https://wiki.uio.no/mn/ibv/aqua/index.php?title=Special:NewPages&feed=atom&hideredirs=1&limit=50&offset=&namespace=0&username=&tagfilter=mn.ibv.aqua - New pages [en]2024-03-29T14:01:25ZFrom mn.ibv.aquaMediaWiki 1.27.4https://wiki.uio.no/mn/ibv/aqua/index.php/WCWC2016-10-18T15:05:13Z<p>Raoulw@uio.no: </p>
<hr />
<div><br />
== Description ==<br />
The WC ('''W'''right '''C'''hu) medium is a commonly used fully-defined medium for culturing of limnic algae. It was first described by Guillard & Lorenzen (1972), and the most-commonly used recipe includes modifications as reported by Makulla (2000).<ref>Guillard, R.R.L. and Lorenzen, C.J. (1972) '''Yellow-green algae with chlorophyllide ''c'''''. ''Journal of Phycology'', 8:1, 10–18. DOI: [https://dx.doi.org/10.1111/j.1529-8817.1972.tb03995.x 10.1111/j.1529-8817.1972.tb03995.x]</ref><ref>Makulla, A. (2000) '''Fatty acid composition of ''Scenedesmus obliquus'': Correlation to dilution rates'''. ''Limnologica'', 30:2, 162–168. DOI: [https://dx.doi.org/10.1016/S0075-9511(00)80011-0 10.1016/S0075-9511(00)80011-0]</ref><br />
== Recipe ==<br />
<br />
Dissolve TES buffer in Type I purified water (e.g., Milli-Q) using a magnetic stirrer and add 1 mL/L of stock solutions and trace metals in numerical order ('''1–7'''). Autoclave appropriately and add 1 mL/L vitamins ('''8''') through a sterile 0.22 μm polystyrene (PES) filter once cooled down to room temperature.<br />
<br />
{| class="wikitable"<br />
!Buffer<br />
!<br />
|-<br />
|Compound<br />
|TES<br />
|-<br />
|[M] g/mol<br />
| 229.25<br />
|-<br />
|mg/5 L<br />
|<nowiki> </nowiki>575<br />
|-<br />
|mg/L<br />
|<nowiki> </nowiki>115<br />
|}<br />
{| class="wikitable"<br />
!Stock solution<br />
!1<br />
!2<br />
!3<br />
!4<br />
!5<br />
!6<br />
|-<br />
|Compound<br />
|CaCl<sub>2</sub> · 2 H<sub>2</sub>O<br />
|MgSO<sub>4</sub> · 7 H<sub>2</sub>O<br />
|NaHCO<sub>3</sub><br />
|K<sub>2</sub>HPO<sub>4</sub><br />
|NaNO<sub>3</sub><br />
| NaSiO<sub>3</sub> · 5 H<sub>2</sub>O<br />
|-<br />
|[M] g/mol<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|g/L<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|g/500 mL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|g/250 mL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|}<br />
{| class="wikitable"<br />
!Stock solution<br />
!7: Trace metals<br />
!<br />
!<br />
!<br />
!<br />
!<br />
!<br />
!<br />
|-<br />
|Compound<br />
|<nowiki> </nowiki>Na<sub>2</sub> · EDTA<br />
|<nowiki> </nowiki>FeCl<sub>3</sub> · 6 H<sub>2</sub>O<br />
|<nowiki> </nowiki>CuSO<sub>4</sub> · 5 H<sub>2</sub>O<br />
|<nowiki> </nowiki>ZnSO<sub>4</sub> · 7 H<sub>2</sub>O<br />
|<nowiki> </nowiki>CoCl<sub>2</sub> · 6 H<sub>2</sub>O<br />
|<nowiki> </nowiki>MnCl<sub>2</sub> · 4 H2O<br />
|<nowiki> </nowiki>NaMoO<sub>4</sub> · 2 H<sub>2</sub>O<br />
|<nowiki> </nowiki>H<sub>3</sub>BO<sub>3</sub><br />
|-<br />
|[M] g/mol<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|g/L<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|g/500 mL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|g/250 mL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|}<br />
{| class="wikitable"<br />
!Stock solution<br />
!8: Vitamins<br />
!<br />
!<br />
|-<br />
|Compound<br />
|<nowiki> </nowiki>Thiamin · HCl<br />
|<nowiki> </nowiki>Biotin<br />
|<nowiki> </nowiki>B<sub>12</sub><br />
|-<br />
|[M] g/mol<br />
|<br />
|<br />
|<br />
|-<br />
|g/L<br />
|<br />
|<br />
|<br />
|-<br />
|g/500 mL<br />
|<br />
|<br />
|<br />
|-<br />
|g/250 mL<br />
|<br />
|<br />
|<br />
|}<br />
<br />
Prepare stock solutions, trace metals, and vitamins in Type I purified water. Stock solution 4 (K<sub>2</sub>HPO<sub>4</sub>) should not be kept in in a polyethylene (PE) bottle and stock solution 6 (NaSiO<sub>3</sub> · 5 H<sub>2</sub>O) should be kept in a polystyrene (PS) bottle instead of a quartz glass bottle.<ref>Hassenteufel, W., Jagitsch, R. & Koczy, F.F. (1963) '''Impregnation of glass surface against sorption of phosphate traces'''. ''Limnology and Oceanography'', 8:2, 152–156. DOI: [https://dx.doi.org/10.4319/lo.1963.8.2.0152 10.4319/lo.1963.8.2.0152]</ref><ref>Harrison, P.J. & Berges, J.A. (2005) '''Marine culture media'''. In: ''Algal culturing techniques'' (ed. R.A. Andersen), 1<sup>st</sup> edition, 596 p. Elsevier Academic Press; Burlington, MA, USA.</ref> For vitamins, prepare 1 mL aliquots and keep at -20 °C; thaw to use.<br />
