Detection of antisense and ribozyme accessible sites on native mRNAs: application to NCOA3 mRNA.

The efficacies of antisense oligonucleotides and ribozymes are greatly dependent on the accessibility of their mRNA targets. Target site accessibility is affected by both RNA structure and the proteins associated along the length of the RNA. To mimic the native state of mRNA for site identification, we have previously used endogenous mRNAs in cellular extracts as targets for defined sequence oligodeoxynucleotides (ODNs) designed to identify both antisense pairing and potential ribozyme cleavage sites. The rationale for this approach is that the specific pairing of an ODN with a mRNA forms a DNA:RNA hybrid that is cleaved by the endogenous RNaseH in the cell extract. To extend the usefulness of this basic approach, we report here the use of semi-random ODN libraries to identify hammerhead ribozyme cleavage sites. Thus, the most accessible sites for antisense and ribozyme base pairing are selected by this approach. A novel feature of the approach described here is the use of terminal transferase-dependent PCR (TDPCR) after reverse transcription to estimate the cleavage efficiency and to precisely determine the RNaseH and ribozyme cleavage sites on mRNAs in cell extracts following treatment with ODN or ribozyme libraries. As a model system, we have targeted the NCOA3 (also known as AIB-1) mRNA in cell extracts. The NCOA3 mRNA encodes a nuclear receptor co-activator that is amplified and over-expressed in a high proportion of breast and ovarian cancers. A highly accessible site on this mRNA was identified, and a ribozyme targeted to this site was demonstrated to effectively downregulate NCOA3 function in cells.

Characterization of an endoprotease (PrpL) encoded by a PvdS-regulated gene in Pseudomonas aeruginosa.

The expression of many virulence factors in Pseudomonas aeruginosa is dependent upon environmental conditions, including iron levels, oxygen, temperature, and osmolarity. The virulence of P. aeruginosa PAO1 is influenced by the iron- and oxygen-regulated gene encoding the alternative sigma factor PvdS, which is regulated through the ferric uptake regulator (Fur). We observed that overexpression of PvdS in strain PAO1 and a DeltapvdS::Gm mutant resulted in increased pyoverdine production and proteolytic activity compared to when PvdS was not overexpressed. To identify additional PvdS-regulated genes, we compared extracellular protein profiles from PAO1 and the DeltapvdS::Gm mutant grown under iron-deficient conditions. A protein present in culture supernatants from PAO1 but not in supernatants from DeltapvdS::Gm was investigated. Amino acid sequence analysis and examination of the genomic database of PAO1 revealed that the N terminus of this 27-kDa protein is identical to that of protease IV of P. aeruginosa strain PA103-29 and is homologous to an endoprotease produced by Lysobacter enzymogenes. In this study, the gene encoding an endoprotease was cloned from PAO1 and designated prpL (PvdS-regulated endoprotease, lysyl class). All (n = 41) but one of the strains of P. aeruginosa, including clinical and environmental isolates, examined carry prpL. Moreover, PrpL production among these strains was highly variable. Analysis of RNase protection assays identified the transcription initiation site of prpL and confirmed that its transcription is iron dependent. In the DeltapvdS::Gm mutant, the level of prpL transcription was iron independent and decreased relative to the level in PAO1. Furthermore, transcription of prpL was independent of PtxR, a PvdS-regulated protein. Finally, PrpL cleaves casein, lactoferrin, transferrin, elastin, and decorin and contributes to PAO1's ability to persist in a rat chronic pulmonary infection model .

Association of steroid receptor coactivator AIB1 with estrogen receptor-alpha in breast cancer cells.

