Studying the Human Gut Microbiota in the Trans-Omics Era - Focus on Metagenomics and Metabonomics

The human gut microbiota comprises a diverse microbial consortium closely co-evolved with the human genome and diet. The importance of the gut microbiota in regulating human health and disease has however been largely overlooked due to the inaccessibility of the intestinal habitat, the complexity of the gut microbiota itself and the fact that many of its members resist cultivation and are in fact new to science. However, with the emergence of 16S rRNA molecular tools and "post-genomics" high resolution technologies for examining microorganisms as they occur in nature without the need for prior laboratory culture, this limited view of the gut microbiota is rapidly changing. This review will discuss the application of molecular microbiological tools to study the human gut microbiota in a culture independent manner. Genomics or metagenomics approaches have a tremendous capability to generate compositional data and to measure the metabolic potential encoded by the combined genomes of the gut microbiota. Another post-genomics approach, metabonomics, has the capacity to measure the metabolic kinetic or flux of metabolites through an ecosystem at a particular point in time or over a time course. Metabonomics thus derives data on the function of the gut microbiota in situ and how it responds to different environmental stimuli e. g. substrates like prebiotics, antibiotics and other drugs and in response to disease. Recently these two culture independent, high resolution approaches have been combined into a single "transgenomic" approach which allows correlation of changes in metabolite profiles within human biofluids with microbiota compositional metagenomic data. Such approaches are providing novel insight into the composition, function and evolution of our gut microbiota.

Microbial species involved in production of 1,2-sn-diacylglycerol and effects of phosphatidylcholine on human fecal microbiota

1,2-sn-Diacylglycerols (DAGs) are activators of protein kinase C (PKQ, which is involved in the regulation of colonic mucosal proliferation. Extracellular DAG has been shown to stimulate the growth of cancer cell lines in vitro and may therefore play an important role in tumor promotion. DAG has been detected in human fecal extracts and is thought to be of microbial origin. Hitherto, no attempts have been made to identify the predominant fecal bacterial species involved in its production. We therefore used anaerobic batch culture systems to determine whether fecal bacteria could utilize phosphatidylcholine (0.5% [wt/vol]) to produce DAG. Production was found to be dependent upon the presence of the substrate and was enhanced in the presence of high concentrations of deoxycholate (5 and 10 mM) in the growth medium. Moreover, its production increased with the pH, and large inter- and intraindividual variations were observed between cultures seeded with inocula from different individuals. Clostridia and Escherichia coli multiplied in the fermentation systems, indicating their involvement in phosphatidylcholine metabolism. On the other hand, there was a significant decrease in the number of Bifidobacterium spp. in the presence of phosphatidylcholine. Pure-culture experiments showed that 10 of the 12 strains yielding the highest DAG levels (>50 nmol/ml) were isolated from batch culture enrichments run at pH 8.5. We found that the strains capable of producing large amounts of DAG were predominantly Clostridium bifermentans (8 of 12), followed by Escherichia coli (2 of 12). Interestingly, one DAG-producing strain was Bifidobacterium infantis, which is often considered a beneficial gut microorganism. Our results have provided further evidence that fecal bacteria can produce DAG and that specific bacterial groups are involved in this process. Future strategies to reduce DAG formation in the gut should target these species.

Studying the Human Gut Microbiota in the Trans-Omics Era - Focus on Metagenomics and Metabonomics

The human gut microbiota comprises a diverse microbial consortium closely co-evolved with the human genome and diet. The importance of the gut microbiota in regulating human health and disease has however been largely overlooked due to the inaccessibility of the intestinal habitat, the complexity of the gut microbiota itself and the fact that many of its members resist cultivation and are in fact new to science. However, with the emergence of 16S rRNA molecular tools and "post-genomics" high resolution technologies for examining microorganisms as they occur in nature without the need for prior laboratory culture, this limited view of the gut microbiota is rapidly changing. This review will discuss the application of molecular microbiological tools to study the human gut microbiota in a culture independent manner. Genomics or metagenomics approaches have a tremendous capability to generate compositional data and to measure the metabolic potential encoded by the combined genomes of the gut microbiota. Another post-genomics approach, metabonomics, has the capacity to measure the metabolic kinetic or flux of metabolites through an ecosystem at a particular point in time or over a time course. Metabonomics thus derives data on the function of the gut microbiota in situ and how it responds to different environmental stimuli e.g. substrates like prebiotics, antibiotics and other drugs and in response to disease. Recently these two culture independent, high resolution approaches have been combined into a single "transgenomic" approach which allows correlation of changes in metabolite profiles within human biofluids with microbiota compositional metagenomic data. Such approaches are providing novel insight into the composition, function and evolution of our gut microbiota.

