Biomedical subjects

Donald E Riley

Publications and source records attributed to Donald E Riley.

17 recordsLinked to original sources

PubMed2005

Inconsistent localization of gram-positive bacteria to prostate-specific specimens from patients with chronic prostatitis.

OBJECTIVES: To determine the rate of gram-positive localizations and whether repetitive cultures demonstrate consistent localization of gram-positive bacteria in patients with chronic prostatitis symptoms. METHODS: We repeated localization cultures at different visits for untreated patients with chronic prostatitis symptoms. RESULTS: A total of 470 patients with chronic prostatitis had lower urinary tract localization cultures done. Ten-fold increases in the concentrations of gram-positive bacteria were noted when the postprostatic massage (VB3) or expressed prostatic secretions cultures were compared with first-void urine (VB1) cultures from 29 patients (6%). This was comparable to the 7% rate of gram-negative chronic bacterial prostatitis. We studied 49 patients who had undergone 130 repeated localization studies (median 2, range 2 to 4). Repeatedly negative studies were found in 20 patients, including 19 who each had undergone two studies and 1 who had undergone four studies. Of 9 patients who each had undergone three or four studies, 9 demonstrated localization of at least one gram-positive species. Of the 29 patients with gram-positive localizations, 27 (94%) did not have consistent localization of the gram-positive species. CONCLUSIONS: Patients with chronic prostatitis demonstrated localization of gram-positive bacteria, but the results were seldom reproducible in untreated patients. Gram-positive localizations may represent nonpathogens, transient bacterial colonization of the lower urinary tract, or intermittent shedding of prostatic pathogens. The limitations of traditional cultures highlight the need for better diagnostic approaches and improved recommendations for antimicrobial therapy.

Chronic Disease↗

PubMed2004

Short tandem repeat (STR) replacements in UTRs and introns suggest an important role for certain STRs in gene expression and disease.

Some untranslated sequence (UTR)-localized, short tandem repeats (STRs) exhibit evidence of selection pressure, including STR-coupling preferences, STR conservation, interspecies STR-STR replacements, and STR variants implicated in certain diseases. We wished to determine if STR replacements occurred near disease-related genes, including previously unstudied STRs as well as some STRs already implicated in disease. Among nine strong-candidate prostate cancer (CaP)-predisposing genes, three [steroid 5-alpha-reductase 2 (Srd5A-2), macrophage scavenger receptor-1 (MSR-1), and tumor necrosis factor receptor-21 (Tnfr-21)] exhibited striking STR replacements (P<0.001). The glomerular disease-related gene, CD2AP, exhibited an STR replacement flanked by well-conserved sequences, suggesting an STR-focused process. Another glomerular disease-related gene, rabphilin 3A, exhibited at least two STR replacements at the same UTR position comparing Drosophila melanogaster, Mus musculus, and Homo sapiens. Two genes implicated in blood-clotting disorders, von Willebrand factor (vWA) and fibrinogen alpha (FGA), exhibited multiple-intron STR replacements among mammals, extending STR replacement phenomena to introns. Among primates, a tyrosine hydroxylase (THO1) intron STR, previously implicated in both schizophrenia and drug withdrawal delirium, exhibited frequent replacements. Some STR replacements were early events in gene divergence. When STR sequences of closely related species were available, STR replacement was observed to be nearly as rapid as speciation. STR replacements expand the list of STR sequences that may contribute to genetic activity and to disease processes.

Animals↗

PubMed2004

Simple repeat replacements support similar functions of distinct repeats in inter-species mRNA homologs.

Simple repeats are ubiquitous in metazoan genomes, but function has been elusive. We reported that distinct, short tandem repeats (STRs) were coupled with rigorous polarity and register, suggesting order in simple repeat usage. Several STRs that lacked internal, canonical base pairs were associated with mRNAs encoding membrane functions and transcription factors. We hypothesized that diverse, simple repeats, such as (AC)n, (GU)n, (AG)n, (CU)n and (CUUU)n, had similar functions. The hypothesis predicts that closely related mRNAs would sometimes exhibit STR replacements. Comparing aquaporin 3 mRNAs, in rodents and humans, (GU)20 replaced (AG)29. Comparing biglycan mRNAs, (GU)25 replaced (CA)12. Comparing immunoglobulin superfamily member 9 mRNAs, the STR-couple, (CU)17(GU)9 replaced the STR-couple, (GU)19(GC)4. Comparing tumor necrosis factor receptor-21 mRNAs, (GU)24 replaced (CUUU)16. In a collection of 52 rodent-H. sapiens homologous mRNAs that had STRs, six (11.5%) STR-STR replacements occurred, significantly more than expected based on an STR frequency of 0.13% in all reported UTRs (p<0.001). Database studies and the observation of STR replacements among transcript homologs independently support the hypothesis that diverse repeat sequences, such as (AG)n, (AC)n, (GU)n, (CU)n and (CUUU)n, have similar usage that is consistent with analogous functions.

