CiteULike: jyuh's plasmid

Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing

Kourosh Salehi-Ashtiani — 2008-06-28T14:29:01-00:00

Nat Meth, Vol. 5, No. 7. (July 2008), pp. 597-600.

A sequential expression system for high-throughput functional genomic analysis.

KA Woodrow — 2008-07-04T23:29:53-00:00

Proteomics, Vol. 7, No. 21. (November 2007), pp. 3870-3879.

A method employing sequential rounds of cell-free protein synthesis (CFPS) was developed to identify gene products influencing the complex metabolic systems that result in protein accumulation and folding in vitro. The first round of CFPS creates an array of cell extracts individually enriched with a single gene product expressed in-parallel from linear DNA expression templates (ETs). The cell extract is engineered to enhance template stability and to provide reaction conditions conducive for general protein activation. Following first-round expression, linear templates are selectively degraded and a plasmid template for a reporter enzyme is added to initiate a subsequent round of protein expression. Reporter concentration and activity identify first-round gene products that affect amino acid and nucleic acid stability, energy supply, protein expression, stability, and activation. This sequential CFPS system provides a unique format for the functional genomic identification of broadly diverse metabolic activities.

Normalization of full-length enriched cDNA.

EA Bogdanova — 2008-06-25T05:39:00-00:00

Molecular bioSystems, Vol. 4, No. 3. (March 2008), pp. 205-212.

Analysis of rare messages in cDNA libraries is extremely difficult due to the substantial variations in the abundance of different transcripts in cells and tissues. Therefore, for rare transcript searches and analyses, the generation of equalized (normalized) cDNA is essential. Several cDNA normalization methods have been developed since 1990. A number of these methods have been optimized for the normalization of full-length enriched cDNA, and used in various applications, including transcriptome analysis and functional screening of cDNA libraries. One such procedure (named DSN-normalization) is based on the unique properties of duplex-specific nuclease (DSN) from kamchatka crab and allows the generation of normalized cDNA libraries with a high gene discovery rate.

Efficient construction of an inverted minimal H1 promoter driven siRNA expression cassette: facilitation of promoter and siRNA sequence exchange.

H Nassanian — 2008-06-06T12:45:08-00:00

PLoS ONE, Vol. 2, No. 1. (2007)

BACKGROUND: RNA interference (RNAi), mediated by small interfering RNA (siRNA), is an effective method used to silence gene expression at the post-transcriptional level. Upon introduction into target cells, siRNAs incorporate into the RNA-induced silencing complex (RISC). The antisense strand of the siRNA duplex then "guides" the RISC to the homologous mRNA, leading to target degradation and gene silencing. In recent years, various vector-based siRNA expression systems have been developed which utilize opposing polymerase III promoters to independently drive expression of the sense and antisense strands of the siRNA duplex from the same template. PRINCIPAL FINDINGS: We show here the use of a ligase chain reaction (LCR) to develop a new vector system called pInv-H1 in which a DNA sequence encoding a specific siRNA is placed between two inverted minimal human H1 promoters (approximately 100 bp each). Expression of functional siRNAs from this construct has led to efficient silencing of both reporter and endogenous genes. Furthermore, the inverted H1 promoter-siRNA expression cassette was used to generate a retrovirus vector capable of transducing and silencing expression of the targeted protein by>80% in target cells. CONCLUSIONS: The unique design of this construct allows for the efficient exchange of siRNA sequences by the directional cloning of short oligonucleotides via asymmetric restriction sites. This provides a convenient way to test the functionality of different siRNA sequences. Delivery of the siRNA cassette by retroviral transduction suggests that a single copy of the siRNA expression cassette efficiently knocks down gene expression at the protein level. We note that this vector system can potentially be used to generate a random siRNA library. The flexibility of the ligase chain reaction suggests that additional control elements can easily be introduced into this siRNA expression cassette.

A PCR based method to construct small interference RNA expression vectors.

Zhiyong Zhang — 2008-06-04T16:05:20-00:00

Molecular biology reports (12 April 2008)

Small interference RNAs (siRNA) have been shown to be useful in the field of gene therapy and gene function studies. As a siRNA expression vector, pSilencer employ RNA polymerase III promoters and could stably produce siRNA for weeks. But once one siRNA sequence was inserted into the pSilencer vector, the other siRNA sequence will hardly be reconstructed, because the site of siRNA production has been occupied and difficult to be changed, so it is not suitable for screen of effective siRNA sequence. To solve this problem, we constructed the subclone pSilcencer329, which generated from pSilencer3.1, then developed a PCR based method of constructing siRNA expression vectors, and generated pSilencerBCL2L2 recombinants efficiently. This method was proven to be effective, reliable, and less expensive, and thus will be of great help in regular gene silencing studies, and will be especially suitable for large scale gene function analysis.

APPLICATION OF AN ADENOVIRAL VECTOR ENCODING SOLUBLE TRANSFORMING GROWTH FACTOR-beta TYPE II RECEPTOR TO THE TREATMENT OF DIABETIC NEPHROPATHY IN MICE.

