DISI - User contributions [en]

File:Nucleoside Nucleotide.png

2018-01-31T06:51:11Z

Henrrymo: Nucleic acids are organic polymeric macromolecules composed of nucleotide monomers building blocks. A nucleotide is made of nucleobase, a five-carbon sugar and 1-3 phosphate groups. Though the nucleotide normally refers nucleoside monophosphate, now nu...

Nucleic acids are organic polymeric macromolecules composed of nucleotide monomers building blocks. A nucleotide is made of nucleobase, a five-carbon sugar and 1-3 phosphate groups. Though the nucleotide normally refers nucleoside monophosphate, now nucleoside diphosphate or nucleoside triphosphate are also belongs to nucleotides. The base in nucleotides can be either purine or pyrimidine. When the sugars are riboses, the nucleotides are ribonucleotides. While the sugars are deoxyriboses, the nucleotides are deoxyribonucleotides.
https://www.creative-proteomics.com/services/nucleoside-nucleotide-analysis-service.htm

File:Amino acid analysis service.png

2018-01-31T06:50:20Z

Henrrymo: Hydrolysis is typically achieved under acid conditions. A standard procedure is hydrolysis with 6 M hydrochloric acid (24 hours, 110°C). Fragile amino acids, especially tryptophan and cysteine, will be partially destroyed. And then hydrolyzed samples ...

Hydrolysis is typically achieved under acid conditions. A standard procedure is hydrolysis with 6 M hydrochloric acid (24 hours, 110°C). Fragile amino acids, especially tryptophan and cysteine, will be partially destroyed. And then hydrolyzed samples (amino acids) are derivatized pre-column or post column for sensitive detection, separated by RP/SCX column. The use of internal and external standards of known amount is crucial for accurate quantification of each amino acid.
https://www.creative-proteomics.com/application/amino-acid-analysis.htm

File:Sphingolipid Metabolism.png

2018-01-31T06:48:54Z

Henrrymo: Cardiolipin (CL) is made up of two phosphatidyl moieties linked by a glycerol bridge. It is a tetra-acylated glycerophospholipid playing a crucial role in in both prokaryotic and eukaryotic cells. It is located at membranes associated with the producti...

Cardiolipin (CL) is made up of two phosphatidyl moieties linked by a glycerol bridge. It is a tetra-acylated glycerophospholipid playing a crucial role in in both prokaryotic and eukaryotic cells. It is located at membranes associated with the production of an electrochemical gradient assisted in the production of ATP and the transportation of substrates across the cell membrane. CL is abundant in mitochondria of eukaryotic cells, especially the inner membrane of mitochondria. It is necessary for efficient transport of electrons across cytochrome c oxidase by binding this enzyme tightly. Besides, it is also related to the function ATP synthase, the cytochrome bc1 complex and ATP/ADP exchange protein the F0F1. By taking part in cytochrome c release from the mitochondria, CL may play an important role in apoptosis.
https://www.creative-proteomics.com/services/cardiolipins-analysis-service.htm

File:Glycerophospholipids Analysis.png

2018-01-31T06:48:12Z

Henrrymo: Glycerophospholipids are glycerol-based phospholipids. They are the main component of biological membranes. Glycerophospholipids present a significant challenge in high level of accuracy in lipid quantitation, given the headgroup diversity, large numbe...

Glycerophospholipids are glycerol-based phospholipids. They are the main component of biological membranes. Glycerophospholipids present a significant challenge in high level of accuracy in lipid quantitation, given the headgroup diversity, large number of possible acyl chain combinations, and vast range of ionization efficiency of species. The glycerophospholipids include hundreds of analytes encountered in routine profiling and over a thousand species detectable from repeated fragmentation scanning from some samples.
https://www.creative-proteomics.com/services/glycerophospholipids-analysis-service.htm

File:Gene Editing Kits.png

2018-01-31T06:45:21Z

Henrrymo: CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems is a newly developed yet the most popular method for genome editing. Besides the basic employment of gene knock-out, CRISPR/Cas9 system can be applied to selective gene ac...

CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems is a newly developed yet the most popular method for genome editing. Besides the basic employment of gene knock-out, CRISPR/Cas9 system can be applied to selective gene activation and repression, purification of specific genomic DNA and fluorescent protein-tagging in live cells through modifications of the Cas9. Creative Biogene’s series products of CRISPR/Cas9 are mainly used for sgRNA vector constructing, sgRNA identification, screening to select the most active sgRNAs and knockout detection.
https://www.creative-biogene.com/Product/Gene-Editing-Kits.html

File:Tn5 transposase sequence.png

2018-01-31T06:32:00Z

Henrrymo: Robust Tn5 Transposase is a hyperactive form of Tn5 transposase. This enzyme can be used to randomly insert Tn5 transposon into target DNA. Robust Tn5 Transposase recognizes inside end sequences, outside end sequences and mosaic end sequences of Tn5 tr...

