Monitoring integraal duurzame stallen : Peildatum 1 januari 2018

Sinds 2008 voert WUR in opdracht van het ministerie van Landbouw, Natuur en Voedselkwaliteit (LNV) de monitor integraal duurzame stallen uit. De monitor laat zien dat op 1 januari 2018 in Nederland 15,0 % van alle rundvee-, varkens- en pluimveestallen integraal duurzaam is---Since 2008 commissioned by the Ministry of agriculture, nature and food quality (LNV) WUR conducts the monitor integral sustainable stables. The monitor shows that on 1 January 2018 in the Netherlands 15.0% of all cattle, pig and poultry houses are integral sustainabl

Distinct gene expression in demyelinated white and grey matter areas of patients with multiple sclerosis

Demyelination of the central nervous system is a prominent pathological hallmark of multiple sclerosis and affects both white and grey matter. However, demyelinated white and grey matter exhibit clear pathological differences, most notably the presence or absence of inflammation and activated glial cells in white and grey matter, respectively. In order to gain more insight into the differential pathology of demyelinated white and grey matter areas, we micro-dissected neighbouring white and grey matter demyelinated areas as well as normal-appearing matter from leucocortical lesions of human post-mortem material and used these samples for RNA sequencing. Our data show that even neighbouring demyelinated white and grey matter of the same leucocortical have a distinct gene expression profile and cellular composition. We propose that, based on their distinct expression profile, pathological processes in neighbouring white and grey matter are likely different which could have implications for the efficacy of treating grey matter lesions with current anti-inflammatory-based multiple sclerosis drugs

‘To the land or to the sea' : diet and mobility in early medieval Frisia

This study investigated palaeodiet and population mobility in early medieval Frisia through the stable isotope analysis of individuals buried in the fifth–eighth century AD cemetery of Oosterbeintum, a terp site on the northern coast of the Netherlands. The results cast new light on the role of the northern Netherlands in trade and migration in the early medieval period, and have significance for the study of interaction and movement throughout the wider North Sea region. Bone collagen and tooth enamel from humans and animals were analyzed using carbon, nitrogen, oxygen, and strontium isotopes. δ13C and δ15N results indicated that the population had a terrestrial, C3-based diet. High δ15N values were observed in humans and fauna, which are probably related to the terp's salt-marsh location. The δ18O and 87Sr/86Sr data revealed a high proportion of non-locals buried at Oosterbeintum, some of whom had probably migrated from regions as distant and varied as Scandinavia and southern England. It is suggested that this immigration may be associated with Frisian maritime trading activities. New data are also presented from a small number of contemporaneous European sites

Tight cooperation between Mot1p and NC2β in regulating genome-wide transcription, repression of transcription following heat shock induction and genetic interaction with SAGA

TATA-binding protein (TBP) is central to the regulation of eukaryotic transcription initiation. Recruitment of TBP to target genes can be positively regulated by one of two basal transcription factor complexes: SAGA or TFIID. Negative regulation of TBP promoter association can be performed by Mot1p or the NC2 complex. Recent evidence suggests that Mot1p, NC2 and TBP form a DNA-dependent protein complex. Here, we compare the functions of Mot1p and NC2βduring basal and activated transcription using the anchor-away technique for conditional nuclear depletion. Genome-wide expression analysis indicates that both proteins regulate a highly similar set of genes. Upregulated genes were enriched for SAGA occupancy, while downregulated genes preferred TFIID binding. Mot1p and NC2β depletion during heat shock resulted in failure to downregulate gene expression after initial activation, which was accompanied by increased TBP and RNA pol II promoter occupancies. Depletion of Mot1p or NC2β displayed preferential synthetic lethality with the TBP-interaction module of SAGA. Our results support the model that Mot1p and NC2β directly cooperate in vivo to regulate TBP function, and that they are involved in maintaining basal expression levels as well as in resetting gene expression after induction by stress

