Borderline hospitality: homestays as a commercial hospitality development project in Grahamstown, Eastern Cape

This study started as an anthropological investigation of commercial hospitality from the point of view of the hands-on host. The chosen case study for this investigation was the Kwam eMakana Government Initiated Poverty Alleviation Project which offered homestays in the townships of Grahamstown East since 2004. Homestays are the most intimate form of commercial hospitality, one step removed from non-commercial or social hospitality. Even at the homestay level there is a conceptual conflict between poverty and (Westernized) commercial hospitality, however, Kwam homes are more middle class than poor. Later the investigation revealed the deeper-seated form of poverty of the Kwam participants being (almost) illiterate. Kwam was a development project like many others, in which huge amounts of money were spent in the name of the project but very little of the benefits reached the intended beneficiaries. Thus, as fieldwork ensued, the emphasis of research migrated from an empirical study of homestay hospitality, to actively assist with the struggle of the Kwam hostesses to maintain the project and gain autonomy for themselves. This study was from the outset reflexive, as the host’s point of view could technically only be presented by auto-ethnography. Then the investigation shifted to a form of engaged anthropology far exceeding advocacy as it is usually understood. The presentation of this can be called radical reflexivity, while it is simultaneously an ethnographical account in the sense of anthropology ‘at home’. It also implied, besides ethical concerns, revisiting literary sensibilities, such as the use of a third person narrative for the reflexive account. To conceptualize the development process of both Kwam and the research interventions Bourdieu’s ‘totality of capital’ (in which the strands of economic, symbolic, cultural and social capitals intertwine) proved most useful. By assessing the various capitals the development of the project and the power struggles central to it can be understood. This study confirms that long-term anthropological investigation is best suited to the study of development projects, if not necessary for real development to be effected. Reflexivity and ethnography are complementary methods to reveal truths which under certain research circumstances may have been very difficult or even impossible to research

YAC contigs of the Rab1 and wobbler (wr) spinal muscular atrophy gene region on proximal mouse chromosome 11 and of the homologous region on human chromosome 2p

powerful tool to advance the identi®cation of gene com-Despite rapid progress in the physical characteriza- plexes and of disease genes. In this respect, the analysis tion of murine and human genomes, little molecular in- of human chromosomes 16 and 19 (Nowak, 1995) and formation is available on certain regions, e.g., proximal mouse chromosomes 1 (Hunter et al., 1994) and 17 (Cox mouse chromosome 11 (Chr 11) and human chromosome et al., 1993) as well as of human and murine X chromo-2p (Chr 2p). We have localized the wobbler spinal atrophy somes is particularly far advanced (Hamvas et al., 1993). gene wr to proximal mouse Chr 11, tightly linked toRab1, On the other hand, such extensive information is not a gene coding for a small GTP-binding protein, and Glns- available for mouse proximal chromosome 11 (Chr 11) ps1, an intronless pseudogene of the glutamine synthe- and human chromosome 2p (Chr 2p) (Fig. 1; cf. Berry et tase gene. We have now used these markers to construct al., 1995; Nowak, 1995), known to share at least the genesa 1.3-Mb yeast arti®cial chromosome (YAC) contig of the for the reticuloendotheliosis oncogene (Brownell et al.,Rab1 region on mouse Chr 11. Four YAC clones isolated 1985), for a brain-speci®cb-spectrin isoform (Bloom et al.,from two independent YAC libraries were characterized 1992), and for cytoplasmic malate dehydrogenase (Ball etby rare-cutting analysis, ¯uorescence in situ hybridiza-al., 1994). However, comparing the segregation map oftion (FISH), and sequence-tagged site (STS) isolation and the mouse with the human cytogenetic map, a colinearmapping. Rab1 and Glns-ps1 were found to be only 20

The bioluminescent Listeria monocytogenes strain Xen32 is defective in flagella expression and highly attenuated in orally infected BALB/cJ mice

