Updated Publication List Using GFP-Trap Related Products

2011

Courtesey: list prepared by ChromoTek

Kastner, P. M., Schleicher, M., et al. (2011). The NDR Family Kinase NdrA of Dictyostelium Localizes to the Centrosome and Is Required for Efficient Phagocytosis. Traffic. 12: 301-312.

Guizetti, J., Schermelleh, L., et al. (2011). Cortical Constriction During Abscission Involves Helices of ESCRT-III-Dependent Filaments. Science.

Muhlen, S., Ruchaud-Sparagano, M. H., et al. (2011). Proteasome-independent Degradation of Canonical NF{kappa}B Complex Components by the NleC Protein of Pathogenic Escherichia coli. J Biol Chem. 286: 5100-5107.

Speck, J., Arndt, K. M., et al. (2011). Efficient phage display of intracellularly folded proteins mediated by the TAT pathway. Protein Eng Des Sel.

Heinrich, C., Gascon, S., et al. (2011). Generation of subtype-specific neurons from postnatal astroglia of the mouse cerebral cortex. Nat Protoc. 6: 214-228.

Qin, W., Leonhardt, H., et al. (2011). Usp7 and Uhrf1 control ubiquitination and stability of the maintenance DNA methyltransferase Dnmt1. J Cell Biochem. 112: 439-444.

Shen, H., Ferguson, S. M., et al. (2011). Constitutive activated Cdc42-associated kinase (Ack) phosphorylation at arrested endocytic clathrin-coated pits of cells that lack dynamin. Mol Biol Cell. 22: 493-502.

Wilkinson, K. A. and Henley, J. M. (2011). Analysis of metabotropic glutamate receptor 7 as a potential substrate for SUMOylation. Neurosci Lett.

Reininger, L., Wilkes, J. M., et al. (2011). An essential Aurora-related kinase transiently associates with spindle pole bodies during Plasmodium falciparum erythrocytic schizogony. Mol Microbiol. 79: 205-221.

Bubeck, D., Reijns, M. A., et al. (2011). PCNA directs type 2 RNase H activity on DNA replication and repair substrates. Nucleic Acids Res.

Dissanayake, K., Toth, R., et al. (2011). ERK/p90(RSK)/14-3-3 signalling has an impact on expression of PEA3 Ets transcription factors via the transcriptional repressor capicua. Biochem J. 433: 515-525.

Kuipers, M. A., Stasevich, T. J., et al. (2011). Highly stable loading of Mcm proteins onto chromatin in living cells requires replication to unload. J Cell Biol. 192: 29-41.

Frauer, C., Rottach, A., et al. (2011). Different Binding Properties and Function of CXXC Zinc Finger Domains in Dnmt1 and Tet1. PLoS One. 6: e16627.

2010

Paris, L. L., Hu, J., et al. (2010). Regulation of Syk by phosphorylation on serine in the linker insert. J Biol Chem. 285: 39844-39854.

Korzeniowski, M. K., Manjarres, I. M., et al. (2010). Activation of STIM1-Orai1 involves an intramolecular switching mechanism. Sci Signal. 3: ra82.

Chamousset, D., De Wever, V., et al. (2010). RRP1B Targets PP1 to Mammalian Cell Nucleoli and is Associated with Pre-60S Ribosomal Subunits. Mol Biol Cell.

Thorslund, T., McIlwraith, M. J., et al. (2010). The breast cancer tumor suppressor BRCA2 promotes the specific targeting of RAD51 to single-stranded DNA. Nat Struct Mol Biol. 17: 1263-1265.

Erdel, F., Schubert, T., et al. (2010). Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites. Proc Natl Acad Sci U S A.

Geoffroy, M. C., Jaffray, E. G., et al. (2010). Arsenic-induced, SUMO-dependent Recruitment of RNF4 into PML Nuclear Bodies. Mol Biol Cell. (PudMed)

Boulon, S., Pradet-Balade, B., et al. (2010). HSP90 and its R2TP/Prefoldin-like cochaperone are involved in the cytoplasmic assembly of RNA polymerase II. Mol Cell. 39: 912-924.

Schmitz, K. M., Mayer, C., et al. (2010). Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev. 24: 2264-2269.

Bakondi, B. and Spees, J. L. (2010). Human CD133-derived bone marrow stromal cells establish ectopic hematopoietic microenvironments in immunodeficient mice. Biochem Biophys Res Commun. 400: 212-218.

Vermeulen, M., Eberl, H. C., et al. (2010). Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 142: 967-980.

Pozo-Guisado, E., Campbell, D. G., et al. (2010). Phosphorylation of STIM1 at ERK1/2 target sites modulates store-operated calcium entry. J Cell Sci. 123: 3084-3093.

