Aquatic food webs in deep temperate lakes: Key species establish through their autecological versatility

Microbial planktonic communities are the basis of food webs in aquatic ecosystems since they contribute substantially to primary production and nutrient recycling. Network analyses of DNA metabarcoding data sets emerged as a powerful tool to untangle the complex ecological relationships among the key players in food webs. In this study, we evaluated co‐occurrence networks constructed from time‐series metabarcoding data sets (12 months, biweekly sampling) of protistan plankton communities in surface layers (epilimnion) and bottom waters (hypolimnion) of two temperate deep lakes, Lake Mondsee (Austria) and Lake Zurich (Switzerland). Lake Zurich plankton communities were less tightly connected, more fragmented and had a higher susceptibility to a species extinction scenario compared to Lake Mondsee communities. We interpret these results as a lower robustness of Lake Zurich protistan plankton to environmental stressors, especially stressors resulting from climate change. In all networks, the phylum Ciliophora contributed the highest number of nodes, among them several in key positions of the networks. Associations in ciliate‐specific subnetworks resembled autecological species‐specific traits that indicate adaptions to specific environmental conditions. We demonstrate the strength of co‐occurrence network analyses to deepen our understanding of plankton community dynamics in lakes and indicate biotic relationships, which resulted in new hypotheses that may guide future research in climate‐stressed ecosystems

Real life patterns of care and progression free survival in metastatic renal cell carcinoma patients: retrospective analysis of cross-sectional data

Abstract Background Patient characteristics and survival outcomes in randomized trials may be different from those in real-life clinical practice. The objective of this study was to describe treatment pathways, safety, drug costs and survival in patients with metastatic Renal Cell Carcinoma (mRCC) in a real world setting. Methods A retrospective analysis was performed using IQVIA real world oncology cross-sectional survey data, a retrospective treatment database collecting anonymized patient-level data in Europe. Data on treatment naïve patients with mRCC who received a first-line targeted therapy in France were extracted for the period 2005–2015. Descriptive analyses were performed on treatment patterns, patient characteristics and safety profiles. Progression Free Survival (PFS) was determined using Kaplan-Meier survival analysis. Results One thousand three hundred thirty-one patients with mRCC who received a first-line targeted therapy were included. The male/female sex ratio was 2.5 and 66% of patients were aged > 60 years. 83% of patients had clear cell adenocarcinoma. 83% of patients underwent a surgical procedure, 10% had radiotherapy. In patients who received a first-line targeted therapy, 73% received sunitinib. The mean time from diagnosis to first-line treatment by targeted therapies in patients initially diagnosed with metastatic disease was 3.3 months [95% CI:2.5–4.1]. In patients who received second-line targeted therapy n = 257 (19%), the most frequently observed treatment sequences were sunitinib-everolimus (33%) and sunitinib-sorafenib (27%). Adverse events data were available for 501 patients and adverse events were documented in 70% of patients, most frequently diarrhoea. The overall median PFS was 13 months [95% CI:11.5–16]. Conclusion Patient characteristics were consistent with the literature. Treatment patterns appeared to follow current practice guidelines. Despite some variations, PFS in our study seems to be consistent with findings from other real world studies. Nevertheless, PFS results were higher than those observed in clinical trials. Due to the use of cross-sectional data, PFS in our study should be interpreted with caution

An integrative approach sheds new light onto the systematics and ecology of the widespread ciliate genus Coleps (Ciliophora, Prostomatea)

