Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “reverse genetics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 991 records · Page 55Linked to original sources

Delta-mediated specification of midline cell fates in zebrafish embryos.

BACKGROUND: Fate mapping studies have shown that progenitor cells of three vertebrate embryonic midline structures - the floorplate in the ventral neural tube, the notochord and the dorsal endoderm - occupy a common region prior to gastrulation. This common region of origin raises the possibility that interactions between midline progenitor cells are important for their specification prior to germ layer formation. RESULTS: One of four known zebrafish homologues of the Drosophila melanogaster cell-cell signaling gene Delta, deltaA (dlA), is expressed in the developing midline, where progenitor cells of the ectodermal floorplate, mesodermal notochord and dorsal endoderm lie close together before they occupy different germ layers. We used a reverse genetic strategy to isolate a missense mutation of dlA, dlAdx2, which coordinately disrupts the development of floorplate, notochord and dorsal endoderm. The dlAdx2 mutant embryos had reduced numbers of floorplate and hypochord cells; these cells lie above and beneath the notochord, respectively. In addition, mutant embryos had excess notochord cells. Expression of a dominant-negative form of Delta protein driven by mRNA microinjection produced a similar effect. In contrast, overexpression of dlA had the opposite effect: fewer trunk notochord cells and excess floorplate and hypochord cells. CONCLUSION: Our results indicate that Delta signaling is important for the specification of midline cells. The results are most consistent with the hypothesis that developmentally equivalent midline progenitor cells require Delta-mediated signaling prior to germ layer formation in order to be specified as floorplate, notochord or hypochord.

Animals↗

Aromatic interactions define the binding of the alphavirus spike to its nucleocapsid.

BACKGROUND: Most enveloped viruses bud from infected cells by a process in which viral intracellular core components interact with cytoplasmic domains of transmembrane spike glycoproteins. We have demonstrated previously that a tyrosine motif in the cytoplasmic domain of the Semliki Forest virus (SFV) spike glycoprotein E2 is absolutely essential for budding. In contrast, hardly anything is known regarding which region of the capsid protein is involved in spike binding. Therefore, the mechanism by which spikes are selectively sorted into the viral bud or by which energy is provided for envelopment, remains unclear. RESULTS: Molecular models of the SFV capsid protein (SFCP) and the cytoplasmic domain of the spike protein were fitted as a basis for a reverse genetics approach to characterizing the interaction between these two proteins. Biochemical analysis of mutants defined a hydrophobic pocket of the capsid protein that is involved both in spike binding and nucleocapsid assembly. CONCLUSIONS: We suggest that aromatic residues in the capsid protein serve to bind the side chain of the essential E2 tyrosine providing both specificity for spike incorporation and energy for budding. The same hydrophobic pocket also appears to play a role in capsid assembly. Furthermore, the results suggest that budding may occur in the absence of preformed nucleocapsids. This is the first demonstration of the molecular mechanisms of spike-nucleocapsid interactions during virus budding.

Amino Acid Sequence↗

Amplification of B cell antigen receptor signaling by a Syk/ITAM positive feedback loop.

We have established a protocol allowing transient and inducible coexpression of many foreign genes in Drosophila S2 Schneider cells. With this powerful approach of reverse genetics, we studied the interaction of the protein tyrosine kinases Syk and Lyn with the B cell antigen receptor (BCR). We find that Lyn phosphorylates only the first tyrosine whereas Syk phosphorylates both tyrosines of the BCR immunoreceptor tyrosine-based activation motif (ITAM). Furthermore, we show that Syk is a positive allosteric enzyme, which is strongly activated by the binding to the phosphorylated ITAM tyrosines, thus initiating a positive feedback loop at the receptor. The BCR-dependent Syk activation and signal amplification is efficiently counterbalanced by protein tyrosine phosphatases, the activity of which is regulated by H(2)O(2) and the redox equilibrium inside the cell.

Animals↗

Strategies to identify transport systems in plants.

Since the first molecular structures of plant transporters were discovered over a decade ago, considerable advances have been made in the study of plant membrane transport, but we still do not understand transport regulation. The genes encoding the transport systems in the various cell membranes are still to be identified, as are the physiological roles of most transport systems. A wide variety of complementary strategies are now available to study transport systems in plants, including forward and reverse genetics, proteomics, and in silico exploitation of the huge amount of information contained in the completely known genomic sequence of Arabidopsis.

Amino Acid Sequence↗

A new class of lipid desaturase central to sphingolipid biosynthesis and signalling.

Sphingolipids and their phosphorylated metabolites play crucial roles in intracellular signalling in animals, and evidence is emerging for analogous situations in fungi and plants. Central to this signalling pathway is the phosphorylation of the sphingoid long chain base, sphingosine, which yields sphingosine-1-phosphate. Until recently, the enzyme responsible for the biosynthesis of sphingosine was unknown, but the Delta(4)-long chain base desaturase that carries out this reaction has now been identified. Orthologues are present in animals, plants and fungi, raising the possibility of using reverse genetics to determine the contribution of sphingosine-1-phosphate to signalling networks.

