Molecular features of new Peach Latent Mosaic Viroid variants suggest that recombination may have contributed to the evolution of this infectious RNA

Nucleotide sequences of a broad range of Peach Latent Mosaic Viroid (PLMVd) variants were determined. The variants were isolated from peach, pear, and almond tree samples collected in Tunisia. Sequence analysis confirmed the high variability of PLMVd, as no less than 119 new variants were identified. Variations included new polymorphic positions, insertions of 11 to 14 nucleotides, and new mutations within the hammerhead self-cleavage motifs. We provide the first covariation-based evidence for certain stems within the proposed secondary structure. Our covariation analysis also strengthens the view that a pseudoknot closes the replication domain. On the basis of phylogenetic tree studies and informative positions, PLMVd variants are proposed to cluster into groups and subgroups likely to have resulted from recombination events. PLMVd thus emerges as a suitable viroid for retracing the evolution of an RNA genome.

Study of the polymerization step of the rolling circle replication of peach latent mosaic viroid

We have developed an in vitro transcriptional assay using Escherichia coli RNA polymerase to initiate the replication of peach latent mosaic viroid (PLMVd). Regardless of the polarity of the PLMVd strand used as template, initiation in vitro occurred at the same hairpin structure. These initiation sites correspond to the 5'-ends of two small (280 nt) PLMVd-related RNAs found in infected peach leaves. Using a series of truncated PLMVd-derived transcripts, we have demonstrated that the viroid domain composed solely of the self-complementary hammerhead sequences is sufficient to trigger polymerase-driven replication in vitro. These data suggest that the bacterial-like RNA polymerase from peach chloroplasts catalyzes PLMVd replication.

Natural 2',5'-phosphodiester bonds found at the ligation sites of peach latent mosaic viroid

Peach latent mosaic viroid (PLMVd) is a circular RNA pathogen that replicates in a DNA-independent fashion via a rolling circle mechanism. PLMVd has been shown to self-ligate in vitro primarily via the formation of 2',5'-phosphodiester bonds; however, in vivo the occurrence and necessity of this nonenzymatic mechanism are not evident. Here, we unequivocally report the presence of 2', 5'-phosphodiester bonds at the ligation site of circular PLMVd strands isolated from infected peach leaves. These bonds serve to close the linear conformers (i.e., intermediates), yielding circular ones. Furthermore, these bonds are shown to stabilize the replicational circular templates, resulting in a significant advantage in terms of viroid viability. Although the mechanism responsible for the formation of these 2',5'-phosphodiester bonds remains to be elucidated, a hypothesis describing in vivo nonenzymatic self-ligation is proposed. Most significantly, our results clearly show that 2',5'-phosphodiester bonds are still present in nature and that they are of biological importance.

A Canadian isolate of hepatitis D (delta) virus

Hepatitis D (delta) virus (HDV) is an infectious agent that propagates in hepatocytes only in the presence of hepatitis B virus, causing fulminant or chronic hepatitis with liver cirrhosis. HDV is a 36 nm particle that includes a circular RNA genome of 1.7 kilobases with an extensive internal complementary that allows it to fold into a rod-like structure. The relationships among genotypes, sequence variability, geographical distribution and disease severity of HDV remain unknown. Consequently, in the present study, the complete nucleotide sequence of an HDV isolated from a Canadian patient was determined. The viral RNA from serum was amplified using reverse transcription coupled to polymerase chain reaction amplification. The resulting complementary DNA was cloned and sequenced. Sequence analysis revealed that this new isolate contained 1672 nucleotides corresponding to genotype 1, which has a worldwide distribution. Sequencing of four independent clones revealed 17 substitutions, corresponding to an overall sequence variability of 1%. Surprisingly, seven mutations were found in the 48-nucleotide region located between the two highly conserved self-catalytic motifs. This is the first demonstration that many substitutions are identified in this region of HDV, and prompts the present authors to define it as a hypervariable region.

Sequencing of peach latent mosaic viroid variants from nine North American peach cultivars shows that this RNA folds into a complex secondary structure

We sequenced 34 new peach latent mosaic viroid (PLMVd) variants isolated from nine different peach cultivars. This study provides the widest view of PLMVd diversity reported to date and includes the original characterization of North American variants, which cannot be differentiated from European sequences. PLMVd appears as a species in which each isolate is a complex mixture of RNAs. Analysis of base-pair covariations supports the hypothesis that PLMVd folds into a complex branched structure with the potential of including three new pseudoknots. The resulting "globular-like" structure is in contrast to the rod-like one adopted by most other viroids.

The kinetics and magnesium requirements for the folding of antigenomic delta ribozymes

Using an oligonucleotide hybridization assay to gain insight into the folding of delta ribozymes, we demonstrate a correlation between their folding and catalytic behavior. Together with recent structural information on the crystal structure of self-cleaved genomic delta ribozyme, in which the L3 loop interacts with J1/4 to form the newly proposed stem P1.1, we conclude that it is likely that the P1.1 stem forms only in the presence of Mg(2+). This stem can be detected in both the self-cleaved and trans-acting delta ribozymes. When the trans-acting version of antigenomic delta ribozyme was studied, it is demonstrated that its L3 loop requires magnesium and, apparently, formation of the P1 stem for the subsequently formation of the P1.1 stem. Most importantly, the kinetics were monitored, and provide a significant addition to our understanding of ribozyme tertiary structure formation prior to the chemical cleavage step. Using previous kinetic data and our new findings, we discuss the rate-limiting characteristics of delta ribozyme folding.

Mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex, branched secondary structure

We have investigated the secondary structure of peach latent mosaic viroid (PLMVd) in solution, and we present here the first description of the structure of a branched viroid in solution. Different PLMVd transcripts of plus polarity were produced by using the circularly permuted RNA method and the exploitation of RNA internal secondary structure to position the 5' and 3' termini and studied by nuclease mapping and binding shift assays using DNA and RNA oligonucleotides. We show that PLMVd folds into a complex, branched secondary structure. In general, this structure is similar to that reported previously, which was based on sequence comparison and computer modelling. The structural microheterogeneity is apparently limited to only some small domains. More importantly, this structure includes a novel pseudoknot that is conserved in all PLMVd isolates and seems to allow folding into a very compact form. This pseudoknot is also found in chrysanthemum chlorotic mottle viroid, suggesting that it is a unique feature of the viroid members of the PLMVd subgroup.

Long term follow-up of intravesical Bacillus Calmette-Guerin for the treatment of bladder transitional cell carcinoma

OBJECTIVE

To review the long-term follow-up, in terms of recurrence and progression, of transitional cell carcinoma of the bladder treated with intravesical BCG with the following indications: CIS, Ta and T1.

MATERIALS AND METHODS

Ninety-two patients who had received complete course of BCG between 1987 and 1993 were included in the study and followed for an average of 59 months (range 12 to 102).

RESULTS

The recurrence and progression were looked at. Patients treated with BCG for Carcinoma in situ, 11 of 19 (53%) remained tumor-free after 1 or 2 courses of BCG for the duration of the follow-up (mean 4.9 years, range 1.5 to 8.5 years). For patients treated for recurring tumors, 17 of 50 (34%) had no recurrences after 1 or 2 courses of BCG with the same follow-up. When facing multiple tumors, 10 of 23 (43%) patients did not experience recurrences. Therefore, in the 92 patients treated, 38 presented no recurrences after 1 or 2 courses of BCG, for a success rate of 41%. In terms of progression, of the 19 patients treated with BCG for CIS, 4 (21%) went on to develop muscle invasive disease. Of the 50 patients treated for recurrent tumors, 2 (4%) eventually developed lamina propria invasion (initial lesion was a Ta tumor), 4 (8%) carcinoma in situ and 7 (14%) muscle invasive disease, for an overall progression rate of 26% in this group. Of the 25 patients treated for multiple tumors, 1 (4%) developed CIS and 3 (12%) presented with muscle invasive disease, for an overall progression rate of 16% for the duration of the follow-up. Therefore, 21 of 92 (23%) patients had progression of their disease following BCG therapy. No prognostic factors for recurrence or progression could be identified in these tumors.

CONCLUSION

When indications warrant its use, BCG is effective in reducing recurrences and limiting progression in TCC of the bladder. Recurrence within 2 years of treatment is, however, a sign of poor prognosis and other therapeutic options should be sought.

Practice patterns of Canadian urologists in benign prostatic hyperplasia and prostate cancer. Canadian Prostate Health Council

PURPOSE

We reviewed the practice patterns of Canadian urologists in benign prostatic hyperplasia (BPH) and prostate cancer, and assessed the changes that occurred between 1995 and 1998.

MATERIALS AND METHODS

In 1995 and 1998 questionnaires were mailed to all active members of the Canadian Urological Association who practiced adult urology in Canada. Many questions were similar, allowing for the assessment of changes in practice patterns.

RESULTS

A number of changes were observed between 1995 and 1998. Cystoscopy and imaging of the upper urinary tract were used less often to evaluate uncomplicated cases of BPH. However, 39% of respondents continued to perform cystoscopy routinely. Finasteride was no longer administered in men with a smaller prostate. In 1998 before radical prostatectomy 28% of respondents routinely performed a bone scan, 29% cystoscopy and 57% chest x-ray. The number believing that maximal androgen blockade is the most effective hormonal therapy decreased from 90% to 62%, while 24% reported in the 1998 survey that they frequently administered intermittent hormonal therapy. Comparison with an American study from 1995 indicated that American urologists used the American Urological Association symptom score and performed a prostate specific antigen test more frequently than Canadian urologists. However, Canadian urologists performed cystoscopy more frequently.

CONCLUSIONS

These surveys provide a useful insight into the variations in clinical practice of Canadian urologists and help to determine whether changes are occurring in regard to the development of practice guidelines. They also indicate the need to develop further guidelines, and ensure that these guidelines are widely promoted and accepted by the urological community.

Nucleotides -1 to -4 of hepatitis delta ribozyme substrate increase the specificity of ribozyme cleavage

In the past, the use of delta ribozyme as a therapeutic tool was limited because substrate specificity was thought to be determined by only 8 nucleotides. Recently, we have accumulated evidence suggesting that the substrate sequence upstream of the cleavage site, which is not involved in the binding with the delta ribozyme, appears to be essential in the selection of an appropriate cleavage site. To understand the role of this region in efficient cleavage, we synthesized a collection of small substrates that possessed single and multiple mutations in positions -1 to -4 and determined the kinetic parameters of their cleavage using a model antigenomic delta ribozyme. Some substrates were found to be uncleavage, whereas others showed >60-fold difference in relative specificity between the least and most efficiently cleaved substrates. The base at each position from -1 to -4 contributes differently to the ability of a substrate to be cleaved. An optimal sequence for positions -1 to -4 was determined to be -1HRHY(-4) (H = U, C, or A). These results shed light on new features that contribute to the substrate requirement of delta ribozyme cleavage and should increase interest in the use of this unique ribozyme.

