Derrida on the Convention of Textual Spacing

This paper focuses on various textual elements in prose writing (footnotes, titles, and prefaces) such as they determine, and are determined by, the textual spacing of the page. Far from functioning in the way that the typographical, syntactical spaces between words do, or from replicating the pauses punctuating words in speech, such spacing is singularly and irreducibly textual. Functioning like non-phonetic marks such as parentheses, or expressing relations of hierarchy (as between footnote and text), textual spacing’s manifold functions belie their pristine blankness. I look at this textual spacing of the preface, title, and footnote, as its orthodox and deviational modes of functioning come to light in certain of Derrida’s readings. A second phase of analysis focuses on the unconventional spatial organization of certain of Derrida’s own texts—on his juxtaposition of cited texts in a determinate spatial configuration, and his composing of a book comprising two columns facing one another. To make sense of such gestures in the face of the derision they can occasion, I have recourse not, as one might, to French modernist art’s ostentatious engagement and display of its own material conditions, but to the conventional exploitation of textual space as analyzed in the first section devoted to the spacing of footnotes, prefaces, and so on. I conclude Derrida’s gestures to continue the tradition in which prose writing has innovatively availed of textual space to institute such conventional textual components as footnotes, prefaces, and titles—components integral to the apparatus of “the book” that gives material form to or “realizes” the logos. Derrida’s gestures are thus to be judged, not on the basis of the bemusement we might feel at an instance and mode of textual spacing that falls under no familiar convention, but only vis-à-vis their deconstruction of the text as an exhaustible totality of sense, and their visually attesting to the intertextuality interwoven in any text’s composition

Effects of human and porcine bile on the proteome of Helicobacter hepaticus

<p>Abstract</p> <p>Background</p> <p><it>Helicobacter hepaticus </it>colonizes the intestine and liver of mice causing hepatobiliary disorders such as hepatitis and hepatocellular carcinoma, and has also been associated with inflammatory bowel disease in children. In its habitat, <it>H. hepaticus </it>must encounter bile which has potent antibacterial properties. To elucidate virulence and host-specific adaptation mechanisms of <it>H. hepaticus </it>modulated by human or porcine bile, a proteomic study of its response to the two types of bile was performed employing two-dimensional gel electrophoresis (2-DE) and mass spectrometry.</p> <p>Results</p> <p>The 2-DE and mass spectrometry analyses of the proteome revealed that 46 proteins of <it>H. hepaticus </it>were differentially expressed in human bile, 18 up-regulated and 28 down-regulated. In the case of porcine bile, 32 proteins were differentially expressed of which 19 were up-regulated, and 13 were down-regulated. Functional classifications revealed that identified proteins participated in various biological functions including stress response, energy metabolism, membrane stability, motility, virulence and colonization. Selected genes were analyzed by RT-PCR to provide internal validation for the proteomic data as well as provide insight into specific expressions of motility, colonization and virulence genes of <it>H. hepaticus </it>in response to human or porcine bile.</p> <p>Conclusions</p> <p>Overall, the data suggested that bile is an important factor that determines virulence, host adaptation, localization and colonization of specific niches within host environment.</p

Comparative analyses of Campylobacter concisusstrains reveal the genome of the reference strain BAA-1457 is not representative of the species

