Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data.

Trips-Viz (https://trips.ucc.ie/) is an interactive platform for the analysis and visualization of ribosome profiling (Ribo-Seq) and shotgun RNA sequencing (RNA-seq) data. This includes publicly available and user generated data, hence Trips-Viz can be classified as a database and as a server. As a database it provides access to many processed Ribo-Seq and RNA-seq data aligned to reference transcriptomes which has been expanded considerably since its inception. Here, we focus on the server functionality of Trips-viz which also has been greatly improved. Trips-viz now enables visualisation of proteomics data from a large number of processed mass spectrometry datasets. It can be used to support translation inferred from Ribo-Seq data. Users are now able to upload a custom reference transcriptome as well as data types other than Ribo-Seq/RNA-Seq. Incorporating custom data has been streamlined with RiboGalaxy (https://ribogalaxy.ucc.ie/) integration. The other new functionality is the rapid detection of translated open reading frames (ORFs) through a simple easy to use interface. The analysis of differential expression has been also improved via integration of DESeq2 and Anota2seq in addition to a number of other improvements of existing Trips-viz features

skiniry/Trips-Viz

Trips-viz is a transcriptome browser designed to visualize Ribosome profiling and RNA-seq data at the level of a single gene/transcript isoform as opposed to at the genome level. Trips-viz also provides you the ability to vizualize data from a gene under different conditions, get meta-information at an individual dataset level such as read length distribution or triplet periodicity, and provides the ability to find differentially expressed or translated genes

Clinical Applicability of the Macular Degeneration Detection Device (MDD-2): a Novel Photostress Recovery Measurement Device

Background: Diseases affecting the macula, such as age-related macular degeneration (AMD), diabetic retinopathy and central serous retinopathy can result in impaired photostress recovery time (PSRT) despite normal visual acuity and fundoscopic appearance. The MDD-2 Macular Degeneration Detection Device is a novel flash photostress recovery device. In this study, we examine the repeatability of the MDD-2 in a normal population and its suitability for incorporation into routine clinical practice. Methods: One hundred (60 female) subjects (mean age 35+-8 years; range 18 to 66 years) were recruited to partake in this study. The photostress recovery time was measured using the MDD-2 on three occasions in the dominant eye and one final occasion in the non-dominant eye to assess measurement repeatability. All subjects were in good ocular health. Visual acuity and iris colour were recorded for each participant. Results: Repeated measures analysis of variance revealed a statistically significant learning effect on intra-measurement repeatability (p < 0.01). Although paired t-test analysis revealed statistically significant differences between repeated measures both within and between eyes (p < 0.05 for all) the correlation between repeat measurements is statistically significant (p < 0.05 for all), and the coefficient of repeatability reaches clinically acceptable levels once the initial photostress recovery time, which demonstrated increased variability and latency compared to all subsequent measures, is excluded. Conclusion: The MDD-2 provides highly repeatable measurements of photostress recovery time among young naïve subjects, following verbal explanation of the task and only one ‘practise’ measurement. The measurement is also highly repeatable between eyes, providing a potential immediate clinical biomarker of ocular health

Sensory Consumer and Descriptive Analysis of Steaks from Beef Animals Selected from Tough and Tender Animal Genotypes: Genetic Meat Quality Traits Can Be Detected by Consumers

The objective of the present study was to determine if animals who were genetically divergent in the predicted tenderness of their meat actually produced more tender meat, as well as what the implications were for other organoleptic properties of the meat. The parental average genetic merit for meat tenderness was used to locate 20 “Tough genotype” heifers and 17 “Tender genotype” heifers; M. longissimus thoracis steaks from all heifers were subjected to sensory affective analysis (140 consumers) and sensory profiling using two trained sensory panels. All sample steaks were treated identically regarding pre- and post-mortem handling, storage, cooking and presentation (i.e., randomised, blind coded). For the affective consumer study, eight steaks were sectioned from the same location of the striploin muscles from each of the heifers. In total, 108 steaks from the Tender genotype and 118 from the Tough genotype were tested in the consumer study to determine the preference or liking of these steaks for appearance, aroma, flavour, tenderness, juiciness and overall acceptability. The consumer study found that the Tender genotype scored higher (p &lt; 0.0001) for liking of tenderness, juiciness, flavour and overall acceptability compared to the Tough genotype. Similar results were generally found for the separate consumer age cohorts (18–64 years) with lower sensory acuity in the 65+ age cohort. For the descriptive analysis, the Tender genotype scored numerically more tender, juicy and flavoursome, although the differences were only significant for one of the panels. The critical outcome from this study is that parental average genetic merit can be used to pre-select groups of animals for tenderness, which, in turn, can be detected by consumers