Takehito Kondo — 2008-05-30T02:49:50-00:00

Clinical and experimental pharmacology & physiology (23 May 2008)

1. In the present study, we examined the effects of inhibiting transforming growth factor (TGF)-beta in a mouse model of diabetic nephropathy. 2. An adenovirus harbouring the gene encoding soluble TGF-beta type II receptor (Ad.CAG-sTbetaRII), a competitive inhibitor of TGF-beta, was injected into hindlimb muscles (systemic delivery) of mice 5 weeks after the induction of diabetes with streptozotocin. The control group was injected with an adenovirus encoding the LacZ gene (Ad-LacZ). 3. Five weeks after administration, anti-TGF-beta gene therapy was found to have had no effect on renal function, albuminuria or glucose metabolism in mice with diabetic nephropathy. Nonetheless, this gene therapy did significantly reduce fibrosis in both glomeruli and renal tubules. These effects were accompanied by attenuation of the increased expression of alpha-smooth muscle actin normally seen in kidneys of diabetic mice and better preservation of glomerular cell numbers, although the thickness of the glomerular capillary basement membrane was unchanged. The plasma concentration of soluble TGF-beta type II receptor peaked on Day 7 after treatment, but was undetectable by Day 14. Moreover, a second treatment with Ad.CAG-sTbetaRII failed to prolong the interval of gene product expression in the blood. 4. The present anti-TGF-beta gene therapy showed a significant antifibrotic effect in a model of diabetic nephropathy, but failed to improve renal function. The inadequacy of the observed effect is likely due to the relatively short interval of gene product expression. This problem will have to be overcome if gene therapies for slowly progressing diseases, like diabetic nephropathy, are to be realised.

DelsGate, a robust and rapid gene deletion construction method.

MD García-Pedrajas — 2008-05-22T04:32:54-00:00

Fungal genetics and biology : FG & B, Vol. 45, No. 4. (April 2008), pp. 379-388.

With the increasing availability of fungal genome sequences there is great demand for fast, simple high-throughput methods to generate constructs for gene deletion. Here we describe a method that combines PCR and Gateway cloning technology together with use of the I-SceI homing endonuclease to generate precise deletion constructs in a very simple, universal and robust manner in just 2 days. These constructs are then used to produce deletion mutants in the organism of interest following applicable methods for that species. In establishing this protocol we determined empirically that 1 kb was a suitable flank length to facilitate homologous recombination in our species of interest, Ustilago maydis. The method, which we have named DelsGate (Deletions via Gateway), consists of standard PCR of only the 5' and 3' 1 kb gene flanks directly followed by in vitro Gateway cloning and final generation of the circular deletion construct by in vivo recombination in Escherichia coli. For use in DelsGate we have modified a Gateway cloning vector to include selectable markers for transformation of Ascomycetes and the Basidiomycete fungus U. maydis which causes corn smut disease. We have tested the reproducibility of the DelsGate approach by generating deletion constructs for 12 U. maydis genes. Although not tested here, the PCR and transformation steps of DelsGate should be well suited for high-throughput approaches to gene deletion construction in fungal species. DelsGate has the potential to be universal for all organisms with efficient transformation and homologous recombination systems.

Engineering BioBrick vectors from BioBrick parts.

RP Shetty — 2008-05-22T04:30:41-00:00

Journal of biological engineering, Vol. 2, No. 1. (2008)

ABSTRACT: BACKGROUND: The underlying goal of synthetic biology is to make the process of engineering biological systems easier. Recent work has focused on defining and developing standard biological parts. The technical standard that has gained the most traction in the synthetic biology community is the BioBrick standard for physical composition of genetic parts. Parts that conform to the BioBrick assembly standard are BioBrick standard biological parts. To date, over 2,000 BioBrick parts have been contributed to, and are available from, the Registry of Standard Biological Parts. RESULTS: Here we extended the same advantages of BioBrick standard biological parts to the plasmid-based vectors that are used to provide and propagate BioBrick parts. We developed a process for engineering BioBrick vectors from BioBrick parts. We designed a new set of BioBrick parts that encode many useful vector functions. We combined the new parts to make a BioBrick base vector that facilitates BioBrick vector construction. We demonstrated the utility of the process by constructing seven new BioBrick vectors. We also successfully used the resulting vectors to assemble and propagate other BioBrick standard biological parts. CONCLUSION: We extended the principles of part reuse and standardization to BioBrick vectors. As a result, myriad new BioBrick vectors can be readily produced from all existing and newly designed BioBrick parts. We invite the synthetic biology community to (1) use the process to make and share new BioBrick vectors; (2) expand the current collection of BioBrick vector parts; and (3) characterize and improve the available collection of BioBrick vector parts.

Development of a novel Gateway-based vector system for efficient, multiparallel protein expression in Escherichia coli.

F Freuler — 2008-05-22T04:28:38-00:00

Protein expression and purification, Vol. 59, No. 2. (June 2008), pp. 232-241.

We describe a cloning and expression system which is based on the Escherichia coli T7 expression system and Gateway recombination technology. We have produced numerous destination vectors with selected fusion tags and an additional set of entry vectors containing the gene of interest and optional labeling tags. This powerful system enables us to transfer a cDNA to several expression vectors in parallel and combine them with various labeling tags. To remove the attached amino terminal tags along with the unwanted attB1 site, we inserted PreScission protease cleavage sites. In contrast to the commercially available destination vectors, our plasmids provide kanamycin resistance, which can be an advantage when expressing toxic proteins in E. coli. Some small-scale protein expression experiments are shown to demonstrate the usefulness of these novel Gateway vectors. In summary, this system has some benefits over the widely used and commercially available Gateway standard system, and it enables many different combinations for expression constructs from a single gene of interest.

A set of ligation-independent in vitro translation vectors for eukaryotic protein production

Viola Bardoczy — 2008-03-28T17:59:36-00:00

BMC Biotechnology, Vol. 8 (27 March 2008), 32.

Rapid one-step recombinational cloning

Changlin Fu — 2008-05-22T04:20:56-00:00

Nucl. Acids Res., Vol. 36, No. 9. (1 May 2008), e54.

