A systematic dissection of the catalytic and non-catalytic functions of TET1 at the interface of epigenetic regulation

Mammalian DNA consists of millions of base pairs. To fit the DNA into the nucleus of a cell the DNA is condensed into chromosomes. The DNA is wrapped around an histone octamer forming nucleosomes which are the basis of chromatin. Chromatin is the physiological form of DNA and altered by various epigenetic mechanisms, such as DNA methylation, histone modifications and RNA modifications. During development epigenetic mechanisms drive lineage choices and cell identity. In this doctoral work we used next generation sequencing and CRISPR/Cas9 genome engineering to study different epigenetic mechanisms in mESCs. The main focus was to study the non-catalytic functions of the DNA demethylase TET1. I have found that TET1 is involved in heterochromatin formation and retroviral silencing independent of DNA demethylation (Publication I). In the scope of this doctoral work I contributed to other projects with the focus on epigenetic proteins in mESCs. First, description of the role of the UBL domain of UHRF1 in the interplay with DNMT1 and DNA maintenance methylation (Publication II). Second, identification of DPPA3 as a regulator of UHRF1 and critical for global DNA demethylation (Publication III). Third, discovery of TET1 and TET2 stage-specific roles in DNA demethylation during early embryonic development (Publication IV). Last, in the scope of this doctoral work I contributed to study the role and function of the novel RNA methyltransferases METTL5 and METTL6 in the field of epitranscriptomics. METTL5 was found to be a specific ribosomal RNA methyltransferase critical for pluripotency and differentiation (Publication V). METTL6 was discovered as a transfer RNA methyltransferase involved in cancer (Publication VI). In summary, this doctoral work investigated and described novel non-catalytic mechanisms of TET1 and studied various epigenetic modifiers and mechanisms at different epigenetic levels

Large Eddy Simulation of Turbulent Channel Flows by the Rational LES Model

The rational large eddy simulation (RLES) model is applied to turbulent channel flows. This approximate deconvolution model is based on a rational (subdiagonal Pade') approximation of the Fourier transform of the Gaussian filter and is proposed as an alternative to the gradient (also known as the nonlinear or tensor-diffusivity) model. We used a spectral element code to perform large eddy simulations of incompressible channel flows at Reynolds numbers based on the friction velocity and the channel half-width Re{sub tau} = 180 and Re{sub tau} = 395. We compared the RLES model with the gradient model. The RLES results showed a clear improvement over those corresponding to the gradient model, comparing well with the fine direct numerical simulation. For comparison, we also present results corresponding to a classical subgrid-scale eddy-viscosity model such as the standard Smagorinsky model.Comment: 31 pages including 15 figure

Modèles d'endommagement par level-set épaisse : solutions analytiques et simulations

Titre du résumé joint : Modélisation de l'endommagement par l'évolution d'une fonction de niveau le modèle TLS (Thick Level Set)National audienceEn endommagement brutal, la rupture se fait le long d'une frontière mobile accompagnée de discontinuités fortes du gradient du déplacement. On propose un modèle d'endommagement plus régulier fondé sur le mouvement d'une couche de largeur finie lc au sein de laquelle l'endommagement varie de façon continue. Cette approche permet dans un même cadre d'initier et de propager des défauts.See http://hal.archives-ouvertes.fr/docs/00/59/27/32/ANNEX/r_E3IGVTN6.pd

Comparison of Simulator Wear Measured by Gravimetric vs Optical Surface Methods for Two Million Cycles

Understanding wear mechanisms are key for better implants Critical to the success of the simulation Small amount of metal wear can have catastrophic effects in the patient such as heavy metal poisoning or deterioration of the bone/implant interface leading to implant failure Difficult to measure in heavy hard-on-hard implants (metal-on-metal or ceramic-on-ceramic) May have only fractions of a milligram of wear on a 200 g component At the limit of detection of even high-end balances when the component is 200 g and the change in weight is on the order of 0.000 1 grams Here we compare the standard gravimetric wear estimate with A non-contact 3D optical profiling method at each weighing stop A coordinate measuring machine (CMM) at the beginning and end of the ru

Enabling Tipping Dynamics in Food System Transformation: How Information and Experience with Novel Meat Substitutes Can Create Positive Political Feedbacks

The food system causes more than a third of the global anthropogenic greenhouse gas emissions, of which half are from livestock. Shifting towards plant-based diets could significantly reduce deforestation, protect biodiversity, and contribute to achieving the Paris climate targets. Yet, deep-rooted eating habits, pleasure, cultural status symbols, and personal freedom are just a few of many bottlenecks to reduce meat consumption. Here, we argue that technological innovation in meat substitutes, if successfully combined with effective informational triggers for behavioral changes, can foster positive political feedbacks to transform the food system. We are particularly interested in assessing the effects of such triggers on accelerating people's reduction of meat consumption and increasing public support for respective food policies. Using advanced machine learning and survey experiments with citizens (N= 2590) in China and the US, the globally largest meat markets, we find that personal experience with new plant-based meat substitutes strongly predicts individuals' intentions to reduce their meat consumption, eat more substitutes, and support public policies that catalyze a transition to more plant-based diets. We also find that in both countries information about the benefits of plant-based diets can increase citizens' behavioral change intentions and policy support. In China, emphasizing social norms in favor of plant-based diets has particularly strong effects on policy support. In the US, prior experience with innovative meat substitutes potentially can boost the positive effects of informational campaigns on public support for meat reduction policies. Overall, the results offer promising implications for a policy sequencing strategy to create positive political feedbacks and enable socio-technical tipping dynamics for food system transformation by fostering innovation in and experience with meat substitutes and highlighting the co-benefits of plant-based diets