Abstract Background In vivo bioluminescence imaging (BLI) is a powerful method for the analysis of host-pathogen interactions in small animal models. The commercially available bioluminescent Listeria monocytogenes strain Xen32 is commonly used to analyse immune functions in knockout mice and pathomechanisms of listeriosis. Findings To analyse and image listerial dissemination after oral infection we have generated a murinised Xen32 strain (Xen32-mur) which expresses a previously described mouse-adapted internalin A. This strain was used alongside the Xen32 wild type strain and the bioluminescent L. monocytogenes strains EGDe-lux and murinised EGDe-mur-lux to characterise bacterial dissemination in orally inoculated BALB/cJ mice. After four days of infection, Xen32 and Xen32-mur infected mice displayed consistently higher rates of bioluminescence compared to EGDe-lux and EGDe-mur-lux infected animals. However, surprisingly both Xen32 strains showed attenuated virulence in orally infected BALB/c mice that correlated with lower bacterial burden in internal organs at day 5 post infection, smaller losses in body weights and increased survival compared to EGDe-lux or EGDe-mur-lux inoculated animals. The Xen32 strain was made bioluminescent by integration of a lux-kan transposon cassette into the listerial flaA locus. We show here that this integration results in Xen32 in a flaA frameshift mutation which makes this strain flagella deficient. Conclusions The bioluminescent L. monocytogenes strain Xen32 is deficient in flagella expression and highly attenuated in orally infected BALB/c mice. As this listerial strain has been used in many BLI studies of murine listeriosis, it is important that the scientific community is aware of its reduced virulence in vivo

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins

<p>Abstract</p> <p>Background</p> <p>The <it>jumonji C (JmjC) domain containing gene 6 </it>(<it>Jmjd6</it>, previously known as phosphatidylserine receptor) has misleadingly been annotated to encode a transmembrane receptor for the engulfment of apoptotic cells. Given the importance of JmjC domain containing proteins in controlling a wide range of diverse biological functions, we undertook a comparative genomic analysis to gain further insights in <it>Jmjd6 </it>gene organisation, evolution, and protein function.</p> <p>Results</p> <p>We describe here a semiautomated computational pipeline to identify and annotate JmjC domain containing proteins. Using a sequence segment N-terminal of the Jmjd6 JmjC domain as query for a reciprocal BLAST search, we identified homologous sequences in 62 species across all major phyla. Retrieved <it>Jmjd6 </it>sequences were used to phylogenetically analyse corresponding loci and their genomic neighbourhood. This analysis let to the identification and characterisation of a bi-directional transcriptional unit compromising the <it>Jmjd6 </it>and <it>1110005A03Rik </it>genes and to the recognition of a new, before overseen <it>Jmjd6 </it>exon in mammals. Using expression studies, two novel <it>Jmjd6 </it>splice variants were identified and validated <it>in vivo</it>. Analysis of the <it>Jmjd6 </it>neighbouring gene <it>1110005A03Rik </it>revealed an incident deletion of this gene in two out of three earlier reported <it>Jmjd6 </it>knockout mice, which might affect previously described conflicting phenotypes. To determine potentially important residues for <it>Jmjd6 </it>function a structural model of the Jmjd6 protein was calculated based on sequence conservation. This approach identified a conserved double-stranded β^-helix (DSBH) fold and a HxDx_nH facial triad as structural motifs. Moreover, our systematic annotation in nine species identified 313 DSBH fold-containing proteins that split into 25 highly conserved subgroups.</p> <p>Conclusion</p> <p>We give further evidence that <it>Jmjd6 </it>most likely has a function as a nonheme-Fe(II)-2-oxoglutarate-dependent dioxygenase as previously suggested. Further, we provide novel insights into the evolution of Jmjd6 and other related members of the superfamily of JmjC domain containing proteins. Finally, we discuss possibilities of the involvement of <it>Jmjd6 </it>and <it>1110005A03Rik </it>in an antagonistic biochemical pathway.</p

