Jump to content

LabAdviser/314/Preparation 314-307/Soft-matter: Difference between revisions

← Older edit
VisualWikitext
Mktracy (talk | contribs)
NLAB-Employees-701, NLAB-LabmanagerAllUsers, NLAB-Nlab307-labadviser-users-34891
620 edits
Mmat (talk | contribs)
NLAB-Employees-701, NLAB-LabmanagerAllUsers, Administrators
1,957 edits
mNo edit summary
 
(48 intermediate revisions by one other user not shown)
Line 3: Line 3:


''This section is written by DTU Nanolab internal if nothing else is stated.''
''This section is written by DTU Nanolab internal if nothing else is stated.''
[[index.php?title=Category:314]]
[[Category:314]]
[[index.php?title=Category:314-Preparation]]
[[Category:314-Preparation]]


= Plunge Freezer =
= Plunge Freezer =
Line 13: Line 13:
== Leica EM GP2 ==
== Leica EM GP2 ==
Plunge freezing is a cryo-fixation method used to preserve samples in their native state prior to cryo-electron microscopy. The EM GP2 plunge freezes fluid or extremely thin samples spread on an electron microscopy grid into liquid ethane and afterwards excess fluid is removed by automatic blotting. Prior to freezing, the sample is maintained in a temperature and humidity controlled environmental chamber which is adjustable between +4°C and +60°C and room humidity to 99 %.  
Plunge freezing is a cryo-fixation method used to preserve samples in their native state prior to cryo-electron microscopy. The EM GP2 plunge freezes fluid or extremely thin samples spread on an electron microscopy grid into liquid ethane and afterwards excess fluid is removed by automatic blotting. Prior to freezing, the sample is maintained in a temperature and humidity controlled environmental chamber which is adjustable between +4°C and +60°C and room humidity to 99 %.  
The main steps of this technique is as follows:<br />
1. The sample is spread onto a glow discharged EM grid <br />
2. The liquid droplet is then blotted with filter paper until only a very thin film of fluid remains <br />
3. The grid is then rapidly plunged into a cryogen (usually liquid ethane) <br />
4. The grid is afterwards stored in a grid box submerged in liquid nitrogen until finally loaded into the cryo-electron microscope for imaging <br />




[https://labmanager.dtu.dk/view_binary.php?class=MiscDocument&id=15&name=Leica_EM_GP2_Operating_manual.pdf Operating manual] ''- requires login''<br />  
[https://labmanager.dtu.dk/view_binary.php?class=MiscDocument&id=15&name=Leica_EM_GP2_Operating_manual.pdf Operating manual] ''- requires login''<br />  


[[File:Plunge Freezer (2).jpg|400px|left|thumb|Leica EM GP2 Location at DTU Nanolab Building 307 Room 909B]]<br clear="all" />
[[File:IMG_9460_GP2.jpg|400px|left|thumb|Leica EM GP2 Location at DTU Nanolab Building 307 Room 909B]]<br clear="all" />


For further information on the equipment usage or training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].  
For further information on the equipment usage or training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].  
Line 57: Line 50:




[[File:Freeze-substitution EM AFS2.jpg|300px|left|thumb|Leica EM AFS2 Location at DTU Nanolab Building 307]]
[[File:Freeze-substitution EM AFS2.jpg|300px|left|thumb|Leica EM AFS2 Location at DTU Nanolab Building 307 Room 909B]]
[[File:EM FSP.JPG|200px|left|thumb|Leica EM FSP Location at DTU Nanolab Building 307]]<br clear="all" />
[[File:EM FSP.JPG|200px|left|thumb|Leica EM FSP Location at DTU Nanolab Building 307 Room 909B]]<br clear="all" />
For further information on the equipment usage or training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information on the equipment usage or training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


<br clear="all" /> -->
<br clear="all" />


= Microtome =
= Microtome =
Line 68: Line 61:




