Reproducible presentation of images

2018/19 eLife Ambassadors progra

Characterisation of oskar 3’UTR RNA domainsinvolved in early RNA localisation and translationalrepression

Induction of D.melanogaster germ cell formation depends on local activity of the maternal determinant Oskar at the posterior of the embryo. When Oskar is mis-expressed at the anterior, posterior structures develop ectopically, while absence of Oskar leads to loss of abdominal structures and germ cells. Spatial restriction of Oskar protein is achieved by enriching oskar mRNA in the oocyte, localising it to the posterior pole and by maintaining the mRNA translationally silencing during transport. The 3’UTR of oskar RNA contains elements for its translational repression and is, together with splicing, also required for posterior localisation. Intronless reporters bearing the oskar 3’UTR can also localise, however this is an indirect process involving hitch-hiking of the reporter RNA with endogenous oskar mRNA, to the posterior pole. We have analysed the molecular basis of the hitch-hiking process and tested its potential implication in regulation of endogenous oskar RNA in vivo. In vitro the oskar 3’UTR RNA forms RNA-RNA dimers via a specific RNA dimerisation domain. In vivo, this dimerisation domain is necessary - though not sufficient - for efficient hitch-hiking of 3’UTR-containing reporters with endogenous oskar mRNA to the posterior of the oocyte. In contrast, the dimerisation domain is not essential for oskar mRNA localisation. Surprisingly however, offspring of females expressing oskar RNA mutated in its dimerisation domain display patterning defects suggesting Oskar protein over-expression. Consistent with this, we found that in this oskar mutant the mRNA is prematurely and ectopically translated. This ectopic translation is suppressed when dimerisation is restored by co-expressing an oskar RNA bearing compensatory mutations that in vitro restore RNA dimerisation. My work thus revealed a direct role for RNA-RNA interaction in translational repression of oskar mRNA

Insights on poster preparation practices in life sciences

Posters are intended to spark scientific dialogue and are omnipresent at biological conferences. Guides and how-to articles help life scientists in preparing informative visualizations in poster format. However, posters shown at conferences are at present often overloaded with data and text and lack visual structure. Here, I surveyed life scientists themselves to understand how they are currently preparing posters and which parts they struggle with. Biologist spend on average two entire days preparing one poster, with half of the time devoted to visual design aspects. Most receive no design or software training and also receive little to no feedback when preparing their visualizations. In conclusion, training in visualization principles and tools for poster preparation would likely improve the quality of conference posters. This would also benefit other common visuals such as figures and slides, and improve the science communication of researchers overall

Statistical Evaluation of Different Mathematical Models for Diffusion Weighted Imaging of Prostate Cancer Xenografts in Mice

Purpose To evaluate fitting quality and repeatability of four mathematical models for diffusion weighted imaging (DWI) during tumor progression in mouse xenograft model of prostate cancer.Methods Human prostate cancer cells (PC-3) were implanted subcutaneously in right hind limbs of 11 immunodeficient mice. Tumor growth was followed by weekly DWI examinations using a 7T MR scanner. Additional DWI examination was performed after repositioning following the fourth DWI examination to evaluate short term repeatability. DWI was performed using 15 and 12 b-values in the ranges of 0-500 and 0-2000 s/mm(2), respectively. Corrected Akaike information criteria and F-ratio were used to evaluate fitting quality of each model (mono-exponential, stretched exponential, kurtosis, and bi-exponential).Results Significant changes were observed in DWI data during the tumor growth, indicated by ADC(m), ADC(s), and ADC(k). Similar results were obtained using low as well as high b-values. No marked changes in model preference were present between the weeks 1-4. The parameters of the mono-exponential, stretched exponential, and kurtosis models had smaller confidence interval and coefficient of repeatability values than the parameters of the bi-exponential model.Conclusion Stretched exponential and kurtosis models showed better fit to DWI data than the mono-exponential model and presented with good repeatability.</p

A biologist’s guide to planning and performing quantitative bioimaging experiments

Technological advancements in biology and microscopy have empowered a transition from bioimaging as an observational method to a quantitative one. However, as biologists are adopting quantitative bioimaging and these experiments become more complex, researchers need additional expertise to carry out this work in a rigorous and reproducible manner. This Essay provides a navigational guide for experimental biologists to aid understanding of quantitative bioimaging from sample preparation through to image acquisition, image analysis, and data interpretation. We discuss the interconnectedness of these steps, and for each, we provide general recommendations, key questions to consider, and links to high-quality open-access resources for further learning. This synthesis of information will empower biologists to plan and execute rigorous quantitative bioimaging experiments efficiently

Docetaxel chemotherapy response in PC3 prostate cancer mouse model detected by rotating frame relaxations and water diffusion

MRI is a common method of prostate cancer diagnosis. Several MRI-derived markers, including the apparent diffusion coefficient (ADC) based on diffusion-weighted imaging, have been shown to provide values for prostate cancer detection and characterization. The hypothesis of the study was that docetaxel chemotherapy response could be picked up earlier with rotating frame relaxation times TRAFF2 and TRAFF4 than with the continuous wave T1ρ, adiabatic T1ρ, adiabatic T2ρ, T1, T2 or water ADC. Human PC3 prostate cancer cells expressing a red fluorescent protein were implanted in 21 male mice. Docetaxel chemotherapy was given once a week starting 1 week after cell implantation for 10 randomly selected mice, while the rest served as a control group (n = 11). The MRI consisted of relaxation along a fictitious field (RAFF) in the second (RAFF2) and fourth (RAFF4) rotating frames, T1 and T2, continuous wave T1ρ, adiabatic T1ρ and adiabatic T2ρ relaxation time measurements and water ADC. MRI was conducted at 7 T, once a week up to 4 weeks from cell implantation. The tumor volume was monitored using T2-weighted MRI and optical imaging. The histology was evaluated after the last imaging time point. Significantly reduced RAFFn, T1ρ,T2ρ and conventional relaxation times 4 weeks after tumor implantation were observed in the treated tumors compared with the controls. The clearest short- and long-term responses were obtained with T1, while no clear improvement in response to treatment was detected with novel methods compared with conventional methods or with RAFFn compared with all others. The tumor volume decreased after a two-week time point for the treated group and increased significantly in the control group, which was supported by increasing red fluorescent light emission in the control tumors. Decreased relaxation times were associated with successful chemotherapy outcomes. The results indicate altered relaxation mechanisms compared with higher dose chemotherapies previously published

Community-developed checklists for publishing images and image analysis

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However for scientists wishing to publish the obtained images and image analyses results, there are to date no unified guidelines. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here we present community-developed checklists for preparing light microscopy images and image analysis for publications. These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and for reporting image analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby heighten the quality of microscopy data is in publications.Comment: 28 pages, 8 Figures, 3 Supplmentary Figures, Manuscript, Essential recommendations for publication of microscopy image dat

Dimerization of oskar 3’UTRs promotes hitchhiking for RNA localization in of the Drosophila oocyte

<p>Paper publishes 2011 in RNA.</p

Features and changing localization of mRNAs in Drosophila development

<p>Poster for 2014 "Complex life of mRNA" in Heidelberg. Accompanying biorxiv article: http://dx.doi.org/10.1101/008938 </p