High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae

A novel approach for identifying condition-specific regulatory modules in yeast reveals functionally distinct coregulated submodules

5-Deoxy-Δ 12,14 -Prostaglandin J 2 Down-Regulates Activin-Induced Activin Receptor, Smad, and Cytokines Expression via Suppression of NF-B and MAPK Signaling in HepG2 Cells

15-Deoxy-Δ 12,14 -prostaglandin J 2 (15d-PGJ 2 ) and activin are implicated in the control of apoptosis, cell proliferation, and inflammation in cells. We examined both the mechanism by which 15d-PGJ 2 regulates the transcription of activin-induced activin receptors (ActR) and Smads in HepG2 cells and the involvement of the nuclear factor-B (NF-B) and mitogen-activated protein kinase (MAPK) pathways in this regulation. Activin A (25 ng/mL) inhibited HepG2 cell proliferation, whereas 15d-PGJ 2 (2 M and 5 M) had no effect. Activin A and 15d-PGJ 2 showed different regulatory effects on ActR and Smad expression, NF-B p65 activity and MEK/ERK phosphorylation, whereas they both decreased IL-6 production and increased IL-8 production. When costimulated with 15d-PGJ 2 and activin, 15d-PGJ 2 inhibited the activin-induced increases in ActR and Smad expression, and decreased activin-induced IL-6 production. However, it increased activin-induced IL-8 production. In addition, 15d-PGJ 2 inhibited activininduced NF-B p65 activity and activin-induced MEK/ERK phosphorylation. These results suggest that 15d-PGJ 2 suppresses activin-induced ActR and Smad expression, down-regulates IL-6 production, and up-regulates IL-8 production via suppression of NF-B and MAPK signaling pathway in HepG2 cells. Regulation of ActR and Smad transcript expression and cytokine production involves NF-B and the MAPK pathway via interaction with 15d-PGJ 2 /activin/Smad signaling

Primary Malignant Melanoma of the Female Urethra

We report here on a rare case of primary malignant melanoma of the female urethra. A 69-year-old female presented at our hospital with a several month history of dysuria, poor stream, gross hematuria, intermittent blood spots, and a painful mass at the external urethral meatus. The physical examination revealed a soft, small, chestnut-sized lesion through the urethral orifice. The mass was tan colored, ulcerated, covered with necrotic tissue, and protruded from the external urethral meatus. The mass was removed by wide local excision under spinal anesthesia. The pathological diagnosis was malignant melanoma of the urethra. Computed tomography of the abdomen as well as a whole-body bone scan showed no evidence of metastasis. The patient has been free of disease for 6 months postoperatively. We discuss the clinicopathologic features and treatment of this tumor

A New Method of Measuring the Amount of Soft Tissue in Pulmonary Ground-Glass Opacity Nodules: a Phantom Study

OBJECTIVE: To devise a new method to measure the amount of soft tissue in pulmonary ground-glass opacity nodules, and to compare the use of this method with a previous volumetric measurement method by use of a phantom study. MATERIALS AND METHODS: Phantom nodules were prepared with material from fixed normal swine lung. Forty nodules, each with a diameter of 10 mm, were made with a variable mean attenuation. The reference-standard amount of soft tissue in the nodules was obtained by dividing the weight by the specific gravity. The imaging data on the phantom nodules were acquired with the use of a 16-channel multidetector CT scanner. The CT-measured amount of soft tissue of the nodules was calculated as follows: soft tissue amount = volume x (1 + mean attenuation value / 1,000). The relative percentage error (RPE) between the CT-measured amount of the soft tissue and the reference-standard amount of the soft tissue was also measured. The RPEs determined with use of the new method were compared with the RPEs determined with the current volumetric measurement method by the use of the paired t test. RESULTS: The CT-measured amount of soft tissue showed a strong correlation with the reference-standard amount of soft tissue (R(2) = 0.996, p < 0.01). The mean RPE of the CT-measured amount of soft tissue in the nodules was -7.79 +/- 1.88%. The mean RPE of the CT-measured volume was 114.78 +/- 51.02%, which was significantly greater than the RPE of the CT-measured amount of soft tissue (p < 0.01). CONCLUSION: The amount of soft tissue measured by the use of CT reflects the reference-standard amount of soft tissue in the ground-glass opacity nodules much more accurately than does the use of the CT-measured volume

Pulmonary nodular ground-glass opacities in patients with extrapulmonary cancers: what is their clinical significance and how can we determine whether they are malignant or benign lesions?

BACKGROUND: The clinical significance of pulmonary nodular ground-glass opacities (NGGOs) in patients with extrapulmonary cancers is not known, although there is an urgent need for study on this topic. The purpose of this study, therefore, was to investigate the clinical significance of pulmonary NGGOs in these patients, and to develop a computerized scheme to distinguish malignant from benign NGGOs. METHODS: Fifty-nine pathologically proven pulmonary NGGOs in 34 patients with a history of extrapulmonary cancer were studied. We reviewed the CT scan characteristics of NGGOs and the clinical features of these patients. Artificial neural networks (ANNs) were constructed and tested as a classifier distinguishing malignant from benign NGGOs. The performance of ANNs was evaluated with receiver operating characteristic analysis. RESULTS: Twenty-eight patients (82.4%) were determined to have malignancies. Forty NGGOs (67.8%) were diagnosed as malignancies (adenocarcinomas, 24; bronchioloalveolar carcinomas, 16). Among the rest of the NGGOs, 14 were atypical adenomatous hyperplasias, 4 were focal fibrosis, and 1 was an inflammatory nodule. There were no cases of metastasis appearing as NGGOs. Between malignant and benign NGGOs, there were significant differences in lesion size; the presence of internal solid portion; the size and proportion of the internal solid portion; the lesion margin; and the presence of bubble lucency, air bronchogram, or pleural retraction (p < 0.05). Using these characteristics, ANNs showed excellent accuracy (z value, 0.973) in discriminating malignant from benign NGGOs. CONCLUSIONS: Pulmonary NGGOs in patients with extrapulmonary cancers tend to have high malignancy rates and are very often primary lung cancers. ANNs might be a useful tool in distinguishing malignant from benign NGGOs

Complete Genome Sequence of the Metabolically Versatile Plant Growth-Promoting Endophyte Variovorax paradoxus S110

Variovorax paradoxus is a microorganism of special interest due to its diverse metabolic capabilities, including the biodegradation of both biogenic compounds and anthropogenic contaminants. V. paradoxus also engages in mutually beneficial interactions with both bacteria and plants. The complete genome sequence of V. paradoxus S110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes. Genomic analysis has revealed multiple metabolic features for autotrophic and heterotrophic lifestyles. These metabolic diversities enable independent survival, as well as a symbiotic lifestyle. Consequently, S110 appears to have evolved into a superbly adaptable microorganism that is able to survive in ever-changing environmental conditions. Based on our findings, we suggest V. paradoxus S110 as a potential candidate for agrobiotechnological applications, such as biofertilizer and biopesticide. Because it has many associations with other biota, it is also suited to serve as an additional model system for studies of microbe-plant and microbe-microbe interactions