The database of the smallest known auto-replicable RNA species: viroids and viroid-like RNAs

This is an online database in order to facilitate research on viroid, viroid-like RNAs and human hepatitis delta virus by presenting a large number of sequences and related data in a comprehensive and user-friendly format (e.g., position of their self-catalytic domains, open reading frame, prediction of the most stable secondary structures, etc.). This online database is available on the WWW at http://www.callisto.si. usherb.ca/jpperra

Long-term followup of initial Ta grade 1 transitional cell carcinoma of the bladder

PURPOSE

We evaluate the long-term outcome of initial Ta grade 1 transitional cell carcinoma.

MATERIALS AND METHODS

A total of 152 patients with initial Ta grade 1 bladder tumor were followed for a mean of 76 months (range 6 to 241). Recurrence was defined as positive findings on cystoscopy or biopsy. Progression was defined as an increase in tumor grade or stage.

RESULTS

Tumor recurrence in 83 of 152 patients (55%) was noted within 12 months of followup in 38 patients (46%), between 12 and 24 in 11 (13%), and between 24 and 60 in 22 (27%). A significant number of recurrences (12, 14%) were diagnosed more than 60 months after the first tumor. Of 83 patients with recurrence 31 (37%) had progression, including 21 to grade 2 and 2 to grade 3 disease. Carcinoma in situ was diagnosed in 3 patients and 5 had muscle invasive disease. Progression occurred more than 24 months after initial diagnosis in 20 patients and more than 60 months after first tumor event (2 had carcinoma in situ and 2 had muscle invasive disease) in 12.

CONCLUSIONS

Ta grade 1 bladder transitional cell carcinomas have a high recurrence rate and progression is not uncommon. These findings warrant close long-term followup, even when in some settings the trend is to discontinue followup after 5 years without any abnormal findings.

Presence of a coordinated metal ion in a trans-acting antigenomic delta ribozyme

We have investigated the cleavage induced by metal ions in an antigenomic form of a trans-acting delta ribozyme. A specific Mg(2+)-induced cleavage at position G(52)at the bottom of the P2 stem was observed to occur solely within catalytically active ribozyme-substrate complexes (i.e. those that performed the essential conformational transition step). Only the divalent cations which support catalytic activity permitted the detection of specific induced cleavages in this region. Using various mutant ribozymes and substrates, we demonstrated a correlation between enzymatic activity and the Mg(2+)-induced cleavage pattern. We show that the efficiency of the coordination of the magnesium to its binding site is related to the nature of the base pair in the middle of the P1 stem (i.e. Rz(23)-S(8)). Together with additional evidence from nuclease probing experiments that indicates the occurrence of a structural rearrangement involving the bottom of the P2 stem upon formation of the P1 helix, these results show that an intimate relationship exists between the folding and the catalytic activity of the delta ribozyme.

Efficacy of finasteride is maintained in patients with benign prostatic hyperplasia treated for 5 years. The North American Finasteride Study Group

OBJECTIVES

The purpose of this open-label study extension was to assess the long-term safety and efficacy of finasteride in the treatment of men with benign prostatic hyperplasia (BPH).

METHODS

A Phase III North American BPH trial originally enrolled 895 men, 297 of whom were randomized to receive finasteride 5 mg. An enlarged prostate gland by digital rectal examination, symptoms of urinary obstruction, and a maximal urinary flow rate of less than 15 mL/s were required for entry. Patients who completed the initial 12-month, double-blind, placebo-controlled study were invited to participate in an open-label extension for 4 additional years.

RESULTS

Of the 297 patients initially randomized to receive finasteride 5 mg, 259 completed 12 months in the double-blind period and 186 completed 48 months of open-label therapy. Prostate volume reached a nadir of -24.6% at month 24, and the effect was maintained through month 60. Compared with baseline values, month 60 prostate volume was decreased by 22.7% (P<0.001), the quasi-American Urological Association symptom score was decreased by 4.3 points, and maximal urinary flow was increased by 2.3 mL/s (P<0.001) on average. Finasteride was well tolerated, with no significant increase in the prevalence of sexual adverse events over time.

CONCLUSIONS

Patients treated with finasteride 5 mg maintained an initial decrease in prostate volume and improvement in symptom score and maximal urinary flow rate over 5 years.

Mutational analysis of the antigenomic trans-acting delta ribozyme: the alterations of the middle nucleotides located on the P1 stem

Our previous report on delta ribozyme cleavage using a trans -acting antigenomic delta ribozyme and a collection of short substrates showed that the middle nucleotides of the P1 stem, the substrate binding site, are essential for the cleavage activity. Here we have further investigated the effect of alterations in the P1 stem on the kinetic and thermodynamic parameters of delta ribozyme cleavage using various ribozyme variants carrying single base mutations at putative positions reported. The kinetic and thermodynamic values obtained in mutational studies of the two middle nucleotides of the P1 stem suggest that the binding and active sites of the delta ribozyme are uniquely formed. Firstly, the substrate and the ribozyme are engaged in the formation of a helix, known as the P1 stem, which may contain a weak hydrogen bond(s) or a bulge. Secondly, a tertiary interaction involving the base moieties in the middle of the P1 stem likely plays a role in defining the chemical environment. As a con-sequence, the active site might form simultaneously or subsequently to the binding site during later steps of the pathway.