Ceramides↗

When negative is positive in functional genomics.

The post-genomic era has caused classical approaches to analyse gene function to be reviewed and refined. Conventional reverse genetic approaches to predict gene function have drawbacks in terms of genetic redundancy and being limited mainly to well-characterized genomes. The relatively recent use of dominant-negative transgenes has been successful in elaborating certain pathways and it is now possible to extend this technique to convert transcription factors into dominant repressor functions by fusion to repressor domains such as ENGRAILED from Drosophila. This methodology opens up new possibilities to overcome genetic redundancy, to identify novel gene functions and also to apply information on conserved protein domains between species to repress heterologous protein function.

Animals↗

Contribution of the Tos17 retrotransposon to rice functional genomics.

The ongoing international efforts of the Rice Genomic Sequencing Project have already generated a large amount of sequence data. The next important challenge will be to construct saturation mutant lines for the functional analysis of all of the genes revealed by this effort in the context of the rice plant as a whole. Recently, the endogenous retrotransposon Tos17 has been shown to be an efficient insertional mutagen. Considering the ease of mutagenesis with Tos17 and its multiple-copy nature, saturation mutagenesis with this retrotransposon should be feasible in rice. Ongoing reverse-genetics studies, such as the PCR-screening of mutants and cataloguing of mutants by sequencing Tos17-insertion sites, as well as traditional forward-genetics studies, have clearly demonstrated that the Tos17 system can significantly contribute to the functional genomics of rice.

Genome, Plant↗

Protein kinases in the plant defence response.

Protein kinases play a central role in signalling during pathogen recognition and the subsequent activation of plant defence mechanisms. Members of different kinase subfamilies, such as calcium-dependent protein kinases and MAP kinases, are involved. Nevertheless, often, only a single component of a signalling cascade in an experimental plant system has been characterised. The future challenge is to understand how these kinases work, which cellular responses they mediate, and how they fit into the bigger picture of defence signalling. This challenge has become increasingly feasible with the recent introduction of new techniques: these techniques include reverse genetics, which will allow the allocation of biological function to kinase isoforms, (phospho) proteomics combined with mass spectrometry, and transient expression of kinases in a (constitutively) active form, mimicking the induction of defence responses in a biological system.

Adaptation, Physiological↗

Applied plant genomics: the secret is integration.

Although concerted efforts to understand selected botanical models have been made, the resulting basic knowledge varies in its applicability to other diverse species including the major crops. Recent advances in high-throughput genomics are offering new avenues through which to exploit model systems for the study of botanical diversity, providing prospects for crop improvement. In particular, whole-genome sequencing has provided opportunities for the broader application of reverse genetics, expression profiling, and molecular mapping in diverse species.

Arabidopsis↗

Overexpression analysis of plant transcription factors.

Transcription factors (TFs) play important roles in plant development and its response to the environment. A variety of reverse genetics tools have been developed to study TF function, the two most commonly used ones being knockout and overexpression. Because of the unique characteristics and modes of action of TFs, the overexpression strategy has been particularly effective in revealing TF function. Thus, a number of overexpression-based methodologies - constitutive expression, tissue-specific expression, chemically inducible expression and overexpression of modified TFs - have been developed and are used in the analysis of TF function.

Gene Expression Regulation, Developmental↗

Plant ion channels: from molecular structures to physiological functions.

Progress in identification of plant ion channels and development of electrophysiological analyses in heterologous expression systems and in planta, in combination with reverse genetic approaches, are providing the possibility of associating molecular entities with physiological functions. Recently, the first attempts to determine in vivo functions using knockout mutants demonstrated the roles of root ion channels. The search for proteins interacting with such channels leads to an even more complex view of the concerted action in protein networks.

Ion Channels↗

Intranasal immunization with inactivated influenza vaccine.

The development of improved vaccines against epidemic and pandemic influenza virus infection remains a priority in vaccine research. Killed vaccines given by injection are both cost-effective and induce immunity; however, their limitations are well known. Live vaccines have been in development for many years, but difficulties and safety concerns have prohibited their licensing in Western countries. However, the newer technologies of vaccine development, including DNA vaccines and attenuated virus vaccines produced by reverse genetics, remain a hope for the future. With these problems in mind, emphasis has been given to the development of inactivated vaccines that are administered intranasally, either as repeated doses of saline vaccine or in conjunction with suitable carriers or adjuvants. This review describes these latter developments and concludes that this approach offers advantages and should be vigorously researched.

Journal Article↗

Influenza vaccines: new developments.

Current inactivated influenza vaccines are being produced with three influenza virus strains that are recommended annually by the World Health Organization on the basis of information obtained from global influenza surveillance. The use of these vaccines, for which the antigens are produced in embryonated chicken eggs, can result in a significant reduction of influenza-related morbidity and mortality. Nevertheless, there is still a demand for vaccines with a higher efficacy that can be produced more rapidly and more flexibly in response to an epidemic or a pandemic. New developments in the field of influenza vaccine preparation include novel vaccine production technologies, reverse genetics technology for the generation of vaccine strains and novel adjuvants for the improvement of vaccine immunogenicity.

