The Center for Reproducible Science at the University of Zurich

The history of the Center for Reproducible Science at the University of Zurich

Morphological reflectors and molecular predictors of preimplantation developmental competence in bovine oocytes and embryos

The efficiency of in vitro production (IVP) of bovine embryos still remains low, reaching blastocyst rates between 25 and 35 %. Accordingly, the necessity to define reliable predictors for developmental competence is indispensible. Up to now most morphological and molecular markers are subjective and partly invasive and thus relatively inaccurately. Therefore, the aim of the first experiment of the present approach was to evaluate the effect of structural changes in zona pellucidas’ (ZP) morphology during in maturation on developmental competence using polarized light microscopy. Structural changes in terms of number and size of pores were displayed by the Scanning electron microscopy and determined quantitatively in zona pellucida birefringence (ZPB). Immature oocytes classified as high presumble quality oocytes exhibited highest values for birefringence, and in vivo matured oocytes showed the lowest values for birefringence compared to their in vitro matured counterparts. These results implicate, that decreasing values for ZPB during maturation are typical for high developmental competence. In the second study of the present thesis, the transcriptome profile of one blastomere of a bovine 2-cell stage embryo was directly correlated with the developmental potential of the corresponding sister blastomere. Analyses using microarray technology revealed specific molecular fingerprints for blastomeres whose sister blastomere developed to the blastocyst stage in contrast to those blastomeres whose sister blastomeres stopped cleaving after separation or were blocked before embryonic genome activation (EGA). Pathway analyses uncovered, that differentially regulated genes (DEG) were mostly involved in oxidative phosphorilation, oxidative stress response and antioxidant activity. Five candidate genes, namely, NDUFS1, MAPK14, CAT, PRDX1 and PRDX6, which are known to act as either direct or indirect scavengers of reactive oxygen species (ROS), were selected and their expression levels were further characterized using two independent models for developmental competence. Furthermore, ROS staining revealed high ROS accumulations in late cleaved or rather developmentally incompetent 2-cell stage embryos, compared to low ROS levels in early cleaved and therefore presumable highly competent 2-cell stage embryos. Taken together, noninvasive morphological criteria predicting subsequent developmental competence of matured bovine oocytes were identified in this work. Moreover, a direct correlation between molecular mechanisms and the individual developmental competence, which was found to be already determined in the 2-cell stage, could be detected.Untersuchungen boviner Eizellen und Embryonen auf morphologischer und molekularer Ebene zur Identifizierung von entwicklungsrelevanten Markern In Anbetracht der relativ geringen Effizienz der in vitro Produktion (IVP) boviner Embryonen mit Blastozystenraten von 25 bis 35 %, ist es unverzichtbar, zuverlässige Prädiktoren für das Entwicklungspotential von Eizellen und Embryonen zu definieren. Bis heute sind die meisten morphologischen und molekularen Qualitätsparameter subjektiv und von invasiver Natur. Daher war es das Ziel in der ersten Studie der vorliegenden Arbeit, strukturelle Veränderungen in der Zona pellucida (ZP) während der in vitro Maturation (IVM) mit Hilfe der Polarisationslichtmikroskopie quantitativ zu erfassen und mit dem Entwicklungspotential zu korrelieren. Strukturelle Änderungen bezogen auf Anzahl und Größe der Poren in der ZP zeigten sich bei der Analyse mittels eines Rasterelektronenmikroskops und spiegelten sich in der Doppellichtbrechungsintensität der Zona pellucida (ZPB) quantitativ wieder. Immature Eizellen, die als qualitativ sehr gut eingestuft wurden, zeigten die höchsten Werte für die ZPB, wohingegen die in vivo maturierten Eizellen im Vergleich zu den in vitro maturierten die niedrigsten Werte aufwiesen. Diese Ergebnisse implizieren, dass abnehmende Werte für die ZPB während der Maturation als Pärdiktor für hohe Eizellqualität genutzt werden können. Zusammenfassend konnte gezeigt werden, dass die Polarisationslichtmikroskopie als nicht invasisver Prädiktor für das Entwicklungspotential genutzt werden kann. In der zweiten Studie der vorliegenden Arbeit wurde eine direkte Korrelation zwischen dem Transkriptionsprofil einer Blastomere eines bovinen Zweizellers zum Entwicklungspotential der korrespondierenden Schwesterblastomere hergestellt. Beim Vergleich mittels Mikroarraytechnologie wurden spezifische molekulare Fingerabdrücke für Blastomeren ermittelt, deren Schwesterblastomeren sich zur Blastozyste entwickelten im Gegensatz zu denen, deren Schwesterblastomeren sich nicht weiter teilten oder vor der embryonalen Genomaktivierung (EGA) geblockt wurden. Nach Analyse der durch die differentiell regulierten Transkripte betroffenen Stoffwechselwege zeigte sich, dass diese Gene hauptsächlich in oxidative Phosphorilierung, oxidative Stressantwort und antioxidative Aktivität involviert waren. Die Expremierung der daraus selektierten Kandidatengene NDUFS1, MAPK14, CAT, PRDX1 und PRDX6, deren direkte und indirekte Funktionen bei der Eliminierung von freien Radikalen bekannt ist, wurde an Hand von zwei unabhängigen Kompetenzmodellen weiter charakterisiert. Des Weiteren zeigte Färbung, dass spät geteilte Zweizeller mit einem geringeren Entwicklungspotential sehr hohe Anreicherungen an freien Radikalen aufwiesen im Gegensatz zu früh geteilten Zweizellern mit einem hohen Entwicklungspotential, die nur niedrige Anreicherungen zeigten. Schlussfolgernd konnte gezeigt werden, dass spezifische molekulare Mechanismen direkt mit dem Entwicklungspotential korrelieren und es bereits im Zweizeller determinieren

