Detecting laterally transferred genes: use of entropic clustering methods and genome position

Most parametric methods for detecting foreign genes in bacterial genomes use a scoring function that measures the atypicality of a gene with respect to the bulk of the genome. Genes whose features are sufficiently atypical—lying beyond a threshold value—are deemed foreign. Yet these methods fail when the range of features of donor genomes overlaps with that of the recipient genome, leading to misclassification of foreign and native genes; existing parametric methods choose threshold parameters to balance these error rates. To circumvent this problem, we have developed a two-pronged approach to minimize the misclassification of genes. First, beyond classifying genes as merely atypical, a gene clustering method based on Jensen–Shannon entropic divergence identifies classes of foreign genes that are also similar to each other. Second, genome position is used to reassign genes among classes whose composition features overlap. This process minimizes the misclassification of either native or foreign genes that are weakly atypical. The performance of this approach was assessed using artificial chimeric genomes and then applied to the well-characterized Escherichia coli K12 genome. Not only were foreign genes identified with a high degree of accuracy, but genes originating from the same donor organism were effectively grouped

The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.This work was funded by a grant from the CSIRO Transformational Biology Capability Platform to Adnane Nemri. Claire Anderson was supported by an ARC Discovery Grant (DP120104044) awarded to David A. Jones and Peter N. Dodds

Utilization trends of pedicle subtraction osteotomies compared to posterior spinal fusion for deformity: A national database analysis between 2008–2011

BACKGROUND: Increased awareness regarding the importance of the sagittal spinal profile has led to more aggressive correction of sagittal malalignment. The utilization trends of pedicle subtraction osteotomy (PSO) for sagittal plane correction in spinal deformity surgery have not been well characterized. METHODS: A commercially available database (PearlDiver, Inc) was queried for both Private Payor and 5 % Medicare claims from 2008 to 2011. Revision and clarification of the coding guidelines for PSO were introduced in 2008. Patients who had a thoracic and/or lumbar PSO were identified using CPT codes (22206-22208). In order to appropriately interpret trends in PSO use, three comparison groups were identified. Patients who had a diagnosis of adult spine deformity were identified using ICD-9 codes. Patients who had fusion for spine deformity or posterior spine fusion were identified using CPT codes. Differences in annual utilization and demographics between these four groups were then compared. RESULTS: From the Private Payor database, 199 PSOs were identified with the number of PSOs increasing from 33 in 2008, to 61 in 2011, representing a 185 % increase. From the Medicare data, 102 PSOs were identified, increasing from 13 in 2008 to 32 in 2011, a 246 % increase. In contrast, from both databases, there was minimal to no increase in the incidence of adult spine deformity, fusion for spine deformity or posterior spine fusion over the study time interval. CONCLUSION: Over the study time interval, there was up to a 3.2-fold increase in the utilization of PSOs while the diagnosis of adult spine deformity, fusion for spine deformity and posterior spine fusions had minimal to no increase

Hydrophilic polymer embolism identified in brain tumor specimens following Wada testing: A report of 2 cases

Hydrophilic polymers are commonly used as coatings on intravascular medical devices. As intravascular pro-cedures continue to increase in frequency, the risk of embolization of this material throughout the body has become evident. These emboli may be discovered incidentally but can result in serious complications includ-ing death. Here, we report the first two cases of hydrophilic polymer embolism (HPE) identified on brain tu-mor resection following Wada testing. One patient experienced multifocal vascular complications and diffuse cerebral edema, while the other had an uneventful postoperative course. Wada testing is frequently per-formed during preoperative planning prior to epilepsy surgery or the resection of tumors in eloquent brain regions. These cases demonstrate the need for increased recognition of this histologic finding to enable fur-ther correlation with clinical outcomes

Dorsal turning of motor corticospinal axons at the pyramidal decussation requires plexin signaling

