Differences

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--- project:biolab:start [2018/08/21 21:31] – borky is nor member anymore pinky
+++ project:biolab:start [2025/06/15 07:54] (current) – sachy
@@ Line 31: / Line 31: @@
   * electrophysiology (see [[project/biolab/taste]])
   * histology (see [[/project/brmhistology/start]])
+  * mapping of interesting organisms (see [[project:bioosm:start]])
 ===== Contact us! =====
-Currently the core team of biolab is: [[user:chido|]], [[user:pinky]], [[user:jenda]], [[user:pasky]], [[user:mrkva]], [[user:tomsuch]] and [[user:bluebear|]]. Various other members of brmlab conduct occasional experiments. Contact anyone of us - we'll be glad to show you around in person aswell.
+Currently the core team of biolab is: [[user:chido|]], [[user:sachy]], [[user:jenda]], [[user:pasky]], [[user:mrkva]], [[user:sumie-dh]] and [[user:bluebear|]]. Various other members of brmlab conduct occasional experiments. Contact anyone of us - we'll be glad to show you around in person aswell.
 We also have a mailinglist: [[https://brmlab.cz/mailman/listinfo/biolab|biolab@brmlab.cz]] ([[https://brmlab.cz/pipermail/biolab/|archives]]).
@@ Line 41: / Line 42: @@
 ===== The Lab =====
-The Biolab is a large room located downstairs from the main hackerspace premises, right behind the chemistry-focused laboratory, chemlab. The two projects cooperate closely with eachother and share some equipment, but at the same time have their own workspaces and designated material storage to assure safety and viability of both chemistry-related and biology-related experiments. If you are interested in the chemlab project, or would like to use their equipment or material, contact [[user:pinky]].
+The Biolab is a large room located in the main hackerspace premises, right next to the chemistry-focused laboratory, chemlab. The two projects cooperate closely with eachother and share some equipment, but at the same time have their own workspaces and designated material storage to assure safety and viability of both chemistry-related and biology-related work. If you are interested in the chemlab project, or would like to use their equipment or material, contact [[user:sachy]].
-Hackerspace members have access cards, non-members are premitted entry accompanied with members anytime the hackerspace is open.
 We started out in a small space behind the brmlab kitchen: [[http://panora.ma/news/2011/brm-meetup/biolabt.html|Panoramatic view of the old lab]]
@@ Line 51: / Line 50: @@
 TODO Pictures!
-We now have larger premises housing a lab bench, a large microscope (dubbed the macroscope), several smaller optical microscopes, a large freezer, a fridge, a set of micropipettes, an elecrophoresis chamber with power supply, an OpenPCR thermocycler, a shaker, precision scales, a microwave, a computer workstation and basic lab equipment like pipette tips, glassware, chemicals etc.
+We now have larger premises housing a lab bench, a large microscope (dubbed the macroscope), several smaller optical microscopes, a large freezer, a fridge, a set of micropipettes, an elecrophoresis chamber with power supply, an OpenPCR thermocycler, a shaker, precision scales, a microwave, a biological incubator, a flowbox and basic lab equipment like pipette tips, glassware, chemicals etc.
 ** Donations of material are always welcome, since we are self-funded. **
-Contact [[user:chido]] or [[user:pinky]] if you have something you would like to contribute! We do not accept dangerous chemicals or other potentially harmful materials.
+Contact [[user:sumie-dh]] or [[user:sachy]] if you have something you would like to contribute! We do not accept dangerous chemicals or other explicitly harmful materials.
 ===== How to behave in biolab =====
-First and foremost, don't be shy visit - if the door is open, just walk in and say hi, if it's closed, ask a brmlab member upstairs to accompany you!
+First and foremost, don't be shy visit - if the door is open, just walk in and say hi, if it's closed, ask a brmlab member to accompany you!
 In order for the biolab to be able to function safely and be available to a large community of people as equally as possible, there are some basic rules:
-  * **Keep the place clean.** If your work is done, put the place back in order for the next person to make a mess of :) This means wash the glass-ware properly, keep containers closed and the bench clean.
+  * **Keep the place clean.** If your work is done, put the place back in order for the next person to make a mess of :) This means wash used tools and glaseware properly, keep containers closed and the bench clean.
   * **No foods and drinks on the workbenches, inside the freezer, fridge or microvawe.** There's a chill-out corner sharing space with the biolab room, food and drink can be consumed there.
-  * **Do not leave unlabeled and open containers in the lab.** If you want to store something or have a longer-running experiment on the bench, it's no problem to leave it there - just make sure to label it with your name, what it is, and the date you put it there. For safety reasons, **unlabeled stuff will be disposed of.**
+  * **Do not leave unlabeled and open containers in the lab.** If you want to store something or have a longer-running experiment on the bench, it's no problem to leave it there - just make sure to label it with your name, what it is, and the date you put it there. For safety reasons, **unlabeled stuff will be disposed of without prior notice.**
-  * You can use all the equipment present. However, some of the machines require at least a small initial introduction on how to use them without you or the machine in question sustaining any damage. We're assuming the microwave is safe in your hands :) but: talk to [[user:pinky]] if you want to use the **macroscope** and to [[user:chido]] if you'd like to play with the **electrophoresis chamber and open PCR.**
+  * You can use all the equipment present. However, some of the machines require at least a small initial introduction on how to use them without you or the machine in question sustaining any damage. We're assuming the microwave is safe in your hands :) but: talk to [[user:sumie-dh]] if you want to use the **macroscope** and to [[user:chido]] if you'd like to play with the **electrophoresis chamber and open PCR.**
-  * **Discuss your projects with the community.** Basically, anything goes that's safe and legal when it comes to projects you would like to introduce to the lab. But in order to keep the lab a safe and fun place to everyone involved, **please talk to [[user:chido]] about your biolab project and to [[user:pinky]] about your chemlab project first.**
+  * **Discuss your projects with the community.** Basically, anything goes that's safe and legal when it comes to projects you would like to introduce to the lab. But in order to keep the lab a safe and fun place to everyone involved, **please talk to [[user:sumie-dh]] about your biolab project and to [[user:sachy]] about your chemlab project first.**
   * **Some storage places are locked.** Because the hackerspace is open to the public, and some of the reagents are potential health hazards or expensive, we keep the storage locked and an inventory registry. If you would like to access to both, members can help you out.
   * **Be nice to eachother.** No, really, this is important :)
@@ Line 81: / Line 80: @@
   * [[project:biolab:incubator]]
   * [[[equipment:brmicroscopy]]]
+  * big biological incubator
+  * flowbox
 What we'd like to have:
   * a more precise microscope
@@ Line 167: / Line 169: @@
 ====== Current Projects ======
-===== PCR and electrophoresis =====
+~~DIRPICTURES sortByDate sortDesc~~
-DNA electrophoresis using the OpenPCR [[http://openpcr.org/]]
-=== 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:
+===== BioOSM =====
-{{:project:biolab:img_6511.jpg?200|}}
+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.
+===== Planarian working group =====
-{{:project:biolab:img_6512.jpg?200|}}
+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.
-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:
+Onboarding of new members: unlikely but discuss it with members.
-{{:project:2802_e4dd_960.jpeg?nolink&300 |}}
+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
-some notes for using SYBR gold:
+===== Epoxidation of samples =====
-  * DO NOT STORE IN GLASS CONTAINER
-  * protocol: [[https://tools.lifetechnologies.com/content/sfs/manuals/mp11494.pdf]]
-**first test run of the openPCR**
+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 :)
-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:
+===== PCR and electrophoresis =====
-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:
+See [[.pcr]]
-  * 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 =====