A suite of Gateway cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae.
AuthorsAlberti S, Gitler AD, Lindquist S,
JournalYeast
PubMed ID17583893
'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 ... More
The alliance for cellular signaling plasmid collection: a flexible resource for protein localization studies and signaling pathway analysis.
AuthorsZavzavadjian JR, Couture S, Park WS, Whalen J, Lyon S, Lee G, Fung E, Mi Q, Liu J, Wall E, Santat L, Dhandapani K, Kivork C, Driver A, Zhu X, Chang MS, Randhawa B, Gehrig E, Bryan H, Verghese M, Maer A, Saunders B, Ning Y, Subramaniam S, Meyer T, Simon MI, O'Rourke N, Chandy G, Fraser ID,
JournalMol Cell Proteomics
PubMed ID17192258
'Cellular responses to inputs that vary both temporally and spatially are determined by complex relationships between the components of cell signaling networks. Analysis of these relationships requires access to a wide range of experimental reagents and techniques, including the ability to express the protein components of the model cells in ... More
Gateway RFP-fusion vectors for high throughput functional analysis of genes.
AuthorsPark JY, Hwang EM, Park N, Kim E, Kim DG, Kang D, Han J, Choi WS, Ryu PD, Hong SG,
JournalMol Cells
PubMed ID17646710
'There is an increasing demand for high throughput (HTP) methods for gene analysis on a genome-wide scale. However, the current repertoire of HTP detection methodologies allows only a limited range of cellular phenotypes to be studied. We have constructed two HTP-optimized expression vectors generated from the red fluorescent reporter protein ... More
High-throughput yeast two-hybrid assays for large-scale protein interaction mapping.
AuthorsWalhout AJ, Vidal M,
JournalMethods
PubMed ID11403578
'Protein-protein interactions play fundamental roles in many biological processes. Hence, protein interaction mapping is becoming a well-established functional genomics approach to generate functional annotations for predicted proteins that so far have remained uncharacterized. The yeast two-hybrid system is currently one of the most standardized protein interaction mapping techniques. Here, we ... More
Towards a proteome-scale map of the human protein-protein interaction network.
AuthorsRual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M,
JournalNature
PubMed ID16189514
'Systematic mapping of protein-protein interactions, or ''interactome'' mapping, was initiated in model organisms, starting with defined biological processes and then expanding to the scale of the proteome. Although far from complete, such maps have revealed global topological and dynamic features of interactome networks that relate to known biological properties, suggesting ... More
Improved full-length cDNA production based on RNA tagging by T4 DNA ligase.
AuthorsClepet C, Le Clainche I, Caboche M,
JournalNucleic Acids Res
PubMed ID14704363
Second-strand cDNA priming is a central problem for full-length characterization of transcripts. A new strategy using bacteriophage T4 DNA ligase and partially degenerate adapters is proposed for grafting a sequence tag to the end of polyribonucleotides. Based on this RNA tagging system and previously described protocols, a new method for ... More
New recombination methods for Sinorhizobium meliloti genetics.
AuthorsHouse BL, Mortimer MW, Kahn ML,
JournalAppl Environ Microbiol
PubMed ID15128536
The availability of bacterial genome sequences has created a need for improved methods for sequence-based functional analysis to facilitate moving from annotated DNA sequence to genetic materials for analyzing the roles that postulated genes play in bacterial phenotypes. A powerful cloning method that uses lambda integrase recombination to clone and ... More
Homologous high-throughput expression and purification of highly conserved E coli proteins.
AuthorsErgin A, Büssow K, Sieper J, Thiel A, Duchmann R, Adam T,
JournalMicrob Cell Fact
PubMed ID17553160
BACKGROUND: Genetic factors and a dysregulated immune response towards commensal bacteria contribute to the pathogenesis of Inflammatory Bowel Disease (IBD). Animal models demonstrated that the normal intestinal flora is crucial for the development of intestinal inflammation. However, due to the complexity of the intestinal flora, it has been difficult to ... More
Isolation of rat dihydrofolate reductase gene and characterization of recombinant enzyme.
AuthorsWang Y, Bruenn JA, Queener SF, Cody V,
JournalAntimicrob Agents Chemother
PubMed ID11502523
While assays of many antifolate inhibitors for dihydrofolate reductase (DHFR) have been performed using rat DHFR as a target, neither the sequence nor the structure of rat DHFR is known. Here, we report the isolation of the rat DHFR gene through screening of a rat liver cDNA library. The rat ... More
The full-ORF clone resource of the German cDNA Consortium.
AuthorsBechtel S, Rosenfelder H, Duda A, Schmidt CP, Ernst U, Wellenreuther R, Mehrle A, Schuster C, Bahr A, Blöcker H, Heubner D, Hoerlein A, Michel G, Wedler H, Köhrer K, Ottenwälder B, Poustka A, Wiemann S, Schupp I,
JournalBMC Genomics
PubMed ID17974005
BACKGROUND: With the completion of the human genome sequence the functional analysis and characterization of the encoded proteins has become the next urging challenge in the post-genome era. The lack of comprehensive ORFeome resources has thus far hampered systematic applications by protein gain-of-function analysis. Gene and ORF coverage with full-length ... More
High throughput immuno-screening of cDNA expression libraries produced by in vitro recombination; exploring the Plasmodium falciparum proteome.
AuthorsKordai Sowa MP, Sharling L, Humphreys G, Cavanagh DR, Gregory WF, Fenn K, Creasey AM, Arnot DE,
JournalMol Biochem Parasitol
PubMed ID14698438
Improved Plasmodium falciparum cDNA expression libraries were constructed by combining mRNA oligo-capping with in vitro recombination and directional cloning of cDNA inserts into a plasmid vector that expresses sequences as thioredoxin fusion proteins. A novel procedure has also been developed for the rapid identification of seropositive clones on high-density filters, ... More
Human protein factory for converting the transcriptome into an in vitro-expressed proteome,.
AuthorsGoshima N, Kawamura Y, Fukumoto A, Miura A, Honma R, Satoh R, Wakamatsu A, Yamamoto J, Kimura K, Nishikawa T, Andoh T, Iida Y, Ishikawa K, Ito E, Kagawa N, Kaminaga C, Kanehori K, Kawakami B, Kenmochi K, Kimura R, Kobayashi M, Kuroita T, Kuwayama H, Maruyama Y, Matsuo K, Minami K, Mitsubori M, Mori M, Morishita R, Murase A, Nishikawa A, Nishikawa S, Okamoto T, Sakagami N, Sakamoto Y, Sasaki Y, Seki T, Sono S, Sugiyama A, Sumiya T, Takayama T, Takayama Y, Takeda H, Togashi T, Yahata K, Yamada H,
JournalNat Methods
PubMed ID19054851
Appropriate resources and expression technology necessary for human proteomics on a whole-proteome scale are being developed. We prepared a foundation for simple and efficient production of human proteins using the versatile Gateway vector system. We generated 33,275 human Gateway entry clones for protein synthesis, developed mRNA expression protocols for them ... More
DNA cloning using in vitro site-specific recombination.
Authors Hartley J L; Temple G F; Brasch M A;
JournalGenome Res
PubMed ID11076863
As a result of numerous genome sequencing projects, large numbers of candidate open reading frames are being identified, many of which have no known function. Analysis of these genes typically involves the transfer of DNA segments into a variety of vector backgrounds for protein expression and functional analysis. We describe ... More