As an increasing number of genes and open reading frames of unknown function are discovered, expression of the encoded proteins is critical toward establishing function. Accordingly, there is an increased need for highly efficient, high-fidelity methods for directional cloning. Among the available methods, site-specific recombination-based cloning techniques, which eliminate the use of restriction endonucleases and ligase, have been widely used for high-throughput (HTP) procedures. We have developed a recombination cloning method, which uses truncated recombination sites to clone PCR products directly into destination/expression vectors, thereby bypassing the requirement for first producing an entry clone. Cloning efficiencies in excess of 80% are obtained providing a highly efficient method for directional HTP cloning. 10.1093/nar/gkn167

Sequence and Ligation Independent Cloning (SLIC)

2008-05-19T03:14:52-00:00

Bitesize Bio

Get Your Clone 90% Of The Time with Ligation Independent Cloning

2008-05-19T02:03:35-00:00

Bitesize Bio

Heterologous Gene Expression Problems?

2008-05-19T01:58:39-00:00

Bitesize Bio

Sending Plasmids: How to Avoid Jail Time and Shredded Envelopes

2008-05-19T01:51:03-00:00

Bitesize Bio

Another way to get your plasmid through the automatic sorting machines is to spot it onto a very small disc of filter paper. Cut out the filter paper, spot 10 microlitres of plasmid solution onto it, allow it to dry for a few minutes, then cover with sandwich wrap. All the recipient has to do is pop the disc into a microfuge tube containing some clean TE and at least enough DNA for a transformation will re-dissolve into the TE. Make sure the filter paper disc is small enough to allow it to be submerged in 10-50 microlitres in a microfuge tube. The recipient won’t thank you for the task of cramming an A4 piece of filter paper into a small tube. Remove the water The ultimate way to send plasmid DNA is in dried form. It’s a bit more time consuming, but plasmids are much more stable in dried form because the things that degrade DNA - DNases and hydrolyses - require water. So with dried DNA there is no problem if you are shipping your plasmid halfway round the world, it gets stuck in a hot customs room for 2 weeks, then sits on the recipient’s bench for a month. The simplest way to dry a DNA sample is to precipitate it (e.g. by ethanol precipitation), but omit the final resuspension step. A more thorough - although more expensive - method of drying DNA is lyophilization, using a speedvac for example.

GenomeVx: simple web-based creation of editable circular chromosome maps.

GC Conant — 2008-05-13T04:27:39-00:00

Bioinformatics (Oxford, England), Vol. 24, No. 6. (15 March 2008), pp. 861-862.

We describe GenomeVx, a web-based tool for making editable, publication-quality, maps of mitochondrial and chloroplast genomes and of large plasmids. These maps show the location of genes and chromosomal features as well as a position scale. The program takes as input either raw feature positions or GenBank records. In the latter case, features are automatically extracted and colored, an example of which is given. Output is in the Adobe Portable Document Format (PDF) and can be edited by programs such as Adobe Illustrator. AVAILABILITY: GenomeVx is available at http://wolfe.gen.tcd.ie/GenomeVx

New insights into chemical biology from ORFeome libraries

Yoko Yashiroda — 2008-04-26T09:20:42-00:00

Current Opinion in Chemical Biology, Vol. 12, No. 1. (February 2008), pp. 55-59.

As the genomes of many organisms have been sequenced, a variety of global analyses, called [`]omics,' have been initiated. Cloning of the set of all open reading frames encoded by the genome (ORFeome) of an organism is a major challenge, which serves as an indispensable provision before one launches into the ocean of the postgenomic world. A suitable strategy for high-throughput cloning and expression of thousands of genes is crucial to success. Recently developed systems employing site-specific or homologous recombination have made it feasible to manipulate thousands of ORFs en masse. Using these technologies, several recent studies have successfully fished biologically active small molecules and target proteins out of this bountiful ocean.

Receptor-specific regulation of phosphatidylinositol 3'-kinase activation by the protein tyrosine phosphatase Shp2.

SQ Zhang — 2008-02-09T08:52:41-00:00

Mol Cell Biol, Vol. 22, No. 12. (June 2002), pp. 4062-4072.

Receptor tyrosine kinases (RTKs) play distinct roles in multiple biological systems. Many RTKs transmit similar signals, raising questions about how specificity is achieved. One potential mechanism for RTK specificity is control of the magnitude and kinetics of activation of downstream pathways. We have found that the protein tyrosine phosphatase Shp2 regulates the strength and duration of phosphatidylinositol 3'-kinase (PI3K) activation in the epidermal growth factor (EGF) receptor signaling pathway. Shp2 mutant fibroblasts exhibit increased association of the p85 subunit of PI3K with the scaffolding adapter Gab1 compared to that for wild-type (WT) fibroblasts or Shp2 mutant cells reconstituted with WT Shp2. Far-Western analysis suggests increased phosphorylation of p85 binding sites on Gab1. Gab1-associated PI3K activity is increased and PI3K-dependent downstream signals are enhanced in Shp2 mutant cells following EGF stimulation. Analogous results are obtained in fibroblasts inducibly expressing dominant-negative Shp2. Our results suggest that, in addition to its role as a positive component of the Ras-Erk pathway, Shp2 negatively regulates EGF-dependent PI3K activation by dephosphorylating Gab1 p85 binding sites, thereby terminating a previously proposed Gab1-PI3K positive feedback loop. Activation of PI3K-dependent pathways following stimulation by other growth factors is unaffected or decreased in Shp2 mutant cells. Thus, Shp2 regulates the kinetics and magnitude of RTK signaling in a receptor-specific manner.

Phosphoinositide 3-Kinase Is Required for Insulin-Induced but Not for Growth Hormone- or Hyperosmolarity-Induced Glucose Uptake in 3T3-L1 Adipocytes

Hiroshi Sakaue — 2008-02-04T16:09:57-00:00

Mol Endocrinol, Vol. 11, No. 10. (1 September 1997), pp. 1552-1562.

