Epigenetic hereditary transcription profiles III, evidence for an epigenetic network resulting in gender, tissue and age-specific variation in overall transcription

<p>Abstract</p> <p>Background</p> <p>We have previously shown that deviations from the average transcription profile of a group of functionally related genes are not only heritable, but also demonstrate specific patterns associated with age, gender and differentiation, thereby implicating genome-wide nuclear programming as the cause. To determine whether these results could be reproduced, a different micro-array database (obtained from two types of muscle tissue, derived from 81 human donors aged between 16 to 89 years) was studied.</p> <p>Results</p> <p>This new database also revealed the existence of age, gender and tissue-specific features in a small group of functionally related genes. In order to further analyze this phenomenon, a method was developed for quantifying the contribution of different factors to the variability in gene expression, and for generating a database limited to residual values reflecting constitutional differences between individuals. These constitutional differences, presumably epigenetic in origin, contribute to about 50% of the observed residual variance which is connected with a network of interrelated changes in gene expression with some genes displaying a decrease or increase in residual variation with age.</p> <p>Conclusion</p> <p>Epigenetic variation in gene expression without a clear concomitant relation to gene function appears to be a widespread phenomenon. This variation is connected with interactions between genes, is gender and tissue specific and is related to cellular aging.</p> <p>This finding, together with the method developed for analysis, might contribute to the elucidation of the role of nuclear programming in differentiation, aging and carcinogenesis</p> <p>Reviewers</p> <p>This article was reviewed by Thiago M. Venancio (nominated by Aravind Iyer), Hua Li (nominated by Arcady Mushegian) and Arcady Mushegian and J.P.de Magelhaes (nominated by G. Church).</p

Hereditary profiles of disorderly transcription?

BACKGROUND: Microscopic examination of living cells often reveals that cells from some cell strains appear to be in a permanent state of disarray without obvious reason. In all probability such a disorderly state affects cell functioning. The aim of this study was to establish whether a disorderly state could occur that adversely affects gene expression profiles and whether such a state might have biomedical consequences. To this end, the expression profiles of the 14 genes of the proteasome derived from the GEO SAGE database were utilized as a model system. RESULTS: By adopting the overall expression profile as the standard for normal expression, deviation in transcription was frequently observed. Each deviating tissue exhibited its own characteristic profile of over-expressed and under-expressed genes. Moreover such a specific deviating profile appeared to be epigenetic in origin and could be stably transmitted to a clonal derivative e.g. from a precancerous normal tissue to its tumor. A significantly greater degree of deviation was observed in the expression profiles from the tumor tissues. The changes in the expression of different genes display a network of interdependencies. Therefore our hypothesis is that deviating profiles reflect disorder in the localization of genes within the nucleus The underlying cause(s) for these disorderly states remain obscure; it could be noise and/or deterministic chaos. Presence of mutational damage does not appear to be predominantly involved. CONCLUSION: As disturbances in expression profiles frequently occur and have biomedical consequences, its determination could prove of value in several fields of biomedical research. REVIEWERS: This article was reviewed by Trey Ideker, Itai Yanai and Stephan Bec

F-18-fluorodeoxyglucose positron emission tomography combined with CT in critically ill patients with suspected infection

Contains fulltext : 88623.pdf (publisher's version ) (Closed access)PURPOSE: To assess the value of F-18-fluorodeoxyglucose positron emission tomography (FDG-PET) combined with CT in critically ill patients suspected of having an infection. METHODS: FDG-PET CT scans requested for evaluation of a suspected infection or inflammatory process in critically ill, mechanically ventilated patients were analyzed (blinded for the final clinical diagnosis) and compared with clinical follow-up. RESULTS: Thirty-five FDG-PET/CT scans performed in 33 ICU patients (28 adults and 5 children), median age 58 years (range 1 month-72 years), were analyzed. Twenty-one FDG-PET/CT scans were true positive. Three FDG-PET/CT scans were considered false positive, in one case leading to additional diagnostic procedures (specificity 79%). Additionally, 11 true negatives were found (sensitivity 100%), leading to an overall accuracy of 91%. CONCLUSIONS: FDG-PET/CT scanning is of additional value in the evaluation of suspected infection in critically ill patients in whom conventional diagnostics did not lead to a diagnosis. Apart from the high accuracy, in this study it appeared that, in addition to conventional diagnostic techniques that were routinely performed, a normal FDG-PET/CT ruled out important infections requiring prolonged antibiotic therapy or drainage. Since sensitivity is lower in highly metabolic active tissues (e.g., endocarditis, meningitis), the FDG-PET/CT scan is not suited to detect infections in these tissues.01 maart 201

