The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this work, we explore a new source of phylogenetic information, the distribution of protein structural domains within fully sequenced prokaryotic genomes. The evolution of the structural domains we use has been studied extensively, allowing us to base our phylogenetic methods on testable theoretical models of structural evolution. We find that the methods that produce reasonable phylogenetic relationships are indeed the methods that are most consistent with theoretical evolutionary models. This work represents, to our knowledge, the first such theoretically motivated phylogeny, as well as the first application of structural information to phylogeny on this scale. Our results have strong implications for the phylogenetic relationships among prokaryotic organisms and for the understanding of protein evolution as a whole.[Supplemental material is available online at www.genome.org and http://paradox.harvard.edu/∼eric/struct_phylo.htm.]Our understanding of the evolution of protein structures has advanced considerably in the past several years (Dokholyan et al. 2002;Koonin et al. 2002;Deeds et al. 2004). This advance has relied, at least in part, on the application of graph theoretic methods to the representation and analysis of structural similarity between protein domains (Dokholyan et al. 2002;Deeds et al. 2003Deeds et al. , 2004. One such application is the Protein Domain Universe Graph (or PDUG), a graph in which a nonredundant set of all known protein structural domains (Holm and Sander 1996; Dietmann and Holm 2001) are represented as nodes, and the structural similarity between domains is used to define edges between them (Dokholyan et al. 2002). The distribution of edges per node in this graph, (known as the degree distribution or p(k)), was shown to follow a power law, i.e., Dokholyan et al. 2002). This degree distribution is markedly different from that of random graphs (Albert and Barabasi 2002) or structural similarity graphs based on complete sets of model polymer structures (Deeds et al. 2003). Graphs with degree distributions similar to that of the PDUG have been produced via evolutionary models that are divergent in nature (Dokholyan et al. 2002;Deeds et al. 2003Deeds et al. , 2004, and these findings have provided further support for a divergent picture of protein structural evolution in the debate between divergent and convergent scenarios of protein structural evolution (Dokholyan et al. 2002;Koonin et al. 2002;Deeds et al. 2003Deeds et al. , 2004.The structural domains used to create the PDUG correspond to families of similar sequences that adopt highly similar structures (Dokholyan et al. 2002). Domains from the PDUG may thus be assigned to the proteomes of an organism based on the prese...

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In contrast to prior retrospective studies, our prospective data suggest that the IL-1 cluster gene variation is not associated with risk of athero-thrombotic disorders.

Positive hip cultures are associated with elevated serum WBC, IVDU, high percentage of synovial fluid PMN leukocytes, and fluid aspirate turbidity. Reaspiration of lavage fluid with either nonbacteriostatic saline or contrast material can yield positive cultures.

IntroductionIn liver stereotactic body radiotherapy, reduction of normal tissue irradiation requires daily image guidance. This is typically accomplished by imaging a surrogate to the tumor. The surrogate is often an implanted metal fiducial marker. There are few reports addressing the specific risks of hepatic fiducial marker implantation. These risks are assumed to be similar to percutaneous liver biopsies which are associated with a 1-4% complication rate - almost always pain or bleeding. To the best of our knowledge, we present the first case of such a fiducial marker migrating to the heart.Case presentationAn 81-year-old Caucasian man (5 years post-gastrectomy for a gastric adenocarcinoma) was referred post-second line palliative chemotherapy for radiotherapy of an isolated liver metastasis. It was decided to proceed with treatment and platinum fiducials were chosen for radiation targeting. Under local anesthesia, three Nester embolization coils (Cook Medical Inc., Bloomington, IN, USA) were implanted under computed tomography guidance. Before the placement of each coil, the location of the tip of the delivery needle was confirmed by computed tomography imaging. During the procedure, the third coil unexpectedly migrated through the hepatic vein to the inferior vena cava and lodged at the junction of the vena cava and the right atrium. The patient remained asymptomatic. He was immediately referred to angiography for extraction of the coil. Using fluoroscopic guidance, an EN Snare Retrieval System (Hatch Medical L.L.C., Snellville, GA, USA) was introduced through a jugular catheter; it successfully grasped the coil and the coil was removed. The patient was kept overnight for observation and no immediate or delayed complications were encountered due to the migration or retrieval of the coil. He subsequently went on to be treated using the remaining fiducials.ConclusionImplanted fiducial markers are increasingly used for stereotactic radiotherapy. There is sparse literature on the risks of such procedures. Although uncommon, the risk of migration does exist and therefore physicians (surgeons, oncologists and radiologists) and patients should be aware of this possibility.