== References ==</div>Raoulw@uio.nohttps://wiki.uio.no/mn/ibv/aqua/index.php/ADaMADaM2016-10-17T14:16:13Z<p>Raoulw@uio.no: </p>
<hr />
<div><br />
== Description ==<br />
<br />
ADaM is short for "'''A'''achener '''Da'''phnien-'''M'''edium" and is an easy to prepare, well-established medium for a variety of ''Daphnia'' and other limnic zooplankton species. Internal analysis in the AQUA laboratory has revealed the medium is virtually free from dissolved organic carbon (DOC), nitrogen (N), and phosphorus (P); it is therefore also suited for stoichiometric studies. The following recipe is based on the original publication by Klüttgen et al.<ref>Klüttgen, B., Dülmer, U., Engels, M. & Ratte, H.T. (1994) '''ADaM, an artificial freshwater for the culture of zooplankton.''' ''Water Research'', 28:3, 743–746. DOI: [https://dx.doi.org/10.1016/0043-1354(94)90157-0 10.1016/0043-1354(94)90157-0]</ref>, with a modified selenium content first mentioned in Ebert et al.<ref>Ebert, D., Zschokke-Rohringer, C.D. & Carius, H.J. (1998) '''Within- and between-population variation for resistance of ''Daphnia magna ''to the bacterial endoparasite ''Pasteuria ramosa''.''' ''Proceedings of the Royal Society B'', 265:1410, 2127–2134. DOI: [https://dx.doi.org/10.1098/rspb.1998.0549 10.1098/rspb.1998.0549]</ref>. <br />
== Recipe ==<br />
<br />
To prepare ADaM, a high quality sea salt for scientific purposes is needed. Specifically, two sea salts have been frequently used in laboratories all over the world to prepare ADaM (this section will be updated soon to accommodate purchase links):<br />
* Crystal Sea<sup>®</sup> Bioassay Laboratory Formula (Marine Enterprises International; Baltimore, MD, USA)<br />
* hw-Marinemix<sup>®</sup> professional (Wiegandt; Krefeld, Germany)<br />
<br />
<nowiki> </nowiki>To complete the medium, three stock solutions are needed. They should be prepared in quartz glass bottles using Type I purified water (e.g. Milli-Q water) and autoclaved after visible solution of the compounds. Stock solutions A and B can be prepared as 1 litre, while for stock solution C, 100 mL suffice. <br />
{| class="wikitable"<br />
!Stock solution<br />
!Compound<br />
!g/L<br />
|-<br />
|A<br />
|CaCl<sub>2</sub> • H<sub>2</sub>O<br />
|117.60<br />
|-<br />
|B<br />
|NaHCO<sub>3</sub><br />
|25.20<br />
|-<br />
|C<br />
|SeO<sub>2</sub><br />
|0.07<br />
|}<br />
<br />
The medium itself is prepared by first dissolving sea salt in distilled water using a magnetic stirrer for at least 15 minutes and subsequently adding stock solutions A, B, and C (in this order).<br />
{| class="wikitable"<br />
!Final volume (L)<br />
!Sea salt (g)<br />
!Stock solution A (mL)<br />
!Stock solution B (mL)<br />
!Stock solution C (mL)<br />
|-<br />
|10<br />
|3.33<br />
|23<br />
|22<br />
|1<br />
|-<br />
|50<br />
|16.60<br />
|115<br />
|110<br />
|5<br />
|-<br />
|60<br />
|19.90<br />
|138<br />
|132<br />
|6<br />
|}<br />
<br />
The finished medium should be aerated through a 0.22 μm polystyrene filter for at least a day before use and kept in darkness (e.g. by covering it with aluminium foil) to minimize bacterial growth.<br />
<br />
== References ==</div>Raoulw@uio.nohttps://wiki.uio.no/mn/ibv/aqua/index.php/3D_printing3D printing2016-10-12T14:50:03Z<p>Janheu@uio.no: Created page with "The Aqua Section has a 3D printer ( Ultimaker 2+), where you can parts for your experiemtnal setups and replacement parts. == Models == You can either search the internet f..."</p>
<hr />
<div>The Aqua Section has a 3D printer ( Ultimaker 2+), where you can parts for your experiemtnal setups and replacement parts. <br />
<br />
== Models ==<br />
<br />
You can either search the internet for free 3D models to print or make your own. Free models can for example be found at Thingiverse[http://www.thingiverse.com]. <br />
<br />
If you want to make your own custom designs, the best way to start is to use the website Tinkercad[http://www.tinkercad.com] and then download the .stl file in the end. <br />
