MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data

The identification of potential regulatory motifs in new sequence data is increasingly important for experimental design. Those motifs are commonly located by matches to IUPAC strings derived from consensus sequences. Although this method is simple and widely used, a major drawback of IUPAC strings is that they necessarily remove much of the information originally present in the set of sequences. Nucleotide distribution matrices retain most of the information and are thus better suited to evaluate new potential sites. However, sufficiently large libraries of pre-compiled matrices are a prerequisite for practical application of any matrix-based approach and are just beginning to emerge. Here we present a set of tools for molecular biologists that allows generation of new matrices and detection of potential sequence matches by automatic searches with a library of pre-compiled matrices. We also supply a large library (> 200) of transcription factor binding site matrices that has been compiled on the basis of published matrices as well as entries from the TRANSFAC database, with emphasis on sequences with experimentally verified binding capacity. Our search method includes position weighting of the matrices based on the information content of individual positions and calculates a relative matrix similarity. We show several examples suggesting that this matrix similarity is useful in estimating the functional potential of matrix matches and thus provides a valuable basis for designing appropriate experiments.

TRANSFAC: an integrated system for gene expression regulation

TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/). Its content has been enhanced, in particular by information about training sequences used for the construction of nucleotide matrices as well as by data on plant sites and factors. Moreover, TRANSFAC has been extended by two new modules: PathoDB provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources.

TRANSFAC: a database on transcription factors and their DNA binding sites

TRANSFAC is a database about eukaryotic transcription regulating DNA sequence elements and the transcription factors binding to and acting through them. This report summarizes the present status of this database and accompanying retrieval tools.

Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms

TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles. In addition to being updated and extended by new features, it has been complemented now by a series of additional database modules. Among them, modules which provide data about signal transduction pathways (TRANSPATH) or about cell types/organs/developmental stages (CYTOMER) are available as well as an updated version of the previously described COMPEL database. The databases are available on the WWW at http://transfac.gbf.de/

TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation

Three databases that provide data on transcriptional regulation are described. TRANSFAC is a database on transcription factors and their DNA binding sites. TRRD (Transcription Regulatory Region Database) collects information about complete regulatory regions, their regulation properties and architecture. COMPEL comprises specific information on composite regulatory elements. Here, we describe the present status of these databases and the first steps towards their federation.

Antibiotic treatment in preterm premature rupture of membranes and neonatal morbidity: a metaanalysis

OBJECTIVE

We performed a metaanalysis of seven published randomized clinical trials to estimate more precisely the effect of prophylactic antibiotics on neonatal mortality, clinical sepsis of the neonate, respiratory distress syndrome, intraventricular hemorrhage, and necrotizing enterocolitis.

STUDY DESIGN

To evaluate the effect of antibiotic treatment unaffected by other forms of treatment such as tocolytics or corticosteroids, investigations in which these additional measures were used were not included. We analyzed study patients and methods and abstracted quantitative outcome data. For each outcome both odds ratios and 95% confidence intervals were calculated.

RESULTS

Among the 657 patients from seven trials published between 1989 and 1994, antibiotic therapy significantly reduced the risk of neonatal sepsis by 68% (odds ratio 0.32, 95% confidence interval 0.16 to 0.65, p=0.001) and that of intraventricular hemorrhage by 50% (odds ratio 0.50, 95% confidence interval 0.28 to 0.89, p=0.019). In contrast, no significant effect of antibiotics on overall neonatal mortality (odds ratio 0.92, 95% confidence interval 0.46 to 1.81), respiratory distress syndrome (odds ratio 0.84, 95% confidence interval 0.58 to 1.22), or necrotizing enterocolitis (odds ratio 1.27, 95% confidence interval 0.61 to 2.62) was found.

CONCLUSION

This metaanalysis supports an improvement of neonatal morbidity in mothers with preterm premature rupture of membranes treated prenatally with different antibiotic regimens.

Closure or nonclosure of the visceral peritoneum at cesarean delivery

OBJECTIVE

Our purpose was to determine whether nonclosure of the visceral peritoneum at low transverse cesarean delivery has advantages over suture peritonization with regard to postoperative morbidity.

STUDY DESIGN

A prospective randomized trial of 549 women undergoing cesarean section was carried out; 262 were randomized to nonclosure and 287 to closure of the visceral peritoneum. Perioperative, intraoperative, and postoperative management decisions were made without reference to treatment groups. Statistical analysis compared intraoperative and postoperative outcome between the two groups.

RESULTS

Operating and anesthesia times were significantly shorter in patients receiving nonclosure. The incidence of febrile morbidity and cystitis and the need for antibiotics and narcotics were all significantly greater when the peritoneum was closed. Hospital stay was significantly shorter after nonclosure.

CONCLUSION

Nonclosure of the visceral peritoneum is associated with lower febrile and infectious morbidity. Routine closure of the visceral peritoneum should be abandoned at cesarean delivery.