Robust Tn5 Transposase is a hyperactive form of Tn5 transposase. This enzyme can be used to randomly insert Tn5 transposon into target DNA. Robust Tn5 Transposase recognizes inside end sequences, outside end sequences and mosaic end sequences of Tn5 transposon.
https://www.creative-biogene.com/Robust-Tn5-Transposase-EMQZ1422-1271506-26.html

File:Cell lines knock out.png

2018-01-31T06:30:37Z

Henrrymo: CRISPR/Cas9 system consists of a “guide” RNA (gRNA) and a bacterial CRISPR-associated endonuclease (Cas9). The gRNA is a short synthetic RNA composed of a Cas9-binding “scaffold” sequence and ∼20 nucleotide “targeting” sequence that defin...

CRISPR/Cas9 system consists of a “guide” RNA (gRNA) and a bacterial CRISPR-associated endonuclease (Cas9). The gRNA is a short synthetic RNA composed of a Cas9-binding “scaffold” sequence and ∼20 nucleotide “targeting” sequence that defines the target genomic site to be modified. Cas9 contains two nuclease domains to induce site-specific DNA cleavage. It’s a scalable genome-wide editing technology for its ease of generating gRNAs. The simplicity and high-efficiency of CRISPR/Cas9 system make it a preferable genomic knockout method to the traditional ZFN and TALEN system. Our scientists are experts at performing gene knockout with CRISPR/Cas9, from designing gRNA constructs to transfection and single clone generation of a wide range of cells, including difficult-to-transfect and tumor cell lines.
https://www.creative-biogene.com/Services/Stable-cell-line-generation/Custom-Genome-Editing-Cell-Lines.html

File:Nuclear receptor screening.png

2018-01-31T06:29:37Z

Henrrymo: Nuclear receptors (NRs) are a class of proteins responsible for sensing steroid and thyroid hormones and certain other molecules. There are 48 genes in the human genome that code for the NRs. The myriad molecular pathways modulated by NRs including but...

Nuclear receptors (NRs) are a class of proteins responsible for sensing steroid and thyroid hormones and certain other molecules. There are 48 genes in the human genome that code for the NRs. The myriad molecular pathways modulated by NRs including but not limited to inflammation, lipid metabolism, apoptosis, extracellular matrix regulation, energy metabolism, and angiogenesis. These pathways’ processes can impact human health, such as general homeostasis, growth, and proliferation, which enable NRs to become the important therapeutic targets in the pathology of cancer, inflammation, and many other diseases for decades.
https://www.creative-biogene.com/Services/Drug-Discovery-Services/Nuclear-Receptor-Screening-Assays.html

File:BAC Library.png

2018-01-31T06:26:57Z

Henrrymo: Bacterial Artificial Chromosome (BAC) acts as a vector to artificially carry DNA into the cell of a bacterium, such as Escherichia coli, to make a BAC clone. In general, BAC clones can carry inserts of DNA up to 200,000 base pairs long. Recently, BAC i...

Bacterial Artificial Chromosome (BAC) acts as a vector to artificially carry DNA into the cell of a bacterium, such as Escherichia coli, to make a BAC clone. In general, BAC clones can carry inserts of DNA up to 200,000 base pairs long. Recently, BAC is used to create BAC libraries which are preferable for genome sequencing, physical maps constructing, and gene cloning. As a leading supplier in BAC library construction services, Creative Biogene is committed to providing you the most affordable BAC library construction services with fastest turnaround time to satisfy your downstream needs.
https://www.creative-biogene.com/Services/BAC-Library-Construction-Service

File:Acyl CoAs.png

2018-01-02T05:47:11Z

Henrrymo: [https://www.creative-proteomics.com/services/acyl-coas-analysis-service.htm Acyl-CoAs] only exist inside the cells and their profiling inside the cells can give you some clues of the local metabolic status. Since each organ exerts its specific functio...

[https://www.creative-proteomics.com/services/acyl-coas-analysis-service.htm Acyl-CoAs] only exist inside the cells and their profiling inside the cells can give you some clues of the local metabolic status. Since each organ exerts its specific function and has its specific energetic demand, each organ is therefore expected to show a different acyl-CoA profile.

File:Sphingomyelin Profiling.png

2018-01-02T05:46:09Z

Henrrymo: [https://www.creative-proteomics.com/services/sphingomyelin-profiling-service.htm Sphingomyelin profiling] service provides data on all individual molecular species. We recommend these profiling scans at the semi-quantitative level, which allows direct...

