DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus

Background: DNA methylation is of pivotal importance during development. Previous genome-wide studies identified numerous differentially methylated regions upon differentiation of stem cells, many of them associated with transcriptional start sites. Results: We present the first genome-wide, single-base-resolution view into DNA methylation dynamics during differentiation of a mammalian epithelial stem cell: the mouse small intestinal Lgr5+ stem cell. Very little change was observed at transcriptional start sites and our data suggest that differentiation-related genes are already primed for expression in the stem cell. Genome-wide, only 50 differentially methylated regions were identified. Almost all of these loci represent enhancers driving gene expression in the differentiated part of the small intestine. Finally, we show that binding of the transcription factor Tcf4 correlates with hypo-methylation and demonstrate that Tcf4 is one of the factors contributing to formation of differentially methylated regions. Conclusions: Our results reveal limited DNA methylation dynamics during small intestine stem cell differentiation and an impact of transcription factor binding on shaping the DNA methylation landscape during differentiation of stem cells in vivo

Quantum Holonomy in Three-dimensional General Covariant Field Theory and Link Invariant

We consider quantum holonomy of some three-dimensional general covariant non-Abelian field theory in Landau gauge and confirm a previous result partially proven. We show that quantum holonomy retains metric independence after explicit gauge fixing and hence possesses the topological property of a link invariant. We examine the generalized quantum holonomy defined on a multi-component link and discuss its relation to a polynomial for the link.Comment: RevTex, 12 pages. The metric independence of path integral measure is justified and the case of multi-component link is discussed in detail. To be published in Physical Review

Fasting before living-kidney donation:effect on donor well-being and postoperative recovery: study protocol of a multicenter randomized controlled trial

BACKGROUND: One of the main effectors on the quality of life of living-kidney donors is postoperative fatigue. Caloric restriction (CR) and short-term fasting (STF) are associated with improved fitness and increased resistance to acute stress. CR/STF increases the expression of cytoprotective genes, increases immunomodulation via increased anti-inflammatory cytokine production, and decreases the expression of pro-inflammatory markers. As such, nutritional preconditioning by CR or STF represents a non-invasive and cost-effective method that could mitigate the effects of acute surgery-induced stress and postoperative fatigue. To investigate whether preoperative STF contributes to a reduction in fatigue after living-kidney donation, a randomized clinical trial is indicated. METHODS: We aim to determine whether 2.5 days of fasting reduces postoperative fatigue score in subjects undergoing living-kidney donation. In this randomized study, the intervention group will follow a preoperative fasting regime for 2.5 days with a low-dose laxative, while the control group will receive standard care. The main study endpoint is postoperative fatigue, 4 weeks after living-kidney donation. Secondary endpoints include the effect of preoperative fasting on postoperative hospital admission time, the feasibility of STF, and the postoperative recovery of donor and recipient kidney function. This study will provide us with knowledge of the feasibility of STF and confirm its effect on postoperative recovery. DISCUSSION: Our study will provide clinically relevant information on the merits of caloric restriction for living-kidney donors and recipients. We expect to reduce the postoperative fatigue in living-kidney donors and improve the postoperative recovery of living-kidney recipients. It will provide evidence on the clinical merits and potential caveats of preoperative dietary interventions. TRIAL REGISTRATION: Netherlands Trial Register NL9262. EudraCT 2020-005445-16. MEC Erasmus MC MEC-2020-0778. CCMO NL74623.078.21 SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13063-021-05950-x

Improving outcomes for donation after circulatory death kidney transplantation:Science of the times

The use of kidneys donated after circulatory death (DCD) remains controversial due to concerns with regard to high incidences of early graft loss, delayed graft function (DGF), and impaired graft survival. As these concerns are mainly based on data from historical cohorts, they are prone to time-related effects and may therefore not apply to the current timeframe. To assess the impact of time on outcomes, we performed a time-dependent comparative analysis of outcomes of DCD and donation after brain death (DBD) kidney transplantations. Data of all 11,415 deceased-donor kidney transplantations performed in The Netherlands between 1990-2018 were collected. Based on the incidences of early graft loss, two eras were defined (1998-2008 [n = 3,499] and 2008-2018 [n = 3,781]), and potential time-related effects on outcomes evaluated. Multivariate analyses were applied to examine associations between donor type and outcomes. Interaction tests were used to explore presence of effect modification. Results show clear time-related effects on posttransplant outcomes. The 1998-2008 interval showed compromised outcomes for DCD procedures (higher incidences of DGF and early graft loss, impaired 1-year renal function, and inferior graft survival), whereas DBD and DCD outcome equivalence was observed for the 2008-2018 interval. This occurred despite persistently high incidences of DGF in DCD grafts, and more adverse recipient and donor risk profiles (recipients were 6 years older and the KDRI increased from 1.23 to 1.39 and from 1.35 to 1.49 for DBD and DCD donors). In contrast, the median cold ischaemic period decreased from 20 to 15 hours. This national study shows major improvements in outcomes of transplanted DCD kidneys over time. The time-dependent shift underpins that kidney transplantation has come of age and DCD results are nowadays comparable to DBD transplants. It also calls for careful interpretation of conclusions based on historical cohorts, and emphasises that retrospective studies should correct for time-related effects