A Simplified Water Accounting Procedure to Assess Climate Change Impact on Water Resources for Agriculture across Different European River Basins

[EN] European agriculture and water policies require accurate information on climate change impacts on available water resources. Water accounting, that is a standardized documentation of data on water resources, is a useful tool to provide this information. Pan-European data on climate impacts do not recognize local anthropogenic interventions in the water cycle. Most European river basins have a specific toolset that is understood and used by local experts and stakeholders. However, these local tools are not versatile. Thus, there is a need for a common approach that can be understood by multi-fold users to quantify impact indicators based on local data and that can be used to synthesize information at the European level. Then, policies can be designed with the confidence that underlying data are backed-up by local context and expert knowledge. This work presents a simplified water accounting framework that allows for a standardized examination of climate impacts on water resource availability and use across multiple basins. The framework is applied to five different river basins across Europe. Several indicators are extracted that explicitly describe green water fluxes versus blue water fluxes and impacts on agriculture. The examples show that a simplified water accounting framework can be used to synthesize basin-level information on climate change impacts which can support policymaking on climate adaptation, water resources and agriculture.This research was funded by Horizon 2020 IMPREX project, grant number 641811Hunink, J.; Simons, G.; Suárez-Almiñana, S.; Solera Solera, A.; Andreu Álvarez, J.; Giuliani, M.; Zamberletti, P.... (2019). A Simplified Water Accounting Procedure to Assess Climate Change Impact on Water Resources for Agriculture across Different European River Basins. Water. 11(10):1-29. https://doi.org/10.3390/w11101976S1291110Jacob, D., Kotova, L., Teichmann, C., Sobolowski, S. P., Vautard, R., Donnelly, C., … van Vliet, M. T. H. (2018). Climate Impacts in Europe Under +1.5°C Global Warming. Earth’s Future, 6(2), 264-285. doi:10.1002/2017ef000710Koutroulis, A. G., Grillakis, M. G., Daliakopoulos, I. N., Tsanis, I. K., & Jacob, D. (2016). Cross sectoral impacts on water availability at +2 °C and +3 °C for east Mediterranean island states: The case of Crete. Journal of Hydrology, 532, 16-28. doi:10.1016/j.jhydrol.2015.11.015Dezsi, Ş., Mîndrescu, M., Petrea, D., Rai, P. K., Hamann, A., & Nistor, M.-M. (2018). High-resolution projections of evapotranspiration and water availability for Europe under climate change. International Journal of Climatology, 38(10), 3832-3841. doi:10.1002/joc.5537Forzieri, G., Feyen, L., Russo, S., Vousdoukas, M., Alfieri, L., Outten, S., … Cid, A. (2016). Multi-hazard assessment in Europe under climate change. 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Freshwater vulnerability under high end climate change. A pan-European assessment. Science of The Total Environment, 613-614, 271-286. doi:10.1016/j.scitotenv.2017.09.074Lobanova, A., Liersch, S., Nunes, J. P., Didovets, I., Stagl, J., Huang, S., … Krysanova, V. (2018). Hydrological impacts of moderate and high-end climate change across European river basins. Journal of Hydrology: Regional Studies, 18, 15-30. doi:10.1016/j.ejrh.2018.05.003Beck, H. E., Vergopolan, N., Pan, M., Levizzani, V., van Dijk, A. I. J. M., Weedon, G. P., … Wood, E. F. (2017). Global-scale evaluation of 22 precipitation datasets using gauge observations and hydrological modeling. Hydrology and Earth System Sciences, 21(12), 6201-6217. doi:10.5194/hess-21-6201-2017Naz, B. S., Kurtz, W., Montzka, C., Sharples, W., Goergen, K., Keune, J., … Kollet, S. (2019). Improving soil moisture and runoff simulations at 3 km over Europe using land surface data assimilation. Hydrology and Earth System Sciences, 23(1), 277-301. doi:10.5194/hess-23-277-2019Haro, D., Solera, A., Paredes, J., & Andreu, J. (2014). Methodology for Drought Risk Assessment in Within-year Regulated Reservoir Systems. Application to the Orbigo River System (Spain). Water Resources Management, 28(11), 3801-3814. doi:10.1007/s11269-014-0710-3Zaniolo, M., Giuliani, M., Castelletti, A. F., & Pulido-Velazquez, M. (2018). Automatic design of basin-specific drought indexes for highly regulated water systems. Hydrology and Earth System Sciences, 22(4), 2409-2424. doi:10.5194/hess-22-2409-2018Koutroulis, A. G., Tsanis, I. K., Daliakopoulos, I. N., & Jacob, D. (2013). Impact of climate change on water resources status: A case study for Crete Island, Greece. Journal of Hydrology, 479, 146-158. doi:10.1016/j.jhydrol.2012.11.055Vargas-Amelin, E., & Pindado, P. (2014). The challenge of climate change in Spain: Water resources, agriculture and land. Journal of Hydrology, 518, 243-249. doi:10.1016/j.jhydrol.2013.11.035Giuliani, M., Li, Y., Castelletti, A., & Gandolfi, C. (2016). A coupled human-natural systems analysis of irrigated agriculture under changing climate. Water Resources Research, 52(9), 6928-6947. doi:10.1002/2016wr019363Giuliani, M., & Castelletti, A. (2016). Is robustness really robust? How different definitions of robustness impact decision-making under climate change. Climatic Change, 135(3-4), 409-424. doi:10.1007/s10584-015-1586-9Grindlay, A. L., Zamorano, M., Rodríguez, M. I., Molero, E., & Urrea, M. A. (2011). Implementation of the European Water Framework Directive: Integration of hydrological and regional planning at the Segura River Basin, southeast Spain. Land Use Policy, 28(1), 242-256. doi:10.1016/j.landusepol.2010.06.005Quevauviller, P., Barceló, D., Beniston, M., Djordjevic, S., Harding, R. J., Iglesias, A., … Werner, M. (2012). Integration of research advances in modelling and monitoring in support of WFD river basin management planning in the context of climate change. Science of The Total Environment, 440, 167-177. doi:10.1016/j.scitotenv.2012.07.055Edens, B., & Graveland, C. (2014). Experimental valuation of Dutch water resources according to SNA and SEEA. Water Resources and Economics, 7, 66-81. doi:10.1016/j.wre.2014.10.003Pedro-Monzonís, M., Jiménez-Fernández, P., Solera, A., & Jiménez-Gavilán, P. (2016). The use of AQUATOOL DSS applied to the System of Environmental-Economic Accounting for Water (SEEAW). Journal of Hydrology, 533, 1-14. doi:10.1016/j.jhydrol.2015.11.034Gouveia, C. M., Trigo, R. M., Beguería, S., & Vicente-Serrano, S. M. (2017). Drought impacts on vegetation activity in the Mediterranean region: An assessment using remote sensing data and multi-scale drought indicators. 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Water Accounting Plus (WA+) – a water accounting procedure for complex river basins based on satellite measurements. doi:10.5194/hessd-9-12879-2012Karimi, P., Bastiaanssen, W. G. M., Molden, D., & Cheema, M. J. M. (2013). Basin-wide water accounting based on remote sensing data: an application for the Indus Basin. Hydrology and Earth System Sciences, 17(7), 2473-2486. doi:10.5194/hess-17-2473-2013Orth, R., & Destouni, G. (2018). Drought reduces blue-water fluxes more strongly than green-water fluxes in Europe. Nature Communications, 9(1). doi:10.1038/s41467-018-06013-7Van den Hurk, B., Hirschi, M., Schär, C., Lenderink, G., van Meijgaard, E., van Ulden, A., … Jones, R. (2005). Soil Control on Runoff Response to Climate Change in Regional Climate Model Simulations. Journal of Climate, 18(17), 3536-3551. doi:10.1175/jcli3471.1Bergström, S., Carlsson, B., Gardelin, M., Lindström, G., Pettersson, A., & Rummukainen, M. (2001). 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Linking Pan-European data to the local scale for decision making for global change and water scarcity within water resources planning and management. Science of The Total Environment, 603-604, 126-139. doi:10.1016/j.scitotenv.2017.05.259Huang, Z., Hejazi, M., Tang, Q., Vernon, C. R., Liu, Y., Chen, M., & Calvin, K. (2019). Global agricultural green and blue water consumption under future climate and land use changes. Journal of Hydrology, 574, 242-256. doi:10.1016/j.jhydrol.2019.04.046Kahil, M. T., Connor, J. D., & Albiac, J. (2015). Efficient water management policies for irrigation adaptation to climate change in Southern Europe. Ecological Economics, 120, 226-233. doi:10.1016/j.ecolecon.2015.11.004Velasco-Muñoz, J., Aznar-Sánchez, J., Belmonte-Ureña, L., & López-Serrano, M. (2018). Advances in Water Use Efficiency in Agriculture: A Bibliometric Analysis. Water, 10(4), 377. doi:10.3390/w10040377Berbel, J., & Mateos, L. (2014). 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The Sigma-trial protocol: a prospective double-blind multi-centre comparison of laparoscopic versus open elective sigmoid resection in patients with symptomatic diverticulitis