[https://www.creative-proteomics.com/services/sphingomyelin-profiling-service.htm Sphingomyelin profiling] service provides data on all individual molecular species. We recommend these profiling scans at the semi-quantitative level, which allows direct comparison between samples or treatments.

File:Post translational modification glycosylation.png

2018-01-02T05:44:38Z

Henrrymo: [https://www.creative-proteomics.com/services/Glycosylation-analysis-of-protein.htm Post translational modification glycosylation] is critical for a wide range of biological processes, including the attachment of cell to the extracellular matrix and in...

[https://www.creative-proteomics.com/services/Glycosylation-analysis-of-protein.htm Post translational modification glycosylation] is critical for a wide range of biological processes, including the attachment of cell to the extracellular matrix and intracellular protein-ligand interactions.

File:Stabe isotope protein standard.png

2018-01-02T05:42:36Z

Henrrymo: [https://www.creative-proteomics.com/products/stable-isotope-labeled-full-length-ms-protein-standard_103.htm Stable isotope protein standard] based on alphabetical.

[https://www.creative-proteomics.com/products/stable-isotope-labeled-full-length-ms-protein-standard_103.htm Stable isotope protein standard] based on alphabetical.

Contract Research Organizations

2016-11-24T06:25:43Z

Henrrymo:

Contract research organizations are companies that will perform specific in vitro and in vivo assays to testing the activity of compounds or therapies. Listed here are companies that the Shoichet lab has either worked with or considered working with in the past.

==[http://pdsp.med.unc.edu PDSP]==
The NIMH Psychoactive Drug Screening Program run by the Roth lab at UNC Chapel Hill, has been a close collaborator in performing in vitro binding and functional assays for almost all GPCR targets and and several transporters. If the PDSP has the assay, they are typically our first choice.

To submit compounds for screening:
# Login to the [https://pdspdb.unc.edu/html/pdspV2/web/index.php PDSP].
# Create a new request
** Provide the grant number, name name, known activity and rational
** Add the compounds and requested assays

Here is the address to send compounds vis FedEx (good as of 11/2014)

PDSP
Attn: Xi-Ping Huang
120 Mason Farm Rd
2113 Genetic Medicine Bldg
Chapel Hill, NC 27514
TEL: (919)-966-8777

When sending compounds provide:
* Shoichet Lab
* project name
* compound id, amount submitted, molecular weight (they usually would like at least 10 mg)
* label the vials with the ID/name and the PDSP# assigned (they will send you labels)

==[https://www.eurofinspanlabs.com/Panlabs Eurofins Panlabs]==
Located in Taiwan, they have 1,350 assays covering the following target classes
*Cytokine/Chemokine (41)
*GPCR (270)
*Ion Channel (41)
*Kinase (154)
*Nuclear Receptor (16)
*Other (15)
*Phosphatase (31)
*Phosphodiesterase (19)
*Protease (51)
*Transporter (19)
They were used by both Henry Lin and Matthew O'Meara (2013-2014) and they gave reasonable results at reasonable prices.

The shoichet lab contact there has been (10/14):
Judy Winslow, phone #: 425-785-3736, email: JudyWinslow@eurofins.com.

==[http://www.reactionbiology.com Reaction Biology]==
Located in Pennsylvania, Reaction Biology specializes in Kinase assays and have a few epigenetic and other assays:
*HMT/DNMT Assays
*HDAC/HAT Assays
*Bromodomain Assays
*DUB Assays
*Protease Assays
*PDE Assays
*CYP/hERG/Bcl/HSP90 Assays
*Cell Assays
*Phosphatase Assays

Their tag line is ''With the largest functional kinase activity assay panel in the industry, RBC provides kinase, epigenetic, and other profiling services to over 590 companies worldwide. RBC specializes in custom assay conditions, high quality reproducible data, and outstanding service.''

* ~104.00USD for 10 dose IC50 singlet curve (with 20% academic discount)
*They have a minimum order of 300USD order

==[http://www.carnabio.com/english CarnaBio]==
Located in Japan, CarnBio has an extensive Kinase pannel of 311 targets and a 2-week turn around. Christian Laggner used them for the kinase assays in [http://www.nature.com/nchembio/journal/v8/n2/abs/nchembio.732.html (Laggner NatChemBio 2012)].

==[http://www.multispaninc.com Multispan]==
In Hayward CA, Multispan 230 validated GPCR assays. 320 human GPCR and 180 murine GPCR cDNAs are cloned for custom assays. Apparently Mike Keiser has used them, though if PDSP has the target/assay that is the way to go.

