Zebrafish

Lesley and Katie's Logbook KMH's Milestone Map LGS's Milestone Map and Report KMH Particle Physics Summary

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 * [|http://www.nd.edu/~danio/]**

NEW READINGS!! After talking to Dr. L a bit about the nitrification cycle, I decided to do a little research and learn more about it so we can better understand our fish. Here is what I found: Like all living creatures, fish give off waste products (pee and poo). These nitrogenous waste products break down into ammonia (NH3), which is highly toxic to most fish. In nature,waste products become diluted to low concentrations because of the high volume of water. In aquariums, however, it can take as little as a few hours for ammonia concentrations to reach toxic levels. You must be careful that the concentration is not too high to stress fish. Emergency action may need to be taken!! Water change and zeolite clay are a few suggestions. The ``nitrogen cycle'' is the process that converts ammonia into other (pretty harmless) nitrogen compounds. Fortunately, bacteria can do this conversion for us! Some species convert ammonia (NH3) to nitrite (N02-), while others convert nitrite to nitrate (NO3-). Thus, __//**cycling the tank**//__ refers to the process of establishing bacterial colonies in the filter bed that convert ammonia --> nitrite --> nitrate. The species of nitrifying bacteria that is needed is are present everywhere, even in the air. Therefore, once you have an ammonia source in your tank, it's only a matter of time before they establish a colony in your filter bed.The fish poop contains the ammonia that the bacteria live on. __//**Don't overfeed them!**//__ More food means more ammonia! Multiple websites even suggested zebra danios (zebrafish) to catalyze the nitrogen cycle in your tank. Sounds like we're doing well!

SPEEDING UP CYCLING (for the impatient :) http://fins.actwin.com/mirror/begin-cycling.html#speed-cycling

][|The Zebrafish Project.ppt] Male and Female Wildtype Zebrafish

//Different stages of Zebrafish Development (Top, left) A 90 minutes old Zebrafish embryo; (Top, right) A two day old Zebrafish embryo/fry; (Bottom) An Adult Zebrafish.//
 * [|www.pdn.cam.ac.uk/ staff/lewis/]**

In case you haven't noticed, Katie and I aren't in class very much. The reason is because we have (successfully) set up a zebrafish lab upstairs in the storage room off of Mrs. Brunner's lab on the third floor. So far, we have been able to keep the population stable but are having trouble with breeding. We've decided to monitor the breeding much more carefully and make adjustments accordingly. Stand by! (And please feel free to come see it!)
 * __11/12/07__**

The Zebrafish Information Network ([|http://zfin.org)], the model organism database for zebrafish, provides the central location for gathered zebrafish genetic, genomic and developmental data. Extensive data integration of mutant phenotypes, genes, expression patterns, sequences, genetic markers, morpholinos, map positions, publications and community resources facilitates the use of the zebrafish as a model for studying gene function, development, behavior and disease. Access to ZFIN data is provided via web-based query forms and through bulk data files. ZFIN is the definitive source for zebrafish gene and allele nomenclature, the zebrafish anatomical ontology (AO) and for zebrafish gene ontology (GO) annotations. ZFIN plays an active role in the development of cross-species ontologies such as the phenotypic quality ontology (PATO) and the gene ontology (GO). Recent enhancements to ZFIN include (i) a new home page and navigation bar, (ii) expanded support for genotypes and phenotypes, (iii) comprehensive phenotype annotations based on anatomical, phenotypic quality and gene ontologies, (iv) a BLAST server tightly integrated with the ZFIN database via ZFIN-specific datasets, (v) a global site search and (vi) help with hands-on resources. CHECK THIS OUT!
 * __ZFIN:__ Zebrafish Information Network**


 * Biology-blog.com**
 * http://www.biology-blog.com/blogs/permalinks/9-2007/microinjection-of-zebrafish-embryos.html**

EXCEPTIONAL ARTICLES: Department of Cell Biology and Anatomy and Genetics, LSU Health Sciences Center, MEB-6A12, 1901 Perdido Street, New Orleans, LA 70112, USA. The presence of cilia in many vertebrate cell types and its function has been ignored for many years. Only in the past few years has its importance been rediscovered. In part, this was triggered by the realization that many gene products mutated in polycystic kidney diseases are localized to cilia and dysfunctional cilia result in kidney disease. Another breakthrough was the observation that the establishment of the left-right body axis is dependent on cilia function. Since then, many other developmental paradigms have been shown to rely on cilia-dependent signaling. In addition to mouse and Chlamydomonas, lower vertebrate model systems such as zebrafish, medaka and Xenopus have provided important new insights into cilia signaling and its role during embryonic development. This review will summarize those studies. We will also illustrate how these lower vertebrates are promising model systems for future studies defining the physiological function of cilia during organogenesis and disease pathophysiology. PMID: 17981674 [PubMed - in process.
 * [|**Wessely O**], [|**Obara T**].

[|Zebrafish: Cure for Blindness?]
 * __Zebrafish Study May Point Way to Blindness Cure__**


 * __VITAMIN D__**

Over the summer, as you may well know, Katie and I worked for QuarkNet but our project was mainly through NDerC. We worked with a Notre Dame doctoral student who studies the leishmania, a parasite spread by the bite of an infected sand fly, that has been infecting our soldiers in the Middle East. His focus was the influence of vitamin D receptors in the infection. Although we ourselves did not work on this project, we had some VERY interesting lunch conversations (to say the least). We even, on a few occasions, got to help out in his lab. Although we didn't have a license to work with the mice ourselves, we did observe his work with them. Anyway, Katie and I learned alot about vitamin D over those two months, and so when it came time to start our own research, we realized we might be able to incorporate our small knowledge of vitamin D into our fish. So, naturally, we went to PubMed! There is research going on currently of the study of vitamin D using zebrafish but not much. There may be a lot of room to study it. This is still a work in progress though! The following is a great article about the functional evolution of vitamin D receptors (in which they used zebrafish as their study animal). [|Functional evolution of vitamin D]

[|**//Notre Dame Center for Zebrafish Studies//**]
 * //__NOTRE DAME: The Center for Zebrafish Studies__//**