BACKGROUND: Diverticulosis is a common disease in the western society with an incidence of 33-66%. 10-25% of these patients will develop diverticulitis. In order to prevent a high-risk acute operation it is advised to perform elective sigmoid resection after two episodes of diverticulitis in the elderly patient or after one episode in the younger ( 50 years or in case of progressive abdominal complaints due to strictures caused by a previous episode of diverticulits. The diagnosis is confirmed by CT-scan, barium enema and/or coloscopy.It is required that the participating surgeons have performed at least 15 laparoscopic and open sigmoid resections. Open resection is performed by median laparotomy, laparoscopic resection is approached by 4 or 5 cannula. Sigmoid and colon which contain serosal changes or induration are removed and a tension free anastomosis is created. After completion of either surgical procedure an opaque dressing will be used, covering from 10 cm above the umbilicus to the pubic bone. Surgery details will be kept separate from the patient's notes.Primary endpoints are the postoperative morbidity and mortality. We divided morbidity in minor (e.g. wound infection), major (e.g. anastomotic leakage) and late (e.g. incisional hernias) complications, data will be collected during hospital stay and after six weeks and six months postoperative. Secondary endpoints are the operative and the postoperative recovery data. Operative data include duration of the operation, blood loss and conversion to laparotomy. Post operative recovery consists of return to normal diet, pain, analgesics, general health (SF-36 questionnaire) and duration of hospital stay. DISCUSSION: The Sigma-trial is a prospective, multi-center, double-blind, randomized study to define the role of laparoscopic sigmoid resection in patients with symptomatic diverticuliti

On Spatially Distributed Hydrological Ecosystem Services: Bridging the Quantitative Information Gap using Remote Sensing and Hydrological Models

One of the ways in which the CGIAR Research Program on Water, Land and Ecosystems (WLE) addresses the challenge of achieving sustainable growth is by improving our understanding of tradeoffs and synergies related to water, food, environment and energy. Essential to the success of these efforts is the availability of quantitative data on these tradeoffs and synergies, and how they vary across space and time. Specifically for the countries sharing the Mekong River, WLE Greater Mekong seeks to drive and inform research and dialogue around the rivers of the region. Hydrological EcoSystem Services (HESS) are heavily affected by intensive development across the region, such as the construction of hydropower dams and land use changes - in particular deforestation, urbanization and agricultural intensification. The full extent of such changes in the agro-ecological system is often unknown, and it is a challenge to account for tradeoffs in HESS in policy processes. As in many other areas of the world, improving governance and management of water resources and associated land and ecosystems in the Greater Mekong region is not only a matter of generating more data. Sharing of knowledge and practices is a key focus of WLE Greater Mekong, which we strive to promote by enhancing the accessibility of valuable information to a wide diversity of regional stakeholders, and promoting dialogue by facilitating the creation of communities of practice. This white paper demonstrates state-of-the-art methods for assessing different HESS and their tradeoffs under different development scenarios. It explores opportunities for spatial monitoring of HESS and predicting changes under different future scenarios, information that is essential for achieving a balanced and healthy agro-ecological system. By relying on tools in the public domain and leveraging the resulting HESS data through online information platforms, this white paper is an excellent example of current efforts supported by WLE Greater Mekong to stimulate uptake of ecosystem services assessments in decision-making processes

A tsunami generated by a strike-slip event.: constraints from GPS and SAR data on the 2018 Palu earthquake

A devastating tsunami struck Palu Bay in the wake of the 28 September 2018 Mw = 7.5 Palu earthquake (Sulawesi, Indonesia). With a predominantly strike-slip mechanism, the question remains whether this unexpected tsunami was generated by the earthquake itself, or rather by earthquake-induced landslides. In this study we examine the tsunami potential of the co-seismic deformation. To this end, we present a novel geodetic dataset of GPS and multiple SAR-derived displacement fields to estimate a 3D co-seismic surface deformation field. The data reveal a number of fault bends, conforming to our interpretation of the tectonic setting as a transtensional basin. Using a Bayesian framework, we provide robust finite fault solutions of the co-seismic slip distribution, incorporating several scenarios of tectonically feasible fault orientations below the bay. These finite fault scenarios involve large co-seismic uplift ( > 2 m) below the bay due to thrusting on a restraining fault bend that connects the offshore continuation of two parallel onshore fault segments. With the co-seismic displacement estimates as input we simulate a number of tsunami cases. For most locations for which video-derived tsunami waveforms are available our models provide a qualitative fit to leading wave arrival times and polarity. The modeled tsunamis explain most of the observed runup. We conclude that co-seismic deformation was the main driver behind the tsunami that followed the Palu earthquake. Our unique geodetic dataset constrains vertical motions of the sea floor, and sheds new light on the tsunamigenesis of strike-slip faults in transtensional basins