Animals↗

PubMed2004

Short tandem repeats are associated with diverse mRNAs encoding membrane-targeted proteins.

Within the genomes of multicellular organisms, short tandem repeating sequences (STRs) are ubiquitous, yet usage patterns remain obscure. The repeats (AC)n and (GU)n appear frequently in the untranslated regions (UTRs) of messenger RNAs (mRNAs). To investigate STR usage patterns, we used three approaches: (1) comparisons of individual mRNA database sequences including annotations and linked references, (2) statistical analysis of complete, UTR databases and (3) study of a large gene family, the aquaporins. Among 500 (AC)n- or (GU)n-containing mRNAs, 58 (12%) had known functions. Of these, 50 (86%) encoded proteins whose activities involved membranes or lipids, including integral membrane proteins, peripheral membrane proteins, ion channels, lipid enzymes, receptors and secreted proteins. A control sequence (AU)n also occurred in mRNAs, but only 5% encoded membrane-related functions. Investigation of all reported 3' UTR sequences, demonstrated that the STR (AC)n was 9 times more common in mRNAs encoding membrane functions than in the total UTR database (P < 0.001). Similarly, (GU)n was 8 times more common in membrane-function mRNAs than in the total database (P < 0.001). These observations suggest that (AC)n and (GU)n may be UTR signals for some mRNAs encoding membrane-targeted proteins.

3' Untranslated Regions↗

PubMed2004

Identification and sequencing of bacterial rDNAs in culture-negative amniotic fluid from women in premature labor.

Our objective was to identify bacterial species present in culture-negative but 16S rDNA-positive amniotic fluid samples from women in preterm labor. Amniotic fluid from 69 women in preterm labor was cultured and examined for the proinflammatory cytokine interleukin-6 (IL-6). Polymerase chain reaction technology was used to detect highly conserved bacterial ribosomal DNA sequences (16S rDNAs). As previously reported, 16S rDNAs were identified in 15 (94%) of 16 culture-positive amniotic fluid samples, in 5 (36%) of 14 culture-negative samples with elevated IL-6, and in 1 (3%) of 39 culture-negative samples with low IL-6 levels. Direct sequencing was performed of 16S rDNAs from the 5 culture-negative amniotic fluid specimens with elevated IL-6, followed by database searches and phylogenetic analyses. The bacterial sequences identified included: two Leptotrichia sanguinegens, one human oral bacterium A33, one Fusobacterium nucleatum, and one Ureaplasma urealyticum. Identification and sequencing of 16S rDNAs in amniotic fluid is a promising technique to identify bacterial species associated with elevated IL-6 levels in culture-negative amniotic fluid that may contribute to the etiology of premature labor.

Adult↗

PubMed2004

Chronic prostatitis: Charlottesville to Seattle.

PURPOSE: Since few men with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) have culturable bacteria by traditional approaches, we used sensitive molecular methods to determine presence of fastidious microorganisms. MATERIALS AND METHODS: We evaluated 135 men with CP/CPPS by standardized clinical evaluation, and by lower tract localization cultures and chamber counts of expressed prostatic secretions of leukocytes. We excluded from study patients with bacteriuria, bacterial prostatitis, urethritis or positive urethral cultures. Prostate biopsy was obtained using a double-needle technique to limit contamination. We chose molecular approaches because previous studies had used culture antigen detection in urine, urethral swabs and expressed prostatic secretions. However, interpretation of such studies is complicated because urogenital samples often acquire bacteria while passing through the urethra. We used specific and broad-spectrum polymerase chain reaction (PCR) assays. RESULTS: Only 10 (8%) of the 135 subjects had positive specific PCR assays, including Mycoplasmia genitalium, Chlamydia trachomatis and Trichomonas vaginalis. Our findings suggested that C. trachomatis, T. vaginalis and M. genitalium may be identified in some patients with CP/CPPS, even among men with no evidence of urethritis and with negative urethral cultures and other assays. The broad-spectrum PCR assays provided the most provocative findings. DNA encoding tetracycline resistance was identified in 25% of subjects, and 77% of subjects had evidence of 16S rDNAs. The white blood cell concentration in the prostatic secretions correlated with identification of 16S rDNAs in prostate tissue (p <0.01). CONCLUSIONS: Delineating the precise role of these organisms in the etiology of CP/CPPS may help define better diagnostic and treatment algorithms.

