Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

The three-dimensional arrangement of the human genome comprises a complex network of structural and regulatory chromatin loops important for coordinating changes in transcription during human development. To better understand the mechanisms underlying context-specific 3D chromatin structure and transcription during cellular differentiation, we generated comprehensive in situ Hi-C maps of DNA loops during human monocyte-to-macrophage differentiation. We demonstrate that dynamic looping events are regulatory rather than structural in nature and uncover widespread coordination of dynamic enhancer activity at preformed and acquired DNA loops. Enhancer-bound loop formation and enhancer-activation of preformed loops represent two distinct modes of regulation that together form multi-loop activation hubs at key macrophage genes. Activation hubs connect 3.4 enhancers per promoter and exhibit a strong enrichment for Activator Protein 1 (AP-1) binding events, suggesting multi-loop activation hubs driven by cell-type specific transcription factors may represent an important class of regulatory chromatin structures for the spatiotemporal control of transcription

Opal-CT precipitation in a clayey soil explained by geochemical transport model of dissolved Si (Blégny, Belgium)

Opal-CT precipitation controlling dissolved Si export Dissolved Si (DSi) exported by rivers are controlled by geological, hydrological and biological cycle processes [1]. The DSi concentrations measured in a river of an upstream catchment in eastern Belgium (Blégny, Land of Herve) don’t vary seasonally (6.91±0.94mgL-1; n=363). Si concentrations in pore water are often higher and vary more (8.65±3.65mgL-1; n=128). The decrease of DSi along the flowpath of water is due to sink processes, i.e. precipitation, adsorption or uptake by vegetation. As the DSi in the river does not show any seasonal variation, uptake by vegetation can be ruled out [1] whereas precipitation or adsorption can control the DSi drained by the stream water. This hypothesis is confirmed by XRD and DeMaster analysis. At 0.1m depth the soil is constituted of 62% quartz, 7% K-feldspar, 6% plagioclase, 3.2% carbonates, 18.9% Al-clay, 1.47% Kaolinite, 0.63% Chlorite and 0.2% amorphous Si, probably of biogenic origin. At 1.5m depth, the amounts of several minerals (35.8% quartz, 0.6% K-feldspars, 0.9% plagioclase, Al-clay 14.7%) drop drastically. Carbonates, chlorite and kaolinite are absent whereas 40.4% opal-CT appears. The precipitation of opal-CT controls the DSi export of this catchment. Development of geochemical transport model To descripe DSi export from a catchment a geochemical transport model is developped in HP1 which couples the water flux model Hydrus with the geochemical model PHREEQC [2]. Our model is based on the conceptual model developped in [3]. First results show different DSi export dynamics in the unsaturated zone than in the aquifer due to different pCO2 values and varying soil moisture conditions. Further development of the model will help to find out the reason of opal-CT precipitation in this setting. [1]Fulweiler, Nixon (2005) Biogeochemistry 74:115–130. [2] Simunek, Jacques, van Genuchten, Mallants (2006) JAWRA 42:1537-1547. [3] Ronchi et al. (2013). Silicon, 5(1), 115–133

The BLAST View of the Star Forming Region in Aquila (ell=45deg,b=0deg)

We have carried out the first general submillimeter analysis of the field towards GRSMC 45.46+0.05, a massive star forming region in Aquila. The deconvolved 6 deg^2 (3\degree X 2\degree) maps provided by BLAST in 2005 at 250, 350, and 500 micron were used to perform a preliminary characterization of the clump population previously investigated in the infrared, radio, and molecular maps. Interferometric CORNISH data at 4.8 GHz have also been used to characterize the Ultracompact HII regions (UCHIIRs) within the main clumps. By means of the BLAST maps we have produced an initial census of the submillimeter structures that will be observed by Herschel, several of which are known Infrared Dark Clouds (IRDCs). Our spectral energy distributions of the main clumps in the field, located at ~7 kpc, reveal an active population with temperatures of T~35-40 K and masses of ~10^3 Msun for a dust emissivity index beta=1.5. The clump evolutionary stages range from evolved sources, with extended HII regions and prominent IR stellar population, to massive young stellar objects, prior to the formation of an UCHIIR.The CORNISH data have revealed the details of the stellar content and structure of the UCHIIRs. In most cases, the ionizing stars corresponding to the brightest radio detections are capable of accounting for the clump bolometric luminosity, in most cases powered by embedded OB stellar clusters