<br />
<br />
== Preparing to print==<br />
<br />
Once you have your model file (.stl) you should install the software Cura[https://ultimaker.com/en/products/cura-software] and load your model file. you can choose between different settings and materials. Use PLA plastic if possible. It is non-toxic and gives the best results. <br />
Using Cura load the gcode (the instructions for the printer) onto the sd card of the printer and then choose it on the menu of the printer. <br />
<br />
If it is the first time that you want to use the printer, please ask Jan Heuschele for a small introduction. If you use the printer a lot please buy new PLA plastic at 3Dnet[http://3dnet.no/collections/2-85/products/pla-2-85?variant=1238153711]</div>Janheu@uio.nohttps://wiki.uio.no/mn/ibv/aqua/index.php/SOPsSOPs2016-09-30T14:38:13Z<p>Raoulw@uio.no: /* Growth media */</p>
<hr />
<div><br />
== Standard operation procedures==<br />
No responsibility is taken for the correctness of the information contained in the following SOPs. <br />
<br />
== Machine manuals ==<br />
* Autoclave (4th floor) <br />
* Plate reader (Synergy MX) <br />
<br />
== Toxicology==<br />
* comet assay<br />
* EROD<br />
* PAH metabolites<br />
<br />
== Phytoplankton ==<br />
<br />
=== '''Growth media''' ===<br />
* IMR 1/2 media<br />
* ES media<br />
* [[WC|(modified) WC medium]]<br />
<br />
=== DNA extraction ===<br />
<br />
== Zooplankton ==<br />
<br />
=== Culture media ===<br />
* [[ADaM]]</div>Janheu@uio.nohttps://wiki.uio.no/mn/ibv/aqua/index.php/ScriptsScripts2016-09-29T11:27:10Z<p>Raoulw@uio.no: </p>
<hr />
<div><br />
Here you will find a collection of scripts and code snippets used in R, Python and other programming languages. <br />
<br />
<br />
== R scripts ==<br />
<br />
=== Ecotoxicology ===<br />
<br />
==== Comet assay ====<br />
Some helpful commands to read in all comet assay files simultaneously. The protected <code>.xls</code> files need to be converted to <code>.csv</code> files, e.g. using LibreOffice<ref>https://www.libreoffice.org/</ref>. <br />
* In R, navigate to the folder containing your <code>.csv</code> files using the <code>setwd()</code> command.<br />
* Read in the tail intensity of the <code>.csv</code> files using the following command: <code>pre.data <- data.frame(sapply(list.files(pattern = "*.csv"), FUN = function(x) { read.csv(x, sep = ";", dec = ",")$Tail.Intensity }))</code>, but keep in mind that you may have to adjust the separator and decimal characters. <br />
* Convert the data to a column-based data frame using the median values of the 50 comets scored per sample: <code>data <- data.frame(Tail.Intensity = stack(sapply(pre.data, FUN = "median"))[ , 1])</code>.<br />
* Remember to add the necessary columns, describing e.g. concentration, locations, or treatments before further analysis. <br />
<br />
== Python ==<br />
Linear filming robot. This script allows to film up to 10 bottles. It will move from bottle to bottle and film each of the bottles for a specified number of seconds (HERE variable name).<br />
<br />
<br />
==Arduino ==<br />
<br />
<br />
== ImageJ==<br />
<br />
== References ==</div>Janheu@uio.nohttps://wiki.uio.no/mn/ibv/aqua/index.php/Main_PageMain Page2016-09-13T18:54:13Z<p>Janheu@uio.no: </p>
<hr />
<div>==== Aim of the AQUA wiki ====<br />
This wiki is a collection of useful recipes, scripts, SOPs, and other knowledge to make the work at the AQUA section go as smoothly as possible. <br />
<br />
=== Content ===<br />
* [[SOPs]]<br />
* [[Scripts|Scripts and code snippets]]<br />
* [[3D printing]]<br />
* [[Arrival guide for new employees]] <br />
<br />
== Getting started ==<br />
If you want to contribute to the wiki please log in using your UiO credientials, and you will be granted access within 1 to 2 days (and send a reminder to Jan Heuschele). If you have questions on how to use the wiki please consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information.<br />
* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]<br />
* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]<br />
__FORCETOC__<br />
__NOINDEX__<br />
__NEWSECTIONLINK__</div>MediaWiki default