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Although a major effect of bisphosphonates on bone is inhibition of resorption resulting from their ability to interfere with osteoclast function, these agents also prevent osteoblast and osteocyte apoptosis in vitro and in vivo. However, the contribution of the latter property to the overall beneficial effects of the drugs on bone remains unknown. We compared herein the action on glucocorticoid-induced bone disease of the classical bisphosphonate alendronate with that of IG9402, a bisphosphonate analog that preserves osteoblast and osteocyte viability but does not induce osteoclast apoptosis in vitro. The bisphosphonates were injected daily (2.3mumol/kg) to 5-month-old Swiss Webster mice (6-11 per group), starting three days prior to implantation of pellets releasing the glucocorticoid prednisolone (2.1mg/kg/d). IG9402 did not affect levels of circulating C-telopeptide or osteocalcin, markers of resorption and formation, respectively, nor did it decrease mRNA levels of osteocalcin or collagen1A1 in bone. On the other hand, alendronate decreased all these parameters. Moreover, IG9402 did not reduce cancellous mineralizing surface, mineral apposition rate or bone formation rate, whereas alendronate induced a decrease in each of these bone formation measures. These findings demonstrate that in contrast to alendronate, IG9402 does not inhibit bone turnover. Both alendronate and IG9402, on the other hand, activated survival kinase signaling in vivo, as evidenced by induction of ERK phosphorylation in bone. Furthermore, both bisphosphonates prevented the increase in osteoblast and osteocyte apoptosis as well as the decrease in vertebral bone mass and strength induced by glucocorticoids. We conclude that a bisphosphonate that does not affect osteoclasts prevents osteoblast and osteocyte apoptosis and the loss of bone strength induced by glucocorticoids in mice.

MOTIVATION: The rapidly increasing set of sequenced genomes high-lights the importance of identifying the synteny blocks in multiple and/or highly duplicated genomes. Most synteny block reconstruction algorithms use genes shared over all genomes to construct the synteny blocks for multiple genomes. However, the number of genes shared among all genomes quickly decreases with the increase in the number of genomes. RESULTS: We propose the DRIMM-Synteny algorithm to address this bottleneck and apply it to analyzing genomic architectures of yeast, plant, and mammalian genomes. We further combine synteny block generation with rearrangement analysis to reconstruct the ancestral pre-duplicated yeast genome. CONTACT: kspham@cs.ucsd.edu.

The molecular chaperone heat shock protein 90 (Hsp90) is an important and abundant protein in eukaryotic cells, essential for the activation of a large set of signal transduction and regulatory proteins. During the functional cycle, the Hsp90 dimer performs large conformational rearrangements. The transient N-terminal dimerization of Hsp90 has been extensively investigated, under the assumption that the C-terminal interface is stably dimerized. Using a fluorescence-based single molecule assay and Hsp90 dimers caged in lipid vesicles, we were able to separately observe and kinetically analyze N- and C-terminal dimerizations. Surprisingly, the C-terminal dimer opens and closes with fast kinetics. The occupancy of the unexpected C-terminal open conformation can be modulated by nucleotides bound to the N-terminal domain and by N-terminal deletion mutations, clearly showing a communication between the two terminal domains. Moreover our findings suggest that the C- and N-terminal dimerizations are anticorrelated. This changes our view on the conformational cycle of Hsp90 and shows the interaction of two dimerization domains.

Aberrant promoter DNA-hypermethylation and repressive chromatin constitutes a frequent mechanism of gene inactivation in cancer. There is a great need to dissect the mechanisms underlying this abnormal silencing. Studies have shown changes in nuclear organization of chromatin in tumor cells as well as association of aberrant methylation with long range silencing of neighboring genes. Further, certain tumors show a high incidence of promoter methylation termed as the CpG island methylator phenotype (CIMP). Here we have analyzed the role of nuclear chromatin architecture for genes in hypermethylated inactive versus non-methylated active states and its relation with long range silencing and CIMP. Using combined immunostaining for active/repressive chromatin marks and FISH in colorectal cancer cell lines we show that aberrant silencing of these genes occurs without requirement for their being positioned at heterochromatic domains. Importantly, hypermethylation, even when associated with long-range epigenetic silencing of neighboring genes, occurs independent of their euchromatic or heterochromatic location. The data indicate that, in cancer, extensive changes around promoter chromatin of individual genes, or gene clusters, can potentially occur locally without preference for nuclear position and/or causing repositioning. These findings have important implications for understanding relationships between nuclear organization and gene expression patterns in cancer.

The immunity-related GTPases (IRG proteins) are one of the strongest early resistance systems against intracellular pathogens. The IRG gene family contains 21 copies arranged as tandem gene clusters on two chromosomes in the C57BL/6 mouse genome but has been reduced to only two copies in humans: IRGC and IRGM. IRGC is not involved in immunity, but the human IRGM gene plays a role in autophagy-targeted destruction of Mycobacterium tuberculosis (BCG) and Salmonella typhimurium. Variant IRGM haplotypes have been associated with increased risk for Crohn's disease and correlated with differential expression of IRGM transcripts. This article reviews in detail the studies performed on human samples, in vitro, and in sequence analyses that provide evidence for the unusual evolutionary history of the IRGM locus and the important role of the IRGM gene in autophagy and Crohn's disease in response to pathogenesis.

Abstract Due to improved outcome after surgery for congenital heart defects, children, adolescents, and grown-ups with congenital heart defects become an increasing population. In order to evaluate operative risk and early outcome after mechanical aortic valve replacement (AVR) in this population, we reviewed patients who underwent previous repair of congenital heart defects. Between July 2002 and November 2008, 15 (10 male and 5 female) consecutive patients (mean age 14.5 +/- 10.5 years) underwent mechanical AVR. Hemodynamic indications for AVR were aortic stenosis in four (27%), aortic insufficiency in eight (53%), and mixed disease in three (20%) after previous repair of congenital heart defects. All patients had undergone one or more previous cardiovascular operations due to any congenital heart disease. Concomitant cardiac procedures were performed in all of them. In addition to AVR, in two patients, a mitral valve exchange was performed. One patient received a right ventricle-pulmonary artery conduit replacement as concomitant procedure. The mean size of implanted valves was 23 mm (range 17-29 mm). There were neither early deaths nor late mortality until December 2008. Reoperations were necessary in five (33%) and included implantation of a permanent pacemaker due to complete atrioventricular block in two (15%), mitral valve replacement with a mechanical prosthesis due to moderate to severe mitral regurgitation in one (7%), aortocoronary bypass grafting due to stenosis of a coronary artery in one (7%), and in one (7%), a redo subaortic stenosis resection was performed because of a secondary subaortic stenosis. At the latest clinical evaluation, all patients were in good clinical condition without a pathological increased gradient across the aortic valve prosthesis or paravalvular leakage in echocardiography. Mechanical AVR has excellent results in patients after previous repair of congenital heart defects in childhood, even in combination with complex concomitant procedures. Previous operations do not significantly affect postoperative outcome.