Silver staining protein gels (Stukenberg lab) and Small Molecules for Xenopus Research: Difference between pages

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Protocol submitted by VGP from Stukenberg lab protocols [http://www.xenbase.org/community/person.do?method=display&personId=1311&tabId=0]
==Notice to our users==
Please help us to improve this small molecules wiki and our other wikis by registering for a wiki account through our normal feedback email.


==Important small molecule references==
*[http://www.xenbase.org/literature/article.do?method=display&articleId=35021 Database of Small Molecules by Feldman and Hogue 2006] at [https://pubchem.ncbi.nlm.nih.gov/ PubChem]
*[http://www.xenbase.org/literature/article.do?method=display&articleId=47903 Wnt/Notch by Myers and Krieg 2014]
*[http://www.xenbase.org/literature/article.do?method=display&articleId=970 Ubiquitin-proteasome by Salic and King 2005]


link to protocol page [http://people.virginia.edu/~djb6t/LabWeb/frogs.htm]
==Alphabetical List of Small Molecules With Literature References==


*[[1,3-Dicyclohexylurea]]
*[[11-cis retinal]]
*[[18alpha-glycyrretinic acid]]
*[[2'-deoxyadenosine]]
*[[2-APB]]
*[[3,3,5-triiodothyronine (T3)]]
*[[5HT (seratonin)]]
*[[8-Pcpt-2-O-Me-cAMP-AM]]
*[[activin]]
*[[AG1296]]
*[[AG1879]]
*[[AGN193109]]
*[[alpha-amanitin]]
*[[anandamide]]
*[[apelin]]
*[[aphidicolin]]
*[[AZD1480]]
*[[Bafilomycin A1]]
*[[BAPTA-AM]]
*[[Barasertib]]
*[[Benzaldehyde, 3-allyl-2-(2-(diethylamino)ethoxy)-(DEAB)]]
*[[beta-xyloside]]
*[[blebbistatin]]
*[[BMS-453]]
*[[Brefeldin A (BFA)]]
*[[bumetanide]]
*[[calcium ionophore]]
*[[CGP54626 ]]
*[[Chelerythrine]]
*[[chenodeoxycholic acid]]
*[[chymostatin ]]
*[[Citral]]
*[[Colcemide]]
*[[concanamycin]]
*[[cycloheximide]]
*[[cyclopamine]]
*[[Cyclosporin A]]
*[[Cytochalasin B]]
*[[cytochalasin D]]
*[[D-AP5]]
*[[D-NAME]]
*[[Colcemide|Demecolcine]]
*[[deltamethrin]]
*[[dexamethosone]]
*[[DHT(dihydrotestosterone)]]
*[[diazepam]]
*[[Difopein]]
*[[Diphenyleneiodonium Chloride]]
*[[DMH-1]]
*[[Dorsomorphin]]
*[[DRB]]
*[[Ex-527]]
*[[finasteride]]
*[[folic acid]]
*[[forskolin]]
*[[fusicoccin]]
*[[gallein]]
*[[gentamycin]]
*[[GSK3-inhibitor IX (BIO)]]
*[[GM6001]]
*[[H-89 Dihydrochloride]]
*[[heptanol]]
*[[herbimycin A]]
*[[Hydroxyurea]]
*[[IBMX]]
*[[jasplakinolide]]
*[[6-B345TTQ]]
*[[KT 5720]]
*[[L-NAME]]
*[[lansoprazole]]
*[[latrunculin A]]
*[[latrunculin B]]
*[[LDN-193189]]
*[[leucovorin]]
*[[LiCl]]
*[[LY294002]]
*[[m-3M3FBS]]
*[[methotrexate (MTX)]]
*[[metronidazole]]
*[[Mg132]]
*[[MMP-2 inhibitor II]]
*[[MS-275]]
*[[nicorandil]]
*[[Nicotinamide]]
*[[Nicotinic acid]]
*[[nifedipine]]
*[[nocodazole]]
*[[NSC-87877]]
*[[o-phenanthroline]]
*[[okadaic acid]]
*[[olomoucine]]
*[[ouabain]]
*[[PD173074]]
*[[PD-407824]]
*[[p-MPPI]]
*[[taxol|Paclitaxel]]
*[[phaclofen]]
*[[Picropodophyllin]]
*[[PMA]]
*[[PP2]]
*[[primaquine]]
*[[Progesterone]]
*[[propylthiouracil]]
*[[pyrimethamine]]
*[[quinpirole]]
*[[rac1 inhibitor]]
*[[rapamycin]]
*[[retinoic acid]]
*[[Retinol]]
*[[RO-3306]]
*[[RS67333]]
*[[RU486]]
*[[SAHA]]
*[[SB 203580]]
*[[SB431542]]
*[[SB 505124]]
*[[SCH28080]]
*[[SNAP]]
*[[sodium nitroprusside]]
*[[SP600125 ]]
*[[SU5402]]
*[[SU6656]]
*[[Suramin]]
*[[tautomycin]]
*[[taxol]]
*[[thyroxine (T4)]]
*[[Torin 2]]
*[[Trichostatin A]]
*[[trimetrexate]]
*[[TTNPB]]
*[[Tubercidin]]
*[[tunicamycin]]
*[[Tyrphostin AG 1478]]
*[[U73122]]
*[[Y27632]]
*[[ZM 447439]]