The steroid receptor coactivator AIB1 (amplified in breast cancer-1) is a transcriptional coactivator which has been found to be amplified in breast cancer. We have now investigated the role of the AIB1 protein in breast cancer cell lines. Although detectable levels of AIB1 were present in most cell lines, high levels of AIB1 expression were observed only in the ER-positive cell lines MCF-7 and BT-474 by western blot analysis. Newly developed monoclonal antibodies (mAbs) were used in several assays to show an association between AIBI and estrogen receptor-alpha (ER). AIB1 and ER co-localized to the nucleus of ER positive cell lines as shown by immunofluorescence microscopy, and a functional association of native AIB1 and ER in MCF-7 nuclear extracts was shown by EMSA. Recombinant ER also recruited AIB1 protein from nuclear extracts, shown by EMSA and by precipitation of ER-complex proteins bound to a biotinylated-ERE DNA target. Additionally, anti-AIB1 mAbs were able to immunoprecipitate ER from nuclear extracts of chemically cross-linked cells but not from uncross-linked cells. Both immunoprecipitation and oligonucleotide precipitation studies demonstrated the presence of p300 and CBP as part of the ER transcriptional complex. These results suggest that AIB1 and ER do associate physically in ER-positive breast cancer cell lines. We propose that in AIB1 amplified breast cancers, a heightened AIB1/ER association may play a crucial role in the progression of these tumors.

Primary renal hypoplasia in humans and mice with PAX2 mutations: evidence of increased apoptosis in fetal kidneys of Pax2(1Neu) +/- mutant mice.

PAX2 mutations cause renal-coloboma syndrome (RCS), a rare multi-system developmental abnormality involving optic nerve colobomas and renal abnormalities. End-stage renal failure is common in RCS, but the mechanism by which PAX2 mutations lead to renal failure is unknown. PAX2 is a member of a family of developmental genes containing a highly conserved 'paired box' DNA-binding domain, and encodes a transcription factor expressed primarily during fetal development in the central nervous system, eye, ear and urogenital tract. Presently, the role of PAX2 during kidney development is poorly understood. To gain insight into the cause of renal abnormalities in patients with PAX2 mutations, kidney anomalies were analyzed in patients with RCS, including a large Brazilian kindred in whom a new PAX2 mutation was identified. In a total of 29 patients, renal hypoplasia was the most common congenital renal abnormality. To determine the direct effects of PAX2 mutations on kidney development fetal kidneys of mice carrying a Pax2 (1Neu)mutation were examined. At E15, heterozygous mutant kidneys were approximately 60% of the size of wild-type littermates, and the number of nephrons was strikingly reduced. Heterozygous 1Neu mice showed increased apoptotic cell death during fetal kidney development, but the increased apoptosis was not associated with random stochastic inactivation of Pax2 expression in mutant kidneys; Pax2 was shown to be biallelically expressed during kidney development. These findings support the notion that heterozygous mutations of PAX2 are associated with increased apoptosis and reduced branching of the ureteric bud, due to reduced PAX2 dosage during a critical window in kidney development.

The prevalence of PAX2 mutations in patients with isolated colobomas or colobomas associated with urogenital anomalies.

The PAX2 gene is mutated in patients with ocular colobomas, vesicoureteral reflux (VUR), and kidney anomalies (renal-coloboma syndrome, OMIM 120330). The three abnormalities which make up this syndrome also occur in isolation, but the causal genes are not known. PAX2 encodes a transcription factor of the paired box class of DNA binding proteins, important for the development of the urogenital tract, optic nerve and adjacent retina, inner ear, and CNS. In this paper we have investigated the prevalence of PAX2 mutations in patients with ocular colobomas, microphthalmos, or retinal anomalies, either in isolation or with associated urogenital anomalies. Using PCR-SSCP, most or all exons of PAX2 were examined in blood DNA from 99 patients who have either ocular anomalies alone or a combination of ocular and urogenital conditions. PAX2 mutations were not detected in patients with ocular colobomas, either in isolation or with associated abnormalities, except in one patient with typical renal-coloboma syndrome. We conclude that PAX2 mutations are unlikely to be common in patients with ocular colobomas in isolation or in patients with ocular colobomas and associated anomalies, except for patients with typical renal-coloboma syndrome where PAX2 is known to be the aetiological cause.