==[http://www.chantest.com ChanTest - Now part of Charles River]==
In Cleveland OH, they have a range of Ion Channel assays. Brian says we've used them before and they were reasonable.
They've now been acquired by Charles River.

''ChanTest has developed the world’s most complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers.''

==[http://www.aurorabiomed.com/ion-channel-screening-assays/ Aurora Biomed]==
Aurora’s product range includes automated liquid-handling equipment, atomic absorption spectrometers, atomic fluorescence spectrometers, ion channel screening technology and microwave digestion systems, increasing the efficiency of sample management in a wide range of research applications. We are headquartered in Vancouver, BC, Canada.

Matt worked with Andy Hegel (andrew.hegle@aurorabiomed.com) to test compounds with patch-clamp assays for the Systems SEA project in 2014. They gave us a discount of 200$ per datapoint.

==[http://www.perkinelmer.com/ PerkinElmer]==
AS OF JAN 1 2015 THEY ARE DISCONTINUING THEIR ASSAY SERVICES DIVISION

Large collection of in vitro services including:
* Cytochrome P450
* Cytokine/Chemokine Secretion
* GPCRs
* Ion Channels (Ligand- & Voltage-Gated)
* Kinases
* Nuclear Receptors
* Other - Enzymes
* Other - Receptors
* Phosphodiesterases (PDEs)
* Transporters
and some in vivo services

[http://www.perkinelmer.com/Catalog/Category/ID/Complete-Services-Assay-List Complete Assay Services List]

==[http://optiviabio.com/ Optivia]==
Specialized in transporters, based in the Bay Area.

==[http://www.solvobiotech.com/ Solvo]==
Specialized in transporters, based in the Bay Area.

==[http://www.genscript.com/bio-assay_center.html GenScript]==
They have few assays for different classes of targets

In particular they have a protease panel covering over 70 proteases and can possibly develop further targets

==[http://bpsbioscience.com/ BPS Biosciences]==
Mostly enzymes

==[http://www.invivogen.com/innate-immunity InvivoGen]==
Located in San Diego, focusing on immune response

Assays for Pattern Recognition Receptor activity
* Toll-Like Receptors
* NOD-Like Receptors
* RIG-I-Like Receptors
* C-type Lectin Receptors
* Cytosolic dsDNA Sensors
* Inflammasome
* Autophagy & Innate Immunity
* PRR & PAMPs Detection

==[http://indigobiosciences.com/screening-services/nuclear-receptor-assays/ INDIGO Biosciences]==
Located in Pennsylvania, they can do nuclear hormone assay.

3,500 minimum order size e.g. 1 compound at 5 receptors at 10 doses each

==[http://www.soralabs.com/services/ Sora Labs]==
It looks like they have some enzyme assays that they can run.

==[http://www.fluofarma.com/ FlouFarma]==
Located in France, high content screening of live cells

==[http://www.cytoskeleton.com/custom-services/compound-screening Cytoskeleton]==
Compound screening against tubulin, microtubule, myosin, sarcomere, kinesin and small G-proteins.

==[https://www.caymanchem.com/app/template/services%2CHome.vm Cayman Chemical]==
* Assay Services
Biochemists with experience in the areas of eicosanoids, steroids, oxidative stress, and inhibitor screening
Use Cayman’s extensive line of well-characterized biochemical kits
Enzyme immunoassay, colorimetric, and fluorometric assays available
* Screening Services
Comprehensive screening laboratory focused on epigenetics
Backed by our core strengths in protein production, assay development, chemical synthesis, and medicinal chemistry
Capacity to test compounds at a rate of up to 100,000 compounds per week
Ability to profile compounds against a broad epigenetic enzyme panel
Includes assays for methyltransferases, demethylases, acetyltransferases, deacetylases (HDACs and SIRTS), and histone code readers (ex. bromodomain proteins)

==[http://www.discoverx.com/ DiscoveRx]==
GPCR, Kinases, Nuclear Receptors, Epigenetic Targets and Signaling Pathways

==[http://www.hdbiosciences.com/EngHTS.htm HD Biosciences]==
HD Biosciences Co., Ltd. is a Shanghai-based, biology-focused preclinical drug discovery contract research organization (CRO). They do hit identification, hit-to-lead, assay development in major target classes, such as GPCRs, kinases, ion channels and transporters, and in a high-throughput screening format using plate-based platforms. Our screening capabilities span from cell line generation, biochemical, and cell-based functional assays for receptors, enzymes and ion channels in a variety of techniques, including:

