Artificial escape from XCI by DNA methylation editing of the CDKL5 gene.

A significant number of X-linked genes escape from X chromosome inactivation and are associated with a distinct epigenetic signature. One epigenetic modification that strongly correlates with X-escape is reduced DNA methylation in promoter regions. Here, we created an artificial escape by editing DNA methylation on the promoter of CDKL5, a gene causative for an infantile epilepsy, from the silenced X-chromosomal allele in human neuronal-like cells. We identify that a fusion of the catalytic domain of TET1 to dCas9 targeted to the CDKL5 promoter using three guide RNAs causes significant reactivation of the inactive allele in combination with removal of methyl groups from CpG dinucleotides. Strikingly, we demonstrate that co-expression of TET1 and a VP64 transactivator have a synergistic effect on the reactivation of the inactive allele to levels >60% of the active allele. We further used a multi-omics assessment to determine potential off-targets on the transcriptome and methylome. We find that synergistic delivery of dCas9 effectors is highly selective for the target site. Our findings further elucidate a causal role for reduced DNA methylation associated with escape from X chromosome inactivation. Understanding the epigenetics associated with escape from X chromosome inactivation has potential for those suffering from X-linked disorders

Feeding the Worlth Healthily: the Challenge of Measuring the effects of Agriculture on Health

Agricultural production, food systems and population health are intimately linked. While there is a strong evidence base to inform our knowledge of what constitutes a healthy human diet, we know little about actual food production or consumption in many populations and how developments in the food and agricultural system will affect dietary intake patterns and health. The paucity of information on food production and consumption is arguably most acute in low- and middle-income countries, where it is most urgently needed to monitor levels of under-nutrition, the health impacts of rapid dietary transition and the increasing ‘double burden’ of nutrition-related disease. Food availability statistics based on food commodity production data are currently widely used as a proxy measure of national-level food consumption, but using data from the UK and Mexico we highlight the potential pitfalls of this approach. Despite limited resources for data collection, better systems of measurement are possible. Important drivers to improve collection systems may include efforts to meet international development goals and partnership with the private sector. A clearer understanding of the links between the agriculture and food system and population health will ensure that health becomes a critical driver of agricultural change

Enhancing the Social Capital of Learning Communities by Using an Ad Hoc Transient Communities Service

Fetter, S., Berlanga, A. J., & Sloep, P. B. (2009). Enhancing the Social Capital of Learning Communities by Using an Ad Hoc Transient Communities Service. In M. Spaniol, Q. Li, R. Klamma & R. W. H. Lau (Eds.), Proceedings of the 8th International Conference Advances in Web-based Learning - ICWL 2009 (pp. 150-157). August, 19-21, 2009, Aachen, Germany. Lecture Notes in Computer Science 5686; Berlin, Heidelberg: Springer-Verlag.In online learning, communities can help to enhance learning. However, because of the dynamic nature of communities, attaining and sustaining these communities can be difficult. One aspect that has an influence on, and is influenced by these dynamics is the social capital of a community. Features of social capital are the social network structure, the sense of belonging and, the support received and provided. It is hypothesized that these features can be improved by using Ad Hoc Transient Communities (AHTCs). Through an AHTC learners are brought together for a specific, learning-related goal (‘ad hoc’) and for only a limited amount of time (‘transience’). To test whether the use of AHTCs has a positive influence on the social capital, a learner support service which enables the use of AHTCs is proposed. Furthermore, requirements, pre-requisites, and future research are discussed.The work on this publication has been sponsored by the TENCompetence Integrated Project that is funded by the European Commission's 6th Framework Programme, priority IST/Technology Enhanced Learning. Contract 027087 [http://www.tencompetence.org

Patterning the geographies of organ transplantation: corporeality, generosity and justice

publication-status: PublishedThis is the author's post-print version of an article published in Transactions of the Institute of British Geographers, 2006, Vol. 31, Issue 3 pp. 257 – 271 Copyright © 2006 Institute of British Geographers / Royal Geographical Society. The definitive version is available at www3.interscience.wiley.comOrgan transplantation is now an established treatment for patients with end-stage organ failure, yet there are spatial inequalities in access to this procedure. This paper explores the uneven geographies of kidney transplantation in London, arguing that inequalities in access to organ transplantation are created through interlocking spatialities of corporeal difference, enacted through global movements of populations, national organ transplantation protocols and the internal immunological spaces of the body. The combination of these processes, operating at different scales, has produced a distinctive configuration in the embodiment of risk in relation to kidney transplants, particularly born by London's Black and Asian communities. Two ethical dimensions to this geography of organ transplantation are explored here: the ethical responsiveness to others shaping the generous practices of organ donation, and the medical practices categorizing difference through techniques of blood typing, tissue matching and the spatial organization of organ transplantation. In concluding, I argue both are critical to understanding the links between ethics and justice in the geographies of organ exchange in London. Further, I suggest geography is central to political debate about the exchange of biological material elsewhere, for it is only through tracing the intersection of ethical, corporeal and technological practices in situ that we can fully reflect on questions of justice within the developing bioeconomy

Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy

Infants with KMT2A-rearranged B-cell acute lymphoblastic leukemia (ALL) have a dismal prognosis. Survival outcomes have remained static in recent decades despite treatment intensification and novel therapies are urgently required. KMT2A-rearranged infant ALL cells are characterized by an abundance of promoter hypermethylation and exhibit high BCL-2 expression, highlighting potential for therapeutic targeting. Here, we show that hypomethylating agents exhibit in vitro additivity when combined with most conventional chemotherapeutic agents. However, in a subset of samples an antagonistic effect was seen between several agents. This was most evident when hypomethylating agents were combined with methotrexate, with upregulation of ATP-binding cassette transporters identified as a potential mechanism. Single agent treatment with azacitidine and decitabine significantly prolonged in vivo survival in KMT2A-rearranged infant ALL xenografts. Treatment of KMT2A-rearranged infant ALL cell lines with azacitidine and decitabine led to differential genome-wide DNA methylation, changes in gene expression and thermal proteome profiling revealed the target protein-binding landscape of these agents. The selective BCL-2 inhibitor, venetoclax, exhibited in vitro additivity in combination with hypomethylating or conventional chemotherapeutic agents. The addition of venetoclax to azacitidine resulted in a significant in vivo survival advantage indicating the therapeutic potential of this combination to improve outcome for infants with KMT2A-rearranged ALL

Identification of a humanized mouse model for functional testing of immune-mediated biomaterial foreign body response.

Biomedical devices comprise a major component of modern medicine, however immune-mediated fibrosis and rejection can limit their function over time. Here, we describe a humanized mouse model that recapitulates fibrosis following biomaterial implantation. Cellular and cytokine responses to multiple biomaterials were evaluated across different implant sites. Human innate immune macrophages were verified as essential to biomaterial rejection in this model and were capable of cross-talk with mouse fibroblasts for collagen matrix deposition. Cytokine and cytokine receptor array analysis confirmed core signaling in the fibrotic cascade. Foreign body giant cell formation, often unobserved in mice, was also prominent. Last, high-resolution microscopy coupled with multiplexed antibody capture digital profiling analysis supplied spatial resolution of rejection responses. This model enables the study of human immune cell-mediated fibrosis and interactions with implanted biomaterials and devices

Elucidation on the Effect of Operating Temperature to the Transport Properties of Polymeric Membrane Using Molecular Simulation Tool

Existing reports of gas transport properties within polymeric membrane as a direct consequence of operating temperature are in a small number and have arrived in diverging conclusion. The scarcity has been associated to challenges in fabricating defect free membranes and empirical investigations of gas permeation performance at the laboratory scale that are often time consuming and costly. Molecular simulation has been proposed as a feasible alternative of experimentally studied materials to provide insights into gas transport characteristic. Hence, a sequence of molecular modelling procedures has been proposed to simulate polymeric membranes at varying operating temperatures in order to elucidate its effect to gas transport behaviour. The simulation model has been validated with experimental data through satisfactory agreement. Solubility has shown a decrement in value when increased in temperature (an average factor of 1.78), while the opposite has been observed for gas diffusivity (an average factor of 1.32) when the temperature is increased from 298.15Â K to 323.15Â K. In addition, it is found that permeability decreases by 1.36 times as the temperature is increased

Active Chromatin Marks Are Retained on X Chromosomes Lacking Gene or Repeat Silencing Despite XIST/Xist Expression in Somatic Cell Hybrids

X-chromosome inactivation occurs early in mammalian development and results in the inactive X chromosome acquiring numerous hallmarks of heterochromatin. While XIST is a key player in the inactivation process, the method of action of this ncRNA is yet to be determined.To assess which features of heterochromatin may be directly recruited by the expression and localization of the XIST RNA we have analyzed a mouse/human somatic cell hybrid in which expression of human and mouse XIST/Xist has been induced from the active X by demethylation. Such hybrids had previously been demonstrated to disconnect XIST/Xist expression from gene silencing and we confirm maintenance of X-linked gene expression, even close to the Xist locus, despite the localized expression of mouse Xist.Loss of the active chromatin marks H3 acetylation and H3 lysine 4 methylation was not observed upon XIST/Xist expression, nor was there a gain of DNA methylation; thus these marks of facultative heterochromatin are not solely dependent upon Xist expression. Cot-1 holes, regions of depleted RNA hybridization with a Cot-1 probe, were observed upon Xist expression; however, these were at reduced frequency and intensity in these somatic cells. Domains of human Cot-1 transcription were observed corresponding to the human chromosomes in the somatic cell hybrids. The Cot-1 domain of the X was not reduced with the expression of XIST, which fails to localize to the human X chromosome in a mouse somatic cell background. The human inactive X in a mouse/human hybrid cell also shows delocalized XIST expression and an ongoing Cot-1 domain, despite X-linked gene silencing. These results are consistent with recent reports separating Cot-1 silencing from genic silencing, but also demonstrate repetitive element expression from an otherwise silent X chromosome in these hybrid cells