The regulatory mechanism of glucose uptake in 3T3-L1 adipocytes was investigated with the use of recombinant adenovirus vectors encoding various dominant negative proteins. Infection with a virus encoding a mutant regulatory subunit of phosphoinositide (PI) 3-kinase that does not bind the 110-kDa catalytic subunit (Deltap85) inhibited the insulin-induced increase in PI 3-kinase activity coprecipitated by antibodies to phosphotyrosine and glucose uptake in a virus dose-dependent manner. Overexpression of a dominant negative RAS mutant in which Asp57 is replaced with tyrosine (RAS57Y) or of a dominant negative SOS mutant that lacks guanine nucleotide exchange activity (DeltaSOS) abolished the insulin-induced increase in mitogen-activated protein kinase activity, but had no effect on PI 3-kinase activity or glucose uptake. Although GH and hyperosmolarity attributable to 300 mM sorbitol each promoted glucose uptake and translocation of glucose transporter (GLUT)4 to an extent comparable to that of insulin, these stimuli triggered little or no association of PI 3-kinase activity with tyrosine-phosphorylated proteins. Overexpression of Deltap85 or treatment of cells with wortmannin, an inhibitor of PI 3-kinase activity, had no effect on glucose uptake or translocation of GLUT4 stimulated by GH or hyperosmolarity. Moreover, overexpression of DeltaSOS or RAC17N also did not affect the increase in glucose uptake induced by these stimuli. A serine/threonine kinase Akt, a constitutively active mutant of which was previously shown to stimulate glucose uptake, is activated by insulin, GH, and hyperosmolarity to [~]4-fold, [~]2.1-fold, and [~]2.3-fold over basal level, respectively. These results suggest that insulin-induced but neither GH- or hyperosmolarity-induced glucose uptake is PI 3-kinase-dependent, and neither RAS nor RAC is required for glucose uptake induced by these stimuli in 3T3-L1 adipocytes. 10.1210/me.11.10.1552

The human estrogen receptor has two independent nonacidic transcriptional activation functions.

L Tora — 2008-02-04T02:00:58-00:00

Cell, Vol. 59, No. 3. (3 November 1989), pp. 477-487.

plasmid hEG0: We have previously reported the presence of a hormone-inducible transcriptional activation function (TAF-2) within the region of the estrogen receptor (ER) that contains the hormone binding domain. We show here that the N-terminal A/B region of the ER contains an independent constitutive activation function (TAF-1) that exhibits cell type specificity since it activates transcription efficiently in chicken embryo fibroblasts, but only poorly in HeLa cells. By analyzing the ability of TAF-1, TAF-2, and the GAL4 and VP16 acidic activating domains (AADs) to homosynergize and heterosynergize with one another and with the factor binding to the upstream element (UE) of the adenovirus 2 major late promoter, we show that the activation properties of TAF-1 and TAF-2 are different and distinct from those of AADs, in agreement with the absence of acidic amino acid stretches in TAF-1 and TAF-2.

Integrative genomic approaches identify IKBKE as a breast cancer oncogene.

JS Boehm — 2007-09-03T15:15:38-00:00

Cell, Vol. 129, No. 6. (15 June 2007), pp. 1065-1079.

Addgene: The karyotypic chaos exhibited by human epithelial cancers complicates efforts to identify mutations critical for malignant transformation. Here we integrate complementary genomic approaches to identify human oncogenes. We show that activation of the ERK and phosphatidylinositol 3-kinase (PI3K) signaling pathways cooperate to transform human cells. Using a library of activated kinases, we identify several kinases that replace PI3K signaling and render cells tumorigenic. Whole genome structural analyses reveal that one of these kinases, IKBKE (IKKepsilon), is amplified and overexpressed in breast cancer cell lines and patient-derived tumors. Suppression of IKKepsilon expression in breast cancer cell lines that harbor IKBKE amplifications induces cell death. IKKepsilon activates the nuclear factor-kappaB (NF-kappaB) pathway in both cell lines and breast cancers. These observations suggest a mechanism for NF-kappaB activation in breast cancer, implicate the NF-kappaB pathway as a downstream mediator of PI3K, and provide a framework for integrated genomic approaches in oncogene discovery.

Impaired microRNA processing enhances cellular transformation and tumorigenesis

Madhu Kumar — 2007-04-26T11:42:04-00:00

Nature Genetics, Vol. 39, No. 5. (01 April 2007), pp. 673-677.

Forkhead transcription factors are critical effectors of cell death and cell cycle arrest downstream of PTEN.

N Nakamura — 2008-01-31T09:02:22-00:00

Mol Cell Biol, Vol. 20, No. 23. (December 2000), pp. 8969-8982.

Addgene: PTEN acts as a tumor suppressor, at least in part, by antagonizing phosphoinositide 3-kinase (PI3K)/Akt signaling. Here we show that Forkhead transcription factors FKHRL1 and FKHR, substrates of the Akt kinase, are aberrantly localized to the cytoplasm and cannot activate transcription in PTEN-deficient cells. Restoration of PTEN function restores FKHR to the nucleus and restores transcriptional activation. Expression of a constitutively active form of FKHR that cannot be phosphorylated by Akt produces the same effect as reconstitution of PTEN on PTEN-deficient tumor cells. Specifically, activated FKHR induces apoptosis in cells that undergo PTEN-mediated cell death and induces G(1) arrest in cells that undergo PTEN-mediated cell cycle arrest. Furthermore, both PTEN and constitutively active FKHR induce p27(KIP1) protein but not p21. These data suggest that Forkhead transcription factors are critical effectors of PTEN-mediated tumor suppression.

An essential role for Akt1 in dendritic cell function and tumor immunotherapy.

