Characterisation of sugar beet (Beta vulgaris L. ssp. vulgaris) varieties using microsatellite markers

<p>Abstract</p> <p>Background</p> <p>Sugar beet is an obligate outcrossing species. Varieties consist of mixtures of plants from various parental combinations. As the number of informative morphological characteristics is limited, this leads to some problems in variety registration research.</p> <p>Results</p> <p>We have developed 25 new microsatellite markers for sugar beet. A selection of 12 markers with high quality patterns was used to characterise 40 diploid and triploid varieties. For each variety 30 individual plants were genotyped. The markers amplified 3-21 different alleles. Varieties had up to 7 different alleles at one marker locus. All varieties could be distinguished. For the diploid varieties, the expected heterozygosity ranged from 0.458 to 0.744. The average inbreeding coefficient F_iswas 0.282 ± 0.124, but it varied widely among marker loci, from F_is= +0.876 (heterozygote deficiency) to F_is= -0.350 (excess of heterozygotes). The genetic differentiation among diploid varieties was relatively constant among markers (F_st= 0.232 ± 0.027). Among triploid varieties the genetic differentiation was much lower (F_st= 0.100 ± 0.010). The overall genetic differentiation between diploid and triploid varieties was F_st= 0.133 across all loci. Part of this differentiation may coincide with the differentiation among breeders' gene pools, which was F_st= 0.063.</p> <p>Conclusions</p> <p>Based on a combination of scores for individual plants all varieties can be distinguished using the 12 markers developed here. The markers may also be used for mapping and in molecular breeding. In addition, they may be employed in studying gene flow from crop to wild populations.</p

Single-center experience with ipilimumab in an expanded access program for patients with pretreated advanced melanoma.

Ipilimumab, a CTLA-4-blocking monoclonal antibody, improved the overall survival (OS) of advanced melanoma patients treated in prospective clinical trials. We here report a study on the outcome of patients with pretreated advanced melanoma offered ipilimumab (at its licensed dose of 3 mg/kg, every 3 wk for a total of 4 doses) in an expanded access program at a single-center university hospital. Of the 50 patients initiating ipilimumab, 31 patients completed induction therapy and 9 patients were offered reinduction therapy. Most immune-related adverse events were mild and reversible. The best objective response rate by mWHO-criteria included 1 complete response and 4 partial responses (best objective response rate of 10%). Two additional patients obtained a partial response by immune-related response criteria. Median OS was 7 months, with a 1- and 2-year survival rate of 45.2% and 28.8%, respectively. Long-term disease control with ipilimumab was observed in 7 patients of which 4 received reinduction. Baseline serum C-reactive protein (CRP) and the absolute lymphocyte count (ALC) measured on week 6 significantly correlated with OS. In conclusion, in this single-center experience with ipilimumab for advanced pretreated melanoma patients, clinical outcome was comparable with the results of published prospective studies. Reinduction therapy was of importance for maintaining long-term disease control in the majority of responding patients. Baseline CRP and ALC at week 6 deserve further prospective evaluation as prognostic and/or predictive (surrogate) markers.Journal ArticleSCOPUS: ar.jinfo:eu-repo/semantics/publishe

Randomized phase II study of axitinib versus physicians best alternative choice of therapy in patients with recurrent glioblastoma

We conducted a randomized, non-comparative, multi center, phase II clinical trial in order to investigate the efficacy of axitinib, an oral small molecule tyrosine kinase inhibitor with high affinity and specificity for the vascular endothelial growth factor receptors, in patients with recurrent glioblastoma following prior treatment with radiation and temozolomide. Forty-four patients were randomly assigned to receive treatment with axitinib (5 mg BID starting dose; N = 22) or “physicians best alternative choice of therapy” that consisted of bevacizumab (N = 20) or lomustine (N = 2). Six-month progression-free survival served as the primary endpoint. The estimated 6-month progression-free survival rate was 34 % (95 % CI 14–54) for patients treated with axitinib and 28 % (95 % CI 8–48) with best alternative treatment; median overall survival was 29 and 17 weeks, respectively. Objective responses according to RANO criteria were documented in 28 % of patients treated with axitinib and 23 % of patients treated with best alternative therapy. A decrease in maximal uptake of 18F-fluoro-ethyl-tyrosine (18F-FET) by the glioblastoma on PET imaging was documented in 85 % of patients at the time of response on axitinib. Corticosteroid treatment could be stopped in four and tapered in seven out of the 15 patients who were treated with steroids at baseline in the axitinib cohort. Most frequent axitinib related grade ≥3 adverse events consisted of fatigue (9 %), diarrhea (9 %), and oral hyperesthesia (4.5 %). We conclude that axitinib has single-agent clinical activity and a manageable toxicity profile in patients with recurrent glioblastoma.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Effects of wheat bran applied to maternal diet on the intestinal architecture and immune gene expression in suckling piglets

International audienceThe strategy of improving the growth and health of piglets through maternal fiber diet intervention has attracted increasing attention. Therefore, 15 sows were conducted to a wheat bran (WB) group, in which the sows' diets included 25% of WB in gestation and 14% in lactation, and a control (CON) group, in which the sows' diets at all stages of reproduction did not contain WB. The results show that maternal high WB intervention seems not to have an impact on the growth of the offspring or the villus height of the duodenum, and the ratio of villi/crypts in the duodenum and jejunum were all higher in piglets born from WB sows, which may indicate that WB piglets had a larger absorption area and capacity for nutrients. The peroxisome proliferator-activated receptor gamma (PPARγ) and interleukin 6 (IL6) expression levels were notably upregulated in the ileal mucosa of WB piglets, while no immune-related genes in the colonic mucosa were affected by the maternal WB supplementation. In conclusion, adding a high proportion of wheat bran to the sow's gestation and lactation diet can affect the intestinal architecture and the expression of some inflammation genes, to some extent, in the ileal mucosa in the progeny

