Laboratory of Animal Model Organisms

 

 

Head:


Agata Tyczewska, PhD

 


   

Staff:

Joanna Gracz Bernaciak, PhD Eng.;

Karol Kołodziejczak, MSc Eng.

 

 

 

Laboratory affiliated to the Department of Integrative Biology

 

Keywords:

Caenorhabditis elegans, microinjection, Caenorhabditis elegans, C. elegans, MediaJet, Mediaclave, Tissue Lyser, PC-100 micro needle puller, nutrient media Integra

 

Offer:

  • Nutrient media sterilization (from 1 l to 10 l)
  • Petri plates pouring, up to 900 plates per hour (Ø 35 mm, 60 mm, 90 mm)
  • Microneedle preparation
  • Microinjections (possibility to use with C. elegans, cell nuclei and cytomplasm of adherent cells, pronucleuses of fertilized mouse oocytes, Xenopus laevis oocytes, fish embryos in early development phases)

 

Equipment:

  • Mediaclave 10, Integra
  • MediaJet vario, with sets for Ø 35 mm, 60 mm, 90 mm Petri plates, Integra
  • PC-100 microneedle puller, Narishige
  • Axio Vert.A1 microscope (Zeiss), with the Eppendorf microinjection set mounted:
    the InjectMan ®4 micromanipulator with dynamic motion control and the programmable FemtoJet ®4i micro diaphragm with integrated pressure supply
  • Tissue Lyser with 2 x 24 Adapter Set for 2 ml tubes, and Grinding Jar Set (stainless steel, 2 x 10 ml)

Since the 1960s, the nematode Caenorhabditis elegans has been used as model organisms for the investigation of a variety of biological processes. As a transparent, multi-cellular, eukaryotic organism, C. elegans not only facilitates the study of cellular differentiation and other developmental processes, it is also an excellent genetic model system. In 1963, Sydney Brenner (2002 Nobel prize in Physiology or Medicine shared with Bob Horvitz and John Sulston) proposed using C. elegans as a model organism for the investigation primarily of neural development in animals. It is a multicellular eukaryotic organism, yet is simple enough to be studied in great detail. The transparency of C. elegans facilitates the study of cellular differentiation and other developmental processes in the intact organism. The C. elegans genome is about 100 million base pairs long and consists of six chromosomes and a mitochondrial genome. The genome contains an estimated 20,470 protein-coding genes. About 35% of C. elegans genes have human homologs. C. elegans is highly amendable to functional genetics because of its short generation time, ease of use, and wealth of available gene-alteration techniques <http://www.wormbook.org/chapters/www_frmutagenesis/frmutagenesis.html>.
C. elegans strains are cheap to breed and can be frozen. When subsequently thawed, they remain viable, allowing long-term storage. Maintenance is easy when compared to other multicellular model organisms, a few hundred nematodes can be kept on a single agar plate and suitable growth medium.
A list of core Web resources most useful to someone studying C. elegans is presented below.

  1. WormBook <http://www.wormbook.org> is a comprehensive, open-access collection of original, peer-reviewed chapters covering topics related to the biology of C. elegans and other nematodes. Wormbook also contains: WormMethods, a collection of protocols for nematode researchers; WormHistory, personal perspectives on C. elegans research; and the Worm Breeder's Gazette, an informal, non-refereed, biannual newsletter for the interchange of ideas and information related to C. elegans and other nematodes.

  2. WormBase <http://www.wormbase.org> is a major repository for C. elegans information, including genomic, genetic, anatomy, people, and literature. WormBase also integrates genetic map information with that of physical map. Genetic Interval Search <http://wormbase.org/db/searches/interval> can return a list of genes that have the potential to map within a specified genetic interval. SNP, Visible Marker, and Strain Search <http://wormbase.org/db/searches/strains> is particularly useful for finding markers for genetic mapping experiments in a small interval.

  3. Caenorhabditis Genetics Center (CGC) <http://biosci.umn.edu/CGC/CGChomepage.htm> is a resource center for C. elegans genetics. It is responsible for gene nomenclature, strain collection and distribution, and genetic map construction. CGC homepage is a portal that has links to these and some other related services useful to C. elegans geneticists.

  4. WormBase Gene Summary <http://www.wormbase.org/db/gene/gene>. Each gene in WormBase has a summary page which collates together several different aspects of a gene, including identification, genetic and genomic location, function, reagents and bibliography.

  5. WormBase Genome Browser <http://www.wormbase.org/db/seq/gbrowse/wormbase> is a physical map browser. Using Genome Browser, one can search and display sequences and sequence-related features; one can also zoom in or out and move along on a chromosome.

  6. WormAtlas <http://www.wormatlas.org/> provides anatomical information of C. elegans. The front page lists several useful entry points. One can use the simple text search tool to search the site for information that relates to anatomical terms (e.g. PVT, name of a neuron). Another good way to use this site is to read sections of the "handbook".

  7. The Nematode Expression Pattern Database (NEXTDB) <http://nematode.lab.nig.ac.jp/db/keysrch.html> provides access to C. elegans EST sequences obtained by Yuji Kohara's laboratory and some other experimental results derived from them, such as expression patterns determined by in situ hybridization, which can be searched via a text query tool.

  8. BCGSC Expression Patterns <http://elegans.bcgsc.ca/perl/eprofile/browse> lists GFP expression data which can be browsed directly or searched by gene name, tissue pattern or life stage.

  9. Textpresso <http://www.textpresso.org> allows text searches on primarily C. elegans literature, including published papers, personal communications and meeting reports. Two major features distinguish Textpresso from other literature search tools: that it searches full-text contents of publications, and in addition to text strings, that it can search for groups of terms (categories).

  10. NCBI:

    a. NCBI PubMed <https://www.ncbi.nlm.nih.gov/pubmed/>allows queries on articles in a large collection of biomedical journals. Coverage of PubMed is broad and usually up to date but some literature relevant to C. elegans studies is not covered. Also, Pubmed searches are limited to citations and abstracts.

    b. NCBI AceView <http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm> shows clustering of EST sequences, their alignments to the genome, and annotation of genes, including gene structure, biological function, and bibliography.

    c. NCBI GenBank <http://www.ncbi.nlm.nih.gov/Genbank/index.html> is a repository of sequences from many phylogenetically diverse organisms including the worm.

    d. NCBI Blast <http://www.ncbi.nlm.nih.gov/BLAST/> offers a very extensive set of blast services. Here, different types of blast searches can be performed against all available sequences in GenBank database. One can even download programs to install and run locally.

Based on WormBook