Cloning and characterization of the human PAX2 promoter.

PAX2, a member of the PAX gene family of developmental transcription factors, is expressed at high levels in the developing eyes, ears, central nervous and urogenital systems, as well as in Wilms' tumor and renal cell carcinoma. Expression of PAX2 in the urogenital system is associated with proliferating cells of the ureteric bud and the differentiating nephrogenic mesenchyme. To date, little is known about the molecular mechanisms controlling the regulation of PAX2 expression. This report describes the cloning and characterization of the human PAX2 gene promoter and localization of the transcription start sites in fetal kidney and Wilms' tumor. We identified two transcription start sites in a Wilms' tumor sample, which were found to be different from that in fetal kidney. The activity of a deletion series of the PAX2 promoter was assessed in NIH-3T3, COS-7, 293, and Madin-Darby canine kidney cells. Although some differences were observed in the activity of each promoter construct, the profile of activity for the promoter fragment series was similar in each experiment, regardless of cell type. The WT1 tumor suppressor protein, which has previously been shown to repress murine Pax2 expression in vitro, was shown to also repress expression from the human PAX2 promoter.

Differential regulation of the human Wilms tumour suppressor gene (WT1) promoter by two isoforms of PAX2.

PAX2 is a member of the paired box family of genes with an important role in kidney, genital tract and eye development. Another gene essential for kidney and genital tract development is the Wilms tumour gene, WT1. PAX2 and WT1 encode transcription factors expressed during fetal kidney development in patterns that overlap both spatially and temporally. The overlap of PAX2 and WT1 expression in fetal kidney prompted us to determine whether PAX2 regulates the WT1 gene. To investigate this possibility, the WT1 promoter and a series of WT1 promoter deletion fragments were cloned into a luciferase reporter vector, and used in co-transfection experiments with PAX2 expression constructs. PAX2 transactivated the WT1 promoter up to 35-fold in CHO-K1 cells, and from four- to sevenfold in 293 cells. Two regions of the WT1 promoter were required in the same promoter construct for efficient transactivation by PAX2 in CHO-K1 cells, and purified recombinant PAX2 protein was found to bind to two sites in the WT1 promoter, at -205/-230 and +377/+402. Removal of WT1 promoter sequences containing the -205/-230, or +377/+402 binding sites abolished transactivation of the WT1 promoter by PAX2 in CHO-K1 cells, and had a differential effect on transactivation of the WT1 promoter in 293 cells, depending on the PAX2 isoform used. A fragment containing the -205/-230 site alone could be transactivated by PAX2. These findings suggest that PAX2 is a tissue-specific modulator of WT1 expression, and is involved in cell growth control via WT1.

Further delineation of renal-coloboma syndrome in patients with extreme variability of phenotype and identical PAX2 mutations.

Renal-coloboma syndrome is a recently described autosomal dominant syndrome of abnormal optic nerve and renal development. Two families have been reported with renal-coloboma syndrome and mutations of the PAX2 gene. The PAX2 gene, which encodes a DNA-binding protein, is expressed in the developing ear, CNS, eye, and urogenital tract. Ocular and/or renal abnormalities have been consistently noted in the five reports of patients with renal-coloboma syndrome, to date, but PAX2 expression patterns suggest that auditory and CNS abnormalities may be additional features of renal-coloboma syndrome. To determine whether additional clinical features are associated with PAX2 mutations, we have used PCR-SSCP to identify PAX2 gene mutations in patients. We report here four patients with mutations in exon 2, one of whom has severe ocular and renal disease, microcephaly, and retardation, and another who has ocular and renal disease with high-frequency hearing loss. Unexpectedly, extreme variability in clinical presentation was observed between a mother, her son, and an unrelated patient, all of whom had the same PAX2 mutation as previously described in two siblings with renal-coloboma syndrome. These results suggest that a sequence of seven Gs in PAX2 exon 2 may be particularly prone to mutation.