Dongsu Park — 2006-12-08T17:00:45-00:00

Nat Biotechnol (3 December 2006)

Addgene: Current dendritic cell (DC) vaccine preparations involving ex vivo differentiation and maturation produce short-lived, transiently active DCs that may curtail T-cell responses in vivo. We demonstrate that Akt1, downregulation of which decreases DC lifespan, is critical for proinflammatory signal-mediated DC survival and maturation. Lipopolysaccharide or CD40 signaling stabilizes Akt1, promoting both activation and Bcl-2-dependent survival of DCs. Expression of a potent allele encoding a lipid raft-targeted Akt1, M(F)-DeltaAkt, is sufficient for maturation and survival of murine bone marrow-derived DCs in vivo. M(F)-DeltaAkt-transduced DCs enhanced T-cell proliferation, activation and long-term memory responses, enabling eradication of large pre-established lymphomas and aggressive B16 melanomas. Human myeloid DCs expressing constitutively active M(F)-DeltahAkt also survived significantly longer and promoted antigen-specific T-cell responses. Thus, Akt1 is a critical regulator of DC lifespan, and its manipulation in DCs can improve the clinical efficacy of DC-based tumor vaccines.

CRE recombinase-inducible RNA interference mediated by lentiviral vectors.

G Tiscornia — 2007-07-14T04:31:07-00:00

Proc Natl Acad Sci U S A, Vol. 101, No. 19. (11 May 2004), pp. 7347-7351.

Addgene: Recently, several systems designed to trigger RNA interference by using small hairpin RNA driven by polymerase III promoters have been described. Here, we report a lentiviral-mediated small interfering RNA delivery system that can be induced by CRE recombinase. The system consists of a lentiviral vector carrying a mouse U6 promoter that is separated from a small hairpin RNA by a random DNA stuffer sequence flanked by modified loxP sites. The silencing cassette is not expressed until activated by addition of CRE recombinase delivered by a lentiviral vector. We have used this system to show specific down-regulation of GFP and two endogenous genes (the tumor suppressor p53 and the NF-kappaB transcription factor subunit p65) in vitro. Furthermore, down-regulation of both p53 and p65 resulted in the expected effect on downstream genes and cellular phenotype. We foresee multiple applications of this system both in vitro and in vivo to down-regulate specific targets in a tissue-specific and localized manner.

Delivery of the Cre recombinase by a self-deleting lentiviral vector: efficient gene targeting in vivo.

A Pfeifer — 2008-01-31T05:56:17-00:00

Proc Natl Acad Sci U S A, Vol. 98, No. 20. (25 September 2001), pp. 11450-11455.

Addgene: The Cre recombinase (Cre) from bacteriophage P1 is an important tool for genetic engineering in mammalian cells. We constructed lentiviral vectors that efficiently deliver Cre in vitro and in vivo. Surprisingly, we found a significant reduction in proliferation and an accumulation in the G(2)/M phase of Cre-expressing cells. To minimize the toxic effect of Cre, we designed a lentiviral vector that integrates into the host genome, expresses Cre in the target cell, and is subsequently deleted from the genome in a Cre-dependent manner. Thus, the activity of Cre terminates its own expression (self-deleting). We showed efficient modification of target genes in vitro and in the brain after transduction with the self-deleting vectors. In contrast to sustained Cre expression, transient expression of Cre from the self-deleting vector induced significantly less cytotoxicity. Such a self-deleting Cre vector is a promising tool for the induction of conditional gene modifications with minimal Cre toxicity in vivo.

Cre-loxP system as a versatile tool for conferring increased levels of tissue-specific gene expression from a weak promoter.

Shingo Nakamura — 2008-01-31T02:15:02-00:00

Mol Reprod Dev (28 December 2007)

Attempts to image reporter gene expression driven by weak promoters are often hampered by the poor transcriptional activity of such promoters. Most tissue-specific promoters are weak compared with stronger but constitutively expressing viral promoters. In this study, we validated methods of enhancing the transcriptional activity of weak promoters using a Cre-loxP system in vitro and in vivo. We constructed a tester vector, pCTL, which carries a strong systemic cytomegalovirus enhancer/ chicken beta-actin promoter (CAG), loxP-flanked CAT, and firefly luciferase (luc) cDNAs. Herpes simplex virus-thymidine kinase (HSV-tk) promoter was used as a weak and systemic promoter and ligated to Cre for construction of pTC. Luc activity was higher (about 10-fold enhancement) in co-transfected (with pCTL and pTC) than in singly (with HSV-tk promoter-driven luc expression vector pTL) transfected NIH3T3 cells. In vivo electroporation-mediated gene delivery of both pCTL and pTC into murine oviductal epithelium yielded results (about 16-fold enhancement) similar to those obtained with in vitro-transfected NIH3T3 cells. To evaluate tissue-specific enhancement of gene expression, podocyte (glomerular visceral epithelial cell)-specific nephrin promoter was ligated to the Cre gene or luc cDNA to create pNC and pNL, respectively. We achieved 2.4-fold improvement of luc gene expression in the mouse kidney in vivo when pCTL and pNC were co-transfected via the tail vein via the lipoplex method. The combination of a weak tissue-specific promoter with the Cre-loxP system could thus be used to enhance the strength of tissue-specific promoters in vitro and in vivo. Mol. Reprod. Dev. (c) 2007 Wiley-Liss, Inc.