Overexpression of coconut AINTEGUMENTA-like gene, CnANT, promotes in vitro regeneration in transgenic Arabidopsis

Knowledge of the molecular biological changes underlying the process of embryogenesis is important for the improvement of somatic embryogenesis of coconut. Among the transcription factors that control the transition from vegetative to embryogenic growth, members of APETALA2/Ethylene-responsive element binding protein domain family play an important role in promoting embryo development. Significant insights into the role of AP2 genes have been obtained by the ectopic expression of AP2 sub family genes in transgenic Arabidopsis. A homolog of the AINTEGUMENTA-like gene that encodes the two AP2 domains and the linker region was identified in the coconut genome. Phylogenetic analysis showed that this gene, CnANT, encodes a protein that branched with BABY BOOM/PLETHORA clade in the AINTEGUMENTA-like major clade and was similar to the oil palm EgAP2-1 protein. According to real time RT-PCR results, higher expression of CnANT was observed in more mature zygotic embryos. Also, high CnANT expression was recorded in embryogenic callus compared to other stages of somatic embryogenesis. We examined the effect of ectopic CnANT expression on the development and regenerative capacity of transgenic Arabidopsis. Overexpression of CnANT in Arabidopsis induced hormone free regeneration of explants. Furthermore, ectopic expression of CnANT enhanced regeneration in vitro and suggested a role for this gene in cell proliferation during in vitro culture.

Neuronal-glial populations form functional networks in a biocompatible 3D scaffold

Monolayers of neurons and glia have been employed for decades as tools for the study of cellular physiology and as the basis for a variety of standard toxicological assays. A variety of three dimensional (3D) culture techniques have been developed with the aim to produce cultures that recapitulate desirable features of intact. In this study, we investigated the effect of preparing primary mouse mixed neuron and glial cultures in the inert 3D scaffold, Alvetex. Using planar multielectrode arrays, we compared the spontaneous bioelectrical activity exhibited by neuroglial networks grown in the scaffold with that seen in the same cells prepared as conventional monolayer cultures. Two dimensional (monolayer; 2D) cultures exhibited a significantly higher spike firing rate than that seen in 3D cultures although no difference was seen in total signal power (<50 Hz) while pharmacological responsiveness of each culture type to antagonism of GABAAR, NMDAR and AMPAR was highly comparable. Interestingly, correlation of burst events, spike firing and total signal power (<50 Hz) revealed that local field potential events were associated with action potential driven bursts as was the case for 2D cultures. Moreover, glial morphology was more physiologically normal in 3D cultures. These results show that 3D culture in inert scaffolds represents a more physiologically normal preparation which has advantages for physiological, pharmacological, toxicological and drug development studies, particularly given the extensive use of such preparations in high throughput and high content systems.

The circulation of romances from England in late-medieval Ireland

The fifteenth century saw a striking upturn in the number of texts from foreign vernaculars that were translated into Irish. Indeed, one might go so far as to speak in terms of a ‘translation trend’ in Ireland during the mid to late fifteenth century. A notable feature of this trend is that a particularly high number of these Irish translations are of romances; contextual and textual evidence suggests that the original exemplars for many of these translated texts appear to have come from England, though not all of them were necessarily in English. Irish translations of eight romances have survived to the present day: Guy of Warwick; Bevis of Hampton; La Queste de Saint Graal; Fierabras; Caxton’s Recuyell of the Histories of Troie; William of Palerne; the Seven Sages of Rome; and Octavian. This paper addresses two aspects of these texts of particular relevance to romance scholars who do not work within the sphere of Celtic studies. Firstly, it argues that certain aspects of the dissemination and reception of romance in Ireland are quite distinctive. Manuscript and textual evidence suggests that the religious orders, particularly the Franciscans, seem to have played a role in the importation and translation of these narratives. Secondly, examination of the Irish versions of romance tends to bear out an observation made by Flower many years ago, but not pursued by subsequent scholars: ‘texts of an unusual kind were current in Ireland, and it may be that interesting discoveries are to be made here’. Certain narrative features of several of these Irish translations diverge from all the surviving versions of the relevant romance in other languages and may witness to a variant exemplar that has since been lost from its own linguistic corpus.

