GIS linked environmental process models

In recent years there has been a great effort to combine the technologies and techniques of GIS and process models. This project examines the issues of linking a standard current generation 2½d GIS with several existing model codes. The focus for the project has been the Shropshire Groundwater Scheme, which is being developed to augment flow in the River Severn during drought periods by pumping water from the Shropshire Aquifer. Previous authors have demonstrated that under certain circumstances pumping could reduce the soil moisture available for crops. This project follows earlier work at Aston in which the effects of drawdown were delineated and quantified through the development of a software package that implemented a technique which brought together the significant spatially varying parameters. This technique is repeated here, but using a standard GIS called GRASS. The GIS proved adequate for the task and the added functionality provided by the general purpose GIS - the data capture, manipulation and visualisation facilities - were of great benefit. The bulk of the project is concerned with examining the issues of the linkage of GIS and environmental process models. To this end a groundwater model (Modflow) and a soil moisture model (SWMS2D) were linked to the GIS and a crop model was implemented within the GIS. A loose-linked approach was adopted and secondary and surrogate data were used wherever possible. The implications of which relate to; justification of a loose-linked versus a closely integrated approach; how, technically, to achieve the linkage; how to reconcile the different data models used by the GIS and the process models; control of the movement of data between models of environmental subsystems, to model the total system; the advantages and disadvantages of using a current generation GIS as a medium for linking environmental process models; generation of input data, including the use of geostatistic, stochastic simulation, remote sensing, regression equations and mapped data; issues of accuracy, uncertainty and simply providing adequate data for the complex models; how such a modelling system fits into an organisational framework

Cloning, purification and characterization of the 6-phospho-3-hexulose isomerase YckF from Bacillus subtilis

The enzyme 6-phospho-3-hexulose isomerase (YckF) from Bacillus subtilis has been prepared and crystallized in a form suitable for X-ray crystallographic analysis. Crystals were grown by the hanging-drop method at 291 K using polyethylene glycol 2000 monomethylether as precipitant. They diffract beyond 1.7 A using an in-house Cu Kalpha source and belong to either space group P6(5)22 or P6(1)22, with unit-cell parameters a = b = 72.4, c = 241.2 A, and have two molecules of YckF in the asymmetric unit

Microbial Reduction of U(VI) under Alkaline Conditions: Implications for Radioactive Waste Geodisposal

Although there is consensus that microorganisms significantly influence uranium speciation and mobility in the subsurface under circumneutral conditions, microbiologically mediated U(VI) redox cycling under alkaline conditions relevant to the geological disposal of cementitious intermediate level radioactive waste, remains unexplored. Here, we describe microcosm experiments that investigate the biogeochemical fate of U(VI) at pH 10–10.5, using sediments from a legacy lime working site, stimulated with an added electron donor, and incubated in the presence and absence of added Fe(III) as ferrihydrite. In systems without added Fe(III), partial U(VI) reduction occurred, forming a U(IV)-bearing non-uraninite phase which underwent reoxidation in the presence of air (O2) and to some extent nitrate. By contrast, in the presence of added Fe(III), U(VI) was first removed from solution by sorption to the Fe(III) mineral, followed by bioreduction and (bio)magnetite formation coupled to formation of a complex U(IV)-bearing phase with uraninite present, which also underwent air (O2) and partial nitrate reoxidation. 16S rRNA gene pyrosequencing showed that Gram-positive bacteria affiliated with the Firmicutes and Bacteroidetes dominated in the post-reduction sediments. These data provide the first insights into uranium biogeochemistry at high pH and have significant implications for the long-term fate of uranium in geological disposal in both engineered barrier systems and the alkaline, chemically disturbed geosphere

The RNA landscape of the human placenta in health and disease

AbstractThe placenta is the interface between mother and fetus and inadequate function contributes to short and long-term ill-health. The placenta is absent from most large-scale RNA-Seq datasets. We therefore analyze long and small RNAs (~101 and 20 million reads per sample respectively) from 302 human placentas, including 94 cases of preeclampsia (PE) and 56 cases of fetal growth restriction (FGR). The placental transcriptome has the seventh lowest complexity of 50 human tissues: 271 genes account for 50% of all reads. We identify multiple circular RNAs and validate 6 of these by Sanger sequencing across the back-splice junction. Using large-scale mass spectrometry datasets, we find strong evidence of peptides produced by translation of two circular RNAs. We also identify novel piRNAs which are clustered on Chr1 and Chr14. PE and FGR are associated with multiple and overlapping differences in mRNA, lincRNA and circRNA but fewer consistent differences in small RNAs. Of the three protein coding genes differentially expressed in both PE and FGR, one encodes a secreted protein FSTL3 (follistatin-like 3). Elevated serum levels of FSTL3 in pregnant women are predictive of subsequent PE and FGR. To aid visualization of our placenta transcriptome data, we develop a web application (https://www.obgyn.cam.ac.uk/placentome/).</jats:p

The RNA landscape of the human placenta in health and disease.