Spatiotemporal dynamics of RhoA activity in migrating cells

Olivier Pertz — 2006-03-20T13:27:42-00:00

Nature (19 March 2006)

Addgene: Rho family GTPases regulate the actin and adhesion dynamics that control cell migration. Current models postulate that Rac promotes membrane protrusion at the leading edge and that RhoA regulates contractility in the cell body. However, there is evidence that RhoA also regulates membrane protrusion. Here we use a fluorescent biosensor, based on a novel design preserving reversible membrane interactions, to visualize the spatiotemporal dynamics of RhoA activity during cell migration. In randomly migrating cells, RhoA activity is concentrated in a sharp band directly at the edge of protrusions. It is observed sporadically in retracting tails, and is low in the cell body. RhoA activity is also associated with peripheral ruffles and pinocytic vesicles, but not with dorsal ruffles induced by platelet-derived growth factor (PDGF). In contrast to randomly migrating cells, PDGF-induced membrane protrusions have low RhoA activity, potentially because PDGF strongly activates Rac, which has previously been shown to antagonize RhoA activity. Our data therefore show that different extracellular cues induce distinct patterns of RhoA signalling during membrane protrusion.

Sirtuins deacetylate and activate mammalian acetyl-CoA synthetases.

WC Hallows — 2008-01-29T03:56:15-00:00

Proc Natl Acad Sci U S A, Vol. 103, No. 27. (5 July 2006), pp. 10230-10235.

Addgene: Silent Information Regulator 2 (Sir2) enzymes (or sirtuins) are NAD(+)-dependent deacetylases that modulate gene silencing, aging and energy metabolism. Previous work has implicated several transcription factors as sirtuin targets. Here, we investigated whether mammalian sirtuins could directly control the activity of metabolic enzymes. We demonstrate that mammalian Acetyl-CoA synthetases (AceCSs) are regulated by reversible acetylation and that sirtuins activate AceCSs by deacetylation. Site-specific acetylation of mouse AceCS1 on Lys-661 was identified by using mass spectrometry and a specific anti-acetyl-AceCS antibody. SIRT1 was the only member of seven human Sir2 homologues capable of deacetylating AceCS1 in cellular coexpression experiments. SIRT1 expression also led to a pronounced increase in AceCS1-dependent fatty-acid synthesis from acetate. Using purified enzymes, only SIRT1 and SIRT3 exhibited high catalytic efficiency against acetylated AceCS1. In mammals, two AceCSs have been identified: cytoplasmic AceCS1 and mitochondrial AceCS2. Because SIRT3 is localized to the mitochondria, we investigated whether AceCS2 also might be regulated by acetylation, and specifically deacetylated by mitochondrial SIRT3. AceCS2 was completely inactivated upon acetylation and was rapidly reactivated by SIRT3 deacetylation. Lys-635 of mouse AceCS2 was identified as the targeted residue. Using reversible acetylation to modulate enzyme activity, we propose a model for the control of AceCS1 by SIRT1 and of AceCS2 by SIRT3.

A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C.

JD Violin — 2008-01-29T03:28:09-00:00

J Cell Biol, Vol. 161, No. 5. (9 June 2003), pp. 899-909.

Addgene: Signals transduced by kinases depend on the extent and duration of substrate phosphorylation. We generated genetically encoded fluorescent reporters for PKC activity that reversibly respond to stimuli activating PKC. Specifically, phosphorylation of the reporter expressed in mammalian cells causes changes in fluorescence resonance energy transfer (FRET), allowing real time imaging of phosphorylation resulting from PKC activation. Targeting of the reporter to the plasma membrane, where PKC is activated, reveals oscillatory phosphorylation in HeLa cells in response to histamine. Each oscillation in substrate phosphorylation follows a calcium oscillation with a lag of approximately 10 s. Novel FRET-based reporters for PKC translocation, phosphoinositide bisphosphate conversion to IP3, and diacylglycerol show that in HeLa cells the oscillatory phosphorylations correlate with Ca2+-controlled translocation of conventional PKC to the membrane without oscillations of PLC activity or diacylglycerol. However, in MDCK cells stimulated with ATP, PLC and diacylglycerol fluctuate together with Ca2+ and phosphorylation. Thus, specificity of PKC signaling depends on the local second messenger-controlled equilibrium between kinase and phosphatase activities to result in strict calcium-controlled temporal regulation of substrate phosphorylation.

High-efficiency FLP and PhiC31 site-specific recombination in mammalian cells.

CS Raymond — 2008-01-29T03:08:35-00:00

PLoS ONE, Vol. 2, No. 1. (2007)

Addgene: DNA site-specific recombinases (SSRs) such as Cre, FLPe, and phiC31, are powerful tools for analyzing gene function in vertebrates. While the availability of multiple high-efficiency SSRs would facilitate a wide array of genomic engineering possibilities, efficient recombination in mammalian cells has only been observed with Cre recombinase. Here we report the de novo synthesis of mouse codon-optimized FLP (FLPo) and PhiC31 (PhiC31o) SSRs, which result in recombination efficiencies similar to Cre.

An in vitro recombination method to convert restriction- and ligation-independent expression vectors.

Feng Guo — 2008-01-25T15:52:03-00:00

Biotechnol J (6 December 2007)

In recent years, restriction-less recombination cloning systems based on site-specific recombinase with high efficiency have been proven to be very successful. Thus, it is desirable to convert existing conventional vectors to recombination vectors. In this report, we describe the conversion of a set of widely used conventional vectors to Gateway(R) recombination expression vectors. An attB cassette flanked by several restriction enzyme sites was inserted in a cloning vector, and then subcloned into existing vectors to be converted to construct intermediate vectors containing the attB cassette, which were then converted to recombination expression vectors by in vitro recombination. The intermediate vectors generated in this study can be used for releasing the attB cassette to convert other vectors using the same protocol described here. With the increasing number of recombination vectors constructed with this protocol, the likeliness of releasing the attB cassette from an existing vector, rather than synthesizing it with PCR, will increase. The final expression vectors can also be used for releasing the attR cassette for constructing new vectors.

