isONform: reference-free transcriptome reconstruction from Oxford Nanopore data.

MOTIVATION: With advances in long-read transcriptome sequencing, we can now fully sequence transcripts, which greatly improves our ability to study transcription processes. A popular long-read transcriptome sequencing technique is Oxford Nanopore Technologies (ONT), which through its cost-effective sequencing and high throughput, has the potential to characterize the transcriptome in a cell. However, due to transcript variability and sequencing errors, long cDNA reads need substantial bioinformatic processing to produce a set of isoform predictions from the reads. Several genome and annotation-based methods exist to produce transcript predictions. However, such methods require high-quality genomes and annotations and are limited by the accuracy of long-read splice aligners. In addition, gene families with high heterogeneity may not be well represented by a reference genome and would benefit from reference-free analysis. Reference-free methods to predict transcripts from ONT, such as RATTLE, exist, but their sensitivity is not comparable to reference-based approaches. RESULTS: We present isONform, a high-sensitivity algorithm to construct isoforms from ONT cDNA sequencing data. The algorithm is based on iterative bubble popping on gene graphs built from fuzzy seeds from the reads. Using simulated, synthetic, and biological ONT cDNA data, we show that isONform has substantially higher sensitivity than RATTLE albeit with some loss in precision. On biological data, we show that isONform's predictions have substantially higher consistency with the annotation-based method StringTie2 compared with RATTLE. We believe isONform can be used both for isoform construction for organisms without well-annotated genomes and as an orthogonal method to verify predictions of reference-based methods. AVAILABILITY AND IMPLEMENTATION: https://github.com/aljpetri/isONform.

Decrease in circulating plasmacytoid dendritic cells during short-term systemic normobaric hypoxia.

BACKGROUND: During exposure to high altitude, the immune system is altered. During hypoxia, an increase in interleukin (IL)-6 and high sensitivity C-reactive protein (hs-CRP), and an increase in natural killer cells and decrease in T cells in blood was shown. However, the impact of hypoxia on dendritic cells has not been investigated yet. MATERIAL AND METHODS: Twelve healthy volunteers were subjected to a transient normobaric hypoxia for 6·5 h simulating an oxygen concentration at 5500 m. During exposure to hypoxia, blood samples were collected and analysed by flow cytometrical cell sorting (FACS) for circulating myeloid (mDCs) and plasmacytoid (pDCs) DCs. Serum levels of IL-6 and tumour necrosis factor (TNF)-α were analysed. In a cell culture hypoxia chamber, blood samples were subjected to the same hypoxia and analysed regarding DCs. RESULTS: Exposure to normobaric hypoxia induced a significant decrease in circulating pDCs about 45% (P = 0·001) but not of mDC compared to baseline normoxia. Furthermore, we observed a significant increase of TNF-α about 340% (P = 0·03) and of IL-6 about 286% (P = 0·002). In cell culture experiments exposure of blood to hypoxia led to no significant changes in DCs, so that a direct cytotoxic effect was excluded. During hypoxia, we observed a transient increase in stromal-derived factor 1 (SDF-1) which is important for pDC tissue recruitment. CONCLUSIONS: We show a significant decrease in circulating pDCs during hypoxia in parallel to a pro-inflammatory response. Further studies are necessary to evaluate whether the decrease in circulating pDCs might be the result of an enhanced tissue recruitment.

Experimental evaluation of the JenaClip transcatheter aortic valve.

OBJECTIVE: Transcatheter techniques of aortic valve replacement are a treatment option for valvular heart disease in high-risk surgical candidates. We evaluated a self-expanding valve system with a novel mechanism of fixation in an experimental setting in an acute animal model and ex vivo in aortic root specimens. METHOD: A self-expanding nitinol stent containing a pericardial tissue valve was implanted in a transapical approach in 15 sheeps. The valve was introduced under fluoroscopic guidance through a 22F sheath by means of a specially designed delivery catheter. Deployment was performed on the beating heart without cardiopulmonary bypass or rapid ventricular pacing and facilitated by positioning feelers anchoring the device to the native aortic cusps. To investigate release and anchoring of the device during retrograde implantation, the stent was also implanted in aortic root specimens obtained from an autopsy series. RESULTS: In animal experiments, stent deployment was primarily successful in 12 (80%) animals. Positioning feelers facilitated implantation by confirming the correct implantation plane of the stent and anchoring to the native aortic cusps. If primary location was not satisfactory the stent was retracted into the catheter and repositioned. After successful implantation no significant changes of hemodynamics were observed. Two animals (13%) developed ventricular fibrillation early in this experimental series due to displacement of one positioning element into a coronary ostium, major regurgitation was observed in two animals. Ex vivo evaluation of the device in aortic root specimens proved feasibility of stent release and leaflet fixation; ex vivo implantation was successful in all cases. CONCLUSION: In this study, we demonstrate feasibility of a leaflet-fixation device in nondiseased aortic valves. The JenaClip provides an effective concept of fixation with positioning feelers that allows exact positioning without outflow obstruction and anchoring the valve to the native leaflets. Further studies are necessary to investigate this concept in diseased aortic valves.