Exotoxin A production in Pseudomonas aeruginosa requires the iron-regulated pvdS gene encoding an alternative sigma factor.

Exotoxin A (ETA) is secreted by Pseudomonas aeruginosa under iron-limiting growth conditions. The ETA structural gene, toxA, is regulated at the transcriptional level by the gene products of the regAB operon. The expression of both toxA and regAB is repressed under iron-replete conditions, suggesting a role for the ferric uptake regulator (Fur) in regulation of ETA synthesis; however, the Fur protein does not interact directly with the toxA or the regAB promoters. Evidence is presented that the iron control of ETA synthesis is mediated by a Fur-regulated alternative sigma factor, PvdS, which had initially been identified as a positive activator for the production of the siderophore pyoverdin. In a delta pvdS deletion mutant, ETA was produced at low levels of less than 5% compared to wild type, but still in response to iron starvation, and introduction of a functional pvdS gene on a plasmid fully restored wild-type levels and normal iron regulation of ETA synthesis. Therefore, a functional pvdS locus is essential for ETA production. Neither toxA nor regAB mRNA was detectable in a delta pvdS mutant. Overexpression of pvdS from the tac promoter on a plasmid resulted in a high-level and iron-independent production of ETA in wild-type PAO1, in the delta pvdS strain, but not in a delta regA strain as a host. These findings suggest that PvdS is required for the activation of the regAB promoters. The transcription of regAB and toxA after induction of the P tac-pvdS gene was monitored in cells grown in high-iron medium. While both regAB and toxA were highly expressed during all growth phases under microaerobic conditions, toxA transcripts were detected only during the exponential but not the early stationary phase of growth under aerobic conditions. These results suggest that a second regulatory mechanism besides the Fur-PvdS system is involved in iron regulation of ETA production.

Cloning and characterization of pvdS, a gene required for pyoverdine synthesis in Pseudomonas aeruginosa: PvdS is probably an alternative sigma factor.

Cells of Pseudomonas aeruginosa secrete a fluorescent yellow-green siderophore, pyoverdine, when grown under iron-deficient conditions. We describe here the cloning and characterization of a gene, pvdS, which is required for this process. The pvdS gene is required for expression from promoters of at least two pyoverdine synthesis genes and can cause expression from these promoters in Escherichia coli, where they are otherwise inactive. Sequencing of pvdS revealed that it is a member of a subfamily of RNA polymerase sigma factors which direct the synthesis of extracellular products by bacteria. The pvdS gene is expressed only in iron-starved bacteria, and in E. coli cells at least, expression is regulated by the Fur repressor protein. We propose that in iron-rich cells of P. aeruginosa, Fur binds to the pvdS promoter and prevents expression of the gene; under conditions of iron starvation, repression is relieved and PvdS is made, reprogramming the cells for pyoverdine synthesis.

Assessment of antibiotic aerosol generation using commercial jet nebulizers.

The performance of 14 commercial jet nebulisers has been assessed; Unineb, Suremist (Unimed (UK) Ltd), Micro-Cirrus (Intersurgical Ltd), Pulmo-Neb (DeVilbiss Health Care UK Ltd), Side-Stream (Medic-Aid Ltd), Micro-Neb III (Lifecare Ltd), RespirGard (Marquest Medical Products Inc), Aeromist, Venticaire (S and W Vickers Ltd), Up-Draft II, Ava-Neb, Up-Draft (Hudson Respiratory Care Inc), Bennett/Twin, Raindrop (Puritan-Bennett Corporation). The units were operated with a high flow compressor (Maxi III, Medix Ltd) at 101/min. Performance was assessed by measuring the fraction of the initial mass of drug released as an aerosol and nebulisation time for initial drug volume of 2-6mls, and the mass median diameter and mass fraction of the aerosol in particles < 5.17 microns diameter. The Side-Stream nebuliser gave the best performance, although incorporation of a filter to trap exhaled antibiotic may prove difficult. The Micro-Cirrus generated a particularly fine aerosol. The Raindrop nebuliser performed well, while the Up-Draft II nebulised efficiently but was associated with extended nebulisation times which may limit its utility.