Improved recombinational stability of lentiviral expression vectors using reduced-genome Escherichia coli.

CS Chakiath — 2007-12-31T15:33:44-00:00

Biotechniques, Vol. 43, No. 4. (October 2007)

Lentiviral expression clones, which contain long direct repeats, often show dramatic instability in Escherichia coli, leading to difficulties in obtaining valid clones. We show that the reduced-genome E. coli strain MDS42 is capable of stabilizing lentiviral expression clones containing direct repeats, and outperforms many commonly used cloning strains for this purpose. In addition, the strain has several characteristics that make it highly amenable for use in recombinational cloning systems.

A versatile approach to multiple gene RNA interference using microRNA-based short hairpin RNAs

Xiaocui Zhu — 2007-10-31T09:34:58-00:00

BMC Molecular Biology, Vol. 8 (30 October 2007), 98.

Protein fabrication automation.

JC Cox — 2007-10-31T16:19:39-00:00

Protein Sci, Vol. 16, No. 3. (March 2007), pp. 379-390.

Facile "writing" of DNA fragments that encode entire gene sequences potentially has widespread applications in biological analysis and engineering. Rapid writing of open reading frames (ORFs) for expressed proteins could transform protein engineering and production for protein design, synthetic biology, and structural analysis. Here we present a process, protein fabrication automation (PFA), which facilitates the rapid de novo construction of any desired ORF from oligonucleotides with low effort, high speed, and little human interaction. PFA comprises software for sequence design, data management, and the generation of instruction sets for liquid-handling robotics, a liquid-handling robot, a robust PCR scheme for gene assembly from synthetic oligonucleotides, and a genetic selection system to enrich correctly assembled full-length synthetic ORFs. The process is robust and scalable.

Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

K Colwill — 2007-10-31T16:11:56-00:00

BMC Biotechnol, Vol. 6 (2006)

Addgene: BACKGROUND: Recombinational systems have been developed to rapidly shuttle Open Reading Frames (ORFs) into multiple expression vectors in order to analyze the large number of cDNAs available in the post-genomic era. In the Creator system, an ORF introduced into a donor vector can be transferred with Cre recombinase to a library of acceptor vectors optimized for different applications. Usability of the Creator system is impacted by the ability to easily manipulate DNA, the number of acceptor vectors for downstream applications, and the level of protein expression from Creator vectors. RESULTS: To date, we have developed over 20 novel acceptor vectors that employ a variety of promoters and epitope tags commonly employed for proteomics applications and gene function analysis. We also made several enhancements to the donor vectors including addition of different multiple cloning sites to allow shuttling from pre-existing vectors and introduction of the lacZ alpha reporter gene to allow for selection. Importantly, in order to ameliorate any effects on protein expression of the loxP site between a 5' tag and ORF, we introduced a splicing event into our expression vectors. The message produced from the resulting 'Creator Splice' vector undergoes splicing in mammalian systems to remove the loxP site. Upon analysis of our Creator Splice constructs, we discovered that protein expression levels were also significantly increased. CONCLUSION: The development of new donor and acceptor vectors has increased versatility during the cloning process and made this system compatible with a wider variety of downstream applications. The modifications introduced in our Creator Splice system were designed to remove extraneous sequences due to recombination but also aided in downstream analysis by increasing protein expression levels. As a result, we can now employ epitope tags that are detected less efficiently and reduce our assay scale to allow for higher throughput. The Creator Splice system appears to be an extremely useful tool for proteomics.

Vectors for co-expression of an unrestricted number of proteins.

C Scheich — 2007-10-27T07:20:20-00:00

Nucleic Acids Res, Vol. 35, No. 6. (2007)

Addgene: A vector system is presented that allows generation of E. coli co-expression clones by a standardized, robust cloning procedure. The number of co-expressed proteins is not limited. Five 'pQLink' vectors for expression of His-tag and GST-tag fusion proteins as well as untagged proteins and for cloning by restriction enzymes or Gateway cloning were generated. The vectors allow proteins to be expressed individually; to achieve co-expression, two pQLink plasmids are combined by ligation-independent cloning. pQLink co-expression plasmids can accept an unrestricted number of genes. As an example, the co-expression of a heterotetrameric human transport protein particle (TRAPP) complex from a single plasmid, its isolation and analysis of its stoichiometry are shown. pQLink clones can be used directly for pull-down experiments if the proteins are expressed with different tags. We demonstrate pull-down experiments of human valosin-containing protein (VCP) with fragments of the autocrine motility factor receptor (AMFR). The cloning method avoids PCR or gel isolation of restriction fragments, and a single resistance marker and origin of replication are used, allowing over-expression of rare tRNAs from a second plasmid. It is expected that applications are not restricted to bacteria, but could include co-expression in other hosts such as Bacluovirus/insect cells.

PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories

Alexandre Angers-Loustau — 2007-09-17T19:44:52-00:00

BMC Molecular Biology, Vol. 8 (17 September 2007), 77.

Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC

Mamie Li — 2007-02-28T17:20:15-00:00

Nature Methods, Vol. 4, No. 3. (11 February 2007), pp. 251-256.

Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells.

D Yang — 2007-05-10T08:56:59-00:00

Proc Natl Acad Sci U S A, Vol. 99, No. 15. (23 July 2002), pp. 9942-9947.