Chronic Disease↗

PubMed2003

Transcribed short tandem repeats occur in couples with strongly preferred registers.

Short tandem repeats (STRs) have been widely observed, but most STRs have no recognized organization or function. Here we show that for diverse mRNAs, 84% of (GC)(n) repeats were found unexpectedly coupled with another STR, (GU)(n). These STR couples exhibited preferred polarity and register. In 3(') untranslated mRNA sequences (UTRs) 100% of (GC)(n>6) repeats were tightly coupled with (GU)(n). For (GC)(n), stem folding energy correlated with the length and number of neighboring, non-folding (GU)(n) partners (p=0.014). Approximately 20% of (AU)(n>/=14) repeats were coupled with (GU)(n). The STR couple (AC)(n)(AG)(n) also exhibited polarity and register preferences. The sequence arrangement at STR-couple joints was conserved rigorously, suggesting that these sequences were under selection pressure. Some STR couples may function as mRNA processing landmarks, based on alternative transcript comparisons. These observations suggest that some transcribed STRs may be functional UTR signals with predictable organization and usage patterns.

3' Untranslated Regions↗

PubMed2003

Application of real-time polymerase chain reaction technology to detect prostatic bacteria in patients with chronic prostatitis/chronic pelvic pain syndrome.

To investigate the potential association between prostate infection and chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS), we used molecular approaches described in previous reports. These methods employed standard polymerase chain (PCR) reaction assays to provide a qualitative evaluation of prostatic bacterial species. Here, we report on the detection of prostatic bacteria using a real-time PCR. Template DNAs were examined from prostatic tissue samples from patients with CP/CPPS. Two PCR primer sets were used: one that amplifies a portion of all known bacterial ribosomal DNAs (16S rDNAs) and one that is specific for Escherichia coli as opposed to related, E. coli-like bacteria. The 16S rDNA real-time PCR assay detected bacterial DNAs in eight (26%) of 31 samples from patients with CP/CPPS, including three samples (10%) that were also positive by the E. coli real-time PCR assay. These E. coli positives were quantified at approximately 10(3) cfu/ml of tissue digested. Quantification, speed and specificity make real-time PCR a promising approach for the quantitative detection and identification of prostatic bacteria from CP/CPPS patients.

Biopsy↗

PubMed2003

Epidemiology of prostatitis: new evidence for a world-wide problem.

We review new data on the epidemiology of chronic prostatitis. These population-based studies used reasonable case-definitions to survey various populations from North America, Europe and Asia. Overall, 2-10% of adult men suffer from symptoms compatible with chronic prostatitis at any time and approximately 15% of men suffer from symptoms of prostatitis at some point in their lives. Other epidemiologic data suggest that chronic prostatitis may be associated with an increased risk for development of benign prostatic hyperplasia and prostate cancer. These data suggest that chronic prostatitis is an important international health care problem that merits increased priority from clinicians and researchers.

Adult↗

PubMed2003

Counting leukocytes in expressed prostatic secretions from patients with chronic prostatitis/chronic pelvic pain syndrome.

OBJECTIVES: The evaluation of WBCs in EPS is recommended for classifying patients with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) but no agreement has been reached on the optimal method. We sought to determine the relationship between the expressed prostatic secretions (EPS) leukocyte (WBC) count per high-power field (evaluated by a more quantitative wet mount method and the traditional gram-stained smear method used in clinical microbiology laboratories) and the EPS WBC concentration to determine whether quantitative methods are necessary for accurate patient classification. METHODS: EPS collected from 94 patients with CP/CPPS were evaluated by gram-stained smear, a standardized wet mount, and a hemocytometer method. RESULTS: The gram-stained smear detected EPS WBCs in 21 (22%) of 94 subjects compared with 78 (83%) by the standardized wet mount and 57 (60%) by the hemocytometer method. The gram-stained EPS WBC count correlated poorly with the WBC concentration by hemocytometer (R(2) = 0.051, P = 0.03). Although the standardized EPS WBC count correlated better with the concentration by hemocytometer, the correlation coefficient remained low (R(2) = 0.244, P <0.0001). CONCLUSIONS: The standardized wet mount proved superior to the gram-stained smear, but both methods lacked precision. Quantitative determination of the EPS WBC concentration by a counting chamber method proved to be the superior evaluation for research studies of CP/CPPS.