Kaidi, A., Weinert, B. T., et al. (2010). Human SIRT6 promotes DNA end resection through CtIP deacetylation. Science. 329: 1348-1353.

Dzamko N., et al. (2010). Inhibition of LRRK2 kinase activity leads to dephosphorylation of Ser910/Ser935, disruption of 14-3-3 binding and altered cytoplasmic localization. Biochem J 430: 405-413.

Nichols R. J., et al. (2010). 14-3-3 binding to LRRK2 is disrupted by multiple Parkinson’s disease-associated mutations and regulates cytoplasmic localization. Biochem J 430: 393-404.

Polo S. E., et al. (2010). Regulation of DNA-damage responses and cell-cycle progression by the chromatin remodelling factor CHD4. EMBO J.

Babiano R., et al. (2010). Ribosomal protein L35 is required for 27SB pre-rRNA processing in Saccharomyces cerevisiae. Nucleic Acids Res 38: 5177-5192.

Loiseau P., et al. (2010). Drosophila PAT1 is required for Kinesin-1 to transport cargo and to maximize its motility. Development 137: 2763-2772.

Dubin, M., Fuchs, J., et al. (2010). Dynamics of a novel centromeric histone variant CenH3 reveals the evolutionary ancestral timing of centromere biogenesis. Nucleic Acids Res.

Pabis, M., Neufeld, N., et al. (2010). Binding properties and dynamic localization of an alternative isoform of the cap-binding complex subunit CBP20. Nucleus. 1: 412-421.

Van Dessel N., et al. (2010). The phosphatase interactor NIPP1 regulates the occupancy of the histone methyltransferase EZH2 at Polycomb targets. Nucleic Acids Res.

Rass U., et al. (2010). Mechanism of Holliday junction resolution by the human GEN1 protein. Genes Dev 24: 1559-1569.

MacKay C., et al. (2010). Identification of KIAA1018/FAN1, a DNA repair nuclease recruited to DNA damage by monoubiquitinated FANCD2. Cell 142: 65-76.

Ommen G., et al. (2010). The co-chaperone SGT of Leishmania donovani is essential for the parasite’s viability. Cell Stress Chaperones 15: 443-455.

Fulcher A. J., et al. (2010). Binding of p110 retinoblastoma protein inhibits nuclear import of simian virus SV40 large tumor antigen. J Biol Chem 285: 17744-17753.

Taniue K., et al. (2010). Sunspot, a link between Wingless signaling and endoreplication in Drosophila. Development 137: 1755-1764.

Kovanich, D., van der Heyden, M. A., et al. (2010). Sphingosine kinase interacting protein is an A-kinase anchoring protein specific for type I cAMP-dependent protein kinase. Chembiochem. 11: 963-971.

Boulon S., et al. (2010). Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners. Mol Cell Proteomics 9: 861-879.

Slabicki M., et al. (2010). A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. PLoS Biol 8: e1000408.

Laxman, S., Sutter, B. M., et al. (2010). Behavior of a metabolic cycling population at the single cell level as visualized by fluorescent gene expression reporters. PLoS One. 5: e12595.

Bergbauer, M., Kalla, M., et al. (2010). CpG-methylation regulates a class of Epstein-Barr virus promoters. PLoS Pathog. 6.

Kalla M., et al. (2010). AP-1 homolog BZLF1 of Epstein-Barr virus has two essential functions dependent on the epigenetic state of the viral genome. Proc Natl Acad Sci U S A 107: 850-855.

Bellanger S., et al. (2010). The human papillomavirus type 18 E2 protein is a cell cycle-dependent target of the SCFSkp2 ubiquitin ligase. J Virol 84: 437-444.

New Product of the Week 032111-032711: Chromotek-GFP-multiTrap®

Promotion of the week 032111-032711: 10% off on all mWasabi and mTFP1 organelle marker fusion vectors. Email abbashussain@allelebiotech.com and include the code FUSION to redeem this offer.

Tags: anti-GFP, anti-RFP, camelid antibodies, Chromotek, GFP booster, GFP-Trap, Multi-Trap, single domain antibodies

New Frontiers for Research Tool Development in the New Year

Optogenetics
Chosen as the Method of the Year 2010 by Nature Method and mentioned in a number of year-end recaps, this is a technology that allows the use of light to precisely (at least in a temporal sense) control engineered proteins within a targeted cell population. For example, by introducing light-activated channelrhodopsins into neurons, one can use a pulse of light to initiate a movement of ion across the cell membrane. The technology, first reported in 2005 then made headlines as a major impact on neurosciences since 2007, is now being combined with other components in controlling a broader array of biological events, such as DNA binding, enzyme activities, etc. Looking forward, a few areas will be more than likely the frontlines of moving optogenetics into more labs:

Additional combinations: The few known channelrhodopsins and their fast growing variations will be combined with more “effecter” domains to control different events. The challenge will be to find ways to use the structural changes or any responses channelrhodopsins have to stimulating lights in order to trigger a reaction in the associated effecter domain.