Small interfering RNA (siRNA) has become a powerful tool for selectively silencing gene expression in cultured mammalian cells. Because different siRNAs of the same gene have variable silencing capacities, RNA interference with synthetic siRNA is inefficient and cost intensive, especially for functional genomic studies. Here we report the use of Escherichia coli RNase III to cleave double-stranded RNA (dsRNA) into endoribonuclease-prepared siRNA (esiRNA) that can target multiple sites within an mRNA. esiRNA recapitulates the potent and specific inhibition by long dsRNA in Drosophila S2 cells. In contrast to long dsRNA, esiRNA mediates effective RNA interference without apparent nonspecific effect in cultured mammalian cells. We found that sequence-specific interference by esiRNA and the nonspecific IFN response activated by long dsRNA are independent pathways in mammalian cells. esiRNA works by eliciting the destruction of its cognate mRNA. Because of its simplicity and potency, this approach is useful for analysis of mammalian gene functions.

A suite of Gateway((R)) cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae.

Simon Alberti — 2007-08-26T10:39:32-00:00

Yeast (21 June 2007)

Addgene: In the post-genomic era, academic and biotechnological research is increasingly shifting its attention from single proteins to the analysis of complex protein networks. This change in experimental design requires the use of simple and experimentally tractable organisms, such as the unicellular eukaryote Saccharomyces cerevisiae, and a range of new high-throughput techniques. The Gateway((R)) system has emerged as a powerful high-throughput cloning method that allows for the in vitro recombination of DNA with high speed, accuracy and reliability. Two Gateway-based libraries of overexpression plasmids containing the entire complement of yeast open reading frames (ORFs) have recently been completed. In order to make use of these powerful resources, we adapted the widely used pRS series of yeast shuttle vectors for use in Gateway-based cloning. The resulting suite of 288 yeast Gateway vectors is based upon the two commonly used GPD and GAL1 promoter expression systems that enable expression of ORFs, either constitutively or under galactose-inducible conditions. In addition, proteins of interest can be fused to a choice of frequently used N- or C-terminal tags, such as EGFP, ECFP, EYFP, Cerulean, monomeric DsRed, HA or TAP. We have made this yeast Gateway((R)) vector kit available to the research community via the non-profit Addgene Plasmid Repository (http://www.addgene.org/yeast_gateway). Copyright (c) 2007 John Wiley & Sons, Ltd.

Spatio-temporal dynamics of protein kinase B/Akt signaling revealed by a genetically encoded fluorescent reporter.

MT Kunkel — 2007-07-13T01:32:26-00:00

J Biol Chem, Vol. 280, No. 7. (18 February 2005), pp. 5581-5587.

Addgene: The serine/threonine kinase protein kinase B (PKB)/Akt is a critical regulator of insulin signaling, cell survival, and oncogenesis. The activation mechanisms of this key kinase are well characterized. In contrast, inactivation of PKB signaling by phosphatases is less well understood. To study the dynamics of PKB signaling in live cells, we generated a genetically encoded fluorescent reporter for PKB activity that reversibly responds to stimuli activating phosphatidylinositol 3-kinase. Specifically, phosphorylation of the reporter expressed in mammalian cells causes changes in fluorescence resonance energy transfer, allowing real-time imaging of phosphorylation catalyzed by PKB. Because of its reversibility, the reporter also allows termination of PKB signaling by phosphatases to be monitored. We found that PKB signaling in the cytosol was more rapid and more transient compared with that in the nucleus, suggesting the presence of differentially regulated phosphatase activity in these two compartments. Furthermore, targeting of the reporter to the plasma membrane, where PKB is activated, resulted in accelerated and prolonged response compared with the response in the cytosol, suggesting that release of PKB or its substrates from the membrane is required for desensitization of PKB signaling. These data reveal spatio-temporal gradients of both signal propagation and signal termination in PKB signaling.

A versatile tool for conditional gene expression and knockdown

Jolanta Szulc — 2006-01-25T10:48:15-00:00

Nature Methods, Vol. 3, No. 2. (23 January 2006), pp. 109-116.

Addgene: Drug-inducible systems allowing the control of gene expression in mammalian cells are invaluable tools for genetic research, and could also fulfill essential roles in gene- and cell-based therapy. Currently available systems, however, often have limited in vivo functionality because of leakiness, insufficient levels of induction, lack of tissue specificity or prohibitively complicated designs. Here we describe a lentiviral vector-based, conditional gene expression system for drug-controllable expression of polymerase (Pol) II promoter-driven transgenes or Pol III promoter-controlled sequences encoding small inhibitory hairpin RNAs (shRNAs). This system has great robustness and versatility, governing tightly controlled gene expression in cell lines, in embryonic or hematopoietic stem cells, in human tumors xenotransplanted into nude mice, in the brain of rats injected intraparenchymally with the vector, and in transgenic mice generated by infection of fertilized oocytes. These results open up promising perspectives for basic or translational research and for the development of gene-based therapeutics.

Controlled expression of transgenes introduced by in vivo electroporation.

T Matsuda — 2007-06-27T07:22:31-00:00

Proc Natl Acad Sci U S A, Vol. 104, No. 3. (16 January 2007), pp. 1027-1032.

Addgene: In vivo electroporation is a powerful technique for the introduction of genes into organisms. Temporal and spatial regulation of expression of introduced genes, or of RNAi, would further enhance the utility of this method. Here we demonstrate conditional regulation of gene expression from electroporated plasmids in the postnatal rat retina and the embryonic mouse brain. For temporal regulation, Cre/loxP-mediated inducible expression vectors were used in combination with a vector expressing a conditionally active form of Cre recombinase, which is activated by 4-hydroxytamoxifen. Onset of gene expression was regulated by the timing of 4-hydroxytamoxifen administration. For spatial regulation, transgenes were expressed by using promoters specific for rod photoreceptors, bipolar cells, amacrine cells, Müller glia or progenitor cells. Combinations of these constructs will facilitate a variety of experiments, including cell-type-specific gene misexpression, conditional RNAi, and fate mapping of progenitor and precursor cells.