Doubled haploid ramets via embryogenesis of haploid tissue cultures

Tissue culture in the oil palm business is generally concerned with the multiplication (clonal production) of dura, pisifera and tenera palms. These are all normal diploids (2n=2x=36). Sumatra Bioscience has pioneered haploid tissue culture of oil palm (n=x=18). Haploid oil palm is the first step in producing doubled haploid palms which in turn provide parental lines for F1 hybrid production. Chromosome doubling is known to occur during embryogenesis in other haploid cultures, e.g. barley anther culture. Haploid tissue cultures in oil palm were therefore set up to investigate and exploit spontaneous chromosome doubling during embryogenesis. Flow cytometry of embryogenic tissue showed the presence of both haploid (n) and doubled haploid (2n) cells indicating spontaneous doubling. Completely doubled haploid ramets were regenerated suggesting that doubling occurred during the first mitoses of embryogenesis. This is the first report of doubled haploid production in oil palm via haploid tissue culture. The method provides a means of producing a range of doubled haploids in oil palm from the 1,000 plus haploids available at Sumatra Bioscience, in addition the method also produced doubled haploid (and haploid) clones. 1.

Modern lovers

Modern Lovers was a survey show of contemporary art practices in dialogue with modernism, bringing together established and emerging artists based in London and international artists from Berlin, Jerusalem and Zagreb. The show features video, film, installation, sculpture, music and performance work that addresses the legacy of the avant garde and the survival of its aesthetics within contemporary culture. In 1976, as punk rock was busy smashing the cultural rubble left behind by the second world war and rejecting the consumer society that had emerged from the ruins, one band bravely announced that it wanted no part in this destruction. Jonathan Richman's Modern Lovers sang about how they still loved the old world. Neither parents nor girlfriends could understand, but the decaying inner city with its false promises of progress still held a fascination for Richman, who claimed he wanted to keep his place in this arcane landscape. Punk's assault on culture was the logical conclusion of modernism's linear narrative of art as a force of innovation that must reject preceding artistic movements to establish new ones. Echoing the negations of Dada, it set out to put an end to this narrative, an end to culture. It is partly because of this inherently destructive and totalising side of Modernism that it has come under harsh critique in the post modern era. Nevertheless, we are still caught up in the same dialectic of progress, revolution and destruction. Post modernism has failed to unseat our desire for the revolutionary moment, even as it has been co-opted to the degree of meaninglessness by the discourses of marketing and Capitalism. But, like Jonathan Richman, the artists in the exhibition "Modern Lovers" keep returning to modernism for something else. Instead of taking it at its word when it proffers revolution, they turn to it in search of reform. Still loving the old world and desiring a dialogue with the past, perhaps as an antidote to the eternal present of Capitalism, they are willing to engage with its aesthetics and ideas on equal ground. Leaving behind the ironic deconstructions of post modernism, they find perspectives worth salvaging and juxtapose them with contemporary visual productions. Trading in the grand narratives of modernity for a more personal approach, they don't seek the purity of form that drove the avant garde movements that inspire them but rather revel in adulteration, dilution and contamination of the past by the present". A live performance by sala-manca was sponsored by the British Council and took place May 26th, 19:00. MODERN LOVERS was accompanied by a catalogue (14.80 cm x 14.80 cm) including essays by Avi Pitchon, the sala-manca group and the curators. A discussion panel about the exhibition themes, as well as the catalogue launch,took place at Goldsmiths College's cinema on the 27th of May at 14:00, chaired by Dr. Suhail Malik (Senior Lecturer & Course Leader Postgraduate Fine Art Critical Studies at Goldsmiths College) and with the participation of Tom Morton (curator, Cubitt Gallery, and regular contributor to Frieze magazine), sala-manca (artist group), Dr. Amanda Beech (artist, curator and senior lecturer at the Wimbledon School of Art), Matthew Poole (course director of MA Gallery Studies, dept. of Art History and Theory at the University of Essex).

Enhanced viability of corneal epithelial cells for efficient transport/storage using a structurally-modified calcium alginate hydrogel

Aims: Therapeutic limbal epithelial stem cells could be managed more efficiently if clinically validated batches were transported for ‘on-demand’ use. Materials & methods: In this study, corneal epithelial cell viability in calcium alginate hydrogels was examined under cell culture, ambient and chilled conditions for up to 7 days. Results: Cell viability improved as gel internal pore size increased, and was further enhanced with modification of the gel from a mass to a thin disc. Ambient storage conditions were optimal for supporting cell viability in gel discs. Cell viability in gel discs was significantly enhanced with increases in pore size mediated by hydroxyethyl cellulose. Conclusion: Our novel methodology of controlling alginate gel shape and pore size together provides a more practical and economical alternative to established corneal tissue/cell storage methods.