The signals that determine activation and repression of specific genes in response to appropriate stimuli are one of the most important, but least understood, types of information encoded in genomic DNA. The nucleotide sequence patterns, or motifs, preferentially bound by various transcription factors have been collected in databases. However, these motifs appear to be individually too short and degenerate to enable detection of functional enhancer and silencer elements within a large genome. Several groups have proposed that dense clusters of motifs may diagnose regulatory regions more accurately. Cluster-Buster is the third incarnation of our software for finding clusters of pre-specified motifs in DNA sequences. We offer a Cluster-Buster web server at http://zlab.bu.edu/cluster-buster/.

The phosphorylated acidic glycoproteins bone sialoprotein (BSP) and osteopontin (OPN) bind to hydroxyapatite (HA) crystals and may be involved in the regulation of bone mineralization. The HA-binding properties of these proteins have been attributed to glutamic acid-rich sequences in BSP and aspartic acid-rich sequences in OPN. The present study examines the roles of these polycarboxylate sequences in the binding of BSP and OPN to HA. Porcine BSP, OPN and the synthetic polypeptides poly-L-glutamic acid [Poly(Glu)] and poly-L-aspartic acid [Poly(Asp)] were labeled with fluorescein isothiocyanate and their binding to HA determined by fluorimetry. From the binding isotherms, dissociation constants (KDs) for all the reagents tested were determined to be in the micromolar range. The saturation binding capacities of HA for Poly(Glu), Poly(Asp), BSP and OPN were similar (500-600 micrograms/m2). To investigate the role of glutamic acid-rich and aspartic acid-rich sequences in the binding to HA of BSP and OPN, respectively, competitive binding studies with Poly(Glu) and Poly(Asp) were performed. Poly(Glu) was able to displace a maximum of 100% of Poly(Glu), 81% of OPN, 68% of BSP and 65% of Poly(Asp). Poly(Asp) was able to displace a maximum of 100% of Poly(Glu), 99% of Poly(Asp), 95% of OPN and 89% of BSP. These results are consistent with the view that BSP and OPN bind to HA via their polycarboxylate sequences, but suggest a complex mode of interaction between polyelectrolytes and ionic crystals.

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Introduction: Ovarian fibroma is an uncommon, benign, stromal neoplasm that is a mixture of collagen-producing mesenchymal cells. There are varying sonographic and computed tomography features described in literature of smaller scale studies. Case Report: We describe a case of an ovarian fibroma presenting as a midline pelvic mass mimicking a vaginal cuff tumour in a 67-year-old patient with surgical history of a hysterectomy. Computed tomography and ultrasound were utilised to evaluate the mass and guide management of the patient. The mass was initially suspected on CT-guided biopsy as a vaginal spindle cell epithelioma amongst other potential differential considerations. With robot-assisted laparoscopic surgery and histologic analysis, the true diagnosis of an ovarian fibroma was reached. Discussion: An ovarian fibroma is an uncommon, benign, stromal ovarian tumour, representing just 1-4% of all ovarian tumours. Its widely varying imaging features present a challenge when radiologically evaluating ovarian fibromas or pelvic tumours, as the differential diagnoses are extensive and ovarian fibromas are often misdiagnosed until surgical resection. We highlight the features of ovarian fibromas and the potential value of pelvic/transvaginal ultrasonography in management of ovarian fibroma and other pelvic masses. Conclusion: The use of computed tomography and ultrasound aided in the diagnostic and treatment pathway of this patient with a pelvic mass. There is high utility of sonography in evaluating such tumours to elucidate salient features, expedite diagnosis, and guide further management.