Effects of Wheat Bran Applied to Maternal Diet on the Intestinal Architecture and Immune Gene Expression in Suckling Piglets

The strategy of improving the growth and health of piglets through maternal fiber diet intervention has attracted increasing attention. Therefore, 15 sows were conducted to a wheat bran (WB) group, in which the sows’ diets included 25% of WB in gestation and 14% in lactation, and a control (CON) group, in which the sows’ diets at all stages of reproduction did not contain WB. The results show that maternal high WB intervention seems not to have an impact on the growth of the offspring or the villus height of the duodenum, and the ratio of villi/crypts in the duodenum and jejunum were all higher in piglets born from WB sows, which may indicate that WB piglets had a larger absorption area and capacity for nutrients. The peroxisome proliferator-activated receptor gamma (PPARγ) and interleukin 6 (IL6) expression levels were notably upregulated in the ileal mucosa of WB piglets, while no immune-related genes in the colonic mucosa were affected by the maternal WB supplementation. In conclusion, adding a high proportion of wheat bran to the sow’s gestation and lactation diet can affect the intestinal architecture and the expression of some inflammation genes, to some extent, in the ileal mucosa in the progeny.</jats:p

Identification of non-invasive biomarkers for treatment response in neuroblastoma by circulating miRNA profiling

Introduction: An outstanding question in neuroblastoma treatment is whether clinically useful biomarkers of response to therapy can be identified. Biomarkers that allow monitoring of targeted drug pathway activation are highly desirable for the clinical follow-up of patients treated with such drugs. Minimally-invasive methods for patient follow-up, like measuring expression levels of miRNAs in serum, may be an elegant approach to obtain a higher specificity, sensitivity and lower handling time than other currently used biomarkers. Method: MYCN/ALKR1279Q transgenic mice were treated with crizotinib. Mice carrying orthotopic xenografts of SH-SY5Y cells were treated with RG7388 or temsirolimus. Serum samples of these mice were collected at different time points before, during and after treatment as well as matching end-point tumor material. Small RNA sequencing was optimized for low input and depleted for abundant non-relevant RNA sequences. Small RNA sequencing and whole miRNome RT-qPCR was performed to identify circulating miRNAs that are responsive to treatment or tumor cell engraftment. Results: We were able to observe expression changes for dozens up to one hundred circulating miRNAs, some of which had a >10 fold change in expression value. miRNAs showed differential expression both as a result of treatment and tumor cell engraftment. These include miRNAs with known roles in neuroblastoma tumor biology like the oncogenic miR-17-92 cluster. Moreover, for some miRNAs expression changes were found to be possibly drug-specific. Conclusion: These data encourage further investigation of circulating miRNAs as biomarkers for treatment response, also in a clinical setting

A harmonized single-cell transcriptomic atlas of human neuroblastoma

Background: Single-cell and single-nucleus RNA sequencing (scRNA-seq or snRNA-seq) are powerful technologies to study the transcriptomic heterogeneity of tumors, including neuroblastoma. Previous studies using scRNA-seq and snRNA-seq were focused on tumoral heterogeneity and aggressiveness in relation to normal developmental and cell-of-origin. While useful, these studies have also raised novel questions. Aims: At present, a comprehensive overview of these studies and data is lacking. In this study, we present a meta-analysis of published scRNA-seq and snRNA-seq datasets for neuroblastoma patient tumors. We compared wet lab and bioinformatics processing procedures across these studies and combined data to form an integrated transcriptomic atlas of human neuroblastoma tumors. Methods: We reviewed all published scRNA-seq and snRNA-seq (n=9) studies and collected metadata, including patient information, sample processing details, wet lab protocol, and bioinformatics approaches (quality control, canonical gene marker selection, and cell type annotation). Thereafter, selected studies were combined to generate a cellular atlas, using benchmarked integration tools to correct for technical bias while preserving biological heterogeneity. Results: Different wet lab protocols and bioinformatics pipelines were applied across the different studies. Most notably, this resulted in a discrepancy in the tumoral composition obtained with scRNA-seq compared to snRNA-seq, with a lack of neuroendocrine cells in scRNA-seq data. Data from more than 50 tumors across various studies (performed on the 10X Genomics platform) were normalized to largely overcome differences in the applied wet lab and bioinformatics approaches. As a result, a harmonized atlas of the transcriptomic landscape of human neuroblastoma tumors was generated. This atlas allows for gaining a more comprehensive view of the heterogeneity of malignant cells and the tumor microenvironment. To illustrate the power of the generated cell atlas as a framework for future single-cell studies, we mapped newly generated scRNA-seq and snRNA-seq data to this reference atlas for cell annotation and observed agreement with manual cell annotation. Conclusion: Our study provides a comprehensive and harmonized view of the single-cell transcriptomic landscape of neuroblastoma and serves as a valuable reference resource for newly generated scRNA-seq and snRNA-seq data