<p>Abstract</p> <p>Background</p> <p>Several studies have shown that significant genotypic heterogeneity exists among <it>Campylobacter concisus </it>strains. Recently, the genome of <it>C. concisus </it>UNSWCD, isolated from a patient with Crohn's disease, was sequenced.</p> <p>Results</p> <p>In this study, comparative analyses were performed between strain UNSWCD and BAA-1457, isolated from a patient with acute gastroenteritis. Searches between <it>C. concisus </it>UNSWCD and BAA-1457 showed that 76% of genes were homologues, whereas those between <it>C. jejuni </it>strains showed 90-91% to be homologues, indicating substantial variation exists within these two <it>C. concisus </it>genomes. More specific bidirectional homology searches identified 1593 genes that are shared between these strains, and 115 and 281 genes unique to UNSWCD and BAA-1457, respectively. Significantly, differences in the type of flagellin glycosylation pathways between the two strains were identified and confirmed by PCR. The protein profiles of UNSWCD, BAA-1457 and a further six strains of <it>C. concisus </it>were compared and analyzed bioinformatically, and this differentiated the strains into four clades. BAA-1457 was found to be highly divergent (average similarity: 56.8%) from the other seven strains (mean average similarity ± standard deviation: 64.7 ± 1.7%). Furthermore, searches for homologues of the 1593 proteins found to be common between UNSWCD and BAA-1457 were conducted against all available bacterial genomes, and 18 proteins were found to be unique to <it>C. concisus</it>, of which 6 were predicted to be secreted, and may represent good markers for detection of this species.</p> <p>Conclusions</p> <p>This study has elucidated several features that may be responsible for the heterogeneity that exists among <it>C. concisus </it>strains, and has determined that the strain BAA-1457 is genetically atypical to other <it>C. concisus </it>strains and is not a good candidate reference strain.</p

Shotgun redox proteomics: identification and quantitation of carbonylated proteins in the UVB resistant marine bacterium, Photobacterium angustum S14

UVB oxidizes proteins through the generation of reactive oxygen species. One consequence of UVB irradiation is carbonylation, the irreversible formation of a carbonyl group on proline, lysine, arginine or threonine residues. In this study, redox proteomics was performed to identify carbonylated proteins in the UVB resistant marine bacterium Photobacterium angustum. Mass-spectrometry was performed with either biotin-labeled or dinitrophenylhydrazide (DNPH) derivatized proteins. The DNPH redox proteomics method enabled the identification of 62 carbonylated proteins (5% of 1221 identified proteins) in cells exposed to UVB or darkness. Eleven carbonylated proteins were quantified and the UVB/dark abundance ratio was determined at both the protein and peptide levels. As a result we determined which functional classes of proteins were carbonylated, which residues were preferentially modified, and what the implications of the carbonylation were for protein function. As the first large scale, shotgun redox proteomics analysis examining carbonylation to be performed on bacteria, our study provides a new level of understanding about the effects of UVB on cellular proteins, and provides a methodology for advancing studies in other biological systems

Examination of the Anaerobic Growth of Campylobacter concisus

Campylobacter concisus is an oral bacterium that is associated with intestinal diseases. C. concisus was previously described as a bacterium that requires H2-enriched microaerobic conditions for growth. The level of H2 in the oral cavity is extremely low, suggesting that C. concisus is unlikely to have a microaerobic growth there. In this study, the anaerobic growth of C. concisus was investigated. The growth of fifty-seven oral C. concisus strains and six enteric C. concisus strains under various atmospheric conditions including anaerobic conditions with and without H2 was examined. The atmospheric conditions were generated using commercially available gas-generation systems. C. concisus putative virulence proteins were identified using mass spectrometry analysis. Under anaerobic conditions, 92% of the oral C. concisus strains (52/57) and all six enteric strains grew without the presence of H2 and the presence of H2 greatly increased C. concisus growth. An oral C. concisus strain was found to express a number of putative virulence proteins and the expression levels of these proteins were not affected by H2. The levels of H2 appeared to affect the optimal growth of C. concisus. This study provides useful information in understanding the natural colonization site and pathogenicity of C. concisus

Changes in the plasma proteome at asymptomatic and symptomatic stages of autosomal dominant Alzheimer\u27s disease

