Difference between revisions of "Overview"
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|Prayag Murawala | |Prayag Murawala | ||
|Limb bud and limb blastema | |Limb bud and limb blastema | ||
| − | |[[File:PM-28.png| | + | |[[File:PM-28.png|180px|thumb|left|Limb bud expression]] |
|Germ-line transmitted | |Germ-line transmitted | ||
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|Prayag Murawala | |Prayag Murawala | ||
|Bone and fibroblast | |Bone and fibroblast | ||
| − | |[[File:PM-33 whole animal.png| | + | |[[File:PM-33 whole animal.png|80px|thumb|left|Bone expression]] [[File:PM-33.png|80px|thumb|left|Bone expression in Limb bud]] |
| − | [[File:PM-33.png| | ||
|Germ-line transmitted | |Germ-line transmitted | ||
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Revision as of 18:53, 24 January 2013
Introduction
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.
Axolotl
Maintaining the axolotls
Feeding
Artemia (Brine shrimp eggs)
Brine shrimp eggs are metabolically inactive and can remain in total stasis for two years while in dry oxygen-free conditions, even at temperatures below freezing. This characteristic is called cryptobiosis meaning "hidden life" (also called diapause). While in cryptobiosis, brine shrimp eggs can survive temperatures of liquid air (−190 °C or −310.0 °F) and a small percentage can survive above boiling temperature (105 °C or 221 °F) for up to two hours.
Once placed in brine (salt) water, the cyst-like eggs hatch within a few hours. The nauplii, or larvae, are less than 0.5 mm in length when they first hatch. Brine shrimp have a biological life cycle of one year, during which they grow to a mature length of around one centimeter on average. This short life span, along with other characteristics such as their ability to remain dormant for long periods, has made them invaluable in scientific research, including space experiments. This ability has also enabled the use of a hybrid of brine shrimp, bred to grow larger and live longer, as Sea-Monkeys.
Artemia Hatching Preparation: Protocol for 15 Ltr.
Switch on the bubbler.
Take the warm water from the tap and fill it into the container, meanwhile add 325 ml volume of salt (Red Sea Coral pro Salt), when the 15 Ltr. container is filled up the salt should be dissolved already.
Switch on the heating. And make sure that the light on the top is on ☺
Add 50-60 ml full of dried artemia (Stored at 40C) to this.
Hatching preparation
- The following protocol is considered for 15 l solution.
- Switch on the bubbler.
- Take the warm water from the tap and fill it into the container, meanwhile add 325 ml volume of salt (Red Sea Coral pro Salt), when the 15 Ltr. container is filled up the salt should be dissolved already.
- Switch on the heating. And make sure that the light on the top is on.
- Add 50-60 ml full of dried artemia (Stored at 40C) to this.
Keep it like this for 2 days with aeration. And >200 Lux of light.
Usually they hatch within few hours but It is good to keep for 2 days to achieve a good hatching.
During these two days temperature can be 18°-20°C.
Make sure hatching container is not getting clogged during these two days.
Lab duties
- Antibiotics
- Benzocaine
- Fibronectin
- Gelatine
- Liquid nitrogen
- Primary antibodies
- Secondary antibodies
- Serum immunostaining
- Autoclave
- Cryostat
- Dissecting microscopes
- Leica confocal microscope
- Vacuum pumps
- Waterbath
- Ordering common stuff
- Heat-shock competent cells
Chemicals
Hardware
General
Protocols
- Blastema cells
- Baculovirus titration
- Myoblasts electroporation
- Adhesive cell culture
- Electroporation of blastema cells
- Electroporation of neural epithelia cells (axolotl spinal cord)
- mESC culture/Cyst formation
- Neurosphere culture
Cell culture
Histology
Molecular biology
Booking calendars
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.
- Fluorescence microscopes
- Microinjectors and electroporators
- Confocal microscopes
- Cryostats
- Microtome
Transgenic lines
Axolotl (A.mexicanum)
| Name | Construct | Method of transgenesis | Author | Tissue | Image | Remarks |
|---|---|---|---|---|---|---|
| PM28 | Prrx1-TFP-NLS-T2A-mERt-Cre-ERt | Sce1 | Prayag Murawala | Limb bud and limb blastema | Germ-line transmitted | |
| PM33 | Col1A2-TFP-NLS-T2A-mERt-Cre-ERt | Sce1 | Prayag Murawala | Bone and fibroblast | Germ-line transmitted |
Frog (X.levies)
Digital data
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. Select a category from the list below in order to view or download the data.
Presentations
| Title | Summary | Author | Date | Type | Link |
|---|---|---|---|---|---|
| Assembling the transcriptome: first results | The presentation contains an overview of several commonly used sequencing and assembly methods. It also presents preliminary results. | Sergej Novojilov | Sep-04-2012 | Group meeting presentation | tba |
| Assembling the transcriptome: first results | The presentation contains an overview of several commonly used sequencing and assembly methods. It also presents preliminary results. | Sergej Novojilov | Sep-04-2012 | Group meeting presentation | tba |
Theses
| Title | Summary | Author | Link |
|---|---|---|---|
| Test | Test | John Doe | tba |
Databases
- Axolotl EST database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.
- Axologle database contains several different Axolotl transciptome assemblies
Datasets
Next generation sequencing
- Mature and regenerating spinal cord
Name Description Type Reads Links Author Remarks Mature spinal cord Mature axolotl spinal cord Illumina, paired-end, 100bp 65,753,941 tba Akira Tazaki Injured spinal cord Injured axolotl spinal cord, 6dpi Illumina, paired-end, 100bp 78,459,950 tba Akira Tazaki - Axolotl limb
Name Description Type Reads Links Author Remarks Mature limb Mature axolotl forelimb Illumina, single-end, 76bp 65,934,228 tba Dunja Knapp Amputated limb (36h) Amputated axolotl forelimb (36hpa) Illumina, single-end, 76bp 65,250,768 tba Dunja Knapp Amputated limb (72h) Amputated axolotl forelimb (72hpa) Illumina, single-end, 76bp 62,970,898 tba Dunja Knapp Lateral wound (36h) Injured (lateral wound) axolotl forelimb (36hpw) Illumina, single-end, 76bp 66,361,470 tba Dunja Knapp Lateral wound (72h) Injured (lateral wound) axolotl forelimb (72hpw) Illumina, single-end, 76bp 64,133,834 tba Dunja Knapp
Images
In-situ images
Antibody staining
Change list
This section is an attempt to make people catalog the changes they might have introduced to the data, protocols, chemicals and so on.