Delta ribozyme has the ability to cleave in transan mRNA

We report here the first demonstration of the cleavage of an mRNA in trans by delta ribozyme derived from the antigenomic version of the human hepatitis delta virus (HDV). We characterized potential delta ribozyme cleavage sites within HDV mRNA sequence (i.e. C/UGN6), using oligonucleotide binding shift assays and ribonuclease H hydrolysis. Ribozymes were synthesized based on the structural data and then tested for their ability to cleave the mRNA. Of the nine ribozymes examined, three specifically cleaved a derivative HDV mRNA. All three active ribozymes gave consistent indications that they cleaved single-stranded regions. Kinetic characterization of the ability of ribozymes to cleave both the full-length mRNA and either wild-type or mutant small model substrate suggests: (i) delta ribozyme has turnovers, that is to say, several mRNA molecules can be successively cleaved by one ribozyme molecule; and (ii) the substrate specificity of delta ribozyme cleavage is not restricted to C/UGN6. Specifically, substrates with a higher guanosine residue content upstream of the cleavage site (i.e. positions -4 to -2) were always cleaved more efficiently than wild-type substrate. This work shows that delta ribozyme constitutes a potential catalytic RNA for further gene-inactivation therapy.

The viroid and viroid-like RNA database

This is an online database to facilitate research on viroid, viroid-like RNAs and human hepatitis delta virus (vHDV) by presenting a large number of sequences and related data in a comprehensive and user-friendly format (e.g. position of their self-catalytic domains, open reading frame of the vHDV, prediction of the most stable secondary structures, etc.). Most of these RNA species share a common proposed replication pattern known as a DNA-independent rolling circle mechanism. Together, these species form the 'brotherhood' of the smallest known auto-replicable RNAs. This online database is available on the World Wide Web at http://www.callisto.si.usherb.ca/jpperra

Identification of a Crohn's disease specific transcript with potential as a diagnostic marker

BACKGROUND

A long time goal of the medical research community has been the identification of a reliable and valid marker for Crohn's disease.

AIM

To identify differences in the genetic expression patterns of healthy and diseased tissues.

METHOD

The RNA arbitrarily primed polymerase chain reaction (RAP-PCR) procedure was modified to improve its potential to identify clinical markers in heterogeneous RNA populations.

RESULTS

With this procedure, a 1065 bp PCR product associated with the inflammation that occurs in Crohn's disease was identified, cloned and sequenced. Northern blot hybridisations showed that this novel sequence originates from a unique RNA species of 3.1 kb. Dot blot hybridisations clearly showed that this RNA species was specific to Crohn's disease. Moreover, its abundance seemed to correlate with the severity of inflammation. Finally, this RNA species was also detected in macroscopically normal areas from Crohn's disease specimens, suggesting that it appears either early during the disease or at least before severe manifestations.

CONCLUSION

This finding of a 3.1 kb RNA species permits the discrimination of Crohn's disease manifestations. Although further clinical work is required, this transcript appears to have definite potential as a diagnostic marker.

The viroid and viroid-like RNA database

The viroid and viroid-like RNA database is a compilation of all natural sequences published in journals or available from the GenBank and EMBL nucleotide sequence libraries. Several information regarding these RNA species such as the position of their self-catalytic domains and the open reading frame of the human hepatitits delta virus are provided. The database also includes a determination of the likely ancestral sequence of most species and a prediction of the most stable secondary structures of these sequences. This online database is available on the World Wide Web (http://www.callisto.si.usherb.ca/[symbol: see text]jpperra ). It should provide an excellent reference point for further phylogenetic and structure-function studies of these RNA species.

Peach latent mosaic viroid is locked by a 2',5'-phosphodiester bond produced by in vitro self-ligation

Although some viroid-like satellite RNAs possess self-cleavage and self-ligation activities, we show that the peach latent mosaic viroid (PLMVd) is unique among all known viroids since it also has such activities. These catalytic activities should have important roles in the rolling circle replication of PLMVd. According to this proposed mechanism, self-cleavage of the multimeric strands occurs via hammerhead structures producing monomers possessing 2',3'-cyclic phosphate and 5'-hydroxyl termini. In the most stable predicted secondary structure for PLMVd these two extremities are juxtaposed, in order for self-ligation to occur. To establish the nature of the phosphodiester bond produced by self-ligation, we followed the classical procedure of complete enzymatic RNA hydrolysis coupled with thin layer chromatography fractionation. Using this procedure, we report that the self-ligation of PLMVd transcripts produces almost exclusively the 2',5' isomer (>96%). Primer extension assays also revealed that reverse transcriptase can read througth this 2', 5' linkage, suggesting that it does not prevent further replication of the viroid. Moreover, we have observed that this 2',5' linkage is resistant to the debranching activity contained in nuclear extracts, as well as being capable of preventing further viroid self-cleavage. Thus, if viroids do indeed self-ligate in vivo, the resulting 2', 5'-phosphodiester bond could contribute to the stability of these RNA species. Finally, an analysis of both the sequence and the structural requirements for hammerhead self-cleavage and self-ligation suggests that these two RNA processes may be interrelated. We hypothesize that the intramolecular self-ligation which produces circular conformers may contribute to the circularization step of the rolling circle replication, while the intermolecular non-enzymatic ligation is a potential mechanism for the sequence reassortment of viroids and viroid-like species.

Update of the viroid and viroid-like sequence database: addition of a hepatitis delta virus RNA section

Recently, we developed and made available an online database that includes all the reported (to our knowledge) viroid and viroid-like RNA sequences [Bussire,F., Lafontaine,D. and Perreault,J.-P. (1996)Nucleic Acids Res.24, 1793-1798]. We report here an update of this catalogue which includes the addition of a new section devoted to human hepatitis delta virus (vHDV) sequences. This new section comprises all available vHDV sequences, irrespective of their completeness, which have been either published or were available from nucleic acid libraries. Additional structural characteristics of the vHDV genome, such as the positions of the self-catalytic domains, the antigen open reading frames, etc., are also included. The catalogue is available on the World Wide Web (see text) in a user-friendly form. It should provide an excellent reference point for further molecular studies of these small circular pathogenic RNAs.