* Fluorescence (e.g. HTRF, FP, FRET, FLIPR, Flexstation)
* Absorbance
* Luminescence (e.g. luciferase, b-lactamase, deGFP, reporter gene)
* Radiometrics (e.g. SPA, MicroBeta, Filtration)
* Electrophysiology (e.g. patch clamps)
* ImageXpress (e.g. live cell image HCA/HCS)

==[http://www.absorption.com/resources/assay-data-sheets/ Absorption Systems]==
Absorption Systems is a preclinical CRO. They have locations in Exton, PA, San Diego, CA, and Panama City, Panama. They work with a wide variety of customers in the pharmaceutical and biotech industry, including small virtual pharma companies, large pharma companies with weekly programs, and specialty CROs looking for services that complement their own offerings. In vitro and in vivo areas of speciality include:

* BCS + Biowaivers
* Wound healing and psoriasis disease models
* Formulation
* Metabolism
* Permeability
* Pharmacokinetics
* Protein binding (e.g. fraction bound in plasma)
* Toxicology
* Transporters

==[http://www.cyprotex.com/toxicology Cyprotex]==
Cyprotex is a contract research organization specializing in preclinical ADME-Tox with offices in the UK and US.

Permeability & Transporters
* Caco-2 permeability
* Transporter interactions
* PAMPA-GI and PAMPA-BBB
* MDCK and MDR1-MDCK
* Transdermal absorption
* Intranasal absorption

Distribution - reversible/time dependent
* Plasma protein binding
* Whole blood binding
* Blood to plasma ratio
* Brain tissue binding
* Microsomal binding

Metabolism
* Metabolic stability microsomes, hepatocytes, S9, plasma/blood
* Metabolite profiling and identification
* Reaction phenotyping
* CYP inhibition
* UGT inhibition
* MAO inhibition
* CYP induction
* PXR and AhR nuclear

receptor activation
* 3D microtissues

==[http://www.brunswicklabs.com/biological-analysis Brunswick Labs]==
Brunswick Laboratories is an independent, full-service bioanalytical laboratory specializing in the science of Antioxidants, Oxidative Stress, Anti-inflammatory, Synthetic and Natural Compound Bioanalysis.

+1-508-281-6660
blservices@brunswicklabs.com
200 Turnpike Road, Southborough, MA 01772, USA

* Bioavailability, BioAbsorption, and BioUptake study via Caco-2 human intestinal cells
* Anti-inflammatory: LOX, COX, TNF-alpha, NFkB, Interleukins (ILs), and PGE2 as biomarkers
* Oxidative Stress Analysis for biological samples
* Antioxidation effect in a biological system: Nrf2, Cellular Antioxidant Assay (CAA)
* Diabetes and Weight Management: insulin secretion, insulin receptor activity, glucose uptake, glucose metabolism, and carbohydrate digestion as biomarkers
* Detoxification and Liver Function: Phase I and Phase II liver enzymes, liver function biomakers in serum
* Energy metabolism investigation via human cells
* Anti-cancer Function evaluation: cancer cell viability, proliferation, apoptosis, and invasion as biomarkers
* Anti-aging Assays: SIRT-1, telomerase activity as biomarkers
* Preclinical Investigations for Skin Care Products: UV protection, melanin (age spot) inhibition, anti-aging, anti-inflammatory

==[http://biotoxsciences.com/In_Vitro_Services BioToxSciences]==
http://biotoxsciences.com/In_Vitro_Services

Based in San Diego, they have a range of in-vitro functional assays

==Other CROs==
* [http://www.ricerca.com Ricerca]
* [http://www.amsbio.com/ amsbio] not really a CRO but apparently they can do assays
* [http://stores.arraybridge.com/enzyme-assays/ ArrayBridge] The have ~850 enzymes listed that they say they have assays for, but little detail on what services they actually provide.
* [http://www.sbdrugdiscovery.com/screening-assays SB Drug Discovery] 50 PDEs, 50 Ion Channels, NHRs, GPCRs, Inflammation
* [http://www.discoverx.com/services/drug-discovery-development-services DiscoverRX] Kinase, Epigenetic, GPCR
* [http://metislabs.com/radioligand-binding-assays.html MetisLab] Radioligand assays for GPCRs
* [http://www.creative-biogene.com/ Creative Biogene] Transfected Stable Cell Lines
* [http://www.creative-bioarray.com/ Creative Bioarray] Human Umbilical Cord Primary Cells

== CRO sourcing services ==
* [https://www.scienceexchange.com]
* [https://www.assaydepot.com]

https://www.genoway.com/services/catalog-models/mouse-knockouts.htm?utm_source=emailing&utm_medium=email&utm_content=01122015&utm_campaign=01122015