Archive for March, 2011

Updated Publication List Using GFP-Trap Related Products


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.


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.

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Recap from the San Diego Entrepreneur Exchange March Event on Green Energy

With the recent concerns about the safety of nuclear power originated from the Japan earthquake and Tsunami, it should be beneficial for us to recap what we have learned at the latest SDEE conference two days before the natural disaster hit Japan.

Ron Pitt, CEO of EcoDog:
Solar energy is a great source of energy but it’s limited by the supply of silicon. Furthermore solar panels have a life of about 20 years, at which point they need to be replaced. It’s important that we take steps to alleviate our dependence on oil and deal with the current crisis, but it is also imperative that we employ forward thinking, and expand the time scale so our fix doesn’t last 20 years, or even 200 years but much longer.

Barry Toyonaga, CBO of Kent BioEnergy:
Algea is probably the most efficient way of removing waste material in waters and to entice nutrition to soil. Even the biomass after use has been shown for making bricks in a recent conference in Japan. It is important to use every aspect of our raw material, we must be so efficient to the point where no useless waste is generated by the end of our process.

Steve Mayfield, Director of the San Diego Center for Algae Biotechnology, UCSD:
The energy generated from petroleum-derived fuels as well as chemicals are used for high efficiency production of food. The emission of CO2 peaked by many magnitudes in recent centuries and coincided with human population explosion. The fast depletion of oil will soon reduce humans’ abilities to produce food at such high efficiency, and unavoidably will lead to famine and population reduction. The recent unrest in Africa is not a fight for democracy but a fight for food (which we can’t agree).

The green industry is young and needs supporting roles even after high rollers like Sapphire Energy, a company spun out by Mayfield and recently received major equity investment from Monsanto, take all the spotlight. There are engineering work to be done to process the oil produced by algae, to manage production and transportation, etc.

Sandy Madigan, CEO of Strategic Enzyme Applications:
Lignin is a naturally present macromolecule in wood and other plants, it is very carbon rich and one of the few natural sources aromatic compounds can be derived from. If broken down effectively lignin can serve as an alternative source of carbon compounds, with the current source being petroleum. Furthermore, as a source of aromatics, it has the potential to provide an exact fuel replacement, as opposed to most current research looking for fuel alternatives.

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Thursday, March 17th, 2011 Allele Mail Bag, Open Forum No Comments

Legoland TALES of Binding DNA by Design

Imagine that you could have a protein that binds to a sequence in a chromosome where you want to activate transcription, nick or break DNA to target insertion or recombination, or create a DNA lesion for screening DNA repair pathway factors…imagine that you could build such proteins very much like putting together legos. Yes, it is possible based on findings about transcription activator-like effector (TALE) proteins. These are plant pathogen transcription factors naturally used to facilitate invasion of host species which have been rekindled to direct DNA binding in other species (1, 2).

Previously, zinc-finger nucleases (ZFNs) have been the focus of genomic modification tool development, but with only limited success. It is not easy to design or select a ZFN using available technologies. In comparison, TALEs have a modular 34 amino acid domain as a basic unit that recognizes a DNA base, with specificity mostly determined by residues 12 and 13. In other words, by using as few as 4 modules with dedicated diamino acids 12 and 13, one can create a protein that binds any DNA sequence.

However, it is not necessarily an easy construct to make because the highly repetitive sequence of TALEs causes plasmid instability during cloning. A team at Harvard recently published a method of minimizing repetitiveness and allowing step-wise ligation; (3). Other aspects of using TALEs involve the designing of an effector domain, e.g. DNAase or transcription activation domain, and packaging the “warhead” in a delivery vehicle such as a lentivirus. The unfolding of the TALEs is just starting, the future seems exciting.

1. J. Boch et al. Science 326, 1509 (2009); published online 29 October 2009
2. M. J. Moscou, and A. J. Bogdanove, Science 326, 1501 (2009)
3. Zhang, F. et al. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat. Biotechnol. 29, 149–153 (2011).

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Wednesday, March 9th, 2011 Open Forum No Comments

Recombinase-Mediated Cassette Exchange (RMCE) and Integrase Swappable in vivo Targeting Element (InSITE)

Genetic switches that can turn on expression of genes of interest in specific tissues or time frames have been used in dissecting biological processes. For example, the yeast-derived transcription factor Gal4 and its upstream activating sequence (UAS) are widely adopted in Drosophila for directing gene expressions.

RMCE was designed to replace existing gene control cassette such as UAS-Gal4 with others through the functions of recombinases, such as Cre, Flp, ?C31. Multiple recombination systems were recently combined to form a flexible enhancer trap, InSITE, for exchanging Gal4 with any other sequence (1). The purpose is to use different existing fly lines that express recombinases in various types of cells.

Related to this topic, UAS-Gal4 was combined with “intra-cassette” recombination for selecting one of the three fluorescent proteins (FPs) in tandem in order to label individual neurons in a setup called “Brainbow”, which was first created in mouse, and recently in flies (2). We expect that InSITE and Drosophila Brainbow would be put together for even broader use of different fly lines and in more cell lineage studies.

One technical barrier for effective use of these systems is the lack of high quality FPs that could provide better brightness and narrower emission spectrum than those currently available. For this reason, the above referenced fly Brainbow research relied heavily on using antibodies against tags fused to the FPs, rendering live cell imaging unobtainable in most cases.

A number of the new FPs in Allele Biotech’s pipeline will be introduced to the field soon, such as the Lancelet YFP, that is ~10X brighter than EGFP, with a very narrow emission bandwidth.

(1) Gahl et Al. 2011,
(2) Hampel et al. 2011,

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Wednesday, March 2nd, 2011 Fluorescent proteins No Comments