Massive Genomic Decay in Serratia symbiotica, a Recently Evolved Symbiont of Aphids

All vertically transmitted bacterial symbionts undergo a process of genome reduction over time, resulting in tiny, gene-dense genomes. Comparison of genomes of ancient bacterial symbionts gives only limited information about the early stages in the transition from a free-living to symbiotic lifestyle because many changes become obscured over time. Here, we present the genome sequence for the recently evolved aphid symbiont Serratia symbiotica. The S. symbiotica genome exhibits several of the hallmarks of genome evolution observed in more ancient symbionts, including elevated rates of evolution and reduction in genome size. The genome also shows evidence for massive genomic decay compared with free-living relatives in the same genus of bacteria, including large deletions, many pseudogenes, and a slew of rearrangements, perhaps promoted by mobile DNA. Annotation of pseudogenes allowed examination of the past and current metabolic capabilities of S. symbiotica and revealed a somewhat random process of gene inactivation with respect to function. Analysis of mutational patterns showed that deletions are more common in neutral DNA. The S. symbiotica genome provides a rare opportunity to study genome evolution in a recently derived heritable symbiont

Evaluation of agricultural management from field to catchment scale: Development of a parsimonious agro-hydrological model

Due to the increasing world population and prosperity, global food production needs a 70% increase by 2050. To achieve this taking into account the limited land and water resources, an increase in productivity needs to be accompanied by an increase in crop water productivity. Improved agricultural management is one of the key solutions for upgrading (crop) water productivity, especially in rainfed cropping systems in drought-prone regions. However, agricultural management practices are only sustainable if they are selected considering their suitability under changing environmental conditions. Also, their potential impact on regional water availability should be taken into account. Agro-hydrological models are suitable tools to investigate the impact of several agricultural management strategies under various environmental conditions. While simple crop and hydrological models are limited with respect to the number and accuracy of the processes they incorporate, complex models have high demand for data. Due to these limitations, there is a need for new agro-hydrological models that accurately simulate both crop productivity and water availability in agricultural catchments but have low data and calibration requirements. This study aimed at developing a widely applicable, parsimonious agro-hydrological model, AquaCrop-Hydro, by linking the process-based AquaCrop crop water productivity model with a conceptual hydrological model. First, the AquaCrop submodel to simulate the effect of agricultural management at field scale was evaluated and further improved. AquaCrop can simulate the effect of various agricultural management practices on the soil water balance, crop canopy development, crop transpiration and crop (water) productivity of an agricultural field. Next to irrigation management, the model considers crop management, soil management, field surface management, mulches, soil fertility management and weed management. Two of these practices were further studied in detail. First, AquaCrop’s semi-quantitative simulation procedure to simulate crop response to soil fertility stress was elaborately discussed and evaluated against field experimental data of maize and wheat in Nepal, quinoa in Bolivia and tef in Ethiopia. Second, a new procedure to simulate crop production in weed-infested fields was developed and tested against field data of barley in Ethiopia and winter wheat in Australia. Evaluation of simulation results showed that AquaCrop performed well to simulate the soil water content, crop development and production under various environmental conditions and different water, soil fertility and weed infestation levels. Furthermore, a scenario analysis demonstrated that AquaCrop enables efficient analysis of a broad range of agricultural management practices in order to develop management strategies that are tailored to the local agronomic and environmental conditions. Subsequently, the AquaCrop model was linked to a conceptual hydrological model. The resulting AquaCrop-Hydro model was evaluated and applied to the Plankbeek catchment, an agricultural catchment in Flanders, Belgium. Comparison against historical observations showed that AquaCrop-Hydro performed well to simulate crop production and river discharge at the outlet of the catchment. Moreover, an impact analysis demonstrated AquaCrop-Hydro's ability to evaluate various agricultural management strategies for climate change adaptation with respect to their effect on crop production as well as water availability. Finally, the strengths and limitations of AquaCrop-Hydro as compared to other agro-hydrological models was assessed. The model is widely applicable to agricultural catchments with varying characteristics. Due to its parsimonious nature it is especially useful for application in data-scarce regions, where it provides good estimates while alleviating the burden of high data and calibration requirements. Although there is room to improve model accuracy and functionality, AquaCrop-Hydro can be applied to evaluate agricultural management strategies and support sustainable water management from field to catchment scale.nrpages: 224status: publishe

