation to install AIR and AIR applications together (this method may not work on some types and versions of browsers).

Here is the link to seamless installation.


  If the seamless installation does not work properly, please download the applications one-by-one from the link given below. Start by installing AIR, followed by "sample.air". (If the file name of "sample.air" is changed to "sample.zip" after downloading, please change it back to "sample.air."

AIR (Software to run "air" applications)


sample.air ("air" application developed as a sample):


   Please try to submit your original AIR applications.






Editor's NoteF  Prof. Urushihara provided us the topic on cellular slime molds, which were newly adopted in the second National BioResource Project. I was impressed by a movie that she had presented at the panel exhibition site of the Biochemistry and Molecular Biology (BMB) conference 2007; this movie showed aggregation of single cells. Cellular slime molds are definitely a fascinating creature. According to Prof. Urushihara, it is not very difficult to culture cellular slime molds; therefore, in the near future, cellular slime molds may become as popular as Escherichia coli among researchers. I sincerely appreciate the contribution of Prof. Urushihara.
  Somei-yoshino cherry blossoms in the front of the National Institute of Genetics are in full bloom. Yaezakura (double petaled cherry blossoms) in the institute will soon be blooming prolifically. (Y.Y.)

Contact AddressF
1111 Yata, Mishima-shi, Shizuoka 411-8540, Japan
Center for Genetic Resource Information, National Institute of Genetics
Tel: 055-981-6885 (Yamazaki)@
E-mail: brnews@chanko.lab.nig.ac.jp

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