The autosomal dominant form of Alzheimer\u27s disease (ADAD) is far less prevalent than late onset Alzheimer\u27s disease (LOAD), but enables well-informed prospective studies, since symptom onset is near certain and age of onset is predictable. Our aim was to discover plasma proteins associated with early AD pathology by investigating plasma protein changes at the asymptomatic and symptomatic stages of ADAD. Eighty-one proteins were compared across asymptomatic mutation carriers (aMC, n = 15), symptomatic mutation carriers (sMC, n = 8) and related noncarriers (NC, n = 12). Proteins were also tested for associations with cognitive measures, brain amyloid deposition and glucose metabolism. Fewer changes were observed at the asymptomatic than symptomatic stage with seven and 16 proteins altered significantly in aMC and sMC, respectively. This included complement components C3, C5, C6, apolipoproteins A-I, A-IV, C-I and M, histidine-rich glycoprotein, heparin cofactor II and attractin, which are involved in inflammation, lipid metabolism and vascular health. Proteins involved in lipid metabolism differed only at the symptomatic stage, whereas changes in inflammation and vascular health were evident at asymptomatic and symptomatic stages. Due to increasing evidence supporting the usefulness of ADAD as a model for LOAD, these proteins warrant further investigation into their potential association with early stages of LOAD

Integrating proteomic data with metabolic modeling provides insight into key pathways of Bordetella pertussis biofilms

Pertussis, commonly known as whooping cough is a severe respiratory disease caused by the bacterium, Bordetella pertussis. Despite widespread vaccination, pertussis resurgence has been observed globally. The development of the current acellular vaccine (ACV) has been based on planktonic studies. However, recent studies have shown that B. pertussis readily forms biofilms. A better understanding of B. pertussis biofilms is important for developing novel vaccines that can target all aspects of B. pertussis infection. This study compared the proteomic expression of biofilm and planktonic B. pertussis cells to identify key changes between the conditions. Major differences were identified in virulence factors including an upregulation of toxins (adenylate cyclase toxin and dermonecrotic toxin) and downregulation of pertactin and type III secretion system proteins in biofilm cells. To further dissect metabolic pathways that are altered during the biofilm lifestyle, the proteomic data was then incorporated into a genome scale metabolic model using the Integrative Metabolic Analysis Tool (iMAT). The generated models predicted that planktonic cells utilised the glyoxylate shunt while biofilm cells completed the full tricarboxylic acid cycle. Differences in processing aspartate, arginine and alanine were identified as well as unique export of valine out of biofilm cells which may have a role in inter-bacterial communication and regulation. Finally, increased polyhydroxybutyrate accumulation and superoxide dismutase activity in biofilm cells may contribute to increased persistence during infection. Taken together, this study modeled major proteomic and metabolic changes that occur in biofilm cells which helps lay the groundwork for further understanding B. pertussis pathogenesis

Characterization of an archaeal virus-host system reveals massive genomic rearrangements in a laboratory strain

Halophilic archaea (haloarchaea) are known to exhibit multiple chromosomes, with one main chromosome and one or several smaller secondary chromosomes or megaplasmids. Halorubrum lacusprofundi, a model organism for studying cold adaptation, exhibits one secondary chromosome and one megaplasmid that include a large arsenal of virus defense mechanisms. We isolated a virus (Halorubrum tailed virus DL1, HRTV-DL1) infecting Hrr. lacusprofundi, and present an in-depth characterization of the virus and its interactions with Hrr. lacusprofundi. While studying virus-host interactions between Hrr. lacusprofundi and HRTV-DL1, we uncover that the strain in use (ACAM34_UNSW) lost the entire megaplasmid and about 38% of the secondary chromosome. The loss included the majority of virus defense mechanisms, making the strain sensitive to HRTV-DL1 infection, while the type strain (ACAM34_DSMZ) appears to prevent virus replication. Comparing infection of the type strain ACAM34_DSMZ with infection of the laboratory derived strain ACAM34_UNSW allowed us to identify host responses to virus infection that were only activated in ACAM34_UNSW upon the loss of virus defense mechanisms. We identify one of two S-layer proteins as primary receptor for HRTV-DL1 and conclude that the presence of two different S-layer proteins in one strain provides a strong advantage in the arms race with viruses. Additionally, we identify archaeal homologs to eukaryotic proteins potentially being involved in the defense against virus infection