<p>Abstract</p> <p>Background</p> <p>The development of the corticospinal tract (CST) in higher vertebrates relies on a series of axon guidance decisions along its long projection pathway. Several guidance molecules are known to be involved at various decision points to regulate the projection of CST axons. However, previous analyses of the CST guidance defects in mutant mice lacking these molecules have suggested that there are other molecules involved in CST axon guidance that are yet to be identified. In this study, we investigate the role of plexin signaling in the guidance of motor CST axons <it>in vivo</it>.</p> <p>Results</p> <p>Expression pattern studies show that <it>plexin-A3</it>, <it>plexin-A4</it>, and <it>neuropilin-1 </it>are expressed in the developing cerebral cortex when the motor CST axons originating from layer V cortical neurons are guided down to the spinal cord. By analyzing mutant mice, we show that motor CST axons that turn dorsally to cross the midline at the pyramidal decussation require plexin-A3 and plexin-A4 signaling. Although other CST guidance defects are found in neuropilin-1 mutants, this dorsal turning defect is not observed in either neuropilin-1 or neuropilin-2 mutants, suggesting that the local cues that activate plexin signaling at the dorsal turning point are membrane-bound semaphorins. Further expression pattern study and mutant analysis indicate that Sema6A is one of the local cues for motor CST axon turning at the pyramidal decussation.</p> <p>Conclusion</p> <p>Dorsal turning and midline crossing at the pyramidal decussation is a crucial step to properly direct CST axons into the dorsal spinal cord. We show that the signaling of plexin-A3, plexin-A4, and Sema6A is at least partially required for dorsal turning of the CST axons, while neuropilin-1 is required for proper fasciculation of the tract at midline crossing. Together with previous reports, these results demonstrate that several guidance cues are specifically utilized to regulate the dorsal turning and midline crossing of developing CST axons.</p

Activation mapping in patients with coronary artery disease with multiple ventricular tachycardia configurations: Occurrence and therapeutic implications of widely separate apparent sites of origin

Catheter or intraoperative activation mapping studies, or both, were performed in 17 patients with coronary artery disease with two to four distinct configurations of ventricular tachycardia, resistant to a mean of 12.1 ± 6.0 antiarrhythmic drug trials per patient. Mapping studies were performed to guide anticipated surgical ablation of arrhythmias. Activation map data were adequate to determine sites of origin of 30 (64%) of 47 observed tachycardia configurations. These 30 ventricular tachycardias (26 observed clinically) were mapped to 22 separate endocardial sites of origin. Sites of origin of distinct tachycardias were identical or closely adjacent (within 3 cm) in six patients and widely separate (≥4 cm) in eight patients (47% of the group). Activation maps were not adequate to determine sites of origin of 17 (36%) of the 47 tachycardias, including all configurations in three patients.Fifteen patients underwent surgery for control of ventricular tachycardia: aggressive, map-guided endocardial resection (mean 26.5 ± 14.2 cm2) in 12 patients with identified sites of tachycardia origin and extensive resection of visible endocardial scar (2 patients) or encircling endocardial ventriculotomy (1 patient) in those in whom the sites of origin of all clinical tachycardias remained undetermined. Two inoperable patients were treated with amiodarone. During postoperative electrophysiologic tests (11 of 13 surgical survivors), ventricular tachyarrhythmias were initially uninducible in only 4 of 11 patients. However, in two patients only nonclinical arrhythmias (ventricular flutter) were induced. Six (21%) of 29 clinical tachycardias whose sites of origin were either not determined or not resected (right septum or papillary muscle) remained inducible in five patients. Using previously ineffective antiarrhythmic drugs, initially inducible arrhythmias became uninducible (two patients), or harder to induce than preoperatively (five patients). As a result of surgical resections alone or in combination with previously ineffective drugs (and amiodarone in two inoperable patients), there were no recurrences of ventricular tachycardia in 14 (93%) of 15 patients discharged during 19.0 ± 14.3 months of follow-up study.Thus, activation mapping may commonly reveal separate apparent sites of origin for clinically observed, morphologically distinct, highly drug-refractory ventricular tachycardias in patients with coronary artery disease with multiple tachycardia configurations. Extensive surgical resection of identified sites of origin may be required to ablate arrhythmias in these patients. Tachycardias whose sites of origin are not identified or resected may remain inducible. However, aggressive surgical excisions may alter regions involved in the genesis or maintenance of these arrhythmias because they become more difficult to induce postoperatively, more amenable to drug therapy and do not recur