Silver Staining Protocol (Not Compatible with Mass Spec)
The Following are in need of standardization and curation
*[[AM251]]
*[[AM281]]
*[[AP1510]]
*[[AR-A014418]]
*[[BHQ]]
*[[b-aminoproprionitrile]]
*[[beclomethasone]]
*[[Butyrate]]
*[[calcicludine]]
*[[Calyculin A]]
*[[celastrol]]
*[[celecoxib]]
*[[chromanol 293B]]
*[[chlorate]]
*[[cytochalasin D]]
*[[colchicine]]
*[[dimethyloxallyl glycine (DMOG)]]
*[[diclofenac]]
*[[etoposide]]
*[[IWR1]]
*[[GW843682X]]
*[[leptomycin B]]
*[[LY320135]]
*[[methylcellulose (MC)]]
*[[methimazole]]
*[[MBCD or MBetaCD]]
*[[MS222]]
*[[nicardipine]]
*[[Nu6102]]
*[[phenylthiourea|phenylthiourea (PTU)]]
*[[purmorphamine]]
*[[Pyrazoleanthrone]]
*[[R(+)BayK 8644]]
*[[RHC80267]]
*[[RL-3]]
*[[SAG]]
*[[SB-431542]]
*[[TG003]]
*[[Thapsigargin]]
*[[U0126]]
*[[ursodeoxycholic acid]]
*[[Echinomycin]]
*[[Gö 6983]]
*[[phenylhydrazine]]
*[[ω-conotoxin–GVIA]]
*[[flunarizine]]
*[[tetrodotoxin]]
*[[veratridine]]
*[[NBI-27914]]


==Small Molecules Affecting Pathways==
===cAMP===
*[[IBMX]]
*[[RU486]]


Notes:
===CDK/Cyclins===
Be careful not to touch gel during any step of the procedure with either a gloved or ungloved hand, finger etc…
*[[olomoucine]]
Use MilliQ-H2O for all steps
*[[RO-3306]]
Perform all incubations in well washed glass dishes.


===ERK/MAPK===
*[[U0126]]
===Folic Acid===
*[[Methotrexate (MTX)]]


1. Remove gels from glass plates in which they were run:
===JAK/STAT===
*[[AZD1480]]
2. Incubate in 50% Methanol, 10% Glacial Acetic Acid, 40% H2O for 30 minutes (100 ml)
 
===JNK===
3. Incubate in 5% Methanol, 7% Acetic Acid (Glacial), 88% H2O for 30 minutes (100ml)
*[[SP600125]]
*[[Pyrazoleanthrone]]
4. Incubate in 10% Gluteraldehyde made up in H2O from 25% stock (25 ml) for 30 minutes.
 
===Nitric Oxide===
5. Wash 4 x 20-30 minutes in H2O using 200-300 ml per wash.
*[[sodium nitroprusside]]
 
6. Makes 2 Solutions, A and B:    A) 3 ml of 30% Ammonia Hydroxide, 0.25 g NaOH in 190 ml H2O.  B) 1.2g Silver Nitrate (AgNO3) into 10 ml of H2O. 
===PDGF===
*[[AG1296]]
7. Add solution B to A slowly, mix gently, and add to gel, incubate for 30 minutes.
*[[AP1510]]
 
8. Make developer and stop solutions (see below).
===Retinoic Acid===
*[[AGN193109]]
9. Perform 5 x 1 minute washes with H2O, using 200 ml’s per wash.
*[[Citral]]
*[[retinoic acid]]
10. Add developer solution (~100 ml) and wait and watch gel until you see bands come up. Quickly remove developer solution and add stop solution. (Developer Solution: 0.1g Citric Acid, 1ml 37% formaldehyde into 1L H2O. Stop Solution: 190 ml H2O and 10 ml Acetic Acid, Glacial)
*[[Retinol]]
*[[TTNPB]]
11. After 10 minutes in Stop Solution wash thoroughly
*[[BMS-453]]
 
===Shh===
*[[cyclopamine]]
*[[purmorphamine]]
*[[Vismodegib]]
 
===TGF-beta/BMP===
*[[SB-431542]]
*[[SB505124]]
 
===Thyroid Signaling===
*[[PTU]]
 
===Wnt===
*[[LiCl]]
*[[GSK3-inhibitor IX (BIO)]]
*[[IWR1]]
 
===Epigenetics===
*[[Ex-527]]
 
===Protease Inhibitors===
*[[chymostatin]]
*[[GM6001|GM6001 (MMP inhibitor)]]
*[[o-phenanthroline|o-phenanthroline(MMP inhibitor)]]
*[[BB-94|BB-94 MMP inhibitor]]
*[[GI254023X| GI254023X MMP10 inhibitor]]
 