Using an expert survey and user feedback to construct PRECHECK: A checklist to evaluate preprints on COVID-19 and beyond

Background: The quality of COVID-19 preprints should be considered with great care, as their contents can influence public policy. Efforts to improve preprint quality have mostly focused on introducing quick peer review, but surprisingly little has been done to calibrate the public’s evaluation of preprints and their contents. Purpose: The PRECHECK project aimed to generate a tool to teach and guide scientifically literate non-experts to critically evaluate preprints, on COVID-19 and beyond. Methods: To create a checklist, we applied a 4-step procedure consisting of an initial internal review, an external review by a pool of experts (methodologists, meta-researchers/experts on preprints, journal editors, and science journalists), a final internal review, and an implementation stage. For the external review step, experts rated the relevance of each element of the checklist on five-point Likert scales, and provided written feedback. After each internal review round, we applied the checklist on a set of high-quality preprints from an online list of milestone research works on COVID-19 and low-quality preprints, which were eventually retracted, to verify whether the checklist can discriminate between the two categories. Results: At the external review step, 26 of the 54 contacted experts responded. The final checklist contained 4 elements (Research question, Study type, Transparency and integrity, and Limitations), with ‘superficial’ and ‘deep’ levels for evaluation. When using both levels of evaluation, the checklist was effective at discriminating high- from low-quality preprints. Its usability was confirmed in workshops with our target audience: Bachelors students in Psychology and Medicine, and science journalists. Conclusions: We created a simple, easy-to-use tool for helping scientifically literate non-experts navigate preprints with a critical mind. We believe that our checklist has great potential to help guide decisions about the quality of preprints on COVID-19 in our target audience and that this extends beyond COVID-19

The influence of comorbidities on the treatment outcome in symptomatic lumbar spinal stenosis: A systematic review and meta-analysis

Background Lumbar spinal stenosis (LSS) affects mainly elderly patients. To this day, it is unclear whether comorbidities influence treatment success. The aim of this systematic review and meta-analysis was to assess the impact of comorbidities on the treatment effectiveness in symptomatic LSS. Methods We conducted a systematic review and meta-analysis and reviewed prospective or retrospective studies from Medline, Embase, Cochrane Library and CINAHL from inception to May 2020, including adult patients with LSS undergoing surgical or conservative treatment. Main outcomes were satisfaction, functional and symptoms improvement, and adverse events (AE). Proportions of outcomes within two subgroups of a comorbidity were compared with risk ratio (RR) as summary measure. Availability of ≥3 studies for the same subgroup and outcome was required for meta-analysis. Results Of 72 publications, 51 studies, mostly assessing surgery, there was no evidence reported that patients with comorbidities were less satisfied compared to patients without comorbidities (RR 1.06, 95% confidence interval (CI) 0.77 to 1.45, 94%), but they had an increased risk for AE (RR 1.46, 95% CI 1.06 to 2.01, 72%). A limited number of studies found no influence of comorbidities on functional and symptoms improvement. Older age did not affect satisfaction, symptoms and functional improvement, and AE (age >80 years RR 1.22, 95% CI 0.98 to 1.52, 60%). Diabetes was associated with more AE (RR 1.72, 95% CI 1.19 to 2.47, 58%). Conclusion In patients with LSS and comorbidities (in particular diabetes), a higher risk for AE should be considered in the treatment decision. Older age alone was not associated with an increased risk for AE, less functional and symptoms improvement, and less treatment satisfaction

Changes in Stroke Rehabilitation during the Sars-Cov-2 Shutdown in Switzerland

INTRODUCTION: Many stroke survivors require continuous outpatient rehabilitation therapy to maintain or improve their neurological functioning, independ-ence, and quality of life. In Switzerland and many other countries, the shutdown to contain SARS-CoV-2 infections led to mobility restrictions and a decrease in therapy delivery. This study investigated the impact of the COVID-19 shutdown on stroke survivors' access to therapy, physical activity, functioning and mood. METHODS: A prospective observational cohort study in stroke subjects. At 4 time-points (before, during, after the shutdown, and at 3-month follow-up), the amount of therapy, physical activities, motor func-tion, anxiety, and depression were assessed. RESULTS: Thirty-six community-dwelling stroke subjects (median 70 years of age, 10 months post--stroke) were enrolled. Therapy reductions related to the shutdown were reported in 72% of subjects. This decrease was associated with significantly extended sedentary time and minimal deterioration in physical activity during the shutdown. Both parameters improved between reopening and 3-month follow-up. Depressive symptoms increased slightly during the observation period. Patients more frequently report-ed on self-directed training during shutdown. CONCLUSION: The COVID-19 shutdown had measurable immediate, but no persistent, effects on post--stroke outcomes, except for depression. Importantly, a 2-month reduction in therapy may trigger improvements when therapy is fully re-initiated thereafter