University of Bern

About: University of Bern is a education organization based out in Bern, Switzerland. It is known for research contribution in the topics: Population & Large Hadron Collider. The organization has 35422 authors who have published 79413 publications receiving 3125088 citations. The organization is also known as: Bern University & UNIBE.

Guidelines for the use and interpretation of assays for monitoring autophagy

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Strengthening the reporting of observational studies in epidemiology (STROBE) statement: guidelines for reporting observational studies

Abstract: Poor reporting of research hampers assessment and makes it less useful. An international group of methodologists, researchers, and journal editors sets out guidelines to improve reports of observational studies

Loss on ignition as a method for estimating organic and carbonate content in sediments: reproducibility and comparability of results.

Abstract: Five test runs were performed to assess possible bias when performing the loss on ignition (LOI) method to estimate organic matter and carbonate content of lake sediments. An accurate and stable weight loss was achieved after 2 h of burning pure CaCO3 at 950 °C, whereas LOI of pure graphite at 530 °C showed a direct relation to sample size and exposure time, with only 40-70% of the possible weight loss reached after 2 h of exposure and smaller samples losing weight faster than larger ones. Experiments with a standardised lake sediment revealed a strong initial weight loss at 550 °C, but samples continued to lose weight at a slow rate at exposure of up to 64 h, which was likely the effect of loss of volatile salts, structural water of clay minerals or metal oxides, or of inorganic carbon after the initial burning of organic matter. A further test-run revealed that at 550 °C samples in the centre of the furnace lost more weight than marginal samples. At 950 °C this pattern was still apparent but the differences became negligible. Again, LOI was dependent on sample size. An analytical LOI quality control experiment including ten different laboratories was carried out using each laboratory's own LOI procedure as well as a standardised LOI procedure to analyse three different sediments. The range of LOI values between laboratories measured at 550 °C was generally larger when each laboratory used its own method than when using the standard method. This was similar for 950 °C, although the range of values tended to be smaller. The within-laboratory range of LOI measurements for a given sediment was generally small. Comparisons of the results of the individual and the standardised method suggest that there is a laboratory-specific pattern in the results, probably due to differences in laboratory equipment and/or handling that could not be eliminated by standardising the LOI procedure. Factors such as sample size, exposure time, position of samples in the furnace and the laboratory measuring affected LOI results, with LOI at 550 °C being more susceptible to these factors than LOI at 950 °C. We, therefore, recommend analysts to be consistent in the LOI method used in relation to the ignition temperatures, exposure times, and the sample size and to include information on these three parameters when referring to the method.

Stent-retriever thrombectomy after intravenous t-PA vs. t-PA alone in stroke

Abstract: BACKGROUND Among patients with acute ischemic stroke due to occlusions in the proximal anterior intracranial circulation, less than 40% regain functional independence when treated with intravenous tissue plasminogen activator (t-PA) alone. Thrombectomy with the use of a stent retriever, in addition to intravenous t-PA, increases reperfusion rates and may improve long-term functional outcome. METHODS We randomly assigned eligible patients with stroke who were receiving or had received intravenous t-PA to continue with t-PA alone (control group) or to undergo endovascular thrombectomy with the use of a stent retriever within 6 hours after symptom onset (intervention group). Patients had confirmed occlusions in the proximal anterior intracranial circulation and an absence of large ischemic-core lesions. The primary outcome was the severity of global disability at 90 days, as assessed by means of the modified Rankin scale (with scores ranging from 0 [no symptoms] to 6 [death]). RESULTS The study was stopped early because of efficacy. At 39 centers, 196 patients underwent randomization (98 patients in each group). In the intervention group, the median time from qualifying imaging to groin puncture was 57 minutes, and the rate of substantial reperfusion at the end of the procedure was 88%. Thrombectomy with the stent retriever plus intravenous t-PA reduced disability at 90 days over the entire range of scores on the modified Rankin scale (P<0.001). The rate of functional independence (modified Rankin scale score, 0 to 2) was higher in the intervention group than in the control group (60% vs. 35%, P<0.001). There were no significant between-group differences in 90-day mortality (9% vs. 12%, P = 0.50) or symptomatic intracranial hemorrhage (0% vs. 3%, P = 0.12). CONCLUSIONS In patients receiving intravenous t-PA for acute ischemic stroke due to occlusions in the proximal anterior intracranial circulation, thrombectomy with a stent retriever within 6 hours after onset improved functional outcomes at 90 days. (Funded by Covidien; SWIFT PRIME ClinicalTrials.gov number, NCT01657461.)