Summary Visualizations of Gene Ontology Terms With GO-Figure!

The Gene Ontology (GO) is a cornerstone of functional genomics research that drives discoveries through knowledge-informed computational analysis of biological data from large-scale assays. Key to this success is how the GO can be used to support hypotheses or conclusions about the biology or evolution of a study system by identifying annotated functions that are overrepresented in subsets of genes of interest. Graphical visualizations of such GO term enrichment results are critical to aid interpretation and avoid biases by presenting researchers with intuitive visual data summaries. Amongst current visualization tools and resources there is a lack of standalone open-source software solutions that facilitate explorations of key features of multiple lists of GO terms. To address this we developed GO-Figure!, an open-source Python software for producing user-customisable semantic similarity scatterplots of redundancy-reduced GO term lists. The lists are simplified by grouping together terms with similar functions using their quantified information contents and semantic similarities, with user-control over grouping thresholds. Representatives are then selected for plotting in two-dimensional semantic space where similar terms are placed closer to each other on the scatterplot, with an array of user-customisable graphical attributes. GO-Figure! offers a simple solution for command-line plotting of informative summary visualizations of lists of GO terms, designed to support exploratory data analyses and dataset comparisons

Treatment options in extra-articular distal radius fractures:a systematic review and meta-analysis

PURPOSE: This systematic literature review aimed to make a detailed overview on the clinical and functional outcomes and to get insight into the possible superiority of a treatment method for extra-articular distal radius fractures. METHODS: Embase, Medline, Cochrane Library, Web of Science, and Google Scholar were searched for studies describing treatment results. Five treatment modalities were compared: plaster cast immobilization, K-wire fixation, volar plating, external fixation, and intramedullary fixation. RESULTS: Out of 7,054 screened studies, 109 were included in the analysis. Overall complication rate ranged from 9% after plaster cast treatment to 18.5% after K-wire fixation. For radiographic outcomes, only volar tilt in the plaster cast group was lower than in the other groups. Apart from better grip strength after volar plating, no clear functional differences were found across treatment groups. CONCLUSION: Current literature does not provide uniform evidence to prove superiority of a particular treatment method when looking at complications, re-interventions, and long-term functional outcomes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00068-021-01679-z

Green genes: bioinformatics and systems-biology innovations drive algal biotechnology.

Many species of microalgae produce hydrocarbons, polysaccharides, and other valuable products in significant amounts. However, large-scale production of algal products is not yet competitive against non-renewable alternatives from fossil fuel. Metabolic engineering approaches will help to improve productivity, but the exact metabolic pathways and the identities of the majority of the genes involved remain unknown. Recent advances in bioinformatics and systems-biology modeling coupled with increasing numbers of algal genome-sequencing projects are providing the means to address this. A multidisciplinary integration of methods will provide synergy for a systems-level understanding of microalgae, and thereby accelerate the improvement of industrially valuable strains. In this review we highlight recent advances and challenges to microalgal research and discuss future potential.We acknowledge support from the EU FP7 project SPLASH (Sustainable PoLymers from Algae Sugars and Hydrocarbons), grant agreement number 311956.This is the accepted manuscript. The final version is available from Cell/Elsevier at http://www.sciencedirect.com/science/article/pii/S016777991400196

PURA syndrome : clinical delineation and genotype-phenotype study in 32 individuals with review of published literature

Background De novo mutations in PURA have recently been described to cause PURA syndrome, a neurodevelopmental disorder characterised by severe intellectual disability (ID), epilepsy, feeding difficulties and neonatal hypotonia. Objectives T o delineate the clinical spectrum of PURA syndrome and study genotype-phenotype correlations. Methods Diagnostic or research-based exome or Sanger sequencing was performed in individuals with ID. We systematically collected clinical and mutation data on newly ascertained PURA syndrome individuals, evaluated data of previously reported individuals and performed a computational analysis of photographs. We classified mutations based on predicted effect using 3D in silico models of crystal structures of Drosophila-derived Pur-alpha homologues. Finally, we explored genotypephenotype correlations by analysis of both recurrent mutations as well as mutation classes. Results We report mutations in PURA (purine-rich element binding protein A) in 32 individuals, the largest cohort described so far. Evaluation of clinical data, including 22 previously published cases, revealed that all have moderate to severe ID and neonatal-onset symptoms, including hypotonia (96%), respiratory problems (57%), feeding difficulties (77%), exaggerated startle response (44%), hypersomnolence (66%) and hypothermia (35%). Epilepsy (54%) and gastrointestinal (69%), ophthalmological (51%) and endocrine problems (42%) were observed frequently. Computational analysis of facial photographs showed subtle facial dysmorphism. No strong genotype-phenotype correlation was identified by subgrouping mutations into functional classes. Conclusion We delineate the clinical spectrum of PURA syndrome with the identification of 32 additional individuals. The identification of one individual through targeted Sanger sequencing points towards the clinical recognisability of the syndrome. Genotype-phenotype analysis showed no significant correlation between mutation classes and disease severity.Peer reviewe

RNA sequencing of Cutaneotrichosporon curvatum ATCC 20509 in two conditions. C/N of 2.8 and 28

RNA sequencing data used in: Genome-scale metabolic modelling underscores the potential of Cutaneotrichosporon curvatum ATCC 20509 as cell factories for biofuels production

RNA sequencing of Cutaneotrichosporon curvatum ATCC 20509 in two conditions. C/N of 2.8 and 28

RNA sequencing data used in: Genome-scale metabolic modelling underscores the potential of Cutaneotrichosporon curvatum ATCC 20509 as cell factories for biofuels production