Characterization of stable RNAs from the resected intestinal tissues of individuals with either Crohn's disease or ulcerative colitis

Circular RNAs reminiscent of viroids and the human hepatitis delta virus have been proposed as possible nonconventional pathogens responsible for Crohn's disease and ulcerative colitis, two inflammatory bowel diseases. Consequently, RNA was extracted from various areas of intestinal tissues from individuals with either Crohn's disease or ulcerative colitis as well as several appropriate control diseases, and analyzed by two-dimensional gel electrophoresis. No circular viroid-like RNAs (< 1500 nucleotides) were detected, confirming a previous report that was limited to the investigation of small RNAs (< 300 nucleotides). However, three small, unusually stable, linear RNAs were shown to be associated to both Crohn's disease and ulcerative colitis tissues: a specific 28S ribosomal RNA cleavage product characterized previously; a 5.8S ribosomal RNA conformer; and a fragment homologous to transcripts from DNA CpG islands. The two last RNAs were detected prior to visible morphological tissue alterations, suggesting that they are produced early during the inflammation and that they have value as molecular diagnostic tools for the inflammatory bowel diseases. The potential cellular mechanisms producing these RNAs and their involvement in inflammatory bowel disease are discussed.

Efficacy and safety of finasteride therapy for benign prostatic hyperplasia: results of a 2-year randomized controlled trial (the PROSPECT study). PROscar Safety Plus Efficacy Canadian Two year Study

OBJECTIVE

To evaluate the efficacy and safety of 2 years' treatment of moderate benign prostatic hyperplasia (BPH) with finasteride.

DESIGN

Double-blind, parallel-group, placebo-controlled, multicentre, prospective randomized study.

SETTING

Outpatient care in 28 centres across Canada.

PARTICIPANTS

Men aged 45 to 80, in good health, with moderate BPH and no evidence of prostate cancer. A total of 613 men were entered into the study; 472 completed the 2 years of treatment.

INTERVENTION

After 1 month of receiving a placebo (run-in period), patients were given either finasteride (5 mg/d) or a placebo for 2 years.

OUTCOME MEASURES

EFFICACY

changes from baseline in BPH symptom scores, maximum urinary flow rates and prostate volume.

SAFETY

onset, course and resolution of all adverse events during the treatment period.

RESULTS

In the efficacy analyses the mean BPH symptom scores decreased 2.1 points (from 15.8 to 13.7) in the finasteride group, as compared with a decrease of 0.7 points (from 16.6 to 15.9) in the placebo group (P < or = 0.01). The maximum urinary flow rate increased by a mean of 1.4 mL/s (from 11.1 to 12.5 mL/s) in the finasteride group, as compared with an increase of 0.3 mL/s (from 10.9 to 11.2 mL/s) in the placebo group (p < or = 0.01). The mean prostate volume decreased by 21% (from a mean volume of 44.1 cm3 at baseline) in the treatment group; it increased by 8.4% (from a mean volume of 45.8 cm3 at baseline) in the placebo group (p < or = 0.01). In the safety analysis, the proportion of patients who experienced any adverse event was similar in the two groups (81.0% in the treatment group and 81.2% in the placebo group). However, the incidence of adverse events related to sexual dysfunction were significantly higher in the finasteride group than in the placebo group (ejaculation disorder 7.7% v. 1.7% and impotence 15.8% v. 6.3%; p < or = 0.01 for both parameters).

CONCLUSION

Finasteride is a well-tolerated and effective alternative to watchful waiting in the treatment of moderate BPH.

[Ureteroscopy versus in situ extracorporeal shockwave lithotripsy in the treatment of calculi of the distal ureter]

In a retrospective study from a unique center (St. Luc Hospital, Montreal) stone clearance of 88 consecutive distal ureteral calculi (below pelvic brim) treated by extracorporeal shock wave lithotripsy in situ were compared to a group of 94 distal ureteral calculi treated by ureteroscopy during the same period. Our results show 84% success rate for ureteroscopy which is clearly superior than 58% stone clearance rate at 3 month follow-up for ESWL Success rate was influenced by stone size in the ESWL group but not in the ureteroscopy group. This study reveals similar success rate for calculi smaller than 6 mm but for larger calculi, success rate of ureteroscopy is significantly superior.

Compilation and analysis of viroid and viroid-like RNA sequences

We have created a catalogue comprising all viroid and viroid-like RNA sequences which to our knowledge have been either published or were available from on-line sequence libraries as of October 1, 1995. In the development of this catalogue nomenclature ambiguities were removed, the likely ancestral sequence of most species was determined and the most stable secondary structures of these sequences were predicted using the MulFold package. Only viroids of PSTVd-type possessed a rod-like secondary structure, while most other viroids adopted branched secondary structures. Several viroids have predicted secondary structures that include either a Y or cruciform structure reminiscent of the tRNA-like end of virus genomes at an extremity. However, it remains unknown whether or not these predicted structures are adopted in solution, and if they serve a particular function in vivo. Additional information such as the position of the self-catalytic domains are included in the catalogue. An analysis of the data compilated in the catalogue is included. The catalogue will be available on the world wide web (http://www.callistro.si.usherb.ca/jpperra), on computer disk and in printed form. It should provide an excellent reference point for further studies.

