From Steele Lab
Basal Metazoan Genome Resources
- Hydra genome browser
- Nematostella genome browser at JGI
- Hydra magnipapillata Unigene Database at NCBI
- Trichoplax genome browser at JGI
- Acropora digitifera genome browser
Sequence Alignment, Assembly, and Analysis Servers
- ClustalW Server - A server for doing Clustal alignments of sequences
- CAP3 Assembler - A server for assembling sequences using CAP3
- SignalP Server - A server for identifying signal sequences in proteins
Cnidarian cDNA and Genomic Library Resources
- Well Locator for Hydra cDNA clones
- Hydra cDNA Clone Plate Inventory (Excel file)
- Nematostella BAC Library - CHORI
DNA, RNA, and Protein amounts in Hydra
There are various values in the literature for the amounts of DNA, RNA, and protein in a Hydra polyp.
Stuart Clarkson reported the following values in his 1969 JEEM paper.
4.5 µg of RNA in a Hydra littoralis polyp 17-20 hours after feeding
13.96 µg of protein in a Hydra littoralis polyp 17-20 hours after feeding
1 µg of DNA in a Hydra littoralis polyp starved for 2 days
Cook and Kelty reported the following protein value in their 1982 JEZ paper.
55 µg of protein in a Hydra littoralis polyp starved for 1 day
Most researchers assume that a well-fed brown Hydra polyp (e.g. H. vulgaris or H. magnipapillata) contains the following amounts of protein and RNA.
10 µg of total RNA (thus about 0.3 µg of polyA+ RNA)
50 µg of protein
Hillier et al. (Genome Research, 2009) reported that both yeast and mammalian cells have 300-350 mRNA molecules per cubic micron of cell volume. Given that it applies to yeast and mammalian cells, this value should also be applicable to Hydra cells.
Transgenic Hydra Lines
- actin promoter-driven GFP in endoderm
- actin promoter-driven RFP in endoderm
- actin promoter-driven RFP in ectoderm
- actin promoter-driven RFP+GFP operon in ectoderm
- actin promoter-driven RFP in ectoderm and actin promoter-driven GFP in endoderm
Hydra strains in the Steele Lab
Hydra vulgaris strain AEP - The AEP strain of Hydra vulgaris is used to generate embryos for production of transgenic Hydra. AEP produces both sperm and eggs, and does so pretty much continuously. Most of the time a given sexual polyp contains only testes or eggs, although occasionally a polyp is seen which contain both testes and an egg. The details of how this strain was generated are not completely clear. Everyone agrees that the founders for this strain were a male strain called CA7, collected from Boulder Creek, south of Susanville, California by Lynne Littlefield and Carolyn Teragawa and a female strain, called PA1, collected from a pond on the Haverford College campus by Carolyn Teragawa. It appears that Boulder Creek drains into the north side of Antelope Lake. Haverford College is in Haverford, Pennsylvania, which is near Philadelphia. There is a single large pond on the campus called the Duck Pond. It seems likely that this is the pond from which PA1 was collected. Both CA7 and PA1 were collected sometime between the late 80s and the early 90s. Lynne and Carolyn were both postdocs in Hans Bode's lab at UC Irvine at the time the CA7 and PA1 strains were brought into the laboratory.
All those involved are in agreement that the initial step in generating the AEP strain was a cross between CA7 and PA1. This cross gave rise to multiple lines designated with letters A, B, C, D, E, etc. Vicki Martin et al. (1997) mention a male E2 line and a female A5 line, which were derived from crossing CA7 and PA1. Pat Bode recalls that crosses among the letter-designated lines (A, B, C, D, E, etc.) were carried out. It is presumed that an AE line was generated by crossing of an A line and an E line. Which A line and which E line were used in this cross is not currently known. The logical final step in the generation of AEP would have been a cross between the presumed AE line and a P line. So AE could have been backcrossed to PA1 to generate AEP.
In an e-mail sent in 2005, Vicki Martin said she thought that a line called PA2 was generated from a cross between CA7 and PA1 and that a cross between a PA2 male and a PA2 female gave rise to AEP. This seems unlikely for two reasons. First, Pat Bode is certain about the production of the A, B, C, D, E, etc. lines from a CA7/PA1 cross and she is certain that crosses among those lines were then carried out. Second, Pat’s recollection makes sense in terms of the nomenclature for AEP. It seems unlikely that AEP would be chosen as the name if the cross was done as Vicki thinks, and Vicki says she doesn’t remember why the line was called AEP. Technau et al. (2003) report crossing AEP females to PA2 males, indicating that a male line called PA2 did, apparently, exist at one point.
Unless documentation is found of exactly how the crosses beyond the initial CA7/PA1 cross were carried out, it won’t be possible to determine the complete pedigree of AEP with certainty.
Hydra vulgaris Zurich strain - This strain was obtained from Monika Hassel's lab when she was at the University of Heidelberg.
Hydra vulgaris from Newport Beach - collected from a small pool located adjacent to Upper Newport Bay.
Hydra oligactis from Daniel Martinez -
Hydra utahensis from Daniel Martinez -
Hydra hymenae from Daniel Martinez -
Hydra magnipapillata strain 105 - This is the strain whose genome was sequenced for the Hydra Genome Project. This strain was also used to construct most of the cDNA libraries used for the Hydra EST Project. This strain originated from a single polyp collected by Dr. Tsutomu Sugiyama in September, 1973 in a swamp adjacent to the National Institute of Genetics in Mishima, Japan (Dr. Toshitaka Fujisawa, unpublished information).
Hydra vulgaris from Australia - This Hydra strain shows the peculiar property of undergoing transverse fission of the polyp at the top of the peduncle just beneath where a bud has emerged.
Hydra Gene Expression Databases
- Molecular Database of Hydra Cells - National Institute of Genetics, Mishima, Japan
Vectors for Transgenic Hydra
We have constructed a number of vectors for use in generating transgenic Hydra. The features of these vectors are described in the following Excel file:
- Laguna Scientific
- Operon Biotechnologies
- UCI Chemical Waste Pickup
- UCI Developmental Biology Center Microscopy Core
- UCI e-Ship
- UCI Computer Store
- Steele Lab Hydra Culture Methods
- Hydra Glossary
Manuals for Kits, Reagents, and Equipment
- NEB mRNA Isolation Kit
- Gene Gun
- GeneRacer Kit
- PTC-100 Thermal Cycler
- Invitrogen TA Cloning Kit
- x-tracta gel extraction tool
The Cnidaria Newsgroup
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Videos of Hydra from YouTube
Hydra cell composition
The paper below contains a detailed analysis of the cell composition of Hydra under various conditions.