De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome.

BACKGROUND: Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited. RESULTS: A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. CONCLUSIONS: We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.

Preliminary Dual-Center Experience with the Bolton Treovance Endograft.

PURPOSE: To present the performance and safety of the Treovance stent graft for endovascular aortic aneurysm repair in a "real-world" patient cohort. METHODS: Patients from 2 centers, deemed unfit for open repair, were electively treated with the Treovance endograft. Clinical preoperative, operative, and up to 1-year postoperative follow-up data of patients were retrospectively analyzed. RESULTS: This study included 46 patients with abdominal aortic aneurysm (44 male), mean age of 78 years ± 8 standard deviation (SD; range: 58-93 years). All met the manufacturer's recommended anatomical requirements: average maximum sac diameter 63 mm ± 10 SD (range: 52-86 mm), proximal neck length 29 mm ± 12 SD (range: 11-60 mm), and neck angulation 30° ± 21 SD (range: 0°-70°). Fourteen had moderate to severe iliac tortuosity. A primary technical success rate of 80% was achieved (100% assisted primary technical success rate): 7 patients required adjunctive procedures intraoperatively and 2 successful treatments for type I endoleaks, which occurred within 24 hours postoperatively. There was 100% survival at 1-year follow-up; however, 4 (8.7%) patients required reintervention: 1 for a type I endoleak, 2 for limb stenosis, and 1 for a type II endoleak with an enlarging sac. No other device-related complications were identified. Reintervention and complication rates in hostile versus nonhostile anatomies were not statistically significant ( P = .28 and P = .42, respectively). CONCLUSION: The Treovance stent graft has a comparable safety profile to other next-generation stent grafts during the first year after endovascular aneurysm repair, which provides a rationale for further interrogation of its outcomes through clinical trials.

Quantification of Lipid-Rich Core in Carotid Atherosclerosis Using Magnetic Resonance T2 Mapping: Relation to Clinical Presentation.

OBJECTIVES: The aim of this study was to: 1) provide tissue validation of quantitative T2 mapping to measure plaque lipid content; and 2) investigate whether this technique could discern differences in plaque characteristics between symptom-related and non-symptom-related carotid plaques. BACKGROUND: Noninvasive plaque lipid quantification is appealing both for stratification in treatment selection and as a possible predictor of future plaque rupture. However, current cardiovascular magnetic resonance (CMR) methods are insensitive, require a coalesced mass of lipid core, and rely on multicontrast acquisition with contrast media and extensive post-processing. METHODS: Patients scheduled for carotid endarterectomy were recruited for 3-T carotid CMR before surgery. Lipid area was derived from segmented T2 maps and compared directly to plaque lipid defined by histology. RESULTS: Lipid area (%) on T2 mapping and histology showed excellent correlation, both by individual slices (R = 0.85, p < 0.001) and plaque average (R = 0.83, p < 0.001). Lipid area (%) on T2 maps was significantly higher in symptomatic compared with asymptomatic plaques (31.5 ± 3.7% vs. 15.8 ± 3.1%; p = 0.005) despite similar degrees of carotid stenosis and only modest difference in plaque volume (128.0 ± 6.0 mm3 symptomatic vs. 105.6 ± 9.4 mm3 asymptomatic; p = 0.04). Receiver-operating characteristic analysis showed that T2 mapping has a good ability to discriminate between symptomatic and asymptomatic plaques with 67% sensitivity and 91% specificity (area under the curve: 0.79; p = 0.012). CONCLUSIONS: CMR T2 mapping distinguishes different plaque components and accurately quantifies plaque lipid content noninvasively. Compared with asymptomatic plaques, greater lipid content was found in symptomatic plaques despite similar degree of luminal stenosis and only modest difference in plaque volumes. This new technique may find a role in determining optimum treatment (e.g., providing an indication for intensive lipid lowering or by informing decisions of stents vs. surgery).

Clostridium septicum sepsis and its implications.

An elderly gentleman, who had 12 years earlier been successfully treated for colon cancer, presented with fever, rigours, right upper quadrant abdominal pain and tenderness. A CT of the abdomen revealed a colonic mass distal to the hepatic flexure with multiple gas locules and a walled off perforation. He underwent a right hemicolectomy. Histology confirmed multifocal colonic adenocarcinoma. His admission blood cultures grew Clostridium septicum. A week postoperatively he developed intermittent fevers and abdominal pain. Repeat CT revealed an abdominal collection adjacent to the new anastomosis, but more importantly, a sharply shouldered aneurysmal dilation of the infra-renal abdominal aorta. These findings prompted immediate surgical drainage of the collection, repair of the anastomostic leak, resection of the infected aortic aneurysm and replacement with a tube graft. This case highlights the clinical significance of C septicum bacteraemia: its association with occult colonic malignancy and with mycotic aneurysm formation. Clostridia isolated from blood cultures should not be dismissed as contaminants but fully identified to ensure appropriate patient management.

The use of oral tacrolimus in a case of short bowel syndrome.

Achieving adequate oral immunosuppression in a renal transplant patient who develops short bowel syndrome provides a significant challenge. We report a case where oral tacrolimus has been used to provide immunosuppression in an established renal transplant patient who developed short bowel syndrome secondary to mesenteric infarction. After reviewing the literature, we conclude that tacrolimus can be used as first-line immunosuppression in patients with short bowel syndrome.