The thermodynamic landscape of carbon redox biochemistry

Redox biochemistry plays a key role in the transduction of chemical energy in all living systems. Observed redox reactions in metabolic networks represent only a minuscule fraction of the space of all possible redox reactions. Here we ask what distinguishes observed, natural redox biochemistry from the space of all possible redox reactions between natural and non-natural compounds. We generate the set of all possible biochemical redox reactions involving linear chain molecules with a fixed numbers of carbon atoms. Using cheminformatics and quantum chemistry tools we analyze the physicochemical and thermodynamic properties of natural and non-natural compounds and reactions. We find that among all compounds, aldose sugars are the ones with the highest possible number of connections (reductions and oxidations) to other molecules. Natural metabolites are significantly enriched in carboxylic acid functional groups and depleted in carbonyls, and have significantly higher solubilities than non-natural compounds. Upon constructing a thermodynamic landscape for the full set of reactions as a function of pH and of steady-state redox cofactor potential, we find that, over this whole range of conditions, natural metabolites have significantly lower energies than the non-natural compounds. For the set of 4-carbon compounds, we generate a Pourbaix phase diagram to determine which metabolites are local energetic minima in the landscape as a function of pH and redox potential. Our results suggest that, across a set of conditions, succinate and butyrate are local minima and would thus tend to accumulate at equilibrium. Our work suggests that metabolic compounds could have been selected for thermodynamic stability, and yields insight into thermodynamic and design principles governing nature’s metabolic redox reactions.https://www.biorxiv.org/content/10.1101/245811v1Othe

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins

<p>Abstract</p> <p>Background</p> <p>The <it>jumonji C (JmjC) domain containing gene 6 </it>(<it>Jmjd6</it>, previously known as phosphatidylserine receptor) has misleadingly been annotated to encode a transmembrane receptor for the engulfment of apoptotic cells. Given the importance of JmjC domain containing proteins in controlling a wide range of diverse biological functions, we undertook a comparative genomic analysis to gain further insights in <it>Jmjd6 </it>gene organisation, evolution, and protein function.</p> <p>Results</p> <p>We describe here a semiautomated computational pipeline to identify and annotate JmjC domain containing proteins. Using a sequence segment N-terminal of the Jmjd6 JmjC domain as query for a reciprocal BLAST search, we identified homologous sequences in 62 species across all major phyla. Retrieved <it>Jmjd6 </it>sequences were used to phylogenetically analyse corresponding loci and their genomic neighbourhood. This analysis let to the identification and characterisation of a bi-directional transcriptional unit compromising the <it>Jmjd6 </it>and <it>1110005A03Rik </it>genes and to the recognition of a new, before overseen <it>Jmjd6 </it>exon in mammals. Using expression studies, two novel <it>Jmjd6 </it>splice variants were identified and validated <it>in vivo</it>. Analysis of the <it>Jmjd6 </it>neighbouring gene <it>1110005A03Rik </it>revealed an incident deletion of this gene in two out of three earlier reported <it>Jmjd6 </it>knockout mice, which might affect previously described conflicting phenotypes. To determine potentially important residues for <it>Jmjd6 </it>function a structural model of the Jmjd6 protein was calculated based on sequence conservation. This approach identified a conserved double-stranded β^-helix (DSBH) fold and a HxDx_nH facial triad as structural motifs. Moreover, our systematic annotation in nine species identified 313 DSBH fold-containing proteins that split into 25 highly conserved subgroups.</p> <p>Conclusion</p> <p>We give further evidence that <it>Jmjd6 </it>most likely has a function as a nonheme-Fe(II)-2-oxoglutarate-dependent dioxygenase as previously suggested. Further, we provide novel insights into the evolution of Jmjd6 and other related members of the superfamily of JmjC domain containing proteins. Finally, we discuss possibilities of the involvement of <it>Jmjd6 </it>and <it>1110005A03Rik </it>in an antagonistic biochemical pathway.</p