Project description:Twelve inshore and six offshore colonies were reciprocally transplanted during 1 year (July 2017- July 2018) at Florida Keys (location). After this period samples were collected from the field and brought to the Experimental Reef Laboratory facilities (RSMAS, Miami) to be acclimated to 30C during 7 days in six aquaria. Three aquaria were keep under initial conditions for the duration of the experiment (30C) and three aquaria had the temperature increased everyday during 7 days to a final temperature of 32C. A total of 56 samples were collected for RNAseq after 6 days of the temperature treatment and stored at -80C.
Project description:The pituitary gland is an important endocrine organ that regulates estrus and reproduction in sheep mainly through hormone synthesis and secretion. In present study, Small-tailed Han sheep (high-reproduction group, HP group), and Wadi sheep (lower-reproduction group, LP group), were used as the experiment materials, and the differential expressed genes (DEGs) were scanned and mined by Oxford Nanopore Technologies (ONT) in pituitary. A total of 7123 DEGs were found, including 3551 genes that were upregulated and 3572 genes that were downregulated in HP group. Go and KEGG related to pituitary function and reproduction were enriched, including reproductive processes, responses to stimuli, and synapses. mTOR signaling pathway, PI3K-Akt signaling pathway, cAMP signaling pathway, ERK1/2 signaling pathways and MAPK signaling pathways. The DEGs detected in this study were involved in the development of tissues and organs and the secretion of hormones in the endocrine system. These findings suggest that these genes might be related to growth, development and the reproduction regulation in sheep, which could provide a scientific basis for elucidating the genetic mechanisms of high reproduction in sheep.
Project description:Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking. We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells. Our findings revealed that blood contamination in the KM samples reduced read quality and altered methylation patterns. Compared with whole-genome bisulfite sequencing (WGBS), the ONT-based methylation profiling can cover more CpG sites (92.4% vs 70%-80%), and exhibit less GC bias with more even genomic coverage. And the ONT methylation calling results showed a high correlation with WGBS results when using shared sites. This study establishes a comprehensive methylation profile for zebrafish KM, paving the way for further investigations into epigenetic regulation and the development of targeted therapies for hematopoietic disorders.
Project description:Higher-order chromatin structure arises from the combinatorial physical interactions of many genomic loci. To investigate this aspect of genome architecture we developed Pore-C, which couples chromatin conformation capture with Oxford Nanopore Technologies (ONT) long reads to directly sequence multi-way chromatin contacts without amplification.
Project description:The femoropopliteal artery is the most common site of disease in patients with peripheral arterial disease and presents some of the greatest challenges for interventional radiology. Many patients can be managed with medical treatment combined with supervised exercise alone. However, a significant proportion, especially those suffering from severe intermittent claudication or critical limb ischemia, will require some form of endovascular or surgical revascularization procedure. During the past few years an endovascular-first approach has gained support from all vascular specialties. Today, even complex lesions can be treated successfully with an endovascular approach. Unfortunately, the unique bio-mechanical properties of this vascular segment have limited long-term patency rates and clinical value of the endovascular options. In this review, the authors discuss the methods and techniques for treatment of femoropopliteal lesions and review the current evidence for commercially available devices on patency outcomes following successful recanalization.
Project description:The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it. The device has a low capital cost, is by far the most portable DNA sequencer available, and can produce data in real-time. It has numerous prospective applications including improving genome sequence assemblies and resolution of repeat-rich regions. Before such a technology is widely adopted, it is important to assess its performance and limitations in respect of throughput and accuracy. In this study we assessed the performance of the MinION by re-sequencing three bacterial genomes, with very different nucleotide compositions ranging from 28.6% to 70.7%; the high G + C strain was underrepresented in the sequencing reads. We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2 kb and 1 kb respectively, while the longest single read was 98 kb. The whole length of a 5 kb rRNA operon was covered by a single read. As the first nanopore-based single molecule sequencer available to researchers, the MinION is an exciting prospect; however, the current error rate limits its ability to compete with existing sequencing technologies, though we do show that MinION sequence reads can enhance contiguity of de novo assembly when used in conjunction with Illumina MiSeq data.
Project description:Pharmacogenomics (PGx) studies the impact of interindividual genomic variation on drug response, allowing the opportunity to tailor the dosing regimen for each patient. Current targeted PGx testing platforms are mainly based on microarray, polymerase chain reaction, or short-read sequencing. Despite demonstrating great value for the identification of single nucleotide variants (SNVs) and insertion/deletions (INDELs), these assays do not permit identification of large structural variants, nor do they allow unambiguous haplotype phasing for star-allele assignment. Here, we used Oxford Nanopore Technologies' adaptive sampling to enrich a panel of 1,036 genes with well-documented PGx relevance extracted from the Pharmacogenomics Knowledge Base (PharmGKB). By evaluating concordance with existing truth sets, we demonstrate accurate variant and star-allele calling for five Genome in a Bottle reference samples. We show that up to three samples can be multiplexed on one PromethION flow cell without a significant drop in variant calling performance, resulting in 99.35% and 99.84% recall and precision for the targeted variants, respectively. This work advances the use of nanopore sequencing in clinical PGx settings.
Project description:Charcot-Marie-Tooth disease type-1A (CMT1A) is one of the most common types of inherited peripheral nerve diseases. It is caused by the trisomy of chromosome 17p12 (c17p12), a large DNA segment of 1.4 Mb containing PMP22 plus eight other genes. The size of c17p12 is formidable for any cloning technique to manipulate, and thus precludes production of models in vitro and in vivo that can precisely recapitulate the genetic alterations in humans with CMT1A. This limitation and other factors have led to several assumptions, which have yet been carefully scrutinized, serving as key principles in our understanding of the disease. For instance, one extra copy of c17p12 in patients with CMT1A results in a higher gene dosage of PMP22, thereby expected to produce a higher level of PMP22 mRNA/proteins that cause the disease. However, there has been increasing evidence that PMP22 levels are highly variable among patients with CMT1A and may fall into the normal range at a given time point. This raises an alternative mechanism causing the disease by dysregulation of PMP22 expression or excessive fluctuation of PMP22 levels, not the absolute increase of PMP22. This has become a pressing issue since recent clinical trials using ascorbic acid failed to alter the clinical outcome of CMT1A patients, leaving no effective therapy for the disease. In this article, we will discuss how this fundamental issue might be investigated. In addition, several other key issues in CMT1A will be discussed, including potential mechanisms responsible for the uniform slowing of conduction velocities. A clear understanding of these issues could radically change how therapies should be developed against CMT1A.