Measurement and prediction of drug solvent losses by evaporation from a jet nebuliser.

The evaporative losses of solvent (water) from a commercial jet nebuliser (Unineb, Unimed Ltd) were estimated and found to be approximately 14% of total nebuliser output. A simple analysis of the nebulisation process then enabled the amount of the drug colomycin released as potentially respirable aerosol to be predicted from measurements of the total nebulisation time. Good agreement was found between the predicted (P) and measured (M) values such that P = 1.07 M (r2 = 0.98). The analysis also indicates that the proportion of the drug released as aerosol will increase as nebulisation proceeds provided nebuliser output is continuous and that for a given initial mass of drug a larger amount of drug is released as an aerosol if the volume of administration used in the nebuliser is as large as possible.

Glutaraldehyde inactivation of exotic animal viruses in swine heart tissue.

Glutaraldehyde, 0.2%, in a 1:100 (wt/vol) ratio, inactivated four animal viruses (foot-and-mouth disease, swine vesicular disease, African swine fever, hog cholera) in swine heart tissues during 11-day exposures at 22 to 26 degrees C.

Inactivation of Milkborne Foot-and-Mouth Disease Virus at Ultra-High Temperatures 1.

Milk from cows with foot-and-mouth disease containing 103-7 to 106-4 plaque-forming units of virus/ml was exposed to several ultra-high temperature treatments for 2-5 sec. Results indicated that the virus in such milk could be reliably inactivated when held at 148 C for 3 sec or longer.

Persistence of Foot-and-Mouth Disease Virus in Dried Casein 1.

Dried casein produced from pasteurized milk of dairy cows infected with foot-and-mouth disease (FMD) virus retained infectivity for cattle in one of seven tests for 42 days of storage at 25 C. Thus, infections FMD virus can persist after pasteurization of the milk at 72 C for 15 sec., acid precipitation and washing of casein, followed by drying of the casein in a hot air flow and conversion to sodium caseinate.

Interferon inducers and foot-and-mouth disease vaccines: influence of two synthetic polynucleotides on antibody response and immunity in guinea pigs and swine.

Polyriboadenylic-polybouridylic acid enhanced the immunological response of guinea pigs to aqueous foot-and-mouth disease virus vaccine. Polyriboninosinic-polyribocytidylic acid enhanced the early antibody production of swine to oil emulsified foot-and-mouth disease virus vaccine. Polyriboninosinic-polyribocytidylic acid alone did not stimulate resistance to foot-and-mouth disease in swine.

Survival of Foot-and-Mouth Disease Virus in Casein and Sodium Caseinate Produced from the Milk of Infected Cows 1.

Milk-borne transmission of foot-and-mouth disease virus (FMDV) was implied during the 1967-1968 epizootic in England. Consequently, experiments were designed to study survival of FMDV in milk and dairy products. As part of these studies, eight batches of casein were prepared from milk collected at various times after infection of cows with FMDV. Raw skimmilk was used in two batches and pasteurized (72 C, 15 sec), skimmilk was used in six. Casein was obtained by acidulation of skimmilk to pH 4.6 with HCI. Each batch was tested for FMDV infectivity either as casein or sodium caseinate in cell cultures and by inoculation of cattle. Samples assayed in cell cultures did not show evidence of infectious FMDV. However, cattle inoculated with these samples became infected with FMDV in one of two trials in which the casein was prepared from raw skimmilk and in three of six trials with skimmilk which was pasteurized. Samples from one of two dried casein batches infected test cattle. Samples from four of six batches of casein prepared from uninfected cows milk to which FMDV was added before pasteurization also infected cattle.