Isotopic characteristics of the Garonne River and its tributaries

The Garonne is the largest river in the south-west of France, and its drainage basin stretches between the Pyrenees and the Massif Central mountains. Until now, no water stable isotope study has been performed on the whole Garonne river basin which is composed of different geological substrata, and where the water resources are limited during the dry summer period. This study focuses on the Garonne river and its tributaries from the Pyre´ne´es foothill upstream to its confluence with the Lot River downstream. The aim of the study is to determine the origins of the surface waters using their chemical and stable isotopic compositions (18O, D and 13C), to better understand their circulation within the drainage basin and to assess the anthropogenic influences. The Garonne displays a specific 18O seasonal effect, and keeps its Pyre´nean characteristics until its confluence with the Tarn River. The difference in the dissolved inorganic carbon (DIC) comes mainly from the change in lithology between the Pyre´ne´es and the Massif Central mountains. Agriculture activity is only detected in the small tributaries

Integration of DNA into bacterial chromosomes from plasmids without a counter-selection marker.

Most bacteria can only be transformed with circular plasmids, so robust DNA integration methods for these rely upon selection of single-crossover clones followed by counter-selection of double-crossover clones. To overcome the limited availability of heterologous counter-selection markers, here we explore novel DNA integration strategies that do not employ them, and instead exploit (i) activation or inactivation of genes leading to a selectable phenotype, and (ii) asymmetrical regions of homology to control the order of recombination events. We focus here on the industrial biofuel-producing bacterium Clostridium acetobutylicum, which previously lacked robust integration tools, but the approach we have developed is broadly applicable. Large sequences can be delivered in a series of steps, as we demonstrate by inserting the chromosome of phage lambda (minus a region apparently unstable in Escherichia coli in our cloning context) into the chromosome of C. acetobutylicum in three steps. This work should open the way to reliable integration of DNA including large synthetic constructs in diverse microorganisms. © 2011 The Author(s)

Spores of Clostridium engineered for clinical efficacy and safety cause regression and cure of tumors in vivo.

Spores of some species of the strictly anaerobic bacteria Clostridium naturally target and partially lyse the hypoxic cores of tumors, which tend to be refractory to conventional therapies. The anti-tumor effect can be augmented by engineering strains to convert a non-toxic prodrug into a cytotoxic drug specifically at the tumor site by expressing a prodrug-converting enzyme (PCE). Safe doses of the favored prodrug CB1954 lead to peak concentrations of 6.3 μM in patient sera, but at these concentration(s) known nitroreductase (NTR) PCEs for this prodrug show low activity. Furthermore, efficacious and safe Clostridium strains that stably express a PCE have not been reported. Here we identify a novel nitroreductase from Neisseria meningitidis, NmeNTR, which is able to activate CB1954 at clinically-achievable serum concentrations. An NmeNTR expression cassette, which does not contain an antibiotic resistance marker, was stably localized to the chromosome of Clostridium sporogenes using a new integration method, and the strain was disabled for safety and containment by making it a uracil auxotroph. The efficacy of Clostridium-Directed Enzyme Prodrug Therapy (CDEPT) using this system was demonstrated in a mouse xenograft model of human colon carcinoma. Substantial tumor suppression was achieved, and several animals were cured. These encouraging data suggest that the novel enzyme and strain engineering approach represent a promising platform for the clinical development of CDEPT

Folded, layered textiles from a Bronze Age pit pyre excavated from Over Barrow 2, Cambridgeshire, England.

The textiles from Over Barrow, Cambridgeshire, England present the opportunity to examine the burial practices at the end of the Early Bronze Age. They were excavated from a pit pyre cremation along with cremated bone, a bone needle/pin and two small sherds of a collared urn. Preserved in charred clumps of multiple layers, they have the potential to provide clues as to how the textiles were used in the cremation, for example, whether they were used as clothing, shrouds or for other purpose such as binding strips. These possibilities raise a number of questions as to the role of textiles in Bronze Age cremation burials in the early second millennium BC in Britain

Learning from the Dead: How Burial Practices in Roman Britain Reflect Changes in Belief and Society

This paper begins by examining the burial traditions of the Iron age Britons and Classical Romans to see how these practices reflect their societal values and belief systems. The funerary methods of both the Britons and Romans are then analyzed following the Roman occupation of Britain in 43 AD to see how these practices changed once the two groups came into contact with each other. The findings show that rather than Romanization, there is a hybridization of burial practices which incorporated and reflect both Roman and British beliefs and values

