The potential of nucleic acid repair in functional genomics.

Chimeric RNA/DNA oligonucleotides have been used successfully to correct point and frameshift mutations in cells as well as in animal and plant models. This approach is one of several nucleic acid repair technologies that will help elucidate the function of newly discovered genes. Understanding the mechanisms by which these different technologies direct gene alteration is essential for progress in their application to functional genomics.

Targeted gene repair in mammalian cells using chimeric RNA/DNA oligonucleotides and modified single-stranded vectors.

Determining the function of newly discovered genes is at the center of the evolving field of genomics. With the elucidation of the human DNA sequence, the importance of single base changes to gene function has become apparent. In some cases, nucleotide alteration accounts for inherited disorders, but in other cases, subtle, even conservative, base changes can influence the function of a gene and its product. To identify how critical genetic changes alter function, molecular tools such as synthetic vectors have been created to direct nucleotide exchange. Some of these vectors, including chimeric RNA/DNA oligonucleotides and modified single-stranded oligonucleotides, have shown promise in the specific alteration of a single base at an exact position within the gene. Here, we describe the activity of the synthetic vectors in a mammalian cell system. The episomal target contains a mutation in the neomycin resistance gene fused to a reporter ligand-binding domain. Correction of the mutated base enables translation of the normal fusion product. This protein can now bind a ligand, resulting in the expression of the fusion protein visualized by green fluorescence. Hence, the activity of any similar vector can be measured easily (and in real time) using confocal microscopy. The system provides the basis for examining the effectiveness of new targeting molecules for creating or repairing single base alterations. In addition, genes suspected of affecting the frequency of repair can be tested through their expression in cells harboring the mutated target plasmid. Once the frequency of exchange in cells is established, the use of these vectors will become commonplace in a process designed to generate specific single base changes in genes involved in signal transduction. Such changes should help define functional domains within these proteins.

An immunohistochemical method for the detection of proteins in the vertebrate lens.

Fluorescence immunohistochemistry has traditionally been difficult or impossible to perform on the vertebrate lens because of its extremely high protein content. Described here is a robust and rapid method for preparing and labeling vertebrate eyes for confocal microscopy. This technique has successfully been applied to localize proteins in the lens epithelium and capsule, as well as the primary and secondary fibers. This technique preserves tissue morphology and coupled with double and triple labeling, has allowed localization of proteins bound to plasma membrane, basement membrane, nucleus, endoplasmic reticulum as well as sub-nuclear compartments. In addition, the present technique has proven useful for fluorescent immunohistochemical analysis of diverse tissues including whole embryos, adult muscle, pancreas, and liver. This procedure allowed us to successfully localize a wide variety of antigens on diverse vertebrate tissues including the more challenging vertebrate lens.

CIB1 deficiency results in impaired thrombosis: the potential role of CIB1 in outside-in signaling through integrin alpha IIb beta 3.

UNLABELLED: Agonist-induced inside-out signaling activates platelet integrin alpha(IIb)beta(3), rendering it to bind plasma fibrinogen (Fg). Fg binding induces outside-in signaling that culminates in platelet aggregation, leading to physiological hemostasis and pathological thrombosis. How outside-in signaling through alpha(IIb)beta(3) regulates hemostasis and thrombosis is not well understood. We have previously shown that CIB1 is involved in regulating alpha(IIb)beta(3) function. OBJECTIVE: To determine the in vivo role of CIB1 in the process of hemostasis and thrombosis. METHODS AND RESULTS: Genetic ablation of Cib1 significantly increased mouse tail bleeding time. Greater than 50% of the Cib1 null mice showed a rebleeding phenotype. Time taken for complete occlusion of carotid artery upon 10% FeCl(3)-induced injury was significantly delayed in the absence of Cib1. This was also associated with unstable thrombus formation. The inside-out signaling appears normal as ADP-, collagen- and PAR4 peptide-induced aggregation and fibrinogen binding was unaffected. The absence of Cib1 also affected the ability of platelets to spread on immobilized Fg, but not filopodia formation. Spreading could be restored in Cib1 null platelets by the addition of exogenous ADP. Outside-in signaling-dependent tyrosine phosphorylation of the integrin beta(3) subunit was significantly reduced in the absence of Cib1 as determined by Western blot analysis. CONCLUSION: Using gene knockout mice, we show for the first time that lack of Cib1 results in impaired thrombosis. CIB1 regulates these processes by affecting platelet spreading, but not platelet filopodia formation. These in vivo and in vitro results clearly show that CIB1 is a key regulator of thrombosis.

Biochemical maturation of Spam1 (PH-20) during epididymal transit of mouse sperm involves modifications of N-linked oligosaccharides.