Intra- and intermolecular nonenzymatic ligations occur within transcripts derived from the peach latent mosaic viroid

We report here the nonenzymatic self-ligation of transcripts corresponding to the peach latent mosaic viroid (PLMVd). This is the first description of this process with viroid sequences, although it has been reported to occur with human hepatitis delta virus RNA. Self-ligation occurs when the 5'-hydroxyl and the 2',3'-cyclic phosphate termini produced by the hammerhead self-cleavage of the viroid RNA are juxtaposed by the viroid rod-like structure, and a phosphodiester bond is formed between the two following hydrolysis of the cyclic phosphate. Unit-length transcripts undergo intramolecular folding, and their subsequent self-ligation produces circular molecules. The self-ligation observed in vitro may contribute to PLMVd circularization during rolling circle replication; however, this does not exclude the possibility that a host RNA ligase catalyzes the ligation steps in vivo. Like self-cleavage, self-ligation is probably an ancestral reaction, and the enzyme-catalyzed ligation most likely evolved from this primitive mechanism. Furthermore, the intermolecular self-ligation of annealed transcripts derived from PLMVd is demonstrated, suggesting a possible mechanism for sequence reassortment in viroids.

An efficient strategy for the synthesis of circular RNA molecules

Images

The RNA of both polarities of the peach latent mosaic viroid self-cleaves in vitro solely by single hammerhead structures

Hammerhead self-cleavage of dimeric, monomeric, truncated and mutated transcripts derived from both polarities of the peach latent mosaic viroid (PLMVd) were characterized. In contrast to some results previously published for a very close sequence variant (see ref. 1), these RNAs exhibit a virtually identical self-cleavage during transcription and after purification. By self-cleavage of dimeric transcripts with normal and mutated hammerhead domains and by complementation experiments, we show that the cleavage reactions involve only single hammerhead structures. This observation contrasts with the case of avocado sunblotch viroid (ASBVd), the other self-cleaving viroid, whose mechanism involves mostly double hammerhead structures, whereas single hammerhead cleavage is associated with viroid-like plant satellite RNAs. The difference in stability between the native secondary structures adopted by viroids and the autocatalytic structures, including the hammerhead motif, governs the efficiency of the self-cleavage reaction. The transition between these conformers is the limiting step in catalysis and is related exclusively to the left arm region of PLMVd secondary structure, which includes the hammerhead sequences. Most of the mutations between the variant we used and the sequence variant previously published are located in this left arm region, which may explain to a great extent the differences in their cleavage efficiency. No interactions with long-range sequences contributing to the autocatalytic tertiary structure were revealed in these experiments.

Pathway of activation by magnesium ions of substrates for the catalytic subunit of RNase P from Escherichia coli

The pathway is described for activation by Mg2+ of substrates for M1 RNA, the catalytic subunit of the RNase P from Escherichia coli. The dissociation constants are reported for binding of Mg2+ to the substrate and for the binding of the metal ion-substrate complex to the enzyme. The enzyme binds the substrate with the same affinity whether or not Mg2+ is already bound to the substate. However, only substrates with bound Mg2+ can make a productive ternary complex when combined with the enzyme. The presence of certain 2'-hydroxyl groups in the substrate is required to stabilize the binding of Mg2+ and, thereby, to increase the lifetime of the ternary complex. An energy profile for the reaction of M1 RNA with a small model substrate is presented and the role of Mg2+ bound to the substrate is discussed.

Staghorn calculi treated by percutaneous nephrolithotomy: risk factors for recurrence

Since 1985 our primary mode of therapy for staghorn calculi has been by percutaneous nephrolithotomy. Between January 1985 and June 1988 we have treated 57 cases using this method. We reviewed the rate of recurrence at a minimum of one-year follow-up and observed a 17 percent recurrence rate. Factors identified that were associated with an increased rate of recurrence were: positive urine cultures during follow-up (55% recurrence vs 12%); stone remnant greater than 5 mm (27.3% recurrence vs 13.8%); and stone complexity (25% recurrence for complex or complete staghorn vs 9.7% for noncomplex or partial staghorn). By identifying these risk factors we think that stone recurrence can be reduced and, with close follow-up, detected earlier to permit less invasive therapy if needed.

Important 2'-hydroxyl groups in model substrates for M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli

The role of 2'-hydroxyl groups in a model substrate for RNase P from Escherichia coli was studied using mixed DNA/RNA derivatives of such a substrate. The presence of the 2'-hydroxyl groups of nucleotides at positions -1 and -2 in the leader sequence and at position 1, as well as at the first C in the 3'-terminal CCA sequence, are important but not absolutely essential for efficient cleavage of the substrate by RNase P or its catalytic RNA subunit, M1 RNA. The 2'-hydroxyl groups in the substrate that are important for efficient cleavage also participate in the binding of Mg2+. An all-DNA external guide sequence (EGS) can efficiently render a potential substrate, derived from the model substrate, susceptible to cleavage by the enzyme or its catalytic RNA subunit. Furthermore, both DNA and RNA EGSs turn over during the reaction with RNase P in vitro. The identity of the nucleotide at position 1 in the substrate, the adjacent Mg(2+)-binding site in the leader sequence, and the junction of the single and double-stranded regions are the important elements in the recognition of model substrates, as well as in the identification of the sites of cleavage in those model substrates.

Relationship between 2'-hydroxyls and magnesium binding in the hammerhead RNA domain: a model for ribozyme catalysis

The use of deoxyribonucleotide substitution in RNA (mixed RNA/DNA polymers) permits an evaluation of the role of 2'-hydroxyl groups in ribozyme catalysis. Specific deoxyribonucleotide substitution at G9 and A13 of the ribozyme decreases the catalytic activity (kcat) of the ribozyme by factors of 14 and 20, respectively. The reduction of the reaction rate concomitant with the absence of these 2'-OHs or the 2'-OH of the substrate U7 position can be partially compensated by increasing the Mg2+ concentration above 10 mM. The KMg of the all-RNA ribozyme is 5.3 mM, and the lack of either of the three influential 2'-OHs increases this value by a factor of approximately 3. These and other reaction constants for the ribozyme and the deoxy-substituted analogues have been determined by assuming a three-step mechanism. The data presented here provide the basis for the formulation of a molecular model of ribozyme activity.