The main steps of this technique proceed as follows:<br />
[https://labmanager.dtu.dk/view_binary.php?class=MiscDocument&id=15&name=EM_UC7_Operating_manual.pdf Operating manual] ''-requires login''<br />
1. Mount sample <br />
2. Mount glass or diamond knife to knife holder <br />
3. Trimming or ultrasectioning of sample <br />
4. Fishing sections <br />
5. Transfer to an EM grid <br />


[[File:IMG_9461_UC7.jpg|400px|left|thumb|Leica EM UC7 Location at DTU Nanolab Building 307 Room 906]]<br clear="all" />


[https://labmanager.dtu.dk/view_binary.php?class=MiscDocument&id=15&name=EM_UC7_Operating_manual.pdf Operating manual] ''-requires login''<br />
'''Requirement for training:'''  
* Completion of the DTU Epoxy course
* Purchased of own diamond knife.


[[File:Leica EM UC7.jpg|400px|left|thumb|Leica EM UC7 Location at DTU Nanolab Building 307 Room 906]]<br clear="all" />


'''Requirement for training:''' Completion of the DTU Epoxy course and purchased of own diamond knife. For further information about the equipment usage or training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information about the equipment usage or training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


<br clear="all" />
<br clear="all" />
Line 88: Line 78:




The main steps of this technique proceed as follows:<br />
[https://labmanager.dtu.dk/view_binary.php?class=MiscDocument&id=15&name=EM_FC7_Operating_manual.pdf Operating manual] ''- requires login''<br />  
1. Set up the cryo chamber EM FC7 to the EM UC7 apparatus <br />
2. Mount both the trim and sectioning diamond knives to the knive holder and set up in the cryo chamber <br />
3. Connect the pump tube between the liquid nitrogen Dewar and the ultramicrotome apparatus <br />
4. Fill up liquid nitrogen Dewar <br />
5. Let equipment to cool down for 1 hour <br />
6. Meanwhile prepare samples (Cut big samples to smaller pieces) <br />
7. Freeze sample in liquid nitrogen and mount sample <br />
8. Trimming and ultrasectioning of sample <br />
9. Collecting sections and transfer to an EM grid <br />


[[File:Leica EM FC7 Cryo-Ultramicrotome.jpg|400px|left|thumb|Leica EM FC7 Location at DTU Nanolab Building 307 Room 906]]<br clear="all" />


[https://labmanager.dtu.dk/view_binary.php?class=MiscDocument&id=15&name=EM_FC7_Operating_manual.pdf Operating manual] ''- requires login''<br />
'''Requirement for training:'''  
* Purchased of own diamond knife.


[[File:Leica EM FC7 Cryo-Ultramicrotome.jpg|400px|left|thumb|Leica EM FC7 Location at DTU Nanolab Building 307 Room 906]]<br clear="all" />


'''Requirement for training:''' Purchased of own diamond knife. For further information about the equipment usage or training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information about the equipment usage or training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


<br clear="all" />
<br clear="all" />
Line 114: Line 96:




[[|300px|thumb|left|LKB Knifemaker Location at DTU Nanolab Building 307 Room 909B]]<br clear="all" />
[[File:IMG_9462_KMR3.jpg|400px|thumb|left|LKB Knifemaker Location at DTU Nanolab Building 307 Room 909B]]<br clear="all" />
For further information about the knifemaker usage and training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information about the knifemaker usage and training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


Line 131: Line 113:
[https://labmanager.dtu.dk/view_binary.php?class=MiscDocument&id=15&name=EM_CPD300_Operating_manual_small.pdf Operating manual] ''- requires login'' <br />  
[https://labmanager.dtu.dk/view_binary.php?class=MiscDocument&id=15&name=EM_CPD300_Operating_manual_small.pdf Operating manual] ''- requires login'' <br />  


[[File:EM CPD300.jpg|300px|thumb|left|Leica EM CPD300 Location at DTU Nanolab Building 314 Room 040]]<br clear="all" />
[[File:IMG_9456_CPD300.jpg|400px|thumb|left|Leica EM CPD300 Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
For further information on the CPD usage or training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information on the CPD usage or training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