Anaerobic Municipal Wastewater Treatment at Low Temperature: Novel High-throughput Methods for Hydrolysis Monitoring and Response to Temperature Shocks in Differently Inoculated Reactors

This dissertation focuses on municipal wastewater, which is produced in everyday household activities. Currently, this wastewater is treated by conventional aerated activated sludge systems. However, these systems are not sustainable since they require substantial amounts of energy for aeration, convert wastewater organic matter only to CO2 and produce large amounts of excess sludge. Anaerobic municipal wastewater treatment (AnMWWT) would tackle all the aforementioned issues, but is challenging at the low wastewater temperatures typical for temperate climate regions, e.g., between 10 °C and 20 °C in Belgium. The main objective of this PhD research was to increase the future applicability of anaerobic municipal wastewater treatment in temperate climate zones. We aimed to achieve this with in-depth experiments organized around three topics. First, we developed a protein hydrolysis assay to quantify the rate at which proteins are converted to peptides and amino acids. A high-throughput assay with a BODIPY FL casein model protein in a 96 well microplate format was developed. This assay provides quantitative results at a high measurement frequency and has a sound theoretical basis. Second, we set out to develop a lipid hydrolysis assay to quantify the rate at which lipids are converted to long-chain fatty acids. A vegetable oil - Rhodamine B lipid emulsion approach in a 96 well microplate format was evaluated with a commercial lipid hydrolysis enzyme, Amano lipase. Third, we aimed to obtain integrated physico-chemical and microbiological knowledge of the changes that occur in anaerobic municipal wastewater treatment when the water temperature drops from 30 °C to 15 °C. In addition, we set out to evaluate the potential of alternative reactor inocula and biofilm-based biomass retention for AnMWWT at a low operational temperature. A lab-scale reactor experiment was conducted over a period of 684 days with a synthetic municipal wastewater fed at a constant rate to the reactor. The operational temperature was varied throughout the experiment from 30 °C to 20 °C, then to 15 °C and again to 30 °C. Polyethylene carriers were added to all reactors to induce biofilm-based biomass retention. The performance and microbial community composition were compared for a traditional sludge digester inoculum (three replicate reactors), a cow rumen inoculum (three replicate reactors) and a sheep rumen inoculum (one reactor). The digester sludge and rumen-inoculated reactors were heavily affected by the stepwise temperature shocks from 30 °C to 20 °C and from 20 °C to 15 °C. A fast increase in the organic acid concentrations with a concomitant drop in biogas production and pH points out inhibition of methanogenesis but not hydrolysis and acidogenesis at low temperature. A steady state with a partial recovery of the initial biogas production rate could be obtained at 20 °C, but not at 15 °C. An adequate reactor performance was obtained in the reactors inoculated with sheep or cow rumen content, but they did not perform better than the digester sludge inoculated reactors. Biomass retention by biofilm formation was intended but was not obtained in this reactor experiment. The combination of turbulence due to continuous mixing and a high hydraulic retention time prevented colonization of the polyethylene carrier surface. The lack of biomass retention most probably affected slow-growing species such as methanogenic Archaea and their syntrophic partners, fatty-acid oxidizing bacteria.status: publishe

Transport of dissolved organic carbon from soil to surface water: Identification and modeling of pathways and controlling factors