Mixed DNA/RNA polymers are cleaved by the hammerhead ribozyme

A series of chemically synthesized oligodeoxyribonucleotides containing one or two ribonucleotides (DNA/RNA mixed polymers) at and/or adjacent to the cleavage site of the substrate can be cleaved by the "hammerhead" ribozyme. In comparison with the all-RNA substrate, the predominantly deoxyribonucleotide substrates have (1) lower optimal temperatures of cleavage, (2) approximately 6-fold higher Km's and 7-fold lower kcat's at 30 degrees C, and (3) 15-fold higher Km's and 8-fold lower kcat's at 37 degrees C. The extent to which the RNA substrate cleavage is inhibited in the presence of an all-DNA (KI = 13 microM) and an RNA substrate analogue with a dC at the cleavage site (KI = 0.96 microM) supports the contention that the formation of the ribozyme-substrate complex with the predominantly deoxyribonucleotide substrates (D substrates) is impaired. The weaker binding of D substrates was confirmed by thermal denaturation and determination of the Tm of the complex. Analysis of the kinetic data also suggests that the conformation of the catalytic core of the ribozyme-substrate complex differs from that of the all-RNA complex, a change that results from the presence of a DNA/RNA heteroduplex in the complex.

Characterization of a chemically synthesized RNA having the sequence of the yeast initiator tRNA(Met)

A 75-unit long oligoribonucleotide corresponding to the sequence of the Saccharomyces cerevisiae initiator tRNA was synthesized chemically. The crude RNA was purified, and the sequence was verified by RNA sequencing techniques. A particularly useful purification step involved hydrophobic chromatography on BND-cellulose. The purified RNA could be aminoacylated to 28% of a bona fide initiator tRNA(Met) sample and threonylated to 76% of the level observed with native tRNA(fMet) from E. coli.

Mixed deoxyribo- and ribo-oligonucleotides with catalytic activity

The RNA of viroids and virusoids in plants, and the RNA transcripts of some tandemly repeated DNA sequences in the newt, can undergo self-catalysed cleavage to generate RNA with 5'-OH and 2',3'-cyclic-phosphate termini. These catalytic RNAs, or ribozymes, form a stem-loop secondary structure called a 'hammerhead' in which the catalytic (ribozyme) and substrate sequences are brought close together. Catalytically active mimics of hammerhead ribozymes can be readily made using oligoribonucleotides. Consequently, hammerhead analogues in which certain ribonucleotides are replaced by different ones have been constructed both to identify consensus residues required for cleavage activity and to determine the details of the cleavage mechanism. But these ribonucleotide-replacements tend to alter the conformation of the hammerhead by changing hydrogen-bonding and stacking potential at the position of substitution. We have now constructed structurally less-disrupted hammerhead analogues in which deoxyribonucleotides, which lack 2'-OH groups, are substituted for ribonucleotides. These mixed RNA-DNA polymers were synthesized using a strategy for the chemical synthesis of RNA that is compatible with DNA synthesis. Analysis of the cleavage products of several of these hammerhead analogues confirms the involvement in the reaction of the 2'-OH adjacent to the cleavage site in the substrate, and demonstrates that some 2'-OH groups in the catalytic region strongly affect activity. The results also indicate that the three-dimensional structure producing nucleic acid-type catalysis is not restricted to RNA.

The synthesis and functional evaluation of RNA and DNA polymers having the sequence of Escherichia coli tRNA(fMet)

Stepwise, solid-phase chemical synthesis has provided long RNA and DNA polymers related to the sequence of Escherichia coli tRNA(fMet). The 34-ribonucleotide oligomer corresponding to the sequence of the 5'-half tRNA molecule has been synthesized and then characterized by gel purification, terminal nucleotide determinations and sequence analysis. This 34-nucleotide oligomer serves as an acceptor in the RNA-ligase-catalyzed reaction with a phosphorylated 43-ribonucleotide oligomer corresponding to the sequence of the 3'-half molecule of tRNA(fMet). The DNA molecule having the sequence of tRNA(fMet) is a 76-deoxyribonucleotide oligomer with a 3'-terminal riboadenosine residue and all U residues replaced by T. These polymers have been compared with an oligodeoxyribonucleotide lacking all 2'-hydroxyl groups except for the 3'-terminal 2'-OH, an oligoribonucleotide lacking modified nucleosides and E. coli tRNA(fMet). The all-RNA 77-nucleotide oligomer can be aminoacylated by E. coli methionyl-tRNA synthetase preparation from E. coli with methionine and threonylated in the A37 position using a yeast extract. In agreement with work by Khan and Roe using tDNA(Phe) and tDNA(Lys), the rA77-DNA(fMet) can be aminoacylated, and preliminary evidence suggests that it can be threonylated to a small extent. Kinetic data support the notion that aminoacylation of tRNA(fMet) does not depend on the presence of 2'-hydroxyl groups with the exception of that in the 3'-terminal nucleotide.

[Immediate complications of transurethral resection of the prostate: study of 1000 consecutive cases]

The authors reviewed the charts of 1000 patients who underwent transurethral resection of the prostate. When the 30-day postoperative period was studied, it was found that 139 patients suffered complications and 6 died. Infectious complications (urinary tract in 63 cases and septicemia in 23 cases) were the commonest followed by hemorrhage and urinary retention. The deaths were related to cardiac problems.