Funder: Department of HealthThe placenta is the interface between mother and fetus and inadequate function contributes to short and long-term ill-health. The placenta is absent from most large-scale RNA-Seq datasets. We therefore analyze long and small RNAs (~101 and 20 million reads per sample respectively) from 302 human placentas, including 94 cases of preeclampsia (PE) and 56 cases of fetal growth restriction (FGR). The placental transcriptome has the seventh lowest complexity of 50 human tissues: 271 genes account for 50% of all reads. We identify multiple circular RNAs and validate 6 of these by Sanger sequencing across the back-splice junction. Using large-scale mass spectrometry datasets, we find strong evidence of peptides produced by translation of two circular RNAs. We also identify novel piRNAs which are clustered on Chr1 and Chr14. PE and FGR are associated with multiple and overlapping differences in mRNA, lincRNA and circRNA but fewer consistent differences in small RNAs. Of the three protein coding genes differentially expressed in both PE and FGR, one encodes a secreted protein FSTL3 (follistatin-like 3). Elevated serum levels of FSTL3 in pregnant women are predictive of subsequent PE and FGR. To aid visualization of our placenta transcriptome data, we develop a web application ( https://www.obgyn.cam.ac.uk/placentome/ )

The RNA landscape of the human placenta in health and disease.

Funder: Department of HealthThe placenta is the interface between mother and fetus and inadequate function contributes to short and long-term ill-health. The placenta is absent from most large-scale RNA-Seq datasets. We therefore analyze long and small RNAs (~101 and 20 million reads per sample respectively) from 302 human placentas, including 94 cases of preeclampsia (PE) and 56 cases of fetal growth restriction (FGR). The placental transcriptome has the seventh lowest complexity of 50 human tissues: 271 genes account for 50% of all reads. We identify multiple circular RNAs and validate 6 of these by Sanger sequencing across the back-splice junction. Using large-scale mass spectrometry datasets, we find strong evidence of peptides produced by translation of two circular RNAs. We also identify novel piRNAs which are clustered on Chr1 and Chr14. PE and FGR are associated with multiple and overlapping differences in mRNA, lincRNA and circRNA but fewer consistent differences in small RNAs. Of the three protein coding genes differentially expressed in both PE and FGR, one encodes a secreted protein FSTL3 (follistatin-like 3). Elevated serum levels of FSTL3 in pregnant women are predictive of subsequent PE and FGR. To aid visualization of our placenta transcriptome data, we develop a web application ( https://www.obgyn.cam.ac.uk/placentome/ )

Franck-Condon Effect in Central Spin System

We study the quantum transitions of a central spin surrounded by a collective-spin environment. It is found that the influence of the environmental spins on the absorption spectrum of the central spin can be explained with the analog of the Franck-Condon (FC) effect in conventional electron-phonon interaction system. Here, the collective spins of the environment behave as the vibrational mode, which makes the electron to be transitioned mainly with the so-called "vertical transitions" in the conventional FC effect. The "vertical transition" for the central spin in the spin environment manifests as, the certain collective spin states of the environment is favored, which corresponds to the minimal change in the average of the total spin angular momentum.Comment: 8 pages, 8 figure

Role of soluble endoglin in BMP9 signaling.

Endoglin (ENG) is a coreceptor of the transforming growth factor-β (TGFβ) family signaling complex, which is highly expressed on endothelial cells and plays a key role in angiogenesis. Its extracellular domain can be cleaved and released into the circulation as soluble ENG (sENG). High circulating levels of sENG contribute to the pathogenesis of preeclampsia (PE). Circulating bone morphogenetic protein 9 (BMP9), a vascular quiescence and endothelial-protective factor, binds sENG with high affinity, but how sENG participates in BMP9 signaling complexes is not fully resolved. sENG was thought to be a ligand trap for BMP9, preventing type II receptor binding and BMP9 signaling. Here we show that, despite cell-surface ENG being a dimer linked by disulfide bonds, sENG purified from human placenta and plasma from PE patients is primarily in a monomeric form. Incubating monomeric sENG with the circulating form of BMP9 (prodomain-bound form) in solution leads to the release of the prodomain and formation of a sENG:BMP9 complex. Furthermore, we demonstrate that binding of sENG to BMP9 does not inhibit BMP9 signaling. Indeed, the sENG:BMP9 complex signals with comparable potency and specificity to BMP9 on human primary endothelial cells. The full signaling activity of the sENG:BMP9 complex required transmembrane ENG. This study confirms that rather than being an inhibitory ligand trap, increased circulating sENG might preferentially direct BMP9 signaling via cell-surface ENG at the endothelium. This is important for understanding the role of sENG in the pathobiology of PE and other cardiovascular diseases.British Heart Foundation, Cancer Genomics Centre Netherlands and from the Netherlands CardioVascular Research Initiative, the Dutch Heart Foundation, Dutch Federation of University Medical Centers, the Netherlands Organization for Health Research and Development, and the Royal Netherlands Academy of Sciences (CVON PHEADRA)

Modelling the atmospheric dispersion of radiotracers in small-scale, controlled detonations: validation of dispersion models using field test data

A series of modelling exercises, based on field tests conducted in the Czech Republic, were carried out by the ‘Urban’ Working Groups as part of the International Atomic Energy Agency’s Environmental Modelling for Radiation Safety II, Modelling and Data for Radiological Impact Assessment (MODARIA) I and MODARIA II international data compilation and model validation programmes. In the first two of these programmes, data from a series of field tests involving dispersion of a radiotracer, 99mTc, from small-scale, controlled detonations were used in a comparison of model predictions with field measurements of deposition. In the third programme, data from a similar field test, involving dispersion of 140La instead of 99mTc, were used. Use of longer-lived 140La as a radiotracer allowed a greater number of measurements to be made over a greater distance from the dispersion point and in more directions than was possible for the earlier tests involving shorter-lived 99mTc. The modelling exercises included both intercomparison of model predictions from several participants and comparison of model predictions with the measured data. Several models (HotSpot, LASAIR, ADDAM/CSA-ERM, plus some research models) were used in the comparisons, which demonstrated the challenges of modelling dispersion of radionuclides from detonations and the need for appropriate meteorological measurements