Species of the genus Coleps are one of the most common planktonic ciliates in lake ecosystems. The study aimed to identify the phenotypic plasticity and genetic variability of different Coleps isolates from various water bodies and from culture collections. We used an integrative approach to study the strains by (i) cultivation in a suitable culture medium, (ii) screening of the morphological variability including the presence/absence of algal endosymbionts of living cells by light microscopy, (iii) sequencing of the SSU and ITS rDNA including secondary structures, (iv) assessment of their seasonal and spatial occurrence in two lakes over a one-year cycle both from morphospecies counts and high-throughput sequencing (HTS), and, (v) proof of the co-occurrence of Coleps and their endosymbiotic algae from HTS-based network analyses in the two lakes. The Coleps strains showed a high phenotypic plasticity and low genetic variability. The algal endosymbiont in all studied strains was Micractinium conductrix and the mutualistic relationship turned out as facultative. Coleps is common in both lakes over the whole year in different depths and HTS has revealed that only one genotype respectively one species, C. viridis, was present in both lakes despite the different lifestyles (mixotrophic with green algal endosymbionts or heterotrophic without algae). Our results suggest a future revision of the species concept of the genus Coleps

Additional file 1: of Real life patterns of care and progression free survival in metastatic renal cell carcinoma patients: retrospective analysis of cross-sectional data

Figure S1. Flow chart of included patients. Table S2. Table resuming patients ‘characteristics. Table S3. Table resuming adverse event data by first-line treatment. (DOCX 37 kb

Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution

Species of the ciliate genus Urotricha are key players in freshwater plankton communities. In the pelagial of lakes, about 20 urotrich species occur throughout an annual cycle, some of which play a pivotal role in aquatic food webs. For example, during the phytoplankton spring bloom, they consume a remarkable proportion of the algal production. In ecological studies, urotrich ciliates are usually merely identified to genus rank and grouped into size classes. This is unsatisfying considering the distinct autecological properties of individual species and their specific spatial and temporal distribution patterns. As a basis for future research, we characterized in detail four common urotrich morphotypes, i.e., specimens identified as U. furcata and tentatively as U. agilis, U. pseudofurcata, and U. castalia, using state-of-the-art methods. We used an integrative polyphasic approach, in which morphological studies (in vivo observation, silver staining methods, scanning electron microscopy) were linked with a molecular approach exploiting four different gene fragments as taxonomic DNA barcodes with different resolution potential (SSU rDNA, ITS-1, ITS-2, hypervariable V4 and V9 regions of the SSU rDNA). We shed light on the diversity of urotrich ciliates as well as on their global distribution patterns, and annual cycles. Additionally, we coupled individual species occurrences and environmental parameters, and subsequently modeled the distribution and occurrence, using logistic regressions. Furthermore, for one strain putatively identified as U. castalia, we ascertained the optimal cultivation media and food preferences. Thereby, our comprehensive view on these important freshwater ciliates that frequently occur in environmental high throughput sequencing datasets worldwide will allow future studies to better exploit protistan plankton data from lakes

Vaccination practices in pediatric transplantation: A survey among member centers of the European reference network <scp>TransplantChild</scp>

Background: There is considerable variation in vaccination practices between pediatric transplant centers. This study aims to evaluate active immunization attitudes and practices among ERN-TransplantChild centers and identify potential areas of improvement that could be addressed by shared evidence-based protocols. Methods: A cross-sectional questionnaire of attitudes and practices toward immunization of pediatric SOT and HSCT candidates and recipients was sent to a representative member of multidisciplinary teams from 27 European centers belonging to the ERN-TransplantChild. Results: A total of 28/62 SOT programs and 6/12 HSCT programs across 21 European centers participated. A quarter of centers did not have an on-site protocol for the immunizations. At the time of transplantation, pediatric candidates were fully immunized (80%-100%) in 57% and 33% of the SOT and HSCT programs. Variations in the time between vaccine administration and admission to the waiting list were reported between the centers, with 2 weeks for inactivated vaccines and variable time (2-4 weeks) for live-attenuated vaccines (LAVs). Almost all sites recommended immunization in the post-transplant period, with a time window of 4-8 months for the inactivated vaccines and 16-24 months for MMR and Varicella vaccines. Only five sites administer LAVs after transplantation, with seroconversion evaluated in 80% of cases. Conclusions: The immunization coverage of European pediatric transplant recipients is still inconsistent and far from adequate. This survey is a starting point for developing shared evidence-based immunization protocols for safe vaccination among pediatric transplant centers and generating new research studies