Electromyographic study of bulbocavernosus muscle in 15 patients with postmicturition dribbling

Fifteen patients with postmicturition dribbling were studied with cystourethroscopy and electromyography of the bulbocavernosus muscle. In all patients the bulbocavernosus reflex and activity of the muscle during and after micturition were normal. No abnormality was found to explain the clinical symptoms.

Interrelationships between circulating vitamin D metabolites in normocalciuric and hypercalciuric renal stone formers

Serum 25-hydroxyvitamin D [25(OH)D], 24,25-dihydroxyvitamin D [24,25(OH)2D] and 1,25-dihydroxyvitamin D [1,25(OH)2D] were studied in renal stone formers while on a diet containing 1,000 or 300 mg calcium per day. The patients were divided into four groups and identified as (a) normocalciuric (NSF), (b) absorptive hypercalciuric (AH), (c) renal hypercalciuric (RH) and (d) as having primary hyperparathyroidism (PHP). The results indicate that, on the 1,000-mg Ca diet, the mean 25(OH)D, 24,25(OH)2D and 1,25(OH)2D concentrations were within the normal range in all groups of patients. On the low-calcium diet, 25(OH)D concentrations decreased significantly in patients with AH and RH while 24,25(OH)2D concentrations were not affected by the low-calcium diet. 1,25(OH)2D concentrations increased significantly during dietary calcium restriction in all groups of patients. When the relationship obtained on each diet between the circulating 25(OH)D concentrations and the 25(OH)D/1,25(OH)2D concentration ratio was compared, it suggested that the increase in the 1,25(OH)2D concentrations during dietary calcium restriction may have been due to an increase in the capacity of the 25(OH)D-1 alpha-hydroxylase, or to an increase in the circulating half-life of the hormone. These results indicate that renal stone formers are able to adapt themselves to dietary calcium restriction as shown by highly significant increases in the circulating 1,25(OH)2D concentrations while on a low-calcium diet. Moreover, the increase in the circulating 1,25(OH)2D concentrations did not happen at the expense of the 24,25(OH)2D production in any of the groups of patients studied.

Influence of dietary calcium on serum 1,25-dihydroxyvitamin D concentrations in renal stone formers

The role of 1,25-dihydroxyvitamin D (1,25(OH)2D) in the pathogenesis of idiopathic hypercalciuria was studied in 37 renal stone formers who, during two 10-day periods, followed first a normal and then a low calcium diet. The following samples were taken during each diet; 24 h urine; fasting blood and urine; blood and urine following a 1 g oral calcium load. Patients were divided according to serum calcium level, 24 h urinary calcium excretion on the first diet and fasting calcium excretion on the second diet. Eight patients were found to be normocalciuric (NSF), 16 had absorptive hypercalciuria (AH), five renal hypercalciuria (RH) and eight primary hyperparathyroidism. In NSF and AH, a positive correlation was found between the fasting and the 24 hour urinary calcium (r = 0.787, P less than 0.001), while negative correlations were found between the fasting urinary calcium and the serum parathyroid hormone (r = -0.703, P less than 0.001) or the fasting urinary cyclic AMP (r = -0.434, P less than 0.01). Patients with RH had higher serum PTH and urinary cAMP levels for a given degree of fasting calciuria mainly on the low calcium diet. Mean serum 1,25(OH)2D was similar in NSF (43.6 +/- 4.5 pg/ml), AH (43.6 +/- 2.3 pg/ml) and RH (40.4 +/- 4.8 pg/ml) on the first diet; increases were similar in all groups after 10 d of calcium restriction. A positive correlation was found between the serum 1,25(OH)2D concentrations and the 24 h urinary calcium excretion on the first diet in NSF (r = 0.889, P less than 0.001) but not in AH or RH. There was no evidence of such correlation with the low calcium diet. No correlation between the calciuric response to calcium loading and the serum concentrations of 1,25(OH)2D was found. The results suggest that serum concentrations of 1,25(OH)2D may be related to urinary calcium excretion in NSF more than in AH or RH. The factors responsible for the hyperabsorption of calcium in the latter patients remain to be elucidated.

Urinary calculi in pregnancy

Between January 1975 and March 1980, 19 pregnant patients with urinary calculi were admitted to hospital, they constituted 0.23% of all women delivered at the Hôpital St-Luc during that period. The symptoms were characteristic: pain in the flank and right lower quadrant, hematuria, frequency and dysuria. Noninterventional therapy was successful in 14 patients. Two patients were operated upon during pregnancy without complications. Ultrasonography is a useful diagnostic procedure during the first trimester. Pyelography should be considered only after adequate time has elapsed to allow spontaneous elimination of the calculi and, if used, one exposure before and one 30 minutes after injection of the contrast material well ensure the radiation dose is low enough to avoid causing any fetal abnormality. The authors believe that treatment must be individualized depending on the location and size of the calculus, the degree of obstruction, presence of infection, age of the fetus and condition of the patient. Spontaneous elimination after hydration and analgesia is the ideal, lumbar ureterolithotomy or basket extraction can be considered, although surgical procedures are best postponed until the postpartum period.

Colorectal neoplasm: a rare complication of ureterosigmoidostomy

A 24-year-old woman had a rectal neoplasm which occurred 20 years after she had undergone ureterosigmoidostomy for exstrophy of the bladder. Only 41 cases of bening or malignant tumours of the large bowel developing after ureterosigmoidostomy have previously been reported in the literature. Adenocarcinoma of the colon is most frequently found and can develop even after urine has been diverted away from the colon. The presenting symptoms are either those of ureteral obstruction or of colorectal neoplasm. This rare complication remains intriguing and the possible pathogenetic mechanisms are discussed.