Severe Acute Hepatocellular Injury Attributed to OxyELITE Pro: A Case Series

Herbal and dietary supplement (HDS) hepatotoxicity is increasingly being reported in the United States. This case series describes the presenting clinical features and outcomes of 7 patients with liver injury attributed to OxyELITE Pro enrolled in the Drug Induced Liver Injury Network (DILIN) study

Use of intraventricular ribbon gauze to reduce particulate emboli during aortic valve replacement

BACKGROUND: The incidence of cerebrovascular accidents following aortic valve surgery remains a devastating complication. The aim of this study was to determine the number of potential embolic material arising during aortic valve replacement and to examine the efficacy of using ribbon gauze in the left ventricle during removal of the native valve and decalcification of the aortic annulus. METHODS: Ribbon gauze was inserted into the left ventricular cavity prior to aortic valve excision in an unselected, prospectively studied series of 30 patients undergoing aortic valve replacement. A further 30 lengths of ribbon gauze were soaked in the pericardiotomy blood of the same patients and all were subjected to histological analysis. RESULTS: The median number of tissue fragments from the aortic valve replacement group was significantly higher than in the control group 5 (0–18) versus 0 (0–1) (p = 3.6 × 10(-5)). The size of tissue fragments varied between 0.1 and 9.0 mm with a mean of 0.61 ± 1.12 mm and a median of 0.2 mm. There was a significantly higher number of tissue fragments associated with patients having surgery for aortic stenosis when compared with patients who had aortic regurgitation with median of 5 (0–18) versus 0 (0–3) (p = 0.8 × 10(-3)). CONCLUSION: Significant capture of particulate debris by the intraventricular ribbon gauze suggests that the technique of left ventricular ribbon gauze insertion during aortic valve excision has merit

Reliability of causality assessment for drug, herbal and dietary supplement hepatotoxicity in the Drug‐Induced Liver Injury Network (DILIN)

Background & AimsBecause of the lack of objective tests to diagnose drug‐induced liver injury (DILI), causality assessment is a matter of debate. Expert opinion is often used in research and industry, but its test–retest reliability is unknown. To determine the test–retest reliability of the expert opinion process used by the Drug‐Induced Liver Injury Network (DILIN).MethodsThree DILIN hepatologists adjudicate suspected hepatotoxicity cases to one of five categories representing levels of likelihood of DILI. Adjudication is based on retrospective assessment of gathered case data that include prospective follow‐up information. One hundred randomly selected DILIN cases were re‐assessed using the same processes for initial assessment but by three different reviewers in 92% of cases.ResultsThe median time between assessments was 938 days (range 140–2352). Thirty‐one cases involved >1 agent. Weighted kappa statistics for overall case and individual agent category agreement were 0.60 (95% CI: 0.50–0.71) and 0.60 (0.52–0.68) respectively. Overall case adjudications were within one category of each other 93% of the time, while 5% differed by two categories and 2% differed by three categories. Fourteen per cent crossed the 50% threshold of likelihood owing to competing diagnoses or atypical timing between drug exposure and injury.ConclusionsThe DILIN expert opinion causality assessment method has moderate interobserver reliability but very good agreement within one category. A small but important proportion of cases could not be reliably diagnosed as ≥50% likely to be DILI.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111130/1/liv12540.pd

Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency

Cytosine DNA bases can be methylated by DNA methyltransferases and subsequently oxidized by TET proteins. The resulting 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) are considered demethylation intermediates as well as stable epigenetic marks. To dissect the contributions of these cytosine modifying enzymes, we generated combinations of Tet knockout (KO) embryonic stem cells (ESCs) and systematically measured protein and DNA modification levels at the transition from naive to primed pluripotency. Whereas the increase of genomic 5-methylcytosine (5mC) levels during exit from pluripotency correlated with an upregulation of the de novo DNA methyltransferases DNMT3A and DNMT3B, the subsequent oxidation steps turned out to be far more complex. The strong increase of oxidized cytosine bases (5hmC, 5fC, and 5caC) was accompanied by a drop in TET2 levels, yet the analysis of KO cells suggested that TET2 is responsible for most 5fC formation. The comparison of modified cytosine and enzyme levels in Tet KO cells revealed distinct and differentiation-dependent contributions of TET1 and TET2 to 5hmC and 5fC formation arguing against a processive mechanism of 5mC oxidation. The apparent independent steps of 5hmC and 5fC formation suggest yet to be identified mechanisms regulating TET activity that may constitute another layer of epigenetic regulation

Hepatic histological findings in suspected drug‐induced liver injury: Systematic evaluation and clinical associations

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102713/1/hep26709.pd