Temporal and Spatial Data Mining with Second-Order Hidden Models

In the frame of designing a knowledge discovery system, we have developed stochastic models based on high-order hidden Markov models. These models are capable to map sequences of data into a Markov chain in which the transitions between the states depend on the \texttt{n} previous states according to the order of the model. We study the process of achieving information extraction fromspatial and temporal data by means of an unsupervised classification. We use therefore a French national database related to the land use of a region, named Teruti, which describes the land use both in the spatial and temporal domain. Land-use categories (wheat, corn, forest, ...) are logged every year on each site regularly spaced in the region. They constitute a temporal sequence of images in which we look for spatial and temporal dependencies. The temporal segmentation of the data is done by means of a second-order Hidden Markov Model (\hmmd) that appears to have very good capabilities to locate stationary segments, as shown in our previous work in speech recognition. Thespatial classification is performed by defining a fractal scanning ofthe images with the help of a Hilbert-Peano curve that introduces atotal order on the sites, preserving the relation ofneighborhood between the sites. We show that the \hmmd performs aclassification that is meaningful for the agronomists.Spatial and temporal classification may be achieved simultaneously by means of a 2 levels \hmmd that measures the \aposteriori probability to map a temporal sequence of images onto a set of hidden classes

Development and implementation of rapid metabolic engineering tools for chemical and fuel production in Geobacillus thermoglucosidasius NCIMB 11955

Background The thermophile Geobacillus thermoglucosidasius has considerable attraction as a chassis for the production of chemicals and fuels. It utilises a wide range of sugars and oligosaccharides typical of those derived from lignocellulose and grows at elevated temperatures. The latter improves the rate of feed conversion, reduces fermentation cooling costs and minimises the risks of contamination. Full exploitation of its potential has been hindered by a dearth of effective gene tools. Results Here we designed and tested a collection of vectors (pMTL60000 series) in G. thermoglucosidasius NCIMB 11955 equivalent to the widely used clostridial pMTL80000 modular plasmid series. By combining a temperature-sensitive replicon and a heterologous pyrE gene from Geobacillus kaustophilus as a counter-selection marker, a highly effective and rapid gene knock-out/knock-in system was established. Its use required the initial creation of uracil auxotroph through deletion of pyrE using allele-coupled exchange (ACE) and selection for resistance to 5-fluoroorotic acid. The turnaround time for the construction of further mutants in this pyrE minus strain was typically 5 days. Following the creation of the desired mutant, the pyrE allele was restored to wild type, within 3 days, using ACE and selection for uracil prototrophy. Concomitant with this process, cargo DNA (pheB) could be readily integrated at the pyrE locus. The system’s utility was demonstrated through the generation in just 30 days of three independently engineered strains equivalent to a previously constructed ethanol production strain, TM242. This involved the creation of two in-frame deletions (ldh and pfl) and the replacement of a promoter region of a third gene (pdh) with an up-regulated variant. In no case did the production of ethanol match that of TM242. Genome sequencing of the parental strain, TM242, and constructed mutant derivatives suggested that NCIMB 11955 is prone to the emergence of random mutations which can dramatically affect phenotype. Conclusions The procedures and principles developed for clostridia, based on the use of pyrE alleles and ACE, may be readily deployed in G. thermoglucosidasius. Marker-less, in-frame deletion mutants can be rapidly generated in 5 days. However, ancillary mutations frequently arise, which can influence phenotype. This observation emphasises the need for improved screening and selection procedures at each step of the engineering processes, based on the generation of multiple, independent strains and whole-genome sequencing

Last rites and human rights: funeral pyres and religious freedom in the United Kingdom

This article considers the litigation in Ghai v Newcastle City Council in which the legality of open air funeral pyres under the Cremation Act 1902, and under the right to freedom of religion and belief in article 9 of the European Convention on Human Rights, was considered. Ultimately the Court of Appeal held that open air funeral pyres within a walled enclosure were not unlawful. But at first instance the Administrative Court, which had assumed that domestic law prohibited such pyres, had held that such a ban would not breach article 9 since it was legitimate to prevent causing offence to the majority of the population. It is the approach of the Administrative Court to article 9 (which was not considered by the Court of Appeal) that forms the basis of the critical analysis in this article. In particular it is argued that the Administrative Court undervalued the right to freedom of religion and belief, as against the need to prevent offence to others, and adopted a stance which was overly deferential to Government and Parliament