<br clear="all" />
<br clear="all" />


= Drying oven =
= Coater =
The TS9026 drying oven is of 26L capacity and is used for epoxy embedding experiments.
== Leica EM ACE600 ==
 
The coater offers 3 applications
* Platinum coating
* Glow discharge
* Carbon coating


Specifications:
* Temperature range is from 2°C to 250°C
* Fan speed is 0 to 10
* Capacity is 26L


[[File:IMG 9634.jpg|400px|thumb|left|TS9026 Drying oven Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
[[File:IMG_9459_ACE600.jpg|400px|thumb|left|Leica EM ACE600 Location at DTU Nanolab Building 307 Room 907]]<br clear="all" />
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information about the coater usage and training contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
 
<br clear="all" />
 
= Sonic Dismembrator =
The Fisherbrand Model 505 sonic dismembrator apparatus applies sound energy to agitate particles in a sample. For biological applications, sonication may be sufficient to disrupt or deactivate a biological material. For example, sonication is often used to disrupt cell membranes and release cellular contents. In nanotechnology sonication is commonly used for evenly dispersing nanoparticles in liquids.
 
[[File:IMG_9633.jpg|400px|thumb|left|Fisherbrand Model 505 Sonic Dismembrator Location at DTU Nanolab Building 314 Room 040]]<br clear="all" />
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


<br clear="all" />
<br clear="all" />
Line 172: Line 145:


[[File:IMG_9636.jpg|400px|thumb|left|Mini tube rotator Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
[[File:IMG_9636.jpg|400px|thumb|left|Mini tube rotator Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
<br clear="all" />
== Centrifuge 5430R ==
Two rotor are available for this centrifuge in the Softmatter lab.
* Rotor FA-45-30-11
Allows max. capacity 30 micro test tubes for 1.5/
2.0 mL and operates at 25000 ×g /15350 rpm
* Rotor F-35-6-30
Allows max. capacity 6 conical tubes for 50 mL or 6 conical tubes for 15 mL and operates at 7745 ×g /7830 rpm
'''Specifications:'''
'''Specifications:'''
* Max. rotor capacity depending on type of rotor: 30 × 1.5/2.0 mL, 6 × 50 mL, 6 × 15 mL
* Max. speed: 25000 ×g (15350 rpm)
* Acceleration/braking time: <25/25 s
* Temperature range: -11 °C to +40 °C
* Run time: 30 s to 99:59 h, infinity
[https://www.eppendorf.com/product-media/doc/en/335227/Centrifugation_Operating-manual_Centrifuge-5430-R.pdf Instruction manual] ''- requires login'' [[File:IMG_9457_Centrifuge 5430R.jpg|400px|thumb|left|Eppendorf centrifuge 5430R Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


Line 188: Line 186:




[https://labmanager.dtu.dk/view_binary.php?class=MiscDocument&id=15&name=Eppendorf_Mini_Spin_plus_centrifuge_Original_Instructions.pdf Instruction manual] ''- requires login'' <br />
[https://labmanager.dtu.dk/view_binary.php?class=MiscDocument&id=15&name=Eppendorf_Mini_Spin_plus_centrifuge_Original_Instructions.pdf Instruction manual] ''- requires login'' <br />[[File:Mini Spin centrifuge.jpg|400px|thumb|left|Eppendorf Mini Spin centrifuge Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
 
[[File:Mini Spin centrifuge.jpg|400px|thumb|left|Eppendorf Mini Spin centrifuge Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


Line 205: Line 200:
*Can be used at 5 to 40 °C (80% relative humidity), in an incubator or cold room
*Can be used at 5 to 40 °C (80% relative humidity), in an incubator or cold room
*Speed range 100 to 2500 (min-1)
*Speed range 100 to 2500 (min-1)