Fetal fibronectin as a marker to predict the onset of term labor and delivery

OBJECTIVE

We examined whether the presence of fetal fibronectin in cervicovaginal secretions may be a marker to predict the onset of term labor and delivery.

STUDY DESIGN

A prospective study was performed in 100 primiparous and multiparous women having reached their expected date of confinement. Fetal fibronectin was assayed by taking samples of both the cervical and vaginal mucus with two different fetal fibronectin tests. The study population was divided into women delivering within 48 hours and women giving birth > 48 hours after sampling.

RESULTS

Seven patients had to be excluded from evaluation. Of the remaining 93 women, 37 were delivered within 48 hours; fetal fibronectin was detected in 30. Fifty-six women were delivered later than 48 hours; 51 of them had negative results for fetal fibronectin (positive accuracy 86%, negative accuracy 88%, p < 0.0001).

CONCLUSION

Fetal fibronectin in the cervicovaginal secretions of women who have reached their expected date of confinement is a useful predictor of the onset of term labor and delivery.

Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements

MOTIVATION

Analysis of unannotated genomic sequences for regulatory regions depends on a reliable recognition of individual cis-acting elements. Since some of them have a very low conserved sequence pattern, additional criteria are required.

RESULTS

Using molecular modelling techniques, we have created a complete database for the conversion of base sequences into profiles of structural parameters of DNA. On this basis, search routines can be developed that scan for profile matches. They may be used instead of or, probably most appropriate in most cases, in combination with conventional sequence pattern searches.

Association between lower urinary tract symptoms and erectile dysfunction

Our aim was to assess the association between lower urinary tract symptoms (LUTS) and erectile dysfunction by means of International Prostate Symptom Score (IPSS) and Sexual Health Inventory for Men (SHIM) questionnaire. A total of 69 eligible patients who were admitted to our outpatient clinic with lower urinary tract symptoms were included in the study. A self administered questionnaire of IPSS and SHIM were given to patients. Demographics and medical history data were recorded. Any risk factor that may be associated with erectile dysfunction, including coronary artery disease, diabetes, hypertension, and smoking status, was determined in each patient. Correlation tests were used to examine the relationship between lower urinary tract symptoms and erectile dysfunction by controlling the effects of age and comorbidities. Mean age was 58.6 +/- 13.1 31-86 years. Mean SHIM and IPSS total score was 14.3 +/- 7.5 and 11.5 +/- 8.1, respectively. Spearman correlation coefficient between IPSS and SHIM scores was found to be -0.41. There was a significant negative correlation with IPSS total scores of moderate degree when both age and presence of risk factor was controlled (r = -0.31; p = 0.009). Storage symptom scores showed significant correlation with SHIM scores (r = -0.33; p = 0.000). The association between SHIM score and each item of IPSS showed significant correlation for urgency, straining and nocturia when age controlled. The degree of bother by LUTS as determined by the IPSS quality of life question was also correlated with SHIM scores; however, this correlation was not significant when age or risk factor for ED was controlled. The presence of LUTS especially storage symptoms is strongly associated with erectile dysfunction independent of age and comorbidities.

Gemeprost for first trimester missed abortion

In 87 patients with a missed abortion prior to 13 weeks, the application of a prostaglandin (PG) E1 derivative (1 mg gemeprost, Cergem) was compared to conventional surgical termination of pregnancy by cervical dilatation and curettage. In 33 patients with PGE1 application, complete expulsion of the abnormal pregnancy occurred after an average of 2.8 +/- 1.5 vaginal suppositories. PGE1 treatment was effective in 76.7%, and surgical management was effective in 90.9% of patients. Sixty percent of the patients in the PGE1 group required analgesia because of uterine pain in comparison to 4.5% in the surgical group. The possibility of medical termination with synthetic PG derivatives should be further investigated.

[Tuboscopy--an endoscopic approach to the intratubal lumen]

A linear everting catheter in combination with a 0.5-mm microendoscope enables the visualization of the tubal lumen. In 35 sterility patients, diagnostic tuboscopies were performed. Physiological and pathological results of tubal mucosa are described. Tuboscopy is a main tool in the diagnosis of the tubal factor. First steps are taken to use tuboscopy not only for diagnostic but also for therapeutic reasons. Yet, the role of this technique in cases of tubal pregnancies cannot be evaluated.

TRANSFAC database as a bridge between sequence data libraries and biological function

The TRANSFAC database contains information about regulatory DNA sequences and the proteins (transcription factors) binding to and acting through them. It may thus serve as a dictionary for the biological meaning of these sequence elements. Moreover, the TRANSFAC data can be used to describe these elements, to define consensi and matrices for elements of certain function, and thus to provide means of identifying regulatory signals in newly unravelled genomic sequences.