Probing photo-ionization: Experiments on positive streamers in pure gasses and mixtures

Positive streamers are thought to propagate by photo-ionization whose parameters depend on the nitrogen:oxygen ratio. Therefore we study streamers in nitrogen with 20%, 0.2% and 0.01% oxygen and in pure nitrogen, as well as in pure oxygen and argon. Our new experimental set-up guarantees contamination of the pure gases to be well below 1 ppm. Streamers in oxygen are difficult to measure as they emit considerably less light in the sensitivity range of our fast ICCD camera than the other gasses. Streamers in pure nitrogen and in all nitrogen/oxygen mixtures look generally similar, but become somewhat thinner and branch more with decreasing oxygen content. In pure nitrogen the streamers can branch so much that they resemble feathers. This feature is even more pronounced in pure argon, with approximately 10^2 hair tips/cm^3 in the feathers at 200 mbar; this density could be interpreted as the free electron density creating avalanches towards the streamer stem. It is remarkable that the streamer velocity is essentially the same for similar voltage and pressure in all nitrogen/oxygen mixtures as well as in pure nitrogen, while the oxygen concentration and therefore the photo-ionization lengths vary by more than five orders of magnitude. Streamers in argon have essentially the same velocity as well. The physical similarity of streamers at different pressures is confirmed in all gases; the minimal diameters are smaller than in earlier measurements.Comment: 28 pages, 14 figures. Major differences with v1: - appendix and spectra removed - subsection regarding effects of repetition frequency added - many more smaller change

Towards a standardised informed consent procedure for live donor nephrectomy:the PRINCE (Process of Informed Consent Evaluation) project-study protocol for a nationwide prospective cohort study

Introduction: Informed consent is mandatory for all (surgical) procedures, but it is even more important when it comes to living kidney donors undergoing surgery for the benefit of others. Donor education, leading to informed consent, needs to be carried out according to certain standards. Informed consent procedures for live donor nephrectomy vary per centre, and even per individual healthcare professional. The basis for a standardised, uniform surgical informed consent procedure for live donor nephrectomy can be created by assessing what information donors need to hear to prepare them for the operation and convalescence. Methods and analysis: The PRINCE (Process of Informed Consent Evaluation) project is a prospective, multicentre cohort study, to be carried out in all eight Dutch kidney transplant centres. Donor knowledge of the procedure and postoperative course will be evaluated by means of pop quizzes. A baseline cohort (prior to receiving any information from a member of the transplant team in one of the transplant centres) will be compared with a control group, the members of which receive the pop quiz on the day of admission for donor nephrectomy. Donor satisfaction will be evaluated for all donors who completed the admission pop-quiz. The primary end point is donor knowledge. In addition, those elements that have to be included in the standardised format informed consent procedure will be identified. Secondary end points are donor satisfaction, current informed consent practices in the different centres (eg, how many visits, which personnel, what kind of information is disclosed, in which format, etc) and correlation of donor knowledge with surgeons' estimation thereof. Ethics and dissemination: Approval for this study was obtained from the medical ethical committee of the Erasmus MC, University Medical Center, Rotterdam, on 18 February 2015. Secondary approval has been obtained from the local ethics committees in six participating centres. Approval in the last centre has been sought. Results: Outcome will be published in a scientific journal

Probing photo-ionization: simulations of positive streamers in varying N2:O2 mixtures

Photo-ionization is the accepted mechanism for the propagation of positive streamers in air though the parameters are not very well known; the efficiency of this mechanism largely depends on the presence of both nitrogen and oxygen. But experiments show that streamer propagation is amazingly robust against changes of the gas composition; even for pure nitrogen with impurity levels below 1 ppm streamers propagate essentially with the same velocity as in air, but their minimal diameter is smaller, and they branch more frequently. Additionally, they move more in a zigzag fashion and sometimes exhibit a feathery structure. In our simulations, we test the relative importance of photo-ionization and of the background ionization from pulsed repetitive discharges, in air as well as in nitrogen with 1 ppm O2 . We also test reasonable parameter changes of the photo-ionization model. We find that photo- ionization dominates streamer propagation in air for repetition frequencies of at least 1 kHz, while in nitrogen with 1 ppm O2 the effect of the repetition frequency has to be included above 1 Hz. Finally, we explain the feather-like structures around streamer channels that are observed in experiments in nitrogen with high purity, but not in air.Comment: 12 figure

Securin (hPTTG1) expression is regulated by β-catenin/TCF in human colorectal carcinoma

Overexpression of the transcriptional activator β-catenin, mostly owing to loss-of-function mutations of the adenomatous polyposis coli (APC) tumour suppressor gene, is crucial for the initiation and progression of human colorectal carcinogenesis. Securin is a regulator of chromosome separation and its overexpression has been shown to be involved in different tumour-promoting processes, like transformation, hyperproliferation and angiogenesis, and correlates with tumour cell invasion. However, the molecular mechanism leading to securin overexpression in human colorectal cancer is unknown. Here we show a correlated high expression of β-catenin and securin (hPTTG1) in colorectal adenomas and carcinomas and further demonstrate that securin is a target of β-catenin transcriptional activation. This implies that deregulation of the β-catenin/T-cell factor-signalling pathway leads to overexpression of securin in human colorectal cancer, which subsequently may contribute to tumour progression