[[File:myPlate magnetic stirrer.jpg|400px|thumb|left|myPlate magnetic stirrer Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
[[File:myPlate magnetic stirrer.jpg|400px|thumb|left|myPlate magnetic stirrer Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
Line 243: Line 239:




[[File:Magnetic hotplate stirrer.jpeg|400px|thumb|left|VWR Magnetic hotplate stirrer Location at DTU Nanolab Building 314 Room 040]]<br clear="all" />
[[File:Magnetic hotplate stirrer.jpeg|400px|thumb|left|VWR Magnetic hotplate stirrer Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


Line 283: Line 279:




[[File:Ohaus Analytical Balance PX224.jpg|400px|thumb|left|Ohaus PX224 analytical balance Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
[[File:IMG_9463_Analytical balance.jpg|400px|thumb|left|Ohaus PX224 analytical balance Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


<br clear="all" />
<br clear="all" />


== pH meter ==
== Midi 40 CO2 Incubator ==
The pH meter allows for accurate pH measurements of chemicals or ideal when making buffers.
The incubator is suitable for the incubation of cell culture and operates at temperatures ranging from 5°C above ambient temperature to 50°C ±0.2°C.
 
Specifications:
* Temperature range is from ambient +5° to 50°C ±0.2°C
* Relative Humidity is <90% at 37°C
* CO2 Sensor is TC Sensor
* Capacity is 40L
 
 
[[File:Midi 40 CO2 Incubator.jpg|400px|thumb|left|Midi 40 CO2 Incubator Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
 
<br clear="all" />
 
== Ultrasonic cleaner ==
The GT SONIC ultrasonic cleaner can be used to remove dirt, grease, corrosion or cleaning electronic and small mechanical parts. Millions of tiny bubbles are created when ultrasonic sound is passed through liquid. These tiny bubbles combined with a huge pressure create incredible cleaning results.
 
 
Specifications:
* Temperature range is from 30°C to 80°C
* Timer can be set from 1 to 99 minutes
* Capacity is 2L
 
 
Four modes are available on the intrument and are as follows:
* '''Degas mode''' - This mode is to be used after a fluid change to rapidly remove air from the fluid so it can provide maximum cleaning effectiveness from the start of the cleaning cycle.
 
* '''Delicate mode''' - The cleaner runs at half power which provides a less aggressive cleaning action for fragile/delicate items.
 
* '''Full-power mode''' - A powerful deep clean that will clean heavily contaminated items.
 
* '''Temperature and Timing mode''' - Allows the user to set both the fluid temperature and duration of the cleaning cycle. These parameters will change depending on the cleaning agent and item being cleaned.
 




[[File:VWR pH meter.jpg|400px|thumb|left|VWR pH meter Location at DTU Nanolab Building 314 Room 040]]<br clear="all" />
[[File:Ultrasonic cleaner.jpg|400px|thumb|left|GT SONIC Ultrasonic cleaner Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


<br clear="all" />
<br clear="all" />


== Midi 40 CO2 Incubator ==
== Drying oven ==
The incubator is suitable for the incubation of cell culture and operates at temperatures ranging from 5°C above ambient temperature to 60°C ±0.2°C.
The TS9026 drying oven is of 26L capacity and is used for epoxy embedding experiments.
 
 
Specifications:
* Temperature range is from ambient to 250°C
* Fan speed is 0 to 10
* Capacity is 26L


[[File:Midi 40 CO2 Incubator.jpg|400px|thumb|left|Midi 40 CO2 Incubator Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
[[File:IMG 9634.jpg|400px|thumb|left|TS9026 Drying oven Location at DTU Nanolab Building 307 Room 903]]<br clear="all" />
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].
For further information on the equipment usage contact mktracy@dtu.dk [https://www.dtu.dk/english/service/phonebook/person?id=141983&cpid=260636&tab=0].


Retrieved from "https://labadviser.nanolab.dtu.dk//index.php?title=LabAdviser/314/Preparation_314-307/Soft-matter"