Six Months of Balloon Treatment does Not Predict the Success of Gastric Banding

BACKGROUND: We studied whether weight loss by intragastric balloon would predict the outcome of subsequent gastric banding with regard to weight loss and BMI reduction. METHODS: A prospective cohort of patients with a body mass index (BMI)>40 kg/m(2) received an intragastric balloon for 6 months followed by laparoscopic adjustable gastric banding (LAGB). Successful balloon-induced weight loss was defined as > or =10% weight loss after 6 months. Successful surgical weight loss was defined as an additional 15% weight loss in the following 12 months. Patients were divided in group A, losing > or =10% of their initial weight with 6 months' balloon treatment, and group B, losing <10% of their initial weight. RESULTS: In 40 patients (32 female, 8 male; age 36.6 yr, range 26-54), the mean BMI decreased from 46.5 to 40.5 kg/m(2) (P <0.001) after 6 months of balloon treatment and to 35.2 kg/m(2) (P <0.001) 12 months after LAGB. Group A (25 patients) and group B (15 patients) had a significant difference in BMI decrease, 12.4 vs 9.0 kg/m(2) (P <0.05), after the total study duration of 18 months. However, there was no difference in BMI reduction (4.7 kg/m(2) vs 5.8 kg/m(2)) in the 12 months after LAGB. 6 patients in group A lost > or =10% of their starting weight during 6 months balloon treatment as well as > or =15% 12 months following LAGB. 6 patients in group B lost <10% of their starting weight after 6 months of BIB, but also lost > or =15% 12 months following LAGB. CONCLUSION: Intragastric balloon did not predict the success of subsequent LAG

The Antioxidant Protein Peroxiredoxin 4 Is Epigenetically Down Regulated in Acute Promyelocytic Leukemia

The antioxidant peroxiredoxin (PRDX) protein family comprises 6 members, which are implicated in a variety of cellular responses, including growth factor signal transduction. PRDX4 resides in the endoplasmic reticulum (ER), where it locally controls oxidative stress by reducing H2O2levels. We recently provided evidence for a regulatory function of PRDX4 in signal transduction from a myeloid growth factor receptor, the granulocyte colony-stimulating factor receptor (G-CSFR). Upon activation, the ligand-induced G-CSFR undergoes endocytosis and routes via the early endosomes where it physically interacts with ER-resident PRDX4. PRDX4 negatively regulates G-CSFR mediated signaling. Here, we investigated whether PRDX4 is affected in acute myeloid leukemia (AML); genomic alterations and expression levels of PRDX4 were investigated. We show that genomic abnormalities involving PRDX4 are rare in AML. However, we find a strong reduction in PRDX4 expression levels in acute promyelocytic leukemia (APL) compared to normal promyelocytes and different molecular subtypes of AML. Subsequently, the possible role of DNA methylation and histone modifications in silencing of PRDX4 in APLs was investigated. We show that the reduced expression is not due to methylation of the CpG island in the promoter region of PRDX4 but correlates with increased trimethylation of histone 3 lysine residue 27 (H3K27me3) and lysine residue 4 (H3K4me3) at the transcriptional start site (TSS) of PRDX4, indicative of a bivalent histone code involved in transcriptional silencing. These findings suggest that the control of G-CSF responses by the antioxidant protein PRDX4 may be perturbed in APL

Integrating Phosphorylation Network with Transcriptional Network Reveals Novel Functional Relationships

Phosphorylation and transcriptional regulation events are critical for cells to transmit and respond to signals. In spite of its importance, systems-level strategies that couple these two networks have yet to be presented. Here we introduce a novel approach that integrates the physical and functional aspects of phosphorylation network together with the transcription network in S.cerevisiae, and demonstrate that different network motifs are involved in these networks, which should be considered in interpreting and integrating large scale datasets. Based on this understanding, we introduce a HeRS score (hetero-regulatory similarity score) to systematically characterize the functional relevance of kinase/phosphatase involvement with transcription factor, and present an algorithm that predicts hetero-regulatory modules. When extended to signaling network, this approach confirmed the structure and cross talk of MAPK pathways, inferred a novel functional transcription factor Sok2 in high osmolarity glycerol pathway, and explained the mechanism of reduced mating efficiency upon Fus3 deletion. This strategy is applicable to other organisms as large-scale datasets become available, providing a means to identify the functional relationships between kinases/phosphatases and transcription factors

Characterization of bovine embryos cultured under conditions appropriate for sustaining human naïve pluripotency.