Tracking mechanisms: A platter of fluorescent proteins (FPs) will be used as an independent tracking method to follow cells being targeted. FPs that have optical spectra that do not interfere with the optogenetic molecules will be tested and established. In addition, FPs with less toxicity, narrower excitation and emission peaks, and more tolerance to different cellular environment will be preferred and eventually set up as standards.

Delivery tools: To bring the optogenetic reagents into cells like neurons researchers will most likely rely on lentiviral vectors in most cases. Other vehicles such as baculovirus, MMLV-based retrovirus, even herpes virus may find broader applications in this field. Pre-packaged lentiviruses and MMLV-retroviruses already contain optogenetic constructs will become popular products.

VHH Antibodies
The small capture polypeptides based on single-domain Camelid antibodies (nanobodies, nano antbodies or nAbs) and similar VHH domains will become much dramatically more popular this year, judging from the significant increase in demands of the only camelid reagent products, GFP-Trap and RFP-Trap, in 2010. There are a number of NIH initiated programs that aim to find capture reagents that eventually target the complete human proteome. One of the key criteria for the current phase of the relevant NIH Director’s Initiative is ability to co-immunoprecipitate. The Human Proteome Organization (HUPO) recently expressed frustration due to the lack of high quality capture reagents necessary to isolate and identify most proteins. HUPO promotes global research on proteins in order to decode the human proteome. From what we have learned from dozens of publications showing the use of GFP-Trap, VHH molecules pulls down GFP-tagged proteins with unprecedented efficiency and purity. VHH antibodies show strong affinity and specificity, at a level superior or comparable to monoclonal antibodies. In addition, VHH antibodies are increasingly appreciated for their capabilities to recognize concave epitopes by their relatively convex-shaped paratopes. VHH nanobodies are small (~12-15 kD), with a limited number of functionally important disulfide bonds, can be expressed very well in E. coli, and are amazingly stable in extreme denaturing conditions such as heat and acid. They have been shown to be better suited for in vivo and trans-cellular membrane delivery than other antibodies. It should not be surprising that one day in the coming years VHH antibodies will be more dominant than monoclonal antibodies.

Super-Resolution Imaging
One of the goals of developing technologies such as photoactivated localization microscopy (PALM) and related super-resolution imaging (SRI) techniques was to achieve electron microscopy (EM) level resolution without using EM. Now new developments show that maybe combining EM and photoactivable FPs would provide more specific and more detailed morphology. It would be anticipated that more photoconvertible FPs will prove to work well for one type of SRI or another. The event that will bring this technology to nearly every cell biology lab is the improvement and availability of necessary instruments that some companies have already begun to commercialize.

New Product of the Week 010311-010911:

Human let-7b miRNA minigene on lentivirus with RFP reporter, ABP-RP-MILT7BLP

Promotion of the Week 010311-010911:

15% off mWasabi-based organelle markers carried on baculo2mammalian system if order this week (On-Demand products will require about 3-4 weeks for virus packaging after an order is placed). Use code 0103BACFP on fax or email order.

Tags: alpaca antibodies, camelid antibodies, channelrhodopsin, EM, halorhodopsin, optogenetic, PALM, photoactivable FP, photoconvertible FP, STED, STORM, VHH, VHH antibodies

BioTechniques Publishes Article on Single Domain Antibodies

Many blogs start by asking “Did you know…” to intrigue you to read along. So here it goes:

Did you know that there are more than 300,000 antibodies that are commercially available? And yes, many antibody companies are still generating more antibodies at ever faster pace and in a more systematic way. There are companies that plan to make peptide or short protein fragments for making antibodies against all human proteins or subproteome, others develop antibodies particularly suitable for demanding assays such as ChIP-CHIP. Government activities such as the National Cancer Institute (NCI)’s Clinical Proteomic Technologies Initiative (CPTI) and the Road Map program under the NIH Director’s Office also set goals of producing comprehensive sets of widely usable, renewable, affinity reagents for clinical cancer samples or the human proteome. Apparently people do not think the 300,000 available antibodies are sufficient for what they do.