==Small Molecules affecting Biological Functions & Processes==
===Angiogenesis===
*[[dimethyloxallyl glycine (DMOG)]]
*[[herbimycin A]]
*[[Suramin]]
 
===Apoptosis===
*[[cycloheximide]]
*[[alpha-amanitin]]
*[[Cyclosporin A]]
*[[2,2ʹ-Methylenebis(1,3-cyclohexanedione)]]
*[[NS3694]]
 
===Autophagy===
*[[LY-294002]]
 
===Calcium Signaling===
*[[nifedipine]]
*[[R(+)BayK 8644]]
*[[nicardipine]]
*[[deltamethrin]]
*[[BHQ]]
*[[Thapsigargin]]
 
===Circadian Rhythm===
*[[quinpirole]]
 
===Cytoskeletal Inhibitors===
*[[Cytochalasin B]]
*[[cytochalasin D]]
*[[Colcemide]]
*[[jasplakinolide]] is an activator
*[[latrunculin B]]
*[[taxol]]
*[[taxol|Paclitaxel]]
 
===Cell Cycle, including mitosis===
*[[Colcemide]]
*[[Hydroxyurea]]
*[[olomoucine]]
*[[PD-407824]]
===Cilia===
*[[methylcellulose (MC)]]
 
===DNA Damage/Repair===
*[[etoposide]]
*[[Hydroxyurea]]
 
===DNA Synthesis===
*[[Calyculin A]]
 
===Growth Cone, Filopodia, and other Cytoskeletal projections===
*[[PP2]]
*[[SU6656]]
*[[cytochalasin D]] 0.1 uM Sigma
*[[latrunculin B]] 30nM Sigma
*[[colchicine]] 12.5uM Sigma
*[[nocodazole]] 0.1uM Sigma
*[[RHC80267]]
 
===Hatching===
*[[ouabain]]
 
===Left-Right Patterning===
*[[methylcellulose (MC)]]
 
===Metamorphosis===
*[[3,3,5-triiodothyronine (T3)]]
*[[methimazole]]
*[[propylthiouracil]]
*[[thyroxine (T4)]]
 
===Neurotransmission===
*[[diazepam]]
*[[p-MPPI]]
*[[phaclofen]]
*[[RS67333]]
*[[deltamethrin]]
 
===Protein Recycling===
*[[primaquine]]
 
==Drugs by Gene Class==
 
===Channels, including ATPases===
*[[ouabain]]
*[[AM251]]
*[[AM281]]
*[[LY320135]]
===G Protein Receptors===
*[[purmorphamine]]
===Kinases===
*[[KT 5720]]
*[[olomoucine]]
*[[PD-407824]]
*[[SB 203580]]
*[[Y27632]]
*[[ZM 447439]]
 
===Phosphatases===
*[[Cyclosporin A]]
*[[deltamethrin]]
*[[okadaic acid]]
*[[tautomycin]]
*[[Calyculin A]]
 
===Small GTPases===
 
 
===Protein Synthesis===
*[[anisomycin]] 40uM Sigma
*[[cycloheximide]] 40uM
 
===Retinoids===
*[[TTNPB]] Sigma
 
==Textpresso Small Molecules to Research==
*[http://www.xenbase.org/literature/article.do?method=display&articleId=43038 importazole inhibits importin]
*[http://www.xenbase.org/literature/article.do?method=display&articleId=42068 M119]
*[http://www.xenbase.org/literature/article.do?method=display&articleId=42068 GBG or GBetaGamma or G Protein Beta Gamma]
*[[LY-294002| LY-294002 inhibits PI3K and autophagy]]
 
==Models of Anemia==
*[[Phenylhydrazine]]

Revision as of 08:37, 7 November 2018

Notice to our users

Please help us to improve this small molecules wiki and our other wikis by registering for a wiki account through our normal feedback email.

Important small molecule references

Alphabetical List of Small Molecules With Literature References

The Following are in need of standardization and curation

Small Molecules Affecting Pathways

cAMP

CDK/Cyclins

ERK/MAPK

Folic Acid

JAK/STAT

JNK

Nitric Oxide

PDGF

Retinoic Acid

Shh

TGF-beta/BMP

Thyroid Signaling

Wnt

Epigenetics

Protease Inhibitors

Small Molecules affecting Biological Functions & Processes

Angiogenesis

Apoptosis

Autophagy

Calcium Signaling

Circadian Rhythm

Cytoskeletal Inhibitors

Cell Cycle, including mitosis

Cilia

DNA Damage/Repair

DNA Synthesis

Growth Cone, Filopodia, and other Cytoskeletal projections

Hatching

Left-Right Patterning

Metamorphosis

Neurotransmission

Protein Recycling

Drugs by Gene Class

Channels, including ATPases

G Protein Receptors

Kinases

Phosphatases

Small GTPases

Protein Synthesis

Retinoids

Textpresso Small Molecules to Research

Models of Anemia

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