Major flaws in conflict prevention policies towards Africa : the conceptual deficits of international actors’ approaches and how to overcome them

Current thinking on African conflicts suffers from misinterpretations oversimplification, lack of focus, lack of conceptual clarity, state-centrism and lack of vision). The paper analyses a variety of the dominant explanations of major international actors and donors, showing how these frequently do not distinguish with sufficient clarity between the ‘root causes’ of a conflict, its aggravating factors and its triggers. Specifically, a correct assessment of conflict prolonging (or sustaining) factors is of vital importance in Africa’s lingering confrontations. Broader approaches (e.g. “structural stability”) offer a better analytical framework than familiar one-dimensional explanations. Moreover, for explaining and dealing with violent conflicts a shift of attention from the nation-state towards the local and sub-regional level is needed.Aktuelle Analysen afrikanischer Gewaltkonflikte sind häufig voller Fehlinterpretationen (Mangel an Differenzierung, Genauigkeit und konzeptioneller Klarheit, Staatszentriertheit, fehlende mittelfristige Zielvorstellungen). Breitere Ansätze (z. B. das Modell der Strukturellen Stabilität) könnten die Grundlage für bessere Analyseraster und Politiken sein als eindimensionale Erklärungen. häufig differenzieren Erklärungsansätze nicht mit ausreichender Klarheit zwischen Ursachen, verschärfenden und auslösenden Faktoren. Insbesondere die richtige Einordnung konfliktverlängernder Faktoren ist in den jahrzehntelangen gewaltsamen Auseinandersetzungen in Afrika von zentraler Bedeutung. Das Diskussionspapier stellt die große Variationsbreite dominanter Erklärungsmuster der wichtigsten internationalen Geber und Akteure gegenüber und fordert einen Perspektivenwechsel zum Einbezug der lokalen und der subregionalen Ebene für die Erklärung und Bearbeitung gewaltsamer Konflikte

An analysis of the warm-season diurnal cycle over the continental united states and northern Mexico in general circulation models

The diurnal cycle of warm-season rainfall over the continental United States and northern Mexico is analyzed in three global atmospheric general circulation models (AGCMs) from NCEP, GFDL, and the NASA Global Modeling Assimilation Office (GMAO). The results for each model are based on an ensemble of five summer simulations forced with climatological sea surface temperatures. Although the overall patterns of time-mean (summer) rainfall and low-level winds are reasonably well simulated, all three models exhibit substantial regional deficiencies that appear to be related to problems with the diurnal cycle. Especially prominent are the discrepancies in the diurnal cycle of precipitation over the eastern slopes of the Rocky Mountains and adjacent Great Plains, including the failure to adequately capture the observed nocturnal peak. Moreover, the observed late afternoon-early evening eastward propagation of convection from the mountains into the Great Plains is not adequately simulated, contributing to the deficiencies in the diurnal cycle in the Great Plains. In the southeast United States, the models show a general tendency to rain in the early afternoon - several hours earlier than observed. Over the North American monsoon region in the southwest United States and northern Mexico, the phase of the broadscale diurnal convection appears to be reasonably well simulated, though the coarse resolution of the runs precludes the simulation of key regional phenomena. All three models employ deep convection schemes that assume fundamentally the same buoyancy closure based on simplified versions of the Arakawa-Schubert scheme. Nevertheless, substantial differences between the models in the diurnal cycle of convection highlight the important differences in their implementations and interactions with the boundary layer scheme. An analysis of local diurnal variations of convective available potential energy (CAPE) shows an overall tendency for an afternoon peak - a feature well simulated by the models. The simulated diurnal cycle of rainfall is in phase with the local CAPE variation over the southeast United States and the Rocky Mountains where the local surface boundary forcing is important in regulating the diurnal cycle of convection. On the other hand, the simulated diurnal cycle of rainfall tends to be too strongly tied to CAPE over the Great Plains, where the observed precipitation and CAPE are out of phase, implying that free atmospheric large-scale forcing plays a more important role than surface heat fluxes in initiating or inhibiting convection.open383