In mammalian preimplantation development, pluripotent cells are set aside from cells that contribute to extra-embryonic tissues. Although the pluripotent cell population of mouse and human embryos can be cultured as embryonic stem cells, little is known about the pathways involved in formation of a bovine pluripotent cell population, nor how to maintain these cells in vitro. The objective of this study was to determine the transcriptomic profile related to bovine pluripotency. Therefore, in vitro derived embryos were cultured in various culture media that recently have been reported capable of maintaining the naïve pluripotent state of human embryonic cells. Gene expression profiles of embryos cultured in these media were compared using microarray analysis and quantitative RT-PCR. Compared to standard culture conditions, embryo culture in 'naïve' media reduced mRNA expression levels of the key pluripotency markers NANOG and POU5F1. A relatively high percentage of genes with differential expression levels were located on the X-chromosome. In addition, reduced XIST expression was detected in embryos cultured in naïve media and female embryos contained fewer cells with H3K27me3 foci, indicating a delay in X-chromosome inactivation. Whole embryos cultured in one of the media, 5iLA, could be maintained until 23 days post fertilization. Together these data indicate that 'naïve' conditions do not lead to altered expression of known genes involved in pluripotency. Interestingly, X-chromosome inactivation and development of bovine embryos were dependent on the culture conditions

Non-operative vs. operative treatment for multiple rib fractures after blunt thoracic trauma: a multicenter prospective cohort study

Background: Patients with multiple rib fractures without a clinical flail chest are increasingly being treated with rib fixation; however, high-quality evidence to support this development is lacking. Methods: We conducted a prospective multicenter observational study comparing rib fixation to non-operative treatment in all patients aged 18 years and older with computed tomography confirmed multiple rib fractures without a clinical flail chest. Three centers performed rib fixation as standard of care. For adequate comparison, the other three centers performed only non-operative treatment. As such clinical equipoise formed the basis for the comparison in this study. Patients were matched using propensity score matching. Results: In total 927 patients with multiple rib fractures were included. In the three hospitals that performed rib fixation, 80 (14%) out of 591 patients underwent rib fixation. From the nonoperative centers, on average 71 patients were adequately matched to 71 rib fixation patients after propensity score matching. Rib fixation was associated with an increase in hospital length of stay (HLOS) of 4.9 days (95%CI 0.8–9.1, p = 0.02) and a decrease in quality of life (QoL) measured by the EQ5D questionnaire at 1 year of 0.1 (95% CI − 0.2–0.0, p = 0.035) compared to non-operative treatment. A subgroup analysis of patients who received operative care within 72 h showed a similar decrease in QoL. Up to 22 patients (28%) who underwent surgery experienced implant-related irritation. Conclusions: We found no benefits and only detrimental effects associated with rib fixation. Based on these results, we do not recommend rib fixation as the standard of care for patients with multiple rib fractures. Trial registration: Registered in the Netherlands Trial Register NTR6833 on 13/11/2017

NF-Y Recruits Ash2L to Impart H3K4 Trimethylation on CCAAT Promoters

BACKGROUND: Different histone post-translational modifications (PTMs) are crucial in the regulation of chromatin, including methylations of H3 at Lysine 4 by the MLL complex. A relevant issue is how this is causally correlated to the binding of specific transcription factors (TFs) in regulatory regions. NF-Y is a TF that regulates 30% of mammalian promoters containing the widespread CCAAT element. We and others established that the presence of H3K4me3 is dependent upon the binding of NF-Y. Here, we investigate the mechanisms of H3K4me3 deposition by NF-Y. METHODS: We employed Chromatin Immunoprecipitation in cells in which Ash2L and NF-Y subunits were knocked down by RNAi, to monitor the presence of histones PTMs and components of the MLL complex. We performed gene expression profiling of Ash2L-knocked down cells and analyzed the regulated genes. We performed ChIPs in leukemic cells in which MLL1 is devoid of the methyltransferase domain and fused to the AF4 gene. RESULTS: Knock down of the Ash2L subunit of MLL leads to a decrease in global H3K4me3 with a concomitant increase in H3K79me2. Knock down of NF-Y subunits prevents promoter association of Ash2L, but not MLL1, nor WDR5, and H3K4me3 drops dramatically. Endogenous NF-Y and Ash2L specifically interact in vivo. Analysis of the promoters of Ash2L regulated genes, identified by transcriptional profiling, suggests that a handful TF binding sites are moderately enriched, among which the CCAAT box. Finally, leukemic cells carrying the MLL-AF4 translocation show a decrease of H3K4me3, absence of Ash2L and increase in H3K79me2, while NF-Y binding was not significantly affected. CONCLUSIONS: Three types of conclusions are reached: (i) H3K4 methylation is not absolutely required for NF-Y promoter association. (ii) NF-Y acts upstream of H3K4me3 deposition by recruiting Ash2L. (iii) There is a general cross-talk between H3K4me3 and H3K79me2 which is independent from the presence of MLL oncogenic fusions