Body Fluids↗

PubMed2002

Diverse eukaryotic transcripts suggest short tandem repeats have cellular functions.

Previously thought "junk" DNA, short tandem repeats consisting of (GATA)n, or its compliment, were found in varied metazoan eukaryotic genomes but were rare in yeast and bacterial genomes. The (GATA)n sequence was found in cDNAs encoding mRNAs with known functions. At least 16 of 18 such transcripts encode membrane-associated proteins including: plasma membranes, synapses, mitochondrial membranes, nuclear envelopes, and brush border membranes. Flanking sequences were diverse but (GATA)n sequences clustered around 500 bases from stop codons. The (GATA)n sequences occurred in both orientations and showed constrained polymorphism. In sets of splice variants with and without (GAUA)n, the STR containing transcripts were the most abundant. These observations suggest that (GATA)n sequences probably function. In many cases, the function may be to encode post-transcriptional signals for mRNAs encoding membrane-associated proteins.

Animals↗

PubMed2002

X Chromosomal short tandem repeat polymorphisms near the phosphoglycerate kinase gene in men with chronic prostatitis.

Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) causes substantial morbidity afflicting approximately 10% of adult males. Treatment is often empirical and ineffective since the etiology is unknown. Other prostate and genitourinary diseases have genetic components suggesting that CP/CPPS may also be influenced by genetic predisposition. We recently reported a highly polymorphic short tandem repeat (STR) locus near the phosphoglycerate kinase gene within Xq11-13. Because this STR is in a region known to predispose towards other prostate diseases, we compared STR polymorphisms in 120 CP/CPPS patients and 300 control blood donors. Nine distinct allele sizes were detected, ranging from 8 to 15 repeats of the tetrameric STR plus a mutant allele (9.5) with a six base deletion in the flanking DNA sequence. The overall allele size distribution in the CP/CPPS patients differed from controls (Chi-square=19.252, df=8, P=0.0231). Frequencies of two specific alleles, 9.5 and 15, differed significantly in CP/CPPS vs. control subjects and allele 10 differed with marginal significance. Alleles 9.5 and 10 were both more common in CP/CPPS patients than controls while allele 15 was less common. These observations suggest that Xq11-13 may contain one or more genetic loci that predispose toward CP/CPPS. Further investigations involving family studies, larger patient populations, and other control groups may help elucidate this potential genetic predisposition in CP/CPPS.

Alleles↗

PubMed2002

The NIH Consensus concept of chronic prostatitis/chronic pelvic pain syndrome compared with traditional concepts of nonbacterial prostatitis and prostatodynia.

The new National Institutes of Health (NIH) consensus classification identifies chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) based on the presence or absence of leukocytes in expressed prostatic secretions (EPS), postprostatic massage urine (VB3), or seminal fluid analysis. The purpose of this review is to determine the effect of the new classification on the proportion of symptomatic patients diagnosed with inflammation. We compare and contrast the new consensus classification with the traditional classification of prostatitis syndromes, then review how these changes effect patient classification in our clinical practice. Thorough clinical and microbiologic examination of 140 patients attending the University of Washington Prostatitis Clinic included evaluation of first void urine, mid-stream urine, EPS, VB3, and semen specimens. Inflammation was documented in 111 (26%) of 420 samples including 39 EPS samples, 32 VB3 samples, and 40 SFA specimens. Of the 140 patients, 73 (52%) had inflammatory CP/CPPS according to the NIH consensus criteria, but only 39 (28%) had nonbacterial prostatitis according to traditional EPS criteria (P < 0.001). The new NIH consensus concept of inflammatory CP/CPPS includes almost twice as many patients as the traditional category of nonbacterial prostatitis.

Chronic Disease↗

PubMed2002

Symptoms and inflammation in chronic prostatitis/chronic pelvic pain syndrome.

OBJECTIVES: To evaluate the possibility that patients with inflammatory and noninflammatory chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) might present with different symptoms. Patients with CP/CPPS present with characteristic symptoms without bacteriuria. The new National Institutes of Health consensus suggests that CP/CPPS can be divided into inflammatory and noninflammatory categories. METHODS: Standardized symptom surveys were completed by 130 subjects who met the criteria for CP/CPPS after clinical examination and urethral, urine, expressed prostatic secretion (EPS), and seminal fluid analysis evaluations. RESULTS: When classified by either EPS or postprostatic massage urine (VB3) findings, subjects with and without inflammation had similar symptoms. However, when classified using the combination of EPS, VB3, and seminal fluid analysis, subjects with inflammatory CP/CPPS had more severe (P <0.02) and more frequent symptoms, in particular, difficulty reaching erection (P <0.01), weak urinary stream (P <0.01), urinary frequency (P = 0.03), and penile pain (P = 0.04). CONCLUSIONS: The increased severity and frequency of symptoms among patients with inflammatory CP/CPPS provide empirical support for the new consensus classification on the basis of the combination of EPS, VB3, and seminal fluid analysis findings.