Indirect immunofluorescence of mouse caput and caudal sperm shows distinctly different distributions of Spaml protein, which is associated with structural and functional differences of the molecule. Spam1 is uniformly distributed over the surface of the head of caput sperm while in caudal sperm, light and confocal microscopy demonstrate that it is localized to the anterior and posterior regions. The hyaluronidase activity of Spaml in acrosome-intact caput sperm was significantly lower (4.3-fold; P < 0.0001) than that of caudal sperm. The increase in enzymatic activity in caudal sperm is accompanied by a reduction in the molecular weight (MW): in extracts from caput sperm there was a major band at approximately 74 kDa and a minor band at approximately 67 kDa; while for the cauda there was a major band at approximately 67 kDa and minor bands at approximately 70 and -56 kDa. Additionally, the bands from caput sperm were 4.9 to 7.7-fold less intense than those from caudal sperm. This decreased affinity for the polyclonal anti-Spaml suggests the presence of different surface characteristics of the molecule from the two epididymal regions. Computer analysis of the protein structure from Spam1 cDNA sequence reveals four putative N-linked glycosylation sites, and enzymatic deglycosylation suggests that all sites are functional. After endoglycosidase activity of extracts from caput and caudal sperm, both show a major band with a MW of approximately 56 kDa, the size of the membrane-anchored polypeptide backbone. Based on the difference in size and intensity of the Spaml bands and hyaluronidase activities from caput and caudal sperm, the data suggest that the activation of Spaml during epididymal maturation is regulated by deglycosylation.

An improved method for affinity probe localization in whole cells of filamentous fungi.

The fungal cell wall, though phylogenetically variable, acts universally as a potent barrier to probing intracellular structures. Thus, the use of high-molecular-weight probes such as antibodies and lectins has proven a formidable challenge. We have devised a preparative method for use with various affinity probes that can be applied to a broad spectrum of filamentous fungal species and used for imaging whole cells. In this study, confocal imaging of whole-mount fungal hyphae after freeze substitution, methacrylate embedment/de-embedment, and infiltration with affinity probes has yielded remarkably improved renderings of the three-dimensional distribution of both microtubules (using antibodies against both alpha- and beta-tubulin) and concanavalin A binding sites. Using this protocol we have been able to document: (1) the three-dimensional distribution of microtubules in all regions of hyphae, (2) the presence of apparent foci for cytoplasmic microtubules, (3) persistent cytoplasmic microtubules during mitosis, and (4) a three-dimensional view of many compartments of the endomembrane system including Golgi-equivalent organelles and apical vesicles. The last result represents the first direct confirmation of apical vesicles comprising the Spitzenkörper.

Characterization of MGC2, a Mycoplasma gallisepticum cytadhesin with homology to the Mycoplasma pneumoniae 30-kilodalton protein P30 and Mycoplasma genitalium P32.

A second cytadhesin-like protein, MGC2, was identified in the avian respiratory pathogen Mycoplasma gallisepticum. The 912-nucleotide mgc2 gene encodes a 32.6-kDa protein with 40.9 and 31.4% identity with the M. pneumoniae P30 and M. genitalium P32 cytadhesins, respectively. Functional studies with reverse transcription-PCR, immunoblotting, double-sided immunogold labeling, and attachment inhibition assays demonstrated homology to the human mycoplasmal P30 and P32 cytadhesins. These findings suggest that there is a family of cytadhesin genes conserved among pathogenic mycoplasmas infecting widely divergent hosts.

In vitro and in vivo nucleotide exchange directed by chimeric RNA/DNA oligonucleotides in Saccharomyces cerevisae.

Targeted gene repair directed by chimeric RNA/DNA oligonucleotides has proven successful in eukaryotic cells including animal and plant models. In many cases, however, there has been a disparity in the levels of gene correction or frequency. While the delivery of these chimera into the nucleus and the long-term stability or purity of these molecules may contribute to this variability, understanding the molecular regulation of conversion is the key to improving or stabilizing frequency. To this end, we have identified genes that control targeted repair, using the genetically tractable organism, Saccharomyces cerevisae and a bank of yeast mutants. Results from experiments in cell-free extracts focused our attention on RAD52, RAD1 and RAD59 as central regulatory factors. RAD1 and RAD59 appear to be required for high levels of conversion whereas RAD52 appears to act, surprisingly, in a suppressive fashion. Results from the in vitro experiments were translated into targeting experiments in vivo. Here, mutations in a fusion construct, containing a marker gene, were converted to wild type, evidenced by the expression of green fluorescence in converted cells. Because the repaired fusion gene contains a corrected neomycin sequence, cells were subsequently placed under G418 selection and conversion confirmed at the genetic level. Taken together, these results establish, for the first time, genes that participate in the regulation of targeted gene repair and provide a novel system for evaluating true frequencies of correction. Importantly, this system enables visualization of corrected (green) and uncorrected (clear) cells enabling measurements of conversion in real time.