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--- project:biolab:start [2019/09/20 18:17] – added current projects sachy
+++ project:biolab:start [2025/06/15 07:54] (current) – sachy
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 ====== Current Projects ======
-===== BioOSM =====
+~~DIRPICTURES sortByDate sortDesc~~
-Some members are collecting photos and other evidence of (micro)organisms which can (not) be seen from behind the computer screen. Please see the [[project:bioosm:start|BioOSM project pages]].
-===== Platyhelmithes / Flatworms =====
-We are cultivating flatworms! Flatworms (plostenky in Czech) are famous for their regeneration abilities - cut them in half, get two fully functional animals. Cut their head, and get two full heads on one body. The non-sexual species are actually reproduced by tearing themself in half!
+===== BioOSM =====
-===== Epoxidation of samples =====
+Some members are collecting photos and other evidence of (micro)organisms which can (not) be seen from behind the computer screen. Please see the [[project:bioosm:start|BioOSM project pages]]. Project is closely knitted with Planarian working group.
-Recently we learned how to pour our macroscopic samples into a transparent epoxide to be able to show them without risking damage. No more fridges full of formaldehyde bottles :)
+===== Planarian working group =====
+External project led by sumie-dh. Project is  beyond 'normal' naturalist way of doing and following certain goals and plans. If you want taste topics like how to deal with unknown [possibly] new species in your collections, how to manage fieldwork plans, messing with keys and searching for resources, research ideas and workflow designs in taxonomy, curating of own sample collection in +- standardized ways, WSI processing and dealing with presentation of your results outside of 'hackerspace setup' talk to members of planarian working group > [[user:sumie-dh]]| [[user:sachy]]. Forget anything DIY in this project ;]
+Overview of currently solved topics is on: https://bioosm.brmlab.cz/histolka/project_imagery/project_imagery.htm
+Note this is only fragment of running things, we are going on own pace, slowly but surely forward, this is speed of planarian.
+Onboarding of new members: unlikely but discuss it with members.
+Planarian samples welcomed but keep permit logic in mind in case of foreign samples or those from local national parks.
+Finished fieldwork sessions:
+  * 2024: First record of the land planarian species Rhynchodemus sylvaticus (Leidy,1852) in a naturalized area of Czechia  [manuscript soon, waiting for DNA barcoding]
+  * 2023-2024: Sexual strains of Girardia tigrina in Central Bohemian region - self-funded, further work ongoing
+  * 2022: Mapovánı́ ploštěnky Dugesia gonocephala v povodı́ Svinenského potoka - grant CSOP_122210, further work ongoing
+  * 2021: Mapovánı́ ploštěnky Crenobia alpina v okolı́ Hojné vody - grant CSOP_122123
-===== PCR and electrophoresis =====
+===== Epoxidation of samples =====
-DNA electrophoresis using the OpenPCR [[http://openpcr.org/]]
+Recently we learned how to pour our macroscopic samples into a transparent epoxide to be able to show them without risking damage. No more fridges full of formaldehyde bottles :)
-=== Status ===
-  * openPCR working, dry run successful (SW: [[https://github.com/cathalgarvey/OpenPyCR]], running.)
-  * Taq/dNTP PCR mix obtained from [[http://www.openbiotech.com]]
-  * electrophoresis working, tested at hackathon
-  * got chemicals:
-    * TAE buffer [[http://letters.cathalgarvey.me/cargo-cults-and-electrophoresis/]])
-    * ddH2O
-    * PCR grade agarose (quite little, expensive)
-    * EtBr
-    * SYBR Gold (thanks [[user:Mrkva]] and [[user:barney]]!)
-    * some DNA fragments for experimentation (pTracer plasmids)
-  * freezer (-20°C) for DNA/enzyme storage is ready
-  * we have a wonderful power supply (up to 300V) thanks to Tomsuch
-  * transilluminator built from blue LEDs
-the first test run with crude agar, self made TAE, DIY loading dye (cresol red+sucrose), 60V (with the power source from hwlab), 1.5h:
-{{:project:biolab:img_6511.jpg?200|}}
-{{:project:biolab:img_6512.jpg?200|}}
+===== PCR and electrophoresis =====
-second test run with agarose and several restriction digest samples using a strong laser and SYBR gold for visualization - blue light filter from infra-soldering station:
+See [[.pcr]]
-{{:project:2802_e4dd_960.jpeg?nolink&300 |}}
-some notes for using SYBR gold:
-  * DO NOT STORE IN GLASS CONTAINER
-  * protocol: [[https://tools.lifetechnologies.com/content/sfs/manuals/mp11494.pdf]]
-**first test run of the openPCR**
-Template: pTracer plasmid
-Primers: inf pTracer F + R (10uM) designed by [[user:chido]] to amplify the GFP/Bsd gene
-PCR mix:
-  dH2O 33ul
-  mastermix Openbiotech 5x 10 ul
-  primer F 2ul
-  primer R 2ul
-  template 1ng/ul 3ul
- total volume 50 ul
-Thermocycler settings:
-°C 60 sec
-°C 30 sec
-°C 30 sec
-°C 60 sec
-  x30
-°C 20 sec
-SYBR gold gel stain:
-ml TAE, 0.3g agarose gel
-  stained in 10ul SYBR gold diluted in 100ml TAE, 40 min
-Results:
-We obtained the desired product using Openbiotech master mix that has been stored in -20 °C, but there was no product at all when using a mastermix that has been stored in the fridge. We aliquoted both SYBR gold gel stain and the PCR mastermix so thawing the stock solution is not necessary.
-OpenPCR works fine! Pictures and analyzed gel coming soon. Next step: devise a protocol for DNA isolation that can be used as a PCR template.
-Useful links:
-  * primer design guide: [[http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html]]
-  * paper on horses/rats/cockroaches detection in food via PCR [[http://journals.tubitak.gov.tr/veterinary/issues/vet-07-31-3/vet-31-3-3-0601-30.pdf]]
-  * there are online companies that will synthetize custom primers for a fee [[http://www.operon.com]][[http://www.biogen.cz]]
 ===== Fun with Bioluminescence =====