Analysis of Variance↗

PubMed2002

Chronic prostatitis: epidemiology and role of infection.

We review the epidemiology of chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and the role of infectious agents, emphasizing critical data necessary to define current research issues. The epidemiologic literature is limited, but the worldwide prevalence appears to be in the range of 2% to 10%, indicating that CP/CPPS represents an important international health problem. Recent molecular studies have documented bacterial DNA sequences in prostate tissue from CP/CPPS patients. These data suggest that colonization and/or infection occurs in the prostates of many patients with CP/CPPS. Further molecular research is needed to define the role of bacteria in the etiology of CP/CPPS.

Chronic Disease↗

PubMed2002

Prostatitis: what is the role of infection.

Although bacterial prostatitis is a common diagnosis, well documented infections of the prostate are uncommon. Culture studies of prostate tissue led our group to hypothesize that bacterial colonization/invasion of the prostate gland might occur more commonly than is appreciated by standard microbiological techniques. Specific polymerase chain reaction (PCR) assays were used for each of the pathogens previously implicated in chronic prostatitis as well as broad-spectrum PCR assays to identify tetracycline resistance genes and bacterial ribosomal-encoding genes (16S rDNAs), followed by cloning and sequencing of the PCR products. Only ten (8%) of the 135 patients with chronic prostatitis had positive specific PCR assays including: Mycoplasma genitalium in four men, Chlamydia trachomatis in three and Trichomonas vaginalis in two, as well as one man positive for both M. genitalium and C. trachomatis. In contrast to the specific probes, the broad-spectrum PCR assays had a substantial proportion of positives. We found evidence of tetracycline resistance in 25% of patients. 16S rDNA-encoding sequences in 77% of the subjects. The tetracycline resistance positives were a subset of the 16S rDNA positive patients. Patients with 16S rDNA-encoding sequences were significantly more likely to have expressed prostatic secretion leukocytes. Many patients with chronic prostatitis/chronic pelvic pain syndrome have a wide variety of bacterial DNA-encoding sequences despite extensive negative microbiological investigations. Understanding the precise role of infection in this syndrome may well lead to better methods to elucidate the microbiology of the prostate in health and disease.

Bacteria↗

PubMed2002

Bacteria in the chronic prostatitis-chronic pelvic pain syndrome: molecular approaches to critical research questions.

PURPOSE: There is a pressing need to determine the causes and consequences of, and optimal therapy for the chronic prostatitis-chronic pelvic pain syndrome. MATERIALS AND METHODS: New data suggest that bacterial infection may be critical in some patients. We examined the rationale for and technical approaches to hypothesis driven studies of bacteria in the chronic prostatitis-chronic pelvic pain syndrome. RESULTS: The first hypothesis was that patients with the chronic prostatitis-chronic pelvic pain syndrome have prostatic bacteria that distinguish them from controls. In pilot studies patients with inflamed expressed prostatic secretions were more likely to have bacterial DNAs, that is 16S ribosomal DNAs. Current goals are to clone, sequence and compare ribosomal DNAs from patients and controls to determine which bacteria are most specific to the chronic prostatitis-chronic pelvic pain syndrome and which should be targeted in clinical trials. The second hypothesis was that bacterial viability correlates with the severity of the chronic prostatitis-chronic pelvic pain syndrome. Quantitative assays for bacterial elongation factor messenger RNA (tufA messenger RNA) provide tools to correlate bacterial viability with patient characteristics, will provide insights into the potential value of antimicrobial therapy and identify characteristics that distinguish patients most likely to respond. The third hypothesis was that patients with prostatic bacteria have similar bacteria in expressed prostatic secretions or on seminal fluid analysis and, furthermore, these bacteria differ from bacteria in controls. These studies would determine whether expressed prostatic secretions or seminal fluid analysis can be used to identify prostatic bacteria and may result in clinical methods for noninvasive diagnosis of prostatic infection. CONCLUSIONS: These studies should provide important insights into the causes of the chronic prostatitis-chronic pelvic pain syndrome and may elucidate optimal clinical evaluation and treatment in patients.

Bacteria↗