Did you know that conventional antibodies commonly used as reagents are ~150kDa in molecular weight and can hardly be used inside live cells? Ulrich Rothbauer, professor in the department of biology at Ludwig Maximilians University, who is working with colleagues to develop tools to study cellular processes in living cells. “These antibodies have to assemble four different chains, two heavy and two light, and they’re assembled by disulfide bonds that cannot be correctly formed in the reducing environment of the cytoplasm. You cannot express such a huge complex molecule in living cells. You can [introduce] them by microinjection, for example, but it’s not applicable for high-throughput cell imaging.” [1] Antibody fragments such as scFv, Fab, and similar derivatives have been developed over the years to certain level of success, but not as widely accepted or practically amenable to replacing conventional antibodies.

Did you know that camel, llama, and shark naturally produce single heavy chain antibodies that can function as 13-16kDa fragments (yes if you have read previous Allele Blogs http://allelebiotech.com/blogs/2009/08/camelid-antibodies/)? They can easily be produced in bacteria, used directly inside live cells via transgene, fused to other proteins as a fusion tag, linked to DNA oligos as a detection module, or immobilized on beads for pull down or co-IP. Currently, these antibodies need to be selected by display after obtaining immunized antibody libraries. There is generally no commercial service for creating custom camelid antibodies at this time due to patent and other issues. Existing products are available for jelly fish GFP and DsRed derived RFP fusions. Publications using such a limited number of camelid antibodies have been amazing so far—dozens in top journals within the last few months and after only a short period of time since product launch.

New Product of the Week 05-09-10 to 05-16-10: RFP-Trap for mCherry, mRFP1, mOrange, mPlum, and mRuby etc.

Promotion of the Week 05-09-10 to 05-16-10: Purchase our ThermoExp500 PCR Thermocycer for $4,650.00, and qualify for $200 off or for a $300 credit toward any other Allele Biotech product or service! http://www.allelebiotech.com/allele3/EQ.php

Original BioTechniques Article http://www.biotechniques.com/news/biotechniquesNews/biotechniques-257771.html?utm_source=BioTechniques+Newsletters+%2526+e-Alerts&utm_campaign=b94f127de0-Methods+Newsletter&utm_medium=email

Tags: Alpaca, camelid antibodies, Chromotek, Fab, GFP-Trap, Hc antibodies, mCherry, mOrange, mPlum, mRFP1, mRuby, nAbs, RFP-Trap, scFv, single domain antibodies, VHH, VHH antibodies

Anti-GFP antibody choices

A variety of anti-GFP antibodies are now provided to fluorescent protein users. In addition to the monoclonal anti-GFP antibody that has been introduced together with the GFP-Trap product group, Allele Biotech also has a strong anti-GFP polyclonal product, and a new rat anti-GFP monoclonal antibody. The availability of these different species specificity should allow users to have options in staining, detection, co-IP, double-labeling, etc.

New Product of the Week 04-05-10 to 04-11-10: Rat anti-AvGFP antibody, ACT-CM-MRGFP10

Promotion of the Week 04-05-10 to 04-11-10: Buy any Allele Biotech/Orbigen’s polyclonal antibody, get another of equal or less value at 60% off (if you are not a fan or friend through Allele’s online social networks, the discount is 30%).

Tags: 3H9, anti-GFP, antibodies, camelid antibodies, Chromotek, GFP booster, GFP detection, monoclonal, polyclonal, rat monoclonal

10 Years of Allele Biotech

Facts about Allele’s 10 years in business:

Products

New product lines added in 2009: iPS cells, Camelid Antibodies, DNA synthesis chemicals, Recombinant Proteins

Highlights: HiTiter Lentiviral Systems, Baculovirus for Mammalian Expression (BacMam), Feeder Cells, shRNA on Viral Vectors, shRNA Validation FP Vector, ProperFold Protein Folding Vector, Validated AllHPLC synthetic siRNA

New Service Groups in 2009: Viral Packaging, RNAi Validation/Screening, FP-based Assay Development

Numbers

Since April, we have added at least one new product every week! We currently run one new promotion per week as well.

A bit of history–did you know that…

Allele Biotech obtained 5 NIH grants in its first three years since establishment. As a matter of fact, Allele Biotech was funded entirely by NIH grants

Allele filed its first patent application in its second year of operation, which was on DNA-driven RNAi and resulted in an outlicensing deal with Promega. As result of the applications, Allele has received 3 US patents on DNA-encoded shRNA, siRNA using promoters such as U6 and H1.

During the past 10 years, Allele was the first to sell U6-based RNAi vectors, the only supplier of bFGF-expressing feeder cells for iPSC, most likely a top 3 provider of baculovirus expression systems, camelid antibody products, iPS creating viral particles, and the most active commercial developer of fluorescent proteins.

Tags: 10 years in business, Allele Anniversary, camelid antibodies, NIH grants, oligos, RNAi