Animals↗

Protein kinases as drug targets in parasitic protozoa.

The importance of protein kinases in cell signaling and cell cycle control has led to detailed structural and functional studies in various eukaryotes, and hence to the synthesis of specific chemical inhibitors for managing disease. Here, the current progress in applying developments from the wider protein kinase field to parasitic protozoa is reviewed. The availability of genome sequence data for several parasites has led to the identification of many protein kinases. Reverse genetics studies, including gene knockout and 'chemical genetics', can help to define the roles of the protein kinases and validate them as drug targets. In addition, screening chemical libraries with active recombinant protein kinases can identify lead compounds for drug design.

Animals↗

Confronting the avian influenza threat: vaccine development for a potential pandemic.

Sporadic human infection with avian influenza viruses has raised concern that reassortment between human and avian subtypes could generate viruses of pandemic potential. Vaccination is the principal means to combat the impact of influenza. During an influenza pandemic the immune status of the population would differ from that which exists during interpandemic periods. An emerging pandemic virus will create a surge in worldwide vaccine demand and new approaches in immunisation strategies may be needed to ensure optimum protection of unprimed individuals when vaccine antigen may be limited. The manufacture of vaccines from pathogenic avian influenza viruses by traditional methods is not feasible for safety reasons as well as technical issues. Strategies adopted to overcome these issues include the use of reverse genetic systems to generate reassortant strains, the use of baculovirus-expressed haemagglutinin or related non-pathogenic avian influenza strains, and the use of adjuvants to enhance immunogenicity. In clinical trials, conventional surface-antigen influenza virus vaccines produced from avian viruses have proved poorly immunogenic in immunologically naive populations. Adjuvanted or whole-virus preparations may improve immunogenicity and allow sparing of antigen.

Animals↗

New angles in mycology: studies in directional growth and directional motility.

Mycology is changing as an era of extensive genome sequencing comes of age and provides vital information that enables questions to be addressed about fungi in all the major taxonomic groups. As technology transfer facilitates what was once only possible for a very small number of model species, it becomes possible to explore the biology and biodiversity of fungi as a whole. The availability of genome sequence information and reverse genetic technologies allows hypotheses that emerge from biological observations to be tested. Genomic and post-genomic technologies will underline the importance of fungi as excellent models for the study of fundamental biological phenomena. Two enduring areas of research in my own laboratory are described that are now being extended using post-genomic approaches. These projects relate to how fungal hyphae extend and guide their tips and secondly how plant pathogenic oomycete zoospores are guided on their journey to the plant surface.

Fungi↗

Use of mutated FLP recognition target (FRT) sites for the exchange of expression cassettes at defined chromosomal loci.

Using the FLP/FRT system for site-specific recombination and the wild-type recognition site (FRT) in conjunction with certain mutant FRT sites, it becomes possible to provoke, with high yield, a double-reciprocal crossover event in cultured mammalian cells. It is demonstrated that this technology enables a targeting of expression cassettes to appropriate chromosomal reference sites in the recipient cell to improve the concepts of reverse genetics. The design of mutant FRT sites promoting such a process will be delineated. Our results show that the five spacer mutations tested are functional as the wild type but differ in the extent of their cross-recombination, which has to be minimized for their simultaneous usage.

Animals↗

Araneoid egg case silk: a fibroin with novel ensemble repeat units from the black widow spider, Latrodectus hesperus.

Araneoid spiders use specialized abdominal glands to manufacture up to seven different protein-based silks/glues that have diverse physical properties. The fibroin sequences that encode egg case fibers (cover silk for the egg case sac) and the secondary structure of these threads have not been previously determined. In this study, MALDI tandem TOF mass spectrometry (MS/MS) and reverse genetics were used to isolate the first egg case fibroin, named tubuliform spidroin 1 (TuSp1), from the black widow spider, Latrodectus hesperus. Real-time quantitative PCR analysis demonstrates TuSp1 is selectively expressed in the tubuliform gland. Analysis of the amino acid composition of raw egg case silk closely aligns with the predicted amino acid composition from the primary sequence of TuSp1, which supports the assertion that TuSp1 represents a major component of egg case fibers. TuSp1 is composed of highly homogeneous repeats that are 184 amino acids in length. The long stretches of polyalanine and glycine-alanine subrepeats, which account for the crystalline regions of minor ampullate and major ampullate fibers, are very poorly represented in TuSp1. However, polyserine blocks and short polyalanine stretches were highly iterated within the primary sequence, and (13)C NMR spectroscopy demonstrated that the majority of alanine was found in a beta-sheet structure in post-spun egg case silk. The TuSp1 repeat unit does not display substantial sequence similarity to any previously described fibroin genes or proteins, suggesting that TuSp1 is a highly divergent member of the spider silk gene family.

Amino Acid Sequence↗