Dissolved organic carbon (DOC) in the surface water is an important component of the global carbon cycle. Due to its active and mobile nature, it affects aquatic ecosystems in several ways and plays a significant role in the cycling and distribution of carbon within and between ecosystems. Although the estimated annual flux of DOC from the land to the oceans is ±0.4 Pg C/year, almost half the current net terrestrial uptake of ±0.9 Pg C/year, the factors controlling the transport of DOC from the soil to the surface water are not clear. Previous research on the transport of DOC in the soil and on the factors controlling DOC export towards the river system has mostly been carried out in forest and wetland areas. However, agricultural land use can lead to significant surface runoff and thereby enable a surface runoff pathway for the transport of DOC. Little information is available on the transport of DOC through surface runoff from agricultural fields and on the factors controlling this transport. At the catchment scale, previous work has mainly focused on either regular sampling during baseflow conditions or high-frequency monitoring during a limited number of events, leading only to a partial understanding of the factors controlling the DOC transport. Although experimental data on DOC export from catchments are available, efforts to model the DOC export are scarce. Therefore, the general aim of this work was to determine the factors controlling the transport of dissolved organic carbon from the soil to the surface water and to identify and model the transport pathways. Field experiments were conducted at different temporal and spatial scales. At the plot scale, rainfall simulations were carried out to identify the effect of soil properties, field characteristics and hydrological conditions on DOC export by surface runoff from agricultural fields. Additionally, the temporal evolution of DOC concentrations and specific UV absorbance (SUVA) values in runoff water during a rainfall event was observed. SUVA is an indicator of the aromaticity and the recalcitrant nature of DOM, whereby higher SUVA values are measured when the DOM is more aromatic. Four small headwater catchments contrasting in land use and hydrogeology were monitored to study the transport pathways delivering DOC towards the surface water at the catchment scale. Stream water was sampled on a regular base during dry weather conditions and at high frequency during rainfall events, to observe the temporal variation of DOC concentrations both seasonally and at the time scale of a rain event. Stream water, groundwater, soil pore water, precipitation/throughfall and riparian zone water samples were additionally analyzed for silica and major cations, allowing an end-member mixing analysis that gained insight into the contributing pathways delivering DOC at the catchment outlet during different flow regimes. For the Blégny grassland catchment, stream water DOC concentrations were modeled as a simple mixture of DOC from the different transport pathways delivering water at the catchment outlet. Therefore, discharge measured at the catchment outlet was modeled as a combination of discharge from different components using the FLEX hydrological model and the WETSPRO model. Results from the rainfall simulations showed that the antecedent rainfall conditions are the most important control on DOC concentrations and quality in surface runoff water from agricultural fields. Lower amounts of rainfall before the experiment, or lower initial moisture content of the soil lead to high concentrations of low aromatic DOC in the runoff water. Soil and field characteristics only have limited effect on DOC concentrations in runoff. Overall, DOC concentrations in runoff water are highest and SUVA values are lowest at the start of a rainfall event. In the stream water from small headwater catchments, DOC concentrations and SUVA values were higher in forest catchments than in pasture catchments. In our study catchments, no seasonal variation in baseflow stream DOC concentrations was observed. During rainfall events in all catchments however, both DOC concentrations and SUVA values increased with discharge, reached a maximum and decreased again as discharge returned to pre-event baseflow values. Overall, the majority of the total annual export of DOC from the study catchments was transported to the catchment outlet during times when discharge was elevated in response to a rainfall event. The changes in concentrations and quality of DOC during discharge events could be attributed to a change in contributions of transport pathways of water to the stream. In the forested catchments with deep groundwater tables and thick unsaturated zones, the main contributions to the stream water during baseflow was via the groundwater. Rising stream DOC concentrations during rainfall events were attributed to additional throughfall and riparian zone transport pathways. In the grassland catchments with shallow groundwater tables, stream flow mainly originated from shallow groundwater discharged at seeps. During rain events, an additional transport pathway through the organic rich top soil layer and water from the riparian zone caused DOC concentration to rise. The importance of the contributing pathways in the grassland catchment changed seasonally and depended on the degree of saturation of the catchment soils. The WETSPRO model calculating DOC concentrations in the stream water as a mixture of DOC from the different transport pathways, was able to reproduce DOC concentrations observed in the Blégny catchment. As the FLEX hydrological model however did not succeed in an accurate prediction of discharge measured in the field, modeled subflows of the FLEX model did not allow a good prediction of the observed variation in stream water DOC concentrations. Overall, this research showed that on agricultural soils that generate considerable amounts of surface runoff during a rainfall event, surface runoff is an important pathway for the transport of DOC from the soil to the surface water. In future research, this transport pathway thus deserves our increased interest. At the catchment scale, the majority of the total annual export of DOC for the study catchments was transported to the catchment outlet during times when discharge was elevated in response to a rainfall event. This proves the value of our work, whereby regular sampling during dry weather baseflow conditions was combined with high-frequency monitoring during a great number of rainfall events. Our results also show that hydrological modeling of observed discharge as the sum of discharges from different transport components, combined with chemical analysis of the contributing sources waters, successfully